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Sample records for ccl3l1-ccr5 genotype influences

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

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

    2008-01-01

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

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

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    Hemant Kulkarni

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

  3. Role of CCL3L1-CCR5 genotypes in the epidemic spread of HIV-1 and evaluation of vaccine efficacy.

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    Hemant Kulkarni

    Full Text Available BACKGROUND: Polymorphisms in CCR5, the major coreceptor for HIV, and CCL3L1, a potent CCR5 ligand and HIV-suppressive chemokine, are determinants of HIV-AIDS susceptibility. Here, we mathematically modeled the potential impact of these genetic factors on the epidemic spread of HIV, as well as on its prevention. METHODS AND RESULTS: Ro, the basic reproductive number, is a fundamental concept in explaining the emergence and persistence of epidemics. By modeling sexual transmission among HIV+/HIV- partner pairs, we find that Ro estimates, and concordantly, the temporal and spatial patterns of HIV outgrowth are highly dependent on the infecting partners' CCL3L1-CCR5 genotype. Ro was least and highest when the infected partner possessed protective and detrimental CCL3L1-CCR5 genotypes, respectively. The modeling data indicate that in populations such as Pygmies with a high CCL3L1 gene dose and protective CCR5 genotypes, the spread of HIV might be minimal. Additionally, Pc, the critical vaccination proportion, an estimate of the fraction of the population that must be vaccinated successfully to eradicate an epidemic was 1, to prevent epidemic spread, population groups defined by specific CCL3L1-CCR5 genotypes might require repeated vaccination, or as our models suggest, a vaccine with an efficacy of >70%. Further, failure to account for CCL3L1-CCR5-based genetic risk might confound estimates of vaccine efficacy. For example, in a modeled trial of 500 subjects, misallocation of CCL3L1-CCR5 genotype of only 25 (5% subjects between placebo and vaccine arms results in a relative error of approximately 12% from the true vaccine efficacy. CONCLUSIONS: CCL3L1-CCR5 genotypes may impact on the dynamics of the HIV epidemic and, consequently, the observed heterogeneous global distribution of HIV infection. As Ro is lowest when the infecting partner has beneficial CCL3L1-CCR5 genotypes, we infer that therapeutic vaccines directed towards reducing the infectivity

  4. The influence of temperature on photosynthesis of different tomato genotypes

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    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

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

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

    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.

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

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

    2012-01-01

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

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

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    E.M. Colin; 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

  8. 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.

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

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

  10. Influence of genotype on the quality of sheep leather

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    Manuel Antônio Chagas Jacinto

    2011-08-01

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

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

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

    2012-01-01

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

  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. 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.

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

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    Pierre Junca

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

  19. 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.

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

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

    2012-01-01

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

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

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

    2017-01-01

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

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

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    Sergio Henao Osorio

    2010-05-01

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

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

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

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

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    Mamta eSharma

    2016-03-01

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

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

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    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

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

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    Esther M Opmeer

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

  7. 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. PMID:27014287

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    Science.gov (United States)

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

    2016-04-01

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

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Cheryl L Peterson

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    OpenAIRE

    Sergio Henao Osorio; Johanna Aristizábal Galvis

    2010-01-01

    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 ...

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

    OpenAIRE

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2003-03-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    OpenAIRE

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

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Marija Uremović

    2003-12-01

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

  4. 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.

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

    Science.gov (United States)

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

    2016-07-01

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

  6. THE INFLUENCE OF GENOTYPE OF RAMS ON THE QUALITATIVE CHARACTERISTICS OF MEAT

    Directory of Open Access Journals (Sweden)

    Kolosov Y. A.

    2016-03-01

    Full Text Available The article presents the results of the qualitative assessment of meat of crossbred rams. The analysis of the data shows that crossbred rams of 2, 3 and 4 groups increased the absolute mass of muscle tissue compared with purebred 12.3; of 18.2 and 25.6%, respectively. Fine-wooled rams were superior in the relative content of bone in carcasses of crossbred 1.1- 4.2 percent. Output of pulp for 1 kg of bones had the advantage of crossbred rams 2, 3 and 4 groups compared with purebred 0.12; 0.24 percent and 0.44 kg respectively. The analysis of the data shows that in carcasses of young animals of all the groups the greatest specific weight took cuts of the 1st sort. Nevertheless, the valuable parts to carcass weight balance was higher in the carcasses of the crossbred calves. So, rams 2, 3 and 4 groups, this advantage was 1.9; 4.5 and 4.7%, respectively. Thus, the analysis of a complex of indicators characterizing the quality of meat rams of different genotypes revealed that the superiority for the studied indices took place for two - and three-bred animals. These options of both simple and complex industrial crossing are promising and can be implemented and used in the farms of Merino and crossbred sheep

  7. 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.

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

    Science.gov (United States)

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

    2011-07-01

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

  9. 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.

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

    OpenAIRE

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

    2009-01-01

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

  11. 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

  12. 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

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

    OpenAIRE

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

    2014-01-01

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

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

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    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.

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

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    Giovanni Bittante

    2013-09-01

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

  16. 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.

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

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    Vanessa Chaia Kaippert

    2013-06-01

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

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

    Science.gov (United States)

    Cherian, Mathew P

    2012-01-01

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

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

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    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.

  20. [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.

  1. 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.

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

    OpenAIRE

    Giovanni Bittante; Rina Verdiglione

    2013-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

  4. Pigeonpea genotypes influence parasitization preference and survival and development of the Helicoverpa armigera larval parasitoid, Campoletis chlorideae.

    Science.gov (United States)

    Hugar, Shiddalingappa V; Sharma, Hari C; Basavan Goud, Kondikallu

    2014-01-01

    Studies were undertaken to identify pigeonpea, Cajanus cajan (L.) Millspaugh and the wild relative of pigeonpea, Cajanus scarabaeoides (L.) (accession ICPW 125,) genotypes that are hospitable to the pod borer, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) larval parasitoid, Campoletis chlorideae Uchida (Hymenoptera: Ichneumonidae) for the management of this pest in pigeonpea based cropping systems. Percentage parasitization of the H. armigera larvae by the C. chlorideae females was greater under no-choice conditions than under multi-choice conditions because of forced parasitization under no-choice conditions. Lowest parasitization was recorded on the wild relative, ICPW 125, which may be due to long nonglandular hairs and low survival of H. armigera larvae. Parasitization of H. armigera larvae was greater under no-choice, dual-choice and/or multi-choice conditions on ICPL 87, ICPL 87119 and ICPL 87091, which are susceptible to H. armigera, than on the pod borer-resistant genotypes ICPL 332WR, ICPL 84060 and ICPB 2042; while survival and development of the parasitoid was better on H. armigera larvae fed on ICPL 87, ICPL 87119, LRG 41, ICP 7035 and ICPL 87091 than on ICPL 332WR, ICPL 84060, ICPB 2042 and ICPW 125. The genotypes ICPL 87, ICPL 87119, LRG 42 and ICPL 87091 that are hospitable to C. chloridae, are better suited for use in integrated pest management to minimize the losses due to H. armigera in pigeonpea. PMID:25110629

  5. Growth, carcass traits and palatability: can the influence of the feeding regimes explain the variability found on those attributes in different Uruguayan genotypes?

    Science.gov (United States)

    Brito, G; San Julián, R; La Manna, A; Del Campo, M; Montossi, F; Banchero, G; Chalkling, D; Soares de Lima, J M

    2014-11-01

    It is well known what genetic and nutritional factors affect growth and meat quality, but there is less information related to interactive importance of them during the productive process. These systems are mainly based on rangelands affecting animal growth in early stages of life thus producing smaller cattle and reduced retail yield comparing with well grown calves. During the last ten years, Uruguayan livestock production systems have been intensified using improved pastures, concentrates and better genetic. The main breeds in Uruguay are Hereford, Angus and their crosses. These British breeds are under genetic evaluation programs which consider carcass trait parameters. It is important for beef industry to know if interactions between genotype and nutrition during growth and fattening phases are influencing production, efficiency, carcass weight and meat quality attributes. The aim of this article is to present information obtained under different feeding strategies during the post weaning and fattening and their influence on those attributes. PMID:25048096

  6. 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

  7. 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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Benedikt Klauke

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

  11. 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.

  12. 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...

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. 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

  17. Fat mass and apolipoprotein E genotype influence serum lipoprotein levels in early adulthood, whereas birth size does not

    NARCIS (Netherlands)

    R.W.J. Leunissen (Ralph); G.F. Kerkhof (Gerthe); Th. Stijnen (Theo); A.C.S. Hokken-Koelega (Anita)

    2008-01-01

    textabstractBackground/Objectives: An association between an unfavorable lipid profile and low birth weight has been reported, although this association remains controversial. We hypothesized that birth size does not have any influence on serum lipid levels but fat accumulation during childhood has.

  18. 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.

  19. 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. PMID:18254590

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

    Science.gov (United States)

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

    1995-10-01

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

  1. 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

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-07-01

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

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

    Directory of Open Access Journals (Sweden)

    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

  5. 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

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Dylan B. Jackson

    2015-12-01

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

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

    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

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

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    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.

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

    Science.gov (United States)

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

    2006-09-01

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

  11. 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.

  12. ApoE genotype and familial Alzheimer's disease: a possible influence on age of onset in APP717 Val-->Ile mutated families.

    Science.gov (United States)

    Nacmias, B; Latorraca, S; Piersanti, P; Forleo, P; Piacentini, S; Bracco, L; Amaducci, L; Sorbi, S

    1995-01-01

    Recent studies have shown a genetic association of the apolipoprotein E (ApoE) epsilon 4 allele with late onset familial and sporadic Alzheimer's disease (AD). In this study we analysed the possible association of the genetic polymorphism of the ApoE gene with age of onset in Italian familial Alzheimer's disease (FAD) families including two early onset familial Alzheimer's (EOFAD) families with the APP717 Val-->Ile mutation in the amyloid precursor protein (APP) gene on chromosome 21. In none of the FAD families analysed was there a significant effect of the ApoE genotype on the age of onset with the exception of one of the two mutated EOFAD families in which the epsilon 2 allele delayed the age of onset. PMID:7746463

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

    Science.gov (United States)

    Bahreini, Rassol; Currie, Robert W

    2015-08-01

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

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Said Y ALkindi

    2015-10-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  17. 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

  18. 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.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Sabro Nielsen, P.

    1996-12-31

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

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

    Science.gov (United States)

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

    2016-06-01

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

  2. 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.

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

    Science.gov (United States)

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

  4. 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...

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

    OpenAIRE

    Roghieh Hajiboland; Naier Beiramzadeh

    2008-01-01

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

  6. 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....

  7. Influence of Genotype over Microtubers Production

    OpenAIRE

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

    2010-01-01

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

  8. Influence of Genotype over Microtubers Production

    Directory of Open Access Journals (Sweden)

    Andreea NISTOR

    2010-06-01

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

  9. 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....

  10. 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.

  11. Aphid and ladybird beetle abundance depend on the interaction of spatial effects and genotypic diversity.

    Science.gov (United States)

    Genung, Mark A; Crutsinger, Gregory M; Bailey, Joseph K; Schweitzer, Jennifer A; Sanders, Nathan J

    2012-01-01

    Intraspecific variation and genotypic diversity of host-plants can affect the structure of associated arthropod communities and the dynamics of populations. Similarly, neighboring plants can also affect interactions between host-plants and their associated arthropods. However, most studies on the effects of host-plant genotypes have largely ignored the potential effects of neighboring host-plants on arthropod communities. In this study, we used a common garden experiment to ask how spatial effects of neighboring patches, along with genotype identity and genotypic diversity in tall goldenrod (Solidago altissima), affect the abundances of a common goldenrod herbivore (Uroleucon nigrotuberculatum) and their dominant predator (Harmonia axyridis, a ladybird beetle). Aphid abundance varied 80-fold among genotypes, while ladybird beetle abundance was not affected by genotype identity. Additionally, there were strong effects of neighboring plots: aphid abundance in a focal plot was positively correlated to aphid abundance in nearby plots, suggesting strong spatial patterning in the abundance of aphids. Neither aphid nor ladybird beetle abundance was affected by genotypic diversity. However, focal plot genotypic diversity mediated the strength of the neighborhood effect (i.e., strong effects for genotype polyculture focal plots and weak effects for genotype monoculture focal plots). Our results show that aphids were directly influenced by host-plant genotype identity while ladybird beetles responded mainly to prey abundance, and suggest that genotypic diversity can influence the effects of spatial processes on the plant-herbivore interactions. PMID:21805301

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

    Directory of Open Access Journals (Sweden)

    Janaína Luz Narciso-Schiavon

    2010-06-01

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

  13. 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 availabil......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....

  14. 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

  15. Noise in Genotype Selection Model

    Institute of Scientific and Technical Information of China (English)

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

    2003-01-01

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

  16. 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.

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

    OpenAIRE

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

    2012-01-01

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

  18. Genotype Specification Language.

    Science.gov (United States)

    Wilson, Erin H; Sagawa, Shiori; Weis, James W; Schubert, Max G; Bissell, Michael; Hawthorne, Brian; Reeves, Christopher D; Dean, Jed; Platt, Darren

    2016-06-17

    We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility. PMID:26886161

  19. Current software for genotype imputation

    OpenAIRE

    Ellinghaus David; Schreiber Stefan; Franke Andre; Nothnagel Michael

    2009-01-01

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

  20. Personal genotypes are teachable moments

    OpenAIRE

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

    2013-01-01

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

  1. 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

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

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

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

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

    Science.gov (United States)

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

    2013-12-01

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

  4. Cerebral Hemorrhage and APOE genotype

    Institute of Scientific and Technical Information of China (English)

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

    2000-01-01

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

  5. 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.

  6. 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....

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

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  8. 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.

  9. 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...

  10. 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...

  11. 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

  12. 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.

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

    Science.gov (United States)

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

    2005-11-01

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

  14. 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.

  15. 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.

  16. Current software for genotype imputation

    Directory of Open Access Journals (Sweden)

    Ellinghaus David

    2009-07-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  18. 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

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

    Directory of Open Access Journals (Sweden)

    Nathalie Balandraud

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  2. 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.

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

    Science.gov (United States)

    Grettenberger, Ian M; Tooker, John F

    2016-09-01

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

  4. 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.

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

    Institute of Scientific and Technical Information of China (English)

    Mei Su; Xilong Zhang; Shicheng Su

    2009-01-01

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

  6. 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.

  7. 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

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

    OpenAIRE

    Amir Hossein SHIRANI RAD; ABBASIAN, Abouzar

    2011-01-01

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

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

    OpenAIRE

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

    2011-01-01

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

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

    OpenAIRE

    Hanna Bandurska; Halina Gniazdowska-Skoczek

    2014-01-01

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

  11. 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.

  12. 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.

  13. 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.

