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Sample records for genetic polymorphisms related

  1. Genetic polymorphisms related to testosterone metabolism in intellectually gifted boys.

    Science.gov (United States)

    Celec, Peter; Tretinárová, Denisa; Minárik, Gabriel; Ficek, Andrej; Szemes, Tomáš; Lakatošová, Silvia; Schmidtová, Eva; Turňa, Ján; Kádaši, Ľudevít; Ostatníková, Daniela

    2013-01-01

    Prepubertal testosterone levels are lower in intellectually gifted boys. The aim of this pilot study was to analyze potential genetic factors related to testosterone metabolism in control and gifted boys. Intellectually gifted (IQ>130; n = 95) and control (n = 67) boys were genotyped. Polymorphisms of interests were chosen in genes including androgen and estrogen receptors, 5-alpha reductase, aromatase and sex hormone binding globulin. Significant differences between control and gifted boys in genotype distributions were found for ESR2 (rs928554) and SHBG (rs1799941). A significantly lower number of CAG repeats in the AR gene were found in gifted boys. Our results support the role of genetic factors related to testosterone metabolism in intellectual giftedness. Increased androgen signaling might explain previous results of lower testosterone levels in intellectually gifted boys and add to the understanding of variability in cognitive abilities.

  2. Genetic Polymorphisms Related to Testosterone Metabolism in Intellectually Gifted Boys

    Science.gov (United States)

    Celec, Peter; Tretinárová, Denisa; Minárik, Gabriel; Ficek, Andrej; Szemes, Tomáš; Lakatošová, Silvia; Schmidtová, Eva; Turňa, Ján; Kádaši, Ľudevít; Ostatníková, Daniela

    2013-01-01

    Prepubertal testosterone levels are lower in intellectually gifted boys. The aim of this pilot study was to analyze potential genetic factors related to testosterone metabolism in control and gifted boys. Intellectually gifted (IQ>130; n = 95) and control (n = 67) boys were genotyped. Polymorphisms of interests were chosen in genes including androgen and estrogen receptors, 5-alpha reductase, aromatase and sex hormone binding globulin. Significant differences between control and gifted boys in genotype distributions were found for ESR2 (rs928554) and SHBG (rs1799941). A significantly lower number of CAG repeats in the AR gene were found in gifted boys. Our results support the role of genetic factors related to testosterone metabolism in intellectual giftedness. Increased androgen signaling might explain previous results of lower testosterone levels in intellectually gifted boys and add to the understanding of variability in cognitive abilities. PMID:23382957

  3. Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder

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    Mayor-Olea Alvaro

    2011-05-01

    Full Text Available Abstract Background Temporomandibular disorder (TMD is a multifactorial syndrome related to a critical period of human life. TMD has been associated with psychological dysfunctions, oxidative state and sexual dimorphism with coincidental occurrence along the pubertal development. In this work we study the association between TMD and genetic polymorphisms of folate metabolism, neurotransmission, oxidative and hormonal metabolism. Folate metabolism, which depends on genes variations and diet, is directly involved in genetic and epigenetic variations that can influence the changes of last growing period of development in human and the appearance of the TMD. Methods A case-control study was designed to evaluate the impact of genetic polymorphisms above described on TMD. A total of 229 individuals (69% women were included at the study; 86 were patients with TMD and 143 were healthy control subjects. Subjects underwent to a clinical examination following the guidelines by the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD. Genotyping of 20 Single Nucleotide Polymorphisms (SNPs, divided in two groups, was performed by multiplex minisequencing preceded by multiplex PCR. Other seven genetic polymorphisms different from SNPs (deletions, insertions, tandem repeat, null genotype were achieved by a multiplex-PCR. A chi-square test was performed to determine the differences in genotype and allelic frequencies between TMD patients and healthy subjects. To estimate TMD risk, in those polymorphisms that shown significant differences, odds ratio (OR with a 95% of confidence interval were calculated. Results Six of the polymorphisms showed statistical associations with TMD. Four of them are related to enzymes of folates metabolism: Allele G of Serine Hydoxymethyltransferase 1 (SHMT1 rs1979277 (OR = 3.99; 95%CI 1.72, 9.25; p = 0.002, allele G of SHMT1 rs638416 (OR = 2.80; 95%CI 1.51, 5.21; p = 0.013, allele T of Methylentetrahydrofolate

  4. Identification of trends in scientific publications related to genetic polymorphisms in gestational diabetes mellitus.

