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Sample records for ccl3l1-ccr5 genotype influences

  1. CCL3L1-CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1-infected individuals.

    Science.gov (United States)

    Ahuja, Sunil K; Kulkarni, Hemant; Catano, Gabriel; Agan, Brian K; Camargo, Jose F; He, Weijing; O'Connell, Robert J; Marconi, Vincent C; Delmar, Judith; Eron, Joseph; Clark, Robert A; Frost, Simon; Martin, Jeffrey; Ahuja, Seema S; Deeks, Steven G; Little, Susan; Richman, Douglas; Hecht, Frederick M; Dolan, Matthew J

    2008-04-01

    The basis for the extensive variability seen in the reconstitution of CD4(+) T cell counts in HIV-infected individuals receiving highly active antiretroviral therapy (HAART) is not fully known. Here, we show that variations in CCL3L1 gene dose and CCR5 genotype, but not major histocompatibility complex HLA alleles, influence immune reconstitution, especially when HAART is initiated at CCR5 genotypes favoring CD4(+) T cell recovery are similar to those that blunted CD4(+) T cell depletion during the time before HAART became available (pre-HAART era), suggesting that a common CCL3L1-CCR5 genetic pathway regulates the balance between pathogenic and reparative processes from early in the disease course. Hence, CCL3L1-CCR5 variations influence HIV pathogenesis even in the presence of HAART and, therefore, may prospectively identify subjects in whom earlier initiation of therapy is more likely to mitigate immunologic failure despite viral suppression by HAART. Furthermore, as reconstitution of CD4(+) cells during HAART is more sensitive to CCL3L1 dose than to CCR5 genotypes, CCL3L1 analogs might be efficacious in supporting immunological reconstitution.

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

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

    2008-01-01

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

  3. Polymorphisms of CCL3L1/CCR5 genes and recurrence of hepatitis B in liver transplant recipients

    Institute of Scientific and Technical Information of China (English)

    HongLi; Hai-YangXie; LinZhou; Wei-LinWang; Ting-BoLiang; MinZhang; Shu-SenZheng

    2011-01-01

    BACKGROUND: The genetic diversity of chemokines and chemokine receptors has been associated with the outcome of hepatitis B virus infection. The aim of this study was to evaluate whether the copy number variation in the CCL3L1 gene and the polymorphisms of CCR5Δ32 and CCR5-2459A→G (rs1799987) are associated with recurrent hepatitis B in liver transplantation for hepatitis B virus infection-related end-stage liver disease. METHODS: A total of 185 transplant recipients were enrolled in this study. The genomic DNA was extracted from whole blood, the copy number of the CCL3L1 gene was determined by a quantitative real-time PCR based assay, CCR5Δ32 was detected by a sizing PCR method, and a single-nucleotide polymorphism in CCR5-2459 was detected by restriction fragment length polymorphismPCR. RESULTS:  No CCR5Δ32 mutation was detected in any of the individuals from China. Neither copy number variation nor polymorphism in CCR5-2459 was associated with post-transplant re-infection with hepatitis B virus. However, patients with fewer copies ( CONCLUSION: Patients possessing the compound decreased functional genotype of both CCL3L1 and CCR5 genes might be more likely to have recurrence of hepatitis B after transplantation.

  4. Role of CCL3L1-CCR5 Genotypes in the Epidemic Spread of HIV-1 and Evaluation of Vaccine Efficacy

    Science.gov (United States)

    2008-08-01

    The rarity of HIV infection via cross- species transmission from chimpanzee to Pygmies contrasts with the fact that documented zoonosis of other viruses...viral zoonosis ? In this respect, it is noteworthy that compared to other African populations that reside in geographical proximity (e.g., non-Pygmy

  5. Outcomes of Highly Active Antiretroviral Therapy in the Context of Universal Access to Healthcare: The U.S. Military HIV Natural History Study

    Science.gov (United States)

    2010-05-27

    CCL3L1- CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1- infected individuals. Nat Med 2008, 14:413...Riley ED, Bangsberg DR: Food insecurity is associated with incomplete HIV RNA suppression among homeless and marginally housed HIV- infected ...increases in HIV- infected adults experiencing 4 years of viral suppression on antiretroviral therapy. Aids 2003, 17:1907-1915. 48. Kaufmann GR, Furrer

  6. Cyclooxygenase 2 genotypes influence prostate cancer susceptibility in Japanese Men.

    Science.gov (United States)

    Sugie, Satoru; Tsukino, Hiromasa; Mukai, Shoichiro; Akioka, Takahiro; Shibata, Norihiko; Nagano, Masafumi; Kamoto, Toshiyuki

    2014-03-01

    This study aims to evaluate the relationship between the cyclooxygenase 2 (COX2) G1195A (rs689465) polymorphism and the risk of prostate cancer in a Japanese population and the associations between COX2 polymorphisms and clinicopathological characteristics, including Gleason grade and prostate-specific antigen (PSA) grade. We recruited 134 patients with prostate cancer and 86 healthy controls matched for age and smoking status. The COX2 G1195A polymorphism status was determined by polymerase chain reaction and restriction fragment length polymorphism analysis. Genotype distributions (p = 0.028) and allelic frequencies (p = 0.014) differed significantly between prostate cancer and control groups in terms of the COX2 G1195A polymorphism (Pearson's χ (2) test). Logistic regression analysis of case and control outcomes showed an odds ratio between the GG and AA genotypes of 3.15 (95% confidence interval = 1.27-8.08, p = 0.014), indicating an increased risk of prostate cancer associated with the AA genotype. Subset analysis revealed no significant associations between this polymorphism and clinicopathological characteristics of prostate cancer. This study demonstrated a relationship between the COX2 G1195A variant and prostate cancer risk. This polymorphism may merit further investigation as a potential genomic marker for the early detection of prostate cancer. Our results support the hypothesis that rs689465 influences susceptibility to prostate cancer; however, prostate cancer progression was not associated with rs689465 in a Japanese population.

  7. 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. Correlati

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

    Science.gov (United States)

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

    2013-04-01

    Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SL(G) carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to L(A)L(A) carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function.

  9. Interaction between vitamin D receptor genotype and estrogen receptor alpha genotype influences vertebral fracture risk

    NARCIS (Netherlands)

    E.M. Colin (Edgar); A.G. Uitterlinden (André); A.P. Bergink (Arjan); M. van de Klift (Marjolein); Y. Fang (Yue); P.P. Arp (Pascal); H.A.P. Pols (Huib); J.P.T.M. van Leeuwen (Hans); J.B.J. van Meurs (Joyce); A. Hofman (Albert)

    2003-01-01

    textabstractIn view of the interactions of vitamin D and the estrogen endocrine system, we studied the combined influence of polymorphisms in the estrogen receptor (ER) alpha gene and the vitamin D receptor (VDR) gene on the susceptibility to osteoporotic vertebral fractures in 634

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

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    van Houwelingen Hans C

    2008-08-01

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

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

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    Maxine Caws

    2008-03-01

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

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

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

    2008-01-01

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

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

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    J. A. Monge-Argilés

    2016-01-01

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

  14. Genotypic and climatic influence on the antioxidant activity of flavonoids in Kale (Brassica oleracea var. sabellica).

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    Zietz, Michaela; Weckmüller, Annika; Schmidt, Susanne; Rohn, Sascha; Schreiner, Monika; Krumbein, Angelika; Kroh, Lothar W

    2010-02-24

    The influence of genotype and climatic factors, e.g. mean temperature and mean global radiation level, on the antioxidant activity of kale was investigated. Therefore, eight kale cultivars, hybrid and traditional, old cultivars, were grown in a field experiment and harvested at four different times. In addition to the investigation of the total phenolic content, the overall antioxidant activity was determined by TEAC assay and electron spin resonance spectrometry. A special aim was to characterize the contribution of single flavonoids to the overall antioxidant activity using an HPLC-online TEAC approach. The antioxidant activity and the total phenolic content were influenced by the genotype and the eco-physiological factors. The HPLC-online TEAC results showed that not all flavonol glycosides contribute to the overall antioxidant activity in the same manner. Taking the results of the structural analysis obtained by HPLC-ESI-MS(n) into account, distinct structure-antioxidant relationships have been observed.

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

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    Christine T Shiner

    2016-05-01

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

  16. Influence of Atg5 mutation in SLE depends on functional IL-10 genotype.

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    Patricia López

    Full Text Available Increasing evidence supports the involvement of autophagy in the etiopathology of autoimmune diseases. Despite the identification of autophagy-related protein (Atg-5 as one of the susceptibility loci in systemic Lupus erythematosus (SLE, the consequences of the carriage of these mutations for patients remain unclear. The present work analyzed the association of Atg5 rs573775 single nucleotide polymorphism (SNP with SLE susceptibility, IFNα, TNFα and IL-10 serum levels, and clinical features, in 115 patients and 170 healthy individuals. Patients who where carriers of the rs573775 T* minor allele presented lower IFNα levels than those with the wild genotype, whereas the opposite result was detected for IL-10. Thus, since IL-10 production was regulated by rs1800896 polymorphisms, we evaluated the effect of this Atg5 mutation in genetically high and low IL-10 producers. Interestingly, we found that the rs573775 T* allele was a risk factor for SLE in carriers of the high IL-10 producer genotype, but not among genetically low producers. Moreover, IL-10 genotype influences SLE features in patients presenting the Atg5 mutated allele. Specifically, carriage of the rs573775 T* allele led to IL-10 upregulation, reduced IFNα and TNFα production and a low frequency of cytopenia in patients with the high IL-10 producer genotype, whereas patients with the same Atg5 allele that were low IL-10 producers presented reduced amounts of all these cytokines, had a lower prevalence of anti-dsDNA antibodies and the latest onset age. In conclusion, the Atg5 rs573775 T* allele seems to influence SLE susceptibility, cytokine production and disease features depending on other factors such as functional IL-10 genotype.

  17. Environmental influences on epistatic interactions: viabilities of cytochrome c genotypes in interpopulation crosses.

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    Willett, Christopher S; Burton, Ronald S

    2003-10-01

    The genetic incompatibilities that underlie F2 hybrid breakdown and reproductive isolation between allopatric populations may be susceptible to environmental interactions. Here we show that epistatic interactions between cytochrome c (CYC) alleles and mitochondrial DNA (mtDNA) variation are dramatically influenced by environmental temperature in interpopulation hybrids of the copepod Tigriopus californicus. CYC is a nuclear-encoded gene that functionally interacts with electron transport system (ETS) complexes composed in part of mtDNA-encoded proteins. Previous studies have provided evidence for functional coadaptation between CYC and ETS complex IV (cytochrome c oxidase) and for cytoplasmic effects on the fitness of CYC genotype in copepod hybrids. In this study, selection on CYC genotype is shown to continue into advanced generation hybrids (F2-F8) increasing the likelihood that CYC itself is involved in the interaction (and not a linked factor). Relative viabilities varied markedly between copepods raised in two different temperature/light regimes. These results suggest that both intrinsic coadaptation and extrinsic selection will influence the outcome of natural hybridizations between populations. Furthermore, the results indicate that the fitness of particular hybrid genotypes depends on additional non-mtDNA encoded genes that interact with CYC.

  18. Sex influences on the penetrance of HLA shared-epitope genotypes for rheumatoid arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, J.M. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

    1996-02-01

    The association between rheumatoid arthritis (RA) and HLA DRB1 alleles may arise through linkage disequilibrium with a disease locus or the direct involvement of HLA alleles in RA. In support of the latter possibility, the shared-epitope hypothesis has been postulated, stating that conformationally similar DR{beta} chains encoded by several DRB1 alleles confer disease susceptibility. To examine these alternative hypotheses of marker-disease association and to investigate gender differences in RA susceptibility, we analyzed the distributions of PCR-based DRB1 genotypes of 309 Caucasian RA patients and 283 Caucasian controls. Initially, the marker-association-segregation {chi}{sup 2} method was used to evaluate evidence for linkage disequilibrium and the direct involvement of markers DR4 Dw4, DR4 Dw14, and DR1 in RA susceptibility. Additional shared-epitope models that grouped DRB1 alleles into five classes (*0401, *0404/*0102, *0405/*0408/*0101, *1001, and all others) and postulated relationships between genotypes and RA susceptibility were also fitted to observed genotypic distributions by the method of minimal {chi}{sup 2}. For females, a linkage-disequilibrium model provided a good fit to the data, as did a shared-epitope model with RA most penetrant among individuals with the *0401, *0401 genotype. For males, the best model indicated highest RA penetrance among shared-epitope compound heterozygotes. Clinically, male RA patients had more subcutaneous nodules and greater use of slowly acting antirheumatic drugs, while female RA patients had earlier disease onset. This study therefore suggests that sex-related factors influence the RA penetrance associated with DRB1 shared-epitope genotypes and that DRB1 effects on RA prognosis and pathogenesis should be considered separately for men and women. 67 refs., 7 tabs.

  19. Influence of metabolic genotypes on biomarkers of exposure to 1,3-butadiene in humans.

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    Fustinoni, Silvia; Soleo, Leonardo; Warholm, Margareta; Begemann, Petra; Rannug, Agneta; Neumann, Hans-G; Swenberg, James A; Vimercati, Luigi; Colombi, Antonio

    2002-10-01

    Carcinogenicity of 1,3-butadiene (BD) has been linked to its metabolic activation of genotoxic epoxides. The inherited variations in the activity of BD-metabolizing enzymes may be responsible for individual differences that modulate the effects of BD exposure. In this study, 40 Italian subjects (30 BD-exposed workers and 10 clerks) were investigated to evaluate the role of genetic polymorphism of cytochromes P450 2E1, microsomal epoxide hydrolase, glutathione transferases GSTM1, GSTP1, GSTT1, and alcohol dehydrogenase, on urinary N-acetyl-S-(3,4-hydroxybutyl)-L-cysteine (MI) and hemoglobin N-(2,3,4-trihydroxybutyl)-valine adducts (THBVal). Median urinary MI and THBVal levels were 1.71 mg/g creatinine and 37.0 pmol/g globin in BD-exposed workers (exposure range, 4-201 microg/m(3)) and 1.42 mg/g creatinine and 35.3 pmol/g globin in unexposed subjects. No difference between the two groups was observed. Among all subjects, MI and THBVal levels were significantly correlated (r = 0.333). Smoking positively influenced the formation of THBVal. Higher THBVal levels were found in subjects with GSTM1 null and GSTT1 null genotypes; borderline influences were also noticed for CYP2E1(G(-35)T). An additive effect of combined polymorphisms for CYP2E1, GSTM1, and GSTT1 genes on the THBVal levels was suggested. A multiple linear regression analysis, where each factor contributed significantly, correlated THBVal levels with smoking, CYP2E1(G(-35)T), GSTT1, and GSTM1 genotypes (r = 0.698). Our results indicate that the THBVal level is influenced by genotypes, and that the analysis of combined polymorphisms may be the key to a better understanding of the role played by polymorphism of BD-metabolizing enzymes.

  20. BDNF genotype influence the efficacy of rTMS in stroke patients.

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    Uhm, Kyeong Eun; Kim, Yun-Hee; Yoon, Kyung Jae; Hwang, Jung Min; Chang, Won Hyuk

    2015-05-06

    Brain-derived neurotrophic factor (BDNF) genotype can influence neural response to repetitive transcranial magnetic stimulation (rTMS) in normal individuals. In this study we established personalized stimulus intensity of facilitatory rTMS according to BDNF genotype in stroke patients. Twenty-two chronic stroke patients were enrolled. All patients underwent three different sessions of rTMS over the ipsilesional M1 in randomized order with a washout period exceeding 24h: first condition, high-frequency rTMS with sub-threshold intensity; second condition, high-frequency rTMS with supra-threshold intensity; third condition, sham rTMS. Cortical excitability in the affected hemisphere was assessed with motor evoked potentials (MEPs) before and after stimulation. Data were analyzed according to BDNF genotype. Six [27.3%] and 16 [72.7%] participants were classified in the Val/Val group and Met allele group, respectively. In each group, significant increases were observed in the amplitude of MEPs after the stimulation in the first and second conditions (prTMS is used for the modulation of cortical excitability in patients with chronic stroke.

  1. Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

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    NIDELET, Thibault; MARTIN, Juliette; LEGRAND, Judith; DILLMANN, Christine; BOURGAIS, Aurélie; de VIENNE, Dominique; SHERLOCK, Gavin; SICARD, Delphine

    2015-01-01

    Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged towards a different life-history strategy. However, phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. In a fifth of our evolution experiments, mutations in the same gene, BMH1, were selected, in three out of the six ancestral genotypes. Two types of BMH1 mutation with opposite phenotypic effects on several traits were found. The evolution of most traits, as well as the occurrence of BMH1 mutations, was significantly influenced by the ancestral strain. However, this effect could not be easily predicted from ancestors’ phylogeny or past-selection. All together, our data demonstrate that phenotypic and its underlying genotypic convergence depends on a complex interplay between the evolutionary environment, pleiotropy and the ancestor genetic background but are not straightforwardly predicable. PMID:24164389

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

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    Junca, Pierre; Carcaud, Julie; Moulin, Sibyle; Garnery, Lionel; Sandoz, Jean-Christophe

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Pierre Junca

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

  4. Social environment influences the relationship between genotype and gene expression in wild baboons.

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    Runcie, Daniel E; Wiedmann, Ralph T; Archie, Elizabeth A; Altmann, Jeanne; Wray, Gregory A; Alberts, Susan C; Tung, Jenny

    2013-05-19

    Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression in the wild baboons of the Amboseli basin. We found evidence for a number of gene-environment interactions (GEIs) associated with variation in the social environment, encompassing social environments experienced in adulthood as well as persistent effects of early life social environment. Social connectedness, maternal dominance rank and group size all interacted with genotype to influence gene expression in at least one sex, and either in early life or in adulthood. These results suggest that social and behavioural variation, akin to other factors such as age and sex, can impact the genotype-phenotype relationship. We conclude that GEIs mediated by the social environment are important in the evolution and maintenance of individual differences in wild social mammals, including individual differences in responses to social stressors.

  5. Influence of DNMT genotype on global and site specific DNA methylation patterns in neonates and pregnant women.

    Directory of Open Access Journals (Sweden)

    Catherine Potter

    Full Text Available This study examines the relationship between common genetic variation within DNA methyltransferase genes and inter-individual variation in DNA methylation. Eleven polymorphisms spanning DNMT1 and DNMT3B were genotyped. Global and gene specific (IGF2, IGFBP3, ZNT5 DNA methylation was quantified by LUMA and bisulfite Pyrosequencing assays, respectively, in neonatal cord blood and in maternal peripheral blood. Associations between maternal genotype and maternal methylation (n (≈ 333, neonatal genotype and neonatal methylation (n (≈ 454, and maternal genotype and neonatal methylation (n (≈ 137 were assessed. The findings of this study provide some support to the hypothesis that genetic variation in DNA methylating enzymes influence DNA methylation at global and gene-specific levels; however observations were not robust to correction for multiple testing. More comprehensive analysis of the influence of genetic variation on global and site specific DNA methylation is warranted.

  6. Influence of Acanthamoeba genotype on clinical course and outcomes for patients with Acanthamoeba keratitis in Spain.

    Science.gov (United States)

    Arnalich-Montiel, Francisco; Lumbreras-Fernández, Blanca; Martín-Navarro, Carmen M; Valladares, Basilio; Lopez-Velez, Rogelio; Morcillo-Laiz, Rafael; Lorenzo-Morales, Jacob

    2014-04-01

    Genotype T4 is by far the most frequent genotype of Acanthamoeba keratitis (AK) and therefore has been considered the most virulent. This study included 14 cases of AK of genotype T4 and three cases of non-T4 genotype. We found that cases of non-T4 genotype had a worse response to medical therapy, greater need for surgical intervention, greater risk of extracorneal involvement, and remarkably poorer final visual outcome than those of T4 genotype, suggesting an association between Acanthamoeba virulence and genotype that requires additional case investigation.

  7. MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance.

    Science.gov (United States)

    McGivney, Beatrice A; Browne, John A; Fonseca, Rita G; Katz, Lisa M; Machugh, David E; Whiston, Ronan; Hill, Emmeline W

    2012-12-01

    Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development. A MSTN SNP significantly associated with Thoroughbred horse racing phenotypes has recently been identified as well as significant reductions in Thoroughbred skeletal muscle gene expression for three transcripts 400-1500 base pairs downstream of the MSTN gene following a period of training. Together, these findings indicate that MSTN genotypes may influence MSTN gene expression. To investigate this, MSTN mRNA expression was measured in biopsies from the middle gluteal muscle from 60 untrained yearling Thoroughbreds (C/C, n = 15; C/T, n = 28; T/T, n = 17) using two independent real-time qRT-PCR assays. MSTN gene expression was also evaluated in a subset (N = 33) of these animals using samples collected after a ten-month period of training. A significant association was observed between genotype and mRNA abundance for the untrained horses (assay I, P = 0.0237; assay II, P = 0.003559), with the C/C cohort having the highest MSTN mRNA levels, the T/T group the lowest levels and the C/T group intermediate levels. Following training, there was a significant decrease in MSTN mRNA (-3.35-fold; P = 6.9 × 10(-7) ), which was most apparent for the C/C cohort (-5.88-fold, P = 0.001). These data demonstrate the tight relationship between phenotype, genotype and gene expression at the MSTN gene in Thoroughbred racehorses.

  8. Grain characteristics, chemical composition, and functional properties of rye (Secale cereale L.) as influenced by genotype and harvest year.

    Science.gov (United States)

    Hansen, Hanne B; Møller, Birthe; Andersen, Sven B; Jørgensen, Johannes R; Hansen, Ase

    2004-04-21

    Grain characteristic, chemical composition, and functional properties of rye were measured in 19 different cultivars grown in one location in up to 3 years. The cultivars included 8 adapted hybrids, 7 adapted population cultivars, and 4 nonadapted population cultivars. The results showed a significant influence of both harvest year and genotype on grain characteristics, chemical composition, and functional properties of the grain. Multivariate data analysis confirmed that the variations in the data were explained by yearly and genotype differences. Calculations of variance components showed that the variations in plant height, harvest yield, and protein content were mainly due to genotype differences and to a lesser extent to differences among harvest years. The kernel weight, hardness index, and content of dietary fiber components, however, were more strongly influenced by the harvest year than by the genotype. Differences in starch properties measured by falling number (FN), amylograph peak viscosity, and temperature at peak viscosity were more strongly influenced by harvest year. The water absorption was strongly influenced by genotype effects, compared to yearly differences. FN and amylograph peak temperature were positively correlated (r = 0.94). No correlation was found between the water absorption and the relative proportion of water-extractable arabinoxylan (AX) compared to the total AX content. However, the degree of ferulic acid cross-linking showed a negative correlation (r = -0.70) with the water absorption.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sergio Henao Osorio

    2010-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Mamta eSharma

    2016-03-01

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

  12. Serotonin transporter genotype and mild traumatic brain injury independently influence resilience and perception of limitations in veterans.

    Science.gov (United States)

    Graham, David P; Helmer, Drew A; Harding, Mark J; Kosten, Thomas R; Petersen, Nancy J; Nielsen, David A

    2013-06-01

    Evidence indicates that individuals with the 5-HTTLPR variant short/short genotype have increased sensitivity to both positive and negative perceptions of perceived social support. The aim of this study was to evaluate this association among Veterans in the context of mild traumatic brain injury (TBI). As part of a larger TBI center, we performed a cross-sectional study of 67 OEF/OIF/OND Veterans (41 with TBI and 26 controls without TBI) who completed the questionnaires and consented to genetic testing. The primary measures included the Connor-Davidson Resilience Scale (CDRISC) and the Perceived Limitations in community participation subscale of the Community Reintegration of Service Members Instrument (CRIS-PL). Both 5-HTTLPR genotype and TBI status were independently associated with the CRIS-PL (p = .009 for genotype, p = .001 for TBI) and the CDRISC (p = .015 for genotype, p = .003 for TBI) scores. This study suggests that both the 5-HTTLPR genotype and TBI status independently, in an almost equal but opposite direction, influence resilience and perceived limitations to social participation. Further, resilience appears more sensitive to perceived limitations in Veterans carrying an S'S' genotype than in L' carriers, but only in the context of having sustained a TBI. While having a TBI appeared to increase a Veteran's sensitivity to social stress, the Veteran's who were L' allele carriers with a TBI fared the worst, with lower resilience and more perceived limitations for community participation compared to L' carrier Veterans without a TBI or Veterans with the S'S' genotype regardless of TBI status.

  13. The influence of irradiance and external CO2 concentration on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Nilwik, H.J.M.; Gosiewski, W.; Bierhuizen, J.F.

    1982-01-01

    With 4 genotypes of tomato, irradiance and CO2-response curves of net photosynthesis were analysed by means of curve fitting. Estimated values of the light compensation point Ic showed small but significant differences between the genotypes, the overall value being in the order of 8 W m−2. The photo

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

    Directory of Open Access Journals (Sweden)

    Esther M Opmeer

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

  15. Influences of Cadmium on Grain Mineral Nutrient Contents of Two Rice Genotypes Differing in Grain Cadmium Accumulation

    Institute of Scientific and Technical Information of China (English)

    CHENG Wang-da; YAO Hai-gen; ZHANG Hong-mei; TAO Xian-guo

    2009-01-01

    A pot experiment was conducted to study the effects of Cd on grain Cd, K, P, Mg, Zn, Cu, Pb, Fe and Mn accumulation in two rice genotypes (Xiushui 63 and Xiushui 217) differing in grain Cd accumulation under four Cd levels, i.e. 0, 0.5, 2.5 and 12.5 mg/kg. Rice genotype greatly affected the grain K content, but not significantly for P, Mg, Zn, Cu, Pb, Fe and Mn contents. There were remarkable effects of additional Cd on the contents of P, Mg and Zn in grains, while not significant for K, Cu, Pb, Fe and Mn contents. No significant differences were found in the interaction of genotype by additional Cd on these nine element contents. The low grain Cd accumulation genotype Xiushui 217 had significantly higher grain K, Mg, Cu and Mn contents than the high grain Cd accumulation genotype Xiushui 63, but the case was opposite for Zn, Pb and Fe contents. It also showed that Cd addition levels significantly influenced the K, P, Mg, Zn, Cu, Pb, Fe and Mn contents in rice grains. Grain K, P, Mg, Zn, Fe and Mn contents reduced with the increasing rate of Cd addition.

  16. Maternal environment influences cocaine intake in adulthood in a genotype-dependent manner.

    Directory of Open Access Journals (Sweden)

    Rixt van der Veen

    Full Text Available BACKGROUND: Accumulating epidemiological evidence points to the role of genetic background as a modulator of the capacity of adverse early experiences to give rise to mental illness. However, direct evidence of such gene-environment interaction in the context of substance abuse is scarce. In the present study we investigated whether the impact of early life experiences on cocaine intake in adulthood depends on genetic background. In addition, we studied other behavioral dimensions associated with drug abuse, i.e. anxiety- and depression-related behaviors. METHODOLOGY/PRINCIPAL FINDINGS: For this purpose, we manipulated the maternal environment of two inbred mouse strains, the C57BL/6J and DBA/2J by fostering them with non-related mothers, i.e. the C3H/HeN and AKR strains. These mother strains show respectively high and low pup-oriented behavior. As adults, C57BL/6J and DBA/2J were tested either for cocaine intravenous self-administration or in the elevated plus-maze and forced swim test (FST. We found that the impact of maternal environment on cocaine use and a depression-related behavior depends upon genotype, as cocaine self-administration and behavior in the FST were influenced by maternal environment in DBA/2J, but not in C57BL/6J mice. Anxiety was not influenced by maternal environment in either strain. CONCLUSIONS/SIGNIFICANCE: Our experimental approach could contribute to the identification of the psychobiological factors determining the susceptibility or the resilience of certain individuals to develop psychopathologies.

  17. Influence of hepatitis C virus and IL28B genotypes on liver stiffness

    DEFF Research Database (Denmark)

    Lundbo, Lene Fogt; Clausen, Louise Nygaard; Weis, Nina;

    2014-01-01

    OBJECTIVE: Liver fibrosis has been associated with hepatitis C virus (HCV) genotype and genetic variation near the interleukin 28B (IL28B) gene, but the relative contribution is unknown. We aimed to investigate the relation between HCV genotypes, IL28B and development of liver stiffness. PATIENTS....... 235 were male, 297 Caucasians, and 223 had been exposed to HCV through intravenous drug use. The overall median TE value was 7.4 kPa (interquartile range (IQR) 5.7-12.1). HCV replication was enhanced in patients carrying the IL28B CC genotype compared to TT and TC (5.8 vs. 5.4 log10 IU/mL, p = 0.......03). Patients infected with HCV genotype 3 had significantly higher TE values (8.2 kPa; IQR, 5.9-14.5) compared to genotype 1 (6.9 kPa; IQR, 5.4-10.9) and 2 (6.7 kPa; IQR, 4.9-8.8) (p = 0.02). Within patients with genotype 3, IL28B CC genotype had the highest TE values (p = 0.04). However, in multivariate...

  18. Environmental Influences on Pigeonpea-Fusarium udum Interactions and Stability of Genotypes to Fusarium Wilt.

    Science.gov (United States)

    Sharma, Mamta; Ghosh, Raju; Telangre, Rameshwar; Rathore, Abhishek; Saifulla, Muhammad; Mahalinga, Dayananda M; Saxena, Deep R; Jain, Yogendra K

    2016-01-01

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

  19. Influence of delta virus infection on the virologic status in Egyptian patients with chronic hepatitis B virus genotype D.

    Science.gov (United States)

    Fouad, Rabab; Abdo, Mahmoud; Eldeen, Hadeel Gamal; Sabry, Dina; Atef, Mira; Ahmed, Rasha; Zayed, Naglaa

    2016-05-01

    Hepatitis delta virus (HDV) usually have an unfavorable clinical outcome in chronic hepatitis B virus (HBV) patients. In Egypt, data about epidemiology, the spectrum of disease, and impact of HDV on HBV infection are rare. To assess the prevalence, clinical and virological characteristics of HDV infection among Egyptian patients with chronic HBV. Adult patients with Hepatitis B surface antigen (HBsAg)-positive were evaluated for the presence of HDV using anti HDV-IgG and HDV RNA by RT-PCR. Routine laboratory investigations, genotypes and subtypes for both HBV and HDV, abdominal sonography, and transient elastography (TE) were done. Liver biopsy was performed only in whenever indicated. One hundred and twenty-one treatment-naïve chronic HBV patients were included. Wild HBV genotype-D2 was found in 98.2% and 81.9% were HBeAg negative. Prevalence of HDV was 8.3% by anti-HDV IgG and 9.9% by RT-PCR. Wild HDV genotype-IIb was reported in 83.3%. HDV infection was more common in males, 90.9% of delta patients were HBeAg negative. Compared to the mono-infected HBV, concomitant HBV/HDV infection was not associated with more derangment in ALT nor advanced stage of fibrosis. 66.7% of HDV patients had significantly lower HBV-DNA level compared to the non-delta patients (P genotype-D was associated with HDV genotype-IIb. Delta infection was associated with negative HBeAg status, reduction of HBV replication, but neither influenced the clinical course nor increased significant liver damage risk.

  20. Differential influence of the 5-HTTLPR genotype, neuroticism and real-life acute stress exposure on appetite and energy intake.

    Science.gov (United States)

    Capello, Aimée E M; Markus, C Rob

    2014-06-01

    Stress or negative mood often promotes energy intake and overeating. Since the serotonin transporter-linked polymorphic region (5-HTTLPR) is found to mediate stress vulnerability as well as to influence energy intake, this gene may also influence the negative effects of stress exposure on overeating. Moreover, since stress proneness also reflects cognitive stress vulnerability - as often defined by trait neuroticism - this may additionally predispose for stress-induced overeating. In the present study it was investigated whether the 5-HTTLPR genotype interacted with neuroticism on changes in mood, appetite and energy intake following exposure to a real-life academic examination stressor. In a balanced-experimental design, homozygous S-allele and L-allele carriers (N = 94) with the lowest and highest neuroticism scores were selected from a large database of 5-HTTLPR genotyped students. Mood, appetite and energy intake were measured before and after a 2-hour academic examination and compared with a control day. Examination influenced appetite for particular sweet snacks differently depending on 5-HTTLPR genotype and neuroticism. S/S compared with L/L subjects reported greater examination stress, and this was accompanied by a more profound post-stress increase in appetite for sweet snacks. Data also revealed a 5-HTTLPR genotype by trait neuroticism interaction on energy intake, regardless of examination. These results consolidate previous assumptions of 5-HTTLPR involvement in stress vulnerability and suggest 5-HTTLPR and neuroticism may influence stress-induced overeating depending on the type of food available. These findings furthermore link previous findings of increased risk for weight gain in S/S-allele carriers, particularly with high scores on trait neuroticism, to increased energy intake.

  1. Influence of Genotype, Environment, and Gypsy Moth Herbivory on Local and Systemic Chemical Defenses in Trembling Aspen (Populus tremuloides).

    Science.gov (United States)

    Rubert-Nason, Kennedy F; Couture, John J; Major, Ian T; Constabel, C Peter; Lindroth, Richard L

    2015-07-01

    Numerous studies have explored the impacts of intraspecific genetic variation and environment on the induction of plant chemical defenses by herbivory. Relatively few, however, have considered how those factors affect within-plant distribution of induced defenses. This work examined the impacts of plant genotype and soil nutrients on the local and systemic phytochemical responses of trembling aspen (Populus tremuloides) to defoliation by gypsy moth (Lymantria dispar). We deployed larvae onto foliage on individual tree branches for 15 days and then measured chemistry in leaves from: 1) branches receiving damage, 2) undamaged branches of insect-damaged trees, and 3) branches of undamaged control trees. The relationship between post-herbivory phytochemical variation and insect performance also was examined. Plant genotype, soil nutrients, and damage all influenced phytochemistry, with genotype and soil nutrients being stronger determinants than damage. Generally, insect damage decreased foliar nitrogen, increased levels of salicinoids and condensed tannins, but had little effect on levels of a Kunitz trypsin inhibitor, TI3. The largest damage-mediated tannin increases occurred in leaves on branches receiving damage, whereas the largest salicinoid increases occurred in leaves of adjacent, undamaged branches. Foliar nitrogen and the salicinoid tremulacin had the strongest positive and negative relationships, respectively, with insect growth. Overall, plant genetics and environment concomitantly influenced both local and systemic phytochemical responses to herbivory. These findings suggest that herbivory can contribute to phytochemical heterogeneity in aspen foliage, which may in turn influence future patterns of herbivory and nutrient cycling over larger spatial scales.

  2. Influence of porcine coat colour genotypes on haematological parameters, piglet birth weight and body weight gain until weaning.

    Science.gov (United States)

    Fésüs, L; Zsolnai, A; Komlósi, I

    2005-04-01

    Two F2 generations of an intercross between Hampshire boars and Hungarian Large White sows were produced to estimate the effects of the porcine KIT genotypes (II, Ii and ii) on quantitative and qualitative haematological indices, on piglet birth weight and growth performance until weaning. Piglets carrying the I allele had significantly fewer lymphocytes (p = 0.041) than the ii homozygotes, heterozygotes had measures between the two homozygotes. KIT genotypes did not influence white blood cells, red blood cells, haemoglobin and haematocrite. II genotype piglets were significantly lighter at birth than the ones carrying the recessive i allele, the effect of KIT genotypes on gain until weaning was not significant, but II piglets tended to gain less. The results of this study support the hypothesis of M. Johansson, H. Ellegren, L. Marklund, U. Gustavsson, E. Ringmar-Cederberg, K. Andersson, I. Edfors-Lilja and L. Andersson [(1992) Genomics, 14, 965] that the pleiotrophic effect of the porcine KIT mutations on haematopoietic cells must be mild.

  3. Lactase non-persistent genotype influences milk consumption and gastrointestinal symptoms in Northern Russians

    Directory of Open Access Journals (Sweden)

    Khabarova Yulia

    2011-11-01

    Full Text Available Abstract Background Milk is an important source of nutrients. The consumption of milk, however, may cause abdominal complaints in lactose intolerant individuals. The frequency of -13910C/C genotype is known to be high among Northern Russians, exceeding the prevalence in northern Europe. In our study we tested two hypotheses: 1 subjects with lactase non-persistent genotype (-13910C/C have more gastrointestinal (GI symptoms associated with milk 2 subjects with lactase non-persistence avoid using milk. Methods In total, 518 students aged 17 to 26 years were randomly selected from different departments in the Northern State Medical University (NSMU for genotyping the lactase activity-defining -13910C/T variant. All subjects filled in a questionnaire covering their personal data, self-reported GI symptoms and milk consumption habits. Results Northern Russians consume very small amounts of milk daily. Among carriers of the lactase non-persistent (LNP genotype there were 10 percentage units of milk-consumers fewer than among lactase-persistent (LP subjects (p = 0.03. Complaints of GI disorders caused by milk were different between the genotypes (p = 0.02. Among all types of food analyzed only milk was associated with increased GI symptoms among subjects with the LNP genotype (OR = 1.95, CI 1.03-3.69 Conclusions Subjects with -13910C/C have more GI symptoms from milk. Subjects with lactase non-persistent genotype avoid using milk. In the case of increasing milk consumption symptoms may increase the need for medical consultation. It is thus important either for people themselves or for health care staff to be aware of lactase persistence/non-persistence.

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

    Directory of Open Access Journals (Sweden)

    Gordana Brankovic

    2015-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Li Yi

    2004-06-01

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

  6. Adolescent age moderates genetic and environmental influences on parent-adolescent positivity and negativity: Implications for genotype-environment correlation.

    Science.gov (United States)

    Marceau, Kristine; Knopik, Valerie S; Neiderhiser, Jenae M; Lichtenstein, Paul; Spotts, Erica L; Ganiban, Jody M; Reiss, David

    2016-02-01

    We examined how genotype-environment correlation processes differ as a function of adolescent age. We tested whether adolescent age moderates genetic and environmental influences on positivity and negativity in mother-adolescent and father-adolescent relationships using parallel samples of twin parents from the Twin and Offspring Study in Sweden and twin/sibling adolescents from the Nonshared Environment in Adolescent Development Study. We inferred differences in the role of passive and nonpassive genotype-environment correlation based on biometric moderation findings. The findings indicated that nonpassive gene-environment correlation played a stronger role for positivity in mother- and father-adolescent relationships in families with older adolescents than in families with younger adolescents, and that passive gene-environment correlation played a stronger role for positivity in the mother-adolescent relationship in families with younger adolescents than in families with older adolescents. Implications of these findings for the timing and targeting of interventions on family relationships are discussed.

  7. Influence of plant species on population dynamics, genotypic diversity and antibiotic production by indigenous Pseudomonas spp

    NARCIS (Netherlands)

    Bergsma-Vlami, M.; Prins, M.E.; Raaijmakers, J.M.

    2005-01-01

    The population dynamics, genotypic diversity and activity of naturally-occurring 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. was investigated for four plant species (wheat, sugar beet, potato, lily) grown in two different soils. All four plant species tested, except lily and in some

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Long-term yield studies in perennial crops like miscanthus are important to determine mean annual energy yield and the farmer’s economy. In two Danish field trials, annual yield of two miscanthus genotypes was followed over a 20-year period. The trials were established in 1993 on loamy sand in Fo...

  9. Protective effect of NSAIDs on cancer and influence of COX-2 C-765G genotype

    NARCIS (Netherlands)

    C. Siemes (Claire); L.E. Visser (Loes); J.W.W. Coebergh (Jan Willem); A. Hofman (Albert); A.G. Uitterlinden (André); B.H.Ch. Stricker (Bruno)

    2008-01-01

    textabstractPurpose: Inhibition of COX-2 enzymes is a frequently suggested mechanism for the beneficial effects of NSAIDs on carcinogenesis. The aim of this study was to explore the role of cumulative NSAID use on four common non-skin related cancers and modification by COX-2 G-765C genotype. Patien

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

    Directory of Open Access Journals (Sweden)

    Margarita Miranda

    2013-06-01

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

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

    OpenAIRE

    2008-01-01

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

  12. Influence of genotype and sex on the response of growing pigs to recombinant porcine somatotropin.

    Science.gov (United States)

    Krick, B J; Roneker, K R; Boyd, R D; Beermann, D H; David, P J; Meisinger, D J

    1992-10-01

    The dose-dependent effects of porcine somatotropin (pST) on growth performance and composition of carcass gain were investigated in 150 growing pigs. The experiment involved two genotypes (barrows from the Pig Improvement Company [PIC] and a University of Nebraska [NEB] gene pool line) and two sexes (PIC barrows and boars). At 30 kg, pigs were randomly assigned within each genotype and sex subclass to receive daily i.m. injections of 50, 100, 150, or 200 micrograms of pST/kg BW or an equivalent volume of an excipient. A diet (3.5 Mcal of DE/kg) supplemented with crystalline amino acids and containing 22.5% CP was available on an ad libitum basis until pigs were slaughtered at approximately 90 kg live weight. Excipient-treated PIC barrows exhibited faster and more efficient growth (P less than .001) and a higher capacity for carcass protein accretion (P less than .001) but similar rates of lipid deposition compared to excipient-treated NEB barrows. Within the PIC genotype, control boars grew at a rate similar to that of barrows, but they were more efficient (P less than .05) and deposited more carcass protein (P less than .05) and less lipid (P less than .001). Carcass protein accretion rate increased (P less than .001) up to approximately 150 micrograms of pST.kg BW-1.d-1, whereas lipid deposition decreased (P less than .001) with each incremental dose of pST. Although differences between PIC boars and barrows for all criteria were negated with increasing pST dose, they were maintained between the two genotypes. Polynomial regressions suggested that a slightly higher pST dose was required to optimize the feed:gain ratio compared with rate of gain and that the dose (micrograms per kilogram BW per day) was a function of the genotype and sex (feed:gain: 185, 170, and 155; rate of gain: 155, 155, and 125 for NEB barrows, PIC barrows, and PIC boars, respectively).

  13. Does COMT genotype influence the effects of d-amphetamine on executive functioning?

    Science.gov (United States)

    Wardle, M C; Hart, A B; Palmer, A A; de Wit, H

    2013-02-01

    In a widely cited study, Mattay et al. reported that amphetamine (0.25 mg/kg oral, or 17 mg for a 68 kg individual) impaired behavioral and brain indices of executive functioning, measured using the Wisconsin Card Sorting Task (WCST) and N-Back working memory task, in 6 individuals homozygous for the met allele of the val158met polymorphism in the catechol-O-methyltransferase (COMT) gene, whereas it improved executive functioning in 10 individuals homozygous for the more active val allele. We attempted to replicate their behavioral findings in a larger sample, using similar executive functioning tasks and a broader range of amphetamine doses. Over four sessions, n = 200 healthy normal adults received oral placebo, d-amphetamine 5, 10, and 20 mg (average of 0.07, 0.15 and 0.29 mg/kg), under counterbalanced double-blind conditions and completed WCST and N-back tests of executive functioning. Amphetamine had typical effects on blood pressure and processing speed but did not affect executive functioning. COMT genotype (val158met) was not related to executive functioning under placebo or amphetamine conditions, even when we compared only the homozygous val/val and met/met genotypes at the highest dose of amphetamine (20 mg). Thus, we were not able to replicate the behavioral interaction between COMT and amphetamine seen in Mattay et al. We discuss possible differences between the studies and the implications of our findings for the use of COMT genotyping to predict clinical responses to dopaminergic drugs, and the use of intermediate phenotypes in genetic research.

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

    Directory of Open Access Journals (Sweden)

    Viktor A. Nedovic

    2007-01-01

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

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

    Science.gov (United States)

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

    2011-07-01

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

  16. The influence and possible recombination of genotypes on the production of microspore embryoids in anther cultures of Solanum tuberosum and dihaploid hybrids.