  14. Genome complexity reduction for SNP genotyping analysis

    OpenAIRE

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

    2002-01-01

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

  15. Parallel genotypic adaptation: when evolution repeats itself

    OpenAIRE

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

    2005-01-01

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

  16. Additional novel Cryptosporidium genotypes in ornamental fishes.

    Science.gov (United States)

    Morine, M; Yang, R; Ng, J; Kueh, S; Lymbery, A J; Ryan, U M

    2012-12-21

    Current knowledge on the prevalence and genotypes of Cryptosporidium in fishes is still limited. This study investigated the prevalence of Cryptosporidium species in 171 ornamental fishes, belonging to 33 species, collected from 8 commercial aquariums around Perth, Western Australia. All samples were screened by nested PCR targeting the 18S rRNA locus. A total of 6 positives were identified by PCR at the 18S locus from 4 different species of fishes (red eye tetra, Moenkhausia sanctaefilomenae; gold gourami, Trichogaster trichopterus; neon tetra, Paracheirodon innesi; goldfish, Carassius auratus auratus), giving an overall prevalence of 3.5% (6/171). Four different genotypes were identified, only one of which has been previously reported in fish; piscine genotype 4 in a neon tetra isolate, a rat genotype III-like isolate in a goldfish, a novel genotype in three isolates from red eye (piscine genotype 7) which exhibited a 3.5% genetic distance from piscine genotype 1 and a piscine genotype 6-like from a gold gourami (1% genetic distance). Further biological and genetic characterisation is required to determine the relationship of these genotypes to established species and strains of Cryptosporidium. PMID:22819587

  17. Hepatitis C virus genotypes in Myanmar

    Science.gov (United States)

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

    2016-01-01

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

  18. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

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

    2015-01-01

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

  19. Genotyping and surveillance for scrapie in Finnish sheep

    Directory of Open Access Journals (Sweden)

    Hautaniemi Maria

    2012-07-01

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

  20. 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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Qureshi Huma

    2007-11-01

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

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

    OpenAIRE

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

    1993-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

    Objective: The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. Methods: One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Results: Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. Conclusion: The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required. PMID:26649001

  5. 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.

  6. 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....

  7. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Seliussen Bjørghild B

    2011-04-01

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

  10. 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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  13. 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.

  14. 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.

  15. Effect of chronic radiation on rape genotype formation

    International Nuclear Information System (INIS)

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

  16. 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

  17. 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.

  18. 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.

  19. Naturally occurrisng and induced genotypes of high lysine sorghum

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Amy J Schuh

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

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

    OpenAIRE

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

    2007-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ali Ijaz

    2011-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

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

  4. 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,...

  5. 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....

  6. 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...

  7. 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.

  8. Multiple Centroid Methodology to analyze genotype adaptability

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2009-01-01

    Full Text Available This study was carried out to propose a modification of the centroid method. The method is modified in thechoice of the ideotype, to be defined according to the researcher's interest, using the bi-segmented regression model, ratherthan based on experimental data, which limit the comparison of genotypes. To illustrate the method, one trait was simulatedin 25 genotypes in 8 environments. For the simulations and statistical analyses the software package GENES was used. Themultiple centroid is more flexible than the original centroid method, since it can be used according to the researcher's objectiveand the desired recommendation strategy. It is also readily interpretable for recommendation and unambiguous. Besides, thenumber of genotypes of interest can be compared, making a detailed study possible, by separating the genotypes intorecommendation classes.

  9. Drought Resistance in Bread Wheat Genotypes

    OpenAIRE

    ÖZTÜRK, Ali

    1998-01-01

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

  10. HCV genotyping using statistical classification approach

    Directory of Open Access Journals (Sweden)

    Norris Ellie D

    2009-07-01

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

  11. 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.

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

    Science.gov (United States)

    Ruta, Simona; Cernescu, Costin

    2015-10-14

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

  13. 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

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

    Science.gov (United States)

    Wang, Wei-Bung; Jiang, Tao

    2011-04-01

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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    Bohinc Tanja

    2014-01-01

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

  17. 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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Objective. This study aimed to determine if the activity of the environmentally influenced cytochrome P450 enzyme CYP1A2, alone or in combination with CYP2D6*4 genotype, discriminates subgroups of oral lichen planus (OLP) according to lifestyle factors and clinical manifestations. Study Design. A...

  1. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

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

  2. 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.

  3. 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.

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

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2012-10-01

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

  6. 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.

  7. 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.

  8. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna

    2013-01-01

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

  9. 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

  10. Differential Genotypic Responses of String Wheat Early Seedling Growth to Limited Moisture Conditions

    Directory of Open Access Journals (Sweden)

    Boubaker, M.

    1995-01-01

    Full Text Available The objective of this study was to measure the genotypic response of spring wheat seedling growth in a range of osmotic media and to determine which genotype could be identified as drought tolerant. Six durum wheat cultivars were subjected to moisture stress using polyethylene glycol PEG-9000. Aqueous solutions of 0, -3, -6 and -9 bars were prepared. For each cultivar 20 seeds were germinated in these solutions in a growth chamber. After 2 weeks, number of roots, leaf number, coleoptile length, seedling height, root length, first and second leaf length, and dry matter weight were measured. All traits measured were significantly influenced by water stress. The water stress treatments of -6 and -9 bars gave lower rates of seedling growth than the 0 and -3 bars treatments. The results suggest that good seedling vigor under water stress condition is a useful selection criterion. An ideotype for a drought tolerant wheat genotype should have good seedling vigor.

  11. 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

  12. 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

  13. 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

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

    Institute of Scientific and Technical Information of China (English)

    陈冰; 蔡卫民

    2003-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Fernanda Salamoni Becker

    2014-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Zhihui Zhang

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

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

    Directory of Open Access Journals (Sweden)

    Myo Nyein Aung

    2010-01-01

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

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

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2014-01-01

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

  19. 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.

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

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    Dinu Gavojdian

    2014-05-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2011-05-01

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

  7. 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

  8. 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.

  9. Carbon isotope fractionation for cotton genotype selection

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    Giovani Greigh de Brito

    2014-09-01

    Full Text Available The objective of this work was to evaluate the carbon isotope fractionation as a phenomic facility for cotton selection in contrasting environments and to assess its relationship with yield components. The experiments were carried out in a randomized block design, with four replicates, in the municipalities of Santa Helena de Goiás (SHGO and Montividiu (MONT, in the state of Goiás, Brazil. The analysis of carbon isotope discrimination (Δ was performed in 15 breeding lines and three cultivars. Subsequently, the root growth kinetic and root system architecture from the selected genotypes were determined. In both locations, Δ analyses were suitable to discriminate cotton genotypes. There was a positive correlation between Δ and seed-cotton yield in SHGO, where water deficit was more severe. In this site, the negative correlations found between Δ and fiber percentage indicate an integrative effect of gas exchange on Δ and its association with yield components. As for root robustness and growth kinetic, the GO 05 809 genotype performance contributes to sustain the highest values of Δ found in MONT, where edaphoclimatic conditions were more suitable for cotton. The use of Δ analysis as a phenomic facility can help to select cotton genotypes, in order to obtain plants with higher efficiency for gas exchange and water use.

  10. 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.

  11. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

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

    2016-04-01

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

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

    International Nuclear Information System (INIS)

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

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

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    Luciana Rodrigues

    2011-12-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  15. 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....

  16. 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.

  17. Silhouette scores for assessment of SNP genotype clusters

    OpenAIRE

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

    2005-01-01

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

  18. Micropropagation of six Paulownia genotypes through tissue culture

    OpenAIRE

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

    2014-01-01

    We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline), P. elongata and hybrid line P. elongata P. fortunei). Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seed...

  19. CYP2D6 genotype dependent oxycodone metabolism in postoperative patients.

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    Ulrike M Stamer

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

  20. Genotyping of Chlamydia trachomatis by Microsphere Suspension Array▿

    OpenAIRE

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

    2008-01-01

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

  1. 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...

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

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

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

  3. 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...

  4. Genotyping-by-Sequencing in Plants

    Directory of Open Access Journals (Sweden)

    Gregory D. May

    2012-09-01

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

  5. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  7. 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.

  8. 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.

  9. 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.

  10. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

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

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

    Directory of Open Access Journals (Sweden)

    Giovanni Barosi

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

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

    OpenAIRE

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

    2011-01-01

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

  13. 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.

  14. Impact of apolipoprotein E genotype variation on means, variances, and correlations of plasma lipid, lipoprotein, and apolipoprotein traits in octogenarians

    Energy Technology Data Exchange (ETDEWEB)

    Haviland, M.B.; Sing, C.F. [Univ. of Michigan, Ann Arbor, MI (United States); Lussier-Cacan, S.; Davignon, J. [Clinical Research Inst. of Montreal (Canada)

    1995-09-25

    The impact of apolipoprotein (apo) E genotype variation on means, variances and correlations between plasma lipid traits was studied in male and female octogenarians. Females had significantly higher mean levels of all 10 of the measured plasma lipid traits than males. The subset of concomitants (i.e., age, height, weight, body mass index, glucose and uric acid) that made a statistically significant contribution to interindividual variability was different in males and females for every trait considered. Gender-specific associations between variation in apo E genotype and variation in particular measures of lipid metabolism, adjusted for concomitant variation, were observed: in females there were no statistically significant associations while in males the means of the three common apo E genotypes were significantly different for adjusted measures of total cholesterol, low density lipoprotein cholesterol and low density lipoprotein-apo B. The common apo E genotypes were heterogeneous with respect to intragenotypic variance for adjusted log-transformed triglyceride levels in females only. Finally, the three common apo E genotypes were heterogeneous with respect to the correlation between traits, adjusted for concomitant variation, and gender influenced the manner in which the genotypes differed for specific correlations. This study documents that variation in the apo E gene has a significant impact on means, variances and correlations of plasma lipid traits in octogenarians, but the effects are context-, that is, gender- and age-, dependent. 65 refs., 4 figs., 3 tabs.

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

    OpenAIRE

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

    2012-01-01

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

  16. CYP2D6 genotype and phenotype relationship in South Indians

    Directory of Open Access Journals (Sweden)

    Naveen A

    2006-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Feng Lin

    2015-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

  19. 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

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

    Science.gov (United States)

    Voss-Fels, Kai; Snowdon, Rod J

    2016-04-01

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

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

    Directory of Open Access Journals (Sweden)

    K. Yanar

    2016-01-01

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

  2. 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.

  3. 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.

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

    Science.gov (United States)

    Yanar, K; Çakatay, U; Aydın, S; Verim, A; Atukeren, P; Özkan, N E; Karatoprak, K; Cebe, T; Turan, S; Ozkök, E; Korkmaz, G; Cacına, C; Küçükhüseyin, O; Yaylım, İ

    2016-01-01

    Nitric oxide synthase (eNOS/NOS3) is responsible for the endothelial synthesis of nitric oxide (NO(•)). G894T polymorphism leads to the amino acid substitution from Glu298Asp that causes lower NOS3 activity and basal NO(•) production in NOS3 894T (298Asp) allele carriers compared with the GG homozygotes. NO(•) acts as an antioxidant protecting against Fenton's reaction which generates highly reactive hydroxyl radicals. Allelic variation of NOS3 may influence an individual's risk of laryngeal cancer (LC). In the current study we have examined the possible relationship between NOS3 G894T genotypes and various systemic oxidative damage markers such as protein carbonyl, advanced oxidation protein products, Cu, Zn-superoxide dismutase, thiol group fractions, and lipid hydroperoxides in LC patients. Genotyping was carried out by PCR-RFLP. In LC patients with TT genotype, Cu, Zn-superoxide dismutase activities and nonprotein thiol levels were significantly higher than the controls. In patients with GT and GG genotype, high levels of lipid hydroperoxides showed statistical significance when compared to controls. Our results indicate a potential relationship among G894T polymorphism of NOS3, and impaired redox homeostasis. Further studies are required to determine the role of NOS3 gene polymorphism and impaired plasma redox homeostasis. PMID:26682008

  5. 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.

  6. 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. PMID:26655153

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

    Directory of Open Access Journals (Sweden)

    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.

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

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    Miklós Bálint

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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. Geographic distribution of hepatitis C virus genotypes in Brazil

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    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.

  15. Noninvasive fetal RhD genotyping

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  16. 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).

  17. 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.

  18. 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).

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

    Institute of Scientific and Technical Information of China (English)

    王芳芳; 尤崇革; 李光迪; 潘云燕; 郜莉娜; 李菲菲

    2011-01-01

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

  20. 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.

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

    OpenAIRE

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

    2013-01-01

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

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

    OpenAIRE

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

    2013-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

  4. Antioxidant capacity of anthocyanins from acerola genotypes

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Arroxelas Galvão De Lima

    2011-03-01

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

  5. Noninvasive fetal RhD genotyping.

    Science.gov (United States)

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

    2014-04-01

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

  6. 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.

  7. Selection of red raspberry genotypes (Rubus idaeus L.)

    OpenAIRE

    Fotirić Milica; Nikolić Mihailo; Milivojević Jasminka; Nikolić Dragan 2

    2009-01-01

    Pomological properties of seedlings obtained by open pollination of Meeker's yellow clone were investigated. From over a 100 seedlings obtained from this progeny, 16 genotypes with red fruits were selected on the Experimental Station 'Radmilovac' that belongs to the Faculty of Agriculture in Belgrade. Dunnett-test was used for single testing of physical and chemical traits of raspberry genotypes. It was found that majority of selected genotypes were in t...

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

    Science.gov (United States)

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

    2016-01-01

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

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Tofig Allahverdiyev

    2015-04-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Science.gov (United States)

    Minihane, Anne Marie

    2016-03-01

    At a population level, cardioprotective and cognitive actions of the fish oil (FO) derived long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been extensively demonstrated. In addition to dietary intake, which is limited for many individuals, EPA and DHA status is dependent on the efficiency of their biosynthesis from α-linolenic acid. Gender and common gene variants have been identified as influencing the rate-limiting desaturase and elongase enzymes. Response to a particular intake or status is also highly heterogeneous and likely influenced by genetic variants which impact on EPA and DHA metabolism and tissue partitioning, transcription factor activity, or physiological end-point regulation. Here, available literature relating genotype to tissue LC n-3 PUFA status and response to FO intervention is considered. It is concluded that the available evidence is relatively limited, with much of the variability unexplained, though APOE and FADS genotypes are emerging as being important. Although genotype × LC n-3 PUFA interactions have been described for a number of phenotypes, few have been confirmed in independent studies. A more comprehensive understanding of the genetic, physiological and behavioural modulators of EPA and DHA status and response to intervention is needed to allow refinement of current dietary LC n-3 PUFA recommendations and stratification of advice to "vulnerable" and responsive subgroups. PMID:26950146

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

    Science.gov (United States)

    Liebe, Sebastian; Varrelmann, Mark

    2016-01-01

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

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

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    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.

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

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    Ana Marjanović-jeromela

    2008-12-01

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

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

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    Elcio Santos

    2015-06-01

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

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

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    Nikolić Nataša P.

    2010-01-01

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

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

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    Humphries Steve E

    2008-08-01

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

  1. 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.

  2. Belief propagation in genotype-phenotype networks.

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  4. 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

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

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    Jiban Shrestha

    2013-06-01

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

  6. Dysregulation Of Innate Immunity In HCV Genotype 1 IL28B Unfavorable Genotype Patients: Impaired Viral Kinetics And Therapeutic Response

    Science.gov (United States)

    Naggie, Susanna; Osinusi, Anu; Katsounas, Antonios; Lempicki, Richard; Herrmann, Eva; Thompson, Alexander J; Clark, Paul J; Patel, Keyur; Muir, Andrew J; McHutchison, John G; Schlaak, Joerg F; Trippler, Martin; Shivakumar, Bhavana; Masur, Henry; Polis, Michael A.; Kottilil, Shyam

    2012-01-01

    Recent studies have shown that a single nucleotide polymorphism upstream of the interleukin (IL)-28B gene plays a major role in predicting therapeutic response in HCV-infected patients treated with pegylated interferon-alpha (IFN)/ribavirin. We sought to investigate the mechanism of the IL28B polymorphism, specifically as it relates to early HCV viral kinetics (VK), IFN pharmacokinetics (PK), IFN pharmacodynamics (PD), and gene expression profiles. Two prospective cohorts (HIV/HCV co-infected and HCV mono-infected) completing treatment with IFN/ribavirin were enrolled. Patients (N=88; 44 HIV/HCV and 44 HCV) were genotyped at the polymorphic site rs12979860. In the HIV/HCV cohort frequent serum sampling was completed for HCV RNA and IFN-levels. DNA microarray of PBMCs and individual expression of interferon stimulated genes (ISGs) were quantified on IFN-therapy. The IL28B favorable (CC) genotype was associated with improved therapeutic response compared to unfavorable (CT/TT) genotypes. Patients with favorable genotype had greater first and second phase VK (P=0.004 and P=0.036, respectively), IFN maximum anti-viral efficiency (P=0.007) and infected cell death loss (P=0.009) compared to unfavorable genotypes. Functional annotation analysis of DNA microarray data was consistent with depressed innate immune function, particularly of NK cells, from patients with unfavorable genotypes (P<0.004). Induction of innate immunity genes was also lower in unfavorable genotype. ISG expression at baseline and induction with IFN was independent of IL28B genotype. Conclusions Carriers of the IL28B favorable genotype were more likely to have superior innate immune response to IFN-therapy compared to unfavorable genotypes, this suggests the unfavorable genotype has aberrant baseline induction of innate immune response pathways resulting in impaired virologic response. IL28B genotype is associated with more rapid viral kinetics and improved treatment response outcomes independent of

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

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

    2015-06-01

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

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

    OpenAIRE

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

    2005-01-01

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

  9. SNP GENOTYPING BY TAQMAN ALLELE DISCRIMINATION TECHNIQUE

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    Lucian Negura

    2015-07-01

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

  10. A new genotype of Arthroderma benhamiae.

    Science.gov (United States)

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

    2008-11-01

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

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

    International Nuclear Information System (INIS)

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

  12. 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.

