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Sample records for sp mouse genotype

  1. High-throughput mouse genotyping using robotics automation.

    Science.gov (United States)

    Linask, Kaari L; Lo, Cecilia W

    2005-02-01

    The use of mouse models is rapidly expanding in biomedical research. This has dictated the need for the rapid genotyping of mutant mouse colonies for more efficient utilization of animal holding space. We have established a high-throughput protocol for mouse genotyping using two robotics workstations: a liquid-handling robot to assemble PCR and a microfluidics electrophoresis robot for PCR product analysis. This dual-robotics setup incurs lower start-up costs than a fully automated system while still minimizing human intervention. Essential to this automation scheme is the construction of a database containing customized scripts for programming the robotics workstations. Using these scripts and the robotics systems, multiple combinations of genotyping reactions can be assembled simultaneously, allowing even complex genotyping data to be generated rapidly with consistency and accuracy. A detailed protocol, database, scripts, and additional background information are available at http://dir.nhlbi.nih.gov/labs/ldb-chd/autogene/.

  2. Genetic characterization and improved genotyping of the dysferlin-deficient mouse strain Dysf (tm1Kcam).

    Science.gov (United States)

    Wiktorowicz, Tatiana; Kinter, Jochen; Kobuke, Kazuhiro; Campbell, Kevin P; Sinnreich, Michael

    2015-01-01

    Mouse models of dysferlinopathies are valuable tools with which to investigate the pathomechanisms underlying these diseases and to test novel therapeutic strategies. One such mouse model is the Dysf (tm1Kcam) strain, which was generated using a targeting vector to replace a 12-kb region of the dysferlin gene and which features a progressive muscular dystrophy. A prerequisite for successful animal studies using genetic mouse models is an accurate genotyping protocol. Unfortunately, the lack of robustness of currently available genotyping protocols for the Dysf (tm1Kcam) mouse has prevented efficient colony management. Initial attempts to improve the genotyping protocol based on the published genomic structure failed. These difficulties led us to analyze the targeted locus of the dysferlin gene of the Dysf (tm1Kcam) mouse in greater detail. In this study we resequenced and analyzed the targeted locus of the Dysf (tm1Kcam) mouse and developed a novel PCR protocol for genotyping. We found that instead of a deletion, the dysferlin locus in the Dysf (tm1Kcam) mouse carries a targeted insertion. This genetic characterization enabled us to establish a reliable method for genotyping of the Dysf (tm1Kcam) mouse, and thus has made efficient colony management possible. Our work will make the Dysf (tm1Kcam) mouse model more attractive for animal studies of dysferlinopathies.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  4. DRD4 genotype predicts longevity in mouse and human.

    Science.gov (United States)

    Grady, Deborah L; Thanos, Panayotis K; Corrada, Maria M; Barnett, Jeffrey C; Ciobanu, Valentina; Shustarovich, Diana; Napoli, Anthony; Moyzis, Alexandra G; Grandy, David; Rubinstein, Marcelo; Wang, Gene-Jack; Kawas, Claudia H; Chen, Chuansheng; Dong, Qi; Wang, Eric; Volkow, Nora D; Moyzis, Robert K

    2013-01-02

    Longevity is influenced by genetic and environmental factors. The brain's dopamine system may be particularly relevant, since it modulates traits (e.g., sensitivity to reward, incentive motivation, sustained effort) that impact behavioral responses to the environment. In particular, the dopamine D4 receptor (DRD4) has been shown to moderate the impact of environments on behavior and health. We tested the hypothesis that the DRD4 gene influences longevity and that its impact is mediated through environmental effects. Surviving participants of a 30-year-old population-based health survey (N = 310; age range, 90-109 years; the 90+ Study) were genotyped/resequenced at the DRD4 gene and compared with a European ancestry-matched younger population (N = 2902; age range, 7-45 years). We found that the oldest-old population had a 66% increase in individuals carrying the DRD4 7R allele relative to the younger sample (p = 3.5 × 10(-9)), and that this genotype was strongly correlated with increased levels of physical activity. Consistent with these results, DRD4 knock-out mice, when compared with wild-type and heterozygous mice, displayed a 7-9.7% decrease in lifespan, reduced spontaneous locomotor activity, and no lifespan increase when reared in an enriched environment. These results support the hypothesis that DRD4 gene variants contribute to longevity in humans and in mice, and suggest that this effect is mediated by shaping behavioral responses to the environment.

  5. Sp5 induces the expression of Nanog to maintain mouse embryonic stem cell self-renewal.

    Science.gov (United States)

    Tang, Ling; Wang, Manman; Liu, Dahai; Gong, Mengting; Ying, Qi-Long; Ye, Shoudong

    2017-01-01

    Activation of signal transducer and activator of transcription 3 (STAT3) by leukemia inhibitory factor (LIF) maintains mouse embryonic stem cell (mESC) self-renewal. Our previous study showed that trans-acting transcription factor 5 (Sp5), an LIF/STAT3 downstream target, supports mESC self-renewal. However, the mechanism by which Sp5 exerts these effects remains elusive. Here, we found that Nanog is a direct target of Sp5 and mediates the self-renewal-promoting effect of Sp5 in mESCs. Overexpression of Sp5 induced Nanog expression, while knockdown or knockout of Sp5 decreased the Nanog level. Moreover, chromatin immunoprecipitation (ChIP) assays showed that Sp5 directly bound to the Nanog promoter. Functional studies revealed that knockdown of Nanog eliminated the mESC self-renewal-promoting ability of Sp5. Finally, we demonstrated that the self-renewal-promoting function of Sp5 was largely dependent on its zinc finger domains. Taken together, our study provides unrecognized functions of Sp5 in mESCs and will expand our current understanding of the regulation of mESC pluripotency.

  6. An enzyme-linked immunosorbent assay (ELISA) for quantification of mouse surfactant protein D (SP-D)

    DEFF Research Database (Denmark)

    Hansen, Soren; Schmidt, Vivi; Steffensen, Maria Abildgaard

    2008-01-01

    characterized and validated for use in sandwich enzyme-linked immunosorbent assay (ELISA). Based on two of these, we established an ELISA that allows for measurements of mouse SP-D in various body fluids. The final ELISA was optimized and calibrated with a standard of purified recombinant mouse SP-D, which......Surfactant protein D (SP-D) is a pattern recognition molecule of the collectin family of C-type lectins. It is found in the airways and at mucosal surfaces. SP-D is part of the innate immune system where it neutralizes and leads to elimination of microorganisms. It regulates the functions of other...... innate immune cells, such as macrophages and neutrophils. It also modulates the adaptive immune response by interacting with antigen-presenting cells and T cells. Monoclonal anti-mouse-SP-D antibodies were raised from SP-D deficient mice using recombinant SP-D as antigen. Ten monoclonal antibodies were...

  7. Electroretinographic genotype-phenotype correlations for mouse and man at the dmd/DMD locus

    Energy Technology Data Exchange (ETDEWEB)

    Millers, D.M.; Weleber, R.G.; Woodward, W.R. [Oregon Health Sciences Univ., Portland, OR (United States)] [and others

    1994-09-01

    Reduced or absent b-waves in the dark-adapted electroretinogram (ERG) of Duchenne and Becker muscular dystrophy (DMD/BMD) patients led to the identification of dystrophin in human retina and the proposal that it plays a role in retinal electrophysiology. Study of a large group of Duchenne and Becker muscular dystrophy males to determine their ocular characteristics indicated that there were position-specific effects of deletions, with 3{prime} defects associated with severe electroretinographic changes, whereas some 5{prime} patients demonstrated less severe, or even normal, ERGs. We studied the mdx mouse, a model with X-linked muscular dystrophy and defective full-length dystrophin, which failed to show any ERG abnormalities. Given the presence of alternate isoforms of dystrophin in retina, and the 5{prime} deletion DMD/BMD patients with normal ERGs, we studied mouse models with differing dystrophin mutations (mdx{sup Cv3}, mdx{sup Cv5}) to determine the usefulness of alternate strains as models for the visual effects of dystropin. Abnormal ERGs similar to those seen in DMD/BMS patients exist in the mdx{sup Cv3} strain of muscular dystrophy mice. Normal ERGs were found the mdx{sup Cv5} strain. The mutations in the mdx and mdx{sup Cv5} mice have been mapped to the 5{prime} end of the dmd gene, while the mutation in the mdx{sup Cv3} mouse is in the 3{prime} end. Thus, there are position effects of the gene defect on the ERG phenotype that are conserved in the mouse. Such genotype-phenotype correlations may reflect differential expression of shorter isoforms of dystrophin.

  8. A rapid genotyping method for an obligate fungal pathogen, Puccinia striiformis f.sp. tritici, based on DNA extraction from infected leaf and Multiplex PCR genotyping

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    Enjalbert Jérôme

    2011-07-01

    Full Text Available Abstract Background Puccinia striiformis f.sp. tritici (PST, an obligate fungal pathogen causing wheat yellow/stripe rust, a serious disease, has been used to understand the evolution of crop pathogen using molecular markers. However, numerous questions regarding its evolutionary history and recent migration routes still remains to be addressed, which need the genotyping of a large number of isolates, a process that is limited by both DNA extraction and genotyping methods. To address the two issues, we developed here a method for direct DNA extraction from infected leaves combined with optimized SSR multiplexing. Findings We report here an efficient protocol for direct fungal DNA extraction from infected leaves, avoiding the costly and time consuming step of spore multiplication. The genotyping strategy we propose, amplified a total of 20 SSRs in three Multiplex PCR reactions, which were highly polymorphic and were able to differentiate different PST populations with high efficiency and accuracy. Conclusion These two developments enabled a genotyping strategy that could contribute to the development of molecular epidemiology of yellow rust disease, both at a regional or worldwide scale.

  9. The loss-of-allele assay for ES cell screening and mouse genotyping.

    Science.gov (United States)

    Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

    2010-01-01

    Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction

  10. HFE Genotype Restricts the Response to Paraquat in a Mouse Model of Neurotoxicity.

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    Nixon, Anne M; Meadowcroft, Mark D; Neely, Elizabeth B; Snyder, Amanda M; Purnell, Carson J; Wright, Justin; Lamendella, Regina; Nandar, Wint; Huang, Xuemei; Connor, James R

    2018-05-01

    Parkinson's disease is marked clinically by motor dysfunction and pathologically by dopaminergic cell loss in the substantia nigra and iron accumulation in the substantia nigra. The driver underlying iron accumulation remains unknown and could be genetic or environmental. The HFE protein is critical for the regulation of cellular iron uptake. Mutations within this protein are associated with increased iron accumulation including in the brain. We have focused on the commonly occurring H63D variant of the HFE gene as a disease modifier in a number of neurodegenerative diseases. To investigate the role of H63D HFE genotype, we generated a mouse model in which the wild-type (WT) HFE gene is replaced by the H67D gene variant (mouse homolog of the human H63D gene variant). Using paraquat toxicity as the model for Parkinson's disease, we found that WT mice responded as expected with significantly greater motor function, loss of tyrosine hydroxylase staining and increase microglial staining in the substantia nigra, and an increase in R 2 relaxation rate within the substantia nigra of the paraquat-treated mice compared to their saline-treated counterparts. In contrast, the H67D mice showed a remarkable resistance to paraquat treatment; specifically differing from the WT mice with no changes in motor function or changes in R 2 relaxation rates following paraquat exposure. At baseline, there were differences between the H67D HFE mice and WT mice in gut microbiome profile and increased L-ferritin staining in the substantia nigra that could account for the resistance to paraquat. Of particular note, the H67D HFE mice regardless of whether or not they were treated with paraquat had significantly less tyrosine hydroxylase immunostaining than WT. Our results clearly demonstrate that the HFE genotype impacts the expression of tyrosine hydroxylase in the substantia nigra, the gut microbiome and the response to paraquat providing additional support that the HFE genotype is a disease

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  12. Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.

    Science.gov (United States)

    Osawa, Ro; Fujisawa, Tomohiko; Pukall, Rüdiger

    2006-07-01

    A Gram-positive, rod-shaped, non-endospore-forming bacterium, strain ASB1(T), able to degrade tannin, was isolated from faeces of the Japanese large wood mouse, Apodemus speciosus. Comparative analysis of the 16S rRNA gene sequence revealed that the strain could be assigned as a member of the genus Lactobacillus. The nearest phylogenetic neighbours were determined as Lactobacillus animalis DSM 20602(T) (98.9 % 16S rRNA gene sequence similarity) and Lactobacillus murinus ASF 361 (98.9 %). Subsequent polyphasic analysis, including automated ribotyping and DNA-DNA hybridization experiments, confirmed that the isolate represents a novel species, for which the name Lactobacillus apodemi sp. nov. is proposed. The DNA G+C content of the novel strain is 38.5 mol%. The cell-wall peptidoglycan is of type A4alpha L-lys-D-asp. The type strain is ASB1(T) (=DSM 16634(T)=CIP 108913(T)).

  13. Bat ticks revisited: Ixodes ariadnae sp. nov. and allopatric genotypes of I. vespertilionis in caves of Hungary.

    Science.gov (United States)

    Hornok, Sándor; Kontschán, Jenő; Kováts, Dávid; Kovács, Richárd; Angyal, Dorottya; Görföl, Tamás; Polacsek, Zsolt; Kalmár, Zsuzsa; Mihalca, Andrei D

    2014-04-27

    In Europe two ixodid bat tick species, Ixodes vespertilionis and I. simplex were hitherto known to occur. Bat ticks were collected from cave walls and bats in Hungary. Their morphology and genotypes were compared with microscopy and conventional PCR (followed by sequencing), respectively. A year-round activity of I. vespertilionis was observed. Molecular analysis of the cytochrome oxidase subunit I (COI) gene of twenty ticks from different caves showed that the occurrence of the most common genotype was associated with the caves close to each other. A few specimens of a morphologically different tick variant were also found and their COI analysis revealed only 86-88% sequence homology with I. simplex and I. vespertilionis, respectively. The microenvironment of caves (well separated from each other) appears to support the existence of allopatric I. vespertilionis COI genotypes, most likely related to the distance between caves and to bat migration over-bridging certain caves. The name I. ariadnae sp. nov. is given to the new tick species described here for the first time.

  14. Bound volatile precursors in genotypes in the pedigree of 'Marion' blackberry (Rubus sp.).

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    Du, Xiaofen; Finn, Chad E; Qian, Michael C

    2010-03-24

    Glycosidically bound volatiles and precursors in genotypes representing the pedigree for 'Marion' blackberry were investigated over two growing seasons. The volatile precursors were isolated using a C18 solid-phase extraction column. After enzymatic hydrolysis, the released volatiles were analyzed using stir bar sorptive extraction gas chromatography-mass spectrometry (GC-MS) and direct microvial insert thermal desorption GC-MS. The most abundant volatile precursors in the genotypes were alcohols, followed by shikimic acid derivatives. High amounts of furanone glycosides were also detected, while norisoprenoids only existed in a small amount in blackberries. The volatile precursor composition in the genotypes in the 'Marion' pedigree was very similar to their free volatile distribution. 'Logan' and 'Olallie' predominantly had bound norisoprenoids. Wild 'Himalaya' predominated with terpene alcohol and furaneol glycosides, whereas 'Santiam' and 'Chehalem' contained a high level of terpene alcohol glycosides. A similar inheritance pattern was also observed for some volatile precursors in the genotypes in the 'Marion' pedigree. A high content of linalool, hydroxylinalool, and alpha-ionol glycosides in 'Olallie' and a low content in 'Chehalem' resulted in a moderate level in their offspring 'Marion', while a low content of (E)-linalool oxide precursor in 'Olallie' and a high content in 'Chehalem' also resulted in a moderate level in 'Marion'. However, the concentration of furaneol glycosides in 'Marion' exceeded that of its two parents.

  15. Mel-18 controls the enrichment of tumor-initiating cells in SP fraction in mouse breast cancer.

    Science.gov (United States)

    Janakiraman, Harinarayanan; Nobukiyo, Asako; Inoue, Hiroko; Kanno, Masamoto

    2011-06-01

    Side population (SP) cell analysis has been used to identify and isolate a minor population of cells with stem cell properties in normal tissues and in many cancers including breast cancer cells. However, the molecular mechanisms that operate in tumor-initiating cells (TICs) in SP fraction remain unclear. The Polycomb group genes, including Bmi1 and Mel-18, have been implicated in the maintenance of hematopoietic stem cells (HSCs) and suggested to be oncogenic and tumor suppressive, respectively, in breast cancer. In this study, we determined the critical role of Mel-18 in the enrichment mechanisms of TICs with the SP phenotype in a mouse breast cancer cell line, MMK3, that was established from a breast cancer developed spontaneously in Mel-18+/- mice. The Mel-18 protein expression level significantly correlates to the percentage of SP fraction in the mouse breast cancer cell line MMK3 series. The comparison between MMK3V3 (V3) cells containing one copy of the Mel-18 gene and MMK3S2 (S2) cells having twice the amount of Mel-18 expression clearly demonstrates the above relationship. Similar results obtained with the percentage of ALDH+ cells in V3 and S2 further confirmed the correlation between protein expression level of Mel-18 and the TICs. More importantly, transplantation of SP and non-SP cells of V3 and S2 cells into the NOD/SCID mice clearly showed that the heterozygous level of Mel-18 leads to the disappearance of enrichment of TICs into SP fraction in vivo. Stem cell pathway focused gene expression profiling of V3 and S2 cells revealed that the genes Abcg2, Aldh1a1 and Dhh were highly down-regulated in V3 compared to S2. These results indicate that the precise Mel-18 expression level controls TIC enrichment mechanisms through the regulation of channel molecule of Abcg2 and functional TIC marker of Aldhlal. In conclusion, our findings revealed the significance of fine-tuning mechanisms for Mel-18 protein expression level in the maintenance of TIC into SP

  16. Biochemical and molecular characterization of the antioxidative system of Coffea sp. under cold conditions in genotypes with contrasting tolerance.

    Science.gov (United States)

    Fortunato, Ana S; Lidon, Fernando C; Batista-Santos, Paula; Leitão, António Eduardo; Pais, Isabel P; Ribeiro, Ana I; Ramalho, José Cochicho

    2010-03-15

    Low positive temperature (chilling) is frequently linked to the promotion of oxidative stress conditions, and is of particular importance in the coffee plant due to its severe impact on growth, development, photosynthesis and production. Nevertheless, some acclimation ability has been reported within the Coffea genus, and is possibly related to oxidative stress control. Using an integrated biochemical and molecular approach, the characterization of the antioxidative system of genotypes with different cold acclimation abilities was performed. Experiments were carried out using 1.5-year-old coffee seedlings of Coffea canephora cv. Apoatã, C. arabica cv. Catuaí, C. dewevrei and 2 hybrids, Icatu (C. arabicaxC. canephora) and Piatã (C. dewevreixC. arabica) subjected to a gradual cold treatment and a recovery period. Icatu showed the greatest ability to control oxidative stress, as reflected by the enhancement of several antioxidative components (Cu,Zn-SOD and APX activities; ascorbate, alpha-tocopherol and chlorogenic acids (CGAs) contents) and lower reactive oxygen species contents (H(2)O(2) and OH). Gene expression studies show that GRed, DHAR and class III and IV chitinases might also be involved in the cold acclimation ability of Icatu. Catuaí showed intermediate acclimation ability through the reinforcement of some antioxidative molecules, usually to a lesser extent than that observed in Icatu. On the other hand, C. dewevrei showed the poorest response in terms of antioxidant accumulation, and also showed the greatest increase in OH values. The difference in the triggering of antioxidative traits supports the hypothesis of its importance to cold (and photoinhibition) tolerance in Coffea sp. and could provide a useful probe to identify tolerant genotypes. Copyright 2009 Elsevier GmbH. All rights reserved.

  17. Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation.

    Science.gov (United States)

    Sun, Lu; Zhu, Ganghui; Liao, Xiaoyong; Yan, Xiulan

    2017-11-01

    The effects of two Pteris vittata L. accessions and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) on arsenic (As) uptake and phenanthrene dissipation were studied. The Alcaligenes sp. survived in the rhizosphere and improved soil As bioavailability with co-exposure. However, bacterial inoculation altered Pteris vittata L. stress tolerance, and substantially affected the As distribution in the rhizosphere of the two P. vittata accessions. Bacterial inoculation was beneficial to protect the Guangxi accession against the toxic effects, and significantly increased plant As and phenanthrene removal ratios by 27.8% and 2.89%, respectively. In contrast, As removal was reduced by 29.8% in the Hunan accession, when compared with corresponding non-inoculated treatments. We conclude that plant genotype selection is critically important for successful microorganism-assisted phytoremediation of soil co-contaminated with As and PAHs, and appropriate genotype selection may enhance remediation efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

    NARCIS (Netherlands)

    Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

    2013-01-01

    Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

  19. Wnt/β-catenin and LIF-Stat3 signaling pathways converge on Sp5 to promote mouse embryonic stem cell self-renewal.

    Science.gov (United States)

    Ye, Shoudong; Zhang, Dongming; Cheng, Fei; Wilson, Daniel; Mackay, Jeffrey; He, Kan; Ban, Qian; Lv, Feng; Huang, Saifei; Liu, Dahai; Ying, Qi-Long

    2016-01-15

    Activation of leukemia inhibitor factor (LIF)-Stat3 or Wnt/β-catenin signaling promotes mouse embryonic stem cell (mESC) self-renewal. A myriad of downstream targets have been identified in the individual signal pathways, but their common targets remain largely elusive. In this study, we found that the LIF-Stat3 and Wnt/β-catenin signaling pathways converge on Sp5 to promote mESC self-renewal. Forced Sp5 expression can reproduce partial effects of Wnt/β-catenin signaling but mimics most features of LIF-Stat3 signaling to maintain undifferentiated mESCs. Moreover, Sp5 is able to convert mouse epiblast stem cells into a naïve pluripotent state. Thus, Sp5 is an important component of the regulatory network governing mESC naïve pluripotency. © 2016. Published by The Company of Biologists Ltd.

  20. Myostatin genotype regulates muscle-specific miRNA expression in mouse pectoralis muscle

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    Cheng Ye

    2010-11-01

    Full Text Available Abstract Background Loss of functional Myostatin results in a dramatic increase in skeletal muscle mass. It is unknown what role miRNAs play in Myostatin mediated repression of skeletal muscle mass. We hypothesized that Myostatin genotype would be associated with the differential expression of miRNAs in skeletal muscle. Findings Loss of functional Myostatin resulted in a significant increase (p .2 on miR-24 expression level. Myostatin genotype did not affect the expression level of MyoD or Myogenin (P > 0.5. Conclusions Myostatin may regulates the expression of miRNAs such as miR-133a, miR-133b, miR-1, and miR-206 in skeletal muscle as it has been observed that the expression of those miRNAs are significantly higher in myostatin null mice compared to wild type and heterozygous mice. In contrast, expression of myogenic factors such as MyoD or Myogenin has not been affected by myostatin in the muscle tissue.

  1. Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease.

    Science.gov (United States)

    Bloom, Seth M; Bijanki, Vinieth N; Nava, Gerardo M; Sun, Lulu; Malvin, Nicole P; Donermeyer, David L; Dunne, W Michael; Allen, Paul M; Stappenbeck, Thaddeus S

    2011-05-19

    The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here, we fulfilled Koch's postulates in host-genotype-specific fashion using a mouse model of IBD with human-relevant disease-susceptibility mutations. From screening experiments we isolated common commensal Bacteroides species, introduced them into antibiotic-pretreated mice, and quantitatively reisolated them in culture. The bacteria colonized IBD-susceptible and -nonsusceptible mice equivalently, but induced disease exclusively in susceptible animals. Conversely, commensal Enterobacteriaceae were >100-fold enriched during spontaneous disease, but an Enterobacteriaceae isolate failed to induce disease in antibiotic-pretreated mice despite robust colonization. We thus demonstrate that IBD-associated microbiota alterations do not necessarily reflect underlying disease etiology. These findings establish important experimental criteria and a conceptual framework for understanding microbial contributions to IBD. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease

    Science.gov (United States)

    Bloom, Seth M.; Bijanki, Vinieth N.; Nava, Gerardo M.; Sun, Lulu; Malvin, Nicole P.; Donermeyer, David L.; Dunne, W. Michael; Allen, Paul M.; Stappenbeck, Thaddeus S.

    2011-01-01

    SUMMARY The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here we fulfilled Koch’s postulates in host-genotype-specific fashion using a mouse model of IBD with human-relevant disease-susceptibility mutations. From screening experiments we isolated common commensal Bacteroides species, introduced them into antibiotic-pretreated mice, and quantitatively re-isolated them in culture. The bacteria colonized IBD-susceptible and non-susceptible mice equivalently, but induced disease exclusively in susceptible animals. Conversely, commensal Enterobacteriaceae were >100-fold enriched during spontaneous disease but an Enterobacteriaceae isolate failed to induce disease in antibiotic-pretreated mice despite robust colonization. We thus demonstrate that IBD-associated microbiota alterations do not necessarily reflect underlying disease etiology. These findings establish important experimental criteria and a conceptual framework for understanding microbial contributions to IBD. PMID:21575910

  3. Guerrerostrongylus marginalis n. sp. (Trichostrongyloidea: Heligmonellidae from the Guianan arboreal mouse (Oecomys auyantepui from French Guiana

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    Weirich Jessica M.

    2016-01-01

    Full Text Available Based on the number and arrangement of cuticular ridges and configuration of the dorsal ray, nematode specimens collected from the small intestine of eight Guianan arboreal mice, Oecomys auyantepui (Rodentia: Sigmodontinae, in French Guiana are herein described and characterized. Guerrerostrongylus marginalis n. sp. (Heligmosomoidea: Heligmonellidae shows a synlophe consisting of more than 40 ridges and a unique bursal arrangement with ray 8 (externo-dorsal extending to the edge of the bursal margin, and appearing more prominent than the dorsal ray. This bursal arrangement is common in members of Hassalstrongylus Durette-Desset, 1971, but uncommon in the other four species in Guerrerostrongylus Sutton & Durette-Desset, 1991. The placement of the new species in Guerrerostrongylus is based on the number and nature of cuticular ridges and the ray arrangement and symmetry of the caudal bursa. Diagnostic characteristics of Guerrerostrongylus marginalis n. sp. include the length of ray 8 relative to bursal margin, the relative size of the spicules and vestibule, and the number of eggs in the uterus. We propose an amendment to the generic diagnosis of Guerrerostrongylus to modify the characters of the long rays 6 (postero-lateral, rays 8 (externo-dorsal, and dorsal ray as diagnostic, since at least ray 6 appears to be short in two different species in the genus, namely G. ulysi Digiani, Notarnicola & Navone, 2012 and G. marginalis n. sp.

  4. Molecular analysis of Ixodes rugicollis, Candidatus Neoehrlichia sp. (FU98) and a novel Babesia genotype from a European badger (Meles meles).

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    Hornok, Sándor; Trauttwein, Klaudia; Takács, Nóra; Hodžić, Adnan; Duscher, Georg Gerhard; Kontschán, Jenő

    2017-01-01

    The European badger (Meles meles) is a widespread mammal in most countries of the European continent, with increasingly recognized veterinary/medical importance owing to its preferred habitats (including pastures and urban environments), broad spectrum of food items, and role as a game hunting target. However, ticks and tick-borne pathogens associated with badgers are only partly known, and most of them have not yet been analysed with molecular biological methods The aim of this study was to perform molecular taxonomic analysis of ticks collected from a road-killed European badger, as well as to molecularly investigate its ticks and blood sample for the presence of Anaplasmataceae and piroplasms. Ticks from the badger were morphologically identified as females of Ixodes rugicollis. Based on its cytochrome oxidase subunit I (COI) and 16S rRNA sequences, I. rugicollis phylogenetically clustered together with I. lividus and I. arboricola, i.e. other members of the subgenus Pholeoixodes. The blood sample of the badger contained the DNA of Candidatus Neoehrlichia sp. (FU98) recently identified in red fox in Austria and the Czech Republic. This genotype is most closely related to Ca. N. lotoris (from raccoons in North America), and has lower sequence identity with the I. ricinus-transmitted zoonotic agent, Ca. N. mikurensis found in Eurasia. In the blood of the badger and in one female I. rugicollis, the DNA of a new Babesia genotype was also present, which differed from a piroplasm detected in M. meles in Spain, and clustered phylogenetically in the B. microti clade. Phylogenetic analysis of I. rugicollis (based on two genetic markers) confirms its status in subgenus Pholeoixodes. Ca. Neoehrlichia sp. (FU98) was identified for the first time in M. meles and in Hungary. In addition, a molecularly previously not yet characterized Babesia genotype occurs in badgers in Central Europe. Copyright © 2016 Elsevier GmbH. All rights reserved.

  5. Genotype-dependent activity of tryptophan hydroxylase-2 determines the response to citalopram in a mouse model of depression.

    Science.gov (United States)

    Cervo, Luigi; Canetta, Alessandro; Calcagno, Eleonora; Burbassi, Silvia; Sacchetti, Giuseppina; Caccia, Silvio; Fracasso, Claudia; Albani, Diego; Forloni, Gianluigi; Invernizzi, Roberto W

    2005-09-07

    Polymorphism of tryptophan hydroxylase, the rate-limiting enzyme in the synthesis of brain serotonin (5-HT), is associated with less synthesis of brain 5-HT in DBA/2J and BALB/c than in C57BL/6J and 129/Sv mice. We selected the forced swimming test, a mouse model used to assess the antidepressant potential of drugs, and neurochemical techniques to study strain differences in the response to citalopram, a selective 5-HT reuptake inhibitor. Citalopram reduced immobility time in C57BL/6J and 129/Sv mice but had no such effect in DBA/2J and BALB/c mice. The drug reduced accumulation of 5-hydroxytryptophan (5-HTP), an indicator of 5-HT synthesis, in C57BL/6J and 129/Sv mice but much less in DBA/2J and BALB/c mice. Pretreatment with tryptophan raised 5-HTP accumulation and reinstated the antidepressant-like effect of citalopram in DBA/2J and BALB/c mice, whereas pharmacological inhibition of 5-HT synthesis prevented the effect of citalopram in C57BL/6J and 129/Sv mice. Because there were no strain differences in catecholamine synthesis, locomotor activity, and brain levels of citalopram at the end of the behavioral test, the results suggest that the failure of citalopram to reduce immobility time in DBA/2J and BALB/c mice is attributable to genotype-dependent impairment of 5-HT synthesis. Interstrain comparisons could probably be a useful strategy for understanding the mechanisms underlying the response to selective serotonin reuptake inhibitors.

  6. Formation of protein hydroperoxides in mouse myeloma cell line Sp2/0-Ag14

    International Nuclear Information System (INIS)

    Du, J.; Gebicki, J.

    2000-01-01

    Full text: Free radicals generated by normal cell metabolism or from environmental sources can cause damage to DNA, proteins and lipids-the important components of mammalian cells. As function molecules and cell constituent, the abundant and easily available nature of proteins make them the prime target of free radicals. Previous research in our lab have shown protein hydroperoxides in turn can react with other proteins, result in the lose of enzymatic function of the later, or crosslink with DNA, which may interfere gene transcription if not repaired. The formation of protein hydroperoxides in Sp2/0-Ag14 cells was induced by exposing them to peroxyl radical or gamma radiation. Cells were then washed and precipitated by tichloroacetic acid. Concentration of protein and lipid hydroperoxides were measured by FOX assay. No significant amount of lipid peroxides were detected. The effects of reducing agents dithiothreitol, glutathione, sodium borohydride identified the nature of protein hydroperoxides. The life time of cell protein hydroperoxides is about 2 hours

  7. TCDD-induced transcriptional profiles in different mouse strains that have an identical AhR genotype

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Qing; Suzuki, Junko S.; Tohyama, Chiharu; Ohsako, Seiichiroh [Environmental Health Sciences Division, National Institute for Environmental Studies, Onogawa, Tsukuba (Japan); Takei, Teiji [Environmental Health and Safety Division, Ministry of the Environment, Kasumigaseki, Tokyo (Japan); Lin, Tinmin; Peterson, R.E. [Wisconsin Univ., Wisconsin, MA (United States). School of Pharmacy and Molecular and Environmental Toxicology Center

    2004-09-15

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that is known to cause hepatotoxicity, teratogenicity and carcinogenicity. A characteristic feature in the toxicity of TCDD is exceptionally large differences in susceptibility among animal species or even strains belonging to the same species. These strain differences in susceptibility to TCDD have now been elucidated to be due to the difference in ligand binding affinity or transcriptional activity of the aryl hydrocarbon receptor (AhR). Actually the C57BL/6 type AhR (AhR{sup b}) showed 6-fold higher ligand binding affinity than the DBA/2 type AhR (AhR{sup d}). The H/W rat AhR has a C-terminal truncation of the transactivating domain compared to the L-E rat AhR. On the other hand, there is considerable species variability in response sensitivity to TCDD that cannot be ascribed simply to polymorphisms of the AhR gene. A non-AhR gene susceptibility loci for hepatic porphyria has been observed in mice treated with iron compounds prior to TCDD injection by using a quantitative trait locus analysis of an F2 intercross between susceptible C57BL/6 and resistant DBA/2 stains. In the rat, a gene B with Han/Wistar type AhR is likely to be involved in resistance to TCDD lethality. These observations suggest that other modulating genes, so-called ''modifier genes'', have profound effects on the AhR-mediated gene expression phenotype. Based on the nucleotide sequence of the AhR coding region, the BALB/c, CBA/J, and C3H/He mouse strains are clustered together on a single branch. In the present study, we try to confirm the existence of modifiers by using microarray analysis to examine hepatic gene expression after TCDD exposure in BALB/c, CBA/J, and C3H/He mice. To recognize the existence of a modifier besides the AhR, it is a prerequisite experimental condition that the analyzed strains have an identical AhR genotype. Therefore, we selected BALB/c, CBA/J, and C3H/He mice as the model

  8. Phenotypic and genotypic Characterization of facultative and obligate Alkalophilic Bacillus sp. isolated from Saudi Arabia alkaline soils

    Directory of Open Access Journals (Sweden)

    Assaeedi Abdulrahman

    2014-10-01

    Full Text Available Isolation and identification of new alkalophilic Bacillus strains have been increasing interest due to their possessing valuable and commercially interesting enzymes. In the present study, a total six obligate and facultative alkalophilic isolates were isolated from desert soil around the Al-qunfotha city, Saudi Arabia. All isolates were phenotypically and genotypically characterized. Among these isolates; AS3, AS4, AS5 and AS6 could grow at pH 9, 10, 11 and 12, but could not grow at pH 7, indicates that these isolates are obligate alkalophiles. While, isolates AS1 and AS2 grew at pH ranged from 7 to 10, but could not grow at pH 11 and 12, suggesting that they could be facultative alkalophiles. All isolates could hydrolyze casein and starch, indicating that they possess interesting amylase and protease enzymes. Based on 16S rDNA data, the phylogenetic analysis of these strains showed that all six alkalophilic Bacillus belonged to Bacillus cohnii with 99% similarity. The nucleotide sequences of 16S rRNA gene for the six isolates were deposited in a Gene-bank under accession numbers; KP053301, KP053302, KP053303, KP053304, KP053305 and KP053306, respectively.

  9. Molecular evidence of the multiple genotype infection of a wild Hokkaido brown bear (Ursus arctos yesoensis) by Babesia sp. UR1.

    Science.gov (United States)

    Jinnai, Michio; Kawabuchi-Kurata, Takako; Tsuji, Masayoshi; Nakajima, Rui; Hirata, Haruyuki; Fujisawa, Kohei; Shiraki, Hiromi; Asakawa, Mitsuhiko; Nasuno, Toyohiko; Ishihara, Chiaki

    2010-10-11

    A frozen-stored blood clot of a wild brown bear cub Ursus arctos yesoensis that had been captured in Hokkaido, Japan was examined for piroplasma infection using polymerase chain reaction (PCR). Two 18S ribosomal RNA gene (SSU rDNA) sequences were generated. One 1565-bp sequence showed the highest similarity with B. gibsoni (95.9% identity) but, phylogenetically, was found to belong to a distinct lineage. The other sequence (1709-bp) could not be definitively assigned to a described taxon, sharing only limited homology to the closest named species (90.1% identity with C. felis). In order to enhance information obtained from the SSU rDNA sequence, further detection and sequence analysis of the CCTeta gene sequence were done revealing the simultaneous presence of three closely related genotypes (all in a monophyletic lineage) within a single bear host. This finding suggested the possibility that a new Babesia species (Babesia sp. UR1) might have been maintained in nature in wild brown bears. While the parasite's biology is yet unknown, to our knowledge, this is, excepting the single case documentation in 1910 of a hemoparasite in a bear at Russian zoo, the first reported case of piroplasms inhabiting a bear species. Copyright 2010 Elsevier B.V. All rights reserved.

  10. Caracterização físico-química dos frutos de genótipos de bananeira produzidos em Botucatu-SP Fruit physicochemical characterization of banana genotypes produced in Botucatu-SP

    Directory of Open Access Journals (Sweden)

    Dayana Portes Ramos

    2009-01-01

    Full Text Available O conhecimento dos atributos pós-colheita dos frutos de novos genótipos é uma importante informação que auxilia o melhorista em sua tomada de decisão. Neste trabalho, objetivou-se avaliar as características físico-químicas de frutos de genótipos de 3 grupos genômicos de bananeira: 'Nanicão-IAC-2001', 'Grande Naine', 'Caipira' e 'Nam' (AAA; 'Maçã', 'Thap Maeo', 'Prata Anã' e 'Prata Zulu' (AAB; 'Fhia 01', 'Fhia 18', 'Prata Graúda' e 'Tropical' (AAAB, no município de Botucatu-SP. As características avaliadas foram: textura, pH, acidez titulável, sólidos solúveis, açúcares solúveis totais, teores de amido e potássio. Foi adotado o delineamento experimental inteiramente casualizado, com 12 tratamentos (genótipos, cinco repetições, sendo que em cada repetição utilizaram-se cinco frutos. Utilizou-se o teste de tukey (Pd" 0,05 para a comparação entre médias de genótipos, dentro de cada grupo genômico. Os resultados mostraram que no grupo AAA, Nam se destacou apresentando frutos mais firmes, com maior teor de sólidos solúveis e amido. Do grupo AAB, 'Prata Zulu' apresentou frutos mais firmes, com maior teor de açúcares solúveis totais e amido e menor acidez. No grupo dos híbridos AAAB, 'Tropical' apresentou maior teor de potássio e amido, no entanto, menor teor de sólidos solúveis e açúcares solúveis totais.The knowledge of the post-harvest characteristics of new banana genotypes is important an information that helps the breeder in making a decision. This work had the objective of evaluating the fruit physical and chemical characteristics of genotypes of three banana genomic groups: 'Nanicão-IAC-2001', 'Grande Naine', 'Caipira', and 'Nam' (AAA; 'Maçã', 'Thap Maeo', 'Prata Anã', and 'Prata Zulu' (AAB; 'Fhia 01', 'Fhia 18', 'Prata Graúda', and 'Tropical' (AAAB in Botucatu region, São Paulo state, Brazil. The evaluated characteristics were: firmness, pH, titratable acidity, soluble solids, total soluble

  11. Differentially Expressed Genes in Resistant and Susceptible Common Bean (Phaseolus vulgaris L. Genotypes in Response to Fusarium oxysporum f. sp. phaseoli.

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    Renfeng Xue

    Full Text Available Fusarium wilt of common bean (Phaseolus vulgaris L., caused by Fusarium oxysporum Schlechtend.:Fr. f.sp. phaseoli (Fop, is one of the most important diseases of common beans worldwide. Few natural sources of resistance to Fop exist and provide only moderate or partial levels of protection. Despite the economic importance of the disease across multiple crops, only a few of Fop induced genes have been analyzed in legumes. Therefore, our goal was to identify transcriptionally regulated genes during an incompatible interaction between common bean and the Fop pathogen using the cDNA amplified fragment length polymorphism (cDNA-AFLP technique. We generated a total of 8,730 transcript-derived fragments (TDFs with 768 primer pairs based on the comparison of a moderately resistant and a susceptible genotype. In total, 423 TDFs (4.9% displayed altered expression patterns after inoculation with Fop inoculum. We obtained full amplicon sequences for 122 selected TDFs, of which 98 were identified as annotated known genes in different functional categories based on their putative functions, 10 were predicted but non-annotated genes and 14 were not homologous to any known genes. The 98 TDFs encoding genes of known putative function were classified as related to metabolism (22, signal transduction (21, protein synthesis and processing (20, development and cytoskeletal organization (12, transport of proteins (7, gene expression and RNA metabolism (4, redox reactions (4, defense and stress responses (3, energy metabolism (3, and hormone responses (2. Based on the analyses of homology, 19 TDFs from different functional categories were chosen for expression analysis using quantitative RT-PCR. The genes found to be important here were implicated at various steps of pathogen infection and will allow a better understanding of the mechanisms of defense and resistance to Fop and similar pathogens. The differential response genes discovered here could also be used as

  12. Mouse arsenic (+3 oxidation state) methyltransferase genotype affects metabolism and tissue dosimetry of arsenicals after arsenite administration in drinking water.

    Science.gov (United States)

    Chen, Baowei; Arnold, Lora L; Cohen, Samuel M; Thomas, David J; Le, X Chris

    2011-12-01

    Arsenic (+3 oxidation state) methyltransferase (As3mt) catalyzes methylation of inorganic arsenic (iAs) producing a number of methylated arsenic metabolites. Although methylation has been commonly considered a pathway for detoxification of arsenic, some highly reactive methylated arsenicals may contribute to toxicity associated with exposure to inorganic arsenic. Here, adult female wild-type (WT) C57BL/6 mice and female As3mt knockout (KO) mice received drinking water that contained 1, 10, or 25 ppm (mg/l) of arsenite for 33 days and blood, liver, kidney, and lung were taken for arsenic speciation. Genotype markedly affected concentrations of arsenicals in tissues. Summed concentrations of arsenicals in plasma were higher in WT than in KO mice; in red blood cells, summed concentrations of arsenicals were higher in KO than in WT mice. In liver, kidney, and lung, summed concentrations of arsenicals were greater in KO than in WT mice. Although capacity for arsenic methylation is much reduced in KO mice, some mono-, di-, and tri-methylated arsenicals were found in tissues of KO mice, likely reflecting the activity of other tissue methyltransferases or preabsorptive metabolism by the microbiota of the gastrointestinal tract. These results show that the genotype for arsenic methylation determines the phenotypes of arsenic retention and distribution and affects the dose- and organ-dependent toxicity associated with exposure to inorganic arsenic.

  13. Phenotypic and genotypic characteristics of novel mouse cell line (NIH/3T3-adapted human enterovirus 71 strains (EV71:TLLm and EV71:TLLmv.

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    Carla Bianca Luena Victorio

    Full Text Available Since its identification in 1969, Enterovirus 71 (EV71 has been causing periodic outbreaks of infection in children worldwide and most prominently in the Asia-Pacific Region. Understanding the pathogenesis of Enterovirus 71 (EV71 is hampered by the virus's inability to infect small animals and replicate in their derived in vitro cultured cells. This manuscript describes the phenotypic and genotypic characteristics of two selected EV71 strains (EV71:TLLm and EV71:TLLmv, which have been adapted to replicate in mouse-derived NIH/3T3 cells, in contrast to the original parental virus which is only able to replicate in primate cell lines. The EV71:TLLm strain exhibited productive infection in all primate and rodent cell lines tested, while EV71:TLLmv exhibited greater preference for mouse cell lines. EV71:TLLmv displayed higher degree of adaptation and temperature adaptability in NIH/3T3 cells than in Vero cells, suggesting much higher fitness in NIH/3T3 cells. In comparison with the parental EV71:BS strain, the adapted strains accumulated multiple adaptive mutations in the genome resulting in amino acid substitutions, most notably in the capsid-encoding region (P1 and viral RNA-dependent RNA polymerase (3D. Two mutations, E167D and L169F, were mapped to the VP1 canyon that binds the SCARB2 receptor on host cells. Another two mutations, S135T and K140I, were located in the VP2 neutralization epitope spanning amino acids 136-150. This is the first report of human EV71 with the ability to productively infect rodent cell lines in vitro.

  14. Quantitative trait loci mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 in Citrullus lanatus var. citroides using genotyping-by-sequencing

    Science.gov (United States)

    One of the most devastating watermelon diseases worldwide, Fusarium wilt, is caused by Fusarium oxysporum f. sp. niveum (Fon). Spread of the particularly virulent Fon race 2 in the United States, coupled with the lack of resistance in edible cultivars of the sweet cultivated watermelon Citrullus lan...

  15. Características estruturais e morfológicas de genótipos de Pennisetum sp. sob pastejo no período de seca Structural and morphological characteristics of Pennisetum sp. genotypes under grazing during the dry period

    Directory of Open Access Journals (Sweden)

    Márcio Vieira da Cunha

    2007-06-01

    Full Text Available O experimento foi realizado com o objetivo de estudar características estruturais e morfológicas de cinco genótipos de Pennisetum sp. (CE 08 A.D., Venezuela, HV-241, Elefante B e Hexaplóide sob pastejo no período de seca na Zona da Mata de Pernambuco. Os genótipos foram manejados sob lotação rotacionada (44 dias de descanso e quatro dias de pastejo ao longo de dois ciclos de pastejo. Os dados foram analisados em delineamento experimental de blocos ao acaso com parcelas subdivididas (os genótipos representaram as parcelas e os ciclos de pastejo, as subparcelas e quatro repetições. Houve variação nas características estruturais e morfológicas de genótipos de Pennisetum sp. Os genótipos CE 08 A.D. e Elefante B apresentaram maior densidade de lâmina foliar verde, menor porcentagem de material morto e maior densidade de perfilhos basais remanescentes e aéreos novos, com médias de 5,0±0,4 kg de MS/ha/cm, 33,0±0,2%, 22,0±0,2 e 146,0±0,4 perfilhos/m², respectivamente. O HV-241 apresentou alta participação de material morto em sua biomassa aérea (55,6±0,3%, o que pode ser atribuído à alta mortalidade de perfilhos (19,0±0,3 e 114,0±0,4 perfilhos basais e aéreos mortos/m², respectivamente. Os genótipos CE 08 A.D. e Elefante B destacaram-se como promissores para utilização sob pastejo no período de seca. O genótipo HV-241, híbrido de capim-elefante com o milheto, foi mais afetado pelos efeitos do estresse hídrico no período seco do ano.The experiment was carried out to study structural and morphologic characteristics of five Pennisetum sp. genotypes (CE 08 A.D., Venezuela, HV-241, Elephant B and Hexaplóide under grazing during the dry period in Pernambuco Forest Zone. Genotypes were managed under rotational stocking (44 days of resting and four days of grazing period. The experimental design was randomized blocks in a split plot arrangement, and four replications. The genotypes represented the plots, and grazing

  16. Challenge pools of hepatitis C virus genotypes 1-6 prototype strains: replication fitness and pathogenicity in chimpanzees and human liver-chimeric mouse models

    DEFF Research Database (Denmark)

    Bukh, Jens; Meuleman, Philip; Tellier, Raymond

    2010-01-01

    Chimpanzees represent the only animal model for studies of the natural history of hepatitis C virus (HCV). To generate virus stocks of important HCV variants, we infected chimpanzees with HCV strains of genotypes 1-6 and determined the infectivity titer of acute-phase plasma pools in additional a...

  17. Genotypic and phenotypic characterization of the Sdccag8Tn(sb-Tyr2161B.CA1C2Ove mouse model.

    Directory of Open Access Journals (Sweden)

    Katie Weihbrecht

    Full Text Available Nephronophthisis-related ciliopathies (NPHP-RC are a group of disorders that present with end-stage renal failure in childhood/adolescence, kidney cysts, retinal degeneration, and cerebellar hypoplasia. One disorder that shares clinical features with NPHP-RC is Bardet-Biedl Syndrome (BBS. Serologically defined colon cancer antigen 8 (SDCCAG8; also known as NPHP10 and BBS16 is an NPHP gene that is also associated with BBS. To better understand the patho-mechanisms of NPHP and BBS caused by loss of SDCCAG8 function, we characterized an SDCCAG8 mouse model (Sdccag8Tn(sb-Tyr2161B.CA1C2Ove generated by Sleeping Beauty Transposon (SBT-mediated insertion mutagenesis. Consistent with the previously reported, independent SDCCAG8 mouse models, our mutant mice display pre-axial polydactyly in their hind limbs. In addition, we report patterning defects in the secondary palate, brain abnormalities, as well as neonatal lethality associated with developmental defects in the lung in our mouse model. The neonatal lethality phenotype is genetic background dependent and rescued by introducing 129S6/SvEvTac background. Genetic modifier(s responsible for this effect were mapped to a region between SNPs rs3714172 and rs3141832 on chromosome 11. While determining the precise genetic lesion in our mouse model, we found that SBT insertion resulted in a deletion of multiple exons from both Sdccag8 and its neighboring gene Akt3. We ascribe the patterning defects in the limb and the secondary palate as well as lung abnormalities to loss of SDCCAG8, while the developmental defects in the brain are likely due to the loss of AKT3. This mouse model may be useful to study features not observed in other SDCCAG8 models but cautions are needed in interpreting data.

  18. Challenge Pools of Hepatitis C Virus Genotypes 1–6 Prototype Strains: Replication Fitness and Pathogenicity in Chimpanzees and Human Liver–Chimeric Mouse Models

    Science.gov (United States)

    Bukh, Jens; Meuleman, Philip; Tellier, Raymond; Engle, Ronald E.; Feinstone, Stephen M.; Eder, Gerald; Satterfield, William C.; Govindarajan, Sugantha; Krawczynski, Krzysztof; Miller, Roger H.; Leroux-Roels, Geert; Purcell, Robert H.

    2010-01-01

    Chimpanzees represent the only animal model for studies of the natural history of hepatitis C virus (HCV). To generate virus stocks of important HCV variants, we infected chimpanzees with HCV strains of genotypes 1–6 and determined the infectivity titer of acute-phase plasma pools in additional animals. The courses of first- and second-passage infections were similar, with early appearance of viremia, HCV RNA titers of >104.7 IU/mL, and development of acute hepatitis; the chronicity rate was 56%. The challenge pools had titers of 103–105 chimpanzee infectious doses/mL. Human liver–chimeric mice developed high-titer infections after inoculation with the challenge viruses of genotypes 1–6. Inoculation studies with different doses of the genotype 1b pool suggested that a relatively high virus dose is required to consistently infect chimeric mice. The challenge pools represent a unique resource for studies of HCV molecular virology and for studies of pathogenesis, protective immunity, and vaccine efficacy in vivo. PMID:20353362

  19. Preventive and therapeutic administration of an indigenous Lactobacillus sp. strain against Proteus mirabilis ascending urinary tract infection in a mouse model.

    Science.gov (United States)

    Fraga, Martín; Scavone, Paola; Zunino, Pablo

    2005-07-01

    Probiotics are increasingly being considered as non-pharmaceutical and safe potential alternatives for the treatment and prevention of a variety of pathologies including urinary tract infections. These are the most common infections in medical practice and are frequently treated with antibiotics, which have generated an intense selective pressure over bacterial populations. Proteus mirabilis is a common cause of urinary tract infections in catheterised patients and people with abnormalities of the urinary tract. In this work we isolated, identified and characterised an indigenous Lactobacillus murinus strain (LbO2) from the vaginal tract of a female mouse. In vitro characterisation of LbO2 included acid and bile salts tolerance, growth in urine, adherence to uroepithelial cells and in vitro antimicrobial activity. The selected strain showed interesting properties, suitable for its use as a probiotic. The ability of LbO2 to prevent and even treat ascending P. mirabilis urinary tract infection was assessed using an experimental model in the mouse. Kidney and bladder P. mirabilis counts were significantly lower in mice preventively treated with the probiotic than in non-treated mice. When LbO2 was used for therapeutic treatment, bladder counts of treated mice were significantly lower although no significant differences were detected in P. mirabilis kidney colonisation of treated and non-treated animals. These results are encouraging and prompt further research related to probiotic strains and the basis of their effects for their use in human and animal health.

