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Sample records for china genotypic heterogeneity

  1. Heterogeneous recombination among Hepatitis B virus genotypes.

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    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

    2017-10-01

    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Prevalence and genotypes of Enterocytozoon bieneusi in China.

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    Wang, Sha-Sha; Wang, Rong-Jun; Fan, Xian-Cheng; Liu, Ting-Li; Zhang, Long-Xian; Zhao, Guang-Hui

    2018-07-01

    Enterocytozoon bieneusi has been considered as the most frequently diagnosed microsporidian species in humans and various animal species, accounting for more than 90% of the cases of human microsporidiosis. Spores of this pathogen excreted from both symptomatic and asymptomatic hosts into environment also would be an important source of waterborne outbreak of microsporidiosis. Due to limited effective drugs available but with too much side effects to mammals (eg. toxic), accurate characterization of E. bieneusi in both humans and animals is essential to implement effective control strategies to this pathogen. In China, E. bieneusi infection was presented in humans and some animals with high prevalence. Analysis of genetic variations of the internal transcribed spacer (ITS) sequences found 361 genotypes in China, and some novel genotypes were identified in some specific hosts. Additionally, associations between infections and some risk factors were also observed. In the present article, we reviewed the current status of prevalence, genotypes, multilocus genotypes (MLGs) in humans, various animals and waters in China. These findings will provide basic information for developing effective control strategies against E. bieneusi infection in China as well as other countries. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Molecular characterisation and prevalence of a new genotype of Cyprinid herpesvirus 2 in mainland China.

    Science.gov (United States)

    Li, Lijuan; Luo, Yangzhi; Gao, Zexia; Huang, Jian; Zheng, Xianghai; Nie, Huihui; Zhang, Junmei; Lin, Li; Yuan, Junfa

    2015-06-01

    Cyprinid herpesvirus 2 (CyHV-2, species Cyprinid herpesvirus 2) has been confirmed as a causative agent of the acute haematopoietic necrosis disease outbreak in farmed goldfish (Carassius auratus L.) and gibel carp (Carassius auratus gibelio Bloch). In this study, we present the genomic characteristics of a variant CyHV-2 strain (SY-C1) isolated from farmed gibel carp in mainland China and its comparative genomics analysis with the CyHV-2 reference strain ST-J1. Overall, the full-length genome of SY-C1 shares 98.8% homology with that of ST-J1. Sequence comparisons between SY-C1 and ST-J1 indicate that the variations include single-nucleotide mutations, insertions, deletions, and rearrangements, which suggested that SY-C1 is different from ST-J1 and represents a new genotype. Therefore, we propose that the identified CyHV-2 can be divided into 2 different genotypes and be named China genotype (C genotype) and Japan genotype (J genotype) according to their isolation loci. Furthermore, epidemiological surveys indicate that the dominant genotype of CyHV-2 circulating in mainland China is closer to the China genotype than the Japan genotype.

  4. Seroprevalence and genotype of Chlamydia in pet parrots in China.

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    Zhang, N-Z; Zhang, X-X; Zhou, D-H; Huang, S-Y; Tian, W-P; Yang, Y-C; Zhao, Q; Zhu, X-Q

    2015-01-01

    Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06-40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

  5. Firm and Product Heterogeneity in China's Automotive Exports

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    Jing Wang

    2015-12-01

    Full Text Available The main purpose of this paper is to provide an in-depth analysis of the anatomy of China's automotive exports, relying on the literature on firm and product heterogeneity. For this purpose, we use highly disaggregated HS 8-digit product-category level data collected by the Chinese Customs Office for 2000 and 2008, and we distinguish between foreign firms, domestic public firms, and domestic private firms. We also decompose automotive products into autos and auto parts and components (P/C. We then calculate both the extensive margins – number of products exported – and intensive margins – average value of exports per product – of China's automotive exports. We estimate gravity equations to assess the determinants of China's exports of autos and auto P/C. Overall, our analysis yields a number of new, interesting stylized facts about China's automotive exports by confirming the need for taking into account different types of heterogeneity in analyzing international trade.

  6. Phenotypic and genotypic heterogeneity of Lynch syndrome: a complex diagnostic challenge.

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    Lynch, Henry T; Lanspa, Stephen; Shaw, Trudy; Casey, Murray Joseph; Rendell, Marc; Stacey, Mark; Townley, Theresa; Snyder, Carrie; Hitchins, Megan; Bailey-Wilson, Joan

    2018-07-01

    Lynch syndrome is the hereditary disorder that most frequently predisposes to colorectal cancer as well as predisposing to a number of extracolonic cancers, most prominently endometrial cancer. It is caused by germline mutations in the mismatch repair genes. Both its phenotype and genotype show marked heterogeneity. This review gives a historical overview of the syndrome, its heterogeneity, its genomic landscape, and its implications for complex diagnosis, genetic counseling and putative implications for immunotherapy.

  7. First insight into the genotypic diversity of clinical Mycobacterium tuberculosis isolates from Gansu Province, China.

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    Jie Liu

    Full Text Available BACKGROUND: Investigations of Mycobacterium tuberculosis genetic diversity in China have indicated a significant regional distribution. The aim of this study was to characterize the genotypes of clinical M. tuberculosis isolates obtained from Gansu, which has a special geographic location in China. METHODOLOGY/PRINCIPAL FINDINGS: A total of 467 clinical M. tuberculosis strains isolated in Gansu Province were genotyped by 15-locus mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR and spoligotyping. The results showed that 445 isolates belonged to six known spoligotype lineages, whereas 22 isolates were unknown. The Beijing genotype was the most prevalent (87.58%, n = 409, while the shared type 1 was the dominant genotype (80.94%, n = 378. The second most common lineage was the T lineage, with 25 isolates (5.35%, followed by the H lineage with 5 isolates (1.07%, the MANU family (0.64%, 3 isolates, the U family (0.43%, 2 isolates and the CAS lineage with 1 isolate (0.21%. By using the VNTR15China method, we observed 15 groups and 228 genotypes among the 467 isolates. We found no association between the five larger groups (including the Beijing genotype and sex, age, or treatment status, and there was no noticeable difference in the group analysis in different areas. In the present study, seven of the 15 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. CONCLUSIONS/SIGNIFICANCE: The Beijing genotype is the predominant genotype in Gansu province. We confirm that VNTR15China is suitable for typing Beijing strains in China and that it has a better discriminatory power than spoligotyping. Therefore, the use of both methods is the most suitable for genotyping analysis of M. tuberculosis.

  8. Molecular characterization and multilocus genotypes of Enterocytozoon bieneusi among horses in southwestern China

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    Lei Deng

    2016-10-01

    Full Text Available Abstract Background Enterocytozoon bieneusi is one of the most prevalent causative species of diarrhea and enteric diseases in various hosts. E. bieneusi has been identified in humans, mammals, birds, rodents and reptiles in China, but few studies have reported E. bieneusi in horses. Therefore, the present study was conducted to assess the prevalence, molecular characteristics and zoonotic potential of E. bieneusi among horses in southwestern China. Findings Three hundred and thirty-three fecal specimens were collected from horses on five farms in the Sichuan and Yunnan provinces of southwestern China. The prevalence of E. bieneusi was 22.5 % (75/333, as determined by nested polymerase chain reaction and sequencing analysis of the internal transcribed spacer region of the ribosomal RNA gene of E. bieneusi. Altogether, 10 genotypes were identified among the 75 E. bieneusi-positive samples: four of these genotypes were known (horse1, horse2, SC02 and D and six were novel (SCH1-4 and YNH1-2. Multilocus sequence typing using three microsatellites (MS1, MS3 and MS7 and one minisatellite (MS4 revealed three, two, three and three genotypes at these four loci, respectively. In phylogenetic analysis, all the genotypes of E. bieneusi obtained in this study were clustered into three distinct groups: D, SC02 and SCH1-3 were clustered into group 1 (zoonotic potential; SCH4 was clustered into group 2 (cattle-hosted; whereas horse2, YNH1 and YNH2 were clustered into group 6 (unclear zoonotic potential. Conclusions This is the first report of E. bieneusi among horses in southwestern China. This is also the first multilocus genotyping analysis using microsatellite and minisatellite markers of E. bieneusi in horses. The presence of genotype D, which was previously identified in humans, and genotypes SC02 and SCH1-3, which belong to potential zoonotic group 1, these results indicate that horses are a potential source of human E. bieneusi infections in China.

  9. Heterogeneity and compartmentalization of Pneumocystis carinii f. sp. hominis genotypes in autopsy lungs

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Lundgren, Bettina; Lundgren, Jens Dilling

    2001-01-01

    The extent and importance of genotype heterogeneity of Pneumocystis carinii f. sp. hominis within lungs have not previously been investigated. Two hundred forty PCR clones obtained from respiratory specimens and lung segments from three patients with fatal P. carinii pneumonia were investigated....... Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mtLSU rRNA sequence types was observed in different lung segments. In conclusion, the interpretation of genotype data and in particular ITS sequence types...... in the assessment of epidemiological questions should be cautious since genotyping done on respiratory samples cannot a priori be assumed to represent all genotypes present within the lung....

  10. Genotyping of Brucella melitensis and Brucella abortus strains currently circulating in Xinjiang, China.

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    Sun, Ming-Jun; Di, Dong-Dong; Li, Yan; Zhang, Zhi-Cheng; Yan, Hao; Tian, Li-Li; Jing, Zhi-Gang; Li, Jin-Ping; Jiang, Hai; Fan, Wei-Xing

    2016-10-01

    Brucellosis is a well-known zoonotic disease that can cause severe economic and healthcare losses. Xinjiang, one of the biggest livestock husbandry sectors in China, has gone through increasing incidence of brucellosis in cattle and small ruminants recently. In this paper, 50 B. melitensis strains and 9 B. abortus strains collected from across Xinjiang area (from 2010 to 2015) were genotyped using multiple locus variable-number tandem-repeat (VNTR) analysis (MLVA) and multi-locus sequence typing (MLST). Based on 8 loci (MLVA-8), 50 B. melitensis strains were classified into three genotypes. Genotypes 42 (n=38, 76%) and 63 (n=11, 22%) were part of the East Mediterranean group, and one genotype with pattern of 1-5-3-13-2-4-3-2 represents a single-locus variant from genotype 63. MLVA-16 resolved 50 B. melitensis strains into 28 genotypes, of which 15 are unique to Xinjiang and 10 are in common with those in adjacent country Kazakhstan and neighboring provinces of China. Minimum Spanning Tree (MST) analysis implies that B. melitensis strains collected from across Kazakhstan, Xinjiang and China areas may share a common origin. Nine B. abortus strains were sorted into three genotypes by MLVA-8, genotypes 36 (n=7, 77.8%), 86 (n=1, 11.1%) and a new genotype with pattern of 4-5-3-13-2-2-3-1. Each B. abortus strain showed distinct MLVA-16 genotypes, suggesting that B. abortus species may possess more genetic diversity than B. melitensis. Using MLST, most B. melitensis strains (n=49) were identified as sequence type ST8, and most B. abortus strains (n=8) were recognized as ST2. Two new sequence types, ST37 and ST38, represented by single strain from B. melitensis and B. abortus species respectively, were also detected in this study. These results could facilitate the pathogen surveillance in the forthcoming eradication programs and serve as a guide in source tracking in case of new outbreaks occur. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Prevalence and Correlation with Clinical Diseases of Helicobacter pylori cagA and vacA Genotype among Gastric Patients from Northeast China

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    Faisal Aziz

    2014-01-01

    Full Text Available Helicobacter pylori vacA and cagA genes have significant genetic heterogenicity, resulting in different clinical outcomes. Northeast part of China has reported high prevalence of H. pylori infections and gastric cancer. Hence, we investigated the H. pylori cagA and vacA genotypes with clinical outcomes in Northeast China. Gastric tissue samples (n=169, chronic gastritis (GIs, gastric ulcer (GU, and gastric cancer (GC were analysed for 16S rRNA ureA, cagA, and cagA genotypes by PCR. A total of 141 (84% cases were found positive for H. pylori by 16S rRNA and ureA. GC showed high H. pylori infection (93% compared with GIs (72% and GU (84%. The vacAs1am1 was highly found in GC (40% and GU (36%, vacAs1am2 in GIs (33%, vacAs1bm1 (14% and vacAs1bm2 (8% in GU cases, and s2m1 in normal cases (33%, while vacAs1cm1 showed low frequency in GIs (2% and GU (3% and GC showed negative result. The East-Asian cagA strain was highly observed in GC (43%, as compared to GIs (41% and GU (20%. The East-Asian cagA/vacAs1am1 was significantly higher in GC (23% than in GU (22% and GIs (145 patients. The East-Asian type cagA with vacAs1a and vacAm1 is the most predominant genotype in H. pylori strains of Northeast China.

  12. Multilocus genotyping of Giardia duodenalis in captive non-human primates in Sichuan and Guizhou provinces, Southwestern China.

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    Zhijun Zhong

    Full Text Available Giardia duodenalis is a common human and animal pathogen. It has been increasingly reported in wild and captive non-human primates (NHPs in recent years. However, multilocus genotyping information for G. duodenalis infecting NHPs in southwestern China is limited. In the present study, the prevalence and multilocus genotypes (MLGs of G. duodenalis in captive NHPs in southwestern China were determined. We examined 207 fecal samples from NHPs in Sichuan and Guizhou provinces, and 16 specimens were positive for G. duodenalis. The overall infection rate was 7.7%, and only assemblage B was identified. G. duodenalis was detect positive in northern white-cheeked gibbon (14/36, 38.9%, crab-eating macaque (1/60, 1.7% and rhesus macaques (1/101, 0.9%. Multilocus sequence typing based on beta-giardin (bg, triose phosphate isomerase (tpi and glutamate dehydrogenase (gdh revealed nine different assemblage B MLGs (five known genotypes and four novel genotypes. Based on a phylogenetic analysis, one potentially zoonotic genotype of MLG SW7 was identified in a northern white-cheeked gibbon. A high degree of genetic diversity within assemblage B was observed in captive northern white-cheeked gibbons in Southwestern China, including a potentially zoonotic genotype, MLG SW7. To the best of our knowledge, this is the first report using a MLGs approach to identify G. duodenalis in captive NHPs in Southwestern China.

  13. Single endemic genotype of measles virus continuously circulating in China for at least 16 years.

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    Yan Zhang

    Full Text Available The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%-100% and 84.7%-100%, H1b were 97.1%-100% and 95.3%-100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR. Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years.

  14. Single Endemic Genotype of Measles Virus Continuously Circulating in China for at Least 16 Years

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    Wang, Huiling; Zhu, Zhen; Ji, Yixin; Liu, Chunyu; Zhang, Xiaojie; Sun, Liwei; Zhou, Jianhui; Lu, Peishan; Hu, Ying; Feng, Daxing; Zhang, Zhenying; Wang, Changyin; Fang, Xueqiang; Zheng, Huanying; Liu, Leng; Sun, Xiaodong; Tang, Wei; Wang, Yan; Liu, Yan; Gao, Hui; Tian, Hong; Ma, Jiangtao; Gu, Suyi; Wang, Shuang; Feng, Yan; Bo, Fang; Liu, Jianfeng; Si, Yuan; Zhou, Shujie; Ma, Yuyan; Wu, Shengwei; Zhou, Shunde; Li, Fangcai; Ding, Zhengrong; Yang, Zhaohui; Rota, Paul A.; Featherstone, David; Jee, Youngmee; Bellini, William J.; Xu, Wenbo

    2012-01-01

    The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%–100% and 84.7%–100%, H1b were 97.1%–100% and 95.3%–100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years. PMID:22532829

  15. New coxsackievirus B4 genotype circulating in Inner Mongolia Autonomous Region, China.

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    Xiaoling Tian

    Full Text Available Hand, foot, and mouth disease (HFMD surveillance was initiated in the Inner Mongolia Autonomous Region of China in 2007, a crucial scrutiny for monitoring the prevalence of enterovirus serotypes associated with HFMD patients. However, this surveillance mostly focused on enterovirus 71 (EV-A71 and coxsackievirus A16; therefore, information on other enterovirus serotypes is limited. To identify the other circulating enterovirus serotypes in the HFMD outbreaks in Inner Mongolia in 2010, clinical samples from HFMD patients were investigated. Six coxsackievirus B4 (CVB4 strains were isolated and phylogenetic analyses of VP1 sequences were performed. Full-length genome sequences of two representative CVB4 isolates were acquired and similarity plot and bootscanning analyses were performed. The phylogenetic dendrogram indicated that all CVB4 strains could be divided into 5 genotypes (Genotypes I-V with high bootstrap support (90-100%. The CVB4 prototype strain (JVB was the sole member of genotype I. CVB4 strains belonging to genotype II, which were once common in Europe and the Americas, seemingly disappeared and gave way to genotype III and IV strains, which appear to be the dominant circulating strains in the world. All Chinese CVB4 strains belonged to Genotype V, a newly identified genotype supported by a high bootstrap value (100%, and are circulating only in mainland of China. Intertypic recombination occurred in the Chinese CVB4 strains with novel unknown serotype EV-B donor sequences. Two Chinese CVB4 strains had a virulent residue at position 129 of VP1, and one strain also had a virulent residue at position 16 of VP4. Increased surveillance is needed to monitor the emergence of new genetic lineages of enteroviruses in areas that are often associated with large-scale outbreaks. In addition, continued monitoring of enteroviruses by clinical surveillance and genetic characterization should be enhanced.

  16. Enterovirus genotypes causing hand foot and mouth disease in Shanghai, China: a molecular epidemiological analysis

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    2013-01-01

    Background A rapid expansion of hand, foot, and mouth disease (HFMD) outbreaks has occurred and caused deaths in China in recent years, but little is known about the other etiologic agents except enterovirus 71 (EV71) and coxsackievirus A 16 (CA16). The objective of this study is to determine the genotype compositions of enterovirus causing HFMD in Shanghai and identify any associations between enterovirus types and clinical manifestations. Methods Stool specimens were collected from patients hospitalized for treatment of HFMD, from May 2010 to April 2011. Enterovirus was detected by reverse transcription PCR and directly genotyped by sequencing the PCR products. Phylogenetic analysis was based on the VP1 partial gene. Results Of 290 specimens, 277 (95.5%) tested positive for enterovirus. The major genotypes were EV71 (63.8%), CA10 (9.0%), CA6 (8.3%), CA16 (6.9%), CA12 (2.4%), and CA4 (1.4%). The EV71 strains belonged to the C4a subtype and CA16 belonged to the B subtype. CA6 was closely related to strains detected in Japan, Taiwan and China, and CA10, CA12 and CA4 were phylogenetically similar to other strains circulating in China. Mean hospital stays and the prevalence of complications in patients with EV71 infection were higher than those in patients in CA6, CA10 or CA16 infection (P enterovirus genotypes. It deserves our attention as early identification of enterovirus genotypes is important for diagnosis and treatment of HFMD patients. PMID:24148902

  17. Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China

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    It is the first report on SSR-based molecular evaluation of genetic variability among sugarcane genotypes from the Karst region of China that provides useful information for local sugarcane improvement. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred l...

  18. The first report of human-derived G10 genotype of Echinococcus canadensis in China and possible sources and routes of transmission.

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    Yang, Dong; Zhang, Tiemin; Zeng, Zhaolin; Zhao, Wei; Zhang, Weizhe; Liu, Aiqin

    2015-10-01

    Cystic echinococcosis (CE) is one of the most important parasitic zoonoses. 10 distinct genotypes, designated G1-G10 genotypes of Echinococcus granulosus sensu lato (s.l.), have been split into 4 species: Echinococcus granulosus sensu stricto (s.s.) (G1-G3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and Echinococcus canadensis (G6-G10); Echinococcus felidis has also been suggested as a sister taxon of E. granulosus s.s. recently. Four genotypes belonging to two species (G1 and G3 genotypes of E. granulosus s.s., and G6 and G7 genotypes of E. canadensis) have been identified in humans and animals in China. In the present study, a human-derived hydatid cyst from a patient in northeastern China's Heilongjiang Province was identified as G10 genotype of E. canadensis based on mitochondrial cytochrome c oxidase subunit I (cox1), cytochrome b (cytb) and NADH dehydrogenase subunit 1 (nad1) genes. Homology analysis showed the cox1 gene sequence of G10 genotype of E. canadensis had 100% homology with those from wolves in Mongolia and from a moose in Russia. The cytb and nad1 gene sequences of G10 genotype of E. canadensis had 100% homology with the complete sequence from a moose in Finland at an amino acid level. The infection source of the CE patient here might be primarily attributable to wolves. This is the first report of G10 genotype of E. canadensis in a human in China. The finding of G10 genotype of E. canadensis in China shows that this genotype possibly has a more wide geographical distribution than previously considered. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Nationwide prevalence of human papillomavirus infection and viral genotype distribution in 37 cities in China.

    Science.gov (United States)

    Wang, Rong; Guo, Xiao-Lei; Wisman, G Bea A; Schuuring, Ed; Wang, Wen-Feng; Zeng, Zheng-Yu; Zhu, Hong; Wu, Shang-Wei

    2015-07-04

    Type-specific high-risk HPV (hrHPV) infection is related to cervical carcinogenesis. The prevalence of hrHPV infection varies geographically, which might reflect the epidemiological characteristics of cervical cancer among different populations. To establish a foundation for HPV-based screening and vaccination programs in China, we investigated the most recent HPV prevalence and genotypic distributions in different female age groups and geographical regions in China. In 2012, a total of 120,772 liquid-based cytological samples from women enrolled for population- or employee-based cervical screening in 37 Chinese cities were obtained by the Laboratory of Molecular Infectious Diseases of Guangzhou KingMed. A total of 111,131 samples were tested by Hybrid Capture II and the other 9,641 were genotyped using the Tellgenplex™ HPV DNA Assay. The total positive rate for hrHPV was 21.07 %, which ranged from 18.42 % (Nanchang) to 31.94 % (Haikou) and varied by region. The regions of Nanchang, Changsha, Hangzhou, Chengdu, Fuzhou, Guangdong, and Guiyang could be considered the low prevalence regions. Age-specific prevalence showed a "two-peak" pattern, with the youngest age group (15-19 years) presenting the highest hrHPV infection rate (30.55 %), followed by a second peak for the 50-60-year-old group. Overall, the most prevalent genotypes were HPV16 (4.82 %) and HPV52 (4.52 %), followed by HPV58 (2.74 %). Two genotypes HPV6 (4.01 %) and HPV11 (2.29 %) were predominant in the low-risk HPV (lrHPV) type, while the mixed genotypes HPV16 + 52 and HPV52 + 58 were most common in women with multiple infections. This study shows that HPV infection in China has increased to the level of an "HPV-heavy-burden" zone in certain regions, with prevalence varying significantly among different ages and regions. Data from this study represent the most current survey of the nationwide prevalence of HPV infection in China, and can serve as valuable reference to guide nationwide cervical cancer

  20. Immunogenicity of mumps virus vaccine candidates matching circulating genotypes in the United States and China.

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    Zengel, James; Phan, Shannon I; Pickar, Adrian; Xu, Pei; He, Biao

    2017-07-13

    Mumps virus (MuV) causes acute infection in humans with characteristic swelling of the parotid gland. While vaccination has greatly reduced the incidence of MuV infection, there have been multiple large outbreaks of mumps virus (MuV) in highly vaccinated populations. The most common vaccine strain, Jeryl Lynn, belongs to genotype A, which is no longer a circulating genotype. We have developed two vaccine candidates that match the circulating genotypes in the United States (genotype G) and China (genotype F). We found that there was a significant decrease in the ability of the Jeryl Lynn vaccine to produce neutralizing antibody responses to non-matched viruses, when compared to either of our vaccine candidates. Our data suggests that an updated vaccine may allow for better immunity against the circulating MuV genotypes G and F. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. A new genotype of Cryptosporidium from giant panda (Ailuropoda melanoleuca) in China.

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    Liu, Xuehan; He, Tingmei; Zhong, Zhijun; Zhang, Hemin; Wang, Rongjun; Dong, Haiju; Wang, Chengdong; Li, Desheng; Deng, Jiabo; Peng, Guangneng; Zhang, Longxian

    2013-10-01

    Fifty-seven fecal samples were collected from giant pandas (Ailuropoda melanoleuca) in the China Conservation and Research Centre for the Giant Panda (CCRCGP) in Sichuan and examined for Cryptosporidium oocysts by Sheather's sugar flotation technique. An 18-year-old male giant panda was Cryptosporidium positive, with oocysts of an average size of 4.60×3.99 μm (n=50). The isolate was genetically analyzed using the partial 18S rRNA, 70 kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein (COWP) and actin genes. Multi-locus genetic characterization indicated that the present isolate was different from known Cryptosporidium species and genotypes. The closest relative was the Cryptosporidium bear genotype, with 11, 10, and 6 nucleotide differences in the 18S rRNA, HSP70, and actin genes, respectively. Significant differences were also observed in the COWP gene compared to Cryptosporidium mongoose genotype. The homology to the bear genotype at the 18S rRNA locus was 98.6%, which is comparable to that between Cryptosporidium parvum and Cryptosporidium hominis (99.2%), or between Cryptosporidium muris and Cryptosporidium andersoni (99.4%). Therefore, the Cryptosporidium in giant pandas in this study is considered as a new genotype: the Cryptosporidium giant panda genotype. © 2013 Elsevier Ireland Ltd. All rights reserved.

  2. Characterization of Prototheca zopfii Genotypes Isolated from Cases of Bovine Mastitis and Cow Barns in China.

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    Shahid, Muhammad; Ali, Tariq; Zhang, Limei; Hou, Rongguang; Zhang, Shiyao; Ding, Laidi; Han, Dandan; Deng, Zhaoju; Rahman, Abdur; Han, Bo

    2016-04-01

    Protothecal mastitis, caused mostly by Prototheca zopfii (P. zopfii), is increasing in dairy herds and is being reported globally. The present study was aimed at studying the epidemiology of mastitis and at molecular characterization of P. zopfii isolates from dairy herds and their surroundings in three provinces of China using microbiological, biochemical and molecular methods, and antibiotic susceptibility tests. Samples from milk (n = 620) of mastitic cows and their barns sources (n = 410) including feces, feed, bedding materials and drinking water were analyzed. Among other pathogens recovered from mastitic milk, 84 (13.5%) of the isolates were identified as P. zopfii. All of the P. zopfii isolates recovered from milk were recognized as genotype 2, whereas 58 (73.4%) and 21 (26.6%) isolates from environmental sources were found to be P. zopfii genotypes 1 and 2, respectively. The isolates were susceptible to some antibiotics and antifungal agents, including amikacin (78.1%), streptomycin (58.5%), gentamicin (17.8%), amphotericin B (68.6%) and nystatin (64.4%). Additionally, the two genotypes displayed versatile patterns of susceptibility to different antimicrobials agents. Phylogeny of the genotypes on the basis of 18S SSU rDNA and 28S SSU rDNA was also investigated. The isolates of the two genotypes separated into different clades, and no interrelationship was observed among these as shown by phylogenetic analysis. The genotype 1 isolates from cow barn sources were non-pathogenic and may not present any risk of mastitis. We conclude that P. zopfii genotype 2 might play an important role in bovine mastitis in China.

  3. Enterovirus genotypes causing hand foot and mouth disease in Shanghai, China: a molecular epidemiological analysis.

    Science.gov (United States)

    Xu, Menghua; Su, Liyun; Cao, Lingfeng; Zhong, Huaqing; Dong, Niuniu; Xu, Jin

    2013-10-22

    A rapid expansion of hand, foot, and mouth disease (HFMD) outbreaks has occurred and caused deaths in China in recent years, but little is known about the other etiologic agents except enterovirus 71 (EV71) and coxsackievirus A 16 (CA16). The objective of this study is to determine the genotype compositions of enterovirus causing HFMD in Shanghai and identify any associations between enterovirus types and clinical manifestations. Stool specimens were collected from patients hospitalized for treatment of HFMD, from May 2010 to April 2011. Enterovirus was detected by reverse transcription PCR and directly genotyped by sequencing the PCR products. Phylogenetic analysis was based on the VP1 partial gene. Of 290 specimens, 277 (95.5%) tested positive for enterovirus. The major genotypes were EV71 (63.8%), CA10 (9.0%), CA6 (8.3%), CA16 (6.9%), CA12 (2.4%), and CA4 (1.4%). The EV71 strains belonged to the C4a subtype and CA16 belonged to the B subtype. CA6 was closely related to strains detected in Japan, Taiwan and China, and CA10, CA12 and CA4 were phylogenetically similar to other strains circulating in China. Mean hospital stays and the prevalence of complications in patients with EV71 infection were higher than those in patients in CA6, CA10 or CA16 infection (P treatment of HFMD patients.

  4. Imported Genotype 2B Rubella Virus Caused the 2012 Outbreak in Anqing City, China.

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    Zhen Zhu

    Full Text Available A rubella outbreak occurred in Anqing city of Anhui province, China, from February to July of 2012, and a total of 241 clinically diagnosed or lab-confirmed patients were reported. The highest number of rubella cases during this outbreak was recorded in teenagers between 10 and 19 years of age who had not previously received the rubella vaccine. Genotyping results indicated that the genotype 2B rubella virus (RV was responsible for the outbreak. However, a phylogenetic analysis showed that the genotype 2B RVs isolated in Anqing City were not related to 2B RVs found in other cities of Anhui province and in other provinces of China, thus providing evidence for importation. After importation, the transmission of Anqing RVs was interrupted owing to an effective immunization campaign against rubella, suggesting the timeliness and effectiveness of contingency vaccination. Strengthening rubella surveillance, including the integration of epidemiologic information and laboratory data, is a vital strategy for rubella control and elimination. In addition, except for routine immunization, targeted supplementary immunization activities aimed at susceptible groups according to sero-epidemiological surveillance data also play a key role in stopping the continuous transmission of rubella viruses and in preventing further congenital rubella syndrome cases.

  5. A new trend of genotype distribution of hepatitis B virus infection in southeast China (Fujian), 2006-2013.

    Science.gov (United States)

    Wei, D H; Liu, H Z; Huang, A M; Liu, X L; Liu, J F

    2015-10-01

    HBV genotypes have specific geographical distributions and can serve as epidemiological markers. Accumulated data have shown that the major HBV genotypes in China are B and C. Here, the HBV genotypes were examined from 6817 blood samples, which were collected from patients with chronic HBV infection in Fujian Province during 2006-2013; genotype B was identified in 3384 patients (49·6%), while genotype C was identified in 3430 patients (50·3%). The percentage of patients infected with genotype C gradually increased with age from 39·5% (patients aged 50 years), reaching a peak of 67·3% in the 45-50 years age group. These results clearly demonstrate that the genotype distribution of HBV in Fujian Province has significantly changed in recent years with almost equal numbers of genotype B and genotype C infections existing in the entire patient population, while higher incidence of genotype C infection exists in older patients, but genotype B is no longer dominant in the Fujian area as previously reported.

  6. Molecular characterization and multi-locus genotypes of Enterocytozoon bieneusi from captive red kangaroos (Macropus Rufus in Jiangsu province, China.

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    Zhijun Zhong

    Full Text Available Enterocytozoon bieneusi is the most common pathogen of microsporidian species infecting humans worldwide. Although E. bieneusi has been found in a variety of animal hosts, information on the presence of E. bieneusi in captive kangaroos in China is limited. The present study was aimed at determining the occurrence and genetic diversity of E. bieneusi in captive kangaroos. A total of 61 fecal specimens (38 from red kangaroos and 23 from grey kangaroos were collected from Nanjing Hongshan Forest Zoo and Hongshan Kangaroo Breeding Research Base, Jiangsu province, China. Using the nested PCR amplification ITS gene of rRNA of E. bieneusi, totally 23.0% (14/61 of tested samples were PCR-positive with three genotypes (i.e. one known genotype, CHK1, and two novel genotypes, CSK1 and CSK2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7 and one minisatellite (MS4 revealed one, five, two, and one types at these four loci, respectively. In phylogenetic analysis, the two genotypes, CHK1 and CSK1, were clustered into a new group of unknown zoonotic potential, and the novel genotype CSK2 was clustered into a separate clade with PtEb and PtEbIX. To date, this is the first report on the presence of E. bieneusi in captive red kangaroos in Jiangsu province, China. Furthermore, a high degree of genetic diversity was observed in the E. bieneusi genotype and seven MLGs (MLG1-7 were found in red kangaroos. Our findings suggest that infected kangaroo may act as potential reservoirs of E. bieneusi and be source to transmit infections to other animal.

  7. Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype.

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    Lin, Yi-Hua; Gao, San-Ji; Damaj, Mona B; Fu, Hua-Ying; Chen, Ru-Kai; Mirkov, T Erik

    2014-06-01

    Sugarcane yellow leaf virus (SCYLV; genus Polerovirus, family Luteoviridae) is a recombinant virus associated with yellow leaf disease, a serious threat to sugarcane in China and worldwide. Among the nine known SCYLV genotypes existing worldwide, COL, HAW, REU, IND, CHN1, CHN2, BRA, CUB and PER, the last five have been reported in China. In this study, the complete genome sequences (5,880 nt) of GZ-GZ18 and HN-CP502 isolates from the Chinese provinces of Guizhou and Hainan, respectively, were cloned, sequenced and characterized. Phylogenetic analysis showed that, among 29 SCYLV isolates described worldwide, the two Chinese isolates clustered together into an independent clade based on the near-complete genome nucleotide (ORF0-ORF5) or amino acid sequences of individual genes, except for the MP protein (ORF4). We propose that the two isolates represent a novel genotype, CHN3, diverging from other genotypes by 1.7-13.6 % nucleotide differences in ORF0-ORF5, and 2.7-28.1 %, 1.8-20.4 %, 0.5-5.1 % and 2.7-15.9 % amino acid differences in P0 (ORF0), RdRp (RNA-dependent RNA polymerase) (ORF1+2), CP (coat protein) (ORF3) and RT (readthrough protein) (ORF3+5), respectively. CHN3 was closely related to the BRA, HAW and PER genotypes, differing by 1.7-3.8 % in the near-complete genome nucleotide sequence. Recombination analysis further identified CHN3 as a new recombinant strain, arising from the major parent CHN-HN1 and the minor parent CHN-GD-WY19. Recombination breakpoints were distributed mostly within the RdRp region in CHN3 and the four significant recombinant genotypes, IND, REU, CUB and BRA. Recombination is considered to contribute significantly to the evolution and emergence of such new SCYLV variants.

  8. New Genotypes of Enterocytozoon bieneusi Isolated from Sika Deer and Red Deer in China

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    Jianying Huang

    2017-05-01

    Full Text Available To examine the occurrence and genotype distribution of Enterocytozoon bieneusi in cervids, 615 fecal samples were collected from red deer (Cervus elaphus and sika deer (Cervus nippon on 10 different farms in Henan and Jilin Province. Enterocytozoon bieneusi was identified and genotyped with a nested PCR analysis of the internal transcribed spacer (ITS region of the rRNA genes, showing an average infection rate of 35.9% (221/615. In this study, 25 ITS genotypes were identified including seven known genotypes (BEB6, EbpC, EbpA, D, HLJDI, HLJD-IV, and COS-I and 18 novel genotypes (designated JLD-I to JLD-XIV, HND-I to HND-IV. Among these, BEB6 (131/221, 59.3% was the predominant genotype (P < 0.01, followed by HLJDI (18/221, 8.1% and JLD-VIII (16/221, 7.2%. BEB6 has recently been detected in humans and nonhuman primates in China. The phylogenetic analysis showed that BEB6, HLJDI, HLJD-IV, COS-I, and 10 novel genotypes (JLD-VII to JLD-XIV, HND-III to HND-IV clustered in group 2. Genotype D, EbpC, and EbpA, known to cause human microsporidiosis worldwide, clustered in group 1, the members of which have zoonotic potential, together with eight novel genotypes (JLD-I to JLD-VI, HND-I to HND-II. Therefore, deer may play a role in the transmission of E. bieneusi to humans.

  9. Enzootic genotype S of H9N2 avian influenza viruses donates internal genes to emerging zoonotic influenza viruses in China.

    Science.gov (United States)

    Gu, Min; Chen, Hongzhi; Li, Qunhui; Huang, Junqing; Zhao, Mingjun; Gu, Xiaobing; Jiang, Kaijun; Wang, Xiaoquan; Peng, Daxin; Liu, Xiufan

    2014-12-05

    Avian influenza viruses of subtype H9N2 are widely prevalent in poultry in many Asian countries, and the segmented nature of the viral genome results in multiple distinct genotypes via reassortment. In this study, genetic evolution of H9N2 viruses circulating in eastern China during 2007-2013 was analyzed. The results showed that the diversity of the gene constellations generated six distinct genotypes, in which a novel genotype (S) bearing the backbone of A/chicken/Shanghai/F/98-like viruses by acquiring A/quail/Hong Kong/G1/97-like polymerase basic subunit 2 and matrix genes has gradually established its ecological niche and been consistently prevalent in chicken flocks in eastern China since its first detection in 2007. Furthermore, genotype S possessed the peculiarity to donate most of its gene segments to other emerging influenza A viruses in China, including the novel reassortant highly pathogenic avian influenza H5N2, the 2013 novel H7N7, H7N9 and the latest reassortant H10N8 viruses, with potential threat to poultry industry and human health. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Molecular characterization of two genotypes of a new polerovirus infecting brassicas in China.

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    Xiang, Hai-Ying; Dong, Shu-Wei; Shang, Qiao-Xia; Zhou, Cui-Ji; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

    2011-12-01

    The genomic RNA sequences of two genotypes of a brassica-infecting polerovirus from China were determined. Sequence analysis revealed that the virus was closely related to but significantly different from turnip yellows virus (TuYV). This virus and other poleroviruses, including TuYV, had less than 90% amino acid sequence identity in all gene products except the coat protein. Based on the molecular criterion (>10% amino acid sequence difference) for species demarcation in the genus Polerovirus, the virus represents a distinct species for which the name Brassica yellows virus (BrYV) is proposed. Interestingly, there were two genotypes of BrYV, which mainly differed in the 5'-terminal half of the genome.

  11. Association between genotype and drug resistance profiles of Mycobacterium tuberculosis strains circulating in China in a national drug resistance survey

    NARCIS (Netherlands)

    Zhou, Yang; van den Hof, Susan; Wang, Shengfen; Pang, Yu; Zhao, Bing; Xia, Hui; Anthony, Richard; Ou, Xichao; Li, Qiang; Zheng, Yang; Song, Yuanyuan; Zhao, Yanlin; van Soolingen, Dick

    2017-01-01

    We describe the population structure of a representative collection of 3,133 Mycobacterium tuberculosis isolates, collected within the framework of a national resistance survey from 2007 in China. Genotyping data indicate that the epidemic strains in China can be divided into seven major complexes,

  12. Genotypic distribution and phylogenetic characterization of Enterocytozoon bieneusi in diarrheic chickens and pigs in multiple cities, China: potential zoonotic transmission.

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    Wei Li

    Full Text Available This study investigated diarrheic broiler and layer chickens (60 days; n=64 for E. bieneusi genotypes in northeast China and evaluated the potential roles of chickens and pigs in zoonotic transmission of microsporidiosis. Two 45-day-old layer chickens in city Jixi, Heilongjiang province and one 23-day-old broiler chicken in city Songyuan, Jilin province were identified to harbor a human-pathogenic E. bieneusi genotype Henan-IV and a new genotype named CC-1, respectively, by nested PCR and sequence analysis of the ribosomal internal transcribed spacer (ITS. Eleven of 64 (17.2% duodenal mucosal specimens from pigs in city Tianjin, city Tongliao of Inner Mongolia, cities Jilin and Songyuan of Jilin province, and cities Daqing, Harbin, and Suihua of Heilongjiang province, were positive for E. bieneusi, with the infection rates of weaned pigs (35%, 7/20 significantly higher than preweaned ones (3.6%, 1/28; P<0.05. Nucleotide sequences of the ITS were obtained from 6 pig specimens, belonging to 3 known genotypes CHN7, EbpC, and Henan-IV. That the previous reports have described the occurrence of genotypes EbpC and Henan-IV in humans and EbpC in wastewater in central China and the clustering of genotypes CC-1 and CHN7 into a major phylogenetic group of E. bieneusi genotypes with zoonotic potential indicated that chickens and pigs could be potential sources of human micorsporidiosis. To our knowledge, this is the first report describing the existence of zoonotic E. bieneusi genotypes in diarrheic chickens.

  13. Physico-chemical properties, antioxidant activity and mineral contents of pineapple genotypes grown in china.

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    Lu, Xin-Hua; Sun, De-Quan; Wu, Qing-Song; Liu, Sheng-Hui; Sun, Guang-Ming

    2014-06-23

    The fruit physico-chemical properties, antioxidant activity and mineral contents of 26 pineapple [Ananas comosus (L.) Merr.] genotypes grown in China were measured. The results showed great quantitative differences in the composition of these pineapple genotypes. Sucrose was the dominant sugar in all 26 genotypes, while citric acid was the principal organic acid. Potassium, calcium and magnesium were the major mineral constituents. The ascorbic acid (AsA) content ranged from 5.08 to 33.57 mg/100 g fresh weight (FW), while the total phenolic (TP) content varied from 31.48 to 77.55 mg gallic acid equivalents (GAE)/100 g FW. The two parameters in the predominant cultivars Comte de Paris and Smooth Cayenne were relative low. However, MD-2 indicated the highest AsA and TP contents (33.57 mg/100 g and 77.55 mg GAE/100 g FM, respectively), and it also showed the strongest antioxidant capacity 22.85 and 17.30 μmol TE/g FW using DPPH and TEAC methods, respectively. The antioxidant capacity of pineapple was correlated with the contents of phenolics, flavonoids and AsA. The present study provided important information for the further application of those pineapple genotypes.

  14. Analysis of HBV genotype distribution and its association with liver cirrhosis in Xinjiang Uygur Autonomous Region, China

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    WANG Xiaozhong

    2014-12-01

    Full Text Available ObjectiveTo investigate the distribution of hepatitis B virus (HBV genotypes among patients in Xinjiang Uygur Autonomous Region, China, and to explore its association with liver cirrhosis. MethodsHBV genotypes of 1018 hepatitis B patients were determined by PCR analysis. The relationship of HBV genotype with clinical outcomes and relevant chronic liver diseases was assessed by contingency chi-square test, Kruskal-Wallis test, and multivariate unconditional logistic regression analysis. ResultsAmong the 828 patients whose HBV genotyping was completed in this study, type C was the major genotype and the percentage was 54.11% (448/828, 25.15% (200/828 had type B, and 16.18% (134/828 had type D. Among the 116 patients with liver cirrhosis, 20.84% had type C, which was significantly more frequent than other genotypes (P<0.00. The multivariate unconditional logistic regression model identified several risk factors for liver cirrhosis, including duration of hepatitis B≥10 years, C genotype, high HBV DNA viral load, and impaired liver function characterized by abnormal alanine aminotransferase test. Among all these factors, genotype C had the highest relevance to liver cirrhosis (OR=2819. ConclusionThe leading genotype of HBV in Xinjiang Uygur Autonomous Region is type C, followed by type B and type D. Genotype C is an independent risk factor for HBV-related liver cirrhosis.

  15. Heterogeneous convergence of regional house prices and the complexity in China

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    Rui Lin

    2015-12-01

    Full Text Available The purpose of this research is to analyze the convergence of regional house prices and its complexity in China. In this purpose it used nonlinear time varying factor model. The obtained results have provided evidences for the existence of some degree of segmentation in China’s housing market. By further dynamic analysis of the convergence, we have found that important housing policies from Chinese central government can significantly alter the housing market but with a time lag of 4 to 5 months, and that quite different behaviors exist between the new house market and the second-hand house market in China, which provides the evidence for the complexity of housing market in China. Multiple factors together are the driving forces for the regional house price convergence. And the driving forces differ among three clubs. The basic conclusion provided from the realized research is that the conventional definitions of economic regions may not be appropriate to analyze house price segregation in China. Heterogeneous convergence exists in China’s regional house prices, indicating the complexity of regional house prices in China. And housing policies should be implemented with different focus among the regions. The way of the central government is to make housing policies aiming at different sub-markets of the new house market and the second-hand house market.

  16. Prevalence and Genotyping of Cryptosporidium Infection in Pet Parrots in North China

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    Xiao-Xuan Zhang

    2015-01-01

    Full Text Available Cryptosporidiosis is a worldwide zoonosis caused by Cryptosporidium spp., sometimes leading to severe diarrhea in humans and animals. In the present study, 311 parrots, belonging to four species, namely, Budgerigars (Melopsittacus undulatus, Lovebirds (Agapornis sp., Alexandrine parakeets (Psittacula eupatria, and Cockatiel (Nymphicus hollandicus, from Beijing and Weifang cities, were examined for Cryptosporidium spp. infection. Blood samples of each bird were examined using enzyme linked immunosorbent assay (ELISA and fecal samples were examined by Sheather’s sugar flotation technique. Prevalence of Cryptosporidium infection were 3.22% (10/311 and 0.64% (2/311 by ELISA and Sheather’s sugar flotation technique, respectively. Seroprevalence of Cryptosporidium infection in different breeds varied from 0 to 15.39%. Sequencing analysis showed that both positive samples from fecal samples belonged to Cryptosporidium avian genotype V. This is the first report of Cryptosporidium avian genotype V in Budgerigars. The results of the present study provided foundation-data for prevention and control of cryptosporidiosis in pet birds in China.

  17. Prevalence and Genotyping of Cryptosporidium Infection in Pet Parrots in North China.

    Science.gov (United States)

    Zhang, Xiao-Xuan; Zhang, Nian-Zhang; Zhao, Guang-Hui; Zhao, Quan; Zhu, Xing-Quan

    2015-01-01

    Cryptosporidiosis is a worldwide zoonosis caused by Cryptosporidium spp., sometimes leading to severe diarrhea in humans and animals. In the present study, 311 parrots, belonging to four species, namely, Budgerigars (Melopsittacus undulatus), Lovebirds (Agapornis sp.), Alexandrine parakeets (Psittacula eupatria), and Cockatiel (Nymphicus hollandicus), from Beijing and Weifang cities, were examined for Cryptosporidium spp. infection. Blood samples of each bird were examined using enzyme linked immunosorbent assay (ELISA) and fecal samples were examined by Sheather's sugar flotation technique. Prevalence of Cryptosporidium infection were 3.22% (10/311) and 0.64% (2/311) by ELISA and Sheather's sugar flotation technique, respectively. Seroprevalence of Cryptosporidium infection in different breeds varied from 0 to 15.39%. Sequencing analysis showed that both positive samples from fecal samples belonged to Cryptosporidium avian genotype V. This is the first report of Cryptosporidium avian genotype V in Budgerigars. The results of the present study provided foundation-data for prevention and control of cryptosporidiosis in pet birds in China.

  18. Population structure of Phytophthora infestans in China – geographic clusters and presence of the EU genotype Blue_13

    NARCIS (Netherlands)

    Li, Y.; Lee, van der T.A.J.; Zhu, J.H.; Jin, G.H.; Lan, C.Z.; Zhu, S.X.; Zhang, R.F.; Liu, B.W.; Zhao, Z.J.; Kessel, G.J.T.; Huang, S.W.; Jacobsen, E.

    2013-01-01

    The population structure of Phytophthora infestans in China was studied and three mitochondrial haplotypes (Ia, IIa, IIb) were observed. Genetic analysis with 10 highly informative SSR markers identified 68 different genotypes, including three dominant clonal lineages. In the Chinese P. infestans

  19. Cost-effectiveness of daclatasvir plus asunaprevir for chronic hepatitis C genotype 1b treatment-naïve patients in China.

    Science.gov (United States)

    Lu, Yun; Jin, Xiuze; Duan, Cheng-A-Xin; Chang, Feng

    2018-01-01

    Hepatitis C is the second fastest growing infectious disease in China. The standard-of-care for chronic hepatitis C in China is Pegylated interferon plus ribavirin (PR), which is associated with tolerability and efficacy issues. An interferon- and ribavirin-free, all-oral regimen comprising daclatasvir (DCV) and asunaprevir (ASV), which displays higher efficacy and tolerability, has recently been approved in China. This study is to estimate the cost-effectiveness of DCV+ASV (24 weeks) for chronic hepatitis C genotype 1b treatment-naïve patients compared with PR regimen (48 weeks) in China. A cohort-based Markov model was developed from Chinese payer perspective to project the lifetime outcomes of treating 10,000 patients with an average age of 44.5 with two hypothetical regimens, DCV+ASV and PR. Chinese-specific health state costs and efficacy data were used. The annual discount rate was 5%. Base-case analysis and sensitivity analysis were conducted. For HCV Genotype 1b treatment-naïve patients, DCV+ASV proved to be dominant over PR, with a cost saving of ¥33,480(5,096 USD) and gains in QALYs and life years of 1.29 and 0.85, respectively. The lifetime risk of compensated cirrhosis, decompensated cirrhosis, hepatocellular carcinoma and liver-related death was greatly reduced with DCV+ASV. Univariate sensitivity analysis demonstrated that key influencers were the discount rate, time horizon, initial disease severity and sustained virological response rate of DCV+ASV, with all scenarios resulting in additional benefit. Probabilistic sensitivity analysis demonstrated that DCV+ASV has a high likelihood (100%) of being cost-effective. DCV+ASV is not only an effective and well-tolerated regimen to treat chronic HCV genotype 1b infection treatment-naïve patients, but also is more cost-effective than PR regimen. DCV+ASV can benefit both the public health and reimbursement system in China.

  20. Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

    Science.gov (United States)

    Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

    2016-09-17

    Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

  1. Effects of soil nutrient heterogeneity on intraspecific competition in the invasive, clonal plant Alternanthera philoxeroides.

    Science.gov (United States)

    Zhou, Jian; Dong, Bi-Cheng; Alpert, Peter; Li, Hong-Li; Zhang, Ming-Xiang; Lei, Guang-Chun; Yu, Fei-Hai

    2012-03-01

    Fine-scale, spatial heterogeneity in soil nutrient availability can increase the growth of individual plants, the productivity of plant communities and interspecific competition. If this is due to the ability of plants to concentrate their roots where nutrient levels are high, then nutrient heterogeneity should have little effect on intraspecific competition, especially when there are no genotypic differences between individuals in root plasticity. We tested this hypothesis in a widespread, clonal species in which individual plants are known to respond to nutrient heterogeneity. Plants derived from a single clone of Alternanthera philoxeroides were grown in the greenhouse at low or high density (four or 16 plants per 27·5 × 27·5-cm container) with homogeneous or heterogeneous availability of soil nutrients, keeping total nutrient availability per container constant. After 9 weeks, measurements of size, dry mass and morphology were taken. Plants grew more in the heterogeneous than in the homogeneous treatment, showing that heterogeneity promoted performance; they grew less in the high- than in the low-density treatment, showing that plants competed. There was no interactive effect of nutrient heterogeneity and plant density, supporting the hypothesis that heterogeneity does not affect intraspecific competition in the absence of genotypic differences in plasticity. Treatments did not affect morphological characteristics such as specific leaf area or root/shoot ratio. Results indicate that fine-scale, spatial heterogeneity in the availability of soil nutrients does not increase competition when plants are genetically identical, consistent with the suggestion that effects of heterogeneity on competition depend upon differences in plasticity between individuals. Heterogeneity is only likely to increase the spread of monoclonal, invasive populations such as that of A. philoxeroides in China.

  2. Upper mantle low velocity heterogeneities beneath NE China revealed by source- and receiver-side converted waves

    Science.gov (United States)

    Guan, Z.; Niu, F.

    2017-12-01

    Common-conversion-point (CCP) stacking of receiver function is a powerful tool in mapping upper mantle heterogeneities. However, reverberations from shallow boundaries with large velocity contrast could contaminate the imaging profiles severely. Applying the refined Slowness Weighted CCP (SWCCP) stacking technique (Guan and Niu, 2017) on NECESSArray data, we eliminated the multiple effects and systematically imaged the upper mantle low velocity heterogeneities in NE China where there exist rich unconsolidated sediments. The SWCCP profiles reveal a 350 km low velocity heterogeneity which is possibly associated with the Changbai Mountain volcanism and interpreted as a negatively buoyant silicate melt lying atop of the 410 km discontinuity. Besides, the imaging results are also suggestive of a sporadic 580-620 km low velocity heterogeneity locating in the easternmost part of NE China with a velocity contrast comparable with the 660-km discontinuity. In addition, between 42º N and 45º N, we also found a double 660-km discontinuity at the two sides of the localized depression in the longitudinal range of 128º E to 131º E. On the other hand, we gathered USArray and Alaska regional array seismic data of deep earthquakes occurring beneath NE China and the surrounding areas and employed stacking technique to study the source side S-to-P conversions. The source-side stacking also showed a strong S-to-P conversion at 600 km deep, consistent with the SWCCP stacks. Meanwhile, we also confirmed the double 660-km discontinuity feature from the source-side conversions. The receiver- and source-side observations provide strong constraints on these low velocity anomalies that may offer insights on the subduction dynamics of the Pacific plate.

  3. A challenge to the striking genotypic heterogeneity of retinitis pigmentosa: a better understanding of the pathophysiology using the newest genetic strategies

    Science.gov (United States)

    Sorrentino, F S; Gallenga, C E; Bonifazzi, C; Perri, P

    2016-01-01

    Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by a complex association between tremendous genotypic multiplicity and great phenotypic heterogeneity. The severity of the clinical manifestation depends on penetrance and expressivity of the disease-gene. Also, various interactions between gene expression and environmental factors have been hypothesized. More than 250 genes with ~4500 causative mutations have been reported to be involved in different RP-related mechanisms. Nowadays, not more than the 50% of RPs are attributable to identified genes, whereas the rest of molecular defects are still undetectable, especially in populations where few genetic screenings have been performed. Therefore, new genetic strategies can be a remarkably useful tool to aid clinical diagnosis, potentially modifying treatment options, and family counseling. Genome-wide analytical techniques (array comparative genomic hybridization and single-nucleotide polymorphism genotyping) and DNA sequencing strategies (arrayed primer extension, Sanger sequencing, and ultra high-throughput sequencing) are successfully used to early make molecular diagnosis detecting single or multiple mutations in the huge heterogeneity of RPs. To date, further research needs to be carried out to better investigate the genotype/phenotype correlation, putting together genetic and clinical findings to provide detailed information concerning the risk of RP development and novel effective treatments. PMID:27564722

  4. Genotypes of Cryptosporidium spp., Enterocytozoon bieneusi and Giardia duodenalis in dogs and cats in Shanghai, China.

    Science.gov (United States)

    Xu, Hailing; Jin, Yue; Wu, Wenxian; Li, Pei; Wang, Lin; Li, Na; Feng, Yaoyu; Xiao, Lihua

    2016-03-01

    Controversies exist on the potential role of companion animals in the transmission of enteric pathogens in humans. This study was conducted to examine the genotype distribution of Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis in companion animals in Shanghai, China, and to assess their zoonotic potential. Fecal specimens from 485 dogs and 160 cats were examined for the occurrence and genotype distribution of the three pathogens by PCR. PCR products were sequenced to determine the species and genotypes. The χ(2) test was used to compare differences in infection rates between living conditions or age groups. Cryptosporidium spp., E. bieneusi and G. duodenalis were found in 39 (8.0 %), 29 (6.0 %) and 127 (26.2 %) of dogs, and 6 (3.8 %), 9 (5.6 %) and 21 (13.1 %) of cats, respectively. Infection rates of the pathogens in dogs from pet shops and a clinic were higher than those in household dogs, and higher in cats from one animal shelter than from pet shops. No significant differences in infection rates were detected among age groups. Cryptosporidium canis and C. felis were the only Cryptosporidium species found in dogs and cats, respectively. Enterocytozoon bieneusi genotype PtEb IX was the dominant genotype in dogs, whereas Type IV and D were the most common ones in cats. Multi-locus sequence typing at the glutamate dehydrogenase, β-giardin, and triosephosphate isomerase loci revealed the presence of G. duodenalis assemblages A (n = 23), B (n = 1), C (n = 26), and D (n = 58) in dogs (only A in household dogs) and assemblages A (n = 2), B (n = 6), C (n = 2), D (n = 1), and F (n = 7) in cats. Co-infection was detected in 24 dogs and 5 cats, especially those living in crowded conditions. Living condition is a major risk factor affecting the occurrence of enteric protists in companion animals in China, and although dogs and cats can be potential sources of human infections, the different distribution of

  5. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  6. The Transmission Disequilibrium/Heterogeneity Test with Parental-Genotype Reconstruction for Refined Genetic Mapping of Complex Diseases

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    Jing Han

    2012-01-01

    Full Text Available In linkage analysis for mapping genetic diseases, the transmission/disequilibrium test (TDT uses the linkage disequilibrium (LD between some marker and trait loci for precise genetic mapping while avoiding confounding due to population stratification. The sib-TDT (S-TDT and combined-TDT (C-TDT proposed by Spielman and Ewens can combine data from families with and without parental marker genotypes (PMGs. For some families with missing PMG, the reconstruction-combined TDT (RC-TDT proposed by Knapp may be used to reconstruct missing parental genotypes from the genotypes of their offspring to increase power and to correct for potential bias. In this paper, we propose a further extension of the RC-TDT, called the reconstruction-combined transmission disequilibrium/heterogeneity (RC-TDH test, to take into account the identical-by-descent (IBD sharing information in addition to the LD information. It can effectively utilize families with missing or incomplete parental genetic marker information. An application of this proposed method to Genetic Analysis Workshop 14 (GAW14 data sets and extensive simulation studies suggest that this approach may further increase statistical power which is particularly valuable when LD is unknown and/or when some or all PMGs are not available.

  7. Rubella epidemic caused by genotype 1E rubella viruses in Beijing, China, in 2007-2011.

    Science.gov (United States)

    Chen, Meng; Zhu, Zhen; Liu, Donglei; Huang, Guohong; Huang, Fang; Wu, Jiang; Zhang, Tiegang; Xu, Wenbo; Pang, Xinghuo

    2013-04-18

    A series of different rubella vaccination strategies were implemented to control rubella and prevent congenital rubella virus infection in Beijing, China. The rubella vaccine was available in 1995 in Beijing, and was introduced into the Beijing immunization program (vaccine recipients at their own expense vaccination) in 2000, and was introduced into the National Expanded Program on Immunization (vaccine recipients free vaccination) in 2006. Rubella virological surveillance started in Beijing in 2007. The reported rubella incidence rate has decreased dramatically due to the introduction of the vaccine in Beijing since 1995. However, rubella epidemics occurred regardless in 2001 and 2007. The incidence rate among the floating population has gradually increased since 2002, reaching 2 or more times that in the permanent resident population. The peak age of rubella cases gradually changed from tree was constructed based on the World Health Organization standard sequence window for rubella virus isolates. All Beijing rubella virus isolates belong to genotype 1E/cluster1 and were clustered interspersed with viruses from other provinces in China. The effective number of infections indicated by a Bayesian skyline plot remained constant from 2007 to 2011. The proportion of rubella cases among the floating population has increased significantly in Beijing since 2002, and the disease burden gradually shifted to the older age group (15- to 39-year olds), which has become a major group with rubella infection since 2006. Genotype 1E rubella virus continuously caused a rubella epidemic in Beijing in 2007-2011 and was the predominant virus, and all Beijing genotype 1E viruses belong to cluster 1, which is also widely circulated throughout the country.

  8. Genetic characterization of human-derived hydatid cysts of Echinococcus granulosus sensu lato in Heilongjiang Province and the first report of G7 genotype of E. canadensis in humans in China.

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    Tiemin Zhang

    Full Text Available Cystic echinococcosis (CE caused by the larval stage of Echinococcus granulosus sensu lato (s.l. is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1-G10 have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province of northeastern China, no molecular information is available on E. granulosus s.l. To understand and to speculate on possible transmission patterns of E. granulosus s.l., we molecularly identified and genotyped 10 hydatid cysts from hepatic CE patients in Heilongjiang Province based on mitochondrial cytochrome c oxidase subunit I (cox1, cytochrome b (cytb and NADH dehydrogenase subunit 1 (nad1 genes. Two genotypes were identified, G1 genotype (n = 6 and G7 genotype (n = 4. All the six G1 genotype isolates were identical to each other at the cox1 locus; three and two different sequences were obtained at the cytb and nad1 loci, respectively, with two cytb gene sequences not being described previously. G7 genotype isolates were identical to each other at the cox1, cytb and nad1 loci; however, the cytb gene sequence was not described previously. This is the first report of G7 genotype in humans in China. Three new cytb gene sequences from G1 and G7 genotypes might reflect endemic genetic characterizations. Pigs might be the main intermediate hosts of G7 genotype in our investigated area by homology analysis. The results will aid in making more effective control strategies for the prevention of transmission of E. granulosus s.l.

  9. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-01-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different

  10. The genotypic characterization of Cronobacter spp. isolated in China.

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    Jinghua Cui

    Full Text Available Cronobacter spp. (Enterobacter sakazakii is an important pathogen contaminating powdered infant formula (PIF. To describe the genotypic diversity of Cronobacter isolated in China, we identified the isolates using fusA allele sequencing, and subtyped all of the isolates using pulsed-field gel electrophoresis (PFGE, multi-locus sequence typing (MLST, and multiple-locus variable-number tandem-repeat analysis (MLVA. A total of 105 isolates were identified, which included C. sakazakii (58 isolates, C. malonaticus (30 isolates, C. dublinensis (11 isolates, C. turicensis (5 isolates, and C. muytjensii (1 isolate. These isolates were showed to have 85 PFGE-patterns, 71 sequence types (STs, and 55 MLVA-patterns. Comparisons among the three molecular subtyping methods revealed that the PFGE method was the most distinguishable tool in identifying clusters of Cronobacter spp. through DNA fingerprinting, and MLST method came second. However, ESTR-1, ESTR-2, ESTR-3, and ESTR-4 were not effective loci for subtyping Cronobacter spp. such that the MLVA method requires further improvement.

  11. Genetic Characterization of Human-Derived Hydatid Cysts of Echinococcus granulosus Sensu Lato in Heilongjiang Province and the First Report of G7 Genotype of E. canadensis in Humans in China

    Science.gov (United States)

    Zeng, Zhaolin; Zhao, Wei; Liu, Aiqin; Piao, Daxun; Jiang, Tao; Cao, Jianping; Shen, Yujuan; Liu, Hua; Zhang, Weizhe

    2014-01-01

    Cystic echinococcosis (CE) caused by the larval stage of Echinococcus granulosus sensu lato (s.l.) is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1–G10) have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province of northeastern China, no molecular information is available on E. granulosus s.l. To understand and to speculate on possible transmission patterns of E. granulosus s.l., we molecularly identified and genotyped 10 hydatid cysts from hepatic CE patients in Heilongjiang Province based on mitochondrial cytochrome c oxidase subunit I (cox1), cytochrome b (cytb) and NADH dehydrogenase subunit 1 (nad1) genes. Two genotypes were identified, G1 genotype (n = 6) and G7 genotype (n = 4). All the six G1 genotype isolates were identical to each other at the cox1 locus; three and two different sequences were obtained at the cytb and nad1 loci, respectively, with two cytb gene sequences not being described previously. G7 genotype isolates were identical to each other at the cox1, cytb and nad1 loci; however, the cytb gene sequence was not described previously. This is the first report of G7 genotype in humans in China. Three new cytb gene sequences from G1 and G7 genotypes might reflect endemic genetic characterizations. Pigs might be the main intermediate hosts of G7 genotype in our investigated area by homology analysis. The results will aid in making more effective control strategies for the prevention of transmission of E. granulosus s.l. PMID:25329820

  12. Emergence of dengue virus 4 genotype II in Guangzhou, China, 2010: Survey and molecular epidemiology of one community outbreak

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    Jing Qin-Long

    2012-04-01

    Full Text Available Abstract Background The re-emergence of dengue virus 4 (DENV-4 has become a public health concern in South America, Southeast Asia and South Asia. However, it has not been known to have caused a local outbreak in China for the past 20 years. The purpose of this study was to elucidate the epidemiology of one local community outbreak caused by DENV-4 in Guangzhou city, China, in 2010; and to determine the molecular characteristics of the genotype II virus involved. Case presentations During September and October of 2010, one imported case, a Guangzhou resident who travelled back from Thailand, resulted in 18 secondary autochthonous cases in Guangzhou City, with an incidence rate of 5.53 per 10,000 residents. In indigenous cases, 14 serum samples tested positive for IgM against DENV and 7 for IgG from a total of 15 submitted serum samples, accompanied by 5 DENV-4 isolates. With identical envelope gene nucleotide sequences, the two isolates (D10168-GZ from the imported index case and Guangzhou 10660 from the first isolate in the autochthonous cases were grouped into DENV-4 genotype II after comparison to 32 previous DENV-4 isolates from GenBank that originated from different areas. Conclusions Based on epidemiological and phylogenetic analyses, the outbreak, which was absent for 20 years after the DENV-4 genotype I outbreak in 1990, was confirmed as DENV-4 genotype II and initially traced to the imported index case, a Guangzhou resident who travelled back from Thailand.

  13. Prevalence of Human Papillomavirus Genotypes Among Women With High-Grade Cervical Lesions in Beijing, China

    Science.gov (United States)

    Xiao, Meizhu; Xu, Qiuxiang; Li, Hongyan; Gao, Huiqiao; Bie, Yachun; Zhang, Zhenyu

    2016-01-01

    Abstract The aim of the study is to investigate the prevalence of high-risk human papillomavirus (hr-HPV) genotypes among Han women with high-grade cervical lesions in Beijing, China. Cervical cell specimens from patients with histopathologically confirmed cervical lesions at 7 hospitals in Beijing were examined with a validated HPV kit for 13 hr-HPV genotypes during the study period. The patients were divided into a low-grade cervical lesions group (cervical intraepithelial neoplasia grade 1, CIN1) and a high-grade cervical lesions group (CIN2+, including cervical intraepithelial neoplasia grade 2, CIN2; cervical intraepithelial neoplasia grade 3, CIN3; squamous cervical cancer, SCC; and adenocarcinoma of the cervix, ACC) based on the histopathology results. A total of 2817 eligible patients were enrolled, including 610 cases identified as CIN1 and 2207 as CIN2+. The hr-HPV positive rates in the CIN1 and CIN2+ groups were 78.2% (477/610) and 93.3% (2060/2207), respectively. The most frequently detected genotypes were HPV16, 58, 52 and18 in the CIN1 group and HPV16, 58, 33, and 52 in the CIN2+ group, in descending order of prevalence. In addition, the prevalence of HPV18 among the patients with ACC was 28.6% (14/49), significantly >7.2% (54/752) prevalence among the SCC patients (P HPV infections gradually deceased to 44.2% in the CIN2 patients, 36.7% in the CIN3 patients, and 35.3% in the cervical cancer (CC) patients, which included SCC and ACC patients. In cases of multiple hr-HPV infections in the CIN2+ group, double infections accounted for ∼76.6%, and HPV16+58, HPV16+52, and HPV16+18 were the most common combinations, in descending order. The most frequent combination for triple infections was HPV16+58+31, with a rate of 4.2%. The highest positive rate occurred in the ≤24 year-old group for all types of cervical lesions. The prevalence of HPV genotypes in the targeted population with high-grade cervical lesions differs from that of other countries. This

  14. Antibody Detection, Isolation, Genotyping, and Virulence of Toxoplasma gondii in Captive Felids from China

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    Yu-Rong Yang

    2017-07-01

    Full Text Available The felids are the only definitive hosts of Toxoplasma gondii, which could excrete oocysts into the environment and provide an infection source for toxoplasmosis in various warm-blooded animal species, particularly the captive felids that live close to human communities. The infection rate of the captive felids is a perfect standard in detecting the presence of Toxoplasma gondii oocysts in the environment. In this study, sera or tissue samples from zoo (1 young tiger, 2 adult tigers, 6 young lions, farm (10 masked palm civets, and pet hospital (28 cats from Henan Province (China were collected. The sera (n = 47 were tested for immunoglobulin G (IgG antibodies against T. gondii by using modified agglutination test (MAT, whereas the hearts tissue (n = 40 were bioassayed in mice to isolate T. gondii strains. The genotype was distinguished by using PCR-RFLP of 10 loci (SAG1, SAG2, SAG3, GRA6, BTUB, L358, c22-8, PK1, c29-2, and Apico. The detection rate for the T. gondii antibody in captive felids was 21.3% (10/47. One viable T. gondii strain (TgCatCHn4 was obtained from a cat heart tissue, and its genotype was ToxoDB#9. The oocysts of ToxoDB#9 were collected from a T. gondii-free cat. The virulence of TgCatCHn4 was low and no cysts were detected in the brain of mice at 60 days post-inoculation. The finding of the present study suggested a widespread exposure of T. gondii for felids in Henan Province of central China, particularly those from the zoological gardens and homes. ToxoDB#9 was the predominant strain in China. Preventive measures against T. gondii oocyst contamination of various components of the environment should thus be implemented, including providing pre-frozen meat, well-cooked cat food, cleaned fruits and vegetables, monitoring birds and rodents, inactive T. gondii oocysts in felids feces, and proper hygiene.

  15. Genotyping of polymorphic effectors of Toxoplasma gondii isolates from China

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    Weisheng Cheng

    2017-11-01

    Full Text Available Abstract Background Toxoplasma gondii is an opportunistic protozoan apicomplexan and obligate intracellular parasite that infects a wide range of animals and humans. Rhoptry proteins 5 (ROP5, ROP16, ROP18 and dense granules 15 (GRA15 are the important effectors secreted by T. gondii which link to the strain virulence for mice and modulate the host’s response to the parasite. Little has been known about these molecules as well as GRA3 in type Chinese 1 strains that show polymorphism among strains of archetypical genotypes. This study examined the genetic diversity of these effectors and its correlated virulence in mice among T. gondii isolates from China. Results Twenty-one isolates from stray cats were detected, of which 15 belong to Chinese 1, and 6 to ToxoDB #205. Wh6 isolate, a Chinese 1 strain, has an avirulent phenotype. PCR-RFLP results of ROP5 and ROP18 presented few variations among the strains. Genotyping of GRA15 and ROP16 revealed that all the strains belong to type II allele except Xz7 which carries type I allele. ROP16 amino acid alignment at 503 locus demonstrated that 17 isolates are featured as type I or type III (ROP16I/III, and the other 4 as type II (ROP16II. The strains investigated may be divided into four groups based on GRA3 amino acid alignment, and all isolates of type Chinese 1 belong to the μ-1 allele except Wh6 which is identical to type II strain. Conclusions PCR-RFLP and sequence alignment analyses of ROP5, ROP16, ROP18, GRA3, and GRA15 in T. gondii revealed that strains with the same genotype may have variations in some of their key genes. GRA3 variation exhibited by Wh6 strain may be associated with the difference in phenotype and pathogenesis.

  16. Genotyping Cryptosporidium andersoni in cattle in Shaanxi Province, Northwestern China.

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    Guang-Hui Zhao

    Full Text Available The present study examined the prevalence and genotypes of Cryptosporidium andersoni in cattle in Shaanxi province, China. A total of 2071 fecal samples (847 from Qinchuan cattle and 1224 from dairy cattle were examined for the presence of Cryptosporidium oocysts, and 70 samples (3.4% were C. andersoni-positive and those positive samples were identified by PCR amplification of the small subunit ribosomal RNA (SSU rRNA and the Cryptosporidium oocyst wall protein (COWP genes. C. andersoni was the only species found in the examined cattle in this province. Fifty-seven C. andersoni isolates were characterized into 5 MLST subtypes using multilocus sequence typing analysis, including a new subtype in the native beef breed Qinchuan cattle. All of these C. andersoni isolates presented a clonal genetic structure. These findings provide new insights into the genetic structure of C. andersoni isolates in Shaanxi province and basic data of Cryptosporidium prevalence status, which in turn have implications for controlling cryptosporidiosis in this province.

  17. Prevalence of Chlamydia trachomatis Genotypes in Men Who Have Sex with Men and Men Who Have Sex with Women Using Multilocus VNTR Analysis-ompA Typing in Guangzhou, China.

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    Xiaolin Qin

    Full Text Available Chlamydia trachomatis is one of the most prevalent bacterial sexually transmitted infection in China. Although C. trachomatis genotypes can be discriminated by outer membrane protein gene (ompA sequencing, currently available methods have limited resolutions. This study used a high-resolution genotyping method, namely, multilocus variable number tandem-repeat analysis with ompA sequencing (MLVA-ompA, to investigate the local epidemiology of C. trachomatis infections among men who have sex with men (MSM and men who have sex with women (MSW attending a sexually transmitted diseases (STD clinic in Guangzhou, China.Rectal specimens from MSM and urethral specimens from MSW were collected between January 2013 and July 2014 at the Guangdong Provincial Center STD clinic. The specimens were sent to the laboratory for analyses. All specimens that were tested positive for C. trachomatis by the commercial nucleic acid amplification tests were genotyped by MLVA-ompA.Fifty-one rectal specimens from MSM and 96 urethral specimens from MSW were identified with C. trachomatis. One hundred and forty-four of the 147 specimens were fully genotyped by MLVA-ompA. Rectal specimens from MSM were divided into four ompA genotypes and urethral specimens from MSW into nine genotypes. No mixed infections were found among all specimens. The most frequent genotypes were D, G, J, E and F. All specimens were further divided into 46 types after ompA genotyping was combined with MLVA. Genotypes D-8.7.1 and G-3.4a.3 were the most frequent among MSM, whereas genotypes D-3.4a.4, E-8.5.1, F-8.5.1, and J-3.4a.2 were the most frequent subtypes among MSW. The discriminatory index D was 0.90 for MLVA, 0.85 for ompA, and 0.95 for MLVA-ompA.The most prevalent MLVA-ompA genotypes were significantly different between MSM and MSW from Guangzhou, China. Moreover, MLVA-ompA represented a more favorable degree of discrimination than ompA and could be a reliable complement for ompA for the routine

  18. Regional differences in the CO_2 emissions of China's iron and steel industry: Regional heterogeneity

    International Nuclear Information System (INIS)

    Xu, Bin; Lin, Boqiang

    2016-01-01

    Identifying the key influencing factors of CO_2 emissions in China's iron and steel industry is vital for mitigating its emissions and formulating effective environmental protection measures. Most of the existing researches utilized time series data to investigate the driving factors of the industry's CO_2 emission at the national level, but regional differences have not been given appropriate attention. This paper adopts provincial panel data from 2000 to 2013 and panel data models to examine the key driving forces of CO_2 emissions at the regional levels in China. The results show that industrialization dominates the industry's CO_2 emissions, but its effect varies across regions. The impact of energy efficiency on CO_2 emissions in the eastern region is greater than in the central and western regions because of a huge difference in R&D investment. The influence of urbanization has significant regional differences due to the heterogeneity in human capital accumulation and real estate development. Energy structure has large potential to mitigate CO_2 emissions on account of increased R&D investment in energy-saving technology and expanded clean energy use. Hence, in order to effectively achieve emission reduction, local governments should consider all these factors as well as regional heterogeneity in formulating appropriate mitigation policies. - Highlights: • We explore the driving forces of CO_2 emissions in China's steel industry. • Industrialization dominates CO_2 emissions in the iron and steel industry. • Energy structure has large potential to mitigate CO_2 emissions in the steel industry. • The influence of urbanization has significant regional differences.