  13. 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.

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

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    V. Re

    2003-06-01

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

  15. Within-population genetic diversity of Taraxacum officinale (Asteraceae): differential genotype response and effect on interspecific competition.

    Science.gov (United States)

    Vavrek, M

    1998-07-01

    Clonal offspring of five morphologically distinct individuals of Taraxacum officinale were planted in a greenhouse experiment with each of three competitors, Plantago major, Poa pratensis and Trifolium pratense. The competitors were chosen to represent a series of competitive environments experienced by a natural population of T. officinale through the year. Differences in size, morphology, and response to the competitive environments were found among clones and support classification of the five individuals as distinct genotypes. Both differential competitive responses (alteration in performance) and competitive effects (impediment by competitor performance) were exhibited among genotypes. The differential response by the T. officinale genotypes to the competitors indicates that the biotic environment may influence the genetic structure of a population. The biotic environment in this case is determined by the sequential appearance and dominance of competitors in a field rather than the spatial distribution of these competitors. Since competitors change in relative dominance across seasons, competition is likely to be a component of the genotype by season interaction that had been observed in the natural population. Thus, differential responses among genotypes to a temporally and spatially fluctuating biotic environment may contribute to the maintenance of within-population genetic diversity. PMID:21684978

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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...

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

    Science.gov (United States)

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

  2. 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.

  3. 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....

  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...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  5. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

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

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    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.

  8. HCV prevalence and predominant genotype in IV drug users

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    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.

  9. 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.

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Fotirić Milica

    2009-01-01

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

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

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    Dekkers Jack CM

    2006-11-01

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

  13. 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.

  14. 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

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  18. 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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. 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.

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

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    Louis Grandjean

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

  4. Epistatic effect of APP717 mutation and apolipoprotein E genotype in familial Alzheimer's disease.

    Science.gov (United States)

    Sorbi, S; Nacmias, B; Forleo, P; Piacentini, S; Latorraca, S; Amaducci, L

    1995-07-01

    We found a new familial Alzheimer's disease kindred in which the disease cosegregates with the APP717Val-->Ile mutation and in which all of the three most common apolipoprotein E (ApoE) alleles are represented. We studied the relationship between ApoE genotype and the clinical expression of the disease and found that in this amyloid precursor protein-mutated family, ApoE genotype influences the age at onset of the disease. Three mutated subjects heterozygous for the epsilon 4 allele had the earliest age at onset in this family, subjects heterozygous for the epsilon 2 allele had the latest age at onset, and subjects homozygous for the epsilon 3 allele had an intermediate age at onset. In this large kindred we also found an amyloid precursor protein-mutated subject 2.4 standard deviations older than the mean age at onset without clinical signs and symptoms of the disease and carrying the epsilon 2/epsilon 3 genotype. PMID:7611715

  5. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  7. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato.

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    Jan G A M L Uitdewilligen

    Full Text Available Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect. This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1-3 511. Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107 was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60-80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with

  8. 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.

  9. Biological variation in Trichinella species and genotypes.

    Science.gov (United States)

    Bolas-Fernández, F

    2003-06-01

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

  10. 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.

  11. Clinical severity of Mycoplasma pneumoniae (MP infection is associated with bacterial load in oropharyngeal secretions but not with MP genotype

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    Widell Anders

    2010-02-01

    patients, but MP genotype did not influence disease severity. Both MP genotypes co-circulated during recent outbreaks in Sweden.

  12. 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.

  13. 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.

  14. 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

  15. The Impact of CYP2D6 Genotyping on Tamoxifen Treatment

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    Roberta Ferraldeschi

    2010-04-01

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

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  17. 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.

  18. 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

  19. Genotyping of Staphylococcus aureus strains isolated from healthy persistent carriers.

    Science.gov (United States)

    Grzegorczyk, Agnieszka; Malm, Anna

    2014-07-01

    The paper presents results on the relatedness of Staphylococcus aureus strains colonizing the upper respiratory tract isolated from healthy persistent carriers. Genotyping was carried out using two methods--multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and pulsed-field gel electrophoresis (PFGE). By comparison of the results obtained by both methods, good correlations between MLVF and PFGE genotyping of strains isolated from the asymptomatic carriers were observed. Further studies are needed to evaluate methods useful for genotyping of S. aureus strains circulating in the community. PMID:24488811

  20. Genotype networks, innovation, and robustness in sulfur metabolism

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    Wagner Andreas

    2011-03-01

    Full Text Available Abstract Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes

  1. SCREENING OF RICE GENOTYPES FOR THERMOTOLERANCE BY TIR TECHNIQUE

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    K. Renuka Devi

    2013-12-01

    Full Text Available Production of rice--the world's most important crop for ensuring food security and addressing poverty will be defeated as temperatures increase in rice-growing areas with continued climate change. Climate change needs us to look at various alternatives for more drought tolerant and tougher strains and to develop a technique to screen a large number of genotypes for high temperature tolerance. Adapting temperature induction response (TIR technique 100 rice genotypes were screened for thermotolerance. Significant variation for acquired thermotolerance was observed in 100 rice lines. From the 100 genotypes 30 were exhibits themotolerance to induced high temperature.

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

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    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

  3. Evaluation of linear array human papillomavirus genotyping using automatic optical imaging software.

    Science.gov (United States)

    Jeronimo, J; Wentzensen, N; Long, R; Schiffman, M; Dunn, S T; Allen, R A; Walker, J L; Gold, M A; Zuna, R E; Sherman, M E; Wacholder, S; Wang, S S

    2008-08-01

    Variations in biological behavior suggest that each carcinogenic human papillomavirus (HPV) type should be considered individually in etiologic studies. HPV genotyping assays might have clinical applications if they are approved for use by the FDA. A widely used genotyping assay is the Roche Linear Array HPV genotyping test (LA). We used LA to genotype the HPV isolates from cervical specimens from women with the full spectrum of cervical disease: cervical cancer, cervical intraepithelial neoplasia (CIN), and HPV infections. To explore the feasibility and value of the automated reading of the LA results, we custom-designed novel, optical imaging software that provides optical density measurements of LA bands. We compared unmagnified visual examination with the automated measurements. The two measurements were highly associated. By either method, the threshold between a negative and a positive result was fairly sharp, with a clear bimodal distribution. Visually, most positive results were judged to be strong or medium, with fewer equivocal results categorized as weak (9.5% of positive samples), very weak (6.5% of positive samples), or extremely weak (7.7% of positive samples). The automated measurements of the intensities were significantly associated with the strength of the visual categories (P or = 120 units), the bands were almost always categorized visually as negative and positive, respectively. In the equivocal zone (20 to 119 units), specimens were more increasingly likely to be judged to be visually positive as the number of other, definite infections on the same strip increased (P for trend or = 25% of HPV infections; thus, any systematic visual tendency that influences their evaluation when the result is equivocal should be minimized. Therefore, automated reading is probably worth development if easy-to-calibrate hardware and software can be optimized. PMID:18550741

  4. 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.

  5. 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.

  6. Effects of genotype and stocking density on broiler performance under three feeding regimes.

    Science.gov (United States)

    Ligaraba, Tshililo Joyce; Benyi, Kow; Baloyi, Joseph Jumu

    2016-08-01

    Ross 308 and Cobb Avian 48 broilers were used in a 49-day study. The effects of genotype, stocking density, and limited-time feeding on growth performance and carcass characteristics were investigated. Overall, Ross consumed more feed, gained more body weight, and was heavier at marketing age than Cobb. Ross also had a higher drumstick percentage, but the percentages of the other carcass parts were similar in the two genotypes. Birds reared at the stocking density of 30 kg BW/m(2) gained more body weight and were heavier at marketing than those raised at 40 kg BW/m(2), but both groups consumed similar quantities of feed and had similar carcass percentages. Neither genotype nor stocking density influenced feed conversion ratio and mortality rate, but genotype x stocking density interaction significantly affected feed consumption and mortality rate. The feed-restricted birds consumed less feed, gained less weight, were lighter at market age, and had lower percentages of breast, neck, and heart than the full-fed birds. Feed restriction also significantly lowered mortality rate but had insignificant effects on feed conversion ratio and percentages of carcass, breast, back, drumstick, neck, wing, gizzard, heart, liver, and abdominal fat. For profitable poultry production in the tropics and subtropics, it is recommended that Ross 308 raised at the stocking density of 30 kg BW/m(2) and subjected to 10-h daily feed removal from 7 to 35 days of age in a 49-day production period be considered. PMID:27221242

  7. 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.

  8. Hepatitis E Virus Genotype 3 in Sewage and Genotype 1 in Acute Hepatitis Cases, Israel.

    Science.gov (United States)

    Ram, Daniela; Manor, Yossi; Gozlan, Yael; Schwartz, Eli; Ben-Ari, Ziv; Mendelson, Ella; Mor, Orna

    2016-07-01

    Hepatitis E virus (HEV) is an emerging infectious agent in developed countries. HEV genotypes 1 (G1) and 3 (G3) have been identified in environmental and clinical samples in Europe. In Israel, the overall prevalence of anti-HEV IgG antibodies was found to be 10.6%; however, reports of HEV infection are scarce. In this study, the presence of HEV in Israel was investigated using 169 sewage samples from 32 treatment facilities and 49 samples from acute hepatitis patients, all collected between 2013 and 2015. Fourteen sewage samples, from Haifa (11/18 samples), Tel Aviv (2/29 samples), and Beer Sheva (1/17 samples), regions with good sanitary conditions and middle-high socioeconomic populations, were HEV positive. Among the patient samples, 6.1% (3/49) were HEV positive, all returning travelers from India. Genotype analysis revealed G1 HEV in patients and G3 HEV sequences in sewage. Evidence that HEV could be establishing itself in our region may justify more active surveillance to monitor its spread. PMID:27246446

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro

    2013-09-01

    Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

  14. 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.

  15. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  16. 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...

  17. Hepatitis E virus genotype 3 in wild rats, United States.

    Science.gov (United States)

    Lack, Justin B; Volk, Kylie; Van Den Bussche, Ronald A

    2012-08-01

    The role of rodents in the epidemiology of zoonotic hepatitis E virus (HEV) infection has been a subject of considerable debate. Seroprevalence studies suggest widespread HEV infection in commensal Rattus spp. rats, but experimental transmission has been largely unsuccessful and recovery of zoonotic genotype 3 HEV RNA from wild Rattus spp. rats has never been confirmed. We surveyed R. rattus and R. norvegicus rats from across the United States and several international populations by using a hemi-nested reverse transcription PCR approach. We isolated HEV RNA in liver tissues from 35 of 446 rats examined. All but 1 of these isolates was relegated to the zoonotic HEV genotype 3, and the remaining sequence represented the recently discovered rat genotype from the United States and Germany. HEV-positive rats were detected in urban and remote localities. Genetic analyses suggest all HEV genotype 3 isolates obtained from wild Rattus spp. rats were closely related. PMID:22840202

  18. Genotype by Environment Interactions in Cognitive Ability: A Survey of 14 Studies from 4 Countries covering 4 Age Groups

    OpenAIRE

    Molenaar, Dylan; Van der Sluis, Sophie; Boomsma, Dorret I.; Haworth, Claire M. A.; Hewitt, John K.; Martin, Nicholas G.; Plomin, Robert; Wright, Margie J; Dolan, Conor V.

    2013-01-01

    A large part of the variation in cognitive ability is known to be due to genetic factors. Researchers have tried to identify modifiers that influence the heritability of cognitive ability, indicating a genotype by environment interaction (GxE). To date, such modifiers include measured variables like income and socioeconomic status. The present paper focuses on GxE in cognitive ability where the environmental variable is an unmeasured environmental factor that is uncorrelated in family members...

  19. Maternal depressive history, teen 5HTTLPR genotype, and the processing of emotional faces: Exploring mechanisms of risk

    OpenAIRE

    Jacobs, Rachel H.; Pine, Daniel S.; Schoeny, Michael E.; Henry, David B.; Gollan, Jackie K; Moy, Gregory; Cook, Edwin H.; Wakschlag, Lauren S.

    2010-01-01

    Variations in the serotonin transporter gene (5HTTLPR) and biased processing of face-emotion displays both have been implicated in the transmission of depression risk, but little is known about developmental influences on these relationships. Within a community sample of adolescents, we examine whether 5HTTLPR genotype moderates the link between maternal depressive history and errors in face-emotion labeling. When controlling for current levels of depression and anxiety among youth, a two-way...

  20. EFFECT OF DROUGHT STRESS ON SOME PHYSIOLOGICAL TRAITS OF DURUM (TRITICUM DURUM DESF.) AND BREAD (TRITICUM AESTIVUM L.) WHEAT GENOTYPES

    OpenAIRE

    Tofig Allahverdiyev

    2015-01-01

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

  1. Increased plasma membrane cholesterol in cystic fibrosis cells correlates with CFTR genotype and depends on de novo cholesterol synthesis

    OpenAIRE

    Sonawane Nitin D; Previs Stephen F; Jiang Dechen; Ruddy Jennifer; Manson Mary E; West Richard H; Fang Danjun; Burgess James D; Kelley Thomas J

    2010-01-01

    Abstract Background Previous observations demonstrate that Cftr-null cells and tissues exhibit alterations in cholesterol processing including perinuclear cholesterol accumulation, increased de novo synthesis, and an increase in plasma membrane cholesterol accessibility compared to wild type controls. The hypothesis of this study is that membrane cholesterol accessibility correlates with CFTR genotype and is in part influenced by de novo cholesterol synthesis. Methods Electrochemical detectio...

  2. 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.

  3. 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.

  4. Genotypic differences in phosphate nutrition of rice (Oryza Sativa L.)

    International Nuclear Information System (INIS)

    Phosphate uptake and use by five genotypes of paddy rice were studied at five phosphate levels in pot studies for 49 days. For all five P levels there were marked genotypic differences in shoot growth, plant dry weight, root/shoot ratios, phosphate uptake and translocation, P content of roots and shoots, and phosphorus use efficiency of shoots (PUE, g shoot mg P-1 in shoot). There were significant genotypic differences in root weight (4 P levels) and in uptake/mg root (all P levels). These latter may have resulted from differences in root weight/root length conversion, root hair development or uptake characteristics, factors which were not studied specifically. Differences between genotypes and P levels in the percentage translocation were partly explicable by differences in P uptake/plant (r = 0.72) but especially by differences in root/shoot ratios (r = 0.89). Differences in PUE were largely a factor of P percentage of the tops (r = 0.94) but significant differences between genotypes were shown as a function of % P. Differences in net photosynthesis rates were largely, but not entirely, due to differences in P % of the shoots. Key factors in P uptake and use and genotypic differences are root growth, uptake/mg root, root/shoot ratios and PUE. (author). 9 refs, 2 figs, 3 tabs

  5. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  6. Genotyping of Rotavirus by Using RT-PCR Methods

    Directory of Open Access Journals (Sweden)

    Hera Nirwati

    2015-11-01

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

  7. 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.