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    Gomes, J S; Minasi, L B; da Cruz, A D; Rodrigues, F M

    2016-05-09

    Gestational diabetes is a genetic multifactorial systemic disease that has been extensively studied. Consequently, there is a large volume of scientific literature pertaining to genes associated with gestational diabetes. The aim of this study was to characterize the main trends in scientific publications focusing on the associations between genetic polymorphisms and gestational diabetes mellitus (GDM). The related articles were extracted from Scopus using the key words "genetic polymorphism" and "gestational diabetes mellitus"; the collected data focused on various fields (medical, biochemical, etc.) and included papers published within December 2013. One hundred and eighty-three relevant articles published between 1987 and 2013 were identified; we observed a significantly increasing trend in the number of publications pertaining to GDM. A majority of the articles focused on the medical (59.9%), biochemical, and genetics and molecular biological (29.6%) aspects of the disease. The genes coding for transcription factor 7-like 2 and glucokinase (TCF7L2, 29% and GCK, 28%) were predominantly studied and reported. This study helped quantify the growth in research pertaining to GDM; researchers from the USA have published a majority of the publications related to GDM. Several candidate genes have been linked to diabetes; however, the specific gene locus responsible for GDM has not yet been identified. The results of this study could help determine the orientation of future research on genetic factors associated with GDM.

  5. Impact of Genetic Polymorphisms on the Smoking-related Risk of Periodontal Disease: the Population-based Study SHIP

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    Meisel P

    2003-09-01

    Full Text Available Abstract Periodontitis is a bacterial inflammatory disease leading to attachment loss with the consequence of tooth loss. There exists a multifactorial risk pattern including bacterial challenge, smoking, age, sex, diabetes, socio-economic and genetic factors. Smoking has the highest impact on the course of the disease modulated by all the other factors. Here, we report the relationship between smoking and the polymorphisms of genetic polymorphisms inflicted in the pathogenesis. In a randomly selected population-based study, 1083 subjects were typed for the polymorphisms of the IL-1 genotype, Fcγ RIIIb receptor gene, myeloperoxidase and N-acetyltransferase (NAT2 and related to their periodontal state. Smoking behavior was assessed including present and past quality and quantity of smoking. There is a significant dose-effect relationship between the exposure to tobacco smoke and the extent of periodontal disease assessed as attachment loss and tooth loss. Moreover, there are gene-environmental interactions as subjects bearing variant genotypes show an enhanced smoking-associated risk of the disease modulated by these genotypes. In non-smokers, the impact of these genetic polymorphisms is mostly negligible. This study provides support for the hypothesis that subjects bearing genetic variants of polymorphically expressed phenotypes are at an increased risk of periodontitis when smoking. Mostly, this may be accomplished via the influence of smoking-related impairment on defense mechanisms rather than on the pathogenic pathways.

  6. Impact of Genetic Polymorphisms on the Smoking-related Risk of Periodontal Disease: the Population-based Study SHIP

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    Schwahn C

    2003-09-01

    Full Text Available Abstract Periodontitis is a bacterial inflammatory disease leading to attachment loss with the consequence of tooth loss. There exists a multifactorial risk pattern including bacterial challenge, smoking, age, sex, diabetes, socio-economic and genetic factors. Smoking has the highest impact on the course of the disease modulated by all the other factors. Here, we report the relationship between smoking and the polymorphisms of genetic polymorphisms inflicted in the pathogenesis. In a randomly selected population-based study, 1083 subjects were typed for the polymorphisms of the IL-1 genotype, Fcγ RIIIb receptor gene, myeloperoxidase and N-acetyltransferase (NAT2 and related to their periodontal state. Smoking behavior was assessed including present and past quality and quantity of smoking. There is a significant dose-effect relationship between the exposure to tobacco smoke and the extent of periodontal disease assessed as attachment loss and tooth loss. Moreover, there are gene-environmental interactions as subjects bearing variant genotypes show an enhanced smoking-associated risk of the disease modulated by these genotypes. In non-smokers, the impact of these genetic polymorphisms is mostly negligible. This study provides support for the hypothesis that subjects bearing genetic variants of polymorphically expressed phenotypes are at an increased risk of periodontitis when smoking. Mostly, this may be accomplished via the influence of smoking-related impairment on defense mechanisms rather than on the pathogenic pathways.

  7. Genetic contributions to age-related decline in executive function: a 10-year longitudinal study of COMT and BDNF polymorphisms

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    Kirk I Erickson

    2008-09-01

    Full Text Available Genetic variability in the dopaminergic and neurotrophic systems could contribute to age-related impairments in executive control and memory function. In this study we examined whether genetic polymorphisms for catechol-O-methyltransferase (COMT and brain-derived neurotrophic factor (BDNF were related to the trajectory of cognitive decline occurring over a 10-year period in older adults. A single-nucleotide polymorphism (SNP in the COMT (Val158/108Met gene affects the concentration of dopamine in the prefrontal cortex. In addition, a Val/Met substitution in the pro-domain for BDNF (Val66Met affects the regulated secretion and trafficking of BDNF with Met carriers showing reduced secretion and poorer cognitive function. We found that impairments over the 10-year span on a task-switching paradigm did not vary as a function of the COMT polymorphism. However, for the BDNF polymorphism the Met carriers performed worse than Val homozygotes at the first testing session but only the Val homozygotes demonstrated a significant reduction in performance over the 10-year span. Our results argue that the COMT polymorphism does not affect the trajectory of age-related executive control decline, whereas the Val/Val polymorphism for BDNF may promote faster rates of cognitive decay in old age. These results are discussed in relation to the role of BDNF in senescence and the transforming impact of the Met allele on cognitive function in old age.

