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Sample records for ccl3l1-ccr5 genotype influences

  1. The CCL3L1-CCR5 genotype influences the development of AIDS, but not HIV susceptibility or the response to HAART

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    Bhattacharya, Tanmoy [Los Alamos National Laboratory; Stanton, Jennifer [NORTHWESTERN UNIV; Kim, Eun - Young [NORTHWESTERN UNIV; Kunstman, Kevin [NORTHWESTERN UNIV; Phair, John [NORTHWESTERN UNIV; Jacobson, Lisa P [JOHNS HOPKINS UNIV; Wolinsky, Steven M [NORTHWESTERN UNIV

    2008-01-01

    A selective advantage against infectious diseases such as HIV/AIDS is associated with differences in the genes relevant to immunity and virus replication. The CC chemokine receptor 5 (CCR5), the principal coreceptor for HIV, and its chemokine ligands, including CCL3L1, influences the CD4+ target cells susceptibility to infection. The CCL3L1 gene is in a region of segmental duplication on the q-arm of human chromosome 17. Increased numbers of CCL3L1 gene copies that affect the gene expression phenotype might have substantial protective effects. Here we show that the population-specific CCL3L1 gene copy number and the CCR5 {Delta}32 protein-inactivating deletion that categorizes the CCL3L1-CCR5 genotype do not influence HIV/AIDS susceptibility or the robustness of immune recovery after the initiation of highly active antiretroviral therapy (HAART).

  2. CCL3L1-CCR5 genotype improves the assessment of AIDS Risk in HIV-1-infected individuals.

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    Hemant Kulkarni

    Full Text Available BACKGROUND: Whether vexing clinical decision-making dilemmas can be partly addressed by recent advances in genomics is unclear. For example, when to initiate highly active antiretroviral therapy (HAART during HIV-1 infection remains a clinical dilemma. This decision relies heavily on assessing AIDS risk based on the CD4+ T cell count and plasma viral load. However, the trajectories of these two laboratory markers are influenced, in part, by polymorphisms in CCR5, the major HIV coreceptor, and the gene copy number of CCL3L1, a potent CCR5 ligand and HIV-suppressive chemokine. Therefore, we determined whether accounting for both genetic and laboratory markers provided an improved means of assessing AIDS risk. METHODS AND FINDINGS: In a prospective, single-site, ethnically-mixed cohort of 1,132 HIV-positive subjects, we determined the AIDS risk conveyed by the laboratory and genetic markers separately and in combination. Subjects were assigned to a low, moderate or high genetic risk group (GRG based on variations in CCL3L1 and CCR5. The predictive value of the CCL3L1-CCR5 GRGs, as estimated by likelihood ratios, was equivalent to that of the laboratory markers. GRG status also predicted AIDS development when the laboratory markers conveyed a contrary risk. Additionally, in two separate and large groups of HIV+ subjects from a natural history cohort, the results from additive risk-scoring systems and classification and regression tree (CART analysis revealed that the laboratory and CCL3L1-CCR5 genetic markers together provided more prognostic information than either marker alone. Furthermore, GRGs independently predicted the time interval from seroconversion to CD4+ cell count thresholds used to guide HAART initiation. CONCLUSIONS: The combination of the laboratory and genetic markers captures a broader spectrum of AIDS risk than either marker alone. By tracking a unique aspect of AIDS risk distinct from that captured by the laboratory parameters

  3. Nutrient Environments Influence Competition among Aspergillus flavus Genotypes

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    Mehl, Hillary L.; Cotty, Peter J.

    2013-01-01

    The population dynamics of Aspergillus flavus, shaped in part by intraspecific competition, influence the likelihood and severity of crop aflatoxin contamination. Competition for nutrients may be one factor modulating intraspecific interactions, but the influences of specific types and concentrations of nutrients on competition between genotypes of A. flavus have not been investigated. Competition between paired A. flavus isolates on agar media was affected by varying concentrations of carbon...

  4. The influence of genotype on habitat selection of fish and the analysis of population structure

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    Artamonova V.S.

    2016-01-01

    Full Text Available We used salmonids, eel and cod to demonstrate the apparent influence of genotype on the migratory behavior of fish and their selection of habitat. These examples indicate that the connection between specific genotypes and certain patterns of migratory behavior is typical of fish. This should always be taken into account in stock structure analysis.

  5. Rationality and emotionality: serotonin transporter genotype influences reasoning bias

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    Stollstorff, Melanie; Bean, Stephanie E.; Anderson, Lindsay M.; Devaney, Joseph M.; Vaidya, Chandan J.

    2012-01-01

    Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SLG carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief...

  6. Nutrient environment influences competition among Aspergillus flavus genotypes

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    Structures of Aspergillus flavus populations, shaped by intraspecific competition, influence the incidences and severities of crop aflatoxin contamination. Competition for nutrients may be one factor modulating intraspecific interactions, but influences of specific types and concentrations of nutrie...

  7. Influence of genotyping error in linkage mapping for complex traits – an analytic study

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    van Houwelingen Hans C

    2008-08-01

    Full Text Available Abstract Background Despite the current trend towards large epidemiological studies of unrelated individuals, linkage studies in families are still thoroughly being utilized as tools for disease gene mapping. The use of the single-nucleotide-polymorphisms (SNP array technology in genotyping of family data has the potential to provide more informative linkage data. Nevertheless, SNP array data are not immune to genotyping error which, as has been suggested in the past, could dramatically affect the evidence for linkage especially in selective designs such as affected sib pair (ASP designs. The influence of genotyping error on selective designs for continuous traits has not been assessed yet. Results We use the identity-by-descent (IBD regression-based paradigm for linkage testing to analytically quantify the effect of simple genotyping error models under specific selection schemes for sibling pairs. We show, for example, that in extremely concordant (EC designs, genotyping error leads to decreased power whereas it leads to increased type I error in extremely discordant (ED designs. Perhaps surprisingly, the effect of genotyping error on inference is most severe in designs where selection is least extreme. We suggest a genomic control for genotyping errors via a simple modification of the intercept in the regression for linkage. Conclusion This study extends earlier findings: genotyping error can substantially affect type I error and power in selective designs for continuous traits. Designs involving both EC and ED sib pairs are fairly immune to genotyping error. When those designs are not feasible the simple genomic control strategy that we suggest offers the potential to deliver more robust inference, especially if genotyping is carried out by SNP array technology.

  8. GST M1 GENOTYPE INFLUENCES SPERM DNA DAMAGE ASSOCIATED WITH EXPOSURE TO AIR POLLUTION

    Science.gov (United States)

    For Society for Epidemiologic Research Meeting, June 15-18, 2004, Salt Lake City, Utah.Presenter: Sherry G. SelevanGSTM1 GENOTYPE INFLUENCES SPERM DNA DAMAGE ASSOCIATED WITH EXPOSURE TO AIR POLLUTION. J Rubes, SG Selevan*, R. Sram, DPEvenson, SD Perreault. VRI, ...

  9. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis.

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    Maxine Caws

    2008-03-01

    Full Text Available The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP and Toll-like receptor-2 (TLR-2. We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR for causing TBM 0.395, 95% confidence intervals (C.I. 0.193-0.806, P = 0.009, suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15-2.15] than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis.

  10. The Influence of Host and Bacterial Genotype on the Development of Disseminated Disease with Mycobacterium tuberculosis

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    Caws, Maxine; Thwaites, Guy; Dunstan, Sarah; Hawn, Thomas R.; Thi Ngoc Lan, Nguyen; Thuong, Nguyen Thuy Thuong; Stepniewska, Kasia; Huyen, Mai Nguyet Thu; Bang, Nguyen Duc; Huu Loc, Tran; Gagneux, Sebastien; van Soolingen, Dick; Kremer, Kristin; van der Sande, Marianne; Small, Peter; Thi Hoang Anh, Phan; Chinh, Nguyen Tran; Thi Quy, Hoang; Thi Hong Duyen, Nguyen; Quang Tho, Dau; Hieu, Nguyen T.; Torok, Estee; Hien, Tran Tinh; Dung, Nguyen Huy; Thi Quynh Nhu, Nguyen; Duy, Phan Minh; van Vinh Chau, Nguyen; Farrar, Jeremy

    2008-01-01

    The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) and Toll-like receptor-2 (TLR-2). We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR) for causing TBM 0.395, 95% confidence intervals (C.I.) 0.193–0.806, P = 0.009), suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15–2.15]) than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis. PMID:18369480

  11. Influence of genotype on the quality of sheep leather

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    Manuel Antônio Chagas Jacinto

    2011-08-01

    Full Text Available The objective of this study was to evaluate the influence of crossings between sheep breeds on the intrinsic quality of leather. It was used the skins of 36 lambs (18 females and 18 males, resulting from crosses between ewes of a native breed from the Brazilian state of Mato Grosso do Sul and rams of the same native breed as well as the Texel and Santa Inês genetic groups. The animals were raised in confinement until slaughter weight, from 28 to 32 kg. After slaughter, samples were taken from the skins for histological analysis. The skins were tanned with chromium, retanned and greased. It was taken from the leather samples for electromicrographs and for tests for tensile and tear strength (intrinsic quality. Morphological aspects from the skin as well as from the leather help to understand the results found and they evidence that breeds or crossings among breeds interfere in the intrinsic quality of leather and skin of sheep.

  12. Influence of APOE Genotype on Alzheimer’s Disease CSF Biomarkers in a Spanish Population

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    J. A. Monge-Argilés

    2016-01-01

    Full Text Available Objectives. To evaluate the association between apolipoprotein E (APOE genotype and cerebrospinal fluid (CSF levels of Alzheimer’s disease (AD biomarkers and to study the influence of APOE genotype on the development of AD in a Spanish population. Material and Methods. The study comprised 29 amnestic mild cognitive impairment (MCI patients and 27 control subjects. Using ELISA methodology, CSF biomarkers and tau/Aβ ratios were obtained. ANOVA and adjusted odds ratios were calculated. Results. We observed the effect of APOE genotype and age on CSF AD variables. The progression to AD was more clearly influenced by CSF AD variables than by age or APOE status. Conclusions. APOE status influences CSF AD variables. However, the presence of APOE ε4 does not appear to be a deterministic factor for the development of AD, because CSF variables have a greater influence on progression to the disease. These results confirm previous observations and, to our knowledge, are the first published in a Spanish population.

  13. Influence of prenatal iron deficiency and MAOA genotype on response to social challenge in rhesus monkey infants

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    Golub, Mari S.; Hogrefe, Casey E.; Unger, Erica L.

    2012-01-01

    Social and emotional behavior are known to be sensitive to both developmental iron deficiency and monoamine oxidase A (MAOA) gene polymorphisms. In this study, male rhesus monkey infants deprived of dietary iron in utero (ID) were compared to iron sufficient (IS) controls (n=10/group). Half of each group had low MAOA activity genotypes and half had high MAOA activity genotypes. A series of social response tests were conducted at 3 to 14 months of age. MAOA genotype influenced attention to a v...

  14. The Influence of Genotype Polymorphism on Morphine Analgesic Effect for Postoperative Pain in Children

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    Lee, Mi Geum; Kim, Hyun Jung; Lee, Keun Hwa

    2016-01-01

    Background Although opioids are the most commonly used medications to control postoperative pain in children, the analgesic effects could have a large inter-individual variability according to genotypes. The aim of this study was to investigate the association between single nucleotide polymorphisms and the analgesic effect of morphine for postoperative pain in children. Methods A prospective study was conducted in 88 healthy children undergoing tonsillectomy, who received morphine during the operation. The postoperative pain score, frequency of rescue analgesics, and side effects of morphine were assessed in the post-anesthesia care unit. The children were genotyped for OPRM1 A118G, ABCB1 C3435T, and COMT Val158Met. Results Children with at least one G allele for OPRM1 (AG/GG) had higher postoperative pain scores compared with those with the AA genotype at the time of discharge from the post-anesthesia care unit (P = 0.025). Other recovery profiles were not significantly different between the two groups. There was no significant relationship between genotypes and postoperative pain scores in analysis of ABCB1 and COMT polymorphisms. Conclusions Genetic polymorphism at OPRM1 A118G, but not at ABCB1 C3435T and COMT Val158Met, influences the analgesic effect of morphine for immediate acute postoperative pain in children. PMID:26839669

  15. Genotypic influence on aversive conditioning in honeybees, using a novel thermal reinforcement procedure.

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    Pierre Junca

    Full Text Available In Pavlovian conditioning, animals learn to associate initially neutral stimuli with positive or negative outcomes, leading to appetitive and aversive learning respectively. The honeybee (Apis mellifera is a prominent invertebrate model for studying both versions of olfactory learning and for unraveling the influence of genotype. As a queen bee mates with about 15 males, her worker offspring belong to as many, genetically-different patrilines. While the genetic dependency of appetitive learning is well established in bees, it is not the case for aversive learning, as a robust protocol was only developed recently. In the original conditioning of the sting extension response (SER, bees learn to associate an odor (conditioned stimulus - CS with an electric shock (unconditioned stimulus - US. This US is however not a natural stimulus for bees, which may represent a potential caveat for dissecting the genetics underlying aversive learning. We thus first tested heat as a potential new US for SER conditioning. We show that thermal stimulation of several sensory structures on the bee's body triggers the SER, in a temperature-dependent manner. Moreover, heat applied to the antennae, mouthparts or legs is an efficient US for SER conditioning. Then, using microsatellite analysis, we analyzed heat sensitivity and aversive learning performances in ten worker patrilines issued from a naturally inseminated queen. We demonstrate a strong influence of genotype on aversive learning, possibly indicating the existence of a genetic determinism of this capacity. Such determinism could be instrumental for efficient task partitioning within the hive.

  16. Influence of catechol-O-methyltransferase (COMT) genotypes on the prognosis of canine mammary tumors.

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    Dias Pereira, P; Lopes, C C; Matos, A J F; Pinto, D; Gärtner, F; Lopes, C; Medeiros, R

    2009-11-01

    Catechol-O-methyltransferase (COMT) is an important enzyme involved in inactivation of catechol estrogens, which are metabolites with carcinogenic properties. Some investigations in human breast cancer associate a genetic polymorphism in the COMT gene (COMT val158met) with an increased risk and poor clinical progression of the disease. In dogs, there are 2 recognized single nucleotide polymorphisms in the COMT gene (COMTG216A and COMTG482A); however, their influence on the outcome of mammary neoplasms has never been investigated. The purpose of this study is to investigate the influence of COMT in the clinical progression of canine mammary tumors, namely in recurrence, metastasis and survival by testing 2 SNPs (G216A and G482A), and 2 genotypes of the COMT gene. A case series was conducted analyzing genomic DNA samples by polymerase chain reaction-restriction fragment length polymorphism from 80 bitches with mammary tumors. Animals were submitted to an active follow-up study for a period of 24 months after surgery. We observed that bitches carrying both genetic variations simultaneously are more likely to develop recurrence of mammary lesions. Our results demonstrate a possible role for COMT genotypes in the outcome of mammary neoplasms in the dog. Identifying a genetic factor predictive of recurrence may be useful in selecting the most effective surgical approach for canine mammary neoplasms. PMID:19605895

  17. Influence of kinship and MHC class II genotype on visual traits in zebrafish larvae (Danio rerio).

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    Hinz, Cornelia; Gebhardt, Katharina; Hartmann, Alexander K; Sigman, Lauren; Gerlach, Gabriele

    2012-01-01

    Kin recognition can drive kin selection and the evolution of social behaviour. In zebrafish (Danio rerio, Hamilton 1822), kin recognition is based on olfactory and visual imprinting processes. If larvae are exposed to visual and chemical cues of kin at day 5 and 6 post fertilization they will recognize kin throughout life, while exposure to non-kin fails to trigger any recognition. Chemical imprinting signals are transcribed by polymorphic genes of the major histocompatibility complex (MHC) code; however, the underlying mechanism for visual imprinting remains unclear. Here we provide evidence for the existence of family-specific differences in morphometry and pigmentation pattern of six day old zebrafish larvae. While rump, tail and body pigmentation were dependent on relatedness, iris pigmentation and morphometry were also influenced by MHC class II genotype. Our study revealed that the MHC not only influences the chemical signature of individuals, but also their visual appearance. PMID:23251449

  18. Influence of COMT Genotype on Antero-posterior Cortical Functional Connectivity Underlying Interference Resolution.

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    Jaspar, Mathieu; Manard, Marine; Dideberg, Vinciane; Bours, Vincent; Maquet, Pierre; Collette, Fabienne

    2016-02-01

    Genetic variability related to the catechol-O-methyltransferase (COMT) gene (Val(158)Met) has received increasing attention as a possible modulator of executive functioning and its neural correlates. However, this attention has generally centered on the prefrontal cortices because of the well-known direct impact of COMT enzyme on these cerebral regions. In this study, we were interested in the modulating effect of COMT genotype on anterior and posterior brain areas underlying interference resolution during a Stroop task. More specifically, we were interested in the functional connectivity between the right inferior frontal operculum (IFop), an area frequently associated with inhibitory efficiency, and posterior brain regions involved in reading/naming processes (the 2 main non-executive determinants of the Stroop effect). The Stroop task was administered during functional magnetic resonance imaging scanning to 3 groups of 15 young adults divided according to their COMT Val(158)Met genotype [Val/Val (VV), Val/Met (VM), and Met/Met (MM)]. Results indicate greater activity in the right IFop and the left middle temporal gyrus in homozygous VV individuals than in Met allele carriers. In addition, the VV group exhibited stronger positive functional connectivity between these 2 brain regions and stronger negative connectivity between the right IFop and left lingual gyrus. These results confirm the impact of COMT genotype on frontal functions. They also strongly suggest that differences in frontal activity influence posterior brain regions related to a non-executive component of the task. Particularly, changes in functional connectivity between anterior and posterior brain areas might correspond to compensatory processes for performing the task efficiently when the available dopamine level is low. PMID:25205659

  19. Mineral content of sorghum genotypes and the influence of water stress.

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    Paiva, Caroline Liboreiro; Queiroz, Valéria Aparecida Vieira; Simeone, Maria Lúcia Ferreira; Schaffert, Robert Eugene; de Oliveira, Antônio Carlos; da Silva, Camila Santana

    2017-01-01

    Sorghum is a source of several minerals whose content may vary depending on the genotype and the production environment. The objective of this study was to screen sorghum genotypes for mineral content and to investigate the effect of water stress on it. A large variability was observed in the mineral content of 100 sorghum genotypes grown in environments without (WoWS) and with water stress (WthWS). The water stress decreased Mn, P, Mg and S contents in 100, 96, 93 and 56% of genotypes, respectively. The genotypes and other factors seemed to have more impact than water stress on K, Ca, Cu, Fe and Zn levels. In 100 sorghum genotypes, 2 were classified as excellent sources of Fe and 25 of Zn, in both environments. The best two genotypes to Fe content were SC21 and SC655 and to Zn were SC320 and SHAN-QUI-RED which showed great potential for use in biofortification. PMID:27507491

  20. GST M1 GENOTYPE INFLUENCES THE SUSCEPTIBILITY OF MEN TO SPERM DNA DAMAGE ASSOCIATED WITH EXPOSURE TO AIR POLLUTION

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    GSTM1 GENOTYPE INFLUENCES THE SUSCEPTIBILITY OF MEN TO SPERM DNA DAMAGE ASSOCIATED WITH EXPOSURE TO AIR POLLUTION. J. Rubes1, SG Selevan2, R. Sram3, DPEvenson4, SD Perreault5. 1VRI, Brno, CR; 2US EPA/ORD/NCEA, Washington, DC; 3IEM AS CR, Prague, CR; 4SDSU, Brookings, SD; 5US EPA...

  1. Influence of cassava genotype and composite flours’ substitution level on rheological behaviour during bread-making

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    Sergio Henao Osorio

    2010-05-01

    Full Text Available Given increasing dependence on imported wheat, studies have been carried out in Colombia regarding the use of composite wheat-cassava flour in bread-making. A project was carried out from 1986-1991 in which different cassava genotypes, harvest ages, substitution levels and bread acceptability were evaluated. However, these studies did not have any effect on the baking sector because a constant supply of high quality, high volume and reasonably-priced cassava flour was lacking. Based on these studies, this work was aimed at determining the influence of three industrial cassava market genotypes (CMC-40, HMC-1, MCOL-1505, using four wheat-cassava flour composite substitution levels (0%, 5%, 10%, 15% regarding the rheological and fermentative characteristics of dough in bread-making. Farinogram, alveogram, amylogram and falling number index analysis were analysed. Specific volume and acceptability of three types of bread (common, mold and hamburger were evaluated. It was determined that composite flours had higher fiber and reduced sugar content than the wheat flour pattern, thereby increasing wa-ter absorption and available sugar content during fermentation. Dough development time for the composite flours was half the a-verage required for wheat flour and the tolerance index was higher; its stability became reduced due to increased substitution le-vels and its firmness increased due to a rise in water absorption. Falling number values came within an acceptable range (250-400 s. The specific volume of all bread having 5% and 10% substitution was higher than that for the pattern. The best general acceptability was assigned to common and mold type bread from all varieties and substitution levels.

  2. Environmental influences on pigeonpea-Fusarium udum interactions and stability of genotypes to Fusarium wilt.

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    Mamta eSharma

    2016-03-01

    Full Text Available Fusarium wilt (Fusarium udum Butler is an important biotic constraint to pigeonpea (Cajanus cajan L. production worldwide. Breeding for fusarium wilt resistance continues to be an integral part of genetic improvement of pigeonpea. Therefore, the study was aimed to identify and validate resistant genotypes to fusarium wilt and determine the magnitude of genotype × environment (G × E interactions through multi-environment and multi-year screening. Total 976 genotypes including germplasm and breeding lines were screened against wilt in wilt sick plot at Patancheru, India. Ninety two genotypes found resistant to wilt were tested further for two more years in wilt sick plot at Patancheru and Pigeonpea Wilt Nursery (PWN comprising of 29 genotypes was constituted. PWN was evaluated at nine locations representing different agro-climatic zones of India for wilt resistance during two crop seasons 2007/08 and 2008/09. Genotypes (G, environment (E and G × E interactions biplot partitioned main effect into G, E and G × E interactions and significant effects (p≤0.001 were obtained for wilt incidence. Genotype contributed 36.51% of resistance variation followed by environment (29.32%. GGE biplot in integration with boxplot and multiple comparison tests enabled us to identify seven stable genotypes (ICPL 20109, ICPL 20096, ICPL 20115, ICPL 20116, ICPL 20102, ICPL 20106 and ICPL 20094 based on their performance across diverse environments. These genotypes have broad based resistance and can be exploited in pigeonpea breeding program.

  3. Influence of COMT val158met genotype on the depressed brain during emotional processing and working memory.

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    Esther M Opmeer

    Full Text Available Major depressive disorder (MDD has been associated with abnormal prefrontal-limbic interactions and altered catecholaminergic neurotransmission. The val158met polymorphism on the catechol-O-methyltransferase (COMT gene has been shown to influence prefrontal cortex (PFC activation during both emotional processing and working memory (WM. Although COMT-genotype is not directly associated with MDD, it may affect MDD pathology by altering PFC activation, an endophenotype associated with both COMT and MDD. 125 participants, including healthy controls (HC, n=28 and MDD patients were genotyped for the COMT val158met polymorphism and underwent functional magnetic resonance imaging (fMRI-neuroimaging during emotion processing (viewing of emotional facial expressions and a WM task (visuospatial planning. Within HC, we observed a positive correlation between the number of met-alleles and right inferior frontal gyrus activation during emotional processing, whereas within patients the number of met-alleles was not correlated with PFC activation. During WM a negative correlation between the number of met-alleles and middle frontal gyrus activation was present in the total sample. In addition, during emotional processing there was an effect of genotype in a cluster including the amygdala and hippocampus. These results demonstrate that COMT genotype is associated with relevant endophenotypes for MDD. In addition, presence of MDD only interacts with genotype during emotional processing and not working memory.

  4. Productive and reproductive efficiency of different genotypes of goat in Bangladesh influenced by nutritional status

    International Nuclear Information System (INIS)

    lack of sufficient forages. The hilly area remains free of flood, covered by dense forest and has a vast grazing land with low human population density. Animals in this area get sufficient forage naturally. The better performances in growth and reproduction in goats reared in hilly area is certainly for better nutrition that occurs naturally. On the hand, crossbred maintained urban area had better performances over Black Bengal goats. This may be for heterosis effect as well as supplementation of feeds. The preliminary study of this experiment indicates that nutrition as well as genotypes has significant influence in the production and reproduction performances of goats in Bangladesh. In fact, this is the first work on Black Bengal goats in the hilly area and crossbred goats of Bangladesh. Further experiment has been planned for confirming this fact. (author)

  5. Influence of drought on seedling development in different corn genotypes (Zea mays L.)

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    Radić Velimir; Vujaković Milka; Marjanović-Jeromela Ana

    2007-01-01

    Assuming that drought affects corn seed performance, such conditions were simulated in this study in order to examine their effects on seedling geminability and length in several corn genotypes. The study showed that the tested seeds tolerated the stress conditions up to a certain point. The studied genotypes differed in level of resistance to the stress conditions. Salt concentrations were determined, which were capable of negatively affecting seed germinability and seedling growth.

  6. The individual and combined influence of ACE and ACTN3 genotypes on muscle phenotypes before and after strength training.

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    Erskine, R M; Williams, A G; Jones, D A; Stewart, C E; Degens, H

    2014-08-01

    Alternative measures of muscle size, strength, and power to those used in previous studies could help resolve the controversy surrounding associations between polymorphisms of the angiotensin-I converting enzyme (ACE) and α-actinin-3 (ACTN3) genes and skeletal muscle phenotypes, and the responses to resistance training (RT). To this end, we measured quadriceps femoris muscle volume (Vm), physiological cross-sectional area (PCSA), maximum isometric force (Ft), specific force (Ft per unit PCSA), maximum isoinertial strength (1-RM), and maximum power (Wmax ; n = 40) before and after 9-week knee extension RT in 51 previously untrained young men, who were genotyped for the ACE I/D and ACTN3 R577X polymorphisms. ACTN3 R-allele carriers had greater Vm, 1-RM, and Wmax than XX homozygotes at baseline (all P ACTN3 genotype (all P > 0.05). Muscle phenotypes were independent of ACE genotype before (all P > 0.05) and after RT (all P > 0.01). However, people with the "optimal" ACE+ACTN3 genotype combination had greater baseline 1-RM and Wmax compared to those with the "suboptimal" profile (both P ACTN3 R577X polymorphism is associated with human Vm and (independently and in combination with the ACE I/D polymorphism) influences 1-RM and Wmax. PMID:23384112

  7. Does angiotensin-1 converting enzyme genotype influence motor or cognitive development after pre-term birth?

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    Whitelaw Andrew

    2005-02-01

    Full Text Available Abstract Background Raised activity of the renin-angiotensin system (RAS may both amplify inflammatory and free radical responses and decrease tissue metabolic efficiency and thus enhance cerebral injury in the preterm infant. The angiotensin-converting enzyme (ACE DD genotype is associated with raised ACE and RAS activity as well as potentially adverse stimuli such as inflammation. The DD genotype has been associated with neurological impairments in the elderly, and thus may be also associated with poorer motor or cognitive development amongst children born preterm prematurely. Methods The association of DD genotype with developmental progress amongst 176 Caucasian children born at less than 33 weeks gestation (median birthweight 1475 g, range 645–2480 g; gestation 30 weeks, range 22–32; 108 male was examined at 2 and 5 1/2 years of age. Measured neuro-cognitive outcomes were cranial ultrasound abnormalities, cerebral palsy, disability, Griffiths Developmental Quotient [DQ] at 2 yrs, and General Cognitive Ability [British Ability Scales-11] and motor performance [ABC Movement], both performed at 5 1/2 yrs. All outcomes were correlated with ACE genotype. Results The DD genotype was not associated with lower developmental quotients even after accounting for important social variables. Conclusion These data do not support either a role for ACE in the development of cognitive or motor function in surviving infants born preterm or inhibition of ACE as a neuroprotective therapy.

  8. Genotype x Environment interaction for antioxidants and phytic acid contents in bread and durum wheat as influenced by climate

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    Gordana Brankovic

    2015-06-01

    Full Text Available Antioxidants prevent oxidative stress and exert positive health effects. However, phytic acid among them decreases micronutrients absorption, representing also antinutrient to human and non-ruminant animals. Fifteen bread wheat (Triticum aestivum L. and 15 durum wheat (Triticum durum Desf. genotypes were evaluated across six environments to determine contents of phytic acid (PA, inorganic P (Pi, total yellow pigment, total soluble phenolic compounds, free protein sulfhydryl groups (PSH, and also phytic acid P/Pi (Pp/Pi. The objective of this study was to quantify, for each trait the effects of environment, genotype, and their interaction; and the influence of climatic factors on the Genotype x Environment interaction (GEI by the use of the factorial regression. GEI (P < 0.001 prevailed as source of variation over genotype (P < 0.001 in determining PA content in bread and durum wheat (44.3% and 34.7% of sum of squares-SS, respectively, PSH content in bread and durum wheat (27% and 28.4% of SS, respectively and total soluble phenolic compounds content in durum wheat (35.5% of SS. The major contribution to the GEI represented climatic variables during stages of stem elongation for PA and phenolic compounds, and also flowering, fertilization, grain formation and grain filling for PSH. Total yellow pigment and Pi contents in bread and durum wheat were predominantly determined by genotype (P < 0.001. Models of climatic variables proved to be efficient in the explanation of more than 92% of the SS of GEI for PA and antioxidants contents.

  9. Evolution of somatic mutations in mammary tumors in transgenic mice is influenced by the inherited genotype

    Directory of Open Access Journals (Sweden)

    Li Yi

    2004-06-01

    of those cells in MMTV-Wnt1 and MMTV-Neu transgenic mice, respectively. Alternative sources of oncogenic potential, such as a second transgenic oncogene or deficiency of a tumor suppressor gene, can obviate the selective power of those secondary mutations. These observations are consistent with the notion that somatic evolution of mouse mammary tumors is influenced by the specific nature of the inherited cancer-promoting genotype.

  10. Sleep duration, depression, and oxytocinergic genotype influence prepulse inhibition of the startle reflex in postpartum women.

    Science.gov (United States)

    Comasco, Erika; Gulinello, Maria; Hellgren, Charlotte; Skalkidou, Alkistis; Sylven, Sara; Sundström-Poromaa, Inger

    2016-04-01

    The postpartum period is characterized by a post-withdrawal hormonal status, sleep deprivation, and susceptibility to affective disorders. Postpartum mothering involves automatic and attentional processes to screen out new external as well as internal stimuli. The present study investigated sensorimotor gating in relation to sleep duration, depression, as well as catecholaminergic and oxytocinergic genotypes in postpartum women. Prepulse inhibition (PPI) of the startle reflex and startle reactivity were assessed two months postpartum in 141 healthy and 29 depressed women. The catechol-O-methyltransferase (COMT) Val158Met, and oxytocin receptor (OXTR) rs237885 and rs53576 polymorphisms were genotyped, and data on sleep duration were collected. Short sleep duration (less than four hours in the preceding night) and postpartum depression were independently associated with lower PPI. Also, women with postpartum depression had higher startle reactivity in comparison with controls. The OXTR rs237885 genotype was related to PPI in an allele dose-dependent mode, with T/T healthy postpartum women carriers displaying the lowest PPI. Reduced sensorimotor gating was associated with sleep deprivation and depressive symptoms during the postpartum period. Individual neurophysiological vulnerability might be mediated by oxytocinergic genotype which relates to bonding and stress response. These findings implicate the putative relevance of lower PPI of the startle response as an objective physiological correlate of liability to postpartum depression. PMID:26857197

  11. Lack of influence of CYP2D6 genotype on the clearance of (R)-, (S)- and racemic-methadone

    DEFF Research Database (Denmark)

    Coller, J K; Joergensen, C; Foster, D J R;

    2007-01-01

    OBJECTIVE: To investigate the influence of CYP2D6 genotype on the oral clearance of (R)-, (S)- and rac-methadone. METHODS: In this retrospective study, CYP2D6 genotypes were identified in 56 methadone maintained subjects. Plasma concentrations of (R)-, (S)- and rac-methadone were determined by...... stereoselective HPLC and sufficient data were available to estimate the apparent oral clearances of (R)-, (S)- and rac-methadone using a population kinetic model in 37 of the genotyped subjects. RESULTS: The CYP2D6 allele frequencies were similar to those previously reported in Caucasians, the most common being......: CYP2D6*1 (35.2%), CYP2D6*2 (12.0%) and CYP2D6*4 (22.2%). Three unknown SNPs were found in four subjects: 1811G > A (n = 1), 1834C > T (n = 1) and 2720G > C (n = 2). The oral clearances of (R)-, (S)- and rac-methadone varied 5.4-, 6.8- and 6.1-fold, respectively. No significant differences in methadone...

  12. Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils.

    Science.gov (United States)

    Poli, Anna; Lazzari, Alexandra; Prigione, Valeria; Voyron, Samuele; Spadaro, Davide; Varese, Giovanna Cristina

    2016-01-01

    Rhizosphere and root-associated microbiota are crucial in determining plant health and in increasing productivity of agricultural crops. To date, research has mainly focused on the bacterial dimension of the microbiota. However, interest in the mycobiota is increasing, since fungi play a key role in soil ecosystems. We examined the effect of plant genotype, soil, and of Fusarium oxysporum f. sp. lycopersici (Fol) on the cultivable component of rhizosphere and root-associated mycobiota of tomato. Resistant and susceptible varieties were cultivated on two different soils (A and B), under glasshouse conditions. Isolated fungi were identified by morphological and molecular approaches. Differences were found between the rhizosphere and the roots, which in general displayed a lower number of species. The structure of the mycobiota was significantly affected by the soil type in the rhizosphere as well as by the plant genotype within the roots (NPERMANOVA, p soil A, where Penicillium spp. and Fusarium spp. were the dominant responding fungi. Overall, the results indicated that i) soil type and plant genotype affect the fungal communities; ii) plant roots select few species from the rhizosphere; and iii) the fungal community structure is influenced by Fol. PMID:27268246

  13. Parent genotype and environmental factors influence introduction success of the critically endangered Savannas Mint (Dicerandra immaculata var. savannarum.

    Directory of Open Access Journals (Sweden)

    Cheryl L Peterson

    Full Text Available Species previously unknown to science are continually discovered and some of these species already face extinction at the time of their discovery. Conserving new and rare species in these cases becomes a trial-and-error process and conservationists will attempt to manage them by using knowledge of closely related species, or those that fill the same ecological niche, and then adapting the management program as needed. Savannas Mint (Dicerandra immaculata Lakela var. savannarum Huck is a perennial plant that was discovered in Florida scrub habitat at two locations in 1995, but is nearly extinct at these locations. We tested whether shade, leaf litter, propagation method, parent genotype, parent collection site, planting date, and absorbent granules influenced survival, reproduction, and recruitment of Savannas Mint in a population of 1,614 plants that we introduced between June 2006 and July 2009 into a state protected site. Survival and reproduction of introduced plants, and recruitment of new plants, was higher in microhabitats in full sun and no leaf litter and lower in partially shaded habitats. The two sites from which parent plants were collected differentially influenced survival and reproduction of introduced plants. These differences in survival and reproduction are likely due to underlying genetic differences. Differential survival of progeny from different parent genotypes further supports the idea that underlying genetics is an important consideration when restoring plant populations. The most successful progeny of parent genotypes had survival rates nearly 12 times higher than the least successful progeny. We speculate that many of these environmental and genetic factors are likely to influence allopatric congeners and other critically endangered gap specialists that grow in Florida scrub and our results can be used to guide their conservation.

  14. Influence of contrasting environments on seed composition of two quinoa genotypes: nutritional and functional properties

    Directory of Open Access Journals (Sweden)

    Margarita Miranda

    2013-06-01

    Full Text Available Quinoa (Chenopodium quinoa Willd. in Chile represents a source of germplasm with high nutritional value. However, there is little information available related to quinoa seed quality grown under contrasting environments. In this study we evaluated the changes on seed composition of seeds of two lowland/coastal quinoa genotypes grown under arid (Vicuna and cold-temperate (Temuco conditions in Chile. Results showed that in the case of 'Regalona Baer' and 'Villarrica' genotypes the arid location (with irrigation led to a significant increase (P < 0.05 in grain yield (4.2 and 5.1 t ha-1, respectively, soluble dietary fiber (16.8 ± 0.4 and 28.9 ± 2.1 g kg-1 DM, respectively, vitamin B3 (2.44 ± 0.005 and 2.26 ± 0.04 mg 100 g-1 DM, respectively, saponins (3.22 ± 0.38 mg 100 g-1 DM, 'Regalona Baer', phenolic compounds (19.2 ± 5.48 and 31.92 ± 1.14 mg gallic acid 100 g-1 DM, respectively and components of proximate analysis, except protein content. The cold-temperate climate (rainfed affected positively seed size (2.22 ± 0.17 mm 'Villarrica' and 1000 seed weight (3.08 ± 0.08 and 3.29 ± 0.08 g, respectively, as well as insoluble dietary fiber content (112.3 ± 23.8 g kg-1 DM, 'Regalona Baer'. Furthermore, vitamin C was higher in 'Regalona Baer' genotype at arid locality (31.22 ± 4.2 mg 100 g-1 DM, but much higher content was registered in 'Villarrica' genotype at cold-temperate climate (49.3 ± 5.36 mg 100 g-1 DM. The environment-induced relationship among variables and genotypes was consistent with principal component analysis (PCA. The arid region of Vicuna in Chile represents a potential area for quinoa cultivation for lowland/coastal quinoa genotypes, whose nutritional and functional features were affected positively, due to the much more stressing climatic conditions.

  15. Influence of the APOE genotype on hepatic stress response: Studies in APOE targeted replacement mice and human liver cells.

    Science.gov (United States)

    Dose, Janina; Nebel, Almut; Piegholdt, Stefanie; Rimbach, Gerald; Huebbe, Patricia

    2016-07-01

    Apolipoprotein E (APOE) is a multifunctional plasma protein mainly acting in lipid metabolism. Human APOE is polymorphic with three major isoforms (APOE2, APOE3 and APOE4). Up to 75% of the body's APOE is produced by the liver. There is increasing evidence from studies in brain-derived cells that APOE4 affects mitochondrial function and biogenesis as well as stress and inflammatory responses - processes, whose disturbances are considered hallmarks of the ageing process. However, although the liver is the main production site of APOE, knowledge about the impact of the APOE genotype on hepatic stress response-related processes is rather limited. Therefore, we studied biomarkers of oxidative status (glutathione levels, 3-nitrotyrosine adducts, protein carbonyl concentration), ER stress (XBP1(S), BiP, DDIT3), proteasome activity, mitochondrial function (respiratory complexes, ATP levels and mitochondrial membrane potential as well as biomarkers of mitochondrial biogenesis, fission and fusion), autophagy (LC3, LAMP2A), apoptosis (BCL2, BAX, CYCS) and DNA damage in the liver of APOE targeted replacement (TR) mice and in Huh7 hepatocytes overexpressing the APOE3 and the APOE4 isoform, respectively. APOE4 mice exhibited a lower chymotrypsin-like and a higher trypsin-like proteasome activity. Levels of protein carbonyls were moderately higher in liver tissue of APOE4 vs. APOE3 mice. Other biomarkers of oxidative stress were similar between the two genotypes. Under basal conditions, the stress-response pathways investigated appeared largely unaffected by the APOE genotype. However, upon stress induction, APOE4 expressing cells showed lower levels of adenosine triphosphate (ATP) and lower mRNA levels of the ATP-generating complex V of the mitochondrial respiratory chain. Overall, our findings provide evidence for a rather low influence of the APOE genotype on the hepatic stress response processes investigated in this study. PMID:27130033

  16. Former Land Use and Host Genotype Influence the Mycorrhizal Colonization of Poplar Roots

    OpenAIRE

    Felicia Gherghel; David Behringer; Stefanie Haubrich; Maren Schlauß; Christina Fey-Wagner; Karl-Heinz Rexer; Alwin Janßen; Gerhard Kost

    2014-01-01

    The present paper analyses the community structure of ectomycorrhiza (ECM) and arbuscular mycorrhiza (AM) fungi associated with seven different poplar clone types growing in a patch system on soil from four different former land use types, originating from spruce forest, poplar stand, grassland and cornfield. We determined the extent to which ECM and AM play a role on the studied factors (genotype, former land use type and host growth). The diversity of ECM and AM fungal communities was estim...

  17. Influence of Seed Size on Yield, Yield Components and Quality of Three Maize Genotypes

    OpenAIRE

    Aman Ullah Chaudhry; M. Ikram Ullah

    2001-01-01

    A field experiment was conducted to determine the effect of seed size on maize (Zea mays L.) performance. Among three genotypes under study the seed size categories and their interaction showed non significant effect on yield, yield components, photo biomass production and quality of maize under Faisalabad agro-meteorological conditions. All the parameters including germination, number of plants per plot, plant height, number of cobs per plant, number of rows per cob, number of grains p...

  18. The Influence of Host and Bacterial Genotype on the Development of Disseminated Disease with Mycobacterium tuberculosis

    OpenAIRE

    Maxine Caws; Guy Thwaites; Sarah Dunstan; Hawn, Thomas R.; Nguyen Thi Ngoc Lan; Nguyen Thuy Thuong Thuong; Kasia Stepniewska; Mai Nguyet Thu Huyen; Nguyen Duc Bang; Tran Huu Loc; Sebastien Gagneux; Dick van Soolingen; Kristin Kremer; Marianne van der Sande; Peter Small

    2008-01-01

    The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated p...

  19. Immunoglobulin G3 and immunoglobulin M isotype plasma levels are influenced by interleukin-1alpha genotype.

    Science.gov (United States)

    Kilpinen, S; Laine, S; Hulkkonen, J; Hurme, M

    2003-03-01

    The immunoglobulin (Ig) plasma levels are known to be, at least partially, genetically regulated, but all the genes involved are not known. Interleukin-1 (IL-1) is a potent proinflammatory cytokine able to serve as an adjuvant for immune responses. IL-1alpha gene is polymorphic, and at least one of the polymorphisms has been identified in the 5' regulatory region of the promoter, a biallelic base exchange (C-->T) at position -889. We set out to study whether the IL-1alpha genotype might contribute to the genetic component seen in the steady-state antibody levels of healthy individuals. Four hundred healthy blood donors (218 males and 182 females) were genotyped, and the plasma levels of IgM, IgG as well as IgG subclasses were measured. An association was found between IgG3 plasma levels and the IL-1alpha genotype; the 1.1 homozygotes had increased IgG3 levels compared with the 1.2 heterozygotes (P < 0.001 in males and P = 0.04 in females, Mann-Whitney U-test). A similar significant association was also found between IgM plasma levels and the IL-1alpha genotype in males, but it was no longer present in females; the 1.1 homozygotes had higher IgM levels than the 2.2 homozygotes (P = 0.03, Mann-Whitney U-test). The data suggest that IL-1alpha-mediated signals are critical for IgG3 and IgM responses, which are induced by thymus-independent antigens and are important in activating complement. PMID:12641660

  20. Influence of COMT genotype and affective distractors on the processing of self-generated thought

    OpenAIRE

    Kilford, E. J.; Dumontheil, I.; Wood, N. W.; Blakemore, S. J.

    2014-01-01

    The catechol-O-methyltransferase (COMT) enzyme is a major determinant of prefrontal dopamine levels. The Val158Met polymorphism affects COMT enzymatic activity and has been associated with variation in executive function and affective processing. This study investigated the effect of COMT genotype on the flexible modulation of the balance between processing self-generated and processing stimulus-oriented information, in the presence or absence of affective distractors. Analyses included 124 h...

  1. ECO-physiological response of S. vulgaris to CR(VI): Influence of concentration and genotype.

    Science.gov (United States)

    Pradas Del Real, Ana E; García-Gonzalo, Pilar; Gil-Díaz, M Mar; González-Rodríguez, Águeda; Lobo, Carmen; Pérez-Sanz, Araceli

    2016-06-01

    The objective of this work is to study the response of Silene vulgaris to a range of environmentally relevant concentrations of Cr(VI) in order to evaluate its potential use in the phytomanagement of Cr polluted sites. Cuttings of six homogenous genotypes from Madrid (Spain) have been used as plant material. The eco-physiological response of S. vulgaris to Cr(VI) changed with the genotype. The yield dose-response curve was characterized by stimulation at low doses of Cr(VI). The effects of metal concentration were quantified on root dry weight, water content and chlorophyll content, determined by SPAD index. The response was not homogeneous for all studied genotypes. At high doses of Cr(VI), plants increased micronutrient concentration in dry tissues which suggested that nutrient balance could be implicated in the alleviation of Cr toxicity. This work highlights the importance of studying the eco-physiological response of metallophytes under a range of pollutant concentrations to determine the most favorable traits to be employed in the phytomanagement process. PMID:26375321

  2. Long-term Miscanthus Yields Influenced by Location, Genotype, Row Distance, Fertilization and Harvest Season

    DEFF Research Database (Denmark)

    Ugilt Larsen, Søren; Jørgensen, Uffe; Kjeldsen, Jens Bonderup;

    2014-01-01

    Foulum and on coarse sand in Jyndevad. Effects of genotype, row distance and fertilization were investigated. In both trials, yield development over time was characterized by an increase during the first years, optimum yields after 7–8 years and a decrease to a lower level which remained relatively...... constant from year 11 to 20. Spring harvest reduced the yield by 34–42 % compared to autumn harvest. In Foulum annual fertilization with 75 kg ha−1 N increased the yield of the genotype Goliath (Miscanthus sinensis) by 26 %. Additional N fertilization only increased the yield of Goliath little, and the...... genotype Giganteus (Miscanthus × giganteus) did not respond to fertilization at all. The highest mean yield in Foulum for the period 1997–2012 was obtained with the shortest row distance (∼18,000 rather than ∼12,000 plants ha−1) and harvested in late autumn, namely 13.1 and 12.0 Mg ha−1 DM annually for...

  3. Influence of Different Genotypes on Trypsin Inhibitor Levels and Activity in Soybeans

    OpenAIRE

    Nedovic, Viktor A.; Stanojevic, Sladjana P.; Barac, Miroljub B.; Vucelic-Radovic, Biljana V.; Pesic, Mirjana B.

    2007-01-01

    This study describes the relationship between the two major trypsin inhibitors (TI) in soybean, i.e., the Kunitz (KTI) and Bowman-Birk (BBI) trypsin inhibitors, as well as between them and the corresponding trypsin inhibitor activity (TIA). Twelve investigated soybean genotypes showed significant differences in TI levels and TIA. A very strong positive correlation was found between the levels of KTI and total BBI (r = 0.94, P < 0.05). No relationship was found between KTI, BBI or total TI and...

  4. Apolipoprotein E genotypes do not influence the age of onset in Huntington's disease

    OpenAIRE

    Saft, C.; Andrich, J; Brune, N; Gencik, M; Kraus, P; Przuntek, H; Epplen, J

    2004-01-01

    Objective: The ε4 allele of the apolipoprotein E (ApoE) gene has been defined as a critical factor for early onset neurodegeneration in Pick's, Parkinson's, and Alzheimer's disease. Unexpectedly, the ε4 allele appeared to delay the age of onset in Huntington's disease (HD) patients. Furthermore, sex specific effects were reported on earlier age of onset due to the ApoE ε2ε3 genotype in males with HD. The age of onset of HD is known to be negatively correlated with increasing lengths of pathog...

  5. Former Land Use and Host Genotype Influence the Mycorrhizal Colonization of Poplar Roots

    Directory of Open Access Journals (Sweden)

    Felicia Gherghel

    2014-12-01

    Full Text Available The present paper analyses the community structure of ectomycorrhiza (ECM and arbuscular mycorrhiza (AM fungi associated with seven different poplar clone types growing in a patch system on soil from four different former land use types, originating from spruce forest, poplar stand, grassland and cornfield. We determined the extent to which ECM and AM play a role on the studied factors (genotype, former land use type and host growth. The diversity of ECM and AM fungal communities was estimated by morphological and molecular analyses of the 18S and ITS of the rDNA genes. Fifteen ECM fungal taxa and four AM groups were distinguished in the roots of the poplars grown for 18 months on soil originating from the respective land use types. The poplar clones showed significantly different rates of shoot length and AM colonization, especially concerning the occurrence of Glomus intraradices and Scutellospora sp. Populus deltoides had significantly higher Scutellospora sp. abundance. Although ECM abundance and diversity was high, no significant differences between the different land use types was found. However, some ECM fungi like Paxillus involutus, Laccaria proxima and Laccaria tortilis showed significant preferences for specific land use types. Our findings suggest that both factors, former land use type and poplar genotype, are important determinants of mycorrhizal colonization of the host plants.

  6. The Influence of Genotype and Production Conditions on the Fertility of Sows in Outdoor System

    Directory of Open Access Journals (Sweden)

    Marija Uremović

    2003-12-01

    Full Text Available The aim of investigation was detected effect of genotype and climate conditions on fertility of sows kept in the outdoor system. The fertility of Black Slavonian breed, F1-Black Slavonian x Duroc and F1 Swedish Landrace x Large White were proveded in conditions of continental climate and German Landrace in conditions of Mediterran climate. The number of live born piglets per litter was: 7.42, 8.54, 9.80 and 10.35 (P<0.01 and reared piglets per litter was: 6.62, 7.66, 8.03 and 9.45 (P<0.01. Higher death rates of piglets of F1- Swedish Landrace x Large White by 7.28% in relation to the Black Slavonian and by 7.70% in relation to F1 Black Slavonian x Duroc results from higher death rates of this combinations (23.67% during a colde part of the year. The research shows that resistant genotypes: Black Slavonian breed and F1 Black Slavonian x Duroc are suitable for keeping in outdoor in conditions of the conetinetal climate. German Landrace breed provided to be suitable for keeping in the outdoor system of production in conditions of Mediterran climate. That confirm low mortality of piglets of 8,7%.

  7. Influence of genotype and feeding on chemical composition of organic chicken meat

    Directory of Open Access Journals (Sweden)

    Achille Franchini

    2010-01-01

    Full Text Available The aim of this study was to evaluate the effects of different genotypes and of feeding on meat chemical composition, including fatty acid profile, of chickens reared under organic conditions. Twomeat–typefast-growing(FG andmedium-growing(MG, andoneegg-typeslow-growing(SG wo meat–type fast-growing (FG and medium-growing (MG, and one egg-type slow-growing (SG strains were assigned to 2 different diets differing for the protein source: soybean (SB and faba bean (FB in partial substitution of soybean. Genotypemarkedlyaffectedthemeatchemical composition. Genotype markedly affected the meat chemical composition. SG breast and thigh meat showed lower content of lipids (P<0.01 than FG. Thehighestproportions he highest proportions of polyunsaturated fatty acids (PUFA n-6 and n-3 and the lowest proportion of monounsaturated (MUFA (P<0.01, as well as the lowest ratio of PUFA n6/n3 (P<0.01 were found in SG breast and thigh meat. MG showed always intermediate values. Asforfeeding, FBtreatmentproducedonlya As for feeding, FB treatment produced only a slight increment of protein in breast and a decrease of fat and ash in thigh meat. Total PUFA and PUFA n-6 resulted lower in both thigh and breast meat of FB groups compared to SB (P<0.01.

  8. Influence of Different Genotypes on Trypsin Inhibitor Levels and Activity in Soybeans

    Directory of Open Access Journals (Sweden)

    Viktor A. Nedovic

    2007-01-01

    Full Text Available This study describes the relationship between the two major trypsin inhibitors (TI in soybean, i.e., the Kunitz (KTI and Bowman-Birk (BBI trypsin inhibitors, as well as between them and the corresponding trypsin inhibitor activity (TIA. Twelve investigated soybean genotypes showed significant differences in TI levels and TIA. A very strong positive correlation was found between the levels of KTI and total BBI (r = 0.94, P < 0.05. No relationship was found between KTI, BBI or total TI and TIA. Based on this data, it appears that the levels of major TI in soybean are related. Understanding the relationship between trypsin inhibitors and their activities could be useful for further improvement of the health impacts of soy proteins.

  9. Influence of genotype, cultivation system and irrigation regime on antioxidant capacity and selected phenolics of blueberries (Vaccinium corymbosum L.).

    Science.gov (United States)

    Cardeñosa, Vanessa; Girones-Vilaplana, Amadeo; Muriel, José Luis; Moreno, Diego A; Moreno-Rojas, José M

    2016-07-01

    Demand for and availability of blueberries has increased substantially over recent years, driven in part by their health-promoting properties. Three blueberry varieties ('Rocío', V2, and V3) were grown under two cultivation systems (open-field and plastic tunnels) and subjected to two irrigations regimes (100% and 80% of crop evapotranspiration) in two consecutive years (2011-2012). They were evaluated for their phytochemical composition and antioxidant capacity. Genotype influenced the antioxidant capacity and the content of the three groups of phenolics in the blueberries. The antioxidant activity and total flavonols content increased when the blueberries were grown under open-field conditions. Deficit irrigation conditions led to additional positive effects on their phenolics (delphinidn-3-acetilhexoside content was increased under plastic tunnel with deficit irrigation). In conclusion, the amount of phenolic compounds and the antioxidant capacity of blueberries were not negatively affected by water restriction; Moreover, several changes were recorded due to growing system and genotype. PMID:26920295

  10. Independent and Interactive Influences of the APOE Genotype and Beta-Amyloid Burden on Cognitive Function in Mild Cognitive Impairment.

    Science.gov (United States)

    Seo, Eun Hyun; Kim, Sang Hoon; Park, Sang Hag; Kang, Seong-Ho; Choo, Il Han

    2016-02-01

    This study aimed to investigate the independent and interactive influences of apolipoprotein E (APOE) ε4 and beta-amyloid (Aβ) on multiple cognitive domains in a large group of cognitively normal (CN) individuals and patients with mild cognitive impairment (MCI) and Alzheimer's disease (AD). Participants were included if clinical and cognitive assessments, amyloid imaging, and APOE genotype were all available from the Alzheimer's Disease Neuroimaging Initiative database (CN = 324, MCI = 502, AD = 182). Individuals with one or two copies of ε4 were designated as APOE ε4 carriers (ε4+); individuals with no ε4 were designated as APOE ε4 non-carriers (ε4-). Based on mean florbetapir standard uptake value ratios, participants were classified as Aβ burden-positive (Aβ+) or Aβ burden-negative (Aβ-). In MCI, APOE ε4 effects were predominantly observed on frontal executive function, with ε4+ participants exhibiting poorer performances; Aβ positivity had no influence on this effect. Aβ effects were observed on global cognition, memory, and visuospatial ability, with Aβ+ participants exhibiting poorer performances. Measures of frontal executive function were not influenced by Aβ. Interactive effects of APOE ε4+ and Aβ were observed on global cognition and verbal recognition memory. Aβ, not APOE ε4+, influenced clinical severity and functional status. The influences of APOE ε4+ and Aβ on cognitive function were minimal in CN and AD. In conclusion, we provide further evidence of both independent and interactive influences of APOE ε4+ and Aβ on cognitive function in MCI, with APOE ε4+ and Aβ showing dissociable effects on executive and non-executive functions, respectively. PMID:26839485

  11. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

    Science.gov (United States)

    DeAtley, K L; Rincon, G; Farber, C R; Medrano, J F; Luna-Nevarez, P; Enns, R M; VanLeeuwen, D M; Silver, G A; Thomas, M G

    2011-07-01

    ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (PBrangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5. PMID:21357449

  12. ACTN3 genotype influences muscle performance through the regulation of calcineurin signaling.

    Science.gov (United States)

    Seto, Jane T; Quinlan, Kate G R; Lek, Monkol; Zheng, Xi Fiona; Garton, Fleur; MacArthur, Daniel G; Hogarth, Marshall W; Houweling, Peter J; Gregorevic, Paul; Turner, Nigel; Cooney, Gregory J; Yang, Nan; North, Kathryn N

    2013-10-01

    α-Actinin-3 deficiency occurs in approximately 16% of the global population due to homozygosity for a common nonsense polymorphism in the ACTN3 gene. Loss of α-actinin-3 is associated with reduced power and enhanced endurance capacity in elite athletes and nonathletes due to "slowing" of the metabolic and physiological properties of fast fibers. Here, we have shown that α-actinin-3 deficiency results in increased calcineurin activity in mouse and human skeletal muscle and enhanced adaptive response to endurance training. α-Actinin-2, which is differentially expressed in α-actinin-3-deficient muscle, has higher binding affinity for calsarcin-2, a key inhibitor of calcineurin activation. We have further demonstrated that α-actinin-2 competes with calcineurin for binding to calsarcin-2, resulting in enhanced calcineurin signaling and reprogramming of the metabolic phenotype of fast muscle fibers. Our data provide a mechanistic explanation for the effects of the ACTN3 genotype on skeletal muscle performance in elite athletes and on adaptation to changing physical demands in the general population. In addition, we have demonstrated that the sarcomeric α-actinins play a role in the regulation of calcineurin signaling. PMID:24091322

  13. The gender-specific apolipoprotein E genotype influence on the distribution of plasma lipids and apolipoproteins in the population of Rochester, Minnesota. II. Regression relationships with concomitants

    Energy Technology Data Exchange (ETDEWEB)

    Reilly, S.L.; Sing, C.F. (Univ. of Michigan, Ann Arbor (United States)); Ferrell, R.E. (Univ. of Pittsburgh, PA (United States)); Kottke, B.A. (Mayo Clinic, Rochester, MN (United States))

    1992-12-01

    The influence of the apolipoprotein E (Apo E) polymorphism and gender on the regression relationships between each of nine plasma lipid and apolipoprotein traits (total cholesterol; ln triglycerides; high-density-lipoprotein chloesterol; apolipoproteins AI, AII, B, and CII; ln CIII; and ln E) and four concomitants (age, weight, waist-to-hip ratio, and smoking) was studied in 507 unrelated individuals representative of the adult population of Rochester, MN. Analyses are presented separately for females and males. Each lipid and apolipoprotein trait exhibited at least one Apo E genotype-specific regression relationship with the concomitants investigated in this study. In most cases the heterogeneity of regression was associated with differences between the [var epsilon]32 and [var epsilon]33 genotype. This study documents that the influence of Apo E genotype on average levels of plasma lipids and apolipoproteins varies among subdivisions of the population defined by age, body size, and smoking status. 61 refs., 1 fig., 5 tabs.

  14. Growth dynamics of the threatened Caribbean staghorn coral Acropora cervicornis: influence of host genotype, symbiont identity, colony size, and environmental setting.

    Directory of Open Access Journals (Sweden)

    Diego Lirman

    Full Text Available BACKGROUND: The drastic decline in the abundance of Caribbean acroporid corals (Acropora cervicornis, A. palmata has prompted the listing of this genus as threatened as well as the development of a regional propagation and restoration program. Using in situ underwater nurseries, we documented the influence of coral genotype and symbiont identity, colony size, and propagation method on the growth and branching patterns of staghorn corals in Florida and the Dominican Republic. METHODOLOGY/PRINCIPAL FINDINGS: Individual tracking of> 1700 nursery-grown staghorn fragments and colonies from 37 distinct genotypes (identified using microsatellites in Florida and the Dominican Republic revealed a significant positive relationship between size and growth, but a decreasing rate of productivity with increasing size. Pruning vigor (enhanced growth after fragmentation was documented even in colonies that lost 95% of their coral tissue/skeleton, indicating that high productivity can be maintained within nurseries by sequentially fragmenting corals. A significant effect of coral genotype was documented for corals grown in a common-garden setting, with fast-growing genotypes growing up to an order of magnitude faster than slow-growing genotypes. Algal-symbiont identity established using qPCR techniques showed that clade A (likely Symbiodinium A3 was the dominant symbiont type for all coral genotypes, except for one coral genotype in the DR and two in Florida that were dominated by clade C, with A- and C-dominated genotypes having similar growth rates. CONCLUSION/SIGNIFICANCE: The threatened Caribbean staghorn coral is capable of extremely fast growth, with annual productivity rates exceeding 5 cm of new coral produced for every cm of existing coral. This species benefits from high fragment survivorship coupled by the pruning vigor experienced by the parent colonies after fragmentation. These life-history characteristics make A. cervicornis a successful candidate

  15. CNR1 genotype influences HDL-cholesterol response to change in dietary fat intake.

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    Heidi J Silver

    Full Text Available BACKGROUND: Success in further reducing the burden of cardiovascular disease (CVD is threatened by the increasing prevalence of obesity-related atherogenic dyslipidemia. HDL-cholesterol (HDL-C level is inversely correlated with CVD risk; each 1 mg/dl decrease in HDL-C is associated with a 6% reduction in risk. We previously showed that a common CNR1 haplotype, H3 (frequency 20%, is protective against the reduction in HDL-C that typically accompanies weight gain. In the present study, we extend that observation by reporting the effect of CNR1 haplotype on HDL-C response to modification of dietary fat intake in weight maintenance and weight loss. METHODS: Six haplotype tagging SNPs that cover the CNR1 gene locus were genotyped in 590 adults of varying body mass index (cohort 1 is 411 males with BMI 18.5-30.0 kg/m(2; cohort 2 is 71 females with BMI18.5-30.0 kg/m(2; and cohort 3 is 108 females with BMI 30-39.9 kg/m(2. Dietary intakes were modified so that fat intake in the "high fat" condition was 15-20% greater than in the "low fat" condition, and lipid profiles were compared between carriers versus noncarriers for each of the five commonly observed CNR1 haplotypes (H1-H5. RESULTS: In normal to overweight subjects on eucaloric diets, the H3 haplotype was significantly associated with short-term high fat diet induced changes in HDL-C level in females (carriers 5.9 mg/dl>noncarriers, p = 0.007. The H3 haplotype was also significantly associated with HDL-C level after 16 weeks on high fat calorie restricted diet in obese females (carriers 6.8 mg/dl>noncarriers, p = 0.009. CONCLUSION: Variability within the CNR1 gene locus contributes to gender-related differences in the HDL-cholesterol response to change in dietary fat intake. Functional characterization of this relationship in vitro may offer insights that potentially yield therapeutic guidance targeting dietary macronutrient composition, a direction much needed in the current epidemic of

  16. Influence of APOE Genotype on Whole-Brain Functional Networks in Cognitively Normal Elderly

    OpenAIRE

    Seo, Eun Hyun; Lee, Dong Young; Lee, Jong-Min; Park, Jun-Sung; Sohn, Bo Kyung; Choe, Young Min; Byun, Min Soo; Choi, Hyo Jung; Woo, Jong Inn

    2013-01-01

    This study aimed to investigate the influence of apolipoprotein E (APOE) ε4 allele on whole-brain functional networks in cognitively normal (CN) elderly by applying graph theoretical analysis to brain glucose metabolism. Eighty-six CN elderly [28 APOE ε4 carriers (ε4+) and 58 non-carriers (ε4-)] underwent clinical evaluation and resting [18F] fluorodeoxyglucose positron emission tomography scan. Whole-brain functional networks were constructed from correlations of the 90 regions of interest u...