  8. 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.

  9. 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

  10. Forage yield and nitrogen nutrition dynamics of warm-season native forage genotypes under two shading levels and in full sunlight

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    Raquel Santiago Barro

    2012-07-01

    Full Text Available The successful achievement of a highly productive understorey pasture in silvopastoral systems depends on the use of well-adapted forage genotypes, showing good agronomic performance and persistence under shading and grazing. In this study, the herbage dry matter yield (DMY and nitrogen nutrition dynamics were determined in three native warm-season grasses (Paspalum regnellii, Paspalum dilatatum and Paspalum notatum and a forage legume (Arachis pintoi under two shading levels compared with full sun. The experiment was conducted in the Campanha region, Bagé, state of Rio Grande do Sul, Brazil, during two evaluation cycles (2008/2009 and 2009/2010. Three shade cloth levels (0%, 50% and 80% of light restriction were applied to the forage genotypes in a split plot design, in which shading levels were the main plot and forage genotypes were the subplots, with three replications. P. regnellii showed the highest accumulated DMY (1500 and 1700 g m-2, respectively, for the first and second evaluation cycles at all shading levels and showed no DMY decreased under the heavy shade (80%. Average DMY over the four genotypes under the 50% shade level was higher or equal compared with full sun. Influence of rainfall was observed on the DMY performance of all genotypes: the positive effect of moderate shading (50% on P. dilatatum and P. notatum DMY was associated to a low soil water availability status. Increased shading level resulted in high nitrogen nutrition index values on grasses, in comparison with full sun. All genotypes performed well under the moderate shading level, but the DMY of both P. regnellii and P. dilatatum and the herbage N content in P. notatum and A. pintoi of all genotypes stood out, showing that those main genotypes are promising to grow in silvopastoral systems at the Campanha region in southern Brazil.

  11. Hepatitis C virus genotypes: A plausible association with viral loads

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    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.

  12. Skeletal muscle strength in older adults. Angiotensin-converting enzyme (ACE genotype affects: an UPDATE

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    ANA PEREIRA

    2011-06-01

    Full Text Available Problem Statement : Previous studies have associated angiotensin-converting enzyme (ACE with variability inthe skeletal muscle baseline strength, though conclusions have been inconsistent across investigations.Approach: The purpose of this study was to review the most important studies that have been exanimate thepossible association between ACE genotype and skeletal muscle baseline strength in elite male and femaleathletes involved in elderly populations. This research is needed because the possibility that the DD genotypemay be associated with a greater proportion of fast twitch fibers could explain the influence of the ACE D alleleupon strength/ power, particularly at high velocities, but this evidence remains equivocal in older people becausemore studies are necessary.Results: Thus, according to scientific evidence, changes in muscle strength with exercise training in olderindividuals may be dependent on ACE I/D genotype. Of note, the results provide a novel insight that thesegenetic variations may interact to determine muscle mass in older women specially. The determination of thispredisposition in this population, highlighting the interest of study, for the prophylactic attitude on the factorsand causes of aging (sarcopenia, osteoporosis, risk of falls, reduction of functional physical go through thisanalysis.Conclusions/Recommendations: In this work, the state of the art related to the influence of the ACE genotypeon skeletal muscle strength was presented and some important relations were reported

  13. Sublineages of Mycobacterium tuberculosis Beijing genotype strains and unfavorable outcomes of anti-tuberculosis treatment.

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    Hang, Nguyen T L; Maeda, Shinji; Keicho, Naoto; Thuong, Pham H; Endo, Hiroyoshi

    2015-05-01

    The influence of Mycobacterium tuberculosis (MTB) lineages/sublineages on unfavorable tuberculosis (TB) treatment outcomes is poorly understood. We investigated the effects of Beijing genotype sublineages and other factors contributing to treatment outcome. Patients newly diagnosed with sputum smear-positive and culture-positive TB in Hanoi, Vietnam, participated in the study. After receiving anti-TB treatment, they were intensively followed up for the next 16 months. MTB isolates collected before treatment were subjected to drug susceptibility testing, and further analyzed to determine MTB (sub) lineages and their clonal similarities. Of 430 patients, 17 had treatment failure and 30 had TB recurrence. Rifampicin resistance was associated with treatment failure {adjusted odds ratio = 6.64 [95% confidence interval (CI), 1.48-29.73]}. The modern Beijing genotype was significantly associated with recurrent TB within 16 months [adjusted hazard ratio = 3.29 (95% CI, 1.17-9.27)], particularly after adjustment for the relevant antibiotic resistance. Human immunodeficiency virus coinfection and severity on chest radiographs were not significantly associated with unfavorable outcomes. Our findings provide further understanding of the influence of MTB strains on unfavorable treatment outcomes. Multiple risk factors should be considered for the optimal management of TB. PMID:25732626

  14. Vitamin D binding protein genotype is associated with serum 25-hydroxyvitamin D and PTH concentrations, as well as bone health in children and adolescents in Finland.

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    Minna Pekkinen

    Full Text Available Vitamin D binding protein (DBP/group-specific component (Gc, correlates positively with serum vitamin D metabolites, and phenotype influences serum 25-hydroxyvitamin D (S-25(OHD concentration. The protein isoform has been associated with decreased bone mineral density (BMD and increased fracture risk. We examined the role of GC genotypes in S-25(OHD status and BMD in 231 Finnish children and adolescents aged 7-19 yr. BMD was measured with DXA from lumbar spine (LS, total hip, and whole body, and for 175 subjects, radial volumetric BMD was measured with pQCT. Background characteristic and total dietary intakes of vitamin D and calcium were collected. The concentrations of 25(OHD, parathyroid hormone (PTH, calcium and other markers of calcium homeostasis were determined from blood and urine. Genotyping was based on single-nucleotide polymorphism (rs4588 in the GC gene. The genotype distribution was: GC 1/1 68%, GC 1/2 26% and GC 2/2 6%. A significant difference emerged in 25(OHD and PTH concentrations between the genotypes, (p = 0.001 and 0.028 respectively, ANCOVA. There was also a linear trend in: Gc 2/2 had the lowest 25(OHD and PTH concentrations (p = 0.025 and 0.012, respectively. Total hip bone mineral content was associated with GC genotype (BMC (p = 0.05, ANCOVA in boys. In regression analysis, after adjusting for relevant covariates, GC genotype was associated with LS BMC and strength and strain index (SSI Z-score in both genders, and LS BMD in boys. In conclusion, the present study demonstrates the association between GC genotypes and S-25(OHD and PTH concentrations. The results show the influence of DBP genetic variation on bone mass accrual in adolescence.

  15. Effects of Smoking and Genotype on the PSR Index of Periodontal Disease in Adults Aged 18–49

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    Polk, Deborah E.; Wang, Xiaojing; Feingold, Eleanor; Shaffer, John R.; Weeks, Daniel E.; Weyant, Robert J.; Crout, Richard J.; McNeil, Daniel W.; Marazita, Mary L.

    2012-01-01

    Studies have found both genetic and environmental influences on chronic periodontitis. The purpose of this study was to examine the relationships among previously identified genetic variants, smoking status, and two periodontal disease-related phenotypes (PSR1 and PSR2) in 625 Caucasian adults (aged 18–49 years). The PSR Index was used to classify participants as affected or unaffected under the PSR1 and PSR2 phenotype definitions. Using logistic regression, we found that the form of the relationship varied by single nucleotide polymorphism (SNP): For rs10457525 and rs12630931, the effects of smoking and genotype on risk were additive; whereas for rs10457526 and rs733048, smoking was not independently associated with affected status once genotype was taken into consideration. In contrast, smoking moderated the relationships of rs3870371 and rs733048 with affected status such that former and never smokers with select genotypes were at increased genetic risk. Thus, for several groups, knowledge of genotype may refine the risk prediction over that which can be determined by knowledge of smoking status alone. Future studies should replicate these findings. These findings provide the foundation for the exploration of novel pathways by which periodontitis may occur. PMID:23066400

  16. Effects of Smoking and Genotype on the PSR Index of Periodontal Disease in Adults Aged 18–49

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    Mary L. Marazita

    2012-08-01

    Full Text Available Studies have found both genetic and environmental influences on chronic periodontitis. The purpose of this study was to examine the relationships among previously identified genetic variants, smoking status, and two periodontal disease-related phenotypes (PSR1 and PSR2 in 625 Caucasian adults (aged 18–49 years. The PSR Index was used to classify participants as affected or unaffected under the PSR1 and PSR2 phenotype definitions. Using logistic regression, we found that the form of the relationship varied by single nucleotide polymorphism (SNP: For rs10457525 and rs12630931, the effects of smoking and genotype on risk were additive; whereas for rs10457526 and rs733048, smoking was not independently associated with affected status once genotype was taken into consideration. In contrast, smoking moderated the relationships of rs3870371 and rs733048 with affected status such that former and never smokers with select genotypes were at increased genetic risk. Thus, for several groups, knowledge of genotype may refine the risk prediction over that which can be determined by knowledge of smoking status alone. Future studies should replicate these findings. These findings provide the foundation for the exploration of novel pathways by which periodontitis may occur.

  17. [Identification and genetic variability of annatto genotypes (Bixa orellana L.) by means of hydrosoluble proteins and isoenzymes].

    Science.gov (United States)

    Medina, A M; Michelangeli, C; Ramis, C; Díaz, A

    2001-01-01

    In order to identify and to determine the genetic variability of 36 annatto genotypes (Bixa orellana L.) collected in five Venezuelan regions (Oriente, Centro, Llanos, Andes and Amazonas) and in Brazil, hydrosoluble protein patterns as well as specific isozyme patterns (alpha-esterase, beta-esterase and peroxidase) were studied using extracts of germinated annatto seeds with radicles of 10 to 15 mm long. Each electrophoretic system allowed genotype discrimination by means of unique banding patterns: both the hydrosoluble protein and the electrophoretic system of beta-esterase with nine banding patterns each; whilst alpha-esterase and peroxidase discriminated eight and three genotypes, respectively. On the other hand, a combination of all the systems permitted a greater discrimination since 34 out of 36 genotypes could be distinguished. Eight mayor groups were formed that showed high levels of genetic diversity (40 to 60%) with no association between geographic and genetic distances, probably because of human influence in the aleatory distribution of this crop. Results obtained indicated that using electrophoretic banding patterns, a classification system could be established for identification and genetic variability purposes in this species. PMID:11510424

  18. Catechol-O-methyltransferase (COMT Genotype Affects Age-Related Changes in Plasticity in Working Memory: A Pilot Study

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    Stephan Heinzel

    2014-01-01

    Full Text Available Objectives. Recent work suggests that a genetic variation associated with increased dopamine metabolism in the prefrontal cortex (catechol-O-methyltransferase Val158Met; COMT amplifies age-related changes in working memory performance. Research on younger adults indicates that the influence of dopamine-related genetic polymorphisms on working memory performance increases when testing the cognitive limits through training. To date, this has not been studied in older adults. Method. Here we investigate the effect of COMT genotype on plasticity in working memory in a sample of 14 younger (aged 24–30 years and 25 older (aged 60–75 years healthy adults. Participants underwent adaptive training in the n-back working memory task over 12 sessions under increasing difficulty conditions. Results. Both younger and older adults exhibited sizeable behavioral plasticity through training (P<.001, which was larger in younger as compared to older adults (P<.001. Age-related differences were qualified by an interaction with COMT genotype (P<.001, and this interaction was due to decreased behavioral plasticity in older adults carrying the Val/Val genotype, while there was no effect of genotype in younger adults. Discussion. Our findings indicate that age-related changes in plasticity in working memory are critically affected by genetic variation in prefrontal dopamine metabolism.

  19. The Differences among Pear Genotypes to Fire Blight (Erwinia amylovora Attack, Based on Observations of Natural Infection

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    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.

  20. Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA▿

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    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-01-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  1. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  2. Mineral composition of different basil (Ocimum spp. genotypes

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    Ličina Vlado Đ.

    2014-01-01

    Full Text Available This experiment investigated mineral composition of 13 basil genotypes (Ocimum spp. in order to find varieties supporting human dietary intake of essential minerals and to evaluate basil genotypes which could serve for herbal production as raw material in pharmaceutical or food processing industry. In addition, this study tested a potential risk of the accumulation of heavy metals during the commercial production of basil on agricultural soil. Mineral composition of basil genotypes was found to be in association with its genetic potential, where some of them can be used in human nutrition as an additional source of several minerals, particularly micronutrients (Fe, Mn, Zn, which generally improve human immune system. Iron-rich basil genotypes were identified in this experiment, like Compact (3576.0 mg/kg, with Lattuga (1585.6 mg/kg and Blue spice (1167.9 mg/kg genotypes, containing more than 1000 mg/kg of Fe in herbal part on dry basil (d.m.. This attract a special attention as a source of iron, especially for humans with low Fe intake, and consequently, for people with low level of hemoglobin. Basil grown on agricultural soil was tested on the accumulation of heavy metals (Cu, Co, Cu, Ni, Cr, Pb, which were not found to be excessive in herbal parts of the plants. Cluster analysis (CA distinguished Ocmium spp. genotypes in two separate groups. Despite of significant differences among the genotypes, content of Fe, Mn, Co, Cr, Ni and Pb made a clear distinction between the clusters. [Projekat Ministarstva nauke Republike Srbije, br. III46001

  3. Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010.

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    Shak, Emma B; France, Anne Marie; Cowan, Lauren; Starks, Angela M; Grant, Juliana

    2015-01-01

    Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009-December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups. PMID:26556930

  4. Identification of Potato Genotypes Using Digital Image Analysis

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    Máté CSÁK

    2011-07-01

    Full Text Available Based on the fractal analysis of digital images, a new classifying system has been proposed at the Potato Research Centre of Keszthely. It is a qualifying system generating objective values to distinguish potato varieties or detect quality differences within the genotype in a relatively simple way. The goal of the research project was to investigate whether Spectral Fractal Dimension (SFD value of digital images is applicable to describe various quality characters of potato tubers and whether SFD values could be used for the identification of certain varieties – if so, which conditions were the most important to enable this process. Considering the above aims, we developed an evaluation computer program which determines the SFD values of the 4 conditions of potato tubers: skin colour; raw flesh-colour; boiled flesh-colour; greying of flesh-colour after 24 hours in RGB spectrum and in all of its sub-spectrums (R, G, B. In total 2080 digital images of 13 varieties from 4 examining periods were analysed. Based on our results we can conclude that SFD analysis can be used in potato breeding only when digital images were made under well-determined, standardized conditions. Detailed statistical analysis (hypothesis tests, principal component analysis and non-hierarchic cluster analysis showed that SFD was not suitable for qualifying tuber characters within a genotype. When images were examined for different years and the same genotype, it became evident, that there are significant deviations between years and within same genotypes. We could conclude that the identification of genotypes should be related not to one particular SFD value, but to the control of the given year with the known value. When analyzing the differences between genotypes on yearly basis, irrespective of characteristics or the studied spectrum, we could not significantly separate genotypes, although there were some that could be separated, even though genotypes and their

  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. Does sex trade with violence among genotypes in Drosophila melanogaster?

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    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.

  7. Analysis of pomological traits in new promising sweet cherry genotypes

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    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

  8. The quality of silage of different sorghum genotypes

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    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.