  20. Herança da resistência à ferrugem da folha da aveia (Puccinia coronata f. sp. avenae Fraser & Led. em genótipos brasileiros de aveia branca Inheritance of oat leaf rust (Puccinia coronata f. sp. avenae Fraser & Led. resistance in white oat brazilian genotypes

    Directory of Open Access Journals (Sweden)

    Eduardo Alano Vieira

    2006-02-01

    the use of resistant cultivars. However, for the durable resistance to be acquired, it is necessary to know the genetics of resistance to crown rust in oats. Thus, the objective of this work was to determine the type of inheritance of resistance to three Puccinia coronata f. sp. avenae Fraser & Led., isolates (collected in southern Brazil in brazilian white oat genotypes. To determine the inheritance of resistance to each one of three isolates,F2 populations were used generated through artificial crosses, between resistant (R and susceptible (S and between resistant genotypes (R. Thus, F2 populations from the following artificial crosses: i URPEL 15 (R x UFRGS 7 (S, UPF 16 (R x UFRGS 7 (S and URPEL 15 (R x UPF 16 (R, were used to determine the inheritance of resistance to isolate one (1; ii URPEL 15 (R x UFRGS 7 (S, UPF 18 (R x UFRGS 7 (S and URPEL 15 (R x UPF 18 (R, to determine the inheritance of resistance to isolate two (2; iii URPEL 15 (R x UFRGS 7 (S and URPEL 15 (R x UPF 18 (S, to determine the inheritance of resistance to isolate three (3. The obtained results indicate that the genotype URPEL 15 present dominants genes for resistance to the three oat leaf rust isolates evaluated, the cultivar UPF 16 presents a recessive gene for resistance to isolate 1 and the cultivar UPF 18 has a recessive gene of resistence to isolate 2. Also, the resistance genes presented by genotypes URPEL 15, UPF 16 and UPF 18, segregate in an independent manner.

  1. Desmanthus GENOTYPES

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    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

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

  2. A genotype-by-sequencing-single nucleotide polymorphism based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides

    Science.gov (United States)

    Fusarium wilt, a fungal disease caused by Fusarium oxysporum f. sp. niveum (Fon), devastates watermelon crop production worldwide. Several races, which are differentiated by host range, of the pathogen exist. Resistance to Fon race 2, a particularly virulent strain prevalent in the United States, do...

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

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    Didion John P

    2012-01-01

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

  4. Avaliação de genótipos de Leucaena spp. nas condições edafoclimáticas de São Carlos, SP: I. caracterização fenotípica e avaliação agronômica Evaluation of Leucaena spp. genotypes in the edaphic and climatic conditions of São Carlos, SP: I. phenotypical characterization and agronomical evaluation

    Directory of Open Access Journals (Sweden)

    A.C.P. de A. Primavesi

    1994-04-01

    Full Text Available Para avaliar genótipos promissores de Leucaena spp., foi instalado experimento em Latossolo Vermelho-Amarelo distrófico, na área da EMBRAPA-CPPSE em São Carlos, situada a 22°01'S e 47°53'W, com altitude de 856 m e média de precipitação anual de 1502 mm. Foram testados os seguintes genótipos: Leucaena leucocephala cv. Texas 1074 (T1, L.leucocephala 29 A9 (T2, L.leucocephala 11 x L.diversifolia 25 (T3, L.leucocephala 11 x L.leucocephala 26 (T4, L.leucocephala 24-19/2-39 X L.diversifolia 26 (T5 e L.leucocephala cv. Cunningham (testemunha. Através das avaliações efetuadas durante o período de estabelecimento (15 meses, verificou-se que: a as plantas de L.leucocephala 24-19/2-39 x L.diversifolia 26 se mostraram mais ramificadas e com maior produção de sementes; b as plantas de L.leucocephala 11 x L.diversifolia 26 apresentaram a maior produção de matéria seca consumível; c os materiais apresentaram brotação após o corte, semelhante ou inferior à testemunha.To test promising genotypes of Leucaena spp., selected in a breeding program, an experiment was conducted in a distrofic Red-Yellow Latossol, at the experimental station of EMBRAPA/CPPSE, São Carlos,SP, located at 22°01' and 47°53'W, altitude of 856 m and with a mean annual precipitation of 1502 mm. The following genotypes were tested: L.leucocephala cv. Texas 1074 (T1, L.leucocephala 29 A9 (T2, L.leucocephala 11 x L.diversifolia 25 (T3, L.leucocephala 11 x L.diversifolia 26 (T4, L.leucocephala 24-19/2-39 x L.diversifolia 26 (T5 and L.leucocephala cv. Cunningham (control. Evaluations were performed during the establishment period (fifteen months and it was concluded that: a the plants of L.leucocephala 24-19/2-39 x L.diversifolia 26, with early flowering, were the most branched and presented the greatest seed yield; b the plants of L.leucocephala 11 x L.diversifolia 26, showed the greatest edible dry matter yield; c the genotypes presented similar or worse growth, than

  5. Enhancement of clavulanic acid production by Streptomyces sp MU ...

    African Journals Online (AJOL)

    Purpose: To enhance clavulanic acid production using UV-mutagenesis on Streptomyces sp. NRC77. Methods: UV-mutagenesis was used to study the effect of Streptomyces sp. NRC77 on CA production. Phenotypic and genotypic identification methods of the promising mutant strain were characterized. Optimization of the ...

  6. Methylobacterium suomiense sp. nov. and Methylobacterium lusitanum sp. nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria.

    Science.gov (United States)

    Doronina, Nina V; Trotsenko, Yuri A; Kuznetsov, Boris B; Tourova, Tatjana P; Salkinoja-Salonen, Mirja S

    2002-05-01

    Two aerobic, pink-pigmented, facultatively methylotrophic bacteria, strains F20T and RXM(T), are described taxonomically. On the basis of their phenotypic and genotypic properties, the isolates are proposed as novel species of the genus Methylobacterium, Methylobacterium suomiense sp. nov. (type strain F20T = VKM B-2238T = NCIMB 13778T) and Methylobacterium lusitanum sp. nov. (type strain RXMT = VKM B-2239T = NCIMB 13779T).

  7. Influence of genotype and age of explant source on the capacity for ...

    African Journals Online (AJOL)

    ONOS

    2010-04-12

    Apr 12, 2010 ... Key words: Musa, embryogenic callus, genotype, male bud age, Cavendish banana .... ethanol for five minutes, rinsed three times with sterile double-distilled ..... somatic embryogenesis in the hybrid cultivar FHIA-21 (Musa sp.

  8. SP. Pescado

    Directory of Open Access Journals (Sweden)

    Renato Gendre

    2003-12-01

    Full Text Available Nell'occhiello di un articolo dal titolo Il Peru dei de[Jini rosa e de/la grande pioggia si legge: "da una partenza  in aereo al «pescado»  che ti  sfamera."1 Questa parola spagnola, giustamente chiusa tra caporali, a noi pare molto interes­ sante, perche, nonostante l'apparenza, non ha nulla da spartire sotto i1 profilo se­ mantico con l'it. pescato. lnfatti, tutti i piu importanti dizionari della lingua italiana, di ieri e di oggi, etimologici e non 2, registrano  accanto a pescata,  ii lemma pescato, 3 ma lo spiegano come "quantita di pesce catturato nel corso di una battuta o di una stagione di pesca",4 mentre lo sp. pescado  indica i1 "pesce (solo nel senso di: pesGe pescato da mangiare [...]".s

  9. Mouse adhalin

    DEFF Research Database (Denmark)

    Liu, L; Vachon, P H; Kuang, W

    1997-01-01

    . To analyze the biological roles of adhalin, we cloned the mouse adhalin cDNA, raised peptide-specific antibodies to its cytoplasmic domain, and examined its expression and localization in vivo and in vitro. The mouse adhalin sequence was 80% identical to that of human, rabbit, and hamster. Adhalin...... was specifically expressed in striated muscle cells and their immediate precursors, and absent in many other cell types. Adhalin expression in embryonic mouse muscle was coincident with primary myogenesis. Its expression was found to be up-regulated at mRNA and protein levels during myogenic differentiation...

  10. Draft genome sequences of six neonatal meningitis-causing escherichia coli isolates (SP-4, SP-5, SP-13, SP-16, SP-46, and SP-65)

    Science.gov (United States)

    Neonatal meningitis Escherichia coli isolates (SP-4, SP-5, SP-13, SP-16, SP-46, and SP-65) were recovered from infants in the Netherlands from 1989 to 1997. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used to validate food safety processing te...

  11. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Resources For Health Professionals Subscribe Search APOE Genotyping, Cardiovascular Disease Send Us Your Feedback Choose Topic At a ... help understand the role of genetic factors in cardiovascular disease . However, the testing is sometimes used in clinical ...

  12. Radiosensitivity of fingermillet genotypes

    Energy Technology Data Exchange (ETDEWEB)

    Raveendran, T S; Nagarajan, C; Appadurai, R; Prasad, M N; Sundaresan, N [Tamil Nadu Agricultural Univ., Coimbatore (India)

    1984-07-01

    Varietal differences in radiosensitivity were observed in a study involving 4 genotypes of fingermillet (Eleusine coracana (Linn.) Gaertn.) subjected to gamma-irradiation. Harder seeds were found to tolerate a higher dose of the mutagen.

  13. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  14. IDENTIFICATION AND MOLECULAR CLONING OF XENOPUS LAEVIS SP22, A PROTEIN ASSOCIATED WITH FERTILIZATION IN MAMMALS

    Science.gov (United States)

    ABSTRACTSP22 is a protein that has been characterized in rats where it has been related with fertility. SP22 homologues have been studied in mouse and man and a definitive role for the protein has not been assigned yet. By means of a polyclonal IgG to recombinant rat SP22...

  15. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease.

    Science.gov (United States)

    Eppig, Janan T; Blake, Judith A; Bult, Carol J; Kadin, James A; Richardson, Joel E

    2015-01-01

    The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse-human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human-Mouse: Disease Connection, allows users to explore gene-phenotype-disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Surfactant protein D of the innate immune defence is inversely associated with human obesity and SP-D deficiency infers increased body weight in mice

    DEFF Research Database (Denmark)

    Sorensen, G.L.; Hjelmborg, J.V.B.; Leth-Larsen, R.

    2006-01-01

    Surfactant protein D (SP-D) is a key regulator of pathogen-induced inflammation. SP-D is further involved in lipid homeostasis in mouse lung and circulation and recent data have demonstrated that the body mass index (BMI; in kg/m(2)) is influenced by genes in common with SP-D. The objective...

  17. Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria

    Directory of Open Access Journals (Sweden)

    Carly R. Muletz-Wolz

    2017-08-01

    Full Text Available Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, for which probiotic applications as conservation strategies have been proposed. We quantified the inhibition strength of five putatively B. dendrobatidis-inhibitory bacteria isolated from woodland salamander skin against six Batrachochytrium genotypes at two temperatures (12 and 18°C. We selected six genotypes from across the Batrachochytrium phylogeny: B. salamandrivorans, B. dendrobatidis-Brazil and four genotypes of the B. dendrobatidis Global Panzootic Lineage (GPL1: JEL647, JEL404; GPL2: SRS810, JEL423. We performed 96-well plate challenge assays in a full factorial design. We detected a Batrachochytrium genotype by temperature interaction on bacterial inhibition score for all bacteria, indicating that bacteria vary in ability to inhibit Batrachochytrium depending on pathogen genotype and temperature. Acinetobacter rhizosphaerae moderately inhibited B. salamandrivorans at both temperatures (μ = 46–53%, but not any B. dendrobatidis genotypes. Chryseobacterium sp. inhibited three Batrachochytrium genotypes at both temperatures (μ = 5–71%. Pseudomonas sp. strain 1 inhibited all Batrachochytrium genotypes at 12°C and four Batrachochytrium genotypes at 18°C (μ = 5–100%. Pseudomonas sp. strain 2 and Stenotrophomonas sp. moderately to strongly inhibited all six Batrachochytrium genotypes at both temperatures (μ = 57–100%. All bacteria consistently inhibited B. salamandrivorans. Using cluster analysis of inhibition scores, we found that more closely related Batrachochytrium genotypes grouped together

  18. Extraction methods of Amaranthus sp. grain oil isolation.

    Science.gov (United States)

    Krulj, Jelena; Brlek, Tea; Pezo, Lato; Brkljača, Jovana; Popović, Sanja; Zeković, Zoran; Bodroža Solarov, Marija

    2016-08-01

    Amaranthus sp. is a fast-growing crop with well-known beneficial nutritional values (rich in protein, fat, dietary fiber, ash, and minerals, especially calcium and sodium, and containing a higher amount of lysine than conventional cereals). Amaranthus sp. is an underexploited plant source of squalene, a compound of high importance in the food, cosmetic and pharmaceutical industries. This paper has examined the effects of the different extraction methods (Soxhlet, supercritical fluid and accelerated solvent extraction) on the oil and squalene yield of three genotypes of Amaranthus sp. grain. The highest yield of the extracted oil (78.1 g kg(-1) ) and squalene (4.7 g kg(-1) ) in grain was obtained by accelerated solvent extraction (ASE) in genotype 16. Post hoc Tukey's HSD test at 95% confidence limit showed significant differences between observed samples. Principal component analysis (PCA) and cluster analysis (CA) were used for assessing the effect of different genotypes and extraction methods on oil and squalene yield, and also the fatty acid composition profile. Using coupled PCA and CA of observed samples, possible directions for improving the quality of product can be realized. The results of this study indicate that it is very important to choose both the right genotype and the right method of extraction for optimal oil and squalene yield. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  19. ExaSP2

    Energy Technology Data Exchange (ETDEWEB)

    2017-09-08

    ExaSP2 is a reference implementation of typical linear algebra algorithms and workloads for a quantum molecular dynamics (QMD) electronic structure code. The algorithm is based on a recursive second-order Fermi-Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of material systems.

  20. Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA.

    Science.gov (United States)

    Weller, Daniel; Andrus, Alexis; Wiedmann, Martin; den Bakker, Henk C

    2015-01-01

    Sampling of seafood and dairy processing facilities in the north-eastern USA produced 18 isolates of Listeria spp. that could not be identified at the species-level using traditional phenotypic and genotypic identification methods. Results of phenotypic and genotypic analyses suggested that the isolates represent two novel species with an average nucleotide blast identity of less than 92% with previously described species of the genus Listeria. Phylogenetic analyses based on whole genome sequences, 16S rRNA gene and sigB gene sequences confirmed that the isolates represented by type strain FSL M6-0635(T) and FSL A5-0209 cluster phylogenetically with Listeria cornellensis. Phylogenetic analyses also showed that the isolates represented by type strain FSL A5-0281(T) cluster phylogenetically with Listeria riparia. The name Listeria booriae sp. nov. is proposed for the species represented by type strain FSL A5-0281(T) ( =DSM 28860(T) =LMG 28311(T)), and the name Listeria newyorkensis sp. nov. is proposed for the species represented by type strain FSL M6-0635(T) ( =DSM 28861(T) =LMG 28310(T)). Phenotypic and genotypic analyses suggest that neither species is pathogenic. © 2015 IUMS.

  1. AMMI analysis to evaluate the adaptability and phenotypic stability of sugarcane genotypes

    Directory of Open Access Journals (Sweden)

    Luís Cláudio Inácio da Silveira

    2013-02-01

    Full Text Available Sugarcane (Saccharum sp. is one of the most important crops in Brazil. The high demand for sugarcane-derived products has stimulated the expansion of sugarcane cultivation in recent years, exploring different environments. The adaptability and the phenotypic stability of sugarcane genotypes in the Minas Gerais state, Brazil, were evaluated based on the additive main effects and multiplicative interaction (AMMI method. We evaluated 15 genotypes (13 clones and two checks: RB867515 and RB72454 in nine environments. The average of two cuttings for the variable tons of pol per hectare (TPH measure was used to discriminate genotypes. Besides the check RB867515 (20.44 t ha-1, the genotype RB987935 showed a high average TPH (20.71 t ha-1, general adaptability and phenotypic stability, and should be suitable for cultivation in the target region. The AMMI method allowed for easy visual identification of superior genotypes for each set of environments.

  2. Molecular evidence of a new Babesia sp. in goats.

    Science.gov (United States)

    Ozubek, Sezayi; Aktas, Munir

    2017-01-15

    In this study, a novel Babesia sp. infecting goats was detected and its phylogenetic relationship to related species was determined. A total of 200 blood samples collected from sheep (n=78) and goats (n=122) were examined in the study. The V4 hypervariable region of the 18S rRNA gene of the novel Babesia sp. was amplified by PCR and analysed using a reverse line blot hybridization assay adapted for small ruminants. Samples from seven goats hybridized to Theileria/Babesia catch-all and Babesia catch-all probes and did not hybridize to any species-specific probe tested, suggesting the presence of an unrecognized Babesia species or genotype. Sequencing results showed the isolate to clearly differ from ovine Babesia species and genotypes currently available in the GenBank database. The isolate showed 90.9%, 93.5%, and 93.4% identity to B. ovis, B. motasi, and B. crassa, respectively and 91-93% similarity to Babesia genotypes recently described in small ruminants. The highest homology (∼96-97%) observed was with Babesia odocoilei, Babesia sp. EU1, and Babesia divergens. The new isolate was provisionally designated Babesia sp. The study contributes to better insight into the distribution and phylogenetic diversity of piroplasms in small ruminants. The survey indicated a high prevalence of piroplasms in small ruminants (21.5%). Of those detected, T. ovis was the most prevalent (17%), followed by Babesia sp. (3.5%), and B. ovis (2%). Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  4. Avaliação de genótipos de Leucaena spp. nas condições edafoclimáticas de São Carlos,SP: II. determinações bromatológicas no período de estabelecimento Evaluation of Leucaena spp. genotypes in the edaphic and climatic conditions of São Carlos, SP: II. bromatological determinations at the establishment period

    Directory of Open Access Journals (Sweden)

    A.C.P. de A. Primavesi

    1994-04-01

    Full Text Available Em experimento conduzido em Latossolo Vermelho-Amarelo distrófico, em área da EMBRAPA - CPPSE em São Carlos, situada a 22°01'S e 47°53'W, com altitude de 856 m e média de precipitação anual de 1502 mm, procedeu-se a determinação da composição bromatológicade folhas, hastes com diâmetro menor que 6 mm e vagens, de genótipos de leucena. Os genótipos avaliados, foram: L.leucocephala cv. Texas 1074 (TI, L.leucocephala 29 A9 (T2, L.leucocephala 11 x L.dlversifolia 25 (T3, L.leucocephala 11 x L.diversifolia 26 (T4, L.leucocephala 24-19/2-39 x L.diverstfolia 26 (T5 e L.leucocephala c v. Cunningham (testemunha. Verificou-se que: os genótipos avahados não apresentaram diferenças nas determinações bromatológicas, realizadas nas folhas e talos finos; o genótipo T3 registrou o maior teor de proteína bruta (28,06%, de fósforo (0,29% e a maior relação PB/FDN e o menor teor de FDN para vagens; os genótipos apresentaram os seguintes teores médios, em porcentagem, para a composição bromatológicadas folhas, vagens e talos finos, respectivamente: Proteína bruta (18,57; 21,68; 6,41; Fibra detergente neutro (29,09; 41,58; 71,01; Fósforo (0,12; 0,22; 0,06; Cálcio (1,39; 0,36; 0,49; Magnesio (0,51; 0,28; 0,24; Tanino (1,32; 1,15; 0,28 e Digestibilidade "in vitro" (58,39; 61,22; 33,61; os teores de proteína e fósforo apresentaram a seguinte ordem decrescente nas partes das plantas: vagens > folhas > talos finos; os teores de cálcio: folhas > talos finos > vagens e de magnésio: folhas > vagens > talos finos.In a trial conducted on a distrofic Red-Yellow Latossol, at EMBRAPA-CPPSE, São Carlos, located at 22°01'S and 47'53'W, altitude of 856 m and with a mean annual rainfall of 1502 mm, the bromatological composition of leaves, stems smaller than 6 mm diameter and pods of leucena genotypes was determined. The genotypes evaluated were: L.leucocephala cv. Texas 1074 (T1, L.leucocephala 29 A9 (T2, L.leucocephala 11 x L.dlversifolia 25

  5. Centralized mouse repositories.

    Science.gov (United States)

    Donahue, Leah Rae; Hrabe de Angelis, Martin; Hagn, Michael; Franklin, Craig; Lloyd, K C Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T

    2012-10-01

    Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.

  6. HBV genotypic variability in Cuba.

    Directory of Open Access Journals (Sweden)

    Carmen L Loureiro

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

  7. HBV Genotypic Variability in Cuba

    Science.gov (United States)

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

    2015-01-01

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

  8. Transcription factor SP4 is a susceptibility gene for bipolar disorder.

    Directory of Open Access Journals (Sweden)

    Xianjin Zhou

    Full Text Available The Sp4 transcription factor plays a critical role for both development and function of mouse hippocampus. Reduced expression of the mouse Sp4 gene results in a variety of behavioral abnormalities relevant to human psychiatric disorders. The human SP4 gene is therefore examined for its association with both bipolar disorder and schizophrenia in European Caucasian and Chinese populations respectively. Out of ten SNPs selected from human SP4 genomic locus, four displayed significant association with bipolar disorder in European Caucasian families (rs12668354, p = 0.022; rs12673091, p = 0.0005; rs3735440, p = 0.019; rs11974306, p = 0.018. To replicate the genetic association, the same set of SNPs was examined in a Chinese bipolar case control sample. Four SNPs displayed significant association (rs40245, p = 0.009; rs12673091, p = 0.002; rs1018954, p = 0.001; rs3735440, p = 0.029, and two of them (rs12673091, rs3735440 were shared with positive SNPs from European Caucasian families. Considering the genetic overlap between bipolar disorder and schizophrenia, we extended our studies in Chinese trios families for schizophrenia. The SNP7 (rs12673091, p = 0.012 also displayed a significant association. The SNP7 (rs12673091 was therefore significantly associated in all three samples, and shared the same susceptibility allele (A across all three samples. On the other hand, we found a gene dosage effect for mouse Sp4 gene in the modulation of sensorimotor gating, a putative endophenotype for both schizophrenia and bipolar disorder. The deficient sensorimotor gating in Sp4 hypomorphic mice was partially reversed by the administration of dopamine D2 antagonist or mood stabilizers. Both human genetic and mouse pharmacogenetic studies support Sp4 gene as a susceptibility gene for bipolar disorder or schizophrenia. The studies on the role of Sp4 gene in hippocampal development may provide novel insights for the contribution of hippocampal abnormalities in these

  9. Monoclonal antibodies against pregnancy-specific β1-glycoprotein (SP1) in immunohistochemistry and radioimmunoassay

    International Nuclear Information System (INIS)

    Wahlstroem, T.; Heikinheimo, M.

    1983-01-01

    Monoclonal mouse antibodies against pregnancy-specific beta-1-glycoprotein (SP 1 ) have been studied for their suitability in immunoperoxidase staining and radioimmunoassay methodologies. These antibodies were useful in staining normal placentas, hydatidiform moles, invasive moles and choriocarcinomas. They showed good specificity, with minimal background staining, and will thus be superior to conventional polyclonal antisera in immunohistochemistry. However, the presently tested monoclonal anti-SP 1 antibodies were found not to be suitable for radioimmunoassay. (Auth.)

  10. SP-100 Program overview

    International Nuclear Information System (INIS)

    Truscello, V.C.

    1984-01-01

    The SP-100 Program is expected to go through three phases: technology assessment and advancement, ground testing, and flight qualification. Currently the program is in the two- to three-year technology assessment and advancement stage. Goals are to identify the space nuclear power system concept that best meets anticipated requirements of future space missions, assess the technical feasibility of that concept, and establish a cost and schedule for developing the concept. The SP-100 Project Office has begun the implementation activities needed to meet these goals. With regard to refractory alloys, a better data base will be required before we move ahead in the program from technology assessment to ground demonstration

  11. Genetic analyses, phenotypic adaptability and stability in sugarcane genotypes for commercial cultivation in Pernambuco.

    Science.gov (United States)

    Dutra Filho, J A; Junior, T C; Simões Neto, D E

    2015-10-05

    In the present study, we assessed the agro-industrial performance of 22 sugarcane genotypes adaptable to edaphoclimatic conditions in production microregions in the State of Pernambuco, Brazil, and we recommended the commercial cultivation of select genotypes. The variables analyzed were as follows: sucrose percentage in cane juice, tonnage of saccharose per hectare (TPH), sugarcane tonnage per hectare (TCH), fiber, solid soluble contents, total recoverable sugar tonnage (ATR), and total recoverable sugar tonnage per hectare (ATR t/ha). A randomized block design with 4 repeats was used. Combined variance of the experiments, genetic parameter estimates, and environment stratification were analyzed. Phenotypic adaptability and stability were analyzed using the Annicchiarico and Wricke methods and analysis of variance. Genetic gain was estimated using the classic index and sum of ranks. Genotype selection was efficient for TPH, TCH, and ATR t/ha. Genotypes presented a great potential for improvement and a similar response pattern in Litoral Norte and Mata Sul microregions for TPH and TCH and Litoral Norte and Litoral Sul microregions for ATR t/ha. Genotypes SP78-4764, RB813804, and SP79-101 showed better productivity and phenotypic adaptability and stability, according to the Wricke and Annicchiarico methods. These genotypes can be recommended for cultivation in the sugarcane belt in the State of Pernambuco.

  12. Cryptosporidium rubeyi n. sp. (Apicomplexa: Cryptosporidiidae in multiple Spermophilus ground squirrel species

    Directory of Open Access Journals (Sweden)

    Xunde Li

    2015-12-01

    Full Text Available Previously we reported the unique Cryptosporidium sp. “c” genotype (e.g., Sbey03c, Sbey05c, Sbld05c, Sltl05c from three species of Spermophilus ground squirrel (Spermophilus beecheyi, Spermophilus beldingi, Spermophilus lateralis located throughout California, USA. This follow-up work characterizes the morphology and animal infectivity of this novel genotype as the final step in proposing it as a new species of Cryptosporidium. Analysis of sequences of 18S rRNA, actin, and HSP70 genes of additional Cryptosporidium isolates from recently sampled California ground squirrels (S. beecheyi confirms the presence of the unique Sbey-c genotype in S. beecheyi. Phylogenetic and BLAST analysis indicates that the c-genotype in Spermophilus ground squirrels is distinct from Cryptosporidium species/genotypes from other host species currently available in GenBank. We propose to name this c-genotype found in Spermophilus ground squirrels as Cryptosporidium rubeyi n. sp. The mean size of C. rubeyi n. sp. oocysts is 4.67 (4.4–5.0 μm × 4.34 (4.0–5.0 μm, with a length/width index of 1.08 (n = 220. Oocysts of C. rubeyi n. sp. are not infectious to neonatal BALB/c mice and Holstein calves. GenBank accession numbers for C. rubeyi n. sp. are DQ295012, AY462233, and KM010224 for the 18S rRNA gene, KM010227 for the actin gene, and KM010229 for the HSP70 gene.

  13. Cryptosporidium sp. in lizards

    Czech Academy of Sciences Publication Activity Database

    Koudela, Břetislav; Modrý, D.

    1998-01-01

    Roč. 45, č. 1 (1998), s. 8 ISSN 1066-5234. [Cryptosporidium sp. in lazards. 01.01.1998-02.01.1998, Praha] R&D Projects: GA ČR GA508/95/0273; GA AV ČR IPP2020702 Subject RIV: fp - Other Medical Disciplines

  14. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccini coronata f. sp. avenae, the causal agent of oat crown rust

    Science.gov (United States)

    Marisa E. Miller; Ying Zhang; Vahid Omidvar; Jana Sperschneider; Benjamin Schwessinger; Castle Raley; Jonathan M. Palmer; Diana Garnica; Narayana Upadhyaya; John Rathjen; Jennifer M. Taylor; Robert F. Park; Peter N. Dodds; Cory D. Hirsch; Shahryar F. Kianian; Melania. Figueroa

    2018-01-01

    Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting...

  15. Cryptosporidium homai n. sp. (Apicomplexa: Cryptosporidiiae) from the guinea pig (Cavia porcellus).

    Science.gov (United States)

    Zahedi, Alireza; Durmic, Zoey; Gofton, Alexander W; Kueh, Susan; Austen, Jill; Lawson, Malcolm; Callahan, Lauren; Jardine, John; Ryan, Una

    2017-10-15

    The morphological, biological, and molecular characterisation of a new Cryptosporidium species from the guinea pig (Cavia porcellus) are described, and the species name Cryptosporidium homai n. sp. is proposed. Histological analysis conducted on a post-mortem sample from a guinea pig euthanised due to respiratory distress, identified developmental stages of C. homai n. sp. (trophozoites and meronts) along the intestinal epithelium. Molecular analysis at 18S rRNA (18S), actin and hsp70 loci was then conducted on faeces from an additional 7 guinea pigs positive for C. homai n. sp. At the 18S, actin and hsp70 loci, C. homai n. sp. exhibited genetic distances ranging from 3.1% to 14.3%, 14.4% to 24.5%, and 6.6% to 20.9% from other Cryptosporidium spp., respectively. At the 18S locus, C. homai n. sp. shared 99.1% similarity with a previously described Cryptosporidium genotype in guinea pigs from Brazil and it is likely that they are the same species, however this cannot be confirmed as actin and hsp70 sequences from the Brazilian guinea pig genotype are not available. Phylogenetic analysis of concatenated 18S, actin and hsp70 sequences showed that C. homai n. sp. exhibited 9.1% to 17.3% genetic distance from all other Cryptosporidium spp. This clearly supports the validity of C. homai n. sp. as a separate species. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. In vitro rootting of Dioscoreas sp.

    Directory of Open Access Journals (Sweden)

    Irma Quintero

    2003-07-01

    Full Text Available The Universidad de Córdoba s Vegetal Tissue Culture Laboratory evaluated the effect of naphthalenacetic acid (NAA on in vitro rooting of three yam cultivars (Dioscorea sp. in 2000. The effect of four hormone levels (0, 0.3, 0.6 and 0.9 mg/1 was studied on three yam cultivars (Diamantes-22,003 and 005. A random experimental design was used employing 4x3 factorial arrangement and 20 repetitions; each experimental unit consisted of a glass receptacle containing the culture medium and the explant (one segment nodal. The variables considered were the number of roots and their thickness, culture medium oxidation and callus production. Findings showed that both the hormone and genotype had an effect on all those variables considered in the study and interaction was significant (P

  17. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  18. Phenotype adaptability and stability of sugarcane genotypes in the sugarcane belt of the state of Pernambuco, Brazil.

    Science.gov (United States)

    Dutra Filho, J A; Junior, T C; Simões Neto, D E

    2014-08-29

    We assessed the agroindustrial performance of 25 sugarcane genotypes adapted to the edaphoclimatic conditions of the State of Pernambuco, Brazil, within the microregions Mata Norte, Mata Sul, Região Central, Litoral Norte, and Litoral Sul. The variables analyzed were POL tonnage per hectare, sugarcane tonnage per hectare, fiber and total recoverable sugar tonnage per hectare, using a randomized block design with four repetitions. Combined variance of experiments, genetic parameter estimates, decomposition of the genotype-environment interaction, and environment stratification were analyzed. Phenotype adaptability and stability were also analyzed. The various genotypes presented great potential for improvement and a similar response pattern to the microregions Centro and Mata Sul of the state of Pernambuco. Genotypes RB863129, RB867515, RB92579, RB953180, SP81-3250, RB75126, and RB942520 were better in productivity and phenotype adaptability and stability compared to genotypes RB892700, RB943365, SP79-1011, Q138, RB943538, SP78-4764, RB953281, RB943066, RB928064, RB93509, RB72454, RB952675, RB952991, RB943161, RB942898, RB872552, RB952900, and RB942849. These genotypes are recommended as cultivation options in the sugarcane belt in the state of Pernambuco, since they stand out in terms of phenotype adaptability and stability as evaluated using the method by Annicchiarico, Lin and Bins, and the method by Eberhart and Russel.

  19. Effects of Alternaria alternata f.sp. lycopersici toxins on pollen

    NARCIS (Netherlands)

    Bino, R.J.; Franken, J.; Witsenboer, H.M.A.; Hille, J.; Dons, J.J.M.

    1988-01-01

    Effects of the phytotoxic compounds (AAL-toxins) isolated from cell-free culture filtrates of Alternaria alternata f.sp. lycopersici on in vitro pollen development were studied. AAL-toxins inhibited both germination and tube growth of pollen from several Lycopersicon genotypes. Pollen from

  20. Diversity and antimicrobial susceptibility of oxytetracycline-resistant isolates of Stenotrophomonas sp. and Serratia sp. associated with Costa Rican crops.

    Science.gov (United States)

    Rodríguez, C; Wachlin, A; Altendorf, K; García, F; Lipski, A

    2007-12-01

    To ameliorate the identification, evaluate the diversity, and determine the antimicrobial sensitivity of 19 oxytetracycline-resistant isolates of Stenotrophomonas sp. and Serratia sp. associated with Costa Rican crops. Phenotypical, chemotaxonomical, and molecular data allocated most isolates to the species Sten. maltophilia and Ser. marcescens. The API profiles, antimicrobial resistance patterns (ATB system), and BOX-polymerase chain reaction (PCR) genomic fingerprints of isolates of Stenotrophomonas sp. exhibited a higher degree of heterogeneity than those obtained for the isolates of Serratia sp. The former group of bacteria exhibited multiresistance to antimicrobials. In contrast, isolates of Serratia sp. were sensitive to the majority of the drugs tested. Changes in the results of the antibiograms throughout incubation, which indicate an induction of tolerance, were observed for isolates of both the species. Minimum inhibitory concentration of oxytetracycline, determined using E-test stripes, were rather elevated. The occurrence of two species of opportunistic pathogens in crop-associated materials poses a risk to consumers in the community. The phenotypic and genotypic data presented could support epidemiologist and physicians dealing with infections caused by environmental strains of these taxa.

  1. Burkholderia cordobensis sp. nov., from agricultural soils.

    Science.gov (United States)

    Draghi, Walter O; Peeters, Charlotte; Cnockaert, Margo; Snauwaert, Cindy; Wall, Luis G; Zorreguieta, Angeles; Vandamme, Peter

    2014-06-01

    Two Gram-negative, rod-shaped bacteria were isolated from agricultural soils in Córdoba province in central Argentina. Their 16S rRNA gene sequences demonstrated that they belong to the genus Burkholderia, with Burkholderia zhejiangensis as most closely related formally named species; this relationship was confirmed through comparative gyrB sequence analysis. Whole-cell fatty acid analysis supported their assignment to the genus Burkholderia. Burkholderia sp. strain YI23, for which a whole-genome sequence is available, represents the same taxon, as demonstrated by its highly similar 16S rRNA (100% similarity) and gyrB (99.1-99.7%) gene sequences. The results of DNA-DNA hybridization experiments and physiological and biochemical characterization further substantiated the genotypic and phenotypic distinctiveness of the Argentinian soil isolates, for which the name Burkholderia cordobensis sp. nov. is proposed, with strain MMP81(T) ( = LMG 27620(T) = CCUG 64368(T)) as the type strain. © 2014 IUMS.

  2. Four new Mouse Spider species (Araneae, Mygalomorphae, Actinopodidae, Missulena from Western Australia

    Directory of Open Access Journals (Sweden)

    Laura Miglio

    2014-05-01

    Full Text Available Four new species of the Mouse Spider genus Missulena Walckenaer, 1805 (family Actinopodidae are described from Western Australia based on morphological features of adult males. Missulena leniae sp. n. (from the Carnarvon and Yalgoo biogeographic regions, Missulena mainae sp. n. (Carnarvon, Missulena melissae sp. n. (Pilbara and Missulena pinguipes sp. n. (Mallee represent a broad spectrum of morphological diversity found in this genus and differ from other congeners by details of the male copulatory bulb, colour patterns, eye sizes, leg morphology and leg spination. Two of the species, M. pinguipes sp. n. and M. mainae sp. n., are characterised by swollen metatarsi of the fourth legs in males, a feature not previously recorded in the family. A key to males of all named Missulena species from Australia is presented and allows their identification based on external morphology.

  3. 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.

  4. Mouse Models as Predictors of Human Responses: Evolutionary Medicine.

    Science.gov (United States)

    Uhl, Elizabeth W; Warner, Natalie J

    Mice offer a number of advantages and are extensively used to model human diseases and drug responses. Selective breeding and genetic manipulation of mice have made many different genotypes and phenotypes available for research. However, in many cases, mouse models have failed to be predictive. Important sources of the prediction problem have been the failure to consider the evolutionary basis for species differences, especially in drug metabolism, and disease definitions that do not reflect the complexity of gene expression underlying disease phenotypes. Incorporating evolutionary insights into mouse models allow for unique opportunities to characterize the effects of diet, different gene expression profiles, and microbiomics underlying human drug responses and disease phenotypes.

  5. Control of Branchionus sp. and Amoeba sp. in cultures of Arthrospira sp. Control de Branchionus sp. y Amoeba sp. en cultivos de Arthrospira sp.

    Directory of Open Access Journals (Sweden)

    Carlos Méndez

    2012-09-01

    Full Text Available Cultivation of cyanobacterium Arthrospira sp. has been developed in many countries for the production of proteins, pigments and other compounds. Outdoor mass cultures are often affected by biological contamination, drastically reducing productivity as far as bringing death. This study evaluates the control of Branchionus sp. and Amoeba sp. with two chemical compounds: urea (U and ammonium bicarbonate (AB, in laboratory conditions and outdoor mass culture of Arthrospira sp. The lethal concentration 100 (LC100 at 24 h for Branchionus sp. and Amoeba sp. determined was of 60-80 mg L-1 (U and 100-150 mg L-1 (AB. The average effective inhibition concentration for 50% of the population (IC50 in Arthrospira sp., after 72 h, was 80 mg L-1 (U and 150 mg L-1 (AB. The application of doses of 60 mg L-1 (U or 100 mg L-1 (AB in the outdoor mass culture of this contaminated microalga, completely inhibited grazing and did not affect the growth of Arthrospira sp. but rather promoted rapid recovery of algal density at levels prior to infestation. These compounds provided an economical and effective control of predators in cultures of Arthrospira sp.El cultivo de la cianobacteria Arthrospira sp. ha sido desarrollado en muchos países para la obtención de proteínas, pigmentos y otros compuestos. Cultivo que a nivel industrial se ve afectado frecuentemente por contaminación biológica, reduciendo drásticamente la productividad hasta causar la muerte. Este estudio evalúa el control de Branchionus sp. y de Amoeba sp. con dos compuestos químicos, la urea (U y bicarbonato de amonio (AB en cultivos de Arthrospira sp. La concentración letal 100 (LC100 determinada a las 24 h para Branchionus sp. y Amoeba sp. fue de 60-80 mg L-1 (U y 100-150 mg L-1 (AB. La concentración media de inhibición efectiva, después de 72 h, para el 50% de la población (IC50 en Arthrospira fue de 80 mg L-1 (U y 150 mg L-1 (AB. La aplicación de dosis de 60 mg L-1 (U ó 100 mg L-1 (AB en

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Genotype modulates testosterone-dependent activity and reactivity in male mice.

    Science.gov (United States)

    Broida, J; Svare, B

    1983-03-01

    Adult castration significantly reduced the homecage locomotor activity of both inbred C57BL/6J and DBA/2J and outbred Rockland-Swiss (R-S) male mice. Castrated C57BL animals exhibited greater reductions in this behavior than did the other genotypes. Locomotor activity in a novel environment (reactivity) was also reduced by castration but only for inbred males. In both test situations, postcastration reductions in ambulation were prevented by implants of testosterone (T)-containing Silastic capsules. Thus, testicular hormones promote activity and reactivity in the male mouse in a genotype-dependent fashion.

  8. SP mountain data analysis

    Science.gov (United States)

    Rawson, R. F.; Hamilton, R. E.; Liskow, C. L.; Dias, A. R.; Jackson, P. L.

    1981-01-01

    An analysis of synthetic aperture radar data of SP Mountain was undertaken to demonstrate the use of digital image processing techniques to aid in geologic interpretation of SAR data. These data were collected with the ERIM X- and L-band airborne SAR using like- and cross-polarizations. The resulting signal films were used to produce computer compatible tapes, from which four-channel imagery was generated. Slant range-to-ground range and range-azimuth-scale corrections were made in order to facilitate image registration; intensity corrections were also made. Manual interpretation of the imagery showed that L-band represented the geology of the area better than X-band. Several differences between the various images were also noted. Further digital analysis of the corrected data was done for enhancement purposes. This analysis included application of an MSS differencing routine and development of a routine for removal of relief displacement. It was found that accurate registration of the SAR channels is critical to the effectiveness of the differencing routine. Use of the relief displacement algorithm on the SP Mountain data demonstrated the feasibility of the technique.

  9. High-Resolution Maps of Mouse Reference Populations

    Czech Academy of Sciences Publication Activity Database

    Šimeček, Petr; Forejt, Jiří; Williams, R. W.; Shiroishi, T.; Takada, T.; Lu, L.; Johnson, T. E.; Bennett, B.; Deschepper, C. F.; Scott-Boyer, M.P.; de Villena, F.P.M.; Churchill, G. A.

    2017-01-01

    Roč. 7, č. 10 (2017), s. 3427-3434 ISSN 2160-1836 R&D Projects: GA ČR GA16-01969S; GA MŠk(CZ) LM2015040; GA MŠk(CZ) LQ1604 Institutional support: RVO:68378050 Keywords : chromosome substitution strains * recombinant inbred strains * mouse diversity genotyping array * gene conversions Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 2.861, year: 2016

  10. Prevotella timonensis sp. nov., isolated from a human breast abscess.

    Science.gov (United States)

    Glazunova, Olga O; Launay, Thierry; Raoult, Didier; Roux, Véronique

    2007-04-01

    Gram-negative anaerobic rods were isolated from a human breast abscess. Based on genotypic and phenotypic characteristics, the novel strain belonged to the genus Prevotella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that it was closely related to Prevotella buccalis (94 % 16S rRNA gene sequence similarity), Prevotella salivae (90 %) and Prevotella oris (89.1 %). The major cellular fatty acid was C(14 : 0) (19.5 %). The new isolate represents a novel species in the genus Prevotella, for which the name Prevotella timonensis sp. nov. is proposed. The type strain is strain 4401737(T) (=CIP 108522(T)=CCUG 50105(T)).

  11. Nocardiopsis potens sp. nov., isolated from household waste.

    Science.gov (United States)

    Yassin, A F; Spröer, C; Hupfer, H; Siering, C; Klenk, H-P

    2009-11-01

    The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

  12. Gaze beats mouse

    DEFF Research Database (Denmark)

    Mateo, Julio C.; San Agustin, Javier; Hansen, John Paulin

    2008-01-01

    Facial EMG for selection is fast, easy and, combined with gaze pointing, it can provide completely hands-free interaction. In this pilot study, 5 participants performed a simple point-and-select task using mouse or gaze for pointing and a mouse button or a facial-EMG switch for selection. Gaze...

  13. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  14. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  15. Inheritance and Bulked Segregant Analysis of Leaf Rust and Stem Rust Resistance in Durum Wheat Genotypes.

    Science.gov (United States)

    Aoun, Meriem; Kolmer, James A; Rouse, Matthew N; Chao, Shiaoman; Bulbula, Worku Denbel; Elias, Elias M; Acevedo, Maricelis

    2017-12-01

    Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and bulked segregant analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized in durum. The single dominant Lr genes in PI 209274, PI 244061, PI387263, and PI 313096 were mapped to chromosome arms 6BS, 2BS, 6BL, and 6BS, respectively. The Sr gene in PI 534304 mapped to 6AL and is most likely Sr13, while the Sr gene in PI 192051 could be uncharacterized in durum.

  16. SP-100 Test Site

    International Nuclear Information System (INIS)

    Cox, C.M.; Mahaffey, M.K.; Miller, W.C.

    1988-01-01

    Preparatory activities are well under way at Hanford to convert the 309 Containment Building and its associated service wing to a 2.5 MWt nuclear test facility for the SP-100 Ground Engineering System (GES) test. Preliminary design is complete, encompassing facility modifications, a secondary heat transport system, a large vacuum system to enclose the high temperature reactor, a test assembly cell and handling system, control and data processing systems, and safety and auxiliary systems. The design makes extensive use of existing equipment to minimize technical risk and cost. Refurbishment of this equipment is 75% complete. The facility has been cleared of obstructing equipment from its earlier reactor test. Current activities are focusing on definitive design and preparation of the Preliminary Safety Analysis Report (PSAR) aimed at procurement and construction approvals and schedules to achieve reactor criticality by January 1992. 6 refs

  17. Streptococcus moroccensis sp. nov. and Streptococcus rifensis sp. nov., isolated from raw camel milk.

    Science.gov (United States)

    Kadri, Zaina; Amar, Mohamed; Ouadghiri, Mouna; Cnockaert, Margo; Aerts, Maarten; El Farricha, Omar; Vandamme, Peter

    2014-07-01

    Two catalase- and oxidase-negative Streptococcus-like strains, LMG 27682(T) and LMG 27684(T), were isolated from raw camel milk in Morocco. Comparative 16S rRNA gene sequencing assigned these bacteria to the genus Streptococcus with Streptococcus rupicaprae 2777-2-07(T) as their closest phylogenetic neighbour (95.9% and 95.7% similarity, respectively). 16S rRNA gene sequence similarity between the two strains was 96.7%. Although strains LMG 27682(T) and LMG 27684(T) shared a DNA-DNA hybridization value that corresponded to the threshold level for species delineation (68%), the two strains could be distinguished by multiple biochemical tests, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes and by their MALDI-TOF MS profiles. On the basis of these considerable phenotypic and genotypic differences, we propose to classify both strains as novel species of the genus Streptococcus, for which the names Streptococcus moroccensis sp. nov. (type strain, LMG 27682(T)  = CCMM B831(T)) and Streptococcus rifensis sp. nov. (type strain, LMG 27684(T)  = CCMM B833(T)) are proposed. © 2014 IUMS.

  18. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-01-01

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

  19. Atypical Toxoplasma gondii genotype in feral cats from the Fernando de Noronha Island, northeastern Brazil.

    Science.gov (United States)

    Melo, R P B; Almeida, J C; Lima, D C V; Pedrosa, C M; Magalhães, F J R; Alcântara, A M; Barros, L D; Vieira, R F C; Garcia, J L; Mota, R A

    2016-07-15

    Toxoplasma gondii isolates from Brazil have a different phenotypic and genotypic pattern, with predominance of virulent isolates and recombinant genotypes, compared to the North Hemisphere. Considering that a new T. gondii genotype, non-pathogenic to mice, was previously identified from free-range chickens from the Fernando de Noronha Island, Brazil, this study aimed to identify genotypes of this parasite in tissue samples of feral cats (Felis catus) from this Brazilian Island. Anti-T. gondii IgG antibodies were detected in 18/31 (58%) feral cats. Two non-virulent T. gondii isolates were obtained by mouse bioassay. Genotyping was performed by PCR-RFLP using 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, PK1, L358 and Apico) and an atypical strain of T. gondii (ToxoDB #146) was identified. This is the first report of this genotype in feral cats. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    ... x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G x E interaction were highly significant for all yield traits. Variations due to G x E interaction were greater than those due to genotypic differences for all yield traits. Genotype x location x year ...

  1. Effect of Mahanarva fimbriolata (Hemiptera: Cercopidae) Attack on Photosynthetic Parameters of Sugarcane Genotypes of Contrasting Susceptibility.

    Science.gov (United States)

    Soares, Bruno Oliveira; Chaves, Vinicius de Vicente; Tomaz, Adriano Cirino; Kuki, Kacilda Naomi; Peternelli, Luiz Alexandre; Barbosa, Márcio Henrique Pereira

    2017-12-05

    The aim of this study was to compare the effect of spittlebug Mahanarva fimbriolata Stål (Hemiptera: Cercopidae) on photosynthetic parameters of both a susceptible (SP81-3250) and a resistant (H.Kawandang) sugarcane genotype. In the first assay, the susceptibility level of genotypes to spittlebug was confirmed by comparing damage score and chlorophyll content of the plants. In the second assay, the effect of spittlebug nymphs on photosynthetic characteristics was assessed using the following parameters: Net photosynthetic rate (A), carboxylation efficiency (A/Ci), stomata conductance (gS), transpiration (E), electron transport rate (ETR), maximum quantum yield of Photosystem 2 (PSII) (FV/FM), effective quantum yield (Y(II)), photochemical quenching (Y(NPQ)), and nonphotochemical quenching (Y(NO)). Spittlebug nymphs affected the photosynthetic process of the susceptible genotype SP81-3250 by decreasing the Chl content, ETR, FV/FM, and Y(II). However, this genotype was able to maintain A probably due to its ability to maintain stomata aperture, increase the carboxylation efficiency of Rubisco, and dissipate excess energy through the xanthophyll cycle, as Y(NPQ) increased under the spittlebug attack. On the other hand, the spittlebug did not affect Chl content and FV/FM of the H.Kawandang genotype. Furthermore, H.Kawandang increased A to compensate for the sink demand by the spittlebug by increasing stomatal aperture and carboxylation efficiency and increasing efficiency of the photochemical apparatus in converting light energy into chemical products. We can conclude that the feeding habits of spittlebug nymphs have different impacts on photosynthesis of susceptible and resistant sugarcane genotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  3. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  4. Mouse Phenome Database (MPD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Mouse Phenome Database (MPD) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection...

  5. Prolonged Ketamine Effects in Sp4 Hypomorphic Mice: Mimicking Phenotypes of Schizophrenia.

    Directory of Open Access Journals (Sweden)

    Baohu Ji

    Full Text Available It has been well established that schizophrenia patients display impaired NMDA receptor (NMDAR functions as well as exacerbation of symptoms in response to NMDAR antagonists. Abnormal NMDAR signaling presumably contributes to cognitive deficits which substantially contribute to functional disability in schizophrenia. Establishing a mouse genetic model will help investigate molecular mechanisms of hypoglutmatergic neurotransmission in schizophrenia. Here, we examined the responses of Sp4 hypomorphic mice to NMDAR antagonists in electroencephalography and various behavioral paradigms. Sp4 hypomorphic mice, previously reported to have reduced NMDAR1 expression and LTP deficit in hippocampal CA1, displayed increased sensitivity and prolonged responses to NMDAR antagonists. Molecular studies demonstrated reduced expression of glutamic acid decarboxylase 67 (GAD67 in both cortex and hippocampus, consistent with abnormal gamma oscillations in Sp4 hypomorphic mice. On the other hand, human SP4 gene was reported to be deleted in schizophrenia. Several human genetic studies suggested the association of SP4 gene with schizophrenia and other psychiatric disorders. Therefore, elucidation of the Sp4 molecular pathway in Sp4 hypomorphic mice may provide novel insights to our understanding of abnormal NMDAR signaling in schizophrenia.