    Science.gov (United States)

    Jacobsen, E; Sopory, S K

    1978-05-01

    In addition to physical and chemical factors, genotype appears to be a very important factor influencing success in anther culture. Recombination by making crosses with selected responding clones has been introduced as a possible helpful method to positively influence the success and response type via the factor genotype. From the progeny of such a cross, one genotype could be selected, producing in 30 to 40 percent of the cultured anthers, fully developed embryoids and plantlets, which are a mixture of polyploids, dihaploids and monohaploids.Further, a pleiotropic marker 'embryo spot' visible as a 'nodal band' in the plant stage, has been used to confirm the microsporic origin of dihaploids and polyploids and to prove their homozygous nature. This marker also shows potential use in confirming the origin of calli from individual microspores.

  17. A protected area influences genotype-specific survival and the structure of a Canis hybrid zone.

    Science.gov (United States)

    Benson, John F; Patterson, Brent R; Mahoney, Peter J

    2014-02-01

    It is widely recognized that protected areas can strongly influence ecological systems and that hybridization is an important conservation issue. However, previous studies have not explicitly considered the influence of protected areas on hybridization dynamics. Eastern wolves are a species of special concern and their distribution is largely restricted to a protected population in Algonquin Provincial Park (APP), Ontario, Canada, where they are the numerically dominant canid. We studied intrinsic and extrinsic factors influencing survival and cause-specific mortality of hybrid and parental canids in the three-species hybrid zone between eastern wolves, eastern coyotes, and gray wolves in and adjacent to APP. Mortality risk for eastern wolves in areas adjacent to APP was significantly higher than for other sympatric Canis types outside of APP, and for eastern wolves and other canids within APP. Outside of APP, the annual mortality rate of all canids by harvest (24%) was higher than for other causes of death (4-7%). Furthermore, eastern wolves (hazard ratio = 3.5) and nonresidents (transients and dispersing animals, hazard ratio = 2.7) were more likely to die from harvest relative to other Canis types and residents, respectively. Thus, eastern wolves dispersing from APP were especially vulnerable to harvest mortality. For residents, eastern wolf survival was more negatively influenced by increased road density than for other Canis types, further highlighting the sensitivity of eastern wolves to human disturbance. A cycle of dispersal from APP followed by high rates of mortality and hybridization appears to maintain eastern wolves at low density adjacent to APP, limiting the potential for expansion beyond the protected area. However, high survival and numerical dominance of eastern wolves within APP suggest that protected areas can allow rare hybridizing species to persist even if their demographic performance is compromised and barriers to hybridization are largely

  18. Correlation of maturity groups with seed composition in soybeans, as influenced by genotypic variation.

    Directory of Open Access Journals (Sweden)

    Maestri, Damián M.

    1998-12-01

    Full Text Available Seeds of 19 soybean cultivars (Glycine max (L. Merrill with maturity groups V, VI or VII were analyzed for proximate composition, fatty acids and sterols. Protein, oil, carbohydrate and ash contents varied between 344-463 g kg-1, 178-233 g kg-1, 234-338 g kg-1, and 40.0-49.3 g kg-1 of dry matter, respectively. Fatty acid profiles revealed that the major acids were palmitic (9.2-12.5%, oleic (17.7-22.1% and linoleic (53.6-56.9%. Linolenic acid ranged from 8.6 to 10.4%. Sitosterol (48.1-56.8% was the main component of the sterol fraction, followed by campesterol (18.4-21.7% and stigmasterol (13.4-18.0%. Statistically significant differences between genotypes were found for the majority of parameters evaluated, but there are not significant variations among maturity groups.

    Se analizaron la humedad, contenido en proteínas, carbohidratos, grasas y cenizas, y las composiciones en ácidos grasos y esteróles de las semillas de 19 cultivares de soja (Glycine max (L. Merrill con grupos de madurez V, VI o VIl. Los contenidos de proteínas, aceites, carbohidratos y cenizas variaron entre 344-463 g kg-1, 178-233 g kg-1, 234-338 g kg-1 y 40.0-49.3 g kg-1 de materia seca, respectivamente. Los ácidos grasos mayoritarios fueron palmítico (9.2-12.5%, oleico (17.7-22.1% y linoleico (53.6-56.9%. El porcentaje de ácido linolénico varió desde 8.6 hasta 10.4%. El principal componente de la fracción de esteroles del aceite fue el sitosterol (48.1-56.8%, seguido por el campesterol (18.4-21.7% y el estigmasterol (13.4-18.0%. Se encontraron diferencias estadísticamente significativas entre los genotipos para la mayoría de los parámetros evaluados, pero no hubo variaciones significativas entre grupos de madurez.

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

    Directory of Open Access Journals (Sweden)

    Diego Lirman

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

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

    Directory of Open Access Journals (Sweden)

    Chris eBaeken

    2014-06-01

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

  1. Interaction genotype by season and its influence on the identification of beans with high content of zinc and iron

    Directory of Open Access Journals (Sweden)

    Camila Andrade Silva

    2012-01-01

    Full Text Available The mineral contents in common bean seeds are influenced, in addition to genetic variation, by environmental crop conditions, especially by the soil type and chemical composition and by the genotype x environment interaction. This study was carried out to verify if the zinc and iron contents are affected by the crop growing period. Ten lines with high iron and zinc contents and ten with low contents were assessed in three seasons: "wet season" of 2009/2010 (sowing in November; "dry season" of 2010 (sowing in February and "winter season" of 2010 (sowing in July, in Lavras, Minas Gerais State, Brazil. The experimental design used was randomized blocks with three replications and plots consisting of two rows of two meters, with a spacing of 0.50 m. The seeds harvested were assessed in regard to iron and zinc mineral contents. The greatest contents were observed in the winter season and the smallest ones in the dry season, with sowing in February. It was observed that in the mean of the three harvests, the lines classified as having high iron and zinc content exhibited an iron quantity 11.0% and a zinc quantity 6.8% above those of low content. The lines by seasons interaction occurs. However, its interference in identification of the groups with high and low content of the two nutrients is not great.

  2. Association of CCR2-CCR5 haplotypes and CCL3L1 copy number with Kawasaki Disease, coronary artery lesions, and IVIG responses in Japanese children.

    Directory of Open Access Journals (Sweden)

    Manju Mamtani

    Full Text Available BACKGROUND: The etiology of Kawasaki Disease (KD is enigmatic, although an infectious cause is suspected. Polymorphisms in CC chemokine receptor 5 (CCR5 and/or its potent ligand CCL3L1 influence KD susceptibility in US, European and Korean populations. However, the influence of these variations on KD susceptibility, coronary artery lesions (CAL and response to intravenous immunoglobulin (IVIG in Japanese children, who have the highest incidence of KD, is unknown. METHODOLOGY/PRINCIPAL FINDINGS: We used unconditional logistic regression analyses to determine the associations of the copy number of the CCL3L1 gene-containing duplication and CCR2-CCR5 haplotypes in 133 Japanese KD cases [33 with CAL and 25 with resistance to IVIG] and 312 Japanese controls without a history of KD. We observed that the deviation from the population average of four CCL3L1 copies (i.e., four copies was associated with an increased risk of KD and IVIG resistance (adjusted odds ratio (OR=2.25, p=0.004 and OR=6.26, p=0.089, respectively. Heterozygosity for the CCR5 HHF*2 haplotype was associated with a reduced risk of both IVIG resistance (OR=0.21, p=0.026 and CAL development (OR=0.44, p=0.071. CONCLUSIONS/SIGNIFICANCE: The CCL3L1-CCR5 axis may play an important role in KD pathogenesis. In addition to clinical and laboratory parameters, genetic markers may also predict risk of CAL and resistance to IVIG.

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

    Science.gov (United States)

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

    2016-04-06

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

  4. Field-isolated genotypes of Mycobacterium bovis vary in virulence and influence case pathology but do not affect outbreak size.

    Directory of Open Access Journals (Sweden)

    David M Wright

    Full Text Available Strains of many infectious agents differ in fundamental epidemiological parameters including transmissibility, virulence and pathology. We investigated whether genotypes of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB differ significantly in transmissibility and virulence, combining data from a nine-year survey of the genetic structure of the M. bovis population in Northern Ireland with detailed records of the cattle population during the same period. We used the size of herd breakdowns as a proxy measure of transmissibility and the proportion of skin test positive animals (reactors that were visibly lesioned as a measure of virulence. Average breakdown size increased with herd size and varied depending on the manner of detection (routine herd testing or tracing of infectious contacts but we found no significant variation among M. bovis genotypes in breakdown size once these factors had been accounted for. However breakdowns due to some genotypes had a greater proportion of lesioned reactors than others, indicating that there may be variation in virulence among genotypes. These findings indicate that the current bTB control programme may be detecting infected herds sufficiently quickly so that differences in virulence are not manifested in terms of outbreak sizes. We also investigated whether pathology of infected cattle varied according to M. bovis genotype, analysing the distribution of lesions recorded at post mortem inspection. We concentrated on the proportion of cases lesioned in the lower respiratory tract, which can indicate the relative importance of the respiratory and alimentary routes of infection. The distribution of lesions varied among genotypes and with cattle age and there were also subtle differences among breeds. Age and breed differences may be related to differences in susceptibility and husbandry, but reasons for variation in lesion distribution among genotypes require further investigation.

  5. Influence of Rice Genotypes on Folding and Spinning Behaviour of Leaffolder (Cnaphalocrocis medinalis) and Its Interaction with Leaf Damage

    Institute of Scientific and Technical Information of China (English)

    M. PUNITHAVALLI; N. M. MUTHUKRISHNAN; M. BALAJI RAJKUMAR

    2013-01-01

    Folding and spinning behavior of Cnaphalocrocis medinalis (Guenee) (Lepidoptera:Pyralidae) in different categories of rice genotypes viz., resistant, susceptible, hybrid, scented, popular and wild rice genotypes were significantly different. Longer leaf selection time and folding time per primary fold;shorter primary fold and whole leaf fold; lower number of binds per primary fold and whole leaf fold were recorded in resistant and wild rice genotypes. In the correlation analysis, it was found that the leaf folding parameters were positively correlated to leaf folder damage whereas the leaf spinning parameters were negatively correlated. Similarly, the morphological characters differed significantly among the chosen genotypes and were related to leaffolder damage. The leaf width and total productive tiller number were positively correlated to leaffolder infestation. Results also indicated that the trichome density and length, leaf length and plant height might contribute to resistance whereas total number of green leaves had no effect on leaffolder infestation. In the scatter plot analysis between leaf folding and spinning characters and leaffolder damage, the genotypes were separated into four groups viz., resistant (TKM6, Ptb 33, LFR831311, Oryza rhizomatis and O. minuta), moderately resistant (ASD16 and CORH1), moderately susceptible (ADT36, Pusa Basmati and CB200290) and susceptible (IR36 and TN1). The present investigation proved that the leaf morphology viz., leaf length and width, plant height and trichome density and length may play a vital role in resistance against rice leaffolder.

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

    Directory of Open Access Journals (Sweden)

    Vanessa Chaia Kaippert

    2013-06-01

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

  7. Growth and yield components of wheat genotypes as influenced by potassium and farm yard manure on a saline sodic soil

    Directory of Open Access Journals (Sweden)

    Muhammad Ashraf, Muhammad Afzal

    2011-11-01

    Full Text Available The adequate supply of mineral nutrients through chemical fertilizers and manure may help to sustain the crop productivity and ensure plant survival under salinity stress. A field study was conducted on saline sodic soil (ECe = 13 dS m-1, SAR 23.3 (mmol L-11/2, pH = 8.6 of surface 15 cm layer to quantify the effects of potassium (K and farm yard manure (FYM on two wheat genotypes differing in salinity tolerance. Three K levels (0, 80, 120 kg ha-1 and two FYM levels (0, 10 t ha-1 were tested using randomized compete block design (RCBD with three replications. The application of K along with FYM reduced Na+ uptake and accumulation in plant tissue. The K concentration and K+/ Na+ ratio were significantly improved in both wheat genotypes with the supplementation of K and FYM. The grain yield was improved by 40-156% in salt tolerant genotype and 46-206% in salt sensitive genotype with added K and FYM. Similar trend was observed in yield components. Ameliorative effects of added K and FYM were more marked in salt sensitive genotype (Auqab-2000 than in salt tolerant (Inqlab-91. Grain yield of salt sensitive and salt tolerant wheat genotypes was positively correlated with leaf K+ concentration determined at various treatments. Addition of K along with FYM decreased sodium adsorption ratio (SAR and electrical conductivity (EC of soil particularly in upper layers. Therefore, it is concluded that K along with FYM could help to alleviate deleterious effects of salts and thus improve the productivity of salt affected soils.

  8. [Influence of genotype, explant type and component of culture medium on in vitro callus induction and shoot organogenesis of tomato (Solanum lycopersicum L.)].

    Science.gov (United States)

    Khaliluev, M R; Bogoutdinova, L R; Baranova, G B; Baranova, E N; Kharchenko, P N; Dolgov, S V

    2014-01-01

    The influence of explant type as well as of the type of growth regulators and concentration on callus induction processes and somatic organogenesis of shoots was studied in vitro on four tomato genotypes of Russian breeding. Cytological study of callus tissue was conducted. It was established that tomato varieties possess a substantially greater ability to indirect shoot organogenesis compared with the F1 hybrid. The highest frequency of somatic organogenesis of shoots, as well as their number per explant, was observed for most of the genotypes studied during the cultivation of cotyledons on Murashige-Skoog culture medium containing 2 mg/l of zeatin in combination with 0.1 mg/l of 3-indoleacetic acid. An effective protocol of indirect somatic organogenesis of shoots from different explants of tomato varieties with a frequency of more than 80% was developed.

  9. Viral genotype and HLA class II alleles influence on extra-hepatic manifestations of chronic HCV infection

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    M. Galeazzi

    2011-09-01

    Full Text Available Objective: To test whether an association between HCV genotype, HLA class II alleles distribution and extra-hepatic manifestations (EHM can be demonstrated in a group of Italian patients with chronic HCV infection . Methods: Sixty patients affected by HCV infection with EHM were consecutively enrolled. 163 HCV patients without EHM were tested as controls for the prevalence of HCV genotypes, while we referred to literature as to the controls for HLA distribution. HCV-RNA was quantified by a RT-PCR. HLA class II alleles typing was performed using a standard microlymphocytotoxicity assay. We used chi-square or Fisher test (p<0.05 significant. Odds Ratio (OR was performed by 2X2 contingency table. Results: HCV 2c genotype was found in 63.46% of patients compared to 19.63% of controls (p<0.0001; OR=7.11. Furthermore, it correlated with carpal tunnel syndrome (p=0.03; OR=4.5 and autoimmune thyroiditis (p=0.02; OR=9.2. On the contrary, 1b genotype protected from EHM in toto (p=0.0004; OR=0.21 and particularly from carpal tunnel syndrome (p=0.0014; OR=0.07. Moreover, 3a genotype prevented HCV people from having cryoglobulinemia (p=0.05; OR=0.11. As to HLA, DR6 seemed to facilitate EHM in HCV patients (p=0.041; OR=1.61, while DQ2 (p=0.03; OR=0.5 and DQ3 (p=0.002; OR= 0.5 may play a protective role. In addition, HLA DR3 was associated with cryoglobulinemia (p=0.02; OR=9.5. Conclusions: According to our findings, 2c genotype can be considered as a major risk factor for developing HCVrelated EHM, while 1b genotype seems to prevent their onset; there are also evidences suggesting that HLA might play a role in chronic HCV infected patients.

  10. AKT1 G205T Genotype Influences Obesity-Related Metabolic Phenotypes and Their Responses to Aerobic Exercise Training in Older Caucasians

    Science.gov (United States)

    McKenzie, Jennifer A.; Witkowski, Sarah; Ludlow, Andrew T.; Roth, Stephen M.; Hagberg, James M.

    2010-01-01

    As part of the insulin signaling pathway, AKT influences growth and metabolism. The AKT1 gene G205T (rs1130214) polymorphism has potential functional effects. Thus, we determined whether the G205T polymorphism influences metabolic variables and their responses to aerobic exercise training. Following dietary stabilization, healthy, sedentary, 50-75 yr old Caucasian men (n = 51) and women (n = 58) underwent 6 months of aerobic exercise training. Before and after completing the intervention, dual-energy x-ray absorptiometry measured percent body fat, computed tomography measured visceral and subcutaneous fat, and oral glucose tolerance testing measured glucose total area under the curve (AUC), insulin AUC, and insulin sensitivity. Taqman assay determined AKT1 G205T genotypes. At baseline, men with the GG genotype (n = 29) had lower VO2max values (p = 0.026), and higher percent body fat (p = 0.046), subcutaneous fat (p = 0.021), and insulin AUC (p = 0.003) values than T allele carriers (n = 22). Despite their rather disadvantageous starting values, men with the GG genotype seemed to respond to exercise training more robustly than men with the T allele, highlighted by significantly greater fold change improvements in insulin AUC (p = 0.012) and glucose AUC (p = 0.035). Although the GG group also significantly improved VO2max with training, the change in VO2max was not as great as that of the T allele carriers (p = 0.037). In contrast, after accounting for hormone replacement therapy use, none of the variables differed in the women at baseline. As a result of exercise training, women with the T allele (n = 20) had greater fold change improvements in fasting glucose (p = 0.011), glucose AUC (p = 0.017), and insulin sensitivity (p = 0.044) than GG genotype women (n = 38). Our results suggest that the AKT1 G205T polymorphism influences metabolic variables and their responses to aerobic exercise training in older previously sedentary individuals. PMID:21097644

  11. AKT1 G205T genotype influences obesity-related metabolic phenotypes and their responses to aerobic exercise training in older Caucasians.

    Science.gov (United States)

    McKenzie, Jennifer A; Witkowski, Sarah; Ludlow, Andrew T; Roth, Stephen M; Hagberg, James M

    2011-03-01

    As part of the insulin signalling pathway, Akt influences growth and metabolism. The AKT1 gene G205T (rs1130214) polymorphism has potential functional effects. Thus, we determined whether the G205T polymorphism influences metabolic variables and their responses to aerobic exercise training. Following dietary stabilization, healthy, sedentary, 50- to 75-year-old Caucasian men (n = 51) and women (n = 58) underwent 6 months of aerobic exercise training. Before and after completing the intervention, dual-energy X-ray absorptiometry was used to measure percentage body fat, computed tomography to measure visceral and subcutaneous fat, and oral glucose tolerance testing to measure glucose total area under the curve (AUC), insulin AUC and insulin sensitivity. Taqman assay was used to determine AKT1 G205T genotypes. At baseline, men with the GG genotype (n = 29) had lower maximal oxygen consumption (VO2 max) values (P = 0.026) and higher percentage body fat (P = 0.046), subcutaneous fat (P = 0.021) and insulin AUC (P = 0.003) values than T allele carriers (n = 22). Despite their rather disadvantageous starting values, men with the GG genotype seemed to respond to exercise training more robustly than men with the T allele, highlighted by significantly greater fold change improvements in insulin AUC (P = 0.012) and glucose AUC (P = 0.035). Although the GG group also significantly improved VO2 max with training, the change in VO2 max was not as great as that of the T allele carriers (P = 0.037). In contrast, after accounting for hormone replacement therapy use, none of the variables differed in the women at baseline. As a result of exercise training, women with the T allele (n = 20) had greater fold change improvements in fasting glucose (P = 0.011), glucose AUC (P = 0.017) and insulin sensitivity (P = 0.044) than GG genotype women (n = 38). Our results suggest that the AKT1 G205T polymorphism influences metabolic variables and their responses to aerobic exercise training in

  12. Influence of the unsaturated fatty acids on body weight, glucose, and lipids metabolism in obese women with Pro12Pro genotype in PPARγ2 gene

    Directory of Open Access Journals (Sweden)

    Márcia Fófano do Lago

    Full Text Available Background: The type of dietary fatty acid may have different effects on obesity and its complications, however, these effects can be influenced by genes and polymorphisms, such as peroxisome proliferator-activated receptor γ isoform 2 (PPARγ2. Moreover, it is unclear whether the degree of unsaturation of the fat has different effects on lipid and glucose metabolism, and particularly the loss of body weight. Objective: To evaluate the influence of diets rich in polyunsaturated fatty acids (PUFA and monounsaturated fatty acids (MUFA on anthropometric and biochemical variables in obese woman with genotype Pro12Pro on PPARγ2 gene on body weight, glycemic and lipemic profile. Methods: Eighteen obese women with Pro12Pro genotype in PPARγ2 gene were randomized into groups to receive a high PUFAs (PUFA-diet, n = 8 or MUFAs (MUFA-diet, n = 10 diets. Anthropometrics (body mass index [BMI] and waist circumference and biochemical variables (glucose, insulin, HOMA-IR, total cholesterol, LDL-cholesterol, and HDL-cholesterol and triglycerides were evaluated at baseline and after 45 days. Results: Anthropometric and biochemical variables were similar between groups at baseline and after intervention (p > 0.05. BMI decrease only in PUFA-diet (p = 0.01, probably due to the lower lipid content in this diet. MUFA-diet decrease fasting glucose (p = 0.03, insulin (p = 0.03, and HOMA-IR (p = 0.02. Conclusion: Compared to PUFA, MUFA was more efficient to reduce the insulin resistance in obese women with Pro12Pro genotype in PPARγ2, even in high saturated fatty acids and total fat diet.

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

    Directory of Open Access Journals (Sweden)

    Pablito M. Magdalita

    2015-06-01

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

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

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    Natalia M. Araujo

    2009-08-01

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

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

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    Melanie eStollstorff

    2013-07-01

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

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

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    Benedikt Klauke

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

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

    Science.gov (United States)

    Klauke, Benedikt; Winter, Bernward; Gajewska, Agnes; Zwanzger, Peter; Reif, Andreas; Herrmann, Martin J; Dlugos, Andrea; Warrings, Bodo; Jacob, Christian; Mühlberger, Andreas; Arolt, Volker; Pauli, Paul; Deckert, Jürgen; Domschke, Katharina

    2012-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Xinxin Ye; Yibing Ma; Bo Sun

    2012-01-01

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

  19. The influence of genotype on vascular endothelial growth factor and regulation of myocardial collateral blood flow in patients with acute and chronic coronary heart disease

    DEFF Research Database (Denmark)

    Ripa, R.S.; Jorgensen, E.; Baldazzi, F.;

    2009-01-01

    OBJECTIVE: To test the hypothesis that mutations in the vascular endothelial growth factor (VEGF) gene are associated with plasma concentration of VEGF and subsequently the ability to influence coronary collateral arteries in patients with coronary heart disease (CHD). METHODS: Blood samples from...... patients with chronic ischemic heart disease (n=53) and acute coronary syndrome (n=61) were analysed. Coronary collaterals were scored from diagnostic biplane coronary angiograms. RESULTS: The plasma concentration of VEGF was increased in patients with acute compared to chronic CHD (p=0.01). The genotype......-1154 and coronary collateral size (p=0.03) and a significant association between the VEGF plasma concentration and the collateral size (p=0.03). CONCLUSION: VEGF plasma concentration seems related to coronary collateral function in patients with CHD. The results did not support the hypothesis...

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

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    Jorge Luís Ferreira

    2015-08-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  2. Affective and neuroendocrine stress reactivity to an academic examination: influence of the 5-HTTLPR genotype and trait neuroticism.

    Science.gov (United States)

    Verschoor, Ellen; Markus, C Rob

    2011-07-01

    The current study examined the singular and interactive effects of the 5-HTTLPR genotype and trait neuroticism on affective and physiological stress responses to an academic examination in healthy undergraduate students. From 771 students, 46 short/short (S/S)-allele carriers and 48 long/long (L/L)-allele carriers with the lowest and the highest neuroticism scores (80 females, 14 males; mean age±SD: 20.3±1.7 years) were selected. Salivary cortisol concentrations, mood and perceived stress were assessed before and after a 2-h written examination and compared with a control day. Negative mood, perceived stress and cortisol significantly increased during the examination compared to the control day. Negative stress effects on mood and perceived stress were significantly larger for S/S-allele carriers compared to L/L-allele carriers, regardless of trait neuroticism. Since vulnerability to real-life stressors is an important risk factor for depression pathogenesis, this may be a mediating factor making S/S-allele carriers more susceptible for depression symptoms.

  3. 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.

  4. Influence of COMT val158met Genotype on the Depressed Brain during Emotional Processing and Working Memory

    NARCIS (Netherlands)

    Opmeer, Esther M.; Kortekaas, Rudie; van Tol, Marie-Jose; van der Wee, Nic J. A.; Woudstra, Saskia; van Buchem, Mark A.; Penninx, Brenda W.; Veltman, Dick J.; Aleman, Andre

    2013-01-01

    Major depressive disorder (MDD) has been associated with abnormal prefrontal-limbic interactions and altered catecholaminergic neurotransmission. The val158met polymorphism on the catechol-O-methyltransferase (COMT) gene has been shown to influence prefrontal cortex (PFC) activation during both emot

  5. Response of rice genotype to straighthead disease as influenced by arsenic level and water management practices in soil.

    Science.gov (United States)

    Hua, Bin; Yan, Wengui; Yang, John

    2013-01-01

    Arsenic (As) uptake by rice plants and the straighthead disease induced by As-based herbicide are of environmental concerns. Bioavailability or mobility of inorganic As in soil has been reported to be significantly influenced by soil minerals such as iron (hydr) oxide; however, the interactions of organic As such as monosodium methanearsonate (MSMA) with soil minerals are little studied, thus largely unknown. In an effort to minimize the As uptake by rice and determine rice cultivar response to soil MSMA level, a field experiment was conducted on three rice cultivars grown in both MSMA-treated and -untreated soils under continuous or intermittent flood water management practices. Results indicated that the grain yield and the occurrence of straighthead disease were cultivar-dependent and influenced by soil As level and water management practices. Straighthead-resistant cultivars yielded more and had lower grain As than the susceptible ones. Elevated soil As with continuous flood management significantly reduced the grain yield of susceptible cultivars by >89% due to substantially increased straighthead, which were induced by increased As content in grains. Yield reduction by MSMA treatment could be partially mitigated with intermittent flood water practice. The As accumulation was found to be associated with soil iron redox transformation influenced by the water management. This study demonstrates that the selection of less As-susceptible cultivars and intermittent flood water practice could be effective means to lower the As accumulation in grains and minimize the occurrence of the As-induced straighthead symptom and yield reduction.

  6. Genotype and harvest time influence the phytochemical quality of Fino lemon juice (Citrus limon (L.) Burm. F.) for industrial use.

    Science.gov (United States)

    González-Molina, Elena; Moreno, Diego A; García-Viguera, Cristina

    2008-03-12

    Two clonal selections of lemon tree (Citrus limon Burm. f. cv. Fino), named Fino-49-5 and Fino-95, were studied to ascertain the influence of genetic (clone) and environmental (season) factors on the human-health bioactive compounds of lemon juice (vitamin C and flavonoids) and the possible relationship between composition and in vitro antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulfonic acid), and ferric reducing antioxidant power) of the juice. The cultivar Fino-49-5 performed better in terms of flavonoid and vitamin C contents. Variability in the weather conditions determined, at least in part, differences in the content of lemon juice bioactives more importantly than the genetic background did. Therefore, the food industry would have phytochemically rich and nutritive lemons with practically complete independence of the harvest time and the selected cultivar.

  7. The Influence of Genetics on Response to Treatment with Ranibizumab (Lucentis) for Age-Related Macular Degeneration: The Lucentis Genotype Study (An American Ophthalmological Society Thesis)

    Science.gov (United States)

    Francis, Peter James

    2011-01-01

    Purpose Age-related macular degeneration (AMD) has a complex etiology arising from genetic and environmental influences. This past decade have seen several genes associated with the disease. Variants in five genes have been confirmed to play a major role. The objective of this study was to evaluate whether genes influence treatment response to ranibizumab for neovascular AMD. The hypothesis was that an individual’s genetic variation will determine treatment response. Methods The study was a two-site prospective open-label observational study of patients newly diagnosed with exudative (neovascular) AMD receiving intravitreal ranibizumab therapy. Treatment-naïve patients were enrolled at presentation and received monthly “as needed” therapy. Clinical data was collected monthly and DNA extracted. Genotyping was performed using the Illumina (San Diego, California) 660-Quad single-nucleotide polymorphism (SNP) chip. Regression analyses were performed to identify SNPs associated with treatment-response end points. Results Sixty-five patients were enrolled. No serious adverse events were recorded. The primary outcome measure was change in ETDRS visual acuity at 12 months. A SNP in the CFH gene was found to be associated with less improvement in visual acuity while receiving ranibizumab therapy. The C3 gene, among others, was associated with reduced thickening and improved retinal architecture. VEGFA, FLT1, and CFH were associated with requiring fewer ranibizumab injections over the 12-month study. Conclusions This study is one of the first prospective pharmacogenetic study of intravitreal ranibizumab. Although preliminary, the results identify a number of putative genetic variants, which will be further examined by replication and functional studies to elucidate the complete pharmacogenetic architecture of therapy for AMD. PMID:22253485

  8. HFE-Related Hemochromatosis: The Haptoglobin 2-2 Type Has a Significant but Limited Influence on Phenotypic Expression of the Predominant p.C282Y Homozygous Genotype

    Directory of Open Access Journals (Sweden)

    Gérald Le Gac

    2009-01-01

    In this study we investigated influence of Hp2-2 and of potential confounders on the iron indices of 351 p.C282Y homozygous patients. We conclude that there is a cause-and-effect relationship between the Hp2-2 genotype and increased iron indices in p.C282Y homozygous patients. The Hp2-2 effect is, however, limited and only apparent in males.

  9. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    OpenAIRE

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicoch...

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

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    Orwa eAboud

    2015-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Jeeser Alves Almeida

    2012-04-01

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

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

    Science.gov (United States)

    Jackson, Dylan B; Beaver, Kevin M

    2015-12-10

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

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

    Directory of Open Access Journals (Sweden)

    Tetsu Tomita

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

  14. Cortical Dopamine Transmission as Measured with the [11C]FLB 457 - Amphetamine PET Imaging Paradigm Is Not Influenced by COMT Genotype.

    Directory of Open Access Journals (Sweden)

    Rajesh Narendran

    Full Text Available Basic investigations link a Val158Met polymorphism (rs4680 in the catechol-O-methyltransferase (COMT gene to not only its enzymatic activity, but also to its dopaminergic tone in the prefrontal cortex. Previous PET studies have documented the relationship between COMT Val158Met polymorphism and D1 and D2/3 receptor binding potential (BP, and interpreted them in terms of dopaminergic tone. The use of baseline dopamine D1 and D2/3 receptor binding potential (BPND as a proxy for dopaminergic tone is problematic because they reflect both endogenous dopamine levels (a change in radiotracer's apparent affinity and receptor density. In this analysis of 31 healthy controls genotyped for the Val158Met polymorphism (Val/Val, Val/Met, and Met/Met, we used amphetamine-induced displacement of [11C]FLB 457 as a direct measure of dopamine release. Our analysis failed to show a relationship between COMT genotype status and prefrontal cortical dopamine release. COMT genotype was also not predictive of baseline dopamine D2/3 receptor BPND.

  15. Influence of genotype and processing on the in vitro rate of starch hydrolysis and resistant starch formation in peas (Pisum sativum L.).

    Science.gov (United States)

    Skrabanja, V; Liljeberg, H G; Hedley, C L; Kreft, I; Björck, I M

    1999-05-01

    The formation of resistant starch (RS) and the rate of starch hydrolysis were evaluated in vitro in a wild type of green-seeded pea genotype RRRbRb BC3 (33-Am) with 32.7% amylose content and in two mutants RRrbrb BC3 (23-Am) and rrRbRb BC3 (65-Am) with amylose contents of 23.3 and 65.1%, respectively. Pea samples were intact or homogenized and subjected either to autoclaving or to boiling at atmospheric pressure. The amount of RS (total starch basis) varied from 6.2 to 12.9% in the 23-Am products and from 31.2 to 33.4% in the 65-Am products. The RS level of the 33-Am product with a regular amylose content was 11.0%. Both the 23-Am and the 65-Am products were abundant sources of dietary fiber (39 and 34%, dry matter basis, respectively) versus 23% in the regular pea product. The amylose/amylopectin ratio was an important determinant of the rate of starch hydrolysis. The hydrolysis indices (HI) and predicted glycemic indices were lowest in the 65-Am peas (HI range = 42-59) as compared to the 23-Am peas (HI range = 53-84). It is concluded that the pea genotypes covered a wide range in starch availability, which is likely to affect nutritional parameters such as glycemic responses and colonic delivery of starch.

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

    Science.gov (United States)

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

    2006-09-01

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

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

    Science.gov (United States)

    Bahreini, Rassol; Currie, Robert W

    2015-08-01

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

  18. Influences of gestational obesity on associations between genotypes and gene expression levels in offspring following maternal gastrointestinal bypass surgery for obesity.

    Directory of Open Access Journals (Sweden)

    Frédéric Guénard

    Full Text Available METHODS: Whole-genome genotyping and gene expression analyses in blood of 22 BMS and 23 AMS offspring from 19 mothers were conducted using Illumina HumanOmni-5-Quad and HumanHT-12 v4 Expression BeadChips, respectively. Using PLINK we analyzed interactions between offspring gene variations and maternal surgical status on offspring gene expression levels. Altered biological functions and pathways were identified and visualized using DAVID and Ingenuity Pathway Analysis. RESULTS: Significant interactions (p ≤ 1.22 x 10(-12 were found for 525 among the 16,060 expressed transcripts: 1.9% of tested SNPs were involved. Gene function and pathway analysis demonstrated enrichment of transcription and of cellular metabolism functions and overrepresentation of cellular stress and signaling, immune response, inflammation, growth, proliferation and development pathways. CONCLUSION: We suggest that impaired maternal gestational metabolic fitness interacts with offspring gene variations modulating gene expression levels, providing potential mechanisms explaining improved cardiometabolic risk profiles of AMS offspring related to ameliorated maternal lipid and carbohydrate metabolism.

  19. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

  20. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  1. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    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...... 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...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  2. Postmortem Blood Concentrations of R- and S-Enantiomers of Methadone and EDDP in Drug Users: Influence of Co-Medication and P-glycoprotein Genotype

    DEFF Research Database (Denmark)

    Buchard, Anders; Linnet, Kristian; Johansen, Sys Stybe;

    2010-01-01

    We investigated toxicological and pharmacogenetic factors that could influence methadone toxicity using postmortem samples. R- and S-methadone were measured in femoral blood from 90 postmortem cases, mainly drug users. The R-enantiomer concentrations significantly exceeded that of the S-enantiome......We investigated toxicological and pharmacogenetic factors that could influence methadone toxicity using postmortem samples. R- and S-methadone were measured in femoral blood from 90 postmortem cases, mainly drug users. The R-enantiomer concentrations significantly exceeded that of the S......-enantiomers (Wilcoxon's test, p

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

    Directory of Open Access Journals (Sweden)

    Whitney eWeikum

    2013-10-01

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

  4. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Cardiovascular Disease Share this page: Was this page helpful? Also ... of choice to decrease the risk of developing cardiovascular disease (CVD) . However, there is a wide variability in ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Sabro Nielsen, P.

    1996-12-31

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

  6. ABO Genotyping of Complete Hydatidiform Moles

    Directory of Open Access Journals (Sweden)

    R. A. Fisher

    1993-01-01

    Full Text Available It has been suggested that the ABO blood group of a patient and her partner influence the clinical outcome for patients having a pregnancy with a complete hydatidiform mole (CHM. Since CHM lack red blood Cells, it has not previously been possible to type CHM serologically and investigate the relationship between the blood group of the CHM and that of the patient. In the present study we have demonstrated the feasibility of using molecular genotyping to determine the ABO genotype of CHM, the ABO genotype being consistent with the androgenetic origin of CHM in all cases. In the series of 48 cases of CHM, the requirement for chemotherapy was not significantly different in those patients with a CHM of like blood group compared with those with a CHM of unlike blood group.

  7. Axiom turkey genotyping array

    Science.gov (United States)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  8. Hepatitis C viral load, genotype 3 and interleukin-28B CC genotype predict mortality in HIV and hepatitis C-coinfected individuals

    DEFF Research Database (Denmark)

    Clausen Nygaard, Louise; Astvad, Karen; Ladelund, Steen;

    2012-01-01

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

  9. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

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

  10. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

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

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

    DEFF Research Database (Denmark)

    Soriano, Vincent; Mocroft, Amanda; Peters, Lars

    2010-01-01

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

  12. Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

    Science.gov (United States)

    Moskvina, Valentina; Schmidt, Karl Michael

    2006-12-01

    With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

  13. Association between histological findings, aminotransferase levels and viral genotype in chronic hepatitis C infection

    Directory of Open Access Journals (Sweden)

    Amanda Alves Fecury

    2014-02-01

    Full Text Available Introduction: The genomic heterogeneity of hepatitis C virus (HCV influences liver disorders. This study aimed to determine the prevalence of HCV genotypes and to investigate the influence of these genotypes on disease progression. Methods: Blood samples and liver biopsies were collected from HCV-seropositive patients for serological analysis, biochemical marker measurements, HCV genotyping and histopathological evaluation. Results: Hepatitis C virus-ribonucleic acid (HCV-RNA was detected in 107 patients (90.6% with genotype 1 and 9.4% with genotype 3. Patients infected with genotype 1 exhibited higher mean necroinflammatory activity and fibrosis. Conclusions: HCV genotype 1 was the most prevalent and was associated with greater liver dysfunction.

  14. Variability of traits quinoa introduced genotypes (Chenopodium quinoa Willd.)

    OpenAIRE

    Dražić, Slobodan; ŽIVANOVIĆ, Tomislav; Maletić, Radojka; Glamočlija, Đorđe; Žarković, Branka; Dražić, Milena

    2013-01-01

    We analyzed variability and influence of investigated factors on grain yield of quinoa during three year period (2009, 2010, 2011). The experiment was conducted at two locations (Nova Pazova and Surduk), using two introduced genotypes of quinoa: KVL 37 and KVL 52. We detected that location and genotype had important impact. Grain yield varied according to years of study (1224 kg/ha to 1671 kg/ha). Results of regression and correlation analysis indicate on variation of the impact of plant heig...

  15. Changing genotypes of cholera toxin (CT) of Vibrio cholerae O139 in Bangladesh and description of three new CT genotypes.

    Science.gov (United States)

    Bhuiyan, Nurul A; Nusrin, Suraia; Alam, Munirul; Morita, Masatomo; Watanabe, Haruo; Ramamurthy, Thandavarayan; Cravioto, Alejandro; Nair, Gopinath Balakrish

    2009-11-01

    We determined the genotype of cholera toxin by amplifying and sequencing the B-subunit in a sequential collection of 90 strains of Vibrio cholerae O139 isolated over the past 13 years since its first description in 1992. Representative strains isolated during 1993-1997 harboured ctxB of El Tor type (genotype 3). Twenty-six strains isolated during 1999, 2001, 2005 and three strains isolated in 1998, 2000 and 2002 were identified to belong to new ctxB genotypes 4 and 5, respectively. Genotype 5 was similar to genotype 1 except at position 28 (D-->A). The genotype 6 was similar to genotype 4 except at position 34 (H-->P). The implication of switch in terms of function of the toxin and its impact on human disease is unclear. How this change has influenced their prevalence relative to that of V. cholerae O1 in human infection is also not clear. The other common virulence gene clusters including the Vibrio pathogenicity island-1, Vibrio seventh pandemic island (VSP)-I and VSP-II of V. cholerae O139 did not show any remarkable difference from that of the O1 El Tor strains. Overall, the majority of the O139 strains tested in this study were similar to the El Tor strains but had altered ctxB genotype. This change and the impact that it causes to the epidemiology of cholera caused by O139 should be closely monitored.

  16. Hepatitis B virus genotypes and resistance mutations in patients under long term lamivudine therapy: characterization of genotype G in Brazil

    Directory of Open Access Journals (Sweden)

    Brandão Carlos E

    2008-01-01

    Full Text Available Abstract Background Lamivudine is an oral nucleoside analogue widely used for the treatment of chronic hepatitis B. The main limitation of lamivudine use is the selection of resistant mutations that increases with time of utilization. Hepatitis B virus (HBV isolates have been classified into eight genotypes (A to H with distinct geographical distributions. HBV genotypes may also influence pathogenic properties and therapeutic features. Here, we analyzed the HBV genotype distribution and the nature and frequency of lamivudine resistant mutations among 36 patients submitted to lamivudine treatment for 12 to 84 months. Results Half of the patients were homosexual men. Only 4/36 (11% patients were HBV DNA negative. As expected for a Brazilian group, genotypes A (24/32 positive individuals, 75%, D (3/32, 9.3% and F (1/32, 3% were present. One sample was from genotype C, which is a genotype rarely found in Brazil. Three samples were from genotype G, which had not been previously detected in Brazil. Lamivudine resistance mutations were identified in 20/32 (62% HBV DNA positive samples. Mean HBV loads of patients with and without lamivudine resistance mutations were not very different (2.7 × 107 and 6.9 × 107 copies/mL, respectively. Fifteen patients showed the L180M/M204V lamivudine resistant double mutation. The triple mutant rt173V/180M/204V, which acts as a vaccine escape mutant, was found in two individuals. The three isolates of genotype G were entirely sequenced. All three showed the double mutation L180M/M204V and displayed a large genetic divergence when compared with other full-length genotype G isolates. Conclusion A high (55% proportion of patients submitted to long term lamivudine therapy displayed resistant mutations, with elevated viral load. The potential of transmission of such HBV mutants should be monitored. The identification of genotypes C and G, rarely detected in South America, seems to indicate a genotype distribution different

  17. STR MARKERS. GENOTYPING APPLICATIONS

    Directory of Open Access Journals (Sweden)

    I. O. Sirbu

    2001-01-01

    Full Text Available STR (short tandem repeats loci consist of short, repetitive sequence elements of 2-8 bp in length. These abundant repeats are well distributed throughout the human genome and are rich source of highly polymorphic markers. There are literally hundreds of STR systems which have been mapped throughout the human genome. Several dozen have been investigated for application to human identity testing. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use. In this paper we intend (far from being exhaustive to present a synthesis of the characteristics of these genetic markers and their applications in genotyping, giving as an example the use of the STRs in a paternity testing case.

  18. The potential of different lime tree (Tilia spp genotypes for phytoextraction of heavy metals

    Directory of Open Access Journals (Sweden)

    Šijačić-Nikolić Mirjana

    2012-01-01

    Full Text Available The research of heavy metals contents (Pb, Mn, Zn, Ni, Fe in soil in the area of the National Park „Fruška gora”, along the highway M21 shows lower values for manganese, zinc and iron than the maximum allowed quantity prescribed by law. For nickel and lead it shows higher values than maximum allowed quantity. The heavy metals contents in leaves of lime tree in 12 analyzed genotypes are far below average values in accordance with ECCE with all genotypes except genotype 7 for lead and genotypes 7 and 8 for iron. The results of analysis of variance components show that out of four components (locality, genotype, locality x genotype and error only the interaction between locality and genotype does not contribute to variance. The contents of Pb, Mn, Fe and Zn in leaves is primarily influenced by genotype while Ni contents may be considered a consequence of locality. The selection of genotypes which is able to uptake greater quantities of heavy metals than other genotypes may serve as a solid basis for phytoextraction of heavy metals as a technology by which heavy metals, metalloids and radionuclides are extracted from environment through usage of suitable species and plant genotypes able to uptake and accumulate the given pollutants in parts of plant tissue. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Studying climate change and its influence on the environment: Impacts, adaptation and mitigation

  19. Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent.