  9. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

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    Milner Danny A

    2012-02-01

    Full Text Available Abstract Background Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP molecular barcode assay was developed for use in laboratory parasites which estimates genotype number and identifies the predominant genotype. Methods The 24 SNP assay was used to determine predominant genotypes in blood and tissues from autopsy and clinical patients with cerebral malaria. Results Single genotypes were shared between the peripheral blood, the brain, and other tissues of cerebral malaria patients, while malaria-infected patients who died of non-malarial causes had mixed genetic signatures in tissues examined. Children with retinopathy-positive cerebral malaria had significantly less complex infections than those without retinopathy (OR = 3.7, 95% CI [1.51-9.10].The complexity of infections significantly decreased over the malaria season in retinopathy-positive patients compared to retinopathy-negative patients. Conclusions Cerebral malaria patients harbour a single or small set of predominant parasites; patients with incidental parasitaemia sustain infections involving diverse genotypes. Limited diversity in the peripheral blood of cerebral malaria patients and correlation with tissues supports peripheral blood samples as appropriate for genome-wide association studies of parasite determinants of pathogenicity.

  10. STUDY ON CROSSING ABILITY OF ANNUAL CHRYSANTHEMUM GENOTYPES

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    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.

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

    Science.gov (United States)

    Spangler, M L; Robbins, K R; Bertrand, J K; Macneil, M; Rekaya, R

    2009-06-01

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK(P)), the probability of assigning true alleles (AK(G)) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A(-1)). Comparisons of these two methods showed that ACO yielded an increase in AK(P) ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A(-1), with different pedigree sizes and structures. PMID:19220227

  12. UGT2B17 genotype and the pharmacokinetic serum profile of Testosterone during substitution therapy with Testosterone Undecanoate. A retrospective experience from 207 men with hypogonadism.

    OpenAIRE

    Anne Kirstine eBang; Niels eJørgensen; Ewa eRajpert-De Meyts; Anders eJuul

    2013-01-01

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

  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. 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.

  15. 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.

  16. 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. PMID:12676710

  17. Cytological Effects of Space Environment on Different Genotype of Rice

    Institute of Scientific and Technical Information of China (English)

    WEI Li-jun; QIAN Yu; YANG Qian; XU Jian-long; WANG Jun-min; SUN Ye-qing

    2007-01-01

    For exploring the biological effect of space environment on different genotype of rice seeds, the cytological effects of M1 generation after space flight were studied.Twelve different genotypes of rice seeds which belong to different climate ecotype (early, medium and late) of indica and japonica were onboard "Shenzhou 4" spaceship for 162 h.After recovered the total number of mitosis cells and chromosomal aberration were observed.In all the lines the mitotic index (MIs) of space flight are much higher than control, which indicates the stimulate effect of space environment.The cell rate of chromosomal aberration (CRCA) of space flight is also much higher than control, but varies from line to line.It indicates that biological effect of space environment on rice seed dependents not only on flight duration but also on rice genotype.The radiosensitivities of different lines were also discussed according to CRCAs.

  18. Carcass traits and meat quality of two different rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Maria D'Agata

    2012-07-01

    Full Text Available To evaluate the effect of genotype on carcass traits and meat quality, thirty-two rabbits for two genotypes (local population – LP; commercial hybrids – HY were used. Rabbits were weaned at 35 days old and slaughtered at 103 days of age for LP and 87 days of age for HY. Comparing the slaughtering traits of two genotypes, LP provided higher dressing out (59.4% vs 56.2%, Pvs 14.2%, Pvs 22.3, Pvs 8,9%, Pvs 0.86%, Pvs 1.12%; Pvs 19.2%; Pvs 31.6%; Pvs 3.8%; P*, higher redness (a*, yellowness (b* and C* value than HY (P

  19. Genotypic variability for protoplast regeneration in Saintpaulia ionantha (H. Wendl.).

    Science.gov (United States)

    Winkelmann, T; Grunewaldt, J

    1995-08-01

    The behaviour of eleven Saintpaulia ionantha (H. Wendl.) genotypes in protoplast culture was compared. Isolation of protoplasts from young shootlets regenerated in vitro on leaf explants, yielded 0.7 to 1.8 × 10(6) protoplasts per gram fresh weight. In all cultivars and breeding lines tested, cell divisions were observed. The mean division frequencies varied between 1.0 and 5.0% after 14 days, and between 6.4 and 13.8% after 24 days of culture. In ten genotypes callussing and shoot regeneration were achieved. The difference between the genotypes in shoot regeneration rate, between 2 and 68%, was more pronounced. The comparison of four cytokinins indicated hat thidiazuron was most effective for shoot regeneration, but often resulted in poorer shoot quality than benzylaminopurine. PMID:24186626

  20. 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.

  1. Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases

    Institute of Scientific and Technical Information of China (English)

    Na; Han; James; Adams; Wei; Fang; Si-Qing; Liu; Simon; Rayner

    2015-01-01

    Japanese encephalitis is a mosquito borne disease and is the leading cause of viral encephalitis in the Asia-Pacific area. The causative agent, Japanese encephalitis virus(JEV) can be phylogenetically classified into five genotypes based on nucleotide sequence. In recent years, genotype I(GI) has displaced genotype III(GIII) as the dominant lineage, but the mechanisms behind this displacement event requires elucidation. In an earlier study, we compared host variation over time between the two genotypes and observed that GI appears to have evolved to achieve more efficient infection in hosts in the replication cycle, with the tradeoff of reduced infectivity in secondary hosts such as humans. To further investigate this phenomenon, we collected JEV surveillance data on human cases and, together with sequence data, and generated genotype/case profiles from seven Asia-Pacific countries and regions to characterize the GI/GIII displacement event. We found that, when comprehensive and consistent vaccination and surveillance data was available, and the GIII to GI shift occurred within a well-defined time period, there was a statistically significant drop in JEV human cases. Our findings provide further support for the argument that GI is less effective in infecting humans, who represent a dead end host. However, experimental investigation is necessary to confirm this hypothesis. The study highlights the value of alternative approaches to investigation of epidemics, as well as the importance of effective data collection for disease surveillance and control.

  2. 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.

  3. Distribution of Gossypol Glands on Cotton (Gossypium hirsutum L. Genotypes

    Directory of Open Access Journals (Sweden)

    Yuksel BOLEK

    2010-06-01

    Full Text Available Knowing the distribution of gossypol glands in cotton will help to improve advanced cultivars with great economic return. The aim is to compare cotton genotypes for the number and the distribution of gossypol glands found in different plant parts and to determine the genotypes which contain more gossypol glands in their vegetative parts but little or none in their seeds. The intensity and the greatness of the gossypol amount is an important part of defending against plant insects and diseases. Randomized complete block design with two replications was applied at the Agricultural Research Institute of Kahramanmara? during 2006-2007. Thirty seven cotton genotypes belonging to Gossypium hirsutum L. species were the plant material. The number of gossypol glands on stem, boll walls (carpels, leaves and seeds were visually counted and ranged from 0 to 142 per cm2 for stem, 0 to 135 per cm2 for leaf, 0 to 85 per cm2 for boll wall and 0 to 16 per mm2 for embryo (kernel. Number of gossypol glands varied for the genotypes and years but this variance was too low in some genotypes. Genotypes �Acala Royale�, �Acala Prema�, �Deltaopal� and �Carmen� had relatively more gossypol glands on their vegetative parts but less in their seed. Measured parameters were positively and significantly correlated to each other. Correlations for number of gossypol glands between stem and leaf (r=0.77**, boll wall (r=0.65** and seed (r=0.32** were significant.

  4. Whole genome amplification of DNA for genotyping pharmacogenetics candidate genes.

    Directory of Open Access Journals (Sweden)

    Santosh ePhilips

    2012-03-01

    Full Text Available Whole genome amplification (WGA technologies can be used to amplify genomic DNA when only small amounts of DNA are available. The Multiple Displacement Amplification Phi polymerase based amplification has been shown to accurately amplify DNA for a variety of genotyping assays; however, it has not been tested for genotyping many of the clinically relevant genes important for pharmacogenetic studies, such as the cytochrome P450 genes, that are typically difficult to genotype due to multiple pseudogenes, copy number variations, and high similarity to other related genes. We evaluated whole genome amplified samples for Taqman™ genotyping of SNPs in a variety of pharmacogenetic genes. In 24 DNA samples from the Coriell human diversity panel, the call rates and concordance between amplified (~200-fold amplification and unamplified samples was 100% for two SNPs in CYP2D6 and one in ESR1. In samples from a breast cancer clinical trial (Trial 1, we compared the genotyping results in samples before and after WGA for four SNPs in CYP2D6, one SNP in CYP2C19, one SNP in CYP19A1, two SNPs in ESR1, and two SNPs in ESR2. The concordance rates were all >97%. Finally, we compared the allele frequencies of 143 SNPs determined in Trial 1 (whole genome amplified DNA to the allele frequencies determined in unamplified DNA samples from a separate trial (Trial 2 that enrolled a similar population. The call rates and allele frequencies between the two trials were 98% and 99.7%, respectively. We conclude that the whole genome amplified DNA is suitable for Taqman™ genotyping for a wide variety of pharmacogenetically relevant SNPs.

  5. 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

  6. 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 (LSDLSDLSDLSDLSDLSD<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. PMID:26776020

  7. Use of chronic irradiation in formation of new rape genotypes

    International Nuclear Information System (INIS)

    Chronic irradiation of hybrid plants of F1 generation obtained by crossing the Canadian rape without erucic acid with European winter varieties containg this acid, doubled the frequency of winter genotypes and increased significantly the frequency of required recombinations of winter character and absence of erucic acid in F2-M2. Genotypes with a more favourable ratio between linoleic and linolenic acids were obtained in the irradiated F2-M2 population. The obtained radio-induced mutants are used for the production of new varieties of winter rape without erucic acid at the Slapy Breeding Station. (author)

  8. 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

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

    DEFF Research Database (Denmark)

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

    . Chlorophyll a fluorescence has been a versatile tool in photosynthesis research to measure plant responses to various abiotic stresses that affect PSII. We aim to establish a reproducible protocol to measure response of wheat genotypes to high temperature, based on the physiological marker, maximum quantum......%. Our protocol seems to be stable over environments since interaction between genotypes and the three repeated experiments separated in time was not statistically significant. The chlorophyll a fluorescence protocol may enable identification of wheat lines reliably more or less tolerant to heat stress...

  10. 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

  11. 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.

  12. Genotype-phenotype correlation and pregnancy outcomes of partial trisomy 14q: A systematic review.

    Science.gov (United States)

    Bregand-White, Julia; Saller, Devereux N; Clemens, Michele; Surti, Urvashi; Yatsenko, Svetlana A; Rajkovic, Aleksandar

    2016-09-01

    Over the last decade, several advances in ultrasound techniques, increasing availability of whole genome microarray testing, and overall expansion of our knowledge about the human genome have drastically enhanced our ability to detect chromosomal abnormalities prenatally. Despite that, genotype-phenotype correlation is difficult to establish for many chromosomal aberrations, particularly for those that are rare, as it requires thorough analysis of a significant number of cases. This in turn increases the burden of the obstetric provider to appropriately counsel a patient regarding prognosis and pregnancy options in these complicated situations. Our experience in prenatal diagnosis and management of a fetus with multiple anomalies and partial trisomy for the 14q11-q24.2 prompted a comprehensive analysis of the relevant literature. Although complete non-mosaic trisomy 14 is associated with first trimester miscarriages, partial trisomy 14q is a rare condition with undefined genotype-phenotype correlation, preventing accurate prenatal counseling, and informed decision making. We performed a systematic literature review, that aimed to summarize prenatal and postnatal findings of individual case reports on 51 patients with partial trisomy 14q in order to elucidate genotype-phenotype correlation, and to supply healthcare professionals with recommendation on essential fetal and parental testing for accurate diagnosis, pregnancy outcomes, and proper family counseling. Comparison of the clinical findings among the patients with partial 14q trisomy suggest that the resulting phenotype is likely to be influenced by the extent of the 14q trisomy segment, associated chromosomal imbalances, parental origin of the rearrangement, and dosage of the genes within the imprinted 14q32 cluster. © 2016 Wiley Periodicals, Inc. PMID:27286879

  13. UGT2B17 genotype and the pharmacokinetic serum profile of Testosterone during substitution therapy with Testosterone Undecanoate. A retrospective experience from 207 men with hypogonadism.

    Directory of Open Access Journals (Sweden)

    Anne Kirstine eBang

    2013-07-01

    Full Text Available BackgroundTestosterone (T is mainly excreted in the urine as testosterone glucuronide (TG. This glucuronidation is partly dependent on the UGT2B17 genotype, and TG excretion is therefore lower in men having the UGT2B17 deletion. However, the possible influence of UGT2B17 genotype on serum T during androgen therapy is unknown. We retrospectively investigated the possible association between the UGT2B17 gene polymorphism and serum T levels in hypogonadal men during Testosterone undecanoate (TU substitution therapy.Subjects and methods207 patients treated with TU (Nebido® were genotyped by qPCR for the UGT2B17 deletion polymorphism. All were given 1000 mg TU per injection at 0, 6 and 18 weeks. Blood samples were taken 2 and 6 weeks after the 1st and 2nd injection, prior to the 3rd injection, and after 2-3 years of treatment. We analysed for the levels of T, luteinizing hormone, sex-hormone-binding globulin, estradiol, prostate specific antigen, haematocrit, haemoglobin and total cholesterol. ResultsThe UGT2B17 genotype frequency was: ins/ins: 42%, ins/del: 44% and del/del: 14%. During the initial 18 weeks of TU treatment, large intra- and inter-individual variations in serum T levels were observed. Large peaks in T levels, ranging from 6.7 nmol/l to 69.5 nmol/l, were noted 2 weeks after injections, regardless of the genotype. T levels did not differ between the 3 genotypes prior to the 3rd injection, but the del/del group had significantly lower levels of LH. At follow-up after 2-3 years, the injection interval or daily T dosage was not dependent on the UGT2B17 genotype. ConclusionIn conclusion, we found large intra- and inter-individual variations in serum T during standard TU treatment regimen in hypogonadal men. Only subtle differences in serum T and LH were noted according to UGT2B17 genotype, which however suggest that the UGT2B17 genotype exert modest influence on the pharmacokinetic profile of T after TU treatment.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    BACKGROUND: Variables influencing serum hepatitis C virus (HCV) RNA levels and genotype distribution in individuals with human immunodeficiency virus (HIV) infection are not well known, nor are factors determining spontaneous clearance after exposure to HCV in this population. METHODS: All HCV...... antibody (Ab)-positive patients with HIV infection in the EuroSIDA cohort who had stored samples were tested for serum HCV RNA, and HCV genotyping was done for subjects with viremia. Logistic regression was used to identify variables associated with spontaneous HCV clearance and HCV genotype 1. RESULTS......: Of 1940 HCV Ab-positive patients, 1496 (77%) were serum HCV RNA positive. Injection drug users (IDUs) were less likely to have spontaneously cleared HCV than were homosexual men (20% vs. 39%; adjusted odds ratio [aOR], 0.36 [95% confidence interval {CI}, 0.24-0.53]), whereas patients positive...

  15. 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.

  16. 5-HTTLPR Genotype Moderates the Effects of Past Ecstasy Use on Verbal Memory Performance in Adolescent and Emerging Adults: A Pilot Study.