  19. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-12-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different parts of the world over the past decade because of variations in population structure, immigration, and routes of transmission. Genotype differences are of epidemiologic interest and help the study of viral transmission dynamics to trace the source of HCV infection in a given population. HCV genotypes are also of considerable clinical importance because they affect response to antiviral therapy and represent a challenging obstacle for vaccine development.

  20. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

    Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

    2017-11-01

    Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China.

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    Jing Peng

    Full Text Available Little is known about the molecular epidemiology of hepatitis C virus (HCV infection in Central China.A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177; 2a, 13.0% (23/177; 3b, 2.3% (4/177; 6a, 1.1% (2/177; 3a, 0.6% (1/177. Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest.The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province.

  2. Novel HBV recombinants between genotypes B and C in 3'-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients.

    Science.gov (United States)

    Liu, Baoming; Yang, Jing-Xian; Yan, Ling; Zhuang, Hui; Li, Tong

    2018-01-01

    As one of the major global public health concerns, hepatitis B virus (HBV) can be divided into at least eight genotypes, which may be related to disease severity and treatment response. We previously demonstrated that genotypes B and C HBV, with distinct geographical distribution in China, had divergent genotype-dependent amino acid polymorphisms and variations in reverse transcriptase (RT) gene region, a target of antiviral therapy using nucleos(t)ide analogues. Recently recombination between HBV genotypes B and C was reported to occur in the RT region. However, their frequency and clinical significance is poorly understood. Here full-length HBV RT sequences from 201 Chinese chronic hepatitis B (CHB) patients were amplified and sequenced, among which 31.34% (63/201) were genotype B whereas 68.66% (138/201) genotype C. Although no intergenotypic recombination was detected among C-genotype HBV, 38.10% (24/63) of B-genotype HBV had recombination with genotype C in the 3'-terminal RT sequences. The patients with B/C intergenotypic recombinants had significantly (Pdistribution feature in China. Our findings provide novel insight into the virological, clinical and epidemiological features of new HBV B/C intergenotypic recombinants at the 3' end of RT sequences among Chinese CHB patients. The highly complex genetic background of the novel recombinant HBV carrying new mutations affecting RT protein may contribute to an enhanced heterogeneity in treatment response or prognosis among CHB patients. Published by Elsevier B.V.

  3. Phylogenetic analysis of the haemagglutinin gene of canine distemper virus strains detected from breeding foxes, raccoon dogs and minks in China.

    Science.gov (United States)

    Zhao, Jian-Jun; Yan, Xi-Jun; Chai, Xiu-Li; Martella, Vito; Luo, Guo-Liang; Zhang, Hai-Ling; Gao, Han; Liu, Ying-Xue; Bai, Xue; Zhang, Lei; Chen, Tao; Xu, Lei; Zhao, Chun-Fei; Wang, Feng-Xue; Shao, Xi-Qun; Wu, Wei; Cheng, Shi-Peng

    2010-01-06

    Canine distemper virus (CDV) infects a variety of carnivores, including wild and domestic Canidae. Genetic/antigenic heterogeneity has been observed among the various CDV strains, notably in the haemagglutinin (H) gene, that appears as a good target to gather epidemiological information. Based on sequence analysis of the H gene, wild-type CDV strains cluster into distinct geographic lineages (genotypes), irrespective of the species of isolation. The sequence of the H gene of 28 CDV strains detected from both vaccinated and non-vaccinated breeding foxes, raccoon dogs and minks from different geographical areas of China during the years 2004-2008 was determined. All the CDV strains but two (strains HL and HLJ2) were characterized as Asia-1 genotype and were highly similar to each other (96.2-99.7% at the amino acid [aa] level) and to other Asia-1 strains (96.1-99.5% aa) previously detected in China. The CDV strains HL and HLJ2 were both collected from foxes in Heilongjiang province in 2005. Strain HL resembled CDVs of the Arctic genotype (GR88-like) and displayed high aa identity (98.0%) to the Chinese canine strain Liu. By converse, strain HLJ2 was barely related to CDVs of the Asia-2 genotype (88.7-90.3% aa identity), and could represent a novel CDV genotype, tentatively proposed as Asia-3. These results suggest that at least three different CDV genotypes, distantly related (81.8-91.6% aa identity) to the vaccine strains, Onderstepoort-like (America-1 genotype), are currently circulating in breeding foxes, raccoon dogs and minks in China, and that the genotype Asia-1 is predominant. Whether the diversity between wild-type CDVs and the vaccine strains may affect, to some extent, the efficacy of the vaccines deserves further investigations.

  4. Spatial Preference Heterogeneity for Integrated River Basin Management: The Case of the Shiyang River Basin, China

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    Fanus Asefaw Aregay

    2016-09-01

    Full Text Available Integrated river basin management (IRBM programs have been launched in most parts of China to ease escalating environmental degradation. Meanwhile, little is known about the benefits from and the support for these programs. This paper presents a case study of the preference heterogeneity for IRBM in the Shiyang River Basin, China, as measured by the Willingness to Pay (WTP, for a set of major restoration attributes. A discrete choice analysis of relevant restoration attributes was conducted. The results based on a sample of 1012 households in the whole basin show that, on average, there is significant support for integrated ecological restoration as indicated by significant WTP for all ecological attributes. However, residential location induced preference heterogeneities are prevalent. Generally, compared to upper-basin residents, middle sub-basin residents have lower mean WTP while lower sub-basin residents express higher mean WTP. The disparity in utility is partially explained by the difference in ecological and socio-economic status of the residents. In conclusion, estimating welfare benefit of IRBM projects based on sample responses from a specific sub-section of the basin only may either understate or overstate the welfare estimate.

  5. Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan

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    Zhang Jinyong

    2011-09-01

    Full Text Available Abstract Background H. pylori (Helicobacter pylori is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

  6. An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity

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    Struchalin Maksim V

    2012-01-01

    Full Text Available Abstract Background Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties. We and Pare with colleagues (2010 developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants. Results In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests. Conclusions Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context.

  7. Comparison of Detection Rate and Mutational Pattern of Drug-Resistant Mutations Between a Large Cohort of Genotype B and Genotype C Hepatitis B Virus-Infected Patients in North China.

    Science.gov (United States)

    Li, Xiaodong; Liu, Yan; Xin, Shaojie; Ji, Dong; You, Shaoli; Hu, Jinhua; Zhao, Jun; Wu, Jingjing; Liao, Hao; Zhang, Xin-Xin; Xu, Dongping

    2017-06-01

    The study aimed to investigate the association of prevalent genotypes in China (HBV/C and HBV/B) with HBV drug-resistant mutations. A total of 13,847 nucleos(t)ide analogue (NA)-treated patients with chronic HBV infection from North China were enrolled. HBV genotypes and resistant mutations were determined by direct sequencing and confirmed by clonal sequencing if necessary. HBV/B, HBV/C, and HBV/D occupied 14.3%, 84.9%, and 0.8% across the study population, respectively. NA usage had no significant difference between HBV/B- and HBV/C-infected patients. Lamivudine-resistant mutations were more frequently detected in HBV/C-infected patients, compared with HBV/B-infected patients (31.67% vs. 25.26%, p M250 V/I/L substitution (0.67% vs. 1.46%, p < 0.01). Multidrug-resistant mutations (defined as coexistence of mutation to nucleoside and nucleotide analogues) were detected in 104 patients. HBV/C-infected patients had a higher detection rate of multidrug-resistant mutation than HBV/B-infected patients (0.83% vs. 0.35%, p < 0.05). The study for the first time clarified that HBV/C-infected patients had a higher risk to develop multidrug-resistant mutations, compared with HBV/B-infected patients; and HBV/C- and HBV/B-infected patients had different inclinations in the ETV-resistant mutational pattern.

  8. Scrub typhus caused by Orientia tsutsugamushi Kawasaki-related genotypes in Shandong Province, northern China.

    Science.gov (United States)

    Zhang, Luyan; Bi, Zhenwang; Kou, Zengqiang; Yang, Huili; Zhang, Aihua; Zhang, Shoufeng; Meng, Xiangpeng; Zheng, Li; Zhang, Meng; Yang, Hui; Zhao, Zhongtang

    2015-03-01

    Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium and characterized by dramatic genetic diversity. To elucidate the genotypes of O. tsutsugamushi populating in patients in Shandong Province, a new epidemic zone in China, we sequenced partial of the 56-kDa type-specific antigen gene (TSA) and identified the genotypes of 43 O. tsutsugamushi samples from human patients confirmed with scrub typhus from 2010 to 2013. All of the 43 sequences are in the same clade, 39 of them are in one branch and the other four sequences, nominated as SH1002, SH1306, SH1309, and SH1307 are in four separate branches. To clarify the clinical characterizations caused by Kawasaki-related genotypes, we studied the clinical profiles of these 43 scrub typhus patients. Most patients (88.1%) were farmers lived in rural areas. They presented with fever (100.0%), headache (79.1%), dizziness (32.6%), generalized myalgia (48.8%), fatigue (53.5%), anorexia (53.5%), facial flushing (23.3%), conjunctival congestion (11.6%), skin rashes (58.1%) and lymphadenopathy (23.3%). Eschar (97.7%) was quite common in patients, which provided doctors with a luminous clue for diagnosis of scrub typhus. Thrombocytopenia was seen in 23.1% of patients, and three patients (7.0%) had bronchopneumonia. There was no death report in Shandong Province during the study period. The present study provides beneficial data for clinical, serological, and molecular diagnosis of scrub typhus infections, and also provides foundations for subsequent studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Genotypes, Virulence Factors and Antimicrobial Resistance Genes of Staphylococcus aureus Isolated in Bovine Subclinical Mastitis from Eastern China

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    Javed Memon§, Yongchun Yang§, Jam Kashifa, Muhammad Yaqoob, Rehana Buriroa, Jamila Soomroa, Wang Liping and Fan Hongjie*

    2013-11-01

    Full Text Available This study was carried out to determine the genotypes, virulence factors and antimicrobial resistance traits of 34 Staphylococcus aureus isolated from subclinical mastitis in Eastern China. Minimal inhibitory concentration (MIC results showed resistance to erythromycin in all isolates. A high frequency of Methicillin resistant S. aureus (MRSA; 29% was observed and these isolates were also highly resistant to penicillin, oxacillin, oxytetracycline and chloramphenicol than methicillin sensitive S. aureus (MSSA isolates. Thirteen pathogenic factors and seven resistance genes including mecA and blaZ gene were checked through PCR. The spaX gene was found in all isolates, whereas cna, spaIg, nuc, clfA, fnbpB, hlA, hlB and seA were present in 35, 79, 85, 59, 35, 85, 71 and 38% isolates, respectively. Nine isolates carried a group of 8 different virulence genes. Moreover, macrolide resistance genes ermB and ermC were present in all isolates. High resistance rate against methicillin was found but no isolate was positive for mecA gene, whereas blaZ and tetK were detected in 82 and 56% isolates, respectively. Genes; fnbpA, seB, seC, seD, dfrK and tetM were not found in any isolate. The statistical association between phenotypic resistance and virulence genes showed, clfA, fnbpB, hlB and seA, were potentially associated with penicillin G, ciprofloxacin, methicillin, chloramphenicol, trimethoprim and oxytetracycline resistance (P≤0.05. REP-PCR based genotyping showed seven distinct genotypes (A-G prevalent in this region. This study reports the presence of multidrug resistant S. aureus in sub-clinical mastitis which were also highly virulent that could be a major obstacle in the treatment of mastitis in this region of China.

  10. Genetic structure of Phytophthora infestans populations in China indicates multiple migration events.

    Science.gov (United States)

    Guo, Liyun; Zhu, Xiao-Qiong; Hu, Chia-Hui; Ristaino, Jean Beagle

    2010-10-01

    One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the

  11. The Dynamics of Microcystis Genotypes and Microcystin Production and Associations with Environmental Factors during Blooms in Lake Chaohu, China

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    Li Yu

    2014-12-01

    Full Text Available Lake Chaohu, which is a large, shallow, hypertrophic freshwater lake in southeastern China, has been experiencing lake-wide toxic Microcystis blooms in recent decades. To illuminate the relationships between microcystin (MC production, the genotypic composition of the Microcystis community and environmental factors, water samples and associated environmental data were collected from June to October 2012 within Lake Chaohu. The Microcystis genotypes and MC concentrations were quantified using quantitative real-time PCR (qPCR and HPLC, respectively. The results showed that the abundances of Microcystis genotypes and MC concentrations varied on spatial and temporal scales. Microcystis exists as a mixed population of toxic and non-toxic genotypes, and the proportion of toxic Microcystis genotypes ranged from 9.43% to 87.98%. Both Pearson correlation and stepwise multiple regressions demonstrated that throughout the entire lake, the abundances of total and toxic Microcystis and MC concentrations showed significant positive correlation with the total phosphorus and water temperature, suggesting that increases in temperature together with the phosphorus concentrations may promote more frequent toxic Microcystis blooms and higher concentrations of MC. Whereas, dissolved inorganic carbon (DIC was negatively correlated with the abundances of total and toxic Microcystis and MC concentrations, indicating that rising DIC concentrations may suppress toxic Microcystis abundance and reduce the MC concentrations in the future. Therefore, our results highlight the fact that future eutrophication and global climate change can affect the dynamics of toxic Microcystis blooms and hence change the MC levels in freshwater.

  12. The Dynamics of Microcystis Genotypes and Microcystin Production and Associations with Environmental Factors during Blooms in Lake Chaohu, China

    Science.gov (United States)

    Yu, Li; Kong, Fanxiang; Zhang, Min; Yang, Zhen; Shi, Xiaoli; Du, Mingyong

    2014-01-01

    Lake Chaohu, which is a large, shallow, hypertrophic freshwater lake in southeastern China, has been experiencing lake-wide toxic Microcystis blooms in recent decades. To illuminate the relationships between microcystin (MC) production, the genotypic composition of the Microcystis community and environmental factors, water samples and associated environmental data were collected from June to October 2012 within Lake Chaohu. The Microcystis genotypes and MC concentrations were quantified using quantitative real-time PCR (qPCR) and HPLC, respectively. The results showed that the abundances of Microcystis genotypes and MC concentrations varied on spatial and temporal scales. Microcystis exists as a mixed population of toxic and non-toxic genotypes, and the proportion of toxic Microcystis genotypes ranged from 9.43% to 87.98%. Both Pearson correlation and stepwise multiple regressions demonstrated that throughout the entire lake, the abundances of total and toxic Microcystis and MC concentrations showed significant positive correlation with the total phosphorus and water temperature, suggesting that increases in temperature together with the phosphorus concentrations may promote more frequent toxic Microcystis blooms and higher concentrations of MC. Whereas, dissolved inorganic carbon (DIC) was negatively correlated with the abundances of total and toxic Microcystis and MC concentrations, indicating that rising DIC concentrations may suppress toxic Microcystis abundance and reduce the MC concentrations in the future. Therefore, our results highlight the fact that future eutrophication and global climate change can affect the dynamics of toxic Microcystis blooms and hence change the MC levels in freshwater. PMID:25474494

  13. Two different genotypes of H1N2 swine influenza virus isolated in northern China and their pathogenicity in animals.

    Science.gov (United States)

    Yang, Huanliang; Chen, Yan; Qiao, Chuanling; Xu, Chuantian; Yan, Minghua; Xin, Xiaoguang; Bu, Zhigao; Chen, Hualan

    2015-02-25

    During 2006 and 2007, two swine-origin triple-reassortant influenza A (H1N2) viruses were isolated from pigs in northern China, and the antigenic characteristics of the hemagglutinin protein of the viruses were examined. Genotyping and phylogenetic analyses demonstrated different emergence patterns for the two H1N2 viruses, Sw/Hebei/10/06 and Sw/Tianjin/1/07. Sequences for the other genes encoding the internal proteins were compared with the existing data to determine their origins and establish the likely mechanisms of genetic reassortment. Sw/Hebei/10/06 is an Sw/Indiana/9K035/99-like virus, whereas Sw/Tianjin/1/07 represents a new H1N2 genotype with surface genes of classic swine and human origin and internal genes originating from the Eurasian avian-like swine H1N1 virus. Six-week-old female BALB/c mice infected with the Sw/HeB/10/06 and Sw/TJ/1/07 viruses showed an average weight loss of 12.8% and 8.1%, respectively. Healthy six-week-old pigs were inoculated intranasally with either the Sw/HeB/10/06 or Sw/TJ/1/07 virus. No considerable changes in the clinical presentation were observed post-inoculation in any of the virus-inoculated groups, and the viruses effectively replicated in the nasal cavity and lung tissue. Based on the results, it is possible that the new genotype of the swine H1N2 virus that emerged in China may become widespread in the swine population and pose a potential threat to public health. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Two genotypes of H1N2 swine influenza viruses appeared among pigs in China.

    Science.gov (United States)

    Xu, Chuantian; Zhu, Qiyun; Yang, Huanliang; Zhang, Xiumei; Qiao, Chuanling; Chen, Yan; Xin, Xiaoguang; Chen, Hualan

    2009-10-01

    H1N2 is one of the main subtypes of influenza, which circulates in swine all over the world. To investigate the prevalence and genetic of H1N2 in swine of China. Two H1N2 swine influenza viruses were isolated from Tianjin and Guangdong province of China in 2004 and 2006, respectively. The molecular evolution of eight gene segments was analyzed. A/Swine/Tianjin/1/2004 has low identity with A/Swine/Guangdong/2006; in the phylogenetic tree of PA gene, A/Swine/Guangdong/1/2006 and A/Swine/Guangxi/1/2006 along with the H1N2 swine isolates of North America formed a cluster; and A/Swine/Tianjin/2004 and A/Swine/Zhejiang/2004, along with the classical H1N1 swine isolates formed another cluster; except that NA gene of A/Swine/Tianjin/1/2004 fell into the cluster of the H3N2 human influenza virus, indicating the reassortment between H3N2 human and H1N1 swine influenza viruses. Two different genotypes of H1N2 appeared among pigs in China. A/swine/Guangdong/1/06 was probably from H1N2 swine influenza viruses of North America; while A/swine/Tianjin/1/04 maybe come from reassortments of classical H1N1 swine and H3N2 human viruses prevalent in North America.

  15. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...

  16. Genetic variants influencing phenotypic variance heterogeneity.

    Science.gov (United States)

    Ek, Weronica E; Rask-Andersen, Mathias; Karlsson, Torgny; Enroth, Stefan; Gyllensten, Ulf; Johansson, Åsa

    2018-03-01

    Most genetic studies identify genetic variants associated with disease risk or with the mean value of a quantitative trait. More rarely, genetic variants associated with variance heterogeneity are considered. In this study, we have identified such variance single-nucleotide polymorphisms (vSNPs) and examined if these represent biological gene × gene or gene × environment interactions or statistical artifacts caused by multiple linked genetic variants influencing the same phenotype. We have performed a genome-wide study, to identify vSNPs associated with variance heterogeneity in DNA methylation levels. Genotype data from over 10 million single-nucleotide polymorphisms (SNPs), and DNA methylation levels at over 430 000 CpG sites, were analyzed in 729 individuals. We identified vSNPs for 7195 CpG sites (P mean DNA methylation levels. We further showed that variance heterogeneity between genotypes mainly represents additional, often rare, SNPs in linkage disequilibrium (LD) with the respective vSNP and for some vSNPs, multiple low frequency variants co-segregating with one of the vSNP alleles. Therefore, our results suggest that variance heterogeneity of DNA methylation mainly represents phenotypic effects by multiple SNPs, rather than biological interactions. Such effects may also be important for interpreting variance heterogeneity of more complex clinical phenotypes.

  17. Genotype-Phenotype Correlation of Maternally Inherited Disorders due to Mutations in Mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Peterus Thajeb

    2006-09-01

    Full Text Available Mitochondrial disorders are heterogeneous systemic ailments that are most often caused by maternal inheritance of a variety of mutations of the mitochondrial (mt DNA. Paternal inheritance and somatic mutation are rare. The disorders are well recognized not only for the genotypic heterogeneity, but also the phenotypic variation among the affected members of a single family. The genotype-phenotype correlation of the diversity of the syndromic and non-syndromic features of mitochondrial disorders are discussed. Some aspects of the molecular mechanisms of this heterogeneity, and the histopathologic findings are highlighted.

  18. Characterisation of the heterogeneity of karst using electrical geophysics - applications in SW China

    Science.gov (United States)

    Binley, A. M.; Cheng, Q.; Tao, M.; Chen, X.

    2017-12-01

    The southwest China karst region is one of the largest globally continuous karst areas. The great (structural, hydrological and geochemical) complexity of karstic environments and their rapidly evolving nature make them extremely vulnerable to natural and anthropogenic processes/activities. Characterising the location and properties of structures within the karst critical zone, and understanding how the landform is evolving is essential for the mitigation and adaption to locally- and globally-driven changes. Because of the specific nature of karst geology and geomorphology in the humid tropics and subtropics, spatial heterogeneity is high, evidenced by specific landforms features. Such heterogeneity leads to a high dynamic variability of hydrological processes in space and time, along with a complex exchange of surface water and groundwater. Investigating karst hydrogeological features is extremely challenging because of the three-dimensional nature of the system. Observations from boreholes can vary significantly over several metres, making conventional aquifer investigative methods limited. Geophysical methods have emerged as potentially powerful tools for hydrogeological investigations. Geophysical surveys can help to obtain more insight into the complex conduit networks and depth of weathering, both of which can provide quantitative information about the hydrological and hydrochemical dynamics of the system, in addition to providing a better understanding of how critical zone structures have been established and how the landscape is evolving. We present here results from recent geophysical field campaigns in SW China. We illustrate the effectiveness of electrical methods for mapping soil infil in epikarst and report results from field-based investigations along hillslope and valley transects. Our results reveal distinct zones of relatively high electrical conductivity to depths of tens of metres, which we attribute to localised increased fracture density. We

  19. Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China.

    Science.gov (United States)

    Liu, Xuehan; Xie, Na; Li, Wei; Zhou, Ziyao; Zhong, Zhijun; Shen, Liuhong; Cao, Suizhong; Yu, Xingming; Hu, Yanchuan; Chen, Weigang; Peng, Gangneng

    2015-01-01

    A single Cryptosporidium isolate from a squirrel monkey with no clinical symptoms was obtained from a zoo in Ya'an city, China, and was genotyped by PCR amplification and DNA sequencing of the small-subunit ribosomal RNA (SSU rRNA), 70-kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein, and actin genes. This multilocus genetic characterization determined that the isolate was Cryptosporidium hominis, but carried 2, 10, and 6 nucleotide differences in the SSU rRNA, HSP70, and actin loci, respectively, which is comparable to the variations at these loci between C. hominis and the previously reported monkey genotype (2, 3, and 3 nucleotide differences). Phylogenetic studies, based on neighbor-joining and maximum likelihood methods, showed that the isolate identified in the current study had a distinctly discordant taxonomic status, distinct from known C. hominis and also from the monkey genotype, with respect to the three loci. Restriction fragment length polymorphisms of the SSU rRNA gene obtained from this study were similar to those of known C. hominis but clearly differentiated from the monkey genotype. Further subtyping was performed by sequence analysis of the gene encoding the 60-kDa glycoprotein (gp60). Maximum homology of only 88.3% to C. hominis subtype IdA10G4 was observed for the current isolate, and phylogenetic analysis demonstrated that this particular isolate belonged to a novel C. hominis subtype family, IkA7G4. This study is the first to report C. hominis infection in the squirrel monkey and, based on the observed genetic characteristics, confirms a new C. hominis genotype, monkey genotype II. Thus, these results provide novel insights into genotypic variation in C. hominis.

  20. Two-wavelength Method Estimates Heat fluxes over Heterogeneous Surface in North-China

    Science.gov (United States)

    Zhang, G.; Zheng, N.; Zhang, J.

    2017-12-01

    Heat fluxes is a key process of hydrological and heat transfer of soil-plant-atmosphere continuum (SPAC), and now it is becoming an important topic in meteorology, hydrology, ecology and other related research areas. Because the temporal and spatial variation of fluxes at regional scale is very complicated, it is still difficult to measure fluxes at the kilometer scale over a heterogeneous surface. A technique called "two-wavelength method" which combines optical scintillometer with microwave scintillometer is able to measure both sensible and latent heat fluxes over large spatial scales at the same time. The main purpose of this study is to investigate the fluxes over non-uniform terrain in North-China. Estimation of heat fluxes was carried out with the optical-microwave scintillometer and an eddy covariance (EC) system over heterogeneous surface in Tai Hang Mountains, China. EC method was set as a benchmark in the study. Structure parameters obtained from scintillometer showed that the typical measurement values of Cn2 are around 10-13 m-2/3 for microwave scintillometer, and values of Cn2 were around 10-15 m-2/3 for optical scintillometer. The correlation of heat fluxes (H) derived from scintillometer and EC system showed as a ratio of 1.05,and with R2=0.75, while the correlation of latent heat fluxes (LE) showed as 1.29 with R2=0.67. It was also found that heat fluxes derived from the two system showed good agreement (R2=0.9 for LE, R2=0.97 for H) when the Bowen ratio (β) was 1.03, while discrepancies showed significantly when β=0.75, and RMSD in H was 139.22 W/m2, 230.85 W/m2 in LE respectively.Experiment results in our research shows that, the two-wavelength method gives a larger heat fluxes over the study area, and a deeper study should be conduct. We expect that our investigate and analysis can be promoted the application of scintillometry method in regional evapotranspiration measurements and relevant disciplines.

  1. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  2. [Population-based study on infection and genotype distribution of high-risk human among women in rural areas of China, 2014].

    Science.gov (United States)

    Di, J L; Luo, X M; Wu, J L; Song, B; Ma, L

    2017-04-06

    Objective: To explore the epidemiologic characterization of high-risk human papillomavirus (HR-HPV) infection and genotype distribution of HR-HPV among women in rural areas of China. Methods: This study used multiple layers of stratified cluster random sampling method. During January to December in 2014, 117 counties of 27 provinces were selected as the HPV test screening pilot project counties. The women aged 35-64 years with rural areas Hukou in these project counties were selected as the study subjects. A total 457 799 women received HPV DNA test. Among them, 118 237 women from 32 counties in 11 provinces received qualified HPV DNA test by fluorescent PCR to detect HPV genotypes. Results: Among 118 237 rural women, the overall HR-HPV positive infection rate was 7.8% (9 249/118 237). The infection rate increased with age and reached an infection peak at the 60-64 age groups (9.9%, 831/8 394). The HR-HPV positive infection rate in western regions (6.9%, 2 144/31 130) was statistical significantly lower than in central regions (8.2%, 1 894/23 023) and eastern regions (8.1%, 5 211/64 084) (χ(2)=51.46, PChina. The single infection rates were 20.9% (1 355/6 496), 18.7% (1 215/6 496), and 11.2% (725/6 496), respectively. The multiple infection rates were 47.2% (77/163), 17.8% (29/163), and 18.4% (30/163), respectively. Conclusion: The HR-HPV positive infection rate in rural areas of Chinese woman was 7.8%, western region has lower infection rate compared with central and eastern regions. HPV 52 was first of the most common genotypes in rural areas of China.

  3. A capsule/lipopolysaccharide/MLST genotype D/L6/ST11 of Pasteurella multocida is likely to be strongly associated with swine respiratory disease in China.

    Science.gov (United States)

    Peng, Zhong; Wang, Haonan; Liang, Wan; Chen, Yibao; Tang, Xibiao; Chen, Huanchun; Wu, Bin

    2018-01-01

    Pasteurella multocida is a leading cause of respiratory disease in pigs worldwide. In this study, we determined the genetic characteristics of 115 P. multocida isolates from the lungs of pigs with respiratory disease in China in 2015 using capsular typing, lipopolysaccharide (LPS) genotyping, and virulence genotyping based on the detection of virulence-associated genes. The results showed that the isolates belonged to three capsular types: A (49.6%), D (46.1%), and nontypable (4.3%); and two LPS genotypes: L3 (22.6%) and L6 (77.4%). When combining the capsular types with the LPS genotypes, a genotype group D: L6 (46.1%) was the most prevalent among the strains. Among the 23 virulence-associated genes detected in this study, a small number of them displayed a certain level of "genotype-preference". We found that pfhA, hgbA, and hgbB had a close association with P. multocida LPS genotypes, while tadD was more associated with P. multocida capsular types. In addition, multilocus sequence typing (MLST) on 40 P. multocida isolates identified four sequence types: ST3, ST10, ST11, and ST16, and the distribution of ST11 was significantly higher than the other MLST genotypes. Interestingly, all of the ST11 isolates detected in this study were genotype D: L6 strains and they were 100% positive for hgbB. Our data suggest that a capsule/LPS/MLST genotype D/L6/ST11 is likely to be strongly associated with respiratory clinical manifestation of the disease in pigs.

  4. Variance heterogeneity in Saccharomyces cerevisiae expression data: trans-regulation and epistasis.

    Science.gov (United States)

    Nelson, Ronald M; Pettersson, Mats E; Li, Xidan; Carlborg, Örjan

    2013-01-01

    Here, we describe the results from the first variance heterogeneity Genome Wide Association Study (VGWAS) on yeast expression data. Using this forward genetics approach, we show that the genetic regulation of gene-expression in the budding yeast, Saccharomyces cerevisiae, includes mechanisms that can lead to variance heterogeneity in the expression between genotypes. Additionally, we performed a mean effect association study (GWAS). Comparing the mean and variance heterogeneity analyses, we find that the mean expression level is under genetic regulation from a larger absolute number of loci but that a higher proportion of the variance controlling loci were trans-regulated. Both mean and variance regulating loci cluster in regulatory hotspots that affect a large number of phenotypes; a single variance-controlling locus, mapping close to DIA2, was found to be involved in more than 10% of the significant associations. It has been suggested in the literature that variance-heterogeneity between the genotypes might be due to genetic interactions. We therefore screened the multi-locus genotype-phenotype maps for several traits where multiple associations were found, for indications of epistasis. Several examples of two and three locus genetic interactions were found to involve variance-controlling loci, with reports from the literature corroborating the functional connections between the loci. By using a new analytical approach to re-analyze a powerful existing dataset, we are thus able to both provide novel insights to the genetic mechanisms involved in the regulation of gene-expression in budding yeast and experimentally validate epistasis as an important mechanism underlying genetic variance-heterogeneity between genotypes.

  5. Multi-locus genotypes of Enterocytozoon bieneusi in captive Asiatic black bears in southwestern China: High genetic diversity, broad host range, and zoonotic potential.

    Science.gov (United States)

    Deng, Lei; Li, Wei; Zhong, Zhijun; Gong, Chao; Cao, Xuefeng; Song, Yuan; Wang, Wuyou; Huang, Xiangming; Liu, Xuehan; Hu, Yanchun; Fu, Hualin; He, Min; Wang, Ya; Zhang, Yue; Wu, Kongju; Peng, Guangneng

    2017-01-01

    Enterocytozoon bieneusi is an obligate eukaryotic intracellular parasite that infects a wide variety of vertebrate and invertebrate hosts. Although considerable research has been conducted on this organism, relatively little information is available on the occurrence of E. bieneusi in captive Asiatic black bears. The present study was performed to determine the prevalence, genetic diversity, and zoonotic potential of E. bieneusi in captive Asiatic black bears in zoos in southwestern China. Fecal specimens from Asiatic black bears in four zoos, located in four different cities, were collected and analyzed for the prevalence of E. bieneusi. The average prevalence of E. bieneusi was 27.4% (29/106), with the highest prevalence in Guiyang Zoo (36.4%, 16/44). Altogether, five genotypes of E. bieneusi were identified among the 29 E. bieneusi-positive samples, including three known genotypes (CHB1, SC02, and horse2) and two novel genotypes named ABB1 and ABB2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7) and one minisatellite (MS4) revealed V, III, V, and IV genotypes at these four loci, respectively. Phylogenetic analysis showed that the genotypes SC02 and ABB2 were clustered into group 1 of zoonotic potential, the genotypes CHB1 and ABB1 were clustered into a new group, and the genotype horse2 was clustered into group 6 of unclear zoonotic potential. In conclusion, this study identified two novel E. bieneusi genotypes in captive Asiatic black bears, and used microsatellite and minisatellite markers to reveal E. bieneusi genetic diversity. Moreover, our findings show that genotypes SC02 (identified in humans) and ABB2 belong to group 1 with zoonotic potential, suggesting the risk of transmission of E. bieneusi from Asiatic black bears to humans and other animals.

  6. Multi-locus genotypes of Enterocytozoon bieneusi in captive Asiatic black bears in southwestern China: High genetic diversity, broad host range, and zoonotic potential.

    Directory of Open Access Journals (Sweden)

    Lei Deng

    Full Text Available Enterocytozoon bieneusi is an obligate eukaryotic intracellular parasite that infects a wide variety of vertebrate and invertebrate hosts. Although considerable research has been conducted on this organism, relatively little information is available on the occurrence of E. bieneusi in captive Asiatic black bears. The present study was performed to determine the prevalence, genetic diversity, and zoonotic potential of E. bieneusi in captive Asiatic black bears in zoos in southwestern China. Fecal specimens from Asiatic black bears in four zoos, located in four different cities, were collected and analyzed for the prevalence of E. bieneusi. The average prevalence of E. bieneusi was 27.4% (29/106, with the highest prevalence in Guiyang Zoo (36.4%, 16/44. Altogether, five genotypes of E. bieneusi were identified among the 29 E. bieneusi-positive samples, including three known genotypes (CHB1, SC02, and horse2 and two novel genotypes named ABB1 and ABB2. Multi-locus sequence typing using three microsatellites (MS1, MS3, and MS7 and one minisatellite (MS4 revealed V, III, V, and IV genotypes at these four loci, respectively. Phylogenetic analysis showed that the genotypes SC02 and ABB2 were clustered into group 1 of zoonotic potential, the genotypes CHB1 and ABB1 were clustered into a new group, and the genotype horse2 was clustered into group 6 of unclear zoonotic potential. In conclusion, this study identified two novel E. bieneusi genotypes in captive Asiatic black bears, and used microsatellite and minisatellite markers to reveal E. bieneusi genetic diversity. Moreover, our findings show that genotypes SC02 (identified in humans and ABB2 belong to group 1 with zoonotic potential, suggesting the risk of transmission of E. bieneusi from Asiatic black bears to humans and other animals.

  7. National Prociency Testing Result of CYP2D6*10 Genotyping for Adjuvant Tamoxifen Therapy in China.

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    Guigao Lin

    Full Text Available Tamoxifen has been successfully used for treating breast cancer and preventing cancer recurrence. Cytochrome P450 2D6 (CYP2D6 plays a key role in the process of metabolizing tamoxifen to its active moiety, endoxifen. Patients with variants of the CYP2D6 gene may not receive the full benefit of tamoxifen treatment. The CYP2D6*10 variant (the most common variant in Asians was analyzed to optimize the prescription of tamoxifen in China. To ensure referring clinicians have accurate information for genotype-guided tamoxifen treatment, the Chinese National Center for Clinical Laboratories (NCCL organized a national proficiency testing (PT to evaluate the performance of laboratories providing CYP2D6*10 genotyping. Ten genomic DNA samples with CYP2D6 wild-type or CYP2D6*10 variants were validated by PCR-sequencing and sent to 28 participant laboratories. The genotyping results and pharmacogenomic test reports were submitted and evaluated by NCCL experts. Additional information regarding the number of samples tested, the accreditation/certification status, and detecting technology was also requested. Thirty-one data sets were received, with a corresponding analytical sensitivity of 98.2% (548/558 challenges; 95% confidence interval: 96.7-99.1% and an analytic specificity of 96.5% (675/682; 95% confidence interval: 97.9-99.5%. Overall, 25/28 participants correctly identified CYP2D6*10 status in 10 samples; however, two laboratories made serious genotyping errors. Most of the essential information was included in the 20 submitted CYP2D6*10 test reports. The majority of Chinese laboratories are reliable for detecting the CYP2D6*10 variant; however, several issues revealed in this study underline the importance of PT schemes in continued external assessment and provision of guidelines.

  8. Different places, different stories: A study of the spatial heterogeneity of county-level fertility in China

    Directory of Open Access Journals (Sweden)

    Donghui Wang

    2017-08-01

    Full Text Available Background: China has been characterized by persistently low fertility rates since the 1990s. Existing literature has examined the relationship between fertility levels and social, economic, and policy-related determinants. However, the possible spatial variation in these relationships has not been investigated. Objective: The purpose of this study is to examine the potential spatially varying relationships between county-level fertility rates and policy and socioeconomic factors in China. Methods: Using geocoded 2010 county-level census data, this study adopts the geographically weighted regression (GWR method to identify place-specific relationships between county-level total fertility rate (TFR and socioeconomic and policy-related factors. Conclusions: We find that relationships between TFR and widely used social, economic, and policy-related factors (rural Hukou, ethnic minority, female education, net migration rate, poor living standard, sex ratio at birth, fertility policy compliance ratio vary spatially in terms of direction, strength, and magnitude. This spatial variation is largely due to differences in local characteristics. The differences between and the complexities of localities cannot be told by a single story of either government intervention or socioeconomic development. Contribution: This study extends existing fertility research on China by explicitly recognizing the spatial heterogeneity in the impact of policy and socioeconomic factors on the local fertility rate. This study sets the stage for future research that will contextually analyze varying fertility rates at the subnational level in China and other countries.

  9. Heterogeneity and compartmentalization of Pneumocystis carinii f. sp. hominis genotypes in autopsy lungs

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Lundgren, Bettina; Lundgren, Jens Dilling

    2001-01-01

    . Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mtLSU rRNA sequence types was observed in different lung segments. In conclusion, the interpretation of genotype data and in particular ITS sequence types...

  10. Does health insurance reduce out-of-pocket expenditure? Heterogeneity among China's middle-aged and elderly.

    Science.gov (United States)

    Zhang, Anwen; Nikoloski, Zlatko; Mossialos, Elias

    2017-10-01

    China's recent healthcare reforms aim to provide fair and affordable health services for its huge population. In this paper, we investigate the association between China's health insurance and out-of-pocket (OOP) healthcare expenditure. We further explore the heterogeneity in this association. Using data of 32,387 middle-aged and elderly individuals drawn from the 2011 and 2013 waves of China Health and Retirement Longitudinal Study (CHARLS), we report five findings. First, having health insurance increases the likelihood of utilizing healthcare and reduces inpatient OOP expenditure. Second, healthcare benefits are distributed unevenly: while low- and medium-income individuals are the main beneficiaries with reduced OOP expenditure, those faced with very high medical bills are still at risk, owing to limited and shallow coverage in certain aspects. Third, rural migrants hardly benefit from having health insurance, suggesting that institutional barriers are still in place. Fourth, health insurance does not increase patient visits to primary care facilities; hospitals are still the main provider of healthcare. Nonetheless, there is some evidence that patients shift from higher-tier to lower-tier hospitals. Last, OOP spending on pharmaceuticals is reduced for inpatient care but not for outpatient care, suggesting that people rely on inpatient care to obtain reimbursable drugs, putting further pressure on the already overcrowded hospitals. Our findings suggest that China's health insurance system has been effective in boosting healthcare utilization and lowering OOP hospitalization expenditure, but there still remain challenges due to the less generous rural scheme, shallow outpatient care coverage, lack of insurance portability, and an underdeveloped primary healthcare system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. First detection of multiple knockdown resistance (kdr)-like mutations in voltage-gated sodium channel using three new genotyping methods in Anopheles sinensis from Guangxi Province, China.

    Science.gov (United States)

    Tan, Wei L; Li, Chun X; Wang, Zhong M; Liu, Mei D; Dong, Yan D; Feng, Xiang Y; Wu, Zhi M; Guo, Xiao X; Xing, Dan; Zhang, Ying M; Wang, Zhong C; Zhao, Tong Y

    2012-09-01

    To investigate knockdown resistance (kdr)-like mutations associated with pyrethroid resistance in Anopheles sinensis (Wiedemann, 1828), from Guangxi province, southwest China, a segment of a sodium channel gene was sequenced and genotyped using three new genotyping assays. Direct sequencing revealed the presence of TTG-to-TCG and TG-to-TTT mutations at allele position L1014, which led to L1014S and L1014F substitutions in a few individual and two novel substitutions of N1013S and L1014W in two DNA templates. A low frequency of the kdr allele mostly in the heterozygous state of L1014S and L1014F was observed in this mosquito population. In this study, the genotyping of An. sinensis using three polymerase chain reaction-based methods generated consistent results, which agreed with the results of DNA sequencing. In total, 52 mosquitoes were genotyped using a direct sequencing assay. The number of mosquitoes and their genotypes were as follows: L/L = 24, L/S = 19, L/F = 8, and F/W = 1. The allelic frequency of L1014, 1014S, and 1014F were 72, 18, and 9%, respectively.

  12. Epidemiologic and genetic characteristics of mumps viruses isolated in China from 1995 to 2010.

    Science.gov (United States)

    Cui, Aili; Zhu, Zhen; Chen, Meng; Zheng, Huanying; Liu, Leng; Wang, Yan; Ma, Yan; Wang, Changyin; Fang, Xueqiang; Li, Ping; Guan, Ronghui; Wang, Shuang; Zhou, Jianhui; Zheng, Lei; Gao, Hui; Ding, Zhengrong; Li, Liqun; Bo, Fang; Sun, Zhaodan; Zhang, Zhenying; Feng, Daxing; He, Jilan; Chen, Hui; Jin, Li; Rota, Paul A; Xu, Wenbo

    2014-01-01

    The epidemiologic and genetic characteristics of mumps viruses detected in China from 1995 to 2010 were analyzed in this study. Mumps remains endemic in China with a high overall incidence rate. The incidence of mumps in Western China was higher than that in other regions of the country. Each year, most of mumps cases occurred between April and July, but a small peak also occurred in November and December. Mumps cases primarily affected the under 15 year old age group. Virologic data demonstrated that genotype F was the predominant circulating genotype throughout China for at least 15 years and no other genotype was detected between 1995 and 2010. Analysis of sequence data from the small hydrophobic (SH) gene indicated that multiple transmission chains of genotype F were found in various provinces of China, with no apparent chronologic and geographic restriction. This is the first report describing the epidemiology of mumps and genetic characterization of mumps viruses at the national level in China. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.

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    Rumen Kostadinov

    2016-04-01

    Full Text Available When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.

  14. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.

    Science.gov (United States)

    Kostadinov, Rumen; Maley, Carlo C; Kuhner, Mary K

    2016-04-01

    When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.

  15. Subtyping of Cryptosporidium cuniculus and genotyping of Enterocytozoon bieneusi in rabbits in two farms in Heilongjiang Province, China

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    Yang Ziyin

    2016-01-01

    Full Text Available Cryptosporidium spp. and Enterocytozoon bieneusi are two prevalent opportunistic pathogens in humans and animals. Currently, few data are available on genetic characterization of both pathogens in rabbits in China. The aim of the present study was to understand prevalence and genetic characterization of Cryptosporidium spp. and E. bieneusi in rabbits. We collected 215 fecal samples from 150 Rex rabbits and 65 New Zealand White rabbits on two different farms in Heilongjiang Province, China. Cryptosporidium spp. and E. bieneusi were tested by polymerase chain reaction (PCR and sequencing the partial small subunit of ribosomal DNA (SSU rDNA and the internal transcribed spacer (ITS region of rDNA, respectively. Cryptosporidium was detected in 3.3% (5/150 of Rex rabbits and 29.2% (19/65 of New Zealand White rabbits. All the 24 Cryptosporidium isolates were identified as C. cuniculus. Enterocytozoon bieneusi was only found in 14.7% (22/150 of Rex rabbits. Five known genotypes: CHN-RD1 (n = 12, D (n = 3, Type IV (n = 2, Peru6 (n = 1, and I (n = 1, and three novel ones CHN-RR1 to CHN-RR3 (one each were detected. By analyzing the 60-kDa glycoprotein (gp60 gene sequences of C. cuniculus isolates, three subtypes were obtained: VbA28 (n = 2, VbA29 (n = 16, and VbA32 (n = 3. All these three C. cuniculus subtypes were reported previously in humans. Four known E. bieneusi genotypes have been found to be present in humans. The three novel ones fell into zoonotic group 1. The results suggest zoonotic potential of C. cuniculus and E. bieneusi isolates in rabbits.

  16. Multiple-locus variable-number tandem-repeat analysis of pathogenic Yersinia enterocolitica in China.

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    Xin Wang

    Full Text Available The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.

  17. Occurrence, Genotyping, and Antibiotic Susceptibility of Cronobacter spp. in Drinking Water and Food Samples from Northeast China.

    Science.gov (United States)

    Fei, Peng; Jiang, Yichao; Gong, Shaoying; Li, Ran; Jiang, Yan; Yuan, Xiujuan; Wang, Ziyuan; Kang, Huaibin; Ali, Md Aslam

    2018-02-23

    Cronobacter species (formerly Enterobacter sakazakii) are emerging opportunistic bacterial pathogens that can infect both infants and adults. This study was conducted to isolate and genotype diverse Cronobacter species from drinking water, chilled fresh pork, powdered infant formula, instant noodles, cookies, fruits, vegetables, and dishes in Northeast China and to evaluate the antibiotic resistance and susceptibility of the isolates. Thirty-four Cronobacter strains were isolated and identified: 21 C. sakazakii isolates (61.8%), 10 C. malonaticus isolates (29.4%), 2 C. dublinensis isolates (5.9%), and 1 C. turicensis isolate (2.9%). These isolates were further divided into 15 sequence types (STs) by multilocus sequence typing. C. sakazakii ST4 (10 isolates, 29.4%), ST1 (3 isolates, 8.8%), and ST8 (3 isolates, 8.8%) and C. malonaticus ST7 (four isolates, 11.8%) were dominant. Antibiotic susceptibility testing indicated that all 34 Cronobacter isolates were susceptible to ampicillin-sulbactam, cefotaxime, ciprofloxacin, gentamicin, meropenem, tetracycline, piperacillin-tazobactam, and trimethoprim-sulfamethoxazole, 88.2% were susceptible to chloramphenicol, and 67.6% were resistant to cephalothin. The results of this study enhance knowledge about genotyping and antibiotic resistance of these Cronobacter species and could be used to prevent potential hazards caused by these strains in drinking water and various food products.

  18. Measuring energy performance with sectoral heterogeneity: A non-parametric frontier approach

    International Nuclear Information System (INIS)

    Wang, H.; Ang, B.W.; Wang, Q.W.; Zhou, P.

    2017-01-01

    Evaluating economy-wide energy performance is an integral part of assessing the effectiveness of a country's energy efficiency policy. Non-parametric frontier approach has been widely used by researchers for such a purpose. This paper proposes an extended non-parametric frontier approach to studying economy-wide energy efficiency and productivity performances by accounting for sectoral heterogeneity. Relevant techniques in index number theory are incorporated to quantify the driving forces behind changes in the economy-wide energy productivity index. The proposed approach facilitates flexible modelling of different sectors' production processes, and helps to examine sectors' impact on the aggregate energy performance. A case study of China's economy-wide energy efficiency and productivity performances in its 11th five-year plan period (2006–2010) is presented. It is found that sectoral heterogeneities in terms of energy performance are significant in China. Meanwhile, China's economy-wide energy productivity increased slightly during the study period, mainly driven by the technical efficiency improvement. A number of other findings have also been reported. - Highlights: • We model economy-wide energy performance by considering sectoral heterogeneity. • The proposed approach can identify sectors' impact on the aggregate energy performance. • Obvious sectoral heterogeneities are identified in evaluating China's energy performance.

  19. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes.

    Science.gov (United States)

    Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A

    2017-03-21

    It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous). Randomness of genotypes was accounted for by deriving the joint probability mass function of marker genotypes conditional on allelic frequencies and pedigree information. As a consequence, these models incorporated kinship and genotypic information that not only permitted to account for heterogeneity of allelic frequencies, but also to include individuals with missing genotypes at some or all loci without the need for previous imputation. This was possible because the non-observed fraction of the design matrix was treated as an unknown model parameter. For each model, a simpler version ignoring population structure, but still accounting for randomness of genotypes was proposed. Implementation of these models and computation of some criteria for model comparison were illustrated using two simulated datasets. Theoretical and computational issues along with possible applications, extensions and refinements were discussed. Some features of the models developed in this study make them promising for genome-wide prediction, the use of information contained in the probability distribution of genotypes is perhaps the most appealing. Further studies to assess the performance of the models proposed here and also to compare them with conventional models used in genome-wide prediction are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Correlation between genotype and the tetrahydrobiopterin-responsive phenotype in Chinese patients with phenylketonuria.

    Science.gov (United States)

    Tao, Jing; Li, Nana; Jia, Haitao; Liu, Zhen; Li, Xiaohong; Song, Jiaping; Deng, Ying; Jin, Xi; Zhu, Jun

    2015-12-01

    A growing body of research has suggested that tetrahydrobiopterin (BH4) responsive phenotype can be predicted by the phenylalanine hydroxylase (PAH) genotype in patients with phenylketonuria (PKU), but data concerning the association between genotype and BH4 responsiveness are scarce in China. A total of 165 PKU patients from China who had undergone a 24-h loading test with BH4 administration were recruited. Genotyping was performed by the next-generation sequencing (NGS) technique. Using the predicted residual PAH activity, we analyzed the association between genotype and BH4-responsiveness. Among the 165 patients, 40 patients (24.24%) responded to BH4. A total of 74 distinct mutations were observed, including 13 novel mutations. The mutation p.R241C was most frequently associated with response. Two known mutations (p.A322T and p.Q419R) and two novel mutations (p.L98V and IVS3-2A>T) were first reported as responsive to BH4. Residual PAH activity of at least 12.5% was needed for responsive genotypes. Genotype-based predictions of BH4-responsiveness are only for selecting potential responders. Accordingly, it is necessary to test potential responders with a long-term BH4 challenge.

  1. Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers.

    Science.gov (United States)

    Lo, Eugenia; Lam, Nancy; Hemming-Schroeder, Elizabeth; Nguyen, Jennifer; Zhou, Guofa; Lee, Ming-Chieh; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

    2017-12-05

    In Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission. Microsatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission. P. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow. The admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  2. [Evaluation of different sets of variable number of tandem repeats ioci for genotyping Mycobacterium tuberculosis isolates in China].

    Science.gov (United States)

    Liu, Mei; Luo, Tao; Yang, Chongguang; Liu, Qingyun; Gao, Qian

    2015-10-01

    To identify a variable number of tandem repeats (VNTR) typing method that is suitable for molecular epidemiological study of tuberculosis in China. We systematically evaluated the commonly used VNTR typing methods, including 4 methods (MIRU-12, VNTR-15/VNTR-24 and VNTR "24+4") proposed by foreign colleagues and 2 methods (VNTR-L15 and VNTR"9+3") developed by domestic researchers using population-based collection of 891 clinical isolates from 5 provinces across the country. The order (from high to low) of discriminatory power for the 6 VNTR typing methods was VNTR"24+4", VNTR"9+3", VNTR-24, VNTR-15, VNTR-L15 and MIRU-12. The discriminatory power of VNTR"9+3" was comparable with VNTR"24+4" and higher than that of VNTR-15/24. The concordance for defining clustered and unique genotypes between VNTR"9+3" and VNTR"24+4" was 96.59%. Our results suggest that VNTR"9+3" is a suitable method for molecular typing of M. tuberculosis in China by considering its high discriminatory power, high consistency with VNTR"24+4" and relative small number of VNTR locus.

  3. Molecular epidemiology of HCV monoinfection and HIV/HCV coinfection in injection drug users in Liuzhou, Southern China.

    Directory of Open Access Journals (Sweden)

    Yi Tan

    Full Text Available BACKGROUND: Hepatitis C virus (HCV mono-infection and HCV/HIV (human immunodeficiency virus co-infection are growing problems in injection drug users (IDU. Their prevalence and genotypic patterns vary with geographic locations. Access to harm reduction measures is opening up opportunities for improving the HIV/HCV profiling of IDU in China, where IDUs account for a significant proportion of the two infections especially in the southern part of the country. METHODOLOGY/PRINCIPAL FINDINGS: A cross sectional study was conducted. Through the Liuzhou Methadone Clinic, a total of 117 injection drug users (IDUs were recruited from Guangxi, Southern China. A majority of the IDUs (96% were HCV antibody positive, of which 21% were HIV infected. Unlike HCV monoinfection, there was spatial heterogeneity in the distribution of HIV/HCV coinfection, the latter also characterized by a higher prevalence of needle-sharing. Phylogenetic analysis revealed that genotype 6a was predominant in the study population. There were shorter genetic distances among the 6a sequences compared to the other HCV subtypes-1a, 3a, and 3b. CONCLUSION/SIGNIFICANCE: The results suggested that HIV and HCV were introduced at around the same time to the IDU populations in Southern China, followed by their differential spread as determined by the biologic characteristics of the virus and the intensity of behavioural risk. This pattern is different from that in other South East Asian countries where HCV infections have probably predated HIV.

  4. Distribution of human papilloma virus genotype prevalence in invasive cervical carcinomas and precancerous lesions in the Yangtze River Delta area, China.

    Science.gov (United States)

    Wang, Hongyun; Cheng, Xiaodong; Ye, Jing; Xu, Xiuyun; Hong, Ying; Sui, Long; You, Zhixue; Xie, Xing

    2018-04-27

    This study aimed to provide more information for cancer prevention strategies by determining the distribution of human papilloma virus (HPV) genotype prevalence in invasive cervical carcinoma (ICC) and precancerous lesion patients in the Yangtze River Delta area in China. This multi-centre descriptive cross-sectional study involves four university hospitals in the Jiangzhehu area. Women with histologically confirmed cervical intraepithelial neoplasia (CIN) 1, CIN2, CIN3 or ICC who were diagnosed and treated in the four selected hospitals between February 2012 and April 2014 were eligible for recruitment. The average age of the patients was 40.93 ± 11.87 years old, among whom the youngest was 17 years old and the oldest was 76 years old.Those with immunodeficiency diseases or a previous history of cancer or CIN were excluded. HPV genotyping was performed by a central laboratory. The distribution and age and disease specificity of the HPV genotype prevalence were analysed. Of the 2181 collected samples, 251 were ICC and 1930 were CIN. The mean age of cervical cancer and CIN patients was 40.93 ± 11.8 years (range, 17-76 years). The five most commonly identified HPV types in each lesion class were as follows: CIN1: 52, 58, 16, 33, and CP; CIN2: 16, 58, 52, 33, and 31; CIN3: 16, 58, 33, 52, and 31; and ICC: 16, 58, 18, 52, and 33. CIN1 had an earlier age of onset (30-40 years) than CIN2, CIN3, and cervical cancer. The age of onset of cervical cancer exhibited two peaks at 40-44 and 50-54 years of age. In all infected patients, the frequency of HPV infection with a single type was 62.9%, and with multiple types, it was 38.1%. There was no difference in the frequencies of multiple types amongst the different cervical lesions. The most prevalent genotypes in the investigated area (52, 58, 16 and 18) justify the necessity of anti-HPV vaccination in teenagers and young girls under 24 years old in the Yangtze River Delta area in China. Infection with

  5. NS5A Sequence Heterogeneity and Mechanisms of Daclatasvir Resistance in Hepatitis C Virus Genotype 4 Infection.

    Science.gov (United States)

    Zhou, Nannan; Hernandez, Dennis; Ueland, Joseph; Yang, Xiaoyan; Yu, Fei; Sims, Karen; Yin, Philip D; McPhee, Fiona

    2016-01-15

    Daclatasvir is an NS5A inhibitor approved for treatment of infection due to hepatitis C virus (HCV) genotypes (GTs) 1-4. To support daclatasvir use in HCV genotype 4 infection, we examined a diverse genotype 4-infected population for HCV genotype 4 subtype prevalence, NS5A polymorphisms at residues associated with daclatasvir resistance (positions 28, 30, 31, or 93), and their effects on daclatasvir activity in vitro and clinically. We performed phylogenetic analysis of genotype 4 NS5A sequences from 186 clinical trial patients and 43 sequences from the European HCV database, and susceptibility analyses of NS5A polymorphisms and patient-derived NS5A sequences by using genotype 4 NS5A hybrid genotype 2a replicons. The clinical trial patients represented 14 genotype 4 subtypes; most prevalent were genotype 4a (55%) and genotype 4d (27%). Daclatasvir 50% effective concentrations for 10 patient-derived NS5A sequences representing diverse phylogenetic clusters were ≤0.080 nM. Most baseline sequences had ≥1 NS5A polymorphism at residues associated with daclatasvir resistance; however, only 3 patients (1.6%) had polymorphisms conferring ≥1000-fold daclatasvir resistance in vitro. Among 46 patients enrolled in daclatasvir trials, all 20 with baseline resistance polymorphisms achieved a sustained virologic response. Circulating genotype 4 subtypes are genetically diverse. Polymorphisms conferring high-level daclatasvir resistance in vitro are uncommon before therapy, and clinical data suggest that genotype 4 subtype and baseline polymorphisms have minimal impact on responses to daclatasvir-containing regimens. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

  6. Genotype-phenotype associations in children with congenital hyperinsulinism

    DEFF Research Database (Denmark)

    Melikyan, Maria; Brusgaard, Klaus; Petraykina, Elena

    Congenital hyperinsulinism (CHI) is a heterogeneous disease in terms of clinical presentation, genetics and histology. Mutations in eight genes are known to be a cause of CHI, of which ABCC8, KCNJ11 and GCK are among the most common. We investigated genotype-phenotype associations in a cohort...

  7. Heterogeneity of O blood group in India: Peeping through the window of molecular biology.

    Science.gov (United States)

    Gogri, Harita; Ray, Sabita; Agrawal, Snehal; Aruna, S; Ghosh, Kanjaksha; Gorakshakar, Ajit

    2018-01-01

    Molecular genotyping of ABO blood group system has identified more than 60 "O" group alleles based on the single-nucleotide polymorphisms present in the ABO gene. Heterogeneity of O group alleles has been observed in various countries from South America, Europe, Middle East, and Asia. India is a vast country with more than 1300 million population which is divided into various ethnic and tribal groups. However, very little is known about the heterogeneity of O alleles in Indians. A total of 116 O group individuals from the mixed population of Mumbai, India, were enrolled in the present study. DNA was extracted using the standard phenol-chloroform method. The exons 6 and 7 of the ABO gene were genotyped by polymerase chain reaction-single-strand conformation polymorphism and/or DNA sequencing. The genotyping results were compared with our earlier findings. Overall, ten different genotypes were identified. Three rare alleles, namely, O05, O11, and O26 were seen in the mixed group category. These results suggest that there is an internal heterogeneity in the mixed group while Dhodias and Parsis, the groups which were screened earlier, seem to be more homogenous groups. An important piece of information emerges out from this study, that is, O01O02 genotype is expressing some selective force in population groups screened in India as well as many other groups worldwide. In the future, molecular genotyping of the ABO blood group system among different ethnic and tribal Indian groups would help in generating data to fill up the gaps in the molecular ABO map of the world.

  8. Response of water use efficiency and carbon emission to no-tillage and winter wheat genotypes in the North China Plain.

    Science.gov (United States)

    Ren, Yujie; Gao, Chao; Han, Huifang; Li, Quanqi

    2018-04-20

    No-tillage management practices reduce net CO 2 losses from farmland and keep soil from degrading, but also decrease winter wheat grain yield and water use efficiency (WUE) in the North China Plain (NCP). Suitable management practices, namely, the choice of genotypes, could enhance crop yield and WUE; however, how the WUE and CO 2 exchange responds to no-tillage practices and winter wheat genotypes remains unclear. In the 2015-2016 and 2016-2017 winter wheat growing seasons in the NCP, a field experiment was carried out, and tested two tillage methods (no-tillage with mulching and conventional tillage) and two winter wheat genotypes ('Tainong 18' and 'Jimai 22'). The goal of the study was to identify the relationship between winter wheat grain yield, water consumption, and carbon emissions in no-tillage practices. The results showed that, compared to conventional tillage, no-tillage significantly reduced the net CO 2 -C cumulative emissions and water consumption; however, the grain yield was significantly reduced by 6.8% and 12.0% in the first and second growing seasons, respectively. Compared with Jimai 22, Tainong 18 had a compensatory effect on the yield reduction caused by no-tillage. As a result, the yield carbon utilization efficiency (R) and WUE were the highest in no-tillage with Tainong 18 (NT18), and the carbon emission per unit water consumption was the lowest in NT18. The results support the idea that a combination of no-tillage with genotype can improve the regulation of soil carbon emissions and water consumption of winter wheat, thus, providing theoretical support for sustainable crop production and soil development in the NCP. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Screening Chinese soybean genotypes for Agrobacterium-mediated genetic transformation suitability*

    Science.gov (United States)

    Song, Zhang-yue; Tian, Jing-luan; Fu, Wei-zhe; Li, Lin; Lu, Ling-hong; Zhou, Lian; Shan, Zhi-hui; Tang, Gui-xiang; Shou, Hui-xia

    2013-01-01

    The Agrobacterium-mediated transformation system is the most commonly used method in soybean transformation. Screening of soybean genotypes favorable for Agrobacterium-infection and tissue regeneration is the most important step to establish an efficient genetic transformation system. In this study, twenty soybean genotypes that originated from different soybean production regions in China were screened for transient infection, regeneration capacity, and stable transgenic efficiency. Three genotypes, Yuechun 04-5, Yuechun 03-3, and Tianlong 1, showed comparable stable transgenic efficiencies with that of the previously reported American genotypes Williams 82 and Jack in our experimental system. For the Tianlong 1, the average stable transformation efficiency is 4.59%, higher than that of control genotypes (Jack and Williams 82), which is enough for further genomic research and genetic engineering. While polymerase chain reaction (PCR), LibertyLink strips, and β-glucuronidase (GUS) staining assays were used to detect the insertion and expression of the transgene, leaves painted with 135 mg/L Basta could efficiently identify the transformants. PMID:23549846

  10. Hepatitis E Virus Genotype 4 Outbreak, Italy, 2011

    Science.gov (United States)

    Garbuglia, Anna R.; Scognamiglio, Paola; Petrosillo, Nicola; Mastroianni, Claudio Maria; Sordillo, Pasquale; Gentile, Daniele; La Scala, Patrizia; Girardi, Enrico

    2013-01-01

    During 2011, 5 persons in the area of Lazio, Italy were infected with a monophyletic strain of hepatitis E virus that showed high sequence homology with isolates from swine in China. Detection of this genotype in Italy parallels findings in other countries in Europe, signaling the possible spread of strains new to Western countries. PMID:23260079

  11. [Discriminatory power of variable number on tandem repeats loci for genotyping Mycobacterium tuberculosis strains in China].

    Science.gov (United States)

    Chen, H X; Cai, C; Liu, J Y; Zhang, Z G; Yuan, M; Jia, J N; Sun, Z G; Huang, H R; Gao, J M; Li, W M

    2017-06-10

    Objective: Using the standard genotype method, variable number of tandem repeats (VNTR), we constructed a VNTR database to cover all provinces and proposed a set of optimized VNTR loci combinations for each province, in order to improve the preventive and control programs on tuberculosis, in China. Methods: A total of 15 loci VNTR was used to analyze 4 116 Mycobacterium tuberculosis strains, isolated from national survey of Drug Resistant Tuberculosis, in 2007. Hunter-Gaston Index (HGI) was also used to analyze the discriminatory power of each VNTR site. A set combination of 12-VNTR, 10-VNTR, 8-VNTR and 5-VNTR was respectively constructed for each province, based on 1) epidemic characteristics of M. tuberculosis lineages in China, with high discriminatory power and genetic stability. Results: Through the completed 15 loci VNTR patterns of 3 966 strains under 96.36 % (3 966/4 116) coverage, we found seven high HGI loci (including QUB11b and MIRU26) as well as low stable loci (including QUB26, MIRU16, Mtub21 and QUB11b) in several areas. In all the 31 provinces, we found an optimization VNTR combination as 10-VNTR loci in Inner Mongolia, Chongqing and Heilongjiang, but with 8-VNTR combination shared in other provinces. Conclusions: It is necessary to not only use the VNTR database for tracing the source of infection and cluster of M. tuberculosis in the nation but also using the set of optimized VNTR combinations in monitoring those local epidemics and M. tuberculosis (genetics in local) population.

  12. The human endurance athlete: heterogeneity and adaptability of ...

    African Journals Online (AJOL)

    In human subjects, large variations between individuals (up to 3-fold) exist in the capacity for endurance exercise performance. In a heterogeneous population, endurance performance is strongly related to whole body maximal oxygen uptake (VO2 max). This is in part genotype dependent (~25%) but is adaptable with ...

  13. Genotype-Specific Measles Transmissibility: A Branching Process Analysis.

    Science.gov (United States)

    Ackley, Sarah F; Hacker, Jill K; Enanoria, Wayne T A; Worden, Lee; Blumberg, Seth; Porco, Travis C; Zipprich, Jennifer

    2018-04-03

    Substantial heterogeneity in measles outbreak sizes may be due to genotype-specific transmissibility. Using a branching process analysis, we characterize differences in measles transmission by estimating the association between genotype and the reproduction number R among postelimination California measles cases during 2000-2015 (400 cases, 165 outbreaks). Assuming a negative binomial secondary case distribution, we fit a branching process model to the distribution of outbreak sizes using maximum likelihood and estimated the reproduction number R for a multigenotype model. Genotype B3 is found to be significantly more transmissible than other genotypes (P = .01) with an R of 0.64 (95% confidence interval [CI], .48-.71), while the R for all other genotypes combined is 0.43 (95% CI, .28-.54). This result is robust to excluding the 2014-2015 outbreak linked to Disneyland theme parks (referred to as "outbreak A" for conciseness and clarity) (P = .04) and modeling genotype as a random effect (P = .004 including outbreak A and P = .02 excluding outbreak A). This result was not accounted for by season of introduction, age of index case, or vaccination of the index case. The R for outbreaks with a school-aged index case is 0.69 (95% CI, .52-.78), while the R for outbreaks with a non-school-aged index case is 0.28 (95% CI, .19-.35), but this cannot account for differences between genotypes. Variability in measles transmissibility may have important implications for measles control; the vaccination threshold required for elimination may not be the same for all genotypes or age groups.

  14. Report of the third international workshop on molecular blood group genotyping

    NARCIS (Netherlands)

    Daniels, G.; van der Schoot, C. E.; Gassner, C.; Olsson, M. L.

    2009-01-01

    The Third International Society of Blood Transfusion Workshop on Molecular Blood Group Genotyping was held in 2008, with a feedback meeting at the International Society of Blood Transfusion Congress in Macao SAR, China. Thirty-three laboratories participated, eight less than in 2006. Six samples

  15. Genotype by sex and genotype by age interactions with sedentary behavior: the Portuguese Healthy Family Study.

    Directory of Open Access Journals (Sweden)

    Daniel M V Santos

    Full Text Available Sedentary behavior (SB expression and its underlying causal factors have been progressively studied, as it is a major determinant of decreased health quality. In the present study we applied Genotype x Age (GxAge and Genotype x Sex (GxSex interaction methods to determine if the phenotypic expression of different SB traits is influenced by an interaction between genetic architecture and both age and sex. A total of 1345 subjects, comprising 249 fathers, 327 mothers, 334 sons and 325 daughters, from 339 families of The Portuguese Healthy Family Study were included in the analysis. SB traits were assessed by means of a 3-d physical activity recall, the Baecke and IPAQ questionnaires. GxAge and GxSex interactions were analyzed using SOLAR 4.0 software. Sedentary behaviour heritability estimates were not always statistically significant (p>0.05 and ranged from 3% to 27%. The GxSex and GxAge interaction models were significantly better than the single polygenic models for TV (min/day, EEsed (kcal/day, personal computer (PC usage and physical activty (PA tertiles. The GxAge model is also significantly better than the polygenic model for Sed (min/day. For EEsed, PA tertiles, PC and Sed, the GxAge interaction was significant because the genetic correlation between SB environments was significantly different from 1. Further, PC and Sed variance heterogeneity among distinct ages were observed. The GxSex interaction was significant for EEsed due to genetic variance heterogeneity between genders and for PC due to a genetic correlation less than 1 across both sexes. Our results suggest that SB expression may be influenced by the interactions between genotype with both sex and age. Further, different sedentary behaviors seem to have distinct genetic architectures and are differentially affected by age and sex.

  16. Prevalence and genetic characterization of Toxoplasma gondii in donkeys in northeastern China.

    Science.gov (United States)

    Zhang, Xiao-Xuan; Shi, Wei; Zhang, Nian-Zhang; Shi, Kun; Li, Jian-Ming; Xu, Peng; Zhao, Quan; Du, Rui

    2017-10-01

    Toxolasma gondii is one of the most important obligate intracellular protozoan parasites. Recently, toxoplasmosis is of increasing concerns because T. gondii not only has a worldwide distribution but also can infect virtually all warm-blooded hosts including donkeys. However, limited information is available concerning the genetic characterization of T. gondii in donkeys in northeastern China. In this study, a total of 302 brain tissue samples collected from donkeys from Jilin (n=108) and Liaoning (n=194) provinces, northeastern China, were examined for T. gondii infection by semi-nested PCR of B1 gene. The positive samples were genotyped at 11 loci (i.e., SAG1, alternative SAG2, 5'-and 3'-SAG2, SAG3, L358, BTUB, c22-8, GRA6, c29-2, PK1 and Apico) using polymerase chain reaction-restriction fragment length polymorphism technology. Of 302 brain tissue samples, 19 (6.29%) were PCR-positive for T. gondii. The prevalence rates of T. gondii were 6.48% (7/108) and 6.19% (12/194) in Jilin Province and Liaoning Province, respectively. The prevalence of T. gondii in different season groups varied from 5.56% to 7.41%. The prevalence of T. gondii in "Cage-free" donkeys was higher than that in "Captive" donkeys. Of the 19 positive samples, only two isolates were successfully genotyped at all loci, three were genotyped at 9 loci. In total, four samples belong to ToxoDB genotype #9, one belong to ToxoDB genotype #10. This is firstly characterized the T. gondii isolates from donkeys in northeastern China. The results of the present study will improve the information of the distribution of T. gondii genotypes in China. Copyright © 2017. Published by Elsevier B.V.

  17. Inference of Cell Mechanics in Heterogeneous Epithelial Tissue Based on Multivariate Clone Shape Quantification

    Science.gov (United States)

    Tsuboi, Alice; Umetsu, Daiki; Kuranaga, Erina; Fujimoto, Koichi

    2017-01-01

    Cell populations in multicellular organisms show genetic and non-genetic heterogeneity, even in undifferentiated tissues of multipotent cells during development and tumorigenesis. The heterogeneity causes difference of mechanical properties, such as, cell bond tension or adhesion, at the cell–cell interface, which determine the shape of clonal population boundaries via cell sorting or mixing. The boundary shape could alter the degree of cell–cell contacts and thus influence the physiological consequences of sorting or mixing at the boundary (e.g., tumor suppression or progression), suggesting that the cell mechanics could help clarify the physiology of heterogeneous tissues. While precise inference of mechanical tension loaded at each cell–cell contacts has been extensively developed, there has been little progress on how to distinguish the population-boundary geometry and identify the cause of geometry in heterogeneous tissues. We developed a pipeline by combining multivariate analysis of clone shape with tissue mechanical simulations. We examined clones with four different genotypes within Drosophila wing imaginal discs: wild-type, tartan (trn) overexpression, hibris (hbs) overexpression, and Eph RNAi. Although the clones were previously known to exhibit smoothed or convoluted morphologies, their mechanical properties were unknown. By applying a multivariate analysis to multiple criteria used to quantify the clone shapes based on individual cell shapes, we found the optimal criteria to distinguish not only among the four genotypes, but also non-genetic heterogeneity from genetic one. The efficient segregation of clone shape enabled us to quantitatively compare experimental data with tissue mechanical simulations. As a result, we identified the mechanical basis contributed to clone shape of distinct genotypes. The present pipeline will promote the understanding of the functions of mechanical interactions in heterogeneous tissue in a non-invasive manner. PMID

  18. Molecular Epidemiology Study in Xuanwei: the Relationship among
Coal Type, Genotype and Lung Cancer Risk

    Directory of Open Access Journals (Sweden)

    Jihua LI

    2015-01-01

    Full Text Available Background and objective It has been proven that the lung cancer mortality rate in Xuanwei County, China was among the highest in the country and has been associated with exposure to indoor smoky coal emissions that contain high levels of polycyclic aromatic hydrocarbons. This risk may be modified by variation in genetic polymorphisms and coal subtypes. Our objective was to use molecular epidemiological techniques to investigate the relationship among genetic polymorphisms, coal subtype and lung cancer risk in Xuanwei County. Methods On the basis of two population-based case-control studies in residents of Xuanwei County, China, questionnaires covering demographic information, smoking history, family and personal medical history, and information on other variables were administered and buccal cells and sputum samples were collected separately from each subject enrolled to extract DNA. GST superfamily, AKR1C3 superfamily, OGG1 superfamily and other genotype were scanned by useing PCR method. ORs and 95%CIs were used to estimate the association between genotypes, coal subtypes and lung cancer risk factors by conditional Logistic regression using Statistical Analysis Software. Results Compared with subjects who using smokeless coal or wood, smoky coal use was statistically significantly associated with lung cancer risk (OR=7.7, 95%CI: 4.5-13.3. There was marked heterogeneity in risk estimates for specific subtypes of smoky coal. Estimates were highest for coal from the Laibin (OR=24.8, Longtan (OR=11.6 and Baoshan (OR=6.0 coal types, and lower for coal from other types; the risk within the same subtype of coal in male and female were similar. The GSTM1-null genotype, the AKR1C3 (Ex1-70C>G, OGG1 (Ex6-315C>G genotypes were closely associated with increased risk of lung cancer in Xuanwei County, and their odds ratios (95%CI were 2.3 (1.3-4.2, 1.8 (1.0-3.5 and 1.9 (1.1-3.3, respectively. Compared to subjects who with GSTM1-positive and used less than

  19. Establishment of a novel two-probe real-time PCR for simultaneously quantification of hepatitis B virus DNA and distinguishing genotype B from non-B genotypes.