  6. Bradysia sp. em morangueiro Bradysia sp. in strawberry

    Directory of Open Access Journals (Sweden)

    Bernadete Radin

    2009-04-01

    Full Text Available No trabalho, relatam-se os primeiros registros de Bradysia sp. (Insecta: Diptera: Sciaridae em morangueiro (Fragaria x ananassa Duch., cultivado no Município de Eldorado do Sul, RS. O cultivo foi realizado em sacolas com três metros de comprimento, preenchidas com substrato composto de casca de arroz e turfa, dispostas horizontalmente sobre bancadas de madeira, em ambiente protegido. A presença de Bradysia sp. foi observada na segunda quinzena de agosto de 2005. Neste trabalho, estão descritos os sintomas apresentados no morangueiro pela praga, prováveis conseqüências sobre o aparecimento de doenças e uma breve descrição morfológica da Bradysia sp., adulto e fase larval.This paper describes the first record of Bradysia sp. (Insecta; Diptera; Sciaridae in strawberry (Fragaria x ananassa, cultivated in the city of Eldorado do Sul, RS, Brazil. Strawberry was planted in plastic bags filled with a mixture of burnt rice hulls and peat and cultivated in a greenhouse. The presence of Bradysia sp was noticed in the second fortnight of August, 2005. The symptoms in strawberry and the probable consequences in terms of disease arising were described in the present study, as well as the morphological characterization of Bradysia sp. and its illustrations.

  7. Yersinia pekkanenii sp. nov.

    Science.gov (United States)

    Murros-Kontiainen, Anna; Johansson, Per; Niskanen, Taina; Fredriksson-Ahomaa, Maria; Korkeala, Hannu; Björkroth, Johanna

    2011-10-01

    The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA-DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA-DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7.1KOH2(T) ( = DSM 22769(T)  = LMG 25369(T)).

  8. Infectivity of Trichinella spp. recovered from decaying mouse and fox muscle tissue

    DEFF Research Database (Denmark)

    Von Koller, J.; Kapel, C.M.O.; Enemark, Heidi L.

    2001-01-01

    The tolerance to degradation processes in meat of nine Trichinella genotypes was studied in mouse and fox tissue, respectively. Minced muscle tissue with Trichinella larvae of different age was stored at room temperature at 100 % relative humidity. During storage weekly sub samples of the minced...

  9. Antimicrobial peptides from Capsicum sp.

    African Journals Online (AJOL)

    ajl yemi

    2011-12-30

    Dec 30, 2011 ... Key words: Antimicrobial peptides, Capsicum sp, Capsicum chinense, chili pepper, agronomical options, ..... of this human activity is resumed by the simple phrase: produce .... It will be interesting to scale the AMPs extraction.

  10. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

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

    2017-11-01

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

  11. An epistatic effect of KRT25 on SP6 is involved in curly coat in horses.

    Science.gov (United States)

    Thomer, Annika; Gottschalk, Maren; Christmann, Anna; Naccache, Fanny; Jung, Klaus; Hewicker-Trautwein, Marion; Distl, Ottmar; Metzger, Julia

    2018-04-23

    Curly coat represents an extraordinary type of coat in horses, particularly seen in American Bashkir Curly Horses and Missouri Foxtrotters. In some horses with curly coat, a hypotrichosis of variable extent was observed, making the phenotype appear more complex. In our study, we aimed at investigating the genetic background of curly coat with and without hypotrichosis using high density bead chip genotype and next generation sequencing data. Genome-wide association analysis detected significant signals (p = 1.412 × 10 -05 -1.102 × 10 -08 ) on horse chromosome 11 at 22-35 Mb. In this significantly associated region, six missense variants were filtered out from whole-genome sequencing data of three curly coated horses of which two variants within KRT25 and SP6 could explain all hair phenotypes. Horses heterozygous or homozygous only for KRT25 variant showed curly coat and hypotrichosis, whereas horses with SP6 variant only, exhibited curly coat without hypotrichosis. Horses with mutant alleles in both variants developed curly hair and hypotrichosis. Thus, mutant KRT25 allele is masking SP6 allele effect, indicative for epistasis of KRT25 variant over SP6 variant. In summary, genetic variants in two different genes, KRT25 and SP6, are responsible for curly hair. All horses with KRT25 variant are additionally hypotrichotic due to the KRT25 epistatic effect on SP6.

  12. Immunostimulatory mouse granuloma protein.

    Science.gov (United States)

    Fontan, E; Fauve, R M; Hevin, B; Jusforgues, H

    1983-10-01

    Earlier studies have shown that from subcutaneous talc-induced granuloma in mice, a fraction could be extracted that fully protected mice against Listeria monocytogenes. Using standard biochemical procedures--i.e., ammonium sulfate fractionation, preparative electrophoresis, gel filtration chromatography, isoelectric focusing, and preparative polyacrylamide gel electrophoresis--we have now purified an active factor to homogeneity. A single band was obtained in NaDodSO4/polyacrylamide gel with an apparent Mr of 55,000. It migrated with alpha 1-globulins and the isoelectric point was 5 +/- 0.1. The biological activity was destroyed with Pronase but not with trypsin and a monospecific polyclonal rabbit antiserum was obtained. The intravenous injection of 5 micrograms of this "mouse granuloma protein" fully protects mice against a lethal inoculum of L. monocytogenes. Moreover, after their incubation with 10 nM mouse granuloma protein, mouse peritoneal cells became cytostatic against Lewis carcinoma cells.

  13. Burn mouse models

    DEFF Research Database (Denmark)

    Calum, Henrik; Høiby, Niels; Moser, Claus

    2014-01-01

    Severe thermal injury induces immunosuppression, involving all parts of the immune system, especially when large fractions of the total body surface area are affected. An animal model was established to characterize the burn-induced immunosuppression. In our novel mouse model a 6 % third-degree b......Severe thermal injury induces immunosuppression, involving all parts of the immune system, especially when large fractions of the total body surface area are affected. An animal model was established to characterize the burn-induced immunosuppression. In our novel mouse model a 6 % third...... with infected burn wound compared with the burn wound only group. The burn mouse model resembles the clinical situation and provides an opportunity to examine or develop new strategies like new antibiotics and immune therapy, in handling burn wound victims much....

  14. Applications of blood group genotyping

    Directory of Open Access Journals (Sweden)

    Mariza A. Mota

    2006-03-01

    Full Text Available Introduction: The determination of blood group polymorphism atthe genomic level facilitates the resolution of clinical problemsthat cannot be addressed by hemagglutination. They are useful to(a determine antigen types for which currently available antibodiesare weakly reactive; (b type patients who have been recentlytransfused; (c identify fetuses at risk for hemolytic disease of thenewborn; and (d to increase the reliability of repositories of antigennegative RBCs for transfusion. Objectives: This review assessedthe current applications of blood group genotyping in transfusionmedicine and hemolytic disease of the newborn. Search strategy:Blood group genotyping studies and reviews were searched ingeneral database (MEDLINE and references were reviewed.Selection criteria: All published data and reviews were eligible forinclusion provided they reported results for molecular basis ofblood group antigens, DNA analysis for blood group polymorphisms,determination of fetal group status and applications of blood groupgenotyping in blood transfusion. Data collection: All data werecollected based on studies and reviews of blood grouppolymorphisms and their clinical applications.

  15. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  16. Molecular epidemiology and genotyping of hepatitis B virus of HBsAg-positive patients in Oman.

    Science.gov (United States)

    Al Baqlani, Said Ali; Sy, Bui Tien; Ratsch, Boris A; Al Naamani, Khalid; Al Awaidy, Salah; Busaidy, Suleiman Al; Pauli, Georg; Bock, C-Thomas

    2014-01-01

    Hepatitis B virus (HBV) infection is a major global health burden with distinct geographic public health significance. Oman is a country with intermediate HBV carrier prevalence; however, little is known about the incidence of HBV variants in circulation. We investigated the HBV genotype distribution, the occurrence of antiviral resistance, and HBV surface antigen (HBsAg) escape mutations in HBsAg-positive patients in Oman. Serum samples were collected from 179 chronically HBV-infected patients enrolled in various gastroenterology clinics in Oman. HBV genotypes were determined by sequencing and phylogenetic analysis. Mutations in the HBV polymerase and the HBsAg gene were characterized by mutational analysis. HBV genotypes D (130/170; 76.47%) and A (32/170; 18.28%) are predominant in Oman. The HBV genotypes C and E were less frequent (each 1.18%), while the HBV genotypes B, G, F, and H were not detected. Four patients revealed HBV genotype mixtures (HBV-A/D and D/C). The analyses of vaccine escape mutations yield that 148/170 (87.06%) HBV sequences were wild type. 22/170 (12.94%) HBV sequences showed mutations in the "a" determinant of the HBsAg domain. Two patients showed the described HBV vaccine escape mutation sP120T. 8/146 (5.48%) HBV isolates harbored mutations in the HBV polymerase known to confer resistance against antiviral therapy. Especially the lamivudine resistance mutations rtL180M/rtM204V and rtM204I were detected. This study shows the distribution of HBV genotypes, therapy resistance, and vaccine escape mutations in HBV-infected patients in Oman. Our findings will have a major impact on therapy management and diagnostics of chronic HBV infections in Oman to control HBV infection in this intermediate HBV-endemic country.

  17. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

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

    2017-10-01

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

  18. Characterization of mutations at the mouse phenylalanine hydroxylase locus

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, J.D.; Charlton, C.K. [Wichita State Univ., KS (United States)

    1997-02-01

    Two genetic mouse models for human phenylketonuria have been characterized by DNA sequence analysis. For each, a distinct mutation was identified within the protein coding sequence of the phenylalanine hydroxylase gene. This establishes that the mutated locus is the same as that causing human phenylketonuria and allows a comparison between these mouse phenylketonuria models and the human disease. A genotype/phenotype relationship that is strikingly similar to the human disease emerges, underscoring the similarity of phenylketonuria in mouse and man. In PAH{sup ENU1}, the phenotype is mild. The Pah{sup enu1} mutation predicts a conservative valine to alanine amino acid substitution and is located in exon 3, a gene region where serious mutations are rare in humans. In PAH{sup ENU2} the phenotype is severe. The Pah{sup enu2} mutation predicts a radical phenylalanine to serine substitution and is located in exon 7, a gene region where serious mutations are common in humans. In PAH{sup ENU2}, the sequence information was used to devise a direct genotyping system based on the creation of a new Alw26I restriction endonuclease site. 26 refs., 2 figs., 1 tab.

  19. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

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

    2016-07-21

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

  20. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-12-01

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

  1. Blood genotyping for improved outcomes in chronic transfusion patients: current and future perspectives

    Directory of Open Access Journals (Sweden)

    Kutner JM

    2014-09-01

    Full Text Available Jose Mauro Kutner,1 Mariza Mota,1 Fabiana Conti,1 Lilian Castilho1,2 1Hemotherapy and Cell Therapy Department, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; 2Hemocentro Unicamp, Campinas, SP, Brazil Abstract: Blood transfusions are life sustaining in chronically transfused patients. However, certain complications, such as alloimmunization to red blood cells, can create challenges in the management of those patients. Routine phenotyping of blood recipients and the use of phenotype-matched blood units for transfusion have been useful to lower the occurrence of red cell alloantibodies in chronically transfused individuals. Nevertheless, extensive phenotyping is expensive, laborious, and cannot be performed in certain situations. The molecular understanding of blood groups has enabled the design of assays that may be used to better guide matched red blood cell transfusions. This review summarizes key findings related to red cell alloimmunization, the already identified and potential future benefits of blood group genotyping, and how molecular typing is being incorporated in the blood bank's routine to improve clinical and long-term outcomes in chronically transfused patients. Keywords: blood group genotyping, chronically transfused patients, platelet genotyping, RBC alloimmunization

  2. Seroprevalencia de Leptospira sp., Rickettsia sp. Ehrlichia sp. en trabajadores rurales del departamento de Sucre, Colombia Seroprevalence of Leptospira sp., Rickettsia sp. and Ehrlichia sp. in rural workers of Sucre, Colombia

    Directory of Open Access Journals (Sweden)

    Rodrigo Ríos

    2008-06-01

    Full Text Available Objective. Determinar la seroprevalencia de Leptospira sp., Rickettsia sp. y Ehrlichia sp. en trabajadores de áreas rurales del departamento de Sucre. Material y métodos. Se realizó un estudio escriptivo, prospectivo, de corte transversal, que pretendió determinar la seroprevalencia e Leptospira sp., Rickettsia sp. y Ehrlichia sp. en 90 trabajadores de áreas rurales del departamento de Sucre. Se estableció la presencia de anticuerpos séricos anti-IgM específicos anti-Leptospira por la técnica de ELISA indirecta. Para la determinación de Rickettsia sp. y Ehrlichia sp. se uso la técnica de inmunofluorescencia indirecta. Resultados. La población evaluada estaba compuesta por 27 (30% ordeñadores, 21 (23% jornaleros, 18 (20% profesionales del campo y 24 (27% que realizaban otras actividades. Ventidós (24% muestras resultaron positivas en alguna de las pruebas. De éstas, 12 (13,3% fueron positivas para Leptospira sp., 7 (7,8% para Rickettsia sp. y 3 (3,3% ara Ehrlichia sp. Conclusión. Este fue el primer estudio que se llevó a cabo en el departamento de Sucre y permitió demostrar que existe una prevalencia importante de Leptospira p.,Rickettsia sp. y Ehrlichia sp.. Los factores de riesgo ocupacional fueron factores determinantes en la seropositividad.Objective. To determine the seroprevalence of Leptospira sp., Rickettsia sp. and Ehrlichia sp. in agricultural workers of Sucre. Methods. A descriptive prospective cross-sectional study was conducted in ninety rural workers of Sucre. Presence of serum antibodies anti-IgM specific anti-Leptospira by indirect ELISA was established. For the determination of Rickettsia and Ehrlichia indirect inmunoflorescence was used. Results.The population was composed by 27 (30% milkers, 21 (23% day workers, 18 farm professionals (20% and 24 (26% workers in others activities. A total of 22 (24% samples were positive to some test. Twelve (13.3% were positive to Leptospira sp., seven (7.8% to Rickettsia sp

  3. Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk.

    Science.gov (United States)

    von Neubeck, Mario; Huptas, Christopher; Glück, Claudia; Krewinkel, Manuel; Stoeckel, Marina; Stressler, Timo; Fischer, Lutz; Hinrichs, Jörg; Scherer, Siegfried; Wenning, Mareike

    2017-06-01

    Five strains, designated WS 4672T, WS 4998, WS 4992T, WS 4997 and WS 5000, isolated from bovine raw milk formed two individual groups in a phylogenetic analysis. The most similar species on the basis of 16S rRNA gene sequences were Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T showing 99.7-99.6 % similarity. Using rpoD gene sequences Pseudomonas veronii LMG 17761T (93.3 %) was most closely related to strain WS 4672T and Pseudomonas libanensis CIP 105460T to strain WS 4992T (93.3 %). The five strains could be differentiated from their closest relatives and from each other by phenotypic and chemotaxonomic characterization and ANIb values calculated from draft genome assemblies. ANIb values of strains WS 4992T and WS4671T to the closest relatives are lower than 90 %. The major cellular polar lipids of both strains are phosphatidylethanolamine, phosphatidylglycerol, a phospholipid and diphosphatidylglycerol, and their major quinone is Q-9. The DNA G+C content of strains WS 4992T and WS 4672T were 60.0  and 59.7  mol%, respectively. Based on these genotypic and phenotypic traits two novel species of the genus Pseudomonas are proposed: Pseudomonas lactis sp. nov. [with type strain WS 4992T (=DSM 29167T=LMG 28435T) and the additional strains WS 4997 and WS 5000], and Pseudomonasparalactis sp. nov. [with type strain WS 4672T (=DSM 29164T=LMG 28439T) and additional strain WS 4998].

  4. Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.

    Science.gov (United States)

    Lee, Hyo-Jin; Whang, Kyung-Sook

    2016-09-01

    Three novel isolates belonging to the genus Streptomyces, designated JR-35T, JR-46 and WH-9T, were isolated from bamboo forest soil in Damyang, Korea. The 16S rRNA gene sequences of strains JR-35T and JR-46 showed highest similarities with Streptomyces olivochromogenes NBRC 3178T (99.1 %), Streptomyces siamensis KC-038T (98.9 %), Streptomyces chartreusis NBRC 12753T (98.9 %), Streptomyces resistomycificus NRRL ISP-5133T (98.9 %) and Streptomyces bobili JCM 4627T (98.8 %), and strain WH-9Tshowed highest sequence similarities with Streptomyces. bobili JCM 4627T (99.2 %), Streptomyces phaeoluteigriseus NRRL ISP-5182T (99.2 %), Streptomyces alboniger NBRC 12738T (99.2 %), Streptomyces galilaeus JCM 4757T (99.1 %) and Streptomyces pseudovenezuelae NBRC 12904T (99.1 %). The predominant menaquinones were MK-9 (H6) and MK-9 (H8). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0 for strains JR-35T and JR-46 and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 for strain WH-9T. The G+C content of the genomic DNA of strains JR-35T, JR-46 and WH-9T were 69.4, 74.4 and 74.1 mol%, respectively. Based on the phenotypic and genotypic data, the three strains are assigned to two novel species of the genus Streptomyces, for which the names Streptomyces rhizosphaerihabitans sp. nov. (type stain JR-35T=KACC 17181T=NBRC 109807T) and Streptomyces adustus sp. nov. (type strain WH-9T=KACC 17197T=NBRC 109810T) are proposed.

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

    Science.gov (United States)

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

    2015-01-01

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

  6. Colonization, mouse-style

    Directory of Open Access Journals (Sweden)

    Searle Jeremy B

    2010-10-01

    Full Text Available Abstract Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice. See research article: http://www.biomedcentral.com/1471-2148/10/325

  7. SP-100 reactor cell activation

    International Nuclear Information System (INIS)

    Wilcox, A.D.

    1991-09-01

    There are plans to test the SP-100 space reactor for 2 yr in the test facility shown in Figure 1. The vacuum vessel will be in the reactor experiment (RX) cell surrounded by an inert gas atmosphere. It is proposed that the reactor test cell could contain removable-water- shielding tanks to reduce the residual activation dose rates in the test cell after the tests are completed. This reduction will allow the facility to be considered for other uses after the SP-100 tests are completed. The radiation dose rates in the test cell were calculated for several configurations of water-shielding tanks to help evaluate this concept

  8. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  9. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among cultivar, microsatellite markers were used in their analysis. The microsatellite profiles of 44 Musa genotypes of various origins.

  10. In vitro Culture of a Novel Genotype of Ehrlichia sp from Brazil

    Czech Academy of Sciences Publication Activity Database

    Zweygarth, E.; Schol, H.; Lis, K.; Cabezas Cruz, Alejandro; Thiel, C.; Silaghi, C.; Ribeiro, M.F.B.; Passos, L.M.F.

    2013-01-01

    Roč. 60, NOV 2013 (2013), s. 86-92 ISSN 1865-1674 Grant - others:EU(XE) FP7-PEOPLE-ITN No.238511 Institutional support: RVO:60077344 Keywords : Ehrlichia * Rhipicephalus (Boophilus) microplus * in vitro culture * tick cell * DH82 * endothelial cell * cattle * 16S rRNA * Brazil Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.116, year: 2013

  11. First genotyping of Blastocystis sp. in dairy, meat, and cashmere goats in northwestern China.

    Science.gov (United States)

    Song, Jun-Ke; Yin, Yan-Ling; Yuan, Ya-Jie; Tang, Huan; Ren, Guan-Jing; Zhang, Hui-Jun; Li, Zi-Xuan; Zhang, Yan-Ming; Zhao, Guang-Hui

    2017-12-01

    Blastocystis is one of the most common parasites inhabiting in small intestines of human and animals. Although its pathogenicity has been remaining controversial, the possibility of zoonotic transmission between human and animals was recognized. The goat was one of the most important economic animals supplying people with cashmere, meat, and dairy products. However, few studies were to investigate Blastocystis infection in goats. A total of 789 faecal specimens of goats (including 362 of dairy, 193 of meat and 234 of cashmere goats) were collected from multiple regions of Shaanxi province in northwestern China to investigate the colonization frequency and subtypes of Blastocystis, and to assess the zoonotic potential of these goats. The respective colonization frequencies of Blastocystis in dairy, meat and cashmere goats were 54.1% (196/362), 40.4% (78/193) and 78.6% (184/234). The prevalence of Blastocystis in pre-weaned (0-2-month) goats was significantly lower than that in goats of other age groups, and the highest colonization was observed in goats of 7-11-month age group. Sequence analysis of Blastocystis positive samples indicated the presence of seven subtypes in these goats, including six known subtypes (STs1, 3, 4, 5, 10, 14) and one possible novel subtype (isolate Sd26), with the subtype 10 as the predominant one. Additionally, zoonotic subtypes were found in dairy (ST1, ST3 and ST5) and cashmere (ST4 and ST5) goats, but not detected in meat goats. These results showed that Blastocystis is highly prevalent, widely distributed and genetically diverse in goats in Shaanxi province, northwestern China, and zoonotic potential of dairy and cashmere goats to transmit Blastocystis. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Phenotypic and Genotypic Antimicrobial Resistance of Lactococcus Sp. Strains Isolated from Rainbow Trout (Oncorhynchus Mykiss

    Directory of Open Access Journals (Sweden)

    Ture Mustafa

    2015-04-01

    Full Text Available A current profile of antimicrobial resistance and plasmid of 29 Lactococcus garvieae and one Lactococcus lactis strains isolated from rainbow trouts (Oncorhynchus mykiss from farms throughout Turkey were investigated. All isolates were sensitive to penicillin G (90%, ampicillin (86.7%, florfenicol (83.3%, amoxicillin (80.1%, and tetracycline (73.4%, and resistant to trimethoprim+sulfamethoxazole (86.6% and gentamycin (46.6% by disc diffusion method. Twenty-eight (93% isolates had two to seven antibiotic resistance genes (ARGs determined by PCR. The most prevalent ARGs were tetracycline (tetB, erythromycin (ereB, and β-lactam (blaTEM. Bacterial strains were also screened for plasmid DNA by agarose gel electrophoresis and two strains harboured plasmids, with sizes ranging from 3 to 9 kb.

  13. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers.

    Science.gov (United States)

    Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Al-Dhabi, N A; Ignacimuthu, S

    2016-01-01

    We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60-70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard's similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard's similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on

  14. Xenophilus aerolatus sp. nov., isolated from air.

    Science.gov (United States)

    Kim, Soo-Jin; Kim, Yi-Seul; Weon, Hang-Yeon; Anandham, Rangasamy; Noh, Hyung-Jun; Kwon, Soon-Wo

    2010-02-01

    A novel aerobic, Gram-negative, motile, rod-shaped bacterial strain designated 5516S-2(T) was isolated from an air sample taken in Suwon, Republic of Korea. Colonies were yellow-pigmented and circular with entire margins. 16S rRNA gene sequence analysis showed that strain 5516S-2(T) was closely related to Xylophilus ampelinus DSM 7250(T) (97.6 % sequence similarity), Variovorax soli KACC 11579(T) (97.5 %) and Xenophilus azovorans DSM 13620(T) (97.1 %). However, the phylogenetic tree indicated that strain 5516S-2(T) formed a separate clade from Xenophilus azovorans. Strain 5516S-2(T) displayed 42, 31 and 30 % DNA-DNA relatedness to the type strains of Xenophilus azovorans, Xylophilus ampelinus and V. soli, respectively. The major fatty acids (>10 % of total fatty acids) were C(16 : 0) (33.3 %), C(17 : 0) cyclo (18.8 %), C(18 : 1)omega7c (17.5 %) and summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 13.0 %). The DNA G+C content was 69 mol%. The major quinone was ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Genotypic and phenotypic characteristics clearly distinguished strain 5516S-2(T) from closely related species and indicated that it represents a novel species within the genus Xenophilus, for which the name Xenophilus aerolatus sp. nov. is proposed. The type strain is 5516S-2(T) (=KACC 12602(T)=DSM 19424(T)).

  15. Streptomyces xylanilyticus sp. nov., isolated from soil.

    Science.gov (United States)

    Moonmangmee, Duangtip; Kanchanasin, Pawina; Phongsopitanun, Wongsakorn; Tanasupawat, Somboon; Moonmangmee, Somporn

    2017-10-01

    A novel actinomycete, strain SR2-123 T , belonging to the genus Streptomyces, was isolated from a soil sample collected from the Sakaerat Environmental Research Station, Thailand Institute of Scientific and Technological Research, Nakhon Ratchasima Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic study. Strain SR2-123 T contained ll-diaminopimelic acid, glucose, mannose and ribose in whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. Menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid, unknown glycolipids, an unknown aminophospholipid, unknown lipids and an unknown aminolipid. The DNA G+C content was 74.8 mol%. The strain was closely related to Streptomyces coeruleorubidus JCM 4359 T (98.5 %), Streptomyces flavofungini JCM 4753 T (98.5 %), Streptomyces coerulescens NBRC 12758 T (98. 5 %) and Streptomyces alboflavus JCM 4615 T (98.4 %), based on 16S rRNA gene sequence similarities. The novel strain exhibited low DNA-DNA relatedness values with the type strains (11.4-25.0 %) of closely related species. On the basis of phenotypic and genotypic characteristics, strain SR2-123 T could be distinguished from closely related species of the genus Streptomyces and represents a novel species of the genus Streptomyces for which the name Streptomyces xylanilyticus sp. nov. is proposed. The type strain is SR2-123 T (=TISTR 2493 T =KCTC 39909 T ).

  16. The Mouse That Soared

    Science.gov (United States)

    2004-09-01

    Astronomers have used an X-ray image to make the first detailed study of the behavior of high-energy particles around a fast moving pulsar. The image, from NASA's Chandra X-ray Observatory, shows the shock wave created as a pulsar plows supersonically through interstellar space. These results will provide insight into theories for the production of powerful winds of matter and antimatter by pulsars. Chandra's image of the glowing cloud, known as the Mouse, shows a stubby bright column of high-energy particles, about four light years in length, swept back by the pulsar's interaction with interstellar gas. The intense source at the head of the X-ray column is the pulsar, estimated to be moving through space at about 1.3 million miles per hour. VLA Radio Image of the Mouse, Full Field VLA Radio Image of the Mouse, Full Field A cone-shaped cloud of radio-wave-emitting particles envelopes the X-ray column. The Mouse, a.k.a. G359.23-0.82, was discovered in 1987 by radio astronomers using the National Science Foundation's Very Large Array in New Mexico. It gets its name from its appearance in radio images that show a compact snout, a bulbous body, and a remarkable long, narrow, tail that extends for about 55 light years. "A few dozen pulsar wind nebulae are known, including the spectacular Crab Nebula, but none have the Mouse's combination of relatively young age and incredibly rapid motion through interstellar space," said Bryan Gaensler of the Harvard-Smithsonian Center for Astrophysics and lead author of a paper on the Mouse that will appear in an upcoming issue of The Astrophysical Journal. "We effectively are seeing a supersonic cosmic wind tunnel, in which we can study the effects of a pulsar's motion on its pulsar wind nebula, and test current theories." Illustration of the Mouse System Illustration of the Mouse System Pulsars are known to be rapidly spinning, highly magnetized neutron stars -- objects so dense that a mass equal to that of the Sun is packed into a

  17. Bifidobacterium aquikefiri sp. nov., isolated from water kefir.

    Science.gov (United States)

    Laureys, David; Cnockaert, Margo; De Vuyst, Luc; Vandamme, Peter

    2016-03-01

    A novel Bifidobacterium , strain LMG 28769 T , was isolated from a household water kefir fermentation process. Cells were Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, oxidase-negative and facultatively anaerobic short rods. Analysis of its 16S rRNA gene sequence revealed Bifidobacterium crudilactis and Bifidobacterium psychraerophilum (97.4 and 97.1 % similarity towards the respective type strain sequences) as nearest phylogenetic neighbours. Its assignment to the genus Bifidobacterium was confirmed by the presence of fructose 6-phosphate phosphoketolase activity. Analysis of the hsp60 gene sequence revealed very low similarity with nucleotide sequences in the NCBI nucleotide database. The genotypic and phenotypic analyses allowed the differentiation of strain LMG 28769 T from all recognized Bifidobacterium species. Strain LMG 28769 T ( = CCUG 67145 T  = R 54638 T ) therefore represents a novel species, for which the name Bifidobacterium aquikefiri sp. nov. is proposed.

  18. Prevotella maculosa sp. nov., isolated from the human oral cavity.

    Science.gov (United States)

    Downes, Julia; Sutcliffe, Iain C; Booth, Veronica; Wade, William G

    2007-12-01

    Three strains of anaerobic Gram-negative bacilli isolated from human oral sites were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed the strains to constitute a novel group within the genus Prevotella, most closely related to Prevotella oris and Prevotella salivae. A novel species, Prevotella maculosa sp. nov., is proposed to accommodate these strains. Prevotella maculosa is saccharolytic and produces acetic and succinic acids as end products of fermentation. The G+C content of the DNA of the type strain is 48 mol%. The type strain of Prevotella maculosa is W1609(T) (=DSM 19339(T) =CCUG 54766(T)).

  19. Captive-bred neotropical birds diagnosed with Cryptosporidium Avian genotype III.

    Science.gov (United States)

    Silva Novaes, Ricardo; Pires, Marcus Sandes; Sudré, Adriana Pittella; Bergamo do Bomfim, Teresa Cristina

    2018-02-01

    Currently, there are only three valid species of Cryptosporidium infecting avian hosts, namely, Cryptosporidium meleagridis, Cryptosporidium baileyi, Cryptosporidium galli and Cryptosporidium avium in addition to 12 genotypes of unknown species status. The objectives of this study were to microscopically diagnose the presence of Cryptosporidium in birds from a commercial aviary located in Rio de Janeiro, Brazil; genotypically characterize species and/or genotypes of genus Cryptosporidum; and conduct sequencing and phylogenetic analyses to compare the obtained DNA sequences with those deposited in GenBank. A total of 85 fecal samples were collected from wild captive-bred birds: 48 of family Psittacidae and 37 of family Ramphastidae. Initially, a search for the presence of Cryptosporidium sp. oocysts was conducted using the centrifugal-flotation in saturated sugar solution technique, after that, the collected samples were analyzed microscopically. Cryptosporidium infections were only detected in 24.32% of samples belonging to the family Ramphastidae. DNA was extracted from positive samples and molecular diagnostics was applied targeting the 18S rRNA gene, followed by sequencing and phylogenetic analysis. The Cryptosporidium Avian genotype III was diagnosed in this study more closely related to the gastric species. This is the first record of Cryptosporidium Avian genotype III in order Piciformes and family Ramphastidae, where three host species (Ramphastus toco, Ramphastus tucanus, and Pteroglossus bailloni) were positive for the etiologic agent. Based on the molecular data obtained, these wild birds raised in captivity do not represent a source of human cryptosporidiosis, considering that Cryptosporidium Avian genotype III does not constitute a zoonosis. Copyright © 2017. Published by Elsevier B.V.

  20. 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

  1. Common bean genotypes for agronomic and market-related traits in VCU trials

    Directory of Open Access Journals (Sweden)

    Alisson Fernando Chiorato

    2015-02-01

    Full Text Available Value for Cultivation and Use (VCU trials are undertaken when evaluating improved common bean (Phaseolus vulgaris L. lines, and knowledge of agronomic and market-related traits and disease reaction is instrumental in making cultivar recommendations. This study evaluates the yield, cooking time, grain color and reaction to anthracnose (Colletotrichum lindemuthianum, Fusarium wilt (Fusarium oxysporum f. sp. phaseoli and Curtobacterium wilt (Curtobacterium flaccumfaciens pv. flaccumfaciens of 25 common bean genotypes derived from the main common bean breeding programs in Brazil. Seventeen VCU trials were carried out in the rainy season, dry season and winter season from 2009 to 2011 in the state of São Paulo. Analyses of grain color and cooking time were initiated 60 days after harvest, and disease reaction analyses were performed in the laboratory under controlled conditions. In terms of yield, no genotype superior to the controls was observed for any of the seasons under consideration. Grains from the dry season exhibited better color, while the rainy season led to the shortest cooking times. The following genotypes BRS Esteio, BRS Esplendor and IAC Imperador were resistant to anthracnose, Fusarium wilt and Curtobacterium wilt and, in general, genotypes with lighter-colored grains were more susceptible to anthracnose and Fusarium wilt.

  2. Reaction of genotypes of lulo (Solanum quitoense Lam. to Meloidogyne spp. under field conditions

    Directory of Open Access Journals (Sweden)

    Claudia Salazar-González

    2017-05-01

    Full Text Available In Colombia, root-knot nematodes Meloidog yne spp. are considered as one of the main constraints in lulo crop production . These nematodes can cause root damage resulting in low production. The aim of this study was to evaluate under field conditions the reaction of 16 genotypes of lulo, Solanum quitoense Lam. (Solanaceae, of the Castilla variety and the species S. hirtum Vahl., previously selected in a greenhouse experiment and categorized as moderately resistant and resistant to the attack by Meloidog yne sp. A chemical treatment and a control treatment, the latter based on the most susceptible genotype in greenhouse experiments were also included. The experiment was conducted in a lulo grove naturally infested with root-knot nematodes under a randomized complete block design with three replications and nine plants per experimental unit. The response variables were incidence, severity and yield. The incidence was higher than 80 % in all cases, but the severity varied because of their genetic condition; BR03 and BR01 being genotypes with lower rates of severity, with values of 1.0 % and 0.8 %, respectively. The yield analysis of variance showed significant differences, indicating that genotypes SQBR01 and SQLF04, reached the highest values with 4.77 and 4.74 t/ha in a total of three harvests.

  3. Morphology and biomass variations in root system of young tomato plants (Solanum sp.)

    International Nuclear Information System (INIS)

    Álvarez Gil, Marta A.; Fernández, Ana Fita; Ruiz Sánchez, María del C.; Bolarín Jiménez, María del C.

    2016-01-01

    The scarce exploitation of genotypic variability present in plant roots is an attractive breeding choice with regard to abiotic stresses and supports the objective of this work, which is to identify genotypic variation in root system traits of tomato genotypes (Solanum sp.). Thus, five tomato genotypes were studied: the commercial hybrid cultivar Jaguar (S. lycopersicum), Pera, Volgogradiskij and PE-47 entry (S. pennellii), which were collected in Peru, and the interspecific hybrid PeraxPE-47. Plants were grown in hydroponics for 26 days since germination; their roots were extracted and images were digitalized on scanner to evaluate total length, average diameter, the projected area and root length, following the categories per diameter of the whole root system through software Win Rhizo Pro 2003. The dry mass of roots and aerial parts was also recorded. Results indicated that genotypes differed in morphology, length according to diameter, root system spatial configuration and biomass, mainly with respect to the wild salinity resistant species PE-47. The interspecific hybrid PxPE-47 could be used as a rootstock to increase salt tolerance of susceptible cultivars. (author)

  4. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

    Science.gov (United States)

    Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle Pca is dikaryotic with two separate haploid nuclei that may vary in virulence genotypes, which highlights the importance of understan...

  5. Developmental plasticity: re-conceiving the genotype.

    Science.gov (United States)

    Sultan, Sonia E

    2017-10-06

    In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

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

    Science.gov (United States)

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

    2010-08-01

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

  7. Incorrect strain information for mouse cell lines: sequential influence of misidentification on sublines.

    Science.gov (United States)

    Uchio-Yamada, Kozue; Kasai, Fumio; Ozawa, Midori; Kohara, Arihiro

    2017-03-01

    Misidentification or cross-contamination of cell lines can cause serious issues. Human cell lines have been authenticated by short tandem repeat profiling; however, mouse cell lines have not been adequately assessed. In this study, mouse cell lines registered with the JCRB cell bank were examined by simple sequence length polymorphism (SSLP) analysis to identify their strains. Based on comparisons with 7 major inbred strains, our results revealed their strains in 80 of 90 cell lines. However, 12 of the 80 cell lines (15%) were found to differ from registered information. Of them, 4 cell lines originated from the same mouse, which had been generated through mating between two different inbred strains. The genotype of the mouse sample had not been examined after the backcross, leading to strain misidentification in those cell lines. Although 8 other cell lines had been established as sublines of a BALB/c cell line, their SSLP profiles are similar to a Swiss cell line. This affects differences in genotypes between inbred and outbred strains. Because the use of inbred samples and interbreeding between strains are not involved in human materials, our results suggest that the cause and influence of misidentification in mouse cell lines are different from those in human.

  8. Penicillium araracuarense sp. nov., Penicillium elleniae sp. nov., Penicillium penarojense sp. nov., Penicillium vanderhammenii sp. nov. and Penicillium wotroi sp. nov., isolated from leaf litter.

    Science.gov (United States)

    Houbraken, Jos; López-Quintero, Carlos A; Frisvad, Jens C; Boekhout, Teun; Theelen, Bart; Franco-Molano, Ana Esperanza; Samson, Robert A

    2011-06-01

    Several species of the genus Penicillium were isolated during a survey of the mycobiota of leaf litter and soil in Colombian Amazon forest. Five species, Penicillium penarojense sp. nov. (type strain CBS 113178(T) = IBT 23262(T)), Penicillium wotroi sp. nov. (type strain CBS 118171(T) = IBT 23253(T)), Penicillium araracuarense sp. nov. (type strain CBS 113149(T) = IBT 23247(T)), Penicillium elleniae sp. nov. (type strain CBS 118135(T) = IBT 23229(T)) and Penicillium vanderhammenii sp. nov. (type strain CBS 126216(T) = IBT 23203(T)) are described here as novel species. Their taxonomic novelty was determined using a polyphasic approach, combining phenotypic, molecular (ITS and partial β-tubulin sequences) and extrolite data. Phylogenetic analyses showed that each novel species formed a unique clade for both loci analysed and that they were most closely related to Penicillium simplicissimum, Penicillium janthinellum, Penicillium daleae and Penicillium brasilianum. An overview of the phylogeny of this taxonomically difficult group is presented, and 33 species are accepted. Each of the five novel species had a unique extrolite profile of known and uncharacterized metabolites and various compounds, such as penicillic acid, andrastin A, pulvilloric acid, paxillin, paspaline and janthitrem, were commonly produced by these phylogenetically related species. The novel species had a high growth rate on agar media, but could be distinguished from each other by several macro- and microscopical characteristics.

  9. Occurrence of antibodies against Toxoplasma gondii and its isolation and genotyping in donkeys, mules, and horses in Brazil.

    Science.gov (United States)

    Gennari, Solange M; Esmerini, Patrícia de O; Lopes, Marcos G; Soares, Herbert S; Vitaliano, Sérgio N; Cabral, Aline D; Pena, Hilda F J; Horta, Maurício C; Cavalcante, Paulo H; Fortes, Kleber P; Villalobos, Eliana M C

    2015-04-15

    The occurrence of antibodies against Toxoplasma gondii was determined in donkeys, mules, and horses from different regions of Brazil. Serum samples from 304 donkeys (67.11%), 118 horses (26.05%), and 31 mules (6.84%) were analyzed by means of the indirect fluorescent antibody test (cutoff=64). Antibodies against T. gondii were detected in 129 equids (28.47%) (82 donkeys, 32 horses, and 15 mules). Tissue samples from 19 seropositive and 50 seronegative animals were obtained in order to isolate the parasite by means of mouse bioassay, and T. gondii was isolated from a donkey. Through genotypic characterization of the isolate, by means of polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) using 11 genotypic markers, the genotype #163 (TgCkBr220), which has already been described in chickens in Brazil, was identified. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Neues vom Heringsparasiten Ichthyophonus sp.

    OpenAIRE

    Lang, Thomas

    1994-01-01

    Seit dem Massensterben von Heringen entlang der schwedischen Südküste im Sommer 1991, aufgrund einer Infektion mit dem parasitischen Pilz Ichthyophonus sp., wird der Gesundheitszustand der Heringsbestände in den europäischen Seegebieten intensiv überwacht. Diese Untersuchungen, an denen sich auch die Bundesforschungsanstalt für Fischerei beteiligt, werden koordiniert von der "Arbeitsgruppe über Pathologie und Krankheiten mariner Organismen" des Internationalen Rates für Meeresforschung (IC...

  11. 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

  12. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  13. 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,...

  14. 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 Udgivelsesdato...

  15. Assessment of antibiotic susceptibilities, genotypic characteristics ...

    African Journals Online (AJOL)

    Jane

    2011-09-28

    Sep 28, 2011 ... Staphylococcus aureus and Salmonella Typhimurium ... This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and ..... Distribution of reference and virulence genes among antibiotic-sensitive S. aureus (SAS), .... environmental factors such as temperature, water activity,.

  16. Hepatitis C Virus: Viral Quasispecies and Genotypes

    Directory of Open Access Journals (Sweden)

    Kyoko Tsukiyama-Kohara

    2017-12-01

    Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  17. Hepatitis C Virus: Viral Quasispecies and Genotypes.

    Science.gov (United States)

    Tsukiyama-Kohara, Kyoko; Kohara, Michinori

    2017-12-22

    Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  18. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... heat shock proteins; ABA, abscisic acid. Page 2. Amar et al. 323. Figure 1. Seed vigor of M. truncatula genotypes under different salt stress conditions. Results are means ..... (HSPs) that accumulate during seed late maturation.

  19. Hearing impairment in genotyped Wolfram syndrome patients.

    NARCIS (Netherlands)

    Plantinga, R.F.; Pennings, R.J.E.; Huygen, P.L.M.; Bruno, R.; Eller, P.; Barrett, T.G.; Vialettes, B.; Paquis-Fluklinger, V.; Lombardo, F.; Cremers, C.W.R.J.

    2008-01-01

    OBJECTIVES: Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment.

  20. Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya.

    Science.gov (United States)

    Nick, G; de Lajudie, P; Eardly, B D; Suomalainen, S; Paulin, L; Zhang, X; Gillis, M; Lindström, K

    1999-10-01

    SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of Acacia senegal and Prosopis chilensis. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridization, genomic fingerprinting using repetitive sequence-based PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus Sinorhizobium. Two of the strains grouped with Sinorhizobium saheli and seven with Sinorhizobium terangae, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species, Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov.

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

    Science.gov (United States)

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

    2016-09-17

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

  2. Popcorn genotypes resistance to fall armyworm

    Directory of Open Access Journals (Sweden)

    Nádia Cristina de Oliveira

    2018-02-01

    Full Text Available ABSTRACT: The aim of this study was to evaluate popcorn genotypes for resistance to the fall armyworm, Spodoptera frugiperda. The experiment used a completely randomized design with 30 replicates. The popcorn genotypes Aelton, Arzm 05 083, Beija-Flor, Colombiana, Composto Chico, Composto Gaúcha, Márcia, Mateus, Ufvm Barão Viçosa, Vanin, and Viviane were evaluated,along with the common maize variety Zapalote Chico. Newly hatched fall armyworm larvae were individually assessed with regard to biological development and consumption of food. The data were subjected to multivariate analyses of variance and genetic divergence among genotypes was evaluated through the clustering methods of Tocher based on generalized Mahalanobis distances and canonical variable analyses. Seven popcorn genotypes, namely, Aelton, Arzm 05 083, Composto Chico, Composto Gaúcha, Márcia, Mateus, and Viviane,were shown to form a cluster (cluster I that had antibiosis as the mechanism of resistance to the pest. Cluster I genotypes and the Zapalote Chico genotype could be used for stacking genes for antibiosis and non-preference resistance.

  3. Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern.

    Science.gov (United States)

    León, María José; Rodríguez-Olmos, Angel; Sánchez-Porro, Cristina; López-Pérez, Mario; Rodríguez-Valera, Francisco; Soliveri, Juan; Ventosa, Antonio; Copa-Patiño, José Luis

    2015-12-01

    A novel pink-pigmented bacterial strain, UAH-SP71T, was isolated from a saltern located in Santa Pola, Alicante (Spain) and the complete genome sequence was analysed and compared with that of Spiribacter salinus M19-40T, suggesting that the two strains constituted two separate species, with a 77.3% ANI value. In this paper, strain UAH-SP71T was investigated in a taxonomic study using a polyphasic approach. Strain UAH-SP71T was a Gram-stain-negative, strictly aerobic, non-motile curved rod that grew in media containing 5-20% (w/v) NaCl (optimum 10% NaCl), at 5-40 °C (optimum 37 °C) and at pH 5-10 (optimum pH 8). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed thatstrain UAH-SP71T is a member of the genus Spiribacter, showing a sequence similarity of 96.5% with Spiribacter salinus M19-40T. Other related species are also members of the family Ectothiorhodospiraceae, including Arhodomonas recens RS91T (95.5% 16S rRNA gene sequence similarity), Arhodomonas aquaeolei ATCC 49307T (95.4 %) and Alkalilimnicola ehrlichii MLHE-1T (94.9 %). DNA-DNA hybridization between strain UAH-SP71T and Spiribacter salinus M19-40T was 39 %. The major cellular fatty acids of strain UAH-SP71T were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c, C10 : 0 3-OH and C12 : 0, a pattern similar to that of Spiribacter salinus M19-40T. Phylogenetic, phenotypic and genotypic differences between strain UAH-SP71T and Spiribacter salinus M19-40T indicate that strainUAH-SP71T represents a novel species of the genus Spiribacter, for which the name Spiribacter curvatus sp. nov. is proposed. The type strain is UAH-SP71T (5CECT8396T5DSM 28542T).

  4. Mouse Mammary Tumor Virus Signal Peptide Uses a Novel p97-Dependent and Derlin-Independent Retrotranslocation Mechanism To Escape Proteasomal Degradation

    Directory of Open Access Journals (Sweden)

    Hyewon Byun

    2017-03-01

    Full Text Available Multiple pathogens, including viruses and bacteria, manipulate endoplasmic reticulum-associated degradation (ERAD to avoid the host immune response and promote their replication. The betaretrovirus mouse mammary tumor virus (MMTV encodes Rem, which is a precursor protein that is cleaved into a 98-amino-acid signal peptide (SP and a C-terminal protein (Rem-CT. SP uses retrotranslocation for ER membrane extraction and yet avoids ERAD by an unknown mechanism to enter the nucleus and function as a Rev-like protein. To determine how SP escapes ERAD, we used a ubiquitin-activated interaction trap (UBAIT screen to trap and identify transient protein interactions with SP, including the ERAD-associated p97 ATPase, but not E3 ligases or Derlin proteins linked to retrotranslocation, polyubiquitylation, and proteasomal degradation of extracted proteins. A dominant negative p97 ATPase inhibited both Rem and SP function. Immunoprecipitation experiments indicated that Rem, but not SP, is polyubiquitylated. Using both yeast and mammalian expression systems, linkage of a ubiquitin-like domain (UbL to SP or Rem induced degradation by the proteasome, whereas SP was stable in the absence of the UbL. ERAD-associated Derlin proteins were not required for SP activity. Together, these results suggested that Rem uses a novel p97-dependent, Derlin-independent retrotranslocation mechanism distinct from other pathogens to avoid SP ubiquitylation and proteasomal degradation.

  5. Enraizamiento in vitro de Dioscoreas sp. In vitro rootting of Dioscoreas sp.

    Directory of Open Access Journals (Sweden)

    Jarma Alfredo

    2003-12-01

    Full Text Available El presente estudio se realizó en el Laboratorio de Cultivo de Tejidos Vegetales de la Universidad de Córdoba en el año 2000 con el objetivo de evaluar el efecto del ácido naftalenacético (ANA en el medio de cultivo sobre el enraizamiento in vitro de tres cultivares de ñame (Dioscorea sp.. Se estudió el efecto de cuatro concentraciones del regulador de crecimiento (0, 0.3, 0.6 y 0.9 mg/1 sobre tres cultivares de ñame (Diamantes-22, 003 y 005. Se empleó un experimento trifactorial con diseño aleatorio y 20 repeticiones; cada unidad experimental estuvo conformada por un recipiente de vidrio que contenía el medio de cultivo y el explante (segmento nodal. Las variables consideradas fueron número y grosor de raíces, oxidación del medio de cultivo y producción de callo. Los resultados indicaron que tanto la hormona como el genotipo tuvieron efecto sobre todas las variables consi­deradas en el estudio y que la interacción fue importante (PThe Universidad de Córdoba s Vegetal Tissue Culture Laboratory evaluated the effect of naphthalenacetic acid (NAA on in vitro rooting of three yam cultivars (Dioscorea sp. in 2000. The effect of four hormone levels (0, 0.3, 0.6 and 0.9 mg/1 was studied on three yam cultivars (Diamantes-22,003 and 005. A random experimental design was used employing 4x3 factorial arrangement and 20 repetitions; each experimental unit consisted of a glass receptacle containing the culture medium and the explant (one segment nodal. The variables considered were the number of roots and their thickness, culture medium oxidation and callus production. Findings showed that both the hormone and genotype had an effect on all those variables considered in the study and interaction was significant (P <0.05 for callus production and culture medium oxidation. The 005 cultivar showed the greatest root number and thickness values. It was also determined that when a 0.6 and 0.9 mg/1 dose of auxin was applied, root production and

  6. DISTRIBUSI Solen sp DI PERAIRAN KABUPATEN BANGKALAN

    Directory of Open Access Journals (Sweden)

    Eva Ari Wahyuni

    2016-03-01

    Full Text Available DISTRIBUTION OF Solen sp IN BANGKALAN WATERSSolen sp potential needs to be developed on the island of Madura, particularly in Bangkalan. Solen sp utilization has increased which has the potential to overfishing. Therefore, this study aims to determine the density of Solen sp and their ecology in the waters Modung village, Modung District, Bangkalan. The experiment was conducted in April 2015 using the descriptive method. The materials used include Solen sp and physico-chemical parameters of the environment (temperature, salinity, pH, and substrate. The analyzes were conducted at the Laboratory of Marine Science, Department of Marine Sciences, Trunojoyo University of Madura by using the tool grabsampler, sieveshaker, and pipetting with gravimetric method. The analysis shows the range of values of temperature between 29-300C, salinity between 31-32 ppt, pH were 7.9-8.0 and the type of substrate in the form of sandy mud, as well as the density of Solen sp from 8-10 individuals/m2. All measurement results indicate normal conditions and in accordance with the sea water quality standard for marine life, which can be a suitable habitat for the growth and development of Solen sp. This condition is thought to affect the density of Solen sp.Keywords: Bangkalan, density, distribution, Solen sp, substrate.ABSTRAKPotensi Solen sp perlu dikembangkan di pulau Madura, khususnya di Kabupaten Bangkalan. Pemanfaatan Solen sp mengalami peningkatan sehingga berpotensi overfishing. Untuk itu, penelitian ini bertujuan untuk mengetahui kepadatan Solen sp dan ekologinya di perairan desa Modung, Kecamatan Modung, Kabupaten Bangkalan. Penelitian dilaksanakan pada bulan April 2015 dengan metode deskriptif. Materi dan bahan yang digunakan diantaranya Solen sp dan parameter fisika-kimia lingkungan (suhu, salinitas, pH, dan substrat. Analisa dilakukan di Laboratorium Ilmu Kelautan, Program studi/Jurusan Ilmu Kelautan Universitas Trunojoyo Madura dengan menggunakan alat

  7. Effect of doxorubicin/pluronic SP1049C on tumorigenicity, aggressiveness, DNA methylation and stem cell markers in murine leukemia.