    Directory of Open Access Journals (Sweden)

    Natasha E Wright

    Full Text Available Ecstasy use is associated with memory deficits. Serotonin transporter gene (5-HTTLPR polymorphisms have been linked with memory function in healthy samples. The present pilot study investigated the influence of 5-HTTLPR polymorphisms on memory performance in ecstasy users, marijuana-using controls, and non-drug-using controls, after a minimum of 7 days of abstinence.Data were collected from 116 young adults (18-25 years-old, including 45 controls, 42 marijuana users, and 29 ecstasy users, and were balanced for 5-HTTLPR genotype. Participants were abstinent seven days prior to completing memory testing. Three MANCOVAs and one ANCOVA were run to examine whether drug group, 5-HTTLPR genotype, and their interactions predicted verbal and visual memory after controlling for gender, past year alcohol use, other drug use, and nicotine cotinine levels.MANCOVA and ANCOVA analysis revealed a significant interaction between drug group and genotype (p = .03 such that ecstasy users with the L/L genotype performed significantly worse on CVLT-2 total recall (p = .05, short (p = .008 and long delay free recall (p = .01, and recognition (p = .006, with the reverse pattern found in controls. Ecstasy did not significantly predict visual memory. 5-HTTLPR genotype significantly predicted memory for faces (p = .02; short allele carriers performed better than those with L/L genotype.5-HTTLPR genotype moderated the effects of ecstasy on verbal memory, with L/L carriers performing worse compared to controls. Future research should continue to examine individual differences in ecstasy's impact on neurocognitive performance as well as relationships with neuronal structure. Additional screening and prevention efforts focused on adolescents and emerging adults are necessary to prevent ecstasy consumption.

  17. Adaptation and Genotype x Environment Interaction of Flaxseed (Linum usitatissimum L. Genotypes in South Central Chile Adaptación e Interacción Genotipo x Ambiente en Lino (Linum usitatissimum L. en la Zona Centro Sur de Chile

    Directory of Open Access Journals (Sweden)

    Marisol Berti

    2010-09-01

    Full Text Available Flaxseed (Linum usitatissimum L. is imported into Chile mostly for bread making and feed. Identification of genotypes best adapted for seed production in South Central Chile would facilitate producer’s decision. The objective of this study was to determine the adaptation and genotype x environment interaction of 16 flaxseed genotypes (including 10 from North American and six from Argentine sources grown at 11 environments (defined as location-year in Chile from 2003 to 2007. Genotype seed yield was above 5700 kg ha-1 for some environments indicating a high yield potential. According to the AMMI (Additive Main Effects and Multiplicative Interaction and SREG (Sites regression models the 11 environments were classified into four groups by the AMMI and three groups by the SREG models. Genotypes were classified into five groups by the SREG model with four of the groups as single genotypes. Overall mean seed yield was similar for all genotypes; however the genotype Nekoma was the most stable and higher yielding genotype across environments. The environment with the highest yield potential was Chillán 2003-2004, but this location had low yield stability across years. The environments with greatest seed yield potential, Chillán 2003-2004 and Los Ángeles 2004-2005, had irrigation during flowering and seed filling. Seed oil content fluctuated between 420 and 530 g kg-1. The climatic differences among environments did not influence oil composition as expected from previous research. Flaxseed appears adapted to South Central Chile with differences observed among genotypes for biomass and seed yield, harvest index, test weight, oil content, and composition.La semilla de lino (Linum usitatissimum L. se importa a Chile principalmente para panaderías y alimento animal. La identificación de genotipos altamente productivos en la zona Centro Sur de Chile facilitaría la decisión de los productores. El objetivo de este estudio fue determinar la adaptaci

  18. 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.

  19. 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.

  20. The influence of competition and host plant resistance on selection of Phytophthora infestans populations in Michigan State and Northern Ireland

    Science.gov (United States)

    The current investigation used multiple cultivars of potato and genotypes of Phytophthora infestans to study the P. infestans genotype x cultivar interaction, and investigate the potential influence of competition and level of field resistance on selection of the surrounding population of P. infesta...

  1. 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.

  2. 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.

  3. Can genotype determine the sports phenotype? A paradigm shift in sports medicine.

    Science.gov (United States)

    Ghosh, Amit; Mahajan, Preetam B

    2016-06-01

    In last two decades, there has been an evolution in sports medicine. Several researchers have worked on different domains of sports medicine, like strength, endurance, sports injury, and psychology. Besides this, several groups have explored the changes at cellular and molecular levels during exercise, which has led to the development of the new domain in sports science known as genetic medicine. Genetic medicine deals with the genotypic basis of sports phenotype. In this article, we try to provide an up-to-date review on genetic determinants of sports performance, which will be like a journey from the nostalgic past towards the traditional present and the romantic future of sports medicine. Endurance and power performance are two important domains of athletes. They vary in individuals, even among trained athletes. Researches indicate that the genetic makeup of sportsmen play a vital role in their performance. Several genetic factors are reported to be responsible for endurance, power, susceptibility to injury, and even psychology of the individual. Besides this, proper training, nutrition, and environment are also important in shaping their potential. The aim of this discussion is to understand the influence of the environment and the genetic makeup on the performance of the athletes. There is sufficient evidence to suggest that genotype determines the sports phenotype in an athlete. Choosing the right sports activity based on genetic endowment is the key for achieving excellence in sports. PMID:26812785

  4. Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology.

    Science.gov (United States)

    Forsman, Anders

    2014-01-01

    There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109

  5. 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.

  6. Can genotype determine the sports phenotype? A paradigm shift in sports medicine.

    Science.gov (United States)

    Ghosh, Amit; Mahajan, Preetam B

    2016-06-01

    In last two decades, there has been an evolution in sports medicine. Several researchers have worked on different domains of sports medicine, like strength, endurance, sports injury, and psychology. Besides this, several groups have explored the changes at cellular and molecular levels during exercise, which has led to the development of the new domain in sports science known as genetic medicine. Genetic medicine deals with the genotypic basis of sports phenotype. In this article, we try to provide an up-to-date review on genetic determinants of sports performance, which will be like a journey from the nostalgic past towards the traditional present and the romantic future of sports medicine. Endurance and power performance are two important domains of athletes. They vary in individuals, even among trained athletes. Researches indicate that the genetic makeup of sportsmen play a vital role in their performance. Several genetic factors are reported to be responsible for endurance, power, susceptibility to injury, and even psychology of the individual. Besides this, proper training, nutrition, and environment are also important in shaping their potential. The aim of this discussion is to understand the influence of the environment and the genetic makeup on the performance of the athletes. There is sufficient evidence to suggest that genotype determines the sports phenotype in an athlete. Choosing the right sports activity based on genetic endowment is the key for achieving excellence in sports.

  7. A constructive replication of the association between the oxytocin receptor genotype and parenting.

    Science.gov (United States)

    Klahr, Ashlea M; Klump, Kelly; Burt, S Alexandra

    2015-02-01

    Behavioral genetic studies have robustly indicated that parenting behaviors are heritable-that is, individual differences in parenting are at least partially a function of genetic differences between persons. Few studies, however, have sought to identify the specific genetic variants that are associated with individual differences in parenting. Genes that influence the oxytocin system are of particular interest, given the growing body of evidence that points to the role of oxytocin for social behaviors, including parenting. The current study conducted examinations of associations between a variant in the oxytocin receptor gene (OXTR rs53576) and parental warmth, control, and negativity in a sample of 1,000 twin children and their parents (N = 500 families) from the Michigan State University Twin Registry to constructively replicate and extend prior work (Bakermans-Kranenburg & van IJzendoorn, 2008; Michalska et al., 2014). Analyses were conducted both at the level of the child and the level of the parent, allowing us to examine both child-driven (via evocative gene-environment correlation) and parent-driven genetic effects on parenting. Mothers' OXTR genotype predicted her warmth toward her children, even after controlling for child genotype. This association was not found for fathers. These findings add to the growing body of evidence linking oxytocin functioning to parental behavior and also highlight potential etiological differences in parenting across mothers and fathers. PMID:25419912

  8. Multi-Year Assessment of Toxic Genotypes and Microcystin Concentration in Northern Lake Taihu, China

    Science.gov (United States)

    Hu, Lili; Shan, Kun; Lin, Lizhou; Shen, Wei; Huang, Licheng; Gan, Nanqin; Song, Lirong

    2016-01-01

    Lake Taihu is the third-largest freshwater lake in China and has been suffering from cyanobacterial blooms for over two decades. The northern part of the lake, Meiliang Bay, is known to be at high risk of dense and sustained Microcystis blooms and toxins. This study aimed to investigate and record the annual and seasonal dynamics of toxic genotype, Microcystis morphospecies succession and microcystin variation. It also aimed to find out the underlying driving factors influencing the dynamic changes. Microcystin (MC) and the Microcystis genotype were quantified using HPLC and quantitative real-time PCR, respectively. Our study, over three consecutive years, showed that the pattern of morphospecies succession was seasonally distinct and annually consistent. During the same period in 2012, 2013 and 2014, the average MC were, on dry weight basis, 733 μg·g−1, 844 μg·g−1, 870 μg·g−1, respectively. The proportion of toxic Microcystis accounted for 41%, 44% and 52%, respectively. Cell bound microcystin was found to correlate with the percentage of toxic Microcystis. Based on historical and current data, we conclude that annual bloom toxicity was relatively stable or possibly increased over the last decade. PMID:26784229

  9. Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

    Science.gov (United States)

    Séraphin, Marie Nancy; Lauzardo, Michael; Morris, J. Glenn; Blackburn, Jason K.

    2016-01-01

    Background Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts. Methods We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan. Principal Findings Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (immigrants are likely to impact TB control. Due to the monomorphic nature of available markers, whole genome sequencing is needed to conclusively delineate recent transmission events between U.S. and foreign-born persons. PMID:27093156

  10. 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.

  11. Infection of mice with oocysts of Toxoplasma gondii by oral route showed differences of virulence from Brazilian RFLP genotypes BrI and BrIII.

    Science.gov (United States)

    Chiebao, Daniela Pontes; Pena, Hilda Fátima de Jesus; Cabral, Aline Diniz; Rocca, Mayra Pereira; Lopes, Estela Gallucci; Valadas, Samantha Yuri Oshiro Branco; Keid, Lara Borges; Grisi Filho, José Henrique Hildebrand; Soares, Rodrigo Martins

    2016-08-01

    South American strains of Toxoplasma gondii present higher genetic diversity than classical European strains. We compared the virulence of two non-archetypal Brazilian genotypes of T. gondii to mice. Oocysts of four isolates, two genotype BrI (TgCatBr71 and TgShBr11) and two BrIII (TgCatBr74 and TgCatBr60) were obtained from cats fed experimentally infected mice. After sporulation, 5.0×10(1) and 1.0×10(2) oocysts were orally administrated to Swiss albine mice in Experiments #1 and #2, respectively (4-10 mice/group). Humoral response from dead and surviving mice was analyzed on days 9 to 35 post-infection. Microscopic observations of lungs and brains were performed for tachyzoites and cysts visualization in fresh preparations. Negative results were tested by PCR. Virulence after infection with oocysts is dose dependent for genotype BrIII isolates, but not for BrI. Differences in mortality were observed among isolates from genotype BrIII on Experiment #1. Intra-genotype phenotypic variation related to the parasite stage of infection was demonstrated and this characteristic should be further studied and may influence future work regarding the role of virulence amid hosts. PMID:27474004

  12. Epidemiology of HPV genotypes in Uganda and the role of the current preventive vaccines: A systematic review

    Directory of Open Access Journals (Sweden)

    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

  13. Evaluation of cotton genotypes for ginning energy and ginning rate

    Science.gov (United States)

    Reducing ginning energy use through cultivar improvement could reduce ginning and energy cost. The objective of this study was to detect genetic variability for ginning energy and ginning rate. Thirty four conventional and twelve transgenic genotypes were evaluated in 2008 and 2009 for ginning energ...

  14. Peptostreptococcus micros smooth and rough genotypes in periodontitis and gingivitis

    NARCIS (Netherlands)

    Kremer, BHA; Loos, BG; van der Velden, U; van Winkelhoff, AJ; Craandijk, J; Bulthuis, HM; Hutter, J; Varoufaki, AS; van Steenbergen, TJM

    2000-01-01

    Background: Two genotypes can be distinguished within the species Peptostreptococcus micros: a smooth (Sm) and a rough (Rg) type. To date no systematic study has been performed on the prevalence and proportion of both types in untreated periodontitis patients and subjects without destructive periodo

  15. Partitioning of copy-number genotypes in pedigrees

    Directory of Open Access Journals (Sweden)

    Andelfinger Gregor U

    2010-05-01

    Full Text Available Abstract Background Copy number variations (CNVs and polymorphisms (CNPs have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.

  16. Human papillomavirus testing and genotyping in cervical screening

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Lynge, Elsebeth; Bonde, Jesper

    2011-01-01

    Mass vaccination against human papillomavirus (HPV) genotypes 16 and 18 will, in the long term, reduce the incidence of cervical cancer, but screening will remain an important cancer control measure in both vaccinated and unvaccinated women. Since the 1960s, cytology screening has helped to reduc...

  17. Physiological response of soybean genotypes to plant density

    NARCIS (Netherlands)

    Gan, Y; Stulen, [No Value; van Keulen, H; Kuiper, PJC

    2002-01-01

    Response of soybean (Glycine max (L.) Merr.) to plant density has occupied a segment of agronomic research for most of the century. Genotype differences have been noted especially in response to planting date, lodging problems and water limitation. There is limited information on the physiological g

  18. 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.

  19. Antimicrobial susceptibility and tetracycline resistance determinant genotyping of Gallibacterium anatis

    DEFF Research Database (Denmark)

    Bojesen, Anders M.; Vazquez, Maria E.; Bager, Ragnhild J.;

    2011-01-01

    these figures were 67% and 42%, respectively, for the reference strains.Genotyping of tetracycline resistance determinants was performed with primers specific for tet(A–E, H, K–M, O). Strains positive for tet(B), tet(H) and tet(L) were identified, however, in 20 out of 49 tetracycline resistant strains...

  20. Accuracy of genotype imputation in Swiss cattle breeds

    Science.gov (United States)

    The objective of this study was to evaluate the accuracy of imputation from Illumina Bovine3k Bead Chip (3k) and Illumina BovineLD (6k) to 54k chip information in Swiss dairy cattle breeds. Genotype data comprised of 54k SNP chip data of Original Braunvieh (OB), Brown Swiss (BS), Swiss Fleckvieh (SF...

  1. Genotype x environment interaction, environmental heterogeneity, and the lek paradox

    Science.gov (United States)

    Substantial additive genetic variance (VA) often exists for male signaling traits in spite of the directional selection that female choice imposes. One solution to this problem, generally termed the ‘lek paradox’, is that genotype x environment interaction (GEI) occurs and generates a ‘crossover’ of...

  2. Distribution of Candida albicans genotypes among family members

    Science.gov (United States)

    Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

    1999-01-01

    Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

  3. Heterosis in crosses between wheat genotypes with different spike architecture

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    Kobiljski Borislav Đ.

    2002-01-01

    Full Text Available In order to estimate hybrid vigor, wheat genotypes differing in spike architecture (normal, tetrastichon and branched were crossed and the F1 and F2 generations analyzed for the number of fertile spikelets/spike, number of grains/spike and grain weight/spike. The parents used for crossing were Sava (normal spike, Forlani (normal spike, ZG T 171/1 (tetrastichon spike and ZG 172 (branched spike. The F1 and F2 progenies, except those from the cross Sava x Forlani, had a lower number of fertile spikelets/spike compared with the better parent. In the crosses between genotypes with normal and branched spikes, the F1 and F2 progenies formed significantly fewer grains/spike. On the other hand, the F1 of the crosses between genotypes with normal and tetrastichon spike showed a significant level of heterosis with respect to the number of grains/spike, particularly the cross Forlani x ZG T 171/1. In regard to grain weight/spike, significant heterosis was detected in all crosses except Sava x ZG 172.The crosses between genotypes with normal and tetrastichon spikes that exhibited significant heterosis for two main yield components were most promising in the context of hybrid wheat development. Such crosses deserve further attention and investigation.