  17. Influence of polyploidy on insect herbivores of native and invasive genotypes of Solidago gigantea (Asteraceae)

    OpenAIRE

    Helen M. Hull-Sanders; Johnson, Robert H.; Owen, Heather A.; Meyer, Gretchen A.

    2009-01-01

    Herbivores are sensitive to the genetic structure of plant populations, as genetics underlies plant phenotype and host quality. Polyploidy is a widespread feature of angiosperm genomes, yet few studies have examined how polyploidy influences herbivores. Introduction to new ranges, with consequent changes in selective regimes, can lead to evolution of changes in plant defensive characteristics and also affect herbivores. Here, we examine how insect herbivores respond to polyploidy in Solidago ...

  18. The influence of genotype and osmotic stress on germination and seedling of maize

    OpenAIRE

    Mandić V.; Bijelić Z.; Krnjaja V.; Tomić Z.; Simić A.; Ružić-Muslić D.; Gogić M.

    2014-01-01

    The aim of this research was to estimate the influence of different NaCl osmotic solutions (0, -0.3 MPa, -0.6 MPa, -0.9 MPa, -1.2 MPa, -1.5 MPa) on seed germination, and early seedling growth in two maize hybrid different maturity groups (ZP 560 - FAO 500 and ZP 666 - FAO 600). Germination was tested in sterile plastic vessels on filter paper moistened with different NaCl solutions, in the dark at 20 ± 1°C, in laboratory. Results of ANOVA indicated that hyb...

  19. Host Genotype and Hypersensitive Reaction Influence Population Levels of Xanthomonas campestris pv. vitians in Lettuce.

    Science.gov (United States)

    Bull, Carolee T; Gebben, Samantha J; Goldman, Polly H; Trent, Mark; Hayes, Ryan J

    2015-03-01

    Dynamics of population sizes of Xanthomonas campestris pv. vitians inoculated onto or into lettuce leaves were monitored on susceptible and resistant cultivars. In general, population growth was greater for susceptible (Clemente, Salinas 88, Vista Verde) than resistant (Batavia Reine des Glaces, Iceberg, Little Gem) cultivars. When spray-inoculated or infiltrated, population levels of X. campestris pv. vitians were consistently significantly lower on Little Gem than on susceptible cultivars, while differences in the other resistant cultivars were not consistently statistically significant. Populations increased at an intermediate rate on cultivars Iceberg and Batavia Reine des Glaces. There were significant positive correlations between bacterial concentration applied and disease severity for all cultivars, but bacterial titer had a significantly greater influence on disease severity in the susceptible cultivars than in Little Gem and an intermediate influence in Iceberg and Batavia Reine des Glaces. Infiltration of X. campestris pv. vitians strains into leaves of Little Gem resulted in an incompatible reaction, whereas compatible reactions were observed in all other cultivars. It appears that the differences in the relationship between population dynamics for Little Gem and the other cultivars tested were due to the hypersensitive response in cultivar Little Gem. These findings have implications for disease management and lettuce breeding because X. campestris pv. vitians interacts differently with cultivars that differ for resistance mechanisms. PMID:25302523

  20. COMT Val158Met genotypes differentially influence subgenual cingulate functional connectivity in healthy females

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    Chris Baeken

    2014-06-01

    Full Text Available Brain imaging studies have consistently shown subgenual Anterior Cingulate Cortical (sgACC involvement in emotion processing. COMT Val158 and Met158 polymorphisms may influence such emotional brain processes in specific ways. Given that resting-state fMRI (rsfMRI may increase our understanding on brain functioning, we integrated genetic and rsfMRI data and focused on sgACC functional connections. No studies have yet investigated the influence of the COMT Val158Met polymorphism (rs4680 on sgACC resting-state functional connectivity (rsFC in healthy individuals. A homogeneous group of sixty-one Caucasian right-handed healthy female university students, all within the same age range, underwent rsfMRI. Compared to Met158 homozygotes, Val158 allele carriers displayed significantly stronger rsFC between the sgACC and the left parahippocampal gyrus, ventromedial parts of the inferior frontal gyrus, and the nucleus accumbens (NAc. On the other hand, compared to Val158 homozygotes, we found in Met158 allele carriers stronger sgACC rsFC with the medial frontal gyrus, more in particular the anterior parts of the medial orbitofrontal cortex. Although we did not use emotional or cognitive tasks, our sgACC rsFC results point to possible distinct differences in emotional and cognitive processes between Val158 and Met158 allele carriers. However, the exact nature of these directions remains to be determined.

  1. Influence of Genotype and Diet on the Characteristics of Semitendinosus Muscle in Crossbred Young Bulls Derived from Brown Swiss Cow and Double Muscled Bulls

    Directory of Open Access Journals (Sweden)

    Giovanni Bittante

    2013-09-01

    Full Text Available The aim of this study was to evaluate the influence of genotype and diet on the characteristics of muscle fibers and adipocytes of the semitendinosus muscle in crossbred young bulls derived from Brown Swiss cows (B and double-muscled Piemontese (PI or Belgian Blue (BB bulls. For this purpose 24 young bulls divided in 6 groups fed 3 diets have been used: a control diet without supplementation of rumen protected CLA (rpCLA, two other diets added with 8 or 80 g/d of a supplement of rpCLA. The histochemical methods (succinic dehydrogenase and mATPase pointed out the presence of three fiber types: type I, type IIA and type IIX. Results demonstrated that genotype affected both fiber type number and size. While there was no significant difference among the percentages of type I fibers (PI×B 12.73%, BB×B 12.95%, the difference was significant (P<0.05 for IIA fiber type (PI×B 23.03%, BB×B 29.13% and for IIX fiber type (PI×B 64.53%, BB×B 57.84%. All the fiber types of the BB×B genotype had a significantly bigger size (P<0.05 than the fibers of PI×B genotype. The adipocytes analyses showed a significant effect (P<0.05 of genotype on the adipocytes total surface. The level of CLA addition did not affected neither muscle fiber nor adipocytes characteristics.

  2. Influence of Temperature and Humidity on the Stability of Carotenoids in Biofortified Maize (Zea mays L.) Genotypes during Controlled Postharvest Storage.

    Science.gov (United States)

    Ortiz, Darwin; Rocheford, Torbert; Ferruzzi, Mario G

    2016-04-01

    Maize is a staple crop that has been the subject of biofortification efforts to increase the natural content of provitamin A carotenoids. Although significant progress toward increasing provitamin A carotenoid content in maize varieties has been made, postharvest handling factors that influence carotenoid stability during storage have not been fully established. The objectives of this study were to determine carotenoid profiles of six selected provitamin A biofortified maize genotypes at various developmental stages and assess the stability of carotenoids in maize kernels during controlled storage conditions (12 month period), including elevated temperature and relative humidity. There were no significant changes in the content of individual carotenoids within genotypes during kernel development from 45 days after pollination through the time of harvest. Carotenoid losses through traditional grain drying were also minimal (<9%). However, the stability of carotenoids in maize kernels over storage time after harvest was found to be dependent on both temperature and humidity, with variation observed among genotypes. Different forms of provitamin A carotenoids follow similar degradation rates. The genotype C17xDE3 had a degradation rate 2 times faster than those of the other genotypes evaluated (P < 0.001). These differences in carotenoid stability under controlled storage were attributed, in part, to observed differences in the physical properties of the kernels (surface area and porosity). These results support the notion that effective control of moisture content and temperature of the kernels during storage conditions is essential to reduce the speed of degradative reactions. PMID:26939642

  3. Crop genotype and a novel symbiotic fungus influences the root endophytic colonization potential of plant growth promoting rhizobacteria

    OpenAIRE

    Singh, Geeta; Singh, N; Marwaha, T. S.

    2009-01-01

    Effect of plant genotype on the root endophytic colonization ability of a plant growth promoting rhizobacteria (PGPR), Pseudomonas striata was undertaken in this study. Use of a lac-Z tagged P. striata strain showed that, it can exist as an endophyte and the plant genotype determines the performance of the inoculated PGPR. The cultivars of Zea mays L. (maize) and Vigna radiata L. (mung bean) tested showed differential affinity to the PGPR (P. striata) as reflected by a significant variation i...

  4. Influence of the body mass and visceral adiposity on glucose metabolism in obese women with Pro12Pro genotype in PPARgamma2 gene

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    Vanessa Chaia Kaippert

    2013-06-01

    Full Text Available Introduction: Glucose metabolism may be altered in obesity and genotype for PPAR 2 can influence this variable. Objective: To evaluate the influence of body mass (BM and visceral adiposity (VA in glucose metabolism in morbid obese women with Pro12Pro genotype. Methods: Were selected 25 morbidly obese women. Groups were formed according to body mass index (BMI [G1: 40-45 kg/m² (n = 17; G2: > 45 kg/m² (n = 8]. Anthropometric, glycemia and insulinemia assessments (fasting, 60 and 120 minutes after high polyunsaturated fatty acids meal were carried out. The insulin resistance (IR and insulin sensitivity (IS were assessed by HOMA-IR and QUICKI respectively. Results: G2 had higher BMI and waist circumference, compared to G1, impaired fasting glucose, low IS and higher IR. The postprandial glucose was normal, but there was a higher insulin peak one hour after the meal in G2. Conclusion: Increased BM and VA were associated with worse glucose metabolism suggesting metabolic differences between morbid obese with Pro12Pro genotype.

  5. Influence of HLA DQ 2/8 genotypes in predisposing type 1 diabetes in siblings of a Saudi family with paternally inherited chromosomal translocations.

    Science.gov (United States)

    Cherian, Mathew P

    2012-01-01

    Type 1 diabetes is one of the most widely studied complex genetic disorders and the genes in human leukocyte antigen (HLA) locus are reported to account approximately 40%-50% of familial aggregation of type 1 diabetes. Genetic markers are helpful in assessing the risk of type 1 diabetes in the general population as well as in close relatives of a patient with type 1 diabetes. The major genetic determinants of this disease are polymorphisms of class II HLA genes encoding DQ and DR. The major susceptibility genes for type 1 diabetes are in the HLA region, and over 90% of patients carry genotypes DR4, DQ8 and/or DR3, DQ2. Absence of the above alleles makes type 1 diabetes very unlikely, especially if the subject carries protective genotypes such as DR2 and/or DQ6. In this brief report of a consanguineous Saudi family, four offsprings inherited one or both of balanced reciprocal translocations from their father. Two offsprings, one with a translocation and the other without, developed type 1 diabetes during early childhood. Both these diabetic children were found to have HLA genotype DQ 2/8, whereas the father and the youngest daughter, both carrying two sets of balanced translocations as well as the protective HLA genotype DQ6, were free of diabetes during several years of observation. This underscores the influence of HLA genotype DQ 2/8 in the susceptibility and DQ6 in the protective effect on type 1 diabetes even in individuals with gross chromosomal abnormalities. PMID:22876559

  6. Bradykinin Type 2 Receptor BE1 Genotype Influences Bradykinin-Dependent Vasodilation During Angiotensin-Converting Enzyme Inhibition

    OpenAIRE

    Van Guilder, Gary P.; Pretorius, Mias; Luther, James M.; Byrd, J. Brian; Hill, Kevin; Gainer, James V.; Brown, Nancy J.

    2008-01-01

    To test the hypothesis that the bradykinin receptor 2 (BDKRB2) BE1 +9/−9 polymorphism affects vascular responses to bradykinin, we measured the effect of intra-arterial bradykinin on forearm blood flow and tissue-type plasminogen activator (t-PA) release in 89 normotensive, nonsmoking, white American subjects in whom degradation of bradykinin was blocked by enalaprilat. BE1 genotype frequencies were +9/+9:+9/−9:−9/−9=19:42:28. BE1 genotype was associated with systolic blood pressure (121.4±2....

  7. Interferon treatment for chronic hepatitis C infection in hemophiliacs--influence of virus load, genotype, and liver pathology on response.

    Science.gov (United States)

    Hanley, J P; Jarvis, L M; Andrew, J; Dennis, R; Hayes, P C; Piris, J; Lee, R; Simmonds, P; Ludlam, C A

    1996-03-01

    In this study, we assessed the effectiveness of interferon treatment in 31 hemophiliacs with chronic hepatitis C virus (HCV) infection. Interferon alfa-2a (3 MU three times weekly) was administered for 6 months. Response was assessed by both serial alanine transaminase (ALT) and HCV RNA levels measured by a sensitive semiquantitative polymerase chain reaction (PCR) method. HCV genotype was determined by restriction fragment length polymorphism (RFLP), and evidence of changing genotypes during interferon therapy was sought. Severity of liver disease was assessed by both noninvasive and invasive methods, including laparoscopic liver inspection and biopsy. Sustained normalization of ALT levels occurred in eight patients (28%), and seven (24%) became nonviremic as assessed by PCR (<80 HCV/mL). Responders universally cleared HCV RNA within 2 months of starting interferon. Genotype 3a was associated with a favorable response to interferon. No evidence was found for a change in circulating genotype in patients who failed to respond to interferon or who relapsed. This study confirms that response rates to interferon are low in hemophiliacs as compared with other groups with chronic HCV infection. We have also demonstrated that virus load measurement over the first 8 to 12 weeks of treatment is an extremely useful method to identify responders at an early stage. PMID:8634415

  8. Influence of Genotype and Diet on the Characteristics of Semitendinosus Muscle in Crossbred Young Bulls Derived from Brown Swiss Cow and Double Muscled Bulls

    OpenAIRE

    Giovanni Bittante; Rina Verdiglione

    2013-01-01

    The aim of this study was to evaluate the influence of genotype and diet on the characteristics of muscle fibers and adipocytes of the semitendinosus muscle in crossbred young bulls derived from Brown Swiss cows (B) and double-muscled Piemontese (PI) or Belgian Blue (BB) bulls. For this purpose 24 young bulls divided in 6 groups fed 3 diets have been used: a control diet without supplementation of rumen protected CLA (rpCLA), two other diets added with 8 or 80 g/d of a supplement of rpCLA. Th...

  9. Crop genotype and a novel symbiotic fungus influences the root endophytic colonization potential of plant growth promoting rhizobacteria.

    Science.gov (United States)

    Singh, Geeta; Singh, N; Marwaha, T S

    2009-01-01

    Effect of plant genotype on the root endophytic colonization ability of a plant growth promoting rhizobacteria (PGPR), Pseudomonas striata was undertaken in this study. Use of a lac-Z tagged P. striata strain showed that, it can exist as an endophyte and the plant genotype determines the performance of the inoculated PGPR. The cultivars of Zea mays L. (maize) and Vigna radiata L. (mung bean) tested showed differential affinity to the PGPR (P. striata) as reflected by a significant variation in the root endophytic colonization ability of P. striata. Coinoculation with a novel symbiotic fungus Piriformospora indica was found to stimulate endophytic colonization of P. striata in both maize and mungbean. The root exudates of maize and mungbean cultivars showed variations in the total sugar and amino acid contents. However, no consistent relationship was recorded between the concentrations of these metabolites and endophytic colonization of the added PGPR. PMID:23572916

  10. Genotype x Environment interaction for antioxidants and phytic acid contents in bread and durum wheat as influenced by climate

    OpenAIRE

    Gordana Brankovic; Vesna Dragičević; Dejan Dodig; Miroslav Zoric; Desimir Knežević; Sladana Žilić; Srbislav Denčić; Gordana Šurlan

    2015-01-01

    Antioxidants prevent oxidative stress and exert positive health effects. However, phytic acid among them decreases micronutrients absorption, representing also antinutrient to human and non-ruminant animals. Fifteen bread wheat (Triticum aestivum L.) and 15 durum wheat (Triticum durum Desf.) genotypes were evaluated across six environments to determine contents of phytic acid (PA), inorganic P (Pi), total yellow pigment, total soluble phenolic compounds, free protein sulfhydryl groups (PSH), ...

  11. Influence of Changing Rainfall Patterns on the Yield of Rambutan (Nephelium lappaceum L. and Selection of Genotypes in Known Drought-tolerant Fruit Species for Climate Change Adaptation

    Directory of Open Access Journals (Sweden)

    Pablito M. Magdalita

    2015-06-01

    Full Text Available In fruit crop production, rainfall, water stress, temperature, and wind are key variables for success, and the present changes in rainfall patterns could affect the flowering and yield of the rambutan (Nephelium lappaceum L. Other fruit species like macopa (Syzygium samarangense, siniguelas (Spondias purpurea, and native santol or cotton fruit (Sandoricum koetjape remain productive despite extreme climatic changes. This study assessed the influence of rainfall on rambutan yield and evaluated and selected tree genotypes of known drought-tolerant fruit species. Rambutan yield in a selected farm in Calauan, Laguna, Philippines, dropped remarkably from 152.2 kg/tree in 2008 to 8.6 kg/tree in 2009. This reduction could be attributed to the high rainfall in April 2009 at 334.4 mm, and possibly other environmental factors like temperature, relative humidity, solar radiation, and strong wind. Furthermore, wet months in 2009 also inhibited the flowering of rambutan. However, a low yield obtained in 2010 at 45.5 kg/tree could be partly attributed to the very low rainfall in May 2010 at only 9.1 mm. On the other hand, in relation to changing climate, selection of tree genotypes for use as varieties in known drought- and flood-tolerant fruit species based on important fruit qualities like sweetness, juiciness, and high edible portion was done. Among 103 macopa genotypes, Mc-13, 43, and 91 were selected and the best (i.e. , Mc-13 had sweet (7.15 °Brix and crispy fruits weighing 49.44 g, creamy white (RHCC 155 A, and had high edible portion (EP, 93.22%. Among 114 siniguelas genotypes, Sg-41, 42 and 105 were selected and the best selection (i.e., Sg-41, had sweet (12.50 °Brix and juicy fruit weighing 20.42 g, ruby red (RHCC 59 A, and had high EP (83.27%. Among 101 native santol genotypes, Sn-47, 59, and 74 were selected and the best selection (i.e. , Sn-59 had relatively sweet (5.56 °Brix and juicy fruits weighing 51.96 g, maize yellow (RHCC 21 B, and had

  12. Expression of Hepatitis B virus surface antigen (HBsAg from genotypes A, D and F and influence of amino acid variations related or not to genotypes on HBsAg detection

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    Natalia M. Araujo

    2009-08-01

    Full Text Available The impact of hepatitis B virus (HBV genotypes on the sensitivity of surface antigen (HBsAg detection assays has been poorly investigated. Here, plasmids carrying consensus or variant coding sequences for HBV surface proteins from genotypes A, D and F, were constructed. HBsAg levels were evaluated in medium and extracts of transfected CHO cells by a commercial polyclonal-based assay. We show that HBsAg detection values of consensus forms from genotypes D and F were, respectively, 37% and 30% lower than those obtained by genotype A. However, the presence of two single variations, T143M in genotype A, and T125M in genotype D, produced a decrease of 44% and an increase of 34%, respectively, on HBsAg mean values in comparison with their consensus forms. In conclusion, HBsAg detection levels varied among HBV genotypes. However, unique amino acid substitutions not linked to genotypes, such as T125M and T143M described here, should have more implications in HBV immunological diagnostics than the set of variations characteristic of each HBV genotype.

  13. Individual differences in emotion-cognition interactions: Emotional valence interacts with serotonin transporter genotype to influence brain systems involved in emotional reactivity and cognitive control

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    Melanie eStollstorff

    2013-07-01

    Full Text Available The serotonin transporter gene (5-HTTLPR influences emotional reactivity and attentional bias towards or away from emotional stimuli and has been implicated in psychopathological states, such as depression and anxiety disorder. The short allele is associated with increased reactivity and attention towards negatively-valenced emotional information, whereas the long allele is associated with that towards positively-valenced emotional information. The neural basis for individual differences in the ability to exert cognitive control over these bottom-up biases in emotional reactivity and attention is unknown, an issue investigated in the present study. Two groups, homozygous 5-HTTLPR long allele carriers or homozygous short allele carriers, underwent functional magnetic resonance imaging (fMRI while completing an Emotional Stroop-like task that varied with regards to the congruency of task-relevant and task-irrelevant information and the emotional valence of the task-irrelevant information. Behaviorally, participants demonstrated the classic Stroop effect (slower responses for incongruent than congruent trials, which did not differ by 5-HTTLPR genotype. However, fMRI results revealed that genotype influenced the degree to which neural systems were engaged depending on the valence of the conflicting task-irrelevant information. While the Long group recruited prefrontal control regions and superior temporal sulcus during conflict when task-irrelevant information was positively-valenced, the "Short" group recruited these regions when task-irrelevant information was negatively-valenced. Thus, participants successfully engaged cognitive control to overcome conflict in an emotional context using similar neural circuitry, but the engagement of this circuitry depended on emotional valence and 5-HTTLPR status. These results suggest that the interplay between emotion and cognition is modulated, in part, by a genetic polymorphism that influences serotonin

  14. Influence of soil type and genotype on Cd bioavailability and uptake by rice and implications for food safety

    Institute of Scientific and Technical Information of China (English)

    Xinxin Ye; Yibing Ma; Bo Sun

    2012-01-01

    Cadmium (Cd) entering the human body via the food chain is of increasing concern.This study investigates the effects of soil type and genotype on variations in the Cd concentrations of different organs of nine rice plants grown on two types of soils with two Cd levels.Cd concentrations in nine rice cultivars varied significantly with genotype and soil type (P < 0.01).The Cd concentration was higher in red paddy soil (RP) than in yellow clayey paddy soil (YP).The average Cd concentrations of different organs in three rice types were indica > hybrid > japonica for the Cd treatments and controls.The polished grain concentration in YP and RP soils had a range of 0.055-0.23 mg/kg and 0.13-0.36 mg/kg in the Cd treatment,respectively.Two rice cultivars in YP soil and five rice cultivars in RP soil exceeded the concentration limits in the Chinese Food Hygiene Standard (0.2 mg/kg).The Cd concentrations in roots,stems,and leaves were all significantly and positively correlated to that in polished grain in a single test.The Cd concentrations in polished grain were positively and significantly (P < 0.01) correlated with the calculated transfer factors of stem to grain and leaf to grain Cd transfer.The results indicated that the variations of Cd concentration in grain were related to Cd uptake and the remobilization of Cd from stem and leaf to grain.Also,the cultivars with a strong tendency for Cd-accumulation should be avoided in paddy soil with low soil pH and low organic matter content to reduce the risks to human health from high Cd levels in rice.

  15. Affect-modulated startle: interactive influence of catechol-O-methyltransferase Val158Met genotype and childhood trauma.

    Directory of Open Access Journals (Sweden)

    Benedikt Klauke

    Full Text Available The etiology of emotion-related disorders such as anxiety or affective disorders is considered to be complex with an interaction of biological and environmental factors. Particular evidence has accumulated for alterations in the dopaminergic and noradrenergic system--partly conferred by catechol-O-methyltransferase (COMT gene variation--for the adenosinergic system as well as for early life trauma to constitute risk factors for those conditions. Applying a multi-level approach, in a sample of 95 healthy adults, we investigated effects of the functional COMT Val158Met polymorphism, caffeine as an adenosine A2A receptor antagonist (300 mg in a placebo-controlled intervention design and childhood maltreatment (CTQ as well as their interaction on the affect-modulated startle response as a neurobiologically founded defensive reflex potentially related to fear- and distress-related disorders. COMT val/val genotype significantly increased startle magnitude in response to unpleasant stimuli, while met/met homozygotes showed a blunted startle response to aversive pictures. Furthermore, significant gene-environment interaction of COMT Val158Met genotype with CTQ was discerned with more maltreatment being associated with higher startle potentiation in val/val subjects but not in met carriers. No main effect of or interaction effects with caffeine were observed. Results indicate a main as well as a GxE effect of the COMT Val158Met variant and childhood maltreatment on the affect-modulated startle reflex, supporting a complex pathogenetic model of the affect-modulated startle reflex as a basic neurobiological defensive reflex potentially related to anxiety and affective disorders.

  16. Estrogens metabolism associated with polymorphisms: influence of COMT G482a genotype on age at onset of canine mammary tumors.

    Science.gov (United States)

    Dias Pereira, P; Lopes, C C; Matos, A J F; Pinto, D; Gärtner, F; Lopes, C; Medeiros, R

    2008-03-01

    Catechol-O-methyltransferase (COMT) is an important enzyme participating in inactivation of carcinogenic oestrogen metabolites. In humans there is a single nucleotide polymorphism in COMT gene (COMT val158met) that has been associated with an increased risk for developing breast cancer. In dogs, there is a single nucleotide polymorphism in COMT gene (G482A), but its relation with mammary carcinogenesis has never been investigated. The aim of this study was to focus on the evaluation of such polymorphism as a risk factor for the development of mammary tumors in bitches and on the analysis of its relationship with some clinicopathologic features (dog's age and weight, number and histologic type of the lesions, lymph node metastasis) of canine mammary neoplasms. A case-control study was conducted analyzing 90 bitches with mammary tumors and 84 bitches without evidence of neoplastic disease. The COMT G482A polymorphism was analyzed by PCR-RFLP. We found a protective effect of the polymorphism in age of onset of mammary tumors, although we could not establish a significant association between COMT genotype and other clinicopathologic parameters nor with mammary tumor risk overall. Animals carrying the variant allele have a threefold likelihood of developing mammary tumors after 9 years of age in comparison with noncarriers. The Kaplan-Meier method revealed significant differences in the waiting time for onset of malignant disease for A allele carrier (12.46 years) and noncarrier (11.13 years) animals. This investigation constitutes the first case-control study designed to assess the relationship between polymorphic genes and mammary tumor risk in dogs. Our results point to the combined effect of COMT genotype with other genetic and/or environmental risk factors as important key factors for mammary tumor etiopathogenesis. PMID:18424824

  17. The alpha-globin genotype does not influence sickle cell disease severity in a retrospective cross-validation study of the pediatric severity score.

    Science.gov (United States)

    Joly, Philippe; Pondarré, Corinne; Bardel, Claire; Francina, Alain; Martin, Cyril

    2012-01-01

    To validate the recently proposed pediatric severity score (PSS) for sickle cell disease (SCD), we retrospectively assembled clinical data from a cohort of 122 patients with SCD (105 S/S or S/β(0) -thal. and 17 S/C) followed up for at least 2 years. Besides age and α- and β-globin genotypes, four new parameters were also tested against the PSS: duration of data assembly, neonatal screening, use of transcranial Doppler ultrasound to prevent vasculopathies and β-globin gene cluster haplotype. Once again, the PSS clearly differentiated patients by their β-globin genotype (P=0.004) but not by their age during data assembly (P=0.159). But, surprisingly, alpha-gene deletions were not associated with a lower PSS (P=0.604), possibly reflecting the opposite effects of α-thalassemia on global SCD severity. As for the newly tested parameters, the PSS appeared not to be influenced by the duration of data assembly (P=0.071) and neonatal screening (P=0.678) but rather by the introduction of transcranial Doppler ultrasound (P=0.006). Moreover, the Senegal haplotype at the homozygous state may be associated with a lower PSS. Methodologically, our data globally confirm the usefulness of the PSS to identify major etiological factors of SCD gravity. Nevertheless, the score is surely underestimated for patients who have been switched to a chronic therapy before the main SCD complications. Biologically, our study questions about the exact influence of α-thalassemia on global SCD severity. PMID:21910753

  18. Genotype-environment interaction of maternal influence characteristics in Nellore cattle bred in the Brazilian humid tropical regions by reaction norm

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    Jorge Luís Ferreira

    2015-08-01

    Full Text Available Reaction Norm (RN is the study of genotype-environment interaction (GxE that complies with alternative ways of genotypes within different environments. This study was carried out to verify GxE by a reaction norm model of weights at 120 (W120 and 210 (W210 days of age in Nellore cattle raised in the Humid Tropical Regions of Brazil. Environmental gradients were obtained by solutions of contemporary groups which were fitted as co-variables in the random regression model via reaction norms. Mean weight at 120 days of age was 127.97 kg, and environmental gradients ranged between -27 and +26 kg. Average was 185.60 kg at 210 days of age and gradients ranged from -54 to +55 kg. Scale changes in the breeding values and heritability estimates occurred along the gradients for the two weights; the genetic correlations between breeding value breeding values were also similar for both weights. These correlations were high between the close gradients, and low to even negative between extreme environments. Slopes representing the environmental sensitivity were high, with changes of scale and changes in classification of ten bulls with a great numbers of calves for the two traits. When regression slopes of the ten bulls with the highest breeding value breeding values were evaluated, these values were different in W120 from those in W210, perhaps due to the greater influence of maternal effect on W120. These results characterize the influence of GxE on the pre-weaning weights of animals in the humid tropical regions of Brazil. Due to this, it is possible to get greater precision on the predictions of the animals breeding values breeding value. A less biased selection and a greater genetic progress occurred.

  19. Genotype-by-Environment Interactions Influencing the Emergence of rpoS Mutations in Escherichia coli Populations

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    King, Thea; Seeto, Shona; Ferenci, Thomas

    2006-01-01

    Polymorphisms in rpoS are common in Escherichia coli. rpoS status influences a trade-off between nutrition and stress resistance and hence fitness across different environments. To analyze the selective pressures acting on rpoS, measurement of glucose transport rates in rpoS+ and rpoS bacteria was used to estimate the role of Fnc, the fitness gain due to improved nutrient uptake, in the emergence of rpoS mutations in nutrient-limited chemostat cultures. Chemostats with set atmospheres, temper...

  20. Influence of calf genotype on colostral immunoglobulins in Bos taurus and Bos indicus cows and serum immunoglobulins in their calves.

    Science.gov (United States)

    Vann, R C; Holloway, J W; Carstens, G E; Boyd, M E; Randel, R D

    1995-10-01

    Purebred Bos indicus calves are documented to have lower survival rates than Bos taurus calves. Thus, this study was designed to investigate the possibility that this decreased survival rate may be attributed to dam colostral immunoglobulin (Ig) concentrations and subsequent calf serum Ig concentrations. The specific objective was to determine the effect of breed type of calf on colostrum production, immunoglobulin concentrations in colostrum and calf serum, and availability and absorption efficiency of Ig. Brahman (B) and Angus (A) cattle were reciprocally mated to produce calves of the following types: A x A (n = 8), A x B (n = 9), B x B (n = 11), and B x A (n = 11). At birth, calves were separated from their dams and a blood sample was collected before feeding pooled colostrum (30 mL/kg birth weight) at 1 and 6 h of age. From 6 to 12 h of age, each calf was placed in a box that allowed interaction with the dam but prevented suckling. At 12 h of age, each calf was fed its dam's colostrum and placed with the dam. Additional blood samples were collected at 12, 24, and 48 h after birth. Serum and colostrum samples were analyzed for IgG, IgG1, IgG2, IgM, and IgA using single radial immunodiffusion (RID) assay techniques. The cows were hand-milked after induction of milk letdown with oxytocin at 1 and 12 h after calving. Colostrum volume was recorded, and samples were collected. Brahman cows produced more (P x B and A x B breed types of calf. Brahman cows had more Ig available at 1 and 12 h than A cows due to increased production of colostrum. Breed type influenced colostral Ig in cattle. Serum concentrations of total Ig, IgG, IgG1, IgG2, IgM, and IgA in the calf and efficiency of absorption at 6 and 12 h were not affected by breed type, sex of calf, or any interaction. PMID:8617676

  1. Reduced nucleotide excision repair and GSTM1-null genotypes influence anti-B(a)PDE-DNA adduct levels in mononuclear white blood cells of highly PAH-exposed coke oven workers

    Energy Technology Data Exchange (ETDEWEB)

    Sofia Pavanello; Alessandra Pulliero; Ewa Siwinska; Danuta Mielzynska; Erminio Clonfero [University of Padova, Padova (Italy). Occupational Health Section, Department of Environmental Medicine and Public Health

    2005-07-01

    It is important to identify the potential genetic-susceptible factors that are able to modulate individual responses to exposure to carcinogenic polycyclic aromatic hydrocarbons (PAHs). In the present study we evaluated the influence of four polymorphisms of nucleotide excision repair (NER) genes and that of glutathione S-transferase {mu}1 (GSTM1-active or -null) on benzo(a)pyrene diol epoxide (B(a)PDE)-DNA adduct levels from the lympho-monocyte fraction (LMF) of highly PAH benzo(a)pyrene -exposed Polish coke oven workers with individual urinary post-shift excretion of 1-pyrenol exceeding the proposed biological exposure index. The bulky {+-}-r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-B(a)PDE)-DNA adduct levels were detected by high-performance liquid chromatography fluorescence analysis and genotypes by polymerase chain reaction. We found that workers with the low DNA repair capacity of XPC-PAT+/+ and XPA-A23A genotypes had increased anti-B(a)PDE-DNA adduct levels, DNA adducts were also raised in workers without GSTM1 activity. Workers with unfavourable XPC-PAT+/+ and XPA-A23A NER genotypes, alone or combined with GSTM1-null genotype were in the tertile with the highest adduct level. The increase in anti-B(a)PDE-DNA adduct levels was related in a multiple linear regression analysis to PAH exposure lack of GSTM1 activity and to low DNA repair capacity of the XPC-PAT+/+ genotype. The influence of the XPA-A23A genotype was not evident in this statistical analysis, and no associations with XPD polymorphisms, dietary habits or tobacco smoking were found. The modulation of anti-B(a)PDE-DNA adducts in the LMF by GSTM1-null and some low-activity NER genotypes may be considered as a potential genetic susceptibility factor capable of modulating individual responses to PAH genotoxic exposure and the consequent risk of cancer in coke oven workers.

  2. Aging, Alzheimer’s, and APOE genotype influence the expression and neuronal distribution patterns of microtubule motor protein dynactin-P50

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    Orwa eAboud

    2015-03-01

    Full Text Available Reports from neural cell cultures and experimental animal studies provide evidence of age- and disease-related changes in retrograde transport of spent or misfolded proteins destined for degradation or recycling. However, few studies address these issues in human brain from those who either age without dementia and overt neuropathology, or succumb to Alzheimer’s; especially as such propensity may be influenced by APOE genotype. We studied the expression and distribution of the dynein subunit dynactin-P50, the β amyloid precursor protein (βAPP, and hyperphosphorylated tau (P-tau in tissues and tissue sections of brains from non-demented, neuropathology-free patients and from Alzheimer patients, with either APOE ε3,3 or APOE ε4,4. We found that advanced age in patients without dementia or neuropathological change was associated with coordinated increases in dynactin-P50 and βAPP in neurons in pyramidal layers of the hippocampus. In contrast, in Alzheimer’s, βAPP and dynactin were significantly reduced. Furthermore, the dynactin-P50 and βAPP that was present was located primarily in dystrophic neurites in Aβ plaques. Tissues from Alzheimer patients with APOE ε3,3 had less P-tau, more βAPP, dynactin-P50, and synaptophysin than did tissues from Alzheimer patients carrying APOE ε4,4. It is logical to conclude, then, that as neurons age successfully, there is coordination between retrograde delivery and maintenance and repair, as well as between retrograde delivery and degradation and/or recycling of spent proteins. The buildup of proteins slated for repair, synaptic viability, transport, and re-cycling in neuron soma and dystrophic neurites suggest a loss of this coordination in Alzheimer neurons. Inheritance of APOE ε3,3 rather than APOE ε4,4, is associated with neuronal resilience, suggestive of better repair capabilities, more synapses, more efficient transport, and less hyperphosphorylation of tau. We conclude that even in disease

  3. A influência do genótipo da ECA sobre a aptidão cardiovascular de jovens do sexo masculino moderadamente ativos The influence of ACE genotype on cardiovascular fitness of moderately active young men

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    Jeeser Alves Almeida

    2012-04-01

    Full Text Available FUNDAMENTO: O gene da enzima conversora de angiotensina (gene ECA tem sido amplamente estudado em relação a fenótipos de aptidão cardiorrespiratória, contudo a associação do genótipo da ECA com corridas de meia-distância tem sido pouco investigada. OBJETIVO: O presente estudo investigou a possível influência da enzima conversora de angiotensina (ECA (I/D sobre a aptidão cardiovascular e o desempenho em corridas de meia-distância por parte de brasileiros jovens do sexo masculino. A validade da previsão de VO2max em relação ao genótipo da ECA também foi analisada. MÉTODOS: Um grupo homogêneo de homens jovens moderadamente ativos foi avaliado em um teste de corrida (V1600 m; m.min-1 e em um teste adicional em esteira ergométrica para a determinação de VO2max. Posteriormente, o [(0,177*V1600m + 8.101] VO2max real e previsto foi comparado com os genótipos da ECA. RESULTADOS: O VO2max e V1600m registrados para os genótipos DD, ID e II foram 45,6 (1,8; 51,9 (0,8 e 54,4 (1,0 mL.kg-1.min-1 e 211,2 (8,3; 249,1 (4,3 e 258,6 (5,4 m.min-1, respectivamente e foram significativamente mais baixos para os genótipos DD (p BACKGROUND: The angiotensin I-converting enzyme gene (ACE gene has been broadly studied as for cardiorespiratory fitness phenotypes, but the association of the ACE genotype to middle-distance running has been poorly investigated. OBJECTIVE: This study investigated the possible influence of Angiotensin-Converting Enzyme (ACE genotype (I/D on cardiovascular fitness and middle-distance running performance of Brazilian young males. The validity of VO2max to predict the ACE genotype was also analyzed. METHODS: A homogeneous group of moderately active young males were evaluated in a 1,600 m running track test (V1600m; m.min-1 and in an incremental treadmill test for VO2max determination. Subsequently, the actual and the predicted [(0.177*V1600m + 8.101] VO2max were compared to ACE genotypes. RESULTS: The VO2max and V1600m

  4. Influence of fresh forage-based diets and αs₁-casein (CSN1S1) genotype on nutrient intake and productive, metabolic, and hormonal responses in milking goats.

    Science.gov (United States)

    Bonanno, A; Di Grigoli, A; Di Trana, A; Di Gregorio, P; Tornambè, G; Bellina, V; Claps, S; Maggio, G; Todaro, M

    2013-04-01

    Polymorphism at the αS1-casein locus (CSN1S1) in goats influences several milk production traits. Milk from goats carrying strong alleles, which are associated with high αS1-casein (αS1-CN) synthesis, has higher fat and casein contents, longer coagulation time and higher curd firmness than milk from goats with weak alleles linked to low αS1-CN content. Nutrition also affects these milk properties; therefore, it is important to better understand the interaction between dietary characteristics and the CSN1S1 genotype in goats. This study aimed to investigate the effect of fresh forage based diet or energy supplement on feeding behavior, milk production, and metabolic and hormonal parameters of Girgentana goats with different genotypes at CSN1S1 loci. From a group of goats genotyped by PCR at the DNA level, 12 were selected because they had the same genotype for αS2-CN, β-CN, and κ-CN but a different genotype for αS1-CN: 6 were homozygous for strong alleles at the CSN1S1 loci (AA) and 6 were heterozygous for a weak allele (AF). Goats of each genotype were allocated to 3 subgroups and fed 3 diets ad libitum in a 3×3 Latin square design. The diets were sulla (Hedysarum coronarium L.) fresh forage, sulla fresh forage plus 800 g/d of barley meal (SFB), and mixed hay plus 800 g/d of barley meal (MHB). Diet had a stronger effect than CSN1S1 genotype. The SFB diet led to the highest energy intake, dry matter (DM) digestibility, and milk yield. The fresh forage diets (SFF and SFB) increased DM and crude protein (CP) intake, CP digestibility, and milk CN compared with the MHB diet. The diets supplemented with energy (SFB, MHB) reduced milk fat and urea, improved CP utilization for casein synthesis, and limited body fat mobilization, in accordance with a lower level of nonesterified fatty acids and higher levels of glucose and IGF-1. With regard to CSN1S1 genotype, AA goats showed higher CP digestibility and lower free thyroxine hormone and cholesterol levels than AF

  5. The Influence of Nutritional Factors on Verbal Deficits and Psychopathic Personality Traits: Evidence of the Moderating Role of the MAOA Genotype

    Science.gov (United States)

    Jackson, Dylan B.; Beaver, Kevin M.

    2015-01-01

    The current study explores whether: (a) nutritional factors among adolescent males predict their risk of exhibiting verbal deficits and psychopathic traits during adulthood and (b) the link between nutritional factors and these outcomes is conditioned by the MAOA genotype. The study analyzes data from the U.S. National Longitudinal Study of Adolescent Health (Add Health), a nationally representative, genetically informative sample. We find evidence that meal deprivation increases the likelihood of both verbal deficits and psychopathic personality traits, whereas poor quality nutrition increases the risk of verbal deficits. We detect the presence of a number of gene-environment interactions between measures of food quality and MAOA genotype, but no evidence of GxE in the case of meal deprivation. Limitations are noted and avenues for future research are discussed. PMID:26690459

  6. The Influence of Nutritional Factors on Verbal Deficits and Psychopathic Personality Traits: Evidence of the Moderating Role of the MAOA Genotype

    Directory of Open Access Journals (Sweden)

    Dylan B. Jackson

    2015-12-01

    Full Text Available The current study explores whether: (a nutritional factors among adolescent males predict their risk of exhibiting verbal deficits and psychopathic traits during adulthood and (b the link between nutritional factors and these outcomes is conditioned by the MAOA genotype. The study analyzes data from the U.S. National Longitudinal Study of Adolescent Health (Add Health, a nationally representative, genetically informative sample. We find evidence that meal deprivation increases the likelihood of both verbal deficits and psychopathic personality traits, whereas poor quality nutrition increases the risk of verbal deficits. We detect the presence of a number of gene-environment interactions between measures of food quality and MAOA genotype, but no evidence of GxE in the case of meal deprivation. Limitations are noted and avenues for future research are discussed.

  7. Influences of the genotype and of the environment in the inheritable and the correlations among seven characteristics of quality in wheat (Triticum aestivum L.)

    International Nuclear Information System (INIS)

    This study, carried out in 7 towns of Cundinamarca and Boyaca departments, looks for to know the contributions of the genotype, of the environment and its interaction on 7 characteristics of quality, at the same time that to estimate the inheritable of these characters and the different interrelations among them. The contribution of the genotype is bigger than that of the environment in the expression of the hardness of the grain (index of pearly), being its comparable contribution in the expression of the levels of extraction of flour and volume of bread. Nevertheless, the genetic effects seem to be but stable in the volume of the bread that in the other 2 factors of quality. The inheritable values in wide sense bigger than 0.5 make denounce that in all the variables it can reach some progress by means of the selection. The positive correlations between the hecto liter weight and the percentage of extraction of flour, protein percentage in the flour and the volume of the bread, and among this finish and the time of development of the mass and the negative correlations between the hardness index and the percentage of extraction of flour and between the hardness index and the water absorption, they are conserved in most of the individual environment and when considering all the environment; But, the maintenance of such interrelations seems to depend much of the genotype. In anyone of the 3 previous cases, individual environment, all the atmospheres or genotypes, the values of the 5 correlations are low, with few examples of having rising to the 2 superiors at 0.5

  8. The influence of 5-HTTLPR genotype on the association between the plasma concentration and therapeutic effect of paroxetine in patients with major depressive disorder.

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    Tetsu Tomita

    Full Text Available INTRODUCTION: The efficacy of treatment with selective serotonin reuptake inhibitors in patients with major depressive disorder (MDD can differ depending on the patient's serotonin transporter-linked polymorphic region (5-HTTLPR genotype, and the effects of varying plasma concentrations of drugs can also vary. We investigated the association between the paroxetine plasma concentration and clinical response in patients with different 5-HTTLPR genotypes. METHODS: Fifty-one patients were enrolled in this study. The Montgomery-Asberg Depression Rating Scale (MADRS was used to evaluate patients at 0, 1, 2, 4, and 6 weeks. The patients' paroxetine plasma concentrations at week 6 were measured using high-performance liquid chromatography. Additionally, their 5-HTTLPR polymorphisms (alleles S and L were analyzed using a polymerase chain reaction with specific primers. We divided the participants into two groups based on their L haplotype: the SS group and the SL and LL group. We performed single and multiple regression analyses to investigate the associations between MADRS improvement and paroxetine plasma concentrations or other covariates for each group. RESULTS: There were no significant differences between the two groups with regard to demographic or clinical data. In the SS group, the paroxetine plasma concentration was significantly negatively correlated with improvement in MADRS at week 6. In the SL and LL group, the paroxetine plasma concentration was significantly positively correlated with improvement in MADRS at week 6 according to the results of the single regression analysis; however, it was not significantly correlated with improvement in MADRS at week 6 according to the results of the multiple regression analysis. CONCLUSION: Among patients with MDD who do not respond to paroxetine, a lower plasma concentration or a lower oral dose of paroxetine might be more effective in those with the SS genotype, and a higher plasma concentration might

  9. Influence of genotype and diet on steer performance, manure odor, and carriage of pathogenic and other fecal bacteria. I. Animal performance.

    Science.gov (United States)

    Ferrell, C L; Berry, E D; Freetly, H C; Miller, D N

    2006-09-01

    Although Brahman crosses constitute a large portion of US beef cattle, little information is available on their response to diverse feed resources compared with Bos taurus steers. Thus, the objectives were to evaluate genotype and diet effects on steer performance during the growing period and subsequent response to a high grain diet during the finishing period. Fifty-one steers [0 (15), 1/4 (20), 1/2 (7), and 3/4 Brahman (9), with the remaining proportion being MARC III] were allotted to 8 pens. Beginning on December 2, steers were individually fed chopped bromegrass hay (n = 26; DM = 85%, CP = 9.5%, ME = 2.19 Mcal/kg) or a corn silage-based diet (n = 25; DM = 51%, CP = 11.9%, ME = 2.75 Mcal/kg) for 119 d. All steers were then fed a high corn diet (DM = 79%, CP = 11.7%, ME = 3.08 Mcal/kg) to a target BW of 560 kg (176 d). Data were analyzed by ANOVA, with genotype, growing diet, and the 2-way interaction included. The interaction was not significant (P > 0.25). The MARC III and 1/2 Brahman steers weighed more (P Brahman steers initially and at the end of the growing period. Weight of bromegrass-fed (325 kg) steers was less than that of corn silage-fed (384 kg) steers at the end of the growing period. Steer ADG and intake of DM, CP, and ME were less (P = 0.087 to 0.001) for 1/4 and 3/4 Brahman than for 0 or 1/2 Brahman steers during growing, finishing, and total, but efficiency of gain did not differ (P > 0.10). Carcass weight, marbling score, quality grade (P yield grade (P < 0.05) were greater for corn silage-fed than for bromegrass-fed steers. Feed intake and performance, but not efficiency, differed among these genotypes. Compensatory performance during finishing was insufficient to overcome reduced performance during the growing period. PMID:16908657

  10. Influence of Honey Bee Genotype and Wintering Method on Wintering Performance of Varroa destructor (Parasitiformes: Varroidae)-Infected Honey Bee (Hymenoptera: Apidae) Colonies in a Northern Climate.

    Science.gov (United States)

    Bahreini, Rassol; Currie, Robert W

    2015-08-01

    The objective of this study was to assess the effectiveness of a cooperative breeding program designed to enhance winter survival of honey bees (Apis mellifera L.) when exposed to high levels of varroa (Varroa destructor Anderson and Trueman) in outdoor-wintered and indoor-wintered colonies. Half of the colonies from selected and unselected stocks were randomly assigned to be treated with late autumn oxalic acid treatment or to be left untreated. Colonies were then randomly assigned to be wintered either indoors (n = 37) or outdoors (n = 40). Late autumn treatment with oxalic acid did not improve wintering performance. However, genotype of bees affected colony survival and the proportion of commercially viable colonies in spring, as indicated by greater rates of colony survival and commercially viable colonies for selected stock (43% survived and 33% were viable) in comparison to unselected stock (19% survived and 9% were viable) across all treatment groups. Indoor wintering improved spring bee population score, proportion of colonies surviving, and proportion of commercially viable colonies relative to outdoor wintering (73% of selected stock and 41% of unselected stock survived during indoor wintering). Selected stock showed better "tolerance" to varroa as the selected stock also maintained higher bee populations relative to unselected stock. However, there was no evidence of "resistance" in selected colonies (reduced mite densities). Collectively, this experiment showed that breeding can improve tolerance to varroa and this can help minimize colony loss through winter and improve colony wintering performance. Overall, colony wintering success of both genotypes of bees was better when colonies were wintered indoors than when colonies were wintered outdoors. PMID:26470288

  11. SERUM TOTAL BILIRUBIN, NOT CHOLELITHIASIS, IS INFLUENCED BY UGT1A1 POLYMORPHISM, ALPHA THALASSEMIA AND S GENOTYPE: FIRST REPORT ON COMPARISON BETWEEN ARAB-INDIAN AND AFRICAN S GENES

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    Said Y ALkindi

    2015-10-01

    Full Text Available Background: We explored the potential relationship between steady state serum bilirubin levels and the incidence of cholelithiasis in the context of UGT1A1 gene A(TAnTAA promoter polymorphism in Omani sickle cell anemia (SCA patients, homozygotes for African (Benin and Bantu and Arab-Indian bS haplotypes, but sharing the same microgeographical environment and comparable life style factors.   Methods: 136 SCA patients were retrospectively studied in whom imaging data including abdominal CT scan, MRI or Ultrasonography was routinely available. Available data on the mean steady state hematological/biochemical parameters (n=136,  bs haplotypes(n=136, a globin gene status (n=105 and UGT1A1 genotypes(n=133 were reviewed from the respective medical records.   Results: The mean serum total bilirubin level was significantly higher in the homozygous UGT1A1(AT7 group as compared to  UGT1A1(AT6 group. Strikingly, cholelithiasis was not influenced by age, gender, alpha globin genotype or bS haplotypes in this SCA cohort.   Conclusion: As observed in other population groups, the UGT1A1 (AT7 homozygosity was significantly associated with raised serum total bilirubin level, but the prevalence of gallstones in the Omani SCA patients was not associated with a thalassaemia, UGT1A1 polymorphism, or bs haplotypes.

  12. High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits

    Science.gov (United States)

    Ibeagha-Awemu, Eveline M.; Peters, Sunday O.; Akwanji, Kingsley A.; Imumorin, Ikhide G.; Zhao, Xin

    2016-01-01

    High-throughput sequencing technologies have increased the ability to detect sequence variations for complex trait improvement. A high throughput genome wide genotyping-by-sequencing (GBS) method was used to generate 515,787 single nucleotide polymorphisms (SNPs), from which 76,355 SNPs with call rates >85% and minor allele frequency ≥1.5% were used in genome wide association study (GWAS) of 44 milk traits in 1,246 Canadian Holstein cows. GWAS was accomplished with a mixed linear model procedure implementing the additive and dominant models. A strong signal within the centromeric region of bovine chromosome 14 was associated with test day fat percentage. Several SNPs were associated with eicosapentaenoic acid, docosapentaenoic acid, arachidonic acid, CLA:9c11t and gamma linolenic acid. Most of the significant SNPs for 44 traits studied are novel and located in intergenic regions or introns of genes. Novel potential candidate genes for milk traits or mammary gland functions include ERCC6, TONSL, NPAS2, ACER3, ITGB4, GGT6, ACOX3, MECR, ADAM12, ACHE, LRRC14, FUK, NPRL3, EVL, SLCO3A1, PSMA4, FTO, ADCK5, PP1R16A and TEP1. Our study further demonstrates the utility of the GBS approach for identifying population-specific SNPs for use in improvement of complex dairy traits. PMID:27506634

  13. Prenatal serotonin reuptake inhibitor (SRI antidepressant exposure and serotonin transporter promoter genotype (SLC6A4 influence executive functions at 6 years of age

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    Whitney eWeikum

    2013-10-01

    Full Text Available Prenatal exposure to serotonin reuptake inhibitor (SRI antidepressants and maternal depression may affect prefrontal cognitive skills (executive functions; EFs including self-control, working memory and cognitive flexibility. We examined long-term effects of prenatal SRI exposure on EFs to determine whether effects are moderated by maternal mood and/or genetic variations in SLC6A4 (a gene that codes for the serotonin transporter [5-HTT] central to the regulation of synaptic serotonin levels and behavior. Children who were exposed to SRIs prenatally (SRI-exposed N=26 and non-exposed (N=38 were studied at age 6 years (M=6.3 SD=0.5 using the Hearts & Flowers task (H&F to assess EFs. Maternal mood was measured during pregnancy (3rd trimester and when the child was age 6 years (Hamilton Depression Scale. Parent reports of child behavior were also obtained (MacArthur Health & Behavior Questionnaire. Parents of prenatally SRI-exposed children reported fewer child externalizing and inattentive (ADHD behaviors. Generalized estimate equation modeling showed a significant 3-way interaction between prenatal SRI exposure, SLC6A4 variant, and maternal mood at the 6-year time-point on H&F accuracy. For prenatally SRI-exposed children, regardless of maternal mood, the H&F accuracy of children with reduced 5HTT expression (a short [S] allele remained stable. Even with increasing maternal depressive symptoms (though all below clinical threshold, EFs of children with at least one short allele were comparable to children with the same genotype whose mothers reported few if any depressive symptoms – in this sense they showed resilience. Children with two long (L alleles were more sensitive to context. When their mothers had few depressive symptoms, LL children showed extremely good EF performance – better than any other group. When their mothers reported more depressive symptoms, LL children’s EF performance was worse than that of any other group.

  14. Influences of XDH genotype by gene-gene interactions with SUCLA2 for thiopurine-induced leukopenia in Korean patients with Crohn's disease.

    Science.gov (United States)

    Park, Soo-Kyung; Hong, Myunghee; Ye, Byong Duk; Kim, Kyung-Jo; Park, Sang Hyoung; Yang, Dong-Hoon; Hwang, Sung-Wook; Kwak, Min Seob; Lee, Ho-Su; Song, Kyuyoung; Yang, Suk-Kyun

    2016-06-01

    Background The impact of genetic variation in the thiopurine S-methyltransferase (TPMT) gene on thiopurine-induced leukopenia has been well demonstrated. Although xanthine dehydrogenase (XDH) is the second major contributor to azathioprine breakdown, polymorphisms in XDH have rarely been studied in IBD patients. We aim to access association between XDH variants and thiopurine-induced leukopenia by gene-gene interaction in a Crohn's disease (CD) population. Study A total of 964 CD patients treated with thiopurines were recruited from a tertiary referral center. The association between four XDH variants (p.Gly172Arg, p.Asn1109Thr, p.Arg149Cys, and p.Thr910Lys) and thiopurine-induced leukopenia was analyzed in cases with early leukopenia (n = 66), late leukopenia (n = 264), and in controls without leukopenia (n = 632). Three non-synonymous SNPs, which we previously reported association with thiopurine-induced leukopenia, NUDT15 (p.Arg139Cys), SUCLA2 (p.Ser199Thr), and TPMT *3C were selected for epistasis analysis with the XDH variants. Results There was no significant association for two variants of XDH and thiopurine-induced leukopenia. In the epistasis analysis, only XDH (p.Asn1109Thr) * SUCLA2 (p.Ser199Thr) showed a statistically significant association with early leukopenia [odds ratio (OR) = 0.16; p = 0.03]. After genotype stratification, a positive association on the background of SUCLA2 wild-type (199Ser) between the XDH (p.Asn1109Thr) and early leukopenia (OR = 4.39; p = 0.01) was detected. Conclusion Genes associated with thiopurine-induced leukopenia can act in a complex interactive manner. Further studies are warranted to explore the mechanisms underlying the effects of the combination of XDH (p.Asn1109Thr) and SUCLA2 (199Ser) on thiopurine-induced leukopenia. PMID:26863601

  15. The Influence of Multiple Human Papillomavirus Types on the Risk of Genotype-Concordant Incident Infections of the Anus and Cervix: The Hawaii HPV Cohort Study

    OpenAIRE

    Goodman, Marc T.; McDuffie, Katharine; Hernandez, Brenda Y.; Wilkens, Lynne R.; Zhu, Xuemei; Thompson, Pamela J.; Killeen, Jeffrey; Kamemoto, Lori; Shvetsov, Yurii B.

    2011-01-01

    The influence of multiple human papillomavirus (HPV) types on detection of concordant incident HPV infections of the cervix or anus following infection at the other anatomic site was examined in a cohort of 897 women. Multiple HPV infections at the anus were not significantly associated with subsequent acquisition of a concordant cervical infection, whereas prior coinfections in the cervix increased risk of a new cervical HPV infection. Incident anal HPV infections following concordant cervic...

  16. Influence of Changing Rainfall Patterns on the Yield of Rambutan (Nephelium lappaceum L.) and Selection of Genotypes in Known Drought-tolerant Fruit Species for Climate Change Adaptation

    OpenAIRE

    Pablito M. Magdalita; Ronaldo B. Saludes

    2015-01-01

    In fruit crop production, rainfall, water stress, temperature, and wind are key variables for success, and the present changes in rainfall patterns could affect the flowering and yield of the rambutan (Nephelium lappaceum L). Other fruit species like macopa (Syzygium samarangense), siniguelas (Spondias purpurea), and native santol or cotton fruit (Sandoricum koetjape) remain productive despite extreme climatic changes. This study assessed the influence of rainfall on rambutan yield and evalua...

  17. Individual differences in emotion-cognition interactions: Emotional valence interacts with serotonin transporter genotype to influence brain systems involved in emotional reactivity and cognitive control

    OpenAIRE

    Melanie Stollstorff; Yuko Munakata; Devaney, Joseph M.

    2013-01-01

    The serotonin transporter gene (5-HTTLPR) influences emotional reactivity and attentional bias towards or away from emotional stimuli and has been implicated in psychopathological states, such as depression and anxiety disorder. The short allele is associated with increased reactivity and attention towards negatively-valenced emotional information, whereas the long allele is associated with that towards positively-valenced emotional information. The neural basis for individual differences in ...

  18. Individual differences in emotion-cognition interactions: emotional valence interacts with serotonin transporter genotype to influence brain systems involved in emotional reactivity and cognitive control

    OpenAIRE

    Stollstorff, Melanie; Munakata, Yuko; Jensen, Arielle P. C.; Guild, Ryan M.; Smolker, Harry R.; Devaney, Joseph M.; Banich, Marie T.

    2013-01-01

    The serotonin transporter gene (5-HTTLPR) influences emotional reactivity and attentional bias toward or away from emotional stimuli, and has been implicated in psychopathological states, such as depression and anxiety disorder. The short allele is associated with increased reactivity and attention toward negatively-valenced emotional information, whereas the long allele is associated with increased reactivity and attention toward positively-valenced emotional information. The neural basis fo...

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

    International Nuclear Information System (INIS)

    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

  20. Bulky carcinogen-DNA adducts and exposure to environmental and occupational sources of polycyclic aromatic hydrocarbons. Influence of susceptibility genotypes on adduct level

    Energy Technology Data Exchange (ETDEWEB)

    Sabro Nielsen, P.