    Directory of Open Access Journals (Sweden)

    Daria Y Alakhova

    Full Text Available Pluronic block copolymers are potent sensitizers of multidrug resistant cancers. SP1049C, a Pluronic-based micellar formulation of doxorubicin (Dox has completed Phase II clinical trial and demonstrated safety and efficacy in patients with advanced adenocarcinoma of the esophagus and gastroesophageal junction. This study elucidates the ability of SP1049C to deplete cancer stem cells (CSC and decrease tumorigenicity of cancer cells in vivo.P388 murine leukemia ascitic tumor was grown in BDF1 mice. The animals were treated with: (a saline, (b Pluronics alone, (c Dox or (d SP1049C. The ascitic cancer cells were isolated at different passages and examined for 1 in vitro colony formation potential, 2 in vivo tumorigenicity and aggressiveness, 3 development of drug resistance and Wnt signaling activation 4 global DNA methylation profiles, and 5 expression of CSC markers.SP1049C treatment reduced tumor aggressiveness, in vivo tumor formation frequency and in vitro clonogenic potential of the ascitic cells compared to drug, saline and polymer controls. SP1049C also prevented overexpression of BCRP and activation of Wnt-β-catenin signaling observed with Dox alone. Moreover, SP1049C significantly altered the DNA methylation profiles of the cells. Finally, SP1049C decreased CD133(+ P388 cells populations, which displayed CSC-like properties and were more tumorigenic compared to CD133(- cells.SP1049C therapy effectively suppresses the tumorigenicity and aggressiveness of P388 cells in a mouse model. This may be due to enhanced activity of SP1049C against CSC and/or altered epigenetic regulation restricting appearance of malignant cancer cell phenotype.

  8. Substance p regulates puberty onset and fertility in the female mouse.

    Science.gov (United States)

    Simavli, Serap; Thompson, Iain R; Maguire, Caroline A; Gill, John C; Carroll, Rona S; Wolfe, Andrew; Kaiser, Ursula B; Navarro, Víctor M

    2015-06-01

    Puberty is a tightly regulated process that leads to reproductive capacity. Kiss1 neurons are crucial in this process by stimulating GnRH, yet how Kiss1 neurons are regulated remains unknown. Substance P (SP), an important neuropeptide in pain perception, induces gonadotropin release in adult mice in a kisspeptin-dependent manner. Here, we assessed whether SP, through binding to its receptor NK1R (neurokinin 1 receptor), participates in the timing of puberty onset and fertility in the mouse. We observed that 1) selective NK1R agonists induce gonadotropin release in prepubertal females; 2) the expression of Tac1 (encoding SP) and Tacr1 (NK1R) in the arcuate nucleus is maximal before puberty, suggesting increased SP tone; 3) repeated exposure to NK1R agonists prepubertally advances puberty onset; and 4) female Tac1(-/-) mice display delayed puberty; moreover, 5) SP deficiency leads to subfertility in females, showing fewer corpora lutea and antral follicles and leading to decreased litter size. Thus, our findings support a role for SP in the stimulation of gonadotropins before puberty, acting via Kiss1 neurons to stimulate GnRH release, and its involvement in the attainment of full reproductive capabilities in female mice.

  9. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  10. Hybrid radiosity-SP3 equation based bioluminescence tomography reconstruction for turbid medium with low- and non-scattering regions

    Science.gov (United States)

    Chen, Xueli; Zhang, Qitan; Yang, Defu; Liang, Jimin

    2014-01-01

    To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP3 equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP3) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions.

  11. Hybrid radiosity-SP3 equation based bioluminescence tomography reconstruction for turbid medium with low- and non-scattering regions

    International Nuclear Information System (INIS)

    Chen, Xueli; Zhang, Qitan; Yang, Defu; Liang, Jimin

    2014-01-01

    To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP 3 equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP 3 ) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions

  12. Introduction to the SP theory of intelligence

    OpenAIRE

    Wolff, J Gerard

    2018-01-01

    This article provides a brief introduction to the "Theory of Intelligence" and its realisation in the "SP Computer Model". The overall goal of the SP programme of research, in accordance with long-established principles in science, has been the simplification and integration of observations and concepts across artificial intelligence, mainstream computing, mathematics, and human learning, perception, and cognition. In broad terms, the SP system is a brain-like system that takes in "New" infor...

  13. Evaluation of antioxidant and cytotoxic properties of Cynobacteria, Limnothrix sp. and Leptolyngbya sp. from Arabian sea

    Digital Repository Service at National Institute of Oceanography (India)

    Anas, A.; Vinothkumar, S.; Gupta, S.; Jasmin, C.; Joseph, V.; Parameswaran, P.S.; Nair, S.

    The hexane fractions of the marine cyanobacteria: Leptolyngbya sp. and Limnothrix sp., collected from Arabian Sea were found to display promising antioxidant properties than their ethyl acetate fraction during radical scavenging ABTS/DPPH assays (IC...

  14. Xylanolytic enzyme systems in Arthrobacter sp MTCC 5214 and Lactobacillus sp.

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, R.; Jalal, T.

    The production of extracellular xylanolytic enzymes such as xylanase, alfa-L-arabinofuranosidase (alfa-l-AFase), and acetyl xylan esterase (Axe) by marine Arthrobacter sp and Lactobacillus sp was investigated using different carbon sources Induction...

  15. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.

    2006-01-01

    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  16. Borrelia sp. phylogenetically different from Lyme disease- and relapsing fever-related Borrelia spp. in Amblyomma varanense from Python reticulatus.

    Science.gov (United States)

    Trinachartvanit, Wachareeporn; Hirunkanokpun, Supanee; Sudsangiem, Ronnayuth; Lijuan, Wanwisa; Boonkusol, Duangjai; Baimai, Visut; Ahantarig, Arunee

    2016-06-24

    Species of the genus Borrelia are causative agents of Lyme disease and relapsing fever. Lyme disease is the most commonly reported vector-borne disease in the northern hemisphere. However, in some parts of the world Lyme borreliosis and relapsing fever may be caused by novel Borrelia genotypes. Herein, we report the presence of a Borrelia sp. in an Amblyomma varanense collected from Python reticulatus. Ticks were collected from snakes, identified to species level and examined by PCR for the presence of Borrelia spp. flaB and 16S rRNA genes. Phylogenetic trees were constructed using the neighbour-joining method. Three A. varanense ticks collected from P. reticulatus were positive for a unique Borrelia sp., which was phylogenetically divergent from both Lyme disease- and relapsing fever-associated Borrelia spp. The results of this study suggest for the first time that there is a Borrelia sp. in A. varanense tick in the snake P. reticulatus that might be novel.

  17. Diet dominates host genotype in shaping the murine gut microbiota

    Science.gov (United States)

    Carmody, Rachel N.; Gerber, Georg K.; Luevano, Jesus M.; Gatti, Daniel M.; Somes, Lisa; Svenson, Karen L.; Turnbaugh, Peter J.

    2014-01-01

    SUMMARY Mammals exhibit marked inter-individual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88−/−, NOD2−/−, ob/ob, and Rag1−/−), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial groups to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping inter-individual variations in host-associated microbial communities. PMID:25532804

  18. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  19. Precise genotyping and recombination detection of Enterovirus

    Science.gov (United States)

    2015-01-01

    Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

  20. Pengendalian Hayati Penyakit Layu Fusarium Pisang (Fusarium Oxysporum F.sp. Cubense) dengan Trichoderma SP.

    OpenAIRE

    Sudirman, Albertus; Sumardiyono, Christanti; Widyastuti, Siti Muslimah

    2011-01-01

    The aim of this research was to study the inhibiting ability of Trichoderma sp. to control fusarium wilt of banana in greenhouse condition. The experiments consisted of the antagonism test between Trichoderma sp. and Fusarium oxysporum f.sp. cubense (Foc) in vitro using dual culture method and glass house experiment which was arranged in 3×3 Factorial Complete Randomized Design. First factor of the latter experiment was the dose of Trichoderma sp. culture (0, 25, and 50 g per polybag), second...

  1. Selective C(sp2)-C(sp) bond cleavage: the nitrogenation of alkynes to amides.

    Science.gov (United States)

    Qin, Chong; Feng, Peng; Ou, Yang; Shen, Tao; Wang, Teng; Jiao, Ning

    2013-07-22

    Breakthrough: A novel catalyzed direct highly selective C(sp2)-C(sp) bond functionalization of alkynes to amides has been developed. Nitrogenation is achieved by the highly selective C(sp2)-C(sp) bond cleavage of aryl-substituted alkynes. The oxidant-free and mild conditions and wide substrate scope make this method very practical. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. First report of Anisakis sp. in Epinephelus sp. in East Indonesia

    OpenAIRE

    Annytha Ina Rohi Detha; Diana Agustiani Wuri; Julianty Almet; Yuni Riwu; Christin Melky

    2018-01-01

    Objective: The present research was conducted to identify the prevalence of Anisakis sp. as fish-borne zoonoses in Epinephelus sp. in territorial waters of East Nusa Tenggara, Indonesia. Materials and methods: A total of 50 fish (Epinephelus sp.) were collected from Kupang Fish Market in East Nusa Tenggara. Identification of Anisakis sp. was performed based on morphological observations considering shape of ventriculus, boring tooth, and mucron using binocular microscope. Results: Prev...

  3. Use of some chemical inducers to improve wheat resistance to Puccinia striiformis f. Sp. Tritici

    Directory of Open Access Journals (Sweden)

    Al-Maaroof Emad

    2014-01-01

    Full Text Available The effect of DL-β-aminobutyric acid (BABA, benzothiadiazole (BTH, indoleacetic acid (IAA and salicylic acid (SA on induced systemic resistance was investigated in moderately susceptible and susceptible wheat genotypes Tamuz-2 and AL-8/70 against Puccinia striiformis f. sp. tritici. Resistance was characterized by reduced infection of yellow rust disease (Yrd. Changes in peroxidase, phenylalanine ammonia-lyase activities and in total phenolic compound content demonstrated that the resistance to Puccinia striiformis can be induced by BABA, BTH, IAA and SA in these two wheat genotypes. Further studies are needed before a practical method using many analogue compounds, such as potassium phosphate and biotic agent for Yrd resistance in wheat is developed.

  4. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome

    Science.gov (United States)

    Pinter, Stefan F.; Colognori, David; Beliveau, Brian J.; Sadreyev, Ruslan I.; Payer, Bernhard; Yildirim, Eda; Wu, Chao-ting; Lee, Jeannie T.

    2015-01-01

    In mammals, several classes of monoallelic genes have been identified, including those subject to X-chromosome inactivation (XCI), genomic imprinting, and random monoallelic expression (RMAE). However, the extent to which these epigenetic phenomena are influenced by underlying genetic variation is unknown. Here we perform a systematic classification of allelic imbalance in mouse hybrids derived from reciprocal crosses of divergent strains. We observe that deviation from balanced biallelic expression is common, occurring in ∼20% of the mouse transcriptome in a given tissue. Allelic imbalance attributed to genotypic variation is by far the most prevalent class and typically is tissue-specific. However, some genotype-based imbalance is maintained across tissues and is associated with greater genetic variation, especially in 5′ and 3′ termini of transcripts. We further identify novel random monoallelic and imprinted genes and find that genotype can modify penetrance of parental origin even in the setting of large imprinted regions. Examination of nascent transcripts in single cells from inbred parental strains reveals that genes showing genotype-based imbalance in hybrids can also exhibit monoallelic expression in isogenic backgrounds. This surprising observation may suggest a competition between alleles and/or reflect the combined impact of cis- and trans-acting variation on expression of a given gene. Our findings provide novel insights into gene regulation and may be relevant to human genetic variation and disease. PMID:25858912

  5. Micropropagation of pear (Pyrus sp.).

    Science.gov (United States)

    Reed, Barbara M; Denoma, Jeanine; Wada, Sugae; Postman, Joseph

    2013-01-01

    Elements of micropropagation include establishment of shoot tip cultures, proliferation, rooting, and acclimatization of the resulting plantlets. The wide genetic variation in Pyrus makes micropropagation challenging for many genotypes. Initiation of shoots is most successful from forced dormant shoots or from scions grafted onto seedling rootstocks to impose juvenility. Clean shoots are recovered after testing for contaminants at the initiation stage on ½ strength Murashige and Skoog 1962 medium (MS), at pH 6.9 for 1 week or by streaking on nutrient agar. Although pear species and cultivars are cultured on several well-known media, MS is the most commonly used. Our studies showed that multiplication and growth of shoots are best on Pear Medium with higher concentrations of calcium chloride, potassium phosphate, and magnesium sulfate than MS medium and 4.4 μM N(6) benzyladenine. Pear shoots are often recalcitrant to rooting; however, a 5 s dip in 10 mM indole-3-butyric acid or naphthalene acetic acid before planting on basal medium without plant growth regulators is effective for many genotypes. Pear shoots store well at 1-4°C, and can hold for as long as 4 years without reculture. Cryopreservation protocols are available for long-term storage of pear shoot tips. Acclimation of in vitro-rooted or micrografted shoots in a mist bed follows standard procedures.

  6. Fine-scale maps of recombination rates and hotspots in the mouse genome.

    Science.gov (United States)

    Brunschwig, Hadassa; Levi, Liat; Ben-David, Eyal; Williams, Robert W; Yakir, Benjamin; Shifman, Sagiv

    2012-07-01

    Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of recombination hotspot regulation. Population genetic data have been used to map and quantify hotspots in the human genome. Genetic variation in recombination rates and hotspots usage have been explored in human pedigrees, mouse intercrosses, and by sperm typing. These studies pointed to the central role of the PRDM9 gene in hotspot modulation. In this study, we used single nucleotide polymorphisms (SNPs) from whole-genome resequencing and genotyping studies of mouse inbred strains to estimate recombination rates across the mouse genome and identified 47,068 historical hotspots--an average of over 2477 per chromosome. We show by simulation that inbred mouse strains can be used to identify positions of historical hotspots. Recombination hotspots were found to be enriched for the predicted binding sequences for different alleles of the PRDM9 protein. Recombination rates were on average lower near transcription start sites (TSS). Comparing the inferred historical recombination hotspots with the recent genome-wide mapping of double-strand breaks (DSBs) in mouse sperm revealed a significant overlap, especially toward the telomeres. Our results suggest that inbred strains can be used to characterize and study the dynamics of historical recombination hotspots. They also strengthen previous findings on mouse recombination hotspots, and specifically the impact of sequence variants in Prdm9.

  7. Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri.

    Science.gov (United States)

    Shahraki, Abdolrazagh Hashemi; Trovato, Alberto; Mirsaeidi, Mehdi; Borroni, Emanuele; Heidarieh, Parvin; Hashemzadeh, Mohamad; Shahbazi, Narges; Cirillo, Daniela M; Tortoli, Enrico

    2017-06-01

    Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.

  8. Trypanosoma sp. diversity in Amazonian bats (Chiroptera; Mammalia) from Acre State, Brazil.

    Science.gov (United States)

    Dos Santos, Francisco C B; Lisboa, Cristiane V; Xavier, Samanta C C; Dario, Maria A; Verde, Rair de S; Calouro, Armando M; Roque, André Luiz R; Jansen, Ana M

    2017-11-16

    Bats are ancient hosts of Trypanosoma species and their flying ability, longevity and adaptability to distinct environments indicate that they are efficient dispersers of parasites. Bats from Acre state (Amazon Biome) were collected in four expeditions conducted in an urban forest (Parque Zoobotânico) and one relatively more preserved area (Seringal Cahoeira) in Rio Branco and Xapuri municipalities. Trypanosoma sp. infection was detected by hemoculture and fresh blood examination. Isolated parasite species were identified by the similarity of the obtained DNA sequence from 18S rDNA polymerase chain reaction and reference strains. Overall, 367 bats from 23 genera and 32 species were examined. Chiropterofauna composition was specific to each municipality, although Artibeus sp. and Carollia sp. prevailed throughout. Trypanosoma sp. infection was detected in 85 bats (23·2%). The most widely distributed and prevalent genotypes were (in order) Trypanosoma cruzi TcI, T. cruzi marinkellei, Trypanosoma dionisii, T. cruzi TcIV and Trypanosoma rangeli. At least one still-undescribed Trypanosoma species was also detected in this study. The detection of T. cruzi TcI and TcIV (the ones associated with Chagas disease in Amazon biome) demonstrates the putative importance of these mammal hosts in the epidemiology of the disease in the Acre State.

  9. Phylogenetic evidence that two distinct Trichuris genotypes infect both humans and non-human primates.

    Directory of Open Access Journals (Sweden)

    Damiana F Ravasi

    Full Text Available Although there has been extensive debate about whether Trichuris suis and Trichuris trichiura are separate species, only one species of the whipworm T. trichiura has been considered to infect humans and non-human primates. In order to investigate potential cross infection of Trichuris sp. between baboons and humans in the Cape Peninsula, South Africa, we sequenced the ITS1-5.8S-ITS2 region of adult Trichuris sp. worms isolated from five baboons from three different troops, namely the Cape Peninsula troop, Groot Olifantsbos troop and Da Gama Park troop. This region was also sequenced from T. trichiura isolated from a human patient from central Africa (Cameroon for comparison. By combining this dataset with Genbank records for Trichuris isolated from other humans, non-human primates and pigs from several different countries in Europe, Asia, and Africa, we confirmed the identification of two distinct Trichuris genotypes that infect primates. Trichuris sp. isolated from the Peninsula baboons fell into two distinct clades that were found to also infect human patients from Cameroon, Uganda and Jamaica (named the CP-GOB clade and China, Thailand, the Czech Republic, and Uganda (named the DG clade, respectively. The divergence of these Trichuris clades is ancient and precedes the diversification of T. suis which clustered closely to the CP-GOB clade. The identification of two distinct Trichuris genotypes infecting both humans and non-human primates is important for the ongoing treatment of Trichuris which is estimated to infect 600 million people worldwide. Currently baboons in the Cape Peninsula, which visit urban areas, provide a constant risk of infection to local communities. A reduction in spatial overlap between humans and baboons is thus an important measure to reduce both cross-transmission and zoonoses of helminthes in Southern Africa.

  10. Mouse infection models for space flight immunology

    Science.gov (United States)

    Chapes, Stephen Keith; Ganta, Roman Reddy; Chapers, S. K. (Principal Investigator)

    2005-01-01

    Several immunological processes can be affected by space flight. However, there is little evidence to suggest that flight-induced immunological deficits lead to illness. Therefore, one of our goals has been to define models to examine host resistance during space flight. Our working hypothesis is that space flight crews will come from a heterogeneous population; the immune response gene make-up will be quite varied. It is unknown how much the immune response gene variation contributes to the potential threat from infectious organisms, allergic responses or other long term health problems (e.g. cancer). This article details recent efforts of the Kansas State University gravitational immunology group to assess how population heterogeneity impacts host health, either in laboratory experimental situations and/or using the skeletal unloading model of space-flight stress. This paper details our use of several mouse strains with several different genotypes. In particular, mice with varying MHCII allotypes and mice on the C57BL background with different genetic defects have been particularly useful tools with which to study infections by Staphylococcus aureus, Salmonella typhimurium, Pasteurella pneumotropica and Ehrlichia chaffeensis. We propose that some of these experimental challenge models will be useful to assess the effects of space flight on host resistance to infection.

  11. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  12. 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.

  13. Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.

    Science.gov (United States)

    Yang, Deok-Chun; Im, Wan-Taek; Kim, Myung Kyum; Lee, Sung-Taik

    2005-03-01

    Gram-negative, non-spore-forming, rod-shaped bacteria, T7-09(T) and TR6-08(T), were isolated from soil from a ginseng field in South Korea and characterized to determine their taxonomic position. 16S rRNA gene sequence analysis showed that the two isolates shared 99.5 % sequence similarity. Strains T7-09(T) and TR6-08(T) were shown to belong to the Proteobacteria and showed the highest levels of sequence similarity to Pseudoxanthomonas broegbernensis DSM 12573(T) (98.1 %), Pseudoxanthomonas mexicana AMX 26B(T) (97.4-97.5 %), Pseudoxanthomonas japonensis 12-3(T) (96.5-96.6 %), Pseudoxanthomonas taiwanensis ATCC BAA-404(T) (95.7 %) and Xanthomonas campestris ATCC 33913(T) (96.3-96.5 %). The sequence similarity values with respect to any species with validly published names in related genera were less than 96.5 %. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with C(15 : 0) iso as the predominant acid supported the assignment of the novel isolates to the order 'Xanthomonadales'. The two isolates could be distinguished from the established species of the genus Pseudoxanthomonas by the presence of quantitative unsaturated fatty acid C(17 : 1) iso omega9c and by their unique biochemical profiles. The results of DNA-DNA hybridization clearly demonstrated that T7-09(T) and TR6-08(T) represent separate species. On the basis of these data, it is proposed that T7-09(T) (=KCTC 12208(T)=IAM 15116(T)) and TR6-08(T) (=KCTC 12207(T)=IAM 15115(T)) be classified as the type strains of two novel Pseudoxanthomonas species, for which the names Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov., respectively, are proposed.

  14. Substance P as a putative efferent transmitter mediates GABAergic inhibition in mouse taste buds.

    Science.gov (United States)

    Huang, Anthony Y; Wu, Sandy Y

    2018-04-01

    Capsaicin-mediated modulation of taste nerve responses is thought to be produced indirectly by the actions of neuropeptides, for example, CGRP and substance P (SP), on taste cells implying they play a role in taste sensitivity. During the processing of gustatory information in taste buds, CGRP shapes peripheral taste signals via serotonergic signalling. The underlying assumption has been that SP exerts its effects on taste transmitter secretion in taste buds of mice. To test this assumption, we investigated the net effect of SP on taste-evoked ATP secretion from mouse taste buds, using functional calcium imaging with CHO cells expressing high-affinity transmitter receptors as cellular biosensors. Our results showed that SP elicited PLC activation-dependent intracellular Ca 2+ transients in taste cells via neurokinin 1 receptors, most likely on glutamate-aspartate transporter-expressing Type I cells. Furthermore, SP caused Type I cells to secrete GABA. Combined with the recent findings that GABA depresses taste-evoked ATP secretion, the current results indicate that SP elicited secretion of GABA, which provided negative feedback onto Type II (receptor) cells to reduce taste-evoked ATP secretion. These findings are consistent with a role for SP as an inhibitory transmitter that shapes the peripheral taste signals, via GABAergic signalling, during the processing of gustatory information in taste buds. Notably, the results suggest that SP is intimately associated with GABA in mammalian taste signal processing and demonstrate an unanticipated route for sensory information flow within the taste bud. © 2018 The British Pharmacological Society.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  16. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    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

  17. Genomes of the Mouse Collaborative Cross.

    Science.gov (United States)

    Srivastava, Anuj; Morgan, Andrew P; Najarian, Maya L; Sarsani, Vishal Kumar; Sigmon, J Sebastian; Shorter, John R; Kashfeen, Anwica; McMullan, Rachel C; Williams, Lucy H; Giusti-Rodríguez, Paola; Ferris, Martin T; Sullivan, Patrick; Hock, Pablo; Miller, Darla R; Bell, Timothy A; McMillan, Leonard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

    2017-06-01

    The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of

  18. Bioactive secondary metabolites from the endophytic fungus Chaetomium sp. isolated from Salvia officinalis growing in Morocco

    Directory of Open Access Journals (Sweden)

    Ebel R.

    2009-01-01

    Full Text Available This study reports the chemical investigation and cytotoxic activity of the secondary metabolites produced by the endophytic fungus Chaetomium sp. isolated from Salvia officinalis growing in Morocco. This plant was collected from the Beni-Mellal Mountain in Morocco and belongs to the Lamiaceae family and is named in Morocco “Salmia”. The endophytic fungus Chaetomium sp. was isolated from the tissues of the stem of this plant. The fungal strain was identified by PCR. The crude organic extract of the fungal strain was proven to be active when tested for cytotoxicity against L5178Y mouse lymphoma cells. Chemical investigation of the secondary metabolites showed that cochliodinol is the main component beside isocochliodinol. The structures of the isolated compounds were determined on the basis of NMR analysis (1H, 13C, COSY and HMBC as well as by mass spectrometry using ESI (Electron Spray Ionisation as source.

  19. Specialised predation by Palpimanus sp. (Araneae: Palpimanidae ...

    African Journals Online (AJOL)

    This is the first detailed report on the natural prey and the prey-capture tactics of a Palpimanus sp. from Entebbe (Uganda). Although this species fed occasionally on insects, its dominant prey in the field was other spiders, especially jumping spiders (Salticidae) and their eggs. Encounters between Palpimanus sp. and ...

  20. Kultivasi Scenedesmus SP. Pada Medium Air Limbah

    OpenAIRE

    Kawaroe, Mujizat

    2011-01-01

    Proses fotosintesis pada mikroalga membutuhkan CO2 dan cahaya matahari serta nutrien untuk pertumbuhannya. Kultivasi Scenedesmus sp. pada medium air limbah bertujuan guna mencukupi kebutuhan mikroalga akan nutrien dan mengurangi masukan dari bahan kimia yang terkandung dalam air limbah tersebut ke lingkungan. Kultivasi Scenedesmus sp. dilakukan selama tujuh hari pada medium air limbah industri tanpa penambahan nutri...

  1. Construction of a mouse model of factor VIII deficiency by gene targeting

    Energy Technology Data Exchange (ETDEWEB)

    Bi, L.; Lawler, A.; Gearhart, J. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)] [and others

    1994-09-01

    To develop a small animal model of hemophilia A for gene therapy experiments, we set out to construct a mouse model for factor VIII deficiency by gene targeting. First, we screened a mouse liver cDNA library using a human FVIII cDNA probe. We cloned a 2.6 Kb partial mouse factor VIII cDNA which extends from 800 base pairs of the 3{prime} end of exon 14 to the 5{prime} end of exon 26. A mouse genomic library made from strain 129 was then screened to obtain genomic fragments covering the exons desired for homologous recombination. Two genomic clones were obtained, and one covering exon 15 through 22 was used for gene targeting. To make gene targeting constructs, a 5.8 Kb genomic DNA fragment covering exons 15 to 19 of the mouse FVIII gene was subcloned, and the neo expression cassette was inserted into exons 16 and 17 separately by different strategies. These two constructs were named MFVIIIC-16 and MFVIIIC-17. The constructs were linearized and transfected into strain 129 mouse ES cells by electroporation. Factor VIII gene-knockout ES cell lines were selected by G-418 and screened by genomic Southern blots. Eight exon 16 targeted cell lines and five exon 17 targeted cell lines were obtained. Three cell lines from each construct were injected into blastocysts and surgically transferred into foster mothers. Multiple chimeric mice with 70-90% hair color derived from the ES-cell genotype were seen with both constructs. Germ line transmission of the ES-cell genotype has been obtained for the MFVIIIC-16 construct, and multiple hemophilia A carrier females have been identified. Factor VIII-deficient males will be conceived soon.

  2. Prevalence and genetic diversity of the intestinal parasites Blastocystis sp. and Cryptosporidium spp. in household dogs in France and evaluation of zoonotic transmission risk.

    Science.gov (United States)

    Osman, Marwan; Bories, Jessica; El Safadi, Dima; Poirel, Marie-Thérèse; Gantois, Nausicaa; Benamrouz-Vanneste, Sadia; Delhaes, Laurence; Hugonnard, Marine; Certad, Gabriela; Zenner, Lionel; Viscogliosi, Eric

    2015-11-30

    Several parasites including the protozoa Blastocystis sp. and Cryptosporidium spp. may be causative agents of gastrointestinal symptoms in domestic dogs, and there may be a potential risk of transmission to owners. While France is one of the largest European countries in terms of its canine population, little data is available about the molecular epidemiology of these two parasites. The purpose of this study was to determine the prevalence of intestinal parasites in household dogs in France, and to evaluate the zoonotic risk of Blastocystis sp. and Cryptosporidium spp. by genotyping the corresponding isolates. To this end, 116 faecal samples were collected from household dogs regardless of breed, age or gender, living in the Lyons area, France. Various intestinal protozoa and helminths were identified by light microscopy. Screening for Blastocystis sp. and Cryptosporidium spp. were subsequently performed by PCR targeting the small subunit (SSU) rDNA coding region, followed by direct sequencing of the PCR products and analysis of the sequences obtained for genotyping. The overall prevalence of dogs infected with at least one gastrointestinal parasite was 42.2% (49/116). After light microscopy examination of faecal samples, the most common parasites found were the protozoa Giardia sp. (25.0%) and Cystoisospora sp. (19.8%). Using molecular methods, four dogs (3.4%) were shown to be infected by Blastocystis sp. and carried either subtype (ST) 2, commonly identified in various animal groups, or ST10, frequently found in bovids. Three dogs (2.6%) were positive for C. canis, infecting humans episodically. The low prevalence of both parasites, combined with the identification of C. canis and Blastocystis sp. ST2 and ST10 in the canine population, strongly suggests that dogs play a negligible role as zoonotic reservoirs for both parasites and do not seem to be natural hosts of Blastocystis sp. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Guide til gode spørgeskemaer

    DEFF Research Database (Denmark)

    Olsen, Henning

    Spørgeskemaundersøgelser bliver ofte brugt til at dokumentere forskellige forhold og begrunde politiske beslutninger. Men resultaterne kan være forbundet med stor usikkerhed. Det kræver omhu og stor sproglig formåen at udarbejde spørgeskemaer. Seniorforsker Henning Olsen har i flere år arbejdet med...... viden om, hvordan folk forstår sproglige meddelelser og genkalder sig informationer. I guiden behandles emner som fx styrende problemstillinger og spørgsmåls fokus og neutralitet, formulering af åbne eller lukkede spørgsmål og svarkategorier, tematiske spørgeforløb, aflastning af svarpersoners...

  4. Toxoplasma gondii: prevalence and characterization of new genotypes in free-range chickens from south Brazil.

    Science.gov (United States)

    Vieira, Fernando Emmanuel Gonçalves; Sasse, João Pedro; Minutti, Ana Flávia; Miura, Ana Carolina; de Barros, Luiz Daniel; Cardim, Sergio Tosi; Martins, Thais Agostinho; de Seixas, Mércia; Yamamura, Milton Issashi; Su, Chunlei; Garcia, João Luis

    2018-03-01

    Toxoplasma gondii is an intracellular parasite that can infect all warm-blooded animals including humans. Recent studies showed that T. gondii strains from South America are genetically diverse. The present work aimed to determine T. gondii prevalence in free-ranging chicken in northwest Parana state in Brazil by two serological tests, to isolate the parasites from seropositive chickens and to genotype the isolates. Antibodies to T. gondii in 386 serum samples from 24 farms were investigated by immunofluorescence antibody assay (IFA) and modified agglutination test (MAT). Samples having titers ≥ 16 were considered positive for both tests. Among the 386 serum samples, 102 (26.4%) were positive for IFA, 64 (16.6%) were positive for MAT, 47 (12.2%) were positive in both tests, and 119 (30.8%) were positive in at least one of the two tests. Brain and pool of heart, lung, and liver from the 119 seropositive chickens were used for mouse bioassay to isolate the parasites. Thirty eight (31.9%) of these seropositive chickens were considered positives in mouse bioassay and 18 isolates were obtained. The isolates were characterized by 10 PCR-RFLP genetic markers including SAG1, SAG2 (5'-3'SAG2, alt.SAG2), SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico. Results of genotyping were compared with the genotypes in ToxoDB database. It revealed ten genotypes, including ToxoDB PCR-RFLP genotypes #6 (n = 2), #19 (n = 1), #21 (n = 2), #111 (n = 2), #152 (n = 1), and #175 (n = 1) and four new types not described before. Our results confirmed a high genetic diversity of this parasite in southern Brazil and also showed that the use of two serological tests in combination can improve the chance of T. gondii isolation. More studies should be taken to determine the zoonotic potential of chickens in the transmission of T. gondii.

  5. Glyphosate catabolism by Pseudomonas sp

    International Nuclear Information System (INIS)

    Shinabarger, D.L.

    1986-01-01

    The pathway for the degradation of glyphosate (N-phosphonomethylglycine) by Pseudomonas sp. PG2982 has been determined using metabolic radiolabeling experiments. Radiorespirometry experiments utilizing [3- 14 C] glyphosate revealed that approximately 50-59% of the C3 carbon was oxidized to CO 2 . Fractionation of stationary phase cells labeled with [3- 14 C]glyphosate revealed that from 45-47% of the assimilated C3 carbon is distributed to proteins and that amino acids methionine and serine are highly labeled. The nucleic acid bases adenine and guanine received 90% of the C3 label that was incorporated into nucleic acids, and the only pyrimidine base labeled was thymine. Pulse labeling of PG2982 cells with [3- 14 C]glyphosate revealed that [3- 14 C]sarcosine is an intermediate in glyphosate degradation. Examination of crude extracts prepared from PG2982 cells revealed the presence of an enzyme that oxidizes sarcosine to glycine and formaldehyde. These results indicate that the first step in glyphosate degradation by PG2982 is cleavage of the carbon-phosphorus bond, resulting in the release of sarcosine and a phosphate group. The phosphate group is utilized as a source of phosphorus, and the sarcosine is degraded to glycine and formaldehyde. Phosphonate utilization by Pseudomonas sp. PG2982 was investigated. Each of the ten phosphonates tested were utilized as a sole source of phosphorus by PG2982. Representative compounds tested included alkylphosphonates, 1-amino-substituted alkylphosphonates, amino-terminal phosphonates, and an arylphosphonate. PG2982 cultures degraded phenylphosphonate to benzene and produced methane from methylphosphonate. The data indicate that PG2982 is capable of cleaving the carbon-phosphorus bond of several structurally different phosphonates

  6. Mass Spectrometric Characteristics of Prenylated Indole Derivatives from Marine-Derived Penicillium sp. NH-SL.

    Science.gov (United States)

    Ding, Hui; Ding, Wanjing; Ma, Zhongjun

    2017-03-22

    Two prenylated indole alkaloids were isolated from the ethyl acetate extracts of a marine-derived fungus Penicillium sp. NH-SL and one of them exhibited potent cytotoxic activity against mouse hepa 1c1c7 cells. In order to detect other bioactive analogs, we used liquid chromatogram tandem mass spectrometry (LC-MS/MS) to analyze the mass spectrometric characteristics of the isolated compounds as well as the crude extracts. As a result, three other analogs were detected, and their structures were deduced according to the similar fragmentation patterns. This is the first systematic report on the mass spectrometric characteristics of prenylated indole derivatives.

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

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  8. Transcription of human resistin gene involves an interaction of Sp1 with peroxisome proliferator-activating receptor gamma (PPARgamma.

    Directory of Open Access Journals (Sweden)

    Anil K Singh

    2010-03-01

    Full Text Available Resistin is a cysteine rich protein, mainly expressed and secreted by circulating human mononuclear cells. While several factors responsible for transcription of mouse resistin gene have been identified, not much is known about the factors responsible for the differential expression of human resistin.We show that the minimal promoter of human resistin lies within approximately 80 bp sequence upstream of the transcriptional start site (-240 whereas binding sites for cRel, CCAAT enhancer binding protein alpha (C/EBP-alpha, activating transcription factor 2 (ATF-2 and activator protein 1 (AP-1 transcription factors, important for induced expression, are present within sequences up to -619. Specificity Protein 1(Sp1 binding site (-276 to -295 is also present and an interaction of Sp1 with peroxisome proliferator activating receptor gamma (PPARgamma is necessary for constitutive expression in U937 cells. Indeed co-immunoprecipitation assay demonstrated a direct physical interaction of Sp1 with PPARgamma in whole cell extracts of U937 cells. Phorbol myristate acetate (PMA upregulated the expression of resistin mRNA in U937 cells by increasing the recruitment of Sp1, ATF-2 and PPARgamma on the resistin gene promoter. Furthermore, PMA stimulation of U937 cells resulted in the disruption of Sp1 and PPARgamma interaction. Chromatin immunoprecipitation (ChIP assay confirmed the recruitment of transcription factors phospho ATF-2, Sp1, Sp3, PPARgamma, chromatin modifier histone deacetylase 1 (HDAC1 and the acetylated form of histone H3 but not cRel, C/EBP-alpha and phospho c-Jun during resistin gene transcription.Our findings suggest a complex interplay of Sp1 and PPARgamma along with other transcription factors that drives the expression of resistin in human monocytic U937 cells.

  9. Trichoderma sp. dalam Pengendalian Penyakit Layu Fusarium pada Tanaman Tomat

    OpenAIRE

    Novita, Trias

    2013-01-01

    Penelitian ini bertujuan untuk mengetahui peran Trichoderma sp dalam pengendalianpenyakit layu fusarium pada tanaman tomat. Penelitian dilaksanakan di Rumah Kaca FakultasPertanian Universitas Jambi, perlakuannya terdiri dari : t0 = tanpa Trichoderma sp; t1 = 25 gTrichoderma sp/8 kg media; t2 = 50 g Trichoderma sp/8 kg media; t3 = 75 g Trichoderma sp/8 kgmedia; dan t4 = 100 g Trichoderma sp /8 kg media. Hasil penelitian menunjukkan bahwa Trichodermasp berperan dalam mengendalikan penyakit layu...

  10. INTERAKSI ANTARA Trichoderma Harzianum, Penicillium SP. DAN Pseudomonas SP. SERTA KAPASITAS ANTAGONISMENYA TERHADAP Phytophthora CapsicilN VITRO*[Interaction Among Trichoderma Harzianum, Penicillium SP., Pseudomonas SP. and Antagonism Capacities Against Phy

    OpenAIRE

    Suharna, Nandang

    2003-01-01

    A preliminary study has been done to know antagonism capacities of three isolates of Trichoderma harzianum, two isolates of Penicillium sp.and one isolate of Pseudomonas sp.against Phytophthora capsici in vitro and interaction among those six antagonists.The highest antagonism capacity possessed by Penicillium sp. KN1, respectively followed by Penicillium sp.KN2,Pseudomonas sp. GH1 and the three T. harzianum isolates. Except for those three T. harzianum isolates, the two Penicillium sp.isolat...

  11. SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis

    Directory of Open Access Journals (Sweden)

    Mario Saare

    2015-01-01

    Full Text Available The SP100 family members comprise a set of closely related genes on chromosome 2q37.1. The widely expressed SP100 and the leukocyte-specific proteins SP110 and SP140 have been associated with transcriptional regulation and various human diseases. Here, we have characterized the SP100 family member SP140L. The genome sequence analysis showed the formation of SP140L gene through rearrangements of the two neighboring genes, SP100 and SP140, during the evolution of higher primates. The SP140L expression is interferon-inducible with high transcript levels in B cells and other peripheral blood mononuclear cells. Subcellularly, SP140L colocalizes with SP100 and SP140 in nuclear structures that are devoid of SP110, PML, or p300 proteins. Similarly to SP100 and SP140 protein, we detected serum autoantibodies to SP140L in patients with primary biliary cirrhosis using luciferase immunoprecipitation system and immunoblotting assays. In conclusion, our results show that SP140L is phylogenetically recent member of SP100 proteins and acts as an autoantigen in primary biliary cirrhosis patients.

  12. An Affymetrix Microarray Design for Microbial Genotyping

    Science.gov (United States)

    2009-10-01

    les échantillons qui ne se prêtent pas aux méthodes culturales de la microbiologie classique. La puce à ADN est une technologie qui permet la... area of microbial genotyping there are multiple platforms that can identify one or a few microbial targets in a single assay iteration. For most

  13. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    malignant cervical samples ... low- and high-risk HPV genotypes without identifying ... Since these samples were not from “healthy .... major capsid protein, any variation in its coding sequence is .... worldwide: a meta-analysis; Br. J. Cancer 88 63–73.

  14. Physicochemical and sensorial quality of banana genotypes

    Directory of Open Access Journals (Sweden)

    Ronielli Cardoso Reis

    2016-03-01

    Full Text Available Despite the diversity of banana varieties in Brazil, only a few cultivars have the proper agronomic traits and fruit quality for commercial exploitation. This study aimed at evaluating the physicochemical traits and sensorial acceptance of banana genotypes, in order to identify those with potential for commercial growing. Six improved banana genotypes were assessed (BRS Maravilha, PC 0101, FHIA 18, TM 2803, YB 4203 and BRS Caipira, as well as three commercial cultivars (Grand Naine, Pacovan and Prata Anã. Analyses of peel and pulp color, peel thickness, pulp yield, moisture, pH, soluble solids, titratable acidity, total carotenoids and sensorial acceptance were performed. The BRS Maravilha, FHIA 18, YB 4203 and BRS Caipira genotypes presented physicochemical traits similar to the Grand Naine, Pacovan and Prata Anã commercial cultivars. The BRS Maravilha and TM 2803 genotypes had sensorial acceptance similar to the Prata Anã and Grand Naine cultivars, and are therefore promising for commercial growing, with the advantage of being resistant to the black Sigatoka and Panama disease.

  15. Genotyping of human pappilomavirus in cervical precancerous ...

    African Journals Online (AJOL)

    Background: Cervical cancer caused by human papilloma virus (HPV), is the second most common cancer for women. This cancer is distributed worldwide, with ~80% of cases are found in the developing countries. In Indonesia, data of HPV genotypes are still limited and do not represent all regions of the country. Thus ...

  16. 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

  17. Morphometric characteristics of Lotus corniculatus L. genotypes ...

    African Journals Online (AJOL)

    The aim of this study was to examine the degree of variability in morphological and agronomic characteristics of 20 Lotus corniculatus L. local genotypes, and also to set aside germplasm that will be used as a source of genetic basis for improvement of the studied properties. In poor quality soils, L. corniculatus L. plays an ...

  18. Genotype X Fertility Interactions in Seedling Sweetgum

    Science.gov (United States)

    Scott X. Chang; Daniel J. Robison

    2002-01-01

    Genotype x fertility interactions may affect the suitability of sweetgum (Liquidambar styraciflua L.) for specific sites or the efficiency of nutrient use. To gain a better understanding of these interactions, 2-year-old sweetgum seedlings from two half-sib families were tested for growth response to N (0 and 100 kg/ha equivalent) and P (0 and 50 kg...

  19. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    Apr 30, 2014 ... Background and justification: Lack of stable high yielding cultivars is one ... of advanced finger millet genotypes evaluated in multiple environments, and (ii) identify stable high yielding .... for interaction principal component axis (IPCA) n, γgn ..... Table 2: Analysis of variance for grain yield using AMMI model.

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

    Science.gov (United States)

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

    2018-05-01

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

  1. In Vitro Conservation of Sweet Potato Genotypes

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Arrigoni-Blank

    2014-01-01

    Full Text Available The aim of this study was to develop a protocol for the in vitro conservation of sweet potato genotypes using the slow growth technique. The first experiment was conducted in a 4×5×2 factorial scheme, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, five concentrations of abscisic acid (ABA (0.0, 1.0, 2.0, 4.0, and 8.0 mg·L−1, and two temperatures (18 and 25°C. The second experiment was conducted in a 4×3×3 factorial scheme at 18°C, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, three variations of MS salts (50, 75, and 100%, and three concentrations of sucrose (10, 20, and 30 g·L−1. Every three months, we evaluated the survival (%, shoot height, and shoot viability. In vitro conservation of the sweet potato genotypes IPB-052 and IPB-007 was obtained over three and six months, respectively, using MS medium plus 2.0 mg·L−1 of ABA at either 18 or 25°C. Genotypes IPB-072 and IPB-137 can be kept for three and six months, respectively, in MS medium without ABA at 18°C. It is possible to store IPB-052 and IPB-072 for six months and IPB-007 and IPB-137 for nine months using 30 g·L−1 of sucrose and 50% MS salts.

  2. Association of collagen type I alpha1 (COLIA1) Sp1 polymorphism with osteoporotic fracture in Caucasian post-menopausal women: a meta-analysis.

    LENUS (Irish Health Repository)

    Ji, G-R

    2012-01-06

    This study was designed to summarize quantitatively the evidence for a relationship between collagen type I alpha1 (COLIA1) Sp1 polymorphism and osteoporotic fracture risk in Caucasian post-menopausal women. This meta-analysis included 16 studies, which analysed 2294 patients with fractures and 10 285 controls. The combined results showed that there was a significant difference in genotype distribution (SS odds ratio [OR] 0.72; Ss OR 1.18; ss OR 1.97) between patients with fractures and controls. When stratifying by the fracture site, it was found that: (i) patients with vertebral fractures had a significantly higher frequency of the Ss genotype and a lower frequency of the SS genotype than controls; and (ii) patients with non-vertebral fractures had a significantly higher frequency of the ss genotype and a lower frequency of the SS genotype than controls. This meta-analysis suggests that the COLIA1 Sp1 polymorphism may be associated with osteoporotic fracture in Caucasian post-menopausal women.

  3. Fresh Water Cyanobacteria Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 as an Anticancer Drug Resource

    OpenAIRE

    Srivastava, Akanksha; Tiwari, Ratnakar; Srivastava, Vikas; Singh, Tej Bali; Asthana, Ravi Kumar

    2015-01-01

    An increasing number of cancer patients worldwide, especially in third world countries, have raised concern to explore natural drug resources, such as the less explored fresh water filamentous cyanobacteria. Six strains of cyanobacteria (Phormidium sp. CCC727, Geitlerinema sp. CCC728, Arthrospira sp. CCC729, Phormidium sp. CCC731, Phormidium sp. CCC730, and Leptolyngbya sp. CCC732) were isolated (paddy fields and ponds in the Banaras Hindu University, campus) and five strains screened for ant...

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

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Abaidoo, R. C. [Kwame Nkrumah University of Technology, Kumasi (Ghana); International Institute of Tropical Agriculture, Ibadan (Nigeria); Opoku, A.; Boahen, S. [Kwame Nkrumah University of Technology, Kumasi (Ghana); Dare, M. O. [Federal University of Agriculture, Abeokuta (Nigeria)

    2013-11-15

    Variability in the utilization of phosphorus (P) by 64 early-maturing soybean (Glycine max L. Merr.) genotypes under low-P soil conditions were evaluated in 2009 and 2010 at Shika, Nigeria. Fifteen phenotypic variables; number of nodules, nodule dry weight, grain yield, plant biomass, total biomass, biomass N and P content, Phosphorus Utilization Index (PUI), shoot P Utilization efficiency (PUIS), grain P Utilization efficiency (PUIG), Harvest Index (HI), Biological N fixed (BNF), total N fixed and N and P uptake were measured. The four clusters revealed by cluster analysis were basically divided along (1) plant biomass and uptake, (2) nutrient acquisition and utilization and (3) nodulation components. Three early maturing genotypes, TGx1842-14E, TGx1912-11F and TGx1913-5F, were identified as having high P utilization index and low P uptake. These genotypes could be a potential source for breeding for P use efficiency in early maturing soybean genotypes. (author)

  6. Determination of Fatty Acid Metabolism with Dynamic [11C]Palmitate Positron Emission Tomography of Mouse Heart In Vivo

    Directory of Open Access Journals (Sweden)

    Yinlin Li

    2015-09-01

    Full Text Available The goal of this study was to establish a quantitative method for measuring fatty acid (FA metabolism with partial volume (PV and spill-over (SP corrections using dynamic [11C]palmitate positron emission tomographic (PET images of mouse heart in vivo. Twenty-minute dynamic [11C]palmitate PET scans of four 18- to 20-week-old male C57BL/6 mice under isoflurane anesthesia were performed using a Focus F-120 PET scanner. A model-corrected blood input function, by which the input function with SP and PV corrections and the metabolic rate constants (k1–k5 are simultaneously estimated from the dynamic [11C]palmitate PET images of mouse hearts in a four-compartment tracer kinetic model, was used to determine rates of myocardial fatty acid oxidation (MFAO, myocardial FA esterification, myocardial FA use, and myocardial FA uptake. The MFAO thus measured in C57BL/6 mice was 375.03 ± 43.83 nmol/min/g. This compares well to the MFAO measured in perfused working C57BL/6 mouse hearts ex vivo of about 350 nmol/g/min and 400 nmol/min/g. FA metabolism was measured for the first time in mouse heart in vivo using dynamic [11C]palmitate PET in a four-compartment tracer kinetic model. MFAO obtained with this model was validated by results previously obtained with mouse hearts ex vivo.

  7. CRP-ductin, the mouse homologue of gp-340/deleted in malignant brain tumors 1 (DMBT1), binds gram-positive and gram-negative bacteria and interacts with lung surfactant protein D

    DEFF Research Database (Denmark)

    Madsen, Jens; Tornøe, Ida; Nielsen, Ole

    2003-01-01

    CRP-ductin is a protein expressed mainly by mucosal epithelial cells in the mouse. Sequence homologies indicate that CRP-ductin is the mouse homologue of human gp-340, a glycoprotein that agglutinates microorganisms and binds the lung mucosal collectin surfactant protein-D (SP-D). Here we report...... that purified CRP-ductin binds human SP-D in a calcium-dependent manner and that the binding is not inhibited by maltose. The same properties have previously been observed for gp-340 binding of SP-D. CRP-ductin also showed calcium-dependent binding to both gram-positive and -negative bacteria. A polyclonal...... antibody raised against gp-340 reacted specifically with CRP-ductin in Western blots. Immunoreactivity to CRP-ductin was found in the exocrine pancreas, in epithelial cells throughout the gastrointestinal tract and in the parotid ducts. A panel of RNA preparations from mouse tissues was screened for CRP...

  8. Antibacterial Actions and Potential Phototoxic Effects of Volatile oils of Foeniculum sp. (fennel, Salvia sp. (sage, Vitis sp. (grape, Lavandula sp. (lavender

    Directory of Open Access Journals (Sweden)

    Elif Ayse Erdogan Eliuz

    2016-09-01

    Full Text Available In the present study, the volatile compounds of essential oil of Foeniculum vulgare (fennel, Salvia officinalis (sage, Vitis vinifera (grape, Lavandula angustifolia (lavender were analysed by gas chromatography-mass spectrometry (GC-MS using the Nist and Willey libraries. It was determined that the main components of Foeniculum sp. were anethole (41.11%, carvacrol (9.18%. whereas main components of Salvia sp were 1.8 cineole (34.09%, caryophyllene (10.95%, camphor (9.44%, α-pinene (8.42%. Vitis sp. contained linoleic acid (36.98%, 2,4-decadienal (30.79%. Finally, volatile component of Lavandula sp. was linalool (33.57%, linalyl acetate (30.74%. Photoxic antibacterial activity of volatile oil of those plants against Escherichia coli (ATCC 25293, Klebsiella pneumoniae (10031, Salmonella thyphimurium, Bacillus subtilis (ATCC 6633, Staphylococcus aureus (ATCC 25925, Enterococcus feacalis (ATCC 29212 were examined by using disc diffusion method. We demonstrated that volatile oil effectively can be activated by a standard LED light. In vitro, significant phototoxicity was demonstrated by volatile oil of Foeniculum sp. and Vitis sp. (P < 0.05, while minor phototoxicity was induced by Lavandula sp. Therefore, volatile oil of plant can be considered as a potential photosensitizer in the photochemical therapy.

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

    Science.gov (United States)

    Manrubia, Susanna; Cuesta, José A

    2017-04-01

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

  10. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Pollen diversity, viability and floral structure of some Musa genotypes. ... This experiment was designed to study the floral structure, pollen morphology and the potential pollen viability of five Musa genotypes obtained ... HOW TO USE AJOL.

  11. Behavior of durum wheat genotypes under normal irrigation and ...

    African Journals Online (AJOL)

    Behavior of durum wheat genotypes under normal irrigation and drought stress conditions in the greenhouse. ... African Journal of Biotechnology ... Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and ...

  12. Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes

    African Journals Online (AJOL)

    sive protein in human diets with grains containing about. 23–25% protein ... Keywords: heritability, phenotype, principal component analysis, variance. Introduction .... be due to genotype, environment, and the interaction of genotype and ...

  13. magnitude of genotype x environment interaction for bacterial leaf

    African Journals Online (AJOL)

    ACSS

    African Crop Science Journal, Vol. ... effects of treatments into genotype, environment, and genotype x environment (G x E) interactions. Results .... method is economically effective (Niño-Liu et al., ..... This phenomenon indicated differences in.