    Science.gov (United States)

    Wang, Wei; Liang, Hongpin; Zeng, Yongbin; Lin, Jinpiao; Liu, Can; Jiang, Ling; Yang, Bin; Ou, Qishui

    2014-11-01

    Establishment of a simple, rapid and economical method for quantification and genotyping of hepatitis B virus (HBV) is of great importance for clinical diagnosis and treatment of chronic hepatitis B patients. We hereby aim to develop a novel two-probe real-time PCR for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes. Conserved primers and TaqMan probes for genotype B and non-B genotypes were designed. The linear range, detection sensitivity, specificity and repeatability of the method were assessed. 539 serum samples from HBV-infected patients were assayed, and the results were compared with commercial HBV quantification and HBV genotyping kits. The detection sensitivity of the two-probe real-time PCR was 500IU/ml; the linear range was 10(3)-10(9)IU/ml, and the intra-assay CVs and inter-assay CVs were between 0.84% and 2.80%. No cross-reaction was observed between genotypes B and non-B. Of the 539 detected samples, 509 samples were HBV DNA positive. The results showed that 54.0% (275/509) of the samples were genotype B, 39.5% (201/509) were genotype non-B and 6.5% (33/509) were mixed genotype. The coincidence rate between the method and a commercial HBV DNA genotyping kit was 95.9% (488/509, kappa=0.923, PDNA qPCR kit were achieved. A novel two-probe real-time PCR method for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes was established. The assay was sensitive, specific and reproducible which can be applied to areas prevalent with HBV genotypes B and C, especially in China. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. [Polymorphism of vitamin D receptor gene Fok I in Mongolian population of China].

    Science.gov (United States)

    Xing, Shao-ji; Zhou, Li-she; Xu, Xiu-ju

    2006-04-01

    To investigate the polymorphism distribution of vitamin D receptor (VDR) gene Fok I in Mongolian population of China. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to analyze three genotypes FF, Ff and ff in the start codon of VDR gene (Fok I) in unrelated normal healthy Mongolian individuals of China. In the population, we obtained the allelic frequencies of 57% and 43% for (F) and (f) allele and the percentage of genotypes FF, Ff and ff to be 31%, 52%, and 17% respectively. The polymorphism frequency and distribution of this VDR gene Fok I in Mongolian population of China exhibit its own characteristics.

  1. Noninvasive In-Vivo Quantification of Mechanical Heterogeneity of Invasive Breast Carcinomas.

    Directory of Open Access Journals (Sweden)

    Tengxiao Liu

    Full Text Available Heterogeneity is a hallmark of cancer whether one considers the genotype of cancerous cells, the composition of their microenvironment, the distribution of blood and lymphatic microvasculature, or the spatial distribution of the desmoplastic reaction. It is logical to expect that this heterogeneity in tumor microenvironment will lead to spatial heterogeneity in its mechanical properties. In this study we seek to quantify the mechanical heterogeneity within malignant and benign tumors using ultrasound based elasticity imaging. By creating in-vivo elastic modulus images for ten human subjects with breast tumors, we show that Young's modulus distribution in cancerous breast tumors is more heterogeneous when compared with tumors that are not malignant, and that this signature may be used to distinguish malignant breast tumors. Our results complement the view of cancer as a heterogeneous disease on multiple length scales by demonstrating that mechanical properties within cancerous tumors are also spatially heterogeneous.

  2. Bacillus anthracis in China and its relationship to worldwide lineages

    Directory of Open Access Journals (Sweden)

    Schupp James M

    2009-04-01

    Full Text Available Abstract Background The global pattern of distribution of 1033 B. anthracis isolates has previously been defined by a set of 12 conserved canonical single nucleotide polymorphisms (canSNP. These studies reinforced the presence of three major lineages and 12 sub-lineages and sub-groups of this anthrax-causing pathogen. Isolates that form the A lineage (unlike the B and C lineages have become widely dispersed throughout the world and form the basis for the geographical disposition of "modern" anthrax. An archival collection of 191 different B. anthracis isolates from China provides a glimpse into the possible role of Chinese trade and commerce in the spread of certain sub-lineages of this pathogen. Canonical single nucleotide polymorphism (canSNP and multiple locus VNTR analysis (MLVA typing has been used to examine this archival collection of isolates. Results The canSNP study indicates that there are 5 different sub-lineages/sub-groups in China out of 12 previously described world-wide canSNP genotypes. Three of these canSNP genotypes were only found in the western-most province of China, Xinjiang. These genotypes were A.Br.008/009, a sub-group that is spread across most of Europe and Asia; A.Br.Aust 94, a sub-lineage that is present in Europe and India, and A.Br.Vollum, a lineage that is also present in Europe. The remaining two canSNP genotypes are spread across the whole of China and belong to sub-group A.Br.001/002 and the A.Br.Ames sub-lineage, two closely related genotypes. MLVA typing adds resolution to the isolates in each canSNP genotype and diversity indices for the A.Br.008/009 and A.Br.001/002 sub-groups suggest that these represent older and established clades in China. Conclusion B. anthracis isolates were recovered from three canSNP sub-groups (A.Br.008/009, A.Br.Aust94, and A.Br.Vollum in the western most portion of the large Chinese province of Xinjiang. The city of Kashi in this province appears to have served as a crossroads

  3. Hepatitis C virus genotypes among multiply transfused hemoglobinopathy patients from Northern Iraq

    Directory of Open Access Journals (Sweden)

    Adil A Othman

    2014-01-01

    Full Text Available Background and Aim: Owing to the scarcity of data on hepatitis C virus (HCV genotypes in Iraq and due to their epidemiological as well as therapy implications, this study was initiated aiming at determining these genotypes in Northern Iraq. Materials and Methods: A total of 70 HCV antibody positive multi transfused patients with hemoglobinopathies, who had detectable HCV ribonucleic acid, were recruited for genotyping using genotype-specific nested polymerase chain reaction. Results: The most frequent genotype detected was genotype 4 (52.9% followed by 3a (17.1%, 1b (12.9% and 1a (1.4%, while mixed genotypes (4 with either 3a or 1b were detected in 7.1%. Conclusion: The predominance of genotype 4 is similar to other studies from surrounding Eastern Mediterranean Arab countries and to the only earlier study from central Iraq, however the significant high proportion of 3a and scarcity of 1a, are in contrast to the latter study and may be explainable by the differing population interactions in this part of Iraq. This study complements previous studies from Eastern Mediterranean region and demonstrates relative heterogeneity of HCV genotype distribution within Iraq and should trigger further studies in other parts of the country.

  4. Geographic distribution of hepatitis C virus genotype 6 subtypes in Thailand.

    Science.gov (United States)

    Akkarathamrongsin, Srunthron; Praianantathavorn, Kesmanee; Hacharoen, Nisachol; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Tanaka, Yasuhito; Mizokami, Masashi; Poovorawan, Yong

    2010-02-01

    The nucleotide sequence of hepatitis C virus (HCV) genotype 6 found mostly in south China and south-east Asia, displays profound genetic diversity. The aim of this study to determine the genetic variability of HCV genotype 6 (HCV-6) in Thailand and locate the subtype distribution of genotype 6 in various geographic areas. Four hundred nineteen anti-HCV positive serum samples were collected from patients residing in - the central part of the country. HCV RNA positive samples based on reverse transcriptase- polymerase chain reaction (RT-PCR) of the 5'UTR were amplified with primers specific for the core and NS5B regions. Nucleotide sequences of both regions were analyzed for the genotype by phylogenetic analysis. To determine geographic distribution of HCV-6 subtypes, a search of the international database on subtype distribution in the respective countries was conducted. Among 375 HCV RNA positive samples, 71 had HCV-6 based on phylogenetic analysis of partial core and NS5B regions. The subtype distribution in order of predominance was 6f (56%), 6n (22%), 6i (11%), 6j (10%), and 6e (1%). Among the 13 countries with different subtypes of HCV-6, most sequences have been reported from Vietnam. Subtype 6f was found exclusively in Thailand where five distinct HCV-6 subtypes are circulating. HCV-6, which is endemic in south China and south-east Asia, displays profound genetic diversity and may have evolved over a considerable period of time. (c) 2009 Wiley-Liss, Inc.

  5. Population dynamics on heterogeneous bacterial substrates

    Science.gov (United States)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  6. Plant genotypes affect aboveground and belowground herbivore interactions by changing chemical defense.

    Science.gov (United States)

    Li, Xiaoqiong; Guo, Wenfeng; Siemann, Evan; Wen, Yuanguang; Huang, Wei; Ding, Jianqing

    2016-12-01

    Spatially separated aboveground (AG) and belowground (BG) herbivores are closely linked through shared host plants, and both patterns of AG-BG interactions and plant responses may vary among plant genotypes. We subjected invasive (USA) and native (China) genotypes of tallow tree (Triadica sebifera) to herbivory by the AG specialist leaf-rolling weevil Heterapoderopsis bicallosicollis and/or the root-feeding larvae of flea beetle Bikasha collaris. We measured leaf damage and leaves rolled by weevils, quantified beetle survival, and analyzed flavonoid and tannin concentrations in leaves and roots. AG and BG herbivores formed negative feedbacks on both native and invasive genotypes. Leaf damage by weevils and the number of beetle larvae emerging as adults were higher on invasive genotypes. Beetles reduced weevil damage and weevils reduced beetle larval emergence more strongly for invasive genotypes. Invasive genotypes had lower leaf and root tannins than native genotypes. BG beetles decreased leaf tannins of native genotypes but increased root tannins of invasive genotypes. AG herbivory increased root flavonoids of invasive genotypes while BG herbivory decreased leaf flavonoids. Invasive genotypes had lower AG and BG herbivore resistance, and negative AG-BG herbivore feedbacks were much stronger for invasive genotypes. Lower tannin concentrations explained overall better AG and BG herbivore performances on invasive genotypes. However, changes in tannins and flavonoids affected AG and BG herbivores differently. These results suggest that divergent selection on chemical production in invasive plants may be critical in regulating herbivore performances and novel AG and BG herbivore communities in new environments.

  7. Significant impacts of heterogeneous reactions on the chemical composition and mixing state of dust particles: A case study during dust events over northern China

    Science.gov (United States)

    Wang, Zhe; Pan, Xiaole; Uno, Itsushi; Li, Jie; Wang, Zifa; Chen, Xueshun; Fu, Pingqing; Yang, Ting; Kobayashi, Hiroshi; Shimizu, Atsushi; Sugimoto, Nobuo; Yamamoto, Shigekazu

    2017-06-01

    The impact of heterogeneous reactions on the chemical components and mixing state of dust particles are investigated by observations and an air quality model over northern China between March 27, 2015 and April 2, 2015. Synergetic observations were conducted using a polarization optical particle counter (POPC), a depolarized two-wavelength Lidar and filter samples in Beijing. During this period, dust plume passed through Beijing on March 28, and flew back on March 29 because of synoptic weather changes. Mineral dust mixed with anthropogenic pollutants was simulated using the Nested Air Quality Prediction Modeling System (NAQPMS) to examine the role of heterogeneous processes on the dust. A comparison of observations shows that the NAQPMS successfully reproduces the time series of the vertical profile, particulate matter concentration, and chemical components of fine mode (diameter ≤ 2.5 μm) and coarse mode (2.5 μm mixed with dust particles. The significant alterations of the chemical composition and mixing state of particles due to heterogeneous reactions are important for the direct and indirect climate effects of dust and anthropogenic aerosols.

  8. Heterogeneity and loss of soil nutrient elements under aeolian processes in the Otindag Desert, China

    Science.gov (United States)

    Li, Danfeng; Wang, Xunming; Lou, Junpeng; Liu, Wenbin; Li, Hui; Ma, Wenyong; Jiao, Linlin

    2018-02-01

    The heterogeneity of the composition of surface soils that are affected by aeolian processes plays important roles in ecological evolution and the occurrence of aeolian desertification in fragile ecological zones, but the associated mechanisms are poorly understood. Using field investigation, wind tunnel experiments, and particle size and element analyses, we discuss the variation in the nutrient elements of surface soils that forms in the presence of aeolian processes of four vegetation species (Caragana microphylla Lam, Artemisia frigida Willd. Sp. Pl., Leymus chinensis (Trin.) Tzvel. and Stipa grandis P. Smirn) growing in the Otindag Desert, China. These four vegetation communities correspond to increasing degrees of degradation. A total of 40 macro elements, trace elements, and oxides were measured in the surface soil and in wind-transported samples. The results showed that under the different degradation stages, the compositions and concentrations of nutrients in surface soils differed for the four vegetation species. Aeolian processes may cause higher heterogeneity and higher loss of soil nutrient elements for the communities of Artemisia frigida Willd. Sp. Pl., Leymus chinensis (Trin.) Tzvel, and Stipa grandis P. Smirn than for the Caragana microphylla Lam community. There was remarkable variation in the loss of nutrients under different aeolian transportation processes. Over the past several decades, the highest loss of soil elements occurred in the 1970s, whereas the loss from 2011 to the present was generally 4.0% of that in the 1970s. These results indicate that the evident decrease in nutrient loss has played an important role in the rehabilitation that has occurred in the region recently.

  9. Genetic analysis of Asian measles virus strains--new endemic genotype in Nepal.

    Science.gov (United States)

    Truong, A T; Mulders, M N; Gautam, D C; Ammerlaan, W; de Swart, R L; King, C C; Osterhaus, A D; Muller, C P

    2001-07-01

    In many parts of Asia measles virus (MV) continues to be endemic. However, little is known about the genetic characteristics of viruses circulating on this continent. This study reports the molecular epidemiological analysis based on the entire nucleocapsid (N) and hemagglutinin (H) genes of the first isolates from Nepal and Taiwan, as well as of recent MV strains from India, Indonesia, and China. Four isolates collected in various regions in Nepal during 1999 belonged to a new genotype, tentatively called D8. Another Nepalese isolate and one from India belonged to genotype D4. The diversity of the Nepalese strains indicated that measles continues to be endemic in this country. The isolate from Taiwan grouped with D3 viruses and one Chinese strain isolated in The Netherlands was assigned to the previously described clade H, known to be endemic in Mainland China. Molecular characterization emerges as an important tool for monitoring virus endemicity and vaccination efforts.

  10. Root foraging increases performance of the clonal plant Potentilla reptans in heterogeneous nutrient environments.

    Science.gov (United States)

    Wang, Zhengwen; van Kleunen, Mark; During, Heinjo J; Werger, Marinus J A

    2013-01-01

    Plastic root-foraging responses have been widely recognized as an important strategy for plants to explore heterogeneously distributed resources. However, the benefits and costs of root foraging have received little attention. In a greenhouse experiment, we grew pairs of connected ramets of 22 genotypes of the stoloniferous plant Potentilla reptans in paired pots, between which the contrast in nutrient availability was set as null, medium and high, but with the total nutrient amount kept the same. We calculated root-foraging intensity of each individual ramet pair as the difference in root mass between paired ramets divided by the total root mass. For each genotype, we then calculated root-foraging ability as the slope of the regression of root-foraging intensity against patch contrast. For all genotypes, root-foraging intensity increased with patch contrast and the total biomass and number of offspring ramets were lowest at high patch contrast. Among genotypes, root-foraging intensity was positively related to production of offspring ramets and biomass in the high patch-contrast treatment, which indicates an evolutionary benefit of root foraging in heterogeneous environments. However, we found no significant evidence that the ability of plastic foraging imposes costs under homogeneous conditions (i.e. when foraging is not needed). Our results show that plants of P. reptans adjust their root-foraging intensity according to patch contrast. Moreover, the results show that the root foraging has an evolutionary advantage in heterogeneous environments, while costs of having the ability of plastic root foraging were absent or very small.

  11. Population expanding with the phalanx model and lineages split by environmental heterogeneity: a case study of Primula obconica in subtropical China.

    Directory of Open Access Journals (Sweden)

    Hai-Fei Yan

    Full Text Available Current and historical events have both affected the current distribution patterns and intraspecific divergence of plants. While numerous studies have focused on the Qinghai-Tibetan Plateau (QTP, the impacts of such events on the flora of subtropical China remain poorly understood. Subtropical China is famous for its highly complex topography and the limited impact from glaciation during the Pleistocene; this may have resulted in a different genetic legacy for species in this region compared to fully glaciated areas.We used plastid and nuclear DNA sequence data and distribution modeling to analyze the divergence patterns and demographic history of Primula obconica Hance, a widespread herbaceous montane species in subtropical China. The phylogenetic analysis revealed two major lineages (lineage A and lineage B, representing a west-east split into the Yunnan and Eastern groups, and the Sichuan and Central groups, respectively. The Eastern and Central groups comprised relatively new derived haplotypes. Nested Clade Analysis and Bayesian Skyline Plot analyses both indicated that P. obconica mainly experienced a gradual expansion of populations. In addition, the simulated distribution of P. obconica during the Last Glacial Maximum was slightly larger than its present-day distribution.Our results are the first to identify a west-east migration of P. obconica. The gradual expansion pattern and a larger potential distribution range in cold periods detected for P. obconica indicate that the population expansion of this species is consistent with the phalanx model. In addition, the current patterns of genetic differentiation have persisted as a result of the extensive environmental heterogeneity that exists in subtropical China.

  12. Oilseed rape genotypes response to boron toxicity

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    Savić Jasna

    2013-01-01

    Full Text Available Response of 16 oilseed rape genotypes to B (boron toxicity was analyzed by comparing the results of two experiments conducted in a glasshouse. In Experiment 1 plants were grown in standard nutrient solutions with 10 µMB (control and 1000 µM B. Relative root and shoot growth varied from 20-120% and 31-117%, respectively. Variation in B concentration in shoots was also wide (206.5-441.7 µg B g-1 DW as well as total B uptake by plant (62.3-281.2 µg B g1. Four selected genotypes were grown in Experiment 2 in pots filled with high B soil (8 kg ha-1 B; B8. Shoot growth was not affected by B8 treatment, while root and shoot B concentration was significantly increased compared to control. Genotypes Panther and Pronto which performed low relative root and shoot growth and high B accumulation in plants in Experiment 1, had good growth in B8 treatment. In Experiment 2 genotype NS-L-7 had significantly lower B concentration in shots under treatment B8, but also very high B accumulation in Experiment 1. In addition, cluster analyses classified genotypes in three groups according to traits contrasting in their significance for analyzing response to B toxicity. The first group included four varieties based on their shared characteristics that have small value for the relative growth of roots and shoots and large values of B concentration in shoot. In the second largest group were connected ten genotypes that are heterogeneous in traits and do not stand out on any characteristic. Genotypes NS-L-7 and Navajo were separated in the third group because they had big relative growth of root and shoot, but also a high concentration of B in the shoot, and high total B uptake. Results showed that none of tested genotypes could not be recommended for breeding process to tolerance for B toxicity. [Projekat Ministarstva nauke Republike Srbije, br. OI 173028

  13. High prevalence of Hepatitis C virus genotype 6 in Vietnam.

    Science.gov (United States)

    Pham, Duc Anh; Leuangwutiwong, Pornsawan; Jittmittraphap, Akanitt; Luplertlop, Nattanej; Bach, Hoa Khanh; Akkarathamrongsin, Srunthron; Theamboonlers, Apiradee; Poovorawan, Yong

    2009-01-01

    This study aimed to update the prevalence of the various Hepatitis C virus genotypes in Vietnamese blood donors. One hundred and three HCV antibody-positive plasma samples were collected from blood donors at the National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam. All specimens were subjected to RT-PCR of the 5' untranslated region (UTR) to confirm the presence of HCV RNA. The core and NS5B regions of thh positive samples were subsequently amplified by RT-PCR followed by direct sequencing and phylogenetic analysis. Seventy out of 103 samples (68.0%) were RNA positive. Core and NS5B were successfully amplified and sequences were obtained for 70 and 65 samples, respectively. Phylogenetic analysis revealed that genotype 6a was the most predominant among Vietnamese blood donors with a prevalence of 37.1% (26/70), followed by genotype 1a at 30.0% (21/70) and genotype 1b at 17.1% (12/70). The prevalence of two other genotype 6 variants, 6e and 61 was 8.6% and 1.4%, respectively. Further analysis of recent studies showed that the geographic distribution of genotype 6 covered mainly southern China and the mainland of Southeast Asia including Vietnam, Laos, Thailand, and Myanmar. The GenBank accession numbers for the sequences reported in this study are FJ768772-FJ768906.

  14. Interactions between social/ behavioral factors and ADRB2 genotypes may be associated with health at advanced ages in China.

    Science.gov (United States)

    Zeng, Yi; Cheng, Lingguo; Zhao, Ling; Tan, Qihua; Feng, Qiushi; Chen, Huashuai; Shen, Ke; Li, Jianxin; Zhang, Fengyu; Cao, Huiqing; Gregory, Simon G; Yang, Ze; Gu, Jun; Tao, Wei; Tian, Xiao-Li; Hauser, Elizabeth R

    2013-09-09

    1042718 or rs1042719 alleles, compared to the non-carriers. The results indicate significant positive associations of interactions between social/behavioral factors and the ADRB2 genotypes with health outcomes of cognitive function and self-reported health, and negative associations of carrying rs1042718 or rs1042719 minor alleles with negative emotion, at advanced ages in China. Our findings are exploratory rather than causal conclusions. This study implies that near-future health promotion programs considering individuals' genetic profiles, with appropriate protection of privacy/confidentiality, would yield increased benefits and reduced costs to the programs and their participants.

  15. Does urbanization affect energy intensities across provinces in China?Long-run elasticities estimation using dynamic panels with heterogeneous slopes

    International Nuclear Information System (INIS)

    Ma, Ben

    2015-01-01

    as China, error cross-sectional dependence and residual nonstationarity must be tested and properly treated to avoid size distortion and biased estimators. - Highlights: • This paper examines elasticities of urbanization on energy intensities in regional China. • Dynamic panel datasets by energy source are modeled allowing for heterogeneity. • Urbanization drives up energy intensity and electricity intensity rather than coal intensity. • Both the most significant impact channel and an energy transition process are identified. • Residual cross-sectional dependence and nonstationarity cannot be ignored technically

  16. Estimating the numbers of malaria infections in blood samples using high-resolution genotyping data.

    Directory of Open Access Journals (Sweden)

    Amanda Ross

    Full Text Available People living in endemic areas often habour several malaria infections at once. High-resolution genotyping can distinguish between infections by detecting the presence of different alleles at a polymorphic locus. However the number of infections may not be accurately counted since parasites from multiple infections may carry the same allele. We use simulation to determine the circumstances under which the number of observed genotypes are likely to be substantially less than the number of infections present and investigate the performance of two methods for estimating the numbers of infections from high-resolution genotyping data. The simulations suggest that the problem is not substantial in most datasets: the disparity between the mean numbers of infections and of observed genotypes was small when there was 20 or more alleles, 20 or more blood samples, a mean number of infections of 6 or less and where the frequency of the most common allele was no greater than 20%. The issue of multiple infections carrying the same allele is unlikely to be a major component of the errors in PCR-based genotyping. Simulations also showed that, with heterogeneity in allele frequencies, the observed frequencies are not a good approximation of the true allele frequencies. The first method that we proposed to estimate the numbers of infections assumes that they are a good approximation and hence did poorly in the presence of heterogeneity. In contrast, the second method by Li et al estimates both the numbers of infections and the true allele frequencies simultaneously and produced accurate estimates of the mean number of infections.

  17. Dopamine transporter 3'UTR VNTR genotype is a marker of performance on executive function tasks in children with ADHD

    Directory of Open Access Journals (Sweden)

    Polotskaia Anna

    2008-06-01

    Full Text Available Abstract Background Attention-Deficit/Hyperactivity Disorder (ADHD is a heterogeneous disorder from both clinical and pathogenic viewpoints. Executive function deficits are considered among the most important pathogenic pathways leading to ADHD and may index part of the heterogeneity in this disorder. Methods To investigate the relationship between the dopamine transporter gene (SLC6A3 3'-UTR VNTR genotypes and executive function in children with ADHD, 196 children diagnosed with ADHD were sequentially recruited, genotyped, and tested using a battery of three neuropsychological tests aimed at assessing the different aspects of executive functioning. Results Taking into account a correction for multiple comparisons, the main finding of this study is a significant genotype effect on performances on the Tower of London (F = 6.902, p = 0.009 and on the Wechsler Intelligence Scale for Children, Third Edition (WISC-III Freedom From Distractibility Index (F = 7.125, p = 0.008, as well as strong trends on Self Ordered Pointing Task error scores (F = 4,996 p = 0.026 and WISC-III Digit Span performance (F = 6.28, p = 0.023. Children with the 9/10 genotype exhibited, on average, a poorer performance on all four measures compared to children with the 10/10 genotype. No effect of genotype on Wisconsin Card Sorting Test measures of performance was detected. Conclusion Results are compatible with the view that SLC6A3 genotype may modulate components of executive function performance in children with ADHD.

  18. Growth and yield performance of Jerusalem artichoke clones in a semiarid region of China

    NARCIS (Netherlands)

    Liu, Z.X.; Spiertz, J.H.J.; Sha, J.; Xue, S.; Xie, G.H.

    2012-01-01

    This study investigated biomass yield and growth characteristics of 26 Jerusalem artichoke (Helianthus tuberosus L.) clones and assessed it as a bioenergy crop for a semiarid region of the Loess Plateau in China. Genotype, year, and genotype ´ year interaction contributed to differences in crop

  19. Demographic variability and heterogeneity among individuals within and among clonal bacteria strains

    DEFF Research Database (Denmark)

    Jouvet, Lionel; Rodriguez-Rojas, Alexandro; Steiner, Ulrich

    2018-01-01

    to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high...... control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction...

  20. Spatial Heterogeneity of Climate Change Effects on Dominant Height of Larch Plantations in Northern and Northeastern China

    Directory of Open Access Journals (Sweden)

    Hao Zang

    2016-07-01

    Full Text Available Determining the response of dominant height growth to climate change is important for understanding adaption strategies. Based on 550 permanent plots from a national forest inventory and climate data across seven provinces and three climate zones, we developed a climate-sensitive dominant height growth model under a mixed-effects model framework. The mean temperature of the wettest quarter and precipitation of the wettest month were found to be statistically significant explanatory variables that markedly improved model performance. Generally, future climate change had a positive effect on stand dominant height in northern and northeastern China, but the effect showed high spatial variability linked to local climatic conditions. The range in dominant height difference between the current climate and three future BC-RCP scenarios would change from −0.61 m to 1.75 m (−6.9% to 13.5% during the period 2041–2060 and from −1.17 m to 3.28 m (−9.1% to 41.0% during the period 2061–2080 across provinces. The impacts of climate change on stand dominant height decreased as stand age increased. Forests in cold and warm temperate zones had a smaller decrease in dominant height, owing to climate change, compared with those in the mid temperate zone. Overall, future climate change could impact dominant height growth in northern and northeastern China. As spatial heterogeneity of climate change affects dominant height growth, locally specific mitigation measures should be considered in forest management.

  1. Ethnic and geographic variations in HPV prevalence and genotype distribution in north-western Yunnan, China.

    Science.gov (United States)

    Baloch, Zulqarnain; Yuan, Tao; Wang, Binghui; Tai, Wenlin; Feng, Yue; Liu, Yanqing; Li, Xiao; Feng, Yue; Liu, Li; Zhang, A-mei; Wu, Xiaomei; Xia, Xueshan

    2016-03-01

    The prevalence and genotype distribution of human papillomavirus (HPV) vary throughout the world. To assess the prevalence and genotype distribution of HPV among three ethnic groups in two geographic locations in north-western Yunnan, we recruited 522 women in Shangri-le (n = 255) and Lijiang (n = 267). PCR amplification of HPV DNA was performed on cervical cells from these women using two consensus primer systems (MY09/11 and GP5/6). Amplified-HPV DNA was genotyped using the HPV GenoArray test. Geographically, the HPV prevalence was significantly higher (P = 0.002) among Shangri-le women than among Lijiang women. Infections with high-risk (HR)-HPV and with multiple HPV genotypes were also significantly more common (P = 0.001) among women in Shangri-le than women in Lijiang. Additionally, the prevalence of overall, HR-HPV, and single genotype HPV infections was significantly higher (P = 0.001) among Tibetan women than among Naxi and Han women. HPV-16 and HPV-33 were significantly more frequent in Shangri-le women compared with Lijiang (P = 0.006) women. In addition, HPV-16 (9.81%) and HPV-33 (5.88%) were significantly more prevalent in Tibetan women than in Naxi and Han women. Here, for the first time, we highlight the significant variation in the prevalence and genotype distribution of HPV in various populations in the north-western region of Yunnan Province. © 2015 Wiley Periodicals, Inc.

  2. Prevalence, enumeration and pheno- and genotypic characteristics of Listeria monocytogenes isolated from raw foods in South China

    Directory of Open Access Journals (Sweden)

    Moutong eChen

    2015-09-01

    Full Text Available Listeria monocytogenes is an important foodborne pathogen that can cause serious illness in immunocompromised individuals, pregnant women, the elderly, and newborns. The aim of this study was to: (i evaluate the prevalence and contamination level (most probable number, MPN of L. monocytogenes in 567 retail raw foods (fishery products, n=154; raw/fresh meat, n=123; frozen foods, n=110; edible fungi, n=108; vegetables, n=72 collected from South China and (ii to gain further knowledge on the phenotype and genotype distributions of this important foodborne pathogen. Approximately 22% of the samples were positive for L. monocytogenes. The contamination levels were between 0.3 and 10 MPN/g in 75.0%, between 10 and 100 MPN/g in 11.0% and less than 100 MPN/g in 14.0% of the countable samples. Five serogroups were identified among the177 foodborne L. monocytogenes isolates, with1/2a-3a (42.4% and1/2b-3b (26.0% serogroups being the most dominant. Serogroup I.1 and II.2 were only found in the edible mushrooms, while serogroup III was dominant in the fishery products, suggesting that specific serogroups of L. monocytogenes may have distinct ecological niches. Ten (5.6% L. monocytogenes isolates exhibited multidrug resistance. Genetic relatedness analysis revealed the absence of distinct associations between specific food types, antibiotic resistance, serogroups, and genetic diversity. The present study provided the first baseline data on the prevalence, contamination level, and characteristics of L. monocytogenes isolated from raw foods in South China. Some multidrug resistant strains belonged to the epidemiologically important serogroups (I.1 and II.1, implying a potential public health risk. In addition, these findings also provide basic information for the Chinese food safety associated authorities to draft appropriate standards to control L. monocytogenes contamination and improve microbiological safety of raw foods.

  3. A Multianalyzer Machine Learning Model for Marine Heterogeneous Data Schema Mapping

    Science.gov (United States)

    Yan, Wang; Jiajin, Le; Yun, Zhang

    2014-01-01

    The main challenges that marine heterogeneous data integration faces are the problem of accurate schema mapping between heterogeneous data sources. In order to improve the schema mapping efficiency and get more accurate learning results, this paper proposes a heterogeneous data schema mapping method basing on multianalyzer machine learning model. The multianalyzer analysis the learning results comprehensively, and a fuzzy comprehensive evaluation system is introduced for output results' evaluation and multi factor quantitative judging. Finally, the data mapping comparison experiment on the East China Sea observing data confirms the effectiveness of the model and shows multianalyzer's obvious improvement of mapping error rate. PMID:25250372

  4. PeakSeeker: a program for interpreting genotypes of mononucleotide repeats

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    Salipante Stephen J

    2009-02-01

    Full Text Available Abstract Background Mononucleotide repeat microsatellites are abundant, highly polymorphic DNA sequences, having the potential to serve as valuable genetic markers. Use of mononucleotide microsatellites has been limited by their tendency to produce "stutter", confounding signals from insertions and deletions within the mononucleotide tract that occur during PCR, which complicates interpretation of genotypes by masking the true position of alleles. Consequently, microsatellites with larger repeating subunits (dinucleotide and trinucleotide motifs are used, which produce less stutter but are less genetically heterogeneous and less informative. A method to interpret the genotypes of mononucleotide repeats would permit the widespread use of those highly informative microsatellites in genetic research. Findings We have developed an approach to interpret genotypes of mononucleotide repeats using a software program, named PeakSeeker. PeakSeeker interprets experimental electropherograms as the most likely product of signals from individual alleles. Because mononucleotide tracts demonstrate locus-specific patterns of stutter peaks, this approach requires that the genotype pattern from a single allele is defined for each marker, which can be approximated by genotyping single DNA molecules or homozygotes. We have evaluated the program's ability to discriminate various types of homozygous and heterozygous mononucleotide loci using simulated and experimental data. Conclusion Mononucleotide tracts offer significant advantages over di- and tri-nucleotide microsatellite markers traditionally employed in genetic research. The PeakSeeker algorithm provides a high-throughput means to type mononucleotide tracts using conventional and widely implemented fragment length polymorphism genotyping. Furthermore, the PeakSeeker algorithm could potentially be adapted to improve, and perhaps to standardize, the analysis of conventional microsatellite genotypes.

  5. Surfactant protein B deficiency and gene mutations for neonatal respiratory distress syndrome in China Han ethnic population

    Science.gov (United States)

    Yin, Xiaojuan; Meng, Fanping; wang, Yan; Xie, Lu; Kong, Xiangyong; Feng, Zhichun

    2013-01-01

    Objective: To determine whether the SP-B deficiency and gene mutations in exon 4 is associated with neonatal RDS in China Han ethnic population. Methods: The study population consisted of 40 neonates with RDS and 40 neonates with other diseases as control in China Han ethnic population. We Compared SP-B expression in lung tissue and bronchoalveolar lavage fluid with immunoblotting, and analyzed mutations in the SP-B gene with polymerase chain reaction (PCR) and gene sequencing. Results: In RDS group, low mature Surfactant protein B was found in both lung tissue and bronchoalveolar lavage fluid in 8 neonates. In control group, only 4 neonates with low mature Surfactant protein B in both lung tissue and bronchoalveolar lavage fluid. In RDS group, 20 neonates were found to have mutations in exon 4, 12 homozygous mutations with C/C genotype and 8 heterozygous mutations with C/T genotype in surfactant protein B gene+1580 polymorphism. There were 8 cases mutations in control group, 1 in C/C and 7 in C/T genotype. The frequency of homozygotes with C/C genotype was 0.3 and frequency of heterozygotes with C/T genotype was 0.02 in RDS group. In control group, frequency of homozygotes with C/C genotype was 0.025 and frequency of heterozygote with C/T genotype was 0.175. Conclusion: Low mature Surfactant protein B is associated with the pathogenesis of neonatal respiratory distress syndrome (RDS) in China Han ethnic population. Mutations in exon 4 of the surfactant protein B gene demonstrate an association between homozygous mutations with C/C genotype in SP-B gene and neonatal RDS. PMID:23330012

  6. An outbreak of multiple norovirus strains on a cruise ship in China, 2014.

    Science.gov (United States)

    Wang, X; Yong, W; Shi, L; Qiao, M; He, M; Zhang, H; Guo, B; Xie, G; Zhang, M; Jin, M; Ding, J

    2016-01-01

    To determine the cause of an outbreak of acute gastroenteritis that occurred on a cruise ship sailing along the Yangzi River from Chongqing to Nanjing, China. Noroviruses were identified by reverse transcription-PCR (RT-PCR) in rectal swabs from 34 of 54 subjects tested (63·0%). Sequencing and genotyping showed that noroviruses of up to seven different genotypes circulated in this outbreak: noroviruses GI.1, GI.2, GI.3, GI.4, GI.8, GI.9 and an uncommon strain GII.17. Common genotypes were not identified in this event. None of the food or water samples were tested positive for noroviruses. We suspected that it was a point-source infection due to contaminated water or food harvested from contaminated water, taking account of the co-existence of diverse norovirus genotypes. In this study, we presented the molecular investigation of a norovirus outbreak on a cruise in China. We revealed that the outbreak was caused by several different norovirus genotypes and analysed the possible source of infection as well, thus facilitating the evaluation of epidemiological issues regarding noroviruses in this area. © 2015 The Society for Applied Microbiology.

  7. Genetic Polymorphisms of the Mitochondrial Aldehyde Dehydrogenase ALDH2 Gene in a Large Ethnic Hakka Population in Southern China.

    Science.gov (United States)

    Zhong, Zhixiong; Hou, Jingyuan; Li, Bin; Zhang, Qifeng; Li, Cunren; Liu, Zhidong; Yang, Min; Zhong, Wei; Zhao, Pingsen

    2018-04-06

    BACKGROUND Human mitochondrial aldehyde dehydrogenase 2 (ALDH2) plays a critical role in the detoxification of the ethanol metabolite acetaldehyde. The ALDH2*2 (rs671) gene variant is mainly absent among Europeans but is prevalent in populations in East Asia. The aim of this study was to investigate ALDH2*2 mutant alleles and genotype frequencies in the Hakka population of China. MATERIAL AND METHODS Between January 2016 and June 2017, 7,966 unrelated individuals were recruited into the study from the Hakka ethnic population residing in the Meizhou area of Guangdong Province, China, who provided venous blood samples. Genotyping of ALDH2 genotypes were determined using a gene chip platform and confirmed by DNA sequencing. RESULTS In the 7,966 individuals from the Hakka population of China in this study, the frequencies of the ALDH2 genotypes *1/*1, *1/*2 and *2/*2 were 52.03%, 39.67%, and 8.30%, respectively; 47.97% of the individuals were found to carry the ALDH2*2 genotype, which was associated with a deficiency in the aldehyde dehydrogenase (ALDH2) enzyme activity. The frequency of the ALDH2*2 allele was lower than that previously reported in the Japanese population but higher than that reported in other Oriental populations. CONCLUSIONS The findings of this study have provided new information on the ALDH2 gene polymorphisms in the Hakka ethnic population residing in the Meizhou area of Guangdong Province, China, including an understanding of the origin of the atypical ALDH2*2 allele. Also, the study findings may be relevant to the primary care of patients in China.

  8. A cross-sectional study of inpatients with late stage of dementia in Southeast China and the associations between biochemical parameters and apolipoprotein E genotypes

    Directory of Open Access Journals (Sweden)

    Jiang B

    2018-01-01

    Full Text Available Bin Jiang,1,2,* Xue-Ping Zhang,3,* Mei-Fang Chen,3 Zheng Wang,3 Ming-Xue Zhao,3 Bin-Hua Chen,3 Hong-Lei Li1 1Department of Neurology and Research Center of Neurology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 2Department of Neurology, The First Affiliated Hospital of Xiamen University, Xiamen, 3The Seventh People’s Hospital of Hangzhou, Mental Health Center of Zhejiang University School of Medicine, Hangzhou, People’s Republic of China *These authors contributed equally to this work Background: The purpose of this study was to analyze the disease distribution of patients in the late stage of dementia through a cross-sectional investigation and to clarify the association between apolipoprotein E (APOE genotypes and the serum levels of total cholesterol, total triglycerides, and blood glucose in the late-stage Alzheimer’s disease (AD patients.Methods: Patients who were in the late stage of dementia in a mental health center were enrolled in this study. A broad battery of neuropsychological tests and neuroimaging was applied to make the diagnosis. The APOE genotype was determined by the multiplex amplification refractory mutation system polymerase chain reaction. The association between APOE genotype and the blood level of biochemical parameters was studied.Results: A total of 155 patients were enrolled in this study. The majority of patients had AD (67.8%, followed by vascular dementia (15.5%, mixed dementia (9%, and others (7.7%. The APOE ε4 allele frequency was significantly different in the different groups. The serum level of total cholesterol (TC in APOE ε4 carriers was higher than in non-carriers (P<0.05. No statistically significant differences were found in the blood glucose and triglycerides (TG levels between these two groups.Conclusion: To our knowledge, this is the first paper to study the characteristics of late-stage dementia in hospital patients in Southeast China. We found that the

  9. Molecular genotyping of ABO blood groups in some population groups from India.

    Science.gov (United States)

    Ray, Sabita; Gorakshakar, Ajit C; Vasantha, K; Nadkarni, Anita; Italia, Yazdi; Ghosh, Kanjaksha

    2014-01-01

    Indian population is characterized by the presence of various castes and tribal groups. Various genetic polymorphisms have been used to differentiate among these groups. Amongst these, the ABO blood group system has been extensively studied. There is no information on molecular genotyping of ABO blood groups from India. Therefore, the main objective of this study was to characterize the common A, B and O alleles by molecular analysis in some Indian population groups. One hundred samples from the mixed population from Mumbai, 101 samples from the Dhodia tribe and 100 samples from the Parsi community were included in this study. Initially, the samples were phenotyped by standard serologic techniques. PCR followed by single strand conformational polymorphsim (SSCP) was used for molecular ABO genotyping. Samples showing atypical SSCP patterns were further analysed by DNA sequencing to characterize rare alleles. Seven common ABO alleles with 19 different genotypes were found in the mixed population. The Dhodias showed 12 different ABO genotypes and the Parsis revealed 15 different ABO genotypes with six common ABO alleles identified in each of them. Two rare alleles were also identified. This study reports the distribution of molecular genotypes of ABO alleles among some population groups from India. Considering the extremely heterogeneous nature of the Indian population, in terms of various genotype markers like blood groups, red cell enzymes, etc., many more ABO alleles are likely to be encountered.

  10. Heterogeneity of HVR-1 quasispecies is predictive of early but not sustained virological response in genotype 1b-infected patients undergoing combined treatment with PEG- or STD-IFN plus RBV.

    Science.gov (United States)

    Abbate, I; Cappiello, G; Lo Iacono, O; Longo, R; Ferraro, D; Antonucci, G; Di Marco, V; Di Stefano, R; Craxì, A; Solmone, M C; Spanò, A; Ippolito, G; Capobianchi, M R

    2003-01-01

    ISDR mutation pattern and HVR-1 quasispecies were analyzed in HCV genotype 1b-infected patients treated with either PEG- or STD-IFN plus ribavirin, in order to find virological correlates of therapy outcome. ISDR region analysis, performed at baseline (T0) and at 4 weeks of therapy (T1), indicated that ISDR mutation pattern was not predictive of response to treatment. Moreover, no selection of putative resistant strains in the first month of therapy was observed. Viral load was not correlated with any parameter of HVR-1 heterogeneity. Among the HVR-1 heterogeneity parameters considered, complexity was inversely correlated to viral load decline at T1. In univariate analysis, complexity, proportion of non synonymous substitutions (NS) and NS/S ratio were lower in patients showing virological response at 6 months of treatment. Complexity was the only parameter independently associated with both decline of viral load at T1 and virological response after 6 months, even after adjustment for confounding variables. At the end of treatment or later, these correlations were lost. Evolution pattern of the HVR-1 quasispecies indicated a strong selective pressure in sustained responders, with complete substitution of pre-existing quasispecies, while minor changes occured in non responders. In relapsers both patterns were present at a similar rate. In conclusion, this study shows that HVR-1 heterogeneity may be involved in the early response to combined IFN-RBV therapy. The loss of correlation between viral heterogeneity and therapy outcome at 6 months of therapy, or later, suggests that other factors may play a role in maintaining sustained response to treatment.

  11. Fast heterogeneous N2O5 uptake and ClNO2 production in power plant and industrial plumes observed in the nocturnal residual layer over the North China Plain

    Science.gov (United States)

    Wang, Zhe; Wang, Weihao; Tham, Yee Jun; Li, Qinyi; Wang, Hao; Wen, Liang; Wang, Xinfeng; Wang, Tao

    2017-10-01

    Dinitrogen pentoxide (N2O5) and nitryl chloride (ClNO2) are key species in nocturnal tropospheric chemistry and have significant effects on particulate nitrate formation and the following day's photochemistry through chlorine radical production and NOx recycling upon photolysis of ClNO2. To better understand the roles of N2O5 and ClNO2 in the high-aerosol-loading environment of northern China, an intensive field study was carried out at a high-altitude site (Mt. Tai, 1465 m a.s.l.) in the North China Plain (NCP) during the summer of 2014. Elevated ClNO2 plumes were frequently observed in the nocturnal residual layer with a maximum mixing ratio of 2.1 ppbv (1 min), whilst N2O5 was typically present at very low levels (coal-fired industry and power plants in the NCP. The heterogeneous N2O5 uptake coefficient (γ) and ClNO2 yield (ϕ) were estimated from steady-state analysis and observed growth rate of ClNO2. The derived γ and ϕ exhibited high variability, with means of 0.061 ± 0.025 and 0.28 ± 0.24, respectively. These values are higher than those derived from previous laboratory and field studies in other regions and cannot be well characterized by model parameterizations. Fast heterogeneous N2O5 reactions dominated the nocturnal NOx loss in the residual layer over this region and contributed to substantial nitrate formation of up to 17 µg m-3. The estimated nocturnal nitrate formation rates ranged from 0.2 to 4.8 µg m-3 h-1 in various plumes, with a mean of 2.2 ± 1.4 µg m-3 h-1. The results demonstrate the significance of heterogeneous N2O5 reactivity and chlorine activation in the NCP, and their unique and universal roles in fine aerosol formation and NOx transformation, and thus their potential impacts on regional haze pollution in northern China.

  12. Dynamical community structure of populations evolving on genotype networks

    International Nuclear Information System (INIS)

    Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

    2015-01-01

    Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

  13. Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

    Science.gov (United States)

    Clavijo, Gabriel; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; López-Ferber, Miguel

    2010-01-01

    An insect nucleopolyhedrovirus naturally survives as a mixture of at least nine genotypes. Infection by multiple genotypes results in the production of virus occlusion bodies (OBs) with greater pathogenicity than those of any genotype alone. We tested the hypothesis that each OB contains a genotypically diverse population of virions. Few insects died following inoculation with an experimental two-genotype mixture at a dose of one OB per insect, but a high proportion of multiple infections were observed (50%), which differed significantly from the frequencies predicted by a non-associated transmission model in which genotypes are segregated into distinct OBs. By contrast, insects that consumed multiple OBs experienced higher mortality and infection frequencies did not differ significantly from those of the non-associated model. Inoculation with genotypically complex wild-type OBs indicated that genotypes tend to be transmitted in association, rather than as independent entities, irrespective of dose. To examine the hypothesis that virions may themselves be genotypically heterogeneous, cell culture plaques derived from individual virions were analysed to reveal that one-third of virions was of mixed genotype, irrespective of the genotypic composition of the OBs. We conclude that co-occlusion of genotypically distinct virions in each OB is an adaptive mechanism that favours the maintenance of virus diversity during insect-to-insect transmission. PMID:19939845

  14. Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance

    NARCIS (Netherlands)

    Mulder, H.A.; Bijma, P.; Hill, W.G.

    2007-01-01

    There is empirical evidence that genotypes differ not only in mean, but also in environmental variance of the traits they affect. Genetic heterogeneity of environmental variance may indicate genetic differences in environmental sensitivity. The aim of this study was to develop a general framework

  15. Diagnostic Challenges in Retinitis Pigmentosa: Genotypic Multiplicity and Phenotypic Variability

    Science.gov (United States)

    Chang, Susie; Vaccarella, Leah; Olatunji, Sunday; Cebulla, Colleen; Christoforidis, John

    2011-01-01

    Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders. Diagnosis can be challenging as more than 40 genes are known to cause non-syndromic RP and phenotypic expression can differ significantly resulting in variations in disease severity, age of onset, rate of progression, and clinical findings. We describe the clinical manifestations of RP, the more commonly known causative gene mutations, and the genotypic-phenotypic correlation of RP. PMID:22131872

  16. A Multianalyzer Machine Learning Model for Marine Heterogeneous Data Schema Mapping

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    Wang Yan

    2014-01-01

    Full Text Available The main challenges that marine heterogeneous data integration faces are the problem of accurate schema mapping between heterogeneous data sources. In order to improve the schema mapping efficiency and get more accurate learning results, this paper proposes a heterogeneous data schema mapping method basing on multianalyzer machine learning model. The multianalyzer analysis the learning results comprehensively, and a fuzzy comprehensive evaluation system is introduced for output results’ evaluation and multi factor quantitative judging. Finally, the data mapping comparison experiment on the East China Sea observing data confirms the effectiveness of the model and shows multianalyzer’s obvious improvement of mapping error rate.

  17. Clinical features of human metapneumovirus genotypes in children with acute lower respiratory tract infection in Changsha, China.

    Science.gov (United States)

    Zeng, Sai-Zhen; Xiao, Ni-Guang; Zhong, Li-Li; Yu, Tian; Zhang, Bing; Duan, Zhao-Jun

    2015-11-01

    To explore the epidemiological and clinical features of different human metapneumovirus (hMPV) genotypes in hospitalized children. Reverse transcription polymerase chain reaction (RT-PCR) or PCR was employed to screen for both hMPV and other common respiratory viruses in 2613 nasopharyngeal aspirate specimens collected from children with lower respiratory tract infections from September 2007 to February 2011 (a period of 3.5 years). The demographics and clinical presentations of patients infected with different genotypes of hMPV were compared. A total of 135 samples were positive for hMPV (positive detection rate: 5.2%). Co-infection with other viruses was observed in 45.9% (62/135) of cases, and human bocavirus was the most common additional respiratory virus. The most common symptoms included cough, fever, and wheezing. The M gene was sequenced for 135 isolates; of these, genotype A was identified in 72.6% (98/135) of patients, and genotype B was identified in 27.4% (37/135) of patients. The predominant genotype of hMPV changed over the 3.5-year study period from genotype A2b to A2b or B1 and then to predominantly B1. Most of clinical features were similar between patients infected with different hMPV genotypes. These results suggested that hMPV is an important viral pathogen in pediatric patients with acute lower respiratory tract infection in Changsha. The hMPV subtypes A2b and B1 were found to co-circulate. The different hMPV genotypes exhibit similar clinical characteristics. © 2015 Wiley Periodicals, Inc.

  18. Phenotypic diversity of basic characteristics of genotypes from the Serbia onion collection

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    Gvozdanović-Varga Jelica

    2013-01-01

    Full Text Available The onion is a widely distributed vegetable crop, which takes an important place in the vegetable production in Serbia. The traditional planting method is the one from sets. Old cultivars and populations and, in recent years, foreign cultivars are grown. The large variety of genotypes, including both domestic populations and cultivars, comprises the significant gene pool of this region. The onion collection of the Institute of Field and Vegetable Crops in Novi Sad is based on the populations and cultivars from the territory of the former Yugoslavia. This paper reviews 30 onion genotypes on the basic IPGRI descriptors (ANNEX I. Variability of the reviewed characteristics was determined by PC analysis. High variability values have been established for bulb skin color, bulb flesh color, bulb hearting and bulb skin thickness. The genotypes varied in bulb skin color as well as in bulb flesh color from white to dark violet. These two characteristics had the largest impact on clustering, with a single genotype being heterogeneous exactly for these two characteristics. [Projekat Ministarstva nauke Republike Srbije, br. TR 31030

  19. Different region analysis for genotyping Yersinia pestis isolates from China.

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    Yanjun Li

    Full Text Available BACKGROUND: DFR (different region analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion. CONCLUSIONS/SIGNIFICANCE: Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT. DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity.

  20. Implications of Future Water Use Efficiency for Ecohydrological Responses to Climate Change and Spatial Heterogeneity of Atmospheric CO2 in China

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    Zhen Zhang

    2013-01-01

    Full Text Available As the atmospheric carbon dioxide (CO2 increases substantially, the spatial distribution of atmospheric CO2 should be considered when estimating the effects of CO2 on the carbon and water cycle coupling of terrestrial ecosystems. To evaluate this effect on future ecohydrological processes, the spatial-temporal patterns of CO2 were established over 1951 - 2099 according to the IPCC emission scenarios SRES A2 and SRES B1. Thereafter, water use efficiency (WUE was used (i.e., Net Primary Production/Evaportranspiration as an indicator to quantify the effects of climate change and uneven CO2 fertilization in China. We carried out several simulated experiments to estimate WUE under different future scenarios using a land process model (Integrated Biosphere Simulator, IBIS. Results indicated that the geographical distributions of averaged WUE have considerable differences under a heterogeneous atmospheric CO2 condition. Under the SRES A2 scenario, WUE decreased slightly with a 5% value in most areas of the southeastern and northwestern China during the 2050s, while decreasing by approximately 15% in southeastern China during the 2090s. During the period of the 2050s under SRES B1 scenario, the change rate of WUE was similar with that under SRES A2 scenario, but the WUE has a more moderate decreasing trend than that under the SRES A2 scenario. In all, the ecosystems in median and low latitude areas had a weakened effect on resisting extreme climate event such as drought. Conversely, the vegetation in a boreal forest had an enhanced buffering capability to tolerate drought events.

  1. Intra-tumoral Heterogeneity of KRAS and BRAF Mutation Status in Patients with Advanced Colorectal Cancer (aCRC and Cost-Effectiveness of Multiple Sample Testing

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    Susan D. Richman

    2011-01-01

    Full Text Available KRAS mutation status is established as a predictive biomarker of benefit from anti-EGFr therapies. Mutations are normally assessed using DNA extracted from one formalin-fixed, paraffin-embedded (FFPE tumor block. We assessed heterogeneity of KRAS and BRAF mutation status intra-tumorally (multiple blocks from the same primary tumor. We also investigated the utility and efficiency of genotyping a ‘DNA cocktail’ prepared from multiple blocks. We studied 68 consenting patients in two randomized clinical trials. DNA was extracted, from ≥2 primary tumor FFPE blocks per patient. DNA was genotyped by pyrosequencing for KRAS codons 12, 13 and 61 and BRAF codon 600. In patients with heterogeneous mutation status, DNA cocktails were prepared and genotyped. Among 69 primary tumors in 68 patients, 7 (10.1% showed intratumoral heterogeneity; 5 (7.2% at KRAS codons 12, 13 and 2 (2.9% at BRAF codon 600. In patients displaying heterogeneity, the relevant KRAS or BRAF mutation was also identified in ‘DNA cocktail’ samples when including DNA from mutant and wild-type blocks. Heterogeneity is uncommon but not insignificant. Testing DNA from a single block will wrongly assign wild-type status to 10% patients. Testing more than one block, or preferably preparation of a ‘DNA cocktail’ from two or more tumor blocks, improves mutation detection at minimal extra cost.

  2. Coal consumption and economic growth in China

    International Nuclear Information System (INIS)

    Li, Raymond; Leung, Guy C.K.

    2012-01-01

    The aim of this paper is to re-examine the relationship between coal consumption and real GDP of China with the use of panel data. This paper applies modern panel data techniques to help shed light on the importance of the heterogeneity among different regions within China. Empirical analyses are conducted for the full panel as well as three subgroups of the panel. The empirical results show that coal consumption and GDP are both I(1) and cointegrated in all regional groupings. Heterogeneity is found in the GDP equation of the full panel. The regional causality tests reveal that the coal consumption–GDP relationship is bidirectional in the Coastal and Central regions whereas causality is unidirectional from GDP to coal consumption in the Western region. Thus, energy conservation measures will not adversely affect the economic growth of the Western region but such measures will likely encumber the economy of the Coastal and Central regions, where most of the coal intensive industries are concentrated. - Highlights: ► We investigate the relationship between coal consumption and GDP in China. ► Panel data are used to account for the potential heterogeneity across different regions. ► Bidirectional causality is found in the Eastern and Central regions. ► Unidirectional causality from GDP to coal consumption is found in the Western region.

  3. Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray.

    NARCIS (Netherlands)

    Avila-Fernandez, A.; Cantalapiedra, D.; Aller, E.; Vallespin, E.; Aguirre-Lamban, J.; Blanco-Kelly, F.; Corton, M.; Riveiro-Alvarez, R.; Allikmets, R.; Trujillo-Tiebas, M.J.; Millan, J.M.; Cremers, F.P.M.; Ayuso, C.

    2010-01-01

    PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations in 272 Spanish families using a genotyping microarray. METHODS: 272 unrelated Spanish families, 107 with autosomal

  4. Full-length genomic sequence of hepatitis B virus genotype C2 isolated from a native Brazilian patient

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    Mónica Viviana Alvarado-Mora

    2011-06-01

    Full Text Available The hepatitis B virus (HBV is among the leading causes of chronic hepatitis, cirrhosis and hepatocellular carcinoma. In Brazil, genotype A is the most frequent, followed by genotypes D and F. Genotypes B and C are found in Brazil exclusively among Asian patients and their descendants. The aim of this study was to sequence the entire HBV genome of a Caucasian patient infected with HBV/C2 and to infer the origin of the virus based on sequencing analysis. The sequence of this Brazilian isolate was grouped with four other sequences described in China. The sequence of this patient is the first complete genome of HBV/C2 reported in Brazil.

  5. Genotypic diversity of an invasive plant species promotes litter decomposition and associated processes.

    Science.gov (United States)

    Wang, Xiao-Yan; Miao, Yuan; Yu, Shuo; Chen, Xiao-Yong; Schmid, Bernhard

    2014-03-01

    Following studies that showed negative effects of species loss on ecosystem functioning, newer studies have started to investigate if similar consequences could result from reductions of genetic diversity within species. We tested the influence of genotypic richness and dissimilarity (plots containing one, three, six or 12 genotypes) in stands of the invasive plant Solidago canadensis in China on the decomposition of its leaf litter and associated soil animals over five monthly time intervals. We found that the logarithm of genotypic richness was positively linearly related to mass loss of C, N and P from the litter and to richness and abundance of soil animals on the litter samples. The mixing proportion of litter from two sites, but not genotypic dissimilarity of mixtures, had additional effects on measured variables. The litter diversity effects on soil animals were particularly strong under the most stressful conditions of hot weather in July: at this time richness and abundance of soil animals were higher in 12-genotype litter mixtures than even in the highest corresponding one-genotype litter. The litter diversity effects on decomposition were in part mediated by soil animals: the abundance of Acarina, when used as covariate in the analysis, fully explained the litter diversity effects on mass loss of N and P. Overall, our study shows that high genotypic richness of S. canadensis leaf litter positively affects richness and abundance of soil animals, which in turn accelerate litter decomposition and P release from litter.

  6. [Association Between SNP rs6007897 of CELSR1 and Acute Ischemic Stroke in Western China Han Population: a Case-control Study].

    Science.gov (United States)

    Qin, Feng-qin; Yu, Li-hua; Hu, Wen-ting; Guo, Jian; Chen, Ning; Guo, Jiang; Fang, Jing-huan; He, Li

    2015-07-01

    To investigate the relationship between single nucleotide polymorphism (SNP) rs6007897 of CELSR1 and acute ischemic stroke in Western China Han population. All subjects (759 acute ischemic stroke patients and 786 controls) were genotyped using ligation detection reaction (LDR). We analyzed the differences between SNP rs6007897 genotypes and allele frequencies between two groups. Two genotypes (AA, AG) of rs6007897 were found in both stroke and control group. There was no statistically significance between two groups about genotype and allele frequency. After adjusting for risk factors, we found there was no significant association between rs6007897 and ischemic stroke CP = 0.797, odds ratio (OR) = 0.886, 95% confidence interval (CI) = 0.352-2.227). SNP rs6007897 of CELSR1 was not significantly associated with ischemic stroke in Western China Han population.

  7. A novel complex A/C/G intergenotypic recombinant of hepatitis B virus isolated in southern China.

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    Heling Su

    Full Text Available Hepatitis B virus (HBV genotypes and subgenotypes may vary in geographical distribution and virological features. Previous investigations, including ours, showed that HBV genotypes B and C were respectively predominant in South and North China, while genotypes A and D were infrequently detected and genotype G was not found. In this study, a novel A/C/G intergenotype was identified in patients with chronic HBV infection in Guilin, a city in southern China. Initial phylogenetic analysis based on the S gene suggested the HBV recombinant to be genotype G. However, extended genotyping based on the entire HBV genome indicated it to be an A/C/G intergenotype with a closer relation to genotype C. Breakpoint analysis using the SIMPLOT program revealed that the recombinant had a recombination with a arrangement of genotypes A, G, A and C fragments. Compared with the HBV recombinants harboring one or two genotype G fragments found in Asian countries, this Guilin recombinant was highly similar to the Vietnam (98-99% and Long An recombinants (96-99%, but had a relatively low similarity to the Thailand one (89%. Unlike those with the typical genotype G of HBV, the patients with the Guilin recombinant were seropositive for HBeAg. Moreover, a relatively high HBV DNA viral load (>2 × 10(6 IU/ml was detected in the patients, and the analysis of viral replication capacity showed that the Guilin recombinant strains had a competent replication capacity similar to genotypes B and C strains. These findings can aid in not only the clarification of the phylogenetic origin of the HBV recombinants with the genotype G fragment found in Asian countries, but also the understanding of the virological properties of these complicated HBV recombinants.

  8. Spillover of Newcastle disease viruses from poultry to wild birds in Guangdong province, southern China.

    Science.gov (United States)

    Xiang, Bin; Han, Lujie; Gao, Pei; You, Renrong; Wang, Fumin; Xiao, Jiajie; Liao, Ming; Kang, Yinfeng; Ren, Tao

    2017-11-01

    Despite intensive vaccination programs in many countries, including China, Newcastle disease has been reported sporadically and is still a significant threat to the poultry industry in China. Newcastle disease virus (NDV) is infectious for at least 250 bird species, but the role of wild birds in virus epidemiology remains largely unknown. Fourteen NDV isolates were obtained from 2040 samples collected from wild birds or the environment in Guangdong province, southern China, from 2013 to 2015. The isolation rate was the highest in the period of wintering and lowest during the periods of spring migration, nesting, and postnesting. A maximum clade credibility phylogenetic analysis revealed that at least four genotypes circulate in southern China: three class II genotypes (II, VI, and IX) and one class I (1b). We also demonstrated that most isolates from wild birds were highly similar to isolates from poultry, and two isolates were linked to viruses from wild birds in northern China. These data suggested that wild birds could disseminate NDV and poultry-derived viruses may spillover to wild birds. Accordingly, vaccine development and poultry management strategies should be considered to prevent future NDV outbreaks, particularly given the strength of the poultry industry in developing countries, such as China. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. MLVA genotyping of Brucella melitensis and Brucella abortus isolates from different animal species and humans and identification of Brucella suis vaccine strain S2 from cattle in China.

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    Hai Jiang

    Full Text Available In China, brucellosis is an endemic disease and the main sources of brucellosis in animals and humans are infected sheep, cattle and swine. Brucella melitensis (biovars 1 and 3 is the predominant species, associated with sporadic cases and outbreak in humans. Isolates of B. abortus, primarily biovars 1 and 3, and B. suis biovars 1 and 3 are also associated with sporadic human brucellosis. In this study, the genetic profiles of B. melitensis and B. abortus isolates from humans and animals were analyzed and compared by multi-locus variable-number tandem-repeat analysis (MLVA. Among the B. melitensis isolates, the majority (74/82 belonged to MLVA8 genotype 42, clustering in the 'East Mediterranean' group. Two B. melitensis biovar 1 genotype 47 isolates, belonging to the 'Americas' group, were recovered; both were from the Himalayan blue sheep (Pseudois nayaur, a wild animal. The majority of B. abortus isolates (51/70 were biovar 3, genotype 36. Ten B. suis biovar 1 field isolates, including seven outbreak isolates recovered from a cattle farm in Inner Mongolia, were genetically indistinguishable from the vaccine strain S2, based on MLVA cluster analysis. MLVA analysis provided important information for epidemiological trace-back. To the best of our knowledge, this is the first report to associate Brucella cross-infection with the vaccine strain S2 based on molecular comparison of recovered isolates to the vaccine strain. MLVA typing could be an essential assay to improve brucellosis surveillance and control programs.

  10. Epidemiology of zoonotic hepatitis E: a community-based surveillance study in a rural population in China.

    Science.gov (United States)

    Zhu, Feng-Cai; Huang, Shou-Jie; Wu, Ting; Zhang, Xue-Feng; Wang, Zhong-Ze; Ai, Xing; Yan, Qiang; Yang, Chang-Lin; Cai, Jia-Ping; Jiang, Han-Min; Wang, Yi-Jun; Ng, Mun-Hon; Zhang, Jun; Xia, Ning-Shao

    2014-01-01

    Hepatitis E is caused by two viral genotype groups: human types and zoonotic types. Current understanding of the epidemiology of the zoonotic hepatitis E disease is founded largely on hospital-based studies. The epidemiology of hepatitis E was investigated in a community-based surveillance study conducted over one year in a rural city in eastern China with a registered population of 400,162. The seroprevalence of hepatitis E in the cohort was 38%. The incidence of hepatitis E was 2.8/10,000 person-years. Totally 93.5% of the infections were attributed to genotype 4 and the rest, to genotype 1. Hepatitis E accounted for 28.4% (102/359) of the acute hepatitis cases and 68.9% (102/148) of the acute viral hepatitis cases in this area of China. The disease occurred sporadically with a higher prevalence during the cold season and in men, with the male-to-female ratio of 3∶1. Additionally, the incidence of hepatitis E increased with age. Hepatitis B virus carriers have an increased risk of contracting hepatitis E than the general population (OR = 2.5, 95%CI 1.5-4.2). Pre-existing immunity to hepatitis E lowered the risk (relative risk  = 0.34, 95% CI 0.21-0.55) and reduced the severity of the disease. Hepatitis E in the rural population of China is essentially that of a zoonosis due to the genotype 4 virus, the epidemiology of which is similar to that due to the other zoonotic genotype 3 virus.

  11. Epidemiology of zoonotic hepatitis E: a community-based surveillance study in a rural population in China.

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    Feng-Cai Zhu

    Full Text Available BACKGROUND: Hepatitis E is caused by two viral genotype groups: human types and zoonotic types. Current understanding of the epidemiology of the zoonotic hepatitis E disease is founded largely on hospital-based studies. METHODS: The epidemiology of hepatitis E was investigated in a community-based surveillance study conducted over one year in a rural city in eastern China with a registered population of 400,162. RESULTS: The seroprevalence of hepatitis E in the cohort was 38%. The incidence of hepatitis E was 2.8/10,000 person-years. Totally 93.5% of the infections were attributed to genotype 4 and the rest, to genotype 1. Hepatitis E accounted for 28.4% (102/359 of the acute hepatitis cases and 68.9% (102/148 of the acute viral hepatitis cases in this area of China. The disease occurred sporadically with a higher prevalence during the cold season and in men, with the male-to-female ratio of 3∶1. Additionally, the incidence of hepatitis E increased with age. Hepatitis B virus carriers have an increased risk of contracting hepatitis E than the general population (OR = 2.5, 95%CI 1.5-4.2. Pre-existing immunity to hepatitis E lowered the risk (relative risk  = 0.34, 95% CI 0.21-0.55 and reduced the severity of the disease. CONCLUSIONS: Hepatitis E in the rural population of China is essentially that of a zoonosis due to the genotype 4 virus, the epidemiology of which is similar to that due to the other zoonotic genotype 3 virus.

  12. Past and future effects of climate change on spatially heterogeneous vegetation activity in China

    Science.gov (United States)

    Gao, Jiangbo; Jiao, Kewei; Wu, Shaohong; Ma, Danyang; Zhao, Dongsheng; Yin, Yunhe; Dai, Erfu

    2017-07-01

    Climate change is a major driver of vegetation activity but its complex ecological relationships impede research efforts. In this study, the spatial distribution and dynamic characteristics of climate change effects on vegetation activity in China from the 1980s to the 2010s and from 2021 to 2050 were investigated using a geographically weighted regression (GWR) model. The GWR model was based on combined datasets of satellite vegetation index, climate observation and projection, and future vegetation productivity simulation. Our results revealed that the significantly positive precipitation-vegetation relationship was and will be mostly distributed in North China. However, the regions with temperature-dominated distribution of vegetation activity were and will be mainly located in South China. Due to the varying climate features and vegetation cover, the spatial correlation between vegetation activity and climate change may be altered. There will be different dominant climatic factors for vegetation activity distribution in some regions such as Northwest China, and even opposite correlations in Northeast China. Additionally, the response of vegetation activity to precipitation will move southward in the next three decades. In contrast, although the high warming rate will restrain the vegetation activity, precipitation variability could modify hydrothermal conditions for vegetation activity. This observation is exemplified in the projected future enhancement of vegetation activity in the Tibetan Plateau and weakened vegetation activity in East and Middle China. Furthermore, the vegetation in most parts of North China may adapt to an arid environment, whereas in many southern areas, vegetation will be repressed by water shortage in the future.

  13. Population genetics, phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS).

    Science.gov (United States)

    Zhao, Peng; Zhou, Hui-Juan; Potter, Daniel; Hu, Yi-Heng; Feng, Xiao-Jia; Dang, Meng; Feng, Li; Zulfiqar, Saman; Liu, Wen-Zhe; Zhao, Gui-Fang; Woeste, Keith

    2018-04-18

    Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans, Juglandaceae), a widespread, economically important group. We found that the processes of isolation generated diversity during glaciations, but that the recent range expansion of J. regia, probably from multiple refugia, led to hybrid formation both within and between sections of the genus. In southern China, human dispersal of J. regia brought it into contact with J. sigillata, which we determined to be an ecotype of J. regia that is now maintained as a landrace. In northern China, walnut hybridized with a distinct lineage of J. mandshurica to form J. hopeiensis, a controversial taxon (considered threatened) that our data indicate is a horticultural variety. Comparisons among whole chloroplast genomes and nuclear transcriptome analyses provided conflicting evidence for the timing of the divergence of Chinese Juglans taxa. J. cathayensis and J. mandshurica are poorly differentiated based our genomic data. Reconstruction of Juglans evolutionary history indicate that episodes of climatic variation over the past 4.5 to 33.80 million years, associated with glacial advances and retreats and population isolation, have shaped Chinese walnut demography and evolution, even in the presence of gene flow and introgression. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China

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    Mingjun Sun

    2017-12-01

    Full Text Available Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2 was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2 and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS-single-nucleotide polymorphism (SNP-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.

  15. Interactive effects of genotype x environment on the live weight of GIFT Nile tilapias.

    Science.gov (United States)

    Oliveira, Sheila N DE; Ribeiro, Ricardo P; Oliveira, Carlos A L DE; Alexandre, Luiz; Oliveira, Aline M S; Lopera-Barrero, Nelson M; Santander, Victor F A; Santana, Renan A C

    2017-01-01

    In this paper, the existence of a genotype x environment interaction for the average daily weight in GIFT Nile tilapia (Oreochromis niloticus) in different regions in the state of Paraná (Brazil) was analyzed. The heritability results were high in the uni-characteristic analysis: 0.71, 0.72 and 0.67 for the cities of Palotina (PL), Floriano (FL) and Diamond North (DN), respectively. Genetic correlations estimated in bivariate analyzes were weak with values between 0.12 for PL-FL, 0.06 for PL and 0.23 for DN-FL-DN. The Spearman correlation values were low, which indicated a change in ranking in the selection of animals in different environments in the study. There was heterogeneity in the phenotypic variance among the three regions and heterogeneity in the residual variance between PL and DN. The direct genetic gain was greater for the region with a DN value gain of 198.24 g/generation, followed by FL (98.73 g/generation) and finally PL (98.73 g/generation). The indirect genetic gains were lower than 0.37 and greater than 0.02 g/generation. The evidence of the genotype x environment interaction was verified, which indicated the phenotypic heterogeneity of the variances among the three regions, weak genetic correlation and modified rankings in the different environments.

  16. Initial brain aging: heterogeneity of mitochondrial size is associated with decline in complex I-linked respiration in cortex and hippocampus.