    1996-12-31

    PAH exposure, whether it is of occupational or environmental origin, is thought to result in an elevated risk of cancer especially in the lungs. DNA damage is considered an important step in the carcinogenic effect of PAH. Hence, methods that elucidate the steps in the carcinogenic process are important to understand the action of PAH. It may prove useful in the exposure assessment and in combination with classical epidemiological methods give better basis for risk estimation. The objective in this thesis was to evaluate the feasibility of the {sup 32}P-postlabeling method to detect carcinogen-DNA adducts for assessing exposure to DNA damaging compounds in different occupationally and environmentally exposed groups. The studies included groups, that have an elevated cancer risk due to occupational exposure to PAH. Exposure levels were supposed to be relatively low according to reports on occupational and environmental air quality programs. Another aim was to evaluate the influence of polymorphisms in metabolizing enzyme genes on DNA adduct levels. A third objective was to establish some kind of baseline DNA adduct level for individuals with supposed low exposure, and compare it to the more exposed groups. A fourth aim in these studies was to examine if biomarkers of genotoxic exposure could be useful in epidemiological studies to identify groups at risk and thereby contribute with better exposure estimates in the study of PAH related cancer risk. (EG).

  1. Bulky carcinogen-DNA adducts and exposure to environmental and occupational sources of polycyclic aromatic hydrocarbons. Influence of susceptibility genotypes on adduct level

    International Nuclear Information System (INIS)

    PAH exposure, whether it is of occupational or environmental origin, is thought to result in an elevated risk of cancer especially in the lungs. DNA damage is considered an important step in the carcinogenic effect of PAH. Hence, methods that elucidate the steps in the carcinogenic process are important to understand the action of PAH. It may prove useful in the exposure assessment and in combination with classical epidemiological methods give better basis for risk estimation. The objective in this thesis was to evaluate the feasibility of the 32P-postlabeling method to detect carcinogen-DNA adducts for assessing exposure to DNA damaging compounds in different occupationally and environmentally exposed groups. The studies included groups, that have an elevated cancer risk due to occupational exposure to PAH. Exposure levels were supposed to be relatively low according to reports on occupational and environmental air quality programs. Another aim was to evaluate the influence of polymorphisms in metabolizing enzyme genes on DNA adduct levels. A third objective was to establish some kind of baseline DNA adduct level for individuals with supposed low exposure, and compare it to the more exposed groups. A fourth aim in these studies was to examine if biomarkers of genotoxic exposure could be useful in epidemiological studies to identify groups at risk and thereby contribute with better exposure estimates in the study of PAH related cancer risk. (EG)

  2. The influence of AVPR1A genotype on individual differences in behaviors during a mirror self-recognition task in chimpanzees (Pan troglodytes).

    Science.gov (United States)

    Mahovetz, L M; Young, L J; Hopkins, W D

    2016-06-01

    The mark/rouge test has been used to assess mirror self-recognition (MSR) in many species. Despite consistent evidence of MSR in great apes, genetic or non-genetic factors may account for the individual differences in behavioral responses that have been reported. We examined whether vasopressin receptor gene (AVPR1A) polymorphisms are associated with MSR-related behaviors in chimpanzees since vasopressin has been implicated in the development and evolution of complex social relations and cognition and chimpanzees are polymorphic for the presence of the RS3-containing DupB region. We compared a sample of DupB+/- and DupB-/- chimpanzees on a mark test to assess its role on social behavior toward a mirror. Chimpanzees were administered two, 10-min sessions where frequencies of mirror-guided self-directed behaviors, contingent actions and other social behaviors were recorded. Approximately one-third showed evidence of MSR and these individuals exhibited more mirror-guided self-exploratory behaviors and mouth contingent actions than chimpanzees not classified as passers. Moreover, DupB+/- males exhibited more scratching and agonistic behaviors than other male and female cohorts. Our findings support previous studies demonstrating individual differences in MSR abilities in chimpanzees and suggest that AVPR1A partly explains individual differences in MSR by influencing the behavioral reactions of chimpanzees in front of a mirror. PMID:27058969

  3. Sex Genotype and Sex Phenotype Contribute to Growth Differences Between Male and Female Channel Catfish

    Science.gov (United States)

    Channel catfish have an XX:XY genotypic system of sex determination, and until the present study, the influence of sex genotype on growth could not be distinguished from sex phenotype. Genotypic male fish (XY) were produced by mating normal (XX) female fish with YY male fish. A subsample from eac...

  4. Halothane genotype and pork quality. 3. Comminuted meat products derived from the three halothane genotypes.

    Science.gov (United States)

    Fisher, P; Mellett, F D; Hoffman, L C

    2000-02-01

    The effect of the halothane gene on cured meat products was investigated using the meat from 60 Landrace×Large White pigs of known halothane genotype (NN=25, Nn=19, nn=16). Results for the two types of fresh sausage manufactured (with and without rusk) indicated that the NN pigs (15.7%) had lower total moisture losses (Psausage without rusk. Where rusk was added, there were no significant differences between genotypes for moisture losses (NN=12.6%, Nn=13. 0%, nn=14.2%). Taste panel evaluations of the fresh sausages made without rusk indicated no genotypic influence for juiciness, however the sausage made with the rusk was judged the juiciest for the nn genotype, with Nn being intermediate and NN the least juiciest. The smoking and cooking losses during manufacturing of the emulsion product (vienna) indicated that the nn genotype (12.5%) had significantly (P<0.05) higher total losses than the Nn genotype (11. 3%), with NN being intermediate (12.4%). PMID:22060606

  5. 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 Nygaard, Louise; Astvad, Karen; Ladelund, Steen; Larsen, Mette Vang; Schønning, Kristian; Benfield, Thomas

    2012-01-01

    : We hypothesized that hepatitis C virus (HCV) load and genotype may influence all-cause mortality in HIV-HCV-coinfected individuals.......: We hypothesized that hepatitis C virus (HCV) load and genotype may influence all-cause mortality in HIV-HCV-coinfected individuals....

  6. Rhizosphere properties of rice genotypes as influenced by anoxia and availability of zinc and iron Propriedades da rizosfera de genótipos de arroz submetidos à anoxia e a diferentes disponibilidades de zinco e ferro

    OpenAIRE

    Roghieh Hajiboland; Naier Beiramzadeh

    2008-01-01

    The objective of this work was to study possible mechanisms involved in root-induced changes of rhizosphere physicochemical properties of rice genotypes, under anoxia and low supply of Zn and Fe. Two rice genotypes, including an upland and a lowland ones, were grown in hydroponic medium under adequate and low supply of Zn and Fe, with or without aeration. Anoxia increased shoot dry weight, root length and uptake of Zn and Fe in lowland Amol genotype, but reduced these parameters in upland Gas...

  7. Predictors of hepatitis B virus genotype and viraemia in HIV-infected patients with chronic hepatitis B in Europe

    DEFF Research Database (Denmark)

    Soriano, Vincent; Mocroft, Amanda; Peters, Lars; Rockstroh, Juergen; Antunes, Francisco; Kirkby, Nikolai; de Wit, Stephane; Monforte, Antonella d'Arminio; Flisiak, Robert; Lundgren, Jens

    2010-01-01

    Both natural history and treatment outcome of hepatitis B virus (HBV) infection are influenced by genotypes and viral load. Information about factors determining HBV genotype distribution and viraemia in HIV/HBV-co-infected patients is scarce....

  8. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

    the ultimate source of the virus's genetic diversity. HCV circulates as a heterogeneous population of genetically different but closely related genomes known as the quasispecies(15.As only 30-35% of nucleotides actually differ, there is obviously considerable heterogeneity in evolutionary rates among nucleotide sites in the genome. This heterogeneity is the result of variable evolutionary constraints. The 5'-UTR contains extensive secondary RNA structure and is correspondingly the slowest evolving genomic region(16. The next slowest region is the C (Core gene, which evolves three times faster than the 5'- UTR. The envelope genes E1 and E2 constitute the most diverse genome region and evolve about nine times faster than the 5'-UTR(16, probably as a result of their presumed role in evading the host immune response. Genomic Heterogeneity and ClassificationSystemsShortly after its discovery in 1989, it became clear that HCV had substantial nucleotide sequence diversity, with only 66 to 80% overall sequencesimilarity among strains belonging to different genotypes or subtypes(17. HCV isolates show four levels of genomic variations: types, subtypes, isolates, andquasispecies. The overall sequence similarities over complete genomic sequences are at least 91% within quasispecies, approximately 79% (range, 77 to 80% between subtypes, and about 68% (range, 66 to 69% between different types. This quasispecies is composed of a group of heterogeneous RNA sequences centered around a dominant nucleotide sequence that changes, throughout the course of the infection, under the selective pressure of the host immune system(18. More than one genotype can be found in the circulations of some HCV-infected patients, particularly in individuals who have received multiple transfusions and intravenous drug users. These are referred to as mixed-genotype infections(19, 20.The lack of a routinely available cell culture system and an easily available animal model has rendered classification of HCV

  9. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons for this is the...... availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  10. Influence of Genotype over Microtubers Production

    Directory of Open Access Journals (Sweden)

    Andreea NISTOR

    2010-06-01

    Full Text Available In vitro microtuberization represents the transitory phase of in vitro multiplication of a healthy material and on field multiplication. Microtubers production is an efficient method for obtaining a healthy material, thus leading to a reduction of the potato production process with 3-4 years. The microtubers of Romanian varieties were obtained from potato micro-cuttings cultured on Murashige-Skoog medium enriched with Cumarin and Kinetin. Sucrose was found to be the most important stimulus for inducing the microtubers. The cultures were maintained in darkness, at 18-20°C for 8-10 weeks for inducing and growing microtubers. The microtubers are important as they can be produced at any time of the year, they are easy to be transported and deposited.

  11. Influence of Genotype over Microtubers Production

    OpenAIRE

    Andreea NISTOR; Gheorghe CAMPEANU; Nicolae ATANASIU; Nicoleta CHIRU; Diana KARÁCSONYI

    2010-01-01

    In vitro microtuberization represents the transitory phase of in vitro multiplication of a healthy material and on field multiplication. Microtubers production is an efficient method for obtaining a healthy material, thus leading to a reduction of the potato production process with 3-4 years. The microtubers of Romanian varieties were obtained from potato micro-cuttings cultured on Murashige-Skoog medium enriched with Cumarin and Kinetin. Sucrose was found to be the most important stimulus fo...

  12. Differential efficacy of protease inhibitors against HCV genotypes 2a, 3a, 5a, and 6a NS3/4A protease recombinant viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Scheel, Troels K H; Jensen, Tanja B; Ghanem, Lubna; Bukh, Jens

    2011-01-01

    The hepatitis C virus (HCV) genotype influences efficacy of interferon (IFN)-based therapy. HCV protease inhibitors are being licensed for treatment of genotype 1 infection. Because there are limited or no data on efficacy against HCV genotypes 2-7, we aimed at developing recombinant infectious...... cell culture systems expressing genotype-specific nonstructural (NS) protein 3 protease (NS3P)....

  13. Gender influence on treatment of chronic hepatitis C genotype 1 Influência do gênero no tratamento da hepatite C crônica genótipo 1

    Directory of Open Access Journals (Sweden)

    Janaína Luz Narciso-Schiavon

    2010-06-01

    Full Text Available INTRODUCTION: Although various studies have been published regarding the treatment of chronic hepatitis C (CHC with peginterferon (Peg-IFN and ribavirin, little is known regarding the real impact of gender on the characteristics that influence the effectiveness and safety of antiviral treatment for CHC patients. The objective of this study was to evaluate the influence of gender on HCV treatment outcomes. METHODS: A retrospective analytical study was conducted among selected carriers of CHC genotype 1, who were treated with Peg-IFN α-2b at a dose of 1.5 μg/kg or Peg-IFN α-2a at a dose of 180 μg/week plus a ribavirin dose of 1,000-1,250 mg/day, according to weight, between 2001 and 2007. RESULTS: Among 181 patients undergoing treatment, the mean age was 46.4 ± 11.0 years and 46% were women. At baseline, 32% of the patients had advanced fibrosis (F3-F4 Scheuer, and 83% of the subjects had viral load > 400,000 IU/ml, without significant difference between the genders (p = 0.428 and p = 0.452, respectively. When compared with men, women had higher incidence of many adverse events such as anemia (p INTRODUÇÃO: Apesar dos vários estudos publicados a respeito do tratamento da hepatite C crônica (CHC com Peg-Interferon (Peg-IFN e ribavirina, se desconhece o real impacto do gênero sobre as características que influenciam a eficácia e a segurança da terapia antiviral em portadores de CHC. O objetivo deste estudo foi avaliar a influência do gênero no tratamento da CHC. MÉTODOS: Foi realizado um estudo analítico retrospectivo de portadores de CHC genótipo 1 tratados com Peg-IFN α-2b na dose de 1,5μg/kg ou Peg-IFN α-2a na dose de180μg/sem associado à ribavirina 1.000-1.250 mg/dia, de acordo com o peso, entre 2001 e 2007. RESULTADOS: Entre 181 pacientes submetidos ao tratamento, a média de idade foi de 46,4±11,0 anos e 46% eram mulheres. No pré-tratamento, 32% dos pacientes apresentavam fibrose avançada (F3-F4 Scheuer, e 83% dos

  14. Noise in Genotype Selection Model

    Institute of Scientific and Technical Information of China (English)

    AI Bao-Quan; CHEN Wei; WANG Xian-Ju; LIU Guo-Tao; WEN De-Hua; LIU Liang-Gang

    2003-01-01

    We study the steady state properties ofa genotype selection model in presence of correlated Gaussian whitenoise. The effect of the noise on the genotype selection model is discussed. It is found that correlated noise can breakthe balance of gene selection and induce the phase transition which can makes us select one type gene haploid from agene group.

  15. Chemical composition, dietary fibre, tannins and minerals of grain amaranth genotypes.

    Science.gov (United States)

    Mustafa, Arif F; Seguin, Philippe; Gélinas, Bruce

    2011-11-01

    The objective of this study was to determine the chemical composition of 28 white and coloured grain amaranth (Amaranthus spp.) genotypes. Neutral detergent fibre (NDF) concentration was greater while strach concentration was lower for coloured seeds genotypes than white seeds genotypes. Total dietary fibre followed a similar trend to that observed for NDF. Total tannin concentrations ranged between 20.7 and 0 g/kg with total and hydrolysed tannin concentrations being higher for white than for coloured seeds genotypes. Coloured seeds genotypes contained higher Mg and Ca concentrations than white seeds genotypes. However, seed colour had no influence on K, Na and P concentrations. Copper and Fe were the most variable micro-minerals in the evaluated genotypes with no significant effect of seed colour on the concentration of either mineral. PMID:21599462

  16. Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies

    OpenAIRE

    Li, Jing; Du, Yun; Liu, Xian; Shen, Qian-cheng; Huang, Ai-Long; Zheng, Ming-Yue; Luo, Xiao-Min; Jiang, Hua-liang

    2012-01-01

    Aim: To investigate the molecular mechanisms underlying the influence of DNA polymerase from different genotypes of hepatitis B virus (HBV) on the binding affinity of adefovir (ADV). Methods: Computational approaches, including homology modeling, docking, MD simulation and MM/PBSA free energy analyses were used. Results: Sequence analyses revealed that residue 238 near the binding pocket was not only a polymorphic site but also a genotype-specific site (His238 in genotype B; Asn238 in genotyp...

  17. Personal genotypes are teachable moments

    OpenAIRE

    Boguski, Mark S.; Boguski, Robert M; Berman, Michele R

    2013-01-01

    There is an urgent need for effective genomics education for healthcare professionals. Recent analysis of an experimental genomics curriculum showed that medical students' examinations of their own genotypes provide a valuable learning experience. Such experiential learning has a long tradition in medical education and its application to genomics is enabled by increasingly powerful and decreasingly costly genome science and technology. Personal genotyping is an important option to consider wh...

  18. Current software for genotype imputation

    OpenAIRE

    Ellinghaus David; Schreiber Stefan; Franke Andre; Nothnagel Michael

    2009-01-01

    Abstract Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputa...

  19. The vigour of glasshouse roses. Scion rootstock relationships, effects of phenotypic & genotypic variation.

    NARCIS (Netherlands)

    Vries, de D.P.

    1993-01-01

    Glasshouse roses commonly are combination plants, consisting of a scion variety and a rootstock of different genotypes. In this study, various environmental and genotypic factors have been investigated that influence the vigour of rootstocks and scion varieties, separately and in graft combination.I

  20. 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.

  1. Effects of plant genotype and insect dispersal rate on the population dynamics of a forest pest.

    Science.gov (United States)

    Moran, Emily V; Bewick, Sharon; Cobbold, Christina A

    2013-12-01

    It has been shown that plant genotype can strongly affect not only individual herbivore performance, but also community composition and ecosystem function. Few studies, however, have addressed how plant genotype affects herbivore population dynamics. In this paper, we used a simulation modeling approach to ask how the genetic composition of a forest influences pest outbreak dynamics, using the example of aspen (Populus tremuloides) and forest tent caterpillars (FTC; Malacosoma disstria). Specifically, we examined how plant genotype, the relative size of genotypic patches, and the rate of insect dispersal between them, affect the frequency, amplitude, and duration of outbreaks. We found that coupling two different genotypes does not necessarily result in an averaging of insect dynamics. Instead, depending on the ratio of patch sizes, when dispersal rates are moderate, outbreaks in the two-genotype case may be more or less severe than in forests of either genotype alone. Thresholds for different dynamic behaviors were similar for all genotypic combinations. Thus, the qualitative behavior of a stand of two different genotypes can be predicted based on the response of the insect to each genotype, the relative sizes of the two patches, and the scale of insect dispersal. PMID:24597225

  2. Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes.

    Science.gov (United States)

    Davies, Chantel; Ellis, Christopher J; Iason, Glenn R; Ennos, Richard A

    2014-01-01

    Community genetics hypothesizes that within a foundation species, the genotype of an individual significantly influences the assemblage of dependent organisms. To assess whether these intra-specific genetic effects are ecologically important, it is required to compare their impact on dependent organisms with that attributable to environmental variation experienced over relevant spatial scales. We assessed bark epiphytes on 27 aspen (Populus tremula L.) genotypes grown in a randomized experimental array at two contrasting sites spanning the environmental conditions from which the aspen genotypes were collected. We found that variation in aspen genotype significantly influenced bark epiphyte community composition, and to the same degree as environmental variation between the test sites. We conclude that maintaining genotypic diversity of foundation species may be crucial for conservation of associated biodiversity. PMID:24789141

  3. Cerebral Hemorrhage and APOE genotype

    Institute of Scientific and Technical Information of China (English)

    Sun xiaojiang; Wu ping; Zhang jing; Lu shanqing; Li bing

    2000-01-01

    Background and Purpose: Current evidence Suggests that the apolipoprotein E (APOE)ε 4 allele predisposes to cerebral amyloid angiopathy (CAA) whereas ε 2 is associated with CAA-zelated hemorrhage. In this study we examined potential clinical risk factors inpatients with cerebral hemorrhage and assessed these with respect to APOE genotype. Methoeds: 146 patinas with cerebral hemorrhage and 70 normal controls were investigated. APOE genotypes were determined with use of polymerase Chain reaction techniques.Results: The frequency of allele gene ( 0.180 ) and the percentage of the APOE ε 4 genotype in the cerebral hemorrhage group were Significantly higher as compared with the e 4 prequency ( O.O72 ) in the control group respectively ( p=O.O389 ) .Conelusious: APOE ε 4 :allele is a risk gene for cerebral hemorrhage.

  4. Research Status Quo and Future of Low Temperature Wheat Genotypes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Low temperature wheat genotypes are a group of wheat with a slightly low canopy (plant) temperature, and the research on their biological characters and utilization in wheat breeding has been done at home and abroad for more than 20 years, and has made great progress. The research contents and advances include the following respects: Wheat genotypes with slightly low canopy temperature have been verified to exist in nature; these wheat genotypes, which present cold temperature, are superior to conventional wheat materials in some important biological characters and particularly prominently in metabolic function and cellular structure; when they suffer stresses such as drought, high temperature and overcast and rainy weather, they still retain their superiority in some of their important biological characters and therefore have a wide range of ecological adaptability; slightly low canopy temperatures of these genotypes are closely correlated with low temperatures of their second heat sources and their vigorous plants; since their low canopy temperatures can be inherited, they can exert favorable influence on the temperatures of their offspring while crossing with other wheat materials, and in particular, the discovery of cold-source wheat as a contributor to low temperature, has further formed good conditions for breeding high and stable quality low temperature wheat varieties with a high and stable yield. Thus, low temperature wheat genotypes are of great research importance and have great prospects.

  5. 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.

  6. Genotypic and Phenotypic Characterization of Chikungunya Virus of Different Genotypes from Malaysia

    Science.gov (United States)

    Sam, I-Ching; Loong, Shih-Keng; Michael, Jasmine Chandramathi; Chua, Chong-Long; Wan Sulaiman, Wan Yusoff; Vythilingam, Indra; Chan, Shie-Yien; Chiam, Chun-Wei; Yeong, Yze-Shiuan; AbuBakar, Sazaly; Chan, Yoke-Fun

    2012-01-01

    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. PMID:23209750

  7. Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon.

    Science.gov (United States)

    Pasquier, Christophe; Njouom, Richard; Ayouba, Ahidjo; Dubois, Martine; Sartre, Michèle Tagni; Vessière, Aurelia; Timba, Isabelle; Thonnon, Jocelyn; Izopet, Jacques; Nerrienet, Eric

    2005-11-01

    Hepatitis C virus infects humans world-wide. The virus genome varies greatly and it has several genotypes. HCV infection is highly prevalent in Central Africa and Cameroon. Initial studies on the genetic variability of HCV showed infection with HCV genotypes 1, 2, and 4. We have now sequenced the NS5b and E2 regions of 156 HCV isolates collected from patients presenting for diagnosis in Yaounde and used the data to describe the distribution of HCV genotypes and subtypes in patients with hepatitis in Cameroon. Genotype 1 was more frequent than Genotypes 4 and 2. Genotypes 1 and 4 were highly heterogeneous, containing many subtypes described previously (1b, 1c, 1e, 1h, 1l, 4f, 4t, 4p, 4k) and unsubtyped groups. There was a systematic phylogenetic concordance between NS5b and E2 sequence clustering. The Genotype 2 sequences did not vary. Neither subject age nor gender influenced HCV distribution. HCV Genotypes 1 and 4 are very heterogeneous in Cameroon, perhaps due to ancient infections. The homogeneity of HCV Genotype 2 indicates its more recent introduction from western Africa. PMID:16173014

  8. Testing GxG interactions between coinfecting microbial parasite genotypes within hosts

    Directory of Open Access Journals (Sweden)

    Rebecca D Schulte

    2014-05-01

    Full Text Available Host-parasite interactions represent one of the strongest selection pressures in nature. They are often governed by genotype-specific (GxG interactions resulting in host genotypes that differ in resistance and parasite genotypes that differ in virulence depending on the antagonist’s genotype. Another type of GxG interactions, which is often neglected but which certainly influences host-parasite interactions, are those between coinfecting parasite genotypes. Mechanistically, within-host parasite interactions may range from competition for limited host resources to cooperation for more efficient host exploitation. The exact type of interaction, i.e. whether competitive or cooperative, is known to affect life-history traits such as virulence. However, the latter has been shown for chosen genotype combinations only, not considering whether the specific genotype combination per se may influence the interaction (i.e. GxG interactions. Here, we want to test for the presence of GxG interactions between coinfections of the bacterium Bacillus thuringiensis infecting the nematode Caenorhabditis elegans by combining two non-pathogenic and five pathogenic strains in all possible ways. Furthermore, we evaluate whether the type of interaction, reflected by the direction of virulence change of multiple compared to single infections, is genotype-specific. Generally, we found no indication for GxG interactions between non-pathogenic and pathogenic bacterial strains, indicating that virulence of pathogenic strains is equally affected by both non-pathogenic strains. Specific genotype combinations, however, differ in the strength of virulence change, indicating that the interaction type between coinfecting parasite strains and thus the virulence mechanism is specific for different genotype combinations. Such interactions are expected to influence host-parasite interactions and to have strong implications for coevolution.

  9. ACTN3 genotype in Spanish elite swimmers: no "heterozygous advantage".

    Science.gov (United States)

    Ruiz, J R; Santiago, C; Yvert, T; Muniesa, C; Díaz-Ureña, G; Bekendam, N; Fiuza-Luces, C; Gómez-Gallego, F; Femia, P; Lucia, A

    2013-06-01

    The aim of the present case-control study was to examine the association of the ACTN3 R577X genotype with elite swimming status. We compared a group of Spanish (Caucasian) elite swimmers (n = 88) with other cohorts of the same ethnic origin, i.e., nonathletic controls (n = 343) and other types of athletes who are in both end-points of the sports performance continuum, i.e., world-class power (n = 119) and endurance male athletes (n = 154). Swimmers had a lower odds ratio (OR) of having the RX genotype [1.815, 95% confidence intervals (CI): 0.899-3.664] compared with nonathletic controls, yet the association did not reach statistical significance (P = 0.096). Endurance athletes had greater OR of having the XX genotype (OR: 2.88, 95% CI: 1.162-7.135, P = 0.022), or the RX+XX genotype (OR: 1.903, 95% CI: 1.015-3.567, P = 0.045) compared with swimmers. No other association was found. In summary, we did not observe an association between the ACTN3 R577X polymorphism and elite swimmer's status, suggesting that any influence of this polymorphism is not of sufficient magnitude as to significantly influence elite swimming performance, at least in Spanish athletes. PMID:23317015

  10. 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.

  11. HLA-DRB1 genotypes and the risk of developing anti citrullinated protein antibody (ACPA positive rheumatoid arthritis.

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    Nathalie Balandraud

    Full Text Available OBJECTIVE: To provide a table indicating the risk for developing anti citrullinated protein antibody (ACPA positive rheumatoid arthritis (RA according to one's HLA-DRB1 genotype. METHODS: We HLA-DRB1 genotyped 857 patients with ACPA positive RA and 2178 controls from South Eastern and Eastern France and calculated Odds Ratios (OR for developing RA for 106 of 132 possible genotypes accounting for 97% of subjects. RESULTS: HLA-DRB1 genotypic ORs for developing ACPA positive RA range from 28 to 0.19. HLA-DRB1 genotypes with HLA-DRB1*04SE (HLA-DRB1*0404, HLA-DRB1*0405, HLA-DRB1*0408, HLA-DRB1*04∶01, HLA-DRB1*01 are usually associated with high risk for developing RA. The second HLA-DRB1 allele in genotype somewhat modulates shared epitope associated risk. We did not identify any absolutely protective allele. Neither the Reviron, nor the du Montcel models accurately explains our data which are compatible with the shared epitope hypothesis and suggest a dosage effect among shared epitope positive HLA-DRB1 alleles, double dose genotypes carrying higher ORs than single dose genotypes. CONCLUSION: HLA-DRB1 genotypic risk for developing ACPA positive RA is influenced by both HLA-DRB1 alleles in genotype. We provide an HLA-DRB1 genotypic risk table for ACPA positive RA.

  12. Selection of common bean (Phaseolus vulgaris L.) genotypes using a genotype plus genotype x environment interaction biplot.

    Science.gov (United States)

    Corrêa, A M; Teodoro, P E; Gonçalves, M C; Santos, A; Torres, F E

    2016-01-01

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability. PMID:27525915

  13. Phosphorus Use Efficiency by Brazilian Common Bean Genotypes Assessed by the 32P Dilution Technique

    International Nuclear Information System (INIS)

    The objectives of this work were to identify the most efficient common bean (Phaseolus vulgaris L.) genotypes on phosphorus (P) utilization, and verify if P from the seed affects the classification of common bean genotypes on P uptake efficiency when the 32P isotopic dilution technique is used. The experiment was conducted in a greenhouse, and plants were grown in pots with surface samples of a dystrophic Typic Haplustox. The treatments consisted of 50 common bean genotypes and two standard plant species, efficient or inefficient in P uptake. The results were assessed through correlation and cluster analysis (multivariate). Sangue de Boi, Rosinha, Thayu, Grafite, Horizonte, Pioneiro and Jalo Precoce common bean genotypes were the most efficient on P uptake, and Carioca 80, CNF 10, Perola, IAPAR 31, Roxao EEP, Apore, Pioneiro, Pontal, Timbo and Ruda were the most efficient in P utilization. The P derived from seed influences the identification of common bean genotypes for P uptake efficiency. (author)

  14. Phosphorus Use Efficiency by Brazilian Upland Rice Genotypes Evaluated by the 32P Dilution Technique

    International Nuclear Information System (INIS)

    The objectives of this work were to identify the most efficient upland rice genotypes in phosphorus (P) utilization, and to verify if P from the seed affects the classification of upland rice genotypes on P uptake efficiency. The experiment was conducted in a greenhouse of the Center for Nuclear Energy in Agriculture (CENA/USP), Piracicaba, Sao Paulo, Brazil, using the 32P isotope technique, and plants were grown in pots with samples of dystrophic Typic Haplustox (Oxisol). The experimental design was completely randomized with four replications. The treatments consisted of 47 upland rice genotypes and two standard plant species, efficient or inefficient in P uptake. The results were assessed through correlation and cluster analysis (multivariate). The Carisma upland rice genotype was the most efficient in P uptake, and Caripuna was the most efficient on P utilization. The P derived from seed does not influence the identification of upland rice genotypes in P uptake efficiency. (author)

  15. Influência do ambiente no rendimento e na qualidade de grãos de genótipos de trigo com irrigação por aspersão no Estado de São Paulo Environmental influence on grain yield and grain quality of wheat genotypes with sprinkler irrigation in the State of São paulo, Brazil

    Directory of Open Access Journals (Sweden)

    JOÃO CARLOS FELICIO

    2001-01-01

    Full Text Available Avaliaram-se a influência do ambiente em 20 genótipos de trigo, no rendimento e qualidade de grãos, a adaptabilidade e a reação a doenças, em regiões onde a irrigação se faz necessária para permitir o bom desempenho agronômico de um genótipo. Instalaram-se os experimentos em Tatuí, Votuporanga, Ribeirão Preto e Mococa, Estado de São Paulo, no período de 1995-98. Avaliaram-se, também, a tolerância dos genótipos ao alumínio tóxico em solução nutritiva e a qualidade industrial para panificação. Com bom rendimento de grãos destacaram-se: em Tatuí, os genótipos IAC 351, IAC 335, IAC 289 e Mochis; em Votuporanga, IAC 289, TUI"S" e SERI*3/BUC; em Ribeirão Preto e Mococa, o IAC 370. No conceito de genótipo ideal, o IAC 370 apresentou alta capacidade produtiva, foi responsivo à melhoria do ambiente e sensível às condições desfavoráveis do ambiente. Entre as doenças, a ferrugem-da-folha foi a de abrangência generalizada com maior incidência em Tatuí. Anahuac, IAC 287, CAL/CHKW//VEE"S" e IAC 370 foram os mais suscetíveis ao oídio. Os genótipos Anahuac, IAC 287, JCAM//EMU"S"/YACO"S", PFAU e IAC 339 foram os mais sensíveis à toxicidade por Al3+. Os genótipos Anahuac, IAC 24, IAC 287, IAC 289, IAC 334, PFAU, TUI"S", IAC 339, IAC 370 e IAC 351 apresentaram características de farinha com bom potencial para panificação.Environmental influence was evaluated in 20 wheat genotypes in relation to grain yield and quality, adaptability and disease reaction in regions where irrigation is necessary for good agronomical performance. The experiments were carried out at Tatuí, Votuporanga, Ribeirão Preto, and Mococa in the State of São Paulo, Brazil, during 1995-98. Genotypes were also evaluated for tolerance to aluminum toxicity in nutrient solutions and for industrial quality for bread production. The genotypes IAC 351, IAC 335, IAC 289 and Mochis presented high grain yield in Tatuí; IAC 289, TUI"S" and SERI*3/BUC in

  16. Current software for genotype imputation

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    Ellinghaus David

    2009-07-01

    Full Text Available Abstract Genotype imputation for single nucleotide polymorphisms (SNPs has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations.

  17. ACTN3 GENOTYPE IS ASSOCIATED WITH TESTOSTERONE LEVELS OF ATHLETES

    OpenAIRE

    2014-01-01

    α-Actinin-3 (ACTN3) has been proposed to regulate skeletal muscle differentiation and hypertrophy through its interaction with the signalling protein calcineurin. Since the inhibition of calcineurin potentiates the production of testosterone, we hypothesized that α-actinin-3 deficiency (predicted from the ACTN3 XX genotype) may influence serum levels of testosterone of athletes. Objective: To investigate the association of ACTN3 gene R577X polymorphism with resting testosterone levels in athl...

  18. Inter-varietal interactions among plants in genotypically diverse mixtures tend to decrease herbivore performance.

    Science.gov (United States)

    Grettenberger, Ian M; Tooker, John F

    2016-09-01

    Much research has explored the effects of plant species diversity on herbivore populations, but far less has considered effects of plant genotypic diversity, or how abiotic stressors, like drought, can modify effects. Mechanisms by which plant genotypic diversity affects herbivore populations remain largely unresolved. We used greenhouse studies with a model system of wheat (Triticum aestivum L.) and bird cherry-oat aphid (Rhopalosiphum padi L.) to determine whether the genotypic diversity of a plant's neighborhood influences performance and fitness of herbivores on a focal plant and if drought changes the influence of neighborhood diversity. Taken across all varieties we tested, plant-plant interactions in diverse neighborhoods reduced aphid performance and generated associational resistance, although effects on aphids depended on variety identity. In diverse mixtures, drought stress greatly diminished the genotypic diversity-driven reduction in aphid performance. Neighborhood diversity influenced mother aphid size, and appeared to partially explain how plant-plant interactions reduced the number of offspring produced in mixtures. Plant size did not mediate effects on aphid performance, although neighborhood diversity reduced plant mass across varieties and watering treatments. Our results suggest inter-varietal interactions in genotypic mixtures can affect herbivore performance in the absence of herbivore movement and that abiotic stress may diminish any effects. Accounting for how neighborhood diversity influences resistance of an individual plant to herbivores will help aid development of mixtures of varieties for managing insect pests and clarify the role of plant genotypic diversity in ecosystems. PMID:27170329

  19. Yield stability in bread wheat genotypes

    International Nuclear Information System (INIS)

    Stability for grain yield performance and genotype x environment (GxE) interaction was studied in twelve (nine advance genotypes and 3 checks) wheat genotypes evaluated at various locations having different agro-climatic conditions in Sindh province of Pakistan over two years. The combined and individual analysis of variance for locations and years was conducted. Pooled analysis of variance revealed highly significant (p<0.01) difference for genotypes, environments and genotype x environment (GxE) interaction. A joint regression analysis was applied to grain yield data to estimate the stability parameters viz., regression coefficient (b), s.e. (b) and deviation from regression coefficients (S2d) for each genotype. Genotype MSH-14 produced the highest mean yield (5090 kg/ha) in all environments averaged for two years, and had regression coefficient (b) close to unity (0.86) and S2d close to zero (0.7923). This indicated wide adaptation and stability of performance of MSH-14 in all environments. Other high yielding genotypes MSH-03 and MSH-05 ranked second and third showing regression coefficient (b=0.78 and 0.69 respectively) and deviation from regression (S2d= 1.076 and 1.29 respectively) indicating specific adaptability of these genotypes to harsh (un favorable) environments. These findings suggested that both the genotypes could be used as stress tolerant genotypes under stressed environments (such as drought, heat and salinity stress). (author)

  20. Progress in genotyping of Chlamydia trachomatis

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Xiong Likuan

    2014-01-01

    Objective To review the common genotyping techniques of Chlamydia trachomatis in terms of their principles,characteristics,applications and limitations.Data sources Data used in this review were mainly from English literatures of PubMed database.The search terms were "Chlamydia trachomatis" and "genotyping".Meanwhile,data from World Health Organization were also cited.Study selection Original articles and reviews relevant to present review's theme were selected.Results Different genotyping techniques were applied on different occasions according to their characteristics,especially in epidemiological studies worldwide,which pushed the study of Chlamydia trachomatis forward greatly.In addition,summaries of some epidemiological studies by genotyping were also included in this work for reference and comparison.Conclusions A clear understanding of common genotyping techniques could be helpful to genotype C.trachomatis more appropriately and effectively.Furthermore,more studies on the association of genotypes of Ch/amydia trachomatis with clinical manifestations should be performed.

  1. The Correlation of Il28B Genotype With Sustained Virologic Response In Romanian patients With Chronic Hepatitis C

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    Ioan Sporea

    2011-12-01

    Full Text Available Background: Multiple variables influencing the sustained virologic response (SVR in chronic hepatitis C have been evaluated. One of them is genetic polymorphism near the IL28B gene.Objectives: The aim of this study was to evaluate the influence of IL28B genotypes on SVR rates in a group of patients with chronic hepatitis C from the western part of Romania.Patients and Methods: A retrospective study was performed in 107 consecutive patients, previously treated with standard-of-care medication for chronic hepatitis C, identified from the databases of 2 centers. Patient demographics, viral load before treatment and at 12, 24, and 72 weeks from the treatment start, and IL28B genotype were evaluated.Results: Among the 107 patents in the study group, 54 patients had SVR (50.5%, and 62 (57.9% showed a complete early virologic response (cEVR. The SVR rates according to IL28B genotype were as follows: 73.1% in patients with genotype C/C, 40.9% in those with genotype C/T, and 57.1% in those with genotype T/T (i.e., 73.1% among patients with the C/C genotype vs. 43.7% among those with non-C/C genotypes; P = 0.0126. The cEVR rates were 80.8% in patients with the C/C genotype vs. 51.2% in those with non-C/C genotypes (P = 0.011.Conclusions: In our cohort of 107 Caucasian HCV patients, the SVR rate was 50.5% with standard-of-care treatment. The SVR rate was directly related to the IL28B genotype: 73.1% in the C/C genotype vs. 43.7% in non-C/C genotypes (P = 0.0126.

  2. Does copper reduce cadmium uptake by different rice genotypes?

    Institute of Scientific and Technical Information of China (English)

    CUI Yujing; ZHANG Xuhong; ZHU Yongguan

    2008-01-01

    A hydroponics experiment was conducted to investigate the effect of copper (Cu) on cadmium (Cd),calcium (Ca),iron (Fe),and zinc (Zn) uptake by several rice genotypes.The experiment was carried out as a 2×2×4 factorial with four rice genotypes and two levels of Cu and Cd in nutrient solution.Plants were grown in a growth chamber with controlled environment.The results showed a significant difference between the biomass of different rice genotypes (P<0.001).The Cd and Cu concentration in the solution had no significant effect on the biomass.The addition of Cu significantly decreased Cd uptake by shoots and roots of rice (P<0.001).The Cd concentration did not significantly influence Ca uptake by plants,whereas the Cu concentration did (P=0.034).There was a significant influence of Cd on Fe uptake by shoots and roots (P<0.001,P=0.003,respectively).Zn uptake decreased significantly as the addition of Cd and Cu increased in shoots.We concluded that Cu had significant influence on Cd uptake.The possible mechanisms were discussed.

  3. The relative importance of trait vs. genetic differentiation for the outcome of interactions among plant genotypes.

    Science.gov (United States)

    Abbott, Jessica M; Stachowicz, John J

    2016-01-01

    Functional trait differences and genetic distance are increasingly used as metrics to predict the. outcome of species interactions and the maintenance of diversity. We apply these ideas to intraspecific diversity for the seagrass Zostera marina (eelgrass), by explicitly testing the influence of trait distance and genetic relatedness on the outcome of pairwise interactions among eelgrass genotypes. Increasing trait distance (but not relatedness) between eelgrass genotypes decreased the likelihood that both would persist over a year-long field experiment, contrary to our expectations based on niche partitioning. In plots in which one genotype excluded another, the biomass and growth of the remaining genotype increased with the trait distance and genetic relatedness of the initial pair, presumably due to a legacy of past interactions. Together these results suggest that sustained competition among functionally similar genotypes did not produce a clear winner, but rapid exclusion occurred among genotypes with distinct trait combinations. Borrowing from coexistence theory, we argue that fitness differences between genotypes with distinct traits overwhelmed any stabilizing effects of niche differentiation. Previously observed effects of eelgrass genetic diversity on performance may rely on nonadditive interactions among multiple genotypes or sufficient environmental heterogeneity to increase stabilizing forces and/or interactions. PMID:27008778

  4. Variability of leaf characteristics in different pedunculate oak genotypes (Ouercus robur L

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    Nikolić Nataša P.

    2006-01-01

    Full Text Available The objective of this study was to determine genotype influences on pedunculate oak's leaf traits: leaf area, specific leaf area (leaf area per unit of leaf mass, concentration of photosynthetic pigments, rates of photosynthesis and respiration, and nutrient concentrations (nitrogen phosphorus, potassium, calcium, and sodium. Leaf samples were taken from seventeen Q. robur genotypes originating from clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Leaf area of the studied genotypes ranged from 248.4 to 628.8 cm2, SLA from 109.4 to 160.7 cm2 dry matter-1, rates of photosynthesis and respiration from 6.98 to 20.32 and from 6.73 to 14.65 µmol O2 m-2 s-1, respectively. The leaves of genotype 35 contained the highest concentration of photosynthetic pigments, while the lowest were recorded in genotype 29. The following pattern of nutrient concentrations was obtained for the studied genotypes: N>Ca>K>P>Na. Genotype variability of P K, Ca, and Na concentrations was more pronounced when compared with nitrogen. Estimated quantitative differences are the consequence of interaction of certain genotype and common environmental conditions for all trees. These results will provide information on intraspecific variation of the studied leaf characteristics.

  5. Association of adiponectin genotype polymorphisms at positions 45 and 276 with obstructive sleep apnea hypopnea syndrome

    Institute of Scientific and Technical Information of China (English)

    Mei Su; Xilong Zhang; Shicheng Su

    2009-01-01

    Objective: To investigate the relationship between adiponectin genotype polymorphisms and obstructive sleep apnea hypopnea syndrome (OSAHS). Methods: Using the TaqMan polymerase chain reaction(PCR) method, the single nucleotide polymorphisms(SNP)at positions 45 and 276 in the adiponectin gene were determined in Chinese of the Han nationality in the Nanjing district. The OSAHS group consisted of 78 patients, and the control group contained 40 subjects. The association of adiponectin genotype polymorphisms at positions 45 and 276 with obstructive sleep apnea hypopnea syndrome was analyzed. Results: No evidence of a direct association was found between OSAHS and adiponectin genotype SNP at positions 45 and 276(P> 0.05). However, compared with those OSAHS patients having G/T+T/T genotype at position 276, the OSAHS patients with the G/G genotype showed a greater neck circumference(NC), a prolonged duration of the longest apnea event, and elevated levels of blood cholesterol and low-density lipoprotein cholesterol(P < 0.05). Conclusion: No direct association was detected between OSAHS and adiponectin genotype distribution at positions 45 and 276 in Chinese of Han nationality in the Nanjing district. However, OSAHS patients with the adiponectin GIG genotype at position 276 had a larger NC and the longest apnea event compared to those having the adiponectin SNP276 G/T +T/T genotype. This may have an indirect influence on the development of OSAHS.

  6. PEPA-1* genotype affects return rate for hatchery steelhead

    Science.gov (United States)

    Reisenbichler, R.R.; Hayes, M.C.; Rubin, S.P.; Wetzel, L.A.; Baker, B.M.

    2006-01-01

    Allozymes continue to be useful as genetic markers in a variety of studies; however, their utility often hinges on the selective neutrality of the allelic variation. Our study tested for neutrality between the two most common alleles (*100 and *110) at the cytosol nonspecific dipeptidase locus (PEPA-1*) in steelhead Oncorhynchus mykiss from Dworshak National Fish Hatchery in Idaho. We tested for differential growth and survival among fish with the * 100/100, *100/ 110, and *110/110 genotypes rearing in a hatchery or a natural stream. We repeated the study for two year-classes, using heterozygous (*100/110) adults to make the experimental crosses. This design avoided differences in family contribution among genotypes because each cross produced all three genotypes. We divided the progeny from each family into two groups. One group was reared in a hatchery for 1 year and then released for migration to the sea and subsequent return to the hatchery as adults. The other group was released into a natural stream and monitored for 3 years. We found no significant differences in size or survival among PEPA-1* genotypes for either the naturally reared fish or the hatchery-reared fish immediately prior to release as smolts. For females, survival to returning adult also was similar among genotypes; however, hatchery-reared males with the *110/110 genotype returned at a higher rate than did males with the *100/ 100 genotype; heterozygous males were intermediate. These results indicate that selection occurs at the PEPA-1* locus or at one or more loci tightly linked to it. The finding of nearly equal frequencies for these two alleles in the source population suggests that selection differentials among genotypes reverse or vary from year to year; otherwise, steady directional selection would drive the *100 allele to low frequencies or extinction. Locus PEPA-1* seems inappropriate for genetic marks in studies of steelhead that span the full life cycle and probably should be avoided

  7. Genotype and ancestry modulate brain's DAT availability in healthy humans

    International Nuclear Information System (INIS)

    The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [11C] cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms - 3-UTR- and intron 8- VNTRs. The main findings are the following: (1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; (2) ethnic background and age influence the strength of these associations; and (3) age-related changes in DAT availability differ in the 3-UTR and intron8 - genotype groups.

  8. Genotype and ancestry modulate brain's DAT availability in healthy humans.

    Directory of Open Access Journals (Sweden)

    Elena Shumay

    Full Text Available The dopamine transporter (DAT is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3 is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET with [¹¹C]cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms--3-UTR- and intron 8--VNTRs. The main findings are the following: 1 both polymorphisms analyzed as single genetic markers and in combination (haplotype modulate DAT density in midbrain; 2 ethnic background and age influence the strength of these associations; and 3 age-related changes in DAT availability differ in the 3-UTR and intron 8--genotype groups.

  9. Genotype variation in bark texture drives lichen community assembly across multiple environments.

    Science.gov (United States)

    Lamit, L J; Lau, M K; Naesborg, R Reese; Wojtowicz, T; Whitham, T G; Gehring, C A

    2015-04-01

    A major goal of community genetics is to understand the influence of genetic variation within a species on ecological communities. Although well-documented for some organisms, additional research is necessary to understand the relative and interactive effects of genotype and environment on biodiversity, identify mechanisms through which tree genotype influences communities, and connect this emerging field with existing themes in ecology. We employ an underutilized but ecologically significant group of organisms, epiphytic bark lichens, to understand the relative importance of Populus angustifolia (narrowleaf cottonwood) genotype and environment on associated organisms within the context of community assembly and host ontogeny. Several key findings emerged. (1) In a single common garden, tree genotype explained 18-33% and 51% of the variation in lichen community variables and rough bark cover, respectively. (2) Across replicated common gardens, tree genotype affected lichen species richness, total lichen cover, lichen species composition, and rough bark cover, whereas environment only influenced composition and there were no genotype by environment interactions. (3) Rough bark cover was positively correlated with total lichen cover and richness, and was associated with a shift in species composition; these patterns occurred with variation in rough bark cover among tree genotypes of the same age in common gardens and with increasing rough bark cover along a -40 year tree age gradient in a natural riparian stand. (4) In a common garden, 20-year-old parent trees with smooth bark had poorly developed lichen communities, similar to their 10-year-old ramets (root suckers) growing in close proximity, while parent trees with high rough bark cover had more developed communities than their ramets. These findings indicate that epiphytic lichens are influenced by host genotype, an effect that is robust across divergent environments. Furthermore, the response to tree genotype is

  10. Evaluation of Drought Tolerance in Rapeseed Genotypes under Non Stress and Drought Stress Conditions

    OpenAIRE

    Amir Hossein SHIRANI RAD; ABBASIAN, Abouzar

    2011-01-01

    Drought is a wide spread problem seriously influencing rapeseed (Brassica napus L.) production, mostly in dryland regions. This study was conducted to determine drought tolerance genotypes with superiority in different stressed environments. Twenty three rapeseed genotypes were tested in a split plot design based on randomized complete block design (RCBD) with four replications in two years (2008- 2009 and 2009-2010) at Seed and Plant Improvement Institute of Karaj, Iran. Seven drought resist...

  11. Two genotypes of mycorrhizal Pinus pinaster respond differently to cadmium contamination

    OpenAIRE

    Sousa, N. R.; Ramos, Miguel A.; Marques, Ana; Castro, Paula M. L.

    2012-01-01

    Fertilization is one of the main anthropogenic sources of Cd accumulation in agricultural soils and when toxic levels have been reached, food crop production is no longer viable. Adequate strategies for the forestation of agricultural metal contaminated sites are of vital importance. The aim of this work was to evaluate the response of two different genotypes of P. pinaster (A and B) to Cd contamination and to assess how inoculation with ectomycorrhizal fungi influenced each genotype. Seedlin...

  12. The vigour of glasshouse roses. Scion rootstock relationships, effects of phenotypic & genotypic variation.

    OpenAIRE

    De, Vries

    1993-01-01

    Glasshouse roses commonly are combination plants, consisting of a scion variety and a rootstock of different genotypes. In this study, various environmental and genotypic factors have been investigated that influence the vigour of rootstocks and scion varieties, separately and in graft combination.In a field crop of Edelcanina (selections of R.canina L.) rootstock plants, significant phenotypic variation occurred for all plant characters investigated. Nurserymen partly disguise variation by g...

  13. The relationship between ciliary neurotrophic factor (CNTF) genotype and motor unit physiology: preliminary studies

    OpenAIRE

    Ferrell Robert; Hurley Ben; Roth Stephen; Stashuk Daniel; Ling Shari; Conwit Robin A; Metter E Jeffrey

    2005-01-01

    Abstract Background Ciliary neurotrophic factor (CNTF) is important for neuronal and muscle development, and genetic variation in the CNTF gene has been associated with muscle strength. The effect of CNTF on nerve development suggests that CNTF genotype may be associated with force production via its influence on motor unit size and firing patterns. The purpose of this study is to examine whether CNTF genotype differentially affects motor unit activation in the vastus medialis with increasing...

  14. Muscle and genotype effects on fatty acid composition of goat kid intramuscular fat

    OpenAIRE

    Valeriano Domenech; Oliva Polvillo; Pilar Garcia; Adriana Bonvillani; Manuel Juárez; Francisco Peña

    2011-01-01

    Little is known about the fatty acid composition of the major muscles in goats from different breeds. Forty entire male suckling kids, 20 Criollo Cordobes and 20 Anglo Nubian, were slaughtered at 75 days of age and the fatty acid composition of their longissimus thoracis (LT) and semitendinosus (ST) muscles was analysed to clarify the effects of genotype and muscle type on goat kid meat. Genotype had a great influence on the fatty acid composition of goat kid meat. Meat from Criollo Cordobes ...

  15. Spatial Patterns of Ectomycorrhizal Assemblages in a Monospecific Forest in Relation to Host Tree Genotype

    OpenAIRE

    Lang, Christa; Finkeldey, Reiner; Polle, Andrea

    2013-01-01

    Ectomycorrhizas (EcM) are important for soil exploration and thereby may shape belowground interactions of roots. We investigated the composition and spatial structures of EcM assemblages in relation to host genotype in an old-growth, monospecific beech (Fagus sylvatica) forest. We hypothesized that neighboring roots of different beech individuals are colonized by similar EcM assemblages if host genotype had no influence on the fungal colonization and that the similarity would decrease with i...

  16. Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

    OpenAIRE

    BÁLINT, MIKLÓS; Tiffin, Peter; Hallström, Björn; O'Hara, Robert B.; Olson, Matthew S.; Fankhauser, Johnathon D.; Piepenbring, Meike; Schmitt, Imke

    2013-01-01

    Foliar fungal communities of plants are diverse and ubiquitous. In grasses endophytes may increase host fitness; in trees, their ecological roles are poorly understood. We investigated whether the genotype of the host tree influences community structure of foliar fungi. We sampled leaves from genotyped balsam poplars from across the species' range, and applied 454 amplicon sequencing to characterize foliar fungal communities. At the time of the sampling the poplars had been growing in a commo...

  17. Cell membrane stability in two barley genotypes under water stress conditions

    OpenAIRE

    Hanna Bandurska; Halina Gniazdowska-Skoczek

    2014-01-01

    The effect of water stress induced in vitro by polyethylene glycol 6000 (PEG) and under drought stress on cell membrane stability was examined in two barley genotypes, the cultivar Aramir and line R567. The injury of cell membranes was markely influenced by leaf age, leaf position on the stem, and the degree of drought stress. The differences in percentage of injury to cell membrane between these genotypes were also found. The cv. Aramir exhibited a lower percentage injury value as compared t...

  18. Radiosensitivity - a genotype dependent mechanism

    International Nuclear Information System (INIS)

    For determining relative radiosensitivity, bulbs of 3 different sizes of Allium cepa L. having same cell size, chromosome number, ICV, INV and DNA content were exposed to different doses of gamma-rays. Gamma ray induced chromosomal aberrations as the end point of radiosensitivity was studied in root meristem and it was found that the aberration percentage increased with increase in doses in all cases. The medium size was found to be much sensitive indicating genotype dependent mechanism for radiosensitivity. (author). 34 refs., 3 tabs

  19. Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling,docking and dynamics simulation studies

    Institute of Scientific and Technical Information of China (English)

    Jing LI; Yun DU; Xian LIU; Qian-cheng SHEN; Ai-long HUANG; Ming-yue ZHENG; Xiao-min LUO; Hua-liang JIANG

    2013-01-01

    Aim: To investigate the molecular mechanisms underlying the influence of DNA polymerase from different genotypes of hepatitis B virus (HBV) on the binding affinity of adefovir (ADV).Methods: Computational approaches,including homology modeling,docking,MD simulation and MM/PBSA free energy analyses were used.Results: Sequence analyses revealed that residue 238 near the binding pocket was not only a polymorphic site but also a genotypespecific site (His238 in genotype B; Asn238 in genotype C).The calculated binding free-energy supported the hypothesis that the polymerase from HBV genotype C was more sensitive to ADV than that from genotype B.By using MD simulation trajectory analysis,binding free energy decomposition and alanine scanning,some energy variation in the residues around the binding pocket was observed.Both the alanine mutations at residues 236 and 238 led to an increase of the energy difference between genotypes C and B (△△Gc-B),suggesting that these residues contributed to the genotype-associated antiviral variability with regard to the interaction with ADV.Conclusion: The results support the hypothesis that the HBV genotype C polymerase is more sensitive to ADV than that from genotype B.Moreover,residue N236 and the polymorphic site 238 play important roles in contributing to the higher sensitivity of genotype C over B in the interaction with ADV.

  20. Genome complexity reduction for SNP genotyping analysis

    OpenAIRE

    Jordan, Barbara; Charest, Alain; Dowd, John F.; Blumenstiel, Justin P.; Yeh, Ru-Fang; Osman, Asiah; Housman, David E.; Landers, John E.

    2002-01-01

    Efficient single nucleotide polymorphism (SNP) genotyping methods are necessary to accomplish many current gene discovery goals. A crucial element in large-scale SNP genotyping is the number of individual biochemical reactions that must be performed. An efficient method that can be used to simultaneously amplify a set of genetic loci across a genome with high reliability can provide a valuable tool for large-scale SNP genotyping studies. In this paper we describe and characterize a method tha...

  1. Parallel genotypic adaptation: when evolution repeats itself

    OpenAIRE

    Wood, Troy E.; Burke, John M.; Rieseberg, Loren H.

    2005-01-01

    Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic...

  2. Family history and apoE genotype interaction in Alzheimer`s disease (AD)

    Energy Technology Data Exchange (ETDEWEB)

    Jarvik, G.P.; Kukull, W.A.; Goddards, K. [and others

    1994-09-01

    The apoE {epsilon}4 allele is associated with increased risk and decreased age of onset of AD. The {epsilon}4 allele may have opposing effects. We determined that family history of a parent or sib with memory problems (famhx+) modified the effect of apoE genotype in a population-based, case (n=165, 72 famhx+)-control (n=233, 73 famhx+) sample. Logistic regression analyses detected a significant apoE genotype (E) by family history (F) by age (A) interaction (ExFxA, p=0.003) and ExF interaction (p=0.0001) in the prediction of AD. ExFxA remained significant when only {epsilon}4+ genotypes were included (p<0.01). ExFxSex (p=0.04) and ExF (p<0.0001) were significant when only {epsilon}4- genotypes were included. Similary, multiple regression detected significant ExF interaction in the prediction of age of AD onset for {epsilon}4+ genotypes (p=0.04) or {epsilon}4- genotypes (p=0.04). Sex did not interact in the prediction of age of onset. Famhx+ increased risk of AD differentially and reduced age of onset except in {epsilon}2+ genotypes. Family history modifies the apoE genotype influence on risk and onset age of AD, suggesting that non-apoE genetic effects interact with apoE in AD. It is most predictive of risk in those with the {epsilon}2{epsilon}3 genotype. Variation in risk and onset among both {epsilon}4+ and {epsilon}4- genotypes demonstrate that {epsilon}2 and {epsilon}3 mediate {epsilon}4 allele effects in AD.

  3. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-01-01

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients. PMID:26345916

  4. Genotyping and surveillance for scrapie in Finnish sheep

    Directory of Open Access Journals (Sweden)

    Hautaniemi Maria

    2012-07-01

    Full Text Available Abstract Background The progression of scrapie is known to be influenced by the amino acid polymorphisms of the host prion protein (PrP gene. There is no breeding programme for TSE resistance in sheep in Finland, but a scrapie control programme has been in place since 1995. In this study we have analysed PrP genotypes of total of 928 purebred and crossbred sheep together with the data of scrapie survey carried out in Finland during 2002–2008 in order to gain knowledge of the genotype distribution and scrapie prevalence in Finnish sheep. Results The ARQ/ARQ genotype was the most common genotype in all breeds studied. ARR allele frequency was less than 12% in purebred Finnish sheep and in most genotypes heterozygous for ARR, the second allele was ARQ. The VRQ allele was not detected in the Grey race sheep of Kainuu or in the Aland sheep, and it was present in less than 6% of the Finnish Landrace sheep. Leucine was the most prominent amino acid found in codon 141. In addition, one novel prion dimorphisms of Q220L was detected. During the scrapie survey of over 15 000 sheep in 2002–2008, no classical scrapie cases and only five atypical scrapie cases were detected. Conclusions The results indicate that the Finnish sheep populations have genetically little resistance to classical scrapie, but no classical scrapie was detected during an extensive survey in 2002–2008. However, five atypical scrapie cases emerged; thus, the disease is present in the Finnish sheep population at a low level.

  5. The association of complex liver disorders with HBV genotypes prevalent in Pakistan

    Directory of Open Access Journals (Sweden)

    Qureshi Huma

    2007-11-01

    Full Text Available Abstract Background Genotyping of HBV is generally used for determining the epidemiological relationship between various virus strains and origin of infection mostly in research studies. The utility of genotyping for clinical applications is only beginning to gain importance. Whether HBV genotyping will constitute part of the clinical evaluation of Hepatitis B patients depends largely on the availability of the relevance of the evidence based information. Since Pakistan has a HBV genotype distribution which has been considered less virulent as investigated by earlier studies from south East Asian countries, a study on correlation between HBV genotypes and risk of progression to further complex hepatic infection was much needed Methods A total of 295 patients with HBsAg positive were selected from the Pakistan Medical Research Council's (PMRC out patient clinics. Two hundred and twenty six (77% were males, sixty nine (23% were females (M to F ratio 3.3:1. Results Out of 295 patients, 156 (53.2% had Acute(CAH, 71 (24.2% were HBV Carriers, 54 (18.4% had Chronic liver disease (CLD Hepatitis. 14 (4.7% were Cirrhosis and HCC patients. Genotype D was the most prevalent genotype in all categories of HBV patients, Acute (108, Chronic (39, and Carrier (53. Cirrhosis/HCC (7 were HBV/D positive. Genotype A was the second most prevalent with 28 (13% in acute cases, 12 (22.2% in chronics, 14 (19.7% in carriers and 5 (41.7 in Cirrhosis/HCC patients. Mixed genotype (A/D was found in 20 (12.8% of Acute patients, 3 (5.6% of Chronic and 4 (5.6% of carriers, none in case of severe liver conditions. Conclusion Mixed HBV genotypes A, D and A/D combination were present in all categories of patients except that no A/D combination was detected in severe conditions. Genotype D was the dominant genotype. However, genotype A was found to be more strongly associated with severe liver disease. Mixed genotype (A/D did not significantly appear to influence the clinical outcome.

  6. Hepatitis C virus genotypes in Myanmar

    Science.gov (United States)

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

    2016-01-01

    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.