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    Madeleine Hanekom

    Full Text Available BACKGROUND: Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. AIM: This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis strain genotypes in primary Mycobacterial Growth Indicator Tubes (MGIT and Löwenstein-Jensen (LJ cultures to identify mixed infections and to establish whether the growth media influenced the recovery of certain strain genotypes. METHOD: A convenience sample of 206 paired MGIT and LJ M. tuberculosis cultures from pulmonary tuberculosis patients resident in Khayelitsha, South Africa were genotyped using an in-house PCR-based method to detect defined M. tuberculosis strain genotypes. RESULTS: The sensitivity and specificity of the PCR-based method for detecting Beijing, Haarlem, S-family, and LAM genotypes was 100%, and 75% and 50% for detecting the Low Copy Clade, respectively. Thirty-one (15% of the 206 cases showed the presence of more than one M. tuberculosis strain genotype. Strains of the Beijing and Haarlem genotypes were significantly more associated with a mixed infection (on both media when compared to infections with a single strain (Beijing MGIT p = 0.02; LJ, p<0.01 and (Haarlem: MGIT p<0.01; LJ, p = 0.01. Strains with the Beijing genotype were less likely to be with "other genotype" strains (p<0.01 while LAM, Haarlem, S-family and LCC occurred independently with the Beijing genotype. CONCLUSION: The PCR-based method was able to identify mixed infection in at least 15% of the cases. LJ media was more sensitive in detecting mixed infections than MGIT media, implying that the growth characteristics of M. tuberculosis on different media may influence our ability to detect mixed infections. The Beijing and Haarlem genotypes were more likely to occur in a mixed infection than any of the other genotypes tested suggesting pathogen

  20. 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.

  1. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

    Science.gov (United States)

    Karangwa, Consolee K.; Sosnovtsev, Stanislav V.

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining “static”) and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification (“static” versus “evolving”), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as “immunotypes”. We propose that “immunotypes” and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population. PMID:28103318

  2. Evidence of occult HCV genotypes in haemophilic individuals with unapparent HCV mixed infections.

    Science.gov (United States)

    Parodi, C; Culasso, A; Aloisi, N; García, G; Bastón, M; Corti, M; Bianco, R P; Campos, R; Ares, B R; Baré, P

    2008-07-01

    Individuals with haemophilia who received non heat-treated factor concentrates were likely to undergo multiple exposures to the hepatitis C virus (HCV). Therefore, HCV mixed-genotype infections might be more frequent in these patients than in the general population. Their prevalence is extremely variable in similar groups of patients tested by different assays due to the fact that currently available genotyping techniques are not suitable to detect multiple HCV genotypes in a viral population. As an HCV viral reservoir, the peripheral blood mononuclear cell (PBMC) might harbor viral variants distinct from the genotypes detected in plasma. We investigated the presence of HCV genotypes in a group of chronically infected haemophilic patients in the PBMC compartment using a non-stimulated cell culture system that allows the detection of the HCV genome in culture supernatants. We compared them to the HCV genotypes found in plasma samples. Cell culture experiments performed with PBMC demonstrated the presence of additional HCV genotypes that were undetected in the corresponding plasma samples with the same genotyping technique. Although mixed infections at HCV genotype level became evident in 5.6% of the patients (16/288), the culture methodology increased the number of HCV infections with multiple genotypes to 62.5% (10/16) (P HCV viral reservoirs is emphasized. Considering minor strains could influence the outcome of treatment, detection of covert HCV mixed-genotype infections might be essential for choosing the adequate therapeutic regimen.

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

    NARCIS (Netherlands)

    Vries, de D.P.

    1993-01-01

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

  4. Amino acid substitution in P3 of Soybean mosaic virus to convert avirulence to virulence on Rsv4-genotype soybean is influenced by the genetic composition of P3.

    Science.gov (United States)

    Wang, Y; Khatabi, B; Hajimorad, M R

    2015-04-01

    The modification of avirulence factors of plant viruses by one or more amino acid substitutions converts avirulence to virulence on hosts containing resistance genes. Limited experimental studies have been conducted on avirulence/virulence factors of plant viruses, in particular those of potyviruses, to determine whether avirulence/virulence sites are conserved among strains. In this study, the Soybean mosaic virus (SMV)-Rsv4 pathosystem was exploited to determine whether: (i) avirulence/virulence determinants of SMV reside exclusively on P3 regardless of virus strain; and (ii) the sites residing on P3 and crucial for avirulence/virulence of isolates belonging to strain G2 are also involved in virulence of avirulent isolates belonging to strain G7. The results confirm that avirulence/virulence determinants of SMV on Rsv4-genotype soybean reside exclusively on P3. Furthermore, the data show that sites involved in the virulence of SMV on Rsv4-genotype soybean vary among strains, with the genetic composition of P3 playing a crucial role.

  5. Serotonin transporter genotype (5-HTTLPR predicts utilitarian moral judgments.

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    Abigail A Marsh

    Full Text Available BACKGROUND: The psychological and neurobiological processes underlying moral judgment have been the focus of extensive recent research. Here we show that serotonin transporter (5-HTTLPR genotype predicts responses to moral dilemmas featuring foreseen harm to an innocent. METHODOLOGY/PRINCIPAL FINDINGS: Participants in this study judged the acceptability of actions that would unintentionally or intentionally harm an innocent victim in order to save others' lives. An analysis of variance revealed a genotype × scenario interaction, F(2, 63 = 4.52, p = .02. Results showed that, relative to long allele homozygotes (LL, carriers of the short (S allele showed particular reluctance to endorse utilitarian actions resulting in foreseen harm to an innocent individual. LL genotype participants rated perpetrating unintentional harm as more acceptable (M = 4.98, SEM = 0.20 than did SL genotype participants (M = 4.65, SEM = 0.20 or SS genotype participants (M = 4.29, SEM = 0.30. No group differences in moral judgments were observed in response to scenarios featuring intentional harm. CONCLUSIONS/SIGNIFICANCE: The results indicate that inherited variants in a genetic polymorphism that influences serotonin neurotransmission influence utilitarian moral judgments as well. This finding is interpreted in light of evidence that the S allele is associated with elevated emotional responsiveness.

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

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    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.

  7. Modulation of human serum glutathione S-transferase A1/2 concentration by cruciferous vegetables in a controlled feeding study is influenced by GSTM1 and GSTT1 genotypes.

    Science.gov (United States)

    Navarro, Sandi L; Chang, Jyh-Lurn; Peterson, Sabrina; Chen, Chu; King, Irena B; Schwarz, Yvonne; Li, Shuying S; Li, Lin; Potter, John D; Lampe, Johanna W

    2009-11-01

    Glutathione S-transferases (GST) detoxify a wide range of carcinogens. Isothiocyanates (ITC), from cruciferous vegetables, are substrates for and inducers of GST. GST variants may alter ITC clearance such that response to crucifers varies by genotype. In a randomized cross-over trial, we tested the hypothesis that changes in serum GSTA1/2 concentration in response to cruciferous vegetable feeding depends on GSTM1/GSTT1 genotype. Thirty-three men and 34 women (age 20-40 years) ate four 14-day controlled diets--basal (vegetable-free), basal supplemented with two different doses of crucifers ("single dose" and "double dose"), and single-dose cruciferous-plus-apiaceous vegetables--fed per kilogram of body weight. Fasting bloods from days 0, 7, 11, and 14 of each diet period were analyzed for serum GSTA1/2 by ELISA. GSTA1/2 increased with single- and double-dose cruciferous compared with basal diet (10% and 13%, respectively; P = 0.02 and 0.004), but cruciferous-plus-apiaceous did not differ from basal (P = 0.59). Overall, GSTA1/2 was higher in GSTM1-null/GSTT1-null than GSTM1+/GSTT1+ individuals (4,198 +/- 338 and 3,372 +/- 183 pg/mL; P = 0.03). The formal interaction of genotype-by-diet was not statistically significant, but the GSTA1/2 increase during the single-dose cruciferous diet was among GSTM1-null/GSTT1-null individuals (by 28%; P = 0.008), largely explained by GSTM1-null/GSTT1-null men (by 41%; P = 0.01). GSTA1/2 increased during the double-dose cruciferous diet in both GSTM1-null/GSTT1-null men (by 35%; P = 0.04) and GSTM1+/GSTT1+ men (by 26%; P = 0.01) but not in women. In summary, cruciferous vegetable supplementation increased GSTA1/2, but the effect was most marked in GSTM1-null/GSTT1-null men.

  8. Haplotypes versus genotypes on pedigrees

    Directory of Open Access Journals (Sweden)

    Kirkpatrick Bonnie B

    2011-04-01

    Full Text Available Abstract Background Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. Results To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Conclusions Two algorithms are introduced: an exponential-time hidden Markov model (HMM for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data.

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

    Science.gov (United States)

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

    2014-01-01

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

  10. Population samples and genotyping technology.

    Science.gov (United States)

    Mack, S J; Sanchez-Mazas, A; Single, R M; Meyer, D; Hill, J; Dron, H A; Jani, A J; Thomson, G; Erlich, H A

    2007-04-01

    The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high-resolution class I and class II genotype data are being generated for 112 population samples from around the world.

  11. The importance of environment on respiratory genotype/phenotype relationships in the Inuit

    DEFF Research Database (Denmark)

    Candelaria, P V; Backer, Vibeke; Khoo, S-K;

    2010-01-01

    Genetic and environmental influences and their interactions are central to asthma pathogenesis. This study aimed to investigate the effects of different macro-environments on asthma genotype-phenotype associations in two geographically separated populations with common ancestry.......Genetic and environmental influences and their interactions are central to asthma pathogenesis. This study aimed to investigate the effects of different macro-environments on asthma genotype-phenotype associations in two geographically separated populations with common ancestry....

  12. Effects of elevated CO2 and plant genotype on interactions among cotton, aphids and parasitoids

    Institute of Scientific and Technical Information of China (English)

    Yu-Cheng Sun; Li Feng; Feng Gao; Feng Ge

    2011-01-01

    Effects of CO2 level (ambient vs.elevated) on the interactions among three cotton (Gossypium hirsutum) genotypes,the cotton aphid (Aphis gossypii Glover),and its hymenoptera parasitoid (Lysiphlebiajaponica Ashrnead) were quantified.It was hypothesized that aphid-parasitoid interactions in crop systems may be altered by elevated CO2,and that the degree of change is influenced by plant genotype.The cotton genotypes had high (M9101),medium (HZ401) and low (ZMS 13) gossypol contents,and the response to elevated CO2 was genotype-specific.Elevated CO2 increased the ratio of total non-structural carbohydrates to nitrogen (TNC:N) in the high-gossypol genotype and the mediumgossypol genotype.For all three genotypes,elevated CO2 had no effect on concentrations of gossypol and condensed tannins.A.gossypii fitness declined when aphids were reared on the high-gossypol genotype versus the low-gossypol genotype under elevated CO2.Furthermore,elevated CO2 decreased the developmental time of L.japonica associated with the high-gossypol genotype and the low-gossypol genotype,but did not affect parasitism or emergence rates.Our study suggests that the abundance of A.gossypii on cotton will not be directly affected by increases in atmospheric CO2.We speculate that A.gossypii may diminish in pest status in elevated CO2 and high-gossypol genotype environments because of reduced fitness to the high-gossypol genotype and shorter developmental time of L.japonica.

  13. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

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    Owen Michael J

    2006-02-01

    Full Text Available Abstract Background Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs. Results In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of Conclusion Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.

  14. Clinical characteristics and distribution of hepatitis B virus genotypes in Guangxi Zhuang population

    Institute of Scientific and Technical Information of China (English)

    Zhong-Min Huang; Qi-Wen Huang; Ya-Qin Qin; Chun-He Huang; Hou-Ji Qin; Yiao-Nan Zhou; Xiang Xu; Chun-Lei Lu

    2005-01-01

    on clinical parameters are not influenced by differences in genotypes. Further studies are needed to gain an in-depth understanding of the relationship between HBV genotypes and serum HBeAb and HBeAg.

  15. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

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    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.

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

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Scheel, Troels K H; Jensen, Tanja B;

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  18. 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...

  19. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  20. Genotyping with TaqMAMA.

    Science.gov (United States)

    Li, Baohui; Kadura, Ibrahim; Fu, Dong-Jing; Watson, David E

    2004-02-01

    TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

  1. Comparative evaluation of INNO-LiPA HBV assay, direct DNA sequencing and subtractive PCR-RFLP for genotyping of clinical HBV isolates

    Directory of Open Access Journals (Sweden)

    Hasan Fuad

    2010-05-01

    Full Text Available Abstract Genotypes (A to H of hepatitis B virus (HBV influence liver disease progression and response to antiviral therapy in HBV-infected patients. Several methods have been developed for rapid genotyping of HBV strains. However, some of these methods may not be suitable for developing countries. The performance of INNO-LiPA HBV Genotyping assay (LiPA, direct DNA sequencing and subtractive PCR-RFLP of genotype-specific HBV genome regions were evaluated for accurately determining the HBV genotypes by analyzing sera (n = 80 samples from chronic HBV patients. Both, LiPA and DNA sequencing identified 63, 4 and 13 HBV strains as belonging to genotype D, genotype A and mixed genotype A and D, respectively. On the contrary, the PCR-RFLP-based method correctly identified all 4 genotype A but only 56 of 63 genotype D strains. Seven genotype D strains yielded indeterminate results. DNA sequence comparisons showed that a single nucleotide change in the target region generated an additional restriction site for Nla IV that compromised the accuracy of this method. Furthermore, all the mixed genotype A and D strains were identified only as genotype A strains. The data show that the PCR-RFLP-based method incorrectly identified some genotype D strains and failed to identify mixed genotype infections while LiPA and DNA sequencing yielded accurate results.

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

    Science.gov (United States)

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

    2005-11-01

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

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Rebecca D Schulte

    2014-05-01

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

  5. Influência genotípica na absorção e na toxidez de manganês em soja Genotypic influence on the absorption and toxicity of manganese in soybean

    Directory of Open Access Journals (Sweden)

    José Lavres Junior

    2008-02-01

    Full Text Available A toxidez de Mn pode ser um problema comum nas regiões tropicais com predominância de solos ácidos. Entretanto, variações das concentrações desse nutriente nas plantas têm sido atribuídas também a diferenças inter e intra-específicas. O presente estudo foi desenvolvido em casa de vegetação e teve como objetivo avaliar as causas de tolerância diferencial à toxidez de Mn. Os cultivares de soja [Glycine max (L. Merrill] Santa Rosa, IAC-15 e IAC-Foscarin 31 foram cultivados em solução nutritiva (pH 5,0 com cinco doses de Mn (2, 100, 150, 200 e 250 µmol L-1. O delineamento experimental foi o de blocos completos ao acaso em esquema fatorial 5 x 3 (cinco doses de Mn e três cultivares, com três repetições. Os cultivares IAC-15 e Santa Rosa exibiram sintomas visuais de toxidez. As concentrações nas folhas associadas ao excesso foram de 1.000 mg kg-1. Entretanto, o IAC-15 apresentou maior produção de grãos e de matéria seca da parte aérea, acompanhado pelo IAC-Foscarin 31 (intermediário e Santa Rosa (menor produção. O maior comprimento total de raízes, as maiores produções de matéria seca de raízes e o acúmulo de Mn neste tecido, bem como a maior compartimentalização deste nutriente no apoplasto, conferiram ao IAC-Foscarin 31 maior tolerância ao excesso de Mn na solução. Há, pois, indicações de diferenças genotípicas entre os cultivares e de que vários mecanismos atuam conjuntamente na tolerância ao excesso de Mn em solução.Manganese (Mn toxicity may be a constraint for crop production in acid soils of tropical regions. However, variations of Mn concentrations in plant tissues are also related to the genotypic differences. A greenhouse experiment was carried out to evaluate Mn tolerance of three soybean cultivars [Glycine max (L. Merrill]. Cultivars Santa Rosa, IAC-15 and IAC-Foscarin 31 were evaluated under five Mn rates (2, 100, 150, 200, and 250 µmol L-1 in nutrient solution (pH 5.0. The experiment

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

    Directory of Open Access Journals (Sweden)

    JOÃO CARLOS FELICIO

    2001-01-01

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

  7. Two-mode clustering of genotype by trait and genotype by environment data

    NARCIS (Netherlands)

    Hageman, J.A.; Malosetti, M.; Eeuwijk, van F.A.

    2012-01-01

    In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environm

  8. 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 SOURCES...... well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015015969.......: 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...

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

    Science.gov (United States)

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

    2016-08-05

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

  10. Influence of breed and genotype on the onset and distribution of infectivity and disease-associated prion protein in sheep following oral infection with the bovine spongiform encephalopathy agent.

    Science.gov (United States)

    McGovern, G; Martin, S; Jeffrey, M; Bellworthy, S J; Spiropoulos, J; Green, R; Lockey, R; Vickery, C M; Thurston, L; Dexter, G; Hawkins, S A C; González, L

    2015-01-01

    The onset and distribution of infectivity and disease-specific prion protein (PrP(d)) accumulation was studied in Romney and Suffolk sheep of the ARQ/ARQ, ARQ/ARR and ARR/ARR prion protein gene (Prnp) genotypes (where A stands for alanine, R for arginine and Q for glutamine at codons 136, 154 and 171 of PrP), following experimental oral infection with cattle-derived bovine spongiform encephalopathy (BSE) agent. Groups of sheep were killed at regular intervals and a wide range of tissues taken for mouse bioassay or immunohistochemistry (IHC), or both. Bioassay results for infectivity were mostly coincident with those of PrP(d) detection by IHC both in terms of tissues and time post infection. Neither PrP(d) nor infectivity was detected in any tissues of BSE-dosed ARQ/ARR or ARR/ARR sheep or of undosed controls. Moreover, four ARQ/ARQ Suffolk sheep, which were methionine (M)/threonine heterozygous at codon 112 of the Prnp gene, did not show any biological or immunohistochemical evidence of infection, while those homozygous for methionine (MARQ/MARQ) did. In MARQ/MARQ sheep of both breeds, initial PrP(d) accumulation was identified in lymphoreticular system (LRS) tissues followed by the central nervous system (CNS) and enteric nervous system (ENS) and finally by the autonomic nervous system and peripheral nervous system and other organs. Detection of infectivity closely mimicked this sequence. No PrP(d) was observed in the ENS prior to its accumulation in the CNS, suggesting that ENS involvement occurred simultaneously to that of, or followed centrifugal spread from, the CNS. The distribution of PrP(d) within the ENS further suggested a progressive spread from the ileal plexus to other ENS segments via neuronal connections of the gut wall. Differences between the two breeds were noted in terms of involvement of LRS and ENS tissues, with Romney sheep showing a more delayed and less consistent PrP(d) accumulation than Suffolk sheep in such tissues. Whether this

  11. Prevailing HCV genotypes and subtypes among hiv infected patients in Georgia.

    Science.gov (United States)

    Karchava, M; Sharvadze, L; Gatserelia, L; Badridze, N; Tsertsvadze, T

    2009-12-01

    Recent analysis of antiretroviral treatment (ART) program data in Georgia showed that end-stage liver disease was a leading cause of death among HIV/HCV co infected patients in 2005. The objective of this retrospective study was to study prevailing genotypes and subtypes of HCV virus in a cohort of HIV infected patients. The investigation revealed that of 1490 patients, 879 (59%) were hepatitis C antibody positive. Detectable HCV RNA was found among 91% of patients. Median liver HCV RNA level was higher than among mono-infected patients. The most prevalent genotypes were genotype 1 (41.6%), followed by genotype 3 (34.7%) and genotype 2 (17.6%), inter (mix) genotype recombinants were found among 5.8 % of patients. The genotype distribution in our study is slightly different from what was seen in Georgia in 2000. The differences of prevailing HCV genotypes among general population and HIV co infected group was probably attributed to the different methods for sample selection used within our study or possible influence of diverse transmission networks among HIV infected group. Another explanation can be the possible shift from predominance of genotype 1 to non 1 genotypes. The higher number intergenotype recombinant forms might be the result of continues parenteral exposure to different HCV genotypes during drug injection paraphernalia. Our study demonstrated high prevalence of HCV infection among HIV-infected patients and revealed 1b as predominant genotype. IDUs were less likely to spontaneously clear the virus than homosexual man and heterosexually infected woman. A greater HCV RNA levels were associated with a greater chance to be infected with HCV genotypes 1. Possible shift from predominance of genotype 1 to non 1 genotypes can be of option. This shift may have a major and beneficial impact on treatment schedules and costs. The higher number intergenotype recombinant forms might be the results of continues parenteral exposure to different HCV genotypes during

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

    Science.gov (United States)

    Grettenberger, Ian M; Tooker, John F

    2016-09-01

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

  13. Progress in genotyping of Chlamydia trachomatis

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Xiong Likuan

    2014-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    CUI Yujing; ZHANG Xuhong; ZHU Yongguan

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Mei Su; Xilong Zhang; Shicheng Su

    2009-01-01

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

  16. Potential antioxidant response to coffee — A matter of genotype?

    Directory of Open Access Journals (Sweden)

    Ute Hassmann

    2014-12-01

    Full Text Available In a human intervention study, coffee combining natural green coffee bean constituents and dark roast products was identified as a genotype-dependent inducer of the Nrf2/ARE pathway, significantly affecting Nrf2 gene expression and downstream GST1A1 and UGT1A1 gene transcription. The observed transcriptional changes correlated with the presence of specific Nrf2 genotypes suggesting their influence on both Nrf2 and subsequent ARE-dependent GST1A1 and UGT1A1 transcription. While the presence of the −653 SNP seems to be advantageous, resulting in higher Nrf2, GST1A1 and UGT1A1 gene transcription following coffee consumption, in contrast, the presence of the −651 SNP significantly down-regulated the response to the study coffee. Furthermore, the presence of the B/B genotype in GST1A1 along with the frequency of the [TA]6/6 and [TA]7/7 polymorphisms in UGT1A1 appeared to significantly increase sensitivity toward coffee-induced gene transcription. This data suggests that when examining the role of the Nrf2/ARE pathway in the regulation of antioxidative and chemopreventive phase II efficacy, individual genotypes should be included when considering the potency of bioactive food/food constituents and their therapeutic potential.

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

    Directory of Open Access Journals (Sweden)

    Elena Shumay

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

  18. Plant genotype shapes ant-aphid interactions: implications for community structure and indirect plant defense.

    Science.gov (United States)

    Mooney, Kailen A; Agrawal, Anurag A

    2008-06-01

    Little is known about the mechanisms by which plant genotype shapes arthropod community structure. In a field experiment, we measured the effects of milkweed (Asclepias syriaca) genotype and ants on milkweed arthropods. Populations of the ant-tended aphid Aphis asclepiadis and the untended aphid Myzocallis asclepiadis varied eight- to 18-fold among milkweed genotypes, depending on aphid species and whether ants were present. There was no milkweed effect on predatory arthropods. Ants increased Aphis abundance 59%, decreased Myzocallis abundance 52%, and decreased predator abundance 56%. Milkweed genotype indirectly influenced ants via direct effects on Aphis and Myzocallis abundance. Milkweed genotype also modified ant-aphid interactions, influencing the number of ants attracted per Aphis and Myzocallis. While ant effects on Myzocallis were consistently negative, effects on Aphis ranged from antagonistic to mutualistic among milkweed genotypes. As a consequence of milkweed effects on ant-aphid interactions, ant abundance varied 13-fold among milkweed genotypes, and monarch caterpillar survival was negatively correlated with genetic variation in ant abundance. We speculate that heritable variation in milkweed phloem sap drives these effects on aphids, ants, and caterpillars. In summary, milkweed exerts genetic control over the interactions between aphids and an ant that provides defense against foliage-feeding caterpillars.

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

    Science.gov (United States)

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

    2015-04-01

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

  20. Subgenotyping of Genotype C Hepatitis B Virus: Correcting Misclassifications and Identifying a Novel Subgenotype

    OpenAIRE

    Weifeng Shi; Chaodong Zhu; Weimin Zheng; Wei Zheng; Cheng Ling; Carr, Michael J; Higgins, Desmond G.; Zhong Zhang

    2012-01-01

    BACKGROUND: More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist. METHODOLOGY/PRINCIPAL FINDINGS: We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed...

  1. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

    Directory of Open Access Journals (Sweden)

    Justice Kipkorir Rono

    2016-01-01

    Full Text Available The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI and genotype plus genotype by environment (GGE biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P<0.05 affected by environments (E, genotypes (G and genotype by environment interaction (GEI. GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

  2. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

    Science.gov (United States)

    Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

    2016-01-01

    The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P < 0.05) affected by environments (E), genotypes (G) and genotype by environment interaction (GEI). GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield. PMID:27777968

  3. 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.

  4. Rotavirus genotypes in Belarus, 2008-2012.

    Science.gov (United States)

    Semeiko, Galina V; Yermalovich, Marina A; Poliakova, Nadezhda; Mijatovic-Rustempasic, Slavica; Kerin, Tara K; Wasley, Annemarie; Videbaek, Dovile; Gentsch, Jon R; Bowen, Michael D; Samoilovich, Elena O

    2014-12-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.

  5. Influence of fertilization, mulch color, early forcing, fruit order, planting date, shading, growing Environment, and genotype on the contents of selected phenolics in strawberry (Fragaria x ananassa Duch.) fruits.

    Science.gov (United States)

    Anttonen, Mikko J; Hoppula, Kalle I; Nestby, Rolf; Verheul, Michél J; Karjalainen, Reijo O

    2006-04-05

    The influence of agricultural practices (fertilization, mulch color, early forcing, and planting date), environment (light and growing area), cultivar, and fruit order on the selected phenolic content and antioxidant activity in strawberry (Fragaria x ananassa Duch.) fruits was studied. Three different levels of fertilization were given to plants in the fertilization experiment. The lowest fertilization level increased the contents of flavonols and ellagic acid from 19 to 57%. Between cultivars, up to 4-fold differences were found in the flavonol content, and it also varied according to growing environment. Planting date in glasshouse production was important for the phenolic content, and a statistically significant interaction was found between planting date and fruit order. Fruit order caused at highest 1.5-2.0-fold differences in the contents of phenolics. Interestingly, compared with other phenolics, anthocyanins were affected differently by many factors. Thus, the findings show that minor cultivation changes can increase the content of phenolics, especially in under-glass production where conditions can be easily manipulated.

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

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    V. Chaia Kaippert

    2010-08-01

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

  8. Inverse association between obesity predisposing FTO genotype and completed suicide.

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    Izabela Chojnicka

    Full Text Available The A allele of rs9939609 in the FTO gene predisposes to increased body mass index (BMI and obesity. Recently we showed an inverse association between the obesity related A allele of rs9939609 and alcohol dependence which was replicated by others. Since this finding raises a possibility that FTO may be associated with other psychiatric phenotypes, we aimed to examine association of rs9939609 with completed suicide. We genotyped rs9939609 in 912 suicide victims and 733 controls using TaqMan approach. We observed an inverse association between suicide and the rs9939609 A allele (OR = 0.80, P = 0.002, Pcor = 0.006 with genotype distribution suggesting a co-dominant effect. Given the link between alcoholism and suicide under influence of alcohol reported in Polish population, confounding by alcohol addiction was unlikely due to apparently similar effect size among cases who were under influence of ethanol at the time of death (OR = 0.76, P = 0.003, N = 361 and those who were not (OR = 0.80, P = 0.007, N = 469. The search for genotype-phenotype correlations did not show significant results. In conclusion, our study proves that there is an inverse association between rs9939609 polymorphism in FTO gene and completed suicide which is independent from association between FTO and alcohol addiction.

  9. Genotyping and surveillance for scrapie in Finnish sheep

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    Hautaniemi Maria

    2012-07-01

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

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

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    Qureshi Huma

    2007-11-01

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    DEFF Research Database (Denmark)

    Krarup, Henrik Bygum; Andersen, Stig; Madsen, Poul Henning;

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Krarup, Henrik; Andersen, Stig; Madsen, Poul Henning;

    2011-01-01

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

  14. Distribution of HBV genotypes among HBV carriers in Benin:phylogenetic analysis and virological characteristics of HBV genotype E

    Institute of Scientific and Technical Information of China (English)

    Kei Fujiwara; Atsushi Ozasa; Yuko Sakamoto; Isao Arita; Ahmed El-Gohary; Agossou Benoit; Sophie I Ogoundele-Akplogan; Namiko Yoshihara; Ryuzo Ueda; Masashi Mizokami; Yasuhito Tanaka; Etsuro Orito; Tomoyoshi Ohno; Takanobu Kato; Kanji Sugihara; Izumi Hasegawa; Mayumi Sakurai; Kiyoaki Ito

    2005-01-01

    AIM: To determine the distribution of Hepatitis B virus (HBV) genotypes in Benin, and to clarify the virological characteristics of the dominant genotype.METHODS: Among 500 blood donors in Benin, 21 HBsAg-positive donors were enrolled in the study. HBV genotypes were determined by enzyme immunoassay and restriction fragment length polymorphism. Complete genome sequences were determined by PCR and direct sequencing.RESULTS: HBV genotype E (HBV/E) was detected in 20/21 (95.2%), and HBV/A in 1/21 (4.8%). From the age-specific prevalence of HBeAg to anti-HBe seroconversion (SC) in 19 HBV/E subjects, SC was estimated to occur frequently in late teens in HBV/E.The comparison of four complete HBV/E genomes from HBeAg-positive subjects in this study and five HBV/E sequences recruited from the database revealed that HBV/E was distributed throughout West Africa with very low genetic divers ity (nucleotide homology 96.7-99.2%).Based on the sequences in the basic core promoter (BCP)to precore region of the nine HBV/E isolates compared to those of the other genotypes, a nucleotide substitution in the BCP, G1757A, was observed in HBV/E.CONCLUSION: HBV/E is predominant in the Republic of Benin, and SC is estimated to occur in late teens in HBV/E. The specific nucleotide substitution G1757A in BCP, which might influence the virological characteristics,is observed in HBV/E.

  15. 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 SOURCES...... dietary, physical activity, or drug based interventions. Gene by treatment interaction models were fitted to individual participant data from all studies included in this review, using allele dose coding for genetic effects and a common set of covariates. Study level interactions were combined using...... random effect models. Metaregression and subgroup analysis were used to assess sources of study heterogeneity. RESULTS: We identified eight eligible randomised controlled trials for the systematic review and meta-analysis (n=9563). Overall, differential changes in body mass index, body weight, and waist...

  16. Whitefly population dynamics and evaluation of whitefly-transmitted tomato yellow leaf curl virus (TYLCV)-resistant tomato genotypes as whitefly and TYLCV reservoirs.

    Science.gov (United States)

    Srinivasan, Rajagopalbabu; Riley, David; Diffie, Stan; Sparks, Alton; Adkins, Scott

    2012-08-01

    Sweetpotato whitefly, Bemisia tabaci (Gennadius), and whitefly-transmitted tomato yellow leaf curl virus (TYLCV) are major threats to tomato production in the southeastern United States. TYLCV was introduced to Florida from the Caribbean islands and has spread to other southern states of the United States. In Georgia, in recent years, the incidence of TYLCV has been steadily increasing. Studies were conducted to monitor population dynamics of whiteflies in the vegetable production belt of Georgia, to evaluate TYLCV-resistant genotypes against whiteflies and TYLCV, and to assess the potential role of resistant genotypes in TYLCV epidemiology. Monitoring studies indicated that the peak incidence of whiteflies varied seasonally from year to year. In general, whitefly populations were not uniformly distributed. Tomato genotypes exhibited minor differences in their ability to support whitefly populations. TYLCV symptoms were visually undetectable in all but one resistant genotype. The infection rates (visually) in susceptible genotypes ranged from 40 to 87%. Greenhouse inoculations with viruliferous whiteflies followed by polymerase chain reaction (PCR) indicated that up to 100% of plants of resistant genotypes were infected, although predominantly symptomless. TYLCV acquisition by whiteflies from TYLCV-infected genotypes was tested by PCR; TYLCV acquisition rates from resistant genotypes were less than from susceptible genotypes. Nevertheless, this difference did not influence TYLCV transmission rates from resistant to susceptible genotypes. Results emphasize that resistant genotypes can serve as TYLCV and whitefly reservoirs and potentially influence TYLCV epidemics.

  17. Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

    Directory of Open Access Journals (Sweden)

    Emily B M Drummond

    Full Text Available Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects, whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture. Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.

  18. Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

    Science.gov (United States)

    Drummond, Emily B M; Vellend, Mark

    2012-01-01

    Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass) clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects), whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture). Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.

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

    Directory of Open Access Journals (Sweden)

    Mark A Genung

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

  20. Hepatitis B virus genotypes:an overview

    Institute of Scientific and Technical Information of China (English)

    Mamun-Al Mahtab; Salimur Rahman; Mobin Khan; Fazal Karim

    2008-01-01

    BACKGROUND: Hepatitis B virus (HBV) infection is a major cause of mortality and morbidity globally. The quest continues to identify viral factors that inlfuence disease progression and severity as well as responses to treatment of HBV infection. Based on variations in HBV, the virus has been divided into a number of genotypes. DATA SOURCES: Review of published literature on HBV genotypes. RESULTS: HBV genotypes are likely to be important in determining the severity and progression of HBV-induced liver disease as well as responses to different anti-viral agents. CONCLUSION: Although HBV genotyping is not yet recommended for routine use in treating HBV infection, available data suggest that, as in hepatitis C virus infection, HBV genotyping is also likely to become a routine investigation for HBV treatment, perhaps in the not too distant future.

  1. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    of the method on simulated data. We find that even with only a small number of barcode genotypes, Wunderbar is capable of identifying mislabeled samples and sample mix-ups with high sensitivity and specificity, even with a high genotyping error rate and even in the presence of dependency between the individual...... barcode genotypes. To detect mislabeled samples we calculate the probability that the discordance between genotypes in the data and in the independent genotypes can be attributed to random (non-mislabeling) genotyping errors. To identify mix-ups we calculate the probability of identifying the set......Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...

  3. Genotype by environment interaction in adolescents' cognitive aptitude.

    Science.gov (United States)

    Harden, K Paige; Turkheimer, Eric; Loehlin, John C

    2007-03-01

    In a replication of Turkheimer, Haley, Waldron, D'Onofrio, Gottesman II (2003, Socioeconomic status modifies heritability of IQ in young children. Psychological Science, 14:623-628), we investigate genotype-environment (G x E) interaction in the cognitive aptitude of 839 twin pairs who completed the National Merit Scholastic Qualifying Test in 1962. Shared environmental influences were stronger for adolescents from poorer homes, while genetic influences were stronger for adolescents from more affluent homes. No significant differences were found between parental income and parental education interaction effects. Results suggest that environmental differences between middle- to upper-class families influence the expression of genetic potential for intelligence, as has previously been suggested by Bronfenbrenner and Ceci's (1994, Nature-nurture reconceptualized in developmental perspective: a bioecological model Psychological Review, 101:568-586) bioecological model.

  4. A European database of Fusarium graminearum and F. culmorum trichothecene genotypes

    Directory of Open Access Journals (Sweden)

    Matias ePasquali

    2016-04-01

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

  5. 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

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  7. The Role of Haptoglobin Genotypes in Chagas Disease

    Directory of Open Access Journals (Sweden)

    Ninomar Mundaray Fernández

    2014-01-01

    Full Text Available Although the number of people infected with T. cruzi is on the rise, host genetic and immune components that are crucial in the development of the Chagas disease have been discovered. We investigated the frequency of polymorphisms in the gene encoding haptoglobin of patients with chronic Chagas disease. The results suggest that while the HP1-1 genotype may confer protection against infection and the development of chronic Chagas disease due to the rapid metabolism of the Hp1-1-Hb complex and its anti-inflammatory activity, the presence of HP2-2 genotype may increase susceptibility towards a chronic condition of the disease due to a slow metabolism of the Hp2-2-Hb complex, lower antioxidant activity, and increased inflammatory reactivity, which lead to cell damage and a deterioration of the cardiac function. Finally, correlations between HP genotypes in different age groups and cardiac manifestations suggest that HP polymorphism could influence the prognosis of this infectious disease. This study shows some of the relevant aspects of the haptoglobin gene polymorphism and its implications in the T. cruzi infection.

  8. The Role of Haptoglobin Genotypes in Chagas Disease

    Science.gov (United States)

    Mundaray Fernández, Ninomar; Fernández-Mestre, Mercedes

    2014-01-01

    Although the number of people infected with T. cruzi is on the rise, host genetic and immune components that are crucial in the development of the Chagas disease have been discovered. We investigated the frequency of polymorphisms in the gene encoding haptoglobin of patients with chronic Chagas disease. The results suggest that while the HP1-1 genotype may confer protection against infection and the development of chronic Chagas disease due to the rapid metabolism of the Hp1-1-Hb complex and its anti-inflammatory activity, the presence of HP2-2 genotype may increase susceptibility towards a chronic condition of the disease due to a slow metabolism of the Hp2-2-Hb complex, lower antioxidant activity, and increased inflammatory reactivity, which lead to cell damage and a deterioration of the cardiac function. Finally, correlations between HP genotypes in different age groups and cardiac manifestations suggest that HP polymorphism could influence the prognosis of this infectious disease. This study shows some of the relevant aspects of the haptoglobin gene polymorphism and its implications in the T. cruzi infection. PMID:25147423

  9. Flavonoid profile of green asparagus genotypes.

    Science.gov (United States)

    Fuentes-Alventosa, J M; Jaramillo, S; Rodríguez-Gutiérrez, G; Cermeño, P; Espejo, J A; Jiménez-Araujo, A; Guillén-Bejarano, R; Fernández-Bolaños, J; Rodríguez-Arcos, R

    2008-08-27

    The determination of flavonoid profiles from different genotypes of triguero asparagus and their comparison to those from green asparagus commercial hybrids was the main goal of this study. The samples consisted of 32 commercial hybrids and 65 genotypes from the Huetor-Tajar population variety (triguero). The analysis of individual flavonoids by HPLC-DAD-MS has allowed the determination of eight naturally occurring flavonol derivatives in several genotypes of triguero asparagus. Those compounds included mono-, di-, and triglycosides of three flavonols, that is, quercetin, isorhamnetin, and kaempferol. The detailed analysis of the flavonoid profiles revealed significant differences among the distinct genotypes. These have been classified in three distinct groups as the result of a k-means clustering analysis, two of them containing both commercial hybrids and triguero asparagus and another cluster constituted by 21 genotypes of triguero asparagus, which contain several key flavonol derivatives able to differentiate them. Hence, the triglycosides tentatively identified as quercetin-3-rhamnosyl-rutinoside, isorhamnetin-3-rhamnosyl-rutinoside, and isorhamnetin-3-O-glucoside have been detected only in the genotypes grouped in the above-mentioned cluster. On the other hand, the compound tentatively identified as isorhamnetin-3-glucosyl-rutinoside was present in most genotypes of triguero asparagus, whereas it has not been detected in any of the commercial hybrids.

  10. HPV Genotyping 9G Membrane Test

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    Danishmalik Rafiq Sayyed

    2013-11-01

    Full Text Available The results of the genital human papillomavirus (HPV detection in 439 cervical samples by cervical cytology were compared with sequencing analysis and a newly developed HPV genotyping 9G membrane test. The excellent sensitivity and specificity of the HPV genotyping 9G membrane test was assured by a signal to noise ratio of more than 300 and a target hybridization to non-target hybridization ratio of 300 ~ 400 at 25 °C. The final results can be obtained in 29 min by simple loading of the hybridization and washing solutions and scanning the membranes without any drying steps or special handling. The 100% identical results of the HPV genotyping 9G membrane test with sequencing results in 439 clinical samples demonstrate significant clinical application for this test. HPV genotyping 9G membrane tests can identify and discriminate five HR-HPV genotypes which are prevalent in almost 87% of cervical cancer cases. Its simple handling makes the HPV genotyping 9G membrane test a very convenient platform for accurate HPV genotyping.

  11. Influence of Different NH4+/NO3- Ratios on Nitrate Accumulation in Different Genotypes of Chinese Cabbage%铵硝比例对不同基因型小白菜硝酸盐积累影响机理研究

    Institute of Scientific and Technical Information of China (English)

    赵首萍; 张瑞麟; 徐明飞; 郑纪慈

    2011-01-01

    Taking the different genotypes of Chinese cabbage (Brassica campestris ssp. chinensis (L.) Makino) cultivars, hyper nitrate accumulator SYM and low nitrate accumulator HGQGC as materials, we investigated the accumulation of nitrate, nitrate reductase activity (NRA) and the expression levels of NRT1and NRT2 in plant tissue. The results showed that different NH4+/NO3- ratios produced significant influence on nitrate accumulation and this influence varied with genotypes. SYM possessed stronger ability than HGQGC to absorb, accumulate and utilize nitrate especially under higher NO3- proportion treatments, and the NRA of HGQGC was more sensitive than SYM to different NH4+/NO3- ratios. The expressions of NRT1 and NRT2 mainly located in root, and the expression levels of NRT1 was higher significantly than that of NRT2. The expression levels of NRT1 and NRT2 can partly explain the different nitrate accumulations between SYM and HGQGC under different NH4+/NO3- ratios;however, the mechanism of it needs more research.%本研究以前期工作中筛选出的硝酸盐积累量存在显著差异的2个不同基因型小白菜品种为材料,在人工气候箱水培条件下研究了不同铵硝比例对小白菜硝酸盐积累量、硝酸还原酶活性(NRA)和硝酸盐吸收基因NRT1和NRT2的表达量的影响.结果表明,不同铵硝比例对小白菜硝酸盐积累量有显著影响,且存在基因型差异.四月慢对硝酸盐吸收、积累及同化利用的能力都强于华冠青梗菜,尤其是在高NO3-比例处理时.与华冠青梗菜相比,四月慢对NO3-的同化利用的能力更不易受铵硝比例的影响.NRT1和NRT2主要在根部表达,且NRT1的表达量显著高于NRT2,NRT1和NRT2的表达量变化规律只能在一定程度上解释小白菜不同基因型间硝酸盐积累量的差异,小白菜不同基因型品种间硝酸盐积累量差异的机理还需要进一步研究.

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

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    Amy J Schuh

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

  13. HCV genotype-specific correlation with serum markers: Higher predictability for genotype 4a

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    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background Several factors have been proposed to assess the clinical outcome of HCV infection. The correlation of HCV genotypes to possible serum markers in clinical prediction is still controversial. The main objective of this study was to determine the existence of any correlation between HCV genotypes to viral load and different clinical serum markers. Methods We performed a prospective cross-sectional and observational study. About 3160 serum HCV RNA positive patients were chosen from 4020 randomly selected anti-HCV positive patients. Statistical analysis was performed using the SPSS 16 software package. ROC (receiver operating characteristics curves were used to compare diagnostic values of serum markers to predict genotypes. Results The most prevalent genotype was 3a (73.9% followed by 1a (10.7%, 4a (6.4% and 3b (6.1% in Pakistani population. No correlation was found between viral load and serum markers for genotype 3a in a large no. of sample (n = 2336. While significant correlation was observed between viral load and AST in genotype 3b, ALP with viral load and ALT for genotype 1a. Patients with genotype 4a showed a significant inverse correlation with viral load and Hb level and AST with ALP. For genotype 4a, AUC (area under the curve of ALT, ALP, AST, bilirubin, Hb level and viral load was 0.790, 0.763, 0.454, 0.664, 0.458 and 0.872 respectively. Conclusions In conclusion, there was a significant variable response of HCV genotypes with serum markers. Severity of disease is independent of serum marker level in genotype 3a, while the liver damage in genotype 4a may associate with viral cytopathic effect as well as the immune-mediated process. An index using six serum markers may correctly predict genotype 4a in patients with ≥75% accuracy.

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

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    Ali Ijaz

    2011-09-01

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

  15. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots.

    Science.gov (United States)

    Rono, Justice Kipkorir; Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

    2016-01-01

    The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

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

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    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

  17. 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...

  18. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Alzheimer Disease Share this page: Was this page helpful? Formal ... help in the diagnosis of probable late onset Alzheimer disease (AD) in symptomatic adults. It is called susceptibility ...

  19. Can Clustering in Genotype Space Reveal "Niches"?

    Science.gov (United States)

    D'Andrea, Rafael; Ostling, Annette

    2016-01-01

    Community ecology lacks the success enjoyed by population genetics to quantify the relative roles played by deterministic and stochastic processes. It has been proposed that clustered patterns of abundance in genotype space provide evidence of selection in microbial communities, since no such clustering would arise in the absence of selection. We critique this test for its unrealistic null hypothesis. We show mathematically and with simulations that point mutations alone lead to clustering in genotype space by causing correlations between abundances of similar genotypes. We also show potential deviations from the mutation-only pattern caused by immigration from a source pool. Clustered patterns in genotype space may still be revealing of selection if analyzed quantitatively but only if neutral and selective regimes can be distinguished once mutation and immigration are included in the null model.