  8. Genetic diversity and relationships in cultivars of Lolium multiflorum Lam. using sequence-related amplified polymorphism markers.

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    Huang, L K; Jiang, X Y; Huang, Q T; Xiao, Y F; Chen, Z H; Zhang, X Q; Miao, J M; Yan, H D

    2014-12-04

    Sequence-related amplified polymorphism (SRAP) markers were used to analyze and estimate the genetic variability, level of diversity, and relationships among 20 cultivars and strains of annual ryegrass (Lolium multiflorum Lam.). Eighteen SRAP primer combinations generated 334 amplification bands, of which 298 were polymorphic. The polymorphism information content ranged from 0.4715 (me10 + em1) to 0.5000 (me5 + em7), with an average of 0.4921. The genetic similarity coefficient ranged from 0.4304 to 0.8529, and coefficients between 0.65 and 0.90 accounted for 90.00%. The cluster analysis separated the accessions into five groups partly according to their germplasm resource origins.

  9. Type 2 diabetes mellitus-related genetic polymorphisms in microRNAs and microRNA target sites.

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    Gong, Weijing; Xiao, Di; Ming, Guangfeng; Yin, Jiye; Zhou, Honghao; Liu, Zhaoqian

    2014-07-01

    MicroRNAs (miRNAs) are important endogenous regulators in eukaryotic gene expression and a broad range of biological processes. MiRNA-related genetic variations have been proved to be associated with human diseases, such as type 2 diabetes mellitus (T2DM). Polymorphisms in miRNA genes (primary miRNAs, precursor miRNAs, mature miRNAs, and miRNA regulatory regions) may be involved in the development of T2DM by changing the expression and structure of miRNAs and target gene expression. Genetic polymorphisms of the 3'-untranslated region (UTR) in miRNA target genes may destroy putative miRNA binding sites or create new miRNA binding sites, which affects the binding of UTRs with miRNAs, finally resulting in susceptibility to and development of T2DM. Therefore, focusing on studies into genetic polymorphisms in miRNAs or miRNA binding sites will help our understanding of the pathophysiology of T2DM development and lead to better health management. Herein, we review the association of genetic polymorphisms in miRNA and miRNA targets genes with T2DM development.

  10. Evaluation of genetic diversity in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by using rapid amplified polymorphic DNA and sequence-related amplified polymorphism markers.

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    Zhang, J; Zhang, L G

    2014-02-14

    Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement.

  11. Genetic polymorphisms in Kawasaki disease

    Institute of Scientific and Technical Information of China (English)

    Ho-chang KUO; Wei-chiao CHANG

    2011-01-01

    Kawasaki disease (KD) is an acute febrile systemic vasculitis,and the cause of KD is not well understood.It is likely due to multiple interactions between genes and environmental factors.The development of genetic association and genome-wide association studies (GWAS) has opened an avenue to better understanding the molecular mechanisms underlying KD.A novel ITPKC signaling pathway was recently found to be responsible for the susceptibility to KD.Furthermore,the GWAS demonstrated the functionally related susceptibility loci for KD in the Caucasian population.In the last decade,the identification of several genomic regions linked to the pathogenesis of KD has made a major breakthrough in understanding the genetics of KD.This review will focus on genetic polymorphisms associated with KD and describe some of the possible clinical implications and molecular mechanisms that can be used to explain how genetic variants regulate the pathogenesis in KD.