  7. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels;

    2014-01-01

    recover the correct labels. Here we describe a statistical method which given a few extra independent genotypes (barcode genotypes) detects mislabeled samples and recovers the correct labels for sample mix-ups. We have implemented the method in a program (named Wunderbar) and we evaluate the reliability...... of the method on simulated data. We find that even with only a small number of barcode genotypes, Wunderbar is capable of identifying mislabeled samples and sample mix-ups with high sensitivity and specificity, even with a high genotyping error rate and even in the presence of dependency between the...... individual barcode genotypes. To detect mislabeled samples we calculate the probability that the discordance between genotypes in the data and in the independent genotypes can be attributed to random (non-mislabeling) genotyping errors. To identify mix-ups we calculate the probability of identifying the set...

  8. Influencia de la grasa de la dieta en el metabolismo glucídico de mujeres obesas con el genotipo Pro12Pro en el gen PPARgama2 Influence of fat diet in glicidic metabolism in obese women with PRO12PRO genotype in PPARgamma2 gene

    Directory of Open Access Journals (Sweden)

    V. Chaia Kaippert

    2010-08-01

    Full Text Available Introducción: El receptor activado por proliferadores de peroxisomas (PPARγ2 es un factor de transcripción adipogénico que influye en la resistencia a la insulina (RI en la presencia de agonistas como los ácidos grasos poliinsaturados (AGPI. Objetivo: Evaluar la influencia de la grasa de la dieta en el metabolismo glucídico de mujeres con obesidad mórbida y con el genotipo Pro12Pro en el gen PPARγ2. Métodos: Fueron seleccionadas 25 mujeres con genotipo Pro12Pro. La ingesta habitual de lípidos fue estimada por registros alimentarios, siendo utilizada para la división de los grupos, GA (hasta un 30% del valor energético total (VET y GB (por encima de un 30% del VET. Fueron realizadas evaluaciones bioquímicas y antropométricas en ayuno, siguiendo la comida test rica en AGPI n-6 y los análisis bioquímicos postprandiales en GA y GB. La RI y la sensibilidad a la insulina (SI fueron evaluadas por HOMA-IR (Homeostasis Model Assessment y QUICKI (Quantitative Insulin Sensitivity Check Index, respectivamente. Resultados y discusión: GA presentó HOMA-IR y QUICKI normales. GB presentó el índice de masa corporal (IMC, HOMA-IR, ingesta de ácidos grasos saturados (AGS y monoinsaturados (AGMI superiores a GA (p Introduction: The peroxisome proliferator-activated receptor gamma 2 (PPARγ2 is an adipogenic transcription factor that influences in insulin resistance (IR in the presence of agonists such as polyunsaturated fatty acids (PUFA. Objective: Evaluate the influence of dietary fat in glicidic metabolism in morbidly obese women with Pro12Pro genotype in the gene PPARγ2. Methods: Were selected 25 women with genotype Pro12Pro. The fat intake was estimated by food records, being used for the division of groups, GA (until 30% of the total energy expenditure (TEE and GB (greater than 30% of the TEE. Biochemical and anthropometric evaluations were conducted in fasting, following the test meal high in n-6 PUFA and postprandial biochemical

  9. HBeAg and not genotypes predicts viral load in patients with hepatitis B in Denmark: a nationwide cohort study

    DEFF Research Database (Denmark)

    Krarup, Henrik Bygum; Andersen, Stig; Madsen, Poul Henning; Christensen, Peer Brehm; Laursen, Alex Lund; Bentzen-Petersen, Anne; Møller, Jørn Munkhof; Weis, Nina Margrethe

    2011-01-01

    To explore the influence of HBV genotype on viral load in patients with HBV infection, and to investigate the relation to gender, age and country of origin or antibodies against hepatitis Be antigen (anti-HBe).......To explore the influence of HBV genotype on viral load in patients with HBV infection, and to investigate the relation to gender, age and country of origin or antibodies against hepatitis Be antigen (anti-HBe)....

  10. HBeAg and not genotypes predicts viral load in patients with hepatitis B in Denmark: A nationwide cohort study

    DEFF Research Database (Denmark)

    Krarup, Henrik; Andersen, Stig; Madsen, Poul Henning; Christensen, Peer Brehm; Laursen, Alex Lund; Bentzen-Petersen, Anne; Møller, Jørn M; Weis, Nina; Nielsen, Henrik Ib; Tage-Jensen, U.

    2011-01-01

    To explore the influence of HBV genotype on viral load in patients with HBV infection, and to investigate the relation to gender, age and country of origin or antibodies against hepatitis Be antigen (anti-HBe).......To explore the influence of HBV genotype on viral load in patients with HBV infection, and to investigate the relation to gender, age and country of origin or antibodies against hepatitis Be antigen (anti-HBe)....

  11. Does hepatitis C viremia or genotype predict the risk of mortality in individuals co-infected with HIV?

    DEFF Research Database (Denmark)

    Rockstroh, Jürgen K; Peters, Lars; Grint, Daniel;

    2013-01-01

    The influence of HCV-RNA levels and genotype on HCV disease progression is not well studied. The prognostic value of these markers was investigated in HIV/HCV co-infected individuals from the EuroSIDA cohort.......The influence of HCV-RNA levels and genotype on HCV disease progression is not well studied. The prognostic value of these markers was investigated in HIV/HCV co-infected individuals from the EuroSIDA cohort....

  12. 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

    Objective: 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. Methods: 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. Results: 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. Conclusion: 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. PMID:26649001

  13. Estimation of Genotype Distributions and Posterior Genotype Probabilities for β-Mannosidosis in Salers Cattle

    OpenAIRE

    Taylor, J F; Abbitt, B.; Walter, J P; Davis, S. K.; Jaques, J. T.; Ochoa, R. F.

    1993-01-01

    β-Mannosidosis is a lethal lysosomal storage disease inherited as an autosomal recessive in man, cattle and goats. Laboratory assay data of plasma β-mannosidase activity represent a mixture of homozygous normal and carrier genotype distributions in a proportion determined by genotype frequency. A maximum likelihood approach employing data transformations for each genotype distribution and assuming a diallelic model of inheritance is described. Estimates of the transformation and genotype dist...

  14. Genotypic differences in behavioural entropy: unpredictable genotypes are composed of unpredictable individuals

    OpenAIRE

    Stamps, Judy A.; Saltz, Julia B.; Krishnan, V.V.

    2013-01-01

    Intra-genotypic variability (IGV) occurs when individuals with the same genotype, raised in the same environment and then tested under the same conditions, express different trait values. Game theoretical and bet-hedging models have suggested two ways that a single genotype might generate variable behaviour when behavioural variation is discrete rather than continuous: behavioural polyphenism (a genotype produces different types of individuals, each of which consistently expresses a different...

  15. Non-additive effects of genotypic diversity increase floral abundance and abundance of floral visitors.

    Directory of Open Access Journals (Sweden)

    Mark A Genung

    Full Text Available BACKGROUND: In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention. METHODOLOGY/PRINCIPAL FINDINGS: Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1 plant genotype explained 45% and 92% of the variation in flower visitor abundance in 2007 and 2008, respectively; and 2 plant genotypic diversity had a positive and non-additive effect on floral abundance and the abundance of flower visitors, as plots established with multiple genotypes produced 25% more flowers and received 45% more flower visits than would be expected under an additive model. CONCLUSIONS/SIGNIFICANCE: These results provide evidence that declines in genotypic diversity may be an important but little considered factor for understanding plant-pollinator dynamics, with implications for the global decline in pollinators due to reduced plant diversity in both agricultural and natural ecosystems.

  16. Host-parasite Red Queen dynamics with phase-locked rare genotypes.

    Science.gov (United States)

    Rabajante, Jomar F; Tubay, Jerrold M; Ito, Hiromu; Uehara, Takashi; Kakishima, Satoshi; Morita, Satoru; Yoshimura, Jin; Ebert, Dieter

    2016-03-01

    Interactions between hosts and parasites have been hypothesized to cause winnerless coevolution, called Red Queen dynamics. The canonical Red Queen dynamics assume that all interacting genotypes of hosts and parasites undergo cyclic changes in abundance through negative frequency-dependent selection, which means that any genotype could become frequent at some stage. However, this prediction cannot explain why many rare genotypes stay rare in natural host-parasite systems. To investigate this, we build a mathematical model involving multihost and multiparasite genotypes. In a deterministic and controlled environment, Red Queen dynamics occur between two genotypes undergoing cyclic dominance changes, whereas the rest of the genotypes remain subordinate for long periods of time in phase-locked synchronized dynamics with low amplitude. However, introduction of stochastic noise in the model might allow the subordinate cyclic host and parasite types to replace dominant cyclic types as new players in the Red Queen dynamics. The factors that influence such evolutionary switching are interhost competition, specificity of parasitism, and degree of stochastic noise. Our model can explain, for the first time, the persistence of rare, hardly cycling genotypes in populations (for example, marine microbial communities) undergoing host-parasite coevolution. PMID:26973878

  17. The genotype-environment interaction variance in rice-seed protein determination

    International Nuclear Information System (INIS)

    Many environmental factors influence the protein content of cereal seed. This fact procured difficulties in breeding for protein. Yield is another example on which so many environmental factors are of influence. The length of time required by the plant to reach maturity, is also affected by the environmental factors; even though its effect is not too decisive. In this investigation the genotypic variance and the genotype-environment interaction variance which contribute to the total variance or phenotypic variance was analysed, with purpose to give an idea to the breeder how selection should be made. It was found that genotype-environment interaction variance is larger than the genotypic variance in contribution to total variance of protein-seed determination or yield. In the analysis of the time required to reach maturity it was found that genotypic variance is larger than the genotype-environment interaction variance. It is therefore clear, why selection for time required to reach maturity is much easier than selection for protein or yield. Selected protein in one location may be different from that to other locations. (author)

  18. Filling in missing genotypes using haplotypes

    Science.gov (United States)

    Unknown genotypes can be made known (imputed) from observed genotypes at the same or nearby loci of relatives using pedigree haplotyping, or from matching allele patterns (regardless of pedigree) using population haplotyping. Fortran program findhap.f90 was designed to combine population and pedigre...

  19. Human Papillomavirus (HPV) Genotyping: Automation and Application in Routine Laboratory Testing

    Science.gov (United States)

    Torres, M; Fraile, L; Echevarria, JM; Hernandez Novoa, B; Ortiz, M

    2012-01-01

    A large number of assays designed for genotyping human papillomaviruses (HPV) have been developed in the last years. They perform within a wide range of analytical sensitivity and specificity values for the different viral types, and are used either for diagnosis, epidemiological studies, evaluation of vaccines and implementing and monitoring of vaccination programs. Methods for specific genotyping of HPV-16 and HPV-18 are also useful for the prevention of cervical cancer in screening programs. Some commercial tests are, in addition, fully or partially automated. Automation of HPV genotyping presents advantages such as the simplicity of the testing procedure for the operator, the ability to process a large number of samples in a short time, and the reduction of human errors from manual operations, allowing a better quality assurance and a reduction of cost. The present review collects information about the current HPV genotyping tests, with special attention to practical aspects influencing their use in clinical laboratories. PMID:23248734

  20. Human Papillomavirus (HPV) Genotyping: Automation and Application in Routine Laboratory Testing.

    Science.gov (United States)

    Torres, M; Fraile, L; Echevarria, Jm; Hernandez Novoa, B; Ortiz, M

    2012-01-01

    A large number of assays designed for genotyping human papillomaviruses (HPV) have been developed in the last years. They perform within a wide range of analytical sensitivity and specificity values for the different viral types, and are used either for diagnosis, epidemiological studies, evaluation of vaccines and implementing and monitoring of vaccination programs. Methods for specific genotyping of HPV-16 and HPV-18 are also useful for the prevention of cervical cancer in screening programs. Some commercial tests are, in addition, fully or partially automated. Automation of HPV genotyping presents advantages such as the simplicity of the testing procedure for the operator, the ability to process a large number of samples in a short time, and the reduction of human errors from manual operations, allowing a better quality assurance and a reduction of cost. The present review collects information about the current HPV genotyping tests, with special attention to practical aspects influencing their use in clinical laboratories. PMID:23248734

  1. THE CLINICAL PRESENTATION OF AUTOIMMUNE THYROID DISEASE IN MEN IS ASSOCIATED WITH IL12B GENOTYPE

    DEFF Research Database (Denmark)

    Walsh, John P; Berry, Jemma; Liu, Shu; Panicker, Vijay; Dayan, Colin M; Brix, Thomas H; Hegedüs, Laszlo; Hou, Peng; Shi, Bingyin; Morahan, Grant

    2011-01-01

    Background.  Common variants in the interleukin 12B (IL12B) gene are associated with predominantly inflammatory (Th1) or antibody-mediated (Th2) immune responses. Since Hashimoto's disease and Graves' disease are thought to arise from mainly Th1 and Th2 immune responses respectively, we...... hypothesized that IL12B genotype may influence the clinical presentation of autoimmune thyroid disease. Objective.  We tested for differences in IL12B genotype between Graves' disease and Hashimoto's disease. Patients.  We studied a discovery cohort of 203 Australian women and 37 men with autoimmune thyroid...... cohort, rs41292470 and rs3212227 genotypes did not differ significantly between Hashimoto's disease and Graves' disease. In Australian males (but not females), rs6887695 genotype differed between Hashimoto's disease and Graves' disease, with a minor allele frequency (MAF) of 14% and 41% respectively (P=0...

  2. Genotyping errors in a calibrated DNA register: implications for identification of individuals

    Directory of Open Access Journals (Sweden)

    Seliussen Bjørghild B

    2011-04-01

    Full Text Available Abstract Background The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors. Results The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote and three false heterozygotes (i.e., the true genotype was a homozygote. Conclusions To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and

  3. A European Database of Fusarium graminearum and F. culmorum Trichothecene Genotypes.

    Science.gov (United States)

    Pasquali, Matias; Beyer, Marco; Logrieco, Antonio; Audenaert, Kris; Balmas, Virgilio; Basler, Ryan; Boutigny, Anne-Laure; Chrpová, Jana; Czembor, Elżbieta; Gagkaeva, Tatiana; González-Jaén, María T; Hofgaard, Ingerd S; Köycü, Nagehan D; Hoffmann, Lucien; Lević, Jelena; Marin, Patricia; Miedaner, Thomas; Migheli, Quirico; Moretti, Antonio; Müller, Marina E H; Munaut, Françoise; Parikka, Päivi; Pallez-Barthel, Marine; Piec, Jonathan; Scauflaire, Jonathan; Scherm, Barbara; Stanković, Slavica; Thrane, Ulf; Uhlig, Silvio; Vanheule, Adriaan; Yli-Mattila, Tapani; Vogelgsang, Susanne

    2016-01-01

    Fusarium species, particularly Fusarium graminearum and F. culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related variables (sampling method, host cultivar, previous crop, etc.) that would allow more effective analysis of factors influencing the spatial and temporal population distribution, is lacking. Consequently, based on the available data, it is difficult to identify factors influencing chemotype distribution and spread at the European level. Here we describe the results of a collaborative integrated work which aims (1) to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000-2013 and (2) to enhance the standardization of epidemiological data collection. Information on host plant, country of origin, sampling location, year of sampling and previous crop of 1147 F. graminearum, 479 F. culmorum, and 3 F. cortaderiae strains obtained from 17 European countries was compiled and a map of trichothecene type B genotype distribution was plotted for each species. All information on the strains was collected in a freely accessible and updatable database (www.catalogueeu.luxmcc.lu), which will serve as a starting point for epidemiological analysis of potential spatial and temporal trichothecene genotype shifts in Europe. The analysis of the currently available European dataset showed that in F. graminearum, the predominant genotype was 15-acetyldeoxynivalenol (15-ADON) (82.9%), followed by 3-acetyldeoxynivalenol (3-ADON) (13.6%), and nivalenol (NIV) (3.5%). In F. culmorum, the prevalent genotype was 3-ADON (59.9%), while the NIV genotype accounted for the remaining 40.1%. Both, geographical and temporal patterns of trichothecene genotypes distribution were identified. PMID:27092107

  4. A European Database of Fusarium graminearum and F. culmorum Trichothecene Genotypes

    Science.gov (United States)

    Pasquali, Matias; Beyer, Marco; Logrieco, Antonio; Audenaert, Kris; Balmas, Virgilio; Basler, Ryan; Boutigny, Anne-Laure; Chrpová, Jana; Czembor, Elżbieta; Gagkaeva, Tatiana; González-Jaén, María T.; Hofgaard, Ingerd S.; Köycü, Nagehan D.; Hoffmann, Lucien; Lević, Jelena; Marin, Patricia; Miedaner, Thomas; Migheli, Quirico; Moretti, Antonio; Müller, Marina E. H.; Munaut, Françoise; Parikka, Päivi; Pallez-Barthel, Marine; Piec, Jonathan; Scauflaire, Jonathan; Scherm, Barbara; Stanković, Slavica; Thrane, Ulf; Uhlig, Silvio; Vanheule, Adriaan; Yli-Mattila, Tapani; Vogelgsang, Susanne

    2016-01-01

    Fusarium species, particularly Fusarium graminearum and F. culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related variables (sampling method, host cultivar, previous crop, etc.) that would allow more effective analysis of factors influencing the spatial and temporal population distribution, is lacking. Consequently, based on the available data, it is difficult to identify factors influencing chemotype distribution and spread at the European level. Here we describe the results of a collaborative integrated work which aims (1) to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000–2013 and (2) to enhance the standardization of epidemiological data collection. Information on host plant, country of origin, sampling location, year of sampling and previous crop of 1147 F. graminearum, 479 F. culmorum, and 3 F. cortaderiae strains obtained from 17 European countries was compiled and a map of trichothecene type B genotype distribution was plotted for each species. All information on the strains was collected in a freely accessible and updatable database (www.catalogueeu.luxmcc.lu), which will serve as a starting point for epidemiological analysis of potential spatial and temporal trichothecene genotype shifts in Europe. The analysis of the currently available European dataset showed that in F. graminearum, the predominant genotype was 15-acetyldeoxynivalenol (15-ADON) (82.9%), followed by 3-acetyldeoxynivalenol (3-ADON) (13.6%), and nivalenol (NIV) (3.5%). In F. culmorum, the prevalent genotype was 3-ADON (59.9%), while the NIV genotype accounted for the remaining 40.1%. Both, geographical and temporal patterns of trichothecene genotypes distribution were identified. PMID:27092107

  5. Hepatitis C virus genotypes in Serbia and Montenegro: The prevalence and clinical significance

    Institute of Scientific and Technical Information of China (English)

    Neda Svirtlih; Gorana Neskovic; Sonja Zerjav; Vladimir Urban; Dragan Delic; Jasmina Simonovic; Djordje Jevtovic; Ljubisa Dokic; Eleonora Gvozdenovic; Ivan Boricic; Dragica Terzic; Sladjana Pavic

    2007-01-01

    AIM: To investigate the prevalence of hepatitis C virus(HCV) genotypes in Serbia and Montenegro and their influence on some clinical characteristics in patients with chronic HCV infection.METHODS: A total of 164 patients was investigated.Complete history, route of infection, assessment of alcohol consumption, an abdominal ultrasound, standard biochemical tests and liver biopsy were done. Gene sequencing of 5' NTR type-specific PCR or commercial kits was performed for HCV genotyping and subtyping. The SPSS for Windows (version 10.0) was used for univariate regression analysis with further multivariate analysis.RESULTS: The genotypes 1, 2, 3, 4, 1b3a and 1b4 were present in 57.9%, 3.7%, 23.2%, 6.7%, 6.7% and 1.8%of the patients, respectively. The genotype 1 (mainly the subtype 1b) was found to be independent of age in subjects older than 40 years, high viral load, more severe necro-inflammatory activity, advanced stage of fibrosis,and absence of intravenous drug abuse. The genotype 3a was associated with intravenous drug abuse and the age below 40. Multivariate analysis demonstrated age over 40 and intravenous drug abuse as the positive predictive factors for the genotypes 1b and 3a, respectively.CONCLUSION: Tn Serbia and Montenegro, the genotypes 1b and 3a predominate in patients with chronic HCV infection. The subtype 1b is characteristic of older patients, while the genotype 3a is common in drug abusers. Association of the subtype 1b with advanced liver disease, higher viral load and histological activity suggests earlier infection with this genotype and eventually its increased pathogenicity.

  6. Microcystis genotype succession and related environmental factors in Lake Taihu during cyanobacterial blooms.

    Science.gov (United States)

    Wang, Xingyu; Sun, Mengjia; Wang, Jinmei; Yang, Letian; Luo, Lan; Li, Pengfu; Kong, Fanxiang

    2012-11-01

    From spring to autumn, heavy Microcystis blooms always occur in Lake Taihu, although environmental conditions vary markedly. We speculated that Microcystis genotype succession could play an important role in adaptation to environmental changes and long-term maintenance of the high Microcystis biomass. In this study, we investigated Microcystis genotype succession pattern and the related environmental variables in Lake Taihu during cyanobacterial blooms. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction -amplified the genus-specific cpcBA and mcyJ gene fragments was used to monitor the variations of Microcystis genotype and potential microcystin (MC)-producing Microcystis genotype compositions during blooms biweekly in three sites (Meiliang Bay, lake center, and Gonghu Bay) and CANOCO 4.5 for Windows were used for the multivariate statistical analysis of their relationships to environmental variables. DGGE patterns indicated that the number of dominant cpcBA genotype per sample increased from spring to autumn. Principal component analysis ordination plots of DGGE profiles showed clear temporal distribution pattern, but not spatial distribution pattern based on both cpcBA and mcyJ genotype compositions. These results indicated there were relatively gradual successions of Microcystis cpcBA and mcyJ genotype compositions in each site, and no distinct spatial difference among the three sites. Redundancy analyses of the gel patterns showed that, in all the three sites, three environmental factors (nitrate, pH, and chemical oxygen demand) were correlated significantly to successions of both cpcBA and mcyJ genotypes except for mcyJ genotype in the lake center. Spearman's correlations indicated that the three environmental variables were also strongly correlated with chl a and MC concentrations. These results suggested that the environmental factors affecting succession of Microcystis community composition might also influence the growth of

  7. 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

  8. Environmental dependency of amphibian-ranavirus genotypic interactions: evolutionary perspectives on infectious diseases.

    Science.gov (United States)

    Echaubard, Pierre; Leduc, Joel; Pauli, Bruce; Chinchar, V Gregory; Robert, Jacques; Lesbarrères, David

    2014-08-01

    The context-dependent investigations of host-pathogen genotypic interactions, where environmental factors are explicitly incorporated, allow the assessment of both coevolutionary history and contemporary ecological influences. Such a functional explanatory framework is particularly valuable for describing mortality trends and identifying drivers of disease risk more accurately. Using two common North American frog species (Lithobates pipiens and Lithobates sylvaticus) and three strains of frog virus 3 (FV3) at different temperatures, we conducted a laboratory experiment to investigate the influence of host species/genotype, ranavirus strains, temperature, and their interactions, in determining mortality and infection patterns. Our results revealed variability in host susceptibility and strain infectivity along with significant host-strain interactions, indicating that the outcome of an infection is dependent on the specific combination of host and virus genotypes. Moreover, we observed a strong influence of temperature on infection and mortality probabilities, revealing the potential for genotype-genotype-environment interactions to be responsible for unexpected mortality in this system. Our study thus suggests that amphibian hosts and ranavirus strains genetic characteristics should be considered in order to understand infection outcomes and that the investigation of coevolutionary mechanisms within a context-dependent framework provides a tool for the comprehensive understanding of disease dynamics. PMID:25469155

  9. Effect of chronic radiation on rape genotype formation

    International Nuclear Information System (INIS)

    The F1 generation of hybrid plants of the Canadian erucic acid-free rape cross-bred with some European winter rape varieties with a high content of erucic acid were chronically irradiated in a gamma-field with doses ranging from 5978 to 329 R er vegetation. In segregating F2 generations, the irradiation significantly increased the proportion of winter genotypes; a matroclinous influence on the developmental characteristics of plants occurred in irradiated segregating F2 hybrid populations. As against spring rape, winter rape varieties used as the maternal form during hybridization caused a statistically significant increase in the frequency of winter genotypes. The segregation of half-winter forms in irradiated segregating hybrid populations of the F2 generation proved the incomplete dominance of the spring habit of oil rape. Chronic irradiation significantly increased erucic-free (0 - 10% of erucic acid) and low-erucic (10 - 20% of erucic acid) genotype frequencies in segregating F2 generations. Chronic irradiation of the hybrid plants of erucic-free spring rapes and erucic winter rapes with doses ranging from 5978 to 329 R per vegetation, together with the temperature screening of winter forms and with the determination of the fatty acid content, may be considered as an effective method of creating non-erucic and low-erucic winter forms of oil rape. (author)

  10. Naturally occurrisng and induced genotypes of high lysine sorghum

    International Nuclear Information System (INIS)

    The discovery of a high lysine genotype of grain sorghum from a natural population and the identification of a high lysine mutant in a mutagenized population is described. Chemical, genetic and other biological characteristics of the two differently derived high lysine germ plasm types are described. Preliminary results suggest that the protein quality of both sources of high lysine sorghum germ plasm is the same. The factors influencing the biological value of the sorghum grain are discussed briefly, including not only lysine content but also tannin content. A discussion of prolamine protein inheritance in grain is presented with some suggestions for research. (author)

  11. Phylogeography of Japanese encephalitis virus: genotype is associated with climate.

    Directory of Open Access Journals (Sweden)

    Amy J Schuh

    Full Text Available The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV is the most important etiologic agent of epidemic encephalitis worldwide, and is primarily maintained between vertebrate reservoir hosts (avian and swine and culicine mosquitoes. There are five genotypes of JEV: GI-V. In recent years, GI has displaced GIII as the dominant JEV genotype and GV has re-emerged after almost 60 years of undetected virus circulation. JEV is found throughout most of Asia, extending from maritime Siberia in the north to Australia in the south, and as far as Pakistan to the west and Saipan to the east. Transmission of JEV in temperate zones is epidemic with the majority of cases occurring in summer months, while transmission in tropical zones is endemic and occurs year-round at lower rates. To test the hypothesis that viruses circulating in these two geographical zones are genetically distinct, we applied Bayesian phylogeographic, categorical data analysis and phylogeny-trait association test techniques to the largest JEV dataset compiled to date, representing the envelope (E gene of 487 isolates collected from 12 countries over 75 years. We demonstrated that GIII and the recently emerged GI-b are temperate genotypes likely maintained year-round in northern latitudes, while GI-a and GII are tropical genotypes likely maintained primarily through mosquito-avian and mosquito-swine transmission cycles. This study represents a new paradigm directly linking viral molecular evolution and climate.

  12. Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

    OpenAIRE

    Smith, Edward M.; Littrell, Jack; Olivier, Michael

    2007-01-01

    High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit th...

  13. Hepatitis C virus genotypes in Pakistan: a systemic review

    Directory of Open Access Journals (Sweden)

    Ali Ijaz

    2011-09-01

    Full Text Available Abstract Background and aim Phylogenetic analysis has led to the classification of hepatitis C virus (HCV into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011 related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched. Result HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03% cases of genotype 1; 1,085 (3.81% cases of genotype 2; 22,429 (78.96% cases of genotype 3; 453 (1.59% cases of genotype 4; 29 (0.10% cases of genotype 5; 37 (0.13% cases of genotype 6; 1,429 (5.03% cases of mixed genotypes, and 939 (3.30% cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.

  14. 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

  15. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie;

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years....

  16. Genotyping and annotation of Affymetrix SNP arrays

    DEFF Research Database (Denmark)

    Lamy, Philippe; Andersen, Claus Lindbjerg; Wikman, Friedrik;

    2006-01-01

    In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point...... allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose-response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in...... 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization...

  17. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  18. Stability and adaptability analysis of highland rice genotypes resulted from induced mutation

    International Nuclear Information System (INIS)

    Crop performance is determined by its genetic factors, environment factors and genetic x environment interaction. In this study, fifteen mutant lines from twenty genotypes were cultivated across five different environments with three different height altitude areas. The objective of the research was to evaluate the genotype x environment interactions for low temperature tolerance. Three stability analysis methods were applied to analyze the stability of promising rice lines. The significant G x E interactions in all measured agronomic traits were detected. The result showed that OS-30-199 mutant line produced the highest yield (4,69 ton/ha) among genotypes observed which was highly significant over check variety, Sarinah (3,42 ton/ha). IPB117-F-20, RB-10-95, C3-10-171, OS-30-199, KK-10-249 and CM-20-251 lines were classified as stable lines by Finlay- Wilkinson, Eberhart - Russel and Francis - Kannenberg yield stability test. RB-30-82, KN-30-186, Kuning, and IPB97-F-13 genotypes adapted in the optimal environments. KN-10-111, PK-30-131, Randah Batu Hampa and Sarinah genotypes were widely adapted in marginal environments. Most of mutant lines had highly significant yield compared to genotypes observed and adapted to low temperature stress. The difference of high elevations had influenced on yield in dry season while there was no significant effect in rainy seasons across three different high elevation areas. (author)

  19. Injecting drug use: A vector for the introduction of new hepatitis C virus genotypes.

    Science.gov (United States)

    Ruta, Simona; Cernescu, Costin

    2015-10-14

    Hepatitis C virus (HCV) genotypes' monitoring allows real-time insight into the dynamic changes that occur in the global epidemiological picture of HCV infection. Intravenous drug use is currently the primary driver for HCV transmission in developed and developing countries. The distribution of HCV genotypes/subtypes differs significantly between people who inject drugs (PWID) and the general population. HCV genotypes that previously exhibited a limited geographical distribution (3a, 4) are becoming more prevalent in this high-risk group. Immigration from HCV-endemic countries and the evolving networks of HCV transmission in PWID influence HCV genotypes distribution in Europe. Social vulnerabilities (e.g., unemployment, homelessness, and limited access to social and healthcare insurances systems) are important triggers for illicit drug use, which increases the associated risks of HCV infection and the frequent emergence of less prevalent genotypes. Genotype/subtype determination bears important clinical consequences in the progression of liver disease, susceptibility to antiviral therapies and the emergence of resistance-associated variants. An estimated half of the chronically HCV-infected PWID are unaware of their infection, and only one in ten of those diagnosed enter treatment. Nevertheless, PWID exhibit high response rates to new antiviral regimens, and the level of HCV reinfection is unexpectedly low. The focus of the healthcare system must be on the early detection and treatment of infection, to avoid late presentations that are associated with high levels of viremia and liver fibrosis, which may diminish the therapeutic success rate. PMID:26478672

  20. Biological aspects of Bemisia tabaci (Genn.) B biotype (Hemiptera: Aleyrodidae) on six bean genotypes

    International Nuclear Information System (INIS)

    The silverleaf whitefly is one of the most harmful pests that attack bean crops, mainly for extracting large quantities of phloem sap and transmitting the bean golden mosaic virus. Resistant germplasm plants can be an important method for controlling this pest. The biological aspects of Bemisia tabaci B biotype on bean (Phaseolus vulgaris) genotypes were evaluated. The tests were conducted under laboratory conditions, with the following genotypes: Arc 1, Arc 3s, Arc 5s, G13028, G11056 and Porrillo 70. The bean plants in a stage IV-1 were infested during one day with silverleaf white flies. Afterwards the eggs and nymphs were observed until adult emergence. Longevity and fecundity of emerged insects were also evaluated. The longest development time occurred for nymphs fed on Arc 3s genotype (26.5 days), following by G11056 (25.9 days) and G13028 (25.3 days). The development period was 5.5 days longer in Arc 3s when compared with Porrillo 70. Also, the wild genotypes Arc 3s and G11056 showed higher mortality rates (94.7% and 83.1%, respectively), which may suggest antibiosis and/or feeding non preference resistance type. For this reason, although longevity and fecundity were not influenced when the whitefly fed on resistant genotypes (Arc 3s, G11056, G13028 and Arc 5s), those genotypes can be used for bean breeding program towards B. tabaci B biotype. (author)

  1. Quantity of glucosinolates in 10 cabbage genotypes and their impact on the feeding of Mamestra brassicae caterpillars

    Directory of Open Access Journals (Sweden)

    Bohinc Tanja

    2014-01-01

    Full Text Available In 2011, we studied the glucosinolate content in 5 cultivars and 5 cabbage hybrids grown outdoors in order to study their influence on the feeding of cabbage moth caterpillars (Mamestra brassicae. The selected genotypes were categorized into three groups, early (the growth period from 55 to 70 days, mid-early (80-90 days and mid-late (110-140 days, while the samples of cabbage for glucosinolate analysis were taken at five intervals, during which we also assessed genotypes for the extent of damage caused by caterpillars. We found that the feeding of caterpillars affected primarily the mid-early and mid-late genotypes of cabbage, and that the glucosinolate content among the different cabbage genotypes varies. The highest content of the analyzed glucosinolates was established in mid-late genotypes. Glucobrassicin was the only glucosinolate found in all cabbage genotypes, yet its antixenotic effect (r=0.20 was very low. We found that sinalbin negatively affects the feeding of cabbage moth caterpillars in mid-early cabbage genotypes (r=-0.34, while the same effect of sinigrin on the extent of damage can be observed in mid-late genotypes (r=-0.27. We have established a strong or moderate correlation between the gluconapin (r=0.87 and progoitrin (r=0.66 contents in mid-late genotypes and the extent of damage caused by caterpillars. Our research proves that different cabbage genotypes are responsible for different susceptibilities to damage by the cabbage moth, and that one of the factors of natural resistance of cabbage are also glucosinolates. Despite this, due to their variability in cabbage we cannot precisely determine the set of genotypes that would ensure a higher cabbage yield as a result of less damage caused by the cabbage moth. Thus, we need to identify in more detail the reasons for the time and quantum variability of glucosinolates in Brassicaceae.

  2. Drought Resistance in Bread Wheat Genotypes

    OpenAIRE

    ÖZTÜRK, Ali

    1998-01-01

    Development of drought-resistant cultivars is one of the major goals in plant breeding programs. Twentysix wheat genotypes were evaluated for drought resistance using the criteria of leaf relative water content (LRWC), leaf relative water loss (LRWL) and drought susceptibility index (DSI) under Erzurum conditions in the crop seasons of 1995-96 and 1996-97. The results showed that differences among the genotypes in LRWC, LRWL and DSI were significant. In rainfed condition; LRWC, LRWL and DSI ...

  3. Clinical Significance of Hepatitis C Virus Genotypes

    OpenAIRE

    Fatih Yuksel Isiksal

    2000-01-01

    On the basis of phylogenetic analysis of nucleotide sequences, multiple genotypes and subtypes of hepatitis C virus (HCV) have been identified. Characterization of these genetic groups is likely to facilitate and contribute to the development of an effective vaccine against infection with HCV. Differences among HCV genotypes in geographic distributions have provided investigators with an epidemiologic marker that can be used to trace the source of HCV infection in a given population. HCV geno...

  4. Coffee Berry Borer Resistance in Coffee Genotypes

    OpenAIRE

    Gustavo Hiroshi Sera; Tumoru Sera; Dhalton Shiguer Ito; Claudionor Ribeiro Filho; Amador Villacorta; Fabio Seidi Kanayama1; Clayton Ribeiro Alegre; Leandro Del Grossi

    2010-01-01

    The aim of this study was to evaluate the coffee germplasm of the Paraná Agronomic Institute (IAPAR) for resistance to the coffee-berry-borer. Preliminary field evaluation was performed in August 2004 and the fruits of less damaged genotypes in the field were evaluated under controlled condition with obligated and free choice experiments established in a randomized complete design with three replications. The genotypes were evaluated fifteen days after infestation with one borer per fruit in ...

  5. Interleukin 28B Gene Variation at rs12979860 Determines Early Viral Kinetics During Treatment in Patients Carrying Genotypes 2 or 3 of Hepatitis C Virus

    DEFF Research Database (Denmark)

    Lindh, Magnus; Lagging, Martin; Färkkilä, Martti;

    2011-01-01

    Single-nucleotide polymorphisms upstream of the interleukin 28B (interferon λ3) gene (IL28B) strongly influence treatment efficacy in patients carrying hepatitis C virus (HCV) of genotype 1. In patients receiving 12 or 24 weeks of interferon-ribavirin therapy for infection with genotype 2 or 3 (n...

  6. HCV genotyping using statistical classification approach

    Directory of Open Access Journals (Sweden)

    Norris Ellie D

    2009-07-01

    Full Text Available Abstract The genotype of Hepatitis C Virus (HCV strains is an important determinant of the severity and aggressiveness of liver infection as well as patient response to antiviral therapy. Fast and accurate determination of viral genotype could provide direction in the clinical management of patients with chronic HCV infections. Using publicly available HCV nucleotide sequences, we built a global Position Weight Matrix (PWM for the HCV genome. Based on the PWM, a set of genotype specific nucleotide sequence "signatures" were selected from the 5' NCR, CORE, E1, and NS5B regions of the HCV genome. We evaluated the predictive power of these signatures for predicting the most common HCV genotypes and subtypes. We observed that nucleotide sequence signatures selected from NS5B and E1 regions generally demonstrated stronger discriminant power in differentiating major HCV genotypes and subtypes than that from 5' NCR and CORE regions. Two discriminant methods were used to build predictive models. Through 10 fold cross validation, over 99% prediction accuracy was achieved using both support vector machine (SVM and random forest based classification methods in a dataset of 1134 sequences for NS5B and 947 sequences for E1. Prediction accuracy for each genotype is also reported.

  7. Prevalence of genotypic HIV-1 drug resistance in Thailand, 2002

    Directory of Open Access Journals (Sweden)

    Watitpun Chotip

    2003-03-01

    Full Text Available Abstract Background The prices of reverse transcriptase (RT inhibitors in Thailand have been reduced since December 1, 2001. It is expected that reduction in the price of these inhibitors may influence the drug resistance mutation pattern of HIV-1 among infected people. This study reports the frequency of HIV-1 genetic mutation associated with drug resistance in antiretroviral-treated patients from Thailand. Methods Genotypic resistance testing was performed on samples collected in 2002 from 88 HIV-1 infected individuals. Automated DNA sequencing was used to genotype the HIV-1 polymerase gene isolated from patients' plasma. Results Resistance to protease inhibitors, nucleoside and non-nucleoside reverse transcriptase inhibitors were found in 10 (12%, 42 (48% and 19 (21% patients, respectively. The most common drug resistance mutations in the protease gene were at codon 82 (8%, 90 (7% and 54 (6%, whereas resistant mutations at codon 215 (45%, 67 (40%, 41 (38% and 184 (27% were commonly found in the RT gene. This finding indicates that genotypic resistance to nucleoside reverse transcriptase inhibitors was prevalent in 2002. The frequency of resistant mutations corresponding to non-nucleoside reverse transcriptase inhibitors was three times higher-, while resistant mutation corresponding to protease inhibitors was two times lower than those frequencies determined in 2001. Conclusion This study shows that the frequencies of RT inhibitor resistance mutations have been increased after the reduction in the price of RT inhibitors since December 2001. We believe that this was an important factor that influenced the mutation patterns of HIV-1 protease and RT genes in Thailand.

  8. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales.

    Science.gov (United States)

    Smith, Matt J; Pascal, Carita E; Grauvogel, Zac; Habicht, Christopher; Seeb, James E; Seeb, Lisa W

    2011-03-01

    Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA. PMID:21429180

  9. Hepatitis B virus genotype A: design of reference sequences for sub-genotypes.

    Science.gov (United States)

    Cai, Qun; Zhu, Huilan; Zhang, Yafei; Li, Xu; Zhang, Zhenhua

    2016-06-01

    Genotype A of hepatitis B virus (HBV/A) is widespread and is currently divided into six sub-genotypes. Suitable reference sequences for different sub-genotypes can facilitate research on HBV/A. However, the current reference sequences for this virus are insufficient. In the present work, we retrieved 442 full-length HBV/A genomic sequences from the GenBank database and classified them into sub-genotypes by phylogenetic analysis. By the maximum likelihood method using the MEGA6.0 software, we established the reference sequences for different HBV/A sub-genotypes. Our analyses demonstrated that these reference sequences clustered phylogenetically with known strains, indicating that the reference sequences we established indeed belonged to the right sub-genotypes. HBV/A subtype sequences were selected by geographic origins and grouped as sub-genotypes including A1-South Africa, A2-Europe, A3-Cameroon, and A5-Haiti. Reference sequences of sub-genotypes A1, A2, A3, and A5 were constructed and deposited into GenBank (KP234050-KP234053). By applying phylogenetic analyses, we further determined the time to most recent common ancestor of HBV/A lineages. In conclusion, these newly established reference sequences can provide suitable reference standards for studies on the molecular biology and virology of HBV genotype A. PMID:27002608

  10. Inferring haplotypes from genotypes on a pedigree with mutations, genotyping errors and missing alleles.

    Science.gov (United States)

    Wang, Wei-Bung; Jiang, Tao

    2011-04-01

    Inferring the haplotypes of the members of a pedigree from their genotypes has been extensively studied. However, most studies do not consider genotyping errors and de novo mutations. In this paper, we study how to infer haplotypes from genotype data that may contain genotyping errors, de novo mutations, and missing alleles. We assume that there are no recombinants in the genotype data, which is usually true for tightly linked markers. We introduce a combinatorial optimization problem, called haplotype configuration with mutations and errors (HCME), which calls for haplotype configurations consistent with the given genotypes that incur no recombinants and require the minimum number of mutations and errors. HCME is NP-hard. To solve the problem, we propose a heuristic algorithm, the core of which is an integer linear program (ILP) using the system of linear equations over Galois field GF(2). Our algorithm can detect and locate genotyping errors that cannot be detected by simply checking the Mendelian law of inheritance. The algorithm also offers error correction in genotypes/haplotypes rather than just detecting inconsistencies and deleting the involved loci. Our experimental results show that the algorithm can infer haplotypes with a very high accuracy and recover 65%-94% of genotyping errors depending on the pedigree topology. PMID:21523936

  11. MIR137HG risk variant rs1625579 genotype is related to corpus callosum volume in schizophrenia

    NARCIS (Netherlands)

    Patel, V.S.; Kelly, S.; Wright, C.; Gupta, C.N.; Arias Vasquez, A.; Perrone-Bizzozero, N.; Ehrlich, S.; Wang, L.; Bustillo, J.R.; Morris, D.; Corvin, A.; Cannon, D.M.; McDonald, C.; Donohoe, G.; Calhoun, V.D.; Turner, J.A.

    2015-01-01

    Genome-wide association studies implicate the MIR137HG risk variant rs1625579 (MIR137HGrv) within the host gene for microRNA-137 as a potential regulator of schizophrenia susceptibility. We examined the influence of MIR137HGrv genotype on 17 subcortical and callosal volumes in a large sample of indi

  12. Disparate effects of plant genotypic diversity on foliage and litter arthropod communities

    Energy Technology Data Exchange (ETDEWEB)

    Crutsinger, Greg [University of Tennessee, Knoxville (UTK); Reynolds, Nicholas [University of Tennessee, Knoxville (UTK); Classen, Aimee T [ORNL; Sanders, Dr. Nathan James [University of Tennessee, Knoxville (UTK)

    2008-01-01

    Intraspecific diversity within plant species is increasingly recognized as an important influence on the structure of associated arthropod communities, though whether there are congruent responses of above- and belowground communities to intraspecific diversity remains unclear. In this study, we compare the effects of host-plant genotype and genotypic diversity of the perennial plant, Solidago altissima, on the arthropod community associated with living plant tissue (foliage-based community) and microarthropods associated with leaf litter (litter-based community). We found that variation among host-plant genotypes had strong effects on the diversity and composition of foliage-based arthropods, but only weak influence on litter-based microarthropods. Furthermore, host-plant genotypic diversity was positively related to the abundance and diversity of foliage-based arthropods, including herbivore and predator trophic levels. In contrast, there were minimal effects of genotypic diversity in litter on microarthropods. Our study illustrates that incorporating both above- and belowground perspective into community genetics studies leads to very different conclusions about the importance of intraspecific diversity, than when considering aboveground responses in isolation.

  13. Type 2 Diabetes TCF7L2 Risk Genotypes Alter Birth Weight: A Study of 24,053 Individuals

    OpenAIRE

    Freathy, Rachel M. ; Weedon, Michael N. ; Bennett, Amanda ; Hyppönen, Elina ; Relton, Caroline L. ; Knight, Beatrice ; Shields, Beverley ; Parnell, Kirstie S. ; Groves, Christopher J. ; Ring, Susan M. ; Pembrey, Marcus E. ; Ben-Shlomo, Yoav ; Strachan, David P. ; Power, Chris ; Jarvelin, Marjo-Riitta 

    2007-01-01

    The role of genes in normal birth-weight variation is poorly understood, and it has been suggested that the genetic component of fetal growth is small. Type 2 diabetes genes may influence birth weight through maternal genotype, by increasing maternal glycemia in pregnancy, or through fetal genotype, by altering fetal insulin secretion. We aimed to assess the role of the recently described type 2 diabetes gene TCF7L2 in birth weight. We genotyped the polymorphism rs7903146 in 15,709 individual...

  14. Vitamin D and estrogen receptor-alpha genotype and indices of bone mass and bone turnover in Danish girls

    DEFF Research Database (Denmark)

    Cusack, S.; Mølgaard, C.; Michaelsen, K. F.;

    2006-01-01

    environmental factors. VDR genotypes had no effect on bone turnover markers. XX and PP ER alpha genotypes were associated (P <0.05) with reduced levels of urinary pyridinium cross-links, whereas serum osteocalcin was similar among genotypes. These findings suggest that the rate of bone resorption was influenced...... (VDR) (FokI, TaqI) and estrogen receptor-alpha (ER alpha) (PvuII, XbaI), and bone mineral density (BMD), bone mineral content (BMC), and markers of bone turnover in 224 Danish girls aged 11-12 years. BMD and BMC were measured by dual-energy X-ray absorptiometry. Serum osteocalcin, 25(OH)D, and...

  15. COMT Val158Met Genotype Determines the Direction of Cognitive Effects Produced by Catechol-O-Methyltransferase Inhibition

    OpenAIRE

    Farrell, Sarah M.; Tunbridge, Elizabeth M.; Braeutigam, Sven; Harrison, Paul J

    2012-01-01

    Background Catechol-O-methyltransferase (COMT) metabolizes dopamine. The COMT Val158Met polymorphism influences its activity, and multiple neural correlates of this genotype on dopaminergic phenotypes, especially working memory, have been reported. COMT activity can also be regulated pharmacologically by COMT inhibitors. The inverted-U relationship between cortical dopamine signaling and working memory predicts that the effects of COMT inhibition will differ according to COMT genotype. Method...

  16. Age, scrapie status, PrP genotype and follicular dendritic cells in ovine ileal Peyer's patches.

    Science.gov (United States)

    Marruchella, Giuseppe; Ligios, Ciriaco; Di Guardo, Giovanni

    2012-10-01

    Follicular dendritic cells (FDCs) residing within ileal Peyer's patches (PPs) are of crucial relevance for sheep scrapie early pathogenesis and subsequent scrapie prion neuroinvasion. In this study, ileal PP follicles were significantly more numerous in lambs than in adult Sarda breed sheep, with significant differences being also found in lymphoid follicle area, perimeter and FDC density. Furthermore, PrPd deposition within ileal PPs and host's PrP genotype did not significantly influence these parameters. We conclude that age significantly affects FDC density in ileal PPs from Sarda breed ovines, independently from host's scrapie status and PrP genotype. PMID:21962485

  17. FTO genotype is associated with exercise training-induced changes in body composition

    OpenAIRE

    Rankinen, Tuomo; Rice, Treva; Teran-Garcia, Margarita; Rao, D.C.; Bouchard, Claude

    2009-01-01

    The fat mass and obesity associated (FTO) gene is the first obesity-susceptibility gene identified by genome-wide association scans and confirmed in several follow-up studies. Homozygotes for the risk allele (A/A) have 1.67 times greater risk of obesity than those who do not have the allele. However, it is not known if regular exercise-induced changes in body composition are influenced by the FTO genotype. The purpose of our study was to test if the FTO genotype is associated with exercise-in...

  18. Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

    Institute of Scientific and Technical Information of China (English)

    Edward; M.; Smith; Jack; Littrell; Michael; Olivier

    2007-01-01

    High-throughput SNP genotyping platforms use automated genotype calling algo- rithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been opti- mized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be ad- visable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  19. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    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)

  20. Genotyping Pattern Among Iranian HCV Positive Patients

    Directory of Open Access Journals (Sweden)

    A Sarafnejad

    2010-06-01

    Full Text Available Background: Successful treatment to eliminate HCV RNA depends on the identified genotype. In the present study, we compared the frequency of different HCV genotypes, during four years study (2004 till 2008.Methods: Sera specimens were received from 16 provinces of Iran. We used High Pure Viral Nucleic Acid Purification kit for extraction and samples were tested with improved form of RT-PCR technique. HCV genotypes were determined using Amplisense PCR kit and Amplicor HCV Monitoring Version 2 test utilized a reverse transcription (RT-PCR approach to quantitative HCV RNA. Two hundreds six HCV positive specimens were entered to the study out of 389 tested samples.Results: Type 3a was the most frequent type (46.6%, followed by type 1 (including 1a and 1b with 25.73% and 17.47% for each respectively with 43.2%. Looking through collected results of the four years study confirmed the rate of HCV infection in those single genotypes 1b, 3a were slightly increased from 12.22% and 38.88% in the first year to 18.66 and 46.51% in the fourth year of the study period.Conclusion: The analyzed data proved that some patients were infected with two different types. High viral load was also more correlated to genotype 1 than other types.

  1. Genotype variation of hepatitis c virus in district buner swat

    International Nuclear Information System (INIS)

    Objective: To determine the frequency of various genotypes of Hepatitis C virus in District Buner, Swat. Methods: This Descriptive case series study was conducted at District Headquarter Hospital Daggar, and Bilal Medical Trust, Pir Baba, Swat, Pakistan from January 2007 to June 2008. A total of 400 patients, 154 Male and 246 Female aged 16-65 years (Mean age 31+-13 years) without clinical and ultrasonographic evidence of cirrhosis, and with positive Hepatitis C Virus (HCV) antibodies by ELIZA, and HCV RNA detected by PCR were included. Hepatitis C virus genotypes were checked in serum by real time PCR (RT-PCR). Results: Genotype 3 was the most common type accounting for 61.5% of the study population. Amongst the subtypes, 182 (45.5%) had genotype 3a and 64 (16%) had genotype 3b. Thirty-five (8.7%) patients had genotype 1a, 12 (3%) had genotype 1b. Twenty-six (6.5%) patients had genotype 2a. Four (1%) patients had genotype 2b. Three (0.75%) patients had genotype 4a, and 1 (0.25%) had genotype 6a. Sixty-four (16%) patients had mixed infections. Forty (10%) patients had genotype 3a and 3b, 12 (3%) patients had genotype 1a, 1b, and 9 (2.25%) patients had genotype 2a and 1c, 2 (0.5%) had genotype1a, 3a and 1 patient (0.25%) had genotype 1a, 3b. Nine (2.25%) patients had untypable genotype. Conclusion: Genotype 3 with its subtypes 3a and 3b is the commonest Hepatitis C virus present in District Buner, Swat. The others in order of decreasing frequency are genotype 1a, 2a and mixed types. (author)

  2. Relationship among root characteristics and differential potassium uptake and use efficiency of selected cotton genotypes under potassium deficiency stress

    International Nuclear Information System (INIS)

    Potassium (K) uptake and K use efficiency are the most important characters of plant genotypes that determine their biomass production under K deficiency stress. This study reports the influence of some important root characters on the K uptake and use efficiency of three pre-selected cotton genotypes under K deficiency stress. These genotypes included CIM-506, NIAB-78 and NIBGE-2, selected on the basis of their differential K use efficiency i.e., low, medium and high, respectively. Cotton genotypes significantly (p<0.01) differed for their K use efficiency, K uptake of shoot, root and on total basis, tap-root length, lateral root number and specific K absorption rate based on tap root length. While, K accumulation rate, K translocation efficiency, K transport rate and specific K absorption rate based on root dry weight were non-significant. The genotype NIBGE-2 was the most tolerant genotype to K deficiency stress and performed best for all the parameters studied followed by NIAB-78 and CIM-506. A significant correlation was observed between K use efficiency and K uptake of cotton genotypes. The root characteristics viz., tap root length, lateral root number, K accumulation rate and specific K absorption rate directly influence both K uptake and use efficiency of cotton under deficient K condition. K translocation rate and specific K absorption rate, based on root dry weight, directly influence total K uptake but not K use efficiency. These physio-morphological root traits of cotton are highly important while breeding for K-use-efficient cotton genotypes. (author)

  3. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A;

    2015-01-01

    Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate...... adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble, in the...

  4. Carcass traits of four rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Ajda Kermauner

    2010-01-01

    Full Text Available Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A and C exhibited slightly worse carcass traits than rabbits in line C, but the differences were not statistically significant. The Californian breed gave worse results than crossbreeding with line C, though in most cases the differences between AxC and AxCal were not significant. The differences between genotypes in hind leg tissue composition, pH and meat colour were not statistically significant.

  5. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

    Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

    1996-04-01

    A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA

  6. Role of cytochrome P450 genotype in the steps toward personalized drug therapy

    Directory of Open Access Journals (Sweden)

    Cavallari LH

    2011-11-01

    Full Text Available Larisa H Cavallari1,2, Hyunyoung Jeong1,2, Adam Bress11Department of Pharmacy Practice, 2Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USAAbstract: Genetic polymorphism for cytochrome 450 (P450 enzymes leads to interindividual variability in the plasma concentrations of many drugs. In some cases, P450 genotype results in decreased enzyme activity and an increased risk for adverse drug effects. For example, individuals with the CYP2D6 loss-of-function genotype are at increased risk for ventricular arrhythmia if treated with usual does of thioridazine. In other cases, P450 genotype may influence the dose of a drug required to achieve a desired effect. This is the case with warfarin, with lower doses often necessary in carriers of a variant CYP2C9*2 or *3 allele to avoid supratherapeutic anticoagulation. When a prodrug, such as clopidogrel or codeine, must undergo hepatic biotransformation to its active form, a loss-of-function P450 genotype leads to reduced concentrations of the active drug and decreased drug efficacy. In contrast, patients with multiple CYP2D6 gene copies are at risk for opioid-related toxicity if treated with usual doses of codeine-containing analgesics. At least 25 drugs contain information in their US Food and Drug Administration-approved labeling regarding P450 genotype. The CYP2C9, CYP2C19, and CYP2D6 genes are the P450 genes most often cited. To date, integration of P450 genetic information into clinical decision making is limited. However, some institutions are beginning to embrace routine P450 genotyping to assist in the treatment of their patients. Genotyping for P450 variants may carry less risk for discrimination compared with genotyping for disease-associated variants. As such, P450 genotyping is likely to lead the way in the clinical implementation of pharmacogenomics. This review discusses variability in the CYP2C9, CYP2C19, and CYP2D6 genes and the

  7. Yield stability and relationships among stability parameters in faba bean (Vicia faba L.) genotypes

    Institute of Scientific and Technical Information of China (English)

    Tamene Temesgen; Gemechu Keneni; Tadese Sefera; Mussa Jarso

    2015-01-01

    Sixteen faba bean genotypes were evaluated in 13 environments in Ethiopia during the main cropping season for three years (2009–2011). The objectives of the study were to evaluate the yield stability of the genotypes and the relative importance of different stability parameters for improving selection in faba bean. The study was conducted using a randomized complete block design with four replications. G × E interaction and yield stability were estimated using 17 different stability parameters. Pooled analysis of variance for grain yield showed that the main effects of both genotypes and environments, and the interaction effect, were highly significant (P≤0.001) and (P≤0.01), respectively. The environment main effect accounted for 89.27% of the total yield variation, whereas genotype and G × E interaction effects accounted for 2.12% and 3.31%, respectively. Genotypic superiority index (Pi) and FT3 were found to be very informative for selecting both high-yielding and stable faba bean genotypes. Twelve of the 17 stability parameters, including CVi, RS,α,λ, S2di, bi, Si(2), Wi,σi2, EV, P59, and ASV, were influenced simultaneously by both yield and stability. They should accordingly be used as complementary criteria to select genotypes with high yield and stability. Although none of the varieties showed consistently superior performance across all environments, the genotype EK 01024-1-2 ranked in the top third of the test entries in 61.5% of the test environments and was identified as the most stable genotype, with type I stability. EK 01024-1-2 also showed a 17.0%seed size advantage over the standard varieties and was released as a new variety in 2013 for wide production and named “Gora”. Different stability parameters explained genotypic performance differently, irrespective of yield performance. It was accordingly concluded that assessment of G × E interaction and yield stability should not be based on a single or a few stability parameters but

  8. Hepatitis C virus genotype diversity among intravenous drug users in Yunnan Province, Southwestern China.

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    Zhihui Zhang

    Full Text Available BACKGROUND: Recently, high proportions (15.6%-98.7% of intravenous drug users (IDUs in China were found to be positive for hepatitis C virus (HCV. Yunnan Province is located in southwestern China and borders one of the world's most important opium-producing regions, thus it is an important drug trafficking route to other regions of China. METHODOLOGY/PRINCIPAL FINDINGS: Here, we assessed 100 HCV-positive plasma samples from IDUs who were enrolled through the Kunming Center for Disease Control and Prevention in 2012. HCV C/E1 fragments were PCR-amplified and sequenced. We identified eight HCV subtypes (1a, 1b, 3a, 3b, 6a, 6n, 6u and 6v, of which genotype 6 was most predominant (frequency, 47% followed by genotypes 3 (41% and 1 (12%. HCV subtypes 6n (30% and 3b (29% were most common and were identified in 59% of the IDUs. We compared HCV genotypes among IDUs in Yunnan Province with those from other regions and found that the distribution patterns of HCV genotypes in Yunnan Province were similar to those in southern China, but different from those in eastern China. However, the distribution patterns of HCV subtypes varied among Yunnan Province and southern China, despite the shared similar genotypes. A comparison of the current data with those previously reported showed that the frequency of HCV genotype 6 increased from 25% to 47% within 5 years, especially subtypes 6a (5% to 15% and 6n (11.2% to 30%. In contrast, the frequencies of subtypes 3b and 1b decreased by almost 50% within 5 years. CONCLUSION/SIGNIFICANCE: Our results provided further information to support the assertion that drug trafficking routes influence HCV transmission patterns among IDUs in Yunnan Province. The frequency of HCV genotypes and subtypes changed rapidly among IDUs in Yunnan Province and subtypes 6a and 6n may have originated in Vietnam and Myanmar, respectively.

  9. Nucleos(tide analogues treatment outcome in genotype B and C chronic hepatitis B

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    Myo Nyein Aung

    2010-01-01

    Full Text Available Background : Hepatitis B genotypes influence the course and severity of the disease. Aim: To compare the treatment outcome of chronic hepatitis B genotype B and C patients after treating with nucleos(tide analogues for six months. Patients and Methods: Forty chronic hepatitis B patients attending the liver clinic of Hospital for Tropical diseases, Bangkok, were studied in retrospective cohort design. Six genotype B patients (15% and thirty-four genotype C patients (85% were treated. Serum hepatitis B viral load , serum alanine amino transferase level, HBeAg status and alpha-feto protein level were measured at the time of starting nucleos(t analogues therapy, and six months later. Besides, achievement of undetectable viral load was assessed in patients with normal serum alanine amino transferase compared to patients with high serum alanine amino transferase level. Results: After six months of nucleos (t analogues treatment, achievement of undetectable hepatitis B viral load was higher in genotype B patients (66.7% than in genotype C patients (42.4% (Relative Risk=1.57, 0.79-3.14. Biochemical remission, HBeAg seroconversion and tumor marker levels between the two groups were not significantly different. Moreover, achievement of undetectable hepatitis B viral load was significantly higher in normal alanine amino transferase level (75% than in patients with high serum alanine amino transferase level (33.3% on nucleos(tide analogue treatment (Relative Risk=2.25, 1.20- 4.20. Conclusion: Chronic hepatitis B treatment outcome between genotype B and C were not significantly different. Patients with normalized serum alanine amino transferase level tend to achieve undetectable viral load after nucleoside analogues treatment.