  20. HPV genotypes concordance between sex partners.

    Science.gov (United States)

    Benevolo, M; Mottolese, M; Marandino, F; Carosi, M; Diodoro, M G; Sentinelli, S; Visca, P; Rollo, F; Mariani, L; Vocaturo, G; Sindico, R; Di Giannuario, D; Perrone Donnorso, R; Pellicciotta, M; Vocaturo, A

    2007-12-01

    The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

  1. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  2. 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,...

  3. 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....

  4. Evaluation of Mungbean Genotypes Based on Yield Stability and Reaction to Mungbean Yellow Mosaic Virus Disease

    Directory of Open Access Journals (Sweden)

    AKM Mahbubul Alam

    2014-09-01

    Full Text Available This work was conducted to identify mungbean genotypes showing yield stability and resistance to mungbean yellow mosaic virus (MYMV disease. Sixteen genotypes were evaluated in a randomized complete block design with two replications for two years (2011 and 2012 at three locations (Gazipur, Ishurdi and Madaripur of the Bangladesh Agricultural Research Institute. An analysis of variance exhibited significant effects of genotype (G, environment (E, and genotype × environment (G×E on grain yield. Among eight agronomic characters, the principal component 1 (PC1 was always higher than the PC2. Considering G×E interaction, BM6 was the best genotype at all three locations in both years. Based on grain yield and stability performance, BM6 ranked first while the worst performing genotypes were BM1 and G10. Based on discrimination and representation, Gazipur was identified as an ideal environment for these mungbeans. Relationship between soil-plant analysis developments (SPAD value was positive with yield but negative with MYMV severity. BM6, G1 and G2 were considered as promising sources of resistance for low disease score and stable response across the environments. The environment proved to have an influence on MYMV infection under natural infestation. A positive correlation was observed between disease score and the temperature under natural growing condition.

  5. Evaluation of mungbean genotypes based on yield stability and reaction to mungbean yellow mosaic virus disease.

    Science.gov (United States)

    Alam, Akm Mahbubul; Somta, Prakit; Jompuk, Choosak; Chatwachirawong, Prasert; Srinives, Peerasak

    2014-09-01

    This work was conducted to identify mungbean genotypes showing yield stability and resistance to mungbean yellow mosaic virus (MYMV) disease. Sixteen genotypes were evaluated in a randomized complete block design with two replications for two years (2011 and 2012) at three locations (Gazipur, Ishurdi and Madaripur) of the Bangladesh Agricultural Research Institute. An analysis of variance exhibited significant effects of genotype (G), environment (E), and genotype × environment (G×E) on grain yield. Among eight agronomic characters, the principal component 1 (PC1) was always higher than the PC2. Considering G×E interaction, BM6 was the best genotype at all three locations in both years. Based on grain yield and stability performance, BM6 ranked first while the worst performing genotypes were BM1 and G10. Based on discrimination and representation, Gazipur was identified as an ideal environment for these mungbeans. Relationship between soil-plant analysis developments (SPAD) value was positive with yield but negative with MYMV severity. BM6, G1 and G2 were considered as promising sources of resistance for low disease score and stable response across the environments. The environment proved to have an influence on MYMV infection under natural infestation. A positive correlation was observed between disease score and the temperature under natural growing condition.

  6. Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology

    Science.gov (United States)

    Song, Kai; Li, Li; Zhang, Guofan

    2016-01-01

    Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling rate and accuracy as a function of coverage. Having initially identified the appropriate parameter settings for filtering to ensure genotype accuracy, we used two different single-nucleotide polymorphism (SNP) calling pipelines, single-sample and multi-sample. We found that a coverage of 15× was suitable for obtaining sufficient numbers of SNPs with high accuracy. Our work provides guidelines for the selection of sequence coverage when using NGS to investigate species with a high degree of heterozygosity and rapid decay of linkage disequilibrium. PMID:27760996

  7. Mixed models identify physic nut genotypes adapted to environments with different phosphorus availability.

    Science.gov (United States)

    Teodoro, P E; Laviola, B G; Martins, L D; Amaral, J F T; Rodrigues, W N

    2016-08-19

    The aim of this study was to screen physic nut (Jatropha curcas) genotypes that differ in their phosphorous (P) use, using mixed models. The experiment was conducted in a greenhouse located in the experimental area of the Centro de Ciências Agrárias of the Universidade Federal do Espírito Santo, in Alegre, ES, Brazil. The experiment was arranged in a randomized block design, using a 10 x 3-factorial scheme, including ten physic nut genotypes and two environments that differed in their levels of soil P availability (10 and 60 mg/dm(3)), each with four replications. After 100 days of cultivation, we evaluated the plant height, stem diameter, root volume, root dry matter, aerial part dry matter, total dry matter, as well as the efficiency of absorption, and use. The parameters were estimated for combined selection while considering the studied parameters: stability and adaptability for both environments were obtained using the harmonic mean of the relative performance of the predicted genotypic values. High genotype by environment interactions were observed for most physic nut traits, indicating considerable influences of P availability on the phenotypic value. The genotype Paraíso simultaneously presented high adaptability and stability for aerial part dry matter, total dry matter, and P translocation efficiency. The genotype CNPAE-C2 showed a positive response to P fertilization by increasing both the total and aerial part dry matter.

  8. Genotypic Variation for Salinity Tolerance in Sorghum (Sorghum bicolor (L. Moench Genotypes at Early Growth Stages

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    Tigabu, Endalew

    2013-04-01

    Full Text Available Sorghum (Sorghum bicolor L. Moench is the fifth most economically important crop among cereals in the world. Salinity is an abiotic factor which reduces productivity of sorghum. Exploiting genetic variability to identify salt tolerant genotype is one of the strategies used to overcome salinity. Pot experiment was carried out to evaluate the genetic variation of eleven sorghum genotypes for NaCl salinity response at germination and early seedling stages. The experimental treatments were five NaCl salinity levels (0, 2, 4, 8, and 16 dS m-1 and eleven sorghum genotypes (Gambella1107, Melkam, S-35, ESH-2, Gobye, 97MW6130, Meko, 76T1#23, ICSV-111, Abshir and Teshale. The experimental design was completely randomized design with three replicates.Data was analyzed using SAS (version 9.0 statistical software and means were separated by LSD. Germination rate, final germination percentage, seedling shoot length and seedling root length were measured. The ANOVA for treatments, genotypes and their interaction was found to be highly significant (p<0.001 with regard to all parameters. Genotypes Meko, Gambella1107, ICSV-111 and Melkam were found salt tolerant during germination and seedling growth stages. However, genotypes ESH-2 and Gobye were salt sensitive during both stages. The rest sorghum genotypes were intermediate in their salt tolerance. The study affirmed the presence of wide genotypic variation among the sorghum genotypes for NaCl salt tolerance.

  9. Integrating statistical and ecophysiological analysis of genotype by environment interaction for grain filling of barley in Mediterranean areas. II. Grain growth

    NARCIS (Netherlands)

    Voltas, J.; Eeuwijk, van F.A.; Araus, J.L.; Romagosa, I.

    1999-01-01

    In Mediterranean areas, grain growth of temperate cereals often progresses under the harmful influence of drought and high temperature. Genotypic responses are mediated by the specific occurrence of these constraints, thus causing genotype by environment (G × E) interaction. Field experiments were c

  10. Impact of genotype on clinical course in arrhythmogenic right ventricular dysplasia/cardiomyopathy-associated mutation carriers

    NARCIS (Netherlands)

    Bhonsale, Aditya; Groeneweg, Judith A.; James, Cynthia A.; Dooijes, Dennis; Tichnell, Crystal; Jongbloed, Jan D. H.; Murray, Brittney; Riele, Anneline S. J. M. te; van den Berg, Maarten P.; Bikker, Hennie; Atsma, Douwe E.; de Groot, Natasja M.; Houweling, Arjan C.; van der Heijden, Jeroen F.; Russell, Stuart D.; Doevendans, Pieter A.; van Veen, Toon A.; Tandri, Harikrishna; Wilde, Arthur A.; Judge, Daniel P.; van Tintelen, J. Peter; Calkins, Hugh; Hauer, Richard N.

    2015-01-01

    AIMS: We sought to determine the influence of genotype on clinical course and arrhythmic outcome among arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C)-associated mutation carriers. METHODS AND RESULTS: Pathogenic mutations in desmosomal and non-desmosomal genes were identified in

  11. Beijing genotype of Mycobacterium tuberculosis is significantly associated with high-level fluoroquinolone resistance in Vietnam.

    Science.gov (United States)

    Duong, Duy An; Nguyen, Thi Hong Duyen; Nguyen, Thi Ngoc Lan; Dai, Viet Hoa; Dang, Thi Minh Ha; Vo, Sy Kiet; Do, Dang Anh Thu; Nguyen, Van Vinh Chau; Nguyen, Huy Dung; Dinh, Ngoc Sy; Farrar, Jeremy; Caws, Maxine

    2009-11-01

    Consecutive fluoroquinolone (FQ)-resistant isolates (n = 109) identified at the Pham Ngoc Thach Hospital for Tuberculosis, Ho Chi Minh City, Vietnam, were sequenced in the quinolone resistance-determining regions of the gyrA and gyrB genes and typed by large sequence polymorphism typing and spoligotyping to identify the Beijing genotype of Mycobacterium tuberculosis. Beijing genotype prevalence was compared with 109 consecutive isolates from newly presenting patients with pulmonary tuberculosis from the hospital outpatient department. Overall, 82.6% (n = 90/109) of isolates had mutations in gyrAB. Nine novel mutations were identified in gyrB (S486F, N538T, T539P, D500A, D500H, D500N, G509A, E540V, and E540D). The influence of these novel gyrB mutations on FQ resistance is not proven. The Beijing genotype was significantly associated with FQ resistance (odds ratio [OR], 2.39 [95% confidence interval {CI}, 1.34 to 4.25]; P = 0.003). Furthermore, Beijing genotype FQ-resistant isolates were significantly more likely than FQ-resistant isolates of other genotypes to have gyrA mutations (OR, 7.75 [95% CI, 2.84 to 21.15]; P = 0.0001) and high-level (>8 microg/ml) FQ resistance (OR, 11.0 [95% CI, 2.6 to 47.0]; P = 0.001). The underlying mechanism of the association of the Beijing genotype with high-level FQ resistance in this setting remains to be determined. The association of the Beijing genotype with relatively high-level FQ resistance conferred by specific gyrA mutations reported here is of grave concern given the epidemic spread of the Beijing genotype and the current hopes for shorter first-line treatment regimens based on FQs.

  12. Distribution and diversity of hepatitis B virus genotypes in Yunnan, China.

    Science.gov (United States)

    Wang, Binghui; Feng, Yue; Li, Zheng; Duan, Haiping; Zhao, Ting; Zhang, Amei; Liu, Li; Baloch, Zulqarnain; Xia, Xueshan

    2014-10-01

    Hepatitis B virus (HBV) is one of the most prevalent pathogens in the world, and infection with this virus is a serious threat for public health. Yunnan is considered as an important endemic center for blood-borne viruses such as human immunodeficiency virus and hepatitis C virus, in China. However, the distribution and diversity of HBV subgenotypes remain unclear in Yunnan province. In the current study, HBV positive samples were collected from different prefectures of Yunnan province and their molecular epidemiological characters were determined. Phylogenetic analysis on the pre-S/S gene (865 bps) showed the prevalence of four HBV genotypes, including genotype B (24 cases, 33.3%), genotype C (45 cases, 62.5%), genotype I (two cases, 2.78%) and C/D recombinants (one case, 1.39%). The most prevalent genotypes B and C could be sub classified into subgenotype B2 and C1, C2, C5, and C7, respectively. Clusters of subgenotype B2 and C2 consisted of strains from China and other East Asian countries, while subgenotype C1, C5, and C7 and genotype I formed a cluster together with strains from Southeast Asia. Using Bayesian inference from phylogenetic, HBV genotypes B and C were estimated to have originated in 1860s and 1910s with an evolutionary rate of 3.26 and 8.01 × 10(-4) substitutions/site/year, respectively. These findings indicate that the distribution of HBV genotypes in Yunnan was influenced by strains from the rest of China and the neighboring countries.

  13. Coevolution of Drosophila melanogaster mtDNA and Wolbachia genotypes.

    Directory of Open Access Journals (Sweden)

    Yury Ilinsky

    Full Text Available Maternally inherited microorganisms can influence the mtDNA pattern of variation in hosts. This influence is driven by selection among symbionts and can cause the frequency of mitochondrial variants in the population to eventually increase or decrease. Wolbachia infection is common and widespread in Drosophila melanogaster populations. We compared genetic variability of D. melanogaster mitotypes with Wolbachia genotypes among isofemale lines associated with different geographic locations and time intervals to study coevolution of the mtDNA and Wolbachia. Phylogenetic analysis of D. melanogaster mtDNA revealed two clades diverged in Africa, each associated with one of the two Wolbachia genotype groups. No evidence of horizontal transmission of Wolbachia between maternal lineages has been found. All the mtDNA variants that occur in infected isofemale lines are found in uninfected isofemale lines and vice versa, which is indicative of a recent loss of infection from some maternal fly lineages and confirms a significant role of Wolbachia in the D. melanogaster mtDNA pattern of variation. Finally, we present a comparative analysis of biogeographic distribution of D. melanogaster mitotypes all over the world.

  14. ACTN3 R577X Genotypes Associate with Class II and Deep Bite Malocclusions

    Science.gov (United States)

    Zebrick, Brian; Teeramongkolgul, Teesit; Nicot, Romain; Horton, Michael J.; Raoul, Gwenael; Ferri, Joel; Vieira, Alexandre R.; Sciote, James J.

    2014-01-01

    Introduction α-actinins are myofibril anchor proteins which influence contractile properties of skeletal muscle. ACTN2 is expressed in slow type I and fast type II fibers whereas ACTN3 is expressed only in fast fibers. ACTN3 homozygosity for the 577X stop codon (i.e. changing 577RR to 577XX - the R577X polymorphism) results in the absence of α-actinin-3 in about 18% of Europeans, diminished fast contractile ability, enhanced endurance performance and reduced bone mass or bone mineral density. We have examined ACTN3 expression and genetic variation in masseter muscle of orthognathic surgery patients to determine genotype associations with malocclusion. Methods Clinical information, masseter muscle biopsies and saliva samples were obtained from 60 subjects. Genotyping for ACTN3 SNPs, RT-PCR quantitation of muscle gene message and muscle morphometric fiber type properties were compared to determine statistical differences between genotype and phenotype. Results Muscle mRNA expression level was significantly different for ACTN3 SNP genotypes (p<0.01). The frequency of ACTN3 genotypes was significantly different for sagittal and vertical classifications of malocclusion with the clearest association being elevated 577XX genotype in skeletal class II malocclusion (p = 0.003). This genotype also resulted in significantly smaller diameter of fast type II fibers in masseter muscle (p = 0.002). Conclusion ACTN3 577XX is overrepresented in skeletal class II malocclusion, suggesting a biologic influence during bone growth. ACTN3 577XX is underrepresented in deep bite malocclusion, suggesting muscle differences contribute to variations in vertical facial dimensions. PMID:25439211

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Objective. This study aimed to determine if the activity of the environmentally influenced cytochrome P450 enzyme CYP1A2, alone or in combination with CYP2D6*4 genotype, discriminates subgroups of oral lichen planus (OLP) according to lifestyle factors and clinical manifestations. Study Design...... activity. The high-CYP1A2-activity group was more exposed to CYP1A2 inducers than the low-CYP1A2-activity group. In the normal-CYP1A2-activity group, more patients had a CYP2D6*4 genotype (58%) (P = .02), and they presented more symptoms (P = .003) and gingival lesions (P = .03). More patients in the low......-CYP1A2-activity group and without CYP2D6*4 genotype presented red lesions (P = .04). Conclusions. We suggest CYP2D6*4 genotype as a disease-susceptible genotype and low or high CYP1A2 activity levels as indicators of environmental influence in OLP subgroups....

  16. Blood Group ABO Genotyping in Paternity Testing.

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-06-01

    BACKGROUND: The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A(1), A(2), B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. METHODS: The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. RESULTS: The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). CONCLUSION: In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for

  17. Methylation of the oxytocin receptor gene in clinically depressed patients compared to controls: The role of OXTR rs53576 genotype.

    Science.gov (United States)

    Reiner, I; Van IJzendoorn, M H; Bakermans-Kranenburg, M J; Bleich, S; Beutel, M; Frieling, H

    2015-06-01

    The emerging field of epigenetics provides a biological basis for gene-environment interactions relevant to depression. We focus on DNA methylation of exon 1 and 2 of the oxytocin receptor gene (OXTR) promoter. The research aims of the current study were to compare OXTR DNA methylation of depressed patients with healthy control subjects and to investigate possible influences of the OXTR rs53576 genotype. The sample of the present study consisted of 43 clinically depressed women recruited from a psychosomatic inpatient unit and 42 healthy, female control subjects - mean age 30 years (SD = 9). DNA methylation profiles of the OXTR gene were assessed from leukocyte DNA by means of bisulfite sequencing. Depressed female patients had decreased OXTR exon 1 DNA methylation compared to non-depressed women. The association between depression and methylation level was moderated by OXTR rs53576 genotype. Exon 2 methylation was associated with OXTR rs53576 genotype but not with depression. Our findings suggest exon-specific methylation mechanisms. Exon 1 methylation appears to be associated with depressive phenotypes whereas exon 2 methylation is influenced by genotype. Previously reported divergent associations between OXTR genotype and depression might be explained by varying exon 1 methylation. In order to further understand the etiology of depression, research on the interplay between genotype, environmental influences and exon-specific methylation patterns is needed.

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  20. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

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

    2015-01-01

    Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... 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...... samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate...

  1. 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.

  2. An Application of Molecular Genotyping in Mice

    Directory of Open Access Journals (Sweden)

    Underkoffler Lara A.

    2003-01-01

    Full Text Available Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis.

  3. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

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

    1996-04-01

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

  4. Influence of grape genotype, ripening season, seed trace size, and culture date on in ovule embryo development and plant formation Influência do genótipo, época de maturação, tamanho da semente-traço e época da cultura sobre o desenvolvimento do embrião no óvulo e a formação da planta de videira

    Directory of Open Access Journals (Sweden)

    Celso V. Pommer

    1995-01-01

    Full Text Available Eighteen seedless grape genotypes differing in ripening season (early, mid and late and in seed trace size (small, medium and large were harvested at 6, 10, 14, 18 and 22 weeks past bloom (wpb. Using embryo rescue techniques it was studied if embryo do abort as the fruit matures and what percent embryos remain viable at later stages. The size of seed trace was also investigated to determine its influence on embryo viability during maturation. It was found that genotype have great influence on embryo culture traits. Late maturing genotypes showed fewer rescued embryos, germinated embryos and transplantable plants than early and mid season ones. The best culture time for grape embryo rescue is 6 and 10 wpb. At these dates, the largest number of embryos, germinated embryos and transplantable plants were obtained. Genotypes with the largest ratio for seed trace weight/seed trace length (i.e., largest density showed the greatest tendency to have the largest number of ovules with embryos, more germinated embryos and more transplantable plants. The study also showed that it is possible to recover plants from mature fruit harvested late, although at a much reduced rate.Dezoito genótipos de uvas (Vitis vinifera L. apirenas, sem sementes diferindo na época de maturação (precoce, média e tardia c no tamanho da semente-traço (pequena, média e grande, foram colhidos a 6, 10, 14, 18 e 22 semanas após o florescimento. Usando técnicas de resgate de embrião, foi estudado se o embrião aborta à medida que o fruto amadurece e quais percentagens de embriões permanecem viáveis em estádios mais avançados. O tamanho da semente-traço também foi investigado para determinar sua influência na viabilidade do embrião durante a maturação. Verificou-se que o genótipo tem grande influência nas características relacionadas com a cultura de embrião. Genótipos de maturação tardia mostraram menos embriões resgatados e germinados e menos pl

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

    Directory of Open Access Journals (Sweden)

    Cavallari LH

    2011-11-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Tamene; Temesgen; Gemechu; Keneni; Tadese; Sefera; Mussa; Jarso

    2015-01-01

    Sixteen faba bean genotypes were evaluated in 13 environments in Ethiopia during the main cropping season for three years(2009–2011). The objectives of the study were to evaluate the yield stability of the genotypes and the relative importance of different stability parameters for improving selection in faba bean. The study was conducted using a randomized complete block design with four replications. G × E interaction and yield stability were estimated using 17 different stability parameters. Pooled analysis of variance for grain yield showed that the main effects of both genotypes and environments, and the interaction effect, were highly significant(P ≤ 0.001) and(P ≤ 0.01), respectively. The environment main effect accounted for 89.27% of the total yield variation, whereas genotype and G × E interaction effects accounted for 2.12% and 3.31%, respectively.Genotypic superiority index(Pi) and FT3 were found to be very informative for selecting both high-yielding and stable faba bean genotypes. Twelve of the 17 stability parameters,including CVi, RS, α, λ, S2 di, bi, S(2)i, Wi, σ2i, EV, P59, and ASV, were influenced simultaneously by both yield and stability. They should accordingly be used as complementary criteria to select genotypes with high yield and stability. Although none of the varieties showed consistently superior performance across all environments, the genotype EK 01024-1-2ranked in the top third of the test entries in 61.5% of the test environments and was identified as the most stable genotype, with type I stability. EK 01024-1-2 also showed a17.0% seed size advantage over the standard varieties and was released as a new variety in2013 for wide production and named "Gora". Different stability parameters explained genotypic performance differently, irrespective of yield performance. It was accordingly concluded that assessment of G × E interaction and yield stability should not be based on a single or a few stability parameters but rather

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

    Directory of Open Access Journals (Sweden)

    Tamene Temesgen

    2015-06-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Tamene Temesgen; Gemechu Keneni; Tadese Sefera; Mussa Jarso

    2015-01-01

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

  9. Viability of cytochrome c genotypes depends on cytoplasmic backgrounds in Tigriopus californicus.

    Science.gov (United States)

    Willett, C S; Burton, R S

    2001-08-01

    Because of their extensive functional interaction, mitochondrial DNA (mtDNA) and nuclear genes may evolve to form coadapted complexes within reproductively isolated populations. As a consequence of coadaptation, the fitness of particular nuclear alleles may depend on mtDNA genotype. Among populations of the copepod Tigriopus californicus, there are high levels of amino acid substitutions in both the mtDNA genes encoding subunits of cytochrome c oxidase (COX) and the nuclear gene encoding cytochrome c (CYC), the substrate for COX. Because of the functional interaction between enzyme and substrate proteins, we hypothesized that the fitness of CYC genotypes would depend on mtDNA genotype. To test this hypothesis, segregation ratios for CYC and a second nuclear marker (histone H1) unrelated to mitochondrial function were scored in F2 progeny of several reciprocal interpopulation crosses. Genotypic ratios at the CYC locus (but not the H1 locus) differed between reciprocal crosses and differed from expected Mendelian ratios, suggesting that CYC genotypic fitnesses were strongly influenced by cytoplasmic (including mtDNA) background. However, in most cases the nature of the deviations from Mendelian ratios and differences between reciprocal crosses are not consistent with simple coevolution between CYC and mtDNA background. In a cross in which both newly hatched larvae and adults were sampled, only the adult sample showed deviations from Mendelian ratios, indicating that genotypic viabilities differed. In two of six crosses, large genotypic ratio differences for CYC were observed between the sexes. These results suggest that significant variation in nuclear-mtDNA coadaptation may exist between T. californicus populations and that the relative viability of specific cytonuclear allelic combinations is somehow affected by sex.

  10. HPV genotyping and p16 expression in Xingu Indigenous Park, Brazil.

    Science.gov (United States)

    Freitas, V G; Focchi, G R; Pereira, E R; Levi, J E; Speck, N M G; Ribalta, J C

    2016-09-16

    The association between high-risk human papillomavirus (HPV) genotypes and p16 expression in indigenous women from the Xingu Indigenous Park, Brazil, was unknown. This study evaluated p16 expression in women with a histological diagnosis of cervical intraepithelial neoplasia (CIN) 3 or higher and correlated this expression with HPV genotypes to determine possible discrepancies in the expression of this marker. We evaluated 37 previously collected samples with different HPV genotypes and high-grade lesions diagnosed based on cytology, histology, and colposcopy. Immunohistochemical analysis was performed using paraffin-embedded tissue sections and the CINtec® Histology Kit. p16 protein expression was investigated by immunostaining with an anti-p16 antibody. HPV genotyping was performed by reverse hybridization. The age of the study population ranged from 22-75 years (43.81 ± 15.89 years) and parity ranged from 1-11 (5.92 ± 2.58). Thirteen different HPV genotypes were found using the INNO-LiPA kit. Single and multiple infections by HPV were found with prevalence of single infections (P = 0.029). Comparison between HPV genotype and simple or multiple infections was highly significant; it was observed more HPV 52 followed by HPV 16 in single infections (P p16 expression was predominantly diffuse, which was observed in 91.7% of lesions, whereas 8.3% were focal (P p16 expression in high-grade CIN was not influenced by the viral genotype; however, more studies are necessary to further our understanding of this restricted group.

  11. LTA4H genotype is associated with susceptibility to bacterial meningitis but is not a critical determinant of outcome.

    Directory of Open Access Journals (Sweden)

    Sarah J Dunstan

    Full Text Available Adjunctive dexamethasone saves lives in the treatment of tuberculous meningitis but this response is influenced by the patient's LTA4H genotype. Despite less certain benefit, adjunctive dexamethasone is also frequently used in the treatment of pyogenic bacterial meningitis, but the influence of LTA4H genotype on outcomes has not been previously investigated. We genotyped the LTA4H promoter region SNP (rs17525495 in 390 bacterial meningitis patients and 751 population controls. rs17525495 was associated with susceptibility to bacteriologically confirmed bacterial meningitis (P = 0.01, OR 1.27 95% confidence interval [CI] 1.05-1.54 but did not influence clinical presentation, disease severity or survival following dexamethasone treatment.

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

    Directory of Open Access Journals (Sweden)

    Julián F. Mateus-Rodriguez

    2014-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Dinu Gavojdian

    2014-05-01

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

  14. 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...

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

    Directory of Open Access Journals (Sweden)

    Ana Marjanović-Jeromela

    2011-02-01

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

  16. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

    Science.gov (United States)

    Rose, Jed E; Behm, Frédérique M; Drgon, Tomas; Johnson, Catherine; Uhl, George R

    2010-01-01

    Improving and targeting nicotine replacement therapy (NRT) are cost-effective strategies for reducing adverse health consequences for smokers. Treatment studies document the efficacy of precessation NRT and support important roles for level of nicotine dependence and precessation smoking reduction in successful quitting. However, prior work has not identified the optimal precessation dose or means for personalizing NRT. Genome-wide association has identified groups of genomic markers associated with successful quitting, allowing us to develop a v1.0 "quit-success" genotype score. We now report influences of v1.0 quit-success genotype score, level of dependence and precessation smoking reduction in a smoking cessation trial that examined effects of 21 versus 42 mg/24 h precessation NRT. Four hundred seventy-nine smokers were randomized to 21 or 42 mg NRT, initiated 2 wks prior to target quit dates. We monitored self-reported abstinence and end-expired air carbon monoxide (CO). Genotyping used Affymetrix arrays (Santa Clara, CA, USA). The primary outcome was 10-wk continuous smoking abstinence. NRT dose, level of nicotine dependence and genotype scores displayed significant interactive effects on successful quitting. Successful abstinence also was predicted by CO reductions during precessation NRT. These results document ways in which smoking cessation strategies can be personalized based on levels of nicotine dependence, genotype scores and CO monitoring. These assessments, taken together, can help match most smokers with optimal NRT doses and help rapidly identify some who may be better treated using other methods.

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

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    Erzsebet Buta

    2015-01-01

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

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

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    Demir A

    2005-01-01

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

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

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    Margarita Miranda

    2012-12-01

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

  20. Use of supplementary genotypes in AMMI analysis.

    Science.gov (United States)

    Pacheco, R M; Duarte, J B; Vencovsky, R; Pinheiro, J B; Oliveira, A B

    2005-03-01

    Improving stability of crop yield in a target production environment is an important breeding objective. It is well known that selection for better stability generally results in lower mean yields and, conversely, that selection for higher mean yields may lead to poorer stability. This paper explores the equivalence between the singular value decomposition used in AMMI analysis and the spectral decomposition used in principal components analysis. This equivalence enables scores of a "supplementary genotype" made up of the highest yield value within each environment to be obtained, and these may serve as the ideal check treatment for selection purposes. These scores are used to (1) display this check in a biplot graph, thereby providing a qualitative comparison with the real genotypes related to their interaction with environments; (2) obtain estimates of the squared distances from the projection of each real genotype to the projection of the "supplementary treatment", thereby allowing conclusions to be made on the yield stability of each real genotype. This procedure was effective in identifying the most stable soybean cultivars in an example shown for illustration.

  1. Genotype by environment interaction in maize breeding

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    Babić Milosav

    2008-01-01

    Full Text Available Because proximity measures occur in pairs where both, similarity and dissimilarity measures exploit the same type of information, companion classification and ordination techniques can be applied. They complement each other in analysis of genotype by environment interaction (GxE data. Choice of method, companion diagnostics and graphical presentation are required within each of methodologies. By clustering of 12 genotypes into 5 groups, 96.26% of variability for genotypes contained in original data is kept. By applying same analysis for environments, 96.45% of variability contained in original data matrix is kept with grouping of 31 environments into 11 groups. Caused by genotypes and environments grouping 78.10% of GxE variability contained in original data matrix remained in analysis of such two-way reduced data. Based on shown results, it is not possible to define smaller growing regions. Clustering of environment can be useful not only for defining mega environments but also for smaller growing regions defining only in combination with some of additional analysis (AMMI, discrimination analysis, correspondent analysis etc.. In such kind of analysis experience of investigator would be of great importance. Choice of test sites for breeding programme can be made based on obtained grouping to a limited extent (rather for restructuring existing test sites network in order to obtain 'better' information with same number of test sites then for its rationalization with number of test sites decreasing.

  2. Polyembryony in non-apomictic citrus genotypes

    Science.gov (United States)

    Aleza, Pablo; Juárez, José; Ollitrault, Patrick; Navarro, Luis

    2010-01-01

    Background and Aims Adventitious embryony from nucellar cells is the mechanism leading to apomixis in Citrus sp. However, singular cases of polyembryony have been reported in non-apomictic genotypes as a consequence of 2x × 4x hybridizations and in vitro culture of isolated nucelli. The origin of the plants arising from the aforementioned processes remains unclear. Methods The genetic structure (ploidy and allelic constitution with microsatellite markers) of plants obtained from polyembryonic seeds arising from 2x × 4x sexual hybridizations and those regenerated from nucellus culture in vitro was systematically analysed in different non-apomictic citrus genotypes. Histological studies were also conducted to try to identify the initiation process underlying polyembryony. Key Results All plants obtained from the same undeveloped seed in 2x × 4x hybridizations resulted from cleavage of the original zygotic embryo. Also, the plants obtained from in vitro nucellus culture were recovered by somatic embryogenesis from cells that shared the same genotype as the zygotic embryos of the same seed. Conclusions It appears that in non-apomictic citrus genotypes, proembryos or embryogenic cells are formed by cleavage of the zygotic embryos and that the development of these adventitious embryos, normally hampered, can take place in vivo or in vitro as a result of two different mechanisms that prevent the dominance of the initial zygotic embryo. PMID:20675656

  3. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping.

    Science.gov (United States)

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2017-01-01

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  4. Evaluation of glycoprotein B genotypes and load of CMV infecting blood leukocytes on prognosis of AIDS patients

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    Aldo Albuquerque Cunha

    2011-04-01

    Full Text Available BACKGROUND: Cytomegalovirus (CMV remains an important pathogen to immunocompromised patients even in the era of HAART. The present study aimed at evaluating the influence of CMV viral load and its gB genotypes on AIDS patients' outcome. METHODS: Blood samples of 101 AIDS patients were collected and tested for HIV load, CD4 - cell count and opportunistic pathogens, including CMV. Semi-nested PCRs were run to detect CMV genome and in the positive samples, gB genotyping and CMV load were established using enzymatic restriction and real time PCR, respectively. All patients were clinically followed for four years. RESULTS: In thirty patients (31% CMV was detected and all fatal cases (n = 5 occurred in this group of patients (p = 0.007, but only two patients had CMV disease (1.9%. However, viral load was not statistically associated with any analyzed parameter. The most frequently observed CMV genotype was gB2 (45.16% followed by gB3 (35.48%. gB2 genotype was more frequently found in patients with CD4-cell counts under 200 cells/mm³ (p = 0.0017, and almost all fatal cases (80% had gB2 genotype. CONCLUSIONS: Our study suggests that CMV and its polymorphisms in biologically relevant genes, such as the gB encoding ORF, may still influence the prognosis and outcome of AIDS patients. The gB2 genotype was associated to patient's bad outcome.

  5. Identification of zoonotic genotypes of Giardia duodenalis.

    Science.gov (United States)

    Sprong, Hein; Cacciò, Simone M; van der Giessen, Joke W B

    2009-12-01

    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 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 zoonotic

  6. 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...... 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...... 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...

  7. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  8. 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....

  9. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  10. 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...

  11. 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

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

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... was significantly higher for both MinERR and MaxLRT compared with EP and random genotyping methods (either across or within family), for all the proportions of genotyped animals. Power to detect significant QTL (α = 0.01) with 20% genotyping for MinERR and MaxLRT was 80 and 75% of that obtained with complete...... that combining the phenotypic and genotypic information in selective genotyping (e.g. MinERR and MaxLRT) is better than using only the EPs and the combined methods can be considered as alternative approaches to decrease genotyping costs, with unbiased QTL effects, decreased sampling variance of the QTL variance...

  13. Strongyloides stercoralis genotypes in humans in Cambodia.

    Science.gov (United States)

    Schär, Fabian; Guo, Li; Streit, Adrian; Khieu, Virak; Muth, Sinuon; Marti, Hanspeter; Odermatt, Peter

    2014-06-01

    Little is known about the genetic variability of the soil-transmitted nematode, Strongyloides stercoralis, in humans. We sequenced portions of the small subunit rDNA (SSU), including the hyper variable regions (HVR) I and IV from S. stercoralis larvae derived from individuals living in a rural setting in Cambodia. We identified three polymorphic positions, including a previously reported one within the HVR I. HVR IV was invariable. Six different SSU alleles existed in our sample. Although different genotypes of S. stercoralis were found in the same individuals, no heterozygous larvae were found. This indicates that there is no or very little interbreeding between the different genotypes. Further studies are needed to examine if this is because sexual reproduction, which is facultative, is rare in our study area's S. stercoralis population or because what is considered to be S. stercoralis today is actually a complex of closely related species or subspecies.

  14. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island.

    Science.gov (United States)

    Karatapanis, Stylianos; Tsoplou, Panagiota; Papastergiou, Vasilios; Vasiageorgi, Aggeliki; Stampori, Maria; Saitis, Ioannis; Tsitsopoulos, Eustathios; Lisgos, Phillipos; Skorda, Lamprini; Ketikoglou, Ioannis; Goulis, Ioannis

    2012-02-01

    Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region.

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

    DEFF Research Database (Denmark)

    Walsh, John P; Berry, Jemma; Liu, Shu;

    2011-01-01

    hypothesized that IL12B genotype may influence the clinical presentation of autoimmune thyroid disease. Objective.  We tested for differences in IL12B genotype between Graves' disease and Hashimoto's disease. Patients.  We studied a discovery cohort of 203 Australian women and 37 men with autoimmune thyroid......' disease (P=0.005) and Hashimoto's disease (P=0.029). Conclusion.  In men with autoimmune thyroid disease, a common variant located upstream of the IL12B coding region may influence whether patients present with Graves' disease or Hashimoto's disease.......Background.  Common variants in the interleukin 12B (IL12B) gene are associated with predominantly inflammatory (Th1) or antibody-mediated (Th2) immune responses. Since Hashimoto's disease and Graves' disease are thought to arise from mainly Th1 and Th2 immune responses respectively, we...

  16. Hepatitis B virus genotypes and hepatocellular carcinoma in Thailand

    Institute of Scientific and Technical Information of China (English)

    Pisit Tangkijvanich; Varocha Mahachai; Piyawat Komolmit; Juthatip Fongsaru; Apiradee Theamboonlers; Yong Poovorawan

    2005-01-01

    AIM: The role of hepatitis B virus (HBV) genotypes on the clinical features and prognosis of patients with hepatocellular carcinoma (HCC) is currently unknown. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Thai patients.METHODS: HBV genotypes were determined by PCR-RFLP in stored sera of 93 asymptomatic carriers, 103 patients with chronic hepatitis, 60 patients with cirrhosis and 76patients with HCC. The clinical data were analyzed in relation to the HBV genotype.RESULTS: HBV genotypes C and B were predominant in Thailand, accounting for 73% and 21%, respectively. The distributions of genotypes B and C were similar in HCC patients compared to the other groups. Genotype C was significantly more common in HCC patients who were under 40 years old than genotype B (18% vs 0%, P= 0.03), but was significantly less common in patients older than 60 years (26% vs 56.5%, P= 0.01). The positive rate of hepatitis B e antigen (HBeAg) in patients with genotype C was significantly higher than that in patients with genotype B (71.6% vs 44.4%, P = 0.03 in chronic hepatitis; 56.8% vs 11.1%,P = 0.01 in cirrhosis). There were no differences between HCC patients with genotypes B and C regarding tumor staging by CLIP criteria and the overall median survival. Multivariate analyses showed that HBV genotype was not an independent prognostic factor of survival in HCC patients.CONCLUSION: Patients with genotype C had a higher positive rate of HBeAg and exhibited earlier progression of cirrhosis and HCC than those with genotype B. However,there were no differences in the risk of developing HCC and its prognosis between patients with these genotypes.

  17. 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.

  18. Methods on Identification and Screening of Rice Genotypes with High Nitrogen Efficiency

    Institute of Scientific and Technical Information of China (English)

    CHENG Jian-feng; JIANG Han-yan; LIU Yi-bai; DAI Ting-bo; CAO Wei-xing

    2011-01-01

    In order to establish methods for indentification and screening of rice genotypes with high nitrogen (N) efficiency,N absorption efficiency (NAE),N utilization efficiency (NUE) and N harvest index (NHI) in ten rice genotypes were investgated at the elongation,booting,heading and maturity stages under six N levels in a pot experiment with soil-sand mixtures at various ratios.NAE in various rice genotypes firstly increased,peaked under a medium nitrogen rate of 0.177 g/kg and then decreased,but NUE and NHI always decreased with increasing nitrogen levels.NAE in various rice genotypes ever increased with growing process and NUE indicated a descending tendency of elongation stage>heading stage>maturity stage>booting stage.N level influenced rice NAE,NUE and NHI most,followed by genotype,and the both effects were significant at 0.01 level.In addition,the interaction effects of genotype and nitrogen level on rice NAE and NUE were significant at 0.01 level,but not significant on rice NHI.Because the maximum differences of NAE and NUE were found at the elongation stage,it was thought to be the most suitable stage for identification and screening these two paremeters.Therefore,the optimum conditions for identification and screening of rice NAE,NUE and NHI in a pot experiment were the nitrogen rate of 0.157 g/kg at the elongation stage,low nitrogen at the elongation stage,and the nitrogen rate of 0.277 g/kg at the maturity stage,respectively.

  19. Impact of genotype-specific herd immunity on the circulatory dynamism of norovirus: a 10-year longitudinal study of viral acute gastroenteritis.

    Science.gov (United States)

    Sakon, Naomi; Yamazaki, Kenji; Nakata, Keiko; Kanbayashi, Daiki; Yoda, Tomoko; Mantani, Masanobu; Kase, Tetsuo; Takahashi, Kazuo; Komano, Jun

    2015-03-15

    Human norovirus is a major cause of viral acute gastroenteritis worldwide. However, the transition of endemic norovirus genotypes remains poorly understood. The characteristics of natural immunity against norovirus are unclear because few studies have been performed in the natural infection setting. This prospective 10-year surveillance study of acute gastroenteritis in the province of Osaka, Japan, revealed that norovirus spread shows temporal, geographic, and age group-specific features in the humans. Genogroup II genotype 4 (GII.4) was detected in most sporadic pediatric cases, as well as in foodborne and nursing home outbreaks, respectively. The dominant genotypes in outbreaks at childcare facilities and schools shifted every season and involved GI, GII.2, GII.3, GII.4, and GII.6. Evidence at both the facility and individual levels indicated that genotype-specific herd immunity lasted long enough to influence the endemic norovirus genotype in the next season. Thus, norovirus circulates through human populations in a uniquely dynamic fashion.

  20. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  1. Hepatitis B virus taxonomy and hepatitis B virus genotypes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

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

    OpenAIRE

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

    2011-01-01

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

  3. 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

  4. Identification of zoonotic genotypes of Giardia duodenalis.

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    Hein Sprong

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

  5. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

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    Hu Shunling

    2011-03-01

    Full Text Available Abstract Background Six nucleotide (nt insertion in the 5'-noncoding region (NCR of the nucleoprotein (NP gene of Newcaslte disease virus (NDV is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX. Results In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates. Conclusions The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

  6. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

    Science.gov (United States)

    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-12-01

    Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.

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

    KAUST Repository

    McCallum, John A.

    2011-06-01

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

  8. Cannabis and cocaine decrease cognitive impulse control and functional corticostriatal connectivity in drug users with low activity DBH genotypes

    NARCIS (Netherlands)

    Ramaekers, J.G.; van Wel, J.H.; Spronk, D.; Franke, B.; Kenis, G.; Toennes, S.W.; Kuypers, K.P.; Theunissen, E.L.; Stiers, P.; Verkes, R.J.

    2016-01-01

    The dopamine beta-hydroxylase (DbetaH) enzyme transforms dopamine into noradrenaline. We hypothesized that individuals with low activity DBH genotypes (rs1611115 CT/TT) are more sensitive to the influence of cannabis and cocaine on cognitive impulse control and functional connectivity in the limbic

  9. Genotypic and environmental effects on cottonseed oil, nitrogen, and gossypol contents in eighteen years Regional High Quality tests

    Science.gov (United States)

    Determination of environmental influence on seed traits is critical for genetic improvement of seed quality in Upland cotton (Gossypium hirsutum L.). The objective of this study was to analyze the relative contribution of environment and genotype (G) for seed oil, nitrogen (N), and gossypol content...

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

    Science.gov (United States)

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

    2015-07-01

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

  11. Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b▿

    Science.gov (United States)

    Hübschen, Judith M.; Mihneva, Zefira; Mentis, Andreas F.; Schneider, François; Aboudy, Yair; Grossman, Zehava; Rudich, Hagit; Kasymbekova, Kalia; Sarv, Inna; Nedeljkovic, Jasminka; Tahita, Marc C.; Tarnagda, Zekiba; Ouedraogo, Jean-Bosco; Gerasimova, A. G.; Moskaleva, T. N.; Tikhonova, Nina T.; Chitadze, Nazibrola; Forbi, J. C.; Faneye, Adedayo O.; Otegbayo, Jesse A.; Charpentier, Emilie; Muller, Claude P.