  12. Genetic polymorphism of the iron-regulatory protein-1 and -2 genes in age-related macular degeneration.

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    Synowiec, Ewelina; Pogorzelska, Magdalena; Blasiak, Janusz; Szaflik, Jerzy; Szaflik, Jacek Pawel

    2012-06-01

    Iron can be involved in the pathogenesis of AMD through the oxidative stress because it may catalyze the Haber-Weiss and Fenton reactions converting hydrogen peroxide to free radicals, which can induce cellular damage. We hypothesized that genetic polymorphism in genes related to iron metabolism may predispose individuals to the development of AMD and therefore we checked for an association between the g.32373708 G>A polymorphism (rs867469) of the IRP1 gene and the g.49520870 G>A (rs17483548) polymorphism of the IRP2 gene and AMD risk as well as the modulation of this association by some environmental and life-style factors. Genotypes were determined in DNA from blood of 269 AMD patients and 116 controls by the allele-specific oligonucleotide-restriction fragment length polymorphism and the polymerase chain reaction-restriction fragment length polymorphism. An association between AMD, dry and wet forms of AMD and the G/G genotype of the g.32373708 G>A-IRP1 polymorphism was found (OR 3.40, 4.15, and 2.75). On the other hand, the G/A genotype reduced the risk of AMD as well as its dry or wet form (OR 0.23, 0.21, 0.26). Moreover, the G allele of the g.49520870 G>A-IRP2 polymorphism increased the risk of the dry form of the disease (OR 1.51) and the A/A genotype and the A allele decreased such risk (OR 0.43 and 0.66). Our data suggest that the g.32373708 G>A-IRP1 and g.49520870 G>A-IRP2 polymorphisms may be associated with increased risk for AMD.

  13. General and Specific Genetic Polymorphism of Cytokines-Related Gene in AITD

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    Chen Xiaoheng

    2017-01-01

    Full Text Available Autoimmune thyroid disease (AITD shows the highest incidence among organ-specific autoimmune diseases and is the most common thyroid disease in humans, including Graves’ disease (GD and Hashimoto’s thyroiditis (HT. The susceptibility to autoimmune diseases is affected by increased autoantibody levels, susceptibility gene polymorphisms, environmental factors, and psychological factors, but the pathogenesis remains unclear. Various cytokines and related genes encoding them play important roles in the development and progression of AITD. CD152, an expression product of the CTLA-4 gene, downregulates T cell activation. The A/A genotype polymorphism in the CT60 locus may reduce the production of thyroid autoantibodies. The C1858T polymorphism of the PTNP22 gene reduces the expression of its encoded LYP, which increases the risk of GD and HT. GD is an organ-specific autoimmune disease involving increased secretion of thyroid hormone, whereas HT may be associated with the destruction of thyroid gland tissue and hypothyroidism. These two diseases exhibit similar pathogenesis but opposite trends in the clinical manifestations. In this review, we focus on the structure and function of these cytokines and related genes in AITD, as well as the association of polymorphisms with susceptibility to GD and HT, and attempt to describe their differences in pathogenesis and clinical manifestations.

  14. General and Specific Genetic Polymorphism of Cytokines-Related Gene in AITD

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    Yizhou, Mei; Bei, He; Huilong, Li; Xin, Wang; Rui, Hu; Lu, Li

    2017-01-01

    Autoimmune thyroid disease (AITD) shows the highest incidence among organ-specific autoimmune diseases and is the most common thyroid disease in humans, including Graves' disease (GD) and Hashimoto's thyroiditis (HT). The susceptibility to autoimmune diseases is affected by increased autoantibody levels, susceptibility gene polymorphisms, environmental factors, and psychological factors, but the pathogenesis remains unclear. Various cytokines and related genes encoding them play important roles in the development and progression of AITD. CD152, an expression product of the CTLA-4 gene, downregulates T cell activation. The A/A genotype polymorphism in the CT60 locus may reduce the production of thyroid autoantibodies. The C1858T polymorphism of the PTNP22 gene reduces the expression of its encoded LYP, which increases the risk of GD and HT. GD is an organ-specific autoimmune disease involving increased secretion of thyroid hormone, whereas HT may be associated with the destruction of thyroid gland tissue and hypothyroidism. These two diseases exhibit similar pathogenesis but opposite trends in the clinical manifestations. In this review, we focus on the structure and function of these cytokines and related genes in AITD, as well as the association of polymorphisms with susceptibility to GD and HT, and attempt to describe their differences in pathogenesis and clinical manifestations. PMID:28133421

  15. Cigarette smoking, genetic polymorphisms and colorectal cancer risk: the Fukuoka Colorectal Cancer Study

    National Research Council Canada - National Science Library

    Nisa, Hoirun; Kono, Suminori; Yin, Guang; Toyomura, Kengo; Nagano, Jun; Mibu, Ryuichi; Tanaka, Masao; Kakeji, Yoshihiro; Maehara, Yoshihiko; Okamura, Takeshi; Ikejiri, Koji; Futami, Kitaroh; Maekawa, Takafumi; Yasunami, Yohichi; Takenaka, Kenji; Ichimiya, Hitoshi; Terasaka, Reiji

    2010-01-01

    .... We investigated the relation of cigarette smoking and related genetic polymorphisms to colorectal cancer risk, with special reference to the interaction between smoking and genetic polymorphism...