  10. Physical and functional evaluation of extruded flours obtained from different rice genotypes

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    Fernanda Salamoni Becker

    2014-08-01

    Full Text Available The transformation of broken grains into native flours modified by extrusion is an alternative to add value to these co-products from the paddy rice processing. This study aimed to analyze the process of extrusion cooking on the physical and functional characteristics of extruded flours obtained from different rice genotypes (IRGA-417, BRS-Primavera and CNA-8502. The experimental design was completely randomized (3x2 factorial with four original replicates and analysis of variance to assess particle size, instrumental color parameters (L*, a* and b*, water absorption index (WAI, milk absorption index (MAI, oil absorption index (OAI, water solubility index (WSI and milk solubility index (MSI of rice flour. The extrusion process promoted changes in all physical and functional properties of rice flour, but only WSI and color parameters were influenced by genotype and by the industrial processing. Rice flours become darker, tending to a more reddish and yellow coloration after extrusion. Native and extruded rice flours of genotypes IRGA-417, BRS-Primavera and extruded rice flour of genotype CNA-8502 showed finer particles, while native flour of genotype CNA-8502 showed coarser particles. The extruded flours of IRGA-417 genotype obtained higher expansion and luminosity, and lower values of chroma a*, chroma b* and water solubility, while the BRS-Primavera higher values of chroma a* and b*, and lower luminosity and expansion, and CAN-8502 higher water solubility and lower expansion and value of chroma a*. The extrusion process led to flours with high water and milk absorption and solubility, low oil absorption and with potential for application in instant products, regardless of genotype.

  11. ACTN3 genotype in professional soccer players

    OpenAIRE

    Santiago Dorrego, Catalina; González-Freire, Marta; Serratosa Fernández, Luis; Morate, F. J.; Meyer, T.; Gómez Gallego, Félix; Lucía Mulas, Alejandro

    2008-01-01

    The authors studied the frequency distribution of alpha-actinin-3 (ACTN3) R577X genotypes in 60 top-level professional soccer players. The results were compared with those of 52 elite endurance athletes and 123 sedentary controls. The per cent distribution of RR and RX genotypes in soccer players (48.3% and 36.7%) was significantly higher and lower, respectively, than controls (28.5% and 53.7%) and endurance athletes (26.5% and 52%) (p = 0.041). Although there are notable exceptions, elite so...

  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. Carcass traits of four rabbit genotypes

    OpenAIRE

    Ajda Kermauner; Silvester Zgur

    2010-01-01

    Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed) were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A ...

  14. ACE I/D genotype, adiposity, and blood pressure in children

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    Rothschild Max

    2009-03-01

    Full Text Available Abstract Background Angiotensin converting enzyme (ACE is a possible candidate gene that may influence both body fatness and blood pressure. Although several genetic studies have been conducted in adults, relatively few studies have examined the contribution of potential candidate genes, and specifically ACE I/D, on adiposity and BP phenotypes in childhood. Such studies may prove insightful for the development of the obesity-hypertension phenotype early in life. The purpose of this study was to examine differences in body fatness and resting blood pressure (BP by ACE I/D genotype, and determine if the association between adiposity and BP varies by ACE I/D genotype in children. Methods 152 children (75 girls, 77 boys were assessed for body composition (% body fat using dual energy x-ray absorbtiometry and resting BP according to American Heart Association recommendations. Buccal cell samples were genotyped using newly developed PCR-RFLP tests for two SNPs (rs4341 and rs4343 in complete linkage disequilibrium with the ACE I/D polymorphism. Partial correlations were computed to assess the ociations between % body fat and BP in the total sample and by genotype. ANCOVA was used to examine differences in resting BP by ACE I/D genotype and fatness groups. Results Approximately 39% of youth were overfat based on % body fat (>30% fat in girls, 25% fat in boys. Body mass, body mass index, and fat-free mass were significantly higher in the ACE D-carriers compared to the II group (p Conclusion ACE D-carriers are heavier than ACE II children; however, BP did not differ by ACE I/D genotype but was adversely influenced in the overfat D-carriers. Further studies are warranted to investigate the genetics of fatness and BP phenotypes in children.

  15. Genotype by Environment Effects on Potato Mini-Tuber Seed Production in an Aeroponics System

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    Julián F. Mateus-Rodriguez

    2014-11-01

    Full Text Available In order to evaluate the environmental effect on plant development and mini-tuber production of a diverse group of potato genotypes grown under an aeroponic system, a G × E interaction experiment was carried out in greenhouses located at CIP’s experimental stations in La Molina (Lima and Huancayo (Junín. Five contrasting environments were set-up and evaluated. A combined Analysis of Variance was performed for the variables “days to tuber set”, “days to senescence” and “plant height”. An Additive Main Effects and Multiplicative Interaction (AMMI Analysis was performed for yield variables: mini-tuber “weight” and “number of mini-tubers” per plant. There was a high variation in all the responses to the treatments. “Days to tuber set” was influenced by genetic responses, temperature and greenhouse Photosynthetically Active Radiation intensity. Considerable increases in the length of the vegetative cycle and plant height were recorded for all genotypes, and these were particularly notable in the warmer coastal environments. AMMI analysis showed that yield variables were primarily influenced by the genotypic effect followed by the genotype by environment interaction effect. The Venturana variety (T2 was the best performing genotype with a total average mini-tuber “weight” of 644 g per plant while the Chucmarina variety (T1 performed best for the variable “number of mini-tubers” with an overall average of 60.2 mini-tubers per plant. Both showed stability across different environments for these variables. The advanced clones T3 (395434.1, T5 (397077.16 and T6 (397073.16 showed stability for yield variables, but their performance was below the overall average of the trial. It is recommended that the environment and management should ideally be tailored to the genotype as this will result in significant yield gains.

  16. Genotypes and viral load of hepatitis C virus among persons attending a voluntary counseling and testing center in Ethiopia.

    Science.gov (United States)

    Abreha, Tesfay; Woldeamanuel, Yimtubezinash; Pietsch, Corinna; Maier, Melanie; Asrat, Daniel; Abebe, Almaz; Hailegiorgis, Bereket; Aseffa, Abraham; Liebert, Uwe Gerd

    2011-05-01

    The prevalence of different genotypes of hepatitis C virus (HCV) in Ethiopia is not known. HCV genotypes influence the response to therapy with alpha-interferon alone or in combination with ribavirin. A cross sectional study was conducted on attendees of voluntary counseling and testing center. Serum samples from 1,954 (734 HIV positive and 1,220 HIV negative) individuals were screened for HCV antibody. Active HCV infection was confirmed by quantitative PCR in 18 of the 71 samples with anti-HCV antibodies. The HCV viral load ranged from 39,650 to 9,878,341 IU/ml (median 1,589,631 IU/ml) with no significant difference [χ(2)(17) = 18.00, P = 0.389] between persons positive or negative for HIV. The viral load of HCV was, however, higher in older study subjects (r = 0.80, P = 0.000). HCV genotypes were determined using the VERSANT HCV Genotype Assay (LiPA) and sequence analysis of the NS5b region of the HCV genome. Diverse HCV genotypes were found including genotypes 1, 2, 4, and 5. There was no difference in the distribution regarding the HIV status. As in other parts of the world, genotyping of HCV must be considered whenever HCV is incriminated as a cause of hepatitis. PMID:21351106

  17. Genetic diversity and comparison of physicochemical and nutritional characteristics of six quinoa (Chenopodium quinoa willd. genotypes cultivated in Chile

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    Margarita Miranda

    2012-12-01

    Full Text Available The present study was focused on the analysis of agronomical, nutritional, physicochemical, and antioxidant properties of six genetically different quinoa (Chenopodium quinoa Willd genotypes cultivated in three distinctive geographical zones of Chile. Ancovinto and Cancosa genotypes from the northern Altiplano (19 ºS, Cáhuil and Faro from the central region (34 ºS, and Regalona and Villarica from the southern region (39 ºS are representative of high genetic differentiation among the pooled samples, in particular between Altiplano and the central-southern groups. A Common-Garden Assay at 30 ºS showed significant differences among seed origins in all morphometric parameters and also in yields. Altiplano genotypes had larger panicule length but no seed production. A significant influence of the different quinoa genotypes on chemical composition and functional properties was also observed. Protein concentration ranged from 11.13 to 16.18 g.100 g-1 d.m., while total dietary fiber content ranged from 8.07-12.08 g.100 g-1 d.m., and both were the highest in Villarrica ecotype. An adequate balance of essential amino acids was also observed. Sucrose was the predominant sugar in all genotypes. Antioxidant activity was high in all genotypes, and it was highest in Faro genotype (79.58% inhibition.

  18. CYP2D6*10B基因型对中国人普罗帕酮对映体药动学的影响%Influence of CYP2D6*10B genotype on pharmacokinetics of propafenone enantiomers in Chinese subjects

    Institute of Scientific and Technical Information of China (English)

    陈冰; 蔡卫民

    2003-01-01

    AIM: To study the relationship between genotype of CYP2D6*10B and pharmacokinetics of propafenone enantiomers. METHODS: Genotype of 17 healthy Chinese HAN subjects was determined by an allele specific amplification method. The blood samples (0-15 h) of the subjects were taken after oral administration of a single dose (400 mg) of propafenone hydrochloride. Concentrations of propafenone enantiomers in plasma were mea sured by a reverse-phase HPLC with precolumn derivatization. RESULTS: Seventeen subjects characterized for CYP2D6* 1 0B genotype included (* 1/* 1) (n = 4), (* 1/* 10) (n = 5) and (* 10/* 10) (n = 8). The metabolic ratios (lg MR) of the three genotypes were -2.68+0.23, -2.2+0.7, and -1.1 +0.5, respectively. The AUC of the three groups that of *1/*10 group or *1/*1 group, and the CL of both enantiomers in *10/*10 is only half of that of *1/*10 group or * 1/* 1 group (P<0.05). CONCLUSION: CYP2D6* 10B alleles induce the declined activity of CYP2D6 and impair the metabolism of propafenone.

  19. The frequency of GSTT1 null genotype in Turkish population and lung cancer risk

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    Demir A

    2005-01-01

    Full Text Available BACKGROUND : Previous studies have suggested that Glutathione S -transferase (GST genotypes may play a role in determining susceptibility to lung cancer, though the data are often conflicting. In different ethnic groups variations in null allele frequency has been observed. AIMS: We aimed to evaluate whether genetic polymorphisms of Glutathione S -transferase theta (GSTT1 influence individual susceptibility to lung cancer in Turkish population. We tried to clarify the frequencies of GSTM1 gene polymorphisms in a Turkish population. METHODS: DNA samples, extracted from the whole blood were amplified using polymerase chain reaction (PCR method in all of the 68 cases, composed of 31 previously diagnosed lung cancer and 37 healthy controls. RESULTS: The prevalence of GSTT1 null genotype in the lung cancer patients was 29%, compared to 11% in control group. GSTT1 null genotype was found to be higher in cancer group compared to the control group, although it was not statistically significant (OR = 3.37, 95% CI = 0.92-12.32, P = 0.06. There was also no significant relation in GSTT1 genotypes among histopathology types of lung cancers. The frequency of GSTT1 was found to be 25.4% ( n = 952 when the studies of Turkish population were reviewed. CONCLUSION: It can be concluded that carrying the GSTT1 null genotype may be accepted as a weak risk factor for the susceptibility to lung cancer.

  20. Genotype by environment interaction for seed yield per plant in rapeseed using AMMI model

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    Ana Marjanović-Jeromela

    2011-02-01

    Full Text Available The objective of this study was to assess genotype by environment interaction for seed yield per plant in rapeseed cultivars grown in Northern Serbia by the AMMI (additive main effects and multiplicative interaction model. The study comprised 19 rapeseed genotypes, analyzed in seven years through field trials arranged in a randomized complete block design, with three replicates. Seed yield per plant of the tested cultivars varied from 1.82 to 19.47 g throughout the seven seasons, with an average of 7.41 g. In the variance analysis, 72.49% of the total yield variation was explained by environment, 7.71% by differences between genotypes, and 19.09% by genotype by environment interaction. On the biplot, cultivars with high yield genetic potential had positive correlation with the seasons with optimal growing conditions, while the cultivars with lower yield potential were correlated to the years with unfavorable conditions. Seed yield per plant is highly influenced by environmental factors, which indicates the adaptability of specific genotypes to specific seasons.

  1. FT-IR Characterization of Pollen Biochemistry, Viability, and Germination Capacity in Saintpaulia H. Wendl. Genotypes

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    Erzsebet Buta

    2015-01-01

    Full Text Available FT-IR characterization of pollen biochemistry was analyzed to detect possible connection with the viability (by staining with potassium iodide, 25% and the germination capacity (on solid nutrient medium, in 15 Saintpaulia genotypes. Vibrational spectroscopy indicates that the pollen of S. ionantha genotype “Red Velvet” is rich in proteins, lipids, triglycerides, and esters and has a viability of 88.4% and a low germination capacity (27.16%. For S. ionantha “Jolly Red” and “Lucky Ladybug” genotypes, pollen showed high viability (88.81–91.49% and low germination capacity (23.02–9.17%, even though the pollen is rich in carbohydrates. S. ionantha “Aloha Orchid” genotype has the highest percentage of viability (94.32% and germination capacity (45.73% and a rich content of carbohydrates and polygalacturonic acids. In S. rupicola and S. ionantha genotypes, the rich content of polygalacturonic acids, lipids, and carbohydrates favourably influenced the germination capacity. Spectroscopic result indicates, through different absorbance band intensity, a possible link between biochemical composition, viability, and germination capacity of Saintpaulia pollen. To determine exactly the relation between biochemistry and biological processes, it is necessary to initiate quantitative researches.

  2. Implications of Genotype by Environment Interactions in Dairy Sheep Welfare

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    Dinu Gavojdian

    2014-05-01

    Full Text Available Small ruminants are the most extensively farmed livestock species in Europe, as a result being extremely exposed to natural hazards which leads to strong interactions between genotype and environment. Aim of the current review was to outline and discuss the main welfare issues and economic implications with regards to the genotype by environment interactions in dairy sheep. Researches concerning the additive genetic effect on milk yield, shown that this accounts only for 10%, while the milk production is 90% influenced by environmental factors, highlighting the major role that management and nutrition play in the dairy production of sheep. Nowadays, dairy sheep breeds (e.g. Eastern Friesian and Lacaune, are being introduced and reared in various countries under an extremely wide range of rearing conditions, without adequate knowledge on their acclimatization to the new specific conditions. It was concluded that a welfare assessment protocol for dairy sheep does not exist up today, moreover, there is a serious lack of data concerning the genetic and environmental factors affecting the welfare status of dairy sheep at farm level under different production systems.

  3. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52):

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2014-01-01

    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. Cryptosporidium Pig Genotype II in Immunocompetent Man

    Czech Academy of Sciences Publication Activity Database

    Kváč, Martin; Květoňová, Dana; Sak, Bohumil; Ditrich, Oleg

    2009-01-01

    Roč. 15, č. 6 (2009), s. 982-983. ISSN 1080-6040 R&D Projects: GA ČR GP523/07/P117 Institutional research plan: CEZ:AV0Z60220518 Keywords : immunocompetent patients * cryptosporidiosis * Cryptosporidium pig genotype II Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 6.794, year: 2009

  5. Camelina: Adaptation and performance of genotypes

    Science.gov (United States)

    Camelina (Camelina sativa L. Crantz) has shown potential as an alternative and biofuel crop in cereal-based cropping systems. Our study investigated the adaption, performance, and yield stability among camelina genotypes across diverse US Pacific Northwest (PNW) environments. Seven named camelina ge...

  6. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  7. Profile and Functional Properties of Seed Proteins from Six Pea (Pisum sativum Genotypes

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    Nikola Ristic

    2010-12-01

    Full Text Available Extractability, extractable protein compositions, technological-functional properties of pea (Pisum sativum proteins from six genotypes grown in Serbia were investigated. Also, the relationship between these characteristics was presented. Investigated genotypes showed significant differences in storage protein content, composition and extractability. The ratio of vicilin:legumin concentrations, as well as the ratio of vicilin + convicilin: Legumin concentrations were positively correlated with extractability. Our data suggest that the higher level of vicilin and/or a lower level of legumin have a positive influence on protein extractability. The emulsion activity index (EAI was strongly and positively correlated with the solubility, while no significant correlation was found between emulsion stability (ESI and solubility, nor between foaming properties and solubility. No association was evident between ESI and EAI. A moderate positive correlation between emulsion stability and foam capacity was observed. Proteins from the investigated genotypes expressed significantly different emulsifying properties and foam capacity at different pH values, whereas low foam stability was detected. It appears that genotype has considerable influence on content, composition and technological-functional properties of pea bean proteins. This fact can be very useful for food scientists in efforts to improve the quality of peas and pea protein products.

  8. Effect of genotype, finishing system, and sex on physiochemical characteristics of goat meat

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    Luciana Rodrigues

    2011-12-01

    Full Text Available Seventy-eight kids of both sexes and five genotypes were used: Alpine, ½ Boer + ½ Alpine (½ BA, ¾ Boer + ¼ Alpine, ½ Anglo-nubian + ½ Alpine and "tricross" (½ Anglo-nubian + ¼ Boer + ¼ Alpine with initial average weight of 14.1 ± 2.5. The objective was to evaluate the effect of genotype, finishing system, and sex on the physiochemical characteristics of goat meat. Finishing systems were: ST1 - kid + dam in pasture and ST2 - weaned kid and feedlot. Kids in ST1 were kept in an area with Panicum maximum cv. Tanzania, and after grazing, water and mineral salt/mix were fed ad libitum to the animals. The animals in ST2 were confined in collective pens distributed according to genotypes and received diet with 16% CP and 73% TDN. The values of pH, a* (red content, Cooking Loss (CL, and Ether Extract (EE percentage were influenced by genotype. Values for red content (a* and L* (brightness, CL and percentages of moisture, protein, EE, and ash were influenced by the finishing system. Longissimus dorsi muscle from animals ½ BA exhibited better physiochemical characteristics. For greater tenderness and higher percentages of fat, consumers should choose female kid goat meat.

  9. Genotype-environment associations support a mosaic hybrid zone between two tidal marsh birds.

    Science.gov (United States)

    Walsh, Jennifer; Rowe, Rebecca J; Olsen, Brian J; Shriver, W Gregory; Kovach, Adrienne I

    2016-01-01

    Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh-level characteristics in shaping a hybrid zone between two recently diverged avian taxa - Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co-occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space. PMID:26811792

  10. ERIC-PCR genotyping of paenibacillus larvae in southern Italian honey and brood combs.

    Science.gov (United States)

    Di Pinto, Angela; Novello, Lucia; Terio, Valentina; Tantillo, Giuseppina

    2011-11-01

    Given the considerable economic loss to beekeepers worldwide and the possible public health implications related to the presence of antibiotics in honey, an American Foulbrood (AFB) monitoring/prevention program for Paenibacillus larvae is regarded as essential. This study investigates the occurrence and distribution of P. larvae genotypes in honey and brood combs from Apulia (Italy). Genotyping of P. larvae isolates using ERIC-PCR generated a total of four different ERIC banding patterns (ERIC-A, ERIC-B, ERIC-C, ERIC-D), including fragments ranging from 200 to 3000 bp. Considering that the genotype has an influence on P. larvae infections and multi-genotype infections of colonies or apiaries may increase the complexity of P. larvae infections by influencing the type and speed of the development of clinical symptoms, the findings of the present study could be helpful for training veterinarians, bee inspector's extension staff, and beekeepers, thus improving the detection of AFB infections in the field. PMID:21853316

  11. Genotypic Variation of Early Maturing Soybean Genotypes for Phosphorus Utilization Efficiency under Field Grown Conditions

    International Nuclear Information System (INIS)

    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)

  12. Assessment of genetic variation in Bulgarian tomato (Solanum lycopersicum L.) genotypes, using fluorescent SSR genotyping platform

    OpenAIRE

    TODOROVSKA, Elena; IVANOVA, Albena; Daniela GANEVA; Galina PEVICHAROVA; Molle, Emil; Bojinov, Bojin; Radkova, Mariana; Danailov, Zhivko

    2014-01-01

    Genetic variability in modern crops is limited due to domestication and selection processes. Genetic variation in eight Bulgarian tomato varieties and breeding lines (variety Plovdivska karotina, variety IZK Alya, L21β, L53β, L1140, L1116, L975, L984) differing in their morphological and biochemical composition was assessed using a highly efficient and low-cost fluorescent simple sequence repeat (SSR) genotyping platform. Genotyping was conducted with 165 publicly available microsatellite mar...

  13. Staphylococcus aureus genotype B and other genotypes isolated from cow milk in European countries.

    Science.gov (United States)

    Cosandey, A; Boss, R; Luini, M; Artursson, K; Bardiau, M; Breitenwieser, F; Hehenberger, E; Lam, Th; Mansfeld, M; Michel, A; Mösslacher, G; Naskova, J; Nelson, S; Podpečan, O; Raemy, A; Ryan, E; Salat, O; Zangerl, P; Steiner, A; Graber, H U

    2016-01-01

    Staphylococcus aureus is globally one of the most important pathogens causing contagious mastitis in cattle. Previous studies, however, have demonstrated in Swiss cows that Staph. aureus isolated from bovine intramammary infection is genetically heterogeneous, with Staph. aureus genotype B (GTB) and GTC being the most prominent genotypes. In addition, Staph. aureus GTB was found to be contagious, whereas Staph. aureus GTC and all the remaining genotypes were involved in individual cow disease. The aim of this study was to subtype strains of Staph. aureus isolated from bovine mastitic milk and bulk tank milk to obtain a unified view of the presence of bovine staphylococcal subtypes in 12 European countries. A total of 456 strains of Staph. aureus were subjected to different typing methods: ribosomal spacer PCR, detection of enterotoxin genes, and detection of gene polymorphisms (lukE, coa). Major genotypes with their variants were combined into genotypic clusters (CL). This study revealed 5 major CL representing 76% of all strains and comprised CLB, CLC, CLF, CLI, and CLR. The clusters were characterized by the same genetic properties as the Swiss isolates, demonstrating high clonality of bovine Staph. aureus. Interestingly, CLB was situated in central Europe whereas the other CL were widely disseminated. The remaining 24% of the strains comprised 41 genotypes and variants, some of which (GTAM, GTBG) were restricted to certain countries; many others, however, were observed only once. PMID:26585469

  14. CYP2D6 genotype dependent oxycodone metabolism in postoperative patients.

    Directory of Open Access Journals (Sweden)

    Ulrike M Stamer

    Full Text Available BACKGROUND: The impact of polymorphic cytochrome P450 CYP2D6 enzyme on oxycodone's metabolism and clinical efficacy is currently being discussed. However, there are only spare data from postoperative settings. The hypothesis of this study is that genotype dependent CYP2D6 activity influences plasma concentrations of oxycodone and its metabolites and impacts analgesic consumption. METHODS: Patients received oxycodone 0.05 mg/kg before emerging from anesthesia and patient-controlled analgesia (PCA for the subsequent 48 postoperative hours. Blood samples were drawn at 30, 90 and 180 minutes after the initial oxycodone dose. Plasma concentrations of oxycodone and its metabolites oxymorphone, noroxycodone and noroxymorphone were analyzed by liquid chromatography-mass spectrometry with electrospray ionization. CYP2D6 genotyping was performed and 121 patients were allocated to the following genotype groups: PM (poor metabolizer: no functionally active CYP2D6 allele, HZ/IM (heterozygous subjects, intermediate metabolizers with decreased CYP2D6 activity, EM (extensive metabolizers, normal CYP2D6 activity and UM (ultrarapid metabolizers, increased CYP2D6 activity. Primary endpoint was the genotype dependent metabolite ratio of plasma concentrations oxymorphone/oxycodone. Secondary endpoint was the genotype dependent analgesic consumption with calculation of equianalgesic doses compared to the standard non-CYP dependent opioid piritramide. RESULTS: Metabolism differed between CYP2D6 genotypes. Mean (95%-CI oxymophone/oxycodone ratios were 0.10 (0.02/0.19, 0.13 (0.11/0.16, 0.18 (0.16/0.20 and 0.28 (0.07/0.49 in PM, HZ/IM, EM and UM, respectively (p = 0.005. Oxycodone consumption up to the 12(th hour was highest in PM (p = 0.005, resulting in lowest equianalgesic doses of piritramide versus oxycodone for PM (1.6 (1.4/1.8; EM and UM 2.2 (2.1/2.3; p<0.001. Pain scores did not differ between genotypes. CONCLUSIONS: In this postoperative setting, the number of

  15. Silhouette scores for assessment of SNP genotype clusters

    OpenAIRE

    Jonsson Mats; Ahlford Annika; Lovmar Lovisa; Syvänen Ann-Christine

    2005-01-01

    Abstract Background High-throughput genotyping of single nucleotide polymorphisms (SNPs) generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding to the two SNP alleles. In a robust assay the three clusters that define the genotypes are well separated and the distances between the data points within a cluster are short. "Silhouettes" is a graphical aid for interpretation and validation of data clusters that prov...

  16. 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....

  17. Effect of genotype on sugar beet yield and quality

    OpenAIRE

    Nenadić N.; Nedić Milan; Živanović Ljubiša; Kolarić Ljubiša; Gujaničić T.

    2003-01-01

    The effect of a considerable number of both domestic and foreign sugar beet genotypes on root yield and quality was investigated. The data demonstrated the most favorable results of some genotypes for root yield and sugar content. Trials were conducted on rhizomania infested soil, thus tolerant genotypes were used. Susceptible cultivars represented the control. In the trial root yield was high and sugar content low. On average, in the genotypes tested, root yield varied from 73.98 to 93.30 t/...

  18. Micropropagation of six Paulownia genotypes through tissue culture

    OpenAIRE

    Lydia Shtereva; VASSILEVSKA-IVANOVA, Roumiana; Tania Karceva; Boris KRAPTCHEV

    2014-01-01

    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 seed...

  19. 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...

  20. Genotyping of Chlamydia trachomatis by Microsphere Suspension Array▿

    OpenAIRE

    Huang, Chung-Ter; Wong, Wing-Wai; Li, Lan-Hui; Chiang, Chien-Chou; Chen, Bor-Dong; Li, Shu-Ying

    2008-01-01

    The identification of Chlamydia trachomatis genotypes is important for both the study of molecular epidemiology and infection control. We have developed a microsphere suspension array assay that can identify C. trachomatis genotypes rapidly and accurately and also discriminate among multiple genotypes in one clinical specimen.

  1. Angiotensin converting enzyme genotype in cardiovascular disease

    Energy Technology Data Exchange (ETDEWEB)

    Summers, K.M.; Huggard, P.R.; West, M.J. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-09-01

    Angiotensin converting enzyme (ACE) catalyses formation of angiotensin II and degradation of bradykinin, vasoactive peptides with opposing properties. The result of ACE action is to promote vasoconstriction and cell growth. PCR is used to detect a common polymorphism due to the insertion of an Alu repeat element of 287 bp into intron 16. ACE genotype has been implicated in risk for myocardial infarction (MI) and hypertension in humans. We have studied a group of 640 patients (61% male aged 64 {plus_minus} 11 years) with myocardial ischaemic syndromes, followed for 12 months after initial hospital admission. In this group, the frequency of the insertion (I) allele was 0.47 (N=1170 chromosomes), not significantly higher than the frequency of 0.46 in 112 local blood donors (50% male aged 59 {plus_minus}5 years). In the 300 patients with diagnosed MI, I allele frequency was 0.48. This is significantly higher ({chi}{sup 2}=5.78, P=0.015) than the frequency of 0.42 reported in a multi-centre study of ACE genotype in 600 male European patients with MI . There was a non-significant increase in the frequency of a cardiac event within 6 months of hospital admission in those of II genotype (N=464, 47 events to date). These results suggest that in our population, the I allele and/or II genotype may be associated with risk of MI. This contrasts with the study cited above, where the D (deletion) allele and DD genotype frequency were raised in patients compared with controls. Hypertension is associated with the ACE D allele, and does not explain the heart disease risk, which may be associated with the I allele, in this group of survivors of myocardial ischaemic disease. The difference between our results and the previous study may be due to ascertainment or ethnic differences or to problems amplifying the I allele in some heterozygotes. Clearly, the role of ACE genotype in these diseases is complex.

  2. The relationship between ciliary neurotrophic factor (CNTF genotype and motor unit physiology: preliminary studies

    Directory of Open Access Journals (Sweden)

    Ferrell Robert

    2005-09-01

    Full Text Available Abstract Background Ciliary neurotrophic factor (CNTF is important for neuronal and muscle development, and genetic variation in the CNTF gene has been associated with muscle strength. The effect of CNTF on nerve development suggests that CNTF genotype may be associated with force production via its influence on motor unit size and firing patterns. The purpose of this study is to examine whether CNTF genotype differentially affects motor unit activation in the vastus medialis with increasing isometric force during knee extension. Results Sixty-nine healthy subjects were genotyped for the presence of the G and A (null alleles in the CNTF gene (n = 57 G/G, 12 G/A. They were tested using a dynamometer during submaximal isometric knee extension contractions that were from 10–50% of their maximal strength. During the contractions, the vastus medialis was studied using surface and intramuscular electromyography with spiked triggered averaging to assess surface-detected motor unit potential (SMUP area and mean firing rates (mFR from identified motor units. CNTF genotyping was performed using standard PCR techniques from DNA obtained from leucocytes of whole blood samples. The CNTF G/A genotype was associated with smaller SMUP area motor units and lower mFR at higher force levels, and fewer but larger units at lower force levels than G/G homozygotes. The two groups used motor units with different size and activation characteristics with increasing force generation. While G/G subjects tended to utilize larger motor units with increasing force, G/A subjects showed relatively less increase in size by using relatively larger units at lower force levels. At higher force levels, G/A subjects were able to generate more force per motor unit size suggesting more efficient motor unit function with increasing muscle force. Conclusion Differential motor unit responses were observed between CNTF genotypes at force levels utilized in daily activities.

  3. Spatial patterns of ectomycorrhizal assemblages in a monospecific forest in relation to host tree genotype.

    Science.gov (United States)

    Lang, Christa; Finkeldey, Reiner; Polle, Andrea

    2013-01-01

    Ectomycorrhizas (EcM) are important for soil exploration and thereby may shape belowground interactions of roots. We investigated the composition and spatial structures of EcM assemblages in relation to host genotype in an old-growth, monospecific beech (Fagus sylvatica) forest. We hypothesized that neighboring roots of different beech individuals are colonized by similar EcM assemblages if host genotype had no influence on the fungal colonization and that the similarity would decrease with increasing distance of the sampling points. The alternative was that the EcM species showed preferences for distinct beech genotypes resulting in intraspecific variation of EcM-host assemblages. EcM species identities, abundance and exploration type as well as the genotypes of the colonized roots were determined in each sampling unit of a 1 L soil core (r = 0.04 m, depth 0.2 m). The Morisita-Horn similarity indices (MHSI) based on EcM species abundance and multiple community comparisons were calculated. No pronounced variation of MHSI with increasing distances of the sampling points within a plot was found, but variations between plots. Very high similarities and no between plot variation were found for MHSI based on EcM exploration types suggesting homogenous soil foraging in this ecosystem. The EcM community on different root genotypes in the same soil core exhibited high similarity, whereas the EcM communities on the root of the same tree genotype in different soil cores were significantly dissimilar. This finding suggests that spatial structuring of EcM assemblages occurs within the root system of an individual. This may constitute a novel, yet unknown mechanism ensuring colonization by a diverse EcM community of the roots of a given host individual. PMID:23630537

  4. Association of the vitamin D receptor genotype BB with low bone density in hyperthyroidism.

    Science.gov (United States)

    Obermayer-Pietsch, B M; Frühauf, G E; Chararas, K; Mikhail-Reinisch, S; Renner, W; Berghold, A; Kenner, L; Lackner, C

    2000-10-01

    Bone mineral density (BMD) is modulated by genetic and environmental factors or certain diseases. In several conditions such as low calcium intake, an influence of vitamin D receptor (VDR) polymorphisms on BMD has been suggested. In the present study, we investigated the relationship of Bsm I and Fok I polymorphisms of the VDR gene and BMD in patients with hyperthyroidism, a disease that often results in low BMD. Bsm I and Fok I genotypes were determined in 76 postmenopausal hyperthyroid patients and 62 healthy postmenopausal women as controls. Patients and controls were matched for age, time since menopause, and lifestyle factors and were free of estrogen medication. BMD evaluation included axial dual X-ray absorptiometry (DXA) and peripheral quantitative computed tomography (PQCT). Low BMD was defined as -2.5 STD below the young adult mean value. Biochemical parameters investigated were thyroid hormones, osteocalcin, and 25-(OH)-vitamin D3 as well as routine laboratory data. Low BMD was found in 61% of hyperthyroid patients and in only 23% of euthyroid controls. In the group of hyperthyroid patients with low bone density, the BB genotype (VDR Bsm I polymorphisms) was significantly more frequent (39%) than in controls (13%; p = 0.003) and hyperthyroid patients with normal BMD (6%; p = 0.013). The odds ratio (OR) for low BMD in patients with BB genotype was 5.7 (95% CI, 1.7-19.1; p hyperthyroidism alone. The cumulative risk for low BMD in patients with hyperthyroidism and BB genotype was 31.4 (95% CI, 3.9-256; p hyperthyroidism and the genetic background of a BB genotype may promote synergistically the development of low BMD in hyperthyroid patients. Screening for the BB genotype in these patients therefore could help to identify those with particularly high risk for the development of low BMD and allow early treatment. PMID:11028447

  5. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant.

    Science.gov (United States)

    Wagner, Maggie R; Lundberg, Derek S; Del Rio, Tijana G; Tringe, Susannah G; Dangl, Jeffery L; Mitchell-Olds, Thomas

    2016-01-01

    Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments. PMID:27402057

  6. Genotyping-by-Sequencing in Plants

    Directory of Open Access Journals (Sweden)

    Gregory D. May

    2012-09-01

    Full Text Available The advent of next-generation DNA sequencing (NGS technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS. This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.

  7. Canine Hip Dysplasia is Predictable by Genotyping

    Science.gov (United States)

    Guo, Gang; Zhou, Zhengkui; Wang, Yachun; Zhao, Keyan; Zhu, Lan; Lust, George; Hunter, Linda; Friedenberg, Steven; Li, Junya; Zhang, Yuan; Harris, Stephen; Jones, Paul; Sandler, Jody; Krotscheck, Ursula; Todhunter, Rory; Zhang, Zhiwu

    2011-01-01

    Summary Objective To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design Two sets of dogs (6 breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV or phenotype), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results The cross validation showed a strong correlation (r>0.7) between the EBV and the GBV. The independent validation showed a strong correlation (r=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive, and negative predictive value of the genomic data were all above 70%. Conclusions Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. PMID:21215318

  8. Detecting immigration by using multilocus genotypes

    OpenAIRE

    Rannala, Bruce; Mountain, Joanna L.

    1997-01-01

    Immigration is an important force shaping the social structure, evolution, and genetics of populations. A statistical method is presented that uses multilocus genotypes to identify individuals who are immigrants, or have recent immigrant ancestry. The method is appropriate for use with allozymes, microsatellites, or restriction fragment length polymorphisms (RFLPs) and assumes linkage equilibrium among loci. Potential applications include studies of dispersal among natural populations of anim...

  9. Hepatitis B virus taxonomy and hepatitis B virus genotypes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses).The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field,updates several recent reviews on HBV genotypes and subgenotypes.

  10. PON1 Status Does Not Influence Cholinesterase Activity in Egyptian Agricultural Workers Exposed to Chlorpyrifos

    OpenAIRE

    Ellison, Corie A.; Crane, Alice L.; Bonner, Matthew R; Knaak, James B.; Browne, Richard W; Lein, Pamela J; Olson, James R.

    2012-01-01

    Animal studies have shown that paraoxonase 1 (PON1) genotype can influence susceptibility to the organophosphorus pesticide chlorpyrifos (CPF). However, Monte Carlo analysis suggests that PON1 genotype may not affect CPF-related toxicity at low exposure conditions in humans. The current study sought to determine the influence of PON1 genotype on the activity of blood cholinesterase as well as the effect of CPF exposure on serum PON1 in workers occupationally exposed to CPF. Saliva, blood and ...

  11. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  12. Silicon Application Effects on Yield and Growth of Two Cucumber Genotypes in Hydroponics System

    OpenAIRE

    P. Mohaghegh; Shirvani, M; Ghasemi, S.

    2010-01-01

    Silicon (Si) has beneficial effects on the growth, yield, and tolerance of some crops against biotic and abiotic stresses. Considering the absence of Si in the nutrient solutions used in hydroponically-grown cucumber, the present study was conducted to investigate the influence of Si on the growth and yield of two cucumber genotypes (Cucumis sativus L. cvs. Dominus GRC and Super Dominus). In a hydroponic experiment, two cucumber cultivars were exposed to three Si levels (0, 100, and 200 mg L-...

  13. JAK2 V617F genotype is a strong determinant of blast transformation in primary myelofibrosis.

    Directory of Open Access Journals (Sweden)

    Giovanni Barosi

    Full Text Available PURPOSE: The influence of JAK2 V617F mutation on blast transformation (BT and overall survival (OS in primary myelofibrosis (PMF is controversial. In a large cohort of patients we applied competing risks analysis for studying the influence of JAK2V617F mutation on BT in PMF. PATIENTS AND METHODS: In 462 PMF-fibrotic type patients (bone marrow [BM] fibrosis grade >0 we computed the incidence of BT and death in the framework of Cox regression analysis and of Fine and Gray competing risks analysis for BT. RESULTS: At the Cox regression analysis, having either a wild-type (wt or a homozygous JAK2V617F genotype were factors for BT (HR, 1.98 and 2.04, respectively, with respect to the heterozygous genotype, but not for OS. At the competing risks regression analysis, the risk for BT in wt and homozygous V617F patients increased with respect to Cox analysis, giving a sHR of 2.17 and 2.12, respectively. Correcting the results for the variables that could have influence on BT, JAK2V617F wt and homozygous genotypes remained independently associated with BT. In a validation cohort of 133 independent cases with PMF-prefibrotic type (BM fibrosis grade = 0, the BT predictive model including JAK2V617F genotype and older age retained high discriminant capacity (C statistics, 0.70; 95% CI, 0.47 to 0.92. CONCLUSION: The accumulation of mutated alleles in the JAK2V617F clone or the selective acquisition of a proliferative advantage in the wt clone are two relevant routes to BT in PMF. The influence of these results on treatment decisions with anti-JAK2 agents should be tested.

  14. The Interaction of Obesity Related Genotypes, Phenotypes, and Economics: An Experimental Economics Approach with Mice

    OpenAIRE

    Davis, George C.; Jacob, Jacy; Good, Deborah J.

    2011-01-01

    Food intake is greatly influenced by economic factors. Consequently, neuroeconomics has been identified as a new and important area for understanding the interaction between genotypes and phenotypes related to food intake. A foundational element of economics is choice between alternatives. Changing food choices are a central element in the explanation of the increasing obesity rates in human populations. The purpose of this research is to incorporate the key element of choice into the investi...

  15. Genotypic variation in the sulfur assimilation and metabolism of onion (Allium cepa L.) I. Plant composition and transcript accumulation

    KAUST Repository

    McCallum, John A.

    2011-06-01

    Organosulfur compounds are major sinks for assimilated sulfate in onion (Allium cepa L.) and accumulation varies widely due to plant genotype and sulfur nutrition. In order to better characterise sulfur metabolism phenotypes and identify potential control points we compared plant composition and transcript accumulation of the primary sulfur assimilation pathway in the high pungency genotype \\'W202A\\' and the low pungency genotype \\'Texas Grano 438\\' grown hydroponically under S deficient (S-) and S-sufficient (S+) conditions. Accumulation of total S and alk(en)yl cysteine sulfoxide flavour precursors was significantly higher under S+ conditions and in \\'W202A\\' in agreement with previous studies. Leaf sulfate and cysteine levels were significantly higher in \\'W202A\\' and under S+. Glutathione levels were reduced by S- treatment but were not affected by genotype, suggesting that thiol pool sizes are regulated differently in mild and pungent onions. The only significant treatment effect observed on transcript accumulation in leaves was an elevated accumulation of O-acetyl serine thiol-lyase under S-. By contrast, transcript accumulation of all genes in roots was influenced by one or more treatments. APS reductase transcript level was not affected by genotype but was strongly increased by S-. Significant genotype × S treatment effects were observed in a root high affinity-sulfur transporter and ferredoxin-sulfite reductase. ATP sulfurylase transcript levels were significantly higher under S+ and in \\'W202A\\'. © 2011 Elsevier Ltd. All rights reserved.

  16. Regrowth patterns and rosette attributes contribute to the differential compensatory responses of Arabidopsis thaliana genotypes to apical damage.

    Science.gov (United States)

    Scholes, D R; Wszalek, A E; Paige, K N

    2016-03-01

    A plant's compensatory performance refers to its ability to maintain or increase its reproductive output following damage. The ability of a plant to compensate depends on numerous factors including the type, severity, frequency and timing of damage, the environmental conditions and the plant's genotype. Upon apical damage, a cascade of hormonal and genetic responses often produces dramatic changes in a plant's growth, development, architecture and physiology. All else being equal, this response is largely dependent on a plant's genotype, with different regrowth patterns displayed by different genotypes of a given species. In this study, we compare the architectural and growth patterns of two Arabidopsis thaliana genotypes following apical damage. Specifically, we characterise regrowth patterns of the genotypes Columbia-4 and Landsberg erecta, which typically differ in their compensation to apical meristem removal. We report that Landsberg erecta suffered reductions in the number of stems produced, maximum elongation rate, a delay in reaching this rate, lower average rosette quality throughout the growing period, and ultimately, less aboveground dry biomass and seed production when damaged compared to undamaged control plants. Columbia-4 had no reductions in any of these measures and maintained larger rosette area when clipped relative to when unclipped. Based on the apparent influence of the rosette on these genotypes' compensatory performances, we performed a rosette removal experiment, which confirmed that the rosette contributes to compensatory performance. This study provides a novel characterisation of regrowth patterns following apical damage, with insights into those measures having the largest effect on plant performance. PMID:26434737

  17. Hepatitis B virus genotypes in Mongols and Australian Aborigines.

    Science.gov (United States)

    Alestig, E; Hannoun, C; Horal, P; Lindh, M

    2001-12-01

    Hepatitis B virus (HBV) is spread worldwide. Seven genotypes, A-G, have been described, differing by more than 8% of the genome. In eastern Asia and Oceania genotypes B and C are predominant. However, little is known about genotypes in Mongolia and Australian aborigines. We analysed the preS and S regions of HBV from 9 Mongols and 5 Australian Aborigines. All Mongolian strains were of genotype D and were most similar to Central Asian sequences. All the Australian strains were genetically of serotype ayw3, and could not be reliably classified by the S region analysis, but placed on a separate branch. By preS analysis, they were however clearly of genotype C. The 6-7% nucleotide difference from published Asian genotype C sequences suggests that they diverged from Asian genotype C branch more than 1000 years ago. PMID:11811682

  18. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    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

  19. In tribute to Bob Blanchard: Divergent behavioral phenotypes of 16p11.2 deletion mice reared in same-genotype versus mixed-genotype cages.

    Science.gov (United States)

    Yang, Mu; Lewis, Freeman; Foley, Gillian; Crawley, Jacqueline N

    2015-07-01

    Mouse models offer indispensable heuristic tools for studying genetic and environmental causes of neuropsychiatric disorders, including autism. Development of useful animal models of complex human behaviors depends not only on extensive knowledge of the human disease, but also on a deep understanding of animal behavior and ethology. Robert and Caroline Blanchard pioneered a number of elegant social paradigms in rodents. Their early work led to systematic delineations of rodent naturalist defensive behaviors,which were proven to be highly useful models of human psychiatric disorders, including fear and anxiety. Their work using the Visible Burrow System to study social stress in rats represented an unprecedented approach to study biological mechanisms of depression. In recent years, their extensive knowledge of mouse behavior and ethology enabled them to quickly become leading figures in the field of behavioral genetics of autism. To commemorate Robert Blanchard's influences on animal models of human psychiatric disorders, here we describe a study conceptualized and led by Mu Yang who was trained as a graduate student in the Blanchard laboratory in the early 2000s. This investigation focuses on social housing in a genetic mouse model of 16p11.2 deletion syndrome. Heterozygous deletions and duplications of a segment containing about 29 genes on human chromosome 16 appear in approximately 0.5–1% of all cases of autism. 16p11.2 deletion syndrome is also associated with intellectual disabilities and speech impairments. Our previous studies showed that a mouse model of 16p11.2 deletion syndrome exhibited deficits in vocalizations and novel object recognition, as compared to wildtype littermate control cagemates. In the spirit of Bob Blanchard's careful attention to the role of social dominance in rodent behaviors, we became interested in the question of whether behavioral outcomes of a mutation differ when mutants are housed in mixed genotype cages, versus housing only

  20. New Insights into Genotype-phenotype Correlations in Chinese Facioscapulohumeral Muscular Dystrophy: A Retrospective Analysis of 178 Patients

    Directory of Open Access Journals (Sweden)

    Feng Lin

    2015-01-01

    Conclusions: Although the number of D4Z4 repeats is known as one of the critical influences on genotype-phenotype correlation, a majority of phenotypic spectrum was still incompatible with their heterozygous contraction of the D4Z4 repeat, especial in female cases. Our results suggest that there are multi-factors synergistically modulating the phenotypic expression.

  1. CYP2D6 genotype and phenotype relationship in South Indians

    Directory of Open Access Journals (Sweden)

    Naveen A

    2006-01-01

    Full Text Available Background : Genotypes of the drug-metabolizing enzyme CYP2D6 influence plasma levels of 25% of commonlyprescribed drugs. This is the first study in India to investigate the genotype-phenotype relationship of CYP2D6. Aim : To study the influence of some CYP2D6 genotypes on the metabolism of its substrate dextromethorphanin healthy South Indian volunteers and to assess the contribution of the CYP2D6FNx0110 and CYP2D6FNx014 alleles. Materials and Methods : Twenty-six subjects from a previous CYP2D6 genotyping study of healthy volunteerswere included for phenotyping in this study. Selected volunteers belonged to any one of three genotype groups:Group I - two normal activity alleles, Group II - one reduced activity allele and one normal activity allele andGroup III - one loss of function allele along with either a wild type or reduced activity allele. Volunteers werephenotyped for the CYP2D6 enzyme using dextromethorphan as probe drug. Concentrations of the parent drugand metabolite dextrorphan were estimated using high performance liquid chromatography. Metabolic ratioswere calculated as the ratio of parent drug to metabolite in 0-8h urine samples. Statistical Analysis : Metabolic ratios from each genotype group were compared using the Mann-Whitney testat 5% significance, to observe their difference between genotype groups. Results : The mean metabolic ratios±SD in Groups I, II and III were 0.0039±0.0031, 0.0032±0.0017 and0.0391±0.0331 respectively. The mean metabolic ratio of Group III was significantly higher when comparedwith Groups I or II. In heterozygous individuals, the FNx011 or FNx012 alleles compensated for the reduced enzymeactivity due to the FNx0110 allele. However, if a heterozygous individual had a FNx014 allele, the reduced enzyme activitycould not be compensated by the FNx011 or FNx012 alleles. Conclusions : The CYP2D6 enzyme activity was found to be decreased in individuals carrying FNx014 or FNx015 alleles.The FNx011 or FNx

  2. Understanding and utilizing crop genome diversity via high-resolution genotyping.

    Science.gov (United States)

    Voss-Fels, Kai; Snowdon, Rod J

    2016-04-01

    High-resolution genome analysis technologies provide an unprecedented level of insight into structural diversity across crop genomes. Low-cost discovery of sequence variation has become accessible for all crops since the development of next-generation DNA sequencing technologies, using diverse methods ranging from genome-scale resequencing or skim sequencing, reduced-representation genotyping-by-sequencing, transcriptome sequencing or sequence capture approaches. High-density, high-throughput genotyping arrays generated using the resulting sequence data are today available for the assessment of genomewide single nucleotide polymorphisms in all major crop species. Besides their application in genetic mapping or genomewide association studies for dissection of complex agronomic traits, high-density genotyping arrays are highly suitable for genomic selection strategies. They also enable description of crop diversity at an unprecedented chromosome-scale resolution. Application of population genetics parameters to genomewide diversity data sets enables dissection of linkage disequilibrium to characterize loci underlying selective sweeps. High-throughput genotyping platforms simultaneously open the way for targeted diversity enrichment, allowing rejuvenation of low-diversity chromosome regions in strongly selected breeding pools to potentially reverse the influence of linkage drag. Numerous recent examples are presented which demonstrate the power of next-generation genomics for high-resolution analysis of crop diversity on a subgenomic and chromosomal scale. Such studies give deep insight into the history of crop evolution and selection, while simultaneously identifying novel diversity to improve yield and heterosis. PMID:27003869

  3. Relation between Endothelial Nitric Oxide Synthase Genotypes and Oxidative Stress Markers in Larynx Cancer

    Directory of Open Access Journals (Sweden)

    K. Yanar

    2016-01-01

    Full Text Available Nitric oxide synthase (eNOS/NOS3 is responsible for the endothelial synthesis of nitric oxide (NO•. G894T polymorphism leads to the amino acid substitution from Glu298Asp that causes lower NOS3 activity and basal NO• production in NOS3 894T (298Asp allele carriers compared with the GG homozygotes. NO• acts as an antioxidant protecting against Fenton’s reaction which generates highly reactive hydroxyl radicals. Allelic variation of NOS3 may influence an individual’s risk of laryngeal cancer (LC. In the current study we have examined the possible relationship between NOS3 G894T genotypes and various systemic oxidative damage markers such as protein carbonyl, advanced oxidation protein products, Cu, Zn-superoxide dismutase, thiol group fractions, and lipid hydroperoxides in LC patients. Genotyping was carried out by PCR-RFLP. In LC patients with TT genotype, Cu, Zn-superoxide dismutase activities and nonprotein thiol levels were significantly higher than the controls. In patients with GT and GG genotype, high levels of lipid hydroperoxides showed statistical significance when compared to controls. Our results indicate a potential relationship among G894T polymorphism of NOS3, and impaired redox homeostasis. Further studies are required to determine the role of NOS3 gene polymorphism and impaired plasma redox homeostasis.

  4. Karyomorphological and morphometric studies of ploidy levels in some wheat (triticum aestivum L.) genotypes

    International Nuclear Information System (INIS)

    Karyomorphological and morphometric investigations of different ploidy levels of 14 genotypes of Triticum aestivum L. and one genotype of Triticum durum Desf. showed that, total chromosomal length (TCL) varied between genotypes. The highest value (56.21 macro m) was recorded with mean chromosomal length of 8.03 +- 0.81 macro m, while the lowest value of TCL (31.65 macro m) was found with mean chromosomal length (MCL) of 4.52 +- 0.41 macro m. Simple Pearson correlation coefficient (r) between TCL and MCL was the highest (r = 1.0 and P = 0.000). While the correlation coefficients between mean arm ratio (MAR) and parameters: total form (TF), intrachromosomal asymmetry index (A1) and m (karyotype; metacentric region chromosome) as well as the coefficients between TF and m and between A1 and m were the only significant (P<0.01) ones. Intrachromosomal asymmetry had a significant (P = 0.000) effect of total form percent than interchomosomal index. TCL and MCL were the most important karyological features influencing the principal component analysis and had 81.7 % variation, while in combination with MAR revealed 94% variation. Cluster dendrogram revealed close association and adjacent phylogenetic relatedness of tri- and hexaploid and also tetra- and hexaploid genotypes. (author)

  5. Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera).

    Science.gov (United States)

    Bálint, Miklós; Tiffin, Peter; Hallström, Björn; O'Hara, Robert B; Olson, Matthew S; Fankhauser, Johnathon D; Piepenbring, Meike; Schmitt, Imke

    2013-01-01

    Foliar fungal communities of plants are diverse and ubiquitous. In grasses endophytes may increase host fitness; in trees, their ecological roles are poorly understood. We investigated whether the genotype of the host tree influences community structure of foliar fungi. We sampled leaves from genotyped balsam poplars from across the species' range, and applied 454 amplicon sequencing to characterize foliar fungal communities. At the time of the sampling the poplars had been growing in a common garden for two years. We found diverse fungal communities associated with the poplar leaves. Linear discriminant analysis and generalized linear models showed that host genotypes had a structuring effect on the composition of foliar fungal communities. The observed patterns may be explained by a filtering mechanism which allows the trees to selectively recruit fungal strains from the environment. Alternatively, host genotype-specific fungal communities may be present in the tree systemically, and persist in the host even after two clonal reproductions. Both scenarios are consistent with host tree adaptation to specific foliar fungal communities and suggest that there is a functional basis for the strong biotic interaction. PMID:23326555

  6. Different Roles of COMT and HTR2A Genotypes in Working Memory Subprocesses.

    Directory of Open Access Journals (Sweden)

    Hirohito M Kondo

    Full Text Available Working memory is linked to the functions of the frontal areas, in which neural activity is mediated by dopaminergic and serotonergic tones. However, there is no consensus regarding how the dopaminergic and serotonergic systems influence working memory subprocesses. The present study used an imaging genetics approach to examine the interaction between neurochemical functions and working memory performance. We focused on functional polymorphisms of the catechol-O-methyltransferase (COMT Val(158Met and serotonin 2A receptor (HTR2A -1438G/A genes, and devised a delayed recognition task to isolate the encoding, retention, and retrieval processes for visual information. The COMT genotypes affected recognition accuracy, whereas the HTR2A genotypes were associated with recognition response times. Activations specifically related to working memory were found in the right frontal and parietal areas, such as the middle frontal gyrus (MFG, inferior frontal gyrus (IFG, anterior cingulate cortex (ACC, and inferior parietal lobule (IPL. MFG and ACC/IPL activations were sensitive to differences between the COMT genotypes and between the HTR2A genotypes, respectively. Structural equation modeling demonstrated that stronger connectivity in the ACC-MFG and ACC-IFG networks is related to better task performance. The behavioral and fMRI results suggest that the dopaminergic and serotonergic systems play different roles in the working memory subprocesses and modulate closer cooperation between lateral and medial frontal activations.

  7. Genotype and ancestry modulate brain's DAT availability in healthy humans

    Energy Technology Data Exchange (ETDEWEB)

    Shumay, E.; Shumay, E.; Chen, J.; Fowler, J.S.; Volkow, N.D.

    2011-08-01

    The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [{sup 11}C] cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms - 3-UTR- and intron 8- VNTRs. The main findings are the following: (1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; (2) ethnic background and age influence the strength of these associations; and (3) age-related changes in DAT availability differ in the 3-UTR and intron8 - genotype groups.

  8. Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera.

    Directory of Open Access Journals (Sweden)

    Miklós Bálint

    Full Text Available Foliar fungal communities of plants are diverse and ubiquitous. In grasses endophytes may increase host fitness; in trees, their ecological roles are poorly understood. We investigated whether the genotype of the host tree influences community structure of foliar fungi. We sampled leaves from genotyped balsam poplars from across the species' range, and applied 454 amplicon sequencing to characterize foliar fungal communities. At the time of the sampling the poplars had been growing in a common garden for two years. We found diverse fungal communities associated with the poplar leaves. Linear discriminant analysis and generalized linear models showed that host genotypes had a structuring effect on the composition of foliar fungal communities. The observed patterns may be explained by a filtering mechanism which allows the trees to selectively recruit fungal strains from the environment. Alternatively, host genotype-specific fungal communities may be present in the tree systemically, and persist in the host even after two clonal reproductions. Both scenarios are consistent with host tree adaptation to specific foliar fungal communities and suggest that there is a functional basis for the strong biotic interaction.

  9. Effect Of Chitosan Application On The Performance Of Lentil Genotypes Under Rainfed Conditions

    Directory of Open Access Journals (Sweden)

    Janmohammadi Mohsen

    2014-12-01

    Full Text Available In the current study, influences of chitosan solutions on morphological characteristics, growth and yield components of lentil (Lens culinaris Med. under rainfed conditions have been investigated. A field experiment was conducted in the Northwest of Iran using a split-plot experiment based on a completely randomized design with three replications. The response of twelve genotypes with different origins to chitosan application at the sowing (seed soaking, vegetative and reproductive stage (spraying chitosan onto leaves was evaluated. Results revealed that chitosan application could significantly improve the number of pods per plant, 100-seed weight, grain yield per plant and harvest index in comparison to control plants. The comparison of yield components between chitosan treatments showed that spraying chitosan during the reproductive stage was more efficient than in other stages. However, the responses of the number of pods per plants and grain yield per plants to chitosan treatments were significantly different among the genotypes. Although the highest grain yield was recorded in the 78S 26013 genotype (from Jordan, its response to chitosan treatments was different from the other genotypes and showed the best performance in plants obtained from seed soaked in chitosan solutions. We suggest that the application of chitosan as an agronomic management strategy be further investigated for an efficient technique to induce resistance in lentil plants against biotic and drought stress in semi-arid regions.

  10. IDENTIFICATION OF TECHNOLOGICALLY IMPORTANT GENES AND THEIR PRODUCTS IN THE COLLECTION OF BREAD WHEAT GENOTYPES

    Directory of Open Access Journals (Sweden)

    Milan Chňapek

    2015-02-01

    Full Text Available Wheat is the second most cultivated crop on the world and is very important plant for feed not only mankind but also animals. Because of this is necessary to develop new varieties with better properties. Bread making quality of wheat grain is one of the most important paramaters for quality evaluation. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE of wheat storage proteins and allelic specific polymerase chain reaction (AS-PCR are analysis suitable for identification, differentiation and characterization of bread wheat (Triticum aestivum L.. There were analysed 16 genotypes of new varieties of bread wheat in our work by SDS-PAGE and obtained results were verified by AS-PCR. Analysed genotypes of bread wheat genotypes were homogenous and single line with very good bread making quality. Our results confirmed hypothesis, that cultivated bread wheat genotypes are uniformed with high production and quality but there is a risk of sensitivity to environmental conditions. SDS-PAGE analyses of wheat grain proteins are fast and not very expensive technique, which provide us information of bread making quality of grains. However, there is possibility of environmental influence on protein synthesis and because of this is necessary to couple these analysis with analysis of DNA.

  11. Large scale genotyping study for asthma in the Japanese population

    Directory of Open Access Journals (Sweden)

    Shibasaki Masanao

    2009-03-01

    Full Text Available Abstract Background Asthma is a complex phenotype that is influenced by both genetic and environmental factors. Genome-wide linkage and association studies have been performed to identify susceptibility genes for asthma. These studies identified new genes and pathways implicated in this disease, many of which were previously unknown. Objective To perform a large-scale genotyping study to identify asthma-susceptibility genes in the Japanese population. Methods We performed a large-scale, three-stage association study on 288 atopic asthmatics and 1032 controls, by using multiplex PCR-Invader assay methods at 82,935 single nucleotide polymorphisms (SNPs (1st stage. SNPs that were strongly associated with asthma were further genotyped in samples from asthmatic families (216 families, 762 members, 2nd stage, 541 independent patients, and 744 controls (3rd stage. Results SNPs located in the 5' region of PEX19 (rs2820421 were significantly associated with P st to the 3rd stage analyses; however, the P values did not reach statistically significant levels (combined, P = 3.8 × 10-5; statistically significant levels with Bonferroni correction, P = 6.57 × 10-7. SNPs on HPCAL1 (rs3771140 and on IL18R1 (rs3213733 were associated with asthma in the 1st and 2nd stage analyses, but the associations were not observed in the 3rd stage analysis. Conclusion No association attained genome-wide significance, but several loci for possible association emerged. Future studies are required to validate these results for the prevention and treatment of asthma.

  12. Comparison of Structural Architecture of HCV NS3 Genotype 1 versus Pakistani Genotype 3a

    OpenAIRE

    Kaneez Fatima; Esam Azhar; Shilu Mathew; Ghazi Damanhouri; Ishtiaq Qadri

    2014-01-01

    This study described the structural characterization of Pakistani HCV NS3 GT3a in parallel with genotypes 1a and 1b NS3. We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling. Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER. Sixty models were produced and clustered into groups and the best model of PK-NCVI/Pk3a NS3 was sele...

  13. UGT2B17 Genotype and the Pharmacokinetic Serum Profile of Testosterone during Substitution Therapy with Testosterone Undecanoate. A Retrospective Experience from 207 Men with Hypogonadism

    OpenAIRE

    Bang, Anne Kirstine; Jørgensen, Niels; Rajpert-De Meyts, Ewa; Juul, Anders

    2013-01-01

    Background: Testosterone (T) is mainly excreted in the urine as testosterone glucuronide (TG). This glucuronidation is partly dependent on the UGT2B17 genotype, and TG excretion is therefore lower in men having the UGT2B17 deletion. However, the possible influence of UGT2B17 genotype on serum T during androgen therapy is unknown. We retrospectively investigated the possible association between the UGT2B17 gene polymorphism and serum T levels in hypogonadal men during Testosterone undecanoate ...

  14. Bacterial communities associated with Brassica napus L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison

    OpenAIRE

    Croes, S.; Weyens, N; Janssen, J.; Vercampt, H.; Colpaert, JV; CARLEER R.; Vangronsveld, J.

    2013-01-01

    Summary Cultivable bacterial strains associated with field-grown Brassica napus L. (soil, rhizosphere and roots) from a trace elements (Cd, Zn and Pb) contaminated field and a non-contaminated control field were characterized genotypically and phenotypically. Correspondence analysis of the genotypic data revealed a correlation between soil and rhizosphere communities isolated from the same field, indicating that local conditions play a more important role in influencing the composition of (rh...