  4. Childhood Pompe disease: Clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    C.I. van Capelle (Carine); J.C. van der Meijden (J.); J.M.P. van den Hout (Johanna); J. Jaeken; M. Baethmann; T. Voit; M.A. Kroos (Marian); T.G.J. Derks (Terry G J); M.E. Rubio-Gozalbo (Estela); M.A. Willemsen (Michél); R. Lachmann (Robin); E. Mengel; H. Michelakakis (Helen); J.C. de Jongste (Johan); A.J.J. Reuser (Arnold); A.T. van der Ploeg (Ans)

    2016-01-01

    textabstractBackground: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotter

  5. DIFFERENTIATION OF BARLEY GENOTYPES BASED ON DNA POLYMORPHISM

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    Marián Tomka

    2013-02-01

    Full Text Available Identification and characterization of genotypes is essential for improving the quality of cultivated varieties in breeding programs. Information about the origin of varieties can help farmers in selecting appropriate varieties to specific growing conditions or end use of crops. A set of ten microsatellite markers was used to describe genetic diversity in a sample of 30 barley (Hordeum vulgare L. genotypes. A total of 55 different alleles were amplified using ten SSR markers localized on chromosomes 1H, 2H, 3H, 5H, 6H, 7H with an average number of 5.5 alleles per locus. On the basis of allele frequencies we have calculated diversity index, polymorphic information content and index of probability, which have mean values of 0.664; 0.643 and 0.126 respectively. These values indicate high differentiation ability of SSR markers. In the created dendrogram using hierarchical cluster analysis using UPGMA algorithm we were able to differentiate all 30 barley genotypes. The results show that DNA markers are suitable for the identification and differentiation of genotypes and indicated the effectiveness of microsatellite markers to describe genetic diversity.

  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. LHRH and LHR genotypes and prostate cancer incidence and survival.

    Science.gov (United States)

    Ingles, Sue Ann; Liu, Stephen V; Pinski, Jacek

    2013-01-01

    Despite their crucial role in initiating steroid-hormone synthesis, the hypothalamic and pituitary hormones (LH, LHRH) and their receptors have received scant attention in genetic studies of hormone-related diseases. This study included 1,170 men diagnosed with prostate cancer (PC) in Los Angeles County between 1999 and 2003. LHRH and LH receptor genotypes were examined for association with PC survival. Additionally, associations with PC incidence were examined by comparing PC cases to control men of similar age and race/ethnicity. The LHR 312 G allele was found to be associated with increased PC mortality (p=0.01). Ten years after diagnosis, 16% of men carrying two copies of the G allele (genotype GG) had died of PC, compared to 11% of those with genotype AG and 9% of those with AA. In a case-control comparison, this same allele was significantly associated with decreased PC risk: OR=0.68 (95% CI: 0.49, 0.93) for genotype GG vs. AA. These results suggest that androgens may play opposing roles in PC initiation and progression, and highlight the need to include these important but overlooked genes in future studies of PC etiology, prognosis, and treatment.

  8. 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…

  9. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  10. Genotyping of Brazilian Giardia duodenalis human axenic isolates

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    ST Coradi

    2011-01-01

    Full Text Available Giardia duodenalis is a complex species that comprises at least seven distinct genetic groups (A to G, but only genotypes A and B are known to infect humans and a wide variety of other mammals. Regardless of biological, biochemical and antigenic analysis, several isolates maintained in vitro were not genetically typed yet. So, in the present study, five Brazilian axenic isolates obtained from asymptomatic and symptomatic patients were typed in order to determine the major genetic groups to which the isolates belonged. DNA was extracted from axenic trophozoites, fragments of glutamate dehydrogenase (gdh and triosephosphate isomerase (tpi genes were amplified by PCR and the isolate genotyping was carried out using restriction fragment length polymorphism (RFLP and DNA sequencing for both genes. The results revealed that all isolates were assigned to genotype A at both analyzed loci. Indeed, DNA sequence analysis classified the four isolates obtained from asymptomatic individuals into subtype AII, while the isolate obtained from the symptomatic patient was typed as subtype AI. Despite of the limited number of isolates assessed, the findings presented herein provide interesting insights on the occurrence of Giardia genotypes in Brazil and hold the perspective for future molecular and epidemiological investigations.

  11. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya;

    2013-01-01

    achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene...

  12. SHOOT AND ROOT EVALUATIONS ON SEEDLINGS FROM Coffea GENOTYPES

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    RAMOS LUIS CARLOS DA SILVA

    1997-01-01

    Full Text Available Roots and shoots from seedlings of 29 coffee genotypes were studied to better characterize the entries from the Coffea germplasm bank of the Instituto Agronômico (IAC, Campinas, State of São Paulo, Brasil. The varieties were seeded in a randomized complete block design with 6 replications and 10 plants per plot. The characters evaluated were: plant (PL, shoot (SL and root (RL length; total plant (PDM, shoot (SDM, root (RDM and lateral root (LRDM dry matter. A lateral root index (LRI and shoot root dry matter (SRDM = SDM/RDM and length ratios; (SRL = SL/RL were calculated. The dwarf varieties (Catuaí, Icatu-caturra, Vila Sarchi, San Ramon, Vila Lobos, São Bernardo presented higher LRDM and lower SDM than the normal size varieties such as Mundo Novo, Bourbon Vermelho, Arábica, Amarelo de Botucatu, Glaucia, etc. The varieties Macrodiscus, Icatu-caturra, Bourbon Amarelo, Vila Lobos and C. congensis showed higher root development related to shoot. The Arábica coffee standard variety showed intermediary root and shoot development. Genotypes of high yield background were higher in SL and SDM, while the dwarf types had only lower SL than the normal ones, but higher RL and dry matters. Seedlings from genotypes of known higher field drought tolerance had lower SL and RL, but higher RDM. Significant phenotypic and genotypic correlation coefficients were obtained, such the genotypes for PL and PDM (r = 0.64; P = 0.01, SL and SDM (r = 0.40; P = 0.05, SDM and LRDM (r = 0.52; P = 0.05, RDM and LRI (r = 0.68; P = 0.01, LRI and SRDM (r = 0.85; P = 0.01 and LRI and LRDM (r = 0.84; P = 0.01. High genotypic correlations suggest that selection directed to one character will directly affect the other. Conversely, low or non-significant correlations suggest independence of association, an indication that it would be possible to select two characteristics to diverse directions. Selection could be done towards different goals to change root and shoot measures

  13. Serotonin transporter genotype modulates subgenual response to fearful faces using an incidental task.

    Science.gov (United States)

    O'Nions, Elizabeth J P; Dolan, Raymond J; Roiser, Jonathan P

    2011-11-01

    This study assessed the impact of serotonin transporter genotype (5-HTTLPR) on regional responses to emotional faces in the amygdala and subgenual cingulate cortex (sgACC), while subjects performed a gender discrimination task. Although we found no evidence for greater amygdala reactivity or reduced amygdala-sgACC coupling in short variant 5-HTTLPR homozygotes (s/s), we observed an interaction between genotype and emotion in sgACC. Only long variant homozygotes (la/la) exhibited subgenual deactivation to fearful versus neutral faces, whereas the effect in s/s subjects was in the other direction. This absence of subgenual deactivation in s/s subjects parallels a recent finding in depressed subjects [Grimm, S., Boesiger, P., Beck, J., Schuepbach, D., Bermpohl, F., Walter, M., et al. Altered negative BOLD responses in the default-mode network during emotion processing in depressed subjects. Neuropsychopharmacology, 34, 932-943, 2009]. Taken together, the findings suggest that subgenual cingulate activity may play an important role in regulating the impact of aversive stimuli, potentially conferring greater resilience to the effects of aversive stimuli in la/la subjects. Using dynamic causal modeling of functional magnetic resonance imaging data, we explored the effects of genotype on effective connectivity and emotion-specific changes in coupling across a network of regions implicated in social processing. Viewing fearful faces enhanced bidirectional excitatory coupling between the amygdala and the fusiform gyrus, and increased the inhibitory influence of the amygdala over the sgACC, although this modulation of coupling did not differ between the genotype groups. The findings are discussed in relation to the role of sgACC and serotonin in moderating responses to aversive stimuli [Dayan, P., & Huys, Q. J., Serotonin, inhibition, and negative mood. PLoS Comput Biol, 4, e4, 2008; Mayberg, H. S., Liotti, M., Brannan, S. K., McGinnis, S., Mahurin, R. K., Jerabek, P. A., et

  14. Genetic polymorphisms and skin aging: the identification of population genotypic groups holds potential for personalized treatments

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    Naval J

    2014-07-01

    Full Text Available Jordi Naval,1 Vicente Alonso,1,2 Miquel Angel Herranz11Genocosmetics Lab, Barcelona, Spain; 2Dermatology Unit, Hospital Nisa 9 de Octubre, Valencia, SpainIntroduction: Skin changes are among the most visible signs of aging. Skin properties such as hydration, elasticity, and antioxidant capacity play a key role in the skin aging process. Skin aging is a complex process influenced by heritable and environmental factors. Recent studies on twins have revealed that up to 60% of the skin aging variation between individuals can be attributed to genetic factors, while the remaining 40% is due to non-genetic factors. Recent advances in genomics and bioinformatics approaches have led to the association of certain single nucleotide polymorphisms (SNPs to skin properties. Our aim was to classify individuals based on an ensemble of multiple polymorphisms associated with certain properties of the skin for providing personalized skin care and anti-aging therapies.Methods and results: We identified the key proteins and SNPs associated with certain properties of the skin that contribute to skin aging. We selected a set of 13 SNPs in gene coding for these proteins which are potentially associated with skin aging. Finally, we classified a sample of 120 female volunteers into ten clusters exhibiting different skin properties according to their genotypic signature.Conclusion: This is the first study that describes the actual frequency of genetic polymorphisms and their distribution in clusters involved in skin aging in a Caucasian population. Individuals can be divided into genetic clusters defined by genotypic variables. These genotypic variables are linked with polymorphisms in one or more genes associated with certain properties of the skin that contribute to a person's perceived age. Therefore, by using this classification, it is possible to characterize human skin care and anti-aging needs on the basis of an individual's genetic signature, thus opening the door

  15. Salinity Responses of Grafted Grapevines: Effects of Scion and Rootstock Genotypes

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    Nuray SIVRITEPE

    2010-12-01

    Full Text Available Two-year-old Sultana and Mke vines (Vitis vinifera L. grafted onto Rupestris du Lot (Vitis rupestris Scheele and 110 R (Vitis berlandieri Vitis rupestris were grown in soil, sand, sphagnum peat and farmyard manure mixture (2:1:1:1 v/v irrigated with 0.3, 2.7 and 5.45 dS m-1 NaCl solutions for a period of 60 days. Biomass accumulation, relative chlorophyll content, leaf water potential, stomatal conductance and transpiration were significantly reduced by salinity in all graft combinations. The inhibiting effect of salinity on growth varied according to the characteristics of the scion genotype and the level of salinity. The results imply the predominance of the scion genotype in determining variation in the leaf-level physiological characteristics of grafted vines because stomatal conductance and transpiration were higher in Sultana than in Mke at the same leaf water potential and the level of salinity, regardless of the rootstock genotype. NaCl treatments did not affect leaf Cu concentration while inducing significant Na, K, Ca, N, P, Mg, Fe, Mn and Zn elevations in the leaves of all scion/rootstock combinations. While salinity caused an increase in N content and a decrease in K content in the roots of all graft combinations, it had no influence on Ca, P, Cu and Zn concentrations. In contrast to the Sultana grafted vines, NaCl salinity led to a decrease in Mg, Fe and Mn concentrations in the roots of Mke grafted vines. Nevertheless, ion accumulation in leaves and roots of grafted vines under saline or non-saline conditions was controlled predominantly by the genotype of the scion. In response to salinity, Sultana grafts accumulated higher amounts of ions in their leaves than in their roots. However, in Mke, higher ion concentrations were seen in the roots. Therefore, the increase in the transport of inorganic ions up to the leaves seems to be the major component of osmotic adjustment in salt-stressed Sultana vines.

  16. Lactase persistence genotypes and malaria susceptibility in Fulani of Mali

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    Dolo Amagana

    2011-01-01

    Full Text Available Abstract Background Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene. Methods To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali. Results Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29. Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11. Conclusions Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason

  17. Genotypes and antibiotic resistance of canine Campylobacter jejuni isolates.

    Science.gov (United States)

    Amar, Chantal; Kittl, Sonja; Spreng, David; Thomann, Andreas; Korczak, Bożena M; Burnens, André P; Kuhnert, Peter

    2014-01-10

    Campylobacter jejuni is the most important cause of bacterial gastroenteritis in humans. It is a commensal in many wild and domestic animals, including dogs. Whereas genotypes of human and chicken C. jejuni isolates have been described in some detail, only little information on canine C. jejuni genotypes is available. To gain more information on genotypes of canine C. jejuni and their zoonotic potential, isolates from routine diagnostics of diarrheic dogs as well as isolates of a prevalence study in non-diarrheic dogs were analyzed. Prevalence of thermophilic Campylobacter among non-diarrheic dogs was 6.3% for C. jejuni, 5.9% for Campylobacter upsaliensis and 0.7% for Campylobacter coli. The C. jejuni isolates were genotyped by multi locus sequence typing (MLST) and flaB typing. Resistance to macrolides and quinolones was genetically determined in parallel. Within the 134 genotyped C. jejuni isolates 57 different sequence types (ST) were found. Five STs were previously unrecognized. The most common STs were ST-48 (11.2%), ST-45 (10.5%) and ST-21 (6.0%). Whereas no macrolide resistance was found, 28 isolates (20.9%) were resistant to quinolones. ST-45 was significantly more prevalent in diarrheic than in non-diarrheic dogs. Within the common time frame of isolation 94% of the canine isolates had a ST that was also found in human clinical isolates. In conclusion, prevalence of C. jejuni in Swiss dogs is low but there is a large genetic overlap between dog and human isolates. Given the close contact between human and dogs, the latter should not be ignored as a potential source of human campylobacteriosis. PMID:24210812

  18. Subtyping novel zoonotic pathogen Cryptosporidium chipmunk genotype I.

    Science.gov (United States)

    Guo, Yaqiong; Cebelinski, Elizabeth; Matusevich, Christine; Alderisio, Kerri A; Lebbad, Marianne; McEvoy, John; Roellig, Dawn M; Yang, Chunfu; Feng, Yaoyu; Xiao, Lihua

    2015-05-01

    Cryptosporidium chipmunk genotype I is an emerging zoonotic pathogen in humans. The lack of subtyping tools makes it impossible to determine the role of zoonotic transmission in epidemiology. To identify potential subtyping markers, we sequenced the genome of a human chipmunk genotype I isolate. Altogether, 9,509,783 bp of assembled sequences in 853 contigs were obtained, with an N50 of 117,886 bp and >200-fold coverage. Based on the whole-genome sequence data, two genetic markers encoding the 60-kDa glycoprotein (gp60) and a mucin protein (ortholog of cgd1_470) were selected for the development of a subtyping tool. The tool was used for characterizing chipmunk genotype I in 25 human specimens from four U.S. states and Sweden, one specimen each from an eastern gray squirrel, a chipmunk, and a deer mouse, and 4 water samples from New York. At the gp60 locus, although different subtypes were seen among the animals, water, and humans, the 15 subtypes identified differed mostly in the numbers of trinucleotide repeats (TCA, TCG, or TCT) in the serine repeat region, with only two single nucleotide polymorphisms in the nonrepeat region. Some geographic differences were found in the subtype distribution of chipmunk genotype I from humans. In contrast, only two subtypes were found at the mucin locus, which differed from each other in the numbers of a 30-bp minisatellite repeat. Thus, Cryptosporidium chipmunk genotype I isolates from humans and wildlife are genetically similar, and zoonotic transmission might play a potential role in human infections. PMID:25762767

  19. A novel hepatitis C virus genotyping method based on liquid microarray.

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    Cesar A B Duarte

    Full Text Available The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%. The concordance between the two methods was 100% for genotype determination (74/74. At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively. Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype "1" subtypes (1a and 1b were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

  20. Emergence of Hepatitis B Virus Genotype F in Aligarh Region of North India

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    Hiba Sami

    2013-01-01

    Full Text Available Introduction. HBV genotypes and subtypes are useful clinical and epidemiological markers. In this study prevalent HBV genotypes were assessed in relation to serological profile and clinical status. Material & Methods. 107 cases of HBV were genotyped. Detailed clinical history was elicited from them. HBsAg, HBeAg, anti-HBs, anti-HBe, and anti-HBc-IgM were assessed. HBV genotyping was performed using Kirschberg's type specific primers (TSP-PCR, heminested PCR, and Naito's monoplex PCR. Nucleotide sequencing was performed. Results. A total of 97 (91% were genotyped following the methods of Kirschberg et al./Naito et al. Genotype D was by far the most prevalent genotype 91 (85.04% in this region. A surprising finding was the detection of genotype F in 5 (4.67% of our patients. Genotype A strangely was observed only in one case. In 85.7% genotype D was associated with moderate to severe liver disease, 43.9% HBeAg, and 18.7% anti-HBc-IgM positivity. Majority of genotype F (80% was seen in mild to moderate liver disease. It was strongly associated with HBeAg 60% and 20% anti-HBc-IgM positivity. Conclusion. Emergence of genotype F in India merits further study regarding its clinical implications and treatment modalities. Knowledge about HBV genotypes can direct a clinician towards more informed management of HBV patients.