  16. Associations between Salivary Testosterone Levels, Androgen‐Related Genetic Polymorphisms, and Self‐Estimated Ejaculation Latency Time

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    Patrick Jern, PhD

    2014-08-01

    Conclusions: We were unable to find support for the hypothesis suggesting an association between T levels and ELT, possibly because of the low number of phenotypically extreme cases (the sample used in the present study was population based. Our results concerning genetic associations should be interpreted with caution until replication studies have been conducted. Jern P, Westberg L, Ankarberg‐Lindgren C, Johansson A, Gunst A, Sandnabba NK, and Santtila P. Associations between salivary testosterone levels, androgen‐related genetic polymorphisms, and self‐estimated ejaculation latency time. Sex Med 2014;2:107–114.

  17. The study of genetic polymorphisms related to serotonin in Alzheimer's disease: a new perspective in a heterogenic disorder

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    Oliveira J.R.M.

    1999-01-01

    Full Text Available Genetic and environmental factors have been implicated in the development of Alzheimer's disease (AD, the most common form of dementia in the elderly. Mutations in 3 genes mapped on chromosomes 21, 14 and 1 are related to the rare early onset forms of AD while the e4 allele of the apolipoprotein E (APOE gene (on chromosome 19 is the major susceptibility locus for the most common late onset AD (LOAD. Serotonin (5-hydroxytryptamine or 5-HT is a key neurotransmitter implicated in the control of mood, sleep, appetite and a variety of traits and behaviors. Recently, a polymorphism in the transcriptional control region upstream of the 5-HT transporter (5-HTT gene has been studied in several psychiatric diseases and personality traits. It has been demonstrated that the short variant(s of this 5-HTT gene-linked polymorphic region (5-HTTLPR is associated with a different transcriptional efficiency of the 5-HTT gene promoter resulting in decreased 5-HTT expression and 5-HT uptake in lymphocytes. An increased frequency of this 5-HTTLPR short variant polymorphism in LOAD was recently reported. In addition, another common polymorphic variation in the 5-HT2A and 5-HT2C serotonin receptor genes previously analyzed in schizophrenic patients was associated with auditory and visual hallucinations in AD. These observations suggest that the involvement of the serotonin pathway might provide an explanation for some aspects of the affective symptoms commonly observed in AD patients. In summary, research on genetic polymorphisms related to AD and involved in receptors, transporter proteins and the enzymatic machinery of serotonin might enhance our understanding of this devastating neurodegenerative disorder.

  18. The study of genetic polymorphisms related to serotonin in Alzheimer's disease: a new perspective in a heterogenic disorder.

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    Oliveira, J R; Zatz, M

    1999-04-01

    Genetic and environmental factors have been implicated in the development of Alzheimer's disease (AD), the most common form of dementia in the elderly. Mutations in 3 genes mapped on chromosomes 21, 14 and 1 are related to the rare early onset forms of AD while the epsilon 4 allele of the apolipoprotein E (APOE) gene (on chromosome 19) is the major susceptibility locus for the most common late onset AD (LOAD). Serotonin (5-hydroxytryptamine or 5-HT) is a key neurotransmitter implicated in the control of mood, sleep, appetite and a variety of traits and behaviors. Recently, a polymorphism in the transcriptional control region upstream of the 5-HT transporter (5-HTT) gene has been studied in several psychiatric diseases and personality traits. It has been demonstrated that the short variant(s) of this 5-HTT gene-linked polymorphic region (5-HTTLPR) is associated with a different transcriptional efficiency of the 5-HTT gene promoter resulting in decreased 5-HTT expression and 5-HT uptake in lymphocytes. An increased frequency of this 5-HTTLPR short variant polymorphism in LOAD was recently reported. In addition, another common polymorphic variation in the 5-HT2A and 5-HT2C serotonin receptor genes previously analyzed in schizophrenic patients was associated with auditory and visual hallucinations in AD. These observations suggest that the involvement of the serotonin pathway might provide an explanation for some aspects of the affective symptoms commonly observed in AD patients. In summary, research on genetic polymorphisms related to AD and involved in receptors, transporter proteins and the enzymatic machinery of serotonin might enhance our understanding of this devastating neurodegenerative disorder.