  15. Comparative analysis of Paenibacillus larvae genotypes isolated in Connecticut.

    Science.gov (United States)

    Dingman, Douglas W

    2015-08-01

    Ninety-six strains of Paenibacillus larvae, causative agent of American foulbrood in honey bee (Apis mellifera) larvae, collected from Connecticut, USA (CT), honey bees, and 12 P. larvae strains not from CT, were genotyped via ERIC-PCR and XbaI-RFLP analysis. All CT-isolates, five strains isolated in South America, three strains from North America (not CT), and one strain isolated in Australia grouped into the ERIC I genotype. Three P. larvae formerly subsp. pulvifaciens strains grouped into ERIC III and IV genotypes. XbaI-RFLP genotyping showed three genotypes within the CT-isolates, and two were identified as XbaI-RFLP Type I and III. The third XbaI-RFLP genotype (Type Ib) represented one of four new XbaI-RFLP genotypes identified. Comparison of genotype results for the P. larvae strains tested was used to develop a correlation between ERIC-PCR genotyping and XbaI-RFLP genotyping. Sixteen CT-isolates were tetracycline-resistant and demonstrated PCR amplification using oligonucleotide primers for tetL. All 16 isolates grouped within XbaI-RFLP Type Ib, suggesting limited introduction of a tetracycline-resistant strain into CT. PMID:25929327

  16. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

    Full Text Available Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV- RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095 for genotype 1, 4.6% (78 for genotype 2, 30.2% (510 for genotype 3, 0.2% (3 for genotype 4, and 0.1% (2 for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017. In all regions, genotype 1 was the most frequent (51.7 to 74.1%, reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%, especially in Mato Grosso State (25.8%, while genotype 3 was more common in the South (43.2%. Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV.

  17. The interactive effect of MAOA-LPR genotype and childhood physical neglect on aggressive behaviors in Italian male prisoners

    OpenAIRE

    Gorodetsky, Elena; Bevilacqua, Laura; Carli, Vladimir; Sarchiapone, Marco; Roy, Alec; Goldman, David; Enoch, Mary-Anne

    2014-01-01

    Aggressive disorders are moderately heritable; therefore, identification of genetic influences is important. The X-linked MAOA gene, encoding the MAOA enzyme, has a functional 30bp repeat polymorphism in the promoter region (MAOA-LPR) that has been shown to influence aggression. Childhood trauma is a known risk factor for numerous psychopathologies in adulthood including aggressive behaviors. We investigated the interactive effect of MAOA-LPR genotype and a history of childhood trauma in pred...

  18. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  19. Celer: an Efficient Program for Genotype Elimination

    CERN Document Server

    De Francesco, Nicoletta; Martini, Luca; 10.4204/EPTCS.33.4

    2010-01-01

    This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  20. OPTIMIZATION TECHNIQUES FOR PCRRFLP FOR GENOTYPING SHEEP

    Directory of Open Access Journals (Sweden)

    Shirokova N. V.

    2015-11-01

    Full Text Available Diagnosis by PCR-RFLP (polymerase chain reaction – polymorphism of the lengths of restriction fragments is the standard analysis of point mutations for the diagnosis of allelic polymorphism of candidate genes related with productive qualities of farm animals. Along the length of the fragments (RFLP make a conclusion about the absence or presence of the point mutation, and homozygosity or heterozygosity of the individual. The aim of our work was the optimization of protocols for conducting PCR-RFLP analysis for genotyping sheep for genes of the growth hormone gene differential growth factor and gene of calpastatin

  1. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    With the completion of Human Genome Project,International HapMap Project and the publication of copy number variation in human genome,a great number of accurate,rapid,and cost-effective technologies for SNP analysis have been developed,promoting the research of the complex diseases.This article presents a review of widely used genotyping techniques,and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai(CHGCs).

  2. Noninvasive fetal RhD genotyping

    DEFF Research Database (Denmark)

    Clausen, Frederik Banch; Damkjær, Merete Berthu; Dziegiel, Morten Hanefeld

    2014-01-01

    Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries, ant...... undergone technical improvements and rapid clinical implementation. As a screening assay, the sensitivity is >99.3% from a gestational age of approximately 10-11weeks. In addition, fetal RhD genotyping is widely used to assess the risk of HDFN in anti-D immunized women....

  3. Celer: an Efficient Program for Genotype Elimination

    Directory of Open Access Journals (Sweden)

    Nicoletta De Francesco

    2010-08-01

    Full Text Available This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  4. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    SHI JinXiu; WANG Ying; HUANG Wei

    2009-01-01

    With the completion of Human Genome Project, International HapMap Project and the publication of copy number variation in human genome, a great number of accurate, rapid, and cost-effective tech-nologies for SNP analysis have been developed, promoting the research of the complex diseases. This article presents a review of widely used genotyping techniques, and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai (CHGCs).

  5. A Rapid PCR-HRM Genotyping Technique for the Single Nucleotide Polymorphisms of Genes that Influence Response to Warfarin Dose%PCR-HRM技术在华法林最佳用药剂量关联基因单核苷酸多态性检测中的应用

    Institute of Scientific and Technical Information of China (English)

    王芳芳; 尤崇革; 李光迪; 潘云燕; 郜莉娜; 李菲菲

    2011-01-01

    目的 最新研究显示华法林最佳用药剂量关联基因CYP2C9,CYP4F2和VKORC1可指导临床个体化用药,该成果的临床应用有赖于临床快速分子诊断方法的建立,为此该论文建立PCR-HRM(High-resolution melting)技术检测华法林最佳用药剂量关联基因单核苷酸多态性(SNP)并进行应用评价.方法 采用国际最前沿的基因突变筛查技术-HRM和新型荧光染料Eva Green对华法林最佳用药剂量关联基因CYP2C9*2,CYP2C9*3,CYP4F2 V433M和VKORC1 1173C/T四个SNP位点先进行染料法荧光PCR,接着进行PCR产物的高分辨熔解,依据熔解峰的特点进行SNP分型即PCR-HRM技术建立,最后通过检测临床181例标本进行临床应用评价.结果 在181例服用华法林的患者中检测到CYP2C9*2杂合子2例,CYP2C9*3杂合子15例,CYP4F2 V433M杂合子74例,纯合子14例,VKORC1 1173C/T杂合子33例.随机选择各类基因型PCR产物共24例进行测序,验证结果与检测结果一致.结论 PCR-HRM技术检测华法林最佳用药剂量关联基因SNP是一种灵敏、简便、快捷的低成本检测方法,可用于临床常规化分子诊断.%Objective The latest studies showed that the Warfarin opitimal dosage associated genes of CYP2C9,CYP4F2,VKORC1 could guide clinical individualized medicine. It was essential to develop a rapid molecular diagnosis method for the clinical application of the achievement,so this paper reported and evaluated the PCR-HRM technique detecting the single nucleotide polymorphisms (SNPs) of the genes in clinical application. Methods The four SNPs of CYPZC9 * 2.CYP2C9 * 3,CYP4F2 V433M and VKORC1 1173C/T were detected using fluorescent PCR assay with the international cutting-edge gene mutations screening technology -HRM and new dye Eva Green. HRM was performed immediately after finished the amplification of target fragments,then judged the genotypes based on the characteristics of the ampilcons'melting peaks.Using this PCR-HRM technnique,181 cases of

  6. Influência de genótipos de amoreira (Morus sp. e substratos no peso e características de casulos do bicho-da-seda (Bombyx mori L. Influence of mulberry (Morus sp. genotypes and substrates in weight and characteristics of silkworm cocoons (Bombyx mori L.

    Directory of Open Access Journals (Sweden)

    Odinete Murari

    2001-05-01

    Full Text Available Avaliou-se o efeito de três genótipos de amoreira, Morus sp. (Moraceae: Miura, FM Shima Miura e IZ 56/4, três tipos de esteiras de criação: terra compactada, concreto e tela plástica sobre o peso e algumas características industriais de casulos produzidos pelo bicho-da-seda, Bombyx mori (Lepidoptera. Houve influência das interações de genótipos com esteiras de criação sobre o peso dos casulos produzidos. Com relação às características industriais, os tratamentos que mais se sobressaíram foram: Miura / terra compactada, FM-SM / tela plástica, IZ 56/4 / terra compactada e IZ 56/4 / tela plástica.The effect of three genotypes of mulberry, Morus sp. (Moraceae, namely, Miura, FM Shima Miura and IZ 56/4, and three types of rearing substrate comprising compact soil, concrete and plastic screen were estimated on weight and on certain industrial characteristics of Bombyx mori (Lepidoptera cocoons. Genotype interactions with rearing substrates affected weight of cocoons produced. Analysis showed the best treatments for manufacturer parameters were Miura / compact soil, FM-Shima Miura / plastic screen, IZ 56/4 / compact soil and IZ 56/4 / plastic screen.

  7. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  8. Effect of Drought Stress on Some Physiological Traits of Durum (Triticum durum Desf. and Bread (Triticum aestivum L. Wheat Genotypes

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    Tofig Allahverdiyev

    2015-04-01

    Full Text Available Drought is a wide-spread problem seriously influencing wheat production and quality worldwide. We aimed to study adaptive changes in physiological parameters of 6 durum and 7 bread wheat genotypes under drought stress. Water stress caused reduction of leaf gas exchange parameters-photosynthesis rate, stomatal conductance, intercellular CO2 concentration, transpiration rate as well leaf area, dry mass, relative water content, and chlorophyll content. Photosynthesis rate, chlorophyll content were higher in flag leaf of bread wheat genotypes. Photosynthesis rate positively correlated with leaf area, dry mass and relative water content.

  9. Genotype x environment interaction studies in promising early genotypes of rice

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    B.D.Patel, A.M.Mehta, S.G.Patel, S.Takle, S.K.Prajapati and S.K.Patel

    2015-06-01

    Full Text Available Twenty one early rice genotypes including four local check varieties (Gurjari, GR-3, GR-7 and GR-12 were evaluated for their stability parameters with respect to eighteen quantitative and qualitative traits in 3 environments (Nawagam, Dabhoi and Dahod during kharif season of 2012. The genotypes x environments interaction and its G x E (linear component were significant for all the characters except grain length, grain breadth, grain L:B ratio, test weight, kernel length, kernel breadth, kernel L:B ratio, kernel length after cooking, alkali spreading value and amylose content. The non-linear component of G x E interaction was also significant for all the characters except straw yield per plant, grain length, grain breadth, test weight, kernel breadth, kernel L : B ratio, hulling %, kernel length after cooking, alkali spreading value and amylose content when tested against pooled error suggested importance of both linear and non-linear components in building up total G x E interaction. Among twenty one genotypes, only one genotype NWGR-9147 was found stable with wide adaptability for grain yield per plant along with the stability for days to 50% flowering, plant height, straw yield per plant and milling percentage characters hence the cultivar could be used for cultivation over a range of environments.

  10. Antioxidant capacity of anthocyanins from acerola genotypes

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    Vera Lúcia Arroxelas Galvão De Lima

    2011-03-01

    Full Text Available Anthocyanins from 12 acerola genotypes cultivated at the Active Germplasm Bank at Federal Rural University of Pernambuco were isolated for antioxidant potential evaluation. The antioxidant activity and radical scavenging capacity of the anthocyanin isolates were measured according to the β-carotene bleaching method and 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical scavenging assay, respectively. The antioxidant activity varied from 25.58 to 47.04% at 0.2 mg.mL-1, and it was measured using the β-carotene bleaching method. The free radical scavenging capacity increased according to the increase in concentration and reaction time by the DPPH assay. At 16.7 μg.mL-1 concentration and after 5 minutes and 2 hours reaction time, the percentage of scavenged radicals varied from 36.97 to 63.92% and 73.27 to 94.54%, respectively. Therefore, the antioxidant capacity of acerola anthocyanins varied amongst acerola genotypes and methods used. The anthocyanins present in this fruit may supply substantial dietary source of antioxidant which may promote health and produce disease prevention effects.

  11. Noninvasive fetal RhD genotyping.

    Science.gov (United States)

    Clausen, Frederik Banch; Damkjær, Merete Berthu; Dziegiel, Morten Hanefeld

    2014-04-01

    Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries, antenatal prophylaxis is combined with postnatal prophylaxis to further minimize the immunization risk. Due to lack of knowledge of the fetal RhD type, antenatal prophylaxis is given to all D-negative women. In the European population, approximately 40% of pregnant women carry a D-negative fetus and are thus at no risk of immunization. Noninvasive fetal RhD genotyping enables antenatal prophylaxis to be targeted to only those women carrying a D-positive fetus to avoid unnecessary treatment. Based on an analysis of cell-free fetal DNA from the plasma of pregnant women, this approach has recently undergone technical improvements and rapid clinical implementation. As a screening assay, the sensitivity is >99.3% from a gestational age of approximately 10-11 weeks. In addition, fetal RhD genotyping is widely used to assess the risk of HDFN in anti-D immunized women. PMID:24642067

  12. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    Science.gov (United States)

    Sinclair, Elizabeth A.; Poore, Alistair G.B.; Bain, Keryn F.; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  13. Tolerance of upland rice genotypes to water deficit

    OpenAIRE

    Cleber M. Guimarães; Luís F. Stone; Paulo H. N. Rangel; Ana C. de L. Silva

    2013-01-01

    Water deficit is one of the environmental factors that cause a great reduction in the upland rice grain yield. The objective of this study was to evaluate genotypes of upland rice with broad genetic diversity for tolerance to this stress and to identify secondary traits for evaluation of this tolerance. Sixty-four genotypes were evaluated during two years at the Experiment Station of EMATER, in Porangatu, GO, under well-watered and water deficit conditions. The genotypes showed differences in...

  14. Detection of Multiple Human Papillomavirus Genotypes in Anal Carcinoma

    OpenAIRE

    Ramamoorthy, Sonia; Liu, Yu-Tsueng; Luo, Linda; Miyai, Katsumi; Lu, Qing; John M. Carethers

    2010-01-01

    Abstract Infection with human papillomavirus (HPV) is a major risk factor for development of anal squamous cell carcinoma. Despite over 100 genotypes of the virus, HPV 16 and 18 are considered pathogenic as they are seen in the majority of cervical and anal cancers. We have employed a custom microarray to examine DNA for several HPV genotypes. We aimed to determine the accuracy of our microarray in anal cancer DNA for HPV genotypes compared to the DNA sequencing gold standard. Method...

  15. Detection of Multiple Human Papillomavirus Genotypes in Anal Carcinoma

    OpenAIRE

    Luo Linda; Liu Yu-Tsueng; Ramamoorthy Sonia; Miyai Katsumi; Lu Qing; Carethers John M

    2010-01-01

    Abstract Infection with human papillomavirus (HPV) is a major risk factor for development of anal squamous cell carcinoma. Despite over 100 genotypes of the virus, HPV 16 and 18 are considered pathogenic as they are seen in the majority of cervical and anal cancers. We have employed a custom microarray to examine DNA for several HPV genotypes. We aimed to determine the accuracy of our microarray in anal cancer DNA for HPV genotypes compared to the DNA sequencing gold standard. Methods We util...

  16. Genotypic richness predicts phenotypic variation in an endangered clonal plant.

    Science.gov (United States)

    Evans, Suzanna M; Sinclair, Elizabeth A; Poore, Alistair G B; Bain, Keryn F; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  17. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  18. Temperature in the seeds germination of pitaya genotypes

    OpenAIRE

    Alessandro Borini Lone; Ronan Carlos Colombo; Vanessa Favetta; Lúcia Sadayo Assari Takahashi; Ricardo Tadeu de Faria

    2014-01-01

    The optimum temperature for germination of cacti vary with the species. With this work, we aimed to evaluate the seeds germination of pitaya genotypes under different temperatures. The used genotypes were: Hylocereus undatus (PB), H. polyrhizus (PV), Selenicereus megalanthus (PA), H. undatus x H. costaricensis (PH1) and H. costaricensis x H. undatus (PH2). For each genotype we used four replicates of 50 seeds, in a completely randomized design. The sowing was carried out on blotter paper in b...

  19. 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.

  20. Subgrouping of patients with oral lichen planus according to cytochrome P450 enzyme phenotype and genotype

    DEFF Research Database (Denmark)

    Kragelund, Camilla; Jensen, Siri Beier; Hansen, Claus;

    2014-01-01

    Objective. This study aimed to determine if the activity of the environmentally influenced cytochrome P450 enzyme CYP1A2, alone or in combination with CYP2D6*4 genotype, discriminates subgroups of oral lichen planus (OLP) according to lifestyle factors and clinical manifestations. Study Design. A...... total of 111 patients with OLP were categorized according to normal, low, or high CYP1A2 activity and CYP2D6*4 genotype. Lifestyle parameters influencing the CYP1A2 activity and symptoms and manifestations of OLP were recorded. Results. Of the 111 patients, 21% had low, 65% normal, and 14% high CYP1A2...... activity. The high-CYP1A2-activity group was more exposed to CYP1A2 inducers than the low-CYP1A2-activity group. In the normal-CYP1A2-activity group, more patients had a CYP2D6*4 genotype (58%) (P = .02), and they presented more symptoms (P = .003) and gingival lesions (P = .03). More patients in the low...

  1. Effect of Environment and Sugar Beet Genotype on Root Rot Development and Pathogen Profile During Storage.

    Science.gov (United States)

    Liebe, Sebastian; Varrelmann, Mark

    2016-01-01

    Storage rots represent an economically important factor impairing the storability of sugar beet by increasing sucrose losses and invert sugar content. Understanding the development of disease management strategies, knowledge about major storage pathogens, and factors influencing their occurrence is crucial. In comprehensive storage trials conducted under controlled conditions, the effects of environment and genotype on rot development and associated quality changes were investigated. Prevalent species involved in rot development were identified by a newly developed microarray. The strongest effect on rot development was assigned to environment factors followed by genotypic effects. Despite large variation in rot severity (sample range 0 to 84%), the spectrum of microorganisms colonizing sugar beet remained fairly constant across all treatments with dominant species belonging to the fungal genera Botrytis, Fusarium, and Penicillium. The intensity of microbial tissue necrotization was strongly correlated with sucrose losses (R² = 0.79 to 0.91) and invert sugar accumulation (R² = 0.91 to 0.95). A storage rot resistance bioassay was developed that could successfully reproduce the genotype ranking observed in storage trials. Quantification of fungal biomass indicates that genetic resistance is based on a quantitative mechanism. Further work is required to understand the large environmental influence on rot development in sugar beet. PMID:26474333

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

    Science.gov (United States)

    Minihane, Anne Marie

    2016-03-01

    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. PMID:26950146

  3. Genotypic and phenotypic evolution of yeast interspecies hybrids during high-sugar fermentation.

    Science.gov (United States)

    Lopandic, Ksenija; Pfliegler, Walter P; Tiefenbrunner, Wolfgang; Gangl, Helmut; Sipiczki, Matthias; Sterflinger, Katja

    2016-07-01

    The yeasts of the Saccharomyces genus exhibit a low pre-zygotic barrier and readily form interspecies hybrids. Following the hybridization event, the parental genomes undergo gross chromosomal rearrangements and genome modifications that may markedly influence the metabolic activity of descendants. In the present study, two artificially constructed hybrid yeasts (Saccharomyces cerevisiae x Saccharomyces uvarum and S. cerevisiae x Saccharomyces kudriavzevii) were used in order to evaluate the influence of high-sugar wine fermentation on the evolution of their genotypic and phenotypic properties. It was demonstrated that the extent of genomic modifications differs among the hybrids and their progeny, but that stress should not always be a generator of large genomic disturbances. The major genome changes were observed after meiosis in the F1 segregants in the form of the loss of different non-S. cerevisiae chromosomes. Under fermentation condition, each spore clone from a tetrad developed a mixed population characterized by different genotypic and phenotypic properties. The S. cerevisiae x S. uvarum spore clones revealed large modifications at the sequence level of the S. cerevisiae sub-genome, and some of the clones lost a few additional S. cerevisiae and S. uvarum chromosomes. The S. cerevisiae x S. kudriavzevii segregants were subjected to consecutive loss of the S. kudriavzevii markers and chromosomes. Both the hybrid types showed increased ethanol and glycerol production as well as better sugar consumption than their parental strains. The hybrid segregants responded differently to stress and a correlation was found between the observed genotypes and fermentation performances. PMID:27075738

  4. Angiotensin-converting enzyme genotype and late respiratory complications of mustard gas exposure

    Directory of Open Access Journals (Sweden)

    Humphries Steve E

    2008-08-01

    Full Text Available Abstract Background Exposure to mustard gas frequently results in long-term respiratory complications. However the factors which drive the development and progression of these complications remain unclear. The Renin Angiotensin System (RAS has been implicated in lung inflammatory and fibrotic responses. Genetic variation within the gene coding for the Angiotensin Converting Enzyme (ACE, specifically the Insertion/Deletion polymorphism (I/D, is associated with variable levels of ACE and with the severity of several acute and chronic respiratory diseases. We hypothesized that the ACE genotype might influence the severity of late respiratory complications of mustard gas exposure. Methods 208 Kurdish patients who had suffered high exposure to mustard gas, as defined by cutaneous lesions at initial assessment, in Sardasht, Iran on June 29 1987, underwent clinical examination, spirometric evaluation and ACE Insertion/Deletion genotyping in September 2005. Results ACE genotype was determined in 207 subjects. As a continuous variable, FEV1 % predicted tended to be higher in association with the D allele 68.03 ± 20.5%, 69.4 ± 21.4% and 74.8 ± 20.1% for II, ID and DD genotypes respectively. Median FEV1 % predicted was 73 and this was taken as a cut off between groups defined as having better or worse lung function. The ACE DD genotype was overrepresented in the better spirometry group (Chi2 4.9 p = 0.03. Increasing age at the time of exposure was associated with reduced FEV1 %predicted (p = 0.001, whereas gender was not (p = 0.43. Conclusion The ACE D allele is associated with higher FEV1 % predicted when assessed 18 years after high exposure to mustard gas.

  5. Phosphorus use efficiency in pima cotton (Gossypium barbadense L. genotypes

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    Elcio Santos

    2015-06-01

    Full Text Available In the Brazilian Cerrado, P deficiency restricts cotton production, which requires large amounts of phosphate fertilizer. To improve the yield of cotton crops, genotypes with high P use efficiency must be identified and used. The present study evaluated P uptake and use efficiency of different Gossypium barbadense L. genotypes grown in the Cerrado. The experiment was carried out in a greenhouse with a completely randomized design, 15 x 2 factorial treatment structure (15 genotypes x 2 P levels, and four replicates. The genotypes were MT 69, MT 70, MT 87, MT 91, MT 92, MT 94, MT 101, MT 102, MT 103, MT 105, MT 106, MT 110, MT 112, MT 124, and MT 125; P levels were sufficient (1000 mg pot-1, PS treatment or deficient (PD treatment. Dry matter (DM and P levels were determined in cotton plant parts and used to calculate plant P content and use efficiency. In general, DM and P content were higher in the PS than in the PD treatment, with the exception of root DM and total DM in some genotypes. Genotypes also differed in terms of P uptake and use capacity. In the PS treatment, genotypes MT 92 and MT 102 had the highest response to phosphate fertilization. Genotype MT 69 exhibited the most efficient P uptake in the PD treatment. Genotype MT 124 showed the best shoot physiological efficiency, apparent recovery efficiency, and utilization efficiency, whereas MT 110 exhibited the highest root physiological efficiency.

  6. Oil Yield Stability of Winter Rapeseed (Brassica napus L. Genotypes

    Directory of Open Access Journals (Sweden)

    Ana Marjanović-jeromela

    2008-12-01

    Full Text Available The identification of the highest yielding cultivar for a specific environment on the basis of both genotype and genotype x environment interaction could be useful for breeders and producers since yield estimation based only on genotype and environment effects are insufficient. The trial was carried out during six growing seasons using eight registered cultivars of rapeseed developed at European breeding stations and 11 experimental lines developed in the Institute of Field and Vegetable Crops, Novi Sad, Serbia. The objective of the study was to identify genotypes with most stable oil yield by using combination of three parameters: ecovalence (wi, regression coefficient (bi and deviations mean square (s2di (first model and AMMI model analysis (second model. Average oil yield per area of experimental genotypes was higher comparing to registered genotypes. According to the first model, seven experimental lines and two registered varieties (Falcon and Banacanka were estimated as stable and wide adaptable genotypes. A complete positive and highly significant correlation was estimated between wi and s2 di that implies that both of these parameters could be used independently. According to the AMMI models, in the environmental conditions of Northern Serbia, the genotypes UM-8 and UM-11 were the most stable and with high average oil yield. Such genotypes can be implemented in future breeding programs and recommended for growing in South Eastern Europe.

  7. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  8. Variability of acorn anatomical characteristics in Quercus robur L. genotypes

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2010-01-01

    Full Text Available The aim of this study was to examine variability of acorn anatomical characteristics in seventeen Quercus robur L. genotypes. Acorns were collected in clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Microscopic measurements were done for pericarp (total thickness, thickness of exocarp and mesocarp, seed coat (total thickness, thickness of outer epidermis, parenchyma, and inner epidermis, and embryo axis (diameter, thickness of cortical region, and diameter of stellar zone. Obtained results revealed certain divergence between genotypes. The thickness of pericarp varied from 418 to 559 mm (genotypes 20 and 22, respectively. On average, the participation of exocarp in the total thickness of pericarp was 36.3%, of mesocarp 61.0%, while of endocarp 2.6%. The thickness of seed coat for individual genotypes ranged from 71 mm (genotype 28 to 157 mm (genotype 38. In addition, anatomic parameters of embryo axis varied among studied genotypes. The lowest cortical zone thickness and stellar zone diameter were measured in genotype 40, while the highest values in genotype 33.

  9. The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines

    Science.gov (United States)

    Chen, Jiafa; Zavala, Cristian; Ortega, Noemi; Petroli, Cesar; Franco, Jorge; Burgueño, Juan; Costich, Denise E.; Hearne, Sarah J.

    2016-01-01

    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 platforms is

  10. 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

  11. Variability, heritability and genetic advance studies in some indigenous genotypes of basmati rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    C. R. Allam, H.K. Jaiswal , A. Qamar , Challa Venkateshwarlu and Y.S. Reddy

    2015-06-01

    Full Text Available The investigation conducted with 25 rice genotypes comprising both Basmati and non-basmati types revealed significant differences among the genotypes for the yield, its components and some grain quality characteristics. The magnitude of differences between PCV and GCV was relatively low for all the traits, indicating less environmental influence. The GCV was higher for the characters alkali spread value, yield per plant and effective panicles. High heritability coupled with high genetic advance as per cent of mean was recorded for days to 50% flowering, plant height, panicle length, effective panicles per plant, spikelets per panicle, filled grains per panicle, test weight, yield per plant, brown rice length, brown rice L/B ratio, kernel length, kernel L/B ratio, kernel length after cooking, elongation ratio and alkali spread value indicating the additive gene effects in the genetic control of these traits and can be improved by simple selection in the present breeding material.

  12. Genotype by environment interaction and yield stability analysis of quality protein maize genotypes in Terai Region of Nepal

    Directory of Open Access Journals (Sweden)

    Jiban Shrestha

    2013-06-01

    Full Text Available Grain yield stability for the new maize genotypes is an important target in maize breeding programs. The main objective of this study was to identify stable high yielding quality protein maize (QPM genotypes under various locations and years in terai region of Nepal. Six quality protein maize genotypes along with Poshilo Makai-1 (Standard Check and Farmer’s Variety (Local Check were tested at three different locations namely Ayodhyapuri-2, Devendrapur, Madi, Chitwan; Rajahar-8, Bartandi, Rajahar, Nawalparasi; Mangalpur-2, Rampur, Chitwan during 2011 and 2012 spring and winter seasons under rainfed condition. The experiment was conducted using Randomized Complete Block Design with two replications in farmer’s fields. There was considerable variation among genotypes and environments for grain yield. The analysis of variance showed that mean squares of environments (E was highly significant and genotypes (G and genotype x environment interaction (GEI were non significant. The genotypes S03TLYQ- AB02 and RampurS03FQ02 respectively produced the higher mean grain yield 5422±564 kg/ha and 5274±603 kg/ha across the locations. Joint regression analysis showed that RampurS03FQ02 and S03TLYQ-AB02 with regression coefficient 1.10 and 1.22 respectively are the most stable genotypes over the tested environments. The coefficient of determination (R2 for genotypes Rampur S03FQ02 and S03TLYQ-AB02 were as high as 0.954, confirming their high predictability to stability. Further confirmation from GGE biplot analysis showed that maize genotype S03TLYQ-AB02 followed by Rampur S03FQ02 were more stable and adaptive genotypes across the tested environments. Thus these genotypes could be recommended to farmers for general cultivation.

  13. Recurrence of hepatitis C virus genotype- 4 infection following orthotopic liver transplantation: natural history and predictors of outcome

    International Nuclear Information System (INIS)

    There are few reports on hepatitis C virus genotype 4 (HCV-4) recurrences after orthotopic liver transplantation (OLT). Therefore, we undertook a study to determine the epidemiological, clinical and virological characteristics of patients with biopsy-proven recurrent HCV infection and analyzed the factors that influence recurrent disease severity. We also compared disease recurrence and outcomes between HCV-4 and other genotypes. All patients who underwent OLT (locally or abroad) for HCV related hepatic cirrhosis from 1991 to 2006 and had recurrent HCV infection were identified. Clinical, laboratory and pathological data before and after OLT were collected and analyzed. Of 116 patients who underwent OLT for hepatitis C, 46 (39.7%) patients satisfied the criteria of recurrent hepatitis C. Twenty-nine (63%) patients were infected with HCV genotype 4. Mean (SD) for age was 54.9 (10.9) years. Nineteen of the HCV genotype 4 patients (65.5%) were males, 21 (72.4%) received deceased donor grafts, and 7 (24.1%) developed > - 1 acute rejection episodes. Pathologically, 7 (24.1%) and 4 (13.8%) patients had inflammation grade 3-4 and fibrosis stage 3-4, respectively. Follow-up biopsy in 9 (31%) HCV genotype 4 patients showed stable, worse and improved fibrosis stage in 5, 2 and 2 patients, respectively. Of the 7 patients in the recurrent HCV group who died, 6 were infected with genotype 4 and 4 of them died of HCV-related disease. This analysis suggests that HCV recurrence following OLT in HCV-4 patients is not significantly different from its recurrence for other genotypes. (author)

  14. Acanthamoeba genotype T4 from the UK and Iran and isolation of the T2 genotype from clinical isolates

    OpenAIRE

    A.H. Maghsood; Sissons, J.; Rezaian, M.; Nolder, D; Warhurst, D.; Khan, Naveed Ahmed

    2005-01-01

    The majority of the keratitis-causing Acanthamoeba isolates are genotype T4. In an attempt to determine whether predominance of T4 isolates in Acanthamoeba keratitis is due to greater virulence or greater prevalence of this genotype, Acanthamoeba genotypes were determined for 13 keratitis isolates and 12 environmental isolates from Iran. Among 13 clinical isolates, eight (61.5 %) belonged to T4, two (15.3 %) belonged to T3 and three (23 %) belonged to the T2 genotype. In contrast, the majorit...

  15. Belief propagation in genotype-phenotype networks.

    Science.gov (United States)

    Moharil, Janhavi; May, Paul; Gaile, Daniel P; Blair, Rachael Hageman

    2016-03-01

    Graphical models have proven to be a valuable tool for connecting genotypes and phenotypes. Structural learning of phenotype-genotype networks has received considerable attention in the post-genome era. In recent years, a dozen different methods have emerged for network inference, which leverage natural variation that arises in certain genetic populations. The structure of the network itself can be used to form hypotheses based on the inferred direct and indirect network relationships, but represents a premature endpoint to the graphical analyses. In this work, we extend this endpoint. We examine the unexplored problem of perturbing a given network structure, and quantifying the system-wide effects on the network in a node-wise manner. The perturbation is achieved through the setting of values of phenotype node(s), which may reflect an inhibition or activation, and propagating this information through the entire network. We leverage belief propagation methods in Conditional Gaussian Bayesian Networks (CG-BNs), in order to absorb and propagate phenotypic evidence through the network. We show that the modeling assumptions adopted for genotype-phenotype networks represent an important sub-class of CG-BNs, which possess properties that ensure exact inference in the propagation scheme. The system-wide effects of the perturbation are quantified in a node-wise manner through the comparison of perturbed and unperturbed marginal distributions using a symmetric Kullback-Leibler divergence. Applications to kidney and skin cancer expression quantitative trait loci (eQTL) data from different mus musculus populations are presented. System-wide effects in the network were predicted and visualized across a spectrum of evidence. Sub-pathways and regions of the network responded in concert, suggesting co-regulation and coordination throughout the network in response to phenotypic changes. We demonstrate how these predicted system-wide effects can be examined in connection with

  16. Effect of genotype, Cr(III and Cr(VI on plant growth and micronutrient status in Silene vulgaris (Moench

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    A. E. Pradas-del-Real

    2013-06-01

    Full Text Available Chromium released into the environment from industrial activities has become an important environmental concern. Silene vulgaris has been proven to be tolerant to many heavy metals, so it is considered an interesting species in the revegetation and restoration of polluted soils, but no information is available about its response to Cr. The objective of this work was to study uptake and influence on plant growth of Cr(III and Cr(VI in six genotypes (four hermaphrodites and two females of S. vulgaris from different sites of Madrid (Spain. Plants were treated for 12 days with 60 µM of Cr(III or Cr(VI in semihydroponics. Dry weights, soil-plant analysis development values (SPAD reading with chlorophylls and micronutrient and total Cr concentrations were determined. Metal uptake was higher in presence of Cr(VI than of Cr(III and poorly translocated to the shoots. In both cases S. vulgaris did not show visual toxicity symptoms, biomass reduction, or differences among SPAD values as consequence of Cr additions. However genotypes SV36 and SV38 showed Fe and Mn imbalance. This is the first report on the relatively good performance of hermaphrodite and female S. vulgaris genotypes in Cr uptake and physiological traits, but further studies will be necessary to elucidate the mechanisms by which the gender may influence these variables. S. vulgaris presented high diversity at genotypic level; the treatment with hexavalent Cr increased the differences among genotypes so the use of cuttings from an homogeneous genotype seems to be an adequate method for the study of this species.

  17. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B;

    2009-01-01

    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...... 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......, 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...

  18. A new genotype of Arthroderma benhamiae.

    Science.gov (United States)

    Kano, Rui; Sano, Ayako; Makimura, Koichi; Watanabe, Shinichi; Nishimura, Kazuko; Yamaguchi, Hideo; Hasegawa, Atuhiko

    2008-11-01

    Nucleotide sequence analysis of chitin synthase 1 (CHS1) indicated 90% sequence similarities among human and animal isolates of Arthroderma benhamiae. In particular, greater than 99% similarity was noted in the nucleotide sequence among Americano-European race isolates, African race isolates, and five isolates from four-toed hedgehogs (Atelerix albiventris). The phylogenetic analysis indicated that the five isolates from hedgehogs were included in the same cluster and distinct from the Americano-European and the African race standard strains of A. benhamiae. These results were confirmed by ITS analysis. Therefore, it was proposed that genotypes could be established for the isolates of A. benhamiae in association with the mating behavior. PMID:18608884

  19. Medulloblastoma Genotype Dictates Blood Brain Barrier Phenotype.

    Science.gov (United States)

    Phoenix, Timothy N; Patmore, Deanna M; Boop, Scott; Boulos, Nidal; Jacus, Megan O; Patel, Yogesh T; Roussel, Martine F; Finkelstein, David; Goumnerova, Liliana; Perreault, Sebastien; Wadhwa, Elizabeth; Cho, Yoon-Jae; Stewart, Clinton F; Gilbertson, Richard J

    2016-04-11

    The childhood brain tumor, medulloblastoma, includes four subtypes with very different prognoses. Here, we show that paracrine signals driven by mutant β-catenin in WNT-medulloblastoma, an essentially curable form of the disease, induce an aberrant fenestrated vasculature that permits the accumulation of high levels of intra-tumoral chemotherapy and a robust therapeutic response. In contrast, SHH-medulloblastoma, a less curable disease subtype, contains an intact blood brain barrier, rendering this tumor impermeable and resistant to chemotherapy. The medulloblastoma-endothelial cell paracrine axis can be manipulated in vivo, altering chemotherapy permeability and clinical response. Thus, medulloblastoma genotype dictates tumor vessel phenotype, explaining in part the disparate prognoses among medulloblastoma subtypes and suggesting an approach to enhance the chemoresponsiveness of other brain tumors. PMID:27050100

  20. SNP GENOTYPING BY TAQMAN ALLELE DISCRIMINATION TECHNIQUE

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    Lucian Negura

    2015-07-01

    Full Text Available Breast cancer is the most frequent neoplasm in women worldwide and the principal cause of deaths by cancer, the majority being by metastatic disease. About half of breast tumors are hormone dependent, and in post-menopause women the preferred first line treatment uses third generation aromatase inhibitors. Aromatase is encoded by CYP19 gene on 15q21.1, and there is strong evidence that mutations in this gene affect its expression, with directconsequences on cancer phenotype and response to treatment. Several single nucleotide polymorphisms have beenstudied on CYP19A1 transcription variant, notably rs727479, rs10046, rs4646 and rs700518. We implemented a Taqman-based allele discrimination assay for the rapid investigation of the 4 SNPs in CYP19A1. We genotyped 22 metastaticbreast cancer patients by the technique described.

  1. Genotype by environment interaction and breeding for robustness in livestock.

    Science.gov (United States)

    Rauw, Wendy M; Gomez-Raya, Luis

    2015-01-01

    The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond. PMID:26539207

  2. Hepatitis C virus genotypes in Cordoba, Argentina unexpected high prevalence of genotype 2

    Directory of Open Access Journals (Sweden)

    V. Re

    2003-06-01

    Full Text Available To determine hepatitis C virus (HCV genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR. Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%, followed by genotypes 1 (38.3 %, and 3 (5.0%. Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9% was found among patients with acute or chronic HCV infection (without known risk factors. These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.A fin de determinar los genotipos del virus de la hepatitis C (HCV circulantes en la región central de Argentina, se estudiaron 96 individuos anti-HCV positivos. La presencia del ARN de HCV se detectó en 60 muestras mediante RT-nested PCR de la región 5' no codificante (5' NCR. La genotipificación se realizó mediante restricción enzimática y el análisis del polimorfismo de los fragmentos largos de la región 5' NCR combinada con PCR usando primers tipo específico de la región del core. El grupo de individuos estudiados incluyó pacientes hemofílicos y hemodializados, drogadictos intravenosos, donantes de sangre y pacientes con enfermedad hepática aguda y crónica, todos provenientes de Córdoba, Argentina. El genotipo 2 fue el más prevalente (55.0%, seguido por los genotipos 1 (38.3 %, con mayor prevalencia

  3. Paternity testing and delivering trait-predictive genotypic data

    Science.gov (United States)

    In the RosBREED project, the Genotyping Team (Team Leader: Nahla Bassil) leads the effort to obtain DNA data needed to enable marker-assisted breeding for critical fruit quality traits. These data are obtained from reference genotypes of apple, peach, cherry and strawberry carefully chosen to repres...

  4. Genotyping-by-sequencing for plant breeding and genetics

    Science.gov (United States)

    Rapid advances in post-Sanger sequencing technology have brought the $1000 human genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotyping-by-sequencing (GBS) has been developed as...

  5. Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping

    OpenAIRE

    Manichaikul, Ani; Palmer, Abraham A.; Sen, Śaunak; Broman, Karl W.

    2007-01-01

    In the case of selective genotyping, the usual permutation test to establish statistical significance for quantitative trait locus (QTL) mapping can give inappropriate significance thresholds, especially when the phenotype distribution is skewed. A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals.

  6. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador

    Science.gov (United States)

    Recent international demand for “nacional” flavour cacao has increased the need for local cacao producers in Ecuador to use high-yielding “nacional” hybrid genotypes. The relative potential of cacao genotypes over various environments needs to be assessed prior to final selection of potential candid...

  7. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David;

    2013-01-01

    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less c...

  8. Ant colony optimization as a method for strategic genotype sampling.

    Science.gov (United States)

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/ 0.3 and 0.5/0.5. In addition...

  9. Genotypic and Phenotypic Characterization of Chikungunya Virus of Different Genotypes from Malaysia

    OpenAIRE

    Sam, I-Ching; Loong, Shih-Keng; Michael, Jasmine Chandramathi; Chua, Chong-Long; Wan Sulaiman, Wan Yusoff; Vythilingam, Indra; Chan, Shie-Yien; Chiam, Chun-Wei; Yeong, Yze-Shiuan; AbuBakar, Sazaly; Chan, Yoke-Fun

    2012-01-01

    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...

  10. Spontaneous viral clearance, viral load, and genotype distribution of hepatitis C virus (HCV) in HIV-infected patients with anti-HCV antibodies in Europe

    DEFF Research Database (Denmark)

    Soriano, Vincent; Mocroft, Amanda; Rockstroh, Juergen;

    2008-01-01

    , respectively. A greater HCV RNA level was associated with a greater chance of being infected with HCV genotype 1 (aOR, 1.60 per 1 log higher [95% CI, 1.36-1.88]). CONCLUSIONS: More than three-quarters of the HIV- and HCV Ab-positive patients in EuroSIDA showed active HCV replication. Viremia was more frequent......BACKGROUND: Variables influencing serum hepatitis C virus (HCV) RNA levels and genotype distribution in individuals with human immunodeficiency virus (HIV) infection are not well known, nor are factors determining spontaneous clearance after exposure to HCV in this population. METHODS: All HCV...... antibody (Ab)-positive patients with HIV infection in the EuroSIDA cohort who had stored samples were tested for serum HCV RNA, and HCV genotyping was done for subjects with viremia. Logistic regression was used to identify variables associated with spontaneous HCV clearance and HCV genotype 1. RESULTS: Of...

  11. Selection of red raspberry genotypes (Rubus idaeus L.

    Directory of Open Access Journals (Sweden)

    Fotirić Milica

    2009-01-01

    Full Text Available Pomological properties of seedlings obtained by open pollination of Meeker's yellow clone were investigated. From over a 100 seedlings obtained from this progeny, 16 genotypes with red fruits were selected on the Experimental Station 'Radmilovac' that belongs to the Faculty of Agriculture in Belgrade. Dunnett-test was used for single testing of physical and chemical traits of raspberry genotypes. It was found that majority of selected genotypes were in the rank with the standard cultivar Meeker, so the final selection of raspberry genotypes was based on organoleptic characteristics. From 16 examined genotypes nine were selected (I/3/2P, I/6/2, I/8/2, II/2/2P, II/3/4P, II/5/3P, II/8/2, II/8/2P and II/PP/2 for further investigation.

  12. 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.

  13. Fruit characterization of sugar apple genotypes in Presidente Dutra, Bahia

    Directory of Open Access Journals (Sweden)

    Saulo Almeida Sousa

    2006-01-01

    Full Text Available To identify promising genotypes for commercial cultivations and studies of genetic improvement with sugarapple, eight fruits each of 30 genotypes of the species were charactyerized by: length and fruit diameter, fruit mass, pulp mass,seed mass, rind mass and receptacle mass, pulp yield, number of seeds, thickness of the rind, pH, total soluble solids (TSS,total titratable acidity (TTA, vitamin C, TSS/TTA ratio, moisture, ash content, total, reducing and non-reducing sugars.Results were evaluated by descriptive statistics (mean, standard deviations and coefficient of variation and statisticalmultivariate analysis, by grouping techniques and main component analysis. The genotypes were clustered in 10 genticallydivergent groups, which allowed the selection of promising genotypes. The highly variable traits fruit, pulp, and rind massand number of seeds contribute to the differentiation of the evaluated genotypes.

  14. Comparison of genotype and intellectual phenotype in untreated PKU patients.

    Science.gov (United States)

    Ramus, S J; Forrest, S M; Pitt, D B; Saleeba, J A; Cotton, R G

    1993-01-01

    We have screened 55 untreated phenylketonuria patients from 42 families for common mutations of the phenylalanine hydroxylase gene and determined both causative alleles in 12 families. The correlation between genotype and intellectual phenotype of patients in these families was examined. Our results were compared to a study which predicted phenylalanine hydroxylase activity based on genotype and examined its correlation with the biochemical phenotype of treated patients. Some of the intellectual phenotypes of patients in our study correlated well with the predicted activities. However, we found one family with a genotype expected to have no activity of phenylalanine hydroxylase where the patients were not severely retarded. Major differences in intellectual phenotype were found in patients with the same genotype both between unrelated subjects and within families, suggesting that there is not a simple correlation between genotype and intellectual phenotype. Images PMID:8320703

  15. Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

    Science.gov (United States)

    Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

    2010-10-01

    The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns. PMID:20640884

  16. Effect of genotype on sugar beet yield and quality

    Directory of Open Access Journals (Sweden)

    Nenadić N.

    2003-01-01

    Full Text Available The effect of a considerable number of both domestic and foreign sugar beet genotypes on root yield and quality was investigated. The data demonstrated the most favorable results of some genotypes for root yield and sugar content. Trials were conducted on rhizomania infested soil, thus tolerant genotypes were used. Susceptible cultivars represented the control. In the trial root yield was high and sugar content low. On average, in the genotypes tested, root yield varied from 73.98 to 93.30 t/ha and sugar content from 11.90 to 13.36%, depending on weather conditions. Root yield of the genotypes investigated varied from 30.61 to 112.64 t/ha and sugar content from 10.60 to 14.20%. The Swedish cultivar Dorotea (tolerant to both rhizomania and cercospora was the most yielding. The least yielding (susceptible to both rhizomania and cercospora was the domestic cultivar Dana.

  17. Influência de genótipos de couve (Brassica oleracea L. var. acephala DC. na biologia de Plutella xylostella (L., 1758 (Lepidoptera: Plutellidae Influence of cabbage genotypes (Brassica oleracea L. var. acephala DC. on the biology of Plutella xylostella (L., 1758 (Lepidoptera: Plutellidae

    Directory of Open Access Journals (Sweden)

    Arlindo Leal Boiça Junior

    2011-08-01

    Full Text Available Objetivou-se, com este trabalho, avaliar a influência de alguns genótipos de couve (Brassica oleracea L. var. acephala DC. no desenvolvimento de Plutella xylostella (L., 1758 (Lepidoptera: Plutellidae. Os genótipos avaliados foram: Manteiga de Ribeirão Pires I-2620, Roxa I-919, Manteiga de São José, Manteiga de Monte Alegre, Pires 2 de Campinas, Couve Comum, Couve de Arthur Nogueira 2, Couve de Arthur Nogueira 1. Lagartas recém-eclodidas foram mantida em discos foliares de 8 cm de diâmetro para cada genótipo. Foram analisados os seguintes parâmetros: duração e viabilidade das fases larval e pupal, longevidade e fecundidade de adultos, utilizando análises paramétricas e de agrupamentos para interpretação dos dados. Observou-se um prolongamento em dias no ciclo de P. xylostella, aumento no peso de pupa e maiores valores de viabilidade e fecundidade, durante a segunda geração. O genótipo Couve de Arthur Nogueira 2 foi menos favorável ao desenvolvimento de P. xylostella nas duas gerações, e Couve Comum demonstrou maior influência negativa ao inseto na segunda geração. Manteiga de Ribeirão Pires I-2620 foi o mais suscetível nas duas gerações, agrupando com este na segunda geração Pires 2 de Campinas e Manteiga de São José.The purpose of this study was to evaluate the effect of cabbage genotypes (Brassica oleracea L. var. acephala DC. on growth of Plutella xylostella (Lepidoptera: Plutellidae. The genotypes evaluated were: Manteiga of Ribeirão Pires I-2620, Roxa I919, Manteiga of São José, Manteiga of Monte Alegre, Pires 2 of Campinas, Couve Comum, Couve of Arthur Nogueira 2, Couve of Arthur Nogueira 1. Neonate larvae were reared in 8 cm leaf discs of each genotype. The parameters evaluated were: period and viability of the larval and pupal stages, sex ratio, longevity and fecundity of adults. Parametric and Cluster analyses were used for data analysis. Overall, it was observed a developmental delay in the P

  18. Comparison of methods for analysis of selective genotyping survival data

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    Dekkers Jack CM

    2006-11-01

    Full Text Available Abstract Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH, linear regression (LR, and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.

  19. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters...... per family. The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach...

  20. Genotypic diversity of Lactobacillus sanfranciscensis strains isolated from French organic sourdoughs.

    Science.gov (United States)

    Lhomme, Emilie; Onno, Bernard; Chuat, Victoria; Durand, Karine; Orain, Servane; Valence, Florence; Dousset, Xavier; Jacques, Marie-Agnès

    2016-06-01

    Lactobacillus sanfranciscensis is the predominant key lactic acid bacterium in traditionally fermented sourdoughs. Despite its prevalence, sourdough and their related breads could be different regarding their physicochemical and sensorial characteristics. The intraspecific diversity of L. sanfranciscensis might explain these observations. Fifty-nine strains isolated from French sourdoughs were typed by a polyphasic approach including Multilocus Sequence Typing (MLST) and Pulsed-field Gel Electrophoresis (PFGE), in order to study their genotypic diversity. MLST scheme can be reduced from six to four gene fragments (gdh, gyrA, nox and pta) without a major loss of discrimination between strains. The genes mapA and pgmA are not good candidates for inclusion in an MLST scheme to type L. sanfranciscensis strains, as they could not be amplified for a set of 18 strains among the 59 studied. This method revealed 20 sequence types (STs). Of these, 19 STs were grouped in one clonal complex, showing a strong relatedness between these strains. PFGE using SmaI discriminated 41 pulsotypes and so distinguished isolates better than the MLST scheme. Both genotypic methods indicate a low diversity between strains isolated from the same sourdough and a higher diversity between strains isolated from different sourdoughs, suggesting an influence of baker practices and/or environmental conditions on the selection of strains. The use of these two methods targeting genetic variations gives an optimal genotypic characterization of L.sanfranciscensis strains. PMID:27015297

  1. molecular Analysis of two Banana Genotypes Induced in Vitro Under Gamma Rays Stress

    International Nuclear Information System (INIS)

    Shoots of banana genotypes, grand naine and shikita were initiated on murashige and skoog (MS) medium containing 2.0 mg/L benzyl adenine. shoots were irradiated with 60Co, doses 0.0, 15.0, 30.0 and 45.0 Gy. The effect of gamma irradiation on the expression of proteins and randomly amplified polymorphism (RAPD) was investigated. the proteins which have molecular weight between 15.0 and 200.0 KDa were highly affected by gamma-irradiation. variation in protein expression pattern was influenced by several factors including the genotype and the irradiation dose. it was observed that some proteins were de novo by the irradiation treatments and some were absent. Total DNA of the two different genotypes was amplified by polymerase chain reaction (PCR)using ten primers. among which the amplified products of 8 primers (80%) out of the ten showed highly polymorphisms. as the results of irradiation primers A7, A9,A10 and R7 revealed more genomic variation than the other primers(A1,B4,P9 and R6). the use gamma -irradiation for inducing changes in the DNA sequence may be revealed by the protein expression and may change the primers sites which were observed by change in the amplified products

  2. The Association between Mycobacterium Tuberculosis Genotype and Drug Resistance in Peru.

    Directory of Open Access Journals (Sweden)

    Louis Grandjean

    Full Text Available The comparison of Mycobacterium tuberculosis bacterial genotypes with phenotypic, demographic, geospatial and clinical data improves our understanding of how strain lineage influences the development of drug-resistance and the spread of tuberculosis.To investigate the association of Mycobacterium tuberculosis bacterial genotype with drug-resistance. Drug susceptibility testing together with genotyping using both 15-loci MIRU-typing and spoligotyping, was performed on 2,139 culture positive isolates, each from a different patient in Lima, Peru. Demographic, geospatial and socio-economic data were collected using questionnaires, global positioning equipment and the latest national census.The Latin American Mediterranean (LAM clade (OR 2.4, p<0.001 was significantly associated with drug-resistance and alone accounted for more than half of all drug resistance in the region. Previously treated patients, prisoners and genetically clustered cases were also significantly associated with drug-resistance (OR's 2.5, 2.4 and 1.8, p<0.001, p<0.05, p<0.001 respectively.Tuberculosis disease caused by the LAM clade was more likely to be drug resistant independent of important clinical, genetic and socio-economic confounding factors. Explanations for this include; the preferential co-evolution of LAM strains in a Latin American population, a LAM strain bacterial genetic background that favors drug-resistance or the "founder effect" from pre-existing LAM strains disproportionately exposed to drugs.

  3. Replication study of the vitamin D receptor (VDR) genotype association with skeletal muscle traits and sarcopenia.

    Science.gov (United States)

    Walsh, Sean; Ludlow, Andrew T; Metter, E Jeffrey; Ferrucci, Luigi; Roth, Stephen M

    2016-06-01

    Polymorphisms in the vitamin D receptor (VDR) gene are some of the most studied in relation to skeletal muscle traits and significant associations have been observed by multiple groups. One such paper by our group provided the first evidence of a genetic association with sarcopenia in men, but that finding has yet to be replicated in an independent cohort. In the present study, we examined multiple VDR polymorphisms in relation to skeletal muscle traits and sarcopenia in 864 men and women across the adult age span. In addition to VDR genotypes and haplotypes, measurements of skeletal muscle strength and fat-free mass (FFM) were determined in all subjects and a measure of sarcopenia was calculated. We observed significant associations between Fok1 and Bsm1 genotypes and skeletal muscle strength in men and women, though these associations were modest and no significant associations were observed for these polymorphisms and muscle mass traits nor for Bsm1-Taq1 haplotype with muscle strength. Fok1 FF genotype was associated with an increased the risk of sarcopenia in older women compared to f-allele carriers (1.3-fold higher risk). These results support previous findings that VDR genetic variation appears to impact skeletal muscle strength and risk for sarcopenia but the influence is modest. PMID:26415498

  4. KIR-HLA genotypes in HIV-infected patients lacking immunological recovery despite effective antiretroviral therapy.

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    Alessandro Soria

    Full Text Available BACKGROUND: In HIV-infected individuals, mechanisms underlying unsatisfactory immune recovery during effective combination antiretroviral therapy (cART have yet to be fully understood. We investigated whether polymorphism of genes encoding immune-regulating molecules, such as killer immunoglobulin-like receptors (KIR and their ligands class I human leukocyte antigen (HLA, could influence immunological response to cART. METHODS: KIR and HLA frequencies were analyzed in 154 HIV-infected and cART-treated patients with undetectable viral load divided into two groups: 'immunological non responders' (INR, N = 50, CD4(+ T-cell count 350/mm(3. Molecular KIR were typed using polymerase chain reaction-based genotyping. Comparisons were adjusted for baseline patient characteristics. RESULTS: The frequency of KIR2DL3 allele was significantly higher in FR than in INR (83.7% vs. 62%, P = 0.005. The functional compound genotype HLA-C1(+/KIR2DL3(+, even at multivariable analysis, when adjusted for nadir CD4(+ T-cell count, was associated with reduced risk of INR status: odds ratio (95% Confidence Intervals 0.34 (0.13-0.88, P = 0.03. CONCLUSIONS: Reduced presence of the inhibitory KIR2DL3 genotype detected in INR might provoke an imbalance in NK function, possibly leading to increased immune activation, impaired killing of latently infected cells, and higher proviral burden. These factors would hinder full immune recovery during therapy.

  5. Muscle and genotype effects on fatty acid composition of goat kid intramuscular fat

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    Valeriano Domenech

    2011-07-01

    Full Text Available Little is known about the fatty acid composition of the major muscles in goats from different breeds. Forty entire male suckling kids, 20 Criollo Cordobes and 20 Anglo Nubian, were slaughtered at 75 days of age and the fatty acid composition of their longissimus thoracis (LT and semitendinosus (ST muscles was analysed to clarify the effects of genotype and muscle type on goat kid meat. Genotype had a great influence on the fatty acid composition of goat kid meat. Meat from Criollo Cordobes had greater saturated (P<0.001 and lower monounsaturated (P<0.001 and polyunsaturated fatty acids (P=0.002 concentration than meat from Anglo Nubian, showing higher saturated fatty acids (SFA. On the other hand, intramuscular fat content from both genotypes was higher (P=0.042 in ST muscle, while the lowest cholesterol levels were observed in ST of Criollo Cordobes (P=0.038. That higher fat content resulted in lower relative contents of total polyunsaturated (P<0.001 and n-3 (P=0.002 fatty acids due to the lower contribution of the membrane phospholipids.

  6. Dry matter genotypes of Cynodon by microwave and conventional oven methods

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    Euclides Reuter de Oliveira

    2013-02-01

    Full Text Available The aimed of this work was to comparing the drying process in a microwave oven and forced air ventilation, as well as their effects on the chemical composition of different genotypes of the genus Cynodon (Tifton 85, Jiggs, Russell, Tifton 68 and Vaquero collected at different ages cutting (28, 48, 63 and 79 days. The experimental design was a randomized block in a split-plot design, with 4 replicates. There was no difference (P>0.05 between the methods analyzed on the chemical composition of the genotypes studied. Increasing age cutoff negatively influenced (P<0.05 the crude protein content of the different plant parts. A significant increase (P<0.05 of dry matter, neutral detergent fiber, acid detergent fiber and dry matter production was observed with increasing age cut. The use of the microwave oven is a quick and precise method obtain the dry matter content of the fodder showing efficiency similar to the method of drying in an oven with forced air circulation. The genotypes showed better chemical composition results when handled at age 28 days.

  7. Hepatitis A Virus Genotype Distribution during a Decade of Universal Vaccination of Preadolescents

    Directory of Open Access Journals (Sweden)

    Lucía D’Andrea

    2015-03-01

    Full Text Available A universal vaccination program among preadolescents was implemented in Catalonia, Spain, during the period of 1999–2013 and its effectiveness has been clearly demonstrated by an overall significant attack rate reduction. However, reductions were not constant over time, and increases were again observed in 2002–2009 due to the occurrence of huge outbreaks. In the following years, in the absence of large outbreaks, the attack rate decreased again to very low levels. However, an increase of symptomatic cases in the <5 age group has recently been observed. This is an unexpected observation since children younger than 6 are mostly asymptomatic. Such a long vaccination campaign offers the opportunity to analyze not only the effectiveness of vaccination, but also the influence of the circulating genotypes on the incidence of hepatitis A among the different age groups. This study has revealed the emergence of genotype IC during a foodborne outbreak, the short-lived circulation of vaccine-escape variants isolated during an outbreak among the men-having-sex-with-men group, and the association of genotype IIIA with the increase of symptomatic cases among the very young. From a public health perspective, two conclusions may be drawn: vaccination is better at an early age, and the vaccination schedule must be complete and include all recommended vaccine doses.

  8. Genotype-temperature interaction in the regulation of development, growth, and morphometrics in wild-type, and growth-hormone transgenic coho salmon.

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    Mare Lõhmus

    Full Text Available BACKGROUND: The neuroendocrine system is an important modulator of phenotype, directing cellular genetic responses to external cues such as temperature. Behavioural and physiological processes in poikilothermic organisms (e.g. most fishes, are particularly influenced by surrounding temperatures. METHODOLOGY/PRINCIPAL FINDINGS: By comparing the development and growth of two genotypes of coho salmon (wild-type and transgenic with greatly enhanced growth hormone production at six different temperatures, ranging between 8 degrees and 18 degrees C, we observed a genotype-temperature interaction and possible trend in directed neuroendocrine selection. Differences in growth patterns of the two genotypes were compared by using mathematical models, and morphometric analyses of juvenile salmon were performed to detect differences in body shape. The maximum hatching and alevin survival rates of both genotypes occurred at 12 degrees C. At lower temperatures, eggs containing embryos with enhanced GH production hatched after a shorter incubation period than wild-type eggs, but this difference was not apparent at and above 16 degrees C. GH transgenesis led to lower body weights at the time when the yolk sack was completely absorbed compared to the wild genotype. The growth of juvenile GH-enhanced salmon was to a greater extent stimulated by higher temperatures than the growth of the wild-type. Increased GH production significantly influenced the shape of the salmon growth curves. CONCLUSIONS: Growth hormone overexpression by transgenesis is able to stimulate the growth of coho salmon over a wide range of temperatures. Temperature was found to affect growth rate, survival, and body morphology between GH transgenic and wild genotype coho salmon, and differential responses to temperature observed between the genotypes suggests they would experience different selective forces should they ever enter natural ecosystems. Thus, GH transgenic fish would be expected to

  9. 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

  10. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.