  1. Prevalence of hepatitis C genotypes in patients with hepatitis C in Lorestan province (2009-2013

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    Mohammad Reza Nazer

    2014-05-01

    Full Text Available Background: Determining hepatitis C genotypes is important to detect the various aspects of this infection, including its epidemiology, pathogenesis and response to anti-viral treatments. The aim of this study was to investigate the prevalence of hepatitis C genotypes in patients admitted to the Infectious Diseases Clinic in Khorramabad. Methods: Out of all the patients admitted to the Infectious Disease Clinic in Khorramabad in a four-year period (April 2009 to March 2013, 120 patients who met the inclusion criteria of the study were evaluated. The PCR method was used to examine the serums of the patients with hepatitis C in terms of the type of genotype. Results: Out of 120 patients, 101 (84.2% were male and 19 (15.8% were female. The most prevalent genotypes were 3a (65%, 1a (24.2%, 1a/1b (5%, and 2 (1.7%, respectively. The genotypes of 5 patients (4.2% could not be determined. No significant relationships were found between gender and genotype, and age group and genotype. Moreover, 18.3% of the patients were HIV-positive. Conclusion: In this study, genotype 3a, the most prevalent genotype, was not consistent with the prevalent genotypes in Arab, European, American, and African countries. Furthermore, genotype 1a was the second most prevalent genotype, while it has been reported as the most prevalent genotype by numerous studies conducted in Iran.

  2. NS4A protein as a marker of HCV history suggests that different HCV genotypes originally evolved from genotype 1b

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    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background The 9.6 kb long RNA genome of Hepatitis C virus (HCV is under the control of RNA dependent RNA polymerase, an error-prone enzyme, for its transcription and replication. A high rate of mutation has been found to be associated with RNA viruses like HCV. Based on genetic variability, HCV has been classified into 6 different major genotypes and 11 different subtypes. However this classification system does not provide significant information about the origin of the virus, primarily due to high mutation rate at nucleotide level. HCV genome codes for a single polyprotein of about 3011 amino acids which is processed into structural and non-structural proteins inside host cell by viral and cellular proteases. Results We have identified a conserved NS4A protein sequence for HCV genotype 3a reported from four different continents of the world i.e. Europe, America, Australia and Asia. We investigated 346 sequences and compared amino acid composition of NS4A protein of different HCV genotypes through Multiple Sequence Alignment and observed amino acid substitutions C22, V29, V30, V38, Q46 and Q47 in NS4A protein of genotype 1b. Furthermore, we observed C22 and V30 as more consistent members of NS4A protein of genotype 1a. Similarly Q46 and Q47 in genotype 5, V29, V30, Q46 and Q47 in genotype 4, C22, Q46 and Q47 in genotype 6, C22, V38, Q46 and Q47 in genotype 3 and C22 in genotype 2 as more consistent members of NS4A protein of these genotypes. So the different amino acids that were introduced as substitutions in NS4A protein of genotype 1 subtype 1b have been retained as consistent members of the NS4A protein of other known genotypes. Conclusion These observations indicate that NS4A protein of different HCV genotypes originally evolved from NS4A protein of genotype 1 subtype 1b, which in turn indicate that HCV genotype 1 subtype 1b established itself earlier in human population and all other known genotypes evolved later as a result of

  3. The impact in older women of ovarian FMR1 genotypes and sub-genotypes on ovarian reserve.

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    Norbert Gleicher

    Full Text Available We recently associated ovarian FMR1genotypes and sub-genotypes with distinct ovarian aging patterns. How they impact older females is, however, unknown. We, therefore, investigated 217 consecutive first in vitro fertilization (IVF cycles in women >40 assessing oocyte yields, stratified for better (anti-Müllerian hormone, AMH >1.05 ng/mL or poorer (AMH ≤ 1.05 ng/mL functional reserve (FOR. Mean age was 42.4 ± 2.0 years, mean AMH 0.76 ± 0.92 ng/mL and mean oocyte yield 5.3 ± 5.4. Overall, and in women with better FOR, FMR1 did not affect oocyte yields. With poorer FOR (AMH ≤ 1.05 ng/mL women with het-norm/high, however, demonstrated higher oocyte yields (5.0 ± 3.8 than those with het-norm/low sub-genotype 3.1 ± 2.5; P = 0.03, confirmed after log conversion. Known associated with low FOR at young age, het-norm/high, thus, appears to preserve FOR into older age, and both het sub-genotypes appear to expand female reproductive lifespan into opposite directions.

  4. Studies on correlation and path analysis in exotic Genotypes of Italian millet [Setaria italica (L. Beauv

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    P. Lakshmi Prasanna, J.S.V. Samba Murthy, P.V. Ramakumar and V. Srinivasa Rao

    2013-03-01

    Full Text Available Thirty four exotic genotypes of Italian millet studied for correlation and path coefficient analysis during kharif and rabi.The investigation during kharif revealed positive significant correlation of days to 50% flowering, plant height, days tomaturity, number of productive tillers per plant, ear length, ear weight and straw weight with yield per plant where asduring rabi besides these characters flag leaf area and 1000 grain weight were also observed to influence yield. Theassociation of protein content and calcium content with grain yield was in negative direction. The association of carotenewith grain yield was negative in during kharif only. So simultaneous improvement of these traits along with grain yield maynot be possible. The study indicated that direct selection based on the characters, number productive tillers per plant duringkharif whereas in rabi ear weight and straw weight are effective as the association and direct effects were positive for thesetraits during both the seasons.

  5. Effect Of Nacl Salt Stress On Antioxidant Enzymes Of Isabgol Plantago Ovata Forsk. Genotypes

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    Suraj Kala

    2015-02-01

    Full Text Available Abstract Activity of antioxidant enzymes such as superoxide dismutase catalase and peroxidase in leaves of isabgol Plantago ovata Forsk. genotypes viz. GI-2 HI-96 PB-80 and HI-5 were studied under salt stress at different EC levels viz. control without salt 5 and 10 dSm-1 of nutrient supplemented NaCl salt solutions in sand filled polythene bags. Salt stress caused significant increase in the activity of superoxide dismutase catalase and peroxidase. Maximum increase in activity of superoxide dismutase and catalase enzymes was found in the genotype GI-2 and minimum increase in the genotype PB-80. Peroxidase activity was highest in the genotype HI-96 and lowest in the genotype PB-80 under salt stress indicating genotype GI-2 and HI-96 having more capacity of scavenging reactive oxygen species produced due to salt stress and were relatively salt tolerant while genotype PB-80 was salt sensitive among the genotypes studied.

  6. Chlamydia trachomatis Genotypes and the Swedish New Variant among Urogenital Chlamydia trachomatis Strains in Finland

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    Suvi Niemi

    2011-01-01

    Full Text Available Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%, F (28%, and G (13%. Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.

  7. Sugarcane Genotype Performance in Three Environments (Based on Crop Cycle) at Mardan, Pakistan

    Science.gov (United States)

    Sugarcane breeders often face significant genotype x environment interactions in their trials grown under multiple environments. Hence, genotypes need to be tested for their stability across different environments keeping in view the significant interactions. An experiment comprising 28 sugarcane ge...

  8. Biotyping and genotyping (MLVA16 of Brucella abortus isolated from cattle in Brazil, 1977 to 2008.

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    Sílvia Minharro

    Full Text Available Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008 of B. abortus and (ii to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region.

  9. Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia

    Institute of Scientific and Technical Information of China (English)

    Suwarto; Nasrullah

    2011-01-01

    To explore the effect of genotype and genotype × environment interaction on Fe concentration in rice grains,Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007-2008 using the AMMI-biplot method.Experiments were conducted using a randomized completely block design with three replications in eight environments.Results indicated that environment (E),genotype (G) and genotype × environment interaction (GE) significantly affected Fe concentration in rice grains.Environment explained 74.43 % of total (G+E+GE) variation,whereas G and GE captured 5.60% and 19.67%,respectively.Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains.Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.

  10. A Sign of Superspreading in Tuberculosis Highly Skewed Distribution of Genotypic Cluster Sizes

    NARCIS (Netherlands)

    Ypma, Rolf J. F.; Altes, Hester Korthals; van Soolingen, Dick; Wallinga, Jacco; van Ballegooijen, W. Marijn

    2013-01-01

    Background: Molecular typing is a valuable tool for gaining insight into spread of Mycobacterium tuberculosis. Typing allows for clustering of cases whose isolates share an identical genotype, revealing epidemiologic relatedness. Observed distributions of genotypic cluster sizes of tuberculosis (TB)

  11. A sign of superspreading in tuberculosis: highly skewed distribution of genotypic cluster sizes.

    NARCIS (Netherlands)

    Ypma, R.J.; Altes, H.K.; Soolingen, D. van; Wallinga, J.; Ballegooijen, W.M. van

    2013-01-01

    BACKGROUND: Molecular typing is a valuable tool for gaining insight into spread of Mycobacterium tuberculosis. Typing allows for clustering of cases whose isolates share an identical genotype, revealing epidemiologic relatedness. Observed distributions of genotypic cluster sizes of tuberculosis (TB)

  12. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: Efficacy of vaccination

    Science.gov (United States)

    Here we describe the characterization a virulent genotype VII Newcastle disease virus (NDV) from Venezuela and evaluate the efficacy of heterologous genotype commercial vaccination under field and controlled rearing conditions. Biological pathotyping and molecular analysis were applied. Results sh...

  13. A novel hepatitis B virus genotyping system by using restriction fragment length polymorphism patterns of S gene amplicons

    Institute of Scientific and Technical Information of China (English)

    Guo-Bing Zeng; Shu-Juan Wen; Zhan-Hui Wang; Li Yan; Jian Sun; Jin-Lin Hou

    2004-01-01

    AIM: Traditional hepatitis B virus (HBV) genotyping methods using restriction fragment length polymorphism (RFLP) can reliably identify genotypes A to F. As HBV genotypes G and H have been recently identified, this study was to establish an accurate and simple genotyping method for all eight HBV genotypes (A to H).METHODS: Two hundred and forty HBV small S sequences obtained from GeneBank were analysed for restriction enzyme sites that would be genotype-specific. Restriction patterns following digestion with restriction enzymes BsrⅠ,StyⅠ, DpnⅠ, HpaⅡ, and EaeⅠ, were determined to identify all eight HBV genotypes. Mixed genotype infections were confirmed by cloning and further RFLP analysis.RESULTS: The new genotyping method could identify HBV genotypes A to H. Genotypes B and C could be determined by a single step digestion with BsrⅠ and StyⅠ in parallel. This was particularly useful in the Far East where genotypes B and C are predominant. Serum samples from 187 Chinese HBV carriers were analysed with this genotyping system, and the genotype distribution was 1.1% (2), 51.9% (97), 40.6% (76) and 4.8%(9) for genotypes A, B, C, and D, respectively. Mixed genotypes were found in only 3 patients (1.6%). Sequence data analysis confirmed the validity of this new method.CONCLUSION: This HBV genotyping system can identify all eight HBV genotypes. It is accurate and simple, and can be widely used for studies on HBV genotyping.

  14. Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions.

    Science.gov (United States)

    Mattila, Anniina L K

    2015-12-01

    Knowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association of heat-shock protein (Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal-related thermal performance in butterflies and other insects. Such information is needed for predictive

  15. Affective neural responses modulated by serotonin transporter genotype in clinical anxiety and depression.

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    Desmond J Oathes

    Full Text Available Serotonin transporter gene variants are known to interact with stressful life experiences to increase chances of developing affective symptoms, and these same variants have been shown to influence amygdala reactivity to affective stimuli in non-psychiatric populations. The impact of these gene variants on affective neurocircuitry in anxiety and mood disorders has been studied less extensively. Utilizing a triallelic assay (5-HTTLPR and rs25531 to assess genetic variation linked with altered serotonin signaling, this fMRI study investigated genetic influences on amygdala and anterior insula activity in 50 generalized anxiety disorder patients, 26 of whom also met DSM-IV criteria for social anxiety disorder and/or major depressive disorder, and 39 healthy comparison subjects. A Group x Genotype interaction was observed for both the amygdala and anterior insula in a paradigm designed to elicit responses in these brain areas during the anticipation of and response to aversive pictures. Patients who are S/L(G carriers showed less activity than their L(A/L(A counterparts in both regions and less activity than S/L(G healthy comparison subjects in the amygdala. Moreover, patients with greater insula responses reported higher levels of intolerance of uncertainty, an association that was particularly pronounced for patients with two LA alleles. A genotype effect was not established in healthy controls. These findings link the serotonin transporter gene to affective circuitry findings in anxiety and depression psychopathology and further suggest that its impact on patients may be different from effects typically observed in healthy populations.

  16. Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions.

    Science.gov (United States)

    Mattila, Anniina L K

    2015-12-01

    Knowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association of heat-shock protein (Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal-related thermal performance in butterflies and other insects. Such information is needed for predictive

  17. Complex nature of SNP genotype effects on gene expression in primary human leucocytes

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    Dinesen Lotte C

    2009-01-01

    Full Text Available Abstract Background Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence biological function is usually unknown. Methods We correlated gene expression and genetic variation in untouched primary leucocytes (n = 110 from individuals with celiac disease – a common condition with multiple risk variants identified. We compared our observations with an EBV-transformed HapMap B cell line dataset (n = 90, and performed a meta-analysis to increase power to detect non-tissue specific effects. Results In celiac peripheral blood, 2,315 SNP variants influenced gene expression at 765 different transcripts (cis expression quantitative trait loci, eQTLs. 135 of the detected SNP-probe effects (reflecting 51 unique probes were also detected in a HapMap B cell line published dataset, all with effects in the same allelic direction. Overall gene expression differences within the two datasets predominantly explain the limited overlap in observed cis-eQTLs. Celiac associated risk variants from two regions, containing genes IL18RAP and CCR3, showed significant cis genotype-expression correlations in the peripheral blood but not in the B cell line datasets. We identified 14 genes where a SNP affected the expression of different probes within the same gene, but in opposite allelic directions. By incorporating genetic variation in co-expression analyses, functional relationships between genes can be more significantly detected. Conclusion In conclusion, the complex nature of genotypic effects in human populations makes the use of a relevant tissue, large datasets, and analysis of different exons essential to enable the identification of the function for many genetic risk variants in common diseases.

  18. Germination and growth of white oat genotypes seedlings submitted to salt stress

    OpenAIRE

    Fabiana Ca