  19. Obesity-related genetic polymorphisms and adiposity indices in a young Italian population.

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    Bordoni, Laura; Marchegiani, Francesca; Piangerelli, Marco; Napolioni, Valerio; Gabbianelli, Rosita

    2017-02-01

    Pediatric obesity develops when a complex biological predisposition collides with an obesogenic environment. To further elucidate the role of genetics in obesity onset, we performed a candidate-gene association study in a young and sportive Italian population by testing the association of functional polymorphisms in ACE (rs4646994), FTO (rs9939609), MC4R (rs17782313) and PPARG (rs1801282) genes with body mass index (BMI) and waist-to-height ratio (WHtR). We also tested the combinations of identified risk genotypes and epistatic interactions among them to determine the existence of cumulative effects in predicting the predisposition to gain weight. Our results confirm a significant direct influence of MC4R rs17782313 and PPARG rs1801282 on body composition, that is, minor allele homozygotes showed significantly higher BMI (rs17782313, β = 1.258, P = 0.031; rs1801282, β = 6.689, P = 1.2 × 10(-4) ) and WHtR (rs17782313, β = 0.021, P = 0.005; rs1801282, β = 0.069, P = 0.003) values. Moreover, by leveraging multifactor dimensionality reduction and general linear model (GLM) approaches we identified an epistatic interaction between ACE and MC4R, where heterozygosity at ACE rs4646994 seems to protect from the unfavorable predisposition to gain weight given by C/C genotype at MC4R rs17782313 (GLM, P = 0.004). In conclusion, to clarify the role of genetics in multifactorial diseases remains a difficult goal, even for the most investigated polymorphisms and in controlled populations. Further studies on epistasis and gene-gene interaction will help to elucidate this complex scenario. © 2017 IUBMB Life, 69(2):98-105, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

  20. Genetic polymorphisms in obesity-related genes and endometrial cancer risk

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    Chen, Xiaoli; Xiang, Yong-Bing; Long, Ji-Rong; Cai, Hui; Cai, Qiuyin; Cheng, Jiarong; Wen, Wanqing; Gao, Yu-Tang; Zheng, Wei; Shu, Xiao-Ou

    2011-01-01

    Background Obesity is associated with circulating levels of adiponectin and leptin and endometrial cancer risk. Little is known about whether single nucleotide polymorphisms (SNPs) in the genes that encode adiponectin (ADIPOQ), leptin (LEP), adiponectin receptor 1 (ADIPOR1), adiponectin receptor 2 (ADIPOR2), and leptin receptor (LEPR) are associated with endometrial cancer. Methods We selected 87 tagging SNPs to capture common genetic variants in these five genes. These SNPs were evaluated in 1,028 endometrial cancer cases and 1,932 community controls recruited from Chinese women. Logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs). Results Three of the 10 SNPs evaluated in the ADIPOQ gene were significantly associated with reduced cancer risk. The OR for women homozygous for the minor allele (A/A) for rs3774262 was 0.68 (95% CI: 0.48-0.97) compared with women homozygous for the major allele (G/G). Similar results were found for SNPs rs1063539 and rs12629945 in ADIPOQ, which were in linkage disequilibrium with rs3774262. These associations became non-significant after Bonferroni correction was applied. Controls with the minor allele A at rs3774262 had lower weight, waist circumference, hip circumference, and BMI than controls with the major allele G (all P<0.05). Women homozygous for the minor allele (T/T) of rs2071045 in the LEP gene also had significantly lower risk (OR=0.70 (0.54-0.90)) than women homozygous for the major allele (C/C). No other SNPs in the LEP, ADIPOR1, ADIPOR2, or LEPR genes were found to be associated with cancer risk. Conclusions Although a chance finding cannot be ruled out, the consistency of findings for gene-endometrial cancer risk and gene-obesity measurements suggests that genetic polymorphisms in the ADIPOQ genes may play a role in endometrial cancer development. PMID:22038736

  1. Genetic polymorphisms in dopamine-related genes and smoking cessation in women: a prospective cohort study

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    Srinouanprachan Sengkeo

    2007-04-01

    Full Text Available Abstract Background Genes involved in dopaminergic neurotransmission have been suggested as candidates for involvement in smoking behavior. We hypothesized that alleles associated with reduced dopaminergic neurotransmission would be more common in continuing smokers than among women who quit smoking. Methods The study included 593 women aged 26–65 years who participated in a twelve month smoking cessation trial conducted in 1993–1994. Participants were contacted three years after the trial to obtain updated smoking history and biological specimens. Seven polymorphisms were assessed in genes involved in dopamine synthesis (tyrosine hydoxylase [TH], receptor activation (dopamine receptors [DRD2, DRD3, DRD4], reuptake (dopamine transporter [SLC6A3], and metabolism (catechol-o-methyltransferase [COMT]. Smoking cessation was assessed as "short-term" quitting (abstinence for the seven days before the conclusion of the trial and "long-term" quitting (abstinence for the six months before a subsequent interview conducted several years later. Results We observed no association of any polymorphism with either short- or long-term quitting. Although some relative risk estimates were consistent with weak associations, either the direction of effect was opposite of that hypothesized, or results of the short- and long-term cessation endpoints differed. However, effect modification on smoking cessation was observed between DRD2 Taq1A and SLC6A3 VNTR polymorphisms, DRD3 Ser/Gly and d,1-fenfluramine, and DRD4 VNTR and d,1-fenfluramine. Conclusion Although these results fail to support prior findings of independent associations of these polymorphisms with smoking status, our exploratory findings suggestive of gene-gene and gene-treatment interactions warrants further investigation.