    Science.gov (United States)

    Thomsen, Kirsten; Yokota, Takashi; Hasan-Olive, Md Mahdi; Sherazi, Niloofar; Fakouri, Nima Borhan; Desler, Claus; Regnell, Christine Elisabeth; Larsen, Steen; Rasmussen, Lene Juel; Dela, Flemming; Bergersen, Linda Hildegard; Lauritzen, Martin

    2018-01-01

    Brain aging is accompanied by declining mitochondrial respiration. We hypothesized that mitochondrial morphology and dynamics would reflect this decline. Using hippocampus and frontal cortex of a segmental progeroid mouse model lacking Cockayne syndrome protein B (CSB m/m ) and C57Bl/6 (WT) controls and comparing young (2-5 months) to middle-aged mice (13-14 months), we found that complex I-linked state 3 respiration (CI) was reduced at middle age in CSB m/m hippocampus, but not in CSB m/m cortex or WT brain. In hippocampus of both genotypes, mitochondrial size heterogeneity increased with age. Notably, an inverse correlation between heterogeneity and CI was found in both genotypes, indicating that heterogeneity reflects mitochondrial dysfunction. The ratio between fission and fusion gene expression reflected age-related alterations in mitochondrial morphology but not heterogeneity. Mitochondrial DNA content was lower, and hypoxia-induced factor 1α mRNA was greater at both ages in CSB m/m compared to WT brain. Our findings show that decreased CI and increased mitochondrial size heterogeneity are highly associated and point to declining mitochondrial quality control as an initial event in brain aging. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Spatial Factor Analysis for Aerosol Optical Depth in Metropolises in China with Regard to Spatial Heterogeneity

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    Hui Shi

    2018-04-01

    Full Text Available A substantial number of studies have analyzed how driving factors impact aerosols, but they have been little concerned with the spatial heterogeneity of aerosols and the factors that impact aerosols. The spatial distributions of the aerosol optical depth (AOD retrieved by Moderate Resolution Imaging Spectrometer (MODIS data at 550-nm and 3-km resolution for three highly developed metropolises, the Beijing-Tianjin-Hebei (BTH region, the Yangtze River Delta (YRD, and the Pearl River Delta (PRD, in China during 2015 were analyzed. Different degrees of spatial heterogeneity of the AOD were found, which were indexed by Moran’s I index giving values of 0.940, 0.715, and 0.680 in BTH, YRD, and PRD, respectively. For the spatial heterogeneity, geographically weighted regression (GWR was employed to carry out a spatial factor analysis, where terrain, climate condition, urban development, and vegetation coverage were taken as the potential driving factors. The results of the GWR imply varying relationships between the AOD and the factors. The results were generally consistent with existing studies, but the results suggest the following: (1 Elevation increase would more likely lead to a strong negative impact on aerosols (with most of the coefficients ranging from −1.5~0 in the BTH, −1.5~0 in the YRD, and −1~0 in the PRD in the places with greater elevations where the R-squared values are always larger than 0.5. However, the variation of elevations cannot explain the variation of aerosols in the places with relatively low elevations (with R-squared values approximately 0.1, ranging from 0 to 0.3, and approximately 0.1 in the BTH, YRD, and PRD, such as urban areas in the BTH and YRD. (2 The density of the built-up areas made a strong and positive impact on aerosols in the urban areas of the BTH (R-squared larger than 0.5, while the R-squared dropped to 0.1 in the places far away from the urban areas. (3 The vegetation coverage led to a stronger

  18. Prevent cervical cancer by screening with reliable human papillomavirus detection and genotyping

    International Nuclear Information System (INIS)

    Ge, Shichao; Gong, Bo; Cai, Xushan; Yang, Xiaoer; Gan, Xiaowei; Tong, Xinghai; Li, Haichuan; Zhu, Meijuan; Yang, Fengyun; Zhou, Hongrong; Hong, Guofan

    2012-01-01

    The incidence of cervical cancer is expected to rise sharply in China. A reliable routine human papillomavirus (HPV) detection and genotyping test to be supplemented by the limited Papanicolaou cytology facilities is urgently needed to help identify the patients with cervical precancer for preventive interventions. To this end, we evaluated a nested polymerase chain reaction (PCR) protocol for detection of HPV L1 gene DNA in cervicovaginal cells. The PCR amplicons were genotyped by direct DNA sequencing. In parallel, split samples were subjected to a Digene HC2 HPV test which has been widely used for “cervical cancer risk” screen. Of the 1826 specimens, 1655 contained sufficient materials for analysis and 657 were truly negative. PCR/DNA sequencing showed 674 infected by a single high-risk HPV, 188 by a single low-risk HPV, and 136 by multiple HPV genotypes with up to five HPV genotypes in one specimen. In comparison, the HC2 test classified 713 specimens as infected by high-risk HPV, and 942 as negative for HPV infections. The high-risk HC2 test correctly detected 388 (57.6%) of the 674 high-risk HPV isolates in clinical specimens, mislabeled 88 (46.8%) of the 188 low-risk HPV isolates as high-risk genotypes, and classified 180 (27.4%) of the 657 “true-negative” samples as being infected by high-risk HPV. It was found to cross-react with 20 low-risk HPV genotypes. We conclude that nested PCR detection of HPV followed by short target DNA sequencing can be used for screening and genotyping to formulate a paradigm in clinical management of HPV-related disorders in a rapidly developing economy

  19. Identification of zoonotic genotypes of Giardia duodenalis.

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    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  20. HBV Genotype B/C and Response to Lamivudine Therapy: A Systematic Review

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    Xiu-Li Chen

    2013-01-01

    Full Text Available A number of nucleoside analogues such as lamivudine (LAM, actually used for the treatment of chronic hepatitis B, can suppress HBV DNA replication, improve transaminase level and liver histology, and enhance the rate of hepatitis B e antigen (HBeAg clearance. The responses to LAM therapy involve HBeAg clearance and HBV DNA conversion of negative. However, the associations between HBV genotype B/C and response to LAM therapy remain ambiguous. The aim of this meta-analysis is to determine more precise estimations of the relationship. All the publications on the associations between HBV genotype B/C and response to LAM (HBeAg clearance and HBV DNA conversion of negative through June 2013 were collected. Relative risk (RR with 95% confidence intervals (95% CI was calculated in fixed or random model, was calculated to examine heterogeneity, and funnel plots were plotted to examine small study effects with Stata 11 software. Overall, for HBeAg clearance and genotype B/C, the RR (95% CI was 1.27 (0.94–1.71, while for HBV DNA conversion of negative and genotype B/C, the RR (95% CI was 1.07 (0.98–1.17. HBV genotype B/C shows no significance associations with response to lamivudine therapy (HBeAg clearance and HBV DNA conversion of negative.

  1. Molecular characterization of varicella-zoster virus clinical isolates from 2006 to 2008 in a tertiary care hospital, Dublin, Ireland, using different genotyping methods.

    LENUS (Irish Health Repository)

    Roycroft, Emma

    2012-10-01

    Varicella-zoster virus (VZV), a herpesvirus, is a ubiquitous organism that causes considerable morbidity worldwide and can cause severe complications on reactivation. Phylogenetic analysis was performed on 19 clinical VZV isolates (16 zoster and 3 varicella) found in Ireland, between December 2006 and November 2008, in order to determine whether previously reported viral heterogeneity was still present and whether viral recombination was evident. Open reading-frames (ORFs) from genes 1, 21, 50, and 54, were sequenced. Clades 1, 2, 3, and 5 were identified. Four putative recombinant isolates were detected (three clade 3\\/1 and one clade 5\\/3\\/1). Further sequencing and examination of ORF 22 and 21\\/50, did not elucidate the putative recombinant genotypes further. These two previously published genotyping schemes were examined in light of the new consensus genotyping scheme proposed in 2010. Remarkable VZV heterogeneity remains prevalent in Ireland. This is the first evidence of putative VZV recombination found in Ireland.

  2. Heterogeneity of O blood group in India: Peeping through the window of molecular biology

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    Harita Gogri

    2018-01-01

    Results And Discussion: Overall, ten different genotypes were identified. Three rare alleles, namely, O05, O11, and O26 were seen in the mixed group category. These results suggest that there is an internal heterogeneity in the mixed group while Dhodias and Parsis, the groups which were screened earlier, seem to be more homogenous groups. An important piece of information emerges out from this study, that is, O01O02 genotype is expressing some selective force in population groups screened in India as well as many other groups worldwide. Conclusion: In the future, molecular genotyping of the ABO blood group system among different ethnic and tribal Indian groups would help in generating data to fill up the gaps in the molecular ABO map of the world.

  3. Phenotypic and Genotypic Resistance of Salmonella Isolates from Healthy and Diseased Pigs in China During 2008-2015.

    Science.gov (United States)

    Jiu, Yueguang; Zhu, Shun; Khan, Sher Bahadar; Sun, Mengzhen; Zou, Geng; Meng, Xianrong; Wu, Bin; Zhou, Rui; Li, Shaowen

    2017-07-01

    The antimicrobial resistance of Salmonella strains is rapidly increasing worldwide, which poses significant threats to animal and public health. In this study, a total of 249 porcine Salmonella isolates collected in China during 2008-2015 were examined, including 155 clinical isolates from diseased pigs and 94 nonclinical isolates from healthy pigs. Based on the minimum inhibitory concentration of seven antimicrobial agents, 96.4% of the isolates were resistant to at least one of the tested antibiotics and 81.0% of them showed multidrug resistance. The highest antimicrobial resistance was observed for tetracycline (85.9%), and the lowest was found for cefotaxime (13.3%). The isolates from diseased pigs exhibited significantly higher levels of antimicrobial resistance than those from healthy pigs. Twenty-two isolates from healthy pigs were resistant to ciprofloxacin, which may inhibit the curative effectiveness of fluoroquinolones on bacterial food-borne poisoning and infections in humans caused by contaminated food. Moreover, cefotaxime resistance of the strains isolated from diseased pigs during 2013-2015 was significantly higher compared with the strains isolated during 2008-2010. Further study showed that the correlation between phenotypic and genotypic resistance varied among the isolates from different sources, and in many cases, the presence of resistance genes was not consistent with the resistance to the corresponding antimicrobials. These results are very significant for veterinary practice and public health.

  4. Heterogenity of Echinococcus canadensis genotype 6 - the main causative agent of cystic echinococcosis in Birjand, Eastern Iran.

    Science.gov (United States)

    Karamian, Mehdi; Haghighi, Fatemeh; Hemmati, Mina; Taylor, Walter Robert; Salehabadi, Alireza; Ghatee, Mohammad Amin

    2017-10-15

    Little is known about the genotypes of Echinococcus spp. and their life cycles in eastern Iran. We analysed the partial sequences of the nad1 and cox1 genes from 17 isolates from hydatid cyst-infected patients (n=9), camels (n=5) and sheep (n=3) in Birjand, eastern Iran. A new primer pair was also used to amplify the long fragment (1180bp) of the cox1 gene. All camel and eight human isolates were G6 strains of Echinococcus canadensis while one human isolate and the three sheep isolates were G1 genotypes (sheep strain) of E. granulosus sensu stricto (s.s.). Nad1 and cox1 sequence analyses showed high G6 genetic homogeneity, similar to previously reported G6 strains from southeast and central Iran, Sudan and Mauritania. Low nucleotide and haplotype diversity similar to G6 strains from Russia (Altai republic) and Kazakhstan was also found, consistent with a bottleneck effect. In this study, G6 was the most common Echinococcus genotype. Genetic homogeneity of east, southeast and central Iranian G6 and its low genetic diversity may be due limited mobility and contact between humans and camels from other regions because of large, inhospitable deserts. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Widespread Occurrence of Zoonotic Cryptosporidium Species and Subtypes in Dairy Cattle from Northeast China: Public Health Concerns.

    Science.gov (United States)

    Tao, Wei; Li, Yijing; Yang, Hang; Song, Mingxin; Lu, Yixin; Li, Wei

    2018-02-01

    Bovine cryptosporidiosis constitutes a threat to the livestock industry and public health worldwide. In the present study we investigated dairy cattle of all ages in northeast China for the prevalence and genetic traits of Cryptosporidium. Nested polymerase chain reaction of the small subunit rRNA gene was used to identify Cryptosporidium species or genotype. The parasite was detected in 130 of 537 (24.2%) animals sampled from the cities of Harbin (35.2%, 69/196) and Qiqihar (32.1%, 61/190). Cryptosporidium parvum (87/130) was identified as the dominant species by sequence analysis followed by Cryptosporidium bovis (28/130), Cryptosporidium ryanae (5/130), Cryptosporidium andersoni (2/130), Cryptosporidium suis-like genotype (2/130), and mixed C. ryanae/ C. bovis (1/130). Subtyping of C. parvum isolates was based on the DNA polymorphisms of the 60-kDa glycoprotein gene. Subtyping of the C. parvum isolates recognized subtypes IIdA15G1 (24/87) in Harbin and IIdA20G1 (48/87) in Qiqihar. A diversity of Cryptosporidium species/genotype and subtypes was identified in cattle from northeast China. Widespread occurrence of human-pathogenic Cryptosporidium species and subtypes is of public health significance. This is the first study reporting C. parvum subtype IIdA20G1 in China. The findings improve the epidemiological knowledge of bovine cryptosporidiosis in China, highlighting the importance of ongoing Cryptosporidium surveillance.

  6. Molecular evolution of H1N1 swine influenza in Guangdong, China, 2016-2017.

    Science.gov (United States)

    Cai, Mengkai; Huang, Junming; Bu, Dexin; Yu, Zhiqing; Fu, Xinliang; Ji, Chihai; Zhou, Pei; Zhang, Guihong

    2018-06-01

    Swine are the main host of the H1N1 swine influenza virus (SIV), however, H1N1 can also infect humans and occasionally cause serious respiratory disease. To trace the evolution of the SIV in Guangdong, China, we performed an epidemic investigation during the period of 2016-2017. Nine H1N1 influenza viruses were isolated from swine nasal swabs. Antigenic analysis revealed that these viruses belonged to two distinct antigenic groups, represented by A/Swine/Guangdong/101/2016 and A/Swine/Guangdong/52/2017. Additionally, three genotypes, known as GD52/17-like, GD493/17-like and GD101/16-like, were identified by phylogenetic analysis. Importantly, the genotypes including a minimum of 4 pdm/09-origin internal genes have become prevalent in China in recent years. A total of 2966 swine serum samples were used to perform hemagglutination inhibition (HI) tests, and the results showed that the seroprevalence values of SW/GD/101/16 (32.2% in 2016, 32.1% in 2017) were significantly higher than the seroprevalence values of SW/GD/52/17 (18.0% in 2016, 16.7% in 2017). Our study showed that the three reassortant genotypes of H1N1 SIV currently circulating in China are stable, but H1N1pdm09 poses challenges to human health by the introduction of internal genes into these reassortant genotypes. Strengthening SIV surveillance is therefore critical for SIV control and minimizing its potential threat to public health. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Loss of heterozygosity drives clonal diversity of Phytophthora capsici in China.

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    Jian Hu

    Full Text Available Phytophthora capsici causes significant loss to pepper (Capsicum annum in China and our goal was to develop single nucleotide polymorphism (SNP markers for P. capsici and characterize genetic diversity nationwide. Eighteen isolates of P. capsici from locations worldwide were re-sequenced and candidate nuclear and mitochondrial SNPs identified. From 2006 to 2012, 276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH. Analysis of SNPs directly from infected peppers confirmed LOH in field populations. One clonal lineage is dominant throughout much of the country. The overall implications for long-lived genetically diverse clonal lineages amidst a widely dispersed sexual population are discussed.

  8. Molecular Epidemiology of Clostridium difficile Infection in Hospitalized Patients in Eastern China.

    Science.gov (United States)

    Jin, Dazhi; Luo, Yun; Huang, Chen; Cai, Jian; Ye, Julian; Zheng, Yi; Wang, Liqian; Zhao, Peng; Liu, Anbing; Fang, Weijia; Wang, Xianjun; Xia, Shichang; Jiang, Jianmin; Tang, Yi-Wei

    2017-03-01

    Few studies on risk factors for and transmission of Clostridium difficile infection (CDI) in China have been reported. A cross-sectional study was conducted for 3 years in eastern China. Consecutive stool specimens from hospitalized patients with diarrhea were cultured for C. difficile. C. difficile isolates from these patients then were analyzed for toxin genes, genotypes, and antimicrobial resistance. A severity score for the CDI in each patient was determined by a blinded review of the medical record, and these scores ranged from 1 to 6. A total of 397 out of 3,953 patients (10.0%) with diarrhea were found to have CDI. Severity of CDI was mild to moderate, and the average (± standard deviation) severity score was 2.61 ± 1.01. C. difficile was isolated from stool specimens in 432 (10.9%) of all the patients who had diarrhea. C. difficile genotypes were determined by multilocus sequence analysis and PCR ribotyping; sequence type 37 (ST37)/ribotype 017 (RT017) ( n = 68, 16.5%) was the dominant genotype. Eleven patients (16.2%) with this genotype had a CDI severity score of 5. Overall, three RTs and four STs were predominant; these genotypes were associated with significantly different antimicrobial resistance patterns in comparison to all genotypes (χ 2 = 79.56 to 97.76; P < 0.001). Independent risk factors associated with CDI included age greater than 55 years (odds ratio [95% confidence interval], 26.80 [18.76 to 38.29]), previous hospitalization (12.42 [8.85 to 17.43]), previous antimicrobial treatment within 8 weeks (150.56 [73.11 to 310.06]), hospital stay more than 3 days before sampling (2.34 [1.71 to 3.22]), undergoing chemotherapy (3.31 [2.22 to 4.92]), and undergoing abdominal surgery (4.82 [3.54 to 6.55]). CDI is clearly a problem in eastern China and has a prevalence of 10.0% in hospitalized patients. Among risk factors for CDI, the advanced age threshold was younger for Chinese patients than that reported for patients in developed countries

  9. The effect of heterogeneous defectors on the evolution of public cooperation

    Science.gov (United States)

    Chen, Tong; Hu, Xuezhi; Wang, Yongjie; Wang, Le

    2018-06-01

    In recent years,more and more private capital join the construction of cultural facilities and the organization of cultural activities in China. Actually, the organization of cultural activities by crowd-funding mechanism is a kind of multi-player game. Not all players who donate different amount of money are real cooperators. In fact, some cunning defectors may donate a little money to avoid the gossip and punishment. This part of people are very tricky. They could be seen as heterogeneous defectors. The role of heterogeneous defectors is investigated in cooperative behaviors of complex social network. Numerical results show that heterogeneous defectors could be a buffer for maintaining the public pool when synergy factor is low in public goods game (PGG). It is relatively easy to be cooperators for heterogeneous defectors when synergy factor is high in PGG. To better improve cooperation, punishment towards heterogeneous defectors and complete defectors is introduced. We are glad to find that when the defectors' loss is equal to or larger than the altruistic cooperators' punishment cost, the mechanism could make great effect. In addition, the role of heterogeneous defectors depends on the relationship between the punishment cost and the defectors' loss.

  10. Characterizing Traffic Conditions from the Perspective of Spatial-Temporal Heterogeneity

    Directory of Open Access Journals (Sweden)

    Peichao Gao

    2016-03-01

    Full Text Available Traffic conditions are usually characterized from the perspective of travel time or the average vehicle speed in the field of transportation, reflecting the congestion degree of a road network. This article provides a method from a new perspective to characterize traffic conditions; the perspective is based on the heterogeneity of vehicle speeds. A novel measurement, the ratio of areas (RA in a rank-size plot, is included in the proposed method to capture the heterogeneity. The proposed method can be performed from the perspective of both spatial heterogeneity and temporal heterogeneity, being able to characterize traffic conditions of not only a road network but also a single road. Compared with methods from the perspective of travel time, the proposed method can characterize traffic conditions at a higher frequency. Compared to methods from the perspective of the average vehicle speed, the proposed method takes account of the heterogeneity of vehicle speeds. The effectiveness of the proposed method has been demonstrated with real-life traffic data of Shenzhen (a coastal urban city in China, and the advantage of the proposed RA has been verified by comparisons to similar measurements such as the ht-index and the CRG index.

  11. Trends in Hepatitis B Virus Resistance to Nucleoside/Nucleotide Analogs in North China from 2009 to 2016: A Retrospective Study.

    Science.gov (United States)

    Guo, Xianghua; Wu, Jushan; Wei, Feili; Ouyang, Yabo; Li, Qing; Liu, Kai; Wang, Yanjun; Zhang, Yulin; Chen, Dexi

    2018-04-11

    Nucleos(t)ide analogs (NAs) are widely used in anti-hepatitis B virus (HBV) therapy for effective inhibition of HBV replication. However, HBV resistance to NAs has emerged, resulting in virus reactivation and disease recurrence. Big data on the current dynamic of HBV resistance profiles are still rare in China. Herein, we analyzed 4,491 plasma samples with HBV primary genotypic resistance mutations representative of the general HBV resistance situation in northern China from 2009 to 2016. We found that entecavir (ETV), representing 52.8% of 12,713 NAs users in the North of China in 2016, has become the major NA for treating Chinese patients infected with HBV. Despite more than 50% of M204I/V±L180M among all HBV resistance cases annually and extensive exposure of the patients to lamivudine (LAM), telbivudine (LdT), and adefovir dipivoxil (ADV), ETV resistance also showed dramatically increased incidence, which climbed to 17.1% in 2016. Moreover, A181T/V, ETV-resistant mutations, and multidrug-resistant mutations were found more frequently in HBV genotype C than in HBV genotype B, 21.2% vs. 8.5%, 12.5% vs. 7.9%, and 5.9% vs. 3%, respectively, whereas M204I and N236T were more predominant in genotype B than in genotype C, 40.3% vs. 20.8%, and 11.3% vs. 1.8%, respectively. In conclusion, we have reported dynamic changes of HBV NA-resistance mutation patterns and the current NA usage profile for anti-HBV treatment in North China in the past 8 years. Our data provides valuable information on HBV NA resistance that is an important reference for clinics to devise more effective treatment regimens for individual patients. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  12. Geographical distribution of Toxoplasma gondii genotypes in Asia: A link with neighboring continents.

    Science.gov (United States)

    Chaichan, P; Mercier, A; Galal, L; Mahittikorn, A; Ariey, F; Morand, S; Boumédiène, F; Udonsom, R; Hamidovic, A; Murat, J B; Sukthana, Y; Dardé, M L

    2017-09-01

    Defining the pattern of genetic diversity of Toxoplasma gondii is important to understand its worldwide distribution. During the last decades, a large number of studies have been published on Toxoplasma genotypes circulating in Europe, in North and South America. Two continents are still largely unexplored, Africa and, to a less extent, Asia. In this last continent, an increasing number of publications reported genotypes circulating in diverse provinces of China, but very few data are available for other Asian countries. After a systematic database search, 47 papers related to T. gondii genotypes in Asia were analyzed. Genetic characterization of DNA was performed by microsatellite markers, or more usually by a multiplex PCR using 11 PCR-RFLP markers, allowing data comparison to draw a first global picture of the population structure of this parasite throughout Asia. Overall, 390 isolates or DNA extracts were completely typed by PCR-RFLP and/or microsatellite marker methods, revealing 36 different PCR-RFLP or equivalent microsatellite genotypes: 15 genotypes identified by a ToxoDB number and 21 atypical or unique genotypes. The most common genotype found in Asia is the genotype ToxoDB#9 (Chinese 1). The clonal types I, II and II variant, and III were also commonly found in Asia. The geographical distribution of these genotypes across Asia may reflect either a continuum with Europe for the western part of Asia (presence of Type II), or the circulation of strains through animal migration or human activities between Africa and the Southwestern part of Asia (Africa 1 genotype in Turkey or ToxoDB#20 both I Sri-Lanka and in Ethiopia or Egypt). Although there are some indications of a genetic population structure in Southeast Asian countries different from the rest of Asia, more studies in this tropical part of Asia will be necessary for a region which represent as well as Africa one of the missing links of the T. gondii genetic diversity. Copyright © 2017 Elsevier B

  13. Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge.

    Science.gov (United States)

    Alvarez Rojas, Cristian A; Romig, Thomas; Lightowlers, Marshall W

    2014-01-01

    Genetic variability in the species group Echinococcus granulosus sensu lato is well recognised as affecting intermediate host susceptibility and other biological features of the parasites. Molecular methods have allowed discrimination of different genotypes (G1-10 and the 'lion strain'), some of which are now considered separate species. An accumulation of genotypic analyses undertaken on parasite isolates from human cases of cystic echinococcosis provides the basis upon which an assessment is made here of the relative contribution of the different genotypes to human disease. The allocation of samples to G-numbers becomes increasingly difficult, because much more variability than previously recognised exists in the genotypic clusters G1-3 (=E. granulosus sensu stricto) and G6-10 (Echinococcus canadensis). To accommodate the heterogeneous criteria used for genotyping in the literature, we restrict ourselves to differentiate between E. granulosus sensu stricto (G1-3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and E. canadensis (G6-7, G8, G10). The genotype G1 is responsible for the great majority of human cystic echinococcosis worldwide (88.44%), has the most cosmopolitan distribution and is often associated with transmission via sheep as intermediate hosts. The closely related genotypes G6 and G7 cause a significant number of human infections (11.07%). The genotype G6 was found to be responsible for 7.34% of infections worldwide. This strain is known from Africa and Asia, where it is transmitted mainly by camels (and goats), and South America, where it appears to be mainly transmitted by goats. The G7 genotype has been responsible for 3.73% of human cases of cystic echinococcosis in eastern European countries, where the parasite is transmitted by pigs. Some of the samples (11) could not be identified with a single specific genotype belonging to E. canadensis (G6/10). Rare cases of human cystic echinococcosis have been identified as having been caused by

  14. Evaluation on island ecological vulnerability and its spatial heterogeneity.

    Science.gov (United States)

    Chi, Yuan; Shi, Honghua; Wang, Yuanyuan; Guo, Zhen; Wang, Enkang

    2017-12-15

    The evaluation on island ecological vulnerability (IEV) can help reveal the comprehensive characteristics of the island ecosystem and provide reference for controlling human activities on islands. An IEV evaluation model which reflects the land-sea dual features, natural and anthropogenic attributes, and spatial heterogeneity of the island ecosystem was established, and the southern islands of Miaodao Archipelago in North China were taken as the study area. The IEV, its spatial heterogeneity, and its sensitivities to the evaluation elements were analyzed. Results indicated that the IEV was in status of mild vulnerability in the archipelago scale, and population pressure, ecosystem productivity, environmental quality, landscape pattern, and economic development were the sensitive elements. The IEV showed significant spatial heterogeneities both in land and surrounding waters sub-ecosystems. Construction scale control, optimization of development allocation, improvement of exploitation methods, and reasonable ecological construction are important measures to control the IEV. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Phenotypes in defined genotypes including siblings with Usher syndrome.

    Science.gov (United States)

    Malm, Eva; Ponjavic, Vesna; Möller, Claes; Kimberling, William J; Andréasson, Sten

    2011-06-01

    To characterize visual function in defined genotypes including siblings with Usher syndrome. Thirteen patients with phenotypically different subtypes of Usher syndrome, including 3 families with affected siblings, were selected. Genetic analysis and ophthalmological examinations including visual fields, full-field electroretinography (ERG), multifocal electroretinography (mf ERG), and optical coherence tomography (OCT) were assessed. The patients' degree of visual handicap was evaluated by a questionnaire (ADL). Twelve of thirteen patients were genotyped as Usher 1B, 1D, 1F, 2A, 2C or 3A. In 12 of 13 patients examined with ERG the 30 Hz flickering light response revealed remaining cone function. In 3 of the patients with Usher type 1 mf ERG demonstrated a specific pattern, with a sharp distinction between the area with reduced function and the central area with remaining macular function and normal peak time. OCT demonstrated loss of foveal depression with distortion of the foveal architecture in the macula in all patients. The foveal thickness ranged from 159 to 384 µm and was not correlated to retinal function. Three siblings shared the same mutation for Usher 2C but in contrast to previous reports regarding this genotype, 1 of them diverged in phenotype with substantially normal visual fields, almost normal OCT and mf ERG findings, and only moderately reduced rod and cone function according to ERG. Evaluation of visual function comprising both the severity of the rod cone degeneration and the function in the macular region confirm phenotypical heterogeneity within siblings and between different genotypes of Usher syndrome.

  16. Top management team heterogeneity and firm performance: An empirical research on Chinese listed companies

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ping

    2007-01-01

    An empirical study of the 2001-2002 data from 356 Chinese companies listed in the Shanghai and Shenzhen stock exchanges indicates that within the social context of China the characteristics of a firm's top management team have a different impact on firm performance from those of foreign countries. Also, the tenure heterogeneity and functional experience heterogeneity of the top management team are inversely related to firm performance. This paper analyzes and discusses the findings in detail and points out areas for future research.

  17. [The velocity of HCV subtype 6a transmission in southwest China].

    Science.gov (United States)

    Hong, Guo-hu; Tan, Zhao-xia; Guo, Yan; Mao, Qing

    2011-07-01

    To estimate the velocity of HCV subtype 6a transmission in Southwest China. The HCV CE1 region from 61 patients infected with HCV genotype 6 were amplificated by RT-PCR and sequenced. The subtypes were identified, and the period of HCV 6a strains originated in southwest china was estimated by using molecular clock phylogenetic analysis. The velocity of HCV subtype 6a transmission in southwest China was estimated by BEAST v1.6.1 and Tracer v1.5 software theoretically. Most of HCV 6a strains distributed in Southwest China origine around the year 1968 and at last 4 epidemic strains existed. The earlier origine strains could be isolated both in intravenous drug users (IDU) and non-IDU patients. After 1997, the HCV 6a strains transmission in southwest China accelerated and the trend intensified in 2007. HCV 6a strains spread fastly both in IDU and non-IDU patients, which might be the main HCV subtype distributed in Southwest China in the future.

  18. Anal HPV infection in HIV-positive men who have sex with men from China.

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    Lei Gao

    Full Text Available BACKGROUND: Anal HPV infection, which contributes to the development of anal warts and anal cancer, is well known to be common among men who have sex with men (MSM, especially among those HIV positives. However, HIV and anal HPV co-infection among MSM has not been addressed in China. METHODS: A cross-sectional study was conducted in Beijing and Tianjin, China. Study participants were recruited using multiple methods with the collaboration of local volunteer organizations. Blood and anal swabs were collected for HIV-1 serological test and HPV genotyping. RESULTS: A total of 602 MSM were recruited and laboratory data were available for 578 of them (96.0%. HIV and anal HPV prevalence were 8.5% and 62.1%, respectively. And 48 MSM (8.3% were found to be co-infected. The HPV genotypes identified most frequently were HPV06 (19.6%, HPV16 (13.0%, HPV52 (8.5% and HPV11 (7.6%. Different modes of HPV genotypes distribution were observed with respect to HIV status. A strong dose-response relationship was found between HIV seropositivity and multiplicity of HPV genotypes (p<0.001, which is consistent with the observation that anal HPV infection was an independent predictor for HIV infection. CONCLUSIONS: A high prevalence of HIV and anal HPV co-infection was observed in the MSM community in Beijing and Tianjin, China. Anal HPV infection was found to be independently associated with increased HIV seropositivity, which suggests the application of HPV vaccine might be a potential strategy to reduce the acquisition of HIV infection though controlling the prevalence of HPV.

  19. Genetic Characterization of the Hemagglutinin Genes of Wild-Type Measles Virus Circulating in China, 1993–2009

    Science.gov (United States)

    Zhu, Zhen; Liu, Chunyu; Mao, Naiying; Ji, Yixin; Wang, Huiling; Jiang, Xiaohong; Li, Chongshan; Tang, Wei; Feng, Daxing; Wang, Changyin; Zheng, Lei; Lei, Yue; Ling, Hua; Zhao, Chunfang; Ma, Yan; He, Jilan; Wang, Yan; Li, Ping; Guan, Ronghui; Zhou, Shujie; Zhou, Jianhui; Wang, Shuang; Zhang, Hong; Zheng, Huanying; Liu, Leng; Ma, Hemuti; Guan, Jing; Lu, Peishan; Feng, Yan; Zhang, Yanjun; Zhou, Shunde; Xiong, Ying; Ba, Zhuoma; Chen, Hui; Yang, Xiuhui; Bo, Fang; Ma, Yujie; Liang, Yong; Lei, Yake; Gu, Suyi; Liu, Wei; Chen, Meng; Featherstone, David; Jee, Youngmee; Bellini, William J.; Rota, Paul A.; Xu, Wenbo

    2013-01-01

    Background China experienced several large measles outbreaks in the past two decades, and a series of enhanced control measures were implemented to achieve the goal of measles elimination. Molecular epidemiologic surveillance of wild-type measles viruses (MeV) provides valuable information about the viral transmission patterns. Since 1993, virologic surveillnace has confirmed that a single endemic genotype H1 viruses have been predominantly circulating in China. A component of molecular surveillance is to monitor the genetic characteristics of the hemagglutinin (H) gene of MeV, the major target for virus neutralizing antibodies. Principal Findings Analysis of the sequences of the complete H gene from 56 representative wild-type MeV strains circulating in China during 1993–2009 showed that the H gene sequences were clustered into 2 groups, cluster 1 and cluster 2. Cluster1 strains were the most frequently detected cluster and had a widespread distribution in China after 2000. The predicted amino acid sequences of the H protein were relatively conserved at most of the functionally significant amino acid positions. However, most of the genotype H1 cluster1 viruses had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. In addition, the substitution of Pro397Leu in the hemagglutinin noose epitope (HNE) was identified in 23 of 56 strains. The evolutionary rate of the H gene of the genotype H1 viruses was estimated to be approximately 0.76×10−3 substitutions per site per year, and the ratio of dN to dS (dN/dS) was measles in China. PMID:24073194

  20. Association of nNOS Gene Polymorphism with Ischemic Stroke in Han Chinese of North China

    Directory of Open Access Journals (Sweden)

    Yingjie Dai

    2013-01-01

    Full Text Available Nitric oxide (NO is an important messenger molecule and effector molecule. This study aimed to investigate the relation of neuronal nitric oxide synthase (nNOS gene polymorphism with ischemic stroke in Han Chinese of North China. This was a case-control study. A total of 413 patients with ischemic stroke were recruited from Han Chinese of North China. There were 201 males and 212 females. In addition, 477 healthy subjects served as controls including 224 males and 253 females. Multiplex SNaPshot was employed to detect nNOS gene polymorphism (rs2293050, rs2139733, rs7308402, and rs1483757. Results showed that the rs1483757, rs2139733, and rs2293050 genotypes and allele frequencies were comparable between patients and controls. However, ischemic stroke patients had significantly reduced AG genotype and A allele frequency when compared with controls (P=0.037, P=0.041. After adjusting confounding factors (gender, age, smoking, history of drinking, hypertension, and diabetes, AG genotype and A allele were still related to ischemic stroke (OR=0.572, 95% CI: 0.335–0.978, P=0.041; OR=0.611, 95% C: 0.378–0.985, and P=0.041 and both were found to be protective factors. Our results showed that rs7308402 gene polymorphism of nNOS is related to ischemic stroke in Han Chinese of North China.

  1. Kernel machine methods for integrative analysis of genome-wide methylation and genotyping studies.

    Science.gov (United States)

    Zhao, Ni; Zhan, Xiang; Huang, Yen-Tsung; Almli, Lynn M; Smith, Alicia; Epstein, Michael P; Conneely, Karen; Wu, Michael C

    2018-03-01

    Many large GWAS consortia are expanding to simultaneously examine the joint role of DNA methylation in addition to genotype in the same subjects. However, integrating information from both data types is challenging. In this paper, we propose a composite kernel machine regression model to test the joint epigenetic and genetic effect. Our approach works at the gene level, which allows for a common unit of analysis across different data types. The model compares the pairwise similarities in the phenotype to the pairwise similarities in the genotype and methylation values; and high correspondence is suggestive of association. A composite kernel is constructed to measure the similarities in the genotype and methylation values between pairs of samples. We demonstrate through simulations and real data applications that the proposed approach can correctly control type I error, and is more robust and powerful than using only the genotype or methylation data in detecting trait-associated genes. We applied our method to investigate the genetic and epigenetic regulation of gene expression in response to stressful life events using data that are collected from the Grady Trauma Project. Within the kernel machine testing framework, our methods allow for heterogeneity in effect sizes, nonlinear, and interactive effects, as well as rapid P-value computation. © 2017 WILEY PERIODICALS, INC.

  2. Genetic characterizations of Giardia duodenalis in sheep and goats in Heilongjiang Province, China and possibility of zoonotic transmission.

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    Weizhe Zhang

    Full Text Available BACKGROUND: Giardia duodenalis is a widespread intestinal protozoan of both humans and mammals. To date, few epidemiological studies have assessed the potential and importance of zoonotic transmission; and the human giardiasis burden attributable to G. duodenalis of animal origin is unclear. No information about occurrence and genotyping data of sheep and goat giardiasis is available in China. The aim of the present study was to determine prevalence and distribution of G. duodenalis in sheep and goats in Heilongjiang Province, China, and to characterize G. duodenalis isolates and assess the possibility of zoonotic transmission. METHODOLOGY/PRINCIPAL FINDINGS: A total of 678 fecal specimens were collected from sheep and goats on six farms ranging in age from one month to four years in Heilongjiang Province, China. The average prevalence of G. duodenalis infection was 5.0% (34/678 by microscopy after Lugol's iodine staining, with 5.6% (30/539 for the sheep versus 2.9% (4/139 for the goats. Molecular analysis was conducted on 34 G. duodenalis isolates based on the triosephosphate isomerase (tpi gene. 29 tpi gene sequences were successfully obtained and identified as assemblages A (n = 4, B (n = 2 and E (n = 23. High heterogeneity was observed within assemblage E at the tpi locus, with five novel subtypes found out of seven subtypes. Two subtypes of assemblage A were detected, including subtype AI (n = 3 and a novel subtype (designated as subtype AIV (n = 1. Two assemblage B isolates were identical to each other in the tpi gene sequences. CONCLUSIONS/SIGNIFICANCE: This is the first report of G. duodenalis infections in sheep and goats in China. The present data revealed the unique endemicity on prevalence, distribution and genetic characterization of G. duodenalis in sheep and goats in Heilongjiang Province. The findings of assemblages A and B in sheep and goats implied the potential of zoonotic transmission.

  3. Mapping the functional landscape of frequent phenylalanine hydroxylase (PAH) genotypes promotes personalised medicine in phenylketonuria.

    Science.gov (United States)

    Danecka, Marta K; Woidy, Mathias; Zschocke, Johannes; Feillet, François; Muntau, Ania C; Gersting, Søren W

    2015-03-01

    In phenylketonuria, genetic heterogeneity, frequent compound heterozygosity, and the lack of functional data for phenylalanine hydroxylase genotypes hamper reliable phenotype prediction and individualised treatment. A literature search revealed 690 different phenylalanine hydroxylase genotypes in 3066 phenylketonuria patients from Europe and the Middle East. We determined phenylalanine hydroxylase function of 30 frequent homozygous and compound heterozygous genotypes covering 55% of the study population, generated activity landscapes, and assessed the phenylalanine hydroxylase working range in the metabolic (phenylalanine) and therapeutic (tetrahydrobiopterin) space. Shared patterns in genotype-specific functional landscapes were linked to biochemical and pharmacological phenotypes, where (1) residual activity below 3.5% was associated with classical phenylketonuria unresponsive to pharmacological treatment; (2) lack of defined peak activity induced loss of response to tetrahydrobiopterin; (3) a higher cofactor need was linked to inconsistent clinical phenotypes and low rates of tetrahydrobiopterin response; and (4) residual activity above 5%, a defined peak of activity, and a normal cofactor need were associated with pharmacologically treatable mild phenotypes. In addition, we provide a web application for retrieving country-specific information on genotypes and genotype-specific phenylalanine hydroxylase function that warrants continuous extension, updates, and research on demand. The combination of genotype-specific functional analyses with biochemical, clinical, and therapeutic data of individual patients may serve as a powerful tool to enable phenotype prediction and to establish personalised medicine strategies for dietary regimens and pharmacological treatment in phenylketonuria. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  4. Molecular epidemiology, genotype-phenotype correlation and BH4 responsiveness in Spanish patients with phenylketonuria.

    Science.gov (United States)

    Aldámiz-Echevarría, Luis; Llarena, Marta; Bueno, María A; Dalmau, Jaime; Vitoria, Isidro; Fernández-Marmiesse, Ana; Andrade, Fernando; Blasco, Javier; Alcalde, Carlos; Gil, David; García, María C; González-Lamuño, Domingo; Ruiz, Mónica; Ruiz, María A; Peña-Quintana, Luis; González, David; Sánchez-Valverde, Felix; Desviat, Lourdes R; Pérez, Belen; Couce, María L

    2016-08-01

    Phenylketonuria (PKU), the most common inborn error of amino acid metabolism, is caused by mutations in the phenylalanine-4-hydroxylase (PAH) gene. This study aimed to assess the genotype-phenotype correlation in the PKU Spanish population and the usefulness in establishing genotype-based predictions of BH4 responsiveness in our population. It involved the molecular characterization of 411 Spanish PKU patients: mild hyperphenylalaninemia non-treated (mild HPA-NT) (34%), mild HPA (8.8%), mild-moderate (20.7%) and classic (36.5%) PKU. BH4 responsiveness was evaluated using a 6R-BH4 loading test. We assessed genotype-phenotype associations and genotype-BH4 responsiveness in our population according to literature and classification of the mutations. The mutational spectrum analysis showed 116 distinct mutations, most missense (70.7%) and located in the catalytic domain (62.9%). The most prevalent mutations were c.1066-11G>A (9.7%), p.Val388Met (6.6%) and p.Arg261Gln (6.3%). Three novel mutations (c.61-13del9, p.Ile283Val and p.Gly148Val) were reported. Although good genotype-phenotype correlation was observed, there was no exact correlation for some genotypes. Among the patients monitored for the 6R-BH4 loading test: 102 were responders (87, carried either one or two BH4-responsive alleles) and 194 non-responders (50, had two non-responsive mutations). More discrepancies were observed in non-responders. Our data reveal a great genetic heterogeneity in our population. Genotype is quite a good predictor of phenotype and BH4 responsiveness, which is relevant for patient management, treatment and follow-up.

  5. Genome characterization, antigenicity and pathogenicity of a novel infectious bronchitis virus type isolated from south China.

    Science.gov (United States)

    Jiang, Lei; Zhao, Wenjun; Han, Zongxi; Chen, Yuqiu; Zhao, Yan; Sun, Junfeng; Li, Huixin; Shao, Yuhao; Liu, Liangliang; Liu, Shengwang

    2017-10-01

    In 2014, three infectious bronchitis virus (IBV) strains, designated as γCoV/ck/China/I0111/14, γCoV/ck/China/I0114/14 and γCoV/ck/China/I0118/14, were isolated and identified from chickens suspected to be infected with IBV in Guangxi province, China. Based upon data arising from S1 sequence and phylogenetic analyses, the three IBV isolates were genetically different from other known IBV types, which represented a novel genotype (GI-29). Virus cross-neutralization tests, using γCoV/ck/China/I0111/14 as a representative, showed that genotype GI-29 was antigenically different from all other known IBV types, thus representing a novel serotype. Complete genomic analysis showed that GI-29 type viruses were closely related to and might originate from a GX-YL5-like virus by accumulation of substitutions in multiple genes. These GI-29 viral genomes are still evolving and diverging, particularly in the 3' region, although we cannot rule out the possibility of recombination events occurring. For isolate γCoV/ck/China/I0114/14, we found that recombination events had occurred between nsps 2 and 3 in gene 1 which led to the introduction of a 4/91 gene fragment into the γCoV/ck/China/I0114/14 viral genome. In addition, we found that the GI-29 type γCoV/ck/China/I0111/14 isolate was a nephropathogenic strain and high pathogenic to 1-day-old specific pathogen-free (SPF) chickens although cystic oviducts were not observed in the surviving layer chickens challenged with γCoV/ck/China/I0111/14 isolate. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. BDNF genotype interacts with motor-function to influence rehabilitation responsiveness post-stroke

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    Christine T Shiner

    2016-05-01

    Full Text Available Background. Persistent motor impairment is common but highly heterogeneous post-stroke. Genetic polymorphisms, including those identified on the brain derived neurotrophic factor (BDNF and apolipoprotein E (APOE genes, may contribute to this variability by limiting the capacity for use-dependent neuroplasticity, and hence rehabilitation responsiveness.Objective. To determine whether BDNF and APOE genotypes influence motor improvement facilitated by post-stroke upper-limb rehabilitation. Methods. BDNF Val66Met and APOE isoform genotypes were determined using leukocyte DNA for 55 community-dwelling patients 2-123 months post-stroke. All patients completed a dose-matched upper-limb rehabilitation program of either Wii-based Movement Therapy or Constraint-induced Movement Therapy. Upper-limb motor-function was assessed pre- and post-therapy using a suite of functional measures. Results. Motor-function improved for all patients post-therapy, with no difference between therapy groups. In the pooled data, there was no significant effect of BDNF or APOE genotype on motor-function at baseline, or following the intervention. However, a significant interaction between the level of residual motor-function and BDNF genotype was identified (p=0.029, whereby post-therapy improvement was significantly less for Met allele carriers with moderate and high, but not low motor-function. There was no significant association between APOE genotype and therapy outcomes. Conclusions. This study identified a novel interaction between the BDNF Val66Met polymorphism, motor-function status and the magnitude of improvement with rehabilitation in chronic stroke. This polymorphism does not preclude, but may reduce, the magnitude of motor improvement with therapy, particularly for patients with higher but not lower residual motor-function. BDNF genotype should be considered in the design and interpretation of clinical trials.

  7. The influence of 5-HTTLPR transporter genotype on amygdala-subgenual anterior cingulate cortex connectivity in autism spectrum disorder

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    Francisco Velasquez

    2017-04-01

    Full Text Available Social deficits in autism spectrum disorder (ASD are linked to amygdala functioning and functional connection between the amygdala and subgenual anterior cingulate cortex (sACC is involved in the modulation of amygdala activity. Impairments in behavioral symptoms and amygdala activation and connectivity with the sACC seem to vary by serotonin transporter-linked polymorphic region (5-HTTLPR variant genotype in diverse populations. The current preliminary investigation examines whether amygdala-sACC connectivity differs by 5-HTTLPR genotype and relates to social functioning in ASD. A sample of 108 children and adolescents (44 ASD completed an fMRI face-processing task. Youth with ASD and low expressing 5-HTTLPR genotypes showed significantly greater connectivity than youth with ASD and higher expressing genotypes as well as typically developing (TD individuals with both low and higher expressing genotypes, in the comparison of happy vs. baseline faces and happy vs. neutral faces. Moreover, individuals with ASD and higher expressing genotypes exhibit a negative relationship between amygdala-sACC connectivity and social dysfunction. Altered amygdala-sACC coupling based on 5-HTTLPR genotype may help explain some of the heterogeneity in neural and social function observed in ASD. This is the first ASD study to combine genetic polymorphism analyses and functional connectivity in the context of a social task.

  8. Brief communication genotyping of Burkholderia pseudomallei revealed high genetic variability among isolates from a single population group.

    Science.gov (United States)

    Zueter, Abdelrahman Mohammad; Rahman, Zaidah Abdul; Yean, Chan Yean; Harun, Azian

    2015-01-01

    Burkholderia pseudomallei is a soil dwelling Gram-negative bacteria predominates in Southeast Asia zone and the tropical part of Australia. Genetic diversity has been explored among various populations and environments worldwide. To date, little data is available on MLST profiling of clinical B. pseudomallei isolates in peninsular Malaysia. In this brief report, thirteen culture positive B. pseudomallei cases collected from a single population of Terengganu state in the Western Peninsular Malaysia and were confirmed by In-house TTS1-PCR. Isolates were subjected for multi-locus sequence typing (MLST) to explore their genotypic diversity and to investigate for possible clonal clustering of a certain sequence type. Patient's clinical information was examined to investigate for clinical correlation among the different genotypes. In spite of small sample set, MLST results indicated predictive results; considerable genotypic diversity, predominance and novelty among B. pseudomallei collected over a single geographically-located population in Malaysia. Massive genotypic heterogeneity was observed; 8 different sequence types with predominance of sequence type 54 and discovery of two novel sequence types. However, no clear pathogenomic or organ tropism clonal relationships were predicted.

  9. Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

    Science.gov (United States)

    Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

    2010-08-01

    There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

  10. The Intergenerational Inequality of Health in China

    DEFF Research Database (Denmark)

    Eriksson, Tor; Pan, Jay; Qin, Xuezheng

    This paper estimates the intergenerational health transmission in China using the 1991-2009 China Health and Nutrition Survey (CHNS) data. Three decades of persistent economic growth in China has been accompanied by high income inequality, which may in turn be caused by the inequality...... measures and various model specifications, and is robust when unobserved household heterogeneity is removed. We also find that the parents’ (especially the mothers’) socio-economic characteristics and environmental / health care choices are strongly correlated with their own and their children’s health......, supporting the “nature-nurture interaction” hypothesis. The Blinder-Oaxaca decomposition further indicates that 15% to 27% of the rural-urban inequality of child health is attributable to the endowed inequality from their parents’ health. An important policy implication of our study is that the increasing...

  11. HIV-1 genetic diversity and its distribution characteristics among newly diagnosed HIV-1 individuals in Hebei province, China.

    Science.gov (United States)

    Lu, Xinli; Zhao, Cuiying; Wang, Wei; Nie, Chenxi; Zhang, Yuqi; Zhao, Hongru; Chen, Suliang; Cui, Ze

    2016-01-01

    Since the first HIV-1 case in 1989, Hebei province has presented a clearly rising trend of HIV-1 prevalence, and HIV-1 genetic diversity has become the vital barrier to HIV prevention and control in this area. To obtain detailed information of HIV-1 spread in different populations and in different areas of Hebei, a cross-sectional HIV-1 molecular epidemiological investigation was performed across the province. Blood samples of 154 newly diagnosed HIV-1 individuals were collected from ten prefectures in Hebei using stratified sampling. Partial gag and env genes were amplified and sequenced. HIV-1 genotypes were identified by phylogenetic tree analyses. Among the 139 subjects genotyped, six HIV-1 subtypes were identified successfully, including subtype B (41.0 %), CRF01_AE (40.3 %), CRF07_BC (11.5 %), CRF08_BC (4.3 %), unique recombinant forms (URFs) (1.4 %) and subtype C (1.4 %). Subtype B was identified as the most frequent subtype. Two URF recombination patterns were the same as CRF01_AE/B. HIV-1 genotype distribution showed a significant statistical difference in different demographic characteristics, such as source (P  0.05). The differences in HIV-1 genotype distribution were closely associated with transmission routes. Particularly, all six subtype strains were found in heterosexuals, showing that HIV-1 has spread from the high-risk populations to the general populations in Hebei, China. In addition, CRF01_AE instead of subtype B has become the major strain of HIV-1 infection among homosexuals. Our study revealed HIV-1 evolution and genotype distribution by investigating newly diagnosed HIV-1 individuals in Hebei, China. This study provides important information to enhance the strategic plan for HIV prevention and control in China.

  12. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  13. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species

    DEFF Research Database (Denmark)

    Maroso, F.; Hillen, J E J; Pardo, B. G.

    2018-01-01

    ; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use...... a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples...... of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select...

  14. Development of a genotyping microarray for Usher syndrome.

    Science.gov (United States)

    Cremers, Frans P M; Kimberling, William J; Külm, Maigi; de Brouwer, Arjan P; van Wijk, Erwin; te Brinke, Heleen; Cremers, Cor W R J; Hoefsloot, Lies H; Banfi, Sandro; Simonelli, Francesca; Fleischhauer, Johannes C; Berger, Wolfgang; Kelley, Phil M; Haralambous, Elene; Bitner-Glindzicz, Maria; Webster, Andrew R; Saihan, Zubin; De Baere, Elfride; Leroy, Bart P; Silvestri, Giuliana; McKay, Gareth J; Koenekoop, Robert K; Millan, Jose M; Rosenberg, Thomas; Joensuu, Tarja; Sankila, Eeva-Marja; Weil, Dominique; Weston, Mike D; Wissinger, Bernd; Kremer, Hannie

    2007-02-01

    Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons. To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele-specific oligonucleotides corresponding to all 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of >98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.

  15. High prevalence of ACE DD genotype among north Indian end stage renal disease patients

    Directory of Open Access Journals (Sweden)

    Pandirikkal Baburajan Vinod

    2006-10-01

    Full Text Available Abstract Background The Renin-Angiotensin system (RAS is a key regulator of both blood pressure and kidney functions and their interaction. In such a situation, genetic variability in the genes of different components of RAS is likely to contribute for its heterogeneous association in the renal disease patients. Angiotensin converting enzyme-1 (ACE-1 is an important component of RAS which determines the vasoactive peptide Angiotensin-II. Methods In the present study, we have investigated 127 ESRD patients and 150 normal healthy controls from north India to deduce the association between ACE gene polymorphism and ESRD. The inclusion criteria for patients included a constantly elevated serum creatinine level above normal range (ranging from 3.4 to 15.8 and further the patients were recommended for renal transplantation. A total of 150 normal healthy controls were also genotyped for ACE I/D polymorphism. The criterion of defining control sample as normal was totally based on the absence of any kidney disease determined from the serum creatinin level. Genotyping of ACE I/D were assayed by polymerase chain reaction (PCR based DNA amplification using specific flanking primers Based on the method described elsewhere. Results The difference of DD and II genotypes was found highly significant among the two groups (p = 0.025; OR = 3.524; 95%CI = 1.54-8.07. The combined genotype DD v/s ID+II comparison validated that DD genotype is a high risk genotype for ESRD (p = 0.001; OR = 5.74; 95%CI limit = 3.4-8.5. However, no correlation was obtained for different biochemical parameters of lipid profile and renal function among DD and non DD genotype. Interestingly, ~87% of the DD ESRD patients were found hypertensive in comparison to the 65% patients of non DD genotype Conclusion Based on these observations we conclude that ACE DD genotype implicate a strong possible role in the hypertensive state and in renal damage among north Indians. The study will help in

  16. Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas

    OpenAIRE

    Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

    2017-01-01

    In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenu...

  17. Evaluation of High Resolution Melting for MTHFR C677T Genotyping in Congenital Heart Disease.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available High resolution melting (HRM is a simple, flexible and low-cost mutation screening technique. The methylenetetrahydrofolate reductase (MTHFR gene encoding a critical enzyme, potentially affects susceptibility to some congenital defects like congenital heart disease (CHD. We evaluate the performance of HRM for genotyping of the MTHFR gene C677T locus in CHD cases and healthy controls of Chinese Han population.A total of 315 blood samples from 147 CHD patients (male72, female 75 and 168 healthy controls (male 92, female 76 were enrolled in the study. HRM was utilized to genotype MTHFR C677T locus of all the samples. The results were compared to that of PCR-RFLP and Sanger sequencing. The association of the MTHFR C677T genotypes and the risk of CHD was analyzed using odds ratio with their 95% confidence interval (CIs from unconditional logistic regression.All the samples were successfully genotyped by HRM within 1 hour and 30 minutes while at least 6 hours were needed for PCR-RFLP and sequencing. The genotypes of MTHFR C677T CC, CT, and TT were 9.52%, 49.66%, and 40.82% in CHD group but 29.17%, 50% and 20.83% in control group, which were identical using both methods of HRM and PCR-RFLP, demonstrating the sensitivity and specificity of HRM were all 100%.MTHFR C677T is a potential risk factor for CHD in our local residents of Shandong province in China. HRM is a fast, sensitive, specific and reliable method for clinical application of genotyping.

  18. Petroleum refining industry in China

    International Nuclear Information System (INIS)

    Walls, W.D.

    2010-01-01

    The oil refining industry in China has faced rapid growth in oil imports of increasingly sour grades of crude with which to satisfy growing domestic demand for a slate of lighter and cleaner finished products sold at subsidized prices. At the same time, the world petroleum refining industry has been moving from one that serves primarily local and regional markets to one that serves global markets for finished products, as world refining capacity utilization has increased. Globally, refined product markets are likely to experience continued globalization until refining investments significantly expand capacity in key demand regions. We survey the oil refining industry in China in the context of the world market for heterogeneous crude oils and growing world trade in refined petroleum products. (author)

  19. Heterogeneity and differentiation: the end for the Third World??

    Science.gov (United States)

    Abdalla, I

    1978-01-01

    Dependence, with all its corollaries, is the common denominator of Third World countries. Comprehensive decolonization is the only way out. New categories and classifications, i.e., OPEC countries and NICs (Newly Industrialized Countries), fall short of destroying the fundamental community of condition and goal. China is not a Third World country. The case for heterogeneity of Third World countries is a faulty one. The average per capita GNP of the higher income group in 1975 was $1,270.00 against $142.70 for the lower income group, 8.9 times lower. Among OECD countries, Switzerland's per capita is 9.3 times Turkey's, yet no one speaks of heterogeneity within OECD. Development can, and should, proceed according to the conditions of each nation, but differences cannot and should not overshadow the commonality of interests in the Third World.

  20. Corporate Governance During Market Transition: Heterogeneous responses to institutional tensions in China

    NARCIS (Netherlands)

    P-O. Legault Tremblay (Pierre-Olivier)

    2015-01-01

    textabstractCorporate governance in transition economies does not fit in the dominant normative models. China embodies institutional tensions between an inherited system of political governance and new laws transplanted from Western countries that empower external shareholders on capital markets.

  1. Association of vitamin D receptor gene polymorphisms with diabetic dyslipidemia in the elderly male population in North China

    Directory of Open Access Journals (Sweden)

    Xia Z

    2017-10-01

    Full Text Available Zheng Xia,1,* Yazhuo Hu,1,* Zhitao Han,1 Ya Gao,1 Jie Bai,2 Yao He,1 Hua Zhao,3 Honghong Zhang1 1Institute of Geriatrics, Beijing Key Laboratory of Normal Aging and Geriatrics, 2Cinical Laboratory in South Building, Chinese PLA General Hospital & Chinese PLA Medical Academy, Beijing, China; 3Zhantansi Outpatient Department, Chinese PLA 309 Hospital, Beijing, China *These authors contributed equally to this work Background: The prevalence of dyslipidemia is rising alarmingly in elderly Han Chinese male patients with type 2 diabetes mellitus (T2DM. The genetic factors that contribute to the development of diabetic dyslipidemia remain incompletely identified. This study was conducted to assess the association between vitamin D receptor (VDR polymorphisms and development of dyslipidemia in the Han elderly male population with T2DM in North China.Methods: A total of 242 T2DM patients with dyslipidemia (DH group, n=108 or without dyslipidemia (DO group, n=134 and 100 controls were genotyped for ApaI, TaqI and FokI single nucleotide polymorphisms (SNPs of the VDR gene using polymerase chain reaction-restriction fragment length polymorphism and sequencing. The frequency and distribution of the SNPs were compared between cases and controls.Results: The distribution of genotypes of VDR-FokI was significantly different between the control and DM group (P=0.033, as well as between the control and DH subgroup (P=0.011 but not DO subgroup (P=0.111. The frequency of C allele and CC genotype of FokI was significantly higher in the DH patients than in the controls (P=0.015 and P=0.003, respectively. Logistic regression analysis in a dominant model homozygous for the C allele of the FokI SNP showed that CC genotype was associated with DH patients (OR =1.797, 95% CI: 1.077–2.999, P=0.025. Significant associations of the ApaI and TaqI SNPs with either DO or DH subjects were not observed.Conclusion: These findings suggest that CC genotype of VDR-FokI is a risk

  2. HIV-1 molecular epidemiology among newly diagnosed HIV-1 individuals in Hebei, a low HIV prevalence province in China.

    Science.gov (United States)

    Lu, Xinli; Kang, Xianjiang; Liu, Yongjian; Cui, Ze; Guo, Wei; Zhao, Cuiying; Li, Yan; Chen, Suliang; Li, Jingyun; Zhang, Yuqi; Zhao, Hongru

    2017-01-01

    New human immunodeficiency virus type 1 (HIV-1) diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals. The four main genotypes were circulating recombinant form (CRF)01_AE (53.4%), CRF07_BC (23.4%), subtype B (15.9%), and unique recombinant forms URFs (4.9%). Within 1 year, three new genotypes (subtype A1, CRF55_01B, CRF65_cpx), unknown before in Hebei, were first found among men who have sex with men (MSM). All nine genotypes were identified in the sexually contracted HIV-1 population. Among 30 URFs, six recombinant patterns were revealed, including CRF01_AE/BC (40.0%), CRF01_AE/B (23.3%), B/C (16.7%), CRF01_AE/C (13.3%), CRF01_AE/B/A2 (3.3%) and CRF01_AE/BC/A2 (3.3%), plus two potential CRFs. This study elucidated the complicated characteristics of HIV-1 molecular epidemiology in a low HIV-1 prevalence northern province of China and revealed the high level of HIV-1 genetic diversity. All nine HIV-1 genotypes circulating in Hebei have spread out of their initial risk groups into the general population through sexual contact, especially through MSM. This highlights the urgency of HIV prevention and control in China.

  3. HIV-1 molecular epidemiology among newly diagnosed HIV-1 individuals in Hebei, a low HIV prevalence province in China.

    Directory of Open Access Journals (Sweden)

    Xinli Lu

    Full Text Available New human immunodeficiency virus type 1 (HIV-1 diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals. The four main genotypes were circulating recombinant form (CRF01_AE (53.4%, CRF07_BC (23.4%, subtype B (15.9%, and unique recombinant forms URFs (4.9%. Within 1 year, three new genotypes (subtype A1, CRF55_01B, CRF65_cpx, unknown before in Hebei, were first found among men who have sex with men (MSM. All nine genotypes were identified in the sexually contracted HIV-1 population. Among 30 URFs, six recombinant patterns were revealed, including CRF01_AE/BC (40.0%, CRF01_AE/B (23.3%, B/C (16.7%, CRF01_AE/C (13.3%, CRF01_AE/B/A2 (3.3% and CRF01_AE/BC/A2 (3.3%, plus two potential CRFs. This study elucidated the complicated characteristics of HIV-1 molecular epidemiology in a low HIV-1 prevalence northern province of China and revealed the high level of HIV-1 genetic diversity. All nine HIV-1 genotypes circulating in Hebei have spread out of their initial risk groups into the general population through sexual contact, especially through MSM. This highlights the urgency of HIV prevention and control in China.

  4. Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.

    Science.gov (United States)

    Ravago-Gotanco, Rachel; de la Cruz, Talna Lorena; Pante, Ma Josefa; Borsa, Philippe

    2018-01-01

    The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

  5. Hepatitis E virus infection in central China reveals no evidence of cross-species transmission between human and swine in this area.

    Directory of Open Access Journals (Sweden)

    Wen Zhang

    Full Text Available Hepatitis E virus (HEV is a zoonotic pathogen of which several species of animal were reported as reservoirs. Swine stands out as the major reservoir for HEV infection in humans, as suggested by the close genetic relationship of swine and human virus. Since 2000, Genotype 4 HEV has become the dominant cause of hepatitis E disease in China. Recent reports showed that genotype 4 HEV is freely transmitted between humans and swine in eastern and southern China. However, the infection status of HEV in human and swine populations in central China is still unclear. This study was conducted in a rural area of central China, where there are many commercial swine farms. A total of 1476 serum and 554 fecal specimens were collected from the general human and swine populations in this area, respectively. The seroepidemiological study was conducted by enzyme-linked immunosorbent assay. Conserved genomic sequences of open reading frame 2 were detected using reverse transcription-PCR. The results indicated that the overall viral burden of the general human subjects was 0.95% (14/1476, while 7.0% (39/554 of the swine excreted HEV in stool. The positive rate of anti-HEV IgG and IgM in the serum samples was 7.9% (117/1476 and 1.6% (24/1476, respectively. Phylogenetic analysis based on the 150 nt partial sequence of the capsid protein gene showed that the 53 swine and human HEV isolates in the current study all belonged to genotype 4, clustering into three major groups. However, the HEV isolates prevalent in the human and swine populations were classified into known distinct subgenotypes, which suggested that no cross-species transmission between swine and humans had taken place in this area. This result was confirmed by cloning and phylogenetic analysis of the complete capsid protein gene sequence of three representative HEV strains in the three major groups. The cross reactivity between anti-HEV IgG from human sera and the two representative strains from swine in

  6. Serological and molecular epidemiology of Japanese encephalitis virus infections in swine herds in China, 2006-2012.

    Science.gov (United States)

    Chai, Chunxia; Wang, Qiao; Cao, Sanjie; Zhao, Qin; Wen, Yiping; Huang, Xiaobo; Wen, Xintian; Yan, Qiguai; Ma, Xiaoping; Wu, Rui

    2018-01-31

    Japanese encephalitis virus (JEV) is a mosquito-borne, zoonotic flavivirus causing viral encephalitis in humans and reproductive disorder in swine. JEV is prevalent throughout China in human; however, spatiotemporal analysis of JEV in Chinese swine herds has not been reported previously. Herein, we present serological and molecular epidemiological results and estimates of prevalence of JEV infections among swine herds in various regions of China. The results suggest that JEV infections are widespread and genotype I and III strains co-exist in the same regions. Therefore, there is an urgent need to monitor JEV infection status among swine herds in China.

  7. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  8. Individual and Joint Associations of Methylenetetrahydrofolate Reductase C677T Genotype and Plasma Homocysteine With Dyslipidemia in a Chinese Population With Hypertension.

    Science.gov (United States)

    Liu, Yanhong; Li, Kang; Venners, Scott A; Hsu, Yi-Hsiang; Jiang, Shanqun; Weinstock, Justin; Wang, Binyan; Tang, Genfu; Xu, Xiping

    2017-04-01

    We aimed to examine the cross-sectional associations of plasma total homocysteine (tHcy) concentrations and methylenetetrahydrofolate reductase ( MTHFR) C677T genotype with dyslipidemia. A total of 231 patients with mild-to-moderate essential hypertension were enrolled from the Huoqiu and Yuexi communities in Anhui Province, China. Plasma tHcy levels were measured by high-performance liquid chromatography. Genotyping was performed by TaqMan allelic discrimination technique. Compared with MTHFR 677 CC + CT genotype carriers, TT genotype carriers had higher odds of hypercholesterolemia (adjusted odds ratio [OR] [95% confidence interval (CI)]: 2.7 [1.4-5.2]; P = .004) and higher odds of abnormal low-density lipoprotein cholesterol (adjusted OR [95% CI]: 2.3 [1.1-4.8]; P = .030). The individuals with the TT genotype had higher concentrations of log(tHcy) than those with the 677 CC + CT genotype (adjusted β [standard error]: .2 [0.03]; P dyslipidemia in Chinese patients with essential hypertension. Further studies are needed to confirm the role of tHcy and the MTHFR C677T mutation in the development of dyslipidemia in a larger sample.

  9. Primary surveys on molecular epidemiology of bovine viral diarrhea virus 1 infecting goats in Jiangsu province, China.

    Science.gov (United States)

    Mao, Li; Li, Wenliang; Yang, Leilei; Wang, Jianhui; Cheng, Suping; Wei, Yong; Wang, Qiusheng; Zhang, Wenwen; Hao, Fei; Ding, Yonglong; Sun, Yinhua; Jiang, Jieyuan

    2016-09-05

    Bovine viral diarrhea virus (BVDV) is a pathogen of domestic and wildlife animals worldwide and is associated with several diseases. In China, there are many reports about genotyping of BVDV strains originated from cattle and pigs, and some of them focused on the geographical distributions of BVDV. Currently, the goat industry in Jiangsu province of China is under going a rapid expansion. Most of these goat farms are backyard enterprises and in close proximity to pig and cattle farms. However, there was very limited information about BVDV infections in goats. The objective of this study was to assess the frequency of BVDV infections of goats, the relationship of these infections to clinical signs and determine what BVDV genotypes are circulating in Jiangsu province. From 236 goat sera collected from six regions in Jiangsu province between 2011 and 2013, BVDV-1 was identified in 29 samples from the five regions by RT-PCR. The BVDV-1 infections occurred with/without clinical signs. Eight different BVDV-1 strains were identified from these positive samples based on the 5'-untranslated region (5'-UTR) sequences, and further clustered into four BVDV-1 subtypes on the phylogenetic analysis. Three were BVDV-1b, two BVDV-1m, two BVDV-1o, and one BVDV-1p, respectively. To our knowledge, this is the first report to investigate the occurrence of BVDV and the genotypes of BVDV infecting goats in China. The results indicated that BVDV-1 infections were indeed present and the viruses were with genetic variations in Chinese goat herds. The information would be very useful for prevention and control of BVDV-1 infections in China.

  10. Detection of human enterovirus 71 and coxsackievirus A16 in children with hand, foot and mouth disease in China.

    Science.gov (United States)

    Chen, Ling; Mou, Xiaozhou; Zhang, Qiong; Li, Yifei; Lin, Jian; Liu, Fanlong; Yuan, Li; Tang, Yiming; Xiang, Charlie

    2012-04-01

    The aims of the present study were to investigate the genetic characteristics of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) strains in China and to evaluate the relationship between the genotypes of CVA16 and EV71 and their geographical distribution. A total of 399 stool specimens were collected from children with symptoms of hand, foot and mouth disease (HFMD) in Zhejiang Province. The presence of enteroviruses was determined using reverse transcription-semi-nested PCR targeted to the VP1 gene of all human enteroviruses and DNA sequencing. EV71 and CVA16, the major etiological agents of HFMD, were detected in 38.4% (38/99) and 35.4% (35/99) of HEV-A species-positive cases, respectively. Based on the phylogenetic analysis of the VP1 gene, EV71 strains identified in this study belong to subgenotype C4, and CVA16 strains herein were classified into clusters B2a and B2b within the genotype B2. Taking into consideration other published data, we conclude that the genetic characteristics of enteroviruses in China reflect the pattern of the endemic circulation of the subgenotype C4 to EV71 and clusters B2a and B2b within genotype B2 to CVA16, which have been continuously circulating in China since 1997. This observation indicates that the genetic characteristics of enteroviruses in China seem to depend on their special geographical and climatical features allowing them to be sustained with little external effect.

  11. Current situation and challenge of registry in China.

    Science.gov (United States)

    Zhang, Yang; Feng, Yuji; Qu, Zhi; Qi, Yali; Zhan, Siyan

    2014-09-01

    Increasing emphasis has been placed on registries for an organized system used in developing clinical research to improve health care. China has sufficient data that can be applied broadly, but the heterogeneity and irregularity of registries limit their applicability. This article aims to describe the status of registries in China and the related challenges. Patient registries for observational studies were retrieved from the International Clinical Trials Registry to quantitatively evaluate the number of comparatively high-quality registries in China. A literature search was also performed to provide support and updates. A total of 64 patient registries were retrieved from ClinicalTrials.gov using disease, product, and health service as criteria. The sample sizes ranged from 15 to 30,400, with only 12 registries marked as completed. This article describes and compares the detailed information in many aspects. The efficient use of registries has already made considerable progress in China; however, registries still require standardization, high-quality transition, and coordinated development.

  12. Genotypic and geographical distribution of porcine reproductive and respiratory syndrome viruses in mainland China in 1996-2016.

    Science.gov (United States)

    Gao, Jia-Cong; Xiong, Jun-Yao; Ye, Chao; Chang, Xiao-Bo; Guo, Jin-Chao; Jiang, Cheng-Gang; Zhang, Gui-Hong; Tian, Zhi-Jun; Cai, Xue-Hui; Tong, Guang-Zhi; An, Tong-Qing

    2017-09-01

    Porcine reproductive and respiratory syndrome (PRRS) has caused huge economic losses to Chinese swine industry and remains a major threat since it was first reported in 1996. However, investigations of molecular epidemiological and genetic diversity of PRRS viruses (PRRSVs) in China were limited to a small number of representative strains collected in several areas. Moreover, lineage classifications reported by individual researchers were quite different. In the present study, we sequenced ORF5 sequences of 217 PRRSVs from clinical samples, retrieved all the available ORF5 sequences of PRRSVs isolated in China in 1996-2016 (n=2213) from GenBank, and systematically analyzed corresponding epidemiological data. NA-type PRRSVs in China were classified into five lineages: lineage 1, lineage 3, lineage 5, lineage 8, and lineage 9. Most strains in China belonged to lineage 8 (85.6%), with dominant strains being classified as sublineage 8.3 (78.3%). Importantly, the emerging lineage 1 and lineage 3 strains spread rapidly, and their proportions among circulating PRRSVs have significantly increased in recent years. The geographical distribution of different PRRSV lineages in each province was analyzed and possible inter-province transmission routes were outlined for main lineages and sublineages. To our knowledge, this study is the most comprehensive and extensive phylogeographical analysis of PRRSVs in China since PRRS outbreak in 1996. Our dataset can serve as a canonical standard for PRRSV classification and will help to study genetic evolution of PRRSV. The results of the present study may also improve prevention of PRRS in China. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Genotypic and Phenotypic Markers of Livestock-Associated Methicillin-Resistant Staphylococcus aureus CC9 in Humans

    OpenAIRE

    Ye, Xiaohua; Wang, Xiaolin; Fan, Yanping; Peng, Yang; Li, Ling; Li, Shunming; Huang, Jingya; Yao, Zhenjiang; Chen, Sidong

    2016-01-01

    Use of antimicrobials in industrial food animal production is associated with the presence of multidrug-resistant Staphylococcus aureus among animals and humans. The livestock-associated (LA) methicillin-resistant S. aureus (MRSA) clonal complex 9 (CC9) is associated with animals and related workers in Asia. This study aimed to explore the genotypic and phenotypic markers of LA-MRSA CC9 in humans. We conducted a cross-sectional study of livestock workers and controls in Guangdong, China. The ...

  14. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

    Science.gov (United States)

    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

    2018-05-01

    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Regional energy efficiency, carbon emission performance and technology gaps in China: A meta-frontier non-radial directional distance function analysis

    International Nuclear Information System (INIS)

    Yao, Xin; Zhou, Hongchen; Zhang, Aizhen; Li, Aijun

    2015-01-01

    At present, China is the largest primary energy consumer and carbon emitter in the world. Meantime, China is a large transitional economy with significant regional gaps. Against such backgrounds, the calculated results of energy and carbon performance indicators may be biased, without considering heterogeneity across regions. To this end, after incorporating region-heterogeneity, this paper provides detailed information, regarding energy efficiency, carbon emission performance and the potential of carbon emission reductions from regional perspectives, which may be important and useful for policy makers. Our main findings are as follows. Firstly, there is significant group-heterogeneity across regions in China, in terms of energy efficiency and carbon emission performance. Secondly, there are no considerable differences between total-factor and single-factor performance indices, since there is limited substitutability between energy inputs and other production inputs. Finally, significant carbon emission reductions can be made by “catching up” for regions with low energy efficiency and carbon emission performance. Looking ahead, the Chinese government should adopt measures to promote improvements in terms of energy efficiency and carbon emission performance in the short term. -- Highlights: •We adopt a meta-frontier non-radial directional distance function analysis. •We provide detailed information regarding energy and carbon emission performance. •We find that there is significant region-heterogeneity in China. •There are no large differences between total- and single-factor performance indices. •It can make great contributions to carbon emission reductions by “catching up”

  16. Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China.

    Science.gov (United States)

    Gao, San-Ji; Lin, Yi-Hua; Pan, Yong-Bao; Damaj, Mona B; Wang, Qin-Nan; Mirkov, T Erik; Chen, Ru-Kai

    2012-10-01

    Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family.