    Science.gov (United States)

    Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David

    2013-01-01

    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq. PMID:23090981

  11. CHRNA3 genotype, nicotine dependence, lung function and disease in the general population

    DEFF Research Database (Denmark)

    Kaur-Knudsen, Diljit; Nordestgaard, Børge G; Bojesen, Stig E

    2012-01-01

    The CHRNA3 rs1051730 polymorphism has been associated to chronic obstructive pulmonary disease (COPD), lung cancer and nicotine dependence in case-control studies with high smoking exposure; however, its influence on lung function and COPD severity in the general population is largely unknown. We...... genotyped 57,657 adult individuals from the Copenhagen General Population Study, of whom 34,592 were ever-smokers. Information on spirometry, hospital admissions, smoking behaviour and use of nicotinic replacement therapy was recorded. In homozygous (11%), heterozygous (44%) and noncarrier (45%) ever...

  12. The Impact of CYP2D6 Genotyping on Tamoxifen Treatment

    Directory of Open Access Journals (Sweden)

    Roberta Ferraldeschi

    2010-04-01

    Full Text Available Tamoxifen remains a cornerstone of treatment for patients with oestrogen-receptor-positive breast cancer. Tamoxifen efficacy depends on the biotransformation, predominantly via the cytochrome P450 2D6 (CYP2D6 isoform, to the active metabolite endoxifen. Both genetic and environmental (drug-induced factors may alter CYP2D6 enzyme activity directly affecting the concentrations of active tamoxifen metabolites. Several studies suggest that germline genetic variants in CYP2D6 influence the clinical outcomes of patients treated with adjuvant tamoxifen. Here, we review the existing data relating CYP2D6 genotypes to tamoxifen efficacy.

  13. Biological variation in Trichinella species and genotypes.

    Science.gov (United States)

    Bolas-Fernández, F

    2003-06-01

    At present, the genus Trichinella comprises seven species of which five have encapsulated muscle larvae (T. spiralis, T. nativa, T. britovi, T. nelsoni and T. murrelli) and two do not (T. pseudospiralis and T. papuae) plus three genotypes of non-specific status (T6, T8 and T9). The diagnostic characteristics of these species are based on biological, biochemical and genetic criteria. Of biological significance is variation observed among species and isolates in parameters such as infectivity and immunogenicity. Infectivity of Trichinella species or isolates is determined, among other considerations, by the immune status of the host in response to species- or isolate-specific antigens. Common and particular antigens determine the extent of protective responses against homologous or heterologous challenge. The kinetics of isotype, cytokine and inflammatory responses against T. spiralis infections are isolate-dependent. Trichinella spiralis and T. pseudospiralis induce different dose-dependent T-cell polarizations in the early host response, with T. spiralis initially preferentially promoting Th1-type responses before switching to Th2 and T. pseudospiralis driving Th2-type responses from the outset. PMID:12756064

  14. Genotype phenotype classification of hepatocellular adenoma

    Institute of Scientific and Technical Information of China (English)

    Paulette Bioulac-Sage; Jean Frédéric Blanc; Sandra Rebouissou; Charles Balabaud; Jessica Zucman-Rossi

    2007-01-01

    Studies that compare tumor genotype with phenotype have provided the basis of a new histological/molecular classification of hepatocellular adenomas. Based on two molecular criteria (presence of a TCF1/HNF1α or β-catenin mutation), and an additional histological criterion (presence or absence of an inflammatory infiltrate), subgroups of hepatocellular adenoma can be defined and distinguished from focal nodular hyperplasia. Analysis of 96 hepatocellular adenomas performed by a French collaborative network showed that they can be divided into four broad subgroups: the first one is defined by the presence of mutations in TCF1 gene inactivating the hepatocyte nuclear factor 1 (HNF1α); the second by the presence of β-catenin activating mutations; the category without mutations of HNF1α or β-catenin is further divided into 2 subgroups depending on the presence or absence of inflammation. Therefore, the approach to the diagnosis of problematic benign hepatocytic nodules may be entering a new era directed by new molecular information. It is hoped that immunohistological tools will improve significantly diagnosis of liver biopsy in our ability to distinguish hepatocellular adenoma from focal nodular hyperplasia (FNH), and to delineate clinically meaningful entities within each group to define the best clinical management. The optimal care of patients with a liver nodule will benefit from the recent knowledge coming from molecular biology and the combined expertise of hepatologists, pathologists, radiologists, and surgeons.

  15. Genotyping of Canine parvovirus in western Mexico.

    Science.gov (United States)

    Pedroza-Roldán, César; Páez-Magallan, Varinia; Charles-Niño, Claudia; Elizondo-Quiroga, Darwin; De Cervantes-Mireles, Raúl Leonel; López-Amezcua, Mario Alberto

    2015-01-01

    Canine parvovirus (CPV) is one of the most common infectious agents related to high morbidity rates in dogs. In addition, the virus is associated with severe gastroenteritis, diarrhea, and vomiting, resulting in high death rates, especially in puppies and nonvaccinated dogs. To date, there are 3 variants of the virus (CPV-2a, CPV-2b, and CPV-2c) circulating worldwide. In Mexico, reports describing the viral variants circulating in dog populations are lacking. In response to this deficiency, a total of 41 fecal samples of suspected dogs were collected from October 2013 through April 2014 in the Veterinary Hospital of the University of Guadalajara in western Mexico. From these, 24 samples resulted positive by polymerase chain reaction, and the viral variant was determined by restriction fragment length polymorphism. Five positive diagnosed samples were selected for partial sequencing of the vp2 gene and codon analysis. The results demonstrated that the current dominant viral variant in Mexico is CPV-2c. The current study describes the genotyping of CPV strains, providing valuable evidence of the dominant frequency of this virus in a dog population from western Mexico. PMID:25525144

  16. Plant genotype, microbial recruitment and nutritional security

    Directory of Open Access Journals (Sweden)

    Jai Singh Patel

    2015-08-01

    Full Text Available Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome.

  17. Evaluation of linear array human papillomavirus genotyping using automatic optical imaging software.

    Science.gov (United States)

    Jeronimo, J; Wentzensen, N; Long, R; Schiffman, M; Dunn, S T; Allen, R A; Walker, J L; Gold, M A; Zuna, R E; Sherman, M E; Wacholder, S; Wang, S S

    2008-08-01

    Variations in biological behavior suggest that each carcinogenic human papillomavirus (HPV) type should be considered individually in etiologic studies. HPV genotyping assays might have clinical applications if they are approved for use by the FDA. A widely used genotyping assay is the Roche Linear Array HPV genotyping test (LA). We used LA to genotype the HPV isolates from cervical specimens from women with the full spectrum of cervical disease: cervical cancer, cervical intraepithelial neoplasia (CIN), and HPV infections. To explore the feasibility and value of the automated reading of the LA results, we custom-designed novel, optical imaging software that provides optical density measurements of LA bands. We compared unmagnified visual examination with the automated measurements. The two measurements were highly associated. By either method, the threshold between a negative and a positive result was fairly sharp, with a clear bimodal distribution. Visually, most positive results were judged to be strong or medium, with fewer equivocal results categorized as weak (9.5% of positive samples), very weak (6.5% of positive samples), or extremely weak (7.7% of positive samples). The automated measurements of the intensities were significantly associated with the strength of the visual categories (P or = 120 units), the bands were almost always categorized visually as negative and positive, respectively. In the equivocal zone (20 to 119 units), specimens were more increasingly likely to be judged to be visually positive as the number of other, definite infections on the same strip increased (P for trend or = 25% of HPV infections; thus, any systematic visual tendency that influences their evaluation when the result is equivocal should be minimized. Therefore, automated reading is probably worth development if easy-to-calibrate hardware and software can be optimized. PMID:18550741

  18. Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

    Science.gov (United States)

    Picard, Christine; Bosco, Marco

    2008-01-01

    Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

  19. Effects of genotype and stocking density on broiler performance under three feeding regimes.

    Science.gov (United States)

    Ligaraba, Tshililo Joyce; Benyi, Kow; Baloyi, Joseph Jumu

    2016-08-01

    Ross 308 and Cobb Avian 48 broilers were used in a 49-day study. The effects of genotype, stocking density, and limited-time feeding on growth performance and carcass characteristics were investigated. Overall, Ross consumed more feed, gained more body weight, and was heavier at marketing age than Cobb. Ross also had a higher drumstick percentage, but the percentages of the other carcass parts were similar in the two genotypes. Birds reared at the stocking density of 30 kg BW/m(2) gained more body weight and were heavier at marketing than those raised at 40 kg BW/m(2), but both groups consumed similar quantities of feed and had similar carcass percentages. Neither genotype nor stocking density influenced feed conversion ratio and mortality rate, but genotype x stocking density interaction significantly affected feed consumption and mortality rate. The feed-restricted birds consumed less feed, gained less weight, were lighter at market age, and had lower percentages of breast, neck, and heart than the full-fed birds. Feed restriction also significantly lowered mortality rate but had insignificant effects on feed conversion ratio and percentages of carcass, breast, back, drumstick, neck, wing, gizzard, heart, liver, and abdominal fat. For profitable poultry production in the tropics and subtropics, it is recommended that Ross 308 raised at the stocking density of 30 kg BW/m(2) and subjected to 10-h daily feed removal from 7 to 35 days of age in a 49-day production period be considered. PMID:27221242

  20. Evaluation of Soybean and Cowpea Genotypes for Phosphorus Use Efficiency

    International Nuclear Information System (INIS)

    Initial screening of one hundred and fifty-two (152) and fifty (50) genotypes of soybean and cowpea, respectively, were conducted at the early growth stage to evaluate root traits associated with phosphorus (P) efficiency. Fifty soybean genotypes were subsequently selected and evaluated on a tropical low P soil (Lixisol) for growth and yield under low and adequate P availability. Plants were sampled at twelve and thirty days after sowing and at maturity. Six cowpea genotypes were also selected and evaluated in pots filled with Alfisol under low, moderate and high P availability. Plants were sampled at forty days and assessed for shoot yield and nodulation under low P availability. Using Principal Component Analysis (PCA), Phosphorus Efficiency Index (PEI) was used to determine P efficiency of soybean and cowpea genotypes. A wide variation in root traits for soybean and cowpea at the early growth stage was found, and allometric analysis showed a significant correlation between the root and shoot parameters at this stage. The study provided an opportunity to compare root traits of newly developed cowpea genotypes (early maturing, medium maturing, dual purpose and Striga resistant lines) with older released cultivars. There were significant differences in root length among the groups. In general, dual purpose, Striga resistant and medium/early maturing genotypes showed the longest roots while the older varieties showed the least total root length. Field and pot results also showed differential growth of soybean and cowpea with low P availability. Further, PCA of the results indicated that soybean genotypes could be grouped into three distinct P efficiency categories. Retaining the PC and the relative weight for each genotype in combination with yield potential under high P, four categories of responsiveness to P were obtained. Cowpea genotypes were grouped into three P efficiency categories and two categories of responsiveness to P. The study also found genetic

  1. Genotyping of Staphylococcus aureus strains isolated from healthy persistent carriers.

    Science.gov (United States)

    Grzegorczyk, Agnieszka; Malm, Anna

    2014-07-01

    The paper presents results on the relatedness of Staphylococcus aureus strains colonizing the upper respiratory tract isolated from healthy persistent carriers. Genotyping was carried out using two methods--multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and pulsed-field gel electrophoresis (PFGE). By comparison of the results obtained by both methods, good correlations between MLVF and PFGE genotyping of strains isolated from the asymptomatic carriers were observed. Further studies are needed to evaluate methods useful for genotyping of S. aureus strains circulating in the community. PMID:24488811

  2. Genotype networks, innovation, and robustness in sulfur metabolism

    Directory of Open Access Journals (Sweden)

    Wagner Andreas

    2011-03-01

    Full Text Available Abstract Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes

  3. SCREENING OF RICE GENOTYPES FOR THERMOTOLERANCE BY TIR TECHNIQUE

    Directory of Open Access Journals (Sweden)

    K. Renuka Devi

    2013-12-01

    Full Text Available Production of rice--the world's most important crop for ensuring food security and addressing poverty will be defeated as temperatures increase in rice-growing areas with continued climate change. Climate change needs us to look at various alternatives for more drought tolerant and tougher strains and to develop a technique to screen a large number of genotypes for high temperature tolerance. Adapting temperature induction response (TIR technique 100 rice genotypes were screened for thermotolerance. Significant variation for acquired thermotolerance was observed in 100 rice lines. From the 100 genotypes 30 were exhibits themotolerance to induced high temperature.

  4. Biodigestão anaeróbia dos dejetos da bovinocultura de corte: influência do período, do genótipo e da dieta Anaerobic biodigestion of beef cattle manure: influence of period, genotype and diet

    Directory of Open Access Journals (Sweden)

    Marco Antonio Previdelli Orrico Junior

    2012-06-01

    genotypes (Canchim and Nellore and sub-plots by three periods of manure collection (initial, intermediate and final. The efficiency of the composting process was evaluated by reductions of total solids, volatile solids, the most probable number (MPN of total and thermotolerant coliforms, chemical and biochemical demand of oxygen, besides the production and potentials of biogas and methane production. There was no effect of genotype or period on manure composting; however, the increase in the forage proportion in the diet promoted the lower efficiency of the process, in which an increase of 26.31% was found for the volume of methane that was produced with diet with 60% concentrate in relation to the diet with 40% concentrate. Significant reductions in MPN of total and thermotolerant coliforms were also observed at the end of the process, regardless of the treatment tested.

  5. Genotype x environment interaction and the stability and adaptation of some induced sesame genotypes through mutation breeding

    International Nuclear Information System (INIS)

    The present study was conducted to provide information on the effect of genotype X environment interaction on the seed yield and the seed oil content of sesame genotypes, as well as the yield stability and adaptation of each genotype. Ten sesame genotypes, including the local variety Giza 32 and two promising induced gamma ray mutants (Mut. 6 and Mut. 8) as well as seven F5 hybrid populations derived from crossing between the local variety and the two induced mutants, were used in this investigation. These genotype were evaluated in the Experimental Farm Project of the Nuclear Research Centre, Atomic Energy Authority Ishash, and at the Agricultural Experiment and Research Centre, Faculty of Agriculture, Cairo University, Giza, as well as on a private farm at El-Saf during 1992 and 1993. The three locations were chosen to provide differences in soil type, which were classified as clay loam, sandy loam and sandy oil at Giza, Inshas and El-Saf, respectively. Two experiments were conducted at each location over the 2 years. The combinations of 2 years and three locations were considered as six different environments. The results indicated that combined analysis of variance revealed highly significant differences as a result of the environments, genotypes, and their interactions, for data recorded on seed yield and oil content, indicating that the genetic potential of genotypes interacted considerably with the varying environments. 1 fig

  6. Genotype by Environment Interactions in Cognitive Ability: A Survey of 14 Studies from 4 Countries covering 4 Age Groups

    OpenAIRE

    Molenaar, Dylan; Van der Sluis, Sophie; Boomsma, Dorret I.; Haworth, Claire M. A.; Hewitt, John K.; Martin, Nicholas G.; Plomin, Robert; Wright, Margie J; Dolan, Conor V.

    2013-01-01

    A large part of the variation in cognitive ability is known to be due to genetic factors. Researchers have tried to identify modifiers that influence the heritability of cognitive ability, indicating a genotype by environment interaction (GxE). To date, such modifiers include measured variables like income and socioeconomic status. The present paper focuses on GxE in cognitive ability where the environmental variable is an unmeasured environmental factor that is uncorrelated in family members...

  7. The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins

    OpenAIRE

    Zhang, Min; Hang, Xiaomin; Tan, Jing; Yang, Hong

    2015-01-01

    To investigate the influences of host genotype and environment on Bifidobacterium longum subsp. longum inhabiting human intestines at the strain level, six pairs of twins, divided into two groups (children and adults), were recruited. Each group consisted of two monozygotic (MZ) twin pairs and one dizygotic (DZ) twin pair. Child twins had been living together from birth, while adult twins had been living separately for 5 to 10 years. A total of 345 B. longum subsp. longum isolates obtained fr...

  8. Maternal depressive history, teen 5HTTLPR genotype, and the processing of emotional faces: Exploring mechanisms of risk

    OpenAIRE

    Jacobs, Rachel H.; Pine, Daniel S.; Schoeny, Michael E.; Henry, David B.; Gollan, Jackie K; Moy, Gregory; Cook, Edwin H.; Wakschlag, Lauren S.

    2010-01-01

    Variations in the serotonin transporter gene (5HTTLPR) and biased processing of face-emotion displays both have been implicated in the transmission of depression risk, but little is known about developmental influences on these relationships. Within a community sample of adolescents, we examine whether 5HTTLPR genotype moderates the link between maternal depressive history and errors in face-emotion labeling. When controlling for current levels of depression and anxiety among youth, a two-way...

  9. EFFECT OF DROUGHT STRESS ON SOME PHYSIOLOGICAL TRAITS OF DURUM (TRITICUM DURUM DESF.) AND BREAD (TRITICUM AESTIVUM L.) WHEAT GENOTYPES

    OpenAIRE

    Tofig Allahverdiyev

    2015-01-01

    Drought is a wide-spread problem seriously influencing wheat production and quality worldwide. We aimed to study adaptive changes in physiological parameters of 6 durum and 7 bread wheat genotypes under drought stress. Water stress caused reduction of leaf gas exchange parameters-photosynthesis rate, stomatal conductance, intercellular CO2 concentration, transpiration rate as well leaf area, dry mass, relative water content, and chlorophyll content. Photosynthesis rate, chlorophyll content we...

  10. Increased plasma membrane cholesterol in cystic fibrosis cells correlates with CFTR genotype and depends on de novo cholesterol synthesis

    OpenAIRE

    Sonawane Nitin D; Previs Stephen F; Jiang Dechen; Ruddy Jennifer; Manson Mary E; West Richard H; Fang Danjun; Burgess James D; Kelley Thomas J

    2010-01-01

    Abstract Background Previous observations demonstrate that Cftr-null cells and tissues exhibit alterations in cholesterol processing including perinuclear cholesterol accumulation, increased de novo synthesis, and an increase in plasma membrane cholesterol accessibility compared to wild type controls. The hypothesis of this study is that membrane cholesterol accessibility correlates with CFTR genotype and is in part influenced by de novo cholesterol synthesis. Methods Electrochemical detectio...

  11. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  12. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  13. Genotype and SNP calling from next-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Paul, Joshua S.; Albrechtsen, Anders;

    2011-01-01

    Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated...

  14. Cryptosporidium parvum: infectivity and pathogenicity of the 'porcine' genotype

    DEFF Research Database (Denmark)

    Enemark, Heidi L.; Ahrens, Peter; Bille-Hansen, Vivi;

    2003-01-01

    Genetic studies have demonstrated profound differences between the 'porcine' genotype of Cryptosporidium parvum, versus 'human' and 'bovine' genotypes. The study analysed infectivity and pathogenicity of the 'porcine' genotype (CPP-13 isolate) of C. parvum, and compared the results with published...... data on the 'bovine' genotype (CPB-0 isolate). This was investigated in calves and piglets from commercial herds. Piglets were mildly affected by the CPP-13 isolate, contrary to piglets infected with the CPB-0 isolate, which caused diarrhoea of a mean duration of 3.5 days. CPP-13 produced no or very...... mild clinical signs in piglets despite the excretion of high numbers of oocysts. Concomitant infection with rotavirus, however, caused a dramatic aggravation of the clinical signs, and 5 of 6 experimentally infected piglets died. CPP-13 appeared to be adapted to porcine hosts as illustrated by the lack...

  15. Genotypes are useful for more than genomic evaluation

    Science.gov (United States)

    New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low cost genotyping, in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes becam...

  16. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro

    2013-09-01

    Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

  17. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  18. Phasing of many thousands of genotyped samples.

    Science.gov (United States)

    Williams, Amy L; Patterson, Nick; Glessner, Joseph; Hakonarson, Hakon; Reich, David

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources). PMID:22883141

  19. Hepatitis E Virus Genotype 3 in Sewage and Genotype 1 in Acute Hepatitis Cases, Israel.

    Science.gov (United States)

    Ram, Daniela; Manor, Yossi; Gozlan, Yael; Schwartz, Eli; Ben-Ari, Ziv; Mendelson, Ella; Mor, Orna

    2016-07-01

    Hepatitis E virus (HEV) is an emerging infectious agent in developed countries. HEV genotypes 1 (G1) and 3 (G3) have been identified in environmental and clinical samples in Europe. In Israel, the overall prevalence of anti-HEV IgG antibodies was found to be 10.6%; however, reports of HEV infection are scarce. In this study, the presence of HEV in Israel was investigated using 169 sewage samples from 32 treatment facilities and 49 samples from acute hepatitis patients, all collected between 2013 and 2015. Fourteen sewage samples, from Haifa (11/18 samples), Tel Aviv (2/29 samples), and Beer Sheva (1/17 samples), regions with good sanitary conditions and middle-high socioeconomic populations, were HEV positive. Among the patient samples, 6.1% (3/49) were HEV positive, all returning travelers from India. Genotype analysis revealed G1 HEV in patients and G3 HEV sequences in sewage. Evidence that HEV could be establishing itself in our region may justify more active surveillance to monitor its spread. PMID:27246446

  20. Pedigree and genotype errors in the Framingham Heart Study

    OpenAIRE

    Almasy Laura; Brush Gerry

    2003-01-01

    Abstract The pedigree and genotype data from the Framingham Heart Study were examined for errors. Errors in 21 of 329 pedigrees were detected with the program PREST, and of these the errors in 16 pedigrees were resolved. Genotyping errors were then detected with SIMWALK2. Five Mendelian errors were found following the pedigree corrections. Double-recombinant errors were more common, with 142 being detected at mistyping probabilities of 0.25 or greater.

  1. Comparison of genotype and intellectual phenotype in untreated PKU patients.

    OpenAIRE

    Ramus, S.J.; Forrest, S M; Pitt, D B; SALEEBA, J.A.; Cotton, R G

    1993-01-01

    We have screened 55 untreated phenylketonuria patients from 42 families for common mutations of the phenylalanine hydroxylase gene and determined both causative alleles in 12 families. The correlation between genotype and intellectual phenotype of patients in these families was examined. Our results were compared to a study which predicted phenylalanine hydroxylase activity based on genotype and examined its correlation with the biochemical phenotype of treated patients. Some of the intellect...

  2. Different genotypes of alternative small grains in organic farming

    OpenAIRE

    Kovačević Dušan Đ.; Roljević Svetlana; Dolijanović Željko; Đorđević Snežana; Milić Vesna

    2014-01-01

    The main objectives were to examine different genotypes of alternative small grains important for food technology in organic farming conditions on morphological and productive characteristics. Four genotypes of different alternative small grains were included in the trial. Three of them were chosen for specific usage in food technology compact wheat Bambi -Triticum aestivum L. ssp. compactum, spelt Nirvana (Triticum aestivum L. ssp. spelta), durum wheat Dur...

  3. Genotypic differences in phosphate nutrition of rice (Oryza Sativa L.)

    International Nuclear Information System (INIS)

    Phosphate uptake and use by five genotypes of paddy rice were studied at five phosphate levels in pot studies for 49 days. For all five P levels there were marked genotypic differences in shoot growth, plant dry weight, root/shoot ratios, phosphate uptake and translocation, P content of roots and shoots, and phosphorus use efficiency of shoots (PUE, g shoot mg P-1 in shoot). There were significant genotypic differences in root weight (4 P levels) and in uptake/mg root (all P levels). These latter may have resulted from differences in root weight/root length conversion, root hair development or uptake characteristics, factors which were not studied specifically. Differences between genotypes and P levels in the percentage translocation were partly explicable by differences in P uptake/plant (r = 0.72) but especially by differences in root/shoot ratios (r = 0.89). Differences in PUE were largely a factor of P percentage of the tops (r = 0.94) but significant differences between genotypes were shown as a function of % P. Differences in net photosynthesis rates were largely, but not entirely, due to differences in P % of the shoots. Key factors in P uptake and use and genotypic differences are root growth, uptake/mg root, root/shoot ratios and PUE. (author). 9 refs, 2 figs, 3 tabs

  4. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  5. Methylenetetrahydrofolate Reductase Genotypes, Dietary Habits and Susceptibility to Stomach Cancer

    Institute of Scientific and Technical Information of China (English)

    ChangmingGao; TakezakiToshiro; JianzhongWu; JianhuoDing; YantingLiu; SupingLi; PingSu; XuHu; TianliongXu; HamajimaNobuyuki; TajimaKazuo

    2004-01-01

    OBJECTIVE To study the relation among methylenetetrahydrofolate reductase (MTHFR) C677T genotypes, dietary habits and the risk of stomach cancer (SC).METHODS A case-control study was conducted with 107 cases of SC and 200 population-based controls in Chuzhou district, Huaian, Jiangsu province, China. The epidemiological data were collected, and DNA of peripheral blood leukocytes was obtained from all of the subjects..MTHFR genotypes were detected by PCR-RFLP. RESULTS (1) The prevalence of the MTHFR C/T or T/T genotypes was found to be significantly different between controls (68.5%) and SC cases (79.4%,P=0.0416), the increased risk had an adjusted OR of 1.79 (95%C1:1.01-3.19). (2) Among subjects who had a low intake of garlic or Chinese onion, MTHFR C/T or T/T genotypes significantly increased the risk of developing SC. Among non-tea drinkers or among subjects who had a frequent intakeof meat, the carriers of the MTHFR C/T or T/T genotypes had a higher risk of SC than individuals with the C/C type MTHFR. CONCLUSION The polymorphism of MTHFR C677T was associated with increased risk of developing SC, and that individuals with differing genotypes may have different susceptibilities to SC, based on their exposure level to environmental factors.

  6. CYP450 genotype and pharmacogenetic association studies: a critical appraisal.

    Science.gov (United States)

    Shah, Rashmi R; Gaedigk, Andrea; LLerena, Adrián; Eichelbaum, Michel; Stingl, Julia; Smith, Robert L

    2016-02-01

    Despite strong pharmacological support, association studies using genotype-predicted phenotype as a variable have yielded conflicting or inconclusive evidence to promote personalized pharmacotherapy. Unless the patient is a genotypic poor metabolizer, imputation of patient's metabolic capacity (or metabolic phenotype), a major factor in drug exposure-related clinical response, is a complex and highly challenging task because of limited number of alleles interrogated, population-specific differences in allele frequencies, allele-specific substrate-selectivity and importantly, phenoconversion mediated by co-medications and inflammatory co-morbidities that modulate the functional activity of drug metabolizing enzymes. Furthermore, metabolic phenotype and clinical outcomes are not binary functions; there is large intragenotypic and intraindividual variability. Therefore, the ability of association studies to identify relationships between genotype and clinical outcomes can be greatly enhanced by determining phenotype measures of study participants and/or by therapeutic drug monitoring to correlate drug concentrations with genotype and actual metabolic phenotype. To facilitate improved analysis and reporting of association studies, we propose acronyms with the prefixes 'g' (genotype-predicted phenotype) and 'm' (measured metabolic phenotype) to better describe this important variable of the study subjects. Inclusion of actually measured metabolic phenotype, and when appropriate therapeutic drug monitoring, promises to reveal relationships that may not be detected by using genotype alone as the variable. PMID:26780308

  7. Genetic diversity of some chili (Capsicum annuum L. genotypes

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  8. Analyzing genotype-by-environment interaction using curvilinear regression

    Directory of Open Access Journals (Sweden)

    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  9. Genotyping of Rotavirus by Using RT-PCR Methods

    Directory of Open Access Journals (Sweden)

    Hera Nirwati

    2015-11-01

    Full Text Available There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994 and Gentsch et al. (1992. There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990 and Simmond et al. (2008 for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.Key words: rotavirus, G typing, P typing

  10. Forage yield and nitrogen nutrition dynamics of warm-season native forage genotypes under two shading levels and in full sunlight

    Directory of Open Access Journals (Sweden)

    Raquel Santiago Barro

    2012-07-01

    Full Text Available The successful achievement of a highly productive understorey pasture in silvopastoral systems depends on the use of well-adapted forage genotypes, showing good agronomic performance and persistence under shading and grazing. In this study, the herbage dry matter yield (DMY and nitrogen nutrition dynamics were determined in three native warm-season grasses (Paspalum regnellii, Paspalum dilatatum and Paspalum notatum and a forage legume (Arachis pintoi under two shading levels compared with full sun. The experiment was conducted in the Campanha region, Bagé, state of Rio Grande do Sul, Brazil, during two evaluation cycles (2008/2009 and 2009/2010. Three shade cloth levels (0%, 50% and 80% of light restriction were applied to the forage genotypes in a split plot design, in which shading levels were the main plot and forage genotypes were the subplots, with three replications. P. regnellii showed the highest accumulated DMY (1500 and 1700 g m-2, respectively, for the first and second evaluation cycles at all shading levels and showed no DMY decreased under the heavy shade (80%. Average DMY over the four genotypes under the 50% shade level was higher or equal compared with full sun. Influence of rainfall was observed on the DMY performance of all genotypes: the positive effect of moderate shading (50% on P. dilatatum and P. notatum DMY was associated to a low soil water availability status. Increased shading level resulted in high nitrogen nutrition index values on grasses, in comparison with full sun. All genotypes performed well under the moderate shading level, but the DMY of both P. regnellii and P. dilatatum and the herbage N content in P. notatum and A. pintoi of all genotypes stood out, showing that those main genotypes are promising to grow in silvopastoral systems at the Campanha region in southern Brazil.

  11. Vitamin D binding protein genotype is associated with serum 25-hydroxyvitamin D and PTH concentrations, as well as bone health in children and adolescents in Finland.

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    Minna Pekkinen

    Full Text Available Vitamin D binding protein (DBP/group-specific component (Gc, correlates positively with serum vitamin D metabolites, and phenotype influences serum 25-hydroxyvitamin D (S-25(OHD concentration. The protein isoform has been associated with decreased bone mineral density (BMD and increased fracture risk. We examined the role of GC genotypes in S-25(OHD status and BMD in 231 Finnish children and adolescents aged 7-19 yr. BMD was measured with DXA from lumbar spine (LS, total hip, and whole body, and for 175 subjects, radial volumetric BMD was measured with pQCT. Background characteristic and total dietary intakes of vitamin D and calcium were collected. The concentrations of 25(OHD, parathyroid hormone (PTH, calcium and other markers of calcium homeostasis were determined from blood and urine. Genotyping was based on single-nucleotide polymorphism (rs4588 in the GC gene. The genotype distribution was: GC 1/1 68%, GC 1/2 26% and GC 2/2 6%. A significant difference emerged in 25(OHD and PTH concentrations between the genotypes, (p = 0.001 and 0.028 respectively, ANCOVA. There was also a linear trend in: Gc 2/2 had the lowest 25(OHD and PTH concentrations (p = 0.025 and 0.012, respectively. Total hip bone mineral content was associated with GC genotype (BMC (p = 0.05, ANCOVA in boys. In regression analysis, after adjusting for relevant covariates, GC genotype was associated with LS BMC and strength and strain index (SSI Z-score in both genders, and LS BMD in boys. In conclusion, the present study demonstrates the association between GC genotypes and S-25(OHD and PTH concentrations. The results show the influence of DBP genetic variation on bone mass accrual in adolescence.

  12. Catechol-O-methyltransferase (COMT Genotype Affects Age-Related Changes in Plasticity in Working Memory: A Pilot Study

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    Stephan Heinzel

    2014-01-01

    Full Text Available Objectives. Recent work suggests that a genetic variation associated with increased dopamine metabolism in the prefrontal cortex (catechol-O-methyltransferase Val158Met; COMT amplifies age-related changes in working memory performance. Research on younger adults indicates that the influence of dopamine-related genetic polymorphisms on working memory performance increases when testing the cognitive limits through training. To date, this has not been studied in older adults. Method. Here we investigate the effect of COMT genotype on plasticity in working memory in a sample of 14 younger (aged 24–30 years and 25 older (aged 60–75 years healthy adults. Participants underwent adaptive training in the n-back working memory task over 12 sessions under increasing difficulty conditions. Results. Both younger and older adults exhibited sizeable behavioral plasticity through training (P<.001, which was larger in younger as compared to older adults (P<.001. Age-related differences were qualified by an interaction with COMT genotype (P<.001, and this interaction was due to decreased behavioral plasticity in older adults carrying the Val/Val genotype, while there was no effect of genotype in younger adults. Discussion. Our findings indicate that age-related changes in plasticity in working memory are critically affected by genetic variation in prefrontal dopamine metabolism.

  13. The Differences among Pear Genotypes to Fire Blight (Erwinia amylovora Attack, Based on Observations of Natural Infection

    Directory of Open Access Journals (Sweden)

    Adriana F. SESTRAS

    2008-08-01

    Full Text Available Fire blight, caused by the bacterium Erwinia amylovora, is one of the most damaging diseases of pear in the world. In Cluj-Napoca area, situated in central Transylvania, Romania, fire blight was observed first in 1994, very late comparative with the other countries from occidental Europe. The response of the pear cultivars and species from National Pear Collection from Cluj-Napoca to fire blight attack, assessed in natural conditions of infection, range on a large scale of variability, which denotes a strong influence of the genotype in expression of resistance or sensitivity to disease. From all genotypes, about 20.5% have not presented symptoms of attack, among them being the following: 'Blanquet precoce', 'Klementinka', 'Severianka', 'Beurre Bachelier', 'Kieffer Seedling', 'Er Shi Shinge', 'Beurre Amanlis', 'Bristol Cross', 'Beurre Liegel', 'Beurre Lucon', 'Grand Champion', 'Magness', 'Mericourt' etc. and several ancient autochthonous cultivars ('Pere malaiete', 'De zahar de Bihor', 'Cu miez rosu', 'Clopotele', 'Garoafa mare', 'Craiese', 'Para de apa'. Also, there were identified several species of Pyrus with no attack, as P. pollveria, P. common pear, P. lindlezi, P. malifolia, P. persica, P. ussuriensis, P. variolosa. The remarked genotypes could be potential sources for further breeding programmes and increase the number of genotypes available for breeding new pear cultivars resistant to Erwinia attack.

  14. Genotype and environment interaction on yield and quality parameters of organically grown winter wheat – Triticum aestivum L. genotypes

    OpenAIRE

    Dashbaljir, Ichinkhorloo; Liebhard, P.; W. Hartl; Loeschenberger, F.; Weinhappel, M.

    2005-01-01

    The interaction of genotype and environment upon yield and quality parameters of eight winter wheat (Triticum aestivum L.) genotypes was studied under organic conditions in Austria over two growing periods, 2001/2002 and 2002/2003, respectively. Two sites that have significantly different climatic conditions, Innviertel and Marchfeld, were chosen for the field experiment. Study site weather and soil conditions are important yield-affecting factors. Although the yield of Marchfeld-grown ge...

  15. Sublineages of Mycobacterium tuberculosis Beijing genotype strains and unfavorable outcomes of anti-tuberculosis treatment.

    Science.gov (United States)

    Hang, Nguyen T L; Maeda, Shinji; Keicho, Naoto; Thuong, Pham H; Endo, Hiroyoshi

    2015-05-01

    The influence of Mycobacterium tuberculosis (MTB) lineages/sublineages on unfavorable tuberculosis (TB) treatment outcomes is poorly understood. We investigated the effects of Beijing genotype sublineages and other factors contributing to treatment outcome. Patients newly diagnosed with sputum smear-positive and culture-positive TB in Hanoi, Vietnam, participated in the study. After receiving anti-TB treatment, they were intensively followed up for the next 16 months. MTB isolates collected before treatment were subjected to drug susceptibility testing, and further analyzed to determine MTB (sub) lineages and their clonal similarities. Of 430 patients, 17 had treatment failure and 30 had TB recurrence. Rifampicin resistance was associated with treatment failure {adjusted odds ratio = 6.64 [95% confidence interval (CI), 1.48-29.73]}. The modern Beijing genotype was significantly associated with recurrent TB within 16 months [adjusted hazard ratio = 3.29 (95% CI, 1.17-9.27)], particularly after adjustment for the relevant antibiotic resistance. Human immunodeficiency virus coinfection and severity on chest radiographs were not significantly associated with unfavorable outcomes. Our findings provide further understanding of the influence of MTB strains on unfavorable treatment outcomes. Multiple risk factors should be considered for the optimal management of TB. PMID:25732626

  16. Skeletal muscle strength in older adults. Angiotensin-converting enzyme (ACE genotype affects: an UPDATE

    Directory of Open Access Journals (Sweden)

    ANA PEREIRA

    2011-06-01

    Full Text Available Problem Statement : Previous studies have associated angiotensin-converting enzyme (ACE with variability inthe skeletal muscle baseline strength, though conclusions have been inconsistent across investigations.Approach: The purpose of this study was to review the most important studies that have been exanimate thepossible association between ACE genotype and skeletal muscle baseline strength in elite male and femaleathletes involved in elderly populations. This research is needed because the possibility that the DD genotypemay be associated with a greater proportion of fast twitch fibers could explain the influence of the ACE D alleleupon strength/ power, particularly at high velocities, but this evidence remains equivocal in older people becausemore studies are necessary.Results: Thus, according to scientific evidence, changes in muscle strength with exercise training in olderindividuals may be dependent on ACE I/D genotype. Of note, the results provide a novel insight that thesegenetic variations may interact to determine muscle mass in older women specially. The determination of thispredisposition in this population, highlighting the interest of study, for the prophylactic attitude on the factorsand causes of aging (sarcopenia, osteoporosis, risk of falls, reduction of functional physical go through thisanalysis.Conclusions/Recommendations: In this work, the state of the art related to the influence of the ACE genotypeon skeletal muscle strength was presented and some important relations were reported

  17. Identification of a new porcine circovirus type 2 (PCV2) genotype in Danish archive pigsamples

    DEFF Research Database (Denmark)

    Dupont, Kitt; Larsen, Lars Erik

    PCV2 is the major causative agent of postweaning multisystemic wasting syndrome (PMWS) in pigs. Two genotypes of PCV2 have been identified: genotype 1 and 2 (Olvera et al., 2007). PCV2 genotype 2 was involved in the first cases of PMWS in Canada (Hamel et al.,. 1998). PCV2 genotype 1 may be more...

  18. Hepatitis C virus genotypes: A plausible association with viral loads

    Directory of Open Access Journals (Sweden)

    Salma Ghulam Nabi

    2013-01-01

    Full Text Available Background and Aim: The basic aim of this study was to find out the association of genotypes with host age, gender and viral load. Material and Methods: The present study was conducted at Social Security Hospital, Pakistan. This study included 320 patients with chronic hepatitis C virus (HCV infection who were referred to the hospital between November 2011 and July 2012. HCV viral detection and genotyping was performed and the association was seen between genotypes and host age, gender and viral load. Results : The analysis revealed the presence of genotypes 1 and 3 with further subtypes 1a, 1b, 3a, 3b and mixed genotypes 1b + 3a, 1b + 3b and 3a + 3b. Viral load quantification was carried out in all 151 HCV ribonucleic acid (RNA positive patients. The genotype 3a was observed in 124 (82.12% patients, 3b was found in 21 (13.91%, 1a was seen in 2 (1.32%, 1b in 1 (0.66%, mixed infection with 1b + 3a in 1 (0.66%, 1b + 3b in 1 (0.66% and 3a + 3b was also found in 1 (0.66% patient. Viral load quantification was carried out in all 151 HCV RNA positive patients and was compared between the various genotypes. The mean viral load in patients infected with genotype 1a was 2.75 × 10 6 , 1b 3.9 × 10 6 , 3a 2.65 × 10 6 , 3b 2.51 × 10 6 , 1b + 3a 3.4 × 106, 1b + 3b 2.7 × 106 and 3a + 3b 3.5 × 10 6 . An association between different types of genotypes and viral load was observed. Conclusion : Further studies should be carried out to determine the association of viral load with different genotypes so that sufficient data is available and can be used to determine the type and duration of therapy needed and predict disease outcome.

  19. Detection of Multiple Human Papillomavirus Genotypes in Anal Carcinoma

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    Luo Linda

    2010-10-01

    Full Text Available Abstract Infection with human papillomavirus (HPV is a major risk factor for development of anal squamous cell carcinoma. Despite over 100 genotypes of the virus, HPV 16 and 18 are considered pathogenic as they are seen in the majority of cervical and anal cancers. We have employed a custom microarray to examine DNA for several HPV genotypes. We aimed to determine the accuracy of our microarray in anal cancer DNA for HPV genotypes compared to the DNA sequencing gold standard. Methods We utilized a sensitive microarray platform to classify 37 types of mucosal HPVs including 14 known high-risk and 23 low-risk types based on cervical cancer data. We utilized DNA from pathologically confirmed cases of anal squamous cell carcinoma. All samples underwent microarray HPV genotyping and PCR analysis. Results HPV was detected in 18/20 (90% anal cancers. HPV genotypes 16 and 18 were present in the majority of specimens, with HPV 16 being the most common. Eighty percent of anal cancers had at least two HPV types. Ten percent of cases (2/20 tested negative using our microarray; DNA sequencing confirmed the lack of presence of HPV DNA in these samples. Conclusions Microarray technology is an accurate way to screen for various genotypes of HPV in anal cancer, with 100% correlation with genomic DNA detection of HPV. The majority of anal cancers in our study associated with pathogenic HPV 16 and/or 18. Other HPV genotypes are present simultaneously with HPV 16 and 18, and might contribute to its pathogenesis.

  20. Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA▿

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-01-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  1. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  2. UGT2B17 genotype and the pharmacokinetic serum profile of Testosterone during substitution therapy with Testosterone Undecanoate. A retrospective experience from 207 men with hypogonadism.

    OpenAIRE

    Anne Kirstine eBang; Niels eJørgensen; Ewa eRajpert-De Meyts; Anders eJuul

    2013-01-01

    BackgroundTestosterone (T) is mainly excreted in the urine as testosterone glucuronide (TG). This glucuronidation is partly dependent on the UGT2B17 genotype, and TG excretion is therefore lower in men having the UGT2B17 deletion. However, the possible influence of UGT2B17 genotype on serum T during androgen therapy is unknown. We retrospectively investigated the possible association between the UGT2B17 gene polymorphism and serum T levels in hypogonadal men during Testosterone undecanoate (T...

  3. A new genotype calling method for affymetrix SNP arrays.

    Science.gov (United States)

    Fu, Bilin; Xu, Jin

    2011-12-01

    Current genotype-calling methods such as Robust Linear Model with Mahalanobis Distance Classifier (RLMM) and Corrected Robust Linear Model with Maximum Likelihood Classification (CRLMM) provide accurate calling results for Affymetrix Single Nucleotide Polymorphisms (SNP) chips. However, these methods are computationally expensive as they employ preprocess procedures, including chip data normalization and other sophisticated statistical techniques. In the small sample case the accuracy rate may drop significantly. We develop a new genotype calling method for Affymetrix 100 k and 500 k SNP chips. A two-stage classification scheme is proposed to obtain a fast genotype calling algorithm. The first stage uses unsupervised classification to quickly discriminate genotypes with high accuracy for the majority of the SNPs. And the second stage employs a supervised classification method to incorporate allele frequency information either from the HapMap data or from a self-training scheme. Confidence score is provided for every genotype call. The overall performance is shown to be comparable to that of CRLMM as verified by the known gold standard HapMap data and is superior in small sample cases. The new algorithm is computationally simple and standalone in the sense that a self-training scheme can be used without employing any other training data. A package implementing the calling algorithm is freely available at http://www.sfs.ecnu.edu.cn/teachers/xuj_en.html. PMID:22084010

  4. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

    Directory of Open Access Journals (Sweden)

    Milner Danny A

    2012-02-01

    Full Text Available Abstract Background Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP molecular barcode assay was developed for use in laboratory parasites which estimates genotype number and identifies the predominant genotype. Methods The 24 SNP assay was used to determine predominant genotypes in blood and tissues from autopsy and clinical patients with cerebral malaria. Results Single genotypes were shared between the peripheral blood, the brain, and other tissues of cerebral malaria patients, while malaria-infected patients who died of non-malarial causes had mixed genetic signatures in tissues examined. Children with retinopathy-positive cerebral malaria had significantly less complex infections than those without retinopathy (OR = 3.7, 95% CI [1.51-9.10].The complexity of infections significantly decreased over the malaria season in retinopathy-positive patients compared to retinopathy-negative patients. Conclusions Cerebral malaria patients harbour a single or small set of predominant parasites; patients with incidental parasitaemia sustain infections involving diverse genotypes. Limited diversity in the peripheral blood of cerebral malaria patients and correlation with tissues supports peripheral blood samples as appropriate for genome-wide association studies of parasite determinants of pathogenicity.

  5. Physiological and Molecular Analysis of Applied Nitrogen in Rice Genotypes

    Institute of Scientific and Technical Information of China (English)

    Khalid Rehman HAKEEM; Ruby CHANDNA; Altaf AHMAD; Muhammad IQBAL

    2012-01-01

    Ten genotypes of rice (Oryza sativa L.) were grown for 30 d in complete nutrient solution with 1 mmol/L (N-insufficient),4 mmol/L (N-moderate) and 10 mmol/L (N-high) nitrogen levels,and nitrogen efficiency (NE) was analyzed.Growth performance,measured in terms of fresh weight,dry weight and lengths of root and shoot,was higher in N-efficient than in N-inefficient rice genotypes at low N level.Of these 10 genotypes,Suraksha was identified as the most N-efficient,while Vivek Dhan the most N-inefficient.To find out the physiological basis of this difference,the nitrate uptake rate of root and the activities of nitrate assimilatory enzymes in leaves of N-efficient and N-inefficient rice genotypes were studied.Uptake experiments revealed the presence of two separate nitrate transporter systems mediating high- and low-affinity nitrate uptake.Interestingly,the nitrate uptake by the roots of Suraksha is mediated by both high- and low-affinity nitrate transporter systems,while that of Vivek Dhan by only low-affinity nitrate transporter system.Study of the activities and expression levels of nitrate assimilatory enzymes in N-efficient and N-inefficient rice genotypes showed that nitrate reductase (NR) and glutamine svnthetase (GS) play important roles in N assimilation under low-nitrogen conditions.

  6. Ant colony optimization as a method for strategic genotype sampling.

    Science.gov (United States)

    Spangler, M L; Robbins, K R; Bertrand, J K; Macneil, M; Rekaya, R

    2009-06-01

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK(P)), the probability of assigning true alleles (AK(G)) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A(-1)). Comparisons of these two methods showed that ACO yielded an increase in AK(P) ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A(-1), with different pedigree sizes and structures. PMID:19220227

  7. A Preliminary Study of Soybean Genotype Responses to Glyphosate

    Directory of Open Access Journals (Sweden)

    Plamen Marinov-Serafimov

    2009-01-01

    Full Text Available The effect of four application rates of glyphosate (Roundup, 360 g a.i./l – 180; 360; 720 and 1440 g a.i./ha on the survival, dynamics of growth, and accumulation of fresh biomass in g per plant was studied on eight newly-developed Bulgarian lines, varieties and candidate varieties of soybean bred by different methods under greenhouse conditions. The objective of this study was to determine and compare the sensitivities of different soybean genotypes to glyphosate. The studied soybean genotypes showed different levelsof glyphosate sensitivity due to their genetic differences. Glyphosate rates of 180, 360, 720 and 1440 g a.i./ha, applied at the stage of three trifoliate leaves (V4 of soybean had effect on the survival of the studied genotypes and can be presented conditionally in the following order: H (40.6% < G (40.7% < D (51.3% < C (52.6% < F (58.9% < E (60.5% < B (62.0% < A (65.3%. The depression coefficients (B of the studied characteristics dependedmainly on soybean genotypes and the applied herbicide rates. The tested glyphosate rates showed a high (GI 26.5-51.6% to relatively low degree of toxicity (GI 16.0-18.7% in the studied soybean genotypes.

  8. Partial hydatidiform mole: histologic parameters in correlation with DNA genotyping.

    Science.gov (United States)

    Buza, Natalia; Hui, Pei

    2013-05-01

    Histologic diagnosis of partial hydatidiform mole (PHM) continues to be problematic, and DNA genotyping has recently become cost-effective for precise separation of PHM from its mimics. We performed a comprehensive reevaluation of histologic parameters of PHM in correlation with DNA genotyping. A total of 143 early abortion specimens were subjected to genotyping as part of the routine workup, resulting in 60 cases of PHM, 52 cases of various chromosomal trisomies, and 31 cases of nonmolar diploid gestations. All available hematoxylin and eosin slides were reviewed retrospectively by 2 gynecologic pathologists blinded to the genotyping results. Significant histologic overlaps were present among genetically confirmed PHM, hydropic abortions, and chromosomal trisomy syndromes. The following morphologic parameters emerged with diagnostic significance for PHM: villus size, presence of 2 villous populations, round or oval pseudoinclusions, at least moderate villous hydrops, cistern formation, and trophoblastic hyperplasia. The most sensitive morphologic features for PHM included villous hydrops (86% sensitivity) or the presence of at least 1 of the following 3 parameters: 2 villous populations, round or oval pseudoinclusions, and cisterns (84% sensitivity). The presence of cisterns and villous size ≥2.5 mm had the highest positive predictive value (90%) for PHM. In conclusion, no single or combined morphologic features are sufficient for definitive diagnosis of PHM. The presence of any one of the following histologic findings should prompt DNA genotyping workup to rule out PHM: round or oval pseudoincludions, cistern formation, 2 populations of villi, and a villous size of ≥2.5 mm. PMID:23518914

  9. Morpho-physiological adaptations of wheat genotypes to salinity stress

    International Nuclear Information System (INIS)

    To explore morpho-physiological alteration in wheat for salinity tolerance, a glass house experiment was laid out in randomized complete block design (RCBD) with three replications at Nuclear Institute of Agriculture, (NIA) Tando Jam, Pakistan. Studies were conducted with two levels of salinity (Control, and 12 dS m-1 NaCl) and five wheat genotypes. Due to salinity stress morphological and yield attributes like plant height, total tillers, productive tillers, spike length, number of spikelets per spike, number of grain per spike, 1000 grain weight, grain weight per plant were decreased in all wheat genotypes, however, wheat ESW-9525 showed significantly less reduction in all these parameters than other wheat genotypes. Biochemical attributes like proline glycine betaine and total soluble sugars were increased in all the genotypes due to salinity. Wheat genotype Bakhtawar maintained the highest Na while the minimum Na contents were found in ESW-9525 that had the highest correlation with grain yield. The tolerant and stable cultivars were ESW-9525 and Sarsabz which had highest yield at 12 dS m-1 salinity than other cultivars. (author)

  10. Blood group genotyping in a population of highly diverse ancestry.

    Science.gov (United States)

    Pellegrino, J; Castilho, L; Rios, M; De Souza, C A

    2001-01-01

    Accurate phenotyping of red blood cells (RBCs) can be difficult in transfusion-dependent patients such as those with thalassemia and sickle cell anemia because of the presence of previously transfused RBCs in the patient's circulation. Recently, the molecular basis associated with the expression of many blood group antigens was established. This allowed the development of a plethora of polymerase chain reaction (PCR)-based tests for identification of the blood group antigens by testing DNA. The new technologies complement phenotyping and overcome some of the limitations of hemagglutination assays. These molecular assays were developed on the basis of DNA sequences of individuals of Caucasian ancestry. The present study addresses the concern that these genotyping assays may not be applicable to populations of highly diverse ancestry because of variability in intronic regions or because of unrecognized alleles. We determined both phenotype and genotype for RH D, K 1/K 2, JK A/JK B, FY A/ FY B-GATA in 250 normal blood donors using PCR. Phenotype and genotype results agreed in 100% of the cases, indicating that molecular genotyping protocols can be effectively applied to populations with a highly diverse genetic background. However, genotyping for Duffy antigens provided information that could not be obtained by phenotyping. Essentially, 30.5 % of the donors with the FY B gene typed as Fy(b-) because of mutations in the GATA box. This information is very useful for the management of transfusion dependent patients. PMID:11170227

  11. Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

    Indian Academy of Sciences (India)

    Xuixiao Hong; Zhenqiang Su; Weigong Ge; Leming Shi; Roger Perkins; Hong Fang; Donna Mendrick; Weida Tong

    2010-04-01

    Genome-wide association studies (GWAS) examine the entire human genome with the goal of identifying genetic variants (usually single nucleotide polymorphisms (SNPs)) that are associated with phenotypic traits such as disease status and drug response. The discordance of significantly associated SNPs for the same disease identified from different GWAS indicates that false associations exist in such results. In addition to the possible sources of spurious associations that have been investigated and discussed intensively, such as sample size and population stratification, an accurate and reproducible genotype calling algorithm is required for concordant GWAS results from different studies. However, variations of genotype calling of an algorithm and their effects on significantly associated SNPs identified in downstream association analyses have not been systematically investigated. In this paper, the variations of genotype calling using the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) algorithm and the resulting influence on the lists of significantly associated SNPs were evaluated using the raw data of 270 HapMap samples analysed with the Affymetrix Human Mapping 500K Array Set (Affy500K) by changing algorithmic parameters. Modified were the Dynamic Model (DM) call confidence threshold (threshold) and the number of randomly selected SNPs (size). Comparative analysis of the calling results and the corresponding lists of significantly associated SNPs identified through association analysis revealed that algorithmic parameters used in BRLMM affected the genotype calls and the significantly associated SNPs. Both the threshold and the size affected the called genotypes and the lists of significantly associated SNPs in association analysis. The effect of the threshold was much larger than the effect of the size. Moreover, the heterozygous calls had lower consistency compared to the homozygous calls.

  12. Does 5HTTLPR Genotype Moderate the Association of Family Environment With Child Attention-Deficit Hyperactivity Disorder Symptomatology?

    Science.gov (United States)

    Elmore, Alexis L; Nigg, Joel T; Friderici, Karen H; Jernigan, Katherine; Nikolas, Molly A

    2016-01-01

    Problematic family dynamics are common among youth with attention-deficit hyperactivity disorder (ADHD). Multiple mechanisms, including diathesis-stress (vulnerability) and differential susceptibility Gene × Environment interaction effects (G × E), have been proposed to account for this association. G × E effects for ADHD were examined via interactions between a genetic marker hypothesized to influence sensitivity to the environment (the promoter polymorphism of the serotonin transporter gene -5HTTLPR) and family conflict and cohesion in predicting ADHD symptoms. There were 498 youth ages 6-17 years (251 ADHD, 213 non-ADHD) and their parents who completed a multistage, multi-informant assessment (including parent and youth reports on the Family Environment Scale), and saliva sample collection for genotyping. Linear regression analyses examined interactions between 5HTTLPR genotype and the Family Environment Scale scales of conflict and cohesion reported by parent and child. Criteria laid out by Roisman et al. ( 2012 ) were applied to evaluate diathesis stress versus differential susceptibility G × E mechanisms. Results demonstrated interactions between 5HTTLPR genotype and both conflict and cohesion in predicting inattention but not hyperactivity-impulsivity. Both interactions were highly consistent with differential susceptibility models of G × E effects. 5HTTLPR genotype appeared to moderate the relationship between family conflict/cohesion and inattentive symptoms. Interactions highlight the role of 5HTTLPR genotype as a potential marker of environmental sensitivity and provide support for differential susceptibility models of G × E effects for ADHD. PMID:25602736

  13. The multi-systemic nature of diabetes mellitus: Genotype or phenotype?

    Directory of Open Access Journals (Sweden)

    Graham Wilfred Ewing

    2010-01-01

    Full Text Available Background: This article discusses factors which materially influence the diagnosis, prevention and treatment of diabetes mellitus but which may be overlooked by the prevailing biomedical paradigm. That cognition can be mathematically linked to the function of the autonomic nervous system and physiological systems casts new light upon the mechanisms responsible for homeostasis and origins of disease. In particular, it highlights the limitations of the reductionist biomedical approach which considers mainly the biochemistry of single pathologies rather than considering the neural mechanisms which regulate the function of physiological systems, and inherent visceral organs; and which are subsequently manifest as biochemistries of varying degrees of complexity and severity. As a consequence, histopathological tests are fraught with inherent limitations and many categories of drugs are significantly ineffective. Aims: Such limitations may be explained if disease (in particular diabetes mellitus has multiple origins, is multi-systemic in nature and, depending upon the characteristics of each pathology, is influenced by genotype and/or phenotype. Results:This article highlights the influence of factors which are not yet considered re. the aetiology of diabetes mellitus e.g. the influence of light and sensory input upon the stability of the autonomic nervous system; the influence of raised plasma viscosity upon rates of reaction; the influence of viruses and/or of modified live viruses given in vaccinations; systemic instability, in particular the adverse influence of drinks and lack of exercise upon the body′s prevailing pH and its subsequent influence upon levels of magnesium and other essential trace elements. Conclusions: This application of the top-down systems biology approach may provide a plausible and inclusive explanation for the nature and occurrence of diabetes mellitus.

  14. Distribution of Human papilloma virus genotypes in cervical cancer tissues

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    Stamenković M.

    2014-01-01

    Full Text Available Cervical cancer incidence and mortality rates in Serbia are among the highest in Europe and data on Human papilloma virus (HPV type distribution are scarce. The aim of this study was to determine the prevalence of HPV types in archival specimens of cervical cancer tissues of women in the Serbian population. A total of 45 paraffin-embedded tissue samples of cervical carcinoma were used in this study. The procedure included deparaffinization of tissue samples, DNA extraction, PCR, gel electrophoresis and HPV genotyping by direct sequencing. HPV was detected in 32 samples (71%. Genotyping revealed the presence of 6 high-risk HPV types 16, 18, 33, 45, 53 and 58, where HPV type 16 was the most prevalent type (73.7%. The results of this study and further studies will provide more detailed information about HPV genotype distribution and may contribute to the formulation of national guidelines for the prevention of cervical cancer. [175073

  15. CYP2D6 genotype determination in the Danish population

    DEFF Research Database (Denmark)

    Brøsen, K; Nielsen, P N; Brusgaard, K;

    1994-01-01

    CYP2D6 genotyping was carried out by XbaI restriction fragment length polymorphism analysis and polymerase chain reaction in 168 healthy Danish volunteers, 77 extensive metabolizers (EM) and 91 poor metabolizers (PM) of sparteine. All EM were genotyped correctly as heterozygous or homozygous for.......11-9.10). The median difference was 0.09 (95% confidence interval: 0.02-0.16). CYP2D6 phenotyping is a promising tool in tailoring the individual dose of tricyclic antidepressants, some neuroleplics and some antiarrhythmics. However if the genotype test could be improved with regard to both sensitivity in PM...... and the ability to predict CYP2D6 activity in EM then it would be of even greater clinical value in therapeutic drug monitoring. Udgivelsesdato: 1994-null...

  16. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

    Haraldsson, H.M.; Ettinger, U.; Magnusdottir, B.B.;

    2010-01-01

    Neuregulin-1 (NRG-1) is a putative susceptibility gene for schizophrenia but the neurocognitive processes that may involve NRG-1 in schizophrenia are unknown. Deficits in antisaccade (AS) and smooth pursuit eye movements (SPEM) are promising endophenotypes, which may be associated with brain...... dysfunctions underlying the pathophysiology of schizophrenia. The aim of this study was to investigate the associations of NRG-1 genotypes with AS and SPEM in schizophrenia patients and healthy controls. Patients (N = 113) and controls (N = 106) were genotyped for two NRG-1 single nucleotide polymorphisms...... findings of impaired AS and SPEM performance in schizophrenia patients (all P <0.005; all d = 0.5-1.5). SNP8NRG243177 risk allele carriers had marginally increased variability of AS spatial error (P = 0.050, d = 0.3), but there were no significant genotype effects on other eye movement variables and no...

  17. Cytological Effects of Space Environment on Different Genotype of Rice

    Institute of Scientific and Technical Information of China (English)

    WEI Li-jun; QIAN Yu; YANG Qian; XU Jian-long; WANG Jun-min; SUN Ye-qing

    2007-01-01

    For exploring the biological effect of space environment on different genotype of rice seeds, the cytological effects of M1 generation after space flight were studied.Twelve different genotypes of rice seeds which belong to different climate ecotype (early, medium and late) of indica and japonica were onboard "Shenzhou 4" spaceship for 162 h.After recovered the total number of mitosis cells and chromosomal aberration were observed.In all the lines the mitotic index (MIs) of space flight are much higher than control, which indicates the stimulate effect of space environment.The cell rate of chromosomal aberration (CRCA) of space flight is also much higher than control, but varies from line to line.It indicates that biological effect of space environment on rice seed dependents not only on flight duration but also on rice genotype.The radiosensitivities of different lines were also discussed according to CRCAs.