  2. Common genetic polymorphisms within NFκB-related genes and the risk of developing invasive aspergillosis

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    Carmen Belén Lupiañez

    2016-08-01

    Full Text Available Invasive Aspergillosis (IA is an opportunistic infection caused by Aspergillus, a ubiquitously present airborne pathogenic mould. A growing number of studies suggest a major host genetic component in disease susceptibility. Here, we evaluated whether 14 single-nucleotide polymorphisms within NFκB1, NFκB2, RelA, RelB, Rel and IRF4 genes influence the risk of IA in a population of 834 high-risk patients (157 IA and 677 non-IA recruited through a collaborative effort involving the aspBIOmics consortium and four European clinical institutions. No significant overall associations between selected SNPs and the risk of IA were found in this large cohort. Although a hematopoietic stem cell transplantation (HSCT-stratified analysis revealed that carriers of the IRF4rs12203592T/T genotype had a 6-fold increased risk of developing the infection when compared with those carrying the C allele (OR-Rec=6.24, 95%CI 1.25-31.2, P=0.026, the association of this variant with IA risk did not reach significance at experiment-wide significant threshold. In addition, we found an association of the IRF4AATC and IRF4GGTC haplotypes (not including the IRF4rs12203592T risk allele with a decreased risk of IA but the magnitude of the association was similar to the one observed in the single-SNP analysis, which indicated that the haplotypic effect on IA risk was likely due to the IRF4rs12203592 SNP. Finally, no evidence of significant interactions among the genetic markers tested and the risk of IA was found. These results suggest that the SNPs on the studied genes do not have a clinically relevant impact on the risk of developing IA.

  3. Association Study of Vitamin D Receptor (VDR) - Related Genetic Polymorphisms and their Haplotypes with Chronic Periodontitis in Colombian Population

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    Isaza-Guzmán, Diana María; Pineda-Trujillo, Nicolás

    2017-01-01

    Introduction There is strong evidence that both genetic and environmental factors may affect the periodontal clinical status. However, epidemiological evidence on the association between Vitamin D Receptor (VDR) polymorphisms and Chronic Periodontitis (CP) has been inconsistent. Aim The focus of this study was to identify if a possible association between VDR Single-Nucleotide Polymorphisms (SNPs) may be implicated in the aetiopathogenesis of CP in Colombian population. Materials and Methods One hundred and ten CP patients and 50 Healthy Controls (HC) were recruited. Periodontal status was assessed based on probing depth, clinical attachment level, extent, and severity of periodontal breakdown. The polymerase chain reaction-restriction fragment length polymorphism method was used to identify the VDR rs7975232, rs1544410, rs2228570, and rs731236 SNPs from saliva samples. Odds Ratios (ORs) along with their 95% Confidence Intervals (CIs) were computed to compare the distribution of genotypes/alleles between HC and CP patients, alongside with analysis of Linkage Disequilibrium (LD) and haplotype associations between SNPs. Also, an analysis of the interaction between genetic findings and those significant demographic factors was performed for all SNPs. Results There was no association neither between the different genotypes/allele frequencies nor haplotypes and CP. Similarly, no significant differences in extent or severity amongst genotype/allele groups were observed. Even so, interaction analysis revealed significant synergistic interactions between each SNP and age associated with the disease status. Conclusion Although these results do not support that VDR SNPs could be identified as independent risk predictor variables for CP in the Colombian population, synergistic biological interactive effects of all these SNPs related to age might play a significant role in the pathogenic pathways of CP. PMID:28384983

  4. Genetic polymorphisms in the hypothalamic pathway in relation to subsequent weight change - the DIOGenes Study

    NARCIS (Netherlands)

    Huaidong, D.U.; Vimaleswaran, K.S.; Angquist, L.; Hansen, R.D.; A, van der D.L.; Holst, C.; Tjonneland, A.; Overvad, K.; Uhre Jakobsen, M.; Boeing, H.; Meidtner, K.; Palli, D.; Masala, G.; Bouatia-Naji, N.; Saris, W.H.M.; Feskens, E.J.M.; Wareham, N.J.; Sorensen, T.I.A.; Loos, R.J.F.