  17. Development of a genotyping microarray for Usher syndrome

    Science.gov (United States)

    Cremers, Frans P M; Kimberling, William J; Külm, Maigi; de Brouwer, Arjan P; van Wijk, Erwin; te Brinke, Heleen; Cremers, Cor W R J; Hoefsloot, Lies H; Banfi, Sandro; Simonelli, Francesca; Fleischhauer, Johannes C; Berger, Wolfgang; Kelley, Phil M; Haralambous, Elene; Bitner‐Glindzicz, Maria; Webster, Andrew R; Saihan, Zubin; De Baere, Elfride; Leroy, Bart P; Silvestri, Giuliana; McKay, Gareth J; Koenekoop, Robert K; Millan, Jose M; Rosenberg, Thomas; Joensuu, Tarja; Sankila, Eeva‐Marja; Weil, Dominique; Weston, Mike D; Wissinger, Bernd; Kremer, Hannie

    2007-01-01

    Background Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein‐coding exons. Methods: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele‐specific oligonucleotides corresponding to all 298 Usher syndrome‐associated sequence variants known to date, 76 of which are novel, were arrayed. Results Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of >98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. Conclusion The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first‐pass screening tool. PMID:16963483

  18. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

    Science.gov (United States)

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

    2015-01-01

    The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

  19. Selection and Evaluation of Maize Genotypes Tolerance to Low Phosphorus Soils

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J. C.; Jiang, H. M.; Zhang, J. F.; Li, L. L.; Li, G. H. [Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing (China)

    2013-11-15

    Maize species differ in their ability to take up phosphorus (P) from the soil, and these differences are attributed to the morphology and physiology of plants relative to their germplasm base. An effective method of increasing P efficiency in maize is to select and evaluate genotypes that can produce a high yield under P deficient conditions. In this study, 116 maize inbred lines with various genetic backgrounds collected from several Agricultural Universities and Institutes in China were evaluated in a field experiment to identify genotypic differences in P efficiency in 2007. Overall, 15 maize inbred lines were selected from the 116 inbred lines during the 5-year field experimental period based on their 100-grain weight in P-deficient soil at maturity, when compared to the characteristics exhibited in P-sufficient soil. All of the selected lines were evaluated in field experiments from 2008 to 2010 for their tolerance to low-P at the seedling and maturity stages. Inhibition (%) was used and defined as the parameter measured under P limitation compared to the parameters measured under P sufficiency to evaluate the genotypic variation in tolerance. Inhibition of root length, root surface area, volume, root: shoot ratio and P uptake efficiency could be used as indices to assess the genotypic tolerance to P limitation. Low-P tolerant genotypes could uptake more P and accumulate more dry matter at the seedling stage. A strong relationship between the total biomass and root length was exhibited. In order to understand the mechanisms of the genotypic tolerance to low-P soil to utilize P from the sparing soluble P forms, 5 maize genotypes selected out of the 15 maize inbred lines, according to the four quadrant distribution, was used as the criteria in a {sup 32}P isotope tracer experiment to follow the recovery of {sup 32}P in soil P fractions. The {sup 32}P tracer results showed a higher rate for water- soluble P transformation to slowly available P in P deficient soil

  20. [Association of leptin receptor gene polymorphrism with metabolic syndrome in older Han adults from major cities in China].

    Science.gov (United States)

    Wu, Jinghuan; Zhuo, Qin; Chen, Xi; Tian, Yuan; Piao, Jianhua; Yang, Xiaoguang

    2016-05-01

    To investigate the relationship of leptin receptor gene rs1137100 and rs1137101 single nucleotide polymorphrism (SNP) with metabolic syndrome (MS) in older Han adults from major cities in China. A total of 2082 older Han adults were selected from 18 major cities including 15 provinces/municipalities of China National Nutrition and Health Survey in 2002. According to the MS definition proposed by Joint Interim Statement (JIS), the subjects were divided into MS and control groups. Plasma leptin and insulin levels were measured. The genotypes of rs1137100 and rs1137101 were detected by Taqman method. Association of genotypes of leptin receptor gene SNPs with MS was investigated. The MS group showed higher body mass index (BMI), waist circumference, fasting serum glucose, systolic blood pressure (SBP) and diastolic blood pressure (DBP), triglycerides (TG), serum total cholesterol (TC), insulin, homeostasis model of assessment for insulin resistence index (HOMA-IR) and leptin levels than those of control individuals, while the high density lipoprotein cholesterol (HDL-c) was significantly lower than the control group. The, GG, AA, GA genotypes distribution and the A allele frequency of rs1137100 and rs1137101 were similar between the two groups. The DBP and SBP level were obviously higher in AA genotype. The HDL-c concentration Was significantly lower in AA and GA + AA genotype. The AA and GA genotypes carriers in rs1137100 had similar risk for MS when comparing with the GG genotypes, and the OR values were 1.23 (95% CI 0.90-1.67) and 2.23 (95% CI 0.83-6.44), respectively. The AA and GA genotypes carriers in rs1137101 had similar risk for MS when comparing with the GG genotypes, and the OR values were 1.23 (95% CI 0.90-1.67) and 2.23 (95% CI 0.83-6.44), respectively. Leptin receptor genes rs1137100 and rs1137101 are not associated with pathogenesis of MS in older Han adults, but it may relate with hypertension or lipid abnormality.

  1. Genotyping and pathobiologic characterization of canine parvovirus circulating in Nanjing, China.

    Science.gov (United States)

    Zhao, Yanbing; Lin, Yan; Zeng, Xujian; Lu, Chengping; Hou, Jiafa

    2013-08-29

    Canine parvovirus (CPV) is an important pathogen that causes acute enteric disease in dogs. It has mutated and spread throughout the world in dog populations. We provide an update on the molecular characterization of CPV that circulated in Nanjing, a provincial capital in China between 2009 and 2012. Seventy rectal swab samples were collected from the dogs diagnosed with CPV infection in 8 animal hospitals of Nanjing. Sequence analysis of VP2 genes of 31 samples revealed that 29 viral strains belonged to CPV-2a subtype, while other two strains were classified into CPV-2b. To investigate the pathogenicity of the prevalent virus, we isolated CPV-2a and performed the animal experiment. Nine beagles were inoculated with 105.86 of 50% tissue culture infectious doses (TCID50) of the virus. All the experimentally infected beagles exhibited mild to moderate mucoid or watery diarrhea on day 4 post-infection (p.i.). On day 9 p.i., characteristic histopathological lesions were clearly observed in multiple organs of infected dogs, including liver, spleen, kidney, brain and all segments of the small and large intestines, while viral DNA and antigen staining could be detected in the sampled tissues. It is notable that canine parvovirus was isolated in one from two brain samples processed. Our results indicated that CPV-2a is the predominant subtype in Nanjing of China. And this virus caused extensive lesions in a variety of tissues, including the brain.

  2. Toxoplasma gondii, Dirofilaria immitis, feline immunodeficiency virus (FIV), and feline leukemia virus (FeLV) infections in stray and pet cats (Felis catus) in northwest China: co-infections and risk factors.

    Science.gov (United States)

    Cong, Wei; Meng, Qing-Feng; Blaga, Radu; Villena, Isabelle; Zhu, Xing-Quan; Qian, Ai-Dong

    2016-01-01

    This study was conducted to estimate the prevalence of Toxoplasma gondii, Dirofilaria immitis, feline immunodeficiency virus (FIV), and feline leukemia virus (FeLV) infections among stray and pet cats in Lanzhou, northwest China, and to identify the influence of age, gender, and regions on seropositivity. T. gondii antibodies were examined in cat sera by the modified agglutination test (MAT). The circulating antigens of D. immitis and FeLV and specific antibodies to FIV were examined using kits commercially available. The overall prevalence of T. gondii, FIV, FeLV, and D. immitis was 19.34, 9.12, 11.33, and 3.04 %, respectively. For the genetic characterization of T. gondii genotypes in cats, genomic DNA was extracted from the seropositive cats and the T. gondii B1 gene was amplified using a semi-nested PCR. DNA samples giving positive B1 amplification were then genotyped using multilocus PCR-RFLP. Two T. gondii genotypes (ToxoDB#9 and ToxoDB#1) were identified. Results of the multivariate logistic regression analysis showed that older cats are more likely to be seropositive than juveniles for T. gondii, FIV, FeLV, and D. immitis. This is the first report of T. gondii genotypes in cats in northwest China. Moreover, the present study is the first study of retrovirus and D. immitis seroprevalence in cats in China. The results revealed that T. gondii, FIV, and FeLV infections are common in stray and pet cats in northwest China.

  3. Serological and molecular epidemiology of Japanese encephalitis virus infections in swine herds in China, 2006–2012

    Science.gov (United States)

    Chai, Chunxia; Wang, Qiao; Cao, Sanjie; Zhao, Qin; Wen, Yiping; Huang, Xiaobo; Wen, Xintian; Yan, Qiguai; Ma, Xiaoping

    2018-01-01

    Japanese encephalitis virus (JEV) is a mosquito-borne, zoonotic flavivirus causing viral encephalitis in humans and reproductive disorder in swine. JEV is prevalent throughout China in human; however, spatiotemporal analysis of JEV in Chinese swine herds has not been reported previously. Herein, we present serological and molecular epidemiological results and estimates of prevalence of JEV infections among swine herds in various regions of China. The results suggest that JEV infections are widespread and genotype I and III strains co-exist in the same regions. Therefore, there is an urgent need to monitor JEV infection status among swine herds in China. PMID:28693301

  4. Identification and Characterization of Chlamydia abortus Isolates from Yaks in Qinghai, China

    Directory of Open Access Journals (Sweden)

    Zhaocai Li

    2015-01-01

    Full Text Available Recently, the yak population has exhibited reproductive disorders, which are considered to be associated with Chlamydia abortus (C. abortus in Qinghai, China. In this study, a total of 9 aborted fetuses (each from a different herd and 126 vaginal swab samples from the 9 herds were collected and analyzed. C. abortus DNA was detected from all of the 9 aborted fetuses and 30 of the 126 vaginal swab samples (23.81% from yak cows in the selected herds. Four C. abortus strains were isolated from embryonated egg yolk sacs inoculated with foetal organ suspensions. The isolated C. abortus strains were further identified, which showed identical restriction profiles with the C. abortus reference strain using AluI restriction enzyme in the RFLP test. Moreover, the isolated C. abortus strains and C. abortus-positive vaginal swab samples were genotyped by multiple loci variable number tandem repeat analysis and all belonged to the genotype 2 group. These findings suggested that C. abortus played a substantial role in yak abortion in Qinghai, China.

  5. Identification and characterization of Chlamydia abortus isolates from yaks in Qinghai, China.

    Science.gov (United States)

    Li, Zhaocai; Cao, Xiaoan; Fu, Baoquan; Chao, Yilin; Cai, Jinshan; Zhou, Jizhang

    2015-01-01

    Recently, the yak population has exhibited reproductive disorders, which are considered to be associated with Chlamydia abortus (C. abortus) in Qinghai, China. In this study, a total of 9 aborted fetuses (each from a different herd) and 126 vaginal swab samples from the 9 herds were collected and analyzed. C. abortus DNA was detected from all of the 9 aborted fetuses and 30 of the 126 vaginal swab samples (23.81%) from yak cows in the selected herds. Four C. abortus strains were isolated from embryonated egg yolk sacs inoculated with foetal organ suspensions. The isolated C. abortus strains were further identified, which showed identical restriction profiles with the C. abortus reference strain using AluI restriction enzyme in the RFLP test. Moreover, the isolated C. abortus strains and C. abortus-positive vaginal swab samples were genotyped by multiple loci variable number tandem repeat analysis and all belonged to the genotype 2 group. These findings suggested that C. abortus played a substantial role in yak abortion in Qinghai, China.

  6. Spatiotemporal pattern of bacillary dysentery in China from 1990 to 2009: what is the driver behind?

    Directory of Open Access Journals (Sweden)

    Zhiwei Xu

    Full Text Available Little is known about the spatiotemporal pattern of bacillary dysentery (BD in China. This study assessed the geographic distribution and seasonality of BD in China over the past two decades.Data on monthly BD cases in 31 provinces of China from January 1990 to December 2009 obtained from Chinese Center for Disease Control and Prevention, and data on demographic and geographic factors, as well as climatic factors, were compiled. The spatial distributions of BD in the four periods across different provinces were mapped, and heat maps were created to present the seasonality of BD by geography. A cosinor function combined with Poisson regression was used to quantify the seasonal parameters of BD, and a regression analysis was conducted to identify the potential drivers of morbidity and seasonality of BD.Although most regions of China have experienced considerable declines in BD morbidity over the past two decades, Beijing and Ningxia still had high BD morbidity in 2009. BD morbidity decreased more slowly in North-west China than other regions. BD in China mainly peaked from July to September, with heterogeneity in peak time between regions. Relative humidity was associated with BD morbidity and peak time, and latitude was the major predictor of BD amplitude.The transmission of BD was heterogeneous in China. Improved sanitation and hygiene in North-west China, and better access to clean water and food in the big floating population in some metropolises could be the focus of future preventive interventions against BD. BD control efforts should put more emphasis on those dry areas in summer.

  7. Phenotype heterogeneity in cancer cell populations

    International Nuclear Information System (INIS)

    Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean; Escargueil, Alexandre; Lorenzi, Tommaso; Lorz, Alexander; Trélat, Emmanuel

    2016-01-01

    Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as “bet hedging” of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to

  8. Phenotype heterogeneity in cancer cell populations

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Luis [CNRS UMR 7598, LJLL, & INRIA MAMBA team, Sorbonne Universités, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, luis@ann.jussieu.fr (France); Chisholm, Rebecca [School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, rebecca.chisholm@gmail.com (Australia); Clairambault, Jean [INRIA MAMBA team & LJLL, UMR 7598, Sorbonne Universités, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, jean.clairambault@inria.fr, Corresponding author (France); Escargueil, Alexandre [INSERM “Cancer Biology and Therapeutics”, Sorbonne Universités, UPMC Univ Paris 06, UMR-S 938, CDR St Antoine, Hôpital St Antoine, 184 Fbg. St Antoine, 75571 Paris cedex 12, France, alexandre.escargueil@upmc.fr (France); Lorenzi, Tommaso [CMLA, ENS Cachan, 61, Av. du Président Wilson, 94230 Cachan cedex & INRIA MAMBA team, & LJLL, UMR 7598, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, tommaso.lorenzi@gmail.com (France); Lorz, Alexander [Sorbonne Universités, UPMC Univ Paris 06, LJLL, UMR 7598 & INRIA Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, alex.lorz@ann.jussieu.fr (France); Trélat, Emmanuel [Institut Universitaire de France, Sorbonne Universités, UPMC Univ Paris 06, LJLL, UMR 7598, Boîte courrier 187, UPMC Univ Paris 06, 4 Pl. Jussieu, 75252 Paris cedex 05, France, emmanuel.trelat@upmc.fr (France)

    2016-06-08

    Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as “bet hedging” of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to

  9. Phenotype heterogeneity in cancer cell populations

    Science.gov (United States)

    Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean; Escargueil, Alexandre; Lorenzi, Tommaso; Lorz, Alexander; Trélat, Emmanuel

    2016-06-01

    Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as "bet hedging" of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to

  10. Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest.

    Science.gov (United States)

    Xu, Wumei; Ci, Xiuqin; Song, Caiyun; He, Tianhua; Zhang, Wenfu; Li, Qiaoming; Li, Jie

    2016-12-01

    The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty-nine plots of 400 m 2 (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

  11. Genotypic Diversity of Staphylococcus aureus α-Hemolysin Gene (hla and Its Association with Clonal Background: Implications for Vaccine Development.

    Directory of Open Access Journals (Sweden)

    Meng Xiao

    Full Text Available The α-hemolysin, encoded by the hla gene, is a major virulence factor in S. aureus infections. Changes in key amino acid residues of α-hemolysin can result in reduction, or even loss, of toxicity. The aim of this study was to investigate the diversity of the hla gene sequence and the relationship of hla variants to the clonal background of S. aureus isolates. A total of 47 clinical isolates from China were used in this study, supplemented with in silico analysis of 318 well-characterized whole genome sequences from globally distributed isolates. A total of 28 hla genotypes were found, including three unique to isolates from China, 20 found only in the global genomes and five found in both. The hla genotype generally correlated with the clonal background, particularly the multilocus sequence type, but was not related to geographic origin, host source or methicillin-resistance phenotype. In addition, the hla gene showed greater diversity than the seven loci utilized in the MLST scheme for S. aureus. Our investigation has provided genetic data which may be useful for future studies of toxicity, immunogenicity and vaccine development.

  12. Novel mutations and their genotype-phenotype correlations in patients with Noonan syndrome, using next-generation sequencing.

    Science.gov (United States)

    Tafazoli, Alireza; Eshraghi, Peyman; Pantaleoni, Francesca; Vakili, Rahim; Moghaddassian, Morteza; Ghahraman, Martha; Muto, Valentina; Paolacci, Stefano; Golyan, Fatemeh Fardi; Abbaszadegan, Mohammad Reza

    2018-03-01

    Noonan Syndrome (NS) is an autosomal dominant disorder with many variable and heterogeneous conditions. The genetic basis for 20-30% of cases is still unknown. This study evaluates Iranian Noonan patients both clinically and genetically for the first time. Mutational analysis of PTPN11 gene was performed in 15 Iranian patients, using PCR and Sanger sequencing at phase one. Then, as phase two, Next Generation Sequencing (NGS) in the form of targeted resequencing was utilized for analysis of exons from other related genes. Homology modelling for the novel founded mutations was performed as well. The genotype, phenotype correlation was done according to the molecular findings and clinical features. Previously reported mutation (p.N308D) in some patients and a novel mutation (p.D155N) in one of the patients were identified in phase one. After applying NGS methods, known and new variants were found in four patients in other genes, including: CBL (p. V904I), KRAS (p. L53W), SOS1 (p. I1302V), and SOS1 (p. R552G). Structural studies of two deduced novel mutations in related genes revealed deficiencies in the mutated proteins. Following genotype, phenotype correlation, a new pattern of the presence of intellectual disability in two patients was registered. NS shows strong variable expressivity along the high genetic heterogeneity especially in distinct populations and ethnic groups. Also possibly unknown other causative genes may be exist. Obviously, more comprehensive and new technologies like NGS methods are the best choice for detection of molecular defects in patients for genotype, phenotype correlation and disease management. Copyright © 2017 Medical University of Bialystok. Published by Elsevier B.V. All rights reserved.

  13. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  14. Energy consumption-economic growth relationship and carbon dioxide emissions in China

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Li; Dong, Suocheng; Xue, Li; Yang, Quanxi [Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101 (China); Liang [Jinan University, Guangzhou 510632 (China); Wangzhou

    2011-02-15

    This paper applies the panel unit root, heterogeneous panel cointegration and panel-based dynamic OLS to re-investigate the co-movement and relationship between energy consumption and economic growth for 30 provinces in mainland China from 1985 to 2007. The empirical results show that there is a positive long-run cointegrated relationship between real GDP per capita and energy consumption variables. Furthermore, we investigate two cross-regional groups, namely the east China and west China groups, and get more important results and implications. In the long-term, a 1% increase in real GDP per capita increases the consumption of energy by approximately 0.48-0.50% and accordingly increases the carbon dioxide emissions by about 0.41-0.43% in China. The economic growth in east China is energy-dependent to a great extent, and the income elasticity of energy consumption in east China is over 2 times that of the west China. At present, China is subject to tremendous pressures for mitigating climate change issues. It is possible that the GDP per capita elasticity of carbon dioxide emissions would be controlled in a range from 0.2 to 0.3 by the great effort. (author)

  15. Epidemiological and molecular characteristics of emergent dengue virus in Yunnan Province near the China-Myanmar-Laos border, 2013-2015.

    Science.gov (United States)

    Hu, Ting-Song; Zhang, Hai-Lin; Feng, Yun; Fan, Jian-Hua; Tang, Tian; Liu, Yong-Hua; Zhang, Liu; Yin, Xiao-Xiong; Chen, Gang; Li, Hua-Chang; Zu, Jin; Li, Hong-Bin; Li, Yuan-Yuan; Yu, Jing; Zhang, Fu-Qiang; Fan, Quan-Shui

    2017-05-08

    Yunnan Province is located in southwestern China and neighbors the Southeast Asian countries, all of which are dengue-endemic areas. In 2000-2013, sporadic imported cases of dengue fever (DF) were reported almost annually in Yunnan Province. During 2013-2015, we confirmed that a large-scale indigenous DF outbreak emerged in cities of Yunnan Province near the China-Myanmar-Laos border. Epidemiological characteristics of DF in Yunnan Province during 2013-2015 were evaluated by retrospective analysis. A total of 232 dengue virus (DENV)-positive sera were randomly collected for sequence analysis of the capsid/premembrane region of DENV from patients with DF in Yunnan Province. The envelope gene of DENV isolates was also amplified and sequenced. Phylogenetic analyses were performed using the neighbor-joining method with the Tajima-Nei model. Phylogenetically, all DENV-positive samples could be classified into DENV-1 genotype I and DENV-2 Asian I genotype during 2013-2015 and DENV-4 genotype I in 2015 from Ruili City; and DENV-3 genotype II in 2013 and DENV-2 Cosmopolitan genotype in 2015 from Xishuangbanna Prefecture. Our results indicated that imported DF from patients from Laos and Myanmar was the primary cause of the DF epidemic in Yunnan Province. Additionally, DENV strains of all four serotypes were identified in indigenous cases in Yunnan Province during the same time period, while the dengue epidemic pattern observed in southwestern Yunnan showed characteristics of a hypoendemic nature: circulation of DENV-1 and DENV-2 over consecutive years.

  16. Genetic polymorphisms of pharmacogenomic VIP variants in the Kyrgyz population from northwest China.

    Science.gov (United States)

    Yunus, Zulfiya; Liu, Lijun; Wang, Hong; Zhang, Le; Li, Xiaolan; Geng, Tingting; Kang, Longli; Jin, Tianbo; Chen, Chao

    2013-10-15

    Pharmacogenomic variant information is well known for major human populations; however, this information is less commonly studied in minorities. In the present study, we genotyped 85 very important pharmacogenetic (VIP) variants (selected from the PharmGKB database) in the Kyrgyz population and compared our data with other four major human populations including Han Chinese in Beijing, China (CHB), the Japanese in Tokyo, Japan (JPT), a northern and western Europe population (CEU), and the Yoruba in Ibadan, Nigeria (YRI). There were 13, 12 and 16 of the selected VIP variant genotype frequencies in the Kyrgyz which differed from those of the CHB, JPT and CEU, respectively (p<0.005). In the YRI, there were 32 different variants, compared to the Kyrgyz (p<0.005). Genotype frequencies of ADH1B, AHR, CYP3A5, PTGS2, VDR, and VKORC1 in the Kyrgyz differed widely from those in the four populations. Haplotype analyses also showed differences among the Kyrgyz and the other four populations. Our results complement the information provided by the database of pharmacogenomics on Kyrgyz. We provide a theoretical basis for safer drug administration and individualized treatment plans for the Kyrgyz. We also provide a template for the study of pharmacogenomics in various ethnic minority groups in China. © 2013 Elsevier B.V. All rights reserved.

  17. Measuring energy efficiency under heterogeneous technologies using a latent class stochastic frontier approach: An application to Chinese energy economy

    International Nuclear Information System (INIS)

    Lin, Boqiang; Du, Kerui

    2014-01-01

    The importance of technology heterogeneity in estimating economy-wide energy efficiency has been emphasized by recent literature. Some studies use the metafrontier analysis approach to estimate energy efficiency. However, for such studies, some reliable priori information is needed to divide the sample observations properly, which causes a difficulty in unbiased estimation of energy efficiency. Moreover, separately estimating group-specific frontiers might lose some common information across different groups. In order to overcome these weaknesses, this paper introduces a latent class stochastic frontier approach to measure energy efficiency under heterogeneous technologies. An application of the proposed model to Chinese energy economy is presented. Results show that the overall energy efficiency of China's provinces is not high, with an average score of 0.632 during the period from 1997 to 2010. - Highlights: • We introduce a latent class stochastic frontier approach to measure energy efficiency. • Ignoring technological heterogeneity would cause biased estimates of energy efficiency. • An application of the proposed model to Chinese energy economy is presented. • There is still a long way for China to develop an energy efficient regime

  18. Polymorphism of 41 kD Flagellin Gene and Its Human B-Cell Epitope in Borrelia burgdorferi Strains of China

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    Huixin Liu

    2016-01-01

    Full Text Available The 41 kD flagellin of Borrelia burgdorferi (B. burgdorferi is a major component of periplasmic flagellar filament core and a good candidate for serodiagnosis in early stage of Lyme disease. Here, we chose 89 B. burgdorferi strains in China, amplified the gene encoding the 41 kD flagellin, and compared the sequences. The results showed that genetic diversity presented in the 41 kD flagellin genes of all 89 strains among the four genotypes of B. burgdorferi, especially in the genotype of B. garinii. Some specific mutation sites for each genotype of the 41 kD flagellin genes were found, which could be used for genotyping B. burgdorferi strains in China. Human B-cell epitope analysis showed that thirteen of 15 nonsynonymous mutations occurred in the epitope region of 41 kD flagellin and thirty of 42 B-cell epitopes were altered due to all 13 nonsynonymous mutations in the epitope region, which may affect the function of the antigen. Nonsynonymous mutations and changed human B-cell epitopes exist in 41 kD flagellin of B. burgdorferi sensu lato strains; these changes should be considered in serodiagnosis of Lyme disease.

  19. 19-VNTR loci used in genotyping Chinese clinical Mycobacterium tuberculosis complex strains and in association with spoligotyping.

    Science.gov (United States)

    Jiang, Yi; Liu, Hai-can; Zheng, Huajun; Dou, Xiangfeng; Tang, Biao; Zhao, Xiu-qin; Zhu, Yongqiang; Lu, Bing; Wang, Shengyue; Dong, Hai-yan; Zhang, Yuan-yuan; Zhao, Guoping; Wan, Kanglin

    2013-07-01

    Recently, tandem repeat typing has emerged as a rapid and easy method for the molecular epidemiology of the Mycobacterium tuberculosis (M. tuberculosis) complex. In this study, a collection of 19 VNTRs incorporating 15 previously described loci and 4 newly evaluated markers were used to genotype 206 Chinese M. tuberculosis isolates and 9 BCG strains. The discriminatory power was evaluated and compared with that obtained by Spoligotyping. It turned out that 15-locus VNTR could be very useful in M. tuberculosis complex strains genotyping in China. The 4 newly evaluated loci were proved informative and could be useful for future epidemiology studies, especially in Beijing family strains. In addition, a unique pattern of the latter 4 loci were found in Chinese BCG strains. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Estimation of the frequency of occult mutations for an autosomal recessive disease in the presence of genetic heterogeneity: application to genetic hearing loss disorders.

    Science.gov (United States)

    Kimberling, William J

    2005-11-01

    The routine testing for pathologic mutation(s) in a patient's DNA has become the foundation of modern molecular genetic diagnosis. It is especially valuable when the phenotype shows genetic heterogeneity, and its importance will grow as treatments become genotype specific. However, the technology of mutation detection is imperfect and mutations are often missed. This can be especially troublesome when dealing with a recessive disorder where the combination of genetic heterogeneity and missed mutation creates an imprecision in the genotypic assessment of individuals who do not appear to have the expected complement of two pathologic mutations. This article describes a statistical approach to the estimation of the likelihood of a genetic diagnosis under these conditions. In addition to providing a means of testing for missed mutations, it also provides a method of estimating and testing for the presence of genetic heterogeneity in the absence of linkage data. Gene frequencies as well as estimates of sensitivity and specificity can be obtained as well. The test is applied to GJB2 recessive nonsyndromic deafness, Usher syndrome types Ib and IIa, and Pendred-enlarged vestibular aqueduct syndrome. Copyright 2005 Wiley-Liss, Inc.

  1. First identification of porcine parvovirus 7 in China.

    Science.gov (United States)

    Xing, Xiulin; Zhou, Han; Tong, Ling; Chen, Yao; Sun, Yankuo; Wang, Heng; Zhang, Guihong

    2018-01-01

    Porcine parvovirus (PPV) are small, non-enveloped and single-stranded DNA viruses, taxonomically classifiable within the family Parvoviridae. Seven PPV genotypes (PPV1 to PPV7) have been identified to date. PPV7, the most recently discovered PPV genotype, was first reported in US pigs in 2016. To explore PPV7 status in Chinese pig populations a total of 64 serum samples collected from two commercial farms in Guangdong province in 2014 were analyzed. PPV7 DNA was detected in 32.8% (21/64) of tested samples. On the porcine circovirus type 2 (PCV2) positive farm, the prevalence rate of PPV7 was 65.5% (19/29) which was significantly higher than that on the PCV2 negative farm (2/35, 5.7%), indicating a possible association between PCV2 and PPV7 infections. The sequences of three PPV7 strains were determined. Phylogenetic analysis revealed that the identified PPV7 strains circulating in China shared 98.7%-99.7% nucleotide homology with the US strain. Further sequence comparison analysis indicated that GD-2014-2 and GD-2014-3 possess a consecutive 9-nt deletion in the VP gene. This is the first report of the existence of PPV7 in China and this finding will strengthen understanding of the epidemiology of porcine parvovirus in Chinese pigs.

  2. Impact of Pathogen Population Heterogeneity and Stress-Resistant Variants on Food Safety.

    Science.gov (United States)

    Abee, T; Koomen, J; Metselaar, K I; Zwietering, M H; den Besten, H M W

    2016-01-01

    This review elucidates the state-of-the-art knowledge about pathogen population heterogeneity and describes the genotypic and phenotypic analyses of persister subpopulations and stress-resistant variants. The molecular mechanisms underlying the generation of persister phenotypes and genetic variants are identified. Zooming in on Listeria monocytogenes, a comparative whole-genome sequence analysis of wild types and variants that enabled the identification of mutations in variants obtained after a single exposure to lethal food-relevant stresses is described. Genotypic and phenotypic features are compared to those for persistent strains isolated from food processing environments. Inactivation kinetics, models used for fitting, and the concept of kinetic modeling-based schemes for detection of variants are presented. Furthermore, robustness and fitness parameters of L. monocytogenes wild type and variants are used to model their performance in food chains. Finally, the impact of stress-resistant variants and persistence in food processing environments on food safety is discussed.

  3. Association of main folate metabolic pathway gene polymorphisms with neural tube defects in Han population of Northern China.

    Science.gov (United States)

    Fang, Yulian; Zhang, Ruiping; Zhi, Xiufang; Zhao, Linsheng; Cao, Lirong; Wang, Yizheng; Cai, Chunquan

    2018-04-01

    Neural tube defects (NTDs) are one of the most prevalent and the most severe congenital malformations worldwide. Studies have confirmed that folic acid supplementation could effectively reduce NTDs risk, but the genetic mechanism remains unclear. In this study, we explored association of single nucleotide polymorphisms (SNP) within folate metabolic pathway genes with NTDs in Han population of Northern China. We performed a case-control study to compare genotype and allele distributions of SNPs in 152 patients with NTDs and 169 controls. A total of 16 SNPs within five genes were genotyped by the Sequenom MassARRAY assay. Our results indicated that three SNPs associated significantly with NTDs (P<0.05). For rs2236225 within MTHFD1, children with allele A or genotype AA had a high NTDs risk (OR=1.500, 95%CI=1.061~2.120; OR=2.862, 95%CI=1.022~8.015, respectively). For rs1801133 within MTHFR, NTDs risk markedly increased in patients with allele T or genotype TT (OR=1.552, 95%CI=1.130~2.131; OR=2.344, 95%CI=1.233~4.457, respectively). For rs1801394 within MTRR, children carrying allele G and genotype GG had a higher NTDs risk (OR=1.533, 95%CI=1.102~2.188; OR=2.355, 95%CI=1.044~5.312, respectively). Our results suggest that rs2236225 of MTHFD1 gene, rs1801133 of MTHFR gene and rs1801394 of MTRR gene were associated with NTDs in Han population of Northern China.

  4. Investigation of the complexity of streamflow fluctuations in a large heterogeneous lake catchment in China

    Science.gov (United States)

    Ye, Xuchun; Xu, Chong-Yu; Li, Xianghu; Zhang, Qi

    2018-05-01

    The occurrence of flood and drought frequency is highly correlated with the temporal fluctuations of streamflow series; understanding of these fluctuations is essential for the improved modeling and statistical prediction of extreme changes in river basins. In this study, the complexity of daily streamflow fluctuations was investigated by using multifractal detrended fluctuation analysis (MF-DFA) in a large heterogeneous lake basin, the Poyang Lake basin in China, and the potential impacts of human activities were also explored. Major results indicate that the multifractality of streamflow fluctuations shows significant regional characteristics. In the study catchment, all the daily streamflow series present a strong long-range correlation with Hurst exponents bigger than 0.8. The q-order Hurst exponent h( q) of all the hydrostations can be characterized well by only two parameters: a (0.354 ≤ a ≤ 0.384) and b (0.627 ≤ b ≤ 0.677), with no pronounced differences. Singularity spectrum analysis pointed out that small fluctuations play a dominant role in all daily streamflow series. Our research also revealed that both the correlation properties and the broad probability density function (PDF) of hydrological series can be responsible for the multifractality of streamflow series that depends on watershed areas. In addition, we emphasized the relationship between watershed area and the estimated multifractal parameters, such as the Hurst exponent and fitted parameters a and b from the q-order Hurst exponent h( q). However, the relationship between the width of the singularity spectrum (Δ α) and watershed area is not clear. Further investigation revealed that increasing forest coverage and reservoir storage can effectively enhance the persistence of daily streamflow, decrease the hydrological complexity of large fluctuations, and increase the small fluctuations.

  5. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation

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    Martinez Fernando J

    2010-03-01

    Full Text Available Abstract Background Numerous studies have demonstrated associations between genetic markers and COPD, but results have been inconsistent. One reason may be heterogeneity in disease definition. Unsupervised learning approaches may assist in understanding disease heterogeneity. Methods We selected 31 phenotypic variables and 12 SNPs from five candidate genes in 308 subjects in the National Emphysema Treatment Trial (NETT Genetics Ancillary Study cohort. We used factor analysis to select a subset of phenotypic variables, and then used cluster analysis to identify subtypes of severe emphysema. We examined the phenotypic and genotypic characteristics of each cluster. Results We identified six factors accounting for 75% of the shared variability among our initial phenotypic variables. We selected four phenotypic variables from these factors for cluster analysis: 1 post-bronchodilator FEV1 percent predicted, 2 percent bronchodilator responsiveness, and quantitative CT measurements of 3 apical emphysema and 4 airway wall thickness. K-means cluster analysis revealed four clusters, though separation between clusters was modest: 1 emphysema predominant, 2 bronchodilator responsive, with higher FEV1; 3 discordant, with a lower FEV1 despite less severe emphysema and lower airway wall thickness, and 4 airway predominant. Of the genotypes examined, membership in cluster 1 (emphysema-predominant was associated with TGFB1 SNP rs1800470. Conclusions Cluster analysis may identify meaningful disease subtypes and/or groups of related phenotypic variables even in a highly selected group of severe emphysema subjects, and may be useful for genetic association studies.

  6. Crustal heterogeneity and seismotectonics of the region around Beijing, China

    Science.gov (United States)

    Huang, Jinli; Zhao, Dapeng

    2004-07-01

    A detailed three-dimensional (3-D) P-wave velocity model of the crust and uppermost mantle under the Chinese capital (Beijing) region is determined with a spatial resolution of 25 km in the horizontal direction and 4-17 km in depth. We used 48,750 precise P-wave arrival times from 2973 events of local crustal earthquakes, controlled seismic explosions and quarry blasts. These events were recorded by a new digital seismic network consisting of 101 seismic stations equipped with high-sensitivity seismometers. The data are analyzed by using a 3-D seismic tomography method. Our tomographic model provides new insights into the geological structure and tectonics of the region, such as the lithological variations and large fault zones across the major geological terranes like the North China Basin, the Taihangshan and the Yanshan mountainous areas. The velocity images of the upper crust reflect well the surface geological and topographic features. In the North China Basin, the depression and uplift areas are imaged as slow and fast velocities, respectively. The Taihangshan and Yanshan mountainous regions are generally imaged as broad high-velocity zones, while the Quaternary intermountain basins show up as small low-velocity anomalies. Velocity changes are visible across some of the large fault zones. Large crustal earthquakes, such as the 1976 Tangshan earthquake ( M=7.8) and the 1679 Sanhe earthquake ( M=8.0), generally occurred in high-velocity areas in the upper to middle crust. In the lower crust to the uppermost mantle under the source zones of the large earthquakes, however, low-velocity and high-conductivity anomalies exist, which are considered to be associated with fluids. The fluids in the lower crust may cause the weakening of the seismogenic layer in the upper and middle crust and thus contribute to the initiation of the large crustal earthquakes.

  7. Genotype x environment interaction for grain yield of wheat genotypes tested under water stress conditions

    International Nuclear Information System (INIS)

    Sail, M.A.; Dahot, M.U.; Mangrio, S.M.; Memon, S.

    2007-01-01

    Effect of water stress on grain yield in different wheat genotypes was studied under field conditions at various locations. Grain yield is a complex polygenic trait influenced by genotype, environment and genotype x environment (GxE) interaction. To understand the stability among genotypes for grain yield, twenty-one wheat genotypes developed Through hybridization and radiation-induced mutations at Nuclear Institute of Agriculture (NIA) TandoJam were evaluated with four local check varieties (Sarsabz, Thori, Margalla-99 and Chakwal-86) in multi-environmental trails (MET/sub s/). The experiments were conducted over 5 different water stress environments in Sindh. Data on grain yield were recorded from each site and statistically analyzed. Combined analysis of variance for all the environments indicated that the genotype, environment and genotype x environment (GxE) interaction were highly significant (P greater then 0.01) for grain yield. Genotypes differed in their response to various locations. The overall highest site mean yield (4031 kg/ha) recorded at Moro and the lowest (2326 kg/ha) at Thatta. Six genotypes produced significantly (P=0.01) the highest grain yield overall the environments. Stability analysis was applied to estimate stability parameters viz., regression coefficient (b), standard error of regression coefficient and variance due to deviation from regression (S/sub 2/d) genotypes 10/8, BWS-78 produced the highest mean yield over all the environments with low regression coefficient (b=0.68, 0.67 and 0.63 respectively and higher S/sup 2/ d value, showing specific adaptation to poor (un favorable) environments. Genotype 8/7 produced overall higher grain yield (3647 kg/ha) and ranked as third high yielding genotype had regression value close to unity (b=0.9) and low S/sup d/ value, indicating more stability and wide adaptation over the all environments. The knowledge of the presence and magnitude of genotype x environment (GE) interaction is important to

  8. MLVA and LPS Characteristics of Brucella canis Isolated from Humans and Dogs in Zhejiang, China

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    Dongri Piao

    2017-12-01

    Full Text Available BackgroundBrucella canis is a pathogenic bacterium that causes brucellosis in dogs, and its zoonotic potential has been increasing in recent years. B. canis is a rare source of human brucellosis in China, where Brucella melitensis has been the major pathogen associated with human brucellosis outbreaks. In late 2011, a case of a B. canis infection was detected in a human patient in Zhejiang Province, China. To compare the genotypes between strains of B. canis isolated from the patient and from dogs, a multiple-locus variable-number tandem-repeat analysis (MLVA-16 was performed. In addition, the lipopolysaccharide-synthesis-related genes were analyzed with the B. canis reference strain RM6/66.Results32 B. canis strains were divided into 26 genotypes using MLVA-16 [Hunter-Gaston Diversity Index (HGDI = 0.976]. The HGDI indexes for various loci ranged between 0.000 and 0.865. All four Hangzhou isolates were indistinguishable using panel 1 (genotype 3 and panel 2A (genotype 28. However, these strains were distinctly different from other isolates from Beijing, Jiangsu, Liaoning, and Inner Mongolia at Bruce 09. The emergence of a human B. canis infection was limited to an area. Comparative analysis indicated B. canis from canines and humans have no differences in lipopolysaccharide-synthesis locus.ConclusionThe comprehensive approaches have been used to analyze human and canine B. canis isolates, including molecular epidemiological and LPS genetic characteristics. Further detailed analysis of the whole genomic sequencing will contribute to understanding of the pathogenicity of B. canis in humans.

  9. Prevalence and Characterization of Integrons in Multidrug Resistant Acinetobacter baumannii in Eastern China: A Multiple-Hospital Study

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    Jing Chen

    2015-08-01

    Full Text Available Objective: The aim of this multiple-hospital study was to investigate the prevalence of integrons in multidrug-resistant Acinetobacter baumannii (MDRAB in Eastern China, and characterize the integron-integrase genes, so as to provide evidence for the management and appropriate antibiotic use of MDRAB infections. Methods: A total of 425 clinical isolates of A. baumannii were collected from 16 tertiary hospitals in 11 cities of four provinces (Fujian, Jiangsu, Zhejiang and Shandong from January 2009 to June 2012. The susceptibility of A. baumannii isolates to ampicillin/sulbactam, piperacillin/tazobactam, ceftazidime, ceftriaxone, cefepime, aztreonam, meropenem, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, sulfamethoxazole/trimenthoprim, minocycline and imipenem was tested, and integrons and their gene cassettes were characterized in these isolates using PCR assay. In addition, integron-positive A. baumannii isolates were genotyped using pulsed-field gel electrophoresis (PFGE assay, and intI1 gene cassette was sequenced. Results: intI1 gene was carried in 69.6% of total A. baumannii isolates, while intI2 and intI3 genes were not detected. The prevalence of resistance to ampicillin/sulbactam, piperacillin/tazobactam, ceftazidime, ceftriaxone, cefepime, aztreonam, imipenem, meropenem, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin and sulfamethoxazole/trimenthoprim was significantly higher in integron-positive A. baumannii isolates than in negative isolates (all p values <0.05, while no significant difference was observed in the prevalence of minocycline resistance (p > 0.05. PFGE assay revealed 27 PFGE genotypes and 4 predominant genotypes, P1, P4, P7 and P19. The PFGE genotype P1 contained 13 extensive-drug resistant and 89 non-extensive-drug resistant A. baumannii isolates, while the genotype P4 contained 34 extensive-drug resistant and 67 non-extensive-drug resistant isolates, appearing a significant

  10. Assessment of the ripple effects and spatial heterogeneity of total losses in the capital of China after a great catastrophic shock

    Directory of Open Access Journals (Sweden)

    Z. Zhang

    2017-03-01

    introduce the sectors' losses caused by the 2008 Wenchuan earthquake (2008 WCE in Beijing, utilizing the Adaptive Regional Input–Output (ARIO model and the Inter-regional ripple effect (IRRE model. The purpose is to assess the ripple effects of indirect economic loss and spatial heterogeneity of both direct and indirect economic loss at the scale of the smallest administrative divisions of China (streets, villages, and towns. The results indicate that the district of Beijing with the most severe indirect economic loss is the Chaoyang District; the finance and insurance industry (15, see Table 1 of Chaowai Street suffers the most in the Chaoyang District, which is 1.46 times that of its direct economic loss. During 2008–2014, the average annual GDP (gross domestic product growth rate of Beijing was decreased 3.63 % by the catastrophe. Compared with the 8 % of GDP growth rate target, the decreasing GDP growth rate is a significant and noticeable economic impact, and it can be efficiently mitigated by increasing rescue effort and by supporting the industries which are located in the seriously damaged regions.

  11. Geographical and Ethnic Distributions of the MTHFR C677T, A1298C and MTRR A66G Gene Polymorphisms in Chinese Populations: A Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Xingmin Wang

    Full Text Available The geographical and ethnic distributions of the polymorphic methylenetetrahydrofolate reductase (MTHFR mutations (C677T and A1298C and methionine synthase reductase (MTRR mutation (A66G remain heterogeneous in China. The goal of this study was to estimate the pooled frequencies of the alleles and associated genotypes of these gene polymorphisms among healthy populations in Mainland China.We systematically reviewed published epidemiological studies on the distributions of 3 genetic variants in Chinese healthy populations living in Mainland China through a meta-analysis. The relevant electronic databases were searched. All of the raw data of the eligible citations were extracted. The frequency estimates were stratified by geography, ethnicity and sex.Sixty-six studies were identified with a total of 92277 study participants. The meta-analysis revealed that the frequencies of the MTHFR C677T, A1298C, and MTRR A66G gene polymorphisms varied significantly between different ethnic groups and along geographical gradients. The frequencies of the 677T allele and 677TT genotype increased along the southern-central-northern direction across Mainland China (all Pvalues≤0.001. The frequencies of the 1298C, 1298CC, 66G and 66GG genotypes decreased along the south-central-north direction across the country (all Pvalues≤0.001.Our meta-analysis strongly indicates significant geographical and ethnic variations in the frequencies of the C677T, A1298C, and A66G gene polymorphisms in the folate metabolism pathway among Chinese populations.

  12. HBV genotypic variability in Cuba.

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    Carmen L Loureiro

    Full Text Available The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%, mainly A2 (149, 60% but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%, with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7. Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  13. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  14. Desmanthus GENOTYPES

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    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  15. Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction.

    Science.gov (United States)

    Zhang, Xiaoyan; Peng, Yanmei; Wang, Ying; Zhang, Zongying; Li, Dawei; Yu, Jialin; Han, Chenggui

    2016-11-22

    Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV. In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China. The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.

  16. Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

    Science.gov (United States)

    Rubin, Ilan N; Doebeli, Michael

    2017-12-21

    Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into

  17. Comparisons of Adherence to Antiretroviral Therapy in a High-Risk Population in China: A Systematic Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Zhou Huan

    Full Text Available Reports on antiretroviral therapy (ART adherence are scare in China; we performed this meta-analysis to estimate ART adherence rates in different populations at high risk for HIV transmission in China.We searched PubMed, Chinese Biomedical Literature Database (Chinese, China National Knowledge Infrastructure (Chinese, and Wanfang (Chinese to identify studies published from January 1985 to May 2015. We used random-effects meta-analysis to calculate weighted mean estimates across studies and 95% CIs. Data were pooled with proportions transformed prior to pooling using the Freeman-Tukey double arcsine transformation and then back transformed to the original scale. We calculated the I2 (and its 95% confidence intervals and tau2 to assess between-study heterogeneity.We identified 36 eligible articles, including 6885 HIV-positive individuals, reporting ART adherence. Pooled analysis produced an estimate of 77.61% (95% CI = 71.63-83.08 of patients with HIV with adequate adherence; however, high heterogeneity was observed between studies (I2 = 96.60%, 95%CI = 96.00%-97.20%; tau2 = 0.16. Three studies, which included 149 old HIV-infected patients, reported the highest ART adequate adherence rate (89.39%, 95% CI = 72.01-99.26 with high heterogeneity between the studies (I2 = 86.20%, 95%CI = 60.00-95.20%; tau2 = 0.13. While, only two studies, which included 143 heterosexual transmission group (HTG patients, reported the lowest ART adequate adherence rate (51.55%, 95% CI = 41.33-61.71 with low heterogeneity between the studies (I2 = 31.3%, tau2 = 0.007. In the multivariable meta-regression model, high-risk populations was the main factor explaining heterogeneity (variance explained 28.14%.ART adherence in some high-risk populations (e.g., heterosexual transmission group is below the recommended levels for maintaining virologic suppression. It is crucial to develop comprehensive intervention strategies to promote ART adherence in high-risk populations and

  18. First construction of infectious clone for newly emerging mutation porcine circovirus type 2 (PCV2) followed by comparison with PCV2a and PCV2b genotypes in biological characteristics in vitro.

    Science.gov (United States)

    Guo, Long J; Lu, Yue H; Huang, Li P; Wei, Yan W; Wu, Hong L; Liu, Chang M

    2011-06-10

    Porcine circovirus type 2 (PCV2), the causative agent of postweaning multisystemic wasting syndrome (PMWS), is a serious economic problem in the swine industry. Different genotypes (PCV2a, PCV2b and PCV2d) of the virus are present in the clinical cases in China, and it is necessary to elucidate the pathogenic difference among different genotypes of PCV2. In this study, four strains of different genotypes were isolated, two were ordinary strains and another two were mutation strains, which there are one and two amino acids elongation in the capsid protein (Cap) of PCV2, respectively. Representative strains of different genotypes of the virus were constructed by infectious molecular clone and biological characterization of the rescued viruses were identified in vitro. Four PCV2 isolates (PCV2a/CL, PCV2b/YJ, PCV2b/JF and PCV2d/BDH) of different genotypes were isolated from the clinical cases of PMWS in China. Four infectious clones of PCV2 were constructed and the rescued viruses were harvested after transfection into PK15 cells. The rescued viruses were verified by nucleotide sequence analysis, morphology of the viruses and immunoperoxidase monolayer assay (IPMA). The rescued viruses propagated stably after consecutive incubation for more than ten passages, and virus propagation reached its peak 72h post infection (PI), and the virus titers were up to 10⁵·⁷ TCID₅₀/ml. By using neutralizing 1D2 monoclonal antibody (mAb) of PCV2, the antigen capture ELISA showed that only the PCV2a/rCL and PCV2b/rJF strains has immunoreactivity with the 1D2 mAb, however, another two rescued strains (PCV2b/rYJ and PCV2d/rBDH) do not, which indicated the antigenic difference among the rescued viruses of different genotypes. In addition, here is the first report of obtaining the newly emerging PCV2 with mutation in vitro by infectious molecular clone technology. Conclusions drawn from this study show that PCV2 has prevailing differences in genomic and ORF2 gene length and antigen

  19. First construction of infectious clone for newly emerging mutation porcine circovirus type 2 (PCV2 followed by comparison with PCV2a and PCV2b genotypes in biological characteristics in vitro

    Directory of Open Access Journals (Sweden)

    Wu Hong L

    2011-06-01

    Full Text Available Abstract Background Porcine circovirus type 2 (PCV2, the causative agent of postweaning multisystemic wasting syndrome (PMWS, is a serious economic problem in the swine industry. Different genotypes (PCV2a, PCV2b and PCV2d of the virus are present in the clinical cases in China, and it is necessary to elucidate the pathogenic difference among different genotypes of PCV2. In this study, four strains of different genotypes were isolated, two were ordinary strains and another two were mutation strains, which there are one and two amino acids elongation in the capsid protein (Cap of PCV2, respectively. Representative strains of different genotypes of the virus were constructed by infectious molecular clone and biological characterization of the rescued viruses were identified in vitro. Results Four PCV2 isolates (PCV2a/CL, PCV2b/YJ, PCV2b/JF and PCV2d/BDH of different genotypes were isolated from the clinical cases of PMWS in China. Four infectious clones of PCV2 were constructed and the rescued viruses were harvested after transfection into PK15 cells. The rescued viruses were verified by nucleotide sequence analysis, morphology of the viruses and immunoperoxidase monolayer assay (IPMA. The rescued viruses propagated stably after consecutive incubation for more than ten passages, and virus propagation reached its peak 72h post infection (PI, and the virus titers were up to 105.7 TCID50/ml. By using neutralizing 1D2 monoclonal antibody (mAb of PCV2, the antigen capture ELISA showed that only the PCV2a/rCL and PCV2b/rJF strains has immunoreactivity with the 1D2 mAb, however, another two rescued strains (PCV2b/rYJ and PCV2d/rBDH do not, which indicated the antigenic difference among the rescued viruses of different genotypes. In addition, here is the first report of obtaining the newly emerging PCV2 with mutation in vitro by infectious molecular clone technology. Conclusions Conclusions drawn from this study show that PCV2 has prevailing differences

  20. Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

    Science.gov (United States)

    Manrubia, Susanna; Cuesta, José A

    2017-04-01

    An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

  1. Impact of Genotype on EPA and DHA Status and Responsiveness to Increased Intakes

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    Anne Marie Minihane

    2016-03-01

    Full Text Available At a population level, cardioprotective and cognitive actions of the fish oil (FO derived long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA have been extensively demonstrated. In addition to dietary intake, which is limited for many individuals, EPA and DHA status is dependent on the efficiency of their biosynthesis from α-linolenic acid. Gender and common gene variants have been identified as influencing the rate-limiting desaturase and elongase enzymes. Response to a particular intake or status is also highly heterogeneous and likely influenced by genetic variants which impact on EPA and DHA metabolism and tissue partitioning, transcription factor activity, or physiological end-point regulation. Here, available literature relating genotype to tissue LC n-3 PUFA status and response to FO intervention is considered. It is concluded that the available evidence is relatively limited, with much of the variability unexplained, though APOE and FADS genotypes are emerging as being important. Although genotype × LC n-3 PUFA interactions have been described for a number of phenotypes, few have been confirmed in independent studies. A more comprehensive understanding of the genetic, physiological and behavioural modulators of EPA and DHA status and response to intervention is needed to allow refinement of current dietary LC n-3 PUFA recommendations and stratification of advice to “vulnerable” and responsive subgroups.

  2. Prevalence of Celiac Disease Autoimmunity Among Adolescents and Young Adults in China.

    Science.gov (United States)

    Yuan, Juanli; Zhou, Chunyan; Gao, Jinyan; Li, Jingjing; Yu, Fenglian; Lu, Jun; Li, Xin; Wang, Xiaozhong; Tong, Ping; Wu, Zhihua; Yang, Anshu; Yao, Yonghong; Nadif, Sarah; Shu, Heng; Jiang, Xu; Wu, Yujie; Gilissen, Luud; Chen, Hongbing

    2017-10-01

    In China, epidemiologic information on celiac disease autoimmunity is scarce and fragmented. We investigated the prevalence of celiac disease autoimmunity in the general Chinese population. In a cross-sectional prospective study, 19,778 undiagnosed Chinese adolescents and young adults (age, 16-25 y) were recruited from consecutive new students who underwent routine physical examinations at 2 universities in Jiangxi, China, from September 2010 through October 2013; the students were from 27 geographic regions in China. All subjects were tested for serum IgG, IgG against deamidated gliadin peptides (IgG anti-DGP), and IgA anti-tissue transglutaminase antibodies (IgA anti-tTG). We also analyzed HLA genotypes in subgroups of participants with different results from tests for serum markers of celiac disease. A total of 434 students (2.19%) tested positive for serum markers for celiac disease (95% confidence interval [CI], 1.99%-2.41%), 0.36% of the students tested positive for anti-tTG IgA (95% CI, 0.28%-0.46%), and 1.88% tested positive for anti-DGP IgG (95% CI, 1.70%-2.09%). The prevalence of celiac disease autoimmunity (positive results in assays for anti-tTG IgA and anti-DGP-IgG) was 0.06% (95% CI, 0.03%-0.10%). Celiac disease autoimmunity was associated with the consumption of wheat and female sex. The prevalence in the Shandong province in north China, where wheat is a staple in the diet, was 0.76% (95% CI, 0.21%-1.95%). The frequencies of the HLA-DQ2/-DQ8 genotypes associated with celiac disease were higher in subjects with celiac disease autoimmunity, based on detection of both serum markers, than in subjects with positive results from a single test (P celiac disease. The prevalence of celiac disease autoimmunity in the Shandong province in north China, where wheat is a staple in the diet, was 0.76%. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

  3. Concepts of pathogenesis in psoriatic arthritis: genotype determines clinical phenotype.

    LENUS (Irish Health Repository)

    FitzGerald, Oliver

    2015-05-07

    This review focuses on the genetic features of psoriatic arthritis (PsA) and their relationship to phenotypic heterogeneity in the disease, and addresses three questions: what do the recent studies on human leukocyte antigen (HLA) tell us about the genetic relationship between cutaneous psoriasis (PsO) and PsA - that is, is PsO a unitary phenotype; is PsA a genetically heterogeneous or homogeneous entity; and do the genetic factors implicated in determining susceptibility to PsA predict clinical phenotype? We first discuss the results from comparing the HLA typing of two PsO cohorts: one cohort providing the dermatologic perspective, consisting of patients with PsO without evidence of arthritic disease; and the second cohort providing the rheumatologic perspective, consisting of patients with PsA. We show that these two cohorts differ considerably in their predominant HLA alleles, indicating the heterogeneity of the overall PsO phenotype. Moreover, the genotype of patients in the PsA cohort was shown to be heterogeneous with significant elevations in the frequency of haplotypes containing HLA-B*08, HLA-C*06:02, HLA-B*27, HLA-B*38 and HLA-B*39. Because different genetic susceptibility genes imply different disease mechanisms, and possibly different clinical courses and therapeutic responses, we then review the evidence for a phenotypic difference among patients with PsA who have inherited different HLA alleles. We provide evidence that different alleles and, more importantly, different haplotypes implicated in determining PsA susceptibility are associated with different phenotypic characteristics that appear to be subphenotypes. The implication of these findings for the overall pathophysiologic mechanisms involved in PsA is discussed with specific reference to their bearing on the discussion of whether PsA is conceptualised as an autoimmune process or one that is based on entheseal responses.

  4. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  5. Identification of Natural Infections in Sheep/Goats with HoBi-like Pestiviruses in China.

    Science.gov (United States)

    Shi, H; Kan, Y; Yao, L; Leng, C; Tang, Q; Ji, J; Sun, S

    2016-10-01

    The natural infections of HoBi-like pestiviruses in cattle have been reported in South America, Europe and Asia. In China, although the detections of HoBi-like pestivirus have been reported, the epidemiological investigation was limited. From January 2014 to October 2015, several flocks of sheep/goats in Henan province in central China suffered respiratory diseases which were recovered slowly after antibiotics treatment. To test whether it is the HoBi-like pestivirus caused this symptom, 49 serum samples and 22 nasal swabs were then collected for analysis by serology and RT-PCR. Serological result revealed that prevalence of pestivirus in small ruminants was 12.2% (6/49) in central China. Sequence analysis of partial 5'-UTR nucleotides of pestivirus-positive samples suggested that HoBi-like pestivirus might have circulated in sheep/goats of China for a period and have evolved into new genotype clusters. It is apparent that the study provides the molecular evidence of natural infections in goat/sheep species with HoBi-like pestiviruses in China. © 2016 Blackwell Verlag GmbH.

  6. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

    Science.gov (United States)

    Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

    2015-01-01

    Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

  7. Evaluating of the spatial heterogeneity of soil loss tolerance and its effects on erosion risk in the carbonate areas of southern China

    Directory of Open Access Journals (Sweden)

    Y. Li

    2017-05-01

    Full Text Available Soil loss tolerance (T value is one of the criteria in determining the necessity of erosion control measures and ecological restoration strategy. However, the validity of this criterion in subtropical karst regions is strongly disputed. In this study, T value is calculated based on soil formation rate by using a digital distribution map of carbonate rock assemblage types. Results indicated a spatial heterogeneity and diversity in soil loss tolerance. Instead of only one criterion, a minimum of three criteria should be considered when investigating the carbonate areas of southern China because the one region, one T value concept may not be applicable to this region. T value is proportionate to the amount of argillaceous material, which determines the surface soil thickness of the formations in homogenous carbonate rock areas. Homogenous carbonate rock, carbonate rock intercalated with clastic rock areas and carbonate/clastic rock alternation areas have T values of 20, 50 and 100 t/(km2 a, and they are extremely, severely and moderately sensitive to soil erosion. Karst rocky desertification (KRD is defined as extreme soil erosion and reflects the risks of erosion. Thus, the relationship between T value and erosion risk is determined using KRD as a parameter. The existence of KRD land is unrelated to the T value, although this parameter indicates erosion sensitivity. Erosion risk is strongly dependent on the relationship between real soil loss (RL and T value rather than on either erosion intensity or the T value itself. If RL > > T, then the erosion risk is high despite of a low RL. Conversely, if T > > RL, then the soil is safe although RL is high. Overall, these findings may clarify the heterogeneity of T value and its effect on erosion risk in a karst environment.

  8. Using genetic data to estimate diffusion rates in heterogeneous landscapes.

    Science.gov (United States)

    Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

    2016-08-01

    Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

  9. Genetic and phenotypic heterogeneity in tropical calcific pancreatitis.

    Science.gov (United States)

    Paliwal, Sumit; Bhaskar, Seema; Chandak, Giriraj R

    2014-12-14

    Tropical calcific pancreatitis (TCP) is a form of chronic non-alcoholic pancreatitis initially reported in the developing parts of the tropical world. The clinical phenotype of TCP has undergone marked changes since its first description in 1968. The disease is now seen in relatively older people with less severe symptoms. In addition, there are varying reports on the proportion of cases presenting with imaging abnormalities like calcification, ductal dilation, and glandular atrophy. Significant progress has also been made in understanding the etiopathology of TCP. The role of malnutrition and cassava toxicity in its pathogenesis is disproven and few studies have focused on the role of micronutrient deficiency and oxidative stress in the etiopathogenesis of TCP. Emerging evidence support an important role for genetic risk factors in TCP. Several studies have shown that, rather than mutations in trypsinogens, variants in serine protease inhibitor kazal type 1, cathepsin B, chymotrypsin C, cystic fibrosis transmembrane regulator, and carboxypeptidase A1, predict risk of TCP. These studies also provided evidence of mutational heterogeneity between TCP and chronic pancreatitis in Western populations. The current review summarizes recent advances that have implications in the understanding of the pathophysiology and thus, heterogeneity in genotype-phenotype correlations in TCP.

  10. Compositional and isotopic heterogeneities in the Neo-Tethyan upper mantle recorded by coexisting Al-rich and Cr-rich chromitites in the Purang peridotite massif, SW Tibet (China)

    Science.gov (United States)

    Xiong, Fahui; Yang, Jingsui; Xu, Xiangzhen; Kapsiotis, Argyrios; Hao, Xiaolin; Liu, Zhao

    2018-06-01

    The Purang harzburgite massif in SW Tibet (China) hosts abundant chrome ore deposits. Ores consist of 20 to >95% modal chromian spinel (Cr-spinel) with mylonitic fabric in imbricate shaped pods. The composition of Cr-spinel in these ores ranges from Al-rich [Cr#Sp or Cr/(Cr + Al) × 100 = 47.60-57.56] to Cr-rich (Cr#Sp: 62.55-79.57). Bulk platinum-group element (PGE) contents of chromitites are also highly variable ranging from 17.5 ppb to ∼2.5 ppm. Both metallurgical and refractory chromitites show a general enrichment in the IPGE (Os, Ir and Ru) with respect to the PPGE (Rh, Pt and Pd), resulting mostly in right-sloping primitive mantle (PM)-normalized PGE profiles. The platinum-group mineral (PGM) assemblages of both chromitite types are dominated by heterogeneously distributed, euhedral Os-bearing laurite inclusions in Cr-spinel. The Purang chromitites have quite inhomogeneous 187Os/188Os ratios (0.12289-0.13194) that are within the range of those reported for mantle-hosted chromitites from other peridotite massifs. Geochemical calculations demonstrate that the parental melts of high-Cr chromitites were boninitic, whereas those of high-Al chromitites had an arc-type tholeiitic affinity. Chromite crystallization was most likely stimulated by changes in magma compositions due to melt-peridotite interaction, leading to the establishment of a heterogeneous physicochemical environment during the early crystallization of the PGM. The highly variable PGE contents, inhomogeneous Os-isotopic compositions and varying Cr#Sp ratios of these chromitites imply a polygenetic origin for them from spatially distinct melt inputs. The generally low γOs values (different sections of a heterogeneously depleted mantle source region. These melts were most likely produced in the mantle wedge above a downgoing lithospheric slab.

  11. Rotavirus genotype shifts among Swedish children and adults-Application of a real-time PCR genotyping.

    Science.gov (United States)

    Andersson, Maria; Lindh, Magnus

    2017-11-01

    It is well known that human rotavirus group A is the most important cause of severe diarrhoea in infants and young children. Less is known about rotavirus infections in other age groups, and about how rotavirus genotypes change over time in different age groups. Develop a real-time PCR to easily genotype rotavirus strains in order to monitor the pattern of circulating genotypes. In this study, rotavirus strains in clinical samples from children and adults in Western Sweden during 2010-2014 were retrospectively genotyped by using specific amplification of VP 4 and VP 7 genes with a new developed real-rime PCR. A genotype was identified in 97% of 775 rotavirus strains. G1P[8] was the most common genotype representing 34.9%, followed by G2P[4] (28.3%), G9P[8] (11.5%), G3P[8] (8.1%), and G4P[8] (7.9%) The genotype distribution changed over time, from predominance of G1P[8] in 2010-2012 to predominance of G2P[4] in 2013-2014. There were also age-related differences, with G1P[8] being the most common genotype in children under 2 years (47.6%), and G2P[4] the most common in those over 70 years of age (46.1%.). The shift to G2P[4] in 2013-2014 was associated with a change in the age distribution, with a greater number of rotavirus positive cases in elderly than in children. By using a new real-time PCR method for genotyping we found that genotype distribution was age related and changed over time with a decreasing proportion of G1P[8]. Copyright © 2017. Published by Elsevier B.V.

  12. Phylogenetic relationships and pathogenicity variation of two Newcastle disease viruses isolated from domestic ducks in Southern China.

    Science.gov (United States)

    Kang, Yinfeng; Li, Yanling; Yuan, Runyu; Li, Xianwei; Sun, Minhua; Wang, Zhaoxiong; Feng, Minsha; Jiao, Peirong; Ren, Tao

    2014-08-12

    Newcastle disease (ND) is an OIE listed disease caused by virulent avian paramyxovirus type 1 (APMV-1) strains, which is enzootic and causes large economic losses in the poultry sector. Genotype VII and genotype IX NDV viruses were the predominant circulating genotype in China, which may possibly be responsible for disease outbreaks in chicken flocks in recent years. While ducks and geese usually have exhibited inapparent infections. In the present study, we investigate the complete genome sequence, the clinicopathological characterization and transmission of two virulent Newcastle disease viruses, SS-10 and NH-10, isolated from domestic ducks in Southern China in 2010. F, and the complete gene sequences based on phylogenetic analysis demonstrated that SS-10 (genotype VII) and NH-10 (genotype IX) belongs to class II. The deduced amino acid sequence was (112)R-R-Q-K/R-R-F(117) at the fusion protein cleavage site. Animal experiment results showed that the SS-10 virus isolated from ducks was highly pathogenic for chickens and geese, but low pathogenic for ducks. It could be detected from spleen, lung, kidney, trachea, small intestine, bursa of fabricius, thymus, pancreas and cecal tonsils, oropharyngeal and cloacal swabs, and could transmit to the naive contact birds. Moreover, it could transmit to chickens, ducks and geese by naive contact. However, the NH-10 virus isolated from ducks could infect some chickens, ducks and geese, but only caused chickens to die. Additionally, it could transmit to the naive contact chickens, ducks, and geese. The two NDV isolates exhibited different biological properties with respect to pathogenicity and transmission in chickens, ducks and geese. Therefore, no species-preference exists for chicken, duck or goose viruses and more attention should be paid to the trans-species transmission of VII NDVs between ducks, geese and chickens for the control and eradication of ND.

  13. Energy consumption-economic growth relationship and carbon dioxide emissions in China

    Energy Technology Data Exchange (ETDEWEB)

    Fei Li, E-mail: lfly2004@yahoo.com.c [Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101 (China); Dong Suocheng; Xue Li [Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101 (China); Liang Quanxi [Jinan University, Guangzhou 510632 (China); Yang Wangzhou [Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101 (China)

    2011-02-15

    This paper applies the panel unit root, heterogeneous panel cointegration and panel-based dynamic OLS to re-investigate the co-movement and relationship between energy consumption and economic growth for 30 provinces in mainland China from 1985 to 2007. The empirical results show that there is a positive long-run cointegrated relationship between real GDP per capita and energy consumption variables. Furthermore, we investigate two cross-regional groups, namely the east China and west China groups, and get more important results and implications. In the long-term, a 1% increase in real GDP per capita increases the consumption of energy by approximately 0.48-0.50% and accordingly increases the carbon dioxide emissions by about 0.41-0.43% in China. The economic growth in east China is energy-dependent to a great extent, and the income elasticity of energy consumption in east China is over 2 times that of the west China. At present, China is subject to tremendous pressures for mitigating climate change issues. It is possible that the GDP per capita elasticity of carbon dioxide emissions would be controlled in a range from 0.2 to 0.3 by the great effort. - Research Highlights: {yields} The long-run cointegrated relationship between real GDP per capita and energy consumption in China is examined. {yields} GDP per capita elasticity of carbon dioxide emissions is estimated. {yields} Economic growth in east China is energy-dependent to a great extent, and relies on the consumption of the energy more than the west China.

  14. Energy consumption-economic growth relationship and carbon dioxide emissions in China

    International Nuclear Information System (INIS)

    Fei Li; Dong Suocheng; Xue Li; Liang Quanxi; Yang Wangzhou

    2011-01-01

    This paper applies the panel unit root, heterogeneous panel cointegration and panel-based dynamic OLS to re-investigate the co-movement and relationship between energy consumption and economic growth for 30 provinces in mainland China from 1985 to 2007. The empirical results show that there is a positive long-run cointegrated relationship between real GDP per capita and energy consumption variables. Furthermore, we investigate two cross-regional groups, namely the east China and west China groups, and get more important results and implications. In the long-term, a 1% increase in real GDP per capita increases the consumption of energy by approximately 0.48-0.50% and accordingly increases the carbon dioxide emissions by about 0.41-0.43% in China. The economic growth in east China is energy-dependent to a great extent, and the income elasticity of energy consumption in east China is over 2 times that of the west China. At present, China is subject to tremendous pressures for mitigating climate change issues. It is possible that the GDP per capita elasticity of carbon dioxide emissions would be controlled in a range from 0.2 to 0.3 by the great effort. - Research Highlights: → The long-run cointegrated relationship between real GDP per capita and energy consumption in China is examined. → GDP per capita elasticity of carbon dioxide emissions is estimated. → Economic growth in east China is energy-dependent to a great extent, and relies on the consumption of the energy more than the west China.

  15. Clinical and biochemical heterogeneity between patients with glycogen storage disease type IA: the added value of CUSUM for metabolic control.

    Science.gov (United States)

    Peeks, Fabian; Steunenberg, Thomas A H; de Boer, Foekje; Rubio-Gozalbo, M Estela; Williams, Monique; Burghard, Rob; Rajas, Fabienne; Oosterveer, Maaike H; Weinstein, David A; Derks, Terry G J

    2017-09-01

    To study heterogeneity between patients with glycogen storage disease type Ia (GSD Ia), a rare inherited disorder of carbohydrate metabolism caused by the deficiency of glucose-6-phosphatase (G6Pase). Descriptive retrospective study of longitudinal clinical and biochemical data and long-term complications in 20 GSD Ia patients. We included 11 patients with homozygous G6PC mutations and siblings from four families carrying identical G6PC genotypes. To display subtle variations for repeated triglyceride measurements with respect to time for individual patients, CUSUM-analysis graphs were constructed. Patients with different homozygous G6PC mutations showed important differences in height, BMI, and biochemical parameters (i.e., lactate, uric acid, triglyceride, and cholesterol concentrations). Furthermore, CUSUM-analysis predicts and displays subtle changes in longitudinal blood triglyceride concentrations. Siblings in families also displayed important differences in biochemical parameters (i.e., lactate, uric acid, triglycerides, and cholesterol concentrations) and long-term complications (i.e., liver adenomas, nephropathy, and osteopenia/osteoporosis). Differences between GSD Ia patients reflect large clinical and biochemical heterogeneity. Heterogeneity between GSD Ia patients with homozygous G6PC mutations indicate an important role of the G6PC genotype/mutations. Differences between affected siblings suggest an additional role (genetic and/or environmental) of modifying factors defining the GSD Ia phenotype. CUSUM-analysis can facilitate single-patient monitoring of metabolic control and future application of this method may improve precision medicine for patients both with GSD and remaining inherited metabolic diseases.

  16. Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Sonesson, Anna K; Odegård, Jørgen; Rönnegård, Lars

    2013-10-17

    Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects. Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects. Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro

  17. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  18. Genetic relatedness of selected clinical Vibrio cholerae O139 isolates from the southern coastal area of China over a 20-year period.

    Science.gov (United States)

    Li, B S; Xiao, Y; Wang, D C; Tan, H L; Ke, B X; He, D M; Ke, C W; Zhang, Y H

    2016-09-01

    Vibrio cholerae O139 emerged as a causative agent of epidemic cholera in 1992 in India and Bangladesh, and was subsequently reported in China in 1993. The genetic relatedness and molecular characteristics of V. cholerae O139 in Guangdong Province, located in the southern coastal area of China, remains undetermined. In this study, we investigated 136 clinical V. cholerae O139 isolates from 1993 to 2013 in Guangdong. By conventional PCR, 123 (90·4%) isolates were positive for ctxB, ace and zot. Sequencing of the positive amplicons indicated 113 (91·7%) isolates possessed the El Tor allele of ctxB (genotype 3); seven carried the classical ctxB type (genotype 1) and three harboured a novel ctxB type (genotype 5). With respect to tcpA, 123 (90·4%) isolates were positive for the El Tor allele. In addition, pulsed-field gel electrophoresis (with NotI digestion) differentiated the isolates into clusters A and B. Cluster A contained seven of the non-toxigenic isolates from 1998 to 2000; another six non-toxigenic isolates (from 1998 and 2007) and all of the toxigenic isolates formed cluster B. Our results suggest that over a 20-year period, the predominant O139 clinical isolates have maintained a relatively tight clonal structure, although some genetic variance and shift has occurred. Our data highlight the persistence of toxigenic V. cholerae O139 in clinical settings in the southern coastal area of China.

  19. [Spatial heterogeneity in body condition of small yellow croaker in Yellow Sea and East China Sea based on mixed-effects model and quantile regression analysis].

    Science.gov (United States)

    Liu, Zun-Lei; Yuan, Xing-Wei; Yan, Li-Ping; Yang, Lin-Lin; Cheng, Jia-Hua

    2013-09-01

    By using the 2008-2010 investigation data about the body condition of small yellow croaker in the offshore waters of southern Yellow Sea (SYS), open waters of northern East China Sea (NECS), and offshore waters of middle East China Sea (MECS), this paper analyzed the spatial heterogeneity of body length-body mass of juvenile and adult small yellow croakers by the statistical approaches of mean regression model and quantile regression model. The results showed that the residual standard errors from the analysis of covariance (ANCOVA) and the linear mixed-effects model were similar, and those from the simple linear regression were the highest. For the juvenile small yellow croakers, their mean body mass in SYS and NECS estimated by the mixed-effects mean regression model was higher than the overall average mass across the three regions, while the mean body mass in MECS was below the overall average. For the adult small yellow croakers, their mean body mass in NECS was higher than the overall average, while the mean body mass in SYS and MECS was below the overall average. The results from quantile regression indicated the substantial differences in the allometric relationships of juvenile small yellow croakers between SYS, NECS, and MECS, with the estimated mean exponent of the allometric relationship in SYS being 2.85, and the interquartile range being from 2.63 to 2.96, which indicated the heterogeneity of body form. The results from ANCOVA showed that the allometric body length-body mass relationships were significantly different between the 25th and 75th percentile exponent values (F=6.38, df=1737, P<0.01) and the 25th percentile and median exponent values (F=2.35, df=1737, P=0.039). The relationship was marginally different between the median and 75th percentile exponent values (F=2.21, df=1737, P=0.051). The estimated body length-body mass exponent of adult small yellow croakers in SYS was 3.01 (10th and 95th percentiles = 2.77 and 3.1, respectively). The

  20. Detection of PCV2e strains in Southeast China

    Directory of Open Access Journals (Sweden)

    Jiankui Liu

    2018-03-01

    Full Text Available Porcine circovirus 2 (PCV2 has been prevalent in swine herds in China since 2002, causing severe economic loss to the pig industry. The number of live pigs in southeast China is > 20 million. Since information on the genetic variation of PCV2 in the Fujian province is limited, the objective of the present work was to investigate the epidemiological and evolutionary characteristics of PCV2 in southeast China from 2013 to 2017. Of the 685 samples collected from 90 different swine herds from 2013 to 2017, 356 samples from 84 different swine herds were positive for PCV2. PCV2a, PCV2b, PCV2d, and PCV2e co-existed in the Fujian province, with PCV2d being the predominant circulating strain in swineherds and PCV2e being reported for the first time in China. Strikingly, PCV2-FJ-water DNA comes from contaminated river water and not infected animals. Sequence comparison among all isolates indicated that 95 isolates shared approximately 78.7%–100% nucleotide identity and 74.5%–100% amino acid identity for open reading frame 2 (ORF2. Amino acid alignment showed that the Cap protein of PCV2e differed markedly from those of PCV2a, PCV2b, PCV2c, and PCV2d. These results indicated that various PCV2 genotypes exist in China, and that PCV2 is continuously evolving, leading to rapid emergence of new variant stains.