  14. Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea.

    Science.gov (United States)

    Nguyen, Tuan Manh; Kim, Jaisoo

    2017-05-01

    White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11 T , UCM-F25, and UCM-80 T . We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11 T , UCM-F25, and UCM-80 T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11 T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664 T (98.48-98.55%), and the strain UCM-80 T was the closest match with Azohydromonas lata IAM 12599 T (98.34%). The presence of summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c), C 16:0 , summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c) as well as twokinds of hydroxyfatty acids consisting of C 10:0 3-OH and C 12:0 2-OH, and branched fatty acids containing C 16:0 iso and C 17:0 cyclo were detected in all the strains. Phosphatidylethanolamine was a major polar lipid. DNA-DNA relatedness confirmed UCM-11 T , UCM-F25 and UCM-80 T as novel members of the genus Azohydromonas. Based on the morphological, physiological, biochemical and genotypic characteristics, we suggest that strains UCM-11 T , UCM-F25, and UCM-80 T represent novel species within the genus Azohydromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11 T (=KACC 18570 T =NBRC 111646 T ) and UCM-80 T (=KACC 18576 T =NBRC 111658 T ), respectively.

  15. Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system.

    Science.gov (United States)

    Kim, Dong-Uk; Lee, Hyosun; Lee, Ji-Hyeong; Ahn, Jae-Hyung; Lim, Sangyong; Jeong, Sunwook; Park, So Yoon; Seong, Chi Nam; Ka, Jong-Ok

    2015-09-01

    Two bacterial strains, designated MA1002(T) and MA1003(T), were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002(T) were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003(T) were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002(T) contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003(T) had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002(T) and MA1003(T) were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002(T) was phylogenetically related to Deinococcus apachensis DSM 19763(T), D. geothermalis DSM 11300(T), D. aerius TR0125(T) and D. aetherius ST0316(T) (92.9, 92.6, 92.0 and 91.9% sequence similarity, respectively), and MA1003(T) showed the highest sequence similarity to Deinococcus hopiensis KR-140(T) (92.9%) and D. xinjiangensis X-82(T) (91.4%). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002(T) = KACC 17964(T) = NBRC 110141(T)) and Deinococcus carri sp. nov. (type strain is MA1003(T) = KACC 17965(T) = NBRC 110142(T)).

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

    Science.gov (United States)

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

    2015-06-01

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

  17. TurboSP and the Topological Trigger

    CERN Document Server

    Belavin, Vladislav

    2016-01-01

    TurboSP was originally proposed as an alternative to Full stream in LHCb data flow. TurboSP is a data flow strategy which not only selects events that should be preserved, like in Full stream, but also provides selective persistence. This is achieved by saving candidates and subset of the reconstruction. During this summer project we investigated the physics viability of using TurboSP with the topological lines and found out a possibility to reduce the number of kept tracks per event by two times while keeping a ratio of fully picked up interesting decay modes on $\\sim 97 \\%$ level.

  18. 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....

  19. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.

    Science.gov (United States)

    Parida, Swarup K; Kalia, Sanjay K; Kaul, Sunita; Dalal, Vivek; Hemaprabha, G; Selvi, Athiappan; Pandit, Awadhesh; Singh, Archana; Gaikwad, Kishor; Sharma, Tilak R; Srivastava, Prem Shankar; Singh, Nagendra K; Mohapatra, Trilochan

    2009-01-01

    Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

  20. Characterization of Variant Creutzfeldt-Jakob Disease Prions in Prion Protein-humanized Mice Carrying Distinct Codon 129 Genotypes*

    Science.gov (United States)

    Takeuchi, Atsuko; Kobayashi, Atsushi; Ironside, James W.; Mohri, Shirou; Kitamoto, Tetsuyuki

    2013-01-01

    To date, all clinical variant Creutzfeldt-Jakob disease (vCJD) patients are homozygous for methionine at polymorphic codon 129 (129M/M) of the prion protein (PrP) gene. However, the appearance of asymptomatic secondary vCJD infection in individuals with a PRNP codon 129 genotype other than M/M and transmission studies using animal models have raised the concern that all humans might be susceptible to vCJD prions, especially via secondary infection. To reevaluate this possibility and to analyze in detail the transmission properties of vCJD prions to transgenic animals carrying distinct codon 129 genotype, we performed intracerebral inoculation of vCJD prions to humanized knock-in mice carrying all possible codon 129 genotypes (129M/M, 129M/V, or 129V/V). All humanized knock-in mouse lines were susceptible to vCJD infection, although the attack rate gradually decreased from 129M/M to 129M/V and to 129V/V. The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased from 129M/M to 129M/V and to 129V/V. The biochemical properties of protease-resistant abnormal PrP in the brain and transmissibility of these humanized mouse-passaged vCJD prions upon subpassage into knock-in mice expressing bovine PrP were not affected by the codon 129 genotype. These results indicate that individuals with the 129V/V genotype may be more susceptible to secondary vCJD infection than expected and may lack the neuropathological characteristics observed in vCJD patients with the 129M/M genotype. Besides the molecular typing of protease-resistant PrP in the brain, transmission studies using knock-in mice carrying bovine PrP may aid the differential diagnosis of secondary vCJD infection, especially in individuals with the 129V/V genotype. PMID:23792955

  1. Characterization of variant Creutzfeldt-Jakob disease prions in prion protein-humanized mice carrying distinct codon 129 genotypes.

    Science.gov (United States)

    Takeuchi, Atsuko; Kobayashi, Atsushi; Ironside, James W; Mohri, Shirou; Kitamoto, Tetsuyuki

    2013-07-26

    To date, all clinical variant Creutzfeldt-Jakob disease (vCJD) patients are homozygous for methionine at polymorphic codon 129 (129M/M) of the prion protein (PrP) gene. However, the appearance of asymptomatic secondary vCJD infection in individuals with a PRNP codon 129 genotype other than M/M and transmission studies using animal models have raised the concern that all humans might be susceptible to vCJD prions, especially via secondary infection. To reevaluate this possibility and to analyze in detail the transmission properties of vCJD prions to transgenic animals carrying distinct codon 129 genotype, we performed intracerebral inoculation of vCJD prions to humanized knock-in mice carrying all possible codon 129 genotypes (129M/M, 129M/V, or 129V/V). All humanized knock-in mouse lines were susceptible to vCJD infection, although the attack rate gradually decreased from 129M/M to 129M/V and to 129V/V. The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased from 129M/M to 129M/V and to 129V/V. The biochemical properties of protease-resistant abnormal PrP in the brain and transmissibility of these humanized mouse-passaged vCJD prions upon subpassage into knock-in mice expressing bovine PrP were not affected by the codon 129 genotype. These results indicate that individuals with the 129V/V genotype may be more susceptible to secondary vCJD infection than expected and may lack the neuropathological characteristics observed in vCJD patients with the 129M/M genotype. Besides the molecular typing of protease-resistant PrP in the brain, transmission studies using knock-in mice carrying bovine PrP may aid the differential diagnosis of secondary vCJD infection, especially in individuals with the 129V/V genotype.

  2. Transcript profiling and gene characterization of three fatty acid desaturase genes in high, moderate, and low linolenic acid genotypes of flax (Linum usitatissimum L.) and their role in linolenic acid accumulation.

    Science.gov (United States)

    Banik, Mitali; Duguid, Scott; Cloutier, Sylvie

    2011-06-01

    Three genes encoding fatty acid desaturase 3 (fad3a, fad3b, and a novel fad3c) were cloned from four flax genotypes varying in linolenic acid content. Real-time PCR was used to quantify expression levels of the three fad3 genes during seed development. High amounts of both fad3a and fad3b transcripts were observed and reached their peak levels at 20 days after anthesis, except for fad3a from SP2047 where only low level expression was observed throughout seed development. Transcript accumulation of the novel fad3c gene was at similar background levels. The fatty acid composition was analysed for all genotypes and stages of development and compared with the fad3 gene expression patterns. α-Linolenic acid gradually accumulated during seed development, while linoleic acid was transient and decreased in M5791, UGG5-5, and AC McDuff. In contrast, the linolenic acid present in the early stages of development nearly completely disappeared in SP2047, while linoleic acid steadily accumulated. fad3a of the low linolenic acid line SP2047 encoded a truncated protein caused by a premature stop codon resulting from a single point mutation, and the low level of transcript accumulation in this genotype is likely due to nonsense-mediated mRNA decay caused by the premature termination of translation as a result of this early stop codon. Although substantial amounts of transcript accumulation occurred with fad3b of SP2047 genotype, cloning of the gene revealed a mutation in the first histidine box causing an amino acid change. Heterologous expression in yeast of the SP2047 and UGG5-5 fad3b genes showed that the mutation in the histidine box in SP2047 caused the enzyme inactivity. Taken together, these results showed that fad3a and fad3b are responsible for linolenic acid accumulation in flax seeds but did not support a major role for the novel fad3c. These observations were further supported by phenotypic and genotypic assessment of a doubled haploid population. Expression patterns

  3. Pengendalian Hayati Penyakit Layu Fusarium Pisang (Fusarium oxysporum f.sp. cubense dengan Trichoderma sp.

    Directory of Open Access Journals (Sweden)

    Albertus Sudirman

    2011-07-01

    Full Text Available The aim of this research was to study the inhibiting ability of Trichoderma sp. to control fusarium wilt of banana in greenhouse condition. The experiments consisted of the antagonism test between Trichoderma sp. and Fusarium oxysporum f.sp. cubense (Foc in vitro using dual culture method and glass house experiment which was arranged in 3×3 Factorial Complete Randomized Design. First factor of the latter experiment was the dose of Trichoderma sp. culture (0, 25, and 50 g per polybag, second factor was time of Trichoderma culture application (2 weeks before Foc inoculation, at same time with Foc inoculation and 2 weeks after Foc inoculation. Trichoderma sp. was cultured in mixed rice brand and chaff medium. The disease intensity was observed with scoring system of wilting leaves (0–4. The results showed that Trichoderma sp. was antagonistic against Foc in vitro and inhibited 86% of Foc colony development. Mechanism of antagonism between Trichoderma sp. and Foc was hyperparasitism. Trichoderma hyphae coiled around Foc hyphae. Lysis of Foc hyphae was occurred at the attached site of Trichoderma hyphae on Foc hyphae. Added banana seedling with Trichoderma sp. Culture reduced disease intensity of Fusarium wilt. Suggested dose of Trichoderma culture application in glass house was 25 g/polybag, given at the same time with Foc inoculation. Penelitian ini bertujuan untuk mengetahui kemampuan Trichoderma sp. untuk pengendalian penyakit layu fusarium pisang di rumah kaca. Penelitian meliputi pengujian daya hambat Fusarium oxysporum f.sp. cubense (Foc in vitro dan kemampuan menekan intensitas penyakit di rumah kaca. Penelitian in vitro meliputi uji antagonisme dan mekanismenya yang dilakukan secara dual culture. Uji pengaruh Trichoderma sp. terhadap penyakit layu Fusarium dilakukan di rumah kaca dengan Rancangan Acak Lengkap Faktorial. Faktor pertama adalah dosis biakan Trichoderma sp., dengan tiga aras (0, 25, 50 g/per bibit dalam polibag. Faktor kedua

  4. Small constrained SP1-7 analogs bind to a unique site and promote anti-allodynic effects following systemic injection in mice.

    Science.gov (United States)

    Jonsson, A; Fransson, R; Haramaki, Y; Skogh, A; Brolin, E; Watanabe, H; Nordvall, G; Hallberg, M; Sandström, A; Nyberg, F

    2015-07-09

    Previous results have shown that the substance P (SP) N-terminal fragment SP1-7 may attenuate hyperalgesia and produce anti-allodynia in animals using various experimental models for neuropathic pain. The heptapeptide was found to induce its effects through binding to and activating specific sites apart from any known neurokinin or opioid receptor. Furthermore, we have applied a medicinal chemistry program to develop lead compounds mimicking the effect of SP1-7. The present study was designed to evaluate the pharmacological effect of these compounds using the mouse spared nerve injury (SNI) model of chronic neuropathic pain. Also, as no comprehensive screen with the aim to identify the SP1-7 target has yet been performed we screened our lead compound H-Phe-Phe-NH2 toward a panel of drug targets. The extensive target screen, including 111 targets, did not reveal any hit for the binding site among a number of known receptors or enzymes involved in pain modulation. Our animal studies confirmed that SP1-7, but also synthetic analogs thereof, possesses anti-allodynic effects in the mouse SNI model of neuropathic pain. One of the lead compounds, a constrained H-Phe-Phe-NH2 analog, was shown to exhibit a significant anti-allodynic effect. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  5. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    The trials were set up to identify sweetpotato genotypes with adaptation to highland agroecologies with special reference to resistance to Ahemaria blight ... growth and at harvest, four genotypes and the local check, Magabari, bad high levels of resistance toA/Jemaria blight. Eight genotypes had total storage root yield ...

  6. Hepatitis B virus Genotypes in West Azarbayjan Province, Northwest Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari

    2017-12-01

    CONCLUSIONS: The results reveal that D genotype is the main genotype of HBV in West Azarbayjan province. Presence of this genotype conformed with the low rate of acute liver diseases caused by hepatitis B chronic infection, cirrhosis of the liver and hepatocellular carcinoma.

  7. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  8. Introduction to a special issue on genotype by environment interaction

    Science.gov (United States)

    Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

  9. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  10. Effect of Genotype and Age on Some Morphometric, Body Linear ...

    African Journals Online (AJOL)

    A population of 231 roosters of the Nigerian indigenous chickens of normal feathered frizzle feathered and naked neck genotypes was evaluated for the effect of genotype and age on some morphometric body linear measurements and semen characteristics of three Nigerian chicken genotypes. 20 roosters from each ...

  11. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

  12. Relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...

  13. Genotype x Environment Interaction for Tuber Yield, Dry Matter ...

    African Journals Online (AJOL)

    A study was conducted to determine stability of tuber yield, dry matter content and specific gravity, and the nature and magnitude of genotype x environment (G x E) interaction in elite tetraploid potato genotypes. Eleven potato genotypes including two standard checks were evaluated in the eastern part of Ethiopia at ...

  14. [Evaluation of hepatitis B virus genotyping EIA kit].

    Science.gov (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

    2009-01-01

    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  15. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  16. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    Chickpea is the major pulse crop cultivated in Ethiopia. However, its production is constrained due to genotype instability and environmental variability. This research was carried out to examine the magnitude of environmental effect on yield of chickpea genotypes and to investigate the stability and adaptability of genotypes ...

  17. Reactions of some potato genotypes to late blight in Cameroon ...

    African Journals Online (AJOL)

    Reactions of some potato genotypes to late blight in Cameroon. D. K. Njualem, P. Demo, H. A. Mendoza, J. T. Koi, S. F. Nana. Abstract. Field experiments were conducted in Cameroon in 1995 and 1996 to evaluate reactions of different potato genotypes to late blight. There were significant differences among genotypes for ...

  18. Detection of Salmonella sp., Vibrio sp. and total plate count bacteria on blood cockle (Anadara granosa)

    Science.gov (United States)

    Ekawati, ER; Yusmiati, S. N. H.

    2018-01-01

    Blood cockle (Anadara granosa) has high level of zinc and protein, which is beneficial for therapeutic function for malnourished particularly stunting case in children. Zinc in animal foods is more absorbable than that from vegetable food. Blood cockle (Anadara granosa) is rich in nutrient and an excellent environment for the growth of microorganisms. This research aimed to identify the contamination of Salmonella sp., Vibrio sp. and total plate count bacteria on blood cockle (Anadara granosa). This was observation research with laboratory analysis. Salmonella sp. and Vibrio sp. were detected from blood cockle. Total plate count was determine of the total amount of the bacteria. Results detected from 20 samples of blood cockle showed that all samples were negative of Salmonella sp. and 1 sample positive Vibrio sp. The result of total plate count bacteria was < 5 x 105 colony/g sample.

  19. Superhard sp2–sp3 hybrid carbon allotropes with tunable electronic properties

    Directory of Open Access Journals (Sweden)

    Meng Hu

    2016-05-01

    Full Text Available Four sp2–sp3 hybrid carbon allotropes are proposed on the basis of first principles calculations. These four carbon allotropes are energetically more favorable than graphite under suitable pressure conditions. They can be assembled from graphite through intralayer wrinkling and interlayer buckling, which is similar to the formation of diamond from graphite. For one of the sp2–sp3 hybrid carbon allotropes, mC24, the electron diffraction patterns match these of i-carbon, which is synthesized from shock-compressed graphite (H. Hirai and K. Kondo, Science, 1991, 253, 772. The allotropes exhibit tunable electronic characteristics from metallic to semiconductive with band gaps comparable to those of silicon allotropes. They are all superhard materials with Vickers hardness values comparable to that of cubic BN. The sp2–sp3 hybrid carbon allotroes are promising materials for photovoltaic electronic devices, and abrasive and grinding tools.

  20. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

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

    2015-01-01

    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......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...... gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...

  1. FRUIT QUALITY CHARACTERISTICS OF SOME BLUEBERRY GENOTYPES

    Directory of Open Access Journals (Sweden)

    Irina Ancu

    2013-12-01

    Full Text Available In Romania the blueberry breeding program started in 1982 and till now was conducted by dr. Paulina Mladin. For inducing the variability, different genetic resources of American blueberry cultivars (V. corymbosum, V. angustifolium were involved in a high number of crosses. For identify the genotype with the best fruit quality, some biometric quality indicators (average fruit weight, size index and basically chemical compounds of fruits including ascorbic acid, dry matter, ash, soluble solids, total sugar, titratable acidity, tanoid substances, pectic substances, protein crude, phosphorus and potassium were determined. Of the eleven chemical studied properties who reflected the fruits quality, for five of them were found no statistically significant differences. The purpose of this paper work was to evaluate fruit quality and to identify the valuable genotypes resulted from Romanian blueberry breeding program.

  2. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  3. EOP Gold Coral (Gerardia sp.) Growth Measurements

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gold coral (Gerardia sp.) trees that were inspected years earlier on Pisces submersible dives were revisited and their change in size measured. The fishery for...

  4. Metabolites from marine fungus Aspergillus sp.

    Digital Repository Service at National Institute of Oceanography (India)

    Wahidullah, S.; Rajmanickam, R.; DeSouza, L.

    Chemical examination of a methanolic extract of the marine fungus, Aspergillus sp., isolated from marine grass environment, yielded a steroid, ergosterol peroxide (1), and a mixture of known glyceride esters (2,3) of unsaturated fatty acids...

  5. SP (4,R) symmetry in light nuclei

    International Nuclear Information System (INIS)

    Peterson, D.R.

    1979-01-01

    A classification of nuclear states according to the noncompact sympletic Lie algebras sp(2n,R), n = 1, 2, 3, is investigated. Such a classification has recently been shown to be physically meaningful. This classification scheme is the appropriate generalization fo Elliott's SU 3 model of rotational states in deformed light nuclei to include core excitations. A restricted classification according to the Lie algebra, sp(4,R), is motivated. Truncation of the model space to a single sp(4,R) irreducible representation allows the inclusion of states possessing very high excitation energy. An sp(4,R) model study is performed on S = T = 0 positive-parity rotational bands in the deformed light nuclei 16 O and 24 Mg. States are included in the model space that possess up to 10h ω in excitation energy. Results for the B(E2) transition rates compare favorable with experiment, without resort to effective charges

  6. Progress in SP-100 tribological coatings

    International Nuclear Information System (INIS)

    Ring, P.J.; Roy, P.; Schuster, G.B.; Busboom, H.J.

    1992-01-01

    The SP-100 reactor will operate at temperatures up to 1500K in high vacuum. To address the SP-100 needs, a tribology development program has been established at GE to investigate candidate coating materials. Materials were selected based on their high thermodynamic stability, high melting point, compatibility with the substrate, and coefficients of thermal expansion similar to niobium-1% zirconium-the candidate structural material for SP-100. An additional requirement was that the deposition processes should be commercially available to coat large components. This paper presents the details regarding the SP-100 Tribology Development Program including background information, specific bearing requirements, basis for coating material selection, testing methods and the initial results covering the early years of this program

  7. Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil.

    Science.gov (United States)

    Zhang, Jia-Yue; Liu, Xing-Yu; Liu, Shuang-Jiang

    2010-08-01

    Two bacterial strains, DNG5T and V3M1T, isolated from forest soil of the Changbai mountains in China, were characterized using a polyphasic approach. Analysis of their 16S rRNA gene sequences indicated that strains DNG5T and V3M1T were phylogenetically related to members of the genus Agrococcus (96.0-98.4% similarity) and Micrococcus (96.7-98.0% similarity), respectively, within the order Actinomycetales. Strains DNG5T and V3M1T were Gram-stain-positive and strictly aerobic and formed yellow colonies on LB agar. Cells of strain DNG5T were short, non-motile rods, 0.4-0.5x0.8-1.0 microm. Strain DNG5T contained MK-10 and MK-11 as the major respiratory quinones and anteiso-C15:0 (49.2%) and iso-C16:0 (22.4%) as the major fatty acids. The diamino acid in the peptidoglycan of strain DNG5T was 2,4-diaminobutyric acid and the murein was of the acetyl type. Cells of strain V3M1T were cocci, 0.6-0.7 microm in diameter. The cell-wall peptidoglycan of strain V3M1T contained the amino acids lysine, glutamic acid, alanine and glycine. Strain V3M1T contained MK-7, MK-7(H2), MK-8 and MK-8(H2) as respiratory quinones and anteiso-C15:0 (78.2%) and iso-C15:0 (13.1%) as the major cellular fatty acids. The DNA G+C contents of strains DNG5T and V3M1T were 75.9 and 67.2 mol%, respectively. The DNA-DNA relatedness of strain DNG5T to Agrococcus jejuensis DSM 22002T, A. jenensis JCM 9950T, A. baldri JCM 12132T and A. citreus JCM 12398T was 58.3, 43.9, 36.1 and 54.1%, respectively. The DNA-DNA relatedness of strain V3M1T to Micrococcus luteus CGMCC 1.2299T, M. antarcticus CGMCC 1.2373T and M. lylae CGMCC 1.2300T was 57.5, 45.4 and 39.0%, respectively. Combining phenotypic and genotypic traits, strain DNG5T represents a novel species of the genus Agrococcus, for which the name Agrococcus terreus sp. nov. is proposed, with DNG5T (=CGMCC 1.6960T =NBRC 104260T) as the type strain. Strain V3M1T represents a novel species of the genus Micrococcus, for which the name Micrococcus terreus sp. nov. is

  8. Novel approach for CES1 genotyping

    DEFF Research Database (Denmark)

    Bjerre, Ditte; Berg Rasmussen, Henrik

    2018-01-01

    AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed...

  9. TL transgenic mouse strains

    International Nuclear Information System (INIS)

    Obata, Y.; Matsudaira, Y.; Hasegawa, H.; Tamaki, H.; Takahashi, T.; Morita, A.; Kasai, K.

    1993-01-01

    As a result of abnormal development of the thymus of these mice, TCR αβ lineage of the T cell differentiation is disturbed and cells belonging to the TCR γδ CD4 - CD8 - double negative (DN) lineage become preponderant. The γδ DN cells migrate into peripheral lymphoid organs and constitute nearly 50% of peripheral T cells. Immune function of the transgenic mice is severely impaired, indicating that the γδ cells are incapable of participating in these reactions. Molecular and serological analyses of T-cell lymphomas reveal that they belong to the γδ lineage. Tg.Tla a -3-1 mice should be useful in defining the role of TL in normal and abnormal T cell differentiation as well as in the development of T-cell lymphomas, and further they should facilitate studies on the differentiation and function of γδ T cells. We isolated T3 b -TL gene from B6 mice and constructed a chimeric gene in which T3 b -TL is driven by the promoter of H-2K b . With the chimeric gene, two transgenic mouse strains, Tg. Con.3-1 and -2 have been derived in C3H background. Both strains express TL antigen in various tissues including skin. The skin graft of transgenic mice on C3H and (B6 X C3H)F 1 mice were rejected. In the mice which rejected the grafts, CD8 + TCRαβ cytotoxic T cells (CTL) against TL antigens were recognized. The recognition of TL by CTL did not require the antigen presentation by H-2 molecules. The results indicated that TL antigen in the skin becomes a transplantation antigen and behaves like a typical allogeneic MHC class I antigen. The facts that (B6 X C3H)F 1 mice rejected the skin expressing T3 b -TL antigen and induced CTL that killed TL + lymphomas of B6 origin revealed that TL antigen encoded by T3 b -TL is recognized as non-self in B6 mice. Experiments are now extended to analyze immune responses to TL antigen expressed on autochthonous T cell lymphomas. (J.P.N.)

  10. Silencing the SpMPK1, SpMPK2, and SpMPK3 Genes in Tomato Reduces Abscisic Acid—Mediated Drought Tolerance

    Directory of Open Access Journals (Sweden)

    Yan Liang

    2013-11-01

    Full Text Available Drought is a major threat to agriculture production worldwide. Mitogen-activated protein kinases (MAPKs play a pivotal role in sensing and converting stress signals into appropriate responses so that plants can adapt and survive. To examine the function of MAPKs in the drought tolerance of tomato plants, we silenced the SpMPK1, SpMPK2, and SpMPK3 genes in wild-type plants using the virus-induced gene silencing (VIGS method. The results indicate that silencing the individual genes or co-silencing SpMPK1, SpMPK2, and SpMPK3 reduced the drought tolerance of tomato plants by varying degrees. Co-silencing SpMPK1 and SpMPK2 impaired abscisic acid (ABA-induced and hydrogen peroxide (H2O2-induced stomatal closure and enhanced ABA-induced H2O2 production. Similar results were observed when silencing SpMPK3 alone, but not when SpMPK1 and SpMPK2 were individually silenced. These data suggest that the functions of SpMPK1 and SpMPK2 are redundant, and they overlap with that of SpMPK3 in drought stress signaling pathways. In addition, we found that SpMPK3 may regulate H2O2 levels by mediating the expression of CAT1. Hence, SpMPK1, SpMPK2, and SpMPK3 may play crucial roles in enhancing tomato plants’ drought tolerance by influencing stomatal activity and H2O2 production via the ABA-H2O2 pathway.

  11. Cellulose powder from Cladophora sp. algae.

    Science.gov (United States)

    Ek, R; Gustafsson, C; Nutt, A; Iversen, T; Nyström, C

    1998-01-01

    The surface are and crystallinity was measured on a cellulose powder made from Cladophora sp. algae. The algae cellulose powder was found to have a very high surface area (63.4 m2/g, N2 gas adsorption) and build up of cellulose with a high crystallinity (approximately 100%, solid state NMR). The high surface area was confirmed by calculations from atomic force microscope imaging of microfibrils from Cladophora sp. algae.

  12. 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.

  13. Devosia soli sp. nov., isolated from greenhouse soil in Korea.

    Science.gov (United States)

    Yoo, Seung-Hee; Weon, Hang-Yeon; Kim, Byung-Yong; Hong, Seung-Beom; Kwon, Soon-Wo; Cho, Yang-Hee; Go, Seung-Joo; Stackebrandt, Erko

    2006-11-01

    A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5%) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0%. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18:1omega7c and C16:0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA-DNA hybridization experiments (47% relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

  14. Chryseobacterium salipaludis sp. nov., isolated at a wild ass sanctuary.

    Science.gov (United States)

    Divyasree, B; Suresh, G; Sasikala, Ch; Ramana, Ch V

    2018-02-01

    A Gram-stain-negative, rod-shaped, non-motile, aerobic bacterium was isolated from a sediment sample obtained from a wild ass sanctuary in Gujarat, India. The strain designated JC490 T was oxidase- and catalase-positive. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain JC490 T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jeonii AT1047 T (96.4 %) and with other members of the genus Chryseobacterium (<96.3 %). The DNA G+C content of strain JC490 T was 34 mol%. Strain JC490 T had phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and five unidentified polar lipids. Menaquinone-6 was the only respiratory quinone found. Iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH were the major fatty acids of strain JC490 T . On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, it is concluded that strain JC490 T constitutes a novel species of the genus Chryseobacterium, for which the name Chryseobacterium salipaludis sp. nov. is proposed. The type strain is JC490 T (=KCTC 52835 T =LMG 30048 T ).

  15. Actinoplanes sediminis sp. nov., isolated from marine sediment.

    Science.gov (United States)

    Qu, Zhi; Bao, Xiao-Dong; Xie, Qing-Yi; Zhao, You-Xing; Yan, Bing; Dai, Hao-Fu; Chen, Hui-Qin

    2018-01-01

    An actinomycete strain M4I47 T was isolated from sediment from Megas Gialos, Syros, Greece. The results of phylogenetic analysis of the 16S rRNA gene sequence of M4I47 T indicated that the highest similarity was with Actinoplanes atraurantiacus Y16 T (98.9 %), Actinoplanes deccanensis IFO 13994 T (98.8 %), Actinoplanes digitatis IFO 12512 T (98.1 %) and Actinoplanes abujensis A4029 T (98.0 %). The cell wall of the novel isolate contained meso-diaminopimelic acid and the whole-cell sugars were xylose, arabinose and glucose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unknown phospholipid. The DNA G+C content was 71.5 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the most closely related species. On the basis of these phenotypic and genotypic data, M4I47 T represents a novel species of the genus Actinoplanes, for which the name Actinoplanessediminis sp. nov. is proposed. The type strain is M4I47 T (=CCTCC AA 2016022 T =DSM 100965 T ).

  16. Streptomyces solisilvae sp. nov., isolated from tropical forest soil.

    Science.gov (United States)

    Zhou, Shuangqing; Yang, Xiaobo; Huang, Dongyi; Huang, Xiaolong

    2017-09-01

    A novel streptomycete (strain HNM0141T) was isolated from tropical forest soil collected from Bawangling mountain of Hainan island, PR China and its taxonomic position was established in a polyphasic study. The organism had chemical and morphological properties consistent with its classification as a member of the Streptomyces violaceusnigerclade. On the basis of the results of 16S rRNA gene sequence analysis, HNM0141T showed highest similarity to Streptomyces malaysiensisCGMCC4.1900T (99.4 %), Streptomyces samsunensis DSM 42010T (98.9 %), Streptomyces yatensis NBRC 101000T (98.3 %), Streptomyces rhizosphaericus NBRC 100778T (98.0 %) and Streptomyces sporoclivatus NBRC 100767T (97.9 %). The strain formed a well-delineated subclade with S. malaysiensis CGMCC4.1900T and S. samsunensis DSM 42010T. The levels of DNA-DNA relatedness between HNM0141T and S. malaysiensis CGMCC4.1900T and S. samsunensis DSM 42010T were 62 and 44 %, respectively. On the basis of phenotypic and genotypic characteristics, HNM0141T represents a novel species in the S. violaceusnigerclade for which the name Streptomyces solisilvae sp. nov. is proposed. The type strain is HNM0141 T (=CCTCC AA 2016045T=KCTC 39905T).

  17. Serratia ureilytica sp. nov., a novel urea-utilizing species.

    Science.gov (United States)

    Bhadra, Bhaskar; Roy, Pradosh; Chakraborty, Ranadhir

    2005-09-01

    A Gram-negative, rod-shaped, urea-dissolving and non-spore-forming bacterium, designated strain NiVa 51(T), was isolated from water of the River Torsa in Hasimara, Jalpaiguri district, West Bengal, India. On the basis of 16S rRNA gene sequence similarity, strain NiVa 51(T) was shown to belong to the gamma-Proteobacteria and to be related to Serratia marcescens subsp. sakuensis (98.35%) and S. marcescens subsp. marcescens (98.30%); however, strain NiVa 51(T) exhibited only 43.7% similarity to S. marcescens by DNA-DNA hybridization. The G+C content of the genomic DNA of the isolate was 60 mol%. Both biochemical characteristics and fatty acid analysis data supported the affiliation of strain NiVa 51(T) to the genus Serratia. Furthermore, strain NiVa 51(T) was found to utilize urea as nitrogen source. The results of DNA-DNA hybridization as well as physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NiVa 51(T) from recognized Serratia species. Strain NiVa 51(T) therefore represents a novel species, for which the name Serratia ureilytica sp. nov. is proposed, with type strain NiVa 51(T) (=LMG 22860(T)=CCUG 50595(T)).

  18. 10. international mouse genome conference

    Energy Technology Data Exchange (ETDEWEB)

    Meisler, M.H.

    1996-12-31

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  19. Teratology studies in the mouse.

    Science.gov (United States)

    Marsden, Edward; Leroy, Mariline

    2013-01-01

    The rat is the routine species of choice as the rodent model for regulatory safety testing of xenobiotics such as medicinal products, food additives, and other chemicals. However, the rat is not always suitable for pharmacological, toxicological, immunogenic, pharmacokinetic, or even practical reasons. Under such circumstances, the mouse offers an alternative for finding a suitable rodent model acceptable to the regulatory authorities. Since all essential routes of administration are possible, the short reproductive cycle and large litter size of the mouse make it a species well adapted for use in teratology studies. Given that good quality animals, including virgin mated females, can be acquired relatively easily and inexpensively, the mouse has been used in reproductive toxicity studies for decades and study protocols are well established.

  20. Mouse models of Fanconi anemia

    International Nuclear Information System (INIS)

    Parmar, Kalindi; D'Andrea, Alan; Niedernhofer, Laura J.

    2009-01-01

    Fanconi anemia is a rare inherited disease characterized by congenital anomalies, growth retardation, aplastic anemia and an increased risk of acute myeloid leukemia and squamous cell carcinomas. The disease is caused by mutation in genes encoding proteins required for the Fanconi anemia pathway, a response mechanism to replicative stress, including that caused by genotoxins that cause DNA interstrand crosslinks. Defects in the Fanconi anemia pathway lead to genomic instability and apoptosis of proliferating cells. To date, 13 complementation groups of Fanconi anemia were identified. Five of these genes have been deleted or mutated in the mouse, as well as a sixth key regulatory gene, to create mouse models of Fanconi anemia. This review summarizes the phenotype of each of the Fanconi anemia mouse models and highlights how genetic and interventional studies using the strains have yielded novel insight into therapeutic strategies for Fanconi anemia and into how the Fanconi anemia pathway protects against genomic instability.

  1. Mouse models of Fanconi anemia

    Energy Technology Data Exchange (ETDEWEB)

    Parmar, Kalindi; D' Andrea, Alan [Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115 (United States); Niedernhofer, Laura J., E-mail: niedernhoferl@upmc.edu [Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Cancer Institute, 5117 Centre Avenue, Hillman Cancer Center, Research Pavilion 2.6, Pittsburgh, PA 15213-1863 (United States)

    2009-07-31

    Fanconi anemia is a rare inherited disease characterized by congenital anomalies, growth retardation, aplastic anemia and an increased risk of acute myeloid leukemia and squamous cell carcinomas. The disease is caused by mutation in genes encoding proteins required for the Fanconi anemia pathway, a response mechanism to replicative stress, including that caused by genotoxins that cause DNA interstrand crosslinks. Defects in the Fanconi anemia pathway lead to genomic instability and apoptosis of proliferating cells. To date, 13 complementation groups of Fanconi anemia were identified. Five of these genes have been deleted or mutated in the mouse, as well as a sixth key regulatory gene, to create mouse models of Fanconi anemia. This review summarizes the phenotype of each of the Fanconi anemia mouse models and highlights how genetic and interventional studies using the strains have yielded novel insight into therapeutic strategies for Fanconi anemia and into how the Fanconi anemia pathway protects against genomic instability.

  2. Phenotypic and genotypic characterization of two Toxoplasma gondii isolates in free-range chickens from Uberlândia, Brazil.

    Science.gov (United States)

    Lopes, C S; Franco, P S; Silva, N M; Silva, D A O; Ferro, E A V; Pena, H F J; Soares, R M; Gennari, S M; Mineo, J R

    2016-07-01

    The aim of this study was to determine the seroprevalence of Toxoplasma gondii infection in free-range chickens from Uberlândia, Minas Gerais state, Brazil, and characterize the genotypic and phenotypic features of two isolates of this parasite, considering the importance of these hosts in the epidemiology of toxoplasmosis. Serum samples from 108 free-range chickens were obtained from ten different districts, and submitted to the modified agglutination test (MAT) for the presence of anti-T. gondii antibodies, and brain and heart tissue samples from infected chickens were processed for mouse bioassay. An overall seroprevalence of 71·3% was found and antibody titres ranged from 16 to 4096. After confirmation of seropositivity by mouse bioassay, the determination of the T. gondii genotypes of two isolates was performed by PCR-RFLP, using primers for the following markers: SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, new SAG2, Apico and CS3. These T. gondii isolates, designated TgChBrUD1and TgChBrUD2, were obtained from heart samples of free-range chickens. The TgChBrUD1 isolate belonged to ToxoDB PCR-RFLP genotype 11 and the TgChBrUD2 isolate belonged to ToxoDB PCR-RFLP genotype 6. Both isolates demonstrated high virulence in a rodent model, with the TgChBrUD1 isolate able to induce brain cysts, in accord with its pattern of multiplication rates in human fibroblast culture. Taken together, these results reveal high prevalence of T. gondii infection in free-range chickens throughout Uberlândia, indicating an important degree of oocyst environmental contamination and the existence of considerable risk for T. gondii transmission to humans by consumption of free-range chicken as a food source.

  3. Resistance Potential of Bread Wheat Genotypes Against Yellow Rust Disease Under Egyptian Climate.

    Science.gov (United States)

    Mahmoud, Amer F; Hassan, Mohamed I; Amein, Karam A

    2015-12-01

    Yellow rust (stripe rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive foliar diseases of wheat in Egypt and worldwide. In order to identify wheat genotypes resistant to yellow rust and develop molecular markers associated with the resistance, fifty F8 recombinant inbred lines (RILs) derived from a cross between resistant and susceptible bread wheat landraces were obtained. Artificial infection of Puccinia striiformis was performed under greenhouse conditions during two growing seasons and relative resistance index (RRI) was calculated. Two Egyptian bread wheat cultivars i.e. Giza-168 (resistant) and Sakha-69 (susceptible) were also evaluated. RRI values of two-year trial showed that 10 RILs responded with RRI value >6 2 rust. However, further molecular analyses would be performed to confirm markers associated with the resistance and suitable for marker-assisted selection. Resistant RILs identified in the study could be efficiently used to improve the resistance to yellow rust in wheat.

  4. 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

  5. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  6. Preliminary tests for Salix sp. tolerance to heavy metals (Cd, Ni, Pb)

    Science.gov (United States)

    Corneanu, Mihaela; Hernea, Cornelia; Butnariu, Monica; Corneanu, Gabriel; Sărac, Ioan; Hollerbach, Wilhelm; Neţoiu, Constantin; Petcov, Andreea Adriana

    2014-05-01

    The species of Salix genus constitute potential sources of germplasm in the prevention of the environment degradation, and offer remedy for about two third from the all degradation types. The majority of the willow species, present a good adaptation to hypoxic conditions, feature which suggest that they manifest a preference for mineral nutrition in comparison with organic one. Thus, many of willow species can be developed on soils with a big amount of minerals and/or radionuclides, being both phytoremediatory species, as well as pioneer ones, contributing to the restoration of soil. Thus, the willow species, posses the capacity for development in degraded areas, natural or anthropic, as swamps, abandoning crops areas, sandy dune, riparian sandy areas, gravels, a.o. In this paper are present some laboratory comparative tests of heavy metals tolerance on four Salix sp. genotypes: clone 202 (Salix alba), hybrid 892 (Salix alba), Inger (Salix viminalis) and Gudrun (Salix viminalis). The genotypes of Salix alba are native from Romania, produced in the Forest Research and Management Institute Bucharest, while the genotypes of Salix viminalis are native from Sweden, but the plant material was produced under license in Romania by REBINA Agrar SRL. As plant material were used one-year-old cuttings (5-10 cm long), with 2-6 buds each. Per genotype, per heavy metal and each of three concentration five replication were used. There were ten experimental variants for each genotype: three concentrations for each of the heavy metals; concentrations selected, in the accordance SR ISO 11269-2/March 1999 and Control (tap water). The cuttings were maintained in metalic solutions for 15 days. In the days 7th and 15th, were performed biometrical observations on: the roots number and length, the shoots number and length, the leaves number/shoot, viability of the shoots. At the end of the experiment the content in heavy metals was determined in roots and shoots (by atomic absorption

  7. Eugenol oil nanoemulsion: antifungal activity against Fusarium oxysporum f. sp. vasinfectum and phytotoxicity on cottonseeds

    Science.gov (United States)

    Abd-Elsalam, Kamel A.; Khokhlov, Alexei R.

    2015-02-01

    The current research deals with the formulation and characterization of bio-based oil-in-water nanoemulsion. The formulated eugenol oil nanoemulsion was characterized by dynamic light scattering, stability test, transmission electron microscopy and thin layer chromatography. The nanoemulsion droplets were found to have a Z-average diameter of 80 nm and TEM study reveals the spherical shape of eugenol oil nanoemulsion (EON). The size of the nanoemulsion was found to be physically stable up to more than 1-month when it was kept at room temperature (25 °C). The TEM micrograph showed that the EON was spherical in shape and moderately mono or di-dispersed and was in the range of 50-110 nm. Three concentrations of the nanoformulation were used to evalute the anti-fusarium activity both in vitro and in vivo experiments. SDS-PAGE results of total protein from the Fusarium oxysporum f. sp. vasinfectum (FOV) isolate before and after treatment with eugenol oil nanoemulsion indicate that the content of extra cellular soluble small molecular proteins decreased significantly in EON-treated fungus. Light micrographs of mycelia and spores treated with EON showed the disruption of the fungal structures. The analysis of variance (ANOVA) for Fusarium wilt incidence indicated highly significant ( p = 0.000) effects of concentration, genotype, and their interaction. The difference in wilt incidence between concentrations and control was not the same for each genotype, that is, the genotypes responded differently to concentrations. Effects of three EON concentration on germination percentage, and radicle length, were determined in the laboratory. One very interesting finding in the current study is that cotton genotypes was the most important factors in determining wilt incidence as it accounted for 93.18 % of the explained (model) variation. In vitro experiments were conducted to evaluate the potential phytotoxic effect of three EON concentrations. Concentration, genotype and

  8. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  9. Mucispirillum schaedleri gen. nov., sp nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents

    DEFF Research Database (Denmark)

    Robertson, B.R.; O'Rourke, J.L.; Neilan, B.A.

    2005-01-01

    in the domain Bacteria. There was a high level of consensus in results obtained from the phenotypic and genotypic characterization of a number of the isolates, which showed they were distinct from other members of the Deferribacteres. As such, they are proposed to constitute a new genus and species......, Mucispirillum schaedleri gen. nov., sp. nov. These organisms are anaerobic, Gram-negative, spiral-shaped rods with bipolar flagella. The type strain is HRI 117(T) (=ATCC BAA-1009(T) = ACM 5223(T))....

  10. Mouse Resource Browser-a database of mouse databases

    NARCIS (Netherlands)

    Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M.; Schofield, Paul N.; Kollias, George; Aidinis, Vassilis

    2010-01-01

    The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the

  11. Performance of chickpea genotypes under Swat valley conditions

    International Nuclear Information System (INIS)

    Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.

    2004-01-01

    Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

  12. Genotypic Variation in Phosphorus Use Efficiency for Symbiotic Nitrogen Fixation in Voandzou (Vigna Subterranea)

    Energy Technology Data Exchange (ETDEWEB)

    Andriamananjara, A.; Rabeharisoa, L. [Laboratoire des Radio-isotopes, Universite d' Antananarivo, Antananarivo (Madagascar); Abdou, M. Malam [Laboratoire Banques de genes CERRA / KOLLO, Institut National de Recherche Agronomique du Niger (INRAN), Niamey (Niger); Masse, D. [Institut de Recherche pour le Developpement, UMR Eco and Sols, Montpellier, (France); Amenc, L.; Pernot, C.; Drevon, J. J. [Institut National de la Recherche Agronomique, UMR Eco and Sols, Montpellier (France)

    2013-11-15

    Vigna subterranea, known as voandzou or Bambara groundnut as an African indigenous crop which is often neglected or under-used in African subsistence agriculture. Preliminary research and country perceptions have shown its agronomic and nutritional properties, in particular under atypical climates of arid and tropical areas, and in saline soils. There is a high potential to increase the production by optimizing symbiotic nitrogen fixation (SNF) through effective inoculation even in nitrate-rich environments. In this study, Vigna subterranea inoculated with the reference strain of Bradyrhizobium sp. Vigna CB756 was studied in order to assess the symbiotic fixation potential of different cultivars and landraces of Madagascar, Niger and Mali under low-P and sufficient-P conditions. Six voandzou cultivars inoculated with Bradyrhizobium sp. Vigna CB756, were grown under hydroaeroponic culture for 6 weeks supplied with four phosphorus levels of 15, 30, 75 and 250 {mu}mol plant{sup -1} week{sup -1} in order to establish the response curve of voandzou to P supply, and to induce P deficient and sufficient levels. In another experiment five tolerant cultivars with high SNF and five sensitive cultivars with low SNF were chosen after a preliminary screening of 54 voandzou genotypes, including 50 landraces from Madagascar, Niger and Mali supplied with 2 P levels as P deficient and P sufficient (30 and 75 {mu}mol plant{sup -1} week{sup -1} ) under hydroaeroponic conditions. Genotypic variation in SFN for the high phosphorus use efficiency (PUE) was observed among the 54 cultivars and landraces. Variability was especially related to the nodule and shoot biomass, nodule permeability, nodule respiration and gene phytase expression. Contrasting cultivars and landraces in terms of PUE for SNF were selected for further evaluation under field conditions. (author)

  13. Penggunaan Jamur Antagonis Trichoderma SP. Dan Gliocladium SP. Untuk Mengendalikan Penyakit Layu Fusarium Pada Tanaman Bawang Merah (Allium Ascalonicum L.)

    OpenAIRE

    Arie Ramadhina, Arie Ramadhina; Lisnawita, Lisnawita; Lubis, Lahmuddin

    2013-01-01

    The use of antagonism fungus of Trichoderma sp. and Gliocladium sp. for controlling wilt(Fusarium oxysporum) in red onion plants. The aim of the research was to know the effectiviness ofantagonism fungus of Trichoderma sp. and Gliocladium sp. in controlling wilt in red onion plants.The research used non-factorial RAK (random group design) with eight treatments: control, 10grams of F. oxysporum, 12 grams of Trichoderma sp., 18 grams of Trichoderma sp., 24 grams ofTrichoderma sp., and 12 grams ...

  14. A Transgenic Tri-Modality Reporter Mouse

    OpenAIRE

    Yan, Xinrui; Ray, Pritha; Paulmurugan, Ramasamy; Tong, Ricky; Gong, Yongquan; Sathirachinda, Ataya; Wu, Joseph C.; Gambhir, Sanjiv S.

    2013-01-01

    Transgenic mouse with a stably integrated reporter gene(s) can be a valuable resource for obtaining uniformly labeled stem cells, tissues, and organs for various applications. We have generated a transgenic mouse model that ubiquitously expresses a tri-fusion reporter gene (fluc2-tdTomato-ttk) driven by a constitutive chicken β-actin promoter. This "Tri-Modality Reporter Mouse" system allows one to isolate most cells from this donor mouse and image them for bioluminescent (fluc2), fluorescent...

  15. Tachykinins stimulate a subset of mouse taste cells.

    Directory of Open Access Journals (Sweden)

    Jeff Grant

    Full Text Available The tachykinins substance P (SP and neurokinin A (NKA are present in nociceptive sensory fibers expressing transient receptor potential cation channel, subfamily V, member 1 (TRPV1. These fibers are found extensively in and around the taste buds of several species. Tachykinins are released from nociceptive fibers by irritants such as capsaicin, the active compound found in chili peppers commonly associated with the sensation of spiciness. Using real-time Ca(2+-imaging on isolated taste cells, it was observed that SP induces Ca(2+ -responses in a subset of taste cells at concentrations in the low nanomolar range. These responses were reversibly inhibited by blocking the SP receptor NK-1R. NKA also induced Ca(2+-responses in a subset of taste cells, but only at concentrations in the high nanomolar range. These responses were only partially inhibited by blocking the NKA receptor NK-2R, and were also inhibited by blocking NK-1R indicating that NKA is only active in taste cells at concentrations that activate both receptors. In addition, it was determined that tachykinin signaling in taste cells requires Ca(2+-release from endoplasmic reticulum stores. RT-PCR analysis further confirmed that mouse taste buds express NK-1R and NK-2R. Using Ca(2+-imaging and single cell RT-PCR, it was determined that the majority of tachykinin-responsive taste cells were Type I (Glial-like and umami-responsive Type II (Receptor cells. Importantly, stimulating NK-1R had an additive effect on Ca(2+ responses evoked by umami stimuli in Type II (Receptor cells. This data indicates that tachykinin release from nociceptive sensory fibers in and around taste buds may enhance umami and other taste modalities, providing a possible mechanism for the increased palatability of spicy foods.

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

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

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

  17. Hybrid radiosity-SP{sub 3} equation based bioluminescence tomography reconstruction for turbid medium with low- and non-scattering regions

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xueli, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn; Zhang, Qitan; Yang, Defu; Liang, Jimin, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn [School of Life Science and Technology, Xidian University, Xi' an, Shaanxi 710071 (China)

    2014-01-14

    To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP{sub 3} equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP{sub 3}) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions.

  18. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  19. Audioprofiles and antioxidant enzyme genotypes in presbycusis.

    Science.gov (United States)

    Angeli, Simon I; Bared, Anthony; Ouyang, Xiaomei; Du, Li Lin; Yan, Denise; Zhong Liu, Xue

    2012-11-01

    Audiometric patterns have been shown to indirectly provide information regarding the pathophysiology of presbycusis and be useful in the phenotyping of hereditary deafness. Hospital-based cohort study of adults with presbycusis, comparing the association of audiometric patterns and polymorphisms of antioxidant enzymes that have been linked to presbycusis: GSTT1, GSTM1 and NAT2. All subjects underwent a clinical evaluation and completed questionnaires regarding ototoxicity and noise exposure. Pure-tone threshold audiometry was obtained and subjects' audiograms were classified into specific patterns. DNA was extracted from blood and the polymorphisms of GSTT1, GSTM1, and the NAT2 variants (NAT2* 5A; NAT2* 6A,B) were analyzed by PCR. The audiometric patterns that were more prevalent in our cohort were "High-Frequency Steeply Sloping" or HFSS (33%), "High-Frequency Gently Sloping" or HFGS (31%), and "Flat" (27%), with other patterns being rare. We did not find a statistical significant effect of gender, age, hearing level, and ear side on the audiometric pattern. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype. In this cohort, there was a similar prevalence for the three audiometric configurations HFSS, HFGS, and Flat, with other configurations being rare. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype, suggesting that the basal turn of the cochlea is susceptible to GSTT1 regulated oxidative stress. However, further studies of audioprofiles with larger sample sizes may be needed to establish phenotype-genotype correlations in presbycusis. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

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

    Directory of Open Access Journals (Sweden)

    Xiao-Xuan Zhang

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  2. Prototheca zopfii genotype 2 disseminated infection in a dog with neurological signs

    Directory of Open Access Journals (Sweden)

    Luciana Sonne

    Full Text Available ABSTRACT: Prototheca zopfii is an alga that can cause disease in animals and humans. Here, we reported a case of systemic protothecosis in a 2-year-old female Boxer. The animal exhibited tetraparesis and vertical nystagmus. It died two weeks after the onset of clinical signs and was necropsied. At gross examination, whitish areas were identified in the heart. Oval or round structures were observed by microscopic examination, some of which formed morula-like structures compatible with algae in the heart, skeletal muscle, and brain. Growth of Prototheca sp. was observed in the heart after culture at 37°C on Sabouraud agar medium with chloramphenicol. Immunohistochemical analysis of the heart and brain using an anti-Prototheca zopfii polyclonal antibody yielded positive results. Genotyping of the cultured agent from brain and heart samples was performed by restriction fragment length polymorphism of a specific 18S rDNA fragment. P. zopfii genotype 2 was reported to be the cause of disseminated protothecosis in this dog with manifestation in the brain, heart, and skeletal muscle.