    2009-01-01

    Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa. PMID:19741071

  12. 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

  13. Enzymatic Saccharification of Shrub Willow Genotypes with Differing Biomass Composition for Biofuel Production

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    Michelle J. Serapiglia

    2013-03-01

    Full Text Available In the conversion of woody biomass feedstocks into liquid fuel ethanol, the pretreatment process is the most critical and costly step. Variations in biomass composition based on genetic differences or environmental effects have a significant impact on the degree of accessibility accomplished by pretreatment and subsequent sugar release by enzymatic hydrolysis. To evaluate this, biomass from 10 genetically diverse, genotypes of shrub willow (Salix spp. was pretreated with a hot-water process at two levels of severity, hydrolyzed using a combination of two commercial enzyme cocktails, and the release of hexose and pentose monomers was quantified by HPLC. Among the genotypes selected for analysis, cellulose content ranged from 39 to 45% (w/w and lignin content ranged from 20 to 23% (w/w at harvest. Differences in the effectiveness of the pretreatment process were observed among the various willow genotypes. Correlations were identified between total sugar release and % cellulose and % lignin content. There was a significant effect of pretreatment severity on polysaccharide accessibility, but the response to pretreatments was different among the genotypes. At the high severity pretreatment ‘SV1’ was the least recalcitrant with sugar release representing as much as 60% of total biomass. These results suggest that structural, as well as chemical characteristics of the biomass may influence pretreatment and hydrolytic efficiency.

  14. Host Genotype and Coinfection Modify the Relationship of within and between Host Transmission.

    Science.gov (United States)

    Susi, Hanna; Vale, Pedro F; Laine, Anna-Liisa

    2015-08-01

    Variation in individual-level disease transmission is well documented, but the underlying causes of this variation are challenging to disentangle in natural epidemics. In general, within-host replication is critical in determining the extent to which infected hosts shed transmission propagules, but which factors cause variation in this relationship are poorly understood. Here, using a plant host, Plantago lanceolata, and the powdery mildew fungus Podosphaera plantaginis, we quantify how the distinct stages of within-host spread (autoinfection), spore release, and successful transmission to new hosts (alloinfection) are influenced by host genotype, pathogen genotype, and the coinfection status of the host. We find that within-host spread alone fails to predict transmission rates, as this relationship is modified by genetic variation in hosts and pathogens. Their contributions change throughout the course of the epidemic. Host genotype and coinfection had particularly pronounced effects on the dynamics of spore release from infected hosts. Confidently predicting disease spread from local levels of individual transmission, therefore, requires a more nuanced understanding of genotype-specific infection outcomes. This knowledge is key to better understanding the drivers of epidemiological dynamics and the resulting evolutionary trajectories of infectious disease.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-01

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

  16. Hepatitis B virus genotype has no impact on hepatitis B e antigen seroconversion after lamivudine treatment

    Institute of Scientific and Technical Information of China (English)

    Henry Lik-Yuen Chan; May-Ling Wong; Alex Yui Hui; Angel Mei-Ling Chim; Ada Mei-Ling Tse; Lawrence Cheung-Tsui Hung; Francis Ka-Leung Chan; Joseph Jao-Yiu Sung

    2003-01-01

    AIM: To investigate the association of hepatitis B virus (HBV) genotype and HBeAg seroconversion after nucleotide analogue treatment.METHODS: Chronic hepatitis B patients receiving lamivudine followed up for at least 6 months post-treatment were studied. Consecutive treatment-naive patients who were prospectively followed up in the clinic for at least 18 months were studied as controls. HBeAg seroconversion was defined as loss of HBeAg, appearance of anti-HBe and normalization of alanine aminotransferase for at least 6 months.RESULTS: Thirty-five patients on lamivudine and 96 control patients followed up for 39 (18-49) months were studied.Lamivudine was given for 12 (10-18) months, and patients were followed up for 15 (6-34) months after drug cessation.Genotype B and C HBV were found in 43 and 88 patients and HBeAg seroconversion occurred in 12 (28 %) and 16(18 %) patients, respectively (P=0.30). There was no difference in HBeAg seroconversion between patients infected by genotype B and C HBV in the control (35 % vs 21%, P=0.25) and lamivudine-treated (14 % vs 10 %,P=1.00) groups.CONCLUSION: HBeAg seroconversion after treatment by lamivudine was not influenced by the HBV genotype.

  17. N-Acetyltransferase 2 genotype, exfoliated urothelial cells and benzidine exposure.

    Science.gov (United States)

    Ma, Qing-wen; Lin, Guo-fang; Chen, Ji-gang; Guo, Wei-Chao; Qin, Yi-qiu; Golka, Klaus; Shen, Jian-hua

    2012-01-01

    Most studies report an association of the slow N-acetyltransferase 2 (NAT2) status with elevated bladder cancer risk. In this study, NAT2 genotypes and the decades-long records of Papanicolaou's grading of exfoliated urothelial cells in a former benzidine-exposed cohort of the Shanghai dyestuff industry (29 bladder cancer patients; 307 non-cancer cohort members, some of them presenting different grades of pre-malignant alterations of exfoliated urothelial cells) were investigated. The cohort members had been enrolled in regular medical surveillance since mid-1980s. No overall increase of slow NAT2 genotypes in the former benzidine-exposed bladder cancer patients was found, compared with non-diseased members of the same cohort. A lower presentation of the homozygous wild genotype NAT2 4/4 was observed in bladder cancer patients, compared with non-diseased members with averaged Papanicolaou's grading (APG)3 II (OR=0.31, 95 percent CI 0.10-0.96, p=0.034) or with APG less than II (OR=0.36,95 percent CI 0.12-1.10, p=0.063). Nevertheless, neither a protective influence of rapid NAT2 genotypes on bladder cancer risk nor on pre-malignant cytological alterations could be confirmed by the present data.

  18. Phenotypic and genotypic variability of disc flower corolla length and nectar content in sunflower

    Directory of Open Access Journals (Sweden)

    Joksimović Jovan

    2003-01-01

    Full Text Available The nectar content and disc flower corolla length are the two most important parameters of attractiveness to pollinators in sunflower. The phenotypic and genotypic variability of these two traits was studied in four commercially important hybrids and their parental components in a trial with three fertilizer doses over two years. The results showed that, looking at individual genotypes, the variability of disc flower corolla length was affected the most by year (85.38-97.46%. As the study years were extremely different, the phenotypic variance of the hybrids and parental components was calculated for each year separately. In such conditions, looking at all of the crossing combinations, the largest contribution to phenotypic variance of the corolla length was that of genotype: 57.27-61.11% (NS-H-45 64.51-84.84% (Velja; 96.74-97.20% (NS-H-702 and 13.92-73.17% (NS-H-111. A similar situation was observed for the phenotypic variability of nectar content, where genotype also had the largest influence, namely 39.77-48.25% in NS-H-45; 39.06-42.51% in Velja; 31.97-72.36% in NS-H-702; and 62.13-94.96% in NS-H-111.

  19. The ALDH2 genotype, alcohol intake, and liver-function biomarkers among Japanese male workers.

    Science.gov (United States)

    Takeshita, T; Yang, X; Morimoto, K

    2000-06-01

    A highly prevalent, atypical genotype in low Km aldehyde dehydrogenase (ALDH2) may influence alcohol-induced liver injury because of higher production of acetaldehyde in the liver. In the present study, we examined relationships between the ALDH2 genotype, alcohol intake, and liver-function biomarkers among Japanese male workers. Study subjects were 385 male workers in a metal plant in Japan, who were free from hepatic viruses and did not have higher aminotransferase activities (alcohol drinking habits and other lifestyles. The ALDH2 genotype was determined by the PCR method followed by restriction-enzyme digestion. In the moderately and heavily drinking groups, those with ALDH2*1/*2 exhibited significantly lower levels than those with ALDH2*1/*1 for all three parameters of liver function, whereas no such differences were observed in the least-drinking group. Multiple linear-regression analysis, adjusting for age, obesity, and smoking habits, revealed that aspartate aminotransferase activity was positively associated with alcohol intake only in those with ALDH2*1/*1. On the other hand, alanine transferase activity was negatively associated with alcohol intake only in those with ALDH2*1/*2. The present study indicates that effects of alcohol intake on liver-function biomarkers are likely to be modified by the ALDH2 genotype in adult males.

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

    Directory of Open Access Journals (Sweden)

    Janmohammadi Mohsen

    2014-12-01

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

  1. 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

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

    Directory of Open Access Journals (Sweden)

    Odinete Murari

    2001-05-01

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

  3. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-01-01

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

  4. The distribution of hepatitis B virus genotypes in Thailand.

    Science.gov (United States)

    Louisirirotchanakul, Suda; Olinger, Christophe M; Arunkaewchaemsri, Panida; Poovorawan, Yong; Kanoksinsombat, Chinda; Thongme, Chittima; Sa-Nguanmoo, Pattaratida; Krasae, Sasithorn; Theamboonlert, Apiradee; Oota, Sineenart; Fongsatitkul, Ladda; Puapairoj, Chintana; Promwong, Charuporn; Weber, Bernard

    2012-10-01

    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.

  5. Prevalence of hepatitis C virus (HCV) genotypes in Balochistan.

    Science.gov (United States)

    Afridi, Sarwat; Naeem, Muhammad; Hussain, Abid; Kakar, Naseebullah; Babar, Masroor Ellahi; Ahmad, Jamil

    2009-07-01

    A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

  6. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    SHI JinXiu; WANG Ying; HUANG Wei

    2009-01-01

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

  7. Celer: an Efficient Program for Genotype Elimination

    Directory of Open Access Journals (Sweden)

    Nicoletta De Francesco

    2010-08-01

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

  8. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

  9. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

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

  10. Preliminary Studies of the Performance of Quinoa (Chenopodium quinoa Willd.) Genotypes under Irrigated and Rainfed Conditions of Central Malawi.

    Science.gov (United States)

    Maliro, Moses F A; Guwela, Veronica F; Nyaika, Jacinta; Murphy, Kevin M

    2017-01-01

    The goal of sustainable intensification of agriculture in Malawi has led to the evaluation of innovative, regionally novel or under-utilized crop species. Quinoa (Chenopodium quinoa Willd.) has the potential to provide a drought tolerant, nutritious alternative to maize. We evaluated 11 diverse varieties of quinoa for their yield and agronomic performance at two locations, Bunda and Bembeke, in Malawi. The varieties originated from Ecuador, Chile and Bolivia in South America; the United States and Canada in North America; and, Denmark in Europe, and were chosen based on their variation in morphological and agronomic traits, and their potential for adaptation to the climate of Malawi. Plant height, panicle length, days to maturity, harvest index, and seed yield were recorded for each variety under irrigation at Bunda and Bembeke, and under rainfed conditions at Bunda. Plant height was significantly influenced by both genotype and environment. There were also significant differences between the two locations for panicle length whereas genotype and genotype × environment (G × E) interaction were not significantly different. Differences were found for genotype and G × E interaction for harvest index. Notably, differences for genotype, environment and G × E were found for grain yield. Seed yield was higher at Bunda (237-3019 kg/ha) than Bembeke (62-692 kg/ha) under irrigated conditions. The highest yielding genotype at Bunda was Titicaca (3019 kg/ha) whereas Multi-Hued was the highest (692 kg/ha) at Bembeke. Strong positive correlations between seed yield and (1) plant height (r = 0.74), (2) days to maturity (r = 0.76), and (3) biomass (r = 0.87) were found under irrigated conditions. The rainfed evaluations at Bunda revealed significant differences in seed yield, plant biomass, and seed size among the genotypes. The highest yielding genotype was Black Seeded (2050 kg/ha) followed by Multi-Hued (1603 kg/ha) and Bio-Bio (1446 kg/ha). Ecuadorian (257 kg/ha) was the

  11. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    Science.gov (United States)

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  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. 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.

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

    Directory of Open Access Journals (Sweden)

    Anne Marie Minihane

    2016-03-01

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

  15. CFTR genotype-related body water and electrolyte balance during a marathon.

    Science.gov (United States)

    Del Coso, J; Lara, B; Salinero, J J; Areces, F; Ruiz-Vicente, D; Gallo-Salazar, C; Abián-Vicén, J; Cacabelos, R

    2016-09-01

    The aim of this investigation was to determine the influence of CFTR genotype on body water and electrolyte balance during a marathon. Fifty-one experienced runners completed a marathon race. Before and after the race, body mass and a sample of venous blood were obtained. During the race, sweat samples were collected using sweat patches, and fluid and electrolyte intake were obtained using self-reported questionnaires. Thirty-eight participants (74.5% of the total) were 7T/7T homozygotes, 11 (21.6%) were 7T/9T heterozygotes, and one participant presented the rare genotype 5T/7T. Another participant with 9T/9T presented the mutation p.L206W. Participants with 7T/7T showed higher sweat sodium concentrations (42.2 ± 21.6 mmol/L) than 7T/9T (29.0 ± 24.7 mmol/L; P = 0.04). The runner with the 5T/7T genotype (10.2 mmol/L) and the participant with the p.L206W mutation (20.5 mmol/L) exhibited low-range sweat sodium concentrations. However, post-race serum sodium concentration was similar in 7T/7T and 7T/9T (142.1 ± 1.3 and 142.4 ± 1.6 mmol/L, respectively; P = 0.27) and did not show abnormalities in participants with the 5T/7T genotype (140.0 mmol/L) and the p.L206W mutation (143.0 mmol/L). Runners with the CFTR-7T/7T genotype exhibited increased sweat sodium concentrations during a marathon. However, this phenotype was not related with increased likelihood of suffering body water and electrolyte imbalances during real competitions.

  16. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    In prospects of global climate change, heat stress is a rising constraint for the productivity of wheat (Triticum aestivum L.). It is a heat-susceptible crop beyond 17-23oC temperature throughout its phenological stages, flowering phase being the most sensitive stage. Chlorophyll a fluorescence...... for 72h was appropriate to induce genotype dependent variation in Fv/Fm. This standardized protocol was used to phenotype wheat genotypes until the variation in the genotypes was consistently high with increased heritability for the trait, Fv/Fm. Mass screening of 1273 wheat genotypes in a milder stress...

  17. 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.

  18. Trichothecene genotypes of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, Dinorah; Calero, Natalia; Mionetto, Ana; Bettucci, Lina

    2013-03-01

    Gibberella zeae (Schwein.) Petch (anamorph F. graminearum Schwabe) is the primary causal agent of FHB of wheat in Uruguay. In the last decade, F. graminearum has produced destructive epidemics on wheat in Uruguay, causing yield losses and price discounts due to reduced seed quality. Strains of F. graminearum clade usually express one of three strain-specific profiles of trichothecene metabolites: nivalenol and its acetylated derivatives (NIV chemotype), deoxynivalenol and 3-acetyldeoxynivalenol (3-AcDON chemotype), or deoxynivalenol and 15-acetyldeoxynivalenol (15-AcDON chemotype). A multiplex PCR assay of Tri3, Tri5, and Tri7 was used to determine the trichothecene genotype of 111 strains of F. graminearum collected during 2003 and 2009 growing seasons from fields located in the major wheat production area of Uruguay. The result showed that all except one of the isolates were of DON genotype, with the remainder of NIV genotype in years 2003 and 2009. All strains with the DON genotype were also of the 15-AcDON genotype in 2003 and nearly all (45/50) in 2009. No DON/3-AcDON genotypes were found in either growing season. No potential shifts in the populations were found in the trichothecene genotypes between 2003 and the 2009 epidemic FHB harvest seasons. This study provides the first data on trichothecene genotypes of F. graminearum strains isolated from wheat in Uruguay and add to the current regional knowledge of trichothecene genotypes.

  19. Genotype X environment interactions. II. Some genetical considerations.

    Science.gov (United States)

    Mather, K

    1975-08-01

    An algebraic formulation, alternative to that of Mather and Jones (1958) and hierarchial rather than factorial in nauture, is presented for describing the differences among the phenotypes produced by a number of genotypes each grown in each of a number of environments. This formuationdoes not include terms representing statistical interactions between genotypes and environments: it depends instead on comparisons between the different genotypes in their variation over the relevant ranges of environemnts. The two-line case is considered ant eht condition established for linearity of the regress ion of genotype X enviroment interaction (g in Mather and Jones' formulation) on overall effect of the envirronment (e in Mather and Jones' formulation)...

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

    Directory of Open Access Journals (Sweden)

    Jiafa Chen

    Full Text Available Quality control (QC of germplasm identity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotyping methods have been developed from a very limited panel of markers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs. Two QC genotyping strategies were developed, the first is a "rapid QC", employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a "broad QC", employing a larger number of SNP, used to identify each germplasm entry and to measure heterogeneity. The optimal marker selection strategies combined the selection of markers with high minor allele frequency, sampling of clustered SNP in proportion to marker cluster distance and selecting markers that maintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5% contamination in the entry, and approximately a 98% probability to detect a 2% contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different

  1. Stress, genotype and norepinephrine in the prediction of mouse behavior using reinforcement learning.

    Science.gov (United States)

    Luksys, Gediminas; Gerstner, Wulfram; Sandi, Carmen

    2009-09-01

    Individual behavioral performance during learning is known to be affected by modulatory factors, such as stress and motivation, and by genetic predispositions that influence sensitivity to these factors. Despite numerous studies, no integrative framework is available that could predict how a given animal would perform a certain learning task in a realistic situation. We found that a simple reinforcement learning model can predict mouse behavior in a hole-box conditioning task if model metaparameters are dynamically controlled on the basis of the mouse's genotype and phenotype, stress conditions, recent performance feedback and pharmacological manipulations of adrenergic alpha-2 receptors. We find that stress and motivation affect behavioral performance by altering the exploration-exploitation balance in a genotype-dependent manner. Our results also provide computational insights into how an inverted U-shape relation between stress/arousal/norepinephrine levels and behavioral performance could be explained through changes in task performance accuracy and future reward discounting.

  2. Noninvasive fetal RhD genotyping

    DEFF Research Database (Denmark)

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

    2014-01-01

    Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries......, antenatal prophylaxis is combined with postnatal prophylaxis to further minimize the immunization risk. Due to lack of knowledge of the fetal RhD type, antenatal prophylaxis is given to all D-negative women. In the European population, approximately 40% of pregnant women carry a D-negative fetus...... and are thus at no risk of immunization. Noninvasive fetal RhD genotyping enables antenatal prophylaxis to be targeted to only those women carrying a D-positive fetus to avoid unnecessary treatment. Based on an analysis of cell-free fetal DNA from the plasma of pregnant women, this approach has recently...

  3. 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......, 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......, 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...

  4. 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).

  5. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  6. Effect of Phosphorus Deficiency on Leaf Photosynthesis and Carbohydrates Partitioning in Two Rice Genotypes with Contrasting Low Phosphorus Susceptibility

    Institute of Scientific and Technical Information of China (English)

    LI Yong-fu; LUO An-cheng; Muhammad Jaffar HASSAN; WEI Xing-hua

    2006-01-01

    To study the effect of phosphorus (P) deficiency on leaf photosynthesis and carbohydrates partitioning and to determine whether the characteristics of leaf photosynthesis and carbohydrates partitioning are related to iow P tolerance in rice plants, a hydroponic culture experiment supplied with either sufficient P (10 mg/L) or deficient P (0.5 mg/L) was conducted by using two rice genotypes different in their responses to low P stress. Results showed that the plant growth of Zhenongda 454 (low P tolerant genotype) was less affected by P deficiency compared with Sanyang'ai (low P sensitive genotype). Under P-deficient conditions,photosynthetic rates of Zhenongda 454 and Sanyang'ai were decreased by 16% and 35%, respectively, and Zhenongda 454 showed higher photosynthetic rate than Sanyang'ai. Phosphorus deficiency decreased the stomatal conductance for both genotypes, but had no significant influence on leaf internal CO2 concentration (Ci), suggesting that the decrease in leaf photosynthetic rate of rice plants induced by P deficiency was not due to stomatal limitation. Phosphorus deficiency increased the concentration of soluble carbohydrates and sucrose in shoots and roots for both genotypes, and also markedly increased the allocation of soluble carbohydrates and sucrose to roots. Under deficient P supply, Zhenongda 454 had higher root/shoot soluble carbohydrates content ratio and root/shoot sucrose content ratio than Sanyang'ai. In addition, phosphorus deficiency increased the concentration of starch in roots for both genotypes, whereas had no effect on the content of starch in shoots or roots. Compared to genotype Sanyang'ai, the better tolerance to low-P stress of Zhenongda 454 can be explained by the fact that Zhenongda 454 maintains a higher photosynthetic rate and a greater ability to allocate carbohydrates to the roots under P deficiency.

  7. Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs.

    Science.gov (United States)

    Jacobs, Rachel L; Spriggs, Amanda N; MacFie, Tammie S; Baden, Andrea L; Irwin, Mitchell T; Wright, Patricia C; Louis, Edward E; Lawler, Richard R; Mundy, Nicholas I; Bradley, Brenda J

    2016-10-01

    Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations.

  8. 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.

  9. Bayesian prediction of breeding values by accounting for genotype-by-environment interaction in self-pollinating crops.

    Science.gov (United States)

    Bauer, A M; Hoti, F; Reetz, T C; Schuh, W-D; Léon, J; Sillanpää, M J

    2009-06-01

    In self-pollinating populations, individuals are characterized by a high degree of inbreeding. Additionally, phenotypic observations are highly influenced by genotype-by-environment interaction effects. Usually, Bayesian approaches to predict breeding values (in self-pollinating crops) omit genotype-by-environment interactions in the statistical model, which may result in biased estimates. In our study, a Bayesian Gibbs sampling algorithm was developed that is adapted to the high degree of inbreeding in self-pollinated crops and accounts for interaction effects between genotype and environment. As related lines are supposed to show similar genotype-by-environment interaction effects, an extended genetic relationship matrix is included in the Bayesian model. Additionally, since the coefficient matrix C in the mixed model equations can be characterized by rank deficiencies, the pseudoinverse of C was calculated by using the nullspace, which resulted in a faster computation time. In this study, field data of spring barley lines and data of a 'virtual' parental population of self-pollinating crops, generated by computer simulation, were used. For comparison, additional breeding values were predicted by a frequentist approach. In general, standard Bayesian Gibbs sampling and a frequentist approach resulted in similar estimates if heritability of the regarded trait was high. For low heritable traits, the modified Bayesian model, accounting for relatedness between lines in genotype-by-environment interaction, was superior to the standard model.

  10. Association of DD Genotype of Insertion/Deletion Polymorphism of Angiotensin-Converting Enzyme Gene with Systemic Lupus Erythematosus and Lupus Nephropathy

    Directory of Open Access Journals (Sweden)

    Saeedeh Salimi

    2013-10-01

    Full Text Available Background: Systemic lupus erythematosus (SLE is a multisystem disease with unknown etiology. We hypothesized that insertion/deletion (I/D polymorphism of angiotensin-converting enzyme (ACE gene may influence the development and/or progression of SLE and lupus nephritis. Materials and Methods: In a crass sectional case-control study, genomic DNA from 106 SLE patients and 103 healthy controls matched for sex, age, and ethnicity, were genotyped for the (I/D polymorphism of ACE gene by polymerase chain reaction (PCR. Comparison of quantitative variants between two groups was assessed by student t-test and association between qualitative variables was analyzed by the chi-square or Fisher exact tests. Results: The frequency of DD genotype in SLE patients was significantly higher than control group (25.5 % vs. 14 %, and the risk of SLE was 2.2 times greater in subjects with DD genotype than the individual by DI and II genotypes (OR, 2.2 [95% CI, 1.1 to 4.4]; p=0.023. The distribution of D allele in SLE patients was significantly higher (p=0.021 compare to controls (47 and 36.4, respectively. The Risk of nephropathy in SLE patients with DD genotype was three times more than other genotypes (OR, 3 [95% CI, 1.1 to 8]; p=0.027].Conclusion: This study demonstrated that ACE DD genotype acts as a risk factor on SLE and Lupus nephropathy in an Iranian population.

  11. 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

  12. Protein profiles and immunoreactivities of Acanthamoeba morphological groups and genotypes.

    Science.gov (United States)

    Pumidonming, Wilawan; Koehsler, Martina; Leitsch, David; Walochnik, Julia

    2014-11-01

    Acanthamoeba is a free-living protozoan found in a wide variety of habitats. A classification of Acanthamoeba into currently eighteen genotypes (T1-T18) has been established, however, data on differences between genotypes on the protein level are scarce. The aim of this study was to compare protein and immunoreactivity profiles of Acanthamoeba genotypes. Thirteen strains, both clinical and non-clinical, from genotypes T4, T5, T6, T7, T9, T11 and T12, representing three morphological groups, were investigated for their protein profiles and IgG, IgM and IgA immunoreactivities. It was shown that protein and immunoreactivity profiles of Acanthamoeba genotypes T4, T5, T6, T7, T9, T11 and T12 are clearly distinct from each other, but the banding patterns correlate to the morphological groups. Normal human sera revealed anti-Acanthamoeba antibodies against isolates of all investigated genotypes, interestingly, however only very weak IgM and virtually no IgA immunoreactivity with T7 and T9, both representing morphological group I. The strongest IgG, IgM and IgA immunoreactivities were observed for genotypes T4, T5 and T6. Differences of both, protein and immunological patterns, between cytopathic and non-cytopathic strains, particularly within genotype T4, were not at the level of banding patterns, but rather in expression levels.

  13. MLVA genotyping of human Brucella isolates from Peru

    NARCIS (Netherlands)

    H.L. Smits; B. Espinosa; R. Castillo; E. Hall; A. Guillen; M. Zevaleta; R.H. Gilman; P. Melendez; C. Guerra; A. Draeger; A. Broglia; K. Nöckler

    2009-01-01

    Recent human Brucella melitensis isolates from Peru were genotyped by multiple locus variable number repeat analysis. All 24 isolates originated from hospitalized patients living in the central part of Peru and consisted of six genomic groups comprising two to four isolates and nine unique genotypes

  14. Caffeoylquinic Acids in Storage Roots of Sixteen Sweetpotato Genotypes

    Science.gov (United States)

    The contents of chlorogenic acid and the 3,4-, 3,5- and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of sixteen sweetpotato genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele and lo...

  15. Distribution of HCV genotypes in the metropolitan area of Naples

    Directory of Open Access Journals (Sweden)

    Giuseppe Sodano

    2013-08-01

    Full Text Available The Hepatitis C virus is characterized by high genomic variability that leads to the identification of six different genotypes and many subtypes. In this work, we show the prevalence of genotypes in patients living in the metropolitan area of Naples collected in one year, analyzing differences in the distribution depending on sex and age groups.

  16. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  17. Paternity testing and delivering trait-predictive genotypic data

    Science.gov (United States)

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

  18. 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...

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

    Science.gov (United States)

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

  20. The Association of Il28b Genotype with the Histological Features of Chronic Hepatitis C Is HCV Genotype Dependent

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    Roberta D'Ambrosio

    2014-04-01

    Full Text Available The interleukin 28B (IL28B rs12979860 polymorphism is associated with treatment outcome in hepatitis C virus (HCV genotype 1 and 4 patients. Its association with the histological features of chronic hepatitis C and disease severity needs further clarifications. To assess the correlation between IL28B genotype, HCV genotype and liver biopsy findings in untreated patients. Materials and Methods: Pre-treatment liver biopsies from 335 HCV Caucasian patients (59% males, age 50 years enrolled in the MIST study were staged for fibrosis and inflammation according to the METAVIR and the Ishak scoring systems; steatosis was dichotomized as <5% or ≥5%. IL28B was typed by Taqman Single Nucleotide Polymorphism (SNP genotyping assay. HCV genotype was 1 in 151 (45%, 2 in 99 (30%, 3 in 50 (15% and 4 in 35 (10% patients. IL28B genotype was CC in 117 (34%, CT in 166 (49% and TT in 52 (15%. At univariate analysis, the IL28B CC genotype was associated with severe portal inflammation in HCV-1 patients (CC vs. CT/TT: 86% vs. 63%, p = 0.005, severe lobular inflammation in HCV-2 patients (CC vs. CT/TT: 44% vs. 23%, p = 0.03, and less fatty infiltration in HCV-1 patients (CC vs. CT/TT: 72% vs. 51%, p = 0.02. Despite the lack of any association between IL28B and fibrosis stage, in HCV-3 patients IL28B CC correlated with METAVIR F3-F4 (CC vs. CT/TT: 74% vs. 26%, p = 0.05. At multivariate analysis, the genotype CC remained associated with severe portal inflammation in HCV-1, only (Odds Ratio (OR: 95% Confidence Interval (CI: 3.24 (1.23–8.51. IL28B genotype is associated with the histological features of chronic hepatitis C in a HCV genotype dependent manner, with CC genotype being independently associated with severe portal inflammation.

  1. Distribution study of Chlamydia trachomatis genotypes in symptomatic patients in Buenos Aires, Argentina: association between genotype E and neonatal conjunctivitis

    Directory of Open Access Journals (Sweden)

    Corominas Ana I

    2010-02-01

    Full Text Available Abstract Background Chlamydia trachomatis infections are the most prevalent sexually transmitted bacterial infections in the world. There is scarce data available referring to the distribution of C. trachomatis genotypes in Argentina. The aim of this study was to identify the genotypes of C. trachomatis circulating in the metropolitan area of Buenos Aires (Argentina associated with ophthalmia neonatorum and genital infections. Findings From 2001 to 2006, 199 positive samples for C. trachomatis infection from symptomatic adult patients and neonates with ophthalmia neonatorum from two public hospitals were studied. C. trachomatis genotypes were determined by PCR-RFLP of an ompA fragment. Genotype E was the most prevalent regardless of the sample origin (46.3% 57/123 in adults and 72.4% 55/76 in neonates, followed by genotype D (19.5% 24/123 and F (14.6% 18/123 in adults, and G (9.2% 7/76 and D (7.9% 6/76 in neonates. We detected a significantly higher frequency of genotype E (p ophthalmia neonatorum than in genital specimens. Genotype D was associated with genital localization (p Conclusion We found a particularly increased frequency of C. trachomatis genotype E in neonatal conjunctivitis, which may indicate an epidemiological association between this genotype and the newborn population. The present study also contributed to increase the knowledge on genotype distribution of Chlamydia trachomatis in symptomatic adult patients in Buenos Aires, Argentina, in which genotypes E, D and F were the predominant ones.

  2. HCV prevalence and predominant genotype in IV drug users

    Directory of Open Access Journals (Sweden)

    Asad Andalibalshohada

    2014-07-01

    Full Text Available Hepatitis C virus (HCV causes 308000 deaths due to liver cancer and 758000 deaths due to cirrhosis every year. Almost 170 million people have HCV infection around the world. Information regarding this virus helps us to determine the prevalence of other hepatitis C genotypes in population, especially in intravenous drug users. It is assumed that some genotypes are more common in certain areas or groups of people. A recent study strongly confirms the central role of injecting network traits, not only as a transmission factor but also as a predictor of HCV genotype and phylogenetic determination in different communities. Hepatitis C genotypes and subtypes have different prevalence considering the country. Risk factors such as transfusion, hemodialysis, root of acquisition and etc, are detected in intravenous drug users. Several conducted studies have investigated the prevalence, risk factors, and predominance of HCV genotypes infection in different parts of Iran.

  3. Micropropagation of six Paulownia genotypes through tissue culture

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    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.

  4. Effect of genotype on sugar beet yield and quality

    Directory of Open Access Journals (Sweden)

    Nenadić N.

    2003-01-01

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

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

    Science.gov (United States)

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

    2010-10-01

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

  6. 谷胱甘肽转硫酶M1、T1基因型及烟酒嗜好与胃癌易感性的关系%Influence GSTM1 and GSTT1 Genotypes and Smoking, Alcohol Exposure on the Occurrence of Gastric Cancer: Case-control Study from Nanjing,China

    Institute of Scientific and Technical Information of China (English)

    沈孝兵; 浦跃朴; 张娇; 朱良军

    2005-01-01

    [目的]探讨谷胱甘肽转硫酶基因多态性M1(GSTM1)、T1(GSTT1)及烟酒嗜好与胃癌易感性的关系,并对GST基因多态性GSTT1、GSTM1与烟酒暴露在胃癌发生中的交互作用进行分析.[方法]采用1:1配对病例-对照研究方法和PCR技术,检测121例原发性胃癌患者和相应对照的GSTM1和GSTF1基因型,结合研究对象的烟酒嗜好,应用SAS统计分析系统,分析GSTM1和GSTT1基因型及烟酒暴露与胃癌发病的关系,并对基因-基因,基因-烟酒暴露在胃癌发生中的交互作用进行分析.[结果]GSTM1(-)基因型频率在病例组和对照组中分别占44.63%和33.88%,分布无显著性差异(x2=2.6436,P>0.05),GSTF1(-)基因型频率在病例组和对照组中分别为52.89%和44.63%,分布也无显著性差异(χ2=1.1650,P>0.05).吸烟者比非吸烟者发生胃癌的危险高(OR=2.538,95%CI:1.336~4.823);饮酒者比非饮酒者发生胃癌的危险高(oR=2.097,95%CI:1.025~4.291).同时携带GSTM1(-)和GSTT1(-)基因型者发生胃癌的危险性高于GSTM1(+)和GSTT1(+)基因型携带者(OR=2.097,95%CI:1.025~4.291);同时有烟酒嗜好的个体发生胃癌的危险性高于无烟酒嗜好者(OR=2.330,95%CI:1.211~4.482).携带GSTM1(-)和GSTT1(-)且有烟酒嗜好者,发生胃癌的危险显著高于携带GSTM1(+)和GSTT1(+)的无烟酒嗜好者(oR=3.600,95%CI:1.025~12.650).[结论]吸烟、饮酒与胃癌易感性增加有关,GSTM1和GSTT1基因型及烟酒嗜好在胃癌发生中存在一定的交互作用.%[Objective] To determine the association between glutathione-s-transferase genetic polymorphisms(GSTM1,GSTF1) and smoking, alcohol exposure with the risk of gastric cancer and elucidate the action and interaction of gene and environmental factors. [ Methods ] 1:1 Case-control study was conducted and polymerase chain reaction technique was employed to analyse the genetic polymorphisms of GST (GSTM1,GSTT1) genotype in 121 cases of patients with gastric cancer and sex, age

  7. Anther Culture of Chinese Radish ( Raphanus sativus L. var. Longinnatus Bailey): Response of Different Genotypes to the Embryogenesis and the Traits of Regenerated Plantlets

    Institute of Scientific and Technical Information of China (English)

    ZHANG Li

    2011-01-01

    [ Objective] The aims were to ① conduct anther culture of Chinese radish varieties; ② observe the development of embryos from anther culture; ③ study the response of different genotypes to embryogenesis in anther culture; ④ observe the morphology of regenerated plantlets; ⑤ analyze the ploidy level of regenerated plantlets arising from the anther culture process. [ Method]Anthers of 15 genotypes with diverse genetic backgrounds of Chinese radish have been cultured in vitro and induced to undergo embryogenesis and plant formation. [Result] Of 15 genotypes evaluated, four produced embryos. The genotype was the main factor to influence the embryogenesis. The morphology and the ploidy of the regenerated plantlets were observed, and the anther-derived plantlets included a mix of haploids, diploids and hexaploids. Of the plants that regenerated from anther embryos 60% were diploid. [ Conclusion] The plantlets had the high ability to double spontaneously.

  8. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

    Science.gov (United States)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study in 2006-2007 demonstrated a predominant EU genotype ...

  9. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities.

    Science.gov (United States)

    Zancarini, Anouk; Mougel, Christophe; Voisin, Anne-Sophie; Prudent, Marion; Salon, Christophe; Munier-Jolain, Nathalie

    2012-01-01

    Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM). First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.

  10. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities.

    Directory of Open Access Journals (Sweden)

    Anouk Zancarini

    Full Text Available Plant and soil types are usually considered as the two main drivers of the rhizosphere microbial communities. The aim of this work was to study the effect of both N availability and plant genotype on the plant associated rhizosphere microbial communities, in relation to the nutritional strategies of the plant-microbe interactions, for six contrasted Medicago truncatula genotypes. The plants were provided with two different nutrient solutions varying in their nitrate concentrations (0 mM and 10 mM. First, the influence of both nitrogen availability and Medicago truncatula genotype on the genetic structure of the soil bacterial and fungal communities was determined by DNA fingerprint using Automated Ribosomal Intergenic Spacer Analysis (ARISA. Secondly, the different nutritional strategies of the plant-microbe interactions were evaluated using an ecophysiological framework. We observed that nitrogen availability affected rhizosphere bacterial communities only in presence of the plant. Furthermore, we showed that the influence of nitrogen availability on rhizosphere bacterial communities was dependent on the different genotypes of Medicago truncatula. Finally, the nutritional strategies of the plant varied greatly in response to a modification of nitrogen availability. A new conceptual framework was thus developed to study plant-microbe interactions. This framework led to the identification of three contrasted structural and functional adaptive responses of plant-microbe interactions to nitrogen availability.

  11. The effects of an intronic polymorphism in TOMM40 and APOE genotypes in sporadic inclusion body myositis.

    Science.gov (United States)

    Gang, Qiang; Bettencourt, Conceicao; Machado, Pedro M; Fox, Zoe; Brady, Stefen; Healy, Estelle; Parton, Matt; Holton, Janice L; Hilton-Jones, David; Shieh, Perry B; Zanoteli, Edmar; De Paepe, Boel; De Bleecker, Jan; Shaibani, Aziz; Ripolone, Michela; Violano, Raffaella; Moggio, Maurizio; Barohn, Richard J; Dimachkie, Mazen M; Mora, Marina; Mantegazza, Renato; Zanotti, Simona; Hanna, Michael G; Houlden, Henry

    2015-04-01

    A previous study showed that, in carriers of the apolipoprotein E (APOE) genotype ε3/ε3 or ε3/ε4, the presence of a very long (VL) polyT repeat allele in "translocase of outer mitochondrial membrane 40" (TOMM40) was less frequent in patients with sporadic inclusion body myositis (sIBM) compared with controls and associated with a later age of sIBM symptom onset, suggesting a protective effect of this haplotype. To further investigate the influence of these genetic factors in sIBM, we analyzed a large sIBM cohort of 158 cases as part of an International sIBM Genetics Study. No significant association was found between APOE or TOMM40 genotypes and the risk of developing sIBM. We found that the presence of at least 1 VL polyT repeat allele in TOMM40 was significantly associated with about 4 years later onset of sIBM symptoms. The age of onset was delayed by 5 years when the patients were also carriers of the APOE genotype ε3/ε3. In addition, males were likely to have a later age of onset than females. Therefore, the TOMM40 VL polyT repeat, although not influencing disease susceptibility, has a disease-modifying effect on sIBM, which can be enhanced by the APOE genotype ε3/ε3.

  12. Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F.

    Science.gov (United States)

    Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Botelho, Livia; Carrilho, Flair José; Pinho, João Renato Rebello

    2011-01-01

    Hepatitis B is a worldwide health problem affecting about 2 billion people and more than 350 million are chronic carriers of the virus. Nine HBV genotypes (A to I) have been described. The geographical distribution of HBV genotypes is not completely understood due to the limited number of samples from some parts of the world. One such example is Colombia, in which few studies have described the HBV genotypes. In this study, we characterized HBV genotypes in 143 HBsAg-positive volunteer blood donors from Colombia. A fragment of 1306 bp partially comprising HBsAg and the DNA polymerase coding regions (S/POL) was amplified and sequenced. Bayesian phylogenetic analyses were conducted using the Markov Chain Monte Carlo (MCMC) approach to obtain the maximum clade credibility (MCC) tree using BEAST v.1.5.3. Of all samples, 68 were positive and 52 were successfully sequenced. Genotype F was the most prevalent in this population (77%) - subgenotypes F3 (75%) and F1b (2%). Genotype G (7.7%) and subgenotype A2 (15.3%) were also found. Genotype G sequence analysis suggests distinct introductions of this genotype in the country. Furthermore, we estimated the time of the most recent common ancestor (TMRCA) for each HBV/F subgenotype and also for Colombian F3 sequences using two different datasets: (i) 77 sequences comprising 1306 bp of S/POL region and (ii) 283 sequences comprising 681 bp of S/POL region. We also used two other previously estimated evolutionary rates: (i) 2.60 × 10(-4)s/s/y and (ii) 1.5 × 10(-5)s/s/y. Here we report the HBV genotypes circulating in Colombia and estimated the TMRCA for the four different subgenotypes of genotype F.

  13. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    Science.gov (United States)

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  14. Methods of analysis and number of replicates for trials with large numbers of soybean genotypes

    Directory of Open Access Journals (Sweden)

    Gilvani Matei

    Full Text Available ABSTRACT: The aim of this study was to evaluate the experimental precision of different methods of statistical analysis for trials with large numbers of soybean genotypes, and their relationship with the number of replicates. Soybean yield data (nine trials; 324 genotypes; 46 cultivars; 278 lines; agricultural harvest of 2014/15 were used. Two of these trials were performed at the same location, side by side, forming a trial with six replicates. Each trial was analyzed by the randomized complete block, triple lattice design, and use of the Papadakis method. The selective accuracy, least significant difference, and Fasoulas differentiation index were estimated, and model assumptions were tested. The resampling method was used to study the influence of the number of replicates, by varying the number of blocks and estimating the precision measurements. The experimental precision indicators of the Papadakis method are more favorable as compared to the randomized complete block design and triple lattice. To obtain selective accuracy above the high experimental precision range in trials with 324 soybean genotypes, two repetitions can be used, and data can be analyzed using the randomized complete block design or Papadakis method.

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

    Directory of Open Access Journals (Sweden)

    Lucía D’Andrea

    2015-03-01

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

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

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    Valeriano Domenech

    2011-07-01

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

  17. Vasodilatory effect of nitroglycerin in Japanese subjects with different aldehyde dehydrogenase 2 (ALDH2) genotypes.

    Science.gov (United States)

    Miura, Takeshi; Nishinaka, Toru; Terada, Tomoyuki; Yonezawa, Kazuya

    2017-03-23

    The functional genetic polymorphism of aldehyde dehydrogenase 2 (ALDH2) influences the enzymatic activities of its wild type (Glu504 encoded by ALDH2*1) and mutant type (Lys504 encoded by ALDH2*2) proteins. The enzymatic activities of mutant-type ALDH2 are limited compared with those of the wild type. ALDH2 has been suggested as a critical factor for nitroglycerin-mediated vasodilation by some human studies and in vitro studies. Currently, there is no research on direct observations of the vasodilatory effect of nitroglycerin sublingual tablets, which is the generally used dosage form. In the present study, the contribution of ALDH2 to the vasodilatory effect of nitroglycerin sublingual tablets was investigated among three genotype groups (ALDH2*1/*1, ALDH2*1/*2, and ALDH2*2/*2) in Japanese. The results by direct assessments of in vivo nitroglycerin-mediated dilation showed no apparent difference in vasodilation among all genotypes of ALDH2. Furthermore, to analyze the effect of other factors (age and flow-mediated dilation), multiple regression analysis and Pearson's correlation coefficient analysis were carried out. These analyses also indicated that the genotypes of ALDH2 were not related to the degree of vasodilation. These results suggest the existence of other predominant pathway(s) for nitroglycerin biotransformation, at least with regard to clinical nitroglycerin (e.g., a sublingual tablet) in Japanese subjects.

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

    Science.gov (United States)

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

    2016-06-01

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

  19. Corticosterone metabolites in laying hen droppings-Effects of fiber enrichment, genotype, and daily variations.

    Science.gov (United States)

    Alm, M; Holm, L; Tauson, R; Wall, H

    2014-10-01

    There is growing interest and concern for animal welfare in commercial poultry production. To evaluate stress and welfare in an objective and noninvasive way, fecal corticosterone metabolites (FCM) in droppings can be analyzed. However, the influence of diet, genotype, and daily variations in FCM and production of droppings in laying hens has been poorly investigated. This study examined the effect of insoluble fiber by adding 3% ground straw pellets to the feed to Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) hens housed in furnished cages between 20 and 40 wk of age. In total, 960 hens were included in the study. Droppings were collected 4 times per day for 3 consecutive days and analyzed by corticosterone immunoassay. Biological validation confirmed the ability of the assay to detect changes in FCM levels. Inclusion of straw pellets in the feed increased FCM concentration in both hen genotypes and increased excretion rate of FCM in LB hens. The LB hens also produced greater amounts of droppings than LSL hens. Both FCM levels and production of droppings varied during the day, although no distinct diurnal rhythm was found. These findings demonstrate that when using FCM to evaluate stress and welfare in laying hens, many factors (e.g., diet, genotype used, and so on) need to be taken into account to allow accurate interpretation of the results. In addition, under certain conditions, excretion rate of FCM might be more appropriate to use compared with FCM concentration.