  1. A Simple PCR Method for Rapid Genotype Analysis of Mycobacterium ulcerans

    Science.gov (United States)

    Stinear, Timothy; Davies, John K.; Jenkin, Grant A.; Portaels, Françoise; Ross, Bruce C.; OppEdIsano, Frances; Purcell, Maria; Hayman, John A.; Johnson, Paul D. R.

    2000-01-01

    Two high-copy-number insertion sequences, IS2404 and IS2606, were recently identified in Mycobacterium ulcerans and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS2404 and IS2606. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for M. ulcerans, and it has confirmed previous studies suggesting a clonal population structure of M. ulcerans within a geographic region. M. ulcerans isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between M. ulcerans isolates from Africa and southeast Asia. The application of 2426 PCR to total DNA, extracted directly from M. ulcerans-infected tissue specimens without culture, demonstrated the sensitivity and specificity of this method and confirmed for the first time that both animal and human isolates from areas of endemicity in southeast Australia have the same genotype. PMID:10747130

  2. MNS, Duffy, and Kell blood groups among the Uygur population of Xinjiang, China.

    Science.gov (United States)

    Lin, G Y; Du, X L; Shan, J J; Zhang, Y N; Zhang, Y Q; Wang, Q H

    2017-03-15

    Human blood groups are a significant resource for patients, leading to a fierce international competition in the screening of rare blood groups. Some rare blood group screening programs have been implemented in western countries and Japan, but not particularly in China. Recently, the genetic background of ABO and Rh blood groups for different ethnic groups or regions in China has been focused on increasingly. However, rare blood groups such as MN, Duffy, Kidd, MNS, and Diego are largely unexplored. No systematic reports exist concerning the polymorphisms and allele frequencies of rare blood groups in China's ethnic minorities such as Uygur and Kazak populations of Xinjiang, unlike those on the Han population. Therefore, this study aimed to investigate the allele frequencies of rare blood groups, namely, MNS, Duffy, Kell, Dombrock, Diego, Kidd, Scianna, Colton, and Lutheran in the Uygur population of Xinjiang Single specific primer-polymerase chain reaction was performed for genotyping and statistical analysis of 9 rare blood groups in 158 Uygur individuals. Allele frequencies were compared with distribution among other ethnic groups. Observed and expected values of genotype frequencies were compared using the chi-square test. Genotype frequencies obeyed the Hardy-Weinberg equilibrium (P > 0.5) and allele frequencies were stable. Of all subjects detected, 4 cases carried the rare phenotype S - s - of MNS blood group (frequency of 0.0253), and 1 case carried the phenotype Jk a-b- (frequency of 0.0063). Frequencies of the four groups, MNS, Duffy, Dombrock, and Diego, in the Uygur population differed from those in other ethnic groups. Gene distribution of the Kell, Kidd, and Colton was similar to that in Tibetan and Han populations, though there were some discrepancies. Gene distribution of Scianna and Lutheran groups showed monomorphism similar to that in Tibetan and Han populations. These findings could contribute to the investigation of the origin, evolution, and

  3. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  4. Account for sector heterogeneity in China's energy consumption. Sector price indices vs. GDP deflator

    International Nuclear Information System (INIS)

    Ma, Chunbo

    2010-01-01

    A common practice in decomposition analyses is to deflate output indicators to purge the impact of inflation by using a general deflator. This practice fails to account for sector heterogeneity and can be hazardous. Although the general identified patterns are largely correct, the calculated magnitudes can be misleading or even wrongly signed. Instead, it is strongly recommended that sector heterogeneity is accounted for by using individual sector price indices for all relevant sectors instead of one general (GDP) deflator. This paper analyzes this advanced decomposition using Chinese data and compares to the usual method of using only one deflator. It is found that while most differences are only of quantitative quality, some show even a qualitative difference. Furthermore, the rising energy intensity in the early 2000s, which has been discussed by previous studies, vanishes completely. (author)

  5. First molecular characterization of enteric protozoa and the human pathogenic microsporidian, Enterocytozoon bieneusi, in captive snakes in China.

    Science.gov (United States)

    Karim, Md Robiul; Yu, Fuchang; Li, Jian; Li, Junqiang; Zhang, Longxian; Wang, Rongjun; Rume, Farzana Islam; Jian, Fuchun; Zhang, Sumei; Ning, Changshen

    2014-08-01

    Enteric protozoa are frequently found in snakes. Nevertheless, few studies regarding genetic characterization of these parasites have been carried out. We describe here the first molecular survey of protozoan pathogens from snakes in China and the first report on Enterocytozoon bieneusi genotyping in snakes in the world. Here, 240 fecal specimens were collected from two species of captive snakes, Naja naja (Indian cobra) and Ptyas mucosus (Oriental rat snake), in Guangxi Province, China, and examined by PCR amplification of the small subunit-ribosomal RNA of enteric protozoa and the internal transcribed spacer of ribosomal RNA of E. bieneusi. Cryptosporidium serpentis was identified in three specimens (2.1%) of Oriental rat snakes. Caryospora was found in 5.4% specimens, including eight from cobras (8.1%) and five from rat snakes (3.6%), and represented six new species-Caryospora sp. SKC-2014a to Caryospora sp. SKC-2014 f. Three new Eimeria species, Eimeria sp. SKE-2014a to Eimeria sp. SKE-2014c, were detected in three specimens (2.1%) from rat snakes. Additionally, Sarcocystis sp. SKS-2014 was detected in one specimen from a cobra. The infection rates of E. bieneusi were 3.0% in cobras and 5.7% in rat snakes. Sequence analysis of 11 PCR products revealed the presence of six E. bieneusi genotypes-two known genotypes (type IV and Henan V) and four new genotypes (CRep-1 to CRep-4). All six E. bieneusi genotypes belonged to the zoonotic group (group 1). This result raised the possibility that E. bieneusi could be present in animals consumed by snakes. This should be taken into consideration to better understand the diversity of the parasite, its transmission through the predator-prey relationship, and public health implications.

  6. Exploring links between genotypes, phenotypes, and clinical predictors of response to early intensive behavioural intervention in Autism Spectrum Disorder

    Directory of Open Access Journals (Sweden)

    Valsamma eEapen

    2013-09-01

    Full Text Available Autism Spectrum Disorder (ASD is amongst the most familial of psychiatric disorders. Twin and family studies have demonstrated a monozygotic concordance rate of 70–90%, dizygotic concordance of around 10% and more than a 20-fold increase in risk for first-degree relatives. Despite major advances in the genetics of autism, the relationship between different aspects of the behavioural and cognitive phenotype and their underlying genetic liability is still unclear. This is complicated by the heterogeneity of autism, which exists at both genetic and phenotypic levels. Given this heterogeneity, one method to find homogeneous entities and link these with specific genotypes would be to pursue endophenotypes. Evidence from neuroimaging, eye tracking and electrophysiology studies supports the hypothesis that, building on genetic vulnerability, ASD emerges from a developmental cascade in which a deficit in attention to social stimuli leads to impaired interactions with primary caregivers. This results in abnormal development of the neurocircuitry responsible for social cognition, which in turn adversely affects later behavioural and functional domains dependent on these early processes, such as language development. Such a model begets a heterogeneous clinical phenotype, and is also supported by studies demonstrating better clinical outcomes with earlier treatment. Treatment response following intensive early behavioural intervention in ASD is also distinctly variable; however, relatively little is known about specific elements of the clinical phenotype that may predict response to current behavioural treatments. This paper overviews the literature regarding genotypes, phenotypes and predictors of response to behavioural intervention in ASD and presents suggestions for future research to explore linkages between these that would enable better identification of, and increased treatment efficacy for, ASD.

  7. Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes

    Science.gov (United States)

    Yang, Hui; Tang, Ming; Gross, Thilo

    2015-08-01

    One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

  8. Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes.

    Science.gov (United States)

    Yang, Hui; Tang, Ming; Gross, Thilo

    2015-08-21

    One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

  9. [Phenotypic diversity of toxigenic Vibrio cholerae O1 El Tor strains identified in China].

    Science.gov (United States)

    Zhao, Xuan; Zhang, Li; Li, Jie; Kan, Biao; Liang, Weili

    2014-05-01

    To understand the phenotypic diversity of toxigenic Vibrio cholerae O1 El Tor strains isolated from different provinces in China during the last 50 years. Traditional biotyping testings including susceptibility to polymyxin B, sensitivity to group IV phage, Voges-Proskauer test and haemolysis of sheep erythrocytes were conducted. Data from Biotype-specific phenotype analysis revealed that only 133 isolates carried the typical El Tor phenotypes while the other 251 isolates displayed atypical El Tor phenotypes. Combined with ctxB, rstR genotypes and phenotypic characteristics, 64 isolates were identified as typical El Tor biotype, 21 were El Tor variants that showing the typical El Tor biotype-specific phenotype but with ctxB(class). 280 isolates were defined as the hybrid groups with traits of both classical and El Tor biotypes that could be further classified into 45 groups, based on the combination of genotypes of ctxB, rstR and phenotypic characteristics. Toxigenic Vibrio cholerae O1 El Tor strains that isolated from different provinces in China displayed high phenotypic diversity. The traditional biotype traits could not be used to correctly distinguish the two different biotypes.

  10. Genetic polymorphisms in very important pharmacogenomic variants in the Zhuang ethnic group of Southwestern China: A cohort study in the Zhuang population.

    Science.gov (United States)

    Li, Jing; Guo, Chenghao; Yan, Mengdan; Niu, Fanglin; Chen, Peng; Li, Bin; Jin, Tianbo

    2018-04-01

    Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations.We genotyped 80 variants of VIP genes in 100 unrelated healthy Zhuang adults from the Yunnan province of China. Next, we analyzed the genotyping data with Structure and F-statistics (Fst).We compared our data with those of other populations using the HapMap data set, and observed that the frequency distribution of Zhuang population in Yunnan closely resembles that of JPT. Furthermore, population structure and Fst analysis showed that the Zhuang population is closely related to the Shaanxi Han population with respect to genetic background.Our study supplements existing information on Zhuang population pharmacogenomics and provides an extensive overview for developing personalized medicine.

  11. Pathotyping and Phylogenetic Characterization of Newcastle Disease Viruses Isolated in Peru: Defining Two Novel Subgenotypes Within Genotype XII.

    Science.gov (United States)

    Chumbe, Ana; Izquierdo-Lara, Ray; Tataje, Luis; Gonzalez, Rosa; Cribillero, Giovana; González, Armando E; Fernández-Díaz, Manolo; Icochea, Eliana

    2017-03-01

    Infections of poultry with virulent strains of avian paramyxovirus 1 (APMV-1), also known as Newcastle disease viruses (NDVs), cause Newcastle disease (ND). This highly contagious disease affects poultry and many other species of birds worldwide. In countries where the disease is prevalent, constant monitoring and characterization of isolates causing outbreaks are necessary. In this study, we report the results of pathogenicity testing and phylogenetic analyses of seven NDVs isolated from several regions of Peru between 2004 and 2015. Six viruses had intracerebral pathogenicity indices (ICPIs) of between 1.75 and 1.88, corresponding to a velogenic pathotype. The remaining virus had an ICPI of 0.00, corresponding to a lentogenic pathotype. These results were consistent with amino acid sequences at the fusion protein (F) cleavage site. All velogenic isolates had the polybasic amino acid sequence 112 RRQKR↓F 117 at the F cleavage site. Phylogenetic analyses of complete F gene sequences showed that all isolates are classified in class II of APMV-1. The velogenic viruses are classified in genotype XII, while the lentogenic virus is classified in genotype II, closely related to the LaSota vaccine strain. Moreover, tree topology, bootstrap values, and genetic distances observed within genotype XII resulted in the identification of novel subgenotypes XIIa (in South America) and XIIb (in China) and possibly two clades within genotype XIIa. All velogenic Peruvian viruses belonged to subgenotype XIIa. Overall, our results confirm the presence of genotype XII in Peru and suggest that it is the prevalent genotype currently circulating in our country. The phylogenetic characterization of these isolates helps to characterize the evolution of NDV and may help with the development of vaccines specific to our regional necessities.

  12. China organic-rich shale geologic features and special shale gas production issues

    Directory of Open Access Journals (Sweden)

    Yiwen Ju

    2014-06-01

    Full Text Available The depositional environment of organic-rich shale and the related tectonic evolution in China are rather different from those in North America. In China, organic-rich shale is not only deposited in marine environment, but also in non-marine environment: marine-continental transitional environment and lacustrine environment. Through analyzing large amount of outcrops and well cores, the geologic features of organic-rich shale, including mineral composition, organic matter richness and type, and lithology stratigraphy, were analyzed, indicating very special characteristics. Meanwhile, the more complex and active tectonic movements in China lead to strong deformation and erosion of organic-rich shale, well-development of fractures and faults, and higher thermal maturity and serious heterogeneity. Co-existence of shale gas, tight sand gas, and coal bed methane (CBM proposes a new topic: whether it is possible to co-produce these gases to reduce cost. Based on the geologic features, the primary production issues of shale gas in China were discussed with suggestions.

  13. Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2012-02-03

    Pre-treatment HCV quasispecies complexity and diversity may predict response to interferon based anti-viral therapy. The objective of this study was to retrospectively (1) examine temporal changes in quasispecies prior to the start of therapy and (2) investigate extensively quasispecies evolution in a group of 10 chronically infected patients with genotype 3a, treated with pegylated alpha2a-Interferon and ribavirin. The degree of sequence heterogeneity within the hypervariable region 1 was assessed by analyzing 20-30 individual clones in serial serum samples. Genetic parameters, including amino acid Shannon entropy, Hamming distance and genetic distance were calculated for each sample. Treatment outcome was divided into (1) sustained virological responders (SVR) and (2) treatment failure (TF). Our results indicate, (1) quasispecies complexity and diversity are lower in the SVR group, (2) quasispecies vary temporally and (3) genetic heterogeneity at baseline can be use to predict treatment outcome. We discuss the results from the perspective of replicative homeostasis.

  14. Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray.

    Science.gov (United States)

    Ávila-Fernández, Almudena; Cantalapiedra, Diego; Aller, Elena; Vallespín, Elena; Aguirre-Lambán, Jana; Blanco-Kelly, Fiona; Corton, M; Riveiro-Álvarez, Rosa; Allikmets, Rando; Trujillo-Tiebas, María José; Millán, José M; Cremers, Frans P M; Ayuso, Carmen

    2010-12-03

    Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations in 272 Spanish families using a genotyping microarray. 272 unrelated Spanish families, 107 with autosomal recessive RP (arRP) and 165 with sporadic RP (sRP), were studied using the APEX genotyping microarray. The families were also classified by clinical criteria: 86 juveniles and 186 typical RP families. Haplotype and sequence analysis were performed to identify the second mutated allele. At least one-gene variant was found in 14% and 16% of the juvenile and typical RP groups respectively. Further study identified four new mutations, providing both causative changes in 11% of the families. Retinol Dehydrogenase 12 (RDH12) was the most frequently mutated gene in the juvenile RP group, and Usher Syndrome 2A (USH2A) and Ceramide Kinase-Like (CERKL) were the most frequently mutated genes in the typical RP group. The only variant found in CERKL was p.Arg257Stop, the most frequent mutation. The genotyping microarray combined with segregation and sequence analysis allowed us to identify the causative mutations in 11% of the families. Due to the low number of characterized families, this approach should be used in tandem with other techniques.

  15. Associations between STAT Gene Polymorphisms and Psoriasis in Northeastern China.

    Science.gov (United States)

    Zhou, Jing; Li, Yuzhen; Sun, Donglin

    2017-01-01

    Psoriasis is an autoimmune disease with genetic and environmental factors. Based on the roles of STATs (signaling transducers and activators of transcription) in autoimmune diseases, it is assumed STAT gene polymorphisms are associated with psoriasis. To study the association between STAT gene polymorphisms and psoriasis in the northeastern Chinese population. Eight single-nucleotide polymorphisms were genotyped: rs2293152, rs3816769, rs4796793, and rs744166 in STAT3, rs7574865 and rs3024866 in STAT4, and rs324011 and rs3024974 in STAT6, using SNaPshot methods. The genotype, allele, and haplotype frequencies were compared between 400 psoriasis patients and 398 healthy individuals in northeastern China. rs744166GG in STAT3 and rs7574865TT in STAT4 had higher frequencies in the case than the control group, suggesting these 2 genotypes increase the susceptibility to psoriasis (p < 0.05). Three haplotypes (H3, H6, and H7) were found to be associated with psoriasis in the study (p < 0.05). These results indicate a role of STAT genes in the pathogenesis of psoriasis. © 2017 S. Karger AG, Basel.

  16. China's energy consumption: A perspective from Divisia aggregation approach

    International Nuclear Information System (INIS)

    Liao, Hua; Wei, Yi-Ming

    2010-01-01

    China's total energy consumption, according to the official data, decreased impressively during 1997-1998 and increased sharply during 2003-2007, which in turn resulted in energy intensity fluctuation. Many literatures explained this ''unusual phenomenon'' from the perspectives of technical change, economic structure shifting and statistical data quality. They measured aggregate energy in thermal units by using linear summation approaches. In this paper, from the perspectives of heterogeneity and imperfect substitutability among diverse energy types, we further examine China's aggregate energy consumption by using Divisia (Sato-Vartia) approach. The results show that China's aggregate energy consumption and intensity fluctuated slightly less than values calculated by using conventional linear approaches, and the ''unusual phenomenon'' is partly explained. It also implies that China's energy intensity changes in 2006-2007 are slightly more optimistic than those officially reported, and the official communique of provincial energy intensity reduction achievements are partly bias. Some provincial achievement are underestimated or overestimated on some provinces. Our empirical results are also helpful to further research, such as energy-economic modeling, energy price elasticity, and elasticity of substitution among capital-labor-energy-material (KLEM). The difficulties or defects when using Divisia approach are also discussed in this paper. (author)

  17. Estimating elasticity for residential electricity demand in China.

    Science.gov (United States)

    Shi, G; Zheng, X; Song, F

    2012-01-01

    Residential demand for electricity is estimated for China using a unique household level dataset. Household electricity demand is specified as a function of local electricity price, household income, and a number of social-economic variables at household level. We find that the residential demand for electricity responds rather sensitively to its own price in China, which implies that there is significant potential to use the price instrument to conserve electricity consumption. Electricity elasticities across different heterogeneous household groups (e.g., rich versus poor and rural versus urban) are also estimated. The results show that the high income group is more price elastic than the low income group, while rural families are more price elastic than urban families. These results have important policy implications for designing an increasing block tariff.

  18. Genotyping of Giardia lamblia isolates from humans in China and Korea using ribosomal DNA Sequences.

    Science.gov (United States)

    Yong, T S; Park, S J; Hwang, U W; Yang, H W; Lee, K W; Min, D Y; Rim, H J; Wang, Y; Zheng, F

    2000-08-01

    Genetic characterization of a total of 15 Giardia lamblia isolates, 8 from Anhui Province, China (all from purified cysts) and 7 from Seoul, Korea (2 from axenic cultures and 5 from purified cysts), was performed by polymerase chain reaction amplification and sequencing of a 295-bp region near the 5' end of the small subunit ribosomal DNA (eukaryotic 16S rDNA). Phylogenetic analyses were subsequently conducted using sequence data obtained in this study, as well as sequences published from other Giardia isolates. The maximum parsimony method revealed that G. lamblia isolates from humans in China and Korea are divided into 2 major lineages, assemblages A and B. All 7 Korean isolates were grouped into assemblage A, whereas 4 Chinese isolates were grouped into assemblage A and 4 into assemblage B. Two Giardia microti isolates and 2 dog-derived Giardia isolates also grouped into assemblage B, whereas Giardia ardeae and Giardia muris were unique.

  19. Genotyping microarray (gene chip) for the ABCR (ABCA4) gene.

    Science.gov (United States)

    Jaakson, K; Zernant, J; Külm, M; Hutchinson, A; Tonisson, N; Glavac, D; Ravnik-Glavac, M; Hawlina, M; Meltzer, M R; Caruso, R C; Testa, F; Maugeri, A; Hoyng, C B; Gouras, P; Simonelli, F; Lewis, R A; Lupski, J R; Cremers, F P M; Allikmets, R

    2003-11-01

    Genetic variation in the ABCR (ABCA4) gene has been associated with five distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), and age-related macular degeneration (AMD). Comparative genetic analyses of ABCR variation and diagnostics have been complicated by substantial allelic heterogeneity and by differences in screening methods. To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants. The ABCR genotyping microarray (the ABCR400 chip) was constructed by the arrayed primer extension (APEX) technology. Each sequence change in ABCR was included on the chip by synthesis and application of sequence-specific oligonucleotides. We validated the chip by screening 136 confirmed STGD patients and 96 healthy controls, each of whom we had analyzed previously by single strand conformation polymorphism (SSCP) technology and/or heteroduplex analysis. The microarray was >98% effective in determining the existing genetic variation and was comparable to direct sequencing in that it yielded many sequence changes undetected by SSCP. In STGD patient cohorts, the efficiency of the array to detect disease-associated alleles was between 54% and 78%, depending on the ethnic composition and degree of clinical and molecular characterization of a cohort. In addition, chip analysis suggested a high carrier frequency (up to 1:10) of ABCR variants in the general population. The ABCR genotyping microarray is a robust, cost-effective, and comprehensive screening tool for variation in one gene in which mutations are responsible for a substantial fraction of retinal disease. The ABCR chip is a prototype for the next generation of screening and diagnostic tools in ophthalmic genetics, bridging clinical and scientific research. Copyright 2003 Wiley

  20. Heterogeneous characters modeling of instant message services users' online behavior.

    Science.gov (United States)

    Cui, Hongyan; Li, Ruibing; Fang, Yajun; Horn, Berthold; Welsch, Roy E

    2018-01-01

    Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users' online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on.

  1. Spatial genetic structure in natural populations of Phragmites australis in a mosaic of saline habitats in the Yellow River Delta, China.

    Directory of Open Access Journals (Sweden)

    Lexuan Gao

    Full Text Available Determination of spatial genetic structure (SGS in natural populations is important for both theoretical aspects of evolutionary genetics and their application in species conservation and ecological restoration. In this study, we examined genetic diversity within and among the natural populations of a cosmopolitan grass Phragmites australis (common reed in the Yellow River Delta (YRD, China, where a mosaic of habitat patches varying in soil salinity was detected. We demonstrated that, despite their close geographic proximity, the common reed populations in the YRD significantly diverged at six microsatellite loci, exhibiting a strong association of genetic variation with habitat heterogeneity. Genetic distances among populations were best explained as a function of environmental difference, rather than geographical distance. Although the level of genetic divergence among populations was relatively low (F'(ST =0.073, weak but significant genetic differentiation, as well as the concordance between ecological and genetic landscapes, suggests spatial structuring of genotypes in relation to patchy habitats. These findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.

  2. Changes in human parechovirus profiles in hospitalized children with acute gastroenteritis after a three-year interval in Lanzhou, China.

    Directory of Open Access Journals (Sweden)

    Ying Guo

    Full Text Available The changing profile of infection over time for Human Parechoviruses (HPeVs is not well known and no detailed study has been reported to date in China. This investigation on HPeV infection in hospitalized children in Lanzhou, China revealed variations in epidemiological characteristics after a three-year interval. To assess the changes that had occurred, epidemiological and clinical characteristics of HPeVs were characterized and compared with previously reported data by our group. A comparable positivity rate (25.3%, 73/289 was revealed after the three-year interval with the majority of the infected children (95.9%, 70/73 being younger than two years of age. While a temporal change in the seasonal distribution was noted in the current study, HPeVs were more frequently detected during July to November compared to September to December in the previous study. Changes in HPeV genotypes patterns, a temporal change in the prevalence of HPeV1, a younger susceptible age to HPeV3 compared with HPeV1 and a tendency of older children to be infected with HPeV4 are in contrast to our previous report. HPeV2, a rarely reported genotype, was identified for the first time in China. In addition, an exclusive trinucleotide (GAT insertion in the HPeV4 nucleotide sequence was identified. However, the profiles of co-infection with other enteric related viruses were similar to our previous findings. In summary, these data suggest temporal variation in the seasonal distribution of HPeV and changing patterns of HPeV genotypes over time in the study region.

  3. Infection rate of Giardia duodenalis, Cryptosporidium spp. and Enterocytozoon bieneusi in cashmere, dairy and meat goats in China.

    Science.gov (United States)

    Peng, Xian-Qi; Tian, Ge-Ru; Ren, Guan-Jing; Yu, Zheng-Qing; Lok, James Barron; Zhang, Long-Xian; Wang, Xue-Ting; Song, Jun-Ke; Zhao, Guang-Hui

    2016-07-01

    Cryptosporidiosis, microsporidiosis, and giardiasis contribute significantly to the high burden of zoonotic diarrhea worldwide. Goats constitute an important species in animal agriculture by providing cashmere wool, meat, and dairy products for human consumption. However, zoonotic pathogens with the potential to cause morbidity and to degrade production have been reported frequently in goats recently. The present study examined 629 fecal specimens from goats, including 315 cashmere goats, 170 dairy goats and 144 meat goats, in multiple cities of Shaanxi and Henan provinces, northwestern and central China, to investigate the infection rate and species/assemblages/genotypes of Giardia duodenalis, Cryptosporidium spp. and Enterocytozoon bieneusi. Of these samples, 274 (43.6%) were positive for three zoonotic pathogens, including 80 (12.7%), 104 (16.5%) and 179 (28.5%) for G. duodenalis, Cryptosporidium spp. and E. bieneusi, respectively. Infections with G. duodenalis, Cryptosporidium spp. and E. bieneusi existed in meat, dairy and cashmere goats, with the highest infection rate of each pathogen being observed in meat goats. DNA sequencing of the SSU rRNA gene from 104 Cryptosporidium-positive specimens revealed existence of Cryptosporidium xiaoi, and the zoonotic parasites Cryptosporidium parvum and Cryptosporidium ubiquitum. Genotyping of G. duodenalis based on the triosephosphate isomerase (TPI) gene identified parasites from zoonotic assemblage A in four cashmere goats and the animal-adapted assemblage E in a group of 76 goats that included cashmere, dairy and meat animals. Polymorphisms in the ribosomal internal transcribed spacer characterized E. bieneusi genotype CHG1 and a novel genotype named as SX1 in both dairy and cashmere goats, genotypes CHS7 and COSI in meat goats, the genotype CHG2 in dairy goats, and the human-pathogenic genotype BEB6 in dairy and meat goats. This is the first detailed study to compare infection rate of the zoonotic protozoan pathogens

  4. Genetic heterogeneity of Escherichia coli isolated from pasteurized milk in State of Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Karine Oltramari

    2014-04-01

    Full Text Available Food contamination caused by enteric pathogens is a major cause of diarrheal disease worldwide, resulting in high morbidity and mortality and significant economic losses. Bacteria are important agents of foodborne diseases, particularly diarrheagenic Escherichia coli. The present study assessed the genetic diversity and antimicrobial resistance of E. coli isolates from pasteurized milk processed in 21 dairies in northwestern State of Parana, Brazil. The 95 E. coli isolates were subjected to antimicrobial susceptibility testing according to the recommendations of the Clinical and Laboratory Standards Institute and assessed genotypically by Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR. The highest rate of resistance was observed for cephalothin (55.78%. ERIC-PCR revealed high genetic diversity, clustering the 95 bacterial isolates into 90 different genotypic patterns. These results showed a heterogeneous population of E. coli in milk samples produced in the northwestern region of Paraná and the need for good manufacturing practices throughout the processing of pasteurized milk to reduce the risk of foodborne illnesses.

  5. Evolution of Sequence Type 4821 Clonal Complex Meningococcal Strains in China from Prequinolone to Quinolone Era, 1972–2013

    Science.gov (United States)

    Guo, Qinglan; Mustapha, Mustapha M.; Chen, Mingliang; Qu, Di; Zhang, Xi; Harrison, Lee H.

    2018-01-01

    The expansion of hypervirulent sequence type 4821 clonal complex (CC4821) lineage Neisseria meningitidis bacteria has led to a shift in meningococcal disease epidemiology in China, from serogroup A (MenA) to MenC. Knowledge of the evolution and genetic origin of the emergent MenC strains is limited. In this study, we subjected 76 CC4821 isolates collected across China during 1972–1977 and 2005–2013 to phylogenetic analysis, traditional genotyping, or both. We show that successive recombination events within genes encoding surface antigens and acquisition of quinolone resistance mutations possibly played a role in the emergence of CC4821 as an epidemic clone in China. MenC and MenB CC4821 strains have spread across China and have been detected in several countries in different continents. Capsular switches involving serogroups B and C occurred among epidemic strains, raising concerns regarding possible increases in MenB disease, given that vaccines in use in China do not protect against MenB. PMID:29553310

  6. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  7. The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines.

    Directory of Open Access Journals (Sweden)

    Jiafa Chen

    Full Text Available Quality control (QC of germplasm identity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotyping methods have been developed from a very limited panel of markers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs. Two QC genotyping strategies were developed, the first is a "rapid QC", employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a "broad QC", employing a larger number of SNP, used to identify each germplasm entry and to measure heterogeneity. The optimal marker selection strategies combined the selection of markers with high minor allele frequency, sampling of clustered SNP in proportion to marker cluster distance and selecting markers that maintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5% contamination in the entry, and approximately a 98% probability to detect a 2% contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different

  8. The presence of Giardia intestinalis in donkeys, Equus asinus, in China.

    Science.gov (United States)

    Zhang, Xiao-Xuan; Zhang, Fu-Kai; Li, Fa-Cai; Hou, Jun-Ling; Zheng, Wen-Bin; Du, Shuai-Zhi; Zhao, Quan; Zhu, Xing-Quan

    2017-01-03

    Giardia intestinalis is one of the most important zoonotic enteric parasites. As no information regarding prevalence and genotype of G. intestinalis in donkeys (Equus asinus) in China is available, 181 faecal samples from 48 donkeys from Jilin Province, from 104 from Shandong Province and from 29 from Liaoning Province were examined between May and December 2015. Twenty-eight (15.47%) out of 181 donkey samples were tested G. intestinalis-positive by nested amplification of the triosephosphate isomerase (tpi) gene. The prevalence in different regional groups varied from 10.42 to 18.27%. The prevalence in adult and young donkeys was 14.29 and 22.92%, respectively. Otherwise, the prevalence was 11.69% in summer and 18.27% in winter. However, no statistically significant differences were found in relation to region or age group. Sequence analysis of the tpi, glutamate dehydrogenase (gdh) and beta giardin (bg) loci identified 4, 1 and 3 subtypes of assemblage B, respectively. Moreover, four novel multilocus genotypes (MLGs novel-1 to novel-4) were identified in assemblage B. This first report of G. intestinalis in donkeys in China indicates that further studies of nation-wide molecular epidemiology and geographical distribution of Giardia in donkeys are warranted. Effective strategies should be implemented to control G. intestinalis infection in donkeys, other animals and humans.

  9. Phylogenetic characteristics of HIV-1 among travelers entering China from Myanmar: A retrospective study.

    Science.gov (United States)

    Zhang, Li; Wang, Binhui; Liang, Yaobo; Feng, Yue; Dong, Shuwei; Wang, Yajuan; Li, Yaping; Zhang, A-Mei; Liu, Li; Qin, Weihong; Xia, Xueshan

    2017-08-01

    Due to the open policy of the Chinese government, a large number of Burmese individuals enter China at land ports in Yunnan province for travel or business. However, the situation of HIV-1 infection and its phylogenetic characteristics among these travelers remains unclear, which is a potential threat to public health. From January 2003 to December 2012, a total of 1,961 travelers were detected to be positive for HIV-1 infection at land ports between Myanmar and Yunnan province, China. From 1153 (58.8%) Burmese of them, we randomly collected 489 serum samples for HIV-1 subtype/recombinant analysis. Based on successfully obtained 223 gag-RT sequences, 187 of them were genotyped as 2 subtypes and 3 CRFs. CRF01_AE was showed to be the most prevalent genotype (54.3%), followed by subtypes C (13.5%) and B (10.8%). Notably, CRF07_BC (1.3%) and CRF08_BC (4.0%) were mainly distributed in travelers from Shan state and Kachin (91.7%, 11/12), but was not found in travelers from the capital city of Yangon (0/16). Additionally, there were 36 samples (16.1%) were preliminary determined as unique recombinant forms (URFs). The higher HIV-1 infection among entering travelers from Myanmar and its diverse and complex genotypes distribution suggest this bridge population may facilitate the transmission of HIV-1. It is necessary to have the strict monitoring on this population for prevention of HIV-1 cross-border transmission. © 2017 Wiley Periodicals, Inc.

  10. Assessing Light Pollution in China Based on Nighttime Light Imagery

    Directory of Open Access Journals (Sweden)

    Wei Jiang

    2017-02-01

    Full Text Available Rapid urbanization and economic development inevitably lead to light pollution, which has become a universal environmental issue. In order to reveal the spatiotemporal patterns and evolvement rules of light pollution in China, images from 1992 to 2012 were selected from the Defense Meteorological Satellite Program Operational Linescan System (DMSP/OLS and systematically corrected to ensure consistency. Furthermore, we employed a linear regression trend method and nighttime light index method to demonstrate China’s light pollution characteristics across national, regional, and provincial scales, respectively. We found that: (1 China’s light pollution expanded significantly in provincial capital cities over the past 21 years and hot-spots of light pollution were located in the eastern coastal region. The Yangtze River Delta, Pearl River Delta, and Beijing–Tianjin–Hebei regions have formed light pollution stretch areas; (2 China’s light pollution was mainly focused in areas of north China (NC and east China (EC, which, together, accounted for over 50% of the light pollution for the whole country. The fastest growth of light pollution was observed in northwest China (NWC, followed by southwest China (SWC. The growth rates of east China (EC, central China (CC, and northeast China (NEC were stable, while those of north China (NC and south China (SC declined; (3 Light pollution at the provincial scale was mainly located in the Shandong, Guangdong, and Hebei provinces, whereas the fastest growth of light pollution was in Tibet and Hainan. However, light pollution levels in the developed provinces (Hong Kong, Macao, Shanghai, and Tianjin were higher than those of the undeveloped provinces. Similarly, the light pollution heterogeneities of Taiwan, Beijing, and Shanghai were higher than those of undeveloped western provinces.

  11. Prevalence of attention deficit/hyperactivity disorder among children and adolescents in China: a systematic review and meta-analysis.

    Science.gov (United States)

    Wang, Tingting; Liu, Kaihua; Li, Zhanzhan; Xu, Yang; Liu, Yuan; Shi, Wenpei; Chen, Lizhang

    2017-01-19

    Attention deficit/hyperactivity disorder (ADHD), the most common childhood neurobehavioural disorder, can produce a series of negative effects on children, adolescents, and even adults as well as place a serious economic burden on families and society. However, the prevalence of ADHD is not well understood in China. The goal of this study was to estimate the pooled prevalence of ADHD among children and adolescents in China using a systematic review and meta-analysis. A systematic literature search was conducted in PubMed, Web of Science, MEDLINE, CNKI, Wanfang, Weipu and CBM databases, and relevant articles published from inception to March 1, 2016, that provided the prevalence of ADHD among children and adolescents in China were reviewed. The risk of bias in individual studies was assessed using the Risk of Bias Tool for prevalence studies. Pooled-prevalence estimates were calculated with a random-effects model. Sources of heterogeneity were explored using subgroup analyses. Sixty-seven studies with a total of 275,502 individuals were included in this study. The overall pooled-prevalence of ADHD among children and adolescents in China was 6.26% (95% CI: 5.36-7.22%) with significant heterogeneity (I 2  = 99.0%, P China is generally consistent with the worldwide prevalence and shows that ADHD affects quite a large number of people under 18 years old. However, a nationwide study is needed to provide more accurate estimations.

  12. Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China

    Directory of Open Access Journals (Sweden)

    Li Z

    2017-10-01

    Full Text Available Zhao Li,* Zhi-wei Chen,* Hu Li, Hong Ren, Peng Hu Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China *These authors contributed equally to this work. Background: Direct-acting antivirals (DAAs against hepatitis C virus (HCV are potent and highly efficacious. However, resistance-associated substitutions (RASs relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear. Materials and methods: Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1, respectively.Results: The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I was observed in 85.48% (53 of 62 of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H were observed in 42.42% (28 of 66 of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G were observed in 100% (44 of 44 of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported.Conclusion: The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China. Keywords: hepatitis C virus, unstructured proteins, resistance

  13. Maturity group classification and maturity locus genotyping of early-maturing soybean varieties from high-latitude cold regions.

    Science.gov (United States)

    Jia, Hongchang; Jiang, Bingjun; Wu, Cunxiang; Lu, Wencheng; Hou, Wensheng; Sun, Shi; Yan, Hongrui; Han, Tianfu

    2014-01-01

    With the migration of human beings, advances of agricultural sciences, evolution of planting patterns and global warming, soybeans have expanded to both tropical and high-latitude cold regions (HCRs). Unlike other regions, HCRs have much more significant and diverse photoperiods and temperature conditions over seasons or across latitudes, and HCR soybeans released there show rich diversity in maturity traits. However, HCR soybeans have not been as well classified into maturity groups (MGs) as other places. Therefore, it is necessary to identify MGs in HCRs and to genotype the maturity loci. Local varieties were collected from the northern part of Northeast China and the far-eastern region of Russia. Maturity group reference (MGR) soybeans of MGs MG000, MG00, and MG0 were used as references during field experiments. Both local varieties and MGR soybeans were planted for two years (2010-2011) in Heihe (N 50°15', E 127°27', H 168.5 m), China. The days to VE (emergence), R1 (beginning bloom) and R7 (beginning maturity) were recorded and statistically analyzed. Furthermore, some varieties were further genotyped at four molecularly-identified maturity loci E1, E2, E3 and E4. The HCR varieties were classified into MG0 or even more early-maturing. In Heihe, some varieties matured much earlier than MG000, which is the most early-maturing known MG, and clustered into a separate group. We designated the group as MG0000, following the convention of MGs. HCR soybeans had relatively stable days to beginning bloom from emergence. The HCR varieties diversified into genotypes of E1, E2, E3 and E4. These loci had different effects on maturity. HCRs diversify early-maturing MGs of soybean. MG0000, a new MG that matures much earlier than known MGs, was developed. HCR soybean breeding should focus more on shortening post-flowering reproductive growth. E1, E2, E3, and E4 function differentially.

  14. Constraints on small-scale heterogeneity in the lowermost mantle from observations of near podal PcP precursors

    Science.gov (United States)

    Zhang, Baolong; Ni, Sidao; Sun, Daoyuan; Shen, Zhichao; Jackson, Jennifer M.; Wu, Wenbo

    2018-05-01

    Volumetric heterogeneities on large (∼>1000 km) and intermediate scales (∼>100 km) in the lowermost mantle have been established with seismological approaches. However, there are controversies regarding the level of heterogeneity in the lowermost mantle at small scales (a few kilometers to tens of kilometers), with lower bound estimates ranging from 0.1% to a few percent. We take advantage of the small amplitude PcP waves at near podal distances (0-12°) to constrain the level of small-scale heterogeneity within 250 km above the CMB. First, we compute short period synthetic seismograms with a finite difference code for a series of volumetric heterogeneity models in the lowermost mantle, and find that PcP is not identifiable if the small-scale heterogeneity in the lowermost mantle is above 2.5%. We then use a functional form appropriate for coda decay to suppress P coda contamination. By comparing the corrected envelope of PcP and its precursors with synthetic seismograms, we find that perturbations of small-scale (∼8 km) heterogeneity in the lowermost mantle is ∼0.2-0.5% beneath regions of the China-Myanmar border area, Okhotsk Sea and South America. Whereas strong perturbations (∼1.0%) are found beneath Central America. In the regions studied, we find that this particular type of small-scale heterogeneity in the lowermost mantle is weak, yet there are some regions requiring heterogeneity up to 1.0%. Where scattering is stronger, such as under Central America, more chemically complex mineral assemblages may be present at the core-mantle boundary.

  15. Sexually transmitted infections among heterosexual male clients of female sex workers in China: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Megan M McLaughlin

    Full Text Available Female sex workers have been the target of numerous sexually transmitted infection (STI prevention strategies in China, but their male clients have attracted considerably less public health attention and resources. We sought to systematically assess the prevalence of HIV, syphilis, gonorrhea, and chlamydia among heterosexual male clients of female sex workers in China.Original research manuscripts were identified by searching Chinese and English language databases, and 37 studies analyzing 26,552 male clients were included in the review. Client STI prevalence across studies was heterogeneous. Pooled prevalence estimates and 95% confidence intervals were 0.68% (0.36-1.28% for HIV, 2.91% (2.17-3.89% for syphilis, 2.16% (1.46-3.17% for gonorrhea, and 8.01% (4.94-12.72% for chlamydia.The pooled prevalence estimates of HIV, syphilis, gonorrhea, and chlamydia among clients in this review exceed the prevalences previously reported among population-representative samples and low-risk groups in China. However, heterogeneity across studies and sampling limitations prevent definitive conclusions about how the prevalence of STIs in this population compares to the general population. These findings suggest a need for greater attention to clients' sexual risk and disease prevalence in China's STI research agenda in order to inform effective prevention policies.

  16. Environmental determinants of woody plant diversity at a regional scale in China.

    Directory of Open Access Journals (Sweden)

    Hong Qian

    Full Text Available Understanding what drives the geographic variation of species richness across the globe is a fundamental goal of ecology and biogeography. Environmental variables have been considered as drivers of global diversity patterns but there is no consensus among ecologists on what environmental variables are primary drivers of the geographic variation of species richness. Here, I examine the relationship of woody plant species richness at a regional scale in China with sixteen environmental variables representing energy availability, water availability, energy-water balance, seasonality, and habitat heterogeneity. I found that temperature seasonality is the best predictor of woody species richness in China. Other important environmental variables include annual precipitation, mean temperature of the coldest month, and potential evapotranspiration. The best model explains 85% of the variation in woody plant species richness at the regional scale in China.

  17. Clear correlation of genotype with disease phenotype in very-long-chain acyl-CoA dehydrogenase deficiency

    DEFF Research Database (Denmark)

    Andresen, B S; Olpin, S; Poorthuis, B J

    1999-01-01

    Very-long-chain acyl-CoA dehydrogenase (VLCAD) catalyzes the initial rate-limiting step in mitochondrial fatty acid beta-oxidation. VLCAD deficiency is clinically heterogenous, with three major phenotypes: a severe childhood form, with early onset, high mortality, and high incidence of cardiomyop......Very-long-chain acyl-CoA dehydrogenase (VLCAD) catalyzes the initial rate-limiting step in mitochondrial fatty acid beta-oxidation. VLCAD deficiency is clinically heterogenous, with three major phenotypes: a severe childhood form, with early onset, high mortality, and high incidence...... of cardiomyopathy; a milder childhood form, with later onset, usually with hypoketotic hypoglycemia as the main presenting feature, low mortality, and rare cardiomyopathy; and an adult form, with isolated skeletal muscle involvement, rhabdomyolysis, and myoglobinuria, usually triggered by exercise or fasting......-phenotype relationship is in sharp contrast to what has been observed in medium-chain acyl-CoA dehydrogenase deficiency, in which no correlation between genotype and phenotype can be established....

  18. Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

    OpenAIRE

    Luo, Tao; Yang, Chongguang; Gagneux, Sebastien; Gicquel, Brigitte; Mei, Jian; Gao, Qian

    2012-01-01

    The standard 15- and 24-locus variable-number tandem repeat (VNTR) genotyping methods have demonstrated adequate discriminatory power and a small homoplasy effect for tracing tuberculosis (TB) transmission and predicting Mycobacterium tuberculosis lineages in European and North American countries. However, its validity for the definition of transmission in homogenous M. tuberculosis populations in settings with high TB burdens has been questioned. Here, we genotyped a population-based collect...

  19. Complete genome sequence analysis identifies a new genotype of brassica yellows virus that infects cabbage and radish in China.

    Science.gov (United States)

    Zhang, Xiao-Yan; Xiang, Hai-Ying; Zhou, Cui-Ji; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

    2014-08-01

    For brassica yellows virus (BrYV), proposed to be a member of a new polerovirus species, two clearly distinct genotypes (BrYV-A and BrYV-B) have been described. In this study, the complete nucleotide sequences of two BrYV isolates from radish and Chinese cabbage were determined. Sequence analysis suggested that these isolates represent a new genotype, referred to here as BrYV-C. The full-length sequences of the two BrYV-C isolates shared 93.4-94.8 % identity with BrYV-A and BrYV-B. Further phylogenetic analysis showed that the BrYV-C isolates formed a subgroup that was distinct from the BrYV-A and BrYV-B isolates based on all of the proteins except P5.

  20. [Evaluation of hepatitis B virus genotyping EIA kit].

    Science.gov (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

    2009-01-01

    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  1. The Comparison of Growth, Slaughter and Carcass Traits of Meat Chicken Genotype Produced by Back-Crossing with A Commercial Broiler Genotype

    Directory of Open Access Journals (Sweden)

    Musa Sarıca

    2014-01-01

    Full Text Available This study was conducted to determine the growth and some slaughter traits between commercial fast growing chickens and three-way cross M2 genotypes. 260 male female mixed chickens from each genotype was reared 10 replicate per genotype in the same house. Two different slaughtering ages were applied to commercial chickens and slaughtered at 6 and 7 weeks of age for comparing with cross genotypes. F chickens reached to slaughtering age at 42 days, whereas cross groups reached at 49 days. Genotypes consumed same amount of feed until slaughtering ages, but F genotype had better feed conversion ratio. The differences between dressing percentage and carcass parts ratios of genotypes were found significant, and F genotype had higher dressing percentage. Carcass parts of all genotypes were found in acceptable limits.

  2. Surveillance of Hepatitis E Virus Contamination in Shellfish in China

    Directory of Open Access Journals (Sweden)

    Shenyang Gao

    2015-02-01

    Full Text Available Background: Hepatitis E virus (HEV has been confirmed to be a zoonotic virus of worldwide distribution. HEV contamination in the water environment has not been well examined in China. The objective of this study was to evaluate HEV contamination in shellfish in a coastal area of China. Such contamination would be significant for evaluating public health risks. Methods: samples of three species shellfish were collected from thirteen points of estuarine tidal flats around the Bohai Gulf and screened for HEV RNA using an in-house nested RT-PCR assay. The detected HEV-positive samples were further verified by gene cloning and sequencing analysis. Results: the overall HEV-positive detection rate is approximately 17.5% per kilogram of shellfish.  HEV was more common among S. subcrenata (28.2%, followed by A. granosa (14.3% and R. philippinarum (11.5%. The phylogenetic analysis of the 13 HEV strains detected revealed that gene fragments fell into two known 4 sub-genotypes (4b/4d groups and another unknown group. Conclusions: 13 different sub-genotype 4 HEVs were found in contaminated shellfish in the Bohai Gulf rim. The findings suggest that a health risk may exist for users of waters in the Bonhai area and to consumers of shellfish.  Further research is needed to assess the sources and infectivity of HEV in these settings, and to evaluate additional shellfish harvesting areas.

  3. Characterization of Theileria equi genotypes in horses in Israel, the Palestinian Authority and Jordan.

    Science.gov (United States)

    Ketter-Ratzon, Dafna; Tirosh-Levy, Sharon; Nachum-Biala, Yaarit; Saar, Tal; Qura'n, Lara; Zivotofsky, Doni; Abdeen, Ziad; Baneth, Gad; Steinman, Amir

    2017-06-01

    Equine theileriosis caused by Theileria equi is endemic in the Middle East, where it causes a severe disease as well as widespread subclinical infection. The aim of this study was to evaluate the diversity of T. equi genotypes in Israel and the neighboring Palestinian Authority and Jordan. Blood samples from 355 horses from Israel, the Palestinian Authority and Jordan were tested for the prevalence of T. equi DNA. Two hundred and fourteen (60%) were found positive for T. equi infection by PCR. Of those, the 18S rRNA (1458bp) and the EMA-1 (745bp) genes of T. equi were sequenced from 15 horse samples that represent Israel's geographical distribution together with four samples from the Palestinian Authority and two from Jordan. The results were used for genotype characterization and phylogenetic analysis of T. equi in the equine population in Israel and its surroundings. Three 18S rRNA genotype clades were found in Israel (A, C and D) with clade D being the most prevalent and included all four isolates from the PA. In contrast, the EMA-1 gene showed little diversity with all sequences clustering in the same clade apart from one Jordanian sequence. Results suggest that although the Israeli horse population is small and relatively confined geographically, it is probable that the genetic variability, which was found among Israeli horses, is a result of introduction of horses from other countries. It also suggests that the EMA-1 gene is probably not a good target for the evaluation of variance in T. equi populations. Characterization of the different genotypes prevalent in a certain region is important in order to map out the intra-species sequence heterogeneity of the parasite, which is needed in order to develop new diagnostic tools and vaccines. Copyright © 2017 Elsevier GmbH. All rights reserved.

  4. Preliminary study of lateral variation in crustal structure of Northeast China from teleseismic receiver functions

    Science.gov (United States)

    Chen, Youlin; Liu, Ruifeng; Huang, Zhibin; Sun, Li

    2011-02-01

    We conducted comprehensive receiver function analyses for a large amount of high-quality broadband teleseismic waveforms data recorded at 19 China National Digital Seismic Network (CNDSN) stations deployed in Northeast China. An advanced H- κ domain search method was adopted to accurately estimate the crustal thickness and ν P/ ν S ratio. The crust has an average thickness of about 34.4 km. The thinnest crust occurs in the central region of Northeast China, while the thickest crust is beneath the Yanshan belt. The ν P/ ν S ratio is relatively uniform with an average of about 1.733. The highest ν P/ ν S ratio is found beneath the Changbaishan, likely associated with its volcanic activities. We found significant lateral heterogeneity beneath three stations CN2, MDJ, and MIH located along the Suolon suture from the back-zimuthal dependence of Moho depth. The velocity modeling from receiver functions indicated complicated Earth structure beneath these stations with large crust-mantle transition zone, noticeable velocity jump in upper mantle, and low velocity zone in middle crust. Dipping velocity interface in the crust with strike approximately parallel to the Suolon suture and down-dip to the south or southeast might explain the observed lateral heterogeneity.

  5. GxE Interactions Between FOXO Genotypes and Tea Drinking Significantly Affect Cognitive Disability at Advanced Ages in China

    DEFF Research Database (Denmark)

    Zeng, Yi; Chen, Huashuai; Ni, Ting

    2015-01-01

    Logistic regression analysis based on data from 822 Han Chinese oldest old aged 92+ demonstrated that interactions between carrying FOXO1A-266 or FOXO3-310 or FOXO3-292 and tea drinking at around age 60 or at present time were significantly associated with lower risk of cognitive disability...... at advanced ages. Associations between tea drinking and reduced cognitive disability were much stronger among carriers of the genotypes of FOXO1A-266 or FOXO3-310 or FOXO3-292 compared with noncarriers, and it was reconfirmed by analysis of three-way interactions across FOXO genotypes, tea drinking at around...... age 60, and at present time. Based on prior findings from animal and human cell models, we postulate that intake of tea compounds may activate FOXO gene expression, which in turn may positively affect cognitive function in the oldest old population. Our empirical findings imply that the health...

  6. Hepatitis B virus infection in Chinese patients with hepatitis C virus infection: prevalence, clinical characteristics, viral interactions and host genotypes: a nationwide cross-sectional study.

    Science.gov (United States)

    Yan, Li-Bo; Rao, Hui-Ying; Ma, Yuan-Ji; Bai, Lang; Chen, En-Qiang; Du, Ling-Yao; Yang, Rui-Feng; Wei, Lai; Tang, Hong

    2016-10-12

    Little is known about hepatitis B virus (HBV) infection in patients with hepatitis C virus (HCV) infection in China. This study aimed to evaluate the prevalence, clinical characteristics, viral interactions and host genotypes of HBV/HCV dual infection compared with HCV monoinfection. A cross-sectional study. China. 997 patients with HCV from 28 university-affiliated hospitals in China were enrolled in this research. Patients were divided into two subgroups. The prevalence of HBV infection in patients with HCV was 4.11% (41/997). The age-specific prevalence of HBsAg was 0.70%, 3.97% and 5.85% in groups aged 18-30, 30-50 and >50 years old (p=0.057), respectively. Patients with HBV/HCV dual infection and patients with HCV monoinfection had similar HCV viral loads (5.80±0.89 vs 5.83±1.00 log10 IU/mL, p=0.904). The dominant HCV genotype was 1b in both groups (53.65% vs 56.90%, p=0.493). The protective C allele in IL-28B (rs12979860) was also the dominant allele type in both patient groups (85.36% vs 83.99%, p=0.814). Patients with HBV/HCV dual infection had a higher ratio of liver cirrhosis and hepatic decompensation than patients with HCV monoinfection (39.02% vs 17.69%, p=0.001; 31.70% vs 12.13%, p=0.001). The HBV burden was moderate in HCV-infected patients in China. Liver cirrhosis was more common in patients with HBV/HCV dual infection, suggesting the need for closer monitoring of dual-infected individuals. NCT01293279; Post-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  7. Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4.

    Science.gov (United States)

    Yamada, Hiroko; Takahashi, Kazuaki; Lim, Olline; Svay, Somana; Chuon, Channarena; Hok, Sirany; Do, Son Huy; Fujimoto, Mayumi; Akita, Tomoyuki; Goto, Noboru; Katayama, Keiko; Arai, Masahiro; Tanaka, Junko

    2015-01-01

    Hepatitis E virus (HEV) is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years), the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0); HEV RNA was detected in two participants (0.23%) and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%), SS19 (94.37%), and swDQ (91.94%). Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required.

  8. Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4.

    Directory of Open Access Journals (Sweden)

    Hiroko Yamada

    Full Text Available Hepatitis E virus (HEV is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years, the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0; HEV RNA was detected in two participants (0.23% and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%, SS19 (94.37%, and swDQ (91.94%. Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required.

  9. A Hybrid Method for Interpolating Missing Data in Heterogeneous Spatio-Temporal Datasets

    Directory of Open Access Journals (Sweden)

    Min Deng

    2016-02-01

    Full Text Available Space-time interpolation is widely used to estimate missing or unobserved values in a dataset integrating both spatial and temporal records. Although space-time interpolation plays a key role in space-time modeling, existing methods were mainly developed for space-time processes that exhibit stationarity in space and time. It is still challenging to model heterogeneity of space-time data in the interpolation model. To overcome this limitation, in this study, a novel space-time interpolation method considering both spatial and temporal heterogeneity is developed for estimating missing data in space-time datasets. The interpolation operation is first implemented in spatial and temporal dimensions. Heterogeneous covariance functions are constructed to obtain the best linear unbiased estimates in spatial and temporal dimensions. Spatial and temporal correlations are then considered to combine the interpolation results in spatial and temporal dimensions to estimate the missing data. The proposed method is tested on annual average temperature and precipitation data in China (1984–2009. Experimental results show that, for these datasets, the proposed method outperforms three state-of-the-art methods—e.g., spatio-temporal kriging, spatio-temporal inverse distance weighting, and point estimation model of biased hospitals-based area disease estimation methods.

  10. Antimicrobial susceptibility, virulence genes, and randomly amplified polymorphic DNA analysis of Staphylococcus aureus recovered from bovine mastitis in Ningxia, China.

    Science.gov (United States)

    Wang, Dong; Zhang, Limei; Zhou, Xuezhang; He, Yulong; Yong, Changfu; Shen, Mingliang; Szenci, Otto; Han, Bo

    2016-12-01

    Staphylococcus aureusis the leading pathogen involved inbovine mastitis, but knowledgeabout antimicrobial resistance, virulence factors, and genotypes of Staphylococcus aureus resulting in bovine mastitis in Ningxia, China, is limited. Therefore, antimicrobial susceptibility, virulence gene, and randomly amplified polymorphic DNA (RAPD) analyses of Staph. aureus were carried out. A total of 327 milk samples from cows with clinical and subclinical mastitis in 4 regions of Ningxia were used for the isolation and identification of pathogens according to phenotypic and molecular characteristics. Antimicrobial susceptibility against 22 antimicrobial agents was determined by disk diffusion. The presence of 8 virulence genes in Staph. aureus isolates was tested by PCR. Genotypes of isolates were investigated based on RAPD. Results showed that 35 isolates obtained from mastitis milk samples were identified as Staph. aureus. The isolates were resistant to sulfamethoxazole (100%), penicillin G (94.3%), ampicillin (94.3%), erythromycin (68.6%), azithromycin (68.6%), clindamycin (25.7%), amoxicillin (11.4%), and tetracycline (5.7%). All of the isolates contained one or more virulence genes with average (standard deviation) of 6.6±1.6. The most prevalent virulence genes were hlb (97.1%), followed by fnbpA, hla, coa (94.3% each), nuc (85.7%), fnbpB (80%), clfA (77.1%), and tsst-1 (40%). Nine different gene patterns were found and 3 of them were the dominant gene combinations (77.1%). Staphylococcus aureus isolates (n=35) were divided into 6 genotypes by RAPD tying, the genotypes III and VI were the most prevalent genotypes. There was greatvariation in genotypes of Staph. aureus isolates, not only among different farms, but also within the same herd in Ningxia province. The study showed a high incidence of Staph. aureus with genomic variation of resistance genes, which is matter of great concern in public and animal health in Ningxia province of China. Copyright © 2016 American

  11. A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism.

    Science.gov (United States)

    Wood, Corlett W; Stinchcombe, John R

    2017-11-01

    The maintenance of genetic variation in the benefits provided by mutualists is an evolutionary puzzle (Heath & Stinchcombe, ). Over time, natural selection should favour the benefit strategy that confers the highest fitness, eroding genetic variation in partner quality. Yet abundant genetic variation in partner quality exists in many systems (Heath & Stinchcombe, ). One possible resolution to this puzzle is that the genetic identity of both a host and its partner affects the benefits each mutualist provides to the other, a pattern known as a genotype-by-genotype interaction (Figure ). Mounting evidence suggests that genotype-by-genotype interactions between partners are pervasive at the phenotypic level (Barrett, Zee, Bever, Miller, & Thrall, ; Heath, ; Hoeksema & Thompson, ). Ultimately, however, to link these phenotypic patterns to the maintenance of genetic variation in mutualisms we need to answer two questions: How much variation in mutualism phenotypes is attributable to genotype-by-genotype interactions, and what mutualistic functions are influenced by each partner and by the interaction between their genomes? In this issue of Molecular Ecology, Burghardt et al. (2017) use transcriptomics to address both questions in the legume-rhizobia mutualism. © 2017 John Wiley & Sons Ltd.

  12. MLVA and MLST typing of Brucella from Qinghai, China.

    Science.gov (United States)

    Ma, Jun-Ying; Wang, Hu; Zhang, Xue-Fei; Xu, Li-Qing; Hu, Gui-Ying; Jiang, Hai; Zhao, Fang; Zhao, Hong-Yan; Piao, Dong-Ri; Qin, Yu-Min; Cui, Bu-Yun; Lin, Gong-Hua

    2016-04-13

    The Qinghai-Tibet Plateau (QTP) of China is an extensive pastoral and semi-pastoral area, and because of poverty and bad hygiene conditions, Brucella is highly prevalent in this region. In order to adequately prevent this disease in the QTP region it is important to determine the identity of Brucella species that caused the infection. A total of 65 Brucella isolates were obtained from human, livestock and wild animals in Qinghai, a Chinese province in east of the QTP. Two molecular typing methods, MLVA (multi-locus variable-number tandem-repeat analysis) and MLST (multi locus sequence typing) were used to identify the species and genotypes of these isolates. Both MLVA and MLST typing methods classified the 65 isolates into three species, B. melitensis, B. abortus and B. suis, which included 60, 4 and 1 isolates respectively. The MLVA method uniquely detected 34 (Bm01 ~ Bm34), 3 (Ba01 ~ Ba03), and 1 (Bs01) MLVA-16 genotypes for B. melitensis, B. abortus and B. suis, respectively. However, none of these genotypes exactly matched any of the genotypes in the Brucella2012 MLVA database. The MLST method identified five known ST types: ST7 and ST8 (B. melitensis), ST2 and ST5 (B. abortus), and ST14 (B. suis). We also detected a strain with a mutant type (3-2-3-2-?-5-3-8-2) of ST8 (3-2-3-2-1-5-3-8-2). Extensive genotype-sharing events could be observed among isolates from different host species. There were at least three Brucella (B. melitensis, B. abortus and B. suis) species in Qinghai, of which B. melitensis was the predominant species in the area examined. The Brucella population in Qinghai was very different from other regions of the world, possibly owing to the unique geographical characteristics such as extremely high altitude in QTP. There were extensive genotype-sharing events between isolates obtained from humans and other animals. Yaks, sheep and blue sheep were important zoonotic reservoirs of brucellosis causing species found in humans.

  13. Separation of Hepatitis C genotype 4a into IgG-depleted and IgG-enriched fractions reveals a unique quasispecies profile.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2012-02-03

    BACKGROUND: Hepatitis C virus (HCV) circulates in an infected individual as a heterogeneous mixture of closely related viruses called quasispecies. The E1\\/E2 region of the HCV genome is hypervariable (HVR1) and is targeted by the humoral immune system. Hepatitis C virions are found in two forms: antibody associated or antibody free. The objective of this study was to investigate if separation of Hepatitis C virions into antibody enriched and antibody depleted fractions segregates quasispecies populations into distinctive swarms. RESULTS: A HCV genotype 4a specimen was fractionated into IgG-depleted and IgG-enriched fractions by use of Albumin\\/IgG depletion spin column. Clonal analysis of these two fractions was performed and then compared to an unfractionated sample. Following sequence analysis it was evident that the antibody depleted fraction was significantly more heterogeneous than the antibody enriched fraction, revealing a unique quasispecies profile. An in-frame 3 nt insertion was observed in 26% of clones in the unfractionated population and in 64% of clones in the IgG-depleted fraction. In addition, an in-frame 3 nt indel event was observed in 10% of clones in the unfractionated population and in 9% of clones in the IgG-depleted fraction. Neither of these latter events, which are rare occurrences in genotype 4a, was identified in the IgG-enriched fraction. CONCLUSION: In conclusion, the homogeneity of the IgG-enriched species is postulated to represent a sequence that was strongly recognised by the humoral immune system at the time the sample was obtained. The heterogeneous nature of the IgG-depleted fraction is discussed in the context of humoral escape.

  14. First isolation, identification, phenotypic and genotypic characterization of Brucella abortus biovar 3 from dairy cattle in Tanzania.

    Science.gov (United States)

    Mathew, C; Stokstad, M; Johansen, T B; Klevar, S; Mdegela, R H; Mwamengele, G; Michel, P; Escobar, L; Fretin, D; Godfroid, J

    2015-07-21

    Brucellosis is a disease of worldwide public health and economic importance. Successful control is based on knowledge of epidemiology and strains present in an area. In developing countries, most investigations are based on serological assays. This study aimed at investigating a dairy herd experiencing abortions in order to establish within-herd seroprevalence to Brucella spp., identify, characterize Brucella strains by Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA-VNTR) and investigate possible spillover to other species. The within-herd seroprevalence in cattle (n = 200) was 48 % (95 % CI 41-55), using an indirect ELISA, while the Rose Bengal Test (RBT) yielded lower prevalence (21.5 %; 95 % CI 16-27). Two sheep (n = 35) and one goat (n = 50) were seropositive using ELISA while none of the dogs (n = 6) was positive with the RBT. Three Brucella were isolated from an aborted fetus and associated membranes. Real time PCR (IS711), Bruce-ladder and classical biotyping classified the isolates as B. abortus biovar 3. MLVA-VNTR revealed two different but closely related genotypes. The isolates showed unique profiles, providing the first genotypic data from Tanzania. These genotypes were not related to B. abortus biovar 3 reference strain Tulya originally isolated from a human patient in Uganda in 1958, unlike the genotypes isolated and characterized recently in Kenya. High within-herd prevalence, isolation of the pathogen and abortion confirm that B. abortus is circulating in this herd with cattle as reservoir hosts. A low seroprevalence in sheep and goats suggests a spillover of B. abortus from cattle to small ruminants in the herd. This is the first isolation and characterization of B. abortus biovar 3 from a dairy cow with abortion in Tanzania. The origin of the Tanzanian genotypes remain elusive, although they seem to be related to genotypes found in Europe, Turkey and China but not related to B. abortus biovar 3 reference strain or genotypes from

  15. Popcorn genotypes resistance to fall armyworm

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    Nádia Cristina de Oliveira

    2018-02-01

    Full Text Available ABSTRACT: The aim of this study was to evaluate popcorn genotypes for resistance to the fall armyworm, Spodoptera frugiperda. The experiment used a completely randomized design with 30 replicates. The popcorn genotypes Aelton, Arzm 05 083, Beija-Flor, Colombiana, Composto Chico, Composto Gaúcha, Márcia, Mateus, Ufvm Barão Viçosa, Vanin, and Viviane were evaluated,along with the common maize variety Zapalote Chico. Newly hatched fall armyworm larvae were individually assessed with regard to biological development and consumption of food. The data were subjected to multivariate analyses of variance and genetic divergence among genotypes was evaluated through the clustering methods of Tocher based on generalized Mahalanobis distances and canonical variable analyses. Seven popcorn genotypes, namely, Aelton, Arzm 05 083, Composto Chico, Composto Gaúcha, Márcia, Mateus, and Viviane,were shown to form a cluster (cluster I that had antibiosis as the mechanism of resistance to the pest. Cluster I genotypes and the Zapalote Chico genotype could be used for stacking genes for antibiosis and non-preference resistance.

  16. Lack of detection of host associated differences in Newcastle disease viruses of genotype VIId isolated from chickens and geese

    Directory of Open Access Journals (Sweden)

    Wang Yuyang

    2012-09-01

    Full Text Available Abstract Background The goose is usually considered to be resistant even to strains of Newcastle disease virus (NDV that are markedly virulent for chickens. However, ND outbreaks have been frequently reported in goose flocks in China since the late 1990s with the concurrent emergence of genotype VIId NDV in chickens. Although the NDVs isolated from both chickens and geese in the past 15 years have been predominantly VIId viruses, published data comparing goose- and chicken-originated ND viruses are scarce and controversial. Results In this paper, we compared genotype VIId NDVs originated from geese and chickens genetically and pathologically. Ten entire genomic sequences and 329 complete coding sequences of individual genes from genotype VIId NDVs of both goose- and chicken-origin were analyzed. We then randomly selected two goose-originated and two chicken-originated VIId NDVs and compared their pathobiology in both geese and chickens in vivo and in vitro with genotype IV virus Herts/33 as a reference. The results showed that all the VIId NDVs either from geese or from chickens shared high sequence homology and characteristic amino acid substitutions and clustered together in phylogenetic trees. In addition, geese and chickens infected by goose or chicken VIId viruses manifested very similar pathological features distinct from those of birds infected with Herts/33. Conclusions There is no genetic or phenotypic difference between genotype VIId NDVs originated from geese and chickens. Therefore, no species-preference exists for either goose or chicken viruses and more attention should be paid to the trans-species transmission of VIId NDVs between geese and chickens for the control and eradication of ND.

  17. Interactions between Social/ behavioral factors and ADRB2 genotypes may be associated with health at advanced ages in China

    DEFF Research Database (Denmark)

    Zeng, Y.; Cheng, L. G.; Zhao, L.

    2013-01-01

    ages. This study intends to fill in this research gap. Method: We conducted an exploratory analysis, using longitudinal survey phenotype/genotype data from 877 oldest-old aged 90+. To estimate association of GxE interactions with health outcome, adjusted for the potential correlation between genotypes...... and social/behavioral factors and various other potentially confounding factors, we develop and test an innovative three-step procedure which combines logistic regression and structural equation methods. Results: Interaction between regular exercise and carrying rs1042718 minor allele is significantly...... analysis found that, adjusted for the confounding effects of correlation of the ADRB2 SNPs with negative emotion, interaction between negative emotion and carrying rs1042718 or rs1042719 minor allele is significantly and negatively associated with cognitive function. The positive association of regular...

  18. Heterogeneous characters modeling of instant message services users' online behavior.

    Directory of Open Access Journals (Sweden)

    Hongyan Cui

    Full Text Available Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users' online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on.

  19. Heterogeneous characters modeling of instant message services users’ online behavior

    Science.gov (United States)

    Fang, Yajun; Horn, Berthold

    2018-01-01

    Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users’ online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on. PMID:29734327

  20. Risk factors for pulmonary cavitation in tuberculosis patients from China.

    Science.gov (United States)

    Zhang, Liqun; Pang, Yu; Yu, Xia; Wang, Yufeng; Lu, Jie; Gao, Mengqiu; Huang, Hairong; Zhao, Yanlin

    2016-10-12

    Pulmonary cavitation is one of the most frequently observed clinical characteristics in tuberculosis (TB). The objective of this study was to investigate the potential risk factors associated with cavitary TB in China. A total of 385 smear-positive patients were enrolled in the study, including 192 (49.9%) patients with cavitation as determined by radiographic findings. Statistical analysis revealed that the distribution of patients with diabetes in the cavitary group was significantly higher than that in the non-cavitary group (adjusted odds ratio (OR) (95% confidence interval (CI)):12.08 (5.75-25.35), Ptuberculosis strains, 330 strains (85.7%) were classified as the Beijing genotype, which included 260 strains that belonged to the modern Beijing sublineage and 70 to the ancient Beijing sublineage. In addition, there were 80 and 31 strains belonging to large and small clusters, respectively. Statistical analysis revealed that cavitary disease was observed more frequently among the large clusters than the small clusters (P=0.037). In conclusion, our findings demonstrate that diabetes and multidrug resistance are risk factors associated with cavitary TB. In addition, there was no significant difference in the cavitary presentation between patients infected with the Beijing genotype strains and those infected with the non-Beijing genotype strains.

  1. Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site.

    Science.gov (United States)

    Antonescu, Cristina R; Viale, Agnes; Sarran, Lisa; Tschernyavsky, Sylvia J; Gonen, Mithat; Segal, Neil H; Maki, Robert G; Socci, Nicholas D; DeMatteo, Ronald P; Besmer, Peter

    2004-05-15

    Gastrointestinal stromal tumors (GISTs) are specific KIT expressing and KIT-signaling driven mesenchymal tumors of the human digestive tract, many of which have KIT-activating mutations. Previous studies have found a relatively homogeneous gene expression profile in GIST, as compared with other histological types of sarcomas. Transcriptional heterogeneity within clinically or molecularly defined subsets of GISTs has not been previously reported. We tested the hypothesis that the gene expression profile in GISTs might be related to KIT genotype and possibly to other clinicopathological factors. An HG-U133A Affymetrix chip (22,000 genes) platform was used to determine the variability of gene expression in 28 KIT-expressing GIST samples from 24 patients. A control group of six intra-abdominal leiomyosarcomas was also included for comparison. Statistical analyses (t tests) were performed to identify discriminatory gene lists among various GIST subgroups. The levels of expression of various GIST subsets were also linked to a modified version of the growth factor/KIT signaling pathway to analyze differences at various steps in signal transduction. Genes involved in KIT signaling were differentially expressed among wild-type and mutant GISTs. High gene expression of potential drug targets, such as VEGF, MCSF, and BCL2 in the wild-type group, and Mesothelin in exon 9 GISTs were found. There was a striking difference in gene expression between stomach and small bowel GISTs. This finding was validated in four separate tumors, two gastric and two intestinal, from a patient with familial GIST with a germ-line KIT W557R substitution. GISTs have heterogeneous gene expression depending on KIT genotype and tumor location, which is seen at both the genomic level and the KIT signaling pathway in particular. These findings may explain their variable clinical behavior and response to therapy.

  2. Developmental plasticity: re-conceiving the genotype.

    Science.gov (United States)

    Sultan, Sonia E

    2017-10-06

    In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

  3. Performance of chickpea genotypes under Swat valley conditions

    International Nuclear Information System (INIS)

    Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.

    2004-01-01

    Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

  4. Whole-gene analysis of two groups of hepatitis B virus C/D inter-genotype recombinant strains isolated in Tibet, China.

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    Tiezhu Liu

    Full Text Available Tibet is a highly hepatitis B virus (HBV endemic area. Two types of C/D recombinant HBV are commonly isolated in Tibet and have been previously described. In an effort to better understand the molecular characteristic of these C/D recombinant strains from Tibet, we undertook a multistage random sampling project to collect HBsAg positive samples. Molecular epidemiological and bio-informational technologies were used to analyze the characteristics of the sequences found in this study. There were 60 samples enrolled in the survey, and we obtained 19 whole-genome sequences. 19 samples were all C/D recombinant, and could be divided into two sub-types named C/D1 and C/D2 according to the differences in the location of the recombinant breakpoint. The recombination breakpoint of the 10 strains belonging to the C/D1 sub-type was located at nt750, while the 9 stains belonging to C/D2 had their recombination break point at nt1530. According to whole-genome sequence analysis, the 19 identified strains belong to genotype C, but the nucleotide distance was more than 5% between the 19 strains and sub-genotypes C1 to C15. The distance between C/D1with C2 was 5.8±2.1%, while the distance between C/D2 with C2 was 6.4±2.1%. The parental strain was most likely sub-genotype C2. C/D1 strains were all collected in the middle and northern areas of Tibet including Lhasa, Linzhi and Ali, while C/D2 was predominant in Shannan in southern Tibet. This indicates that the two recombinant genotypes are regionally distributed in Tibet. These results provide important information for the study of special HBV recombination events, gene features, virus evolution, and the control and prevention policy of HBV in Tibet.