  18. Genotypic variability for protoplast regeneration in Saintpaulia ionantha (H. Wendl.).

    Science.gov (United States)

    Winkelmann, T; Grunewaldt, J

    1995-08-01

    The behaviour of eleven Saintpaulia ionantha (H. Wendl.) genotypes in protoplast culture was compared. Isolation of protoplasts from young shootlets regenerated in vitro on leaf explants, yielded 0.7 to 1.8 × 10(6) protoplasts per gram fresh weight. In all cultivars and breeding lines tested, cell divisions were observed. The mean division frequencies varied between 1.0 and 5.0% after 14 days, and between 6.4 and 13.8% after 24 days of culture. In ten genotypes callussing and shoot regeneration were achieved. The difference between the genotypes in shoot regeneration rate, between 2 and 68%, was more pronounced. The comparison of four cytokinins indicated hat thidiazuron was most effective for shoot regeneration, but often resulted in poorer shoot quality than benzylaminopurine. PMID:24186626

  19. Carcass traits and meat quality of two different rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Maria D'Agata

    2012-07-01

    Full Text Available To evaluate the effect of genotype on carcass traits and meat quality, thirty-two rabbits for two genotypes (local population – LP; commercial hybrids – HY were used. Rabbits were weaned at 35 days old and slaughtered at 103 days of age for LP and 87 days of age for HY. Comparing the slaughtering traits of two genotypes, LP provided higher dressing out (59.4% vs 56.2%, Pvs 14.2%, Pvs 22.3, Pvs 8,9%, Pvs 0.86%, Pvs 1.12%; Pvs 19.2%; Pvs 31.6%; Pvs 3.8%; P*, higher redness (a*, yellowness (b* and C* value than HY (P

  20. Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases

    Institute of Scientific and Technical Information of China (English)

    Na; Han; James; Adams; Wei; Fang; Si-Qing; Liu; Simon; Rayner

    2015-01-01

    Japanese encephalitis is a mosquito borne disease and is the leading cause of viral encephalitis in the Asia-Pacific area. The causative agent, Japanese encephalitis virus(JEV) can be phylogenetically classified into five genotypes based on nucleotide sequence. In recent years, genotype I(GI) has displaced genotype III(GIII) as the dominant lineage, but the mechanisms behind this displacement event requires elucidation. In an earlier study, we compared host variation over time between the two genotypes and observed that GI appears to have evolved to achieve more efficient infection in hosts in the replication cycle, with the tradeoff of reduced infectivity in secondary hosts such as humans. To further investigate this phenomenon, we collected JEV surveillance data on human cases and, together with sequence data, and generated genotype/case profiles from seven Asia-Pacific countries and regions to characterize the GI/GIII displacement event. We found that, when comprehensive and consistent vaccination and surveillance data was available, and the GIII to GI shift occurred within a well-defined time period, there was a statistically significant drop in JEV human cases. Our findings provide further support for the argument that GI is less effective in infecting humans, who represent a dead end host. However, experimental investigation is necessary to confirm this hypothesis. The study highlights the value of alternative approaches to investigation of epidemics, as well as the importance of effective data collection for disease surveillance and control.

  1. UGT2B17 genotype and the pharmacokinetic serum profile of Testosterone during substitution therapy with Testosterone Undecanoate. A retrospective experience from 207 men with hypogonadism.

    Directory of Open Access Journals (Sweden)

    Anne Kirstine eBang

    2013-07-01

    Full Text Available BackgroundTestosterone (T is mainly excreted in the urine as testosterone glucuronide (TG. This glucuronidation is partly dependent on the UGT2B17 genotype, and TG excretion is therefore lower in men having the UGT2B17 deletion. However, the possible influence of UGT2B17 genotype on serum T during androgen therapy is unknown. We retrospectively investigated the possible association between the UGT2B17 gene polymorphism and serum T levels in hypogonadal men during Testosterone undecanoate (TU substitution therapy.Subjects and methods207 patients treated with TU (Nebido® were genotyped by qPCR for the UGT2B17 deletion polymorphism. All were given 1000 mg TU per injection at 0, 6 and 18 weeks. Blood samples were taken 2 and 6 weeks after the 1st and 2nd injection, prior to the 3rd injection, and after 2-3 years of treatment. We analysed for the levels of T, luteinizing hormone, sex-hormone-binding globulin, estradiol, prostate specific antigen, haematocrit, haemoglobin and total cholesterol. ResultsThe UGT2B17 genotype frequency was: ins/ins: 42%, ins/del: 44% and del/del: 14%. During the initial 18 weeks of TU treatment, large intra- and inter-individual variations in serum T levels were observed. Large peaks in T levels, ranging from 6.7 nmol/l to 69.5 nmol/l, were noted 2 weeks after injections, regardless of the genotype. T levels did not differ between the 3 genotypes prior to the 3rd injection, but the del/del group had significantly lower levels of LH. At follow-up after 2-3 years, the injection interval or daily T dosage was not dependent on the UGT2B17 genotype. ConclusionIn conclusion, we found large intra- and inter-individual variations in serum T during standard TU treatment regimen in hypogonadal men. Only subtle differences in serum T and LH were noted according to UGT2B17 genotype, which however suggest that the UGT2B17 genotype exert modest influence on the pharmacokinetic profile of T after TU treatment.

  2. Shift work in nurses: contribution of phenotypes and genotypes to adaptation.

    Directory of Open Access Journals (Sweden)

    Karen L Gamble

    Full Text Available BACKGROUND: Daily cycles of sleep/wake, hormones, and physiological processes are often misaligned with behavioral patterns during shift work, leading to an increased risk of developing cardiovascular/metabolic/gastrointestinal disorders, some types of cancer, and mental disorders including depression and anxiety. It is unclear how sleep timing, chronotype, and circadian clock gene variation contribute to adaptation to shift work. METHODS: Newly defined sleep strategies, chronotype, and genotype for polymorphisms in circadian clock genes were assessed in 388 hospital day- and night-shift nurses. RESULTS: Night-shift nurses who used sleep deprivation as a means to switch to and from diurnal sleep on work days (∼25% were the most poorly adapted to their work schedule. Chronotype also influenced efficacy of adaptation. In addition, polymorphisms in CLOCK, NPAS2, PER2, and PER3 were significantly associated with outcomes such as alcohol/caffeine consumption and sleepiness, as well as sleep phase, inertia and duration in both single- and multi-locus models. Many of these results were specific to shift type suggesting an interaction between genotype and environment (in this case, shift work. CONCLUSIONS: Sleep strategy, chronotype, and genotype contribute to the adaptation of the circadian system to an environment that switches frequently and/or irregularly between different schedules of the light-dark cycle and social/workplace time. This study of shift work nurses illustrates how an environmental "stress" to the temporal organization of physiology and metabolism can have behavioral and health-related consequences. Because nurses are a key component of health care, these findings could have important implications for health-care policy.

  3. Genotype-phenotype correlation and pregnancy outcomes of partial trisomy 14q: A systematic review.

    Science.gov (United States)

    Bregand-White, Julia; Saller, Devereux N; Clemens, Michele; Surti, Urvashi; Yatsenko, Svetlana A; Rajkovic, Aleksandar

    2016-09-01

    Over the last decade, several advances in ultrasound techniques, increasing availability of whole genome microarray testing, and overall expansion of our knowledge about the human genome have drastically enhanced our ability to detect chromosomal abnormalities prenatally. Despite that, genotype-phenotype correlation is difficult to establish for many chromosomal aberrations, particularly for those that are rare, as it requires thorough analysis of a significant number of cases. This in turn increases the burden of the obstetric provider to appropriately counsel a patient regarding prognosis and pregnancy options in these complicated situations. Our experience in prenatal diagnosis and management of a fetus with multiple anomalies and partial trisomy for the 14q11-q24.2 prompted a comprehensive analysis of the relevant literature. Although complete non-mosaic trisomy 14 is associated with first trimester miscarriages, partial trisomy 14q is a rare condition with undefined genotype-phenotype correlation, preventing accurate prenatal counseling, and informed decision making. We performed a systematic literature review, that aimed to summarize prenatal and postnatal findings of individual case reports on 51 patients with partial trisomy 14q in order to elucidate genotype-phenotype correlation, and to supply healthcare professionals with recommendation on essential fetal and parental testing for accurate diagnosis, pregnancy outcomes, and proper family counseling. Comparison of the clinical findings among the patients with partial 14q trisomy suggest that the resulting phenotype is likely to be influenced by the extent of the 14q trisomy segment, associated chromosomal imbalances, parental origin of the rearrangement, and dosage of the genes within the imprinted 14q32 cluster. © 2016 Wiley Periodicals, Inc. PMID:27286879

  4. The effect of myostatin genotype on body temperature during extreme temperature events.

    Science.gov (United States)

    Howard, J T; Kachman, S D; Nielsen, M K; Mader, T L; Spangler, M L

    2013-07-01

    Extreme heat and cold events can create deleterious physiological changes in cattle as they attempt to cope. The genetic background of animals can influence their response to these events. The objective of the current study was to determine the impact of myostatin genotype (MG) on body temperature during periods of heat and cold stress. Two groups of crossbred steers and heifers of unknown pedigree and breed fraction with varying percentages of Angus, Simmental, and Piedmontese were placed in a feedlot over 2 summers and 2 winters. Before arrival, animals were genotyped for the Piedmontese-derived myostatin mutation (C313Y) to determine their MG as either homozygous normal (0 copy; n = 84), heterozygous (1 copy; n = 96), or homozygous for inactive myostatin (2 copy; n = 59). Hourly tympanic and vaginal temperature measurements were collected for steers and heifers, respectively, for 5 d during times of anticipated heat and cold stress. Mean (±SD) ambient temperature for summer and winter stress events were 24.4 (±4.64) and -1.80 (±11.71), respectively. A trigonometric function (sine + cosine) with periods of 12 and 24 h was used to describe the diurnal cyclical pattern. Hourly body temperature was analyzed within a season, and fixed effects included MG, group, trigonometric functions nested within group, and interaction of MG with trigonometric functions nested within group; random effects were animal and residual (Model [I]). A combined analysis of season and group was also investigated with the inclusion of season as a main effect and the nesting of effects within both group and season (Model [C]). In both models, the residual was fitted using an autoregressive covariance structure. A 3-way interaction of MG, season, and trigonometric function periodicities of 24 h (P 0.05). The current study illustrated that a genotype × environment interaction exists for MG and 1-copy animals were more robust to environmental extremes in comparison with 0- or 2-copy animals

  5. Whole genome amplification of DNA for genotyping pharmacogenetics candidate genes.

    Directory of Open Access Journals (Sweden)

    Santosh ePhilips

    2012-03-01

    Full Text Available Whole genome amplification (WGA technologies can be used to amplify genomic DNA when only small amounts of DNA are available. The Multiple Displacement Amplification Phi polymerase based amplification has been shown to accurately amplify DNA for a variety of genotyping assays; however, it has not been tested for genotyping many of the clinically relevant genes important for pharmacogenetic studies, such as the cytochrome P450 genes, that are typically difficult to genotype due to multiple pseudogenes, copy number variations, and high similarity to other related genes. We evaluated whole genome amplified samples for Taqman™ genotyping of SNPs in a variety of pharmacogenetic genes. In 24 DNA samples from the Coriell human diversity panel, the call rates and concordance between amplified (~200-fold amplification and unamplified samples was 100% for two SNPs in CYP2D6 and one in ESR1. In samples from a breast cancer clinical trial (Trial 1, we compared the genotyping results in samples before and after WGA for four SNPs in CYP2D6, one SNP in CYP2C19, one SNP in CYP19A1, two SNPs in ESR1, and two SNPs in ESR2. The concordance rates were all >97%. Finally, we compared the allele frequencies of 143 SNPs determined in Trial 1 (whole genome amplified DNA to the allele frequencies determined in unamplified DNA samples from a separate trial (Trial 2 that enrolled a similar population. The call rates and allele frequencies between the two trials were 98% and 99.7%, respectively. We conclude that the whole genome amplified DNA is suitable for Taqman™ genotyping for a wide variety of pharmacogenetically relevant SNPs.

  6. Distribution of Gossypol Glands on Cotton (Gossypium hirsutum L. Genotypes

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    Yuksel BOLEK

    2010-06-01

    Full Text Available Knowing the distribution of gossypol glands in cotton will help to improve advanced cultivars with great economic return. The aim is to compare cotton genotypes for the number and the distribution of gossypol glands found in different plant parts and to determine the genotypes which contain more gossypol glands in their vegetative parts but little or none in their seeds. The intensity and the greatness of the gossypol amount is an important part of defending against plant insects and diseases. Randomized complete block design with two replications was applied at the Agricultural Research Institute of Kahramanmara? during 2006-2007. Thirty seven cotton genotypes belonging to Gossypium hirsutum L. species were the plant material. The number of gossypol glands on stem, boll walls (carpels, leaves and seeds were visually counted and ranged from 0 to 142 per cm2 for stem, 0 to 135 per cm2 for leaf, 0 to 85 per cm2 for boll wall and 0 to 16 per mm2 for embryo (kernel. Number of gossypol glands varied for the genotypes and years but this variance was too low in some genotypes. Genotypes �Acala Royale�, �Acala Prema�, �Deltaopal� and �Carmen� had relatively more gossypol glands on their vegetative parts but less in their seed. Measured parameters were positively and significantly correlated to each other. Correlations for number of gossypol glands between stem and leaf (r=0.77**, boll wall (r=0.65** and seed (r=0.32** were significant.

  7. Genotyping of Brucella species using clade specific SNPs

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    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  8. The influence of competition and host plant resistance on selection of Phytophthora infestans populations in Michigan State and Northern Ireland

    Science.gov (United States)

    The current investigation used multiple cultivars of potato and genotypes of Phytophthora infestans to study the P. infestans genotype x cultivar interaction, and investigate the potential influence of competition and level of field resistance on selection of the surrounding population of P. infesta...

  9. 5-HTTLPR Genotype Moderates the Effects of Past Ecstasy Use on Verbal Memory Performance in Adolescent and Emerging Adults: A Pilot Study.

    Directory of Open Access Journals (Sweden)

    Natasha E Wright

    Full Text Available Ecstasy use is associated with memory deficits. Serotonin transporter gene (5-HTTLPR polymorphisms have been linked with memory function in healthy samples. The present pilot study investigated the influence of 5-HTTLPR polymorphisms on memory performance in ecstasy users, marijuana-using controls, and non-drug-using controls, after a minimum of 7 days of abstinence.Data were collected from 116 young adults (18-25 years-old, including 45 controls, 42 marijuana users, and 29 ecstasy users, and were balanced for 5-HTTLPR genotype. Participants were abstinent seven days prior to completing memory testing. Three MANCOVAs and one ANCOVA were run to examine whether drug group, 5-HTTLPR genotype, and their interactions predicted verbal and visual memory after controlling for gender, past year alcohol use, other drug use, and nicotine cotinine levels.MANCOVA and ANCOVA analysis revealed a significant interaction between drug group and genotype (p = .03 such that ecstasy users with the L/L genotype performed significantly worse on CVLT-2 total recall (p = .05, short (p = .008 and long delay free recall (p = .01, and recognition (p = .006, with the reverse pattern found in controls. Ecstasy did not significantly predict visual memory. 5-HTTLPR genotype significantly predicted memory for faces (p = .02; short allele carriers performed better than those with L/L genotype.5-HTTLPR genotype moderated the effects of ecstasy on verbal memory, with L/L carriers performing worse compared to controls. Future research should continue to examine individual differences in ecstasy's impact on neurocognitive performance as well as relationships with neuronal structure. Additional screening and prevention efforts focused on adolescents and emerging adults are necessary to prevent ecstasy consumption.

  10. Use of chronic irradiation in formation of new rape genotypes

    International Nuclear Information System (INIS)

    Chronic irradiation of hybrid plants of F1 generation obtained by crossing the Canadian rape without erucic acid with European winter varieties containg this acid, doubled the frequency of winter genotypes and increased significantly the frequency of required recombinations of winter character and absence of erucic acid in F2-M2. Genotypes with a more favourable ratio between linoleic and linolenic acids were obtained in the irradiated F2-M2 population. The obtained radio-induced mutants are used for the production of new varieties of winter rape without erucic acid at the Slapy Breeding Station. (author)

  11. Nutrient composition of strawberry genotypes cultivated in a horticulture farm.

    Science.gov (United States)

    Hossain, Ashrafi; Begum, Parveen; Salma Zannat, M; Hafizur Rahman, Md; Ahsan, Monira; Islam, Sheikh Nazrul

    2016-05-15

    This article decribes the nutrient composition of four strawberry genotypes cultivated at the Sher-e-Bangla Agriculture University horticulture farm in Dhaka (Bangladesh). AOAC and standard validated methods were employed to analyse the nutrient composition. Protein, fat and ash contents were found to be vary significantly (LSDstrawberries (LSDstrawberry genotypes contained a wide array of minerals including Ca, Mg, Na, K, P, Mn, Zn, Cu and Fe; most of which varied significantly (LSDStrawberries could be a potential dietary supplement for vitamin C along with minerals, particularly for the children who do not like local fruits, but love to eat the colourful strawberries. PMID:26776020

  12. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  13. Two-temperature LATE-PCR endpoint genotyping

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    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

  14. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto;

    . Chlorophyll a fluorescence has been a versatile tool in photosynthesis research to measure plant responses to various abiotic stresses that affect PSII. We aim to establish a reproducible protocol to measure response of wheat genotypes to high temperature, based on the physiological marker, maximum quantum......%. Our protocol seems to be stable over environments since interaction between genotypes and the three repeated experiments separated in time was not statistically significant. The chlorophyll a fluorescence protocol may enable identification of wheat lines reliably more or less tolerant to heat stress...

  15. The microanalysis on resistance of new tomato genotypes

    Directory of Open Access Journals (Sweden)

    Tatiana Calalb

    2013-04-01

    Full Text Available Microscopic study on the leaf of the new tomato genotypes has shown that the most informative structural indicators of drought resistance of these plants are: a presence, level of development and the distribution of protective and glandulartrichomes on the leaves; b presence and occurrence of the cells with oxalate calcium sand in the leaf mesophyll. Statistical processing of the results determines that new tomato genotypes “Line 50” – ‚Prizor’ × (‚Prizor’ × Lycopersicon hirsutum and “Line 47” – ‘Friguşor’ × (Lycopersicon peruvianum × ‚Victoria’ are resistant to drought.

  16. Positive Effects of Plant Genotypic and Species Diversity on Anti-Herbivore Defenses in a Tropical Tree Species

    Science.gov (United States)

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A.

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  17. Positive effects of plant genotypic and species diversity on anti-herbivore defenses in a tropical tree species.

    Directory of Open Access Journals (Sweden)

    Xoaquín Moreira

    Full Text Available Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves. We found that both forms of plant diversity had positive effects on stem (but not leaf defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer

  18. Positive effects of plant genotypic and species diversity on anti-herbivore defenses in a tropical tree species.

    Science.gov (United States)

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  19. Human alpha-actinin-3 genotype association with exercise-induced muscle damage and the repeated-bout effect.

    Science.gov (United States)

    Venckunas, Tomas; Skurvydas, Albertas; Brazaitis, Marius; Kamandulis, Sigitas; Snieckus, Audrius; Moran, Colin N

    2012-12-01

    Alpha-actinin-3 (ACTN3) is an integral part of the Z line of the sarcomere. The ACTN3 R577X (rs1815739) polymorphism determines the presence or absence of functional ACTN3, which may influence the extent of exercise-induced muscle damage. This study aimed to compare the impact of, and recovery from, muscle-damaging eccentric exercise on subjects with or without functional ACTN3. Seventeen young men (20-33 years old), homozygous for the R (n = 9) or X (n = 8) alleles, performed two bouts of stretch-shortening exercise (50 drop jumps) two weeks apart. Muscle soreness, plasma creatine kinase (CK) activity, jump height, maximal voluntary isometric torque (MVC), peak concentric isokinetic torque (IT), and electrically stimulated knee extension torques at 20 and 100 Hz were measured at baseline and at a number of time points up to 14 days after each bout. There were no significant baseline differences between the groups. However, significant time point × genotype interactions were observed for MVC (p = 0.021) and IT (p = 0.011) for the immediate effect of eccentric exercise in bout 1. The RR group showed greater voluntary force decrements (RR vs. XX: MVC, -33.3% vs. -24.5%; IT, -35.9% vs. -23.2%) and slower recovery. A repeated-bout effect was clearly observed, but there were no differences by genotype group. The ACTN3 genotype modulates the response of muscle function to plyometric jumping exercise, although the differences are modest. The ACTN3 genotype does not influence the clearly observed repeated-bout effect; however, XX homozygotes recover baseline voluntary torque values faster and thus may be able to undertake more frequent training sessions. PMID:22891846

  20. Adaptation and Genotype x Environment Interaction of Flaxseed (Linum usitatissimum L. Genotypes in South Central Chile Adaptación e Interacción Genotipo x Ambiente en Lino (Linum usitatissimum L. en la Zona Centro Sur de Chile

    Directory of Open Access Journals (Sweden)

    Marisol Berti

    2010-09-01

    Full Text Available Flaxseed (Linum usitatissimum L. is imported into Chile mostly for bread making and feed. Identification of genotypes best adapted for seed production in South Central Chile would facilitate producer’s decision. The objective of this study was to determine the adaptation and genotype x environment interaction of 16 flaxseed genotypes (including 10 from North American and six from Argentine sources grown at 11 environments (defined as location-year in Chile from 2003 to 2007. Genotype seed yield was above 5700 kg ha-1 for some environments indicating a high yield potential. According to the AMMI (Additive Main Effects and Multiplicative Interaction and SREG (Sites regression models the 11 environments were classified into four groups by the AMMI and three groups by the SREG models. Genotypes were classified into five groups by the SREG model with four of the groups as single genotypes. Overall mean seed yield was similar for all genotypes; however the genotype Nekoma was the most stable and higher yielding genotype across environments. The environment with the highest yield potential was Chillán 2003-2004, but this location had low yield stability across years. The environments with greatest seed yield potential, Chillán 2003-2004 and Los Ángeles 2004-2005, had irrigation during flowering and seed filling. Seed oil content fluctuated between 420 and 530 g kg-1. The climatic differences among environments did not influence oil composition as expected from previous research. Flaxseed appears adapted to South Central Chile with differences observed among genotypes for biomass and seed yield, harvest index, test weight, oil content, and composition.La semilla de lino (Linum usitatissimum L. se importa a Chile principalmente para panaderías y alimento animal. La identificación de genotipos altamente productivos en la zona Centro Sur de Chile facilitaría la decisión de los productores. El objetivo de este estudio fue determinar la adaptaci

  1. Differences in ovarian aging patterns between races are associated with ovarian genotypes and sub-genotypes of the FMR1 gene

    Directory of Open Access Journals (Sweden)

    Gleicher Norbert

    2012-09-01

    Full Text Available Abstract Background Ovarian aging patterns differ between races, and appear to affect fertility treatment outcomes. What causes these differences is, however, unknown. Variations in ovarian aging patterns have recently been associated with specific ovarian genotypes and sub-genotypes of the FMR1 gene. We, therefore, attempted to determine differences in how functional ovarian reserve (FOR changes with advancing age between races, and whether changes are associated with differences in distribution of ovarian genotypes and sub-genotypes of the FMR1 gene. Methods We determined in association with in vitro fertilization (IVF FOR in 62 young Caucasian, African and Asian oocyte donors and 536 older infertility patients of all three races, based on follicle stimulating hormone (FSH, anti-Müllerian hormone (AMH and oocyte yields, and investigated whether differences between races are associated with differences in distribution of FMR1 genotypes and sub-genotypes. Results Changes in distribution of mean FSH, AMH and oocyte yields between young donors and older infertility patients were significant (all P FMR1 genotypes and sub-genotypes in patients varied significantly between races, with Asians demonstrating fewer het-norm/low sub-genotypes than Caucasians and Africans (P = 0.012. Conclusion FOR changes in different races at different rates, and appears to parallel ovarian FMR1 genotypes and sub-genotype distributions. Differences in ovarian aging between races may, therefore, be FMR1-associated.

  2. Genotyping analysis for the 46 C/T polymorphism of coagulation factor XII and the involvement of factor XII activity in patients with recurrent pregnancy loss.

    Directory of Open Access Journals (Sweden)

    Eriko Asano

    Full Text Available BACKGROUND: Established causes of recurrent pregnancy loss (RPL include antiphospholipid syndrome, uterine anomalies, parental chromosomal abnormalities, particularly translocations and abnormal embryonic karyotype. A systematic review concluded that coagulation factor XII (FXII deficiency was associated with RPL. However, it could not be established whether the 46 C/T SNP of FXII or low activity of FXII was a risk factor for RPL, because of the small sample size. METHODS AND FINDINGS: We conducted a cross-sectional and cohort study in 279 patients with two or more unexplained consecutive pregnancy losses and 100 fertile women. The association between the lupus anticoagulant (LA activity and FXII activity was examined. The frequency of the CC, CT and TT genotypes and the FXII activity were also compared between the patients and controls. Subsequent miscarriage rates among the CC, CT, TT genotypes and according to the FXII activity was examined. LA was associated with reduced FXII activity. The CT, but not the TT, genotype was confirmed to be a risk factor for RPL in the cross-sectional study using multivariate logistic regression analysis (OR, 2.8; 95% CI, 1.37-5.85. The plasma FXII activity in the patients was similar to that in the controls. Neither low FXII activity nor the CT genotype predicted the subsequent pregnancy outcome in the cohort study. On the other hand, and intermediate FXII activity level of 85-101% was predictive of subsequent miscarriage. CONCLUSIONS: Low FXII activity was not associated with RPL. The FXII gene was found to be one of the significant susceptibility genes for RPL, similar to the FV Leiden mutation. However, the clinical influence of the CT genotype might be relatively small, because the presence/absence of this genotype did not have any predictive value for the subsequent pregnancy outcome. This was the first study indicating the influence of FXII 46C/T on further pregnancy outcomes.

  3. The value of molecular stratification for CEBPA(DM) and NPM1(MUT) FLT3(WT) genotypes in older patients with acute myeloid leukaemia.

    Science.gov (United States)

    Dickson, Glenda J; Bustraan, Sophia; Hills, Robert K; Ali, Akbar; Goldstone, Anthony H; Burnett, Alan K; Linch, David C; Gale, Rosemary E

    2016-02-01

    Older adult patients (≥60 years) with acute myeloid leukaemia (AML) are generally considered to be poor-risk and there is limited information available regarding risk stratification based on molecular characterization in this age group, particularly for the double-mutant CEBPA (CEBPA(DM) ) genotype. To investigate whether a molecular favourable-risk genotype can be identified, we investigated CEBPA, NPM1 and FLT3 status and prognostic impact in a cohort of 301 patients aged 60 years or more with intermediate-risk cytogenetics, all treated intensively. Overall survival (OS) at 1 year was highest in the 12 patients (4%) that were CEBPA(DM) compared to the 76 (28%) with a mutant NPM1 and wild-type FLT3 (NPM1(MUT) FLT3(WT) ) genotype or all other patients (75%, 54%, 33% respectively), with median survival 15·2, 13·6 and 6·6 months, although the benefit was short-term (OS at 3 years 17%, 29%, 12% respectively). Combination of the CEBPA(DM) and NPM1(MUT) FLT3(WT) genotype patients defined a molecular group with favourable prognosis (P < 0·0001 in multivariate analysis), with 57% of patients alive at 1 year compared to 33% for all other patients. Knowledge of genotype in older cytogenetically intermediate-risk patients might influence therapy decisions. PMID:26847745

  4. Caffeine and 3-km cycling performance: Effects of mouth rinsing, genotype, and time of day.

    Science.gov (United States)

    Pataky, M W; Womack, C J; Saunders, M J; Goffe, J L; D'Lugos, A C; El-Sohemy, A; Luden, N D

    2016-06-01

    We assessed the efficacy of caffeine mouth rinsing on 3-km cycling performance and determined whether caffeine mouth rinsing affects performance gains influenced by the CYP1A2 polymorphism. Thirty-eight recreational cyclists completed four simulated 3-km time trials (TT). Subjects ingested either 6 mg/kg BW of caffeine or placebo 1 h prior to each TT. Additionally, 25 mL of 1.14% caffeine or placebo solution were mouth rinsed before each TT. The treatments were Placebo, caffeine Ingestion, caffeine Rinse and Ingestion+Rinse. Subjects were genotyped and classified as AA homozygotes or AC heterozygotes for the rs762551 polymorphism of the CYP1A2 gene involved in caffeine metabolism. Magnitude-based inferences were used to evaluate treatment differences in mean power output based on a predetermined meaningful treatment effect of 1.0%. AC heterozygotes (4.1%) and AA homozygotes (3.4%) benefited from Ingestion+Rinse, but only AC performed better with Ingestion (6.0%). Additionally, Rinse and Ingestion+Rinse elicited better performance relative to Placebo among subjects that performed prior to 10:00 h (Early) compared with after 10:00 h (Late). The present study provides additional evidence of genotype and time of day factors that affect the ergogenic value of caffeine intake that may allow for more personalized caffeine intake strategies to maximize performance. PMID:26062916

  5. Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

    Science.gov (United States)

    Séraphin, Marie Nancy; Lauzardo, Michael; Morris, J. Glenn; Blackburn, Jason K.

    2016-01-01

    Background Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts. Methods We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan. Principal Findings Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (immigrants are likely to impact TB control. Due to the monomorphic nature of available markers, whole genome sequencing is needed to conclusively delineate recent transmission events between U.S. and foreign-born persons. PMID:27093156

  6. Can genotype determine the sports phenotype? A paradigm shift in sports medicine.

    Science.gov (United States)

    Ghosh, Amit; Mahajan, Preetam B

    2016-06-01

    In last two decades, there has been an evolution in sports medicine. Several researchers have worked on different domains of sports medicine, like strength, endurance, sports injury, and psychology. Besides this, several groups have explored the changes at cellular and molecular levels during exercise, which has led to the development of the new domain in sports science known as genetic medicine. Genetic medicine deals with the genotypic basis of sports phenotype. In this article, we try to provide an up-to-date review on genetic determinants of sports performance, which will be like a journey from the nostalgic past towards the traditional present and the romantic future of sports medicine. Endurance and power performance are two important domains of athletes. They vary in individuals, even among trained athletes. Researches indicate that the genetic makeup of sportsmen play a vital role in their performance. Several genetic factors are reported to be responsible for endurance, power, susceptibility to injury, and even psychology of the individual. Besides this, proper training, nutrition, and environment are also important in shaping their potential. The aim of this discussion is to understand the influence of the environment and the genetic makeup on the performance of the athletes. There is sufficient evidence to suggest that genotype determines the sports phenotype in an athlete. Choosing the right sports activity based on genetic endowment is the key for achieving excellence in sports. PMID:26812785

  7. Several Fruit Characteristics of Rosa sp. Genotypes from the Northeastern Region of Romania

    Directory of Open Access Journals (Sweden)

    Craita Maria ROSU

    2011-11-01

    Full Text Available There is great evidence regarding the beneficial influence of rose hips on human and animal health. In this respect, fruits of native populations of Rosa spp. collected from the northeastern part of Romania (400-1060 m altitude were assayed for nutritional and some morphological properties, in order to select the best genotypes. The results show a great quantitative variability of analyzed genotypes, regarding dimensions and biochemical indicators as follow: ascorbic acid: 866.91 mg/100 g fw (R. rubiginosa, 615.98 mg/100 g fw (R. caesia; carotenes: 34.95 mg/100 g fw (R. subcanina, 24.64 mg/100 g fw (R. nitidula; protein content: 0.47 g/100 g fw (R. micrantha, 0.25 g/100 g fw (R. caesia; total sugars: 17.63 g/100 g fw (R. andegavensis, 11.55 g/100 g fw (R. caryophyllacea. The fruits length, width and dry weight were: 25 mm (R. canina, 12 mm (R. micrantha, 16.5 mm (R. corymbifera, 8 mm (R. micrantha and 25% dry weight (R. rubiginosa, 38% dry weight (R. nitidula, respectively. The present study demonstrates the existence of a rich rose germplasm source in north-east area, with good biotechnological fruit quality, which recommends them as functional foods according to their chemical contents (R. rubiginosa, R. vosagiaca, R. subcanina, R. canina and R. caryophyllacea and also as sources for natural colorants in food technology.

  8. A constructive replication of the association between the oxytocin receptor genotype and parenting.

    Science.gov (United States)

    Klahr, Ashlea M; Klump, Kelly; Burt, S Alexandra

    2015-02-01

    Behavioral genetic studies have robustly indicated that parenting behaviors are heritable-that is, individual differences in parenting are at least partially a function of genetic differences between persons. Few studies, however, have sought to identify the specific genetic variants that are associated with individual differences in parenting. Genes that influence the oxytocin system are of particular interest, given the growing body of evidence that points to the role of oxytocin for social behaviors, including parenting. The current study conducted examinations of associations between a variant in the oxytocin receptor gene (OXTR rs53576) and parental warmth, control, and negativity in a sample of 1,000 twin children and their parents (N = 500 families) from the Michigan State University Twin Registry to constructively replicate and extend prior work (Bakermans-Kranenburg & van IJzendoorn, 2008; Michalska et al., 2014). Analyses were conducted both at the level of the child and the level of the parent, allowing us to examine both child-driven (via evocative gene-environment correlation) and parent-driven genetic effects on parenting. Mothers' OXTR genotype predicted her warmth toward her children, even after controlling for child genotype. This association was not found for fathers. These findings add to the growing body of evidence linking oxytocin functioning to parental behavior and also highlight potential etiological differences in parenting across mothers and fathers. PMID:25419912

  9. Multi-Year Assessment of Toxic Genotypes and Microcystin Concentration in Northern Lake Taihu, China

    Science.gov (United States)

    Hu, Lili; Shan, Kun; Lin, Lizhou; Shen, Wei; Huang, Licheng; Gan, Nanqin; Song, Lirong

    2016-01-01

    Lake Taihu is the third-largest freshwater lake in China and has been suffering from cyanobacterial blooms for over two decades. The northern part of the lake, Meiliang Bay, is known to be at high risk of dense and sustained Microcystis blooms and toxins. This study aimed to investigate and record the annual and seasonal dynamics of toxic genotype, Microcystis morphospecies succession and microcystin variation. It also aimed to find out the underlying driving factors influencing the dynamic changes. Microcystin (MC) and the Microcystis genotype were quantified using HPLC and quantitative real-time PCR, respectively. Our study, over three consecutive years, showed that the pattern of morphospecies succession was seasonally distinct and annually consistent. During the same period in 2012, 2013 and 2014, the average MC were, on dry weight basis, 733 μg·g−1, 844 μg·g−1, 870 μg·g−1, respectively. The proportion of toxic Microcystis accounted for 41%, 44% and 52%, respectively. Cell bound microcystin was found to correlate with the percentage of toxic Microcystis. Based on historical and current data, we conclude that annual bloom toxicity was relatively stable or possibly increased over the last decade. PMID:26784229

  10. Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology.

    Science.gov (United States)

    Forsman, Anders

    2014-01-01

    There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109

  11. Genetic polymorphisms and skin aging: the identification of population genotypic groups holds potential for personalized treatments

    Directory of Open Access Journals (Sweden)

    Naval J

    2014-07-01

    Full Text Available Jordi Naval,1 Vicente Alonso,1,2 Miquel Angel Herranz11Genocosmetics Lab, Barcelona, Spain; 2Dermatology Unit, Hospital Nisa 9 de Octubre, Valencia, SpainIntroduction: Skin changes are among the most visible signs of aging. Skin properties such as hydration, elasticity, and antioxidant capacity play a key role in the skin aging process. Skin aging is a complex process influenced by heritable and environmental factors. Recent studies on twins have revealed that up to 60% of the skin aging variation between individuals can be attributed to genetic factors, while the remaining 40% is due to non-genetic factors. Recent advances in genomics and bioinformatics approaches have led to the association of certain single nucleotide polymorphisms (SNPs to skin properties. Our aim was to classify individuals based on an ensemble of multiple polymorphisms associated with certain properties of the skin for providing personalized skin care and anti-aging therapies.Methods and results: We identified the key proteins and SNPs associated with certain properties of the skin that contribute to skin aging. We selected a set of 13 SNPs in gene coding for these proteins which are potentially associated with skin aging. Finally, we classified a sample of 120 female volunteers into ten clusters exhibiting different skin properties according to their genotypic signature.Conclusion: This is the first study that describes the actual frequency of genetic polymorphisms and their distribution in clusters involved in skin aging in a Caucasian population. Individuals can be divided into genetic clusters defined by genotypic variables. These genotypic variables are linked with polymorphisms in one or more genes associated with certain properties of the skin that contribute to a person's perceived age. Therefore, by using this classification, it is possible to characterize human skin care and anti-aging needs on the basis of an individual's genetic signature, thus opening the door

  12. Serotonin transporter genotype modulates subgenual response to fearful faces using an incidental task.

    Science.gov (United States)

    O'Nions, Elizabeth J P; Dolan, Raymond J; Roiser, Jonathan P

    2011-11-01

    This study assessed the impact of serotonin transporter genotype (5-HTTLPR) on regional responses to emotional faces in the amygdala and subgenual cingulate cortex (sgACC), while subjects performed a gender discrimination task. Although we found no evidence for greater amygdala reactivity or reduced amygdala-sgACC coupling in short variant 5-HTTLPR homozygotes (s/s), we observed an interaction between genotype and emotion in sgACC. Only long variant homozygotes (la/la) exhibited subgenual deactivation to fearful versus neutral faces, whereas the effect in s/s subjects was in the other direction. This absence of subgenual deactivation in s/s subjects parallels a recent finding in depressed subjects [Grimm, S., Boesiger, P., Beck, J., Schuepbach, D., Bermpohl, F., Walter, M., et al. Altered negative BOLD responses in the default-mode network during emotion processing in depressed subjects. Neuropsychopharmacology, 34, 932-943, 2009]. Taken together, the findings suggest that subgenual cingulate activity may play an important role in regulating the impact of aversive stimuli, potentially conferring greater resilience to the effects of aversive stimuli in la/la subjects. Using dynamic causal modeling of functional magnetic resonance imaging data, we explored the effects of genotype on effective connectivity and emotion-specific changes in coupling across a network of regions implicated in social processing. Viewing fearful faces enhanced bidirectional excitatory coupling between the amygdala and the fusiform gyrus, and increased the inhibitory influence of the amygdala over the sgACC, although this modulation of coupling did not differ between the genotype groups. The findings are discussed in relation to the role of sgACC and serotonin in moderating responses to aversive stimuli [Dayan, P., & Huys, Q. J., Serotonin, inhibition, and negative mood. PLoS Comput Biol, 4, e4, 2008; Mayberg, H. S., Liotti, M., Brannan, S. K., McGinnis, S., Mahurin, R. K., Jerabek, P. A., et

  13. Salinity Responses of Grafted Grapevines: Effects of Scion and Rootstock Genotypes

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    Nuray SIVRITEPE

    2010-12-01

    Full Text Available Two-year-old Sultana and Mke vines (Vitis vinifera L. grafted onto Rupestris du Lot (Vitis rupestris Scheele and 110 R (Vitis berlandieri Vitis rupestris were grown in soil, sand, sphagnum peat and farmyard manure mixture (2:1:1:1 v/v irrigated with 0.3, 2.7 and 5.45 dS m-1 NaCl solutions for a period of 60 days. Biomass accumulation, relative chlorophyll content, leaf water potential, stomatal conductance and transpiration were significantly reduced by salinity in all graft combinations. The inhibiting effect of salinity on growth varied according to the characteristics of the scion genotype and the level of salinity. The results imply the predominance of the scion genotype in determining variation in the leaf-level physiological characteristics of grafted vines because stomatal conductance and transpiration were higher in Sultana than in Mke at the same leaf water potential and the level of salinity, regardless of the rootstock genotype. NaCl treatments did not affect leaf Cu concentration while inducing significant Na, K, Ca, N, P, Mg, Fe, Mn and Zn elevations in the leaves of all scion/rootstock combinations. While salinity caused an increase in N content and a decrease in K content in the roots of all graft combinations, it had no influence on Ca, P, Cu and Zn concentrations. In contrast to the Sultana grafted vines, NaCl salinity led to a decrease in Mg, Fe and Mn concentrations in the roots of Mke grafted vines. Nevertheless, ion accumulation in leaves and roots of grafted vines under saline or non-saline conditions was controlled predominantly by the genotype of the scion. In response to salinity, Sultana grafts accumulated higher amounts of ions in their leaves than in their roots. However, in Mke, higher ion concentrations were seen in the roots. Therefore, the increase in the transport of inorganic ions up to the leaves seems to be the major component of osmotic adjustment in salt-stressed Sultana vines.

  14. Genotypes of Helicobacter pylori in patients with peptic ulcer bleeding

    OpenAIRE

    Perng, Chin-Lin; Lin, Hwai-Jeng; Lo, Wen-Ching; Tseng, Guan-Ying; Sun, I-Chen; Ou, Yueh-Hsing

    2004-01-01

    AIM: Helicobacter pylori causes chronic gastritis, peptic ulcer, gastric cancer and MALT-lymphoma. Different genotypes of Helicobacter pylori are confirmed from diverse geographic areas. Its association with bleeding peptic ulcer remains controversial. The aim of this study was to investigate the Helicobacter pylori vacA alleles, cagA and iceA in patients with bleeding peptic ulcer.

  15. Evaluation of cotton genotypes for ginning energy and ginning rate

    Science.gov (United States)

    Reducing ginning energy use through cultivar improvement could reduce ginning and energy cost. The objective of this study was to detect genetic variability for ginning energy and ginning rate. Thirty four conventional and twelve transgenic genotypes were evaluated in 2008 and 2009 for ginning energ...

  16. New Hepatitis E Virus Genotype in Camels, the Middle East

    Science.gov (United States)

    Lau, Susanna K.P.; Teng, Jade L.L.; Tsang, Alan K. L.; Joseph, Marina; Wong, Emily Y.M.; Tang, Ying; Sivakumar, Saritha; Xie, Jun; Bai, Ru; Wernery, Renate; Wernery, Ulrich; Yuen, Kwok-Yung

    2014-01-01

    In a molecular epidemiology study of hepatitis E virus (HEV) in dromedaries in Dubai, United Arab Emirates, HEV was detected in fecal samples from 3 camels. Complete genome sequencing of 2 strains showed >20% overall nucleotide difference to known HEVs. Comparative genomic and phylogenetic analyses revealed a previously unrecognized HEV genotype. PMID:24856611

  17. New Hepatitis E Virus Genotype in Camels, the Middle East

    OpenAIRE

    Woo, Patrick C. Y.; Lau, Susanna K. P.; Teng, Jade L. L.; Tsang, Alan K. L.; Joseph, Marina; Wong, Emily Y.M.; Tang, Ying; Sivakumar, Saritha; Xie, Jun; Bai, Ru; Wernery, Renate; Wernery, Ulrich; Yuen, Kwok-Yung

    2014-01-01

    In a molecular epidemiology study of hepatitis E virus (HEV) in dromedaries in Dubai, United Arab Emirates, HEV was detected in fecal samples from 3 camels. Complete genome sequencing of 2 strains showed >20% overall nucleotide difference to known HEVs. Comparative genomic and phylogenetic analyses revealed a previously unrecognized HEV genotype.

  18. Human papillomavirus testing and genotyping in cervical screening

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Lynge, Elsebeth; Bonde, Jesper

    2011-01-01

    Mass vaccination against human papillomavirus (HPV) genotypes 16 and 18 will, in the long term, reduce the incidence of cervical cancer, but screening will remain an important cancer control measure in both vaccinated and unvaccinated women. Since the 1960s, cytology screening has helped to reduce...

  19. Diversity of Enterocytozoon bieneusi genotypes among small rodentsin southwestern Poland

    Czech Academy of Sciences Publication Activity Database

    Perec Matysiak, A.; Buńkowska-Gawlik, K.; Kváč, Martin; Sak, Bohumil; Hildebrand, J.; Leśniańska, K.

    2015-01-01

    Roč. 214, 2015-Dec-15 (2015), s. 242-246. ISSN 0304-4017 R&D Projects: GA ČR GA14-20684S Institutional support: RVO:60077344 Keywords : Enterocytozoon bieneusi * Small rodents * Genotyping Subject RIV: FN - Epidemiology, Contagious Diseases ; Clinical Immunology Impact factor: 2.460, year: 2014

  20. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  1. Unidirectional Suppression of Anaplasma phagocytophilum Genotypes in Infected Lambs

    OpenAIRE

    Stuen, Snorre; Dahl, Hilde; Bergström, Karin; Moum, Truls

    2005-01-01

    Five-month-old lambs were simultaneously infected with different doses of two 16S rRNA genetic variants of Anaplasma phagocytophilum and thereafter followed for clinical observation and blood sampling. The result of the study indicates a unidirectional suppression of genotypes in infected lambs, at least during a certain period of an A. phagocytophilum infection.

  2. Distribution of Candida albicans genotypes among family members

    Science.gov (United States)

    Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

    1999-01-01

    Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

  3. Iterative combination of national phenotype, genotype, pedigree, and foreign information

    Science.gov (United States)

    Single step methods can combine all sources of information into accurate rankings for animals with and without genotypes. Equations that require inverting the genomic relationship matrix G work well with limited numbers of animals, but equivalent models without inversion are needed as numbers increa...

  4. Speech Characteristics Associated with Three Genotypes of Ataxia

    Science.gov (United States)

    Sidtis, John J.; Ahn, Ji Sook; Gomez, Christopher; Sidtis, Diana

    2011-01-01

    Purpose: Advances in neurobiology are providing new opportunities to investigate the neurological systems underlying motor speech control. This study explores the perceptual characteristics of the speech of three genotypes of spino-cerebellar ataxia (SCA) as manifest in four different speech tasks. Methods: Speech samples from 26 speakers with SCA…

  5. Genotyping of Brazilian Giardia duodenalis human axenic isolates

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    ST Coradi

    2011-01-01

    Full Text Available Giardia duodenalis is a complex species that comprises at least seven distinct genetic groups (A to G, but only genotypes A and B are known to infect humans and a wide variety of other mammals. Regardless of biological, biochemical and antigenic analysis, several isolates maintained in vitro were not genetically typed yet. So, in the present study, five Brazilian axenic isolates obtained from asymptomatic and symptomatic patients were typed in order to determine the major genetic groups to which the isolates belonged. DNA was extracted from axenic trophozoites, fragments of glutamate dehydrogenase (gdh and triosephosphate isomerase (tpi genes were amplified by PCR and the isolate genotyping was carried out using restriction fragment length polymorphism (RFLP and DNA sequencing for both genes. The results revealed that all isolates were assigned to genotype A at both analyzed loci. Indeed, DNA sequence analysis classified the four isolates obtained from asymptomatic individuals into subtype AII, while the isolate obtained from the symptomatic patient was typed as subtype AI. Despite of the limited number of isolates assessed, the findings presented herein provide interesting insights on the occurrence of Giardia genotypes in Brazil and hold the perspective for future molecular and epidemiological investigations.

  6. Partitioning of copy-number genotypes in pedigrees

    Directory of Open Access Journals (Sweden)

    Andelfinger Gregor U

    2010-05-01

    Full Text Available Abstract Background Copy number variations (CNVs and polymorphisms (CNPs have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.

  7. Heterosis in crosses between wheat genotypes with different spike architecture

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    Kobiljski Borislav Đ.

    2002-01-01

    Full Text Available In order to estimate hybrid vigor, wheat genotypes differing in spike architecture (normal, tetrastichon and branched were crossed and the F1 and F2 generations analyzed for the number of fertile spikelets/spike, number of grains/spike and grain weight/spike. The parents used for crossing were Sava (normal spike, Forlani (normal spike, ZG T 171/1 (tetrastichon spike and ZG 172 (branched spike. The F1 and F2 progenies, except those from the cross Sava x Forlani, had a lower number of fertile spikelets/spike compared with the better parent. In the crosses between genotypes with normal and branched spikes, the F1 and F2 progenies formed significantly fewer grains/spike. On the other hand, the F1 of the crosses between genotypes with normal and tetrastichon spike showed a significant level of heterosis with respect to the number of grains/spike, particularly the cross Forlani x ZG T 171/1. In regard to grain weight/spike, significant heterosis was detected in all crosses except Sava x ZG 172.The crosses between genotypes with normal and tetrastichon spikes that exhibited significant heterosis for two main yield components were most promising in the context of hybrid wheat development. Such crosses deserve further attention and investigation.

  8. Mycotoxin chemistry meets genomics: When is a genotype a chemotype?

    Science.gov (United States)

    The chemotype of a microbial or plant species has traditionally been defined as its profile of secondary metabolites, while the genotype is its DNA sequence. For the fungus Fusarium, DNA sequence analysis has associated diversity of trichothecene biosynthetic (TRI) genes with diversity of trichothe...

  9. High-Throughput, Large-Scale SNP Genotyping: Bioinformatics Considerations

    OpenAIRE

    Margetic, Nino

    2004-01-01

    In order to provide a high-throughput, large-scale genotyping facility at the national level we have developed a set of inter-dependent information systems. A combination of commercial, publicly-available and in-house developed tools links a series of data repositories based both on flat files and relational databases providing an almost complete semi-automated pipeline.

  10. Prevalence of American Foulbrood and Paenibacillus Larvae Genotypes in Bulgaria

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    Nikolina V. RUSENOVA

    2016-01-01

    Full Text Available This study aimed to analyse the prevalence of American foulbrood and Paenibacillus larvae genotypes in Bulgaria. For this purpose, data concerning American foulbrood outbreaks were used. Also, available data on the number of destroyed bee families covering a twenty-five-year period (1989 - 2013 was collected from the register of Bulgarian Food Safety Agency. In addition, Paenibacillus larvae genotypes in 15 apiaries were established by rep - PCR with BOXA1R and MBOREP1 primers. Results showed broad incidence of the disease, particularly at the beginning of the analysed period, with a tendency to reduction of affected apiaries and bee families at the end of the period. A statistically significant prevalence of American foulbrood in South Bulgaria compared to the northern regions was observed. Genotyping of Paenibacillus larvae revealed two genotypes: ab and AB, with the preponderance of the more virulent AB in South Bulgaria. The obtained results showed the need for conducting regular mandatory screening of bee colonies for early diagnostics of the disease and the implementation of relevant measures for American foulbrood prevention and control.

  11. A simple and robust approach for genotyping in Musaceae

    Czech Academy of Sciences Publication Activity Database

    Hřibová, Eva; Christelová, Pavla; Roux, N.; Doležel, Jaroslav

    2013-01-01

    Roč. 986, April 2013 (2013), s. 241-246. ISSN 0567-7572 Grant ostatní: GA MŠk(CZ) ED0007/01/01 Institutional research plan: CEZ:AV0Z50380511 Keywords : fragment analysis * genotyping platform * microsatellite markers Subject RIV: EB - Genetics ; Molecular Biology http://www.actahort.org/books/986/986_25.htm

  12. Selecting additional tag SNPs for tolerating missing data in genotyping

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    Chen Ting

    2005-11-01

    Full Text Available Abstract Background Recent studies have shown that the patterns of linkage disequilibrium observed in human populations have a block-like structure, and a small subset of SNPs (called tag SNPs is sufficient to distinguish each pair of haplotype patterns in the block. In reality, some tag SNPs may be missing, and we may fail to distinguish two distinct haplotypes due to the ambiguity caused by missing data. Results We show there exists a subset of SNPs (referred to as robust tag SNPs which can still distinguish all distinct haplotypes even when some SNPs are missing. The problem of finding minimum robust tag SNPs is shown to be NP-hard. To find robust tag SNPs efficiently, we propose two greedy algorithms and one linear programming relaxation algorithm. The experimental results indicate that (1 the solutions found by these algorithms are quite close to the optimal solution; (2 the genotyping cost saved by using tag SNPs can be as high as 80%; and (3 genotyping additional tag SNPs for tolerating missing data is still cost-effective. Conclusion Genotyping robust tag SNPs is more practical than just genotyping the minimum tag SNPs if we can not avoid the occurrence of missing data. Our theoretical analysis and experimental results show that the performance of our algorithms is not only efficient but the solution found is also close to the optimal solution.

  13. DIFFERENTIATION OF BARLEY GENOTYPES BASED ON DNA POLYMORPHISM

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    Marián Tomka

    2013-02-01

    Full Text Available Identification and characterization of genotypes is essential for improving the quality of cultivated varieties in breeding programs. Information about the origin of varieties can help farmers in selecting appropriate varieties to specific growing conditions or end use of crops. A set of ten microsatellite markers was used to describe genetic diversity in a sample of 30 barley (Hordeum vulgare L. genotypes. A total of 55 different alleles were amplified using ten SSR markers localized on chromosomes 1H, 2H, 3H, 5H, 6H, 7H with an average number of 5.5 alleles per locus. On the basis of allele frequencies we have calculated diversity index, polymorphic information content and index of probability, which have mean values of 0.664; 0.643 and 0.126 respectively. These values indicate high differentiation ability of SSR markers. In the created dendrogram using hierarchical cluster analysis using UPGMA algorithm we were able to differentiate all 30 barley genotypes. The results show that DNA markers are suitable for the identification and differentiation of genotypes and indicated the effectiveness of microsatellite markers to describe genetic diversity.

  14. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya;

    2013-01-01

    achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene...

  15. Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Tanja B; Mathiesen, Christian K;

    2011-01-01

    To facilitate genotype-specific high-throughput studies of hepatitis C virus (HCV), we have developed reporter viruses using JFH1-based recombinants expressing core-nonstructural protein 2 (NS2) of genotype 1 to 7 prototype isolates. We introduced enhanced green fluorescent protein (EGFP) into NS5A...... deletions in EGFP, while 2a(J6)¿40 did not show an impaired viability. We further developed panels of JFH1-based genotype 1 to 7 core-NS2 recombinants expressing EGFP- or RLuc-NS5A¿40 fusion proteins. In cell culture, the different EGFP recombinants showed growth characteristics comparable to those...... of these reporter viruses for high-throughput fluorescence- and luminescence-based studies of HCV-receptor interactions and serum-neutralizing antibodies was demonstrated. Finally, using RLuc viruses, we showed that the genotype-specific core-NS2 sequence did not influence the response to alfa-2b interferon (IFN...

  16. A novel hepatitis C virus genotyping method based on liquid microarray.

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    Cesar A B Duarte

    Full Text Available The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%. The concordance between the two methods was 100% for genotype determination (74/74. At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively. Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype "1" subtypes (1a and 1b were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

  17. Prevalence of hepatitis C genotypes in patients with hepatitis C in Lorestan province (2009-2013

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    Mohammad Reza Nazer

    2014-05-01

    Full Text Available Background: Determining hepatitis C genotypes is important to detect the various aspects of this infection, including its epidemiology, pathogenesis and response to anti-viral treatments. The aim of this study was to investigate the prevalence of hepatitis C genotypes in patients admitted to the Infectious Diseases Clinic in Khorramabad. Methods: Out of all the patients admitted to the Infectious Disease Clinic in Khorramabad in a four-year period (April 2009 to March 2013, 120 patients who met the inclusion criteria of the study were evaluated. The PCR method was used to examine the serums of the patients with hepatitis C in terms of the type of genotype. Results: Out of 120 patients, 101 (84.2% were male and 19 (15.8% were female. The most prevalent genotypes were 3a (65%, 1a (24.2%, 1a/1b (5%, and 2 (1.7%, respectively. The genotypes of 5 patients (4.2% could not be determined. No significant relationships were found between gender and genotype, and age group and genotype. Moreover, 18.3% of the patients were HIV-positive. Conclusion: In this study, genotype 3a, the most prevalent genotype, was not consistent with the prevalent genotypes in Arab, European, American, and African countries. Furthermore, genotype 1a was the second most prevalent genotype, while it has been reported as the most prevalent genotype by numerous studies conducted in Iran.

  18. RAPD analysis of the genetic polymorphism in european wheat genotypes

    Directory of Open Access Journals (Sweden)

    Tímea Kuťka Hlozáková

    2016-01-01

    Full Text Available Wheat (Triticum aestivum L. is one of the main crops for human nutrition. The genetic variability of grown wheat has been reduced by modern agronomic practices, which inturn prompted the importance of search for species that could be useful as a genepool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to analyze the genetic diversity among 24 European wheat genotypes based on Random Amplified Polymorphism (RAPD markers. A total of 29 DNA fragments were amplified with an average 4.83 polymorphic fragments per primer. The primer producing the most polymorphic fragments was SIGMA-D-P, where 7 polymorphic amplification products were detected. The lowest number of amplified fragments (3 was detected by using the primer OPB-08. The size of amplified products varied between 300 bp (OPE-07 to 3000 bp (SIGMA-D-P. The diversity index (DI of the applied RAPD markers ranged from 0.528 (OPB-07 to 0.809 (SIGMA-D-P with an average of 0.721. The polymorphism information content (PIC of the markers varied from 0.469 (OPB-07 to 0.798 (SIGMA-D-P with an average 0.692. Probability of identity (PI was low ranged from 0.009 (SIGMA-D-P to 0.165 (OPB-07 with an avarage 0.043. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. Within the dendrogram was separated the unique genotype Insegrain (FRA from the rest of 23 genotypes which were further subdivided into two subclusters. In the first subclaster were grouped 13 genotypes and the second subcluster involved 10 genotypes. The first subcluster also included the genotype Bagou from France, in which were detected novel high - molecular - weight glutenin subunits using SDS-PAGE. Using 6 RAPD markers only two wheat genotypes have not been distinguished. Through that the information about genetic similarity and differences will be helpful to avoid any possibility of elite germplasm becoming genetically uniform

  19. Genotypes and antibiotic resistance of canine Campylobacter jejuni isolates.

    Science.gov (United States)

    Amar, Chantal; Kittl, Sonja; Spreng, David; Thomann, Andreas; Korczak, Bożena M; Burnens, André P; Kuhnert, Peter

    2014-01-10

    Campylobacter jejuni is the most important cause of bacterial gastroenteritis in humans. It is a commensal in many wild and domestic animals, including dogs. Whereas genotypes of human and chicken C. jejuni isolates have been described in some detail, only little information on canine C. jejuni genotypes is available. To gain more information on genotypes of canine C. jejuni and their zoonotic potential, isolates from routine diagnostics of diarrheic dogs as well as isolates of a prevalence study in non-diarrheic dogs were analyzed. Prevalence of thermophilic Campylobacter among non-diarrheic dogs was 6.3% for C. jejuni, 5.9% for Campylobacter upsaliensis and 0.7% for Campylobacter coli. The C. jejuni isolates were genotyped by multi locus sequence typing (MLST) and flaB typing. Resistance to macrolides and quinolones was genetically determined in parallel. Within the 134 genotyped C. jejuni isolates 57 different sequence types (ST) were found. Five STs were previously unrecognized. The most common STs were ST-48 (11.2%), ST-45 (10.5%) and ST-21 (6.0%). Whereas no macrolide resistance was found, 28 isolates (20.9%) were resistant to quinolones. ST-45 was significantly more prevalent in diarrheic than in non-diarrheic dogs. Within the common time frame of isolation 94% of the canine isolates had a ST that was also found in human clinical isolates. In conclusion, prevalence of C. jejuni in Swiss dogs is low but there is a large genetic overlap between dog and human isolates. Given the close contact between human and dogs, the latter should not be ignored as a potential source of human campylobacteriosis. PMID:24210812

  20. Subtyping novel zoonotic pathogen Cryptosporidium chipmunk genotype I.

    Science.gov (United States)

    Guo, Yaqiong; Cebelinski, Elizabeth; Matusevich, Christine; Alderisio, Kerri A; Lebbad, Marianne; McEvoy, John; Roellig, Dawn M; Yang, Chunfu; Feng, Yaoyu; Xiao, Lihua

    2015-05-01

    Cryptosporidium chipmunk genotype I is an emerging zoonotic pathogen in humans. The lack of subtyping tools makes it impossible to determine the role of zoonotic transmission in epidemiology. To identify potential subtyping markers, we sequenced the genome of a human chipmunk genotype I isolate. Altogether, 9,509,783 bp of assembled sequences in 853 contigs were obtained, with an N50 of 117,886 bp and >200-fold coverage. Based on the whole-genome sequence data, two genetic markers encoding the 60-kDa glycoprotein (gp60) and a mucin protein (ortholog of cgd1_470) were selected for the development of a subtyping tool. The tool was used for characterizing chipmunk genotype I in 25 human specimens from four U.S. states and Sweden, one specimen each from an eastern gray squirrel, a chipmunk, and a deer mouse, and 4 water samples from New York. At the gp60 locus, although different subtypes were seen among the animals, water, and humans, the 15 subtypes identified differed mostly in the numbers of trinucleotide repeats (TCA, TCG, or TCT) in the serine repeat region, with only two single nucleotide polymorphisms in the nonrepeat region. Some geographic differences were found in the subtype distribution of chipmunk genotype I from humans. In contrast, only two subtypes were found at the mucin locus, which differed from each other in the numbers of a 30-bp minisatellite repeat. Thus, Cryptosporidium chipmunk genotype I isolates from humans and wildlife are genetically similar, and zoonotic transmission might play a potential role in human infections. PMID:25762767