    2011-01-01

    Background: Single nucleotide polymorphisms (SNPs) in genes encoding the components involved in the hypothalamic pathway may influence weight gain and dietary factors may modify their effects. \\\\ Aim: We conducted a case-cohort study to investigate the associations of SNPs in candidate genes with

  5. Genetic polymorphisms and drug metabolism

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    Vita Dolžan

    2007-12-01

    Full Text Available Background: It is estimated that genetic factors account for 15–30 % of variability in drug response, however for some drugs this may be the major determinant in drug response. Pharmacogenetics aims to identify genetic sources of variability in response to drugs by studying genetic variations affecting drug metabolizing enzymes, transporters and drug targets thus causing interindividual variability in drug levels (pharmacokinetics, drug response (pharmacodynamics and side effects. Extensive information on genetic variability in drug metabolizing enzymes, transporters and targets is available from public databases. Drugs are metabolized in two phases. In Phase I drug is metabolically activated to reactive electrophilic form, mostly by cytochromes P450 (CYPs, to be conjugated to some endogenous compound by Phase II enzymes: UDP-glucuronosyltransferases (UGTs, N-acetyl-transferases (NATs, glutathione S-transferases (GSTs, or others. Genetic polymorphism of many enzymes involved in this process leads to inter-individual variations in metabolism and pharmacokinetics of drugs and could therefore influence drug response. Genetic polymorphism is the occurrence of two or more alleles at a given locus of which the rare allele has a frequency of at least 1 % or more in a given population. The understanding of a patient’s genotype and its corresponding effect on drug response could help distinguish between responders and non-responders of a specific drug treatment and help to choose the most effective drug and optimal dose. A large number of different methodologies have been developed for genotyping, however at present predictive genotyping for drug metabolizing enzymes does not occur routinely in the clinical practice.Conclusions: There is increasing evidence that genotyping for polymorphic drug metabolizing enzymes, in particular CYPs has potential to improve drug therapy and achieve higher response rates and reduced adverse effects. Open questions

  6. Genetic polymorphism of interleukin-6 influences susceptibility to HBV-related hepatocellular carcinoma in a male Chinese Han population.

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    Tang, Shengli; Yuan, Yufeng; He, Yueming; Pan, Dingyu; Zhang, Yongxi; Liu, Yuanyuan; Liu, Quanyan; Zhang, Zhonglin; Liu, Zhisu

    2014-04-01

    As a multifunctional cytokine, interleukin-6 (IL-6) plays a key role in chronic inflammation as well as tumor growth and progression of hepatitis B virus (HBV) infection. Recent studies have implicated that single nucleotide polymorphism (SNP) -572C>G (rs1800796) located within the promoter region of IL-6 gene was associated with susceptibility to several diseases. Here, a case-control study was undertaken to investigate the association between this polymorphism and HBV-related hepatocellular carcinoma (HCC) susceptibility in a Chinese Han population. A total of 900 patients with chronic HBV infection, including 505 HBV-related HCC patients and 395 HBV infected patients without HCC were enrolled, and rs1800796 polymorphism was genotyped by the TaqMan method and DNA sequencing technology. The results indicated no significant association between rs1800796 polymorphism and the risk of HBV-related HCC in all subjects; however, a significant difference was identified in male subjects. Under the dominant model, male subjects with the G allele (CG/GG) have higher susceptibility to HBV-related HCC than those with CC genotype after adjusting confounding factors (P=0.012, odds ratio [OR] 1.68, 95% confidence interval [95% CI] 1.15-2.42). Our results suggested that rs1800796 polymorphism of IL-6 gene was associated with susceptibility to HBV-related HCC in a male Chinese Han population.

  7. Genetic polymorphism and its potential relation to environmental stress in five populations of the European flounder Platichthys flesus, along the French Atlantic coast.

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    Marchand, J; Evrard, E; Guinand, B; Cachot, J; Quiniou, L; Laroche, J

    2010-08-01

    In this study, new DNA markers were explored for the flounder Platichthys flesus. cDNA and genomic sequences of the genes encoding the glyceraldehyde-3-phosphate-deshydrogenase (GAPDH), the cytosolic creatine kinase (CK), the prostaglandin D synthase (PGDS) and the betaine homocysteine methyltransferase (BHMT) were characterized. The tumour suppressor p53 gene structure was already described. A PCR-SSCP (Single Strand Conformation Polymorphism) analysis was finally conducted to study the genetic polymorphism of different populations of flounders collected along the French Atlantic coast. Four highly contaminated French estuaries (Seine, Vilaine, Loire and Gironde) were sampled and compared to a reference estuary (Ster) to explore possible selective effect of the environment on specific allelic frequencies. Our results showed that two loci p53 and PGDS, could be potential markers of chemical stress: p53A allele frequency increased in contaminated systems compared to the reference system. In the Vilaine estuary, PGDS polymorphism could be related to pesticide stress.

  8. Genetic Polymorphisms of Glutathione-Related