  5. Genomic selection in mink yield higher accuracies with a Bayesian approach allowing for heterogeneous variance than a GBLUP model

    DEFF Research Database (Denmark)

    Villumsen, Trine Michelle; Su, Guosheng; Cai, Zexi

    2018-01-01

    by sequencing. Four live grading traits and four traits on dried pelts for size and quality were analysed. GWAS analysis detected significant SNPs for all the traits. The single-trait Bayesian model resulted in higher accuracies for the genomic predictions than the single-trait GBLUP model, especially......The accuracy of genomic prediction for mink was compared for single-trait and multiple-trait GBLUP models and Bayesian models that allowed for heterogeneous (co)variance structure over the genome. The mink population consisted of 2,103 brown minks genotyped with the method of genotyping...... for the traits measured on dried pelts. We expected the multiple-trait models to be superior to the single trait models since the multiple-trait model can make use of information when traits are correlated. However, we did not find a general improvement in accuracies with the multiple-trait models compared...

  6. Genetic variations of the NPC1L1 gene associated with hepatitis C virus (HCV) infection and biochemical characteristics of HCV patients in China.

    Science.gov (United States)

    Zhang, A-Mei; Zhang, Cheng-Lin; Song, Yuzhu; Zhao, Ping; Feng, Yue; Wang, Binghui; Li, Zheng; Liu, Li; Xia, Xueshan

    2016-12-01

    About 2% of the world population is infected with hepatitis C virus (HCV), a leading cause of hepatic cirrhosis and hepatocellular carcinoma. The Niemann-Pick C1-like 1 cholesterol absorption receptor (NPC1L1) was recently identified to be an important factor for HCV entry into host cells. Whether genetic variations of the NPC1L1 gene are associated with HCV infection is unknown. In this study, five single nucleotide polymorphisms (SNPs) of the NPC1L1 gene were analyzed in 261 HCV-infected individuals and 265 general controls from Yunnan Province, China. No significant differences were identified in genotypes or alleles of the SNPs between the two groups. After constructing haplotypes based on the five SNPs, a significant difference between HCV-infected individuals and general controls was shown for two haplotypes. Haplotype GCCTT appeared to be a protective factor and haplotype GCCCT was a risk factor for HCV-infected individuals. Genotypes of four SNPs correlated with biochemical characteristics of HCV-infected persons. Genotypes of SNPs rs799444 and rs2070607 were correlated with total bilirubin. Genotype TT of rs917098 was a risk factor for the gamma-glutamyltransferase level. Furthermore, HCV-infected individuals carrying genotype GG of rs41279633 showed statistically higher gamma-glutamyltransferase levels than HCV-infected persons with GT and TT. The results of this study identified the association between genetic susceptibility of the NPC1L1 gene and HCV infection, as well as biochemical characteristics of HCV-infected persons in Yunnan, China. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  7. Metafroniter energy efficiency with CO2 emissions and its convergence analysis for China

    International Nuclear Information System (INIS)

    Li, Ke; Lin, Boqiang

    2015-01-01

    This paper measures the energy efficiency performance with carbon dioxide (CO 2 ) emissions in 30 provinces in China during the period of 1997–2011 using a meta-frontier framework with the improved directional distance function (DDF). We construct a new environmental production possibility set by combining the super-efficiency and sequential data envelopment analysis (DEA) models to avoid “discriminating power problem” and “technical regress” when evaluating efficiency by DDF. Then, it is used in a meta-frontier framework to reflect the technology heterogeneities across east, central and west China. The results indicate that eastern China achieved the highest progress inefficiency relative to the metafrontier, followed by western and the central China. By focusing on technology gaps, we offer some suggestions for the different groups based on group-frontier and meta-frontier analyses. The inefficiency can be attributed to managerial failure for eastern and western China, and technological differences for central China. The convergence analysis shows that energy and CO 2 emission governance will produce negative effects on economic growth, and it is suitable and acceptable to introduce rigorous environmental measures in eastern China. - Highlights: • We present an improved DEA model to calculate the directional distance function. • The improved directional distance function combines with a meta-frontier analysis. • The reasons of energy inefficiency are varied for different regions. • Convergence analysis means east China should introduce rigorous environmental policy

  8. Cancer stem cell marker Musashi-1 rs2522137 genotype is associated with an increased risk of lung cancer.

    Directory of Open Access Journals (Sweden)

    Xu Wang

    Full Text Available Gene single nucleotide polymorphisms (SNPs have been extensively studied in association with development and prognosis of various malignancies. However, the potential role of genetic polymorphisms of cancer stem cell (CSC marker genes with respect to cancer risk has not been examined. We conducted a case-control study involving a total of 1000 subjects (500 lung cancer patients and 500 age-matched cancer-free controls from northeastern China. Lung cancer risk was analyzed in a logistic regression model in association with genotypes of four lung CSC marker genes (CD133, ALDH1, Musashi-1, and EpCAM. Using univariate analysis, the Musashi-1 rs2522137 GG genotype was found to be associated with a higher incidence of lung cancer compared with the TT genotype. No significant associations were observed for gene variants of CD133, ALDH1, or EpCAM. In multivariate analysis, Musashi-1 rs2522137 was still significantly associated with lung cancer when environmental and lifestyle factors were incorporated in the model, including lower BMI; family history of cancer; prior diagnosis of chronic obstructive pulmonary disease, pneumonia, or pulmonary tuberculosis; occupational exposure to pesticide; occupational exposure to gasoline or diesel fuel; heavier smoking; and exposure to heavy cooking emissions. The value of the area under the receiver-operating characteristic (ROC curve (AUC was 0.7686. To our knowledge, this is the first report to show an association between a Musashi-1 genotype and lung cancer risk. Further, the prediction model in this study may be useful in determining individuals with high risk of lung cancer.

  9. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.

    2006-01-01

    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  10. Identification of the -α(2.4) Deletion in One Family and in One Hb H Disease Patient in Guangxi, People's Republic of China.

    Science.gov (United States)

    Pang, Wanrong; Sun, Lei; Long, Ju; Weng, Xunjin; Ye, Xuehe; Wang, Junjie; Liao, Yan; Tang, Weijun; Fan, Zuqian; Wu, Suping; Song, Chuanlu; Wei, Xiaoying; Zhang, Chenghong

    2016-06-01

    The 2.4 kb (or -α(2.4)) deletion in the α-globin gene cluster (NG_000006.1) is an α(+)-thalassemia (α(+)-thal) allele. The molecular basis of -α(2.4) is a deletion from 36860 to 39251 of the α-globin gene cluster. It was reported by three research groups in 2005, 2012 and 2014, respectively. In routine thalassemia screening studies by this research group, we found an individual with the -α(2.4)/αα genotype and an Hb H (β4) disease patient whose genotype was - -(SEA)/-α(2.4). Samples from the parents of the carrier of the -α(2.4)/αα genotype were collected to perform pedigree analysis, and the proband's mother's genotype was diagnosed to be - -(SEA)/-α(2.4). The research revealed that the -α(2.4) allele exists in the population of southern Guangxi, People's Republic of China.

  11. Integrative Genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data

    Directory of Open Access Journals (Sweden)

    Eric eGamazon

    2013-05-01

    Full Text Available Given recent advances in the generation of high-throughput data such as whole genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs, demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical FDR when p-values for the observed and simulated phenotypes are available.

  12. Variants of Interleukin-7/Interleukin-7 Receptor Alpha are Associated with Both Neuromyelitis Optica and Multiple Sclerosis Among Chinese Han Population in Southeastern China

    Directory of Open Access Journals (Sweden)

    Jing-Cong Zhuang

    2015-01-01

    Full Text Available Background: Neuromyelitis optica (NMO and multiple sclerosis (MS are autoimmune demyelinating diseases of the central nerve system. Interleukin-7 (IL-7 and interleukin-7 receptor alpha (IL-7Rα were proved to be important in the pathogenesis of both diseases because of the roles they played in the differentiations of autoimmune lymphocytes. The variants of both genes had been identified to be associated with MS susceptibility in Caucasian, Japanese and Korean populations. However, the association of these variants with NMO and MS has not been well studied in Chinese Southeastern Han population. Here, we aimed to evaluate the association of six IL-7 variants (rs1520333, rs1545298, rs4739140, rs6993386, rs7816065, and rs2887502 and one variant of IL-7RA (rs6897932 with NMO and MS among Chinese Han population in southeastern China. Methods: Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MassARRAY system and Sanger sequencing were used to determine the variants of IL-7 and IL-7RA in 167 NMO patients, 159 MS patients and 479 healthy controls among Chinese Han population in southeastern China. Samples were excluded if the genotyping success rate <90%. Results: Statistical differences were observed in the genotypes of IL-7 rs1520333 in MS patients and IL-7RA rs6897932 in NMO patients, compared with healthy controls (P = 0.035 and 0.034, respectively. There was a statistically significant difference in the genotypes of IL-7 rs2887502 between MS and NMO patients (P = 0.014. And there were statistically significant differences in the rs6897932 genotypes (P = 0.004 and alleles (P = 0.042 between NMO-IgG positive patients and healthy controls. Conclusions: The study suggested that among Chinese Han population in southeastern China, the variant of IL-7RA (rs6897932 was associated with NMO especially NMO-IgG positive patients while the variant of IL-7 (rs1520333 with MS patients. And the genotypic differences of IL-7 rs2887502

  13. Variants of Interleukin-7/Interleukin-7 Receptor Alpha are Associated with Both Neuromyelitis Optica and Multiple Sclerosis Among Chinese Han Population in Southeastern China

    Institute of Scientific and Technical Information of China (English)

    Jing-Cong Zhuang; Lei Wu; Mei-Zhen Qian; Ping-Ping Cai; Qi-Bing Liu; Gui-Xian Zhao; Zhen-Xin Li

    2015-01-01

    Background: Neuromyelitis optica (NMO) and multiple sclerosis (MS) are autoimmune demyelinating diseases of the central nerve system.Interleukin-7 (IL-7) and interleukin-7 receptor alpha (IL-7Rα) were proved to be important in the pathogenesis of both diseases because of the roles they played in the differentiations of autoimmune lymphocytes.The variants of both genes had been identified to be associated with MS susceptibility in Caucasian, Japanese and Korean populations.However, the association of these variants with NMO and MS has not been well studied in Chinese Southeastern Han population.Here, we aimed to evaluate the association of six IL-7 variants (rs 1520333, rs1545298, rs4739140, rs6993386, rs7816065, and rs2887502) and one variant of IL-7RA (rs6897932) with NMO and MS among Chinese Han population in southeastem China.Methods: Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MassARRAY system) and Sanger sequencing were used to determine the variants ofIL-7 and IL-7RA in 167 NMO patients, 159 MS patients and 479 healthy controls among Chinese Han population in southeastern China.Samples were excluded if the genotyping success rate <90%.Results: Statistical differences were observed in the genotypes ofIL-7 rs 1520333 in MS patients and IL-7RA rs6897932 in NMO patients,compared with healthy controls (P =0.035 and 0.034, respectively).There was a statistically significant difference in the genotypes of IL-7 rs2887502 between MS and NMO patients (P =0.014).And there were statistically significant differences in the rs6897932 genotypes (P =0.004) and alleles (P =0.042) between NMO-IgG positive patients and healthy controls.Conclusions: The study suggested that among Chinese Han population in southeastern China, the variant of IL-7RA (rs6897932) was associated with NMO especially NMO-IgG positive patients while the variant of IL-7 (rs1520333) with MS patients.And the genotypic differences ofIL-7 rs2887502 between MS and NMO

  14. Hepatitis E Virus Genotype 4 Sequences Detected in Sewage from Treatment Plants of China

    OpenAIRE

    Li, Heng; Li, Wei; She, Ruiping; Yu, Liang; Wu, Qiaoxing; Yang, Jingling; Hu, Fengjiao; Soomro, Majid Hussain; Shi, Ruihan; Hao, Wenzhuo; Zhao, Yue; Mao, Jingjing

    2017-01-01

    The aim of this study was to investigate the occurrence of hepatitis E virus (HEV) in sewage samples in Shen Zhen, China. Sewage samples were collected from 152 sewage plants including livestock sewage, domestic sewage and treated sewage from May to July of 2015. Two of 152 samples were HEV positive (1.32%) from the livestock sewage plants. Partial ORF2 fragments of HEV were sequenced and a phylogenetic tree was constructed using MEGA5.1. Blast and phylogenetic analyses showed that both of th...

  15. Complete genome sequence of a novel H9N2 subtype influenza virus FJG9 strain in China reveals a natural reassortant event.

    Science.gov (United States)

    Xie, Qingmei; Yan, Zhuanqiang; Ji, Jun; Zhang, Huanmin; Liu, Jun; Sun, Yue; Li, Guangwei; Chen, Feng; Xue, Chunyi; Ma, Jingyun; Bee, Yingzuo

    2012-09-01

    A/chicken/FJ/G9/09 (FJ/G9) is an H9N2 subtype avian influenza virus (H9N2 AIV) strain causing high morbidity that was isolated from broilers in Fujian Province of China in 2009. FJ/G9 has been used as the vaccine strain against H9N2 AIV infection in Fujian Province of China. Here, we report the complete genome sequence of FJ/G9 with natural six-way reassortment, which is the most complex genotype strain in China and even in the world so far. The present findings will aid in understanding the complexity and diversity of H9N2 subtype avian influenza virus.

  16. Revisiting genotype-phenotype overlap in neurogenetics: triplet-repeat expansions mimicking spastic paraplegias.

    Science.gov (United States)

    Bettencourt, Conceição; Quintáns, Beatriz; Ros, Raquel; Ampuero, Israel; Yáñez, Zuleima; Pascual, Samuel Ignacio; de Yébenes, Justo García; Sobrido, María-Jesús

    2012-09-01

    Hereditary spastic paraplegias (HSPs) constitute a heterogeneous group of neurological disorders, characterized primarily by progressive spasticity and weakness of the lower limbs. HSPs are caused by mutations in multiple genes (at least 48 loci and 28 causative genes). The clinical spectrum of HSPs is wide and important differences have been reported between patients with distinct mutations in the same gene, or even between different family members bearing the same mutation. Many patients with HSP present clinical deficits related to the involvement of neuronal systems other than corticospinal tracts, namely, peripheral nerves, sensory, or cerebellar pathways. These cases may be difficult to differentiate from other neurological diseases (e.g., hereditary ataxias), also genetically and clinically heterogeneous. As an illustration of how overlapping this genotype-phenotype relationship is, and the difficulties that it brings upon the development of neurogenetic algorithms and databases, we review the main clinical and genetic features of HSPs, and summarize reports on cases of triplet-repeat spinocerebellar ataxias that can mimic HSP phenotypes. This complex scenario makes the necessity of high-quality, curated mutation databases even more urgent, in order to develop adequate diagnostic guidelines, correct interpretation of genetic testing, and appropriate genetic counseling. © 2012 Wiley Periodicals, Inc.

  17. Grain yield stability of early maize genotypes

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    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  18. [Epidemiological characteristics of diarrheagenic Escherichia coli among diarrhea outpatients in China, 2012-2015].

    Science.gov (United States)

    Zhang, Z K; Lai, S J; Yu, J X; Yang, W Q; Wang, X; Jing, H Q; Li, Z J; Yang, W Z

    2017-04-10

    Objective: To understand the epidemiological characteristics of diarrheagenic Escherichia (E.) coli (DEC) among diarrhea outpatients in China. Methods: Diarrhea surveillance program was conducted in outpatient and emergency departments from 170 hospitals that under the sentinel programs in 27 provinces, from 2012-2015. Clinical and epidemiological data regarding diarrhea patients were collected, with fecal specimens sampled and tested for DEC in 92 network-connected laboratories. Results: Among all the 46 721 diarrhea cases, 7.7 % of them appeared DEC positive in those with geographic heterogeneity. In 2 982 cases (6.4 % ) with available data on PCR subtypes of DEC, enteroaggregative E. coli (EAEC, 1 205 cases, 40.4 % ) appeared the most commonly seen pathogens, followed by enteropathogenic E. coli (EPEC, 815 cases, 27.3 % ), and enterotoxigenic E.coli (ETEC, 653 cases, 21.9 % ). The highest positive rate of DEC was observed in outpatients of 25-34 years old (10.1 % ), living in the warm temperate zones (11.1 % ), and with mucous-like stool (9.4 % ). The positive rate of DEC showed a strong seasonal pattern, with peaks in summer, for all the subtypes. Conclusions: DEC seemed easy to be detected among diarrhea outpatients in China, with EAEC, EPEC and ETEC the most commonly identified subtypes. Epidemiological characteristics regarding the heterogeneities of DEC appeared different, in regions, age groups and seasons. Long-term surveillance programs should be strengthened to better understand the epidemiology of DEC, in China.

  19. Effectiveness of interventions for hypertension care in the community – a meta-analysis of controlled studies in China

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    Lu Zuxun

    2012-07-01

    Full Text Available Abstract Background Hypertension is a serious public health problem in China and in other developing countries. Our aim is to conduct a systematic review of studies on the effectiveness of community interventions for hypertension management in China. Methods China National Knowledge Infrastructure, PubMed, and references of retrieved articles were searched to identify randomised or quasi-randomised controlled studies that evaluated community hypertension care in mainland China. One reviewer extracted and a second reviewer checked data from the included studies. Results We included 94 studies, 93 of which were in Chinese language, that evaluated the following interventions: health education, improved monitoring, family-support, self-management, healthcare management changes and training of providers. The study quality was generally poor, with high risk of biased outcome reporting and significant heterogeneity between studies. When reported, the vast majority of the included studies reported statistically significantly improved outcomes in the intervention group. By assuming zero treatment effects for missing outcomes, the weighted reduction in the intervention group was 6∙9 (95% CI: 4∙9 to 8∙9 mm Hg for systolic BP, and 3∙8 (95% CI: 2∙6 to 5∙0 mm Hg for diastolic BP. Exploratory subgroup analyses found no significant differences between different interventions. Conclusions After taking account of possible reporting biases, a wide range of community interventions for hypertension care remain effective. The findings have implications for China and other low and middle income countries facing similar challenges. Because of significant heterogeneity and high risk of bias in the available studies, further well designed studies should be conducted in China to provide high quality evidence to inform policy decisions on hypertension control.

  20. Multilocus Sequence Typing of Pathogenic Candida albicans Isolates Collected from a Teaching Hospital in Shanghai, China: A Molecular Epidemiology Study

    Science.gov (United States)

    Li, Li; Zhang, Qiangqiang; Zhu, Junhao; Gao, Qian; Chen, Min; Zhu, Min

    2015-01-01

    Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In the present study, multilocus sequence typing (MLST) was used to characterize the genetic diversity and population structure of 62 C. albicans isolates collected from 40 patients from Huashan Hospital in Shanghai, China. A total of 50 diploid sequence types (DSTs) were identified in the 62 C. albicans isolates, with 41 newly identified DSTs. Based on cluster analysis, the 62 isolates were classified into nine existing clades and two new clades (namely clades New 1 and New 2). The majority of the isolates were clustered into three clades, clade 6 (37.5%), clade 1 (15.0%) and clade 17 (15.0%). Isolates of clade New 2 were specifically identified in East Asia. We identified three cases of potential nosocomial transmission based on association analysis between patients’ clinical data and the genotypes of corresponding isolates. Finally, by analyzing the genotypes of serial isolates we further demonstrated that the microevolution of C. albicans was due to loss of heterozygosity. Our study represents the first molecular typing of C. albicans in eastern China, and we confirmed that MLST is a useful tool for studying the epidemiology and evolution of C. albicans. PMID:25919124

  1. Mutualism and Adaptive Divergence: Co-Invasion of a Heterogeneous Grassland by an Exotic Legume-Rhizobium Symbiosis

    Science.gov (United States)

    Porter, Stephanie S.; Stanton, Maureen L.; Rice, Kevin J.

    2011-01-01

    Species interactions play a critical role in biological invasions. For example, exotic plant and microbe mutualists can facilitate each other's spread as they co-invade novel ranges. Environmental context may influence the effect of mutualisms on invasions in heterogeneous environments, however these effects are poorly understood. We examined the mutualism between the legume, Medicago polymorpha, and the rhizobium, Ensifer medicae, which have both invaded California grasslands. Many of these invaded grasslands are composed of a patchwork of harsh serpentine and relatively benign non-serpentine soils. We grew legume genotypes collected from serpentine or non-serpentine soil in both types of soil in combination with rhizobium genotypes from serpentine or non-serpentine soils and in the absence of rhizobia. Legumes invested more strongly in the mutualism in the home soil type and trends in fitness suggested that this ecotypic divergence was adaptive. Serpentine legumes had greater allocation to symbiotic root nodules in serpentine soil than did non-serpentine legumes and non-serpentine legumes had greater allocation to nodules in non-serpentine soil than did serpentine legumes. Therefore, this invasive legume has undergone the rapid evolution of divergence for soil-specific investment in the mutualism. Contrary to theoretical expectations, the mutualism was less beneficial for legumes grown on the stressful serpentine soil than on the non-serpentine soil, possibly due to the inhibitory effects of serpentine on the benefits derived from the interaction. The soil-specific ability to allocate to a robust microbial mutualism may be a critical, and previously overlooked, adaptation for plants adapting to heterogeneous environments during invasion. PMID:22174755

  2. Mutualism and adaptive divergence: co-invasion of a heterogeneous grassland by an exotic legume-rhizobium symbiosis.

    Directory of Open Access Journals (Sweden)

    Stephanie S Porter

    Full Text Available Species interactions play a critical role in biological invasions. For example, exotic plant and microbe mutualists can facilitate each other's spread as they co-invade novel ranges. Environmental context may influence the effect of mutualisms on invasions in heterogeneous environments, however these effects are poorly understood. We examined the mutualism between the legume, Medicago polymorpha, and the rhizobium, Ensifer medicae, which have both invaded California grasslands. Many of these invaded grasslands are composed of a patchwork of harsh serpentine and relatively benign non-serpentine soils. We grew legume genotypes collected from serpentine or non-serpentine soil in both types of soil in combination with rhizobium genotypes from serpentine or non-serpentine soils and in the absence of rhizobia. Legumes invested more strongly in the mutualism in the home soil type and trends in fitness suggested that this ecotypic divergence was adaptive. Serpentine legumes had greater allocation to symbiotic root nodules in serpentine soil than did non-serpentine legumes and non-serpentine legumes had greater allocation to nodules in non-serpentine soil than did serpentine legumes. Therefore, this invasive legume has undergone the rapid evolution of divergence for soil-specific investment in the mutualism. Contrary to theoretical expectations, the mutualism was less beneficial for legumes grown on the stressful serpentine soil than on the non-serpentine soil, possibly due to the inhibitory effects of serpentine on the benefits derived from the interaction. The soil-specific ability to allocate to a robust microbial mutualism may be a critical, and previously overlooked, adaptation for plants adapting to heterogeneous environments during invasion.

  3. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  4. Calcium-sensing receptor gene polymorphism (rs7652589) is associated with calcium nephrolithiasis in the population of Yi nationality in Southwestern China.

    Science.gov (United States)

    Li, Hao; Zhang, Jianhua; Long, Jiang; Shi, Jiarun; Luo, Yuhui

    2018-04-16

    The calcium-sensing receptor (CaSR) gene plays an important role in regulating the Ca 2+ balance and reducing the risk for calcium stones. In this study, we evaluated the association of CaSR polymorphisms with calcium nephrolithiasis in the population of Yi nationality in Southwestern China. Biochemical variables were evaluated in 624 calcium nephrolithiasis patients and 470 age-matched healthy controls without a history of nephrolithiasis. CaSR polymorphisms rs7652589, rs1501899, rs1801725 (Ala986Ser), rs1042636 (Arg990Gly) and rs1801726 (Gln1011Glu) were investigated between the calcium nephrolithiasis patients and healthy controls, using direct sequencing. Compared with the healthy controls, serum creatinine and 24-hour urine calcium levels were significantly higher in calcium nephrolithiasis patients. Among these five polymorphisms, the genotypic and allelic frequency distributions of rs7652589 SNP was significantly associated with the risk of calcium nephrolithiasis. However, there were no genotypic or allelic distribution differences for rs1501899, rs1801725, rs1042636, and rs1801726 polymorphisms between calcium nephrolithiasis patients and healthy controls. Moreover, the association between rs7652589 SNP genotypes and the biochemical variables was not found. Our study showed that CaSR rs7652589 polymorphism had a significant effect on the risk of developing calcium nephrolithiasis in the population of Yi nationality in Southwestern China. © 2018 John Wiley & Sons Ltd/University College London.

  5. Recent ecological transitions in China: greening, browning, and influential factors

    Science.gov (United States)

    Lü, Yihe; Zhang, Liwei; Feng, Xiaoming; Zeng, Yuan; Fu, Bojie; Yao, Xueling; Li, Junran; Wu, Bingfang

    2015-03-01

    Ecological conservation and restoration are necessary to mitigate environmental degradation problems. China has taken great efforts in such actions. To understand the ecological transition during 2000-2010 in China, this study analysed trends in vegetation change using remote sensing and linear regression. Climate and socioeconomic factors were included to screen the driving forces for vegetation change using correlation or comparative analyses. Our results indicated that China experienced both vegetation greening (restoration) and browning (degradation) with great spatial heterogeneity. Socioeconomic factors, such as human populations and economic production, were the most significant factors for vegetation change. Nature reserves have contributed slightly to the deceleration of vegetation browning and the promotion of greening; however, a large-scale conservation approach beyond nature reserves was more effective. The effectiveness of the Three-North Shelter Forest Program lay between the two above approaches. The findings of this study highlighted that vegetation trend detection is a practical approach for large-scale ecological transition assessments, which can inform decision-making that promotes vegetation greening via proper socioeconomic development and ecosystem management.

  6. Recent ecological transitions in China: greening, browning, and influential factors.

    Science.gov (United States)

    Lü, Yihe; Zhang, Liwei; Feng, Xiaoming; Zeng, Yuan; Fu, Bojie; Yao, Xueling; Li, Junran; Wu, Bingfang

    2015-03-04

    Ecological conservation and restoration are necessary to mitigate environmental degradation problems. China has taken great efforts in such actions. To understand the ecological transition during 2000-2010 in China, this study analysed trends in vegetation change using remote sensing and linear regression. Climate and socioeconomic factors were included to screen the driving forces for vegetation change using correlation or comparative analyses. Our results indicated that China experienced both vegetation greening (restoration) and browning (degradation) with great spatial heterogeneity. Socioeconomic factors, such as human populations and economic production, were the most significant factors for vegetation change. Nature reserves have contributed slightly to the deceleration of vegetation browning and the promotion of greening; however, a large-scale conservation approach beyond nature reserves was more effective. The effectiveness of the Three-North Shelter Forest Program lay between the two above approaches. The findings of this study highlighted that vegetation trend detection is a practical approach for large-scale ecological transition assessments, which can inform decision-making that promotes vegetation greening via proper socioeconomic development and ecosystem management.

  7. Genotypic diversity of root and shoot characteristics of

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    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  8. Survey of enterovirus infections from hand, foot and mouth disease outbreak in china, 2009

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    Yang Fan

    2011-11-01

    Full Text Available Abstract Background In China, a rapid expansion of Hand, foot, and mouth disease (HFMD outbreaks has occurred since 2004 and HFMD has become an important issue for China. However, people are still only concerned with human enterovirus 71(HEV-71 and coxsackie virus A16 (CV-A16. Much of what is known about the other enterovirus infections relies on fractional evidence and old epidemic data, with little knowledge concerning their distribution. To alert potential threatens of the other enteroviruses, our study genetically characterized specimens from different regions of China and yielded novel information concerning the circulating and phylogenetic characteristics of enteroviral strains from HFMD cases. Findings A total of 301 clinical throat swabs were randomly obtained from patients suffering from HFMD from the southern, northern and central regions of China during outbreaks in 2009. 266 of 301 (88.4% HFMD cases were found positive for HEV and seven genotypes, HEV-71, CV-A16, -B5, -A4, -A6, -A10, and -A12, were detected. Conclusions The HFMD pathogen compositions in the different regions of China were significantly different. HFMD epidemics might persist for a long time in China due to the multiple pathogen compositions, the enteroviral characteristic of recombination and co-infection, the ever-increasing travel and migration and the deficiency of effective vaccine. Our study deserves the attention on HFMD control and vaccine development.

  9. Emergence and diversification of dengue 2 cosmopolitan genotype in Pakistan, 2011.

    Science.gov (United States)

    Khan, Mohammad A; Ellis, Esther M; Tissera, Hasitha A; Alvi, Mohammad Y; Rahman, Fatima F; Masud, Faisal; Chow, Angelia; Howe, Shiqin; Dhanasekaran, Vijaykrishna; Ellis, Brett R; Gubler, Duane J

    2013-01-01

    Major dengue epidemics have been observed in the Indian subcontinent since the 1980s and have occurred with increased hospitalizations and mortality. In 2011, the first major epidemic of dengue occurred in Lahore, the second largest city in Pakistan, and resulted in 21,685 confirmed cases and 350 deaths. To investigate the possible viral causes for the increased epidemic activity, we determined the predominant serotype and characterized the viruses genetically. Of 50 patients carefully selected as probable dengue fever or dengue hemorrhagic fever, 34 were positive by virologic testing (i.e. PCR and/or virus isolation). DENV-2 was detected in 32 patients and DENV-1 in two. A total of 24 partial and three full DENV genomes were sequenced. Phylogenetic analyses of the capsid (C), pre-membrane (prM), and envelope genes comprising 2500 nucleotides in length indicated that all DENV-2 isolates in Pakistan since 2007 form a monophyletic lineage that is endemic in the country. These viruses were all of the cosmopolitan genotype (IV) and most closely related to viruses isolated in India and Sri Lanka in the past two decades. Phylogenetic analyses of data currently available in GenBank suggest that the Cosmopolitan genotype has diverged into two geographically distinct sub-lineages: sub-lineage IV-a has only been observed in Southeast Asia, China and Oceania, while IV-b is prevalent in the Indian subcontinent. These results highlight the increased diversity of dengue viruses as they spread geographically within the region.

  10. A longitudinal study of Stargardt disease: quantitative assessment of fundus autofluorescence, progression, and genotype correlations.

    Science.gov (United States)

    Fujinami, Kaoru; Lois, Noemi; Mukherjee, Rajarshi; McBain, Vikki A; Tsunoda, Kazushige; Tsubota, Kazuo; Stone, Edwin M; Fitzke, Fred W; Bunce, Catey; Moore, Anthony T; Webster, Andrew R; Michaelides, Michel

    2013-12-17

    We characterized subtypes of fundus autofluorescence (AF) and the progression of retinal atrophy, and correlated these findings with genotype in Stargardt disease. Full clinical examination and AF imaging was undertaken in 68 patients with Stargardt disease. The baseline data were compared to those at follow-up. Patients were classified into three AF subtypes: type 1 had a localized low signal at the fovea surrounded by a homogeneous background, type 2 had a localized low signal at the macula surrounded by a heterogeneous background with numerous foci of abnormal signal, and type 3 had multiple low signal areas at the posterior pole with a heterogeneous background. At baseline, there were 19 patients with type 1, 41 with type 2, and 8 with type 3 disease. The areas of reduced AF signal were measured and rate of atrophy enlargement (RAE) was calculated as the difference of the atrophy size over time (mm²) divided by the follow-up interval (years). Molecular screening of ABCA4 was undertaken. The mean follow-up interval was 9.1 years. A total of 42% cases with type 1 disease progressed to type 2, and 12% with type 2 progressed to type 3. The RAE (mm²/y) based upon baseline AF subtypes was significantly different; 0.06 in type 1, 0.67 in type 2, and 4.37 in type 3. ABCA4 variants were identified in 57 patients. There was a significant association between AF subtype and genotype. The AF pattern at baseline influences the enlargement of atrophy over time and has genetic correlates. These data are likely to assist in the provision of counseling on prognosis in Stargardt disease and be valuable for future clinical trials.

  11. Human papillomavirus genotypes and phylogenetic analysis of HPV-16 variants in HIV-1 infected subjects in Italy.

    Science.gov (United States)

    Tanzi, Elisabetta; Amendola, Antonella; Bianchi, Silvia; Fasolo, M Michela; Beretta, Rosangela; Pariani, Elena; Zappa, Alessandra; Frati, Elena; Orlando, Giovanna

    2009-05-29

    A cross-sectional study was carried out to improve the state of evidence regarding the spectrum of HPV types and HPV-16 LCR variants circulating among men and women infected with HIV-1 in Italy. This study, conducted in 518 HIV-positive subjects (346 males and 172 females), showed a high prevalence of HPV anal infections (88.7%) in men and of cervical infections (65.1%) in women. A wide spectrum of HPV genotypes has been observed, as both single and multiple infections. Low-risk HPV types 6, 11 and 61 were frequently detected. HPV-16 was the prevalent high-risk type. Fourteen different HPV-16 LCR variants were found. Ten belonged to the European lineage (78.7% were detected in Italian subjects and 21.3% in foreign-born, all homo/bisexual men), two to the Asiatic lineage and two to the African-2 lineage. This study underlines the great genotypic heterogeneity characterizing anal and cervical HPV infections and the marked polymorphism of the predominant HPV-16 in this high-risk population in Italy.

  12. Genotypic Variation of Early Maturing Soybean Genotypes for Phosphorus Utilization Efficiency under Field Grown Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Abaidoo, R. C. [Kwame Nkrumah University of Technology, Kumasi (Ghana); International Institute of Tropical Agriculture, Ibadan (Nigeria); Opoku, A.; Boahen, S. [Kwame Nkrumah University of Technology, Kumasi (Ghana); Dare, M. O. [Federal University of Agriculture, Abeokuta (Nigeria)

    2013-11-15

    Variability in the utilization of phosphorus (P) by 64 early-maturing soybean (Glycine max L. Merr.) genotypes under low-P soil conditions were evaluated in 2009 and 2010 at Shika, Nigeria. Fifteen phenotypic variables; number of nodules, nodule dry weight, grain yield, plant biomass, total biomass, biomass N and P content, Phosphorus Utilization Index (PUI), shoot P Utilization efficiency (PUIS), grain P Utilization efficiency (PUIG), Harvest Index (HI), Biological N fixed (BNF), total N fixed and N and P uptake were measured. The four clusters revealed by cluster analysis were basically divided along (1) plant biomass and uptake, (2) nutrient acquisition and utilization and (3) nodulation components. Three early maturing genotypes, TGx1842-14E, TGx1912-11F and TGx1913-5F, were identified as having high P utilization index and low P uptake. These genotypes could be a potential source for breeding for P use efficiency in early maturing soybean genotypes. (author)

  13. Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

    Science.gov (United States)

    Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

    2012-01-01

    Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

  14. Heterogeneity in coal composition and implications for lung cancer risk in Xuanwei and Fuyuan counties, China

    NARCIS (Netherlands)

    Downward, George S.; Hu, Wei; Large, David; Veld, Harry; Xu, Jun; Reiss, Boris; Wu, Guoping; Wei, Fusheng; Chapman, Robert S.; Rothman, Nat; Qing, Lan; Vermeulen, Roel

    2014-01-01

    Background: Xuanwei and Fuyuan counties in Yunnan Province, China have among the highest lung cancer rates in the country. This has been associated with the domestic combustion of bituminous coal (referred to as "smoky" coal). Additionally, significant geographical variation in cancer rates among

  15. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  16. Dissemination, divergence and establishment of H7N9 influenza viruses in China.

    Science.gov (United States)

    Lam, Tommy Tsan-Yuk; Zhou, Boping; Wang, Jia; Chai, Yujuan; Shen, Yongyi; Chen, Xinchun; Ma, Chi; Hong, Wenshan; Chen, Yin; Zhang, Yanjun; Duan, Lian; Chen, Peiwen; Jiang, Junfei; Zhang, Yu; Li, Lifeng; Poon, Leo Lit Man; Webby, Richard J; Smith, David K; Leung, Gabriel M; Peiris, Joseph S M; Holmes, Edward C; Guan, Yi; Zhu, Huachen

    2015-06-04

    Since 2013 the occurrence of human infections by a novel avian H7N9 influenza virus in China has demonstrated the continuing threat posed by zoonotic pathogens. Although the first outbreak wave that was centred on eastern China was seemingly averted, human infections recurred in October 2013 (refs 3-7). It is unclear how the H7N9 virus re-emerged and how it will develop further; potentially it may become a long-term threat to public health. Here we show that H7N9 viruses have spread from eastern to southern China and become persistent in chickens, which has led to the establishment of multiple regionally distinct lineages with different reassortant genotypes. Repeated introductions of viruses from Zhejiang to other provinces and the presence of H7N9 viruses at live poultry markets have fuelled the recurrence of human infections. This rapid expansion of the geographical distribution and genetic diversity of the H7N9 viruses poses a direct challenge to current disease control systems. Our results also suggest that H7N9 viruses have become enzootic in China and may spread beyond the region, following the pattern previously observed with H5N1 and H9N2 influenza viruses.

  17. Experimental evidence for competitive growth advantage of genotype VII over VI: implications for foot-and-mouth disease virus serotype A genotype turnover in nature.

    Science.gov (United States)

    Mohapatra, J K; Subramaniam, S; Singh, N K; Sanyal, A; Pattnaik, B

    2012-04-01

    In India, systematic genotype replacement has been observed for serotype A foot-and-mouth disease virus. After a decade of co-circulation of genotypes VI and VII, genotype VII emerged as the single dominant genotype since 2001. To derive possible explanations for such epochal evolution dynamics, in vitro intergenotype growth competition experiments involving both co- and superinfection regimes were conducted. Coinfection of BHK-21 cells demonstrated abrupt loss in the genotype VI viral load with commensurate increase in the load of genotype VII as measured by the genotype differentiating ELISA, RT-PCR and real-time RT-PCR. The superinfection dynamics was shaped by temporal spacing of infection, where the invading genotype VII took more number of passages than coinfection to eventually overtake the resident genotype VI. It was speculated that such superior replicative fitness of genotype VII could have been a possible factor for the ultimate dominance of genotype VII in nature. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. [Genetic differentiation of Isaria farinosa populations in Anhui Province of East China].

    Science.gov (United States)

    Sun, Zhao-Hong; Luan, Feng-Gang; Zhang, Da-Min; Chen, Ming-Jun; Wang, Bin; Li, Zeng-Zhi

    2011-11-01

    Isaria farinosa is an important entomopathogenic fungus. By using ISSR, this paper studied the genetic heterogeneity of six I. farinosa populations at different localities of Anhui Province, East China. A total of 98.5% polymorphic loci were amplified with ten polymorphic primers, but the polymorphism at population level varied greatly, within the range of 59.6%-93.2%. The genetic differentiation index (G(st)) between the populations based on Nei's genetic heterogenesis analysis was 0.3365, and the gene flow (N(m)) was 0.4931. The genetic differentiation between the populations was lower than that within the populations, suggesting that the genetic variation of I. farinosa mainly come from the interior of the populations. The UPGMA clustering based on the genetic similarities between the isolates revealed that the Xishan population was monophylectic, while the other five populations were polyphylectic, with the Yaoluoping population being the most heterogenic and the Langyashan population being the least heterogenic. No correlations were observed between the geographic distance and the genetic distance of the populations. According to the UPGMA clustering based on the genetic distance between the populations, the six populations were classified into three groups, and this classification was accorded with the clustering based on geographic environment, suggesting the effects of environmental heterogeneity on the population heterogeneity.

  19. Maternal education and breastfeeding practices in China: A systematic review and meta-analysis.

    Science.gov (United States)

    Zhao, Jian; Zhao, Yun; Du, Mengran; Binns, Colin W; Lee, Andy H

    2017-07-01

    to examine the association between maternal education and breastfeeding prevalence in China. a systematic review and meta-analysis was conducted based on the literature of observational studies retrieved from electronic databases of CNKI, Medline, Embase, CINHAL, ProQuest and Science Direct. Maternal education was recoded into two binary categorical variables using different cut-off points. Both fixed and random effect models were used to estimate the pooled association between maternal education and breastfeeding prevalence in China. Visual inspection of Galbraith plot for heterogeneity detection, sensitivity analysis and publication bias test were performed. a total of 31 studies were included in the systematic review, and 15 and 26 studies were suitable for meta-analysis in terms of two different cutoff points of maternal education respectively. In the group using 6-year education cut-off (Group 1), the odds of breastfeeding was 10% (pooled OR=0.90, 95% CI: 0.83, 0.97) lower in mothers who had been educated for 'more than 6 years' compared to mothers with '6 years or less' education. In the group using 12-year education cut-off (Group 2), the odds of breastfeeding was 9% (pooled OR=0.91, 95% CI: 0.86, 0.96) lower in mothers who had 'more than 12 years' education compared to mothers who attained '12 years or less' education. There was substantial heterogeneity across the studies in both groups. Through meta-regression analysis, sample size of studies was detected contributing to the heterogeneity in Group 1; however none of study level factors were found to be a source of heterogeneity in Group 2. in the Chinese culture and employment environment, mothers who have attained a higher level of education are less likely to breastfeed their babies compared to mothers with lower education levels. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Heterogeneous network architectures

    DEFF Research Database (Denmark)

    Christiansen, Henrik Lehrmann

    2006-01-01

    is flexibility. This thesis investigates such heterogeneous network architectures and how to make them flexible. A survey of algorithms for network design is presented, and it is described how using heuristics can increase the speed. A hierarchical, MPLS based network architecture is described......Future networks will be heterogeneous! Due to the sheer size of networks (e.g., the Internet) upgrades cannot be instantaneous and thus heterogeneity appears. This means that instead of trying to find the olution, networks hould be designed as being heterogeneous. One of the key equirements here...... and it is discussed that it is advantageous to heterogeneous networks and illustrated by a number of examples. Modeling and simulation is a well-known way of doing performance evaluation. An approach to event-driven simulation of communication networks is presented and mixed complexity modeling, which can simplify...

  1. Open Standards in Practice: An OGC China Forum Initiative

    Science.gov (United States)

    Yue, Peng; Zhang, Mingda; Taylor, Trevor; Xie, Jibo; Zhang, Hongping; Tong, Xiaochong; Yu, Jinsongdi; Huang, Juntao

    2016-11-01

    Open standards like OGC standards can be used to improve interoperability and support machine-to-machine interaction over the Web. In the Big Data era, standard-based data and processing services from various vendors could be combined to automate the extraction of information and knowledge from heterogeneous and large volumes of geospatial data. This paper introduces an ongoing OGC China forum initiative, which will demonstrate how OGC standards can benefit the interaction among multiple organizations in China. The ability to share data and processing functions across organizations using standard services could change traditional manual interactions in their business processes, and provide on-demand decision support results by on-line service integration. In the initiative, six organizations are involved in two “MashUp” scenarios on disaster management. One “MashUp” is to derive flood maps in the Poyang Lake, Jiangxi. And the other one is to generate turbidity maps on demand in the East Lake, Wuhan, China. The two scenarios engage different organizations from the Chinese community by integrating sensor observations, data, and processing services from them, and improve the automation of data analysis process using open standards.

  2. The future of populous economies. China and India shape their destinies.

    Science.gov (United States)

    Livernash, R

    1995-01-01

    Population in 1995 was about 1.2 billion in China and about 935 million in India. Populations are expected to reach respectively 1.5 billion and 1.4 billion by 2025. These two countries now and in the future will average about 35% of total world population. This article compares the current and expected demographic, economic, and environmental conditions in China and India. How these countries manage their growth, poverty, and population will affect the region and the world as well as each nation. China's fertility is now below replacement but population momentum will increase population by about 300 million/year. India's fertility is 3.6 children/woman and India will add 450 million/year. China's population over 60 years old will reach 20% by 2020, while India's will be under 15% in 2025. China will be almost 55% urban by 2025 from 30% in the 1990s, and India will be 45% urban from 27% urban. China's economic growth has averaged over 9%/year compared to India's 5% annual growth during the 1980s and the economic decline during the 1990s. China has 12% of rural population living below the poverty line and India has about 33% of its total population impoverished. China's life expectancy is about 10 years higher. Under-five mortality is 43/1000 live births in China and 131/1000 in India. Poverty-related diseases are still high in India. China is a homogenous population with an authoritarian regime. India is a democracy with a large nongovernmental community and a heterogenous population. India has about 33% of the land area of China but over twice the agricultural land per person. About 50% of China's land and only 25% of India's land is irrigated. Water resources are problems in northern China and much of India. Air and water pollution are problems in both countries. Differences in the population-environment-development context are discussed in terms of the effects of poverty, the constraints posed by development, and the environmental impact of rising per capita

  3. The genotype-phenotype landscape of familial amyotrophic lateral sclerosis in Australia.

    Science.gov (United States)

    McCann, E P; Williams, K L; Fifita, J A; Tarr, I S; O'Connor, J; Rowe, D B; Nicholson, G A; Blair, I P

    2017-09-01

    Amyotrophic lateral sclerosis (ALS) is a clinically and genetically heterogeneous fatal neurodegenerative disease. Around 10% of ALS cases are hereditary. ALS gene discoveries have provided most of our understanding of disease pathogenesis. We aimed to describe the genetic landscape of ALS in Australia by assessing 1013 Australian ALS patients for known ALS mutations by direct sequencing, whole exome sequencing or repeat primed polymerase chain reaction. Age of disease onset and disease duration were used for genotype-phenotype correlations. We report 60.8% of Australian ALS families in this cohort harbour a known ALS mutation. Hexanucleotide repeat expansions in C9orf72 accounted for 40.6% of families and 2.9% of sporadic patients. We also report ALS families with mutations in SOD1 (13.7%), FUS (2.4%), TARDBP (1.9%), UBQLN2 (.9%), OPTN (.5%), TBK1 (.5%) and CCNF (.5%). We present genotype-phenotype correlations between these genes as well as between gene mutations. Notably, C9orf72 hexanucleotide repeat expansion positive patients experienced significantly later disease onset than ALS mutation patients. Among SOD1 families, p.I114T positive patients had significantly later onset and longer survival. Our report highlights a unique spectrum of ALS gene frequencies among patients from the Australian population, and further, provides correlations between specific ALS mutations with disease onset and/or duration. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Determination of genotypic and clinical characteristics of Colombian patients with mucopolysaccharidosis IVA

    Directory of Open Access Journals (Sweden)

    Tapiero-Rodriguez SM

    2018-04-01

    Full Text Available Sandra M Tapiero-Rodriguez,1 Johanna C Acosta Guio,1 Gloria Liliana Porras-Hurtado,2 Natalia García,3 Martha Solano,4 Harry Pachajoa,5 Harvy M Velasco1 1Universidad Nacional de Colombia, Departamento de morfología, Maestría de genética humana, Bogotá, 2Family Compensation Fund of Risaralda, Pereira, 3Faculty of Medicine, Manizales University, Manizales, 4Department of Neuropediatrics, Cardioinfantil Foundation, Bogotá, 5Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras, Universidad ICESI y Fundación Valle del Lili, Cali, Colombia Background: As mucopolysaccharidosis IVA (MPS IVA is the most frequent MPS in Colombia, this paper aims to describe its clinical and mutational characteristics in 32 diagnosed patients included in this study. Methods: Genotyping was completed by amplification and Sanger sequencing of the GALNS gene. The SWISS-model platform was used for bioinformatic analysis, and mutant proteins were generated by homology from the wild-type GALNS code 4FDI template from the Protein Data Bank (PDB database. Docking was performed using the GalNAc6S ligand (PubChem CID: 193456 by AutoDock Vina 1.0 and visualized in PyMOL and LigPlot+. Results: Eleven variants were identified, and one new pathogenic variant was described in the heterozygous state, which is consistent with genotype c. 319 G>T or p.Ala107Ser. The pathogenic variant c.901G>T or p.Gly301Cys was the most frequent mutation with 51.6% of alleles. Docking revealed affinity energy of −5.9 Kcal/mol between wild-type GALNS and the G6S ligand. Some changes were evidenced at the intermolecular interaction level, and affinity energy for each mutant decreased. Conclusion: Clinical variables and genotypic analysis were similar to those reported for other world populations. Genotypic data showed greater allelic heterogeneity than those previously reported. Bioinformatics tools showed differences in the binding interactions of mutant proteins with the G6S

  5. Multilocus genotyping of a ‘Candidatus Phytoplasma aurantifolia’-related strain associated with cauliflower phyllody disease in China

    Science.gov (United States)

    A new cauliflower disease characterized by formation of leaf-like inflorescences and malformed flowers occurred in a seed production filed located in Yunnan, a southwest province of China. In the diseased plants, floral organs in three inner whorls (petals, carpels, and stamens) were under-develope...

  6. Occurrence of canine parvovirus in dogs from Henan province of China in 2009-2014.

    Science.gov (United States)

    Zhao, Zhanqin; Liu, Huisheng; Ding, Ke; Peng, Chunping; Xue, Qiao; Yu, Zuhua; Xue, Yun

    2016-07-04

    There is no information concerning the genotype of Canine parvovirus (CPV) currently circulating in Henan province, China. Therefore, the aim of the present study was to provide insights into the epidemiology and molecular characterization of CPV circulating in Henan province from 2009 to 2014. Nineteen thousand nine hundred seven dogs from pet hospitals in the cities of Luoyang, Anyang, Jiaozuo, Sanmenxia, Xinxiang, Zhengzhou in Henan province between 2009 and 2014 were investigated. Over the 6-year period, 1169 CPV-positive cases were identified and the morbidity of CPV infection ranged from 4.16 to 8.06 %, although morbidity was not significant (P > 0.05) between 2009 and 2014. Factors associated with morbidity included sampling season, dog age, breed, vaccination status, and sex. CPV co-infection with coccidium (10.00 %), canine distemper virus (4.79 %), hookworm (2.40 %), canine coronavirus (1.11 %), roundworm (1.03 %), tapeworm (0.17 %) and Babesia spp. (0.09 %) were observed. The new CPV-2a variant was more prevalent than the new CPV-2b variant in Henan province. CPV 2c was not observed in this study. The epidemiology of CPV infection and identification of the circulating genotypes in Henan province, China from 2009 to 2014 determined that the new CPV-2a variant was more prevalent.

  7. A comparative study on the influential factors of China's provincial energy intensity

    International Nuclear Information System (INIS)

    Yang, Guangfei; Li, Wenli; Wang, Jianliang; Zhang, Dongqing

    2016-01-01

    China has become the largest energy consumer worldwide, and it is important to study the energy intensity to realize the sustainable development goal of China. This paper focuses on investigating the influential factors of China's energy intensity using provincial-level panel data from 1985 to 2012. More specifically, we try to identify which factor is relatively more important to pay attention to. A novel approach based on evolutionary computation is proposed to intelligently mine the intrinsic relations between observed phenomena and to let the important factors automatically emerge from the discovered nonlinear models. However, due to China's vast territory and significant heterogeneities, this approach may fail to examine some detailed or hidden information when analyzing the country as a whole. Instead, we concentrate on the provincial level because the provinces play vital roles in reducing energy intensity in China. From our analytical results, the main findings are as follows: (1) the Total Population is the most important influential factor across China's provinces, while the Energy Price Index has the least impact; and (2) the provinces could be naturally classified into four categories based on the primary factors emerged from data, and such classification could reveal more about the true underlying features of each area. - Highlights: • Identify the important factors of China's energy intensity by symbolic regression. • Analyze China's energy intensity using provincial-level panel data from 1985 to 2012. • Intelligently investigate nonlinear models and the emergence of important factors. • The Total Population is discovered to be the most important influential factor. • Provinces are naturally classified into four categories by the influential factors.

  8. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    ... x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G x E interaction were highly significant for all yield traits. Variations due to G x E interaction were greater than those due to genotypic differences for all yield traits. Genotype x location x year ...

  9. A Geodynamic Study of Active Crustal Deformation and Earthquakes in North China

    Science.gov (United States)

    Yang, Y.; Liu, M.

    2005-12-01

    North China is part of the Archaean Sino-Korean craton, yet today it is a region of intense crustal deformation and earthquakes, including 21 M >=7.0 events since 512 AD. More than half of the large events occurred within the Fen-Wei rift system surrounding the stable Ordos plateau; the largest events (M >=7.3) show a sequential southward migration along the rift. However, since 1695 the Fen-Wei rift has became seismically dormant, while seismicity seems having shifted eastward to the North China plain, marked by the 1996 Tangshan earthquake (M=7.8). We have developed a 3D viscoelastic geodynamic model to study the cause of seismicity and its spatial-temporal pattern in North China. Constrained by crustal kinematics from GPS and neotectonic data, the model shows high deviatoric stress in the North China crust, resulting mainly from compression of the expanding Tibetan Plateau and resistance from the stable Siberian block. Within North China seismicity is largely controlled by lateral heterogeneity of lithospheric structures, which explains the concentration of seismicity in the Fen-Wei rift. Our results show that stress triggering may have contributed to the sequential migration of large events along the rift, and the release and migration of stress and strain energy from these large events may partially explain the intense seismicity in the North China plain in the past 300 years. Comparing the predicted long-term spatial pattern of strain energy with seismic energy release provides some insights of potential earthquake risks in North China.

  10. The Many Faces of Primary Aldosteronism and Cushing Syndrome: A Reflection of Adrenocortical Tumor Heterogeneity.

    Science.gov (United States)

    Mete, Ozgur; Duan, Kai

    2018-01-01

    Adrenal cortical tumors constitute a heterogeneous group of neoplasms with distinct clinical, morphological, and molecular features. Recent discoveries of specific genotype-phenotype correlations in adrenal cortical adenomas have transformed our understanding of their respective endocrine syndromes. Indeed, a proportion of patients with primary aldosteronism are now known to harbor adrenal cortical adenomas with heterogeneous molecular alterations ( KCNJ5, ATP1A1, ATP2B3 , and CACNA1D ) involving the calcium/calmodulin kinase signaling pathway. Several lines of evidence suggest that KCNJ5 -mutant aldosterone-producing adenomas have distinct clinicopathological phenotype compared to those harboring ATP1A1, ATP2B3 , and CACNA1D mutations. Benign adrenal cortical tumors presenting with Cushing syndrome often have diverse mutations ( PRKACA, PRKAR1A, GNAS, PDE11A , and PDE8B ) involving the cyclic AMP signaling pathway. In addition to cortisol-producing adenomas, bilateral micronodular adrenocortical disease and primary bilateral macronodular adrenal hyperplasia (PBMAH) have also expanded the spectrum of benign neoplasms causing adrenal Cushing disease. The recent discovery of inactivating ARMC5 germline mutations in PBMAH has challenged the old belief that this disorder is mainly a sporadic disease. Emerging evidence suggests that PBMAH harbors multiple distinct clonal proliferations, reflecting the heterogeneous genomic landscape of this disease. Although most solitary adrenal cortical tumors are sporadic, there is an increasing recognition that inherited susceptibility syndromes may also play a role in their pathogenesis. This review highlights the molecular and morphological heterogeneity of benign adrenal cortical neoplasms, reflected in the diverse presentations of primary aldosteronism and adrenal Cushing syndrome.

  11. Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

    Science.gov (United States)

    Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

    2011-02-01

    The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

  12. Sequence heterogeneity in the 18S rRNA gene in Theileria equi from horses presented in Switzerland.

    Science.gov (United States)

    Liu, Qin; Meli, Marina L; Zhang, Yi; Meili, Theres; Stirn, Martina; Riond, Barbara; Weibel, Beatrice; Hofmann-Lehmann, Regina

    2016-05-15

    A reverse line blot (RLB) hybridization assay was adapted and applied for equine blood samples collected at the animal hospital of the University of Zurich to determine the presence of piroplasms in horses in Switzerland. A total of 100 equine blood samples were included in the study. The V4 hypervariable region of the 18S rRNA gene was amplified by polymerase chain reaction and analyzed using the RLB assay. Samples from seven horses hybridized to a Theileria/Babesia genus-specific and a Theileria genus-specific probe. Of these, two hybridized also to the Theileria equi-specific probe. The other five positive samples did not hybridize to any of the species-specific probes, suggesting the presence of unrecognized Theileria variants or genotypes. The 18S rRNA gene of the latter five samples were sequenced and found to be closely related to T. equi isolated from horses in Spain (AY534822) and China (KF559357) (≥98.4% identity). Four of the seven horses that tested positive had a documented travel history (France, Italy, and Spain) or lived abroad (Hungary). The present study adds new insight into the presence and sequence heterogeneity of T. equi in Switzerland. The results prompt that species-specific probes must be designed in regions of the gene unique to T. equi. Of note, none of the seven positive horses were suspected of having Theileria infection at the time of presentation to the clinic. Clinicians should be aware of the possibility of equine piroplasma infections outside of endemic areas and in horses without signs of piroplasmosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Prevalence of multiple enteroviruses associated with hand, foot, and mouth disease in Shijiazhuang City, Hebei province, China: outbreaks of coxsackieviruses a10 and b3.

    Directory of Open Access Journals (Sweden)

    Huifang Tian

    Full Text Available Hand, foot, and mouth disease (HFMD has been one of the most common infectious diseases in Shijiazhuang City, as is the situation in China overall. In the National HFMD surveillance system, the pathogen detection was focused on EV-A71 and CVA16, and therefore, information on the other EVs is very limited. In order to identify the circulating EV serotypes in the HFMD outbreaks in Shijiazhuang City during 2010-2012, 4045 patients presented with HFMD were recruited in the study, and clinical samples were investigated. Typing of EV serotypes was performed using the molecular typing methods, and phylogenetic analyses based on entire VP1 sequences of human enterovirus 71 (EV-A71, coxsackievirus A16 (CVA16, CVA10 and CVB3 was performed. The results revealed that EV-A71 and CVA16 were the 2 most important pathogens but the circulating trends of the 2 viruses showed a shift, the spread of EV-A71 became increasingly weak, whereas the spread of CVA16 became increasingly stronger. CVA10 and CVB3 were the third and fourth most prevalent pathogens, respectively. Co-infection of two viruses at the same time was not found in these samples. Based on entire VP1 region sequences, the phylogenetic analysis revealed that C4a subgenotype EV-A71, B1a and B1b subgenotype CVA16 continued to evolve. The CVA10 strains were assigned to 4 genotypes (A-D, whereas the CVB3 strains were assigned to 5 genotypes (A-E, with clear geographical and temporal-specific distributions. The Shijiazhuang CVA10 sequences belonged to 4 epidemic lineages within genotype C, whereas the Shijiazhuang CVB3 sequences belonged to 2 epidemic lineages within genotype E, which may have the same origins as the strains reported in other part of China. CVA10 and CVB3, 2 pathogens that were previously infrequently detected, were identified as pathogens causing the HFMD outbreaks. This study underscores the need for detailed laboratory-based surveillances of HFMD in mainland China.

  14. Genotypic and phenotypic characterization of antimicrobial-resistant Escherichia coli from farm-raised diarrheic sika deer in Northeastern China.

    Directory of Open Access Journals (Sweden)

    Rui Li

    Full Text Available In China, overuse and/or abuse of antimicrobials are common in stockbreeding, which possess high risks of antimicrobial-resistant contaminations. The serogroups, major virulence genes, and antimicrobial resistant patterns of the antimicrobial-resistant Escherichia coli (E. coli were investigated in the feces of diarrheic farm-raised sika deer from 50 farms in three Northeastern provinces of China. A total of 220 E. coli isolates were obtained and characterized. Twenty-eight O serogroups were identified from the obtained E. coli isolates with O2, O26, O128, O142 and O154 being dominant. Nearly all the isolates were resistant to at least four of the tested antimicrobials. More than 90% of the E. coli isolates carried at least one of the tested virulence genes. About 85% of the E. coli isolates carried one or more antimicrobial-resistant genes responsible for resistant phenotypes of sulfonamides, streptomycin/spectionomycin or tetracycline. The antimicrobial resistant level and pathogenic group occurrences of the obtained E. coli isolates were higher than that of livestock and wild animals reported in some developed countries. Thus, the fecal-carrying antimicrobial-resistant E. coli from the farm-raised sika deer is potentially a significant contamination source for freshwater systems and food chain, and may pose great health risks for human and animals in Northeastern China.

  15. Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus in China.

    Directory of Open Access Journals (Sweden)

    Huayuan Huang

    Full Text Available The Chinese crocodile lizard Shinisaurus crocodilurus is a critically endangered species, listed in Appendix II of CITES. Its populations and habitat in China have undergone significant changes in recent years. Understanding the genetic variability and phylogeography of this species is very important for successful conservation. In this study, samples were taken from 11 wild ponds and two captive populations in China. We sequenced mitochondrial CYTB, partial ND6, and partial tRNA-Glu and genotyped 10 microsatellite loci. Our analyses of these data showed low genetic variability, no strong isolation caused by distance, and a lack of a phylogeographic structure in this species. Based on our results, the basal divergence between two clades of S. crocodilurus in China may have been caused by the formation of the Pearl River system. We found a population expansion in one of these clades. Microsatellite analysis indicated the presence of three clusters, separated by significant genetic differences. We found that most individuals in the two captive populations were from the Luokeng (Guangdong and Guangxi wild source populations, respectively.

  16. Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer

    Science.gov (United States)

    Morrison, Carl D.; Liu, Pengyuan; Woloszynska-Read, Anna; Zhang, Jianmin; Luo, Wei; Qin, Maochun; Bshara, Wiam; Conroy, Jeffrey M.; Sabatini, Linda; Vedell, Peter; Xiong, Donghai; Liu, Song; Wang, Jianmin; Shen, He; Li, Yinwei; Omilian, Angela R.; Hill, Annette; Head, Karen; Guru, Khurshid; Kunnev, Dimiter; Leach, Robert; Eng, Kevin H.; Darlak, Christopher; Hoeflich, Christopher; Veeranki, Srividya; Glenn, Sean; You, Ming; Pruitt, Steven C.; Johnson, Candace S.; Trump, Donald L.

    2014-01-01

    Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as “stitchers,” to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication–licensing complex. A second group (two bladder tumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in bladder cancer. PMID:24469795

  17. Effects of grown origin, genotype, harvest year, and their interactions of wheat kernels on near infrared spectral fingerprints for geographical traceability.

    Science.gov (United States)

    Zhao, Haiyan; Guo, Boli; Wei, Yimin; Zhang, Bo

    2014-01-01

    The effects of origin, genotype, harvest year, and their interactions on wheat near infrared (NIR) spectra were studied to find the reasons for differences in NIR fingerprints of wheat from different geographical origins and the stability of NIR fingerprints among different years. Ten varieties were grown in three regions of China for 2 years. 180 kernel samples were analysed by NIR. The spectra after pre-treatment were analysed by principal component analysis, multi-way analysis of variance, and discriminant partial least-squares. The results showed that origin, genotype, year, and their interactions all had significant effects on wheat NIR fingerprints. The second overtones of N-H and C-H stretching vibrations and a combination of stretch and deformation of C-H group in wheat were mainly influenced by the geographical origin. The wavelength ranges 975-990 nm, 1200 nm, and 1355-1380 nm contained plenty of origin information to build robust discriminant models of wheat geographical origin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Clinical Heterogeneity of Atypical Pantothenate Kinase-Associated Neurodegeneration in Koreans

    Directory of Open Access Journals (Sweden)

    Jae-Hyeok Lee

    2016-01-01

    Full Text Available Objective Neurodegeneration with brain iron accumulation (NBIA represents a group of inherited movement disorders characterized by iron accumulation in the basal ganglia. Recent advances have included the identification of new causative genes and highlighted the wide phenotypic variation between and within the specific NBIA subtypes. This study aimed to investigate the current status of NBIA in Korea. Methods We collected genetically confirmed NBIA patients from twelve nationwide referral hospitals and from a review of the literature. We conducted a study to describe the phenotypic and genotypic characteristics of Korean adults with atypical pantothenate kinase-associated neurodegeneration (PKAN. Results Four subtypes of NBIA including PKAN (n = 30, PLA2G6-related neurodegeneration (n = 2, beta-propeller protein-associated neurodegeneration (n = 1, and aceruloplasminemia (n = 1 have been identified in the Korean population. The clinical features of fifteen adults with atypical PKAN included early focal limb dystonia, parkinsonism-predominant feature, oromandibular dystonia, and isolated freezing of gait (FOG. Patients with a higher age of onset tended to present with parkinsonism and FOG. The p.R440P and p.D378G mutations are two major mutations that represent approximately 50% of the mutated alleles. Although there were no specific genotype-phenotype correlations, most patients carrying the p.D378G mutation had a late-onset, atypical form of PKAN. Conclusions We found considerable phenotypic heterogeneity in Korean adults with atypical PKAN. The age of onset may influence the presentation of extrapyramidal symptoms.

  19. Relationship of some upland rice genotype after gamma irradiation

    Science.gov (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

    2018-02-01

    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  20. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    Science.gov (United States)

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

  1. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  2. Meta-analysis on the effectiveness of team-based learning on medical education in China.

    Science.gov (United States)

    Chen, Minjian; Ni, Chunhui; Hu, Yanhui; Wang, Meilin; Liu, Lu; Ji, Xiaoming; Chu, Haiyan; Wu, Wei; Lu, Chuncheng; Wang, Shouyu; Wang, Shoulin; Zhao, Liping; Li, Zhong; Zhu, Huijuan; Wang, Jianming; Xia, Yankai; Wang, Xinru

    2018-04-10

    Team-based learning (TBL) has been adopted as a new medical pedagogical approach in China. However, there are no studies or reviews summarizing the effectiveness of TBL on medical education. This study aims to obtain an overall estimation of the effectiveness of TBL on outcomes of theoretical teaching of medical education in China. We retrieved the studies from inception through December, 2015. Chinese National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Wanfang Database, Chinese Scientific Journal Database, PubMed, EMBASE and Cochrane Database were searched. The quality of included studies was assessed by the Newcastle-Ottawa scale. Standardized mean difference (SMD) was applied for the estimation of the pooled effects. Heterogeneity assumption was detected by I 2 statistics, and was further explored by meta-regression analysis. A total of 13 articles including 1545 participants eventually entered into the meta-analysis. The quality scores of these studies ranged from 6 to 10. Altogether, TBL significantly increased students' theoretical examination scores when compared with lecture-based learning (LBL) (SMD = 2.46, 95% CI: 1.53-3.40). Additionally, TBL significantly increased students' learning attitude (SMD = 3.23, 95% CI: 2.27-4.20), and learning skill (SMD = 2.70, 95% CI: 1.33-4.07). The meta-regression results showed that randomization, education classification and gender diversity were the factors that caused heterogeneity. TBL in theoretical teaching of medical education seems to be more effective than LBL in improving the knowledge, attitude and skill of students in China, providing evidence for the implement of TBL in medical education in China. The medical schools should implement TBL with the consideration on the practical teaching situations such as students' education level.

  3. Unexpected heterogeneity derived from Cas9 ribonucleoprotein-introduced clonal cells at the HPRT1 locus.

    Science.gov (United States)

    Sakuma, Tetsushi; Mochida, Keiji; Nakade, Shota; Ezure, Toru; Minagawa, Sachi; Yamamoto, Takashi

    2018-04-01

    Single-cell cloning is an essential technique for establishing genome-edited cell clones mediated by programmable nucleases such as CRISPR-Cas9. However, residual genome-editing activity after single-cell cloning may cause heterogeneity in the clonal cells. Previous studies showed efficient mutagenesis and rapid degradation of CRISPR-Cas9 components in cultured cells by introducing Cas9 ribonucleoproteins (RNPs). In this study, we investigated how the timing for single-cell cloning of Cas9 RNP-transfected cells affected the heterogeneity of the resultant clones. We carried out transfection of Cas9 RNPs targeting several loci in the HPRT1 gene in HCT116 cells, followed by single-cell cloning at 24, 48, 72 hr and 1 week post-transfection. After approximately 3 weeks of incubation, the clonal cells were collected and genotyped by high-resolution microchip electrophoresis and Sanger sequencing. Unexpectedly, long-term incubation before single-cell cloning resulted in highly heterogeneous clones. We used a lipofection method for transfection, and the media containing transfectable RNPs were not removed before single-cell cloning. Therefore, the active Cas9 RNPs were considered to be continuously incorporated into cells during the precloning incubation. Our findings provide a warning that lipofection of Cas9 RNPs may cause continuous introduction of gene mutations depending on the experimental procedures. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  4. Dynamic heterogeneity in life histories

    DEFF Research Database (Denmark)

    Tuljapurkar, Shripad; Steiner, Uli; Orzack, Steven Hecht

    2009-01-01

    or no fixed heterogeneity influences this trait. We propose that dynamic heterogeneity provides a 'neutral' model for assessing the possible role of unobserved 'quality' differences between individuals. We discuss fitness for dynamic life histories, and the implications of dynamic heterogeneity...... generate dynamic heterogeneity: life-history differences produced by stochastic stratum dynamics. We characterize dynamic heterogeneity in a range of species across taxa by properties of the Markov chain: the entropy, which describes the extent of heterogeneity, and the subdominant eigenvalue, which...... distributions of lifetime reproductive success. Dynamic heterogeneity contrasts with fixed heterogeneity: unobserved differences that generate variation between life histories. We show by an example that observed distributions of lifetime reproductive success are often consistent with the claim that little...

  5. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naïve HIV/HCV Co-Infected Patients in China.

    Directory of Open Access Journals (Sweden)

    Kali Zhou

    Full Text Available The advent of direct-acting agents (DAAs has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China.Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1-6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs were identified in positions associated with HCV resistance.Overall, 72.8% (566/778 of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193 of genotype 1, 100% (23/23 of genotype 2, 100% (237/237 of genotype 3 and 92% (299/325 of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69 patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance.The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed.

  6. Genotype-phenotype correlations in a mountain population community with high prevalence of Wilson's disease: genetic and clinical homogeneity.

    Directory of Open Access Journals (Sweden)

    Relu Cocoş

    Full Text Available Wilson's disease is an autosomal recessive disorder caused by more than 500 mutations in ATP7B gene presenting considerably clinical manifestations heterogeneity even in patients with a particular mutation. Previous findings suggested a potential role of additional genetic modifiers and environment factors on phenotypic expression among the affected patients. We conducted clinical and genetic investigations to perform genotype-phenotype correlation in two large families living in a socio-culturally isolated community with the highest prevalence of Wilson's disease ever reported of 1 ∶ 1130. Sequencing of ATP7B gene in seven affected individuals and 43 family members identified a common compound heterozygous genotype, H1069Q/M769H-fs, in five symptomatic and two asymptomatic patients and detected the presence of two out of seven identified single nucleotide polymorphisms in all affected patients. Symptomatic patients had similar clinical phenotype and age at onset (18 ± 1 years showing dysarthria and dysphagia as common clinical features at the time of diagnosis. Moreover, all symptomatic patients presented Kayser-Fleischer rings and lack of dystonia accompanied by unfavourable clinical outcomes. Our findings add value for understanding of genotype-phenotype correlations in Wilson's disease based on a multifamily study in an isolated population with high extent of genetic and environmental homogeneity as opposed to majority of reports. We observed an equal influence of presumed other genetic modifiers and environmental factors on clinical presentation and age at onset of Wilson's disease in patients with a particular genotype. These data provide valuable inferences that could be applied for predicting clinical management in asymptomatic patients in such communities.

  7. Analysis of hepatitis C virus core/NS5A protein co-localization using novel cell culture systems expressing core-NS2 and NS5A of genotypes 1-7

    DEFF Research Database (Denmark)

    Galli, Andrea; Scheel, Troels K H; Prentoe, Jannick C

    2013-01-01

    Hepatitis C virus (HCV) is an important human pathogen infecting hepatocytes. With the advent of infectious cell culture systems, the HCV particle assembly and release processes are finally being uncovered. The HCV core and NS5A proteins co-localize on cytoplasmic lipid droplets (c......LDs) or on the endoplasmic reticulum (ER) at different stages of particle assembly. Current knowledge on assembly and release is primarily based on studies in genotype 2a cell culture systems; however, given the high genetic heterogeneity of HCV, variations might exist among genotypes. Here, we developed novel HCV strain...... JFH1-based recombinants expressing core-NS2 and NS5A from genotypes 1-7, and analysed core and NS5A co-localization in infected cells. Huh7.5 cells were transfected with RNA of core-NS2/NS5A recombinants and putative adaptive mutations were analysed by reverse genetics. Adapted core-NS2/NS5A...

  8. An epidemiologic survey of methicillin-resistant Staphylococcus aureus by combined use of mec-HVR genotyping and toxin genotyping in a university hospital in Japan.

    Science.gov (United States)

    Nishi, Junichiro; Yoshinaga, Masao; Miyanohara, Hiroaki; Kawahara, Motoshi; Kawabata, Masaharu; Motoya, Toshiro; Owaki, Tetsuhiro; Oiso, Shigeru; Kawakami, Masayuki; Kamewari, Shigeko; Koyama, Yumiko; Wakimoto, Naoko; Tokuda, Koichi; Manago, Kunihiro; Maruyama, Ikuro

    2002-09-01

    To evaluate the usefulness of an assay using two polymerase chain reaction-based genotyping methods in the practical surveillance of methicillin-resistant Staphylococcus aureus (MRSA). Nosocomial infection and colonization were surveyed monthly in a university hospital in Japan for 20 months. Genotyping with mec-HVR is based on the size of the mec-associated hypervariable region amplified by polymerase chain reaction. Toxin genotyping uses a multiplex polymerase chain reaction method to amplify eight staphylococcal toxin genes. Eight hundred nine MRSA isolates were classified into 49 genotypes. We observed differing prevalences of genotypes for different hospital wards, and could rapidly demonstrate the similarity of genotype for outbreak isolates. The incidence of genotype D: SEC/TSST1 was significantly higher in isolates causing nosocomial infections (49.5%; 48 of 97) than in nasal isolates (31.4%; 54 of 172) (P = .004), suggesting that this genotype may represent the nosocomial strains. The combined use of these two genotyping methods resulted in improved discriminatory ability and should be further investigated.