  3. Prediction of direct and indirect genetic gains and genotypic correlations in rubber tree progenies

    Directory of Open Access Journals (Sweden)

    Cecília Khusala Verardi

    2011-09-01

    Full Text Available The objective of this work was to estimate the genetic parameters, genotypic and phenotypic correlations, and direct and indirect genetic gains among and within rubber tree (Hevea brasiliensis progenies. The experiment was set up at the Municipality of Jaú, SP, Brazil. A randomized complete block design was used, with 22 treatments (progenies, 6 replicates, and 10 plants per plot at a spacing of 3x3 m. Three‑year‑old progenies were assessed for girth, rubber yield, and bark thickness by direct and indirect gains and genotypic correlations. The number of latex vessel rings showed the best correlations, correlating positively and significantly with girth and bark thickness. Selection gains among progenies were greater than within progeny for all the variables analyzed. Total gains obtained were high, especially for girth increase and rubber yield, which were 93.38 and 105.95%, respectively. Young progeny selection can maximize the expected genetic gains, reducing the rubber tree selection cycle.

  4. Plant genotypic diversity reduces the rate of consumer resource utilization.

    Science.gov (United States)

    McArt, Scott H; Thaler, Jennifer S

    2013-07-07

    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

  5. Relationship of some upland rice genotype after gamma irradiation

    Science.gov (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

    2018-02-01

    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  6. Interaction of uranium with Pleurotus sp

    International Nuclear Information System (INIS)

    Ohnuki, Toshihiko; Sakamoto, Fuminori; Kozaki, Naofumi; Ozaki, Takuro; Samadfam, Mohammad

    2002-01-01

    Uptake of uranium by higher fungi, such as mushroom is little elucidated. We have studied the interaction of uranium with Pleurotus sp. (a mushroom) in pure culture over a wide range of U concentration (50-3000 mg/L). The Pleurotus sp. was cultured in two different media. One was rice bran medium, and the other was agar (yeast extract, peptone and dextrose) medium. The uptake of uranium in Pleurotus sp. was examined by alpha ray autoradiography (A,A), X-ray fluorescence spectroscopy (XRF) and scanning microcopy (SEM) equipped with EDS. In the agar medium, the higher uranium concentration gave lower growth of mycelia, and no fruiting body was observed. In the rice bran medium, the fruiting body was grown at U concentrations up to 1000 mg/L. The AA and XRF analysis showed that uranium taken up in the fruiting body was below the detection limit. The SEM-EDS analysis indicated that U was distributed in the limited region and was not transported to the mycelia far from U containing medium. It is concluded that uranium affects the growth of Pleurotus sp., and little uranium is taken up by Pleurotus sp. during the growth of both mycelia and fruiting body. (author)

  7. Taxonomy Icon Data: Synechocystis sp.PCC 6803 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Synechocystis sp.PCC 6803 Synechocystis sp.PCC 6803 Synechocystis_sp_PCC_6803_L.png Synecho...cystis_sp_PCC_6803_NL.png Synechocystis_sp_PCC_6803_S.png Synechocystis_sp_PCC_6803_NS.png http://bi...osciencedbc.jp/taxonomy_icon/icon.cgi?i=Synechocystis+sp%2ePCC+6803&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synecho...cystis+sp%2ePCC+6803&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synecho...cystis+sp%2ePCC+6803&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synechocystis

  8. Five novel Wickerhamomyces- and Metschnikowia-related yeast species, Wickerhamomyces chaumierensis sp. nov., Candida pseudoflosculorum sp. nov., Candida danieliae sp. nov., Candida robnettiae sp. nov. and Candida eppingiae sp. nov., isolated from plants

    NARCIS (Netherlands)

    Groenewald, Marizeth; Robert, Vincent; Smith, Maudy Th

    On the basis of nucleotide divergences in the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacers (ITS) domain of the rRNA gene, five novel yeast species, Wickerhamomyces chaumierensis sp. nov. (CBS 8565(T)  = JCM 17246(T)), Candida pseudoflosculorum sp. nov. (CBS 8584(T)  = JCM

  9. Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass.

    Science.gov (United States)

    Doronina, Nina V; Trotsenko, Yuri A; Kolganova, Tatjana V; Tourova, Tatjana P; Salkinoja-Salonen, Mirja S

    2004-09-01

    Strain F31T was isolated from meadow grass (Poa trivialis L.) sampled from the city park in Helsinki. Analysis of phenotypic and genotypic properties showed the strain to be related to the group of obligately methylotrophic non-methane utilizing bacteria (methylobacteria) with the ribulose monophosphate pathway of formaldehyde assimilation. Phylogenetic analysis showed the strain to be closely related to the genus Methylobacillus, and analysis of fatty acid composition confirmed this association. Thus, on the basis of its genotypic and phenotypic properties, the isolate is proposed as a novel species of the genus Methylobacillus, Methylobacillus pratensis sp. nov., with F31T as the type strain (= VKM B-2247T = NCIMB 13994T).

  10. Description of Babesia duncani n.sp. (Apicomplexa: Babesiidae) from humans and its differentiation from other piroplasms.

    Science.gov (United States)

    Conrad, Patricia A; Kjemtrup, Anne M; Carreno, Ramon A; Thomford, John; Wainwright, Katlyn; Eberhard, Mark; Quick, Rob; Telford, Sam R; Herwaldt, Barbara L

    2006-06-01

    The morphologic, ultrastructural and genotypic characteristics of Babesia duncani n.sp. are described based on the characterization of two isolates (WA1, CA5) obtained from infected human patients in Washington and California. The intraerythrocytic stages of the parasite are morphologically indistinguishable from Babesia microti, which is the most commonly identified cause of human babesiosis in the USA. Intraerythrocytic trophozoites of B. duncani n.sp. are round to oval, with some piriform, ring and ameboid forms. Division occurs by intraerythrocytic schizogony, which results in the formation of merozoites in tetrads (syn. Maltese cross or quadruplet forms). The ultrastructural features of trophozoites and merozoites are similar to those described for B. microti and Theileria spp. However, intralymphocytic schizont stages characteristic of Theileria spp. have not been observed in infected humans. In phylogenetic analyses based on sequence data for the complete18S ribosomal RNA gene, B. duncani n.sp. lies in a distinct clade that includes isolates from humans, dogs and wildlife in the western United States but separate from Babesia sensu stricto, Theileria spp. and B. microti. ITS2 sequence analysis of the B. duncani n.sp. isolates (WA1, CA5) show that they are phylogenetically indistinguishable from each other and from two other human B. duncani-type parasites (CA6, WA2 clone1) but distinct from other Babesia and Theileria species sequenced. This analysis provides robust molecular support that the B. duncani n.sp. isolates are monophyletic and the same species. The morphologic characteristics together with the phylogenetic analysis of two genetic loci support the assertion that B. duncani n.sp. is a distinct species from other known Babesia spp. for which morphologic and sequence information are available.

  11. Substituting mouse transcription factor Pou4f2 with a sea urchin orthologue restores retinal ganglion cell development.

    Science.gov (United States)

    Mao, Chai-An; Agca, Cavit; Mocko-Strand, Julie A; Wang, Jing; Ullrich-Lüter, Esther; Pan, Ping; Wang, Steven W; Arnone, Maria Ina; Frishman, Laura J; Klein, William H

    2016-03-16

    Pou domain transcription factor Pou4f2 is essential for the development of retinal ganglion cells (RGCs) in the vertebrate retina. A distant orthologue of Pou4f2 exists in the genome of the sea urchin (class Echinoidea) Strongylocentrotus purpuratus (SpPou4f1/2), yet the photosensory structure of sea urchins is strikingly different from that of the mammalian retina. Sea urchins have no obvious eyes, but have photoreceptors clustered around their tube feet disc. The mechanisms that are associated with the development and function of photoreception in sea urchins are largely unexplored. As an initial approach to better understand the sea urchin photosensory structure and relate it to the mammalian retina, we asked whether SpPou4f1/2 could support RGC development in the absence of Pou4f2. To answer this question, we replaced genomic Pou4f2 with an SpPou4f1/2 cDNA. In Pou4f2-null mice, retinas expressing SpPou4f1/2 were outwardly identical to those of wild-type mice. SpPou4f1/2 retinas exhibited dark-adapted electroretinogram scotopic threshold responses, indicating functionally active RGCs. During retinal development, SpPou4f1/2 activated RGC-specific genes and in S. purpuratus, SpPou4f2 was expressed in photoreceptor cells of tube feet in a pattern distinct from Opsin4 and Pax6. Our results suggest that SpPou4f1/2 and Pou4f2 share conserved components of a gene network for photosensory development and they maintain their conserved intrinsic functions despite vast morphological differences in mouse and sea urchin photosensory structures. © 2016 The Authors.

  12. Mac-1low early myeloid cells in the bone marrow-derived SP fraction migrate into injured skeletal muscle and participate in muscle regeneration

    International Nuclear Information System (INIS)

    Ojima, Koichi; Uezumi, Akiyoshi; Miyoshi, Hiroyuki; Masuda, Satoru; Morita, Yohei; Fukase, Akiko; Hattori, Akihito; Nakauchi, Hiromitsu; Miyagoe-Suzuki, Yuko; Takeda, Shin'ichi

    2004-01-01

    Recent studies have shown that bone marrow (BM) cells, including the BM side population (BM-SP) cells that enrich hematopoietic stem cells (HSCs), are incorporated into skeletal muscle during regeneration, but it is not clear how and what kinds of BM cells contribute to muscle fiber regeneration. We found that a large number of SP cells migrated from BM to muscles following injury in BM-transplanted mice. These BM-derived SP cells in regenerating muscles expressed different surface markers from those of HSCs and could not reconstitute the mouse blood system. BM-derived SP/Mac-1 low cells increased in number in regenerating muscles following injury. Importantly, our co-culture studies with activated satellite cells revealed that this fraction carried significant potential for myogenic differentiation. By contrast, mature inflammatory (Mac-1 high ) cells showed negligible myogenic activities. Further, these BM-derived SP/Mac-1 low cells gave rise to mononucleate myocytes, indicating that their myogenesis was not caused by stochastic fusion with host myogenic cells, although they required cell-to-cell contact with myogenic cells for muscle differentiation. Taken together, our data suggest that neither HSCs nor mature inflammatory cells, but Mac-1 low early myeloid cells in the BM-derived SP fraction, play an important role in regenerating skeletal muscles

  13. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    Science.gov (United States)

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

  14. SP2Bench: A SPARQL Performance Benchmark

    Science.gov (United States)

    Schmidt, Michael; Hornung, Thomas; Meier, Michael; Pinkel, Christoph; Lausen, Georg

    A meaningful analysis and comparison of both existing storage schemes for RDF data and evaluation approaches for SPARQL queries necessitates a comprehensive and universal benchmark platform. We present SP2Bench, a publicly available, language-specific performance benchmark for the SPARQL query language. SP2Bench is settled in the DBLP scenario and comprises a data generator for creating arbitrarily large DBLP-like documents and a set of carefully designed benchmark queries. The generated documents mirror vital key characteristics and social-world distributions encountered in the original DBLP data set, while the queries implement meaningful requests on top of this data, covering a variety of SPARQL operator constellations and RDF access patterns. In this chapter, we discuss requirements and desiderata for SPARQL benchmarks and present the SP2Bench framework, including its data generator, benchmark queries and performance metrics.

  15. The gamma ray spectrometer GA.SP

    Energy Technology Data Exchange (ETDEWEB)

    Bazzacco, D [Instituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova (Italy)

    1992-08-01

    GA.SP is a general purpose 4{pi} detector array for advanced {gamma}-spectroscopy and, in the same time, a suitable system for reaction mechanism studies. The detector is sited at the LNL Tandem+Linac accelerator and has been built as a joint project of INFN Padova, LNL, Milano and Firenze. The array consists of 40 Compton suppressed HPGe detectors and of a 4{pi} calorimeter composed of 80 BGO crystals. The detector houses a reaction chamber of 34 cm diameter where a charged particles multiplicity filter composed of 40 Si detectors is going to be installed. Evaporation residues produced in the centre of GA.SP can be injected into the recoil mass spectrometer (RMS, named CAMEL) in use at LNL, without the need to remove any of the gamma detectors. The coupled operation of GA.SP, RMS and Si ball will give a unique instrument for identification and study of weak reaction channels. (author). 6 figs.

  16. The gamma ray spectrometer GA.SP

    International Nuclear Information System (INIS)

    Bazzacco, D.

    1992-01-01

    GA.SP is a general purpose 4π detector array for advanced γ-spectroscopy and, in the same time, a suitable system for reaction mechanism studies. The detector is sited at the LNL Tandem+Linac accelerator and has been built as a joint project of INFN Padova, LNL, Milano and Firenze. The array consists of 40 Compton suppressed HPGe detectors and of a 4π calorimeter composed of 80 BGO crystals. The detector houses a reaction chamber of 34 cm diameter where a charged particles multiplicity filter composed of 40 Si detectors is going to be installed. Evaporation residues produced in the centre of GA.SP can be injected into the recoil mass spectrometer (RMS, named CAMEL) in use at LNL, without the need to remove any of the gamma detectors. The coupled operation of GA.SP, RMS and Si ball will give a unique instrument for identification and study of weak reaction channels. (author). 6 figs

  17. SP-100/Brayton power system concepts

    International Nuclear Information System (INIS)

    Owen, D.F.

    1989-01-01

    Use of closed Brayton cycle (CBC) power conversion technology has been investigated for use with SP-100 reactors for space power systems. The CBC power conversion technology is being developed by Rockwell International under the Dynamic Isotype Power System (DIPS) and Space Station Freedom solar dynamic power system programs to provide highly efficient power conversion with radioisotype and solar collector heat sources. Characteristics including mass, radiator area, thermal power, and operating temperatures for systems utilizing SP-100 reactor and CBC power conversion technology were determined for systems in the 10-to 100-kWe power range. Possible SP-100 reactor/CBC power system configurations are presented. Advantages of CBC power conversion technology with regard to reactor thermal power, operating temperature, and development status are discussed

  18. Construction of expression vectors for metabolic engineering of the vanillin-producing actinomycete Amycolatopsis sp. ATCC 39116.

    Science.gov (United States)

    Fleige, Christian; Steinbüchel, Alexander

    2014-01-01

    Amycolatopsis sp. ATCC 39116 is able to synthesize the important flavoring agent vanillin from cheap natural substrates. The bacterium is therefore of great interest for the industry and used for the fermentative production of vanillin. In order to improve the production of natural vanillin with Amycolatopsis sp. ATCC 39116, the strain has been genetically engineered to optimize the metabolic flux towards the desired product. Extensive metabolic engineering was hitherto hampered, due to the lack of genetic tools like functional promoters and expression vectors. In this study, we report the establishment of a plasmid-based gene expression system for Amycolatopsis sp. ATCC 39116 that allows a further manipulation of the genotype. Four new Escherichia coli-Amycolatopsis shuttle vectors harboring different promoter elements were constructed, and the functionality of these regulatory elements was proven by the expression of the reporter gene gusA, encoding a β-glucuronidase. Glucuronidase activity was detected in all plasmid-harboring strains, and remarkable differences in the expression strength of the reporter gene depending on the used promoter were observed. The new expression vectors will promote the further genetic engineering of Amycolatopsis sp. ATCC 39116 to get insight into the metabolic network and to improve the strain for a more efficient industrial use.

  19. The Mouse SAGE Site: database of public mouse SAGE libraries

    Czech Academy of Sciences Publication Activity Database

    Divina, Petr; Forejt, Jiří

    2004-01-01

    Roč. 32, - (2004), s. D482-D483 ISSN 0305-1048 R&D Projects: GA MŠk LN00A079; GA ČR GV204/98/K015 Grant - others:HHMI(US) 555000306 Institutional research plan: CEZ:AV0Z5052915 Keywords : mouse SAGE libraries * web -based database Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.260, year: 2004

  20. Antioxidant capacity of anthocyanins from acerola genotypes

    Directory of Open Access Journals (Sweden)

    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.

  1. [Mexican phenotype and genotype Vibrio cholerae 01].

    Science.gov (United States)

    Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J

    1995-01-01

    This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

  2. HFE genotype affects exosome phenotype in cancer.

    Science.gov (United States)

    Mrowczynski, Oliver D; Madhankumar, A B; Slagle-Webb, Becky; Lee, Sang Y; Zacharia, Brad E; Connor, James R

    2017-08-01

    Neuroblastoma is the third most common childhood cancer, and timely diagnosis and sensitive therapeutic monitoring remain major challenges. Tumor progression and recurrence is common with little understanding of mechanisms. A major recent focus in cancer biology is the impact of exosomes on metastatic behavior and the tumor microenvironment. Exosomes have been demonstrated to contribute to the oncogenic effect on the surrounding tumor environment and also mediate resistance to therapy. The effect of genotype on exosomal phenotype has not yet been explored. We interrogated exosomes from human neuroblastoma cells that express wild-type or mutant forms of the HFE gene. HFE, one of the most common autosomal recessive polymorphisms in the Caucasian population, originally associated with hemochromatosis, has also been associated with increased tumor burden, therapeutic resistance boost, and negative impact on patient survival. Herein, we demonstrate that changes in genotype cause major differences in the molecular and functional properties of exosomes; specifically, HFE mutant derived exosomes have increased expression of proteins relating to invasion, angiogenesis, and cancer therapeutic resistance. HFE mutant derived exosomes were also shown to transfer this cargo to recipient cells and cause an increased oncogenic functionality in those recipient cells. Copyright © 2017. Published by Elsevier B.V.

  3. Haplotype-Based Genotyping in Polyploids

    Directory of Open Access Journals (Sweden)

    Josh P. Clevenger

    2018-04-01

    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  4. Hearing impairment in genotyped Wolfram syndrome patients.

    Science.gov (United States)

    Plantinga, Rutger F; Pennings, Ronald J E; Huygen, Patrick L M; Bruno, Rocco; Eller, Philipp; Barrett, Timothy G; Vialettes, Bernard; Paquis-Fluklinger, Veronique; Lombardo, Fortunato; Cremers, Cor W R J

    2008-07-01

    Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment. Pure tone threshold data of 23 Wolfram syndrome patients were used for cross-sectional analysis in subgroups (age less than 16 years or between 19 and 25 years, gender, and origin). All subgroups, with 1 exception, showed a fairly similar type of hearing impairment with, on average, thresholds of about 25 dB (range, 0 to 65 dB) at 0.25 to 1 kHz, gently sloping downward to about 60 dB (range, 25 to 95 dB) at 8 kHz. The subgroup of Dutch women, which was excluded from the calculations of the average hearing thresholds, showed a higher degree of hearing impairment. Only the latter subgroup showed progression; however, contrary to the previous longitudinal analysis, progression was not significant in the present cross-sectional analysis, presumably because of the high degree of cross-subject variability. This unique collection of audiometric data from genotyped Wolfram syndrome patients shows no substantial progression in sensorineural hearing impairment with advancing age, no relation to the types of WFS1 mutations identified, and, with exclusion of the subgroup of Dutch female patients, no significant sex-related differences.

  5. Immortalization and characterization of mouse floxed Bmp2/4 osteoblasts

    International Nuclear Information System (INIS)

    Wu, Li-An; Yuan, Guohua; Yang, Guobin; Ortiz-Gonzalez, Iris; Yang, Wuchen; Cui, Yong; MacDougall, Mary; Donly, Kevin J.; Harris, Stephen; Chen, Shuo

    2009-01-01

    Generation of a floxed Bmp2/4 osteoblast cell line is a valuable tool for studying the modulatory effects of Bmp2 and Bmp4 on osteoblast differentiation as well as relevant molecular events. In this study, primary floxed Bmp2/4 mouse osteoblasts were cultured and transfected with simian virus 40 large T-antigen. Transfection was verified by polymerase chain reaction (PCR) and immunohistochemistry. To examine the characteristics of the transfected cells, morphology, proliferation and mineralization were analyzed, expression of cell-specific genes including Runx2, ATF4, Dlx3, Osx, dentin matrix protein 1, bone sialoprotein, osteopontin, osteocalcin, osteonectin and collagen type I was detected. These results show that transfected floxed Bmp2/4 osteoblasts bypassed senescence with a higher proliferation rate, but retain the genotypic and phenotypic characteristics similar to the primary cells. Thus, we for the first time demonstrate the establishment of an immortalized mouse floxed Bmp2/4 osteoblast cell line.

  6. Immortalization and characterization of mouse floxed Bmp2/4 osteoblasts

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Li-An [Department of Pediatric Dentistry, The University of Texas Health Science Center at San Antonio, TX (United States); Department of Pediatric Dentistry, School of Stomatology, The Fourth Military Medical University, Xi-an (China); Yuan, Guohua; Yang, Guobin [Department of Pediatric Dentistry, The University of Texas Health Science Center at San Antonio, TX (United States); Key Laboratory of Oral Biomedical Engineering Ministry of Education, Wuhan (China); Ortiz-Gonzalez, Iris [Department of Pediatric Dentistry, The University of Texas Health Science Center at San Antonio, TX (United States); Yang, Wuchen; Cui, Yong [Department of Periodontics, Dental School, The University of Texas Health Science Center at San Antonio, TX (United States); MacDougall, Mary [Department of Oral/Maxillofacial Surgery, University of Alabama, Birmingham, AL (United States); Donly, Kevin J. [Department of Pediatric Dentistry, The University of Texas Health Science Center at San Antonio, TX (United States); Harris, Stephen [Department of Periodontics, Dental School, The University of Texas Health Science Center at San Antonio, TX (United States); Chen, Shuo, E-mail: chens0@uthscsa.edu [Department of Pediatric Dentistry, The University of Texas Health Science Center at San Antonio, TX (United States)

    2009-08-14

    Generation of a floxed Bmp2/4 osteoblast cell line is a valuable tool for studying the modulatory effects of Bmp2 and Bmp4 on osteoblast differentiation as well as relevant molecular events. In this study, primary floxed Bmp2/4 mouse osteoblasts were cultured and transfected with simian virus 40 large T-antigen. Transfection was verified by polymerase chain reaction (PCR) and immunohistochemistry. To examine the characteristics of the transfected cells, morphology, proliferation and mineralization were analyzed, expression of cell-specific genes including Runx2, ATF4, Dlx3, Osx, dentin matrix protein 1, bone sialoprotein, osteopontin, osteocalcin, osteonectin and collagen type I was detected. These results show that transfected floxed Bmp2/4 osteoblasts bypassed senescence with a higher proliferation rate, but retain the genotypic and phenotypic characteristics similar to the primary cells. Thus, we for the first time demonstrate the establishment of an immortalized mouse floxed Bmp2/4 osteoblast cell line.

  7. Impaired cholesterol esterification in primary brain cultures of the lysosomal cholesterol storage disorder (LCSD) mouse mutant

    International Nuclear Information System (INIS)

    Patel, S.C.; Suresh, S.; Weintroub, H.; Brady, R.O.; Pentchev, P.G.

    1987-01-01

    Esterification of cholesterol was investigated in primary neuroglial cultures obtained from newborn lysosomal cholesterol storage disorder (LCSD) mouse mutants. An impairment in 3 H-oleic acid incorporation into cholesteryl esters was demonstrated in cultures of homozygous LCSD brain. Primary cultures derived from other phenotypically normal pups of the carrier breeders esterified cholesterol at normal levels or at levels which were intermediary between normal and deficient indicating a phenotypic expression of the LCSD heterozygote genotype. These observations on LCSD mutant brain cells indicate that the defect in cholesterol esterification is closely related to the primary genetic defect and is expressed in neuroglial cells in culture

  8. Modifications of Sp(2) covariant superfield quantization

    Energy Technology Data Exchange (ETDEWEB)

    Gitman, D.M.; Moshin, P.Yu

    2003-12-04

    We propose a modification of the Sp(2) covariant superfield quantization to realize a superalgebra of generating operators isomorphic to the massless limit of the corresponding superalgebra of the osp(1,2) covariant formalism. The modified scheme ensures the compatibility of the superalgebra of generating operators with extended BRST symmetry without imposing restrictions eliminating superfield components from the quantum action. The formalism coincides with the Sp(2) covariant superfield scheme and with the massless limit of the osp(1,2) covariant quantization in particular cases of gauge-fixing and solutions of the quantum master equations.

  9. SP-100 converter multicouple thermoelectric cell

    International Nuclear Information System (INIS)

    Kull, R.A.; Terrill, W.R.

    1990-01-01

    The General Electric Company is under contract to DOE to design, fabricate, and test an SP-100 Ground Engineering System. This paper provides a description of the SP-100 space reactor power system configuration, and a more detailed description of the power conversion subsystem (PCSS) and the key building block of the power converter, the thermoelectric cell. The functions of the various elements of the PCSS and the cells are also presented. These cells convert the thermal energy from the reactor into electrical power at the desired voltage while being conductively coupled to the hot and cold side heat exchangers to maximize the power output and system specific power

  10. Expression and significance of Bax protein in model of radiation injury in mouse skin

    International Nuclear Information System (INIS)

    Feng Yizhong; Mo Yahong

    2002-01-01

    Objective: The study is to find some valuable criteria for diagnosis and treatment of radiation injury in skin. Methods: The expression of Bax protein was studied by SP immunohistochemistry in 40 cases of model of radiation injury in mouse skin. Their relationship relating to radiation dose was also investigated. Results: The expression rates of Bax were 30%, 30%, 70%, 70% in 5 Gy group, 15 Gy group, 30 Gy group, 45 Gy group respectively. There was no significant correlation between the expression of Bax and radiation groups. Conclusions: The experiment shows that radiation can increase the expression of Bax protein which might be related to poor healing in radiation skin injury

  11. Fatty acid composition of Spirulina sp., Chlorella sp. and Chaetoceros sp. microalgae and introduction as potential new sources to extinct omega 3 and omega 6

    Directory of Open Access Journals (Sweden)

    Homan Gorjzdadeh

    2016-05-01

    Full Text Available Background: This study was carried out to determine the oil fatty acids from two special species of microalgae; Spirulina sp.,Chlorella sp. and also Chaetoceros sp. collected from Bahmanshir River. Materials and Methods: Sampling of microalgae Chaetoceros sp. from Bahmanshir River was under taken using bottle samplers during spring season of 2013. Microalgae Spirulina sp. and Chlorella sp. were supplied from Shrimp Research Institute of Iran in Bushehr Province. Samples then were cultured under controlled laboratory conditions and mass culture for 100 liters was undertaken. Isolation of microalgae species from water of cultured media was carried out using filtration and centrifugation methods. The fatty acid compositions were determined by Gas – FID chromatography. Results: Results showed that regarding Saturated Fatty Acids (SFA obtained from purified culture of Chaetoceros sp., Spirulina sp. and Chlorella sp. the maximum amount of total fatty acids were belonged to palmitic acids (C16:0 with 15.21%, 30.1% and 25.17% of total fatty acids  respectively. Analysis of Mono Unsaturated Fatty Acids (MUFA showed that in the Oleic acid was maximum amount of 34% in Spirulina sp. In addition the amount of MUFA in Chlorella sp. was 16.37% of total fatty acids. On the other hand the amount of palmeotic acid in purified culture of Chaetoceros sp. was 30.33% from total content of fatty acids. Analysis of Poly Unsaturated Fatty Acids (PUFA, Linoleic acid (C18:2 (Omega 6, revealed maximum percentage in Spirulina sp. with 18.8%. Results of Alpha linoleic acid (C18:3 (Omega3 analysis showed maximum amount of 9.66% in Chlorella sp. compared to other microalgae with lower omega 3 contents. Spirulina sp. contained maximum amount of Linoleic acid (C18:2 with 18.8% of total fatty acids. Therefore, Spirulina sp. can be considered as a rich source of omega 6 for the purpose of fatty acid extractions. The presence of PUFA in Chlorella sp. and Spirulina sp. was

  12. 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.

  13. The genotype-phenotype map of an evolving digital organism

    OpenAIRE

    Fortuna, Miguel A.; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms fr...

  14. 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.

  15. Candida halmiae sp. nov., Geotrichum ghanense sp. nov. and Candida awuaii sp. nov., isolated from Ghanaian cocoa fermentations

    DEFF Research Database (Denmark)

    Nielsen, Dennis Sandris; Jakobsen, Mogens; Jespersen, Lene

    2010-01-01

    During an investigation of the microbiology of Ghanaian cocoa fermentations, a number of yeast isolates with unusual pheno- and genotypic properties representing three possible novel species were isolated. Members of Group A divided by multilateral budding and ascospores were not produced. Group B...

  16. Halobacterium sp. SP1(1) as a starter culture for accelerating fish sauce fermentation.

    Science.gov (United States)

    Akolkar, A V; Durai, D; Desai, A J

    2010-07-01

    Application of Halobacterium sp. SP1(1) for the acceleration of fish sauce fermentation. Traditional fish sauce fermentation was mimicked using Halobacterium sp. SP1(1) as starter culture. Protease activity, peptide release and α-amino content (parameters used to monitor the progress of the fermentation) were high at day 10 in tests and day 20 in un-inoculated controls. The total protein and nitrogen contents were also high in tests compared with controls. The amino acid profile observed at the end of fermentation in experimental samples, when compared with the commercial sauce preparation, was found to be better with respect to flavour and aroma contributing amino acids as well as essential amino acid lysine. Microflora analysis of the final fish sauce revealed the absence of any nonhalophilic or halotolerant micro-organisms. The protease-producing halophilic isolates obtained from the fish sauce of eviscerated and uneviscerated controls were identified as Halobacterium sp. F1 and F2, respectively, by 16S rDNA sequence analysis. Exogenous augmentation of Halobacterium sp. SP1(1) accelerated the fish sauce fermentation process with an additive effect on the existing natural microflora present in the fish during fermentation. Halobacterium sp SP1(1), therefore, can be used as an important starter culture for accelerating the fish fermentation process, which is attributed to its extracellular protease. The present study is the first report on use of Halobacterium species as a starter culture for accelerating fish sauce fermentation. Use of halobacterial starter cultures may revolutionize the process in fish sauce industries by reducing the fermentation time and making the process more economical with improved nutritive value of product. Journal compilation © 2009 The Society for Applied Microbiology. No claim to Indian Government works.

  17. 76 FR 56876 - Proposed Collection; Comment Request for Forms 9779, 9779(SP), 9783, 9783(SP), 9787, 9787(SP...

    Science.gov (United States)

    2011-09-14

    ... and 9789(SP), Electronic Federal Tax Payment System (EFTPS). DATES: Written comments should be received on or before November 14, 2011 to be assured of consideration. ADDRESSES: Direct all [email protected] . SUPPLEMENTARY INFORMATION: Title: Electronic Federal Tax Payment System (EFTPS). OMB...

  18. Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization.

    Directory of Open Access Journals (Sweden)

    Betânia Paiva Drumond

    Full Text Available The American/Asian genotype of Dengue virus type 2 (DENV-2 was introduced into the Americas in the 80's. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP, Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3 close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1 to 1988/89, followed by the introduction of lineages BR2 (1998-2000 and BR3 (2003-05. Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. SP-A binding sites on bovine alveolar macrophages.

    Science.gov (United States)

    Plaga, S; Plattner, H; Schlepper-Schaefer, J

    1998-11-25

    Surfactant protein A (SP-A) binding to bovine alveolar macrophages was examined in order to characterize SP-A binding proteins on the cell surface and to isolate putative receptors from these cells that could be obtained in large amounts. Human SP-A, unlabeled or labeled with gold particles, was bound to freshly isolated macrophages and analyzed with ELISA or the transmission electron microscope. Binding of SP-A was inhibited by Ca2+ chelation, by an excess of unlabeled SP-A, or by the presence of 20 mg/ml mannan. We conclude that bovine alveolar macrophages expose binding sites for SP-A that are specific and that depend on Ca2+ and on mannose residues. For isolation of SP-A receptors with homologous SP-A as ligand we isolated SP-A from bovine lung lavage. SDS-PAGE analysis of the purified SP-A showed a protein of 32-36 kDa. Functional integrity of the protein was demonstrated. Bovine SP-A bound to Dynabeads was used to isolate SP-A binding proteins. From the fractionated and blotted proteins of the receptor preparation two proteins bound SP-A in a Ca2+-dependent manner, a 40-kDa protein showing mannose dependency and a 210-kDa protein, showing no mannose sensitivity. Copyright 1998 Academic Press.

  2. Dosimetric Studies in Normal Mice of 177Lu-DOTA-SP and 177Lu-DOTA-His2-MG

    International Nuclear Information System (INIS)

    Puerta Yepes, N.; Rojo, A.M.; Lopez Bularte, A.C.; Nevares, N.; Zapata, M.; Perez, J.H.; Crudo, J.

    2010-01-01

    DOTA-Substance-P (SP) and DOTA-minigastrin (His2-MG) labeled with 177 Lu could be used in peptide receptor radionuclide therapy (PRRT) for treatment of various tumour species. Biodistribution studies of both radiopharmaceuticals in normal mice were performed at different times. Absorbed doses in mouse organs were estimated and extrapolated to humans. Dosimetric calculations showed that kidneys received the highest dose, for both radiopharmaceuticals. The Maximum Tolerated Activity (MTA) of 177 Lu-DOTA-SP that can be administered without kidney toxicity are 414 and 422 MBq/kg for the standard adult man and woman, respectively. In the same way, the MTA of 177 Lu-DOTA-His2-MG are 488 and 518 MBq/kg for the standard adult man and woman, respectively. (authors)

  3. Ovos de Toxocara sp. e larvas de Ancylostoma sp. em praça pública de Lavras, MG Toxocara sp. eggs and Ancylostoma sp. larva in public parks, Brazil

    Directory of Open Access Journals (Sweden)

    Antônio Marcos Guimarães

    2005-04-01

    Full Text Available Larva migrans visceral e cutânea são zoonoses parasitárias causadas pela infecção da larva de Toxocara sp. e Ancylostoma sp., respectivamente. O objetivo do estudo foi verificar a contaminação por ovos de Toxocara sp. e ovos e larvas de Ancylostoma sp. em amostras de solos coletadas de praças públicas e de áreas de recreação infantil de Lavras, Estado de Minas Gerais, por meio da técnica de centrífugo-flutuação e do método de Baermann. A ocorrência de ovos de Toxocara sp. e, ovos e larvas de Ancylostoma sp. foi observada em 69,6% (16/23 das amostras de solo coletadas de praças públicas. A contaminação somente por ovos de Ancylostoma sp. em amostras de solo coletadas em escolas/creches foi de 22,2% (4/18. A percentagem de amostras de areia coletadas de escolas/creches contaminadas somente com larvas de Ancylostoma sp. foi de 11,1% (2/18. Praças públicas são as áreas com maior risco potencial de infecção por Toxocara sp. e Ancylostoma sp. Exame coproparasitológico realizado em 174 amostras de fezes de cães observou 58% e 23%, respectivamente, com ovos de Ancylostoma sp. e Toxocara sp.Visceral and cutaneous larva migrans are parasitic zoonoses caused by the infection of larval nematodes Toxocara sp. and Ancylostoma sp. respectively. The objective of this study was to investigate the contamination by Toxocara sp. eggs and Ancylostoma sp. eggs and larva of soil samples collected from public parks and children's playground areas in state of Minas Gerais, Brazil, using both Baermann's method and centrifugal flotation technique. Toxocara sp. and Ancylostoma sp. eggs were observed in soil samples collected from public squares in 17.4% (4/23 and 69.6 (16/23 respectively. In schools and child day care settings the contamination by Ancylostoma sp. larva in sand samples was 11.1% (2/18. Public parks are settings of more potential risk of Toxocara sp. eggs and Ancylostoma sp. infection. Stool parasitology testing of 174 stool

  4. Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

    Science.gov (United States)

    Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

    2012-01-01

    Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

  5. Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes.

    Science.gov (United States)

    Zellmer, Sebastian; Schmidt-Heck, Wolfgang; Godoy, Patricio; Weng, Honglei; Meyer, Christoph; Lehmann, Thomas; Sparna, Titus; Schormann, Wiebke; Hammad, Seddik; Kreutz, Clemens; Timmer, Jens; von Weizsäcker, Fritz; Thürmann, Petra A; Merfort, Irmgard; Guthke, Reinhard; Dooley, Steven; Hengstler, Jan G; Gebhardt, Rolf

    2010-12-01

    The cellular basis of liver regeneration has been intensely investigated for many years. However, the mechanisms initiating hepatocyte "plasticity" and priming for proliferation are not yet fully clear. We investigated alterations in gene expression patterns during the first 72 hours of C57BL/6N mouse hepatocyte culture on collagen monolayers (CM), which display a high basal frequency of proliferation in the absence of cytokines. Although many metabolic genes were down-regulated, genes related to mitogen-activated protein kinase (MAPK) signaling and cell cycle were up-regulated. The latter genes showed an overrepresentation of transcription factor binding sites (TFBS) for ETF (TEA domain family member 2), E2F1 (E2F transcription factor 1), and SP-1 (Sp1 transcription factor) (P ETF, E2F1, and SP-1 and displayed increased expression of E2F1. Cultivation of murine hepatocytes on CM primes cells for proliferation through cytokine-independent activation of MAPK signaling. The transcription factors ETF, E2F1, and SP-1 seem to play a pronounced role in mediating proliferation-dependent differential gene expression. Similar events, but on a shorter time-scale, occur very early after liver damage in vivo. Copyright © 2010 American Association for the Study of Liver Diseases.

  6. 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 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. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  7. Cultures of preimplantation mouse embryos

    International Nuclear Information System (INIS)

    Streffer, C.; Molls, M.

    1987-01-01

    In the preimplantation mouse embryos the chromosomal damage develops through several postradiation cell cycles and mitoses. New chromosome aberrations are seen during the second and third postradiation mitoses. Also, more micronuclei appear during later postradiation interphases. This is in agreement with the assumption that unrepaired chromosomal radiation damage develops during the cell generation cycle to such a form (i.e. double-strand breaks in DNA) that chromosomal breaks occur. This proposition is strengthened by the observation that radiation-induced damage is more rapidly expressed after neutron exposure (first or second postradiation mitosis) than after exposure to X rays at the one- or two-cell stage. The preimplantation mouse embryo culture is an inviting system for additional studies at the molecular level, especially now that within the last few years more sensitive methods have been developed for study of DNA and protein structure, regulation, and synthesis. The results from these studies of cultures of preimplantation mouse embryos present a favorable case for the study of complex biological systems under very defined conditions in vitro for extrapolation to effects in vivo

  8. Mouse Models of Gastric Cancer

    Science.gov (United States)

    Hayakawa, Yoku; Fox, James G.; Gonda, Tamas; Worthley, Daniel L.; Muthupalani, Sureshkumar; Wang, Timothy C.

    2013-01-01

    Animal models have greatly enriched our understanding of the molecular mechanisms of numerous types of cancers. Gastric cancer is one of the most common cancers worldwide, with a poor prognosis and high incidence of drug-resistance. However, most inbred strains of mice have proven resistant to gastric carcinogenesis. To establish useful models which mimic human gastric cancer phenotypes, investigators have utilized animals infected with Helicobacter species and treated with carcinogens. In addition, by exploiting genetic engineering, a variety of transgenic and knockout mouse models of gastric cancer have emerged, such as INS-GAS mice and TFF1 knockout mice. Investigators have used the combination of carcinogens and gene alteration to accelerate gastric cancer development, but rarely do mouse models show an aggressive and metastatic gastric cancer phenotype that could be relevant to preclinical studies, which may require more specific targeting of gastric progenitor cells. Here, we review current gastric carcinogenesis mouse models and provide our future perspectives on this field. PMID:24216700

  9. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes.

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Ormeño-Orrillo, Ernesto; Parma, Marcia Maria; Melo, Itamar Soares; Martínez-Romero, Esperanza; Hungria, Mariangela

    2015-12-01

    Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T

  10. Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut.

    Science.gov (United States)

    Praet, Jessy; Cnockaert, Margo; Meeus, Ivan; Smagghe, Guy; Vandamme, Peter

    2017-06-01

    Spectra of five isolates (LMG 28358 T , LMG 29879 T , LMG 29880 T , LMG 28359 T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359 T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates. Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804 T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804 T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804 T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358 T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359 T as the type strain, Gilliamella bombi sp. nov., with LMG 29879 T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880 T as the type strain. Copyright © 2017 Elsevier GmbH. All rights reserved.

  11. Biosorption of uranium by Azolla, SP, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Vieira, Ludmila C.; Alves, Eliakim G.; Marumo, Julio T., E-mail: lcvieira@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Ferreira, Rafael V. de P., E-mail: rafael@itatijuca.com [Itatijuca Biotech, Sao Paulo, SP (Brazil); Canevesi, Rafael L.S.; Silva, Edson A., E-mail: edson.silva2@unioeste.br [Universidade Estadual do Oeste Parana (UNIOESTE), Toledo, PR (Brazil)

    2015-07-01

    Radioactive liquid waste needs special attention and requires suitable treatment before deposition. Among the potential technologies under development for the treatment of liquid radioactive wastes the biosorption has been highlighted by being an efficient and low cost technique. Biosorption process involves the exchange of ions contained in the biomass matrix by others present in solution. There are many biomasses that could be applied in treatment of radioactive wastes, for example, agricultural residues and macrophyte. The aim of this study is evaluate the ability of the Azolla sp., a floating aquatic plant, to absorb uranium in solution. Azolla sp. is a macrophyte that has been used to treat effluents containing heavy metals. The biosorption capacity of uranium by Azolla sp. was experimentally determined and modeled by isotherms. Experiments were performed to determine metal uptake, and then the solutions were analyzed by inductively coupled plasma optical emission spectrometry (ICP-OES). The isotherms applied to model the data was Langmuir, Freundlich, Sips Toth, Redlich Peternson, Two-Site-Langmuir, Radke Prausnitz to develop a technique for the treatment of radioactive liquid waste generated at the Nuclear and Energy Research Institute (IPEN-CNEN/SP), Brazil. (author)

  12. Biosorption of uranium by Azolla, SP, Brazil

    International Nuclear Information System (INIS)

    Vieira, Ludmila C.; Alves, Eliakim G.; Marumo, Julio T.; Ferreira, Rafael V. de P.; Canevesi, Rafael L.S.; Silva, Edson A.

    2015-01-01

    Radioactive liquid waste needs special attention and requires suitable treatment before deposition. Among the potential technologies under development for the treatment of liquid radioactive wastes the biosorption has been highlighted by being an efficient and low cost technique. Biosorption process involves the exchange of ions contained in the biomass matrix by others present in solution. There are many biomasses that could be applied in treatment of radioactive wastes, for example, agricultural residues and macrophyte. The aim of this study is evaluate the ability of the Azolla sp., a floating aquatic plant, to absorb uranium in solution. Azolla sp. is a macrophyte that has been used to treat effluents containing heavy metals. The biosorption capacity of uranium by Azolla sp. was experimentally determined and modeled by isotherms. Experiments were performed to determine metal uptake, and then the solutions were analyzed by inductively coupled plasma optical emission spectrometry (ICP-OES). The isotherms applied to model the data was Langmuir, Freundlich, Sips Toth, Redlich Peternson, Two-Site-Langmuir, Radke Prausnitz to develop a technique for the treatment of radioactive liquid waste generated at the Nuclear and Energy Research Institute (IPEN-CNEN/SP), Brazil. (author)

  13. Carbon sp chains in graphene nanoholes

    DEFF Research Database (Denmark)

    Castelli, Ivano Eligio; Ferri, Nicola; Onida, Giovanni

    2012-01-01

    Nowadays sp carbon chains terminated by graphene or graphitic-like carbon are synthesized routinely in several nanotech labs. We propose an ab initio study of such carbon-only materials, by computing their structure and stability, as well as their electronic, vibrational and magnetic properties. ...

  14. Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments.

    Science.gov (United States)

    Pohl, Carolina H; Smit, Martha S; Albertyn, Jacobus

    2011-09-01

    Recent rDNA sequencing of 25 isolates from a previous study, during which limonene-utilizing yeasts were isolated from monoterpene-rich environments by using 1,4-disubstituted cyclohexanes as sole carbon sources, led to the identification of four hitherto unknown Rhodotorula species. Analyses of the 26S rDNA D1/D2 region as well as the internal transcribed spacer (ITS) domain indicated that two isolates (CBS 8499(T) and CBS 10736) were identical and were closely related to Rhodotorula cycloclastica, a previously described limonene-utilizing yeast. These novel isolates differed from known yeast species and could be distinguished from R. cycloclastica by standard physiological tests. The other three isolates represent three novel Rhodotorula species, closely related to Sporobolomyces magnisporus. These three species could also be distinguished from other Rhodotorula species by standard physiological tests. Based on these results, we suggest that the new isolates represent novel species, for which the names Rhodotorula eucalyptica sp. nov. (type strain CBS 8499(T)  = NRRL Y-48408(T)), Rhodotorula pini sp. nov. (type strain CBS 10735(T)  = NRRL Y-48410(T)), Rhodotorula bloemfonteinensis sp. nov. (type strain CBS 8598(T)  = NRRL Y-48407(T)) and Rhodotorula orientis sp. nov. (type strain CBS 8594(T)  = NRRL Y-48719(T)) are proposed. R. eucalyptica and R. pini can also utilize limonene.

  15. Test af spørgeskema

    DEFF Research Database (Denmark)

    Hermansen, Jonathan

    2017-01-01

    Denne bog gennemgår alle surveyarbejdets faser og giver en praktisk indføring i •design af undersøgelsen og udvælgelse af stikprøver, •formulering af spørgeskemaer samt indsamling og kodning af data, •metoder til at analysere resultaterne....

  16. Lipid contents of the sponge Haliclona sp.

    Digital Repository Service at National Institute of Oceanography (India)

    Parameswaran, P.S.; Das, B.; Kamat, S.Y.

    Several fatty acids, sterols, batyl alcohol and its analogs and an N-acylated sphingosine (ceramide) have been isolated from the lipid fraction of the extract of the sponge Haliclona sp. The major sterol is found to be cholesterol (54%), followed...

  17. Optisk scanning af spørgeskemaer

    DEFF Research Database (Denmark)

    Paulsen, Aksel

    / 1000 felter= 0.370 (95% CI: 0.160-0.729), (p= 0.020)). Der var ingen statistisk forskel mellem optisk scanning (fejl/ 1000 felter= 0.046 (95% CI: 0.001-0.258)) og manuel dobbelt indtastning (p=1.000). Konklusioner: Optisk scanning er et godt alternativ til manuel dobbelt indtastning for spørgeskema med......Formål og baggrund: Patient rapporterede outcomes i form af spørgeskemaer bruges i øgende grad i sundhedssektoren både i klinisk praksis og forskning. Ofte bruges spørgeskemaer i papirformat. Manuel dobbelt indtastning er defineret som guld standard for overføring af data til et elektronisk format......, men processen er tidkrævende. Optisk scanning af spørgeskemaer med automatisk registrering af svar kan være et alternativ, men videre validering af metoden er nødvendig. Design: 200 patienter blev tilfældigt udvalgt fra en kohorte på 5777 patienter der tidligere havde svaret på to forskellige...

  18. Aerococcus sp. with an antimycobacterial effect

    African Journals Online (AJOL)

    Yomi

    2011-12-21

    Dec 21, 2011 ... In this study, we reported data on a strain that was isolated from different areas of Fez. (Morocco), which ... sp. The antibacterial activity of the genus Aerococcus have .... able to amplify the 16S rRNA gene from eubacteria.

  19. Botrallin from the endophytic fungus Hyalodendriella sp ...

    African Journals Online (AJOL)

    use

    2011-12-12

    Dec 12, 2011 ... Bioassay-guided fractionation of the crude methanol extract of the mycelia from the endophytic fungus. Hyalodendriella sp. Ponipodef12, associated with the hybrid 'Neva' of Populus deltoides Marsh × P. nigra L., led to the isolation of one compound coded as P12-1 which was identified as botrallin (1,7-.

  20. Induction of miR-137 by Isorhapontigenin (ISO) Directly Targets Sp1 Protein Translation and Mediates Its Anticancer Activity Both In Vitro and In Vivo.

    Science.gov (United States)

    Zeng, Xingruo; Xu, Zhou; Gu, Jiayan; Huang, Haishan; Gao, Guangxun; Zhang, Xiaoru; Li, Jingxia; Jin, Honglei; Jiang, Guosong; Sun, Hong; Huang, Chuanshu

    2016-03-01

    Our recent studies found that isorhapontigenin (ISO) showed a significant inhibitory effect on human bladder cancer cell growth, accompanied with cell-cycle G0-G1 arrest as well as downregulation of Cyclin D1 expression at transcriptional level via inhibition of Sp1 transactivation in bladder cancer cells. In the current study, the potential ISO inhibition of bladder tumor formation has been explored in a xenograft nude mouse model, and the molecular mechanisms underlying ISO inhibition of Sp1 expression and anticancer activities have been elucidated both in vitro and in vivo. Moreover, the studies demonstrated that ISO treatment induced the expression of miR-137, which in turn suppressed Sp1 protein translation by directly targeting Sp1 mRNA 3'-untranslated region (UTR). Similar to ISO treatment, ectopic expression of miR-137 alone led to G0-G1 cell growth arrest and inhibition of anchorage-independent growth in human bladder cancer cells, which could be completely reversed by overexpression of GFP-Sp1. The inhibition of miR-137 expression attenuated ISO-induced inhibition of Sp1/Cyclin D1 expression, induction of G0-G1 cell growth arrest, and suppression of cell anchorage-independent growth. Taken together, our studies have demonstrated that miR-137 induction by ISO targets Sp1 mRNA 3'-UTR and inhibits Sp1 protein translation, which consequently results in reduction of Cyclin D1 expression, induction of G0-G1 growth arrest, and inhibition of anchorage-independent growth in vitro and in vivo. Our results have provided novel insights into understanding the anticancer activity of ISO in the therapy of human bladder cancer. ©2016 American Association for Cancer Research.

  1. The astaxanthin dideoxyglycoside biosynthesis pathway in Sphingomonas sp. PB304

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Kim, Jin Ho; Lee, Bun Yeol

    2014-01-01

    A major carotenoid in Sphingomonas sp. PB304, originally isolated from a river in Daejon City, South Korea, was identified as astaxanthin dideoxyglycoside. Gene clusters encoding the astaxanthin dideoxyglycoside biosynthetic enzymes were identified by screening Sphingomonas sp. PB304 fosmid...

  2. SP-100 initial startup and restart control strategy

    Science.gov (United States)

    Halfen, Frank J.; Wong, Kwok K.; Switick, Dennis M.; Shukla, Jaikaran N.

    Startup control strategies for SP-100 are described. Revised control and operating strategies are discussed which have been developed and tested using the SP-100 dynamic simulation model Aries-GFS (Generic Flight System).

  3. Plant genotype, microbial recruitment and nutritional security.

    Science.gov (United States)

    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number 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 (Berendsen et al., 2012; Marques et al., 2014).