  20. Imaging spectroscopy links aspen genotype with below-ground processes at landscape scales.

    Science.gov (United States)

    Madritch, Michael D; Kingdon, Clayton C; Singh, Aditya; Mock, Karen E; Lindroth, Richard L; Townsend, Philip A

    2014-01-01

    Fine-scale biodiversity is increasingly recognized as important to ecosystem-level processes. Remote sensing technologies have great potential to estimate both biodiversity and ecosystem function over large spatial scales. Here, we demonstrate the capacity of imaging spectroscopy to discriminate among genotypes of Populus tremuloides (trembling aspen), one of the most genetically diverse and widespread forest species in North America. We combine imaging spectroscopy (AVIRIS) data with genetic, phytochemical, microbial and biogeochemical data to determine how intraspecific plant genetic variation influences below-ground processes at landscape scales. We demonstrate that both canopy chemistry and below-ground processes vary over large spatial scales (continental) according to aspen genotype. Imaging spectrometer data distinguish aspen genotypes through variation in canopy spectral signature. In addition, foliar spectral variation correlates well with variation in canopy chemistry, especially condensed tannins. Variation in aspen canopy chemistry, in turn, is correlated with variation in below-ground processes. Variation in spectra also correlates well with variation in soil traits. These findings indicate that forest tree species can create spatial mosaics of ecosystem functioning across large spatial scales and that these patterns can be quantified via remote sensing techniques. Moreover, they demonstrate the utility of using optical properties as proxies for fine-scale measurements of biodiversity over large spatial scales.

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

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    Euclides Reuter de Oliveira

    2013-02-01

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

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

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    Alessandro Soria

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

  3. Treatment of genotype 2 and 3 chronic hepatitis C virus-infected patients

    Institute of Scientific and Technical Information of China (English)

    Perdita Wietzke-Braun; Volker Meier; Katrin Neubauer-Saile; Sabine Mihm; Giuliano Ramadori

    2005-01-01

    AIM: Before pegylated interferon alpha (IFN) was introduced for the therapy of chronic hepatitis C virus(HCV)-induced hepatitis, conventional thrice weekly IFN therapy was supplemented by ribavirin. Also, at that time,higher and more frequent doses of IFN were expected to be more effective than the standard regimen of 3 MU thrice weekly. As ribavirin significantly increases side effects and negatively influences the quality of life particularly in young patients, we started a prospective non-randomized study with a daily IFN-2a monotherapy as an initial treatment for chronic hepatitis C.METHODS: Forty-six consecutive chronic HCV-infected patients received 3 MU IFN-2a per day as an initial treatment. Patients with genotype 2 or 3 (n = 12) were treated for 24 wk, and patients with genotypes other than 2 or 3 (n = 34) for 48 wk. Treatment outcome was followed up for 48 wk after the end of treatment (EOT).Virological response was defined as the absence of detectable serum HCV-RNA. Patients without virological response at 12 wk after the start of treatment received RESULTS: During treatment, three genotype 3 patients were excluded from the study due to incompliance. The remaining patients (n = 9) infected with genotype 2 or 3showed an initial virological response rate of 100%. Six patients (66.7%) were still found to be virus-free at the end of follow-up period. In these patients, initial virological response was evident already after 2 wk of treatment. In contrast, initial virological response occurred first after 4 wk of treatment in the three patients who relapsed(33.3%). In comparison, patients infected with genotypes other than 2 or 3 (n = 34) showed an initial virological response rate of only 23.5% (n = 8), and even in combination with ribavirin a sustained virological response(SVR) rate of only 11.8% (n = 4) could be achieved.CONCLUSION: In chronic HCV-infected patients with genotype 2 or 3, a SVR can be expected after 24 wk of daily dose IFN-2a treatment

  4. Association between CYP19A1 genotype and pubertal sagittal jaw growth

    Science.gov (United States)

    He, Shushu; Hartsfield, James K.; Guo, Yujiao; Cao, Yang; Wang, Si; Chen, Song

    2016-01-01

    Introduction Sagittal jaw growth is influenced during puberty by a ratio of androgens and estrogens. The CYP19A1 (formerly CYP19) gene encodes the cytochrome P450 enzyme aromatase (estrogen synthetase), which converts testosterone to estrogen. Genetic variations including single nucleotide polymorphisms might regulate CYP19A1 gene expression or the function of the aromatase protein and thus influence sagittal jaw growth. Methods The annual sagittal jaw growth in 92 pubertal orthodontic patients was determined by using pretreatment and posttreatment cephalometric radiographs. Single nucleotide polymorphisms rs2470144 and rs2445761 were genotyped and haplotypes constructed. Associations between genotypes or haplotypes and the annual sagittal growth were estimated by using JMP (version 9.0; SAS Institute, Cary, NC). Results Two single nucleotide polymorphisms were significantly associated with average differences in annual sagittal jaw growth in boys. Haplotype analysis demonstrated that haplotypes Trs2470144Trs2445761 and Crs2470144Trs2445761 had significant effects on annual sagittal maxillary growth and on mandibular growth in boys. No association was found in girls. Conclusions A quantitative trait locus that influences male pubertal sagittal jaw growth might exist in the CYP19A1 gene, and single nucleotide polymorphisms rs2470144 and rs2445761 might be inside this quantitative trait locus or be linked to it. PMID:23116507

  5. Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy.

    Science.gov (United States)

    Mirandola, Silvia; Sebastiani, Giada; Rossi, Cristina; Velo, Emanuela; Erne, Elke Maria; Vario, Alessandro; Tempesta, Diego; Romualdi, Chiara; Campagnolo, Davide; Alberti, Alfredo

    2012-12-01

    The evolution of hepatitis B virus (HBV) and the role of different variants during antiviral therapy may be influenced by HBV genotype. We have therefore analysed substitutions potentially related to nucleos(t)ide analogues (NAs) resistance at 42 positions within RT-region in a cohort of patients with chronic hepatitis B in relation to HBV-genotype. RT mutations analysis was performed by direct sequencing in 200 NAs-naïve patients and in 64 LAM or LAM+ADV experienced patients with NAs resistance, infected mainly by HBV-genotypes D and A. 27 polymorphic-sites were identified among the 42 positions analysed and 64 novel mutations were detected in 23 positions. Genotype-D displayed the highest mutation frequency (6.4%) among all HBV-genotypes analysed. Single or multiple mutations were detected in 80% of naïve patients. Overall, the most frequent single mutations were at residues rt54, rt53 and rt91 which may associate with significantly lower HBV-DNA levels (p=0.001). Comparison with sequencing data of patients failing LMV or LAM+ADV therapy revealed an higher frequency of novel genotype-specific mutations if compared with naïve patients: 3 mutations under LAM monotherapy in HBV-D (rtS85F; rtL91I; rtC256G) and 3 mutations under ADV therapy in HBV-A (rtI53V; rtW153R; rtF221Y). In HBV-D treated patients the dominant resistance mutation was rtL80V (31.4%) and rtM204I (60%) in LAM+ADV group while LAM-treated patients showed a preference of rtM204V (51.9%). Interestingly, none of HBV-A patients had mutation rtM204I under ADV add-on treatment but all of them had the "V" AA substitution. These results suggested that in patients with CHB, HBV-genotype might be relevant in the evolution and development of drug resistance showing also different mutation patterns in the YMDD motif between HBV genotype D and A.

  6. 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.

  7. Genotype phenotype classification of hepatocellular adenoma

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  8. Plant genotype, microbial recruitment and nutritional security

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    Jai Singh Patel

    2015-08-01

    Full Text Available Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome.

  9. Biodigestão anaeróbia dos dejetos da bovinocultura de corte: influência do período, do genótipo e da dieta Anaerobic biodigestion of beef cattle manure: influence of period, genotype and diet

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    Marco Antonio Previdelli Orrico Junior

    2012-06-01

    genotypes (Canchim and Nellore and sub-plots by three periods of manure collection (initial, intermediate and final. The efficiency of the composting process was evaluated by reductions of total solids, volatile solids, the most probable number (MPN of total and thermotolerant coliforms, chemical and biochemical demand of oxygen, besides the production and potentials of biogas and methane production. There was no effect of genotype or period on manure composting; however, the increase in the forage proportion in the diet promoted the lower efficiency of the process, in which an increase of 26.31% was found for the volume of methane that was produced with diet with 60% concentrate in relation to the diet with 40% concentrate. Significant reductions in MPN of total and thermotolerant coliforms were also observed at the end of the process, regardless of the treatment tested.

  10. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

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    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.

  11. Hepatitis B virus genotypes and lamivudine resistance mutations in Jordan

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To investigate and identify prevalent hepatitis B virus (HBV) genotypes and to explore lamivudine-resistant mutations among treated and untreated patients in Jordan.METHODS: A total of 107 cases with chronic hepatitis B were recruited from different medical centers in Jordan. Serological tests were preformed for all cases using a microparticle enzyme immunoassay. HBV Genotyping was performed for 70 cases using Line probe genotyping assay, The YMDD mutations were explored for 20 cases (4 were lamivudine naive) using the INNO-LiPA HBV DR assay.RESULTS: Genotype D was the only detected genotype. A total of 6 YMDD mutations were detected in 5 treated patients (31%) while one mutation was detected in the naive patients. Seventeen percent of cases were positive for HBeAg and had statistically significant higher levels of serum aminotransferases.CONCLUSION: HBV genotype D appears to be the only circulating type in Jordanian patients. The YMDD mutations were detected in 31% of lamivudine-treated cases with similar patterns to those found in the lit-erature. We also found a relatively low prevalence of HBeAg expression among examined cases (17%). Awareness of these serologic, genotypic and resistance patterns might help in the formulation of management plans and for predicting clinical outcomes. Further larger scale studies are needed to confirm our results and to examine possible associations among clinical, serologic, and genetic patterns of HBV infections in Jordan.

  12. Preliminary report of hepatitis B virus genotype prevalence in Iran

    Institute of Scientific and Technical Information of China (English)

    Seyed-Moayed Alavian; Hossein Keyvani; Mahdi Rezai; Neda Ashayeri; Homa Mohammad Sadeghi

    2006-01-01

    AIM: To determine the prevalence of hepatitis B virus (HBV) genotypes in Iranian hepatitis B surface antigen (HBsAg) carriers, chronic hepatitis B and cirrhotic patients.METIHODS: A total of 109 HBsAg-positive patients were included in this study. HBV genotypes were determined by using INNO-LiPA methodology which is based on the reverse hybridization principle.RESULTS: The distribution of patients with different stages of liver disease was as follows: 95 (86.4%) chronic hepatitis, 11 (10%) liver cirrhosis, and 3 (2.7%)inactive carrier. Of the chronic hepatitis and liver cirrhosis patients, 26.4% were HBeAg-positive while 70% were HBeAg-negative. Genotype D was the only detected type found in all patients. CONCLUSION: Classifying HBV into genotypes has to be cost-effective and clinically relevant. Our study indicates that HBV genotype D prevails in the Mediterranean area, Near and Middle East, and South Asia. Continued efforts for understanding HBV genotype through international co-operation will reveal further virological differences of the genotypes and their clinical relevance.

  13. Imputation of missing genotypes: an empirical evaluation of IMPUTE

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    Steinberg Martin H

    2008-12-01

    Full Text Available Abstract Background Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood. Results We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs. The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans. Conclusion Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.

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

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    Mare Lõhmus

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

  15. FTO genotype is associated with phenotypic variability of body mass index.

    Science.gov (United States)

    Yang, Jian; Loos, Ruth J F; Powell, Joseph E; Medland, Sarah E; Speliotes, Elizabeth K; Chasman, Daniel I; Rose, Lynda M; Thorleifsson, Gudmar; Steinthorsdottir, Valgerdur; Mägi, Reedik; Waite, Lindsay; Smith, Albert Vernon; Yerges-Armstrong, Laura M; Monda, Keri L; Hadley, David; Mahajan, Anubha; Li, Guo; Kapur, Karen; Vitart, Veronique; Huffman, Jennifer E; Wang, Sophie R; Palmer, Cameron; Esko, Tõnu; Fischer, Krista; Zhao, Jing Hua; Demirkan, Ayşe; Isaacs, Aaron; Feitosa, Mary F; Luan, Jian'an; Heard-Costa, Nancy L; White, Charles; Jackson, Anne U; Preuss, Michael; Ziegler, Andreas; Eriksson, Joel; Kutalik, Zoltán; Frau, Francesca; Nolte, Ilja M; Van Vliet-Ostaptchouk, Jana V; Hottenga, Jouke-Jan; Jacobs, Kevin B; Verweij, Niek; Goel, Anuj; Medina-Gomez, Carolina; Estrada, Karol; Bragg-Gresham, Jennifer Lynn; Sanna, Serena; Sidore, Carlo; Tyrer, Jonathan; Teumer, Alexander; Prokopenko, Inga; Mangino, Massimo; Lindgren, Cecilia M; Assimes, Themistocles L; Shuldiner, Alan R; Hui, Jennie; Beilby, John P; McArdle, Wendy L; Hall, Per; Haritunians, Talin; Zgaga, Lina; Kolcic, Ivana; Polasek, Ozren; Zemunik, Tatijana; Oostra, Ben A; Junttila, M Juhani; Grönberg, Henrik; Schreiber, Stefan; Peters, Annette; Hicks, Andrew A; Stephens, Jonathan; Foad, Nicola S; Laitinen, Jaana; Pouta, Anneli; Kaakinen, Marika; Willemsen, Gonneke; Vink, Jacqueline M; Wild, Sarah H; Navis, Gerjan; Asselbergs, Folkert W; Homuth, Georg; John, Ulrich; Iribarren, Carlos; Harris, Tamara; Launer, Lenore; Gudnason, Vilmundur; O'Connell, Jeffrey R; Boerwinkle, Eric; Cadby, Gemma; Palmer, Lyle J; James, Alan L; Musk, Arthur W; Ingelsson, Erik; Psaty, Bruce M; Beckmann, Jacques S; Waeber, Gerard; Vollenweider, Peter; Hayward, Caroline; Wright, Alan F; Rudan, Igor; Groop, Leif C; Metspalu, Andres; Khaw, Kay Tee; van Duijn, Cornelia M; Borecki, Ingrid B; Province, Michael A; Wareham, Nicholas J; Tardif, Jean-Claude; Huikuri, Heikki V; Cupples, L Adrienne; Atwood, Larry D; Fox, Caroline S; Boehnke, Michael; Collins, Francis S; Mohlke, Karen L; Erdmann, Jeanette; Schunkert, Heribert; Hengstenberg, Christian; Stark, Klaus; Lorentzon, Mattias; Ohlsson, Claes; Cusi, Daniele; Staessen, Jan A; Van der Klauw, Melanie M; Pramstaller, Peter P; Kathiresan, Sekar; Jolley, Jennifer D; Ripatti, Samuli; Jarvelin, Marjo-Riitta; de Geus, Eco J C; Boomsma, Dorret I; Penninx, Brenda; Wilson, James F; Campbell, Harry; Chanock, Stephen J; van der Harst, Pim; Hamsten, Anders; Watkins, Hugh; Hofman, Albert; Witteman, Jacqueline C; Zillikens, M Carola; Uitterlinden, André G; Rivadeneira, Fernando; Zillikens, M Carola; Kiemeney, Lambertus A; Vermeulen, Sita H; Abecasis, Goncalo R; Schlessinger, David; Schipf, Sabine; Stumvoll, Michael; Tönjes, Anke; Spector, Tim D; North, Kari E; Lettre, Guillaume; McCarthy, Mark I; Berndt, Sonja I; Heath, Andrew C; Madden, Pamela A F; Nyholt, Dale R; Montgomery, Grant W; Martin, Nicholas G; McKnight, Barbara; Strachan, David P; Hill, William G; Snieder, Harold; Ridker, Paul M; Thorsteinsdottir, Unnur; Stefansson, Kari; Frayling, Timothy M; Hirschhorn, Joel N; Goddard, Michael E; Visscher, Peter M

    2012-10-11

    There is evidence across several species for genetic control of phenotypic variation of complex traits, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ∼170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype), is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ∼0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI, possibly mediated by DNA methylation. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.

  16. Pharmacokinetics of lansoprazole in Chinese healthy subjects in relation to CYP2C19 genotypes

    Institute of Scientific and Technical Information of China (English)

    Yu-rong HU; Hai-ling QIAO; Quan-cheng KAN

    2004-01-01

    AIM: To study the kinetic characteristics of lansoprazole in healthy Chinese subjects in relation to CYP2C19 genotype status for the individualized dose regimen of lansoprazole. METHODS: Nine homozygous extensive metabolizers (homo EMs) and 9 poor metabolizers (PMs) were recruited for the study from a total of 70 healthy Chinese volunteers, whose CYP2C19 genotype status was determined by the PCR-RFLP techniques. After a single oral dose of 30 mg lansoprazole capsule, plasma concentrations of lansoprazole were determined with HPLC method. RESULTS: In Chinese subjects, the allele frequencies of the CYP2C19ml and CYP2C19m2 mutation were 0.35 and 0.07, respectively. The concentration-time curves in the two groups were best fitted to a one-compartment model. In the homo EMs and the PMs groups, the main kinetic parameters were as follows: Tmax(2.44±0.85)and (2.33±0.94) h, Cmax (1.10±0.34) and (1.73±0.56) mg/L, Cl/F (16.55±6.38) and (3.58± 1) L/h, T1/2ke (1.96±0.51)Cmax values existed between the two groups (P<0.01). CONCLUSION: CYP2C19 genotype is the major factor to influence the interindividual kinetic variability of lansoprazole. Individualized dose regimen of lansoprazole, based on identification of genotype, can be of great benefit for the reasonable use of this drug.

  17. Viral and epidemiological determinants of the invasion dynamics of novel dengue genotypes.

    Directory of Open Access Journals (Sweden)

    José Lourenço

    Full Text Available BACKGROUND: Dengue has become a major concern for international public health. Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities. Viral lineage replacement events, caused for example by different levels of cross-protection or differences in viral fitness, have also been linked to a temporary change in dengue epidemiology. A major replacement event was recently described for South-East Asia where the Asian-1 genotype of dengue serotype 2 replaced the resident Asian/American type. Although this was proposed to be due to increased viral fitness in terms of enhanced human-to-mosquito transmission, no major change in dengue epidemiology could be observed. METHODS/RESULTS: Here we investigate the invasion dynamics of a novel, advantageous dengue genotype within a model system and determine the factors influencing the success and rate of fixation as well as their epidemiological consequences. We find that while viral fitness overall correlates with invasion success and competitive exclusion of the resident genotype, the epidemiological landscape plays a more significant role for successful emergence. Novel genotypes can thus face high risks of stochastic extinction despite their fitness advantage if they get introduced during episodes of high dengue prevalence, especially with respect to that particular serotype. CONCLUSION: The rarity of markers for positive selection has often been explained by strong purifying selection whereby the constraints imposed by dengue's two-host cycle are expected to result in a high rate of deleterious mutations. Our results demonstrate that even highly beneficial mutants are under severe threat of extinction, which would suggest that apart from purifying selection, stochastic effects and genetic drift beyond seasonal bottlenecks are equally important in shaping dengue's viral

  18. Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.

    Directory of Open Access Journals (Sweden)

    Weifeng Shi

    Full Text Available BACKGROUND: More than ten subgenotypes of genotype C Hepatitis B virus (HBV have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2, however, inconsistent designations of these subgenotypes still exist. METHODOLOGY/PRINCIPAL FINDINGS: We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%. CONCLUSIONS/SIGNIFICANCE: A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.

  19. Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

    Science.gov (United States)

    Picard, Christine; Bosco, Marco

    2008-01-01

    Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

  20. Variation among genotypes in responses to increasing temperature in a marine parasite: evolutionary potential in the face of global warming?

    Science.gov (United States)

    Berkhout, Boris W; Lloyd, Melanie M; Poulin, Robert; Studer, Anja

    2014-11-01

    Climates are changing worldwide, and populations are under selection to adapt to these changes. Changing temperature, in particular, can directly impact ectotherms and their parasites, with potential consequences for whole ecosystems. The potential of parasite populations to adapt to climate change largely depends on the amount of genetic variation they possess in their responses to environmental fluctuations. This study is, to our knowledge, the first to look at differences among parasite genotypes in response to temperature, with the goal of quantifying the extent of variation among conspecifics in their responses to increasing temperature. Snails infected with single genotypes of the trematode Maritrema novaezealandensis were sequentially acclimatised to two different temperatures, 'current' (15°C) and 'elevated' (20°C), over long periods. These temperatures are based on current average field conditions in the natural habitat and those predicted to occur during the next few decades. The output and activity of cercariae (free-swimming infective stages emerging from snails) were assessed for each genotype at each temperature. The results indicate that, on average, both cercarial output and activity are higher at the elevated acclimation temperature. More importantly, the output and activity of cercariae are strongly influenced by a genotype-by-temperature interaction, such that different genotypes show different responses to increasing temperature. Both the magnitude and direction (increase or decrease) of responses to temperature varied widely among genotypes. Therefore, there is much potential for natural selection to act on this variation, and predicting how the trematode M. novaezealandensis will respond to the climate changes predicted for the next century will prove challenging.

  1. The GSTM1 null genotype increased risk of gastric cancer: a meta-analysis based on 46 studies.

    Directory of Open Access Journals (Sweden)

    Yi Zhao

    Full Text Available BACKGROUND: Glutathione S-transferases M1 (GSTM1 is an important phase II metabolizing enzyme. The null genotype of GSTM1 causes total loss of GSTM1 enzyme activity and numerous studies have investigated the association between GSTM1 null genotype and gastric cancer risk. METHODS: This meta-analysis was designed to investigate the relationship between GSTM1 null genotype and susceptibility to gastric cancer and assess the influence of Helicobacter pylori infection, smoking, Lauren's classification, and other factors. Odds ratios (ORs and 95% confidence intervals (CIs were calculated to estimate the association strength. RESULTS: A total of 46 eligible studies were indentified and analyzed in this meta-analysis, including 8138 cases of gastric cancer and 13867 controls. Pooled results showed that the GSTM1 null genotype was associated with a significantly increased risk of gastric cancer (OR=1.217, 95% CI: 1.113-1.331, P(heterogeneity<0.001. Sub-group analysis suggested that the significant association was only observed in Asians (OR=1.273, 95%: 1.137-1.426, P(heterogeneity= 0.002, but not in Caucasians. The increased risk was found among H. pylori positive population (OR=1.928, 95% CI: 1.028-3.615, P(heterogeneity=0.065, while no association was found among H. pylori negative population (OR=0.969, 95% CI: 0.618-1.521, P(heterogeneity=0.168. For smoking status, the GSTM1 null genotype increased risk of gastric cancer in both ever-smokers and non-smokers. Source of control, sample size, location of tumor and Lauren's classification did not modify the association. CONCLUSIONS: In this meta-analysis based on 46 epidemiological studies, we show that the GSTM1 null genotype is associated with an increased risk of gastric cancer among Asians but not among Caucasians. H. pylori infection but not smoking status could modify the association.

  2. Phasing of many thousands of genotyped samples.

    Science.gov (United States)

    Williams, Amy L; Patterson, Nick; Glessner, Joseph; Hakonarson, Hakon; Reich, David

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources).

  3. Premature ovarian failure : from phenotype to genotype

    NARCIS (Netherlands)

    Knauff, A.H.

    2009-01-01

    Postponement of childbearing has led to increased rates of age-related female subfertility. Age-related decreases in ovarian follicle numbers and decay in oocyte quality influence the natural loss of fecundity and ultimately the start of menopause. The rate of ovarian ageing is highly variable among

  4. 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.

  5. Reduced Uptake of Family Screening in Genotype-Negative Versus Genotype-Positive Long QT Syndrome.

    Science.gov (United States)

    Hanninen, Mikael; Klein, George J; Laksman, Zachary; Conacher, Susan S; Skanes, Allan C; Yee, Raymond; Gula, Lorne J; Leong-Sit, Peter; Manlucu, Jaimie; Krahn, Andrew D

    2015-08-01

    The acceptance and yield of family screening in genotype-negative long QT syndrome (LQTS) remains incompletely characterized. In this study of family screening for phenotype-definite Long QT Syndrome (LQTS, Schwartz score ≥3.5), probands at a regional Inherited Cardiac Arrhythmia clinic were reviewed. All LQTS patients were offered education by a qualified genetic counselor, along with materials for family screening including electronic and paper correspondence to provide to family members. Thirty-eight qualifying probands were identified and 20 of these had family members who participated in cascade screening. The acceptance of screening was found to be lower among families without a known pathogenic mutation (33 vs. 77 %, p = 0.02). A total of 52 relatives were screened; fewer relatives were screened per index case when the proband was genotype-negative (1.7 vs. 3.1, p = 0.02). The clinical yield of screening appeared to be similar irrespective of gene testing results (38 vs. 33 %, p = 0.69). Additional efforts to promote family screening among gene-negative long QT families may be warranted.

  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. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

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    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.

  8. Genotype versus phenotype in families with androgen insensitivity syndrome

    NARCIS (Netherlands)

    Boehmer, ALM; Bruggenwirth, H; Van Assendelft, C; Otten, BJ; Verleun-Mooijman, MCT; Niermeijer, MF; Brunner, HG; Rouwe, CW; Waelkens, JJ; Oostdijk, W; Kleijer, WJ; Van der Kwast, TH; De Vroede, MA; Drop, SLS

    2001-01-01

    Androgen insensitivity syndrome encompasses a wide range of phenotypes, which are caused by numerous different mutations in the AR gene. Detailed information on the genotype/ phenotype relationship in androgen insensitivity syndrome is important for sex assignment, treatment of androgen insensitivit

  9. Molecular methods for genotyping complex copy number polymorphisms.

    Science.gov (United States)

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  10. Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics

    DEFF Research Database (Denmark)

    Engberg, J.; Bang, D. D.; Aabenhus, R.;

    2005-01-01

    The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals and the t...

  11. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  12. Superoxide Dismutase and Catalase Genotypes in Pediatric Migraine Patients.

    Science.gov (United States)

    Saygi, Semra; Erol, İlknur; Alehan, Füsun; Yalçın, Yaprak Yılmaz; Kubat, Gözde; Ataç, Fatma Belgin

    2015-10-01

    This study compared superoxide dismutase (SOD) and catalase (CAT) alleles in 97 consecutive children and adolescents with migraine to 96 healthy children and adolescents. Isolated genomic DNA was used as a template for SOD1 (35 A/C), SOD2 16 C/T, and CAT2 [(-262 C/T) and (-21 A/T)] allele genotyping. The SOD2 16 C/T genotype and C allele frequency differed significantly between controls and migraine (P = .047; P = .038). CAT -21 AA genotype and A allele frequency were significantly higher in both migraine with aura patients (P = .013; P = .004) and migraine without aura patients (P = .003; P = .001) compared to controls. To our knowledge, this is the first demonstration of differences in SOD and CAT genotypes between pediatric migraine patients and age-matched controls. Further studies on the functional implications of these genetic variants on neural antioxidant capacity and the use of antioxidant modulators for migraine treatment are warranted.

  13. Characterization of cowpea genotype resistance to Callosobruchus maculatus

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    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.

  14. Forensic SNP Genotyping using Nanopore MinION Sequencing

    Science.gov (United States)

    Cornelis, Senne; Gansemans, Yannick; Deleye, Lieselot; Deforce, Dieter; Van Nieuwerburgh, Filip

    2017-01-01

    One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies’ (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible. PMID:28155888

  15. Circulation of genotype-I hepatitis B virus in the primitive tribes of Arunachal Pradesh in early sixties and molecular evolution of genotype-I.

    Science.gov (United States)

    Haldipur, Bangari P; Walimbe, Atul M; Arankalle, Vidya A

    2014-10-01

    Retrospective serologic screening of 1077 serum samples collected from the primitive tribe from north-eastern India in 1963 revealed high prevalence of HBV (15% HBsAg carrier rate) and HCV (7% anti-HCV positivity) and co-circulation of multiple HBV genotypes-A, C, D and G. Full genome sequencing classified all the G-genotype samples as genotype-I. Comparison of genotype-I-HBV full-genome sequences representing 1963 (n=5, this study) and 2005 (reported earlier) showed identical recombination break-points of genotypes-A/G/C. Genotype-C and genotype-C-fragment of I-genotype circulating in 1963 were distinctly different. The data demonstrates that the recombination events were not recent. Molecular clock analysis predicted existence of genotype-I in this tribe during 1920s.

  16. Robust SNP genotyping by multiplex PCR and arrayed primer extension

    Directory of Open Access Journals (Sweden)

    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  17. Evaluation of allelopathic potential of safflower genotypes (Carthamus tinctorius L.

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    Motamedi Marzieh

    2016-12-01

    Full Text Available Forty safflower genotypes were grown under normal irrigation and drought stress. In the first experiment, the allelopathic potential of shoot residues was evaluated using the sandwich method. Each genotype residue (0.4 g was placed in a sterile Petri dish and two layers of agar were poured on that. Radish seeds were placed on agar medium. The radish seeds were cultivated without safflower residues as the controls. The length of the radicle, hypocotyl, and fresh biomass weight and seed germination percentages were measured. A pot experiment was also done on two genotypes with the highest and two with the lowest allelopathic activity selected after screening genotypes in the first experiment. Before entering the reproductive phase, irrigation treatments (normal irrigation and drought stress were applied. Shoots were harvested, dried, milled and mixed with the topsoil of new pots and then radish seeds were sown. The pots with safflower genotypes were used to evaluate the effect of root residue allelopathy. The shoot length, fresh biomass weight, and germination percentage were measured. Different safflower genotypes showed varied allelopathic potential. The results of the first experiment showed that Egypt and Iran-Khorasan genotypes caused maximum inhibitory responses and Australia and Iran-Kerman genotypes resulted in minimum inhibitory responses on radish seedling growth. Fresh biomass weight had the most sensitivity to safflower residues. The results of the pot experiment were consistent with the results of in vitro experiments. Residues produced under drought stress had more inhibitory effects on the measured traits. Safflower root residue may have a higher level of allelochemicals or different allelochemicals than shoot residue.

  18. Sex and PRNP genotype determination in preimplantation caprine embryos.

    Science.gov (United States)

    Guignot, F; Perreau, C; Cavarroc, C; Touzé, J-L; Pougnard, J-L; Dupont, F; Beckers, J-F; Rémy, B; Babilliot, J-M; Bed'Hom, B; Lamorinière, J M; Mermillod, P; Baril, G

    2011-08-01

    The objective of this study was to test the accuracy of genotype diagnosis after whole amplification of DNA extracted from biopsies obtained by trimming goat embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer. Whole genome amplification (WGA) was performed using Multiple Displacement Amplification (MDA). Sex and prion protein (PRNP) genotypes were determined. Sex diagnosis was carried out by PCR amplification of ZFX/ZFY and Y chromosome-specific sequences. Prion protein genotype determination was performed on codons 142, 154, 211, 222 and 240. Embryos were collected at day 7 after oestrus and biopsied either immediately after collection (blastocysts and expanded blastocysts) or after 24 h of in vitro culture (compacted morulae). Biopsied embryos were frozen by vitrification. Vitrified whole embryos were kept as control. DNA of biopsies was extracted and amplified using MDA. Sex diagnosis was efficient for 97.4% of biopsies and PRNP genotyping was determined in 78.7% of biopsies. After embryo transfer, no significant difference was observed in kidding rate between biopsied and vitrified control embryos, whereas embryo survival rate was different between biopsied and whole vitrified embryos (p = 0.032). At birth, 100% of diagnosed sex and 98.2% of predetermined codons were correct. Offspring PRNP profiles were in agreement with parental genotype. Whole genome amplification with MDA kit coupled with sex diagnosis and PRNP genotype predetermination are very accurate techniques to genotype goat embryos before transfer. These novel results allow us to plan selection of scrapie-resistant genotypes and kid sex before transfer of cryopreserved embryo.

  19. ABO genotyping in leukemia patients reveals new ABO variant alleles

    OpenAIRE

    Novaretti,M.C.Z.; DOMINGUES, A. E.; MANHANI, R.; Pinto, E M; Dorlhiac-Llacer, P.E.; Chamone, D.A.F.

    2008-01-01

    The ABO blood group is the most important blood group system in transfusion medicine and organ transplantation. To date, more than 160 ABO alleles have been identified by molecular investigation. Almost all ABO genotyping studies have been performed in blood donors and families and for investigation of ABO subgroups detected serologically. The aim of the present study was to perform ABO genotyping in patients with leukemia. Blood samples were collected from 108 Brazilian patients with chronic...

  20. Genotype and SNP calling from next-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Paul, Joshua S.; Albrechtsen, Anders

    2011-01-01

    Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated w...... with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies....

  1. Genetic diversity of some chili (Capsicum annuum L. genotypes

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  2. Genotyping of Rotavirus by Using RT-PCR Methods

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    Hera Nirwati

    2015-11-01

    Full Text Available There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994 and Gentsch et al. (1992. There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990 and Simmond et al. (2008 for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.Key words: rotavirus, G typing, P typing

  3. Methylenetetrahydrofolate Reductase Genotypes, Dietary Habits and Susceptibility to Stomach Cancer

    Institute of Scientific and Technical Information of China (English)

    ChangmingGao; TakezakiToshiro; JianzhongWu; JianhuoDing; YantingLiu; SupingLi; PingSu; XuHu; TianliongXu; HamajimaNobuyuki; TajimaKazuo

    2004-01-01

    OBJECTIVE To study the relation among methylenetetrahydrofolate reductase (MTHFR) C677T genotypes, dietary habits and the risk of stomach cancer (SC).METHODS A case-control study was conducted with 107 cases of SC and 200 population-based controls in Chuzhou district, Huaian, Jiangsu province, China. The epidemiological data were collected, and DNA of peripheral blood leukocytes was obtained from all of the subjects..MTHFR genotypes were detected by PCR-RFLP. RESULTS (1) The prevalence of the MTHFR C/T or T/T genotypes was found to be significantly different between controls (68.5%) and SC cases (79.4%,P=0.0416), the increased risk had an adjusted OR of 1.79 (95%C1:1.01-3.19). (2) Among subjects who had a low intake of garlic or Chinese onion, MTHFR C/T or T/T genotypes significantly increased the risk of developing SC. Among non-tea drinkers or among subjects who had a frequent intakeof meat, the carriers of the MTHFR C/T or T/T genotypes had a higher risk of SC than individuals with the C/C type MTHFR. CONCLUSION The polymorphism of MTHFR C677T was associated with increased risk of developing SC, and that individuals with differing genotypes may have different susceptibilities to SC, based on their exposure level to environmental factors.

  4. Performance of genotype-MTBDR test directly on clinical specimens

    Directory of Open Access Journals (Sweden)

    Gülden Yılmaz

    2012-12-01

    Full Text Available Objectives: Most important point for the control and effective treatment of multidrug resistant tuberculosis (MDR-TBis early diagnosis and rapid determination of the resistance. The aim of this study is to assess the performance of theGenotype-MTBDR assay applied directly on sputum samples and compare the results with those obtained by DNA sequencingand phenotypic susceptibility testing.Materials and methods: Between November 2005 and February 2006, 93 smear and culture positive sputum sampleswere included in the study. Drug susceptibility results for rifampin (RIF and isoniazid (INH, obtained by proportionmethod on L-J medium, Genotype-MTBDR and DNA sequencing were compared.Results: The rate of concordance between the results of the Genotype-MTBDR and DNA sequencing was 93.5% and96.7% for RIF and INH, respectively. Moreover, Genotype-MTBDR detected all the RIF (24 and INH (18 resistant strainsobtained by sequencing (100%. Compared to the DNA sequencing method; the sensitivity, specificity, positive predictiveand negative predictive value for RIF and INH were 100%, 91.3%, 80%, 100% and 100%, 96%, 85.7%, 100% respectively.Conclusion: Genotype-MTBDR, one of molecular assays, distinctly shortens the time for diagnosis and detection of resistanceto INH and RIF, essential for management of MDR-TB. The test appears to have good sensitivity and specificitywhen also used directly on sputum specimens. J Microbiol Infect Dis 2012; 2(4: 135-141Key words: Mycobacterium tuberculosis; drug resistance; genotype-MTBDR.

  5. Analyzing genotype-by-environment interaction using curvilinear regression

    Directory of Open Access Journals (Sweden)

    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  6. Differential activation of dendritic cells by Mycobacterium tuberculosis Beijing genotype.

    Science.gov (United States)

    Reyes-Martínez, Juana Elizabeth; Nieto-Patlán, Erik; Nieto-Patlán, Alejandro; Gonzaga-Bernachi, Job; Santos-Mendoza, Teresa; Serafín-López, Jeanet; Chávez-Blanco, Alma; Sandoval-Montes, Claudia; Flores-Romo, Leopoldo; Estrada-Parra, Sergio; Estrada-García, Iris; Chacón-Salinas, Rommel

    2014-01-01

    Mycobacterium tuberculosis (Mtb) inhibits dendritric cells (DC) function in order to delay T cell response. Furthermore, there is increasing evidence that genetic diversity of Mtb strains can affect their interaction with the immune system. Beijing genotype has attracted attention because of its high prevalence and multi-drug resistance. Although it is known that this genotype is hypervirulent and differentially activates macrophages when compared to other genotypes, little is known about its interaction with DC. In order to address this issue, murine bone marrow derived DC (BMDC) were stimulated with soluble extracts (SE) from BCG, H37Rv, Canetti and Beijing genotypes. We observed that unlike other mycobacteria strains, SE-Beijing was unable to induce maturation of DC as assessed by cell surface MHC-II expression. DC stimulated with SE-Beijing failed to produce IL-12 and TNF-α, but did secrete IL-10. Interestingly, SE-Beijing induced CCR7 and PDL-1 on BMDC, but did not induce the expression of CD86. When BMDC stimulated with SE-Beijing were used to activate CD4+ cells they were unable to induce a Th1 response when compared with less virulent genotypes. These results indicate that Beijing is able to modulate DC activation and function, which may be related to the pathogenesis induced by this genotype.

  7. Serotonergic genotypes, neuroticism, and financial choices.

    Directory of Open Access Journals (Sweden)

    Camelia M Kuhnen

    Full Text Available Life financial outcomes carry a significant heritable component, but the mechanisms by which genes influence financial choices remain unclear. Focusing on a polymorphism in the promoter region of the serotonin transporter gene (5-HTTLPR, we found that individuals possessing the short allele of this gene invested less in equities, were less engaged in actively making investment decisions, and had fewer credit lines. Short allele carriers also showed higher levels of the personality trait neuroticism, despite not differing from others with respect to cognitive skills, education, or wealth. Mediation analysis suggested that the presence of the 5-HTTLPR short allele decreased real life measures of financial risk taking through its influence on neuroticism. These findings show that 5-HTTLPR short allele carriers avoid risky and complex financial choices due to negative emotional reactions, and have implications for understanding and managing individual differences in financial choice.

  8. Effects of data structure on the estimation of covariance functions to describe genotype by envrironment interactions in a reaction norm model

    NARCIS (Netherlands)

    Calus, M.P.L.; Bijma, P.; Veerkamp, R.F.

    2004-01-01

    Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of

  9. TLR4 genotype and environmental LPS mediate RSV bronchiolitis through Th2 polarization

    Science.gov (United States)

    Caballero, Mauricio T.; Serra, M. Elina; Acosta, Patricio L.; Marzec, Jacqui; Gibbons, Luz; Salim, Maximiliano; Rodriguez, Andrea; Reynaldi, Andrea; Garcia, Alejandro; Bado, Daniela; Buchholz, Ursula J.; Hijano, Diego R.; Coviello, Silvina; Newcomb, Dawn; Bellabarba, Miguel; Ferolla, Fausto M.; Libster, Romina; Berenstein, Ada; Siniawaski, Susana; Blumetti, Valeria; Echavarria, Marcela; Pinto, Leonardo; Lawrence, Andrea; Ossorio, M. Fabiana; Grosman, Arnoldo; Mateu, Cecilia G.; Bayle, Carola; Dericco, Alejandra; Pellegrini, Mariana; Igarza, Ignacio; Repetto, Horacio A.; Grimaldi, Luciano Alva; Gudapati, Prathyusha; Polack, Norberto R.; Althabe, Fernando; Shi, Min; Ferrero, Fernando; Bergel, Eduardo; Stein, Renato T.; Peebles, R. Stokes; Boothby, Mark; Kleeberger, Steven R.; Polack, Fernando P.

    2015-01-01

    While 30%–70% of RSV-infected infants develop bronchiolitis, 2% require hospitalization. It is not clear why disease severity differs among healthy, full-term infants; however, virus titers, inflammation, and Th2 bias are proposed explanations. While TLR4 is associated with these disease phenotypes, the role of this receptor in respiratory syncytial virus (RSV) pathogenesis is controversial. Here, we evaluated the interaction between TLR4 and environmental factors in RSV disease and defined the immune mediators associated with severe illness. Two independent populations of infants with RSV bronchiolitis revealed that the severity of RSV infection is determined by the TLR4 genotype of the individual and by environmental exposure to LPS. RSV-infected infants with severe disease exhibited a high GATA3/T-bet ratio, which manifested as a high IL-4/IFN-γ ratio in respiratory secretions. The IL-4/IFN-γ ratio present in infants with severe RSV is indicative of Th2 polarization. Murine models of RSV infection confirmed that LPS exposure, Tlr4 genotype, and Th2 polarization influence disease phenotypes. Together, the results of this study identify environmental and genetic factors that influence RSV pathogenesis and reveal that a high IL-4/IFN-γ ratio is associated with severe disease. Moreover, these molecules should be explored as potential targets for therapeutic intervention. PMID:25555213

  10. Catechol-O-methyltransferase (COMT) Genotype Affects Age-Related Changes in Plasticity in Working Memory: A Pilot Study

    Science.gov (United States)

    Riemer, Thomas G.; Schulte, Stefanie; Onken, Johanna; Heinz, Andreas; Rapp, Michael A.

    2014-01-01

    Objectives. Recent work suggests that a genetic variation associated with increased dopamine metabolism in the prefrontal cortex (catechol-O-methyltransferase Val158Met; COMT) amplifies age-related changes in working memory performance. Research on younger adults indicates that the influence of dopamine-related genetic polymorphisms on working memory performance increases when testing the cognitive limits through training. To date, this has not been studied in older adults. Method. Here we investigate the effect of COMT genotype on plasticity in working memory in a sample of 14 younger (aged 24–30 years) and 25 older (aged 60–75 years) healthy adults. Participants underwent adaptive training in the n-back working memory task over 12 sessions under increasing difficulty conditions. Results. Both younger and older adults exhibited sizeable behavioral plasticity through training (P < .001), which was larger in younger as compared to older adults (P < .001). Age-related differences were qualified by an interaction with COMT genotype (P < .001), and this interaction was due to decreased behavioral plasticity in older adults carrying the Val/Val genotype, while there was no effect of genotype in younger adults. Discussion. Our findings indicate that age-related changes in plasticity in working memory are critically affected by genetic variation in prefrontal dopamine metabolism. PMID:24772423

  11. Catechol-O-methyltransferase (COMT Genotype Affects Age-Related Changes in Plasticity in Working Memory: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Stephan Heinzel

    2014-01-01

    Full Text Available Objectives. Recent work suggests that a genetic variation associated with increased dopamine metabolism in the prefrontal cortex (catechol-O-methyltransferase Val158Met; COMT amplifies age-related changes in working memory performance. Research on younger adults indicates that the influence of dopamine-related genetic polymorphisms on working memory performance increases when testing the cognitive limits through training. To date, this has not been studied in older adults. Method. Here we investigate the effect of COMT genotype on plasticity in working memory in a sample of 14 younger (aged 24–30 years and 25 older (aged 60–75 years healthy adults. Participants underwent adaptive training in the n-back working memory task over 12 sessions under increasing difficulty conditions. Results. Both younger and older adults exhibited sizeable behavioral plasticity through training (P<.001, which was larger in younger as compared to older adults (P<.001. Age-related differences were qualified by an interaction with COMT genotype (P<.001, and this interaction was due to decreased behavioral plasticity in older adults carrying the Val/Val genotype, while there was no effect of genotype in younger adults. Discussion. Our findings indicate that age-related changes in plasticity in working memory are critically affected by genetic variation in prefrontal dopamine metabolism.