  9. Transmission of Hepatitis E Virus in Developing Countries

    Directory of Open Access Journals (Sweden)

    Mohammad S. Khuroo

    2016-09-01

    Full Text Available Hepatitis E virus (HEV, an RNA virus of the Hepeviridae family, has marked heterogeneity. While all five HEV genotypes can cause human infections, genotypes HEV-1 and -2 infect humans alone, genotypes HEV-3 and -4 primarily infect pigs, boars and deer, and genotype HEV-7 primarily infects dromedaries. The global distribution of HEV has distinct epidemiological patterns based on ecology and socioeconomic factors. In resource-poor countries, disease presents as large-scale waterborne epidemics, and few epidemics have spread through person-to-person contact; however, endemic diseases within these countries can potentially spread through person-to-person contact or fecally contaminated water and foods. Vertical transmission of HEV from infected mother to fetus causes high fetal and perinatal mortality. Other means of transmission, such as zoonotic transmission, can fluctuate depending upon the region and strain of the virus. For instance, zoonotic transmission can sometimes play an insignificant role in human infections, such as in India, where human and pig HEV infections are unrelated. However, recently China and Southeast Asia have experienced a zoonotic spread of HEV-4 from pigs to humans and this has become the dominant mode of transmission of hepatitis E in eastern China. Zoonotic HEV infections in humans occur by eating undercooked pig flesh, raw liver, and sausages; through vocational contact; or via pig slurry, which leads to environmental contamination of agricultural products and seafood. Lastly, blood transfusion-associated HEV infections occur in many countries and screening of donors for HEV RNA is currently under serious consideration. To summarize, HEV genotypes 1 and 2 cause epidemic and endemic diseases in resource poor countries, primarily spreading through contaminated drinking water. HEV genotypes 3 and 4 on the other hand, cause autochthonous infections in developed, and many developing countries, by means of a unique zoonotic

  10. Two-temperature LATE-PCR endpoint genotyping

    Directory of Open Access Journals (Sweden)

    Reis Arthur H

    2006-12-01

    Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

  11. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  12. Platelet Immunology in China: Research and Clinical Applications.

    Science.gov (United States)

    Wu, Guoguang; Zhou, Yan; Li, Lilan; Zhong, Zhoulin; Li, Hengchong; Li, Haiyan; Yu, Mei; Shen, Weidong; Ni, Heyu

    2017-04-01

    Immunization against human platelet alloantigens (HPAs) is associated with a number of clinical complications. The detection and identification of clinically relevant platelet antibodies are important for the diagnosis and management of patients affected with immune-mediated thrombocytopenias. Human platelet alloantigen frequencies and the characteristics of antiplatelet antibodies vary widely between ethnic groups. Since 2008, the importance of platelet immunology in the field of transfusion medicine has gained greater recognition by clinical laboratories in China. Laboratories in China have established and improved methods for platelet antibody detection and HPA genotyping techniques, which are used for the diagnosis of alloimmune platelet disorders in clinic and research environments. Research has revealed the frequencies of HPA alleles in different Chinese ethnic groups and compared the differences in HPA gene frequencies between the Chinese Han and other ethnic groups of the world. Production of anti-CD36 isoantibodies is an important risk factor for immune-mediated thrombocytopenia in the Chinese population. Advances in research and clinical application of platelet immunology have significantly improved the clinical diagnosis, treatment including transfusion support, and prevention of alloimmune platelet disorders in the Chinese population. Copyright © 2017. Published by Elsevier Inc.

  13. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  14. Smoking and Inflammatory Bowel Disease: A Comparison of China, India, and the USA.

    Science.gov (United States)

    Wang, Peiqi; Hu, Jun; Ghadermarzi, Shadi; Raza, Ali; O'Connell, Douglas; Xiao, Amy; Ayyaz, Faraz; Zhi, Min; Zhang, Yuanqi; Parekh, Nimisha K; Lazarev, Mark; Parian, Alyssa; Brant, Steven R; Bedine, Marshall; Truta, Brindusa; Hu, Pinjin; Banerjee, Rupa; Hutfless, Susan M

    2018-06-04

    Cigarette smoking is thought to increase the risk of Crohn's disease (CD) and exacerbate the disease course, with opposite roles in ulcerative colitis (UC). However, these findings are from Western populations, and the association between smoking and inflammatory bowel disease (IBD) has not been well studied in Asia. We aimed to compare the prevalence of smoking at diagnosis between IBD cases and controls recruited in China, India, and the USA, and to investigate the impact of smoking on disease outcomes. We recruited IBD cases and controls between 2014 and 2018. All participants completed a questionnaire about demographic characteristics, environmental risk factors and IBD history. We recruited 337 participants from China, 194 from India, and 645 from the USA. In China, CD cases were less likely than controls to be current smokers (adjusted odds ratio [95% CI] 0.4 [0.2-0.9]). There was no association between current or former smoking and CD in the USA. In China and the USA, UC cases were more likely to be former smokers than controls (China 14.6 [3.3-64.8]; USA 1.8 [1.0-3.3]). In India, both CD and UC had similar current smoking status to controls at diagnosis. Current smoking at diagnosis was significantly associated with greater use of immunosuppressants (4.4 [1.1-18.1]) in CD cases in China. We found heterogeneity in the associations of smoking and IBD risk and outcomes between China, India, and the USA. Further study with more adequate sample size and more uniform definition of smoking status is warranted.

  15. Emergence and diversification of dengue 2 cosmopolitan genotype in Pakistan, 2011.

    Directory of Open Access Journals (Sweden)

    Mohammad A Khan

    Full Text Available Major dengue epidemics have been observed in the Indian subcontinent since the 1980s and have occurred with increased hospitalizations and mortality. In 2011, the first major epidemic of dengue occurred in Lahore, the second largest city in Pakistan, and resulted in 21,685 confirmed cases and 350 deaths. To investigate the possible viral causes for the increased epidemic activity, we determined the predominant serotype and characterized the viruses genetically. Of 50 patients carefully selected as probable dengue fever or dengue hemorrhagic fever, 34 were positive by virologic testing (i.e. PCR and/or virus isolation. DENV-2 was detected in 32 patients and DENV-1 in two. A total of 24 partial and three full DENV genomes were sequenced. Phylogenetic analyses of the capsid (C, pre-membrane (prM, and envelope genes comprising 2500 nucleotides in length indicated that all DENV-2 isolates in Pakistan since 2007 form a monophyletic lineage that is endemic in the country. These viruses were all of the cosmopolitan genotype (IV and most closely related to viruses isolated in India and Sri Lanka in the past two decades. Phylogenetic analyses of data currently available in GenBank suggest that the Cosmopolitan genotype has diverged into two geographically distinct sub-lineages: sub-lineage IV-a has only been observed in Southeast Asia, China and Oceania, while IV-b is prevalent in the Indian subcontinent. These results highlight the increased diversity of dengue viruses as they spread geographically within the region.

  16. Simulations of Sulfate-Nitrate-Ammonium (SNA) aerosols during the extreme haze events over Northern China in 2014

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Dan; Liu, Zhiquan; Fast, Jerome D.; Ban, Junmei

    2016-08-30

    Extreme haze events have occurred frequently over China in recent years. Although many studies have investigated the formation mechanisms associated with PM2.5 for heavily polluted regions in China based on observational data, adequately predicting peak PM2.5 concentrations is still challenging for regional air quality models. In this study, we evaluate the performance of one configuration of the Weather Research and Forecasting model coupled with chemistry (WRF-Chem) and use the model to investigate the sensitivity of heterogeneous reactions on simulated peak sulfate, nitrate, and ammonium concentrations in the vicinity of Beijing during four extreme haze episodes in October 2014 over the North China Plain. The highest observed PM2.5 concentration of 469 μg m-3 occurred in Beijing. Comparisons with observations show that the model reproduced the temporal variability in PM2.5 with the highest PM2.5 values on polluted days (defined as days in which observed PM2.5 is greater than 75 μg m-3), but predictions of sulfate, nitrate, and ammonium were too low on days with the highest observed concentrations. Observational data indicate that the sulfur/nitric oxidation rates are strongly correlated with relative humidity during periods of peak PM2.5; however, the model failed to reproduce the highest PM2.5 concentrations due to missing heterogeneous reactions. As the parameterizations of those reactions is not well established yet, estimates of SO2-to-H2SO4 and NO2/NO3-to-HNO3 reaction rates that depend on relative humidity were applied which improved the simulation of sulfate, nitrate, and ammonium enhancement on polluted days in terms of both concentrations and partitioning among those species. Sensitivity simulations showed that the extremely high heterogeneous reaction rates and also higher emission rates than those reported in the emission inventory

  17. Implementation of Cell Samples as Controls in National Proficiency Testing for Clopidogrel Therapy-Related CYP2C19 Genotyping in China: A Novel Approach.

    Directory of Open Access Journals (Sweden)

    Guigao Lin

    Full Text Available Laboratories are increasingly requested to perform CYP2C19 genetic testing when managing clopidogrel therapy, especially in patients with acute coronary syndrome undergoing percutaneous coronary intervention. To ensure high quality molecular testing and ascertain that the referring clinician has the correct information for CYP2C19 genotype-directed antiplatelet therapy, a proficiency testing scheme was set up to evaluate the laboratory performance for the entire testing process. Proficiency panels of 10 cell samples encompassing the common CYP2C19 genetic polymorphisms were distributed to 62 participating laboratories for routine molecular testing and the responses were analyzed for accuracy of genotyping and the reporting of results. Data including the number of samples tested, the accreditation/certification status, and test methodology of each individual laboratory were also reviewed. Fifty-seven of the 62 participants correctly identified the CYP2C19 variants in all samples. There were six genotyping errors, with a corresponding analytical sensitivity of 98.5% (333/338 challenges; 95% confidence interval: 96.5-99.5% and an analytic specificity of 99.6% (281/282; 95% confidence interval: 98.0-99.9%. Reports of the CYP2C19 genotyping results often lacked essential information. In conclusion, clinical laboratories demonstrated good analytical sensitivity and specificity; however, the pharmacogenetic testing community requires additional education regarding the correct reporting of CYP2C19 genetic test results.

  18. The Comparison of Growth, Slaughter and Carcass Traits of Meat Chicken Genotype Produced by Back-Crossing with A Commercial Broiler Genotype

    OpenAIRE

    Musa Sarıca; Umut Sami Yamak; Mehmet Akif Boz; Ahmet Uçar

    2014-01-01

    This study was conducted to determine the growth and some slaughter traits between commercial fast growing chickens and three-way cross M2 genotypes. 260 male female mixed chickens from each genotype was reared 10 replicate per genotype in the same house. Two different slaughtering ages were applied to commercial chickens and slaughtered at 6 and 7 weeks of age for comparing with cross genotypes. F chickens reached to slaughtering age at 42 days, whereas cross groups reached at 49 days. Genot...

  19. Genetic polymorphisms of the CASP8 gene promoter may not be associated with colorectal cancer in Han Chinese from southwest China.

    Directory of Open Access Journals (Sweden)

    Mei-Sheng Xiao

    Full Text Available PURPOSE: Caspase 8 (CASP8 plays a critical role in the apoptotic pathway and aberrant regulation of this pathway causes many diseases including cancers. Genetic variants rs3834129 (CTTACT/- and rs3769821 (T/C in the promoter region of the CASP8 gene were documented to be associated with multiple solid cancers and non-Hodgkin's lymphoma (NHL, respectively, despite of some controversies. We aimed to discern potential association of these two variants and rs113686495 (CTGTCATT/-, as well as CASP8 mRNA and protein expression levels with colorectal cancer (CRC in Han Chinese. METHODS: We genotyped CASP8 genetic variants in 305 CRC patients and 342 healthy individuals from Kunming, Southwest China. Expression levels of CASP8 mRNA and protein were quantified in paired cancerous and paracancerous normal tissues by using real-time quantitative PCR and western blot, respectively. We compared the frequencies of alleles, genotypes, and haplotypes between the cases and controls. Correlation of CASP8 mRNA and protein expression levels in paired cancerous and paracancerous normal tissues from patients with different genotypes and clinical expression were also evaluated. RESULTS: There was no association of the CASP8 genetic variants with CRC in our case-control study. The CASP8 gene mRNA expression levels in cancerous and paracancerous normal tissues were similar and there was no significant difference between subjects with different genotypes and clinical features. However, we found that CASP8 protein level was significantly lower in cancerous tissues than in paired paracancerous normal tissues. CONCLUSIONS: Our results suggest that the three CASP8 genetic variants may not be associated with CRC risk in Han Chinese from southwest China. Aberrant CASP8 protein expression may play a role in the pathogenesis of CRC.

  20. Identifying electricity-saving potential in rural China: Empirical evidence from a household survey

    International Nuclear Information System (INIS)

    Yu, Yihua; Guo, Jin

    2016-01-01

    In recent years, there has been a fast-growing body of literature examining energy-saving potential in relation to electricity. However, empirical studies focusing on non-Western nations are limited. To fill this gap, this study intends to examine the electricity-saving potential of rural households in China using a unique data set from the China Residential Electricity Consumption Survey (CRECS) in collaboration with the China General Social Survey (CGSS), conducted nationwide at the household level in rural China. We use a stochastic frontier model, which allows us to decompose residential electricity consumption into the minimum necessary amount of consumption based on physical characteristics (e.g. house size, house age, number of televisions or refrigerators) and estimate the consumption slack (i.e. the amount of electricity consumption that could be saved), which depends on various factors. We find that rural households in China are generally efficient in electricity saving and the saving potential is affected by (fast) information feedback and social-demographic characteristics, instead of by the (averaged) electricity price, or energy efficiency labelling signals. In addition, we find no evidence of regional heterogeneity on electricity saving potential for rural households. Policy implications are derived. - Highlights: •Electricity saving potential of rural households in China is examined. •Unique survey data from the CRECS in collaboration with the CGSS are used. •A stochastic frontier model is applied. •Information feedback and social-demographic characteristics matter. •Electricity price or energy efficiency tier rating does not matter.

  1. The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China

    Directory of Open Access Journals (Sweden)

    Yang Li

    2018-04-01

    Full Text Available This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%. By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP, and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%. By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.

  2. Heterogeneous cellular networks

    CERN Document Server

    Hu, Rose Qingyang

    2013-01-01

    A timely publication providing coverage of radio resource management, mobility management and standardization in heterogeneous cellular networks The topic of heterogeneous cellular networks has gained momentum in industry and the research community, attracting the attention of standardization bodies such as 3GPP LTE and IEEE 802.16j, whose objectives are looking into increasing the capacity and coverage of the cellular networks. This book focuses on recent progresses,  covering the related topics including scenarios of heterogeneous network deployment, interference management i

  3. Epidemiology of hepatitis C virus and genotype distribution in immigrants crossing to Europe from North and sub-Saharan Africa.

    Science.gov (United States)

    Daw, Mohamed A; El-Bouzedi, Abdallah; Ahmed, Mohamed O; Dau, Aghnyia A; Agnan, Mohamed M

    accounted for 329 (36.1%), 326 (35.8%), and 131 (14.4%) strains, respectively, followed by genotype 3 that accounted for 87 (9.5%) strains. Genotype 5 was isolated mainly from 18 HOA (2%) and 20 West African (2.2%) individuals. The prevalence of HCV is considered high with a unique disparate distribution among African immigrants crossing to Europe. This indicated that the prevalence of HCV is high among these immigrants and thus may be reflected on the HCV prevalence in the guest countries. The broad genetic heterogeneity of HCV genotypes detected here may impact the efficacy of prevention and control efforts for HCV in both Europe and North and sub-Saharan Africa; hence, an integrated global policy of actions is needed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    The trials were set up to identify sweetpotato genotypes with adaptation to highland agroecologies with special reference to resistance to Ahemaria blight ... growth and at harvest, four genotypes and the local check, Magabari, bad high levels of resistance toA/Jemaria blight. Eight genotypes had total storage root yield ...

  5. First genotyping of Blastocystis sp. in dairy, meat, and cashmere goats in northwestern China.

    Science.gov (United States)

    Song, Jun-Ke; Yin, Yan-Ling; Yuan, Ya-Jie; Tang, Huan; Ren, Guan-Jing; Zhang, Hui-Jun; Li, Zi-Xuan; Zhang, Yan-Ming; Zhao, Guang-Hui

    2017-12-01

    Blastocystis is one of the most common parasites inhabiting in small intestines of human and animals. Although its pathogenicity has been remaining controversial, the possibility of zoonotic transmission between human and animals was recognized. The goat was one of the most important economic animals supplying people with cashmere, meat, and dairy products. However, few studies were to investigate Blastocystis infection in goats. A total of 789 faecal specimens of goats (including 362 of dairy, 193 of meat and 234 of cashmere goats) were collected from multiple regions of Shaanxi province in northwestern China to investigate the colonization frequency and subtypes of Blastocystis, and to assess the zoonotic potential of these goats. The respective colonization frequencies of Blastocystis in dairy, meat and cashmere goats were 54.1% (196/362), 40.4% (78/193) and 78.6% (184/234). The prevalence of Blastocystis in pre-weaned (0-2-month) goats was significantly lower than that in goats of other age groups, and the highest colonization was observed in goats of 7-11-month age group. Sequence analysis of Blastocystis positive samples indicated the presence of seven subtypes in these goats, including six known subtypes (STs1, 3, 4, 5, 10, 14) and one possible novel subtype (isolate Sd26), with the subtype 10 as the predominant one. Additionally, zoonotic subtypes were found in dairy (ST1, ST3 and ST5) and cashmere (ST4 and ST5) goats, but not detected in meat goats. These results showed that Blastocystis is highly prevalent, widely distributed and genetically diverse in goats in Shaanxi province, northwestern China, and zoonotic potential of dairy and cashmere goats to transmit Blastocystis. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. A Sharable and Efficient Metadata Model for Heterogeneous Earth Observation Data Retrieval in Multi-Scale Flood Mapping

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    Nengcheng Chen

    2015-07-01

    Full Text Available Remote sensing plays an important role in flood mapping and is helping advance flood monitoring and management. Multi-scale flood mapping is necessary for dividing floods into several stages for comprehensive management. However, existing data systems are typically heterogeneous owing to the use of different access protocols and archiving metadata models. In this paper, we proposed a sharable and efficient metadata model (APEOPM for constructing an Earth observation (EO data system to retrieve remote sensing data for flood mapping. The proposed model contains two sub-models, an access protocol model and an enhanced encoding model. The access protocol model helps unify heterogeneous access protocols and can achieve intelligent access via a semantic enhancement method. The enhanced encoding model helps unify a heterogeneous archiving metadata model. Wuhan city, one of the most important cities in the Yangtze River Economic Belt in China, is selected as a study area for testing the retrieval of heterogeneous EO data and flood mapping. The past torrential rain period from 25 March 2015 to 10 April 2015 is chosen as the temporal range in this study. To aid in comprehensive management, mapping is conducted at different spatial and temporal scales. In addition, the efficiency of data retrieval is analyzed, and validation between the flood maps and actual precipitation was conducted. The results show that the flood map coincided with the actual precipitation.

  7. Assessing accuracy of genotype imputation in American Indians.

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    Alka Malhotra

    Full Text Available Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome. The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.

  8. Porphyromonas gingivalis Fim-A genotype distribution among Colombians

    Science.gov (United States)

    Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

    2015-01-01

    Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

  9. Genetic and antigenic characterization of novel pestivirus genotypes: implications for classification

    International Nuclear Information System (INIS)

    Becher, Paul; Avalos Ramirez, Ramiro; Orlich, Michaela; Cedillo Rosales, Sibilina; Koenig, Matthias; Schweizer, Matthias; Stalder, Hanspeter; Schirrmeier, Horst; Thiel, Heinz-Juergen

    2003-01-01

    Currently, the genus Pestivirus comprises the four approved species Bovine viral diarrhea virus 1 (BVDV-1), BVDV-2, Classical swine fever virus (CSFV), and Border disease virus (BDV) and one tentative fifth species represented by a single strain (H138) isolated from a giraffe in Kenya more than 30 years ago. To further address the issue of heterogeneity of pestiviruses we have determined the entire N pro and E2 coding sequences for several new pestivirus isolates. Interestingly, phylogenetic analysis revealed that one pestivirus isolated in the 1990s in Africa is closely related to strain H138. Moreover, several novel pestiviruses isolated from sheep group together with the previously described strain V60 (Reindeer-1) isolated from a reindeer, whereas one ovine pestivirus strain (Gifhorn) significantly differs from all previously described pestiviruses, including BDV. We propose to term these mainly sheep-derived pestiviruses BDV-2 (V60-like isolates) and BDV-3 (Gifhorn); consequently, the 'classical' BDV isolates should be termed BDV-1. As an additional criterion for segregation of pestiviruses, the antigenic relatedness of pestivirus isolates covering all observed major genotypes was studied by cross-neutralization assays. Analysis of the antigenic similarities indicated the presence of seven major antigenic groups corresponding to BVDV-1, BVDV-2, CSFV, BDV-1, BDV-2, BDV-3, and 'giraffe'. Taking into account the host origin, the lack of differences concerning the course of disease, and the results of our genetic and antigenic analyses, we suggest that BDV-1, BDV-2, and BDV-3 should be considered as major genotypes within the species BDV

  10. Solidago canadensis invasion affects soil N-fixing bacterial communities in heterogeneous landscapes in urban ecosystems in East China.

    Science.gov (United States)

    Wang, Congyan; Jiang, Kun; Zhou, Jiawei; Wu, Bingde

    2018-03-12

    Soil nitrogen-fixing bacterial communities (SNB) can increase the level of available soil N via biological N-fixation to facilitate successful invasion of several invasive plant species (IPS). Meanwhile, landscape heterogeneity can greatly enhance regional invasibility and increase the chances of successful invasion of IPS. Thus, it is important to understand the soil micro-ecological mechanisms driving the successful invasion of IPS in heterogeneous landscapes. This study performed cross-site comparisons, via metagenomics, to comprehensively analyze the effects of Solidago canadensis invasion on SNB in heterogeneous landscapes in urban ecosystems. Rhizospheric soil samples of S. canadensis were obtained from nine urban ecosystems [Three replicate quadrats (including uninvaded sites and invaded sites) for each type of urban ecosystem]. S. canadensis invasion did not significantly affect soil physicochemical properties, the taxonomic diversity of plant communities, or the diversity and richness of SNB. However, some SNB taxa (i.e., f_Micromonosporaceae, f_Oscillatoriaceae, and f_Bacillaceae) changed significantly with S. canadensis invasion. Thus, S. canadensis invasion may alter the community structure, rather than the diversity and richness of SNB, to facilitate its invasion process. Of the nine urban ecosystems, the diversity and richness of SNB was highest in farmland wasteland. Accordingly, the community invasibility of farmland wasteland may be higher than that of the other types of urban ecosystem. In brief, landscape heterogeneity, rather than S. canadensis invasion, was the strongest controlling factor for the diversity and richness of SNB. One possible reason may be the differences in soil electrical conductivity and the taxonomic diversity of plant communities in the nine urban ecosystems, which can cause notable shifts in the diversity and richness of SNB. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Plant genotypic diversity reduces the rate of consumer resource utilization.

    Science.gov (United States)

    McArt, Scott H; Thaler, Jennifer S

    2013-07-07

    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

  12. Distribution of Hepatitis C Virus Genotypes in the South Marmara Region

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    Harun Agca

    2014-03-01

    Full Text Available Aim: Hepatitis C virus (HCV is an important caustive agent of hepatitis, cirrhosis and hepatocellular carcinoma both in our country and the world. Prognosis and response to treatment is related with the genotype of HCV which has six genotypes and over a hundred quasispecies. Knowing the HCV genotype is also important for epidemiological data. In this study we aimed to investigate the HCV genotypes of samples sent to Uludag University Hospital Microbiology Laboratory which is the reference centre in the South Marmara Region. Material and Method: This study was done retrospectively to analyse the HCV patients%u2019 sera sent to our laboratory between July 2010and December 2012 for HCV genotyping. Artus HCV QS-RGQ PCR kit (Qiagene,Hilden, Germany was used in Rotor-Gene Q (Qiagene, Hilden Germany for detection of HCV RNA. HCV RNA positive samples of patients%u2019 sera were were used for genotyping by the Linear Array HCV genotyping test (Roche, NJ, USA.Results: 214 (92.6 % of total 231 patients included in the study were genotype 1, one (0.4 % was genotype 2, nine (3.9 % were genotype 3 and, seven (3.4 % were found genotype 4. Three of genotype 3 patients were of foreign nationality, two were born abroad and one of the genotype 4 patients were born abroad. Discussion: Concordant with our country data the most frequent genotype was 1, genotype 2 was seen in patients especially related with foreign countries and genotype 4 was seen rare. The importance of genotype 1, which is seen more frequent in our country and region is; resistance to antiviral treatment and prolonged treatment duration in chronic hepatitis C patients.

  13. [Diversity and classification system of weed community in Harbin City, China].

    Science.gov (United States)

    Chen, Xiao-Shuang; Liang, Hong; Song, Kun; Da, Liang-Jun

    2014-08-01

    To analyze the causes of weed community diversity and their strategies of adaption to the high heterogeneity of urban habitats, weed communities in the central urban area of Harbin, China were studied, and a classification system was established for the weed communities. There were 175 weed species, belonging to 128 genera and 38 families. The heterogeneous urban habitats and species' temporal niche differentiation resulted in the highly diversified weed communities. The high proportions of mono-species dominance and annual species dominance communities were their response to the unstable urban habitats under human disturbances with high intensities and frequencies. A four-level classification system was established in terms of plant species and habitat conditions. Within this system, the identified 1763 weed communities could be categorized into two types of life form, 5 types of dormancy form, 22 community groups, and 119 dominance communities.

  14. Locus heterogeneity for Waardenburg syndrome is predictive of clinical subtypes.

    Science.gov (United States)

    Farrer, L A; Arnos, K S; Asher, J H; Baldwin, C T; Diehl, S R; Friedman, T B; Greenberg, J; Grundfast, K M; Hoth, C; Lalwani, A K

    1994-10-01

    Waardenburg syndrome (WS) is a dominantly inherited and clinically variable syndrome of deafness, pigmentary changes, and distinctive facial features. Clinically, WS type I (WS1) is differentiated from WS type II (WS2) by the high frequency of dystopia canthorum in the family. In some families, WS is caused by mutations in the PAX3 gene on chromosome 2q. We have typed microsatellite markers within and flanking PAX3 in 41 WS1 kindreds and 26 WS2 kindreds in order to estimate the proportion of families with probable mutations in PAX3 and to study the relationship between phenotypic and genotypic heterogeneity. Evaluation of heterogeneity in location scores obtained by multilocus analysis indicated that WS is linked to PAX3 in 60% of all WS families and in 100% of WS1 families. None of the WS2 families were linked. In those families in which equivocal lod scores (between -2 and +1) were found, PAX3 mutations have been identified in 5 of the 15 WS1 families but in none of the 4 WS2 families. Although preliminary studies do not suggest any association between the phenotype and the molecular pathology in 20 families with known PAX3 mutations and in four patients with chromosomal abnormalities in the vicinity of PAX3, the presence of dystopia in multiple family members is a reliable indicator for identifying families likely to have a defect in PAX3.

  15. Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci.

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    Yanjun Li

    Full Text Available BACKGROUND: The species Yersinia pestis is commonly divided into three classical biovars, Antiqua, Medievalis, and Orientalis, belonging to subspecies pestis pathogenic for human and the (atypical non-human pathogenic biovar Microtus (alias Pestoides including several non-pestis subspecies. Recent progress in molecular typing methods enables large-scale investigations in the population structure of this species. It is now possible to test hypotheses about its evolution which were proposed decades ago. For instance the three classical biovars of different geographical distributions were suggested to originate from Central Asia. Most investigations so far have focused on the typical pestis subspecies representatives found outside of China, whereas the understanding of the emergence of this human pathogen requires the investigation of strains belonging to subspecies pestis from China and to the Microtus biovar. METHODOLOGY/PRINCIPAL FINDINGS: Multi-locus VNTR analysis (MLVA with 25 loci was performed on a collection of Y. pestis isolates originating from the majority of the known foci worldwide and including typical rhamnose-negative subspecies pestis as well as rhamnose-positive subspecies pestis and biovar Microtus. More than 500 isolates from China, the Former Soviet Union (FSU, Mongolia and a number of other foci around the world were characterized and resolved into 350 different genotypes. The data revealed very close relationships existing between some isolates from widely separated foci as well as very high diversity which can conversely be observed between nearby foci. CONCLUSIONS/SIGNIFICANCE: The results obtained are in full agreement with the view that the Y. pestis subsp. pestis pathogenic for humans emerged in the Central Asia region between China, Kazakhstan, Russia and Mongolia, only three clones of which spread out of Central Asia. The relationships among the strains in China, Central Asia and the rest of the world based on the MLVA

  16. Phenotypic and genotypic variation in Iranian Pistachios

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    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  17. The heterogeneous dynamics of economic complexity.

    Science.gov (United States)

    Cristelli, Matthieu; Tacchella, Andrea; Pietronero, Luciano

    2015-01-01

    What will be the growth of the Gross Domestic Product (GDP) or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness) allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.

  18. The Heterogeneous Dynamics of Economic Complexity

    Science.gov (United States)

    Cristelli, Matthieu; Tacchella, Andrea; Pietronero, Luciano

    2015-01-01

    What will be the growth of the Gross Domestic Product (GDP) or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch—Economic Complexity—have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness) allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method—the selective predictability scheme—in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries. PMID:25671312

  19. Seismic attenuation relationship with homogeneous and heterogeneous prediction-error variance models

    Science.gov (United States)

    Mu, He-Qing; Xu, Rong-Rong; Yuen, Ka-Veng

    2014-03-01

    Peak ground acceleration (PGA) estimation is an important task in earthquake engineering practice. One of the most well-known models is the Boore-Joyner-Fumal formula, which estimates the PGA using the moment magnitude, the site-to-fault distance and the site foundation properties. In the present study, the complexity for this formula and the homogeneity assumption for the prediction-error variance are investigated and an efficiency-robustness balanced formula is proposed. For this purpose, a reduced-order Monte Carlo simulation algorithm for Bayesian model class selection is presented to obtain the most suitable predictive formula and prediction-error model for the seismic attenuation relationship. In this approach, each model class (a predictive formula with a prediction-error model) is evaluated according to its plausibility given the data. The one with the highest plausibility is robust since it possesses the optimal balance between the data fitting capability and the sensitivity to noise. A database of strong ground motion records in the Tangshan region of China is obtained from the China Earthquake Data Center for the analysis. The optimal predictive formula is proposed based on this database. It is shown that the proposed formula with heterogeneous prediction-error variance is much simpler than the attenuation model suggested by Boore, Joyner and Fumal (1993).

  20. Systematic review of reporting rates of adverse events following immunization: an international comparison of post-marketing surveillance programs with reference to China.

    Science.gov (United States)

    Guo, Biao; Page, Andrew; Wang, Huaqing; Taylor, Richard; McIntyre, Peter

    2013-01-11

    China is the most populous country in the world, with an annual birth cohort of approximately 16 million, requiring an average of 500 million vaccine doses administered annually. In China, over 30 domestic and less than 10 overseas vaccine manufacturers supply over 60 licensed vaccine products, representing a growing vaccine market mainly due to recent additions to the national immunization schedule, but data on post-marketing surveillance for adverse events following immunization (AEFI) are sparse. To compare reporting rates for various categories of AEFI from China with other routine post-marketing surveillance programs internationally. Systematic review of published studies reporting rates of AEFI by vaccine, category of reaction and age from post-marketing surveillance systems in English and Chinese languages. Overall AEFI reporting rates (all vaccines, all ages) in Chinese studies were consistent with those from similar international studies elsewhere, but there was substantial heterogeneity in regional reporting rates in China (range 2.3-37.8/100,000 doses). The highest AEFI reporting rates were for diphtheria-tetanus-pertussis whole-cell (DTwP) and acellular (DTaP) vaccines (range 3.3-181.1/100,000 doses for DTwP; range 3.5-92.6/100,000 doses for DTaP), with higher median rates for DTwP than DTaP, and higher than expected rates for DTaP vaccine. Similar higher rates for DTwP and DTaP containing vaccines, and relatively lower rates for vaccines against hepatitis B virus, poliovirus, and Japanese encephalitis virus were found in China and elsewhere in the world. Overall AEFI reporting rates in China were consistent with similar post-marketing surveillance systems in other countries. Sources of regional heterogeneity in AEFI reporting rates, and their relationships to differing vaccine manufacturers versus differing surveillance practices, require further exploration. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Formation of nitro-PAHs from the heterogeneous reaction of ambient particle-bound PAHs with NO3/N2O5

    Science.gov (United States)

    Zimmermann, K.; Jariyasopit, N.; Simonich, S. L.; Atkinson, R.; Arey, J.

    2012-12-01

    Polycyclic aromatic hydrocarbons (PAHs) and their nitrated derivatives (nitro-PAHs) have been shown to be mutagenic in bacterial and mammalian assays and are classified as probable human carcinogens. Semi-volatile PAHs partition between the gas and particulate phases, depending on their liquid-phase vapor pressures and ambient temperatures. These PAHs have been extensively measured in ambient particulate matter and can ultimately undergo long-range transport from source regions (e.g., China to the western USA) (1). During transport these particle-bound PAHs may undergo reaction with NO3/N2O5 to form nitro-PAH derivatives. Previous studies of heterogeneous nitration of PAHs have used particles composed of graphite, diesel soot, and wood smoke (2-4). This study investigates the heterogeneous formation of nitro-PAHs from ambient particle-bound PAHs from Beijing, China and sites located within the Los Angeles air basin. These ambient particle samples, along with filters coated with isotopically labeled PAHs, were exposed to a mix of NO2/NO3/N2O5 in a 7000 L Teflon chamber, with analysis focused on the heterogeneous formation of molecular weight 247 and 273 nitro-PAHs. The heterogeneous formation of certain nitro-PAHs (including1-nitropyrene and 1- and 2-nitrotriphenylene) was observed for some, but not all, ambient samples. Formation of nitro-PAHs typically formed through gas-phase reactions (2-nitrofluoranthene and 2-nitropyrene) was not observed. The effect of particle age and local photochemical conditions during sampling on the degree of nitration in environmental chamber reactions, as well as ambient implications, will be presented. 1. Primbs, T.; Simonich, S.; Schmedding, D.; Wilson, G.; Jaffe, D.; Takami, A.; Kato, S.; Hatakeyama, S.; Kajii, Y. Environ. Sci. Technol. 2007, 41, 3551-3558. 2. Esteve, W.; Budzinski, H.; Villenave, E. Atmospheric Environment 2004, 38, 6063-6072. 3. Nguyen, M.; Bedjanian, Y.; Guilloteau, A. Journal of Atmospheric Chemistry 2009, 62

  2. Modeling and validation of directional reflectance for heterogeneous agro-forestry scenarios

    Science.gov (United States)

    Yelu, Z.; Jing, L.; Qinhuo, L.; Huete, A. R.

    2015-12-01

    Landscape heterogeneity is a common natural phenomenon but is seldom considered in current radiative transfer models for predicting the surface reflectance. This paper developed an explicit analytical Radiative Transfer model for heterogeneous Agro-Forestry scenarios (RTAF) by dividing the scenario into non-boundary regions and boundary regions. The scattering contribution of the non-boundary regions that are treated as homogeneous canopies can be estimated from the SAILH model, whereas that of the boundary regions with lengths, widths, canopy heights, and orientations of the field patches, is calculated based on the bidirectional gap probability by considering the interactions and mutual shadowing effects among different patches. The hot spot factor is extended for heterogeneous scenarios, the Hapke model for soil anisotropy is incorporated, and the contributions of the direct and diffuse radiation are separately calculated. The multi-angular airborne observations and the Discrete Anisotropic Radiative Transfer (DART) model simulations were used for validating and evaluating the RTAF model over an agro-forestry scenario in Heihe River Basin, China. It indicates that the RTAF model can accurately simulate the hemispherical-directional reflectance factors (HDRFs) of the heterogeneous agro-forestry scenario, with an RMSE of 0.0016 and 0.0179 in the red and near-infrared (NIR) bands, respectively. The RTAF model was compared with two widely used models, the dominant cover type (DCT) model and the spectral linear mixture (SLM) model, which either neglected the interactions and mutual shadowing effects between the shelterbets and crops, or did not account for the contribution of the shelterbets. Results suggest that the boundary effect can significantly influence the angular distribution of the HDRFs, and consequently enlarged the HDRF variations between the backward and forward directions in the principle plane. The RTAF model reduced the maximum relative error from 25

  3. Hepatitis C Virus: Viral Quasispecies and Genotypes.

    Science.gov (United States)

    Tsukiyama-Kohara, Kyoko; Kohara, Michinori

    2017-12-22

    Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  4. Response of cotton genotypes to boron under-b-adequate conditions

    International Nuclear Information System (INIS)

    Shah, J. A.; Sial, M. A.; Hassan, Z. U.; Rajpar, I.

    2015-01-01

    Balanced boron (B) application is well-known to enhance the cotton production; however, the narrow range between B-deficiency and toxicity levels makes it difficult to manage. Cotton genotypes extensively differ in their response to B requirements. The adequate dose of B for one genotype may be insufficient or even toxic to other genotype. The effects of boron (B) on seed cotton yield and its various yield associated traits were studied on 10 cotton genotypes of Pakistan. The pot studies were undertaken to categorize cotton genotypes using B-deficient (control) and B-adequate (2.0 kg B ha-1) levels arranged in CRD with four repeats. The results indicated that the seed cotton yield, yield attributes and B-uptake of genotypes were comparatively decreased in B-deficient stressed treatment. Genotype NIA-Ufaq exhibited wide range of adaptation and ranked as efficient-responsive, as it produced higher seed cotton yield under both B-regimes. SAU-2 and CIM-506 were highly-efficient and remaining all genotypes were medium-efficient. Genotype Sindh-1 produced low seed cotton yield under B deficient condition and ranked as low-efficient. B-efficient cotton genotypes can be grown in B deficient soils without B application. (author)

  5. Micropropagation of six Paulownia genotypes through tissue culture

    Directory of Open Access Journals (Sweden)

    Lydia Shtereva

    2014-12-01

    Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

  6. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  7. Gene Profiling in Late Blight Resistance in Potato Genotype SD20

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    Xiaohui Yang

    2018-06-01

    Full Text Available Late blight caused by the oomycete fungus Phytophthora infestans (Pi is the most serious obstacle to potato (Solanum tuberosum production in the world. A super race isolate, CN152, which was identified from Sichuan Province, China, could overcome nearly all known late blight resistance genes and caused serious damage in China. The potato genotype SD20 was verified to be highly resistant to CN152; however, the molecular regulation network underlying late blight resistance pathway remains unclear in SD20. Here, we performed a time-course experiment to systematically profile the late blight resistance response genes using RNA-sequencing in SD20. We identified 3354 differentially expressed genes (DEGs, which mainly encoded transcription factors and protein kinases, and also included four NBS-LRR genes. The late blight responsive genes showed time-point-specific induction/repression. Multi-signaling pathways of salicylic acid, jasmonic acid, and ethylene signaling pathways involved in resistance and defense against Pi in SD20. Gene Ontology and KEGG analyses indicated that the DEGs were significantly enriched in metabolic process, protein serine/threonine kinase activity, and biosynthesis of secondary metabolites. Forty-three DEGs were involved in immune response, of which 19 were enriched in hypersensitive response reaction, which could play an important role in broad-spectrum resistance to Pi infection. Experimental verification confirmed the induced expression of the responsive genes in the late blight resistance signaling pathway, such as WRKY, ERF, MAPK, and NBS-LRR family genes. Our results provided valuable information for understanding late blight resistance mechanism of potato.

  8. Identification of a novel frameshift mutation in the ILDR1 gene in a UAE family, mutations review and phenotype genotype correlation.

    Directory of Open Access Journals (Sweden)

    Abdelaziz Tlili

    Full Text Available Autosomal recessive non-syndromic hearing loss is one of the most common monogenic diseases. It is characterized by high allelic and locus heterogeneities that make a precise diagnosis difficult. In this study, whole-exome sequencing was performed for an affected patient allowing us to identify a new frameshift mutation (c.804delG in the Immunoglobulin-Like Domain containing Receptor-1 (ILDR1 gene. Direct Sanger sequencing and segregation analysis were performed for the family pedigree. The mutation was homozygous in all affected siblings but heterozygous in the normal consanguineous parents. The present study reports a first ILDR1 gene mutation in the UAE population and confirms that the whole-exome sequencing approach is a robust tool for the diagnosis of monogenic diseases with high levels of allelic and locus heterogeneity. In addition, by reviewing all reported ILDR1 mutations, we attempt to establish a genotype phenotype correlation to explain the phenotypic variability observed at low frequencies.

  9. The epidemiological characteristics and genetic diversity of dengue virus during the third largest historical outbreak of dengue in Guangdong, China, in 2014.

    Science.gov (United States)

    Sun, Jiufeng; Wu, De; Zhou, Huiqiong; Zhang, Huan; Guan, Dawei; He, Xiang; Cai, Songwu; Ke, Changwen; Lin, Jinyan

    2016-01-01

    The third largest historical outbreak of dengue occurred during July to December 2014, in 20 of 21 cities of Guangdong, China. The epidemiological and molecular characteristics of the introduction, expansion and phylogeny of the DENV isolates involved in this outbreak were investigated. A combination analyses of epidemiological characteristics and genetic diversity of dengue virus was performed in this study. In total, 45,236 cases and 6 fatalities were reported. Unemployed individuals, retirees and retailers were the most affected populations. A total of 6024 cases were verified to have DENV infections by nucleic acid detection, of which 5947, 74 and 3 were confirmed to have DENV-1, -2, and -3 infections, respectively. Phylogenetic analyses of DENV-1 isolates were assigned into three genotypes (I, IV, and V). Genotype V was the predominant genotype that likely originated from Singapore. The DENV-2 isolates were assigned to the Cosmopolitan and Asian I genotypes. A unique DENV-3 isolate (genotype III) shared high similarity with isolates obtained from Guangdong in 2013. A combination analyses demonstrated the multiple geographical origins of this outbreak, and highlight the importance of early detection, the case management and vector surveillance for preventing further dengue epidemics in Guangdong. Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  10. Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010.

    Science.gov (United States)

    Shak, Emma B; France, Anne Marie; Cowan, Lauren; Starks, Angela M; Grant, Juliana

    2015-01-01

    Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009-December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups.

  11. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer.......Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  12. Hepatitis C viral load, genotype 3 and interleukin-28B CC genotype predict mortality in HIV and hepatitis C-coinfected individuals

    DEFF Research Database (Denmark)

    Clausen, Louise Nygaard; Astvad, Karen; Ladelund, Steen

    2012-01-01

    OBJECTIVE: We hypothesized that hepatitis C virus (HCV) load and genotype may influence all-cause mortality in HIV-HCV-coinfected individuals. DESIGN AND METHODS: Observational prospective cohort study. Mortality rates were compared in a time-updated multivariate Poisson regression analysis....... RESULTS: We included 264 consecutive HIV-HCV-coinfected individuals. During 1143 person years at risk (PYR) 118 individuals died [overall mortality rate 10 (95% confidence interval; 8, 12)/100 PYR]. In multivariate analysis, a 1 log increase in HCV viral load was associated with a 30% higher mortality......) CC genotype was associated with 54% higher mortality risk [aMRR: 1.54 (0.89, 3.82] compared to TT genotype. CONCLUSION: High-HCV viral load, HCV genotype 3 and IL28B genotype CC had a significant influence on the risk of all-cause mortality among individuals coinfected with HIV-1. This may have...

  13. Factors Influencing the Spatial Difference in Household Energy Consumption in China

    Directory of Open Access Journals (Sweden)

    Yongxia Ding

    2016-12-01

    Full Text Available What factors determine the spatial heterogeneity of household energy consumption (HEC in China? Can the impacts of these factors be quantified? What are the trends and characteristics of the spatial differences? To date, these issues are still unclear. Based on the STIRPAT model and panel dataset for 30 provinces in China over the period 1997–2013, this paper investigated influences of the income per capita, urbanization level and annual average temperature on HEC, and revealed the spatial effects of these influencing factors. The results show that the income level is the main influencing factor, followed by the annual average temperature. There exists a diminishing marginal contribution with increasing income. The influence of urbanization level varies according to income level. In addition, from the eastern region to western region of China, variances largely depend upon economic level at the provincial level. From the northern region to southern region, change is mainly caused by temperature. The urbanization level has more significant impact on the structure and efficiency of household energy consumption than on its quantity. These results could provide reference for policy making and energy planning.

  14. Exploring unobserved heterogeneity in bicyclists' red-light running behaviors at different crossing facilities.

    Science.gov (United States)

    Guo, Yanyong; Li, Zhibin; Wu, Yao; Xu, Chengcheng

    2018-06-01

    Bicyclists running the red light at crossing facilities increase the potential of colliding with motor vehicles. Exploring the contributing factors could improve the prediction of running red-light probability and develop countermeasures to reduce such behaviors. However, individuals could have unobserved heterogeneities in running a red light, which make the accurate prediction more challenging. Traditional models assume that factor parameters are fixed and cannot capture the varying impacts on red-light running behaviors. In this study, we employed the full Bayesian random parameters logistic regression approach to account for the unobserved heterogeneous effects. Two types of crossing facilities were considered which were the signalized intersection crosswalks and the road segment crosswalks. Electric and conventional bikes were distinguished in the modeling. Data were collected from 16 crosswalks in urban area of Nanjing, China. Factors such as individual characteristics, road geometric design, environmental features, and traffic variables were examined. Model comparison indicates that the full Bayesian random parameters logistic regression approach is statistically superior to the standard logistic regression model. More red-light runners are predicted at signalized intersection crosswalks than at road segment crosswalks. Factors affecting red-light running behaviors are gender, age, bike type, road width, presence of raised median, separation width, signal type, green ratio, bike and vehicle volume, and average vehicle speed. Factors associated with the unobserved heterogeneity are gender, bike type, signal type, separation width, and bike volume. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Molecular Characterization of Streptococcus agalactiae Isolated from Bovine Mastitis in Eastern China

    Science.gov (United States)

    Yang, Yongchun; Liu, Yinglong; Ding, Yunlei; Yi, Li; Ma, Zhe; Fan, Hongjie; Lu, Chengping

    2013-01-01

    One hundred and two Streptococcus agalactiae (group B streptococcus [GBS]) isolates were collected from dairy cattle with subclinical mastitis in Eastern China during 2011. Clonal groups were established by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE), respectively. Capsular polysaccharides (CPS), pilus and alpha-like-protein (Alp) family genes were also characterized by molecular techniques. MLST analysis revealed that these isolates were limited to three clonal groups and were clustered in six different lineages, i.e. ST (sequence type) 103, ST568, ST67, ST301, ST313 and ST570, of which ST568 and ST570 were new genotypes. PFGE analysis revealed this isolates were clustered in 27 PFGE types, of which, types 7, 8, 14, 15, 16, 18, 23 and 25 were the eight major types, comprising close to 70% (71/102) of all the isolates. The most prevalent sequence types were ST103 (58% isolates) and ST568 (31% isolates), comprising capsular genotype Ia isolates without any of the detected Alp genes, suggesting the appearance of novel genomic backgrounds of prevalent strains of bovine S. agalactiae. All the strains possessed the pilus island 2b (PI-2b) gene and the prevalent capsular genotypes were types Ia (89% isolates) and II (11% isolates), the conserved pilus type providing suitable data for the development of vaccines against mastitis caused by S. agalactiae. PMID:23874442

  16. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  17. Characterization of some sunflower genotypes using ISSR markers

    International Nuclear Information System (INIS)

    Mokrani, L.; Nabulsi, I.; MirAli, N.

    2014-01-01

    Sunflower (Helianthus annuus L.) is grown mostly as a source of vegetable oil of high quality and is especially used in food industry. It is generally produced by multinationals and sold as hybrids. Our research, based on two techniques (ISSR and RAPD), is considered as the first one to be interested in molecular characterization of sunflower genotypes in Syria. We used 25 ISSR primers and 13 RAPD primers to study 29 sunflower genotypes and two reference controls belonging to the same family (Calendula officinalis L. and Targets erecta L.). ISSR results revealed a low polymorphism when compared to other studies. We noticed also 11 genotypes genetically related where percent disagreement values (PDV) didn't exceed 1%, they are 7189 - 7191 - 7184 - 7183 - 443 - 441 - Ghab1 -Ghab2 - Ghab3 - Ghab4 - Ghab5 - Madakh halab - Sarghaya4 -Tarkibi knitra. Sarghaya4 and Tarkibi knitra have indeed the lowest yield and some common morphological characters. At the opposite, the genotype Hysum33 has the highest yield and is genetically distant from the other genotypes. All the genotypes could be used in QTL detection as we didn't notice any similarity between them. (author)

  18. Detailed crustal structure of the North China and its implication for seismicity

    Science.gov (United States)

    Jiang, Wenliang; Wang, Xin; Tian, Tian; Zhang, Jingfa; Wang, Donglei

    2014-02-01

    Since the Mesozoic-Cenozoic era the North China Craton has experienced an important tectonic transition and it has given rise to complicated crustal structure and strong earthquake activity. Based on the large-scale surface gravity data, we studied the detailed crustal structure and seismogenic mechanism of the North China. The results indicate that the North China presents typical characteristics of adjoining depression and uplift, alternating basins and hills, inhomogeneous density and also great differences in crustal structure and Moho topography. The upper and middle crustal structures are dominated by the NNE-striking tectonic units, with many faults cut down to the middle crust. The lower crust is characterized by the folding-structure, with high and low-density placed alternately from west to east, presenting lateral heterogeneous feature. Adjusted by the gravity isostasy, Moho topography of the North China fluctuates greatly. Compared with the North China Basin, crustal thickness in the Western Taihang, northern Yanshan and Luzhong areas are much thicker while those densities are lower than the North China Basin. The dominating tectonic direction of the Moho topography strikes NE to NNE and undulates alternately from west to east. The epicenters are mostly concentrated in the upper and middle crust, especially the transitional areas between the high and low-gravity anomalies. The Tancheng earthquake in 1668, Sanhe earthquake in 1673, Tangshan earthquake in 1976, and all other seismic tectonic zones of the North China are all distributed in area where magma moves strongly beneath the crust, which is considered to be related to the movement of the high density, unstable and heat flows along the deep passage from the uppermost and asthenosphere due to the subduction of the Pacific slab towards the Eurasian plate.

  19. Hepatitis C Virus: Viral Quasispecies and Genotypes

    Directory of Open Access Journals (Sweden)

    Kyoko Tsukiyama-Kohara

    2017-12-01

    Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  20. Investigation of genetic diversity and epidemiological characteristics of Pasteurella multocida isolates from poultry in southwest China by population structure, multi-locus sequence typing and virulence-associated gene profile analysis.

    Science.gov (United States)

    Li, Zhangcheng; Cheng, Fangjun; Lan, Shimei; Guo, Jianhua; Liu, Wei; Li, Xiaoyan; Luo, Zeli; Zhang, Manli; Wu, Juan; Shi, Yang

    2018-04-25

    Fowl cholera caused by Pasteurella multocida has always been a disease of global importance for poultry production. The aim of this study was to obtain more information about the epidemiology of avian P. multocida infection in southwest China and the genetic characteristics of clinical isolates. P. multocida isolates were characterized by biochemical and molecular-biological methods. The distributions of the capsular serogroups, the phenotypic antimicrobial resistance profiles, lipopolysaccharide (LPS) genotyping and the presence of 19 virulence genes were investigated in 45 isolates of P. multocida that were associated with clinical disease in poultry. The genetic diversity of P. multocida strains was performed by 16S rRNA and rpoB gene sequence analysis as well as multilocus sequence typing (MLST). The results showed that most (80.0%) of the P. multocida isolates in this study represented special P. multocida subspecies, and 71.1% of the isolates showed multiple-drug resistance. 45 isolates belonged to capsular types: A (100%) and two LPS genotypes: L1 (95.6%) and L3 (4.4%). MLST revealed two new alleles (pmi77 and gdh57) and one new sequence type (ST342). ST129 types dominated in 45 P. multocida isolates. Isolates belonging to ST129 were with the genes ompH+plpB+ptfA+tonB, whereas ST342 included isolates with fur+hgbA+tonB genes. Population genetic analysis and the MLST results revealed that at least one new ST genotype was present in the avian P. multocida in China. These findings provide novel insights into the epidemiological characteristics of avian P. multocida isolates in southwest China.

  1. [Genotypic variability and persistence of Legionella pulsed-field gel electrophoresis patterns in 16 cooling towers in Shanghai, China].

    Science.gov (United States)

    Chen, Ming-liang; Wang, Gang-yi; Chen, Min; Zhou, Hai-jian; Shao, Zhu-jun; Zhang, Xi; Wu, Fan

    2010-07-01

    To investigate the genotypic characteristics and persistence of Legionella pulsed-field gel electrophoresis (PFGE) patterns in 16 air-conditioner cooling towers in six different public sites of Shanghai. From May to October, continuous sampling was operated once per month in 2007. Legionella strains isolated from the 16 cooling towers were confirmed by serological and latex agglutination. PFGE was applied for the fingerprinting of the isolates, while the cluster results of PFGE were analyzed by BioNumerics software. 131 strains of Legionella were isolated, including L. pneumophila, L. bozemanae, L. micdadei and L. anisa. 52 distinguishable PFGE patterns were differentiated among the 16 cooling towers, with 37 patterns were owned by just one cooling tower, which was not shared with other cooling towers, while 15 patterns were shared by more than 2 cooling towers. All the cooling towers had ≥ 2 PFGE patterns, while in 13 cooling towers the same PFGE patterns were recovered during the six months. From June to October of 2007, 18 strains of Legionella belonging to the PFGE pattern of LPAs.SH0078 were isolated continuously from 6 cooling towers. This study demonstrated great genotypic diversity and complexity of Legionella in cooling towers. Persistence of the PFGE patterns was observed in 81.25% of the cooling towers. The PFGE pattern of LPAs. SH0078 was distributed widely, suggesting it might be the dominate strain in Shanghai.

  2. Hazardous waste and environmental trade: China`s issues

    Energy Technology Data Exchange (ETDEWEB)

    Ma Jiang [National Research Center for Science and Technology for Development, Beijing (China)

    1996-12-31

    By presenting some case studies, this paper analyzes China`s situation with regard to hazardous waste: its environmental trade, treatment, and management. The paper describes China`s experiences with the environmental trade of hazardous waste in both the internal and international market. Regulations for managing the import of waste are discussed, as are China`s major approaches to the trading of hazardous waste both at home and overseas. The major reasons for setting up the Asian-Pacific Regional Training Center for Technology Transfer and Environmental Sound Management of Wastes in China and the activities involved in this effort are also described. 1 tab.

  3. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China.

    Directory of Open Access Journals (Sweden)

    Hao Sun

    Full Text Available Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.

  4. Neutralizing antibodies in patients with chronic hepatitis C, genotype 1, against a panel of genotype 1 culture viruses

    DEFF Research Database (Denmark)

    Pedersen, Jannie; Jensen, Tanja B; Carlsen, Thomas H R

    2013-01-01

    , infection treated with pegylated interferon-α and ribavirin. Thirty-nine patients with chronic hepatitis C, genotype 1a or 1b, with either sustained virologic response (n = 23) or non-sustained virologic response (n = 16) were enrolled. Samples taken prior to treatment were tested for their ability...... to neutralize 6 different HCV genotype 1 cell culture recombinants (1a: H77/JFH1, TN/JFH1, DH6/JFH1; 1b: J4/JFH1, DH1/JFH1, DH5/JFH1). The results were expressed as the highest dilution yielding 50% neutralization (NAb50-titer). We observed no genotype or subtype specific differences in NAb50-titers between......The correlation of neutralizing antibodies to treatment outcome in patients with chronic hepatitis C virus (HCV) infection has not been established. The aim of this study was to determine whether neutralizing antibodies could be used as an outcome predictor in patients with chronic HCV, genotype 1...

  5. Clinical application of RT-nested PCR integrated with RFLP in Hantavirus detection and genotyping: a prospective study in Shandong Province, PR China.

    Science.gov (United States)

    Liu, Yun-Xi; Zhao, Zhong-Tang; Cao, Wu-Chun; Xu, Xiao-Qun; Suo, Ji-Jiang; Xing, Yu-Bin; Jia, Ning; Du, Ming-Mei; Liu, Bo-Wei; Yao, Yuan

    2013-01-01

    The aim of the present study was to evaluate the clinical usefulness of applying RT-nested PCR along with RFLP as a method for diagnosis and genotypic differentiation of Hantavirus in the acute-stage sera of HFRS patients as compared to the ELISA technique. A prospective study of patients with suspected HFRS patients was carried out. Sera were collected for serological evaluation by ELISA and RT-nested PCR testing. Primers were selected from the published sequence of the S segment of HTNV strain 76-118 and SEOV strain SR-11, which made it possible to obtain an amplicon of 403 bp by RT-nested PCR. The genotypic differentiations of the RT-nested PCR amplicons were carried out by RFLP. Sequence analyses of the amplicons were used to confirm the accuracy of the results obtained by RFLP. Of the 48 acute-stage sera from suspected HFRS patients, 35 were ELISA-positive while 41 were positive by RT-nested PCR. With Hind III and Hinf I, RFLP profiles of the RT-nested PCR amplicons of the 41 positive sera exhibited two patterns. 33 had RFLP profiles similar to the reference strain R22, and thus belonged to the SEOV type. The other 8 samples which were collected during October-December had RFLP profiles similar to the reference strain 76-118, and thus belonged to the HTNV type. Sequence phylogenetic analysis of RT-nested PCR amplicons revealed sdp1, sdp2 YXL-2008, and sdp3 as close relatives of HTNV strain 76-118, while sdp22 and sdp37 as close relatives of SEOV strain Z37 and strain R22 located in two separate clusters in the phylogenetic tree. These results were identical to those acquired by RFLP. RT-nested PCR integrated with RFLP was a rapid, simple, accurate method for detecting and differentiating the genotypes of Hantavirus in the acute-stage sera of suspected HFRS patients. In Shandong province, the main genotypes of Hantavirus belonged to the SEOV types, while the HTNV types were observed during the autumn-winter season.

  6. Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

    Science.gov (United States)

    Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens

    2013-01-01

    in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

  7. Squamous intraepithelial lesions of the anal squamocolumnar junction: Histopathological classification and HPV genotyping

    Directory of Open Access Journals (Sweden)

    Omar Clavero

    2017-06-01

    Full Text Available Background: Human papillomavirus (HPV-related anal cancer lesions are often found adjacent to the squamocolumnar junction (SCJ. We have assessed the histopathology and associated HPV genotypes in anal SCJ lesions in surgically excised anal warts in HIV-negative and –positive patients. Methods: Histopathology identified 47 squamous intraepithelial lesions (SILs adjacent to the SCJ amongst a total of 145 cases of clinically diagnosed anal condylomata. The anal SCJ lesions were further analyzed with p16, CK7 and p63 immunohistochemistry and HPV genotyping. Results: Sixteen (16/47 of the excised anal wart lesions contained HSIL; Three were HSIL and exclusively associated with oncogenic HPVs. A further thirteen (13/47 were mixed lesions. Of these eight were HSILs with LSIL and six were HSILs with papillary immature metaplasia (PIM; Ten of the mixed lesions were associated with one or more oncogenic HPVs, while three cases were exclusively associated with HPV6. Conclusions: Clinically diagnosed anal warts cannot be assumed to be limited to low-grade lesions as anal warts of the SCJ often show heterogeneous lesions, with coexistence of LSIL, PIM, and HSIL. Lesions showing PIM, however, may mimic HSIL, because they are hypercellular, but lack the nuclear atypia and conspicuous mitotic activity of HSIL; and are p16 negative. Keywords: Anal squamocolumnar junction, Low-grade squamous intraepithelial lesion (LSIL, High-grade squamous intraepithelial lesion (HSIL, Papillary immature metaplasia (PIM, HPV, HIV

  8. Imaging of fast chlorophyll fluorescence induction curve (OJIP) parameters, applied in a screening study with wild barley (Hordeum spontaneum) genotypes under heat stress.

    Science.gov (United States)

    Jedmowski, Christoph; Brüggemann, Wolfgang

    2015-10-01

    We quantified the influence of heat stress (HS) on PSII by imaging of parameters of the fast chlorophyll fluorescence (CF) induction (OJIP) kinetic of 20 genotypes of wild barley (Hordeum spontaneum) covering a broad geographical spectrum. We developed a standardised screening procedure, allowing a repetitive fluorescence measurement of leaf segments. The impact of HS was quantified by calculating a Heat Resistance Index (HRI), derived from the decrease of the Performance Index (PI) caused by HS treatment and following recovery. For the genotype showing the lowest HRI, reduced maximum quantum yield (φP0) and increased relative variable fluorescence of the O-J phase (K-Peak) were detected after HS, whereas the basal fluorescence (F0) remained stable. An additional feature was a lowered fraction of active (QA-reducing) reaction centres (RCs). The disturbances disappeared after one day of recovery. Spatial heterogeneities of fluorescence parameters were detected, as the negative effect of HS was stronger in the leaf areas close to the leaf tip. The results of this study prove that chlorophyll fluorescence imaging (CFI) is suitable for the detection of HS symptoms and that imaging of JIP-Test parameters should be considered in future screening and phenotyping studies aiming for the characterisation of plant genotypes. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Human papillomavirus genotypes in invasive cervical squamous cell carcinoma in Trinidad Genotipos de virus de los papilomas humanos en carcinoma cervicouterino escamocelular invasor en Trinidad

    Directory of Open Access Journals (Sweden)

    Felicia Hosein

    2013-04-01

    Full Text Available OBJECTIVE: To determine the relative contribution of known high-risk human papillomavirus (HPV genotypes to the occurrence of cervical cancers in Trinidad. METHODS: The distribution of HPV genotypes in cases of invasive cervical squamous cell carcinoma in Trinidad was investigated. This study was a follow-up to an investigation of HPV genotypes in 310 nonsymptomatic women in Trinidad. The latter study showed that cervical HPV prevalence and heterogeneity of genotypes were high in the study population; notably, the genotypes targeted by the available HPV prophylactic vaccines were not the most common types. RESULTS: The current study of 85 cases of invasive cervical squamous cell carcinomas demonstrated that the previously observed heterogeneity in HPV genotype distribution is lost in cases of invasive cervical cancer, with the vaccine-targeted HPV types HPV 16 and HPV 18 becoming the most prevalent. CONCLUSIONS: HPV 16 and HPV 18 were the primary HPV genotypes associated with cases of invasive squamous cell carcinoma in the current Trinidad study. This strong association leads us to conclude that the HPV vaccines targeting HPV 16 and HPV 18 may contribute to reducing the cervical cancer burden in Trinidad.OBJETIVO: Determinar la contribución relativa de los diferentes genotipos de virus de los papilomas humanos (VPH conocidos como de alto riesgo para la aparición de cáncer cervicouterino en Trinidad. MÉTODOS: Se investigó la distribución de los genotipos de VPH en casos de carcinoma cervicouterino escamocelular invasor en Trinidad. Este estudio fue la continuación de una investigación de los genotipos de VPH presentes en 310 mujeres asintomáticas en Trinidad. Este último estudio reveló altas prevalencia de VPH en el cuello uterino y heterogeneidad de los genotipos en la población del estudio; cabe destacar que los genotipos a los que se dirigen las vacunas preventivas de la infección por VPH disponibles no fueron los tipos m

  10. Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in deer in Henan and Jilin, China.

    Science.gov (United States)

    Huang, Jianying; Zhang, Zhenjie; Zhang, Yiqi; Yang, Yong; Zhao, Jinfeng; Wang, Rongjun; Jian, Fuchun; Ning, Changshen; Zhang, Wanyu; Zhang, Longxian

    2018-04-12

    Little is known about the prevalence and zoonotic potential of Cryptosporidium spp. and Giardia duodenalis in deer in China. In this study, 662 fecal samples were collected from 11 farms in Henan and Jilin Provinces between July 2013 and August 2014, and were screened for the presence of Cryptosporidium and G. duodenalis with genotyping and subtyping methods. Cryptosporidium spp. and G. duodenalis were detected in 6.80% (45/662) and 1.21% (5/662) of samples, respectively. Six Cryptosporidium species/genotypes were identified based on the small subunit ribosomal ribonucleic acid (SSU rRNA) gene: C. parvum (n = 11); C. andersoni (n = 5); C. ubiquitum (n = 3); C. muris (n = 1); C. suis-like (n = 1); and Cryptosporidium deer genotype (n = 24). When five of the 11 C. parvum isolates were subtyped by sequencing the 60 kDa glycoprotein (gp60) gene, zoonotic subtypes IIaA15G2R2 (n = 4) and IIdA19G1 (n = 1) were found. According to a subtype analysis, three C. ubiquitum isolates belonged to XIIa subtype 2. In contrast, only assemblage E was detected in the five Giardia-positive samples with small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequencing. To our knowledge, this is the first study to report C. andersoni, as well as C. parvum zoonotic subtypes IIaA15G2R2 and IIdA19G1 in cervids. These data, though limited, suggest that cervids may be a source of zoonotic Cryptosporidium and Giardia. Cervids in the present study are likely to be of low zoonotic potential to humans, and more molecular epidemiological studies are required to clarify the prevalence and public health significance of Cryptosporidium and G. duodenalis in cervids throughout China.

  11. Mechanisms of population heterogeneity among molting common mergansers on Kodiak Island, Alaska: Implications for genetic assessments of migratory connectivity

    Science.gov (United States)

    Pearce, John M.; Zwiefelhofer, Denny; Maryanski, Nate

    2009-01-01

    Quantifying population genetic heterogeneity within nonbreeding aggregations can inform our understanding of patterns of site fidelity, migratory connectivity, and gene flow between breeding and nonbreeding areas. However, characterizing mechanisms that contribute to heterogeneity, such as migration and dispersal, is required before site fidelity and migratory connectivity can be assessed accurately. We studied nonbreeding groups of Common Mergansers (Mergus merganser) molting on Kodiak Island, Alaska, from 2005 to 2007, using banding data to assess rates of recapture, mitochondrial (mt) DNA to determine natal area, and nuclear microsatellite genotypes to assess dispersal. Using baseline information from differentiated mtDNA haplogroups across North America, we were able to assign individuals to natal regions and document population genetic heterogeneity within and among molting groups. Band-recovery and DNA data suggest that both migration from and dispersal among natal areas contribute to admixed groups of males molting on Kodiak Island. A lack of differentiation in the Common Merganser's nuclear, bi-parentally inherited DNA, observed across North America, implies that dispersal can mislead genetic assessments of migratory connectivity and assignments of nonbreeding individuals to breeding areas. Thus multiple and independent data types are required to account for such behaviors before accurate assessments of migratory connectivity can be made.

  12. The first report of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area, China.

    Science.gov (United States)

    Zhang, Xueyong; Jian, Yingna; Li, Xiuping; Ma, Liqing; Karanis, Gabriele; Karanis, Panagiotis

    2018-05-01

    Cryptosporidium is one of the most important genera of intestinal zoonotic pathogens, which can infect various hosts and cause diarrhoea. There is little available information about the molecular characterisation and epidemiological prevalence of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area of Qinghai Province, Northwest China. Therefore, the aim of this study was to determine Cryptosporidium species/genotypes and epidemiological prevalence in these mammals by detecting the SSU rRNA gene by PCR amplification. The Cryptosporidium spp. infection rate was 8.9% (8/90) in Qinghai voles and 6.25% (4/64) in wild plateau pikas. Positive samples were successfully sequenced, and the following Cryptosporidium species were found: C. parvum, C. ubiquitum, C. canis and a novel genotype in Qinghai voles and C. parvum and a novel genotype in wild plateau pikas. This is the first report of Cryptosporidium infections in M. fuscus and wild O. curzoniae in Northwest China. The results suggest the possibility of Cryptosporidium species transmission among these two hosts, the environment, other animals and humans and provide useful molecular epidemiological data for the prevention and control of Cryptosporidium infections in wild animals and the surrounding environments. The results of the present study indicate the existence of Cryptosporidium species infections that have potential public health significance. This is the first report of Cryptosporidium multi-species infections in these animal hosts.

  13. Relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...

  14. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

  15. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  16. Comparative salinity responses among tomato genotypes and rootstocks

    International Nuclear Information System (INIS)

    Oztekin, G.B.; Tuzel, Y.

    2011-01-01

    Salinity is a major constraint limiting agricultural crop productivity in the world. However, plant species and cultivars differ greatly in their response to salinity. This study was conducted in a greenhouse to determine the response of 4 commercial tomato rootstocks, 21 cultivars and 8 candidate varieties to salinity stress. Seeds were germinated in peat and when the plants were at the fifth-true leaf stage, salt treatment was initiated except control treatment. NaCl was added to nutrient solution daily with 25 mM concentration and had been reached to 200 mM final concentration. On harvest day, genotypes were classified based on the severity of leaf symptoms caused by NaCl treatment. After symptom scoring, the plants were harvested and leaf number, root length, stem length and diameter per plant were measured. The plants were separated into shoots and roots for dry matter production. Our results showed that, on average, NaCl stress decreased all parameters and the rootstocks gave the highest performance than genotypes. Among all rootstocks, three varieties (2211 and 2275) and ten genotypes (Astona, Astona RN, Caracas, Deniz, Durinta, Export, Gokce, Target, Yeni Talya and 144 HY) were selected as tolerant with slight chlorosis whereas the genotype Malike was selected as sensitive with severe chlorosis. Candidate varieties 2316 and 1482 were the most sensitive ones. Plant growth and dry matter production differed among the tested genotypes. However no correlation was found between plant growth and dry matter production. Rootstock Beaufort gave the highest shoot dry matter although Heman had highest root dry matter. Newton showed more shoot and root dry matter than other genotypes. It is concluded that screening of genotypes based on severity of symptoms at early stage of development and their dry matter production could be used as a tool to indicate genotypic variation to salt stress. (author)

  17. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  18. Significant association between RGS14 rs12654812 and nephrolithiasis risk among Guangxi population in China.

    Science.gov (United States)

    Long, Jun; Chen, Yang; Lin, Haisong; Liao, Ming; Li, Tianyu; Tong, Lei; Wei, Suchun; Xian, Xiaoying; Zhu, Jia; Chen, Jianxin; Tian, Jiarong; Wang, Qiuyan; Mo, Zengnan

    2018-03-26

    Nephrolithiasis is a worldwide health problem that affects almost all populations. This study aimed to evaluate the association between rs12654812 of regulator of G protein signaling 14 (RGS14) gene and nephrolithiasis in the Chinese population. A total of 1541 participators including 830 cases and 711 controls were included from Guangxi area in China. Age, sex, BMI, smoking status, drinking status, creatinine, uric acid, and urea nitrogen were analyzed between the case group and control group. We found that the G/A+A/A genotypes of rs12654812 had a significantly increased nephrolithiasis risk after adjusting age, sex, BMI, smoking, drinking, and hypertension, compared with G/G genotype (OR = 1.361, 95% CI = 1.033-1.794, P = .029). This hazardous effect was more pronounced in subgroup of age < 50, ever smoking, ever drinking, creatinine normal, and high uric acid. The G/A genotype of rs12654812 also had a significantly increased nephrolithiasis risk compared with G/G genotype. The A allele of rs12654812 significantly increased the risk of nephrolithiasis compared with the G allele after adjusting for age, sex, BMI, smoking, drinking and hypertension (OR = 1.277, 95% CI = 1.013-1.609, P = .038). Our results suggest that the RGS14 polymorphism is involved in the etiology of nephrolithiasis and thus may be a genetic marker for nephrolithiasis. © 2018 Wiley Periodicals, Inc.

  19. Evaluating potassium-use-efficiency of five cotton genotypes of pakistan

    International Nuclear Information System (INIS)

    Hassan, Z.U.; Kubar, K.A.

    2014-01-01

    Potassium (K) deficiency in Pakistani soils has been recently reported as the major limiting factor affecting sustainable cotton production. The present study was conducted to envisage how K nutrition affect the growth, biomass production, yield and K-use-efficiency of five cotton genotypes, NIBGE-3701, NIBGE-1524 (Bt-transgenic), Sadori, Sindh-1 and SAU-2 (non-Bt conventional), commonly grown in Pakistan. All five genotypes were raised at deficient and adequate K levels, i.e. 0 and 60 kg K/sub 2/O ha-1, respectively. The experiment was performed in plastic pots following a completely randomized factorial design with three repeats. Adequate K nutrition significantly increased various plant growth traits and yield of all cotton genotypes under study, viz. number of sympodia (21%), number of leaves (34%), leaf dry biomass (30%), shoot dry biomass (31%), number of bolls (50%) and yield of seed cotton (92%). Substantial variations were observed among cotton genotypes for their K-use-efficiency and K-response-efficiency. Sadori and SAU-2 were screened as most K-use-efficient cotton genotypes, while Sindh-1 and SAU-2 were ranked as the most K-responsive cotton genotypes. Interestingly, Sadori did not respond to K nutrition. Moreover, Bt cotton genotypes accumulated more K as compared to non-Bt genotypes. The cotton genotype SAU-2 was identified as efficient-response genotype for better adaptation for both low- and high-K-input sustainable cotton agriculture systems. (author)

  20. High-throughput mouse genotyping using robotics automation.

    Science.gov (United States)

    Linask, Kaari L; Lo, Cecilia W

    2005-02-01

    The use of mouse models is rapidly expanding in biomedical research. This has dictated the need for the rapid genotyping of mutant mouse colonies for more efficient utilization of animal holding space. We have established a high-throughput protocol for mouse genotyping using two robotics workstations: a liquid-handling robot to assemble PCR and a microfluidics electrophoresis robot for PCR product analysis. This dual-robotics setup incurs lower start-up costs than a fully automated system while still minimizing human intervention. Essential to this automation scheme is the construction of a database containing customized scripts for programming the robotics workstations. Using these scripts and the robotics systems, multiple combinations of genotyping reactions can be assembled simultaneously, allowing even complex genotyping data to be generated rapidly with consistency and accuracy. A detailed protocol, database, scripts, and additional background information are available at http://dir.nhlbi.nih.gov/labs/ldb-chd/autogene/.