  4. Sources of Wilhelm Johannsen's genotype theory.

    Science.gov (United States)

    Roll-Hansen, Nils

    2009-01-01

    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5-30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen's concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group - species, subspecies, elementary species - by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171-215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term "genotype" was introduced in W. Johannsen's 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological "type" distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58-59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen's studies of heredity in populations from their start in the early 1890s till his

  5. 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......, 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......, 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...

  6. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  7. Cryptosporidium testudinis sp. n., Cryptosporidium ducismarci Traversa, 2010 and Cryptosporidium tortoise genotype III (Apicomplexa: Cryptosporidiidae) in tortoises

    Czech Academy of Sciences Publication Activity Database

    Ježková, Jana; Horčičková, Michaela; Hlásková, Lenka; Sak, Bohumil; Květoňová, Dana; Novák, J.; Hofmannová, L.; McEvoy, J.; Kváč, Martin

    2016-01-01

    Roč. 63, October 14 (2016), č. článku 035. ISSN 1803-6465 R&D Projects: GA ČR GA15-01090S Institutional support: RVO:60077344 Keywords : morphology * transmission studies * taxonomy * new species * molecular phylogeny Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.082, year: 2016

  8. Investigating Genetic Diversity Among Cotton Genotypes Available in the Iranian Gene Bank (Gossypium sp. Using ISSR Molecular Marker

    Directory of Open Access Journals (Sweden)

    F Shahriari Ahmadi

    2013-04-01

    Full Text Available Cotton is one of the most important world crops and is considered as a major cash crop in the North East of Iran. All selections in plant breeding are based on diversity and an increase in genetic diversity determines the range of selection. In the present study, 24 cultivars of cotton available at the research station for cotton in the East of Iran -Kashmar- were studied using the ISSR marker. A total number of 13 primers, with repeated simple sequences, were used for the amplification of genomic DNA. Overall, 128 bands were obtained, 109 of which showed polymorphism. To evaluate genetic similarity between cultivars, cluster analysis accompanied by the similarity coefficient developed by Jaccard and Nee (1972, were applied using the UPGMA method. Dendrogram analysis showed a high diversity in the cotton cultivars and two main groups with 70 percent genetic similarity dividing the cotton cultivars into two main groups; namely, tetraploid and diploid. The highest polymorphism percentage was related to 5' (CT8RC3' (100% and the lowest belonged to 5' (AG8YA3' and 5' (TC8G3' (25% primers. Based on the similarity matrix, the highest genetic similarity was found in Varamin and Khordad and the lowest in Avangard and Bakhtegan cultivars. Based on the obtained results, ISSR markers can be efficiently used for the investigation of genetic diversity among cotton cultivars.

  9. Pseudomonas versuta sp. nov., isolated from Antarctic soil.

    Science.gov (United States)

    See-Too, Wah Seng; Salazar, Sergio; Ee, Robson; Convey, Peter; Chan, Kok-Gan; Peix, Álvaro

    2017-06-01

    In this study we analysed three bacterial strains coded L10.10 T , A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993 T . Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10 T , A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10 T (LMG 29628 T , DSM 101070 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

  10. Staphylococcus massiliensis sp. nov., isolated from a human brain abscess.

    Science.gov (United States)

    Al Masalma, Mouhamad; Raoult, Didier; Roux, Véronique

    2010-05-01

    Gram-positive, catalase-positive, coagulase-negative, non-motile, non-fermentative and novobiocin-susceptible cocci were isolated from a human brain abscess sample (strain 5402776(T)). This novel strain was analysed by a polyphasic taxonomic approach. The respiratory quinones detected were MK-7 (93 %) and MK-6 (7 %) and the major fatty acids were C(15 : 0) iso (60.5 %), C(17 : 0) iso (8.96 %) C(15 : 0) anteiso (7.93 %) and C(19 : 0) iso (6.78 %). The peptidoglycan type was A3alpha l-Lys-Gly(2-3)-l-Ser-Gly. Based on cellular morphology and biochemical criteria, the new isolate was assigned to the genus Staphylococcus, although it did not correspond to any recognized species. The G+C content of the DNA was 36.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the new isolate was most closely related to Staphylococcus piscifermentans, Staphylococcus condimenti, Staphylococcus carnosus subsp. carnosus, S. carnosus subsp. utilis and Staphylococcus simulans (97.7 %, 97.6 %, 97.6 %, 97.6 % and 96.5 % sequence similarity, respectively). Comparison of tuf, hsp60, rpoB, dnaJ and sodA gene sequences was also performed. In phylogenetic analysis inferred from tuf, dnaJ and rpoB gene sequence comparisons, strain 5402776(T) clustered with Staphylococcus pettenkoferi (93.7 %, 82.5 % and 89 % sequence similarity, respectively) and on phylogenetic analysis inferred from sodA gene sequence comparisons, it clustered with Staphylococcus chromogenes (82.8 %). On the basis of phenotypic and genotypic data, this isolate represents a novel species for which the name Staphylococcus massiliensis sp. nov. is proposed (type strain 5402776(T)=CCUG 55927(T)=CSUR P23(T)).

  11. Hymenobacter seoulensis sp. nov., isolated from river water.

    Science.gov (United States)

    Lee, Jae-Jin; Lee, Yeon-Hee; Park, Su-Jin; Lee, Seung-Yeol; Park, Sangkyu; Kim, Myung Kyum; Ten, Leonid N; Jung, Hee-Young

    2017-04-01

    A Gram-stain-negative, aerobic, rod-shaped, non-motile and pink-pigmented bacterial strain, designated 16F7GT, was isolated from river water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 16F7GT belongs to the genus Hymenobacter. The 16S rRNA gene sequence similarity to members of the genus Hymenobacter ranged from 90.5 to 97.4 %, and the most closely related strains were Hymenobacter rigui WPCB131T (97.4 %) and Hymenobacter xinjiangensis X2-1gT (97.3 %). Strain 16F7GT had <70 % DNA-DNA relatedness with H. rigui (32.8±7.8 %) and H. xinjiangensis (30.2±6.2 %), indicating that it represents a novel genospecies. Cells were catalase- and oxidase-positive. The genomic DNA G+C content was 56.6 mol%. The major fatty acids were summed feature 4 (C17 : 1iso I/C17 : 1 anteiso B; 19.8 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 18.4 %), C15 : 0 iso (17.0 %), C16 : 1ω5c (11.8 %) and C15 : 0 anteiso (9.8 %). The major polar lipid was phosphatidylethanolamine and the predominant respiratory quinone was menaquinone 7 (MK-7). Based on the phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain 16F7GT represents a novel species within the genus Hymenobacter, for which the name Hymenobacter seoulensis sp. nov. is proposed. The type strain is 16F7GT (=KCTC 52197T=JCM 31655T).

  12. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil.

    Science.gov (United States)

    Dahal, Ram Hari; Kim, Jaisoo

    2016-01-01

    An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium, designated strain R49T, was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R49T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes that was distinct from the most closely related genera Dyadobacter (91.98-93.85 % sequence similarity), Persicitalea (88.69 %) and Runella (84.79-85.81 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain R49T was 53.9 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R49T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhabdobacter roseus gen. nov., sp. nov. is proposed. The type strain of Rhabdobacter roseus is R49T ( = KEMB 9005-318T = KACC 18395T = JCM 30685T).

  13. Microvirga soli sp. nov., an alphaproteobacterium isolated from soil.

    Science.gov (United States)

    Dahal, Ram Hari; Kim, Jaisoo

    2017-01-01

    An aerobic, Gram-stain-negative, catalase-positive and oxidase-negative, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium designated strain R491T was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R491T formed a lineage within the family Methylobacteriaceae of the phylum Proteobacteria that was distinct from various species of the genus Microvirga, including Microvirgaaerilata 5420S-16T (97.83 % 16S rRNA gene sequence similarity), Microvirga zambiensis WSM3693T (97.76 %), Microvirga flocculans ATCC BAA-817T (97.41 %), and Microvirga lupini Lut6T, Microvirga subterranea DSM 14364T, Microvirga vignae BR3299T, and Microvirga guangxiensis 25BT (96.99 %). The major polar lipids of strain R491T were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 71.2 %), C16 : 0 (12.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.7 %), and C18 : 0 (4.2 %). The DNA G+C content of strain R491T was 61.8 mol%. DNA-DNA hybridization values between strain R491T and other members of the genus Microvirga ranged from 27 to 57 %. On the basis of phenotypic, genotypic and phylogenetic analyses, strain R491T represents a novel species of the genus Microvirga, for which the name Microvirga soli sp. nov. is proposed. The type strain is R491T (=KEMB 9005-408T=KACC 18969T=NBRC 112417T).

  14. Serratia oryzae sp. nov., isolated from rice stems.

    Science.gov (United States)

    Zhang, Cai-Wen; Zhang, Jun; Zhao, Juan-Juan; Zhao, Xia; Zhao, Dong-Fang; Yin, Hua-Qun; Zhang, Xiao-Xia

    2017-08-01

    A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia. The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA-DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia. Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia, for which the name Serratia oryzae sp. nov. is proposed.

  15. Lactobacillus shenzhenensis sp. nov., isolated from a fermented dairy beverage.

    Science.gov (United States)

    Zou, Yuanqiang; Liu, Feng; Fang, Chengxiang; Wan, Daiwei; Yang, Rentao; Su, Qingqing; Yang, Ruifu; Zhao, Jiao

    2013-05-01

    Two Lactobacillus strains, designated LY-73(T) and LY-30B, were isolated from a dairy beverage, sold in Shenzhen market, China. The two isolates were Gram-positive, non-spore-forming, non-motile, facultatively anaerobic rods that were heterofermentative and did not exhibit catalase activity. Sequencing of the 16S rRNA, pheS and rpoA genes revealed that the two isolates shared 99.5, 99.8 and 99.9 % sequence similarity, which indicates that they belong to the same species. Phylogenetic analysis demonstrated clustering of the two isolates with the genus Lactobacillus. Strain LY-73(T) showed highest 16S rRNA gene sequence similarities with Lactobacillus harbinensis KACC 12409(T) (97.73%), Lactobacillus perolens DSM 12744(T) (96.96 %) and Lactobacillus selangorensis DSM 13344(T) (93.10 %). Comparative analyses of their rpoA and pheS gene sequences indicated that the novel strains were significantly different from other Lactobacillus species. Low DNA-DNA reassociation values (50.5 %) were obtained between strain LY-73(T) and its phylogenetically closest neighbours. The G+C contents of the DNA of the two novel isolates were 56.1 and 56.5 mol%. Straight-chain unsaturated fatty acids C18 : 1ω9c (78.85 and 74.29 %) were the dominant components, and the cell-wall peptidoglycan was of the l-Lys-d-Asp type. Based on phenotypic characteristics, and chemotaxonomic and genotypic data, the novel strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus shenzhenensis sp. nov. is proposed, with LY-73(T) ( = CCTCC M 2011481(T) = KACC 16878(T)) as the type strain.

  16. Evidence that COMT genotype and proline interact on negative-symptom outcomes in schizophrenia and bipolar disorder.

    Science.gov (United States)

    Clelland, C L; Drouet, V; Rilett, K C; Smeed, J A; Nadrich, R H; Rajparia, A; Read, L L; Clelland, J D

    2016-09-13

    Elevated peripheral proline is associated with psychiatric disorders, and there is evidence that proline is a neuromodulator. The proline dehydrogenase (PRODH) gene, which encodes the enzyme that catalyzes proline catabolism, maps to human chromosome 22q11.2, a region conferring risk of schizophrenia. In the Prodh-null mouse, an interaction between elevated peripheral proline and another 22q11.2 gene, catechol-O-methyltransferase (COMT), on neurotransmission and behavior has been reported. We explored the relationship between fasting plasma proline levels and COMT Val(158)Met genotype on symptoms (positive, negative and total) in schizophrenia patients. In an exploratory study we also examined symptom change in patients with bipolar disorder. There was a significant interaction between peripheral proline and COMT on negative symptoms in schizophrenia (PScale for the Assessment of Negative Symptom (SANS) scores. In contrast, high proline was associated with high SANS scores in patients carrying a Met allele. The relationship between proline and COMT also appears to modify negative symptoms across psychiatric illness. In bipolar disorder, a significant interaction was also observed on negative-symptom change (P=0.007, n=43). Negative symptoms are intractable and largely unaddressed by current medications. These data indicate a significant interaction between peripheral proline and COMT genotype, influencing negative symptoms in schizophrenia and bipolar disorder. That high proline has converse effects on symptoms by COMT genotype, may have implications for therapeutic decisions.

  17. Analisis Fosfor pada Cacing Tanah (Megascolex sp. dan Fridericia sp.) Secara Spektrofotometri Sinar Tampak

    OpenAIRE

    Safira, Cut Shafa

    2015-01-01

    Earthworm is natural resource which can be used for medication due to its highly amount of minerals. One of these minerals is phosphorus. The aim of this research are to identify, determine and know the difference content of phosphorus in Megascolex sp. and Fridericia sp. Qualitative analysis shows positive results with addition of ammonium molybdate 4% and BaCl2 5%. Quantitative analysis was done using visible spectrophotometer with ascorbic acid method, measuring blu-colored molybdenum ...

  18. Nanocrystalline sp{sup 2} and sp{sup 3} carbons: CVD synthesis and applications

    Energy Technology Data Exchange (ETDEWEB)

    Terranova, M. L. [Università degli Studi di Roma “Tor Vergata,” via Della Ricerca Scientifica, Dipartimento di Scienze e Tecnologie Chimiche—MinimaLab (Italy); Rossi, M. [Università degli Studi di Roma “Sapienza,” via A. Scarpa, Dipartimento di Scienze di Base e Applicate per l’Ingegneria and Centro di Ricerca per le Nanotecnologie Applicate all’Ingegneria (CNIS) (Italy); Tamburri, E., E-mail: emanuela.tamburri@uniroma2.it [Università degli Studi di Roma “Tor Vergata,” via Della Ricerca Scientifica, Dipartimento di Scienze e Tecnologie Chimiche—MinimaLab (Italy)

    2016-11-15

    The design and production of innovative materials based on nanocrystalline sp{sup 2}- and sp{sup 3}-coordinated carbons is presently a focus of the scientific community. We present a review of the nanostructures obtained in our labs using a series of synthetic routes, which make use of chemical vapor deposition (CVD) techniques for the selective production of non-planar graphitic nanostructures, nanocrystalline diamonds, and hybrid two-phase nanostructures.

  19. Differences in nutrient uptake capacity of the benthic filamentous algae Cladophora sp., Klebsormidium sp. and Pseudanabaena sp. under varying N/P conditions.

    Science.gov (United States)

    Liu, Junzhuo; Vyverman, Wim

    2015-03-01

    The N/P ratio of wastewater can vary greatly and directly affect algal growth and nutrient removal process. Three benthic filamentous algae species Cladophora sp., Klebsormidium sp. and Pseudanabaena sp. were isolated from a periphyton bioreactor and cultured under laboratory conditions on varying N/P ratios to determine their ability to remove nitrate and phosphorus. The N/P ratio significantly influenced the algal growth and phosphorus uptake process. Appropriate N/P ratios for nitrogen and phosphorus removal were 5-15, 7-10 and 7-20 for Cladophora sp., Klebsormidium sp. and Pseudanabaena sp., respectively. Within these respective ranges, Cladophora sp. had the highest biomass production, while Pseudanabaena sp. had the highest nitrogen and phosphorus contents. This study indicated that Cladophora sp. had a high capacity of removing phosphorus from wastewaters of low N/P ratio, and Pseudanabaena sp. was highly suitable for removing nitrogen from wastewaters with high N/P ratio. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Anomalous self potential (sp) log signatures observed in a water ...

    African Journals Online (AJOL)

    Geophysical logging was done after drilling had been completed in a water well at Okwudor, South Eastern Nigeria. Three electric logs were run viz: Self Potential (SP), Resistivity N16″ and N64″ logs. An anomaly was observed in the SP log. The SP results from this well show some deviation from the standard norm.

  1. Biosorption of chromium by mangrove-derived Aplanochytrium sp ...

    African Journals Online (AJOL)

    The microbial dried biomass of Thraustochytrids is used as bioadsorbent for the removal of the chromium in aqueous solution. In this investigation, three species of Thraustochydrids namely Aplanochytrium sp., Thraustochytrium sp. and Schizochytrium sp. were tested for the efficiency of chromium accumulation by culturing ...

  2. Babesia peircei sp. nov. from the jackass penguin

    African Journals Online (AJOL)

    1992-01-09

    Jan 9, 1992 ... An avian piroplasm, Babesia peircei sp. nov. is described from the jackass penguin Spheniscus demersus. Morphological differences between Babesia peircei sp. nov. and the other valid Babesia spp. are discussed together with the possible vectors. 'n Voal-piroplasma, Babesia peircei sp. nov. afkomstig ...

  3. Environmental conditions affecting exopolysaccharide production by Pseudomonas aeruginosa, Micrococcus sp., and Ochrobactrum sp.

    Science.gov (United States)

    Kiliç, Nur Koçberber; Dönmez, Gönül

    2008-06-15

    Three different chromium-resistant microorganisms (Pseudomonas aeruginosa, Micrococcus sp., and Ochrobactrum sp.) were tested with regard to their EPS production at different pH levels, temperatures, Cr(VI) concentrations, and incubation periods. The optimum pH level was 7 for P. aeruginosa and Micrococcus sp., while it was 8 for Ochrobactrum sp. according to the highest EPS amount at 100 mg/L Cr(VI) concentration. The highest production of EPSs by the three bacteria was obtained under different environmental conditions. P. aeruginosa produced the highest EPS (863.3 mg/L) after incubation for 96 h on media with 50 mg/L Cr(VI) at 20 degrees C, Micrococcus sp. gave the highest yield (444.6 mg/L) after incubation for 72 h on media with 100 mg/L Cr(VI) at the same temperature, and Ochrobactrum sp. had the highest production (430.5 mg/L) on media with 150 mg/L Cr(VI) at 30 degrees C at the end of 48 h of incubation.

  4. Remote sensing data of SP Mountain and SP Lava flow in North-Central Arizona

    Science.gov (United States)

    Schaber, G.G.; Elachi, C.; Farr, T.G.

    1980-01-01

    Multifrequency airborne radar image data of SP Mountain [Official name of feature (U.S. Geological Survey, 1970)] and SP flow (and vicinity) in north-central Arizona were obtained in diverse viewing directions and direct and cross-polarization, then compared with surface and aerial photography, LANDSAT multispectral scanner data, airborne thermal infrared imagery, surface geology, and surface roughness statistics. The extremely blocky, basaltic andesite of SP flow is significantly brighter on direct-polarization K-band (0.9-cm wavelength) images than on cross-polarized images taken simultaneously. Conversely, for the longer wavelength (25 cm) L-band radar images, the cross-polarization image returns from SP flow are brighter than the direct-polarized image. This effect is explained by multiple scattering and the strong wavelength dependence of polarization effects caused by the rectilinear basaltic andesite scatters. Two distinct types of surface relief on SP flow, one extremely blocky, the other subdued, are found to be clearly discriminated on the visible and thermal wavelength images but are separable only on the longer wavelength L-band radar image data. The inability of the K- and X- (3-cm wavelength) band radars to portray the differences in roughness between the two SP flow surface units is attributed to the radar frequency dependence of the surface-relief scale, which, described as the Rayleigh criterion, represents the transition between quasispecular and primarily diffuse backscatter. ?? 1980.

  5. Two new species of suctorians, Acineta satyanandani sp. nov. and Paracineta karunakarani sp. nov. epizoic on ostracods

    Digital Repository Service at National Institute of Oceanography (India)

    Santhakumari, V.

    Two, species of protozoic suctorians, Acineta satyanandani sp. nov. and Paracineta karunakarani sp. nov., are described. These were found attached on the body of the marine ostracod, Cypridina dentata (Muller), collected from the shelf and slope...

  6. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  7. 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.

  8. Methods for discovering and validating relationships among genotyped animals

    Science.gov (United States)

    Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, t...

  9. Variation of meat quality traits among five genotypes of chicken.

    Science.gov (United States)

    Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K

    2009-10-01

    The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

  10. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

    Science.gov (United States)

    A number of Bangladeshi wheat genotypes (varieties and advanced lines) have been tested for boron efficiency through sand culture experiments over two years (2007-08 & 2008-09) against two Thai check varieties ‘Fang 60’ (boron efficient) and ‘SW41’ (boron inefficient). Performances of the genotypes ...

  11. Crossbreeding of large white and Nsukka local pigs: Genotype and ...

    African Journals Online (AJOL)

    5-Blood samples from 80 pigs of 4 genotypes - the Nsukka local (Lo), the exotic Large White (LW), the one-way F1 (LW x Lo) and the F2 crosses belonging to 5 age groups, were analyzed, to determine the mean values of the haematological parameters in the genotypes and different age groups and to check if and how the ...

  12. Enhanced fodder yield of maize genotypes under saline irrigation is ...

    African Journals Online (AJOL)

    Poor quality irrigation water adversely affects the growth and yield of crops. This study was designed to evaluate the growth, fodder yield and ionic concentration of three promising maize (Zea mays L.) genotypes under the influence of varying quality irrigation water, with different salinity levels. The genotypes, such as ...

  13. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  14. Application of mixed models for the assessment genotype and ...

    African Journals Online (AJOL)

    Application of mixed models for the assessment genotype and environment interactions in cotton ( Gossypium hirsutum ) cultivars in Mozambique. ... The cultivars ISA 205, STAM 42 and REMU 40 showed superior productivity when they were selected by the Harmonic Mean of Genotypic Values (HMGV) criterion in relation ...

  15. The influence of host genotype X environment Interactions on the ...

    African Journals Online (AJOL)

    Mean squares for environments, genotypes and G x E interactions were highly significant (P<0.0001) for anthracnose infection. Significant G x E interactions, accounting for 19% of the treatment sums of squares, indicated that genotypes responded differentially to anthracnose infection across environments. The additive ...

  16. The genotype-phenotype map of an evolving digital organism.

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna

    2017-02-01

    Full Text Available To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences, which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  17. The genotype-phenotype map of an evolving digital organism.

    Science.gov (United States)

    Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-02-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  18. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.

    1982-01-01

    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1.

  19. characterisation of common bean genotypes based on storage

    African Journals Online (AJOL)

    ACSS

    of pliers and then ground to fine powder with a ... segregation of genotypes were Rm 23.75, 32.50,. 33.75, 22.50 ... Figure 1. Positions of Phaseolus vulgarisL. genotypes on the first and second correspondence scores based on storage protein.

  20. Integrated analysis for genotypic adaptation in rice | Das | African ...

    African Journals Online (AJOL)

    Integrated analysis for genotypic adaptation in rice. S Das, RC Misra, MC Pattnaik, SK Sinha. Abstract. Development of varieties with high yield potential coupled with wide adaptability is an important plant breeding objective. The presence of genotype by environment (GxE) interaction plays a crucial role in determining the ...

  1. Characteristics of Streptococcus mutans genotypes and dental caries in children

    Science.gov (United States)

    Cheon, Kyounga; Moser, Stephen A.; Wiener, Howard W.; Whiddon, Jennifer; Momeni, Stephanie S.; Ruby, John D.; Cutter, Gary R.; Childers, Noel K.

    2013-01-01

    This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5 and 6 yr-old children, considered being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping with repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, filled surfaces (dmfs/DMFS) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity) and 13 genotypes were shared by at least 2 children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and was negatively associated with p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high caries risk community, which suggest fewer decayed surfaces are significantly associated with lower diversity and stability of S. mutans genotypes. PMID:23659236

  2. Beijing/W genotype Mycobacterium tuberculosis and drug resistance.

    NARCIS (Netherlands)

    Glynn, Judith R; Kremer, Kristin; Borgdorff, Martien W; Rodriguez, Mar Pujades; Soolingen, Dick van

    2006-01-01

    Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype's prevalence worldwide, trends over time and with

  3. 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...

  4. Genotype dependent callus induction and shoot regeneration in ...

    African Journals Online (AJOL)

    This study aims to observe the effect of genotype, hormone and culture conditions on sunflower (Helianthus annuus L.) callus induction and indirect plant regeneration. Calli were obtained from hypocotyl and cotyledon explants of five different sunflower genotypes; Trakya 80, Trakya 129, Trakya 259, Trakya 2098 and ...

  5. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    The objective of the study was to differentiate genotypes with higher efficiency and responsiveness to nitrogen supply, to understand how the nitrogen supply can impact the dry matter allocation and the accumulation of this nutrient in the different plant compartments of genotypes of conilon coffee, cultivated under ...

  6. Haemoglobin genotype of children with severe malaria seen at the ...

    African Journals Online (AJOL)

    Abstract: Introduction: Types of haemoglobin (Hb) genotype have been found to be crucial to the rate of red blood cell parasite invasion, multiplication, and destruction as well as outcome of malaria disease. In a bid to provide more information on the relationship between Hb genotype and level of protection conferred by ...

  7. participatory selection of mungbean genotypes in uganda abstract

    African Journals Online (AJOL)

    ACSS

    2017-05-29

    May 29, 2017 ... that there were no significant differences in genotype choices based on gender ... However, there were significant genotype preference differences between eastern and northern regions (χ2 = ..... for southern Ethiopia. ... of improved cowpea cultivars in the Guinea and Sudan savanna zones of north east.

  8. Genetic variation of response to water deficit in parental genotypes ...

    African Journals Online (AJOL)

    dgomi

    In this study, we investigated morphological and photosynthetic responses to water deficit in parental genotypes of M. ... for adaptation to water deficit in legumes is a prerequisite for any research aiming to improve legume yields. ...... tolerant genotypes in rainfed lowland rice. Field Crop. Res. 99:48-58. Rouached A, Slama I, ...

  9. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

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

    2015-01-01

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

  10. Evaluation of sorghum genotypes under drought stress conditions ...

    African Journals Online (AJOL)

    Seven genotypes of sorghum (Sorghum bicolour (L.) Moench) were studied in both drought and normal conditions. In each condition, the genotypes were evaluated using a split plot based randomized complete block design with three replications. Drought tolerance indices including stability tolerance index (STI), mean ...

  11. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  12. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  13. Utrophin Compensates dystrophin Loss during Mouse Spermatogenesis

    OpenAIRE

    Chen, Hung-Chih; Chin, Yu-Feng; Lundy, David J.; Liang, Chung-Tiang; Chi, Ya-Hui; Kuo, Paolin; Hsieh, Patrick C. H.

    2017-01-01

    Duchenne muscular dystrophy (DMD) is an X-linked genetic disorder resulting from mutations in the dystrophin gene. The mdx/utrn ?/? mouse, lacking in both dystrophin and its autosomal homologue utrophin, is commonly used to model the clinical symptoms of DMD. Interestingly, these mice are infertile but the mechanisms underlying this phenomenon remain unclear. Using dystrophin deficient mdx mouse and utrophin haplodeficient mdx/utrn +/? mouse models, we demonstrate the contribution of Dp427 (f...

  14. Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

    Science.gov (United States)

    Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens

    2013-01-01

    in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

  15. Microbiologically influenced corrosion of galvanized steel by Desulfovibrio sp. and Desulfosporosinus sp. in the presence of Ag–Cu ions

    Energy Technology Data Exchange (ETDEWEB)

    Ilhan-Sungur, Esra, E-mail: esungur@istanbul.edu.tr [Istanbul University, Faculty of Science, Department of Biology, 34134 Vezneciler, Istanbul (Turkey); Unsal-Istek, Tuba [Istanbul University, Faculty of Science, Department of Biology, 34134 Vezneciler, Istanbul (Turkey); Cansever, Nurhan [Yıldız Technical University, Faculty of Chemistry-Metallurgy, Metallurgical and Materials Engineering Department, 34210 Esenler, Istanbul (Turkey)

    2015-07-15

    The effects of Ag–Cu ions on the microbiologically induced corrosion of galvanized steel in the presence of Desulfovibrio sp. and Desulfosporosinus sp. were investigated. The corrosion behavior of galvanized steel was analyzed by potentiodynamic polarization and electrochemical impedance spectroscopy. The biofilm, corrosion products and Ag–Cu ions on the surfaces were investigated by using scanning electron microscopy, energy dispersive X-ray spectrometry and elemental mapping. The biofilm layer formed by the Desulfovibrio sp. was stable covering the all surface of galvanized steel coupons, while that by Desulfosporosinus sp. was intermittent, highly porous and heterogeneous. It was found that both of the sulfate reducing bacteria species accelerated corrosion of the galvanized steel. However, it was detected that Desulfosporosinus sp. was more corrosive for galvanized steel than Desulfovibrio sp. Scanning electron microscopy images showed that Desulfovibrio sp. and Desulfosporosinus sp. in biofilm clustered into patches on the galvanized steel surface when the culture contained toxic Ag–Cu ions. The ions affected the growth of the sulfate reducing bacteria strains in different ways and hence the corrosion behaviors. It was observed that the Ag–Cu ions affected negatively growth of Desulfosporosinus sp. especially after 24 h of exposure leading to a decrease in the corrosion rate of galvanized steel. However, Desulfovibrio sp. showed more corrosive effect in the presence of the ions according to the ions-free culture. Energy dispersive X-ray spectrometry analysis showed that corrosion products on the surfaces were mainly composed of Zn, S, Na, O and P. - Highlights: • Galvanized steel was corroded by Desulfosporosinus sp. and Desulfovibrio sp. • Desulfosporosinus sp. is more corrosive than Desulfovibrio sp. • The Ag–Cu ions affected corrosion behavior of Desulfosporosinus sp. and Desulfovibrio sp. on galvanized steel.

  16. In vitro cytotoxicity evaluation of nano-carbon particles with different sp{sup 2}/sp{sup 3} ratios

    Energy Technology Data Exchange (ETDEWEB)

    Li, S.S.; Wu, B.J.; Deng, Q.Y. [Key Laboratory for Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); Guo, Y.B. [The Third People' s Hospital of Chengdu, Sichuan 610031 (China); Leng, Y.X., E-mail: yxleng@263.net [Key Laboratory for Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); Huang, N. [Key Laboratory for Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)

    2017-06-01

    Graphitization occurs during the long-term service of a diamond-like carbon (DLC) modified artificial joint. Then, DLC wear debris, which are carbon particles with different sp{sup 2}/sp{sup 3} ratios and sizes ranging from the nano- to micro-meter scale produced. In this paper, to promote the application of DLC coating for artificial joint modification, the cytotoxicity of DLC debris (nano-carbon particles, NCs) with different sp{sup 2}/sp{sup 3} ratios was studied. The microstructure and physical characteristics of NCs with different sp{sup 2}/sp{sup 3} ratios were investigated by Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), Transmission Electron Microscope (TEM) and Dynamic Light Scattering (DLS). Meanwhile, osteoblasts and macrophages were applied to characterize the cytotoxicity of the NCs. In vitro cytotoxicity assay results indicated that cells incubated with NCs of different sp{sup 2}/sp{sup 3} ratios had greater osteogenic capacity, and these particles caused a weaker immune response in comparison with CoCrMo particles. Taken together, the results indicated that NCs with different sp{sup 2}/sp{sup 3} ratios presented a good cytocompatibility than CoCrMo particles. But no significant differences were observed among NCs with different sp{sup 2}/sp{sup 3} ratios. The better cytocompatibility of NCs is mainly attributable to their surface charge. - Highlights: • NCs with different sp{sup 2}/sp{sup 3} ratios have been successfully prepared by annealing treatment. • NCs with different sp{sup 2}/sp{sup 3} ratios show good osteogenic capacity and lower immune response. • The good cytocompatibility of NCs is mainly dependent on its surface charge.

  17. Microbiologically influenced corrosion of galvanized steel by Desulfovibrio sp. and Desulfosporosinus sp. in the presence of Ag–Cu ions

    International Nuclear Information System (INIS)

    Ilhan-Sungur, Esra; Unsal-Istek, Tuba; Cansever, Nurhan

    2015-01-01

    The effects of Ag–Cu ions on the microbiologically induced corrosion of galvanized steel in the presence of Desulfovibrio sp. and Desulfosporosinus sp. were investigated. The corrosion behavior of galvanized steel was analyzed by potentiodynamic polarization and electrochemical impedance spectroscopy. The biofilm, corrosion products and Ag–Cu ions on the surfaces were investigated by using scanning electron microscopy, energy dispersive X-ray spectrometry and elemental mapping. The biofilm layer formed by the Desulfovibrio sp. was stable covering the all surface of galvanized steel coupons, while that by Desulfosporosinus sp. was intermittent, highly porous and heterogeneous. It was found that both of the sulfate reducing bacteria species accelerated corrosion of the galvanized steel. However, it was detected that Desulfosporosinus sp. was more corrosive for galvanized steel than Desulfovibrio sp. Scanning electron microscopy images showed that Desulfovibrio sp. and Desulfosporosinus sp. in biofilm clustered into patches on the galvanized steel surface when the culture contained toxic Ag–Cu ions. The ions affected the growth of the sulfate reducing bacteria strains in different ways and hence the corrosion behaviors. It was observed that the Ag–Cu ions affected negatively growth of Desulfosporosinus sp. especially after 24 h of exposure leading to a decrease in the corrosion rate of galvanized steel. However, Desulfovibrio sp. showed more corrosive effect in the presence of the ions according to the ions-free culture. Energy dispersive X-ray spectrometry analysis showed that corrosion products on the surfaces were mainly composed of Zn, S, Na, O and P. - Highlights: • Galvanized steel was corroded by Desulfosporosinus sp. and Desulfovibrio sp. • Desulfosporosinus sp. is more corrosive than Desulfovibrio sp. • The Ag–Cu ions affected corrosion behavior of Desulfosporosinus sp. and Desulfovibrio sp. on galvanized steel

  18. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

    Directory of Open Access Journals (Sweden)

    Stephen W. Erickson

    2016-07-01

    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  19. 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.

  20. Steroid metabolism in the mouse placenta

    International Nuclear Information System (INIS)

    Okker-Reitsma, G.H.

    1976-01-01

    The purpose of the study described in this thesis was to investigate the capacity for steroid synthesis of the mouse placenta - especially the production of progesterone, androgens and estrogens - and to determine, if possible, the relation of steroid synthesis to special cell types. In an introductory chapter the androgen production in the mouse placenta is surveyed by means of a histochemical and bioindicator study of different stages of development of the placenta. The metabolism of [ 3 H]-dehydroepiandrosterone and [ 3 H]-progesterone by mouse placental tissue in vitro is studied. The metabolism of [ 3 H]-progesterone by the mouse fetal adrenal in vitro is also studied

  1. Interaction of Sp1 zinc finger with transport factor in the nuclear localization of transcription factor Sp1

    International Nuclear Information System (INIS)

    Ito, Tatsuo; Kitamura, Haruka; Uwatoko, Chisana; Azumano, Makiko; Itoh, Kohji; Kuwahara, Jun

    2010-01-01

    Research highlights: → Sp1 zinc fingers themselves interact with importin α. → Sp1 zinc finger domains play an essential role as a nuclear localization signal. → Sp1 can be transported into the nucleus in an importin-dependent manner. -- Abstract: Transcription factor Sp1 is localized in the nucleus and regulates the expression of many cellular genes, but the nuclear transport mechanism of Sp1 is not well understood. In this study, we revealed that GST-fused Sp1 protein bound to endogenous importin α in HeLa cells via the Sp1 zinc finger domains, which comprise the DNA binding domain of Sp1. It was found that the Sp1 zinc finger domains directly interacted with a wide range of importin α including the armadillo (arm) repeat domain and the C-terminal acidic domain. Furthermore, it turned out that all three zinc fingers of Sp1 are essential for binding to importin α. Taken together, these results suggest that the Sp1 zinc finger domains play an essential role as a NLS and Sp1 can be transported into the nucleus in an importin-dependent manner even though it possesses no classical NLSs.

  2. Molecular epidemiology and genetic diversity of hepatitis B virus genotype E in an isolated Afro-Colombian community.

    Science.gov (United States)

    Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Carrilho, Flair José; Pinho, João Renato Rebello

    2010-02-01

    Hepatitis B virus (HBV) infection is a significant public health concern with 350 million chronic carriers worldwide. Eight HBV genotypes (A-H) have been described so far. Genotype E (HBV/E) is widely distributed in West Africa and has rarely been found in other continents, except for a few cases in individuals with an African background. In this study, we characterized HBV genotypes in Quibdó, Colombia, by partial S/P gene sequencing, and found, for the first time, HBV/E circulating in nine Afro-Colombian patients who had no recent contact with Africa. The presence of HBV/E in this community as a monophyletic group suggests that it was a result of a recent introduction by some Afro-descendent contact or, alternatively, that the virus came with slaves brought to Colombia. By using sequences with sampling dates, we estimated the substitution rate to be about 3.2 x 10(-4) substitutions per site per year, which resulted in a time to the most recent common ancestor (TMRCA) of 29 years. In parallel, we also estimated the TMRCA for HBV/E by using two previously estimated substitution rates (7.7 x 10(-4) and 1.5 x 10(-5) substitutions per site per year). The TMRCA was around 35 years under the higher rate and 1500 years under the slower rate. In sum, this work reports for the first time the presence of an exclusively African HBV genotype circulating in South America. We also discuss the time of the entry of this virus into America based on different substitution rates estimated for HBV.

  3. Identification of Cryptosporidium Species and Genotypes in Scottish Raw and Drinking Waters during a One-Year Monitoring Period▿

    Science.gov (United States)

    Nichols, R. A. B.; Connelly, L.; Sullivan, C. B.; Smith, H. V.

    2010-01-01

    We analyzed 1,042 Cryptosporidium oocyst-positive slides (456 from raw waters and 586 from drinking waters) of which 55.7% contained 1 or 2 oocysts, to determine species/genotypes present in Scottish waters. Two nested PCR-restriction fragment length polymorphism (RFLP) assays targeting different loci (1 and 2) of the hypervariable region of the 18S rRNA gene were used for species identification, and 62.4% of samples were amplified with at least one of the PCR assays. More samples (577 slides; 48.7% from raw water and 51.3% from drinking water) were amplified at locus 1 than at locus 2 (419 slides; 50.1% from raw water and 49.9% from drinking water). PCR at loci 1 and 2 amplified 45.4% and 31.7% of samples containing 1 or 2 oocysts, respectively. We detected both human-infectious and non-human-infectious species/genotype oocysts in Scottish raw and drinking waters. Cryptosporidium andersoni, Cryptosporidium parvum, and the Cryptosporidium cervine genotype (now Cryptosporidium ubiquitum) were most commonly detected in both raw and drinking waters, with C. ubiquitum being most common in drinking waters (12.5%) followed by C. parvum (4.2%) and C. andersoni (4.0%). Numerous samples (16.6% total; 18.9% from drinking water) contained mixtures of two or more species/genotypes, and we describe strategies for unraveling their identity. Repetitive analysis for discriminating mixtures proved useful, but both template concentration and PCR assay influenced outcomes. Five novel Cryptosporidium spp. (SW1 to SW5) were identified by RFLP/sequencing, and Cryptosporidium sp. SW1 was the fourth most common contaminant of Scottish drinking water (3%). PMID:20639357

  4. Therapeutic cloning in the mouse

    Science.gov (United States)

    Mombaerts, Peter

    2003-01-01

    Nuclear transfer technology can be applied to produce autologous differentiated cells for therapeutic purposes, a concept termed therapeutic cloning. Countless articles have been published on the ethics and politics of human therapeutic cloning, reflecting the high expectations from this new opportunity for rejuvenation of the aging or diseased body. Yet the research literature on therapeutic cloning, strictly speaking, is comprised of only four articles, all in the mouse. The efficiency of derivation of embryonic stem cell lines via nuclear transfer is remarkably consistent among these reports. However, the efficiency is so low that, in its present form, the concept is unlikely to become widespread in clinical practice. PMID:12949262

  5. A superhard sp3 microporous carbon with direct bandgap

    Science.gov (United States)

    Pan, Yilong; Xie, Chenlong; Xiong, Mei; Ma, Mengdong; Liu, Lingyu; Li, Zihe; Zhang, Shuangshuang; Gao, Guoying; Zhao, Zhisheng; Tian, Yongjun; Xu, Bo; He, Julong

    2017-12-01

    Carbon allotropes with distinct sp, sp2, and sp3 hybridization possess various different properties. Here, a novel all-sp3 hybridized tetragonal carbon, namely the P carbon, was predicted by the evolutionary particle swarm structural search. It demonstrated a low density among all-sp3 carbons, due to the corresponding distinctive microporous structure. P carbon is thermodynamically stable than the known C60 and could be formed through the single-walled carbon nanotubes (SWCNTs) compression. P carbon is a direct bandgap semiconductor displaying a strong and superhard nature. The unique combination of electrical and mechanical properties constitutes P carbon a potential superhard material for semiconductor industrial fields.

  6. A new inhibitor of synovial phospholipase A2 from fermentations of Penicillium sp. 62-92.

    Science.gov (United States)

    Witter, L; Anke, T; Sterner, O

    1998-01-01

    Penidiamide, a new tripetide containing dehydrotryptamine, glycine and anthranilic acid linked together by two amide bonds, and oxindole were isolated from submerged cultures of Penicillium sp. 62-92. Both compounds preferentially inhibited human synovial phospholipase A2, penidiamide with an IC50 of 30 microM and oxindole of 380 microM. With the exception of U 937 cells (leukemia, human), no cytotoxic activities were detected against HL-60- (leukemia, human), HeLa S3- (epitheloid carcinoma, human), BHK 21- (kidney fibroblasts, hamster), and L1210-cells (leukemia, mouse). No antimicrobial activity was detected for oxindole, and only weak antibacterial activity for penidiamide. The structure of penidiamide was elucidated by spectroscopic methods.

  7. Thalassospiramide G, a New γ-Amino-Acid-Bearing Peptide from the Marine Bacterium Thalassospira sp.

    Directory of Open Access Journals (Sweden)

    Sang Kook Lee

    2013-02-01

    Full Text Available In the chemical investigation of marine unicellular bacteria, a new peptide, thalassospiramide G (1, along with thalassospiramides A and D (2–3, was discovered from a large culture of Thalassospira sp. The structure of thalassospiramide G, bearing γ-amino acids, such as 4-amino-5-hydroxy-penta-2-enoic acid (AHPEA, 4-amino-3,5-dihydroxy-pentanoic acid (ADPA, and unique 2-amino-1-(1H-indol-3-yl ethanone (AIEN, was determined via extensive spectroscopic analysis. The absolute configuration of thalassospiramide D (3, including 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA, was rigorously determined by 1H–1H coupling constant analysis and chemical derivatization. Thalassospiramides A and D (2–3 inhibited nitric oxide (NO production in lipopolysaccharide (LPS-stimulated mouse macrophage RAW 264.7 cells, with IC50 values of 16.4 and 4.8 μM, respectively.

  8. The phenotype, psychotype and genotype of bruxism

    Science.gov (United States)

    Cruz-Fierro, Norma; Martínez-Fierro, Margarita; Cerda-Flores, Ricardo M.; Gómez-Govea, Mayra A.; Delgado-Enciso, Iván; Martínez-De-Villarreal, Laura E.; González-Ramírez, Mónica T.; Rodríguez-Sánchez, Irám Pablo

    2018-01-01

    Bruxism is a jaw muscle activity that involves physio-pathological, psycho-social, hereditary and genetic factors. The purpose of this study was to determine the associations between self-reported bruxism, anxiety, and neuroticism personality trait with the rs6313 polymorphism in the gene HTR2A. A sample of 171 subjects of both sexes (14–53 years of age) was included. The control group (group 1, n=60) exhibited no signs or symptoms of bruxism. The case group had signs and symptoms of bruxism (n=112) and was subdivided into group 2, bruxism during sleep (n=22); group 3, awake bruxism (n=44); and group 4 combined bruxism (n=46). As diagnostic tools, the Self-Reported Bruxism Questionnaire (SBQ), the Beck Anxiety Inventory (BAI) and the Eysenck Personality Questionnaire Revised-Abbreviated (EPQR-A) were used. HTR2A (rs6313) SNPs were determined by qPCR for all the participants. The packages SPSS, maxLik and EPI-INFO were used for data analysis. The combined bruxism group reported higher scores in bruxism symptoms, mean = 32.21; anxiety symptoms, mean = 14.80; and neuroticism, mean = 3.26. Combined bruxism was associated with a higher degree of neuroticism (OR=15.0; CI 1.52–148.32) and anxiety in grade 3-moderate (OR=3.56; CI 1.27–10.03), and grade 4-severe (OR=8.40; CI 1.45–48.61), as determined using EPISODE computer software. Genotypic homogeneity analysis revealed no significant differences in allele frequency (P=0.612) among the four groups. The population was in Hardy-Weinberg equilibrium (maxLik package). In conclusion, the three instruments confirm traits of bruxism, anxiety and neuroticism in individuals with bruxism. These data were ratified when the sample was divided by genotypic homogeneity. On the other hand, there was no significant difference between the groups in the SNPs rs6313 from the HTR2A gene. PMID:29599979

  9. Sp1/3 and NF-1 mediate basal transcription of the human P2X1 gene in megakaryoblastic MEG-01 cells

    Directory of Open Access Journals (Sweden)

    Ennion Steven J

    2006-03-01

    Full Text Available Abstract Background P2X1 receptors play an important role in platelet function as they can induce shape change, granule centralization and are also involved in thrombus formation. As platelets have no nuclei, the level of P2X1 expression depends on transcriptional regulation in megakaryocytes, the platelet precursor cell. Since nothing is known about the molecular mechanisms regulating megakaryocytic P2X1 expression, this study aimed to identify and functionally characterize the P2X1 core promoter utilized in the human megakaryoblastic cell line MEG-01. Results In order to identify cis-acting elements involved in the transcriptional regulation of P2X1 expression, the ability of 4.7 kb P2X1 upstream sequence to drive luciferase reporter gene expression was tested. Low promoter activity was detected in proliferating MEG-01 cells. This activity increased 20-fold after phorbol-12-myristate-13-acetate (PMA induced differentiation. A transcription start site was detected 365 bp upstream of the start codon by primer extension. Deletion analysis of reporter constructs indicated a core promoter located within the region -68 to +149 bp that contained two Sp1 sites (named Sp1a and Sp1b and an NF-1 site. Individual mutations of Sp1b or NF-1 binding sites severely reduced promoter activity whereas triple mutation of Sp1a, Sp1b and NF-1 sites completely abolished promoter activity in both untreated and PMA treated cells. Sp1/3 and NF-1 proteins were shown to bind their respective sites by EMSA and interaction of Sp1/3, NF-1 and TFIIB with the endogenous P2X1 core promoter in MEG-01 cells was demonstrated by chromatin immunoprecipitation. Alignment of P2X1 genes from human, chimp, rat, mouse and dog revealed consensus Sp1a, Sp1b and NF-1 binding sites in equivalent positions thereby demonstrating evolutionary conservation of these functionally important sites. Conclusion This study has identified and characterized the P2X1 promoter utilized in MEG-01 cells and

  10. 25-hydroxycholesterol promotes RANKL-induced osteoclastogenesis through coordinating NFATc1 and Sp1 complex in the transcription of miR-139-5p

    International Nuclear Information System (INIS)

    Zhang, Lishan; Lv, Yinping; Xian, Guozhe; Lin, Yanliang

    2017-01-01

    25-hydroxycholesterol (25-HC) is implicated in many processes, including lipid metabolism and the immune response. However, the role of 25-HC in RANKL-induced osteoclastogenesis remains largely unknown. Our results showed that 25-HC inhibited miR-139-5p expression in mouse bone marrow macrophages (BMMs) cultured in receptor activator of NF-κB ligand (RANKL) and monocyte macrophage colony-stimulating factor (M-CSF). Further investigation suggested that 25-HC promoted the expression of nuclear factor of activated T cell cytoplasmic 1 (NFATc1) and Sp1, especially in the presence of RANKL and M-CSF. Meanwhile, 25-HC induced nuclear translocation of NFATc1, resulting in the interaction between NFATc1 and Sp1 that was confirmed by co-immunoprecipitation. Chromatin immunoprecipitation assay indicated that Sp1 could bind to miR-139-5p promoter, but NFATc1 had no binding capacity. Although forming NFATc1/Sp1 complex increased its binding to miR-139-5p promoter, the complex inhibited the transcriptional activity of Sp1. Inhibition of NFATc1 increase the expression of miR-139-5p, which might be due to the release of free Sp1 that could bind to the promoter of miR-139-5p. Enforced expression of miR-139-5p impaired osteoclastogenesis induced by co-treatment with 25-HC and RANKL. These results suggested that 25-HC induced the interaction between NFATc1 and Sp1, reducing the level of free Sp1 to inhibit miR-139-5p expression and promote osteoclastogenesis. - Highlights: • 25-hydroxycholesterol inhibited miR-139-5p expression in bone marrow macrophages. • 25-hydroxycholesterol promoted the expression of NFATc1 and Sp1. • 25-hydroxycholesterol induced the interaction between NFATc1 and Sp1. • NFATc1/Sp1 complex inhibited the transcription of miR-139-5p. • MiR-139-5p impaired osteoclastogenesis induced by 25-hydroxycholesterol and RANKL.

  11. Sp6 and Sp8 Transcription Factors Control AER Formation and Dorsal-Ventral Patterning in Limb Development

    Science.gov (United States)

    Haro, Endika; Delgado, Irene; Junco, Marisa; Yamada, Yoshihiko; Mansouri, Ahmed; Oberg, Kerby C.; Ros, Marian A.

    2014-01-01

    The formation and maintenance of the apical ectodermal ridge (AER) is critical for the outgrowth and patterning of the vertebrate limb. The induction of the AER is a complex process that relies on integrated interactions among the Fgf, Wnt, and Bmp signaling pathways that operate within the ectoderm and between the ectoderm and the mesoderm of the early limb bud. The transcription factors Sp6 and Sp8 are expressed in the limb ectoderm and AER during limb development. Sp6 mutant mice display a mild syndactyly phenotype while Sp8 mutants exhibit severe limb truncations. Both mutants show defects in AER maturation and in dorsal-ventral patterning. To gain further insights into the role Sp6 and Sp8 play in limb development, we have produced mice lacking both Sp6 and Sp8 activity in the limb ectoderm. Remarkably, the elimination or significant reduction in Sp6;Sp8 gene dosage leads to tetra-amelia; initial budding occurs, but neither Fgf8 nor En1 are activated. Mutants bearing a single functional allele of Sp8 (Sp6−/−;Sp8+/−) exhibit a split-hand/foot malformation phenotype with double dorsal digit tips probably due to an irregular and immature AER that is not maintained in the center of the bud and on the abnormal expansion of Wnt7a expression to the ventral ectoderm. Our data are compatible with Sp6 and Sp8 working together and in a dose-dependent manner as indispensable mediators of Wnt/βcatenin and Bmp signaling in the limb ectoderm. We suggest that the function of these factors links proximal-distal and dorsal-ventral patterning. PMID:25166858

  12. Analysis list: SP2 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SP2 Blood,Liver,Pluripotent stem cell + hg19 http://dbarchive.biosciencedbc.jp/kyus...hu-u/hg19/target/SP2.1.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/SP2.5.tsv http://dbarchive....biosciencedbc.jp/kyushu-u/hg19/target/SP2.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/SP2.Blood.tsv,http:...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/SP2.Liver.tsv,http:...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/SP2.Pluripotent_stem_cell.tsv http://dbarchive.biosciencedbc

  13. Biodegradation of resorcinol byPseudomonas sp.

    Institute of Scientific and Technical Information of China (English)

    Nader Hajizadeh; Najibeh Shirzad; Ali Farzi; Mojtaba Salouti; Azra Momeni

    2016-01-01

    ABSTRACT Objective:To investigate the ability ofPseudomonas sp. isolated from East Azarbaijan, Iran in bioremediation of resorcinol. Methods: Resorcinol biodegradation was evaluated using spectrophotometry and confirmed by gas chromatography-mass spectroscopy. Results:This isolate was able to remove up to 37.12% of resorcinol from contaminated water. Reusability experiments had confirmed the biodegradation process which produced seven intermediate compounds. These intermediates were characterized by gas chromatography-mass spectroscopy technique. The products of resorcinol biodegradation were apparently 1, 4-cyclohexadiene, nonadecene, 2-heptadecanone, 1-isopropyl-2-methoxy-4-methylbenzene, hexadecanoic acid, 9-octadecenoic acid, phenol and 5-methyl-2-(1-methylethyl). Conclusions: The findings revealed thatPseudomonas sp. is able to degrade resorcinol. Because of being an indigenous organism, this isolate is more compatible with the climate of the northwest region of Iran and possibly will be used for degradation of other similar aromatic compounds.