  12. Hepatitis C virus core proteins derived from different quasispecies of genotype 1b inhibit the growth of Chang liver cells

    Institute of Scientific and Technical Information of China (English)

    Xue-Bing Yan; Lei Mei; Xia Feng; Mei-Rong Wan; Zhi Chen; Nicole Pavia; Christian Brechot

    2008-01-01

    AIM: To investigate the influence of different quasispecies of hepatitis C virus (HCV) genotype 1b core protein on growth of Chang liver cells.METHODS: Three eukaryotic expression plasmids (pEGFP-N1/core) that contained different quasispecies truncated core proteins of HCV genotype 1b were constructed. These were derived from tumor (T) and nontumor (NT) tissues of a patient infected with HCV and C191 (HCV-J6). The core protein expression plasmids were transiently transfected into Chang liver cells. At different times, the cell cycle and apoptosis was assayed by flow cytometry, and cell proliferation was assayed by methyl thiazolyl tetrazolium (MTT) assay.RESULTS: The proportion of S-phase Chang liver cells transfected with pEGFP-N1/core was significantly lower than that of cells transfected with blank plasmid at three different times after transfection (all P NT > C191), and apoptosis was increased in cells transfected with pEGFP-N1/core as the transfection time increased (72 h > 48 h > 24 h).CONCLUSION: These results suggest that HCV genotype 1b core protein induces apoptosis, and inhibits cellcycle progression and proliferation of Chang liver cells.Different quasispecies core proteins of HCV genotype 1b might have some differences in the pathogenesis of HCV persistent infection and hepatocellular carcinoma.

  13. Changes of Chlorophyll Index (SPAD, Relative Water Content, Electrolyte Leakage and Seed Yield in Spring Safflower Genotypes under Irrigation Termination

    Directory of Open Access Journals (Sweden)

    B.E. Moosavifar

    2012-04-01

    Full Text Available In order to evaluate the effect of irrigation termination and genotype on chlorophyll index (SPAD, relative water content, electrolyte leakage and seed yield in spring safflower, an experiment was conducted, in a spilt plot arrangement based on randomized complete block design with four replications at Research Farm, Faculty of Agriculture, the University of Birjand, during 2008. Irrigation regimes (full irrigation (whole season irrigation, irrigation until grain filling, flowering and heading-bud and genotypes (Mahali Isfahan (a local variety, Isfahan28 and IL111 were arranged in main and subplots, respectively. Results showed chlorophyll content, relative water content, cell membrane stability and seed yield were influenced by irrigation termination. Provided that with terminating irrigation at an earlier stage, an increase in electrolyte leakage and reduction in relative water content and seed yield was observed in plants. There were negative relations between electrolyte leakage from plants leaf cells and seed yield. Plants which experienced irrigation termination in an earlier growth stage, suffered more damage to their cell membranes, leading to depression of their production potential. Based on the results, Mahali Isfahan and Isfahan28 can be introduced as drought resistant genotypes, because of their lower electrolyte leakage and higher relative water content. But, in general, Mahali Isfahan had the highest seed yield due to its nativeness and high adaptation to arid conditions southern of Khorasan, and therefore this genotype suggests for planting in the region.

  14. The Differences among Pear Genotypes to Fire Blight (Erwinia amylovora Attack, Based on Observations of Natural Infection

    Directory of Open Access Journals (Sweden)

    Adriana F. SESTRAS

    2008-08-01

    Full Text Available Fire blight, caused by the bacterium Erwinia amylovora, is one of the most damaging diseases of pear in the world. In Cluj-Napoca area, situated in central Transylvania, Romania, fire blight was observed first in 1994, very late comparative with the other countries from occidental Europe. The response of the pear cultivars and species from National Pear Collection from Cluj-Napoca to fire blight attack, assessed in natural conditions of infection, range on a large scale of variability, which denotes a strong influence of the genotype in expression of resistance or sensitivity to disease. From all genotypes, about 20.5% have not presented symptoms of attack, among them being the following: 'Blanquet precoce', 'Klementinka', 'Severianka', 'Beurre Bachelier', 'Kieffer Seedling', 'Er Shi Shinge', 'Beurre Amanlis', 'Bristol Cross', 'Beurre Liegel', 'Beurre Lucon', 'Grand Champion', 'Magness', 'Mericourt' etc. and several ancient autochthonous cultivars ('Pere malaiete', 'De zahar de Bihor', 'Cu miez rosu', 'Clopotele', 'Garoafa mare', 'Craiese', 'Para de apa'. Also, there were identified several species of Pyrus with no attack, as P. pollveria, P. common pear, P. lindlezi, P. malifolia, P. persica, P. ussuriensis, P. variolosa. The remarked genotypes could be potential sources for further breeding programmes and increase the number of genotypes available for breeding new pear cultivars resistant to Erwinia attack.

  15. Hepatitis C virus genotypes: A plausible association with viral loads

    Directory of Open Access Journals (Sweden)

    Salma Ghulam Nabi

    2013-01-01

    Full Text Available Background and Aim: The basic aim of this study was to find out the association of genotypes with host age, gender and viral load. Material and Methods: The present study was conducted at Social Security Hospital, Pakistan. This study included 320 patients with chronic hepatitis C virus (HCV infection who were referred to the hospital between November 2011 and July 2012. HCV viral detection and genotyping was performed and the association was seen between genotypes and host age, gender and viral load. Results : The analysis revealed the presence of genotypes 1 and 3 with further subtypes 1a, 1b, 3a, 3b and mixed genotypes 1b + 3a, 1b + 3b and 3a + 3b. Viral load quantification was carried out in all 151 HCV ribonucleic acid (RNA positive patients. The genotype 3a was observed in 124 (82.12% patients, 3b was found in 21 (13.91%, 1a was seen in 2 (1.32%, 1b in 1 (0.66%, mixed infection with 1b + 3a in 1 (0.66%, 1b + 3b in 1 (0.66% and 3a + 3b was also found in 1 (0.66% patient. Viral load quantification was carried out in all 151 HCV RNA positive patients and was compared between the various genotypes. The mean viral load in patients infected with genotype 1a was 2.75 × 10 6 , 1b 3.9 × 10 6 , 3a 2.65 × 10 6 , 3b 2.51 × 10 6 , 1b + 3a 3.4 × 106, 1b + 3b 2.7 × 106 and 3a + 3b 3.5 × 10 6 . An association between different types of genotypes and viral load was observed. Conclusion : Further studies should be carried out to determine the association of viral load with different genotypes so that sufficient data is available and can be used to determine the type and duration of therapy needed and predict disease outcome.

  16. Research on Hepatitis B virus Genotypes and Subgenotypes among Bai Nationality in Dali, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    Wei LI; Yuan-ying SHEN; Xuan-rong ZHANG; Lai-feng REN; Qiang LI; Ru SHEN; Hai-ping ZHAO

    2008-01-01

    To investigate the distribution of hepatitis B virus (HBV) genotypes and subgenotypes among the Bai nationality in Dali, a total of 100 serum samples from patients with chronic HBV-infection were collected for the detection of HBV genotypes and subgenotypes by genotype-specific primers and restriction fragment length polymorphism (RLFP), respectively. Among the 100 samples, the proportions of genotype B, C and mixed genotype (B+C) were 41%, 25% and 34%, respectively. All the genotype B strains belonged to subgenotype Ba. In genotype C, 84% were Subgenotype Cs and 12% were subgenotype Ce. The distribution of genotypes B, C and B+C showed no significant difference between male and female patients (P=0.182) and among the age groups of patients (P=0.812). The rates of HBeAg/HBeAg positivity were no significantly different among genotypes B, genotype C and mixed genotype (B+C) (P=0.077/P=0.663). In Dali, genotypes B, B+C and C existed among Bai nationality with chronic HBV-infection, and genotype B was the major genotype. Subgenotypes Ba and Cs were the predominant strains in patients with HBV genotype B/C infection. The most prominent characteristic was the higher prevalent rate of mixed genotype (B+C) in patients.

  17. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Loy, John Dustin; Clawson, Michael L

    2017-05-01

    Genotype 2M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate genotype 2 strains in veterinary diagnostic laboratories.

  18. 乙型肝炎病毒基因亚型及相关指标临床意义分析%Clinical Correlation Research of Hepatitis B Virus Genotypes

    Institute of Scientific and Technical Information of China (English)

    黄波; 万小涛; 张有辉; 钟方财

    2016-01-01

    目的:探讨乙型肝炎病毒不同基因亚型与病毒复制状况、凝血功能、肝脏功能的关系,以及不同基因亚型的临床意义。方法选取慢性乙型肝炎、肝硬化、肝癌患者血液标本,检测乙型肝炎病毒基因亚型、病毒载量、凝血功能、肝功能等指标,应用统计软件SPSS 16.0进行分析。结果本次调查乙型肝炎病毒基因亚型主要为B型和C型,B型略多于C型。但在肝癌患者中,C型所占比例高于B型(0.05)。结论本地区乙型肝炎病毒基因亚型主要为B型和C型,C型患者肝脏损害较B型重,提示不同基因亚型可能影响患者体内病毒复制,并引起不同临床损害程度的慢性肝病。%Objective To understand the distribution of genotypes in Neijiang area, analyze the relationship of different genotypes with virus replication, liver function and coagulation function, investigate the clinical significance of different genotypes. Methods Serum samples were collected from chronic hepatitis B, liver cirrhosis, hepatic cell carcinoma individuals. Hepatitis B virus genotypes, virus replication, liver function and coagulation function were detected. The data was analyzed with SPSS 16.0.Results The main genotypes in Neijiang area were B and C. The C genotype virus replication was significantly higher than that of B genotype ( ﹤0.05).The proportion of C genotype in hepatic cell carcinoma group exhibited significantly higher than that in B genotype( ﹤0.05).No significant difference was found in liver function between B and C genotypes( >0.05). But significant difference was found in coagulation function between B and C genotypes ( ﹤0.05). Conclusion The main genotypes in Neijiang area were B and C. The liver damage of patients with C genotype is more serious than that of B genotype, which prompts that hepatitis B virus genotypes may influence on in vivo hepatitis B virus replication and may cause chronic liver disease of different

  19. Is incidence of multiple HPV genotypes rising in genital infections?

    Science.gov (United States)

    Sohrabi, Amir; Hajia, Masoud; Jamali, Firouzeh; Kharazi, Faranak

    2017-02-16

    Frequency of cervical cancer related to Human Papilloma Virus (HPV) has increased remarkably in less-developed countries. Hence, applying capable diagnostic methods is urgently needed, as is having a therapeutic strategy as an effective step for cervical cancer prevention. The aim of this study was to investigate the prevalence of various multi-type HPV infection patterns and their possible rising incidence in women with genital infections. This descriptive study was conducted on women who attended referral clinical laboratories in Tehran for genital infections from January 2012 until December 2013. A total of 1387 archival cervical scraping and lesion specimens were collected from referred women. HPV genotyping was performed using approved HPV commercial diagnostic technologies with either INNO-LiPA HPV or Geno Array Test kits. HPV was positive in 563 cases (40.59%) with mean age of 32.35±9.96. Single, multiple HPV genotypes and untypable cases were detected in 398 (70.69%), 160 (28.42%) and 5 (0.89%) cases, respectively. Multiple HPV infections were detected in 92 (57.5%), 42 (26.2%), 17 (10.6%) and 9 (5.7%) cases as two, three, four and five or more genotypes, respectively. The prevalence of 32 HPV genotypes was determined one by one. Seventeen HPV genotypes were identified in 95.78% of all positive infections. Five dominant genotypes, HPV6, 16, 53, 11 and 31, were identified in a total of 52.35%of the HPV positive cases. In the present study, we were able to evaluate the rate of multiple HPV types in genital infections. Nevertheless, it is necessary to evaluate the role of the dominant HPV low-risk types and the new probably high-risk genotypes, such as HPV53, in the increasing incidences of genital infections.

  20. Assessment of HCV genotypes in Yunnan Province of Southwest China.

    Science.gov (United States)

    Li, Qiongfen; Yao, Yufeng; Shen, Yunsong; Cao, Danfeng; Li, Yalin; Zhang, Shuqiong; Cun, Wei; Sun, Mingbo; Yu, Jiankun; Shi, Li; Dong, Shaozhong

    2016-12-23

    Recently, we reported that the frequency of hepatitis C virus (HCV) genotypes and subtypes has rapidly changed among intravenous drug users (IDUs) in Yunnan Province over the last 5 years; this is especially true for subtype 6a which has increased in frequency from 5 to 15%. Here, we assessed 120 HCV-positive plasma samples from the general population (GP). HCV NS5B fragments were amplified and sequenced by PCR. We identified four HCV genotypes (1, 2, 3 and 6) and seven HCV subtypes (1b, 2a, 3a, 3b, 6a, 6n, and 6k) in this population. Genotype 3 was predominant, with a distribution frequency of 0.484, followed by genotype 1 (0.283), genotype 6 (0.133) and genotype 2 (0.100). HCV subtypes 3b (frequency 0.292) and 1b (frequency 0.283) were the most common subtypes. A comparison of the current data with previous results reported for IDUs showed that the distribution frequencies of genotypes 1, 2 and 6 were significantly different between patients in the GP and IDUs (P HCV subtypes, the distribution frequencies of 1b, 2a, 6a, and 6n were significantly different between patients in the GP and IDU groups (P HCV subtype 6a strains isolated from IDUs and the GP were intermixed and not separately clustered. HCV subtype 6a was predominant not only among IDUs but also among those in the GP in the Guangdong Province and Vietnam. However, HCV subtype 6a was predominant only among IDUs and not among those in the GP in the Yunnan and Guangxi Provinces. Our results indicate that the HCV subtype 6a could rapidly spread across China.

  1. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored.

  2. HBV genotypes prevalence, precore and basal core mutants in Morocco.

    Science.gov (United States)

    Baha, Warda; Ennaji, My Mustapha; Lazar, Fatiha; Melloul, Marouane; El Fahime, Elmostafa; El Malki, Abdelouahad; Bennani, Abdelouaheb

    2012-08-01

    The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. The objective of the current study was to find out the pattern of HBV genotypes circulating in Morocco and to investigate the precore (PC) and basal core promoter (BCP) mutants' status in Moroccan chronic hepatitis B patients. Viral genotypes were determined in 221 chronic carriers using INNO-LiPA HBV assay and hemi-nested PCR. Phylogenetic analysis was performed in 70 samples, and multiplex PCR method was used to confirm some genotyping results. PC and CP mutants were determined using Inno-Lipa. All isolates were successfully genotyped. The genotype distribution was D in 90.45% of cases, A (5.9%), E (1 case), and mixed genotypes (5 A/D and 2 D/F) in 3.17% patients. HBV carried in the HBV/D samples could be assigned to D7 (63.3%), D1 (32.7%) and 2% of strains to each D4 and D5, all HBV/A belonged to A2 subgenotype and HBV/E strain could not be sub-genotyped. In 70 studied strains, HBV mutants were detected in 88.6% of cases; PC mutants were detected in (40%) of patients and 21.5% present a mixture of wild type and G1896A mutation. BCP mutants were observed in 65.7% of cases, 22.9% were found to have the T1762/1764A double mutation, 18.6% had A1762/1764T mutation and 22.9% of patients showed the A1762T/G1764A double mutation with either A1762T/G1764T mutation. Co-infection by PC and BCP mutants was detected in 52.9% of cases. Movement from place to place most likely shapes the observed genotype distribution and consequent prevalence of genotypes other than A2 or D7 in this population. High circulation of PC and BCP mutants is common in chronic hepatitis B infection in Morocco.

  3. New technologies for ultra-high throughput genotyping in plants.

    Science.gov (United States)

    Appleby, Nikki; Edwards, David; Batley, Jacqueline

    2009-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready marker technology (MRT); DArT genotyping; SNP genotyping using the Invader assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex system, and Illumina GoldenGate and Infinium methods.

  4. Genotyping of Mycobacterium leprae in Myanmar and possible transmission modes.

    Science.gov (United States)

    Aye, Khin Saw; Oo, Yin Thet Nu; Kyaw, Kyaw; Win, Aye Aye; Matsuoka, Masanori

    2012-09-01

    The polymorphism of TTC repeats in Mycobacterium leprae was examined using bacilli from slit skin samples of leprosy patients attending at Central Special Skin Clinic, Yangon General Hospital and nasal swabs of their contacts to elucidate the possible mode of leprosy transmission. It was found that bacilli with different TTC genotypes were distributed among same household contacts and also harbored bacilli in patients were different TTC genotype from that harbored on the nasal mucus of the healthy contacts. Genotypes of TTC repeats were found to differ between husband under treatment and his wife and also mother under treatment and her sons living in same house. This study revealed that TTC genotype of bacilli harbored by household contacts was different with the TTC genotype by index cases. These results indicate that the family members get transmission from outside the dwellings rather than from commonly supposed their MB index cases. There might have been some infectious sources to which the populace had been commonly exposed outside the dwellings.

  5. Physiological and Molecular Analysis of Applied Nitrogen in Rice Genotypes

    Institute of Scientific and Technical Information of China (English)

    Khalid Rehman HAKEEM; Ruby CHANDNA; Altaf AHMAD; Muhammad IQBAL

    2012-01-01

    Ten genotypes of rice (Oryza sativa L.) were grown for 30 d in complete nutrient solution with 1 mmol/L (N-insufficient),4 mmol/L (N-moderate) and 10 mmol/L (N-high) nitrogen levels,and nitrogen efficiency (NE) was analyzed.Growth performance,measured in terms of fresh weight,dry weight and lengths of root and shoot,was higher in N-efficient than in N-inefficient rice genotypes at low N level.Of these 10 genotypes,Suraksha was identified as the most N-efficient,while Vivek Dhan the most N-inefficient.To find out the physiological basis of this difference,the nitrate uptake rate of root and the activities of nitrate assimilatory enzymes in leaves of N-efficient and N-inefficient rice genotypes were studied.Uptake experiments revealed the presence of two separate nitrate transporter systems mediating high- and low-affinity nitrate uptake.Interestingly,the nitrate uptake by the roots of Suraksha is mediated by both high- and low-affinity nitrate transporter systems,while that of Vivek Dhan by only low-affinity nitrate transporter system.Study of the activities and expression levels of nitrate assimilatory enzymes in N-efficient and N-inefficient rice genotypes showed that nitrate reductase (NR) and glutamine svnthetase (GS) play important roles in N assimilation under low-nitrogen conditions.

  6. The quality of silage of different sorghum genotypes

    Directory of Open Access Journals (Sweden)

    Daniella Cangussú Tolentino

    2016-05-01

    Full Text Available The objective was to select from among 24 sorghum genotypes the superior ones for silage production. The study was conducted in the experimental field of Embrapa Maize & Sorghum, in the municipality of Sete Lagoas, Minas Gerais State. It used 24 forage sorghum genotypes, 21 being hybrids from the crossing of grain sorghum females and forage males (12F38019, 12F38006, 12F40006, 12F40005, 12F40019, 12F37016, 12F37005, 12F37043, 12F39006, 12F39005, 12F39019, 12F38005, 12F38007, 12F37007, 12F39007, 12F40007, 12F38014, 12F37014, 12F39014, 12F40014 e 12F38009 and three witnesses: BRS 610, BRS 655 and Volumax. It estimated productivity per area, in vitro dry matter digestibility, and assessed the bromatological and fermentation characteristics of sorghum silage. In vitro dry matter digestibility, unavailable protein in neutral detergent, neutral detergent fiber corrected for ashes and protein, acid detergent fiber, hemicellulose and lignin differed as to the genotypes tested. The pH and the ammoniacal nitrogen of the silage also showed differences between genotypes. Most of the genotypes tested are favorable for silage production, except the hybrid with higher lignin content 12F370014, and the hybrids 12F37007 and 12F370014, which showed the highest NDFap values.

  7. Does sex trade with violence among genotypes in Drosophila melanogaster?

    Directory of Open Access Journals (Sweden)

    Larry G Cabral

    Full Text Available The evolutionary forces shaping the ability to win competitive interactions, such as aggressive encounters, are still poorly understood. Given a fitness advantage for competitive success, variance in aggressive and sexual display traits should be depleted, but a great deal of variation in these traits is consistently found. While life history tradeoffs have been commonly cited as a mechanism for the maintenance of variation, the variability of competing strategies of conspecifics may mean there is no single optimum strategy. We measured the genetically determined outcomes of aggressive interactions, and the resulting effects on mating success, in a panel of diverse inbred lines representing both natural variation and artificially selected genotypes. Males of one genotype which consistently lost territorial encounters with other genotypes were nonetheless successful against males that were artificially selected for supernormal aggression and dominated all other lines. Intransitive patterns of territorial success could maintain variation in aggressive strategies if there is a preference for territorial males. Territorial success was not always associated with male mating success however and females preferred 'winners' among some male genotypes, and 'losers' among other male genotypes. This suggests that studying behaviour from the perspective of population means may provide limited evolutionary and genetic insight. Overall patterns of competitive success among males and mating transactions between the sexes are consistent with mechanisms proposed for the maintenance of genetic variation due to nonlinear outcomes of competitive interactions.

  8. Analysis of pomological traits in new promising sweet cherry genotypes

    Directory of Open Access Journals (Sweden)

    Fotirić-Akšić Milica

    2013-01-01

    Full Text Available Sweet cherry breeding programs are interested in developing new cultivars that are very early or very late in ripening, high yielding, with excellent fruit size and quality. The aim of this study was to evaluate new, promising, sweet cherry genotypes (G-1 and G-2 for ripening time, fruit morphology and fruit chemical content, and compare it with the standard sweet cherry cultivars (Bigarreau Jaboulay, B. H. Burlat, Seneca, Hedelfiger Riesenkirsche, Germersdorfer Grosse Kirsche, Emperor Francis and Bing. Experiment was done during four consecutive years (2006-2009 in Grocka, near Belgrade. The earliest fruit ripening was recorded in G-2 (22nd April while the latest in `Bing` (2nd June. Fruit weight varied from 5.83 g (G-2 up to 8.93 g (G-1. Soluble solid content and total sugar content were the lowest in genotype G-2 (10.48%; 8.45%, respectively but the highest in Emperor Francis (18.28%; 15.98%, respectively. No matter the fact that some standard cultivars showed better results for some traits, genotypes G-1 and G-2 are considered very promising. So, genotype G-1 could be intended for table consumption since it ripens 2-3 days after cv. B. H. Burlat, but have much higher fruit weight. Also, genotype G-2, the earliest in this trial, showed satisfactory fruit weight for this ripening time, which makes it very interesting for fresh market production. [Projekat Ministarstva nauke Republike Srbije, br. 31063 i br. 31038

  9. STUDY ON CROSSING ABILITY OF ANNUAL CHRYSANTHEMUM GENOTYPES

    Directory of Open Access Journals (Sweden)

    Suneetha Kattera

    2014-03-01

    Full Text Available The experiment comprised of six genotypes viz., NAC-01-10, NAC-02-10, NAC-03-10, NAC-04-10, NAC-05-10, NAC-06-10 selected for petal colour and number of layers of petals to estimate pollen viability, in-vitro pollen germination, stigma receptivity and crossed seed set percentage to find out the crossing ability of genotypes. The present experiment was laid out at the experimental field of Horticulture Section, College of Agriculture, Nagpur, during 2010-11. Pollen viability of six genotypes of annual chrysanthemum showed a range of 69.69% to 86.66% viability, Percentage of germination on the day of anthesis ranged from 22.72% (NAC-06-10 to 66.66% (NAC-01-10. First day pollen pollinated on first day stigma showed 100% stigma receptivity in all six genotypes and the crossed seed set ranged from 61.60% (NAC-04-10 × NAC-05-10 to 92.00% (NAC-01-10 × NAC-04-10 among direct crosses whereas, the percentage ranged from 42.00% (NAC-04-10 × NAC-02-10 to 90.00% (NAC-05-10 × NAC-01-10 among the reciprocal crosses. All the six genotypes are highly suitable for their use as parents in crossing program.

  10. Super-genotype: global monoclonality defies the odds of nature.

    Directory of Open Access Journals (Sweden)

    Johannes J Le Roux

    Full Text Available The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae with differing global (North American and African patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (F(ST = 0.0 and is supported by extreme low quantitative trait variance (Q(ST = 0.00065-0.00952. The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

  11. Super-genotype: global monoclonality defies the odds of nature.

    Science.gov (United States)

    Le Roux, Johannes J; Wieczorek, Ania M; Wright, Mark G; Tran, Carol T

    2007-07-04

    The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae) with differing global (North American and African) patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (F(ST) = 0.0) and is supported by extreme low quantitative trait variance (Q(ST) = 0.00065-0.00952). The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

  12. The multi-systemic nature of diabetes mellitus: Genotype or phenotype?

    Directory of Open Access Journals (Sweden)

    Graham Wilfred Ewing

    2010-01-01

    Full Text Available Background: This article discusses factors which materially influence the diagnosis, prevention and treatment of diabetes mellitus but which may be overlooked by the prevailing biomedical paradigm. That cognition can be mathematically linked to the function of the autonomic nervous system and physiological systems casts new light upon the mechanisms responsible for homeostasis and origins of disease. In particular, it highlights the limitations of the reductionist biomedical approach which considers mainly the biochemistry of single pathologies rather than considering the neural mechanisms which regulate the function of physiological systems, and inherent visceral organs; and which are subsequently manifest as biochemistries of varying degrees of complexity and severity. As a consequence, histopathological tests are fraught with inherent limitations and many categories of drugs are significantly ineffective. Aims: Such limitations may be explained if disease (in particular diabetes mellitus has multiple origins, is multi-systemic in nature and, depending upon the characteristics of each pathology, is influenced by genotype and/or phenotype. Results:This article highlights the influence of factors which are not yet considered re. the aetiology of diabetes mellitus e.g. the influence of light and sensory input upon the stability of the autonomic nervous system; the influence of raised plasma viscosity upon rates of reaction; the influence of viruses and/or of modified live viruses given in vaccinations; systemic instability, in particular the adverse influence of drinks and lack of exercise upon the body′s prevailing pH and its subsequent influence upon levels of magnesium and other essential trace elements. Conclusions: This application of the top-down systems biology approach may provide a plausible and inclusive explanation for the nature and occurrence of diabetes mellitus.

  13. The multi-systemic nature of diabetes mellitus: Genotype or phenotype?

    Directory of Open Access Journals (Sweden)

    Graham Wilfred Ewing

    2010-10-01

    Full Text Available Background: This article discusses factors which materially influence the diagnosis, prevention and treatment of diabetes mellitus but which may be overlooked by the prevailing biomedical paradigm. That cognition can be mathematically linked to the function of the autonomic nervous system and physiological systems casts new light upon the mechanisms responsible for homeostasis and origins of disease. In particular, it highlights the limitations of the reductionist biomedical approach which considers mainly the biochemistry of single pathologies rather than considering the neural mechanisms which regulate the function of physiological systems, and inherent visceral organs; and which are subsequently manifest as biochemistries of varying degrees of complexity and severity. As a consequence, histopathological tests are fraught with inherent limitations and many categories of drugs are significantly ineffective. Aims: Such limitations may be explained if disease (in particular diabetes mellitus has multiple origins, is multi-systemic in nature and, depending upon the characteristics of each pathology, is influenced by genotype and/or phenotype. Results: This article highlights the influence of factors which are not yet considered re. the aetiology of diabetes mellitus e.g. the influence of light and sensory input upon the stability of the autonomic nervous system; the influence of raised plasma viscosity upon rates of reaction; the influence of viruses and/or of modified live viruses given in vaccinations; systemic instability, in particular the adverse influence of drinks and lack of exercise upon the body’s prevailing pH and its subsequent influence upon levels of magnesium and other essential trace elements. Conclusions: This application of the top-down systems biology approach may provide a plausible and inclusive explanation for the nature and occurrence of diabetes mellitus.

  14. Characteristics of general distribution of hepatitis B virus genotypes in China

    Institute of Scientific and Technical Information of China (English)

    Chang-Tai Zhu; Chun-Lei Dong

    2009-01-01

    BACKGROUND:Based on differences in the virus nucleotide sequence, hepatitis B virus (HBV) genotypes are presently divided into genotypes A-H. The geographic distributions of HBV genotypes differ in countries and regions. To determine the general characteristics of their distributions in the mainland of China, we reviewed articles on HBV genotypes published in China. METHODS:The Wanfang Database and the CNKI Database were searched for original articles involving HBV in China, and then the data from the articles were classiifed according to genotype and latitude and analyzed using SPSS 11.0. RESULTS:The main HBV genotypes were C, B and BC, and their rates were 50.99%, 35.58%, 6.07%, respectively;other genotypes were rare. There was a negative correlation between latitude and the rate of genotype B (r=-0.782,P0.05). CONCLUSIONS:In China, HBV genotype C predominates, followed by genotype C and mixed genotype BC; genotypes A, D and others are rare. With an increasing latitude, the distribution of genotype B decreases gradually, while that of genotype C tends to increase. The other genotypes do not show any changes.

  15. The separate and combined effects of MHC genotype, parasite clone, and host gender on the course of malaria in mice

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    Walker Mirjam

    2006-11-01

    Full Text Available Abstract Background The link between host MHC (major histocompatibility complex genotype and malaria is largely based on correlative data with little or no experimental control of potential confounding factors. We used an experimental mouse model to test for main effects of MHC-haplotypes, MHC heterozygosity, and MHC × parasite clone interactions. We experimentally infected MHC-congenic mice (F2 segregants, homo- and heterozygotes, males and females with one of two clones of Plasmodium chabaudi and recorded disease progression. Results We found that MHC haplotype and parasite clone each have a significant influence on the course of the disease, but there was no significant host genotype by parasite genotype interaction. We found no evidence for overdominance nor any other sort of heterozygote advantage or disadvantage. Conclusion When tested under experimental conditions, variation in the MHC can significantly influence the course of malaria. However, MHC heterozygote advantage through overdominance or dominance of resistance cannot be assumed in the case of single-strain infections. Future studies might focus on the interaction between MHC heterozygosity and multiple-clone infections.

  16. On the value of certain genotypic properties for forming exercise-induced bronchial asthma in children

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    Лорина Алімівна Іванова

    2015-10-01

    delM1+ (ІБС 24,2 % genotype , BTLI 35,4 %, and bronchodilation ones – in children with GSTT1+M1del genotype (BDI 21,0 %, BTLI 39,3 %. At exercise-induced bronchial asthma the highest bronchial tubes lability indicators are in children without mutation of eNOS gene exactly at the expense of bronchodilation test with salbutamol (BDI 19,8 %, BTLI 40,0 %.Conclusions. The “null” genotype of GSTT1 and GSTM1, genes more often takes place in children with exercise-induced bronchial asthma and the highest bronchospasm indicators are in patients with GSTT1delM1+ genotype. The mutations of eNOS gene (GT, ТТ genotypes take place in every second child with bronchial asthma but the gene mutation has no essential influence of an intensity of bronchospasm at the same time decreasing the results of bronchomotor tests with salbutamol

  17. Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes.

    Science.gov (United States)

    Laguerre, Gisèle; Louvrier, Philippe; Allard, Marie-Reine; Amarger, Noëlle

    2003-04-01

    Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy.

  18. Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

    Indian Academy of Sciences (India)

    Xuixiao Hong; Zhenqiang Su; Weigong Ge; Leming Shi; Roger Perkins; Hong Fang; Donna Mendrick; Weida Tong

    2010-04-01

    Genome-wide association studies (GWAS) examine the entire human genome with the goal of identifying genetic variants (usually single nucleotide polymorphisms (SNPs)) that are associated with phenotypic traits such as disease status and drug response. The discordance of significantly associated SNPs for the same disease identified from different GWAS indicates that false associations exist in such results. In addition to the possible sources of spurious associations that have been investigated and discussed intensively, such as sample size and population stratification, an accurate and reproducible genotype calling algorithm is required for concordant GWAS results from different studies. However, variations of genotype calling of an algorithm and their effects on significantly associated SNPs identified in downstream association analyses have not been systematically investigated. In this paper, the variations of genotype calling using the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) algorithm and the resulting influence on the lists of significantly associated SNPs were evaluated using the raw data of 270 HapMap samples analysed with the Affymetrix Human Mapping 500K Array Set (Affy500K) by changing algorithmic parameters. Modified were the Dynamic Model (DM) call confidence threshold (threshold) and the number of randomly selected SNPs (size). Comparative analysis of the calling results and the corresponding lists of significantly associated SNPs identified through association analysis revealed that algorithmic parameters used in BRLMM affected the genotype calls and the significantly associated SNPs. Both the threshold and the size affected the called genotypes and the lists of significantly associated SNPs in association analysis. The effect of the threshold was much larger than the effect of the size. Moreover, the heterozygous calls had lower consistency compared to the homozygous calls.

  19. Etanercept reduces matrix metalloproteinase-9 level in children with polyarticular juvenile idiopathic arthritis and TNF-alpha-308GG genotype.

    Science.gov (United States)

    Basic, Jelena; Pavlovic, Dusica; Jevtovic-Stoimenov, Tatjana; Vojinovic, Jelena; Susic, Gordana; Stojanovic, Ivana; Kocic, Gordana; Milosevic, Vuk; Cvetkovic, Tatjana; Marinkovic, Milena; Veljkovic, Andrej

    2010-06-01

    Genetic contribution of tumor necrosis factor polymorphism (TNF-alpha-308G/A) in patients with juvenile idiopathic arthritis (JIA) on response to TNF blocking agents, as well as matrix metalloproteinase-9 (MMP-9) production, is not yet well established. We have investigated whether the TNF-alpha-308G/A polymorphism can influence MMP-9 level and clinical response to etanercept (TNF receptor II-Fc fusion protein) in JIA patients, after 1 year of treatment. A total of 66 patients with polyarticular JIA and 65 healthy children were screened for the polymorphism using the polymerase chain reaction-restriction fragment length polymorphism method. JIA patients donated paired blood samples prior to and 12 months after etanercept therapy. Plasma MMP-9 level was determined using an enzyme-linked immunosorbent assay kit. Clinical assessment was performed according to ACR Pedi 50 improvement criteria. The frequency of the A allele was significantly higher in JIA patients compared to controls (39% vs. 26%, P = 0.026). Patients with the -308GG genotype achieved an ACR Pedi 50 response significantly more frequently than those with the -308AA genotype (P = 0.035). MMP-9 level in patients with the genotype -308GG was significantly decreased after 1 year of treatment with etanercept compared to the value from before (P = 0.036). On the other hand, there was a decrease of MMP-9 levels after treatment, but not statistically significant in patients with the genotypes -308GA/AA. We conclude that etanercept reduces MMP-9 level in children with polyarticular JIA and TNF-alpha-308GG genotype. Our results correlate with findings that the -308A allele is associated with a lower response to etanercept treatment.

  20. A systematic review on the association between the Helicobacter pylori vacA i genotype and gastric disease.

    Science.gov (United States)

    Liu, Xian; He, Bangshun; Cho, William C; Pan, Yuqin; Chen, Jie; Ying, Houqun; Wang, Feng; Lin, Kang; Peng, Hongxin; Wang, Shukui

    2016-05-01

    Helicobacter pylori (H. pylori) has been recognized as a cause of gastrointestinal diseases and progress of the pathology of gastrointestinal diseases is related to the genotype of H. pylori. Published studies have indicated that the H. pylori vacuolating cytotoxin gene A (vacA) i1/i2 genotype is associated with peptic ulcer disease (PUD) and gastric cancer (GC), but their conclusions are inconsistent. This study aimed to further assess the risk of vacA i gene for PUD and/or GC. A systematic search was conducted across three main electronic databases (PubMed, Web of Science, and CNKI). A meta-analysis was then performed on the pooled data of the published articles to estimate the overall influence of vacA i polymorphisms on PUD and/or GC by crude odds ratio (OR) with 95% confidence intervals (CI). The reliability of the results were confirmed by publication bias and sensitivity analysis of included studies. A total of 14 studies were selected according to the specific inclusion and exclusion criteria. The pooled results revealed that patients with GC were more vulnerable to infection by H. pylori i1 genotype (OR = 5.12; 95% CI: 2.66-9.85; P gastritis or nonulcer disease. Moreover, the results of subgroup analysis indicated that the i1 genotype of H. pylori was associated with an increased GC risk (OR = 10.89; 95% CI: 4.11-20.88; P < 0.001) in the Middle Asian population. The H. pylori vacA i1 genotype is associated with an increased GC risk, especially in the Middle Asian population.

  1. Does 5HTTLPR Genotype Moderate the Association of Family Environment With Child Attention-Deficit Hyperactivity Disorder Symptomatology?

    Science.gov (United States)

    Elmore, Alexis L; Nigg, Joel T; Friderici, Karen H; Jernigan, Katherine; Nikolas, Molly A

    2016-01-01

    Problematic family dynamics are common among youth with attention-deficit hyperactivity disorder (ADHD). Multiple mechanisms, including diathesis-stress (vulnerability) and differential susceptibility Gene × Environment interaction effects (G × E), have been proposed to account for this association. G × E effects for ADHD were examined via interactions between a genetic marker hypothesized to influence sensitivity to the environment (the promoter polymorphism of the serotonin transporter gene -5HTTLPR) and family conflict and cohesion in predicting ADHD symptoms. There were 498 youth ages 6-17 years (251 ADHD, 213 non-ADHD) and their parents who completed a multistage, multi-informant assessment (including parent and youth reports on the Family Environment Scale), and saliva sample collection for genotyping. Linear regression analyses examined interactions between 5HTTLPR genotype and the Family Environment Scale scales of conflict and cohesion reported by parent and child. Criteria laid out by Roisman et al. ( 2012 ) were applied to evaluate diathesis stress versus differential susceptibility G × E mechanisms. Results demonstrated interactions between 5HTTLPR genotype and both conflict and cohesion in predicting inattention but not hyperactivity-impulsivity. Both interactions were highly consistent with differential susceptibility models of G × E effects. 5HTTLPR genotype appeared to moderate the relationship between family conflict/cohesion and inattentive symptoms. Interactions highlight the role of 5HTTLPR genotype as a potential marker of environmental sensitivity and provide support for differential susceptibility models of G × E effects for ADHD.

  2. ENVIRONMENTAL AND SOCIO-ECONOMIC ASPECT OF GROWING MISCANTHUS GENOTYPES

    Directory of Open Access Journals (Sweden)

    Marián KOTRLA

    2013-01-01

    Full Text Available Deliberate cultivation of plants for energy biomass is becoming increasingly important. Biomass should significantly contribute to increase the share of renewable energy in the European Union. On the research locality of Slovak University of Agriculture in Nitra localized in the village Kolíňany (Slovak Republic is implemented basic research focused on the growth and production of the two genotypes energy grass Miscanthus. Research is carried out since 2010. In the third year after planting (the year 2012 were confirmed biomass production depending on the genotype of 35.45 and 36.67 t ha-1. Based on the analysis of growth and production performance of Miscanthus genotypes can be evaluated the high environmental and socio-economic aspects of growing energy crops, depending on the specific agro-ecological conditions.

  3. Comparative analysis of minor histocompatibility antigens genotyping methods

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    A. S. Vdovin

    2016-01-01

    Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.

  4. Acanthamoeba T4 genotype associated with keratitis infections in Tunisia.

    Science.gov (United States)

    Dendana, F; Sellami, H; Trabelsi, H; Neji, S; Cheikhrouhou, F; Makni, F; Ayadi, A

    2013-01-01

    Acanthamoeba keratitis (AK) is a sight-threatening infection. We report five cases of AK diagnosed from 2005 to 2009 in the Laboratory of Parasitology-Mycology at Habib Bourguiba Sfax Hospital, Tunisia. All were associated with improper care of contact lenses (rinsing of contact lenses with tap water and inappropriate cleaning) and lens storage. The patients displayed different clinical presentations: corneal inflammation, corneal ulceration, and corneal abscess. The diagnosis was made after direct examination, culture, and polymerase chain reaction amplification with specific primers. The genotype classification was based on the highly variable DF3 region in the 18S rRNA gene. This is the first study characterizing Acanthamoeba genotype in Tunisia and North Africa. All Acanthamoeba isolates were associated to the T4 genotype. Three different DF3 sequence types were related to AK infections T4/10, T4/15, and T4/16.

  5. Cytological Effects of Space Environment on Different Genotype of Rice

    Institute of Scientific and Technical Information of China (English)

    WEI Li-jun; QIAN Yu; YANG Qian; XU Jian-long; WANG Jun-min; SUN Ye-qing

    2007-01-01

    For exploring the biological effect of space environment on different genotype of rice seeds, the cytological effects of M1 generation after space flight were studied.Twelve different genotypes of rice seeds which belong to different climate ecotype (early, medium and late) of indica and japonica were onboard "Shenzhou 4" spaceship for 162 h.After recovered the total number of mitosis cells and chromosomal aberration were observed.In all the lines the mitotic index (MIs) of space flight are much higher than control, which indicates the stimulate effect of space environment.The cell rate of chromosomal aberration (CRCA) of space flight is also much higher than control, but varies from line to line.It indicates that biological effect of space environment on rice seed dependents not only on flight duration but also on rice genotype.The radiosensitivities of different lines were also discussed according to CRCAs.

  6. Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria.

    Science.gov (United States)

    Laatamna, Abd Elkarim; Wagnerová, Pavla; Sak, Bohumil; Květoňová, Dana; Aissi, Miriem; Rost, Michael; Kváč, Martin

    2013-10-18

    Faecal samples from two horse farms in Algeria keeping Arabian, Thoroughbred, and Barb horses were examined for the presence of Cryptosporidium in 2010-2011. A total of 138 faecal samples (16 from a farm keeping 50 animals and 122 from a farm with 267 horses) were screened for Cryptosporidium spp. infection using molecular tools. DNA was extracted from all samples. Nested PCR was performed to amplify fragments of the SSU rDNA and gp60 genes to determine the presence of Cryptosporidium species and genotypes. Sequence analyses of SSU and gp60 genes revealed four animals positive for the presence of subtype XIIIa A22R9 of the Cryptosporidium hedgehog genotype. The infections were not associated with diarrhoea. This study reports, for the first time, the occurrence of Cryptosporidium in Algeria and the first occurrence of the hedgehog genotype in horses. These findings support the potential role of infected horses in sylvatic-domestic transmission of Cryptosporidium.

  7. Noninvasive genotyping of common marmoset (Callithrix jacchus) by fingernail PCR.

    Science.gov (United States)

    Takabayashi, Shuji; Katoh, Hideki

    2015-07-01

    The common marmoset (Callithrix jacchus) is a New World primate that is a useful model for medical studies. In this study, we report a convenient, reliable, and noninvasive procedure to genotype a living common marmoset by using fingernails. This method was used to successfully genotype DNA by restriction fragment length polymorphism (RFLP) PCR without prior purification, by using the KOD FX PCR enzyme kit. Additionally, there is no sample contamination from hematopoietic chimera derived from fused placenta in utero. We compared chimeric levels between various tissues in females with male littermates using quantitative fluorescent (QF)-PCR to prepare a reliable DNA source for genetic analyses, such as genotyping, gene mapping, or genomic sequencing. The chimerism detected appeared to be restricted to lymphatic tissues, such as bone marrow, thymus, spleen, lymph nodes and blood cells. As a result, DNA from fingernails with the quick is the best DNA source for genetic research in living marmosets.

  8. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

    Directory of Open Access Journals (Sweden)

    Vouillamoz, José F.

    2016-07-01

    Full Text Available The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation. Over a two years period, yields in dry leaves ranged from 10 to 170 g m-2, with a percentage of leaves ranging from 53 to 75 %. HPLC analyses showed a notable variability in phytochemical composition, with stevioside content ranging from 0.3 to 7.9 % w/w and rebaudioside A from 0.3 to 6.5 % w/w. Cultivation of S. rebaudiana in Switzerland is feasible. With a density of 10 plants per m2, the potential yields of dry matter are approximately 1-2 t ha-1. The most productive genotypes (Pharmasaat, Hem Zaden, Stepa and Mediplant 3 and 11 will be submitted to the industry for organoleptic evaluation.

  9. Clinical utility of thiopurine S-methyltransferase genotyping.

    Science.gov (United States)

    Corominas, Hèctor; Baiget, Montserrat

    2004-01-01

    Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that plays a major role in the metabolism of thiopurine drugs such as mercaptopurine and azathioprine. The interindividual differences in response to thiopurine administration is in part due to the presence of genetic polymorphisms in the gene that regulates TPMT activity. TPMT genotype correlates well with the in vivo enzyme activity within erythrocytes. Patients with genetically determined decreased TPMT activity develop severe myelosuppression when treated with standard doses of thiopurine drugs because an excess of thioguanine nucleotides accumulates in hematopoietic tissues. TPMT genotyping provides clinicians with a reliable method for identifying TPMT-deficient patients who can benefit from low doses of thiopurine drugs in order to reduce the risk of developing adverse effects. Moreover, the administration of higher doses of the drug could improve therapeutic response in patients in whom the TPMT genotyping demonstrates the absence of mutated alleles.

  10. Relation between hepatitis B virus genotypes and gene mutation of basic core promoter in Li nationality

    Institute of Scientific and Technical Information of China (English)

    Juntao Zeng; Zhengwen Liu; Shiping Zeng; Jing Chen

    2009-01-01

    Objective:To investigate the relation between hepatitis B virus(HBV) genotypes and the double mutation of A-to-T nucleotide(nt) 1762 and G-to-A nt 1764 in basic core promotev(BCP T1762/A1764) in patients of the Li nationality. Methods:Subjects were 125 HBV DNA positive patients that belong to the Li nationality on Hainan Island. HBV DNA genotype was determined by real time fluorimetrypolymerase chain reaction. BCP T1762/A1764 mutation was performed using the direct sequencing method. Results:The prevalence rates of genotype B, genotype C, genotype D, genotype C and D mixed infection(genotype C+D) and genotype B and D mixed infection (genotype B+C) were 31.20%, 53.60%, 12.00%, 2.40% and 0.80% respectively. Mutation frequencies in patients infected with HBV genotype C(58.21%) were significantly higher than in those infected with other genotypes (P <0.01). The serum viral load of the patients with genotype C(5.74±1.21) was also higher than that of those with genotype B(P <0.01). Conclusion:The major genotypes in the Li nationality were genotype C and genotype B. The infection of genotype D and mixed infection also occurred in the Li nationality. Genotype C HBV has a higher replication rate, and the different degrees of pathogenecity among HBV genotypes may be related to BCP T1762/ A1764 mutation frequency.

  11. Genotyping of Brucella species using clade specific SNPs

    Directory of Open Access Journals (Sweden)

    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  12. Photosynthesis, photorespiration and productivity of wheat and soybean genotypes.

    Science.gov (United States)

    Aliyev, Jalal A

    2012-07-01

    The results of the numerous measurements obtained during the last 40 years on gas exchange rate, photosynthetic carbon metabolism by exposition in ¹⁴CO₂ and activities of primary carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC/O), in various wheat and soybean genotypes grown over a wide area in the field and contrasting in photosynthetic traits and productivity are presented in this article. It was established that high productive wheat genotypes (7-9 t ha⁻¹) with the optimal architectonics possess higher rate of CO₂ assimilation during the leaf ontogenesis. Along with the high rate of photosynthesis, high values of photorespiration are characteristic for the high productive genotypes. Genotypes with moderate (4-5 t ha⁻¹) and low (3 t ha⁻¹) grain yield are characterized by relatively low rates of both CO₂ assimilation and photorespiration. A value of photorespiration constitutes 28-35% of photosynthetic rate in contrasting genotypes. The activities of RuBPC and RuBPO were changing in a similar way in the course of the flag leaf and ear elements development. High productive genotypes are also characterized by a higher rate of biosynthesis and total value of glycine-serine and a higher photosynthetic rate. Therefore, contrary to conception arisen during many years on the wastefulness of photorespiration, taking into account the versatile investigations on different aspects of photorespiration, it was proved that photorespiration is one of the evolutionarily developed vital metabolic processes in plants and the attempts to reduce this process with the purpose of increasing the crop productivity are inconsistent.

  13. Shift work in nurses: contribution of phenotypes and genotypes to adaptation.

    Directory of Open Access Journals (Sweden)

    Karen L Gamble

    Full Text Available BACKGROUND: Daily cycles of sleep/wake, hormones, and physiological processes are often misaligned with behavioral patterns during shift work, leading to an increased risk of developing cardiovascular/metabolic/gastrointestinal disorders, some types of cancer, and mental disorders including depression and anxiety. It is unclear how sleep timing, chronotype, and circadian clock gene variation contribute to adaptation to shift work. METHODS: Newly defined sleep strategies, chronotype, and genotype for polymorphisms in circadian clock genes were assessed in 388 hospital day- and night-shift nurses. RESULTS: Night-shift nurses who used sleep deprivation as a means to switch to and from diurnal sleep on work days (∼25% were the most poorly adapted to their work schedule. Chronotype also influenced efficacy of adaptation. In addition, polymorphisms in CLOCK, NPAS2, PER2, and PER3 were significantly associated with outcomes such as alcohol/caffeine consumption and sleepiness, as well as sleep phase, inertia and duration in both single- and multi-locus models. Many of these results were specific to shift type suggesting an interaction between genotype and environment (in this case, shift work. CONCLUSIONS: Sleep strategy, chronotype, and genotype contribute to the adaptation of the circadian system to an environment that switches frequently and/or irregularly between different schedules of the light-dark cycle and social/workplace time. This study of shift work nurses illustrates how an environmental "stress" to the temporal organization of physiology and metabolism can have behavioral and health-related consequences. Because nurses are a key component of health care, these findings could have important implications for health-care policy.

  14. The role of macrosymbiont genotypes and earthworms in the enrichment of soil with biological nitrogen

    Science.gov (United States)

    Nazaryuk, V. M.; Kalimullina, F. R.; Klenova, M. I.

    2010-06-01

    The specific features of the symbiotic apparatus and the accumulation of the plant biomass under the influence of different genotypes of peas ( Pisum sativum L.) on gray forest soils were studied in field conditions. With the alternation of legume and grass cultures, the genotypes of plants with supernodulation were found to affect the microbial nitrogen content in the soil to a greater extent than the concentration of ammonium and nitrate nitrogen. For the growing period, the N content in the microbial biomass increased, on the average, by 1.3 to 1.5 times. The consumption of nitrogen by the plants of the supernodular mutant K-301a was found to be 2.6 and 3.0 times greater than that by the pea plants of the Ramonskii-77 variety and of the K-562a line, respectively. During the after effect of the symbiotically bound air nitrogen, a significant uptake of this element was observed only by the oat plants grown after the K-56 2a. The nitrogen fixation by these plants was 1.3 times more active than that by the peas of the Ramonskii-77 variety. The importance of earthworms (Lumbricidae) and plant residues of different genotypes for the processes of mineralization of organic compounds and accumulation of ammonium, nitrate, and microbial nitrogen in the soils under optimal hydrothermal conditions was revealed. In the experiment, two maximums of the CO2 emission were recorded; they may be related to the periodic production of organic mass by the earthworms and the creation of favorable conditions for microbial activity by them. The accumulation of nitrate nitrogen (up to 150 mg/kg) in the soil was the greatest owing to the interaction between the earthworms and the residues of the supernodular K-301a mutant.

  15. The effect of myostatin genotype on body temperature during extreme temperature events.

    Science.gov (United States)

    Howard, J T; Kachman, S D; Nielsen, M K; Mader, T L; Spangler, M L

    2013-07-01

    Extreme heat and cold events can create deleterious physiological changes in cattle as they attempt to cope. The genetic background of animals can influence their response to these events. The objective of the current study was to determine the impact of myostatin genotype (MG) on body temperature during periods of heat and cold stress. Two groups of crossbred steers and heifers of unknown pedigree and breed fraction with varying percentages of Angus, Simmental, and Piedmontese were placed in a feedlot over 2 summers and 2 winters. Before arrival, animals were genotyped for the Piedmontese-derived myostatin mutation (C313Y) to determine their MG as either homozygous normal (0 copy; n = 84), heterozygous (1 copy; n = 96), or homozygous for inactive myostatin (2 copy; n = 59). Hourly tympanic and vaginal temperature measurements were collected for steers and heifers, respectively, for 5 d during times of anticipated heat and cold stress. Mean (±SD) ambient temperature for summer and winter stress events were 24.4 (±4.64) and -1.80 (±11.71), respectively. A trigonometric function (sine + cosine) with periods of 12 and 24 h was used to describe the diurnal cyclical pattern. Hourly body temperature was analyzed within a season, and fixed effects included MG, group, trigonometric functions nested within group, and interaction of MG with trigonometric functions nested within group; random effects were animal and residual (Model [I]). A combined analysis of season and group was also investigated with the inclusion of season as a main effect and the nesting of effects within both group and season (Model [C]). In both models, the residual was fitted using an autoregressive covariance structure. A 3-way interaction of MG, season, and trigonometric function periodicities of 24 h (P 0.05). The current study illustrated that a genotype × environment interaction exists for MG and 1-copy animals were more robust to environmental extremes in comparison with 0- or 2-copy animals.

  16. Pollen aroma fingerprint of two sunflower (Helianthus annuus L.) genotypes characterized by different pollen colors.

    Science.gov (United States)

    Bertoli, Alessandra; Fambrini, Marco; Doveri, Silvia; Leonardi, Michele; Pugliesi, Claudio; Pistelli, Luisa

    2011-09-01

    Samples of fresh pollen grains, collected from capitula in full bloom from two genotypes of sunflower (Helianthus annuus L.) and characterized by a different color, i.e., white-cream (WC) and orange (O), were analyzed by the HS-SPME (headspacesolid phase microextraction)/GC/MS technique. This study defined for the first time the fingerprint of the sunflower pollen, separated from the disc flowers, to define its contribution to the inflorescence aroma. In the GC/MS fingerprints of the WC and O genotypes, 61 and 62 volatile compounds were identified, respectively. Monoterpene hydrocarbons (34% in O vs. 28% in WC) and sesquiterpene hydrocarbons (37% in O vs. 31% in WC) were ubiquitous in all samples analyzed and represented the main chemical classes. α-Pinene (21% in O vs. 20% in WC) and sabinene (11% in O vs. 6% in WC) were the dominant volatiles, but also a full range of aliphatic hydrocarbons and their oxygenated derivatives gave a decisive contribution to the aroma composition (10% in O vs. 12% in WC). In addition, dendrolasin (3% in O vs. 4% in WC) and some minor constituents such as (E)-hex-2-en-1-ol (0.4% in O vs. 0.1% in WC) were pointed out not only for their contribution to the pollen scent, but also for their well-known role in the plant ecological relationships. Having evaluated two pollen morphs with different carotenoid-based colors, the study sought to highlight also the presence of some volatile precursors or derivatives of these pigments in the aroma. However, the pollen aroma of the two selected genotypes made a specific chemical contribution to the sunflower inflorescence scent without any influence on carotenoid derivatives.

  17. IGKC and FcγR genotypes and humoral immunity to HER2 in breast cancer.

    Science.gov (United States)

    Pandey, Janardan P; Kistner-Griffin, Emily; Black, Laurel; Namboodiri, Aryan M; Iwasaki, Motoki; Kasuga, Yoshio; Hamada, Gerson S; Tsugane, Shoichiro

    2014-02-01

    Immunoglobulin κ constant (IGKC) gene has recently been identified as a strong prognostic marker in several human solid tumors, including breast cancer. Although the mechanisms underlying the IGKC signature are not yet known, identification of tumor-infiltrating plasma cells as the source of IGKC expression strongly suggests a role for humoral immunity in breast cancer progression. The primary aim of the present investigation was to determine whether the genetic variants of IGKC, KM (κ marker) allotypes, are risk factors for breast cancer, and whether they influence the magnitude of humoral immunity to epidermal growth factor receptor 2 (HER2), which is overexpressed in 25-30% of breast cancer patients and is associated with poor prognosis. Using a matched case-control design, we genotyped a large (1719 subjects) study population from Japan and Brazil for KM alleles. Both cases and controls in this study population had been previously characterized for GM (γ marker) and Fcγ receptor (FcγR) alleles, and the cases had also been characterized for anti-HER2 antibodies. Conditional logistic regression analysis of the data showed that KM1 allele additively contributed to the risk of breast cancer in the Japanese subjects from Nagano: Compared to KM3 homozygotes, KM1 homozygotes were almost twice as likely to develop breast cancer (OR=1.77, CI 1.06-2.95). Additionally, KM genotypes-individually and in particular epistatic combinations with FcγRIIa genotypes-contributed to the magnitude of anti-HER2 antibody responsiveness in the Japanese patients. This is the first report implicating KM alleles in the immunobiology of breast cancer.

  18. Two-temperature LATE-PCR endpoint genotyping

    Directory of Open Access Journals (Sweden)

    Reis Arthur H

    2006-12-01

    Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

  19. Two-temperature LATE-PCR endpoint genotyping

    Science.gov (United States)

    Sanchez, J Aquiles; Abramowitz, Jessica D; Salk, Jesse J; Reis, Arthur H; Rice, John E; Pierce, Kenneth E; Wangh, Lawrence J

    2006-01-01

    Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the

  20. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    Wheat (Triticum aestivum L.) is a heat-susceptible crop throughout its phenological stages, flowering phase being the most sensitive stage. Early stress detection method with advanced physiological measurements may provide new dimensions to establish a high throughput phenotyping technique...... yield efficiency of PSII photochemistry (Fv/Fm). We subsequently used this standardized protocol for mass screening of wheat genotypes. Our results showed that the temperature of 40°C in 300 µmol m-2s-1 light for 72 h was appropriate to induce heat stress to reveal genetic variation among genotypes...

  1. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  2. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

    Haraldsson, H.M.; Ettinger, U.; Magnusdottir, B.B.;

    2010-01-01

    Neuregulin-1 (NRG-1) is a putative susceptibility gene for schizophrenia but the neurocognitive processes that may involve NRG-1 in schizophrenia are unknown. Deficits in antisaccade (AS) and smooth pursuit eye movements (SPEM) are promising endophenotypes, which may be associated with brain...... dysfunctions underlying the pathophysiology of schizophrenia. The aim of this study was to investigate the associations of NRG-1 genotypes with AS and SPEM in schizophrenia patients and healthy controls. Patients (N = 113) and controls (N = 106) were genotyped for two NRG-1 single nucleotide polymorphisms...... findings of impaired AS and SPEM performance in schizophrenia patients (all P

  3. [Present and future of genotype-based personalized nutrition].

    Science.gov (United States)

    Sarkadi Nagy, Eszter; Martos, Éva

    2014-05-18

    After the completion of the Human Genome Project, the era of providing personalized dietary advice based on an individual's genetic profile seemed near. Since then more than a decade has passed and the pace of development has been slower than expected. Genotyping single nucleotide polymorphisms which may determine susceptibility to multifactorial diseases is cheaper and more accessible than it was ten years ago. However, few of them are supported by such solid scientific evidence which would justify their use for personalized dietary advice. The future of genotype-based personalized nutrition depends on whether a sufficient amount of gene-diet-disease interactions are identified and scientifically confirmed.

  4. Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

    Directory of Open Access Journals (Sweden)

    Wensheng Wang

    2016-11-01

    Full Text Available Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA

  5. Positive effects of plant genotypic and species diversity on anti-herbivore defenses in a tropical tree species.

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    Xoaquín Moreira

    Full Text Available Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves. We found that both forms of plant diversity had positive effects on stem (but not leaf defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer

  6. 5-HTTLPR Genotype Moderates the Effects of Past Ecstasy Use on Verbal Memory Performance in Adolescent and Emerging Adults: A Pilot Study.

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    Natasha E Wright

    Full Text Available Ecstasy use is associated with memory deficits. Serotonin transporter gene (5-HTTLPR polymorphisms have been linked with memory function in healthy samples. The present pilot study investigated the influence of 5-HTTLPR polymorphisms on memory performance in ecstasy users, marijuana-using controls, and non-drug-using controls, after a minimum of 7 days of abstinence.Data were collected from 116 young adults (18-25 years-old, including 45 controls, 42 marijuana users, and 29 ecstasy users, and were balanced for 5-HTTLPR genotype. Participants were abstinent seven days prior to completing memory testing. Three MANCOVAs and one ANCOVA were run to examine whether drug group, 5-HTTLPR genotype, and their interactions predicted verbal and visual memory after controlling for gender, past year alcohol use, other drug use, and nicotine cotinine levels.MANCOVA and ANCOVA analysis revealed a significant interaction between drug group and genotype (p = .03 such that ecstasy users with the L/L genotype performed significantly worse on CVLT-2 total recall (p = .05, short (p = .008 and long delay free recall (p = .01, and recognition (p = .006, with the reverse pattern found in controls. Ecstasy did not significantly predict visual memory. 5-HTTLPR genotype significantly predicted memory for faces (p = .02; short allele carriers performed better than those with L/L genotype.5-HTTLPR genotype moderated the effects of ecstasy on verbal memory, with L/L carriers performing worse compared to controls. Future research should continue to examine individual differences in ecstasy's impact on neurocognitive performance as well as relationships with neuronal structure. Additional screening and prevention efforts focused on adolescents and emerging adults are necessary to prevent ecstasy consumption.

  7. The Discriminatory Value of CYP2D6 Genotyping in Predicting the Dextromethorphan/Dextrorphan Phenotype in Women with Breast Cancer

    Science.gov (United States)

    Trojan, Andreas; Vergopoulos, Athanasios; Breitenstein, Urs; Seifert, Burkhardt; Rageth, Christoph; Joechle, Wolfgang

    2012-01-01

    Background The growth inhibitory effect of tamoxifen is used for the treatment of breast cancer. Tamoxifen efficacy is mediated by its biotransformation, predominantly via the cytochrome P450 2D6 (CYP2D6) isoenzyme, to the active metabolite endoxifen. We investigated the relationship of CYP2D6 genotypes to the metabolism of dextromethorphan (DM), which is frequently used as a surrogate marker for the formation of endoxifen. Methods The CYP2D6 genotype was determined by polymerase chain reaction (PCR) in previously untreated patients with hormone receptor-positive invasive breast cancer considered to receive antihormonal therapy. The DM/dextrorphan (DX) urinary excretion ratios were obtained in a subset of patients by high-pressure liquid chromatography (HPLC)-mediated urine analysis after intake of 25 mg DM. The relationships of genotype and corresponding phenotype were statistically analyzed for association. Results From 151 patients predicted based on their genotype data for the ‘traditional’ CYP2D6 phenotype classes poor, intermediate, extensive and ultrarapid, 83 patients were examined for their DM/DX urinary ratios. The genotype-based poor metabolizer status correlated with the DM/DX ratios, whereas the intermediate, extensive and ultrarapid genotypes could not be distinguished based on their phenotype. Citalopram intake did not significantly influence the phenotype. Conclusions The DM metabolism can be reliably used to assess the CYP2D6 enzyme activity. The correlation with the genotype can be incomplete and the metabolic ratios do not seem to be compromised by citalopram. DM phenotyping may provide a standardized tool to better assess the CYP2D6 metabolic capacity. PMID:22553469

  8. Paraoxonase 1 genotype-phenotype correlation in patients with metabolic syndrome.

    Science.gov (United States)

    Ciumărnean, Lorena; Dronca, Eleonora; Vesa, Ştefan Cristian; Sâmpelean, Dorel; Buzoianu, Anca Dana; Achimaş-Cadariu, Andrei

    2015-01-01

    The aim of the study was to investigate the influence of three single nucleotide polymorphisms (SNPs) (-108C>T, -162A>G and -909G>C) from the promoter region of paraoxonase 1 (PON1) gene on the enzyme activity, in patients with metabolic syndrome (MS). The study group consisted of 61 individuals with MS and the control group of 73 individuals without MS, matched for age and gender. For each individual, clinical and genetic parameters with possible influence on PON1 activities (paraoxonase, arylesterase and lactonase) were measured. PON1 genotyping was performed with PCR-RFLP, using specific primers and restriction enzymes. We found no differences for distribution of PON1 -108C>T, -162A>G and -909G>C polymorphisms, between the two groups (p-NS). The -108C>T and -909G>C polymorphisms were associated with paraoxonase (p=0.03, p=0.006, respectively), arylesterase (p162A>G polymorphism was not associated with paraoxonase (p-NS) or lactonase (p-NS) activities, but influenced the arylesterase activity (p=0.03). PON1 activities were influenced by all three polymorphisms, regardless of the presence of MS.

  9. Differences in ovarian aging patterns between races are associated with ovarian genotypes and sub-genotypes of the FMR1 gene

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    Gleicher Norbert

    2012-09-01

    Full Text Available Abstract Background Ovarian aging patterns differ between races, and appear to affect fertility treatment outcomes. What causes these differences is, however, unknown. Variations in ovarian aging patterns have recently been associated with specific ovarian genotypes and sub-genotypes of the FMR1 gene. We, therefore, attempted to determine differences in how functional ovarian reserve (FOR changes with advancing age between races, and whether changes are associated with differences in distribution of ovarian genotypes and sub-genotypes of the FMR1 gene. Methods We determined in association with in vitro fertilization (IVF FOR in 62 young Caucasian, African and Asian oocyte donors and 536 older infertility patients of all three races, based on follicle stimulating hormone (FSH, anti-Müllerian hormone (AMH and oocyte yields, and investigated whether differences between races are associated with differences in distribution of FMR1 genotypes and sub-genotypes. Results Changes in distribution of mean FSH, AMH and oocyte yields between young donors and older infertility patients were significant (all P FMR1 genotypes and sub-genotypes in patients varied significantly between races, with Asians demonstrating fewer het-norm/low sub-genotypes than Caucasians and Africans (P = 0.012. Conclusion FOR changes in different races at different rates, and appears to parallel ovarian FMR1 genotypes and sub-genotype distributions. Differences in ovarian aging between races may, therefore, be FMR1-associated.

  10. Pattern and molecular epidemiology of Hepatitis B virus genotypes circulating in Pakistan.

    Science.gov (United States)

    Awan, Zunaira; Idrees, Muhammad; Amin, Irum; Butt, Sadia; Afzal, Samia; Akbar, Haji; Rehman, Irshad-ur; Younas, Saima; Shahid, Muhammad; Lal, Amreek; Saleem, Sana; Rauff, Bisma

    2010-12-01

    The continuously mutating nature of Hepatitis B virus (HBV) is responsible for the emergence of varying genotypes in different regions of the world affecting the disease outcome. The objective of the current study was to find out the pattern of HBV genotypes circulating in Pakistan. HBV genotypes were determined in HBV chronic patients of different age and gender from all the four different geographical regions (provinces) of Pakistan for a period of 2 years (2007-2009). Out of the total 3137 consecutive patients, 300 (175; 58.3% males and 125; 41.7% females) were randomly selected for HBV genotype A through H determination using molecular genotyping methods. Total 269 (89.6%) isolates were successfully genotyped where as 31 (10.3%) samples failed to generate a type-specific PCR band and were found untypable. Out of the successfully genotyped samples, 43 (14.3%) were with type A, 54 (18%) were with type B, 83 (27.6%) were with type C, 39 (13%) were with type D, 2 (0.6%) were with type E, 4 (1.3%) were with genotype F and total 44 (14.6%) were with mixed HBV infections. Of the mixed genotype infection cases, 16 were with genotypes A/D, 9 were B/C, six were A/D/F, five were with genotypes A/F, two were with A/B/D and B/E and one each for A/C as well as A/E genotypes. Four common genotypes of HBV found worldwide (A, B, C & D) were isolated from Pakistan along with uncommon genotypes E and F for the first time in Pakistan. Overall Genotype C is the most prevalent genotype. Genotypes B and C are predominant in Punjab & Balochistan and Khyber Pakhtoonkhwa, respectively whereas genotype A in Sindh.

  11. Genotyping analysis for the 46 C/T polymorphism of coagulation factor XII and the involvement of factor XII activity in patients with recurrent pregnancy loss.

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    Eriko Asano

    Full Text Available BACKGROUND: Established causes of recurrent pregnancy loss (RPL include antiphospholipid syndrome, uterine anomalies, parental chromosomal abnormalities, particularly translocations and abnormal embryonic karyotype. A systematic review concluded that coagulation factor XII (FXII deficiency was associated with RPL. However, it could not be established whether the 46 C/T SNP of FXII or low activity of FXII was a risk factor for RPL, because of the small sample size. METHODS AND FINDINGS: We conducted a cross-sectional and cohort study in 279 patients with two or more unexplained consecutive pregnancy losses and 100 fertile women. The association between the lupus anticoagulant (LA activity and FXII activity was examined. The frequency of the CC, CT and TT genotypes and the FXII activity were also compared between the patients and controls. Subsequent miscarriage rates among the CC, CT, TT genotypes and according to the FXII activity was examined. LA was associated with reduced FXII activity. The CT, but not the TT, genotype was confirmed to be a risk factor for RPL in the cross-sectional study using multivariate logistic regression analysis (OR, 2.8; 95% CI, 1.37-5.85. The plasma FXII activity in the patients was similar to that in the controls. Neither low FXII activity nor the CT genotype predicted the subsequent pregnancy outcome in the cohort study. On the other hand, and intermediate FXII activity level of 85-101% was predictive of subsequent miscarriage. CONCLUSIONS: Low FXII activity was not associated with RPL. The FXII gene was found to be one of the significant susceptibility genes for RPL, similar to the FV Leiden mutation. However, the clinical influence of the CT genotype might be relatively small, because the presence/absence of this genotype did not have any predictive value for the subsequent pregnancy outcome. This was the first study indicating the influence of FXII 46C/T on further pregnancy outcomes.

  12. Comparison of potentials between genotype-based selection and genotypic value-based selection of quantitative traits

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    According to the difference of selection criteria, methods of marker-assisted selection (MAS) of quantitative traits can be divided into genotype-based selection (GS) and genotypic value-based selection (GVS). By means of computer simulation, potentials of the two methods were compared. Results showed that the two methods had similar basic laws and their efficiencies were not significantly different except that GS behaved better in the case where the number of QTLs was large and QTL effects were equal. From the application point of view, combination of GS and GVS should be the development direction of MAS research in the future.

  13. Genotyping Test with Clinical Factors: Better Management of Acute Postoperative Pain?

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    Aline Hajj

    2015-03-01

    Full Text Available Individualization of acute postoperative pain treatment on an evidence-based decision process is a major health concern. The aim of this study is to investigate the influence of genetic and non-genetic factors on the variability of response to morphine in acute postoperative pain. A group of nighty-five patients undergoing major surgery were included prospectively. At 24 h, a logistic regression model was carried out to determine the factors associated with morphine doses given by a Patient Controlled Analgesia device. The dose of morphine was associated with age (p = 0.011, patient weight (p = 0.025 and the duration of operation (p = 0.030. This dose decreased with patient’s age and duration of operation and increased with patient’s weight. OPRM1 and ABCB1 polymorphisms were significantly associated with administered dose of morphine (p = 0.038 and 0.012 respectively. Patients with at least one G allele for c.118A>G OPRM1 polymorphism (AG/GG needed 4 times the dose of morphine of AA patients. Additionally, patients with ABCB1 CT and CC genotypes for c.3435C>T polymorphism were 5.6 to 7.1 times more prone to receive higher dose of morphine than TT patients. Our preliminary results support the evidence that OPRM1/ABCB1 genotypes along with age, weight and duration of operation have an impact on morphine consumption for acute postoperative pain treatment.

  14. Can genotype determine the sports phenotype? A paradigm shift in sports medicine.

    Science.gov (United States)

    Ghosh, Amit; Mahajan, Preetam B

    2016-06-01

    In last two decades, there has been an evolution in sports medicine. Several researchers have worked on different domains of sports medicine, like strength, endurance, sports injury, and psychology. Besides this, several groups have explored the changes at cellular and molecular levels during exercise, which has led to the development of the new domain in sports science known as genetic medicine. Genetic medicine deals with the genotypic basis of sports phenotype. In this article, we try to provide an up-to-date review on genetic determinants of sports performance, which will be like a journey from the nostalgic past towards the traditional present and the romantic future of sports medicine. Endurance and power performance are two important domains of athletes. They vary in individuals, even among trained athletes. Researches indicate that the genetic makeup of sportsmen play a vital role in their performance. Several genetic factors are reported to be responsible for endurance, power, susceptibility to injury, and even psychology of the individual. Besides this, proper training, nutrition, and environment are also important in shaping their potential. The aim of this discussion is to understand the influence of the environment and the genetic makeup on the performance of the athletes. There is sufficient evidence to suggest that genotype determines the sports phenotype in an athlete. Choosing the right sports activity based on genetic endowment is the key for achieving excellence in sports.

  15. The interplay between genotype, metabolic state and cofactor treatment governs phenylalanine hydroxylase function and drug response.

    Science.gov (United States)

    Staudigl, Michael; Gersting, Søren W; Danecka, Marta K; Messing, Dunja D; Woidy, Mathias; Pinkas, Daniel; Kemter, Kristina F; Blau, Nenad; Muntau, Ania C

    2011-07-01

    The discovery of a pharmacological treatment for phenylketonuria (PKU) raised new questions about function and dysfunction of phenylalanine hydroxylase (PAH), the enzyme deficient in this disease. To investigate the interdependence of the genotype, the metabolic state (phenylalanine substrate) and treatment (BH(4) cofactor) in the context of enzyme function in vitro and in vivo, we (i) used a fluorescence-based method for fast enzyme kinetic analyses at an expanded range of phenylalanine and BH(4) concentrations, (ii) depicted PAH function as activity landscapes, (iii) retraced the analyses in eukaryotic cells, and (iv) translated this into the human system by analyzing the outcome of oral BH(4) loading tests. PAH activity landscapes uncovered the optimal working range of recombinant wild-type PAH and provided new insights into PAH kinetics. They demonstrated how mutations might alter enzyme function in the space of varying substrate and cofactor concentrations. Experiments in eukaryotic cells revealed that the availability of the active PAH enzyme depends on the phenylalanine-to-BH(4) ratio. Finally, evaluation of data from BH(4) loading tests indicated that the patient's genotype influences the impact of the metabolic state on drug response. The results allowed for visualization and a better understanding of PAH function in the physiological and pathological state as well as in the therapeutic context of cofactor treatment. Moreover, our data underscore the need for more personalized procedures to safely identify and treat patients with BH(4)-responsive PAH deficiency.

  16. Genotypic diversity of complement component C4 does not predict kidney transplant outcome.

    Science.gov (United States)

    Wahrmann, Markus; Döhler, Bernd; Ruhenstroth, Andrea; Haslacher, Helmuth; Perkmann, Thomas; Exner, Markus; Rees, Andrew J; Böhmig, Georg A

    2011-02-01

    Gene copy number of complement component C4, which varies among individuals, may determine the intrinsic strength of the classical complement pathway. Presuming a major role of complement as an effector in transplant rejection, we hypothesized that C4 genetic diversity may partially explain the variation in allograft outcomes. This retrospective study included 1969 deceased-donor kidney transplants randomly selected from the Collaborative Transplant Study DNA bank. We determined recipient and donor gene copy number of total C4, C4 isotypes (C4A and C4B), and C4 gene length variants (C4L and C4S) by quantitative real-time PCR analysis. Groups defined according to recipient C4 gene copy number (low, intermediate, and high) had similar 10-year allograft survival. Genotypic groups showed comparable rates of graft dysfunction, treatment for rejection, immunological graft loss, hospitalization for infection, malignant disease, and death. Similarly, separate analyses of C4A, C4B, C4L, and C4S; combined evaluation of donor and recipient C4 genotype; or analysis of recipients with higher risk for rejection did not reveal considerable outcome effects. In conclusion, we did not demonstrate that C4 gene copy number associates with transplant outcome, and we found no evidence that the resulting variation in the strength of classical complement activation influences susceptibility to rejection.

  17. Alcohol drinking, mean corpuscular volume of erythrocytes, and alcohol metabolic genotypes in drunk drivers.

    Science.gov (United States)

    Pavanello, Sofia; Snenghi, Rossella; Nalesso, Alessandro; Sartore, Daniela; Ferrara, Santo Davide; Montisci, Massimo

    2012-02-01

    Regular and irregular abuse of alcohol are global health priorities associated with diseases at multiple sites, including cancer. Mechanisms of diseases induced by alcohol are closely related to its metabolism. Among conventional markers of alcohol abuse, the mean corpuscular volume (MCV) of erythrocytes is prognostic of alcohol-related cancer and its predictivity increases when combined with functional polymorphisms of alcohol dehydrogenase (ADH1B [rs1229984] and ADH1C [rs698]) and the mitochondrial aldehyde dehydrogenase (ALDH2 [rs671]). Whether these genetic variants can influence abuse in alcohol drinking and MCV has never been examined in drunk-driving traffic offenders. We examined 149 drunk drivers, diagnosed as alcohol abusers according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth edition Text Revision (DSM-IV-TR) and enrolled in a probation program, and 257 social drinkers (controls), all Caucasian males. Alcohol intake was assessed according to self-reported drink-units/d and MCV unadjusted and adjusted for age, smoking, and body mass index. Multivariable models were used to compute MCV adjusted means. Genotype analyses were performed by PCR on DNA from blood. The adjusted MCV mean was higher in drunk-driving abusers than in controls (92 vs. 91fL; Palcohol drinking, and MCV enlargement. This suggests that drunk drivers with augmented MCV modulated by the alcohol metabolic ADH1B*1/*1 genotype may be at higher risk of driving incapability and of alcohol-related cancer.

  18. Genotype by energy expenditure interaction with metabolic syndrome traits: the Portuguese healthy family study.

    Science.gov (United States)

    Santos, Daniel M V; Katzmarzyk, Peter T; Diego, Vincent P; Souza, Michele C; Chaves, Raquel N; Blangero, John; Maia, José A R

    2013-01-01

    Moderate-to-high levels of physical activity are established as preventive factors in metabolic syndrome development. However, there is variability in the phenotypic expression of metabolic syndrome under distinct physical activity conditions. In the present study we applied a Genotype X Environment interaction method to examine the presence of GxEE interaction in the phenotypic expression of metabolic syndrome. A total of 958 subjects, from 294 families of The Portuguese Healthy Family study, were included in the analysis. Total daily energy expenditure was assessed using a 3 day physical activity diary. Six metabolic syndrome related traits, including waist circumference, systolic blood pressure, glucose, HDL cholesterol, total cholesterol and triglycerides, were measured and adjusted for age and sex. GxEE examination was performed on SOLAR 4.3.1. All metabolic syndrome indicators were significantly heritable. The GxEE interaction model fitted the data better than the polygenic model (pwaist circumference, systolic blood pressure, glucose, total cholesterol and triglycerides. For waist circumference, glucose, total cholesterol and triglycerides, the significant GxEE interaction was due to rejection of the variance homogeneity hypothesis. For waist circumference and glucose, GxEE was also significant by the rejection of the genetic correlation hypothesis. The results showed that metabolic syndrome traits expression is significantly influenced by the interaction established between total daily energy expenditure and genotypes. Physical activity may be considered an environmental variable that promotes metabolic differences between individuals that are distinctively active.

  19. Hepatitis C virus seroprevalence and genotypes in patients with diffuse connective tissue diseases and spondyloarthropathies

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    Barbosa V.S.

    2005-01-01

    Full Text Available Many extrahepatic manifestations, including rheumatic diseases, have been reported to be associated with hepatitis C virus (HCV infection. In order to investigate the prevalence of HCV infection among patients with rheumatic diseases, in the present study we interviewed 367 patients and tested their blood samples for HCV antibodies (anti-HCV by an enzyme-linked immunosorbent assay. Anti-HCV-reactive samples were retested for confirmation by a line immunoassay and also for HCV RNA detection by the polymerase chain reaction. HCV RNA-positive samples were genotyped by INNO-LIPA. An overall HCV infection prevalence of 1.9% (7/367 was found. Of the 7 HCV-infected patients, 4 had systemic lupus erythematosus and 3 rheumatoid arthritis, resulting in positivity rates of 2.3 and 3.4%, respectively. HCV RNA genotyping revealed the presence of subtypes 1a (57.1%, 1b (28.6% and 3a (14.3%. The clinical course was favorable for all HCV-infected patients, except one, who died due to renal insufficiency related to lupus nephritis. These results demonstrate a low HCV infection prevalence among the population studied. In the few positive cases, we observed no adverse influence of this infection on the clinical evolution of the rheumatic disease.

  20. Prior infection of pigs with a genotype 3 swine hepatitis E virus (HEV) protects against subsequent challenges with homologous and heterologous genotypes 3 and 4 human HEV.

    Science.gov (United States)

    Sanford, Brenton J; Dryman, Barbara A; Huang, Yao-Wei; Feagins, Alicia R; Leroith, Tanya; Meng, Xiang-Jin

    2011-07-01

    Hepatitis E virus (HEV) is an important human pathogen. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Genotypes 3 and 4 swine HEV is widespread in pigs and known to infect humans. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In this study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. The control group was inoculated and challenged with PBS buffer. Weekly sera from all pigs were tested for HEV RNA and IgG anti-HEV, and weekly fecal samples were also tested for HEV RNA. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia was not detected and only two pigs challenged with swine HEV had 1-week fecal virus shedding, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenges with homologous and heterologous genotypes 3 and 4 HEV. The results from this study have important implications for future development of an effective HEV vaccine.

  1. Epidemiology of HPV genotypes in Uganda and the role of the current preventive vaccines: A systematic review

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    Namujju Proscovia B

    2011-07-01

    Full Text Available Abstract Background Limited data are available on the distribution of human papillomavirus (HPV genotypes in the general population and in invasive cervical cancer (ICC in Uganda. Yet, with the advent of preventive HPV vaccines that target HPV 16 and 18 responsible for causing about 70% of ICC cases in the world, such information is crucial to predict how vaccination and HPV-based screening will influence prevention of ICC. Methods To review the distribution of HPV infection and prevalent genotypes, electronic databases (e.g. PubMed/MEDLINE and HINARI were searched for peer reviewed English articles on HPV infection up to November 30, 2010. Eligible studies were selected according to the following criteria: DNA-confirmed cervical or male genital HPV prevalence and genotypes, HPV incidence estimates and HPV seroprevalence among participants. Results Twenty studies were included in the review. Among HIV negative adult women, the prevalence of HR-HPV infections ranged from 10.2% -40.0% compared to 37.0% -100.0% among HIV positive women. Among HIV positive young women aged below 25 years, the prevalence of HR-HPV genotypes ranged from 41.6% -75.0% compared to 23.7% -67.1% among HIV negative women. Multiple infections with non vaccine HR-HPV genotypes were frequent in both HIV positive and HIV negative women. The main risk factors for prevalent HPV infections were age, lifetime number of sexual partners and HIV infection. Incident infections with HR-HPV genotypes were more frequent among adult HIV positive than HIV negative women estimated at 17.3 and 7.0 per 100 person-years, respectively. Similarly, incident HR-HPV among young women aged below 25 years were more frequent among HIV positive (40.0 per 100 person-years than HIV negative women (20.3 per 100 person-years women. The main risk factor for incident infection was HIV infection. HPV 16 and 18 were the most common genotypes in ICC with HPV 16/18 contributing up to 73.5% of cases with single

  2. Detection of genotype recycling fraud in U.S. immigrants.

    Science.gov (United States)

    Wenk, Robert E

    2011-01-01

    Relationship testing laboratories provide genetic evidence to support or refute claims of kinship between U.S. citizen petitioners and potential immigrant beneficiaries. One female beneficiary presented a male amelogenin type and alleles at 15 autosomal loci that were identical to an alleged brother's. Laboratory records showed that her alleged father had petitioned to have 15 children emigrate from Ghana. The petitioner's 15 paternity indices exceeded 10⁵, but the children shared only four short tandem repeat (STR) profiles, suggesting fraudulent reuse of genotypes in this alleged pedigree (AP). To determine the extent of this "genotype recycling," I examined the laboratory's 555 APs from Ghana and 532 control APs from Nigeria. Seventeen Ghanaian APs (3.1%) but no Nigerian APs showed genotype recycling. Of 90 tested people in the 17 APs, 56 shared identical STR profiles with others in their AP. Of these 56 people, 10 were petitioners with unexpectedly high parentage indices. Seven of 56 had amelogenin types that disagreed with their declared genders. Database searches for identical multilocus genotypes in allegedly different people would best detect this fraud.

  3. Speech Characteristics Associated with Three Genotypes of Ataxia

    Science.gov (United States)

    Sidtis, John J.; Ahn, Ji Sook; Gomez, Christopher; Sidtis, Diana

    2011-01-01

    Purpose: Advances in neurobiology are providing new opportunities to investigate the neurological systems underlying motor speech control. This study explores the perceptual characteristics of the speech of three genotypes of spino-cerebellar ataxia (SCA) as manifest in four different speech tasks. Methods: Speech samples from 26 speakers with SCA…

  4. Genotyping of FCN and MBL2 Polymorphisms Using Pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans Ole; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...

  5. Nutrient composition of strawberry genotypes cultivated in a horticulture farm.

    Science.gov (United States)

    Hossain, Ashrafi; Begum, Parveen; Salma Zannat, M; Hafizur Rahman, Md; Ahsan, Monira; Islam, Sheikh Nazrul

    2016-05-15

    This article decribes the nutrient composition of four strawberry genotypes cultivated at the Sher-e-Bangla Agriculture University horticulture farm in Dhaka (Bangladesh). AOAC and standard validated methods were employed to analyse the nutrient composition. Protein, fat and ash contents were found to be vary significantly (LSD<0.05), while the variation in moisture (LSD<1.33), dietary fibre (LSD<0.15) and total sugar (LSD<0.09) were found to be insignificant among the genotypes. Vitamin C content ranged from 26.46 mg to 37.77 mg per 100g edible strawberries (LSD<0.060). Amount of carotenoids were found to be very low being in a range of 0.99-3.30 μg per 100g edible fruit. Analysis of mineral revealed that strawberry genotypes contained a wide array of minerals including Ca, Mg, Na, K, P, Mn, Zn, Cu and Fe; most of which varied significantly (LSD<0.05) among the genotypes. Strawberries could be a potential dietary supplement for vitamin C along with minerals, particularly for the children who do not like local fruits, but love to eat the colourful strawberries.

  6. Genotypic characterization of amoeba isolated from Acanthamoeba keratitis in Poland.

    Science.gov (United States)

    Derda, Monika; Solarczyk, Piotr; Cholewiński, Marcin; Hadaś, Edward

    2015-03-01

    Free-living amoebae belonging to the genus Acanthamoeba are the causative factor of many diseases. Among others, they cause Acanthamoeba keratitis (AK), a condition that usually occurs in contact lens wearers, though it is also observed in non-wearers. The number of diagnosed cases of AK increased more than eightfold during 8 years in the USA, and a proportional increase in frequency also occurred in Poland and Europe. Cases of AK are usually diagnosed late, and their therapy is difficult and rarely successful. AK is an uncommon diagnosis in Poland. The increased number of positive cases observed in our laboratory may reflect the growing at-risk population of contact lens wearers. Acanthamoeba as a genus of facultative human parasites is currently classified into 17 genotypes. Isolates belonging to seven genotypes were found to be associated with AK. One genotype in particular, T4, was found to be overrepresented in human disease. The main finding of our study is that in Poland, AK is almost always associated with the T4 genotype.

  7. Genotype-phenotype associations in children with congenital hyperinsulinism

    DEFF Research Database (Denmark)

    Melikyan, Maria; Brusgaard, Klaus; Petraykina, Elena

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

  8. Surveillance for Echinococcus canadensis genotypes in Canadian ungulates.

    Science.gov (United States)

    Schurer, Janna; Shury, Todd; Leighton, Frederick; Jenkins, Emily

    2013-12-01

    The geographic and host distribution, prevalence and genotypes of Echinococcus canadensis in wild ungulates in Canada are des