  14. SP-100 space reactor power system readiness

    International Nuclear Information System (INIS)

    Josloff, A.T.; Matteo, D.N.; Bailey, H.S.

    1992-01-01

    This paper discusses the SP-100 Space Reactor Power System which is being developed by GE, under contract to the U.S. Department of Energy, to provide electrical power in the range of 10's to 100's of kW. The system represents an enabling technology for a wide variety of earth orbital and interplanetary science missions, nuclear electric propulsion (NEP) stages, and lunar/Mars surface power for the Space Exploration Initiative (SEI). The technology and design is now at a state of readiness to support the definition of early flight demonstration missions. Of particular importance is that SP-100 meets the demanding U.S. safety performance, reliability and life requirements. The system is scalable and flexible and can be configured to provide 10's to 100's of kWe without repeating development work and can meet DoD goals for an early, low-power demonstration flight in the 1996-1997 time frame

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

    Science.gov (United States)

    Andersson, Maria; Lindh, Magnus

    2017-11-01

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

  16. Superfield quantization in Sp(2) covariant formalism

    CERN Document Server

    Lavrov, P M

    2001-01-01

    The rules of the superfield Sp(2) covariant quantization of the arbitrary gauge theories for the case of the introduction of the gauging with the derivative equations for the gauge functional are generalized. The possibilities of realization of the expanded anti-brackets are considered and it is shown, that only one of the realizations is compatible with the transformations of the expanded BRST-symmetry in the form of super translations along the Grassmann superspace coordinates

  17. Spøgelsets egne ord

    DEFF Research Database (Denmark)

    Gemzøe, Anker

    2012-01-01

    refleksioner over den gengangerscene, der åbner Shakespeares Hamlet. Ifølge Derridas ’hantologie’ opererer spøgelser i en eksistentiel tidslighed, der har at gøre med sorg, sprog og forvandling. Genremæssigt, tilføjer Gemzøe, har gengangeren det med at husere i tragedien. Med Derridas ’hantologie’ som en af de...

  18. Carbon sp chains in graphene nanoholes

    International Nuclear Information System (INIS)

    Castelli, Ivano E; Ferri, Nicola; Onida, Giovanni; Manini, Nicola

    2012-01-01

    Nowadays sp carbon chains terminated by graphene or graphitic-like carbon are synthesized routinely in several nanotech labs. We propose an ab initio study of such carbon-only materials, by computing their structure and stability, as well as their electronic, vibrational and magnetic properties. We adopt a fair compromise of microscopic realism with a certain level of idealization in the model configurations, and predict a number of properties susceptible to comparison with experiment. (paper)

  19. Carbon sp chains in graphene nanoholes

    Science.gov (United States)

    Castelli, Ivano E.; Ferri, Nicola; Onida, Giovanni; Manini, Nicola

    2012-03-01

    Nowadays sp carbon chains terminated by graphene or graphitic-like carbon are synthesized routinely in several nanotech labs. We propose an ab initio study of such carbon-only materials, by computing their structure and stability, as well as their electronic, vibrational and magnetic properties. We adopt a fair compromise of microscopic realism with a certain level of idealization in the model configurations, and predict a number of properties susceptible to comparison with experiment.

  20. Commercial technologies from the SP-100 program

    International Nuclear Information System (INIS)

    Truscello, V.C.; Fujita, T.; Mondt, J.F.

    1995-01-01

    For more than a decade, Jet Propulsion Labortory and Los Alamos have managed a multi-agency funded effort to develop a space reactor power system. This SP-100 Program has developed technologies required for space power systems that can be implemented in the industrial and commercial sectors to improve competitiveness in the global economy. Initial steps taken to transfer this technology from the laboratories to industrial and commercial entities within United States include: (1) identifying specific technologies having commercial potential; (2) distributing information describing the identified technologies and interacting with interested commercial and industrial entities to develop application-specific details and requirements; and (3) providing a technological data base that leads to transfer of technology or the forming of teaming arrangements to accomplish the transfer by tailoring the technology to meet application-specific requirements. SP-100 technologies having commercial potential encompass fabrication processes, devices, and components. Examples: a process for bonding refractory metals to graphite, a device to sense the position of an actuator and a component to enable rotating machines to operate without supplying lubrication (self-lubricating ball bearing). Shortly after the NASA Regional Technology Transfer Centers widely disseminated information covering SP-100 technologies, over one hundred expressions of interest were received, which indicate that there is a large potential benefit in transferring SP-100 technology. Interactions with industrial and commercial entities have identified a substantial need for creating teaming arrangements involving the interested entity and personnel from laboratories and their contractors, who have the knowledge and ability to tailor the technology to meet application-specific requirements. copyright 1995 American Institute of Physics

  1. Thermomucor abortosporangium sp. nov. (Fungi: Mucorales

    Directory of Open Access Journals (Sweden)

    A. Swathi Sri

    2012-03-01

    Full Text Available Thermomucor abortosporangium A. Swathi Sri & A. Subrahm., sp. nov. is described as the second species of Thermomucor. It differs from the type species of T. indicae-seudaticae in the branching pattern of sporangiophores, size and shape of sporangiospores and production of abortosporangia. Zygospores are reddish brown, globose, psilate, isogamic and formed at low (37°C temperature whilst the higher temperatures are prohibitive. The fungus grows well at 50°C on PDA, SMA and MEA.

  2. Genotyping of vacA alleles of Helicobacter pylori strains recovered ...

    African Journals Online (AJOL)

    commonly detected genotypes in the meat-based foods, viz, vegetable sandwich and ready to eat fish, were vacA ... Keywords: Helicobacter pylori, VacA genotypes, Genotyping, Food items ..... Microbiology and Quality Control, Islamic Azad.

  3. Development of A Mouse Model of Menopausal Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Elizabeth R. Smith

    2014-02-01

    Full Text Available Despite significant understanding of the genetic mutations involved in ovarian epithelial cancer and advances in genomic approaches for expression and mutation profiling of tumor tissues, several key questions in ovarian cancer biology remain enigmatic: the mechanism for the well-established impact of reproductive factors on ovarian cancer risk remains obscure; questions of the cell of origin of ovarian cancer continue to be debated; and the precursor lesion, sequence, or events in progression remain to be defined. Suitable mouse models should complement the analysis of human tumor tissues and may provide clues to these questions currently perplexing ovarian cancer biology.A potentially useful model is the germ cell-deficient Wv (white spotting variant mutant mouse line, which may be used to study the impact of menopausal physiology on the increased risk of ovarian cancer. The Wv mice harbor a point mutation in c-Kit that reduces the receptor tyrosine kinase activity to about 1-5% (it is not a null mutation. Homozygous Wv mutant females have a reduced ovarian germ cell reservoir at birth and the follicles are rapidly depleted upon reaching reproductive maturity, but other biological phenotypes are minimal and the mice have a normal life span. The loss of ovarian function precipitates changes in hormonal and metabolic activity that model features of menopause in humans. As a consequence of follicle depletion, the Wv ovaries develop ovarian tubular adenomas, a benign epithelial tumor corresponding to surface epithelial invaginations and papillomatosis that mark human ovarian aging. Ongoing work will test the possibility of converting the benign epithelial tubular adenomas into neoplastic tumors by addition of an oncogenic mutation, such as of Tp53, to model the genotype and biology of serous ovarian cancer.Model based on the Wv mice may have the potential to gain biological and etiological insights into ovarian cancer development and prevention.

  4. Robust and sensitive analysis of mouse knockout phenotypes.

    Directory of Open Access Journals (Sweden)

    Natasha A Karp

    Full Text Available A significant challenge of in-vivo studies is the identification of phenotypes with a method that is robust and reliable. The challenge arises from practical issues that lead to experimental designs which are not ideal. Breeding issues, particularly in the presence of fertility or fecundity problems, frequently lead to data being collected in multiple batches. This problem is acute in high throughput phenotyping programs. In addition, in a high throughput environment operational issues lead to controls not being measured on the same day as knockouts. We highlight how application of traditional methods, such as a Student's t-Test or a 2-way ANOVA, in these situations give flawed results and should not be used. We explore the use of mixed models using worked examples from Sanger Mouse Genome Project focusing on Dual-Energy X-Ray Absorptiometry data for the analysis of mouse knockout data and compare to a reference range approach. We show that mixed model analysis is more sensitive and less prone to artefacts allowing the discovery of subtle quantitative phenotypes essential for correlating a gene's function to human disease. We demonstrate how a mixed model approach has the additional advantage of being able to include covariates, such as body weight, to separate effect of genotype from these covariates. This is a particular issue in knockout studies, where body weight is a common phenotype and will enhance the precision of assigning phenotypes and the subsequent selection of lines for secondary phenotyping. The use of mixed models with in-vivo studies has value not only in improving the quality and sensitivity of the data analysis but also ethically as a method suitable for small batches which reduces the breeding burden of a colony. This will reduce the use of animals, increase throughput, and decrease cost whilst improving the quality and depth of knowledge gained.

  5. A Naturally Fluorescent Mgp Transgenic Mouse for Angiogenesis and Glaucoma Longitudinal Studies.

    Science.gov (United States)

    Asokan, Priyadarsini; Mitra, Rajendra N; Periasamy, Ramesh; Han, Zongchao; Borrás, Teresa

    2018-02-01

    Our goal was to generate and characterize a new mouse model in which only angiogenesis- and glaucoma-relevant tissues would be naturally fluorescent. The Matrix Gla (MGP) gene is highly expressed in vascular smooth muscle cells (VSMC) and trabecular meshwork (TM). We sought to direct our Mgp-Cre.KI mouse recombinase to VSMC/TM cells to produce their longitudinal fluorescent profiles. Homozygous Mgp-Cre.KI mice were crossed with Ai9 homozygous reporter mice harboring a loxP-flanked STOP cassette preventing transcription of a DsRed fluorescent protein (tdTomato). The F1 double-heterozygous (Mgp-tdTomato) was examined by direct fluorescence, whole mount, histology, and fundus photography. Custom-made filters had 554/23 emission and 609/54 exciter nanometer wavelengths. Proof of concept of the model's usefulness was conducted by inducing guided imaging laser burns. Evaluation of a vessel's leakage and proliferation was followed by noninvasive angiography. The Mgp-tdTomato mouse was viable, fertile, with normal IOP and ERG. Its phenotype exhibited red paws and snout (cartilage expression), which precluded genotyping. A fluorescent red ring was seen at the limbus and confirmed to be TM expression by histology. The entire retinal vasculature was red fluorescent (VSMC) and directly visualized by fundus photography. Laser burns on the Mgp-tdTomato allowed separation of leakiness and neovascularization evaluation parameters. The availability of a transgenic mouse naturally fluorescent in glaucoma-relevant tissues and retinal vasculature brings the unique opportunity to study a wide spectrum of single and combined glaucomatous conditions in vivo. Moreover, the Mgp-tdTomato mouse provides a new tool to study mechanisms and therapeutics of retinal angiogenesis longitudinally.

  6. A Naturally Fluorescent Mgp Transgenic Mouse for Angiogenesis and Glaucoma Longitudinal Studies

    Science.gov (United States)

    Asokan, Priyadarsini; Mitra, Rajendra N.; Periasamy, Ramesh; Han, Zongchao

    2018-01-01

    Purpose Our goal was to generate and characterize a new mouse model in which only angiogenesis- and glaucoma-relevant tissues would be naturally fluorescent. The Matrix Gla (MGP) gene is highly expressed in vascular smooth muscle cells (VSMC) and trabecular meshwork (TM). We sought to direct our Mgp-Cre.KI mouse recombinase to VSMC/TM cells to produce their longitudinal fluorescent profiles. Methods Homozygous Mgp-Cre.KI mice were crossed with Ai9 homozygous reporter mice harboring a loxP-flanked STOP cassette preventing transcription of a DsRed fluorescent protein (tdTomato). The F1 double-heterozygous (Mgp-tdTomato) was examined by direct fluorescence, whole mount, histology, and fundus photography. Custom-made filters had 554/23 emission and 609/54 exciter nanometer wavelengths. Proof of concept of the model's usefulness was conducted by inducing guided imaging laser burns. Evaluation of a vessel's leakage and proliferation was followed by noninvasive angiography. Results The Mgp-tdTomato mouse was viable, fertile, with normal IOP and ERG. Its phenotype exhibited red paws and snout (cartilage expression), which precluded genotyping. A fluorescent red ring was seen at the limbus and confirmed to be TM expression by histology. The entire retinal vasculature was red fluorescent (VSMC) and directly visualized by fundus photography. Laser burns on the Mgp-tdTomato allowed separation of leakiness and neovascularization evaluation parameters. Conclusions The availability of a transgenic mouse naturally fluorescent in glaucoma-relevant tissues and retinal vasculature brings the unique opportunity to study a wide spectrum of single and combined glaucomatous conditions in vivo. Moreover, the Mgp-tdTomato mouse provides a new tool to study mechanisms and therapeutics of retinal angiogenesis longitudinally. PMID:29392320

  7. Genetic Dissection of Trabecular Bone Structure with Mouse Intersubspecific Consomic Strains

    Directory of Open Access Journals (Sweden)

    Taro Kataoka

    2017-10-01

    Full Text Available Trabecular bone structure has an important influence on bone strength, but little is known about its genetic regulation. To elucidate the genetic factor(s regulating trabecular bone structure, we compared the trabecular bone structures of two genetically remote mouse strains, C57BL/6J and Japanese wild mouse-derived MSM/Ms. Phenotyping by X-ray micro-CT revealed that MSM/Ms has structurally more fragile trabecular bone than C57BL/6J. Toward identification of genetic determinants for the difference in fragility of trabecular bone between the two mouse strains, we employed phenotype screening of consomic mouse strains in which each C57BL/6J chromosome is substituted by its counterpart from MSM/Ms. The results showed that many chromosomes affect trabecular bone structure, and that the consomic strain B6-Chr15MSM, carrying MSM/Ms-derived chromosome 15 (Chr15, has the lowest values for the parameters BV/TV, Tb.N, and Conn.D, and the highest values for the parameters Tb.Sp and SMI. Subsequent phenotyping of subconsomic strains for Chr15 mapped four novel trabecular bone structure-related QTL (Tbsq1-4 on mouse Chr15. These results collectively indicate that genetic regulation of trabecular bone structure is highly complex, and that even in the single Chr15, the combined action of the four Tbsqs controls the fragility of trabecular bone. Given that Tbsq4 is syntenic to human Chr 12q12-13.3, where several bone-related SNPs are assigned, further study of Tbsq4 should facilitate our understanding of the genetic regulation of bone formation in humans.

  8. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  9. 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. © 2014 The Author(s).

  10. Take care of your mouse!

    CERN Multimedia

    IT Department

    2011-01-01

    “Stop --- Think --- Click" is the basic recommendation for securely browsing the Internet and for securely reading e-mails. Users who have followed this recommendation in the past were less likely to have their computer infected or their computing account compromised. We would like to thank all those who donated their mouse to the CERN Animal Shelter for Computer Mice (http://cern.ch/c-a-s). For those who still use a mouse, please stay vigilant and  alert: do not click on links whose origin you do not trust or which look like gibberish. Do not install untrusted software or plug-ins, since software from untrusted sources may infect or compromise your computer, or violate copyrights. Finally, take particular care with e-mails: Do not open unexpected or suspicious e-mails or attachments. Delete them if they do not concern you or if they appear strange. If in doubt, or if you have questions, please do not hesitate to contact Computer.Security@cern.ch

  11. Optimization of cellulase production by Penicillium sp.

    Science.gov (United States)

    Prasanna, H N; Ramanjaneyulu, G; Rajasekhar Reddy, B

    2016-12-01

    The production of cellulolytic enzymes (β-exoglucanase, β-endoglucanase and β-glucosidase) by Penicillium sp. on three different media in liquid shake culture conditions was compared. The organism exhibited relatively highest activity of endoglucanase among three enzymes measured at 7-day interval during the course of its growth on Czapek-Dox medium supplemented with 0.5 % (w/v) cellulose. Cellulose at 0.5 %, lactose at 0.5 %, sawdust at 0.5 %, yeast extract at 0.2 % as a nitrogen source, pH 5.0 and 30 °C temperature were found to be optimal for growth and cellulase production by Penicillium sp. Yields of Fpase, CMCase and β-glucosidase, attained on optimized medium with Penicillium sp. were 8.7, 25 and 9.52 U/ml, respectively with increment of 9.2, 5.9 and 43.8-folds over titers of the respective enzyme on unoptimised medium. Cellulase of the fungal culture with the ratio of β-glucosidase to Fpase greater than one will hold potential for biotechnological applications.

  12. Biosorption of 241Am by Candida sp

    International Nuclear Information System (INIS)

    Luo Shunzhong; Zhang Taiming; Liu Ning; Yang Yuanyou; Jin Jiannan; Hua Xinfeng

    2003-01-01

    The biosorption of radionuclide 241 Am from solutions by Candida sp., and the influences of experimental conditions on the adsorption were studied. The results showed that the adsorption equilibrium was achieved within 4h and the optimum pH=2. No significant differences on 241 Am biosorption were observed at 10-45 degree C, or challenged with Au 3+ or Ag + , even 1500 times or 4500 times over 241 Am, respectively. The adsorption rate could reach 97.8% by dry Candida sp. of 0.82 g/L in 241 Am solutions (pH=2) of 5.6-111 MBq/L (44.04-873.0 μg/L) (C 0 ), with maximum adsorption capacity (W) of 63.5 MBq/g (501.8 μg/g), implying that the removal of 241 Am by Candida sp. from solutions was feasible. The relationship between activities (C 0 ) and adsorption capacities (W) of 241 Am indicated that the biosorption process could be described by Langmuir adsorption isotherm

  13. Biosorption of americium-241 by Candida sp

    International Nuclear Information System (INIS)

    Luo Shunzhong; Zhang Taiming; Liu Ning; Yang Yuanyou; Jin Jiannan; Liao Jiali

    2003-01-01

    As an important radioisotope in nuclear industry and other fields, americium-241 is one of the most serious contamination concerns duo to its high toxicity and long half-life. In this experiment, the biosorption of 241 Am from solution by Candida sp., and the effects of various experimental conditions on the adsorption were investigated. The preliminary results showed that the adsorption of 241 Am by Candida sp. was efficient. 241 Am could be removed by Candida sp. of 0.82 g/L (dry weight) from 241 Am solutions of 5.6-111 MBq/L (44.3-877.2 μg/L)(C 0 ), with maximum adsorption rate (R) of 98% and maximum adsorption capacities (W) of 63.5 MBq/g biomass (dry weight) (501.8 μg/g). The biosorption equilibrium was achieved within 4 hour and the optimum pH was pH = 2. No significant differences on 241 Am adsorption were observed at 10 C-45 C, or in solutions containing Au 3+ or Ag + , even 1500 times or 4500 times above the 241 Am concentration, respectively. The relationship between concentrations and adsorption capacities of 241 Am indicated the biosorption process should be described by a Langmuir adsorption isotherm. (orig.)

  14. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Rafaela Morando

    2015-06-01

    Full Text Available The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens. Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green, in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were performed for oviposition in a greenhouse, besides tests for attractiveness and consumption under laboratory conditions (26±2ºC, 65±10% RH, and 14 h light: 10 h dark photophase. In the no-choice test with adults, in the greenhouse, the 'IAC Jabola', Arcelina 1, 'IAC Boreal', 'Flor de Mayo', and 'IAC Formoso' genotypes were the least oviposited, showing antixenosis-type resistance for oviposition. In the free-choice test with larvae, Arcelina 4, 'BRS Horizonte', 'Pérola', H96A102-1-1-1-52, 'IAC Boreal', 'IAC Harmonia', and 'IAC Formoso' were the less consumed genotypes, which indicates antixenosis to feeding. In the no-choice test, all genotypes (except for 'IAPAR 57' expressed moderate levels of antixenosis to feeding against C. includens larvae.

  15. 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

  16. Assessing accuracy of genotype imputation in American Indians.

    Directory of Open Access Journals (Sweden)

    Alka Malhotra

    Full Text Available Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome. The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.

  17. Genetic similarity of soybean genotypes revealed by seed protein

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2005-01-01

    Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

  18. Mouse allergen exposure and immunologic responses: IgE-mediated mouse sensitization and mouse specific IgG and IgG4 levels

    NARCIS (Netherlands)

    Matsui, Elizabeth C.; Krop, Esmeralda J. M.; Diette, Gregory B.; Aalberse, Rob C.; Smith, Abigail L.; Eggleston, Peyton A.

    2004-01-01

    Although there is evidence that contact with mice is associated with IgE-mediated mouse sensitization and mouse specific antibody responses, the exposure-response relationships remain unclear. To determine whether IgE-mediated mouse sensitization and mouse specific IgG (mIgG) and mIgG4 levels

  19. Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles.

    Science.gov (United States)

    Margos, Gabriele; Lane, Robert S; Fedorova, Natalia; Koloczek, Johannes; Piesman, Joseph; Hojgaard, Andrias; Sing, Andreas; Fingerle, Volker

    2016-03-01

    Two species of the genus Borrelia , Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov., were first described by Postic and co-workers on the basis of genetic analyses of several loci. Multilocus sequence analysis of eight housekeeping loci confirmed that these two Borrelia genomospecies are distinct members of the Borrelia burgdorferi sensu lato complex. B. bissettiae sp. nov. was initially described in transmission cycles involving Neotoma fuscipes wood rats and Ixodes pacificus ticks in California, and Neotoma mexicana and Ixodes spinipalpis in Colorado. The preferred host of B. californiensis sp. nov. appears to be the California kangaroo rat, Dipodomys californicus ; Ixodes jellisoni , I. spinipalipis and I. pacificus ticks are naturally infected with it. Thus, the ecological associations of the two genomospecies and their genetic distance from all other known Borrelia genomospecies species justify their description as separate genomospecies: B. bissettiae sp. nov. (type strain DN127 T  = DSM 17990 T  =  CIP 109136 T ) and B. californiensis (type strain CA446 T  = DSM 17989 T  = ATCC BAA-2689 T ).

  20. Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp

    Science.gov (United States)

    Viegelmann, Christina; Margassery, Lekha Menon; Kennedy, Jonathan; Zhang, Tong; O’Brien, Ciarán; O’Gara, Fergal; Morrissey, John P.; Dobson, Alan D. W.; Edrada-Ebel, RuAngelie

    2014-01-01

    Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8) isolated from the sponge Haliclona simulans from Irish waters. Streptomyces strain SM8 extracts showed antibacterial and antifungal activity. NMR analysis of the active fractions proved that hydroxylated saturated fatty acids were the major components present in the antibacterial fractions. Antimycin compounds were initially putatively identified in the antifungal fractions using LC-Orbitrap. Their presence was later confirmed by comparison to a standard. Genomic analysis of Streptomyces sp. SM8 revealed the presence of multiple secondary metabolism gene clusters, including a gene cluster for the biosynthesis of the antifungal antimycin family of compounds. The antimycin gene cluster of Streptomyces sp. SM8 was inactivated by disruption of the antimycin biosynthesis gene antC. Extracts from this mutant strain showed loss of antimycin production and significantly less antifungal activity than the wild-type strain. Three butenolides, 4,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (1), 4,11-dihydroxy-10-methyl-dodec-2-en-1,4-olide (2), and 4-hydroxy-10-methyl-11-oxo-dodec-2-en-1,4-olide (3) that had previously been reported from marine Streptomyces species were also isolated from SM8. Comparison of the extracts of Streptomyces strain SM8 and its host sponge, H. simulans, using LC-Orbitrap revealed the presence of metabolites common to both extracts, providing direct evidence linking sponge metabolites to a specific microbial symbiont. PMID:24893324

  1. Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp.

    Directory of Open Access Journals (Sweden)

    Christina Viegelmann

    2014-06-01

    Full Text Available Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8 isolated from the sponge Haliclona simulans from Irish waters. Streptomyces strain SM8 extracts showed antibacterial and antifungal activity. NMR analysis of the active fractions proved that hydroxylated saturated fatty acids were the major components present in the antibacterial fractions. Antimycin compounds were initially putatively identified in the antifungal fractions using LC-Orbitrap. Their presence was later confirmed by comparison to a standard. Genomic analysis of Streptomyces sp. SM8 revealed the presence of multiple secondary metabolism gene clusters, including a gene cluster for the biosynthesis of the antifungal antimycin family of compounds. The antimycin gene cluster of Streptomyces sp. SM8 was inactivated by disruption of the antimycin biosynthesis gene antC. Extracts from this mutant strain showed loss of antimycin production and significantly less antifungal activity than the wild-type strain. Three butenolides, 4,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (1, 4,11-dihydroxy-10-methyl-dodec-2-en-1,4-olide (2, and 4-hydroxy-10-methyl-11-oxo-dodec-2-en-1,4-olide (3 that had previously been reported from marine Streptomyces species were also isolated from SM8. Comparison of the extracts of Streptomyces strain SM8 and its host sponge, H. simulans, using LC-Orbitrap revealed the presence of metabolites common to both extracts, providing direct evidence linking sponge metabolites to a specific microbial symbiont.

  2. The wobbler mouse, an ALS animal model

    DEFF Research Database (Denmark)

    Moser, Jakob Maximilian; Bigini, Paolo; Schmitt-John, Thomas

    2013-01-01

    This review article is focused on the research progress made utilizing the wobbler mouse as animal model for human motor neuron diseases, especially the amyotrophic lateral sclerosis (ALS). The wobbler mouse develops progressive degeneration of upper and lower motor neurons and shows striking...

  3. Mouse adenovirus type 1 infection of macrophages

    NARCIS (Netherlands)

    Ashley, S.L.; Welton, A.R.; Harwood, K.M.; Rooijen, van N.; Spindler, K.R.

    2009-01-01

    Mouse adenovirus type 1 (MAV-1) causes acute and persistent infections in mice, with high levels of virus found in the brain, spinal cord and spleen in acute infections. MAV-1 infects endothelial cells throughout the mouse, and monocytes/macrophages have also been implicated as targets of the virus.

  4. MMP-8 genotypes influence the inflammatory response in human endotoxemia.

    Science.gov (United States)

    Rella, Judith M; Jilma, Bernd; Fabry, Astrid; Kaynar, A Murat; Mayr, Florian B

    2014-04-01

    Clinical studies have reported associations between MMP-8 genotypes and clinical outcomes without exploring underlying mechanisms. This study aims to understand the influence of the rs1940475 SNP on downstream chemokine and cytokine response in human endotoxemia. Rs1940475 was genotyped in 44 healthy Caucasian males, who were challenged with an intravenous bolus of 2 ng/kg lipopolysaccharide (LPS). Plasma levels of tumor necrosis factor (TNF), interleukin (IL)-6, IL-8, and macrophage inflammatory protein (MIP)-1α were measured at baseline and 2, 4, 6, and 24 h after LPS infusion with high-sensitivity enzyme immunoassays. Peak TNF levels at 2 h after LPS infusion were significantly higher in subjects with AA genotype compared to subjects with AG or GG genotypes (185 pg/mL [IQR, 154-234] vs. 94 pg/mL [IQR, 65-125] vs. 107 pg/mL [IQR, 80-241], respectively; p = 0.03 between groups). Peak IL-6 levels were trend-wise higher in subjects with AA genotype compared to those with AG or GG genotypes (566 pg/mL [IQR, 294-644] vs. 278 pg/mL [IQR, 184-539] and 329 pg/mL [IQR, 240-492], respectively; p = 0.15 between groups). In contrast, peak MIP-1α at 2 h was highest in GG genotype carriers compared to those with AG or AA genotypes (602 pg/mL [IQR, 449-727] vs. 389 pg/mL [IQR, 375-490] and 510 pg/mL [425-813], respectively; p < 0.03 between groups). AA genotype carriers had highest peak TNF and IL-6 levels after LPS challenge, whereas peak MIP-1α levels were highest in GG carriers. This indicates that the rs1940475 SNP modifies the host response to inflammatory stimuli, which may in part explain previously shown associations with clinical outcomes.

  5. EFEKTIFITAS DAYA HAMBAT BAKTERI Streptomyces sp TERHADAP Erwinia sp PENYEBAB PENYAKIT BUSUK REBAH PADA TANAMAN LIDAH BUAYA (Aloe barbadensis Mill

    Directory of Open Access Journals (Sweden)

    SARMILA TASNIM

    2013-05-01

    Full Text Available Streptomyces sp was conducted from December 2010 - June 2011 at the Laboratoryof Microbiology, Biology Department, Math and Science Faculty, UdayanaUniversity Bukit Jimbaran-Bali. Implementation stages of the research consisted ofisolation and testing of the antibiotic activity Streptomyces sp to inhibit growthbacterial pathogens Erwinia sp as a cause of disease in plants fallen foul (Soft rot ofAloe barbadensis Mill.The results of this study have eight isolates of Streptomyces spwith macroscopic and microscopic characters are varied. Furthermore, all isolateswere obtained and then tested against antibiotic activity to inhibit growth the bacteriaErwinia sp. Test results obtained by Streptomyces sp that has the most effective ininhibiting the ability of the bacteria Erwinia sp isolates are Streptomyces sp2for (45%.

  6. 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.

  7. Evaluation of Soybean and Cowpea Genotypes for Phosphorus Use Efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Kumaga, F. K.; Ofori, K.; Adiku, S. K.; Kugblenu, Y. O.; Asante, W.; Seidu, H. [College of Agriculture and Consumer Sciences, University of Ghana, Legon, Accra (Ghana); Adu-Gyamfi, J. J. [Soil and Water Management and Crop Nutrition Laboratory, International Atomic Energy Agency, Vienna (Austria)

    2013-11-15

    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

  8. Phenotypic and Genotypic Characterization of Indigenous Lactobacillus Community from Traditional Istrian Ewe's Cheese

    Directory of Open Access Journals (Sweden)

    Mirna Mrkonjić Fuka

    2012-01-01

    Full Text Available The objective of this study is to describe the diversity of indigenous cultivable community of the lactobacilli associated with the production of traditional Istrian cheese and to get a collection of well characterized strains. Raw milk and cheese samples were collected from three different farms in Istria during ripening. A total of 212 mesophilic and thermophilic Lactobacillus isolates as well as bulk colonies (consortia were investigated using culture-dependent approach combining phenotyping and genotyping. Biochemical fingerprinting with PhenePlate-LB system preliminary grouped 212 isolates in 16 distinct PhP types. Only one representative isolate from each PhP cluster was further analyzed by genotyping for a reliable identification at the genus and species level by employing PCR techniques and sequencing of 16S rRNA genes. Sequence analysis of 16S rRNA revealed the presence of Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus. Lactobacilli were screened for possible resistance against seven selected antibiotics: ampicillin, tetracycline, penicillin, rifampin, clindamycin, erythromycin and vancomycin. Although there was no clear pattern of antimicrobial susceptibility to most tested antibiotics, all representative isolates were resistant to vancomycin. The analysis of bulk colonies by denaturing gradient gel electrophoresis (DGGE identified Lactobacillus plantarum and Lactobacillus brevis as predominant members of Lactobacillus population. Pediococcus pentosaceus, Pediococcus acidilactici, Streptococcus sp. and Leuconostoc mesenteroides were also detected as part of the analysed consortia. The prevalence of identified species and community members of lactobacilli agrees with other studies of raw milk cheese and represents a useful base for further selection.

  9. Nanoscale transformation of sp2 to sp3 of graphite by slow highly charged ion irradiation

    International Nuclear Information System (INIS)

    Meguro, T.; Hida, A.; Koguchi, Y.; Miyamoto, S.; Yamamoto, Y.; Takai, H.; Maeda, K.; Aoyagi, Y.

    2003-01-01

    Nanoscale transformation of electronic states by highly charged ion (HCI) impact on graphite surfaces is described. The high potential energy of slow HCI, which induces multiple emission of electrons from the surface, provides a strong modification of the electronic states of the local area upon graphite surfaces. The HCI impact and the subsequent surface treatment either by electron injection from a scanning tunneling microscopy tip or by He-Cd laser irradiation induce a localized transition from sp 2 to sp 3 hybridization in graphite, resulting in the formation of nanoscale diamond-like structures (nanodiamond) at the impact region. From Raman spectroscopic measurements on sp 2 related peaks, it is found that the HCI irradiation creates vacancy complexes in contrast to ions having a lower charge state, which generate single vacancies. It is of interest that a single impact of HCI creates one nanodiamond structure, suggesting potential applications of HCI in nanoscale material processing

  10. Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil.

    Science.gov (United States)

    Lee, Jae-Chan; Whang, Kyung-Sook

    2015-09-01

    Strains Y-12(T) and Y-47(T) were isolated from mountain forest soil and strain WR43(T) was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10-55 °C (optimal growth at 28-30 °C), at pH 3.0-8.0 (optimal growth at pH 6.0) and in the presence of 0-4.0% (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7%); the similarity between the three sequences ranged from 98.3 to 98.7%. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17  : 0 cyclo and the DNA G+C content of the novel isolates was 61.6-64.4 mol%. DNA-DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50%. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12(T)= KACC 17601(T) = NBRC 109933(T) = NCAIM B 02543(T)), Burkholderia solisilvae sp. nov. (type strain Y-47(T) = KACC 17602(T)= NBRC 109934(T) = NCAIM B 02539(T)) and Burkholderia rhizosphaerae sp. nov. (type strain WR43(T) = KACC 17603(T) = NBRC 109935(T) = NCAIM B 02541(T)) are proposed.

  11. SEE locomotor behavior test discriminates C57BL/6J and DBA/2J mouse inbred strains across laboratories and protocol conditions.

    Science.gov (United States)

    Kafkafi, Neri; Lipkind, Dina; Benjamini, Yoav; Mayo, Cheryl L; Elmer, Gregory I; Golani, Ilan

    2003-06-01

    Conventional tests of behavioral phenotyping frequently have difficulties differentiating certain genotypes and replicating these differences across laboratories and protocol conditions. This study explores the hypothesis that automated tests can be designed to quantify ethologically relevant behavior patterns that more readily characterize heritable and replicable phenotypes. It used SEE (Strategy for the Exploration of Exploration) to phenotype the locomotor behavior of the C57BL/6 and DBA/2 mouse inbred strains across 3 laboratories. The 2 genotypes differed in 15 different measures of behavior, none of which had a significant genotype-laboratory interaction. Within the same laboratory, most of these differences were replicated in additional experiments despite the test photoperiod phase being changed and saline being injected. Results suggest that well-designed tests may considerably enhance replicability across laboratories.

  12. Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).

    Science.gov (United States)

    Endo, Akihito; Futagawa-Endo, Yuka; Schumann, Peter; Pukall, Rüdiger; Dicks, Leon M T

    2012-03-01

    Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3 mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity. Based on the data provided, the five isolates represent five novel species, for which the names Bifidobacterium reuteri sp. nov. (type strain: AFB22-1(T) = JCM 17295(T) = DSM 23975(T)), Bifidobacterium callitrichos sp. nov. (type strain: AFB22-5(T) = JCM 17296(T) = DSM 23973(T)), Bifidobacterium saguini sp. nov. (type strain: AFB23-1(T) = JCM 17297(T) = DSM 23967(T)), Bifidobacterium stellenboschense sp. nov. (type strain: AFB23-3(T) = JCM 17298(T) = DSM 23968(T)) and Bifidobacterium biavatii sp. nov. (type strain: AFB23-4(T) = JCM 17299(T) = DSM 23969(T)) are proposed. Copyright © 2011 Elsevier GmbH. All rights reserved.

  13. Fermentation of Azolla sp. leaves and the utilization as a feed ingredient of tilapia Oreochromis sp.

    Directory of Open Access Journals (Sweden)

    Nur Bambang Priyo Utomo

    2015-03-01

    Full Text Available ABSTRACTThe objective of this study was to study the effect of incubation period on the nutritional content of Azolla sp. meal fermented by Trichoderma harzianum, and its optimum supplementation level in the feed of tilapia Oreochromis sp. In incubation period treatments, fermentation of Azolla meal was performed in two, six, eight, and ten days (AF2, AF6, AF8, AF10 using Trichoderma harzianum as the fermentor. The fish used in this study was tilapia Oreochromis sp. with an average weight of 10.59±1.29 g. The design of the feeding treatments was repeletting commercial feed with Azolla leaves by with different supplementation levels, i.e. 0% (A/control, 30% (B, 60% (C, and 90% (D. Faecal collection for digestibility measurement was conducted for 15 days and fish growth rate was observed for 40 days. Azolla meal fermented for two days (AF2 showed the best results among the other treatments with a crude fiber decrease of 37.19% and protein increase of 38.65%. The results of this study indicate that fermentation can increase the nutritional quality of Azolla meal and its most optimal supplementation level in the diet of tilapia is 30%.Keywords: crude fiber, Azolla sp., tilapiaABSTRAKPenelitian ini bertujuan untuk mengetahui pengaruh lama waktu fermentasi daun mata lele Azolla sp. menggunakan kapang Trichoderma harzianum serta dosis optimal dalam pakan ikan nila Oreochromis sp. Proses fermentasi tepung daun mata lele dilakukan selama dua, enam, delapan, dan sepuluh hari (AF2, AF6, AF8, AF10. Ikan uji pada penelitian ini menggunakan ikan nila Oreochromis sp. dengan bobot rata-rata 10,59±1,29 g yang ditebar sebanyak 6 ekor/akuarium berukuran 50×45×30 cm3. Sebagai pakan perlakuan yakni repeletting daun mata lele dengan pakan komersil pada tingkat suplementasi 0% (A/kontrol, 30% (B, 60% (C, dan 90% (D. Pemeliharaan ikan uji dan pengumpulan data dilakukan dengan mengumpulkan feses ikan untuk uji ketercernaan selama 15 hari dan mengamati pertumbuhan

  14. Isolation of C11 Cyclopentenones from Two Didemnid Species, Lissoclinum sp. and Diplosoma sp.

    Directory of Open Access Journals (Sweden)

    Katsuhiro Ueda

    2009-12-01

    Full Text Available A series of new C11 cyclopentenones 1-7 was isolated, together with four known metabolites 9/10, 12 and 13, from the extract of the didemnid ascidian Lissoclinum sp. The other didemnid ascidian Diplosoma sp. contained didemnenones 1, 2 and 5, and five known metabolites 8-12. The structures of 1-7 were elucidated by spectroscopic analyses. Cytotoxicity of the isolated compounds was evaluated against three human cancer cell lines (HCT116, A431 and A549.

  15. Interspecific variation in anthocyanins, phenolics, and antioxidant capacity among genotypes of highbush and lowbush blueberries (Vaccinium section cyanococcus spp.).

    Science.gov (United States)

    Kalt, W; Ryan, D A; Duy, J C; Prior, R L; Ehlenfeldt, M K; Vander Kloet, S P

    2001-10-01

    Recent interest in the possible protective effects of dietary antioxidant compounds against human degenerative disease has prompted investigation of foods such as blueberries (Vaccinium sp.), which have a high antioxidant capacity. Fruit obtained from genotypes of highbush blueberries (Vaccinium corymbosum L.) and lowbush blueberries (Vaccinium angustifolium Aiton) were analyzed for their antioxidant capacity, their content of anthocyanins, and total phenolic compounds, to evaluate the intraspecific and interspecific variation in these parameters. The method of extraction influenced the composition of fruit extracts; the highest anthocyanin and total phenolic contents and antioxidant capacity were found in extracts obtained using a solvent of acidified aqueous methanol. Regardless of the method, lowbush blueberries were consistently higher in anthocyanins, total phenolics, and antioxidant capacity, compared with highbush blueberries. There was no relationship between fruit size and anthocyanin content in either species.

  16. Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum genotypes

    Directory of Open Access Journals (Sweden)

    Pingchuan Li

    2017-12-01

    Full Text Available Crested wheatgrass [Agropyron cristatum L. (Gaertn.] is an important cool-season forage grass widely used for early spring grazing. However, the genomic resources for this non-model plant are still lacking. Our goal was to generate the first set of next generation sequencing data using the genotyping-by-sequencing technique. A total of 272 crested wheatgrass plants representing seven breeding lines, five cultivars and five geographically diverse accessions were sequenced with an Illumina MiSeq instrument. These sequence datasets were processed using different bioinformatics tools to generate contigs for diploid and tetraploid plants and SNPs for diploid plants. Together, these genomic resources form a fundamental basis for genomic studies of crested wheatgrass and other wheatgrass species. The raw reads were deposited into Sequence Read Archive (SRA database under NCBI accession SRP115373 (https://www.ncbi.nlm.nih.gov/sra?term=SRP115373 and the supplementary datasets are accessible in Figshare (10.6084/m9.figshare.5345092. Keywords: Crested wheatgrass, Genotyping-by-sequencing, Diploid, Tetraploid, Raw sequence data

  17. 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

    2016-01-01

    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

  18. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

    Directory of Open Access Journals (Sweden)

    Katy Denise Heath

    2014-04-01

    Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

  19. Radiosensitivity of mouse germ cells

    International Nuclear Information System (INIS)

    Matsuda, Yoichi; Takeuchi, Toyoko; Maemori, Mamiko; Seki, Naohiko; Tobari, Izuo

    1991-01-01

    To estimate radiosensitivity of mouse germ cells the analysis of chromosome aberrations was performed at diakinesis-metaphase I of spermatocytes and first-cleavage metaphase of one-cell embryos after exposure to radiations at various stages of primary spermatocytes and spermatids. The result provided evidence that there are two major types of DNA damage in X-irradiated sperm : (1) short-lived DNA lesions ; the lesions are subject to repair inhibition by agents added in G 1 , and are converted into chromosome-type aberrations during G 1 , and (2) long-lived DNA lesions ; the lesions persist until S phase and repair of the lesions is inhibited by caffeine, hydroxyurea and arabinofuranosyl cytosine in G 2 . The characteristic of X-ray damage induced in spermiogenic stage and repair mechanism for the damage in the fertilized egg were discussed comparing with the results with two chemicals, methyl methanesulfonate (MMS) and mitomycin C (MMC). (J.P.N.)

  20. Analysis of the genetic diversity of four rabbit genotypes using ...

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

    May 15, 2013 ... consumption and low cost, it has been widely utilized in genetics analysis in ... isozyme variation among the selected individuals within each rabbit genotype. ... with different embryo survival (Bolet and Theau-Clement, 1994).

  1. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    etc

    2015-05-06

    . Combined analysis of variance (ANOVA) for yield and yield components revealed highly significant .... yield stability among varieties, multi-location trials with ... Mean grain yield (kg/ha) of 17 Kabuli-type chickpea genotypes ...

  2. Sofosbuvir based treatment of chronic hepatitis C genotype 3 infections

    DEFF Research Database (Denmark)

    Dalgard, Olav; Weiland, Ola; Noraberg, Geir

    2017-01-01

    BACKGROUND AND AIMS: Chronic hepatitis C virus (HCV) genotype 3 infection with advanced liver disease has emerged as the most challenging to treat. We retrospectively assessed the treatment outcome of sofosbuvir (SOF) based regimes for treatment of HCV genotype 3 infections in a real life setting...... in Scandinavia. METHODS: Consecutive patients with chronic HCV genotype 3 infection were enrolled at 16 treatment centers in Denmark, Sweden, Norway and Finland. Patients who had received a SOF containing regimen were included. The fibrosis stage was evaluated by liver biopsy or transient liver elastography...... was similar for all treatment regimens, but lower in men (p = 0.042), and in patients with decompensated liver disease (p = 0.004). CONCLUSION: We found that sofosbuvir based treatment in a real-life setting could offer SVR rates exceeding 90% in patients with HCV genotype 3 infection and advanced liver...

  3. Evaluation of 14 winter bread wheat genotypes in normal irrigation ...

    African Journals Online (AJOL)

    Evaluation of 14 winter bread wheat genotypes in normal irrigation and stress conditions after anthesis stage. ... African Journal of Biotechnology ... Using biplot graphic method, comparison of indices amounts and mean rating of indices for ...

  4. adaptation of introduced mungbean genotypes in uganda abstract

    African Journals Online (AJOL)

    ACSS

    locations in Uganda, to determine the adaptability of introduced mungbean genotypes, and identify ... The six test multi-locations were grouped into two candidate mega-environments for ..... interactions: Challenges and opportunities for.

  5. cyanide cassava genotypes in acid ultisols of south eastern Nigeria

    African Journals Online (AJOL)

    ENGR C.J

    2014-01-29

    Jan 29, 2014 ... Thirty-eight high and low cyanide cassava genotypes were evaluated for growth and .... sium (K) and sodium (Na) were determined by Flamephoto-metory .... outlined for randomized complete block design (Steel et al., 1997).

  6. 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.

  7. Effects of nutritional supplementation and genotype on milk ...

    African Journals Online (AJOL)

    Effects of nutritional supplementation and genotype on milk production and fertility of lactating dairy ... Bulletin of Animal Health and Production in Africa ... The objective of this study was to determine effects of nutrition on milk production and ...

  8. Effects of genotype x bradyrhizobium inoculation or x fertilizer n ...

    African Journals Online (AJOL)

    Genotype x inoculation interaction was significant only for protein and oil content in one year. .... main-plot factor. ... components and expected genetic gains invoiving yield srrnin. ... Combined analysis of the cu ltivar experiment was carried.

  9. 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.

  10. 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.

  11. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    uvp

    2014-08-24

    Aug 24, 2014 ... Genotype x environment interaction (G x E) in dairy cattle is a contentious ... environments, if it exists, with a negative impact on genetic response ..... interaction for Holstein milk yield in Colombia, Mexico and Puerto Rico.

  12. Giardia and Cryptosporidium species and genotypes in coyotes (Canis latrans).

    Science.gov (United States)

    Trout, James M; Santín, Mónica; Fayer, Ronald

    2006-06-01

    Feces and duodenal scrapings were collected from 22 coyotes (Canis latrans) killed in managed hunts in northeastern Pennsylvania. Polymerase chain reaction (PCR) methods were used to detect Giardia and Cryptosporidium spp. PCR-amplified fragments of Giardia and Cryptosporidium spp. SSU-rRNA genes were subjected to DNA sequence analysis for species/genotype determination. Seven coyotes (32%) were positive for G. duodenalis: three assemblage C, three assemblage D, and one assemblage B. Six coyotes (27%) were positive for Cryptosporidium spp. One isolate shared 99.7% homology with C. muris, whereas five others (23%) shared 100% homology with C. canis, coyote genotype. This is the first report on multiple genotypes of Giardia spp. in coyotes and on the prevalence of Cryptosporidium spp. genotypes in coyotes.

  13. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    2012-10-15

    Oct 15, 2012 ... in human has been paralleled by the simultaneous develop- ment of ... In crop plants, the development of large genotyping arrays started much ..... via deep resequencing of reduced representation libraries with the Illumina ...

  14. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    Lindomar

    2016-08-31

    Aug 31, 2016 ... tolerance to the deficit of these nutrients in the soil. (Colodetti et al., 2014; ... be passive of exploration using genotypes of rapid growth and low nutritional ... amino acids, proteins, nucleotides, hormones and chlorophyll ...

  15. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Prof. Ogunji

    Pollen diversity, viability and floral structure of some Musa genotypes ... at the Faculty of Agriculture & Natural Resources Management farm, Ebonyi State University,. Abakaliki. ..... Roots, tuber, plantains and bananas in human nutrition. Rome,.

  16. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    etc

    2015-05-06

    May 6, 2015 ... 4Ethiopian Institute of Agriculture Research, Debre Zeit Agriculture Research Center, Ethiopia. Received .... interaction on seed yield of Kabuli -chickpea genotypes .... becomes important for the chickpea breeders in terms of.

  17. Assessment of genotype x environment interaction on yield and ...

    African Journals Online (AJOL)

    user

    2011-04-11

    Apr 11, 2011 ... yield and yield components of durum wheat genotypes ... The results of combined analysis of variance showed a strong influence of the ... Stability is defined as the early prediction of environmental im- ... Many resear-.

  18. Genetic diversity of maize genotypes on the basis of morpho ...

    African Journals Online (AJOL)

    Genetic diversity of maize genotypes on the basis of morpho-physiological and simple sequence repeat (SSR) markers. Ashish Kumar, Arunita Rakshit, Naresh K Mangilipelli, Y Varalaxmi, T Vijayalakshmi, Jainender M Vanaja, SK Yadav, B Venkateswarlu, M Maheswari ...

  19. The Comparison of Growth, Slaughter and Carcass Traits of Meat Chicken Genotype Produced by Back-Crossing with A Commercial Broiler Genotype

    Directory of Open Access Journals (Sweden)

    Musa Sarıca

    2014-01-01

    Full Text Available This study was conducted to determine the growth and some slaughter traits between commercial fast growing chickens and three-way cross M2 genotypes. 260 male female mixed chickens from each genotype was reared 10 replicate per genotype in the same house. Two different slaughtering ages were applied to commercial chickens and slaughtered at 6 and 7 weeks of age for comparing with cross genotypes. F chickens reached to slaughtering age at 42 days, whereas cross groups reached at 49 days. Genotypes consumed same amount of feed until slaughtering ages, but F genotype had better feed conversion ratio. The differences between dressing percentage and carcass parts ratios of genotypes were found significant, and F genotype had higher dressing percentage. Carcass parts of all genotypes were found in acceptable limits.

  20. Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar.

    Science.gov (United States)

    Gligor, M; Ganzhorn, J U; Rakotondravony, D; Ramilijaona, O R; Razafimahatratra, E; Zischler, H; Hapke, A

    2009-02-01

    Hybrid zones in ecotones can be useful model systems for the study of evolutionary processes that shape the distribution and discreteness of species. Such studies could be important for an improved understanding of the complex biogeography of Madagascar, which is renowned for its outstanding degree of small-scale endemism. Certain forest remnants in central Madagascar indicate that transitional corridors across the island could have connected microendemics in different forest types in the past. Evolutionary processes in such corridors are difficult to study because most of these corridors have disappeared due to deforestation in central Madagascar. We studied a hybrid zone in one of the few remaining ecotonal corridors between dry and humid forests in Madagascar, which connects two species of mouse lemurs, Microcebus griseorufus in dry spiny forest and Microcebus murinus in humid littoral forest. We sampled 162 mouse lemurs at nine sites across this boundary. Morphometric analyses revealed intermediate morphotypes of many individuals in transitional habitat. Bayesian clustering of microsatellite genotypes and assignment tests yielded evidence for a mixed ancestry of mouse lemurs in the ecotone, where we also observed significant linkage disequilibria and heterozygote deficiency. In contrast to these observations, mitochondrial haplotypes displayed a sharply delimited boundary at the eastern edge of spiny forest, which was noncoincident with the signals from microsatellite data. Among several alternative scenarios, we propose asymmetric nuclear introgression due to male-biased dispersal, divergent environmental selection, and an expansion of dry spiny forest in the course of aridification as a probable explanation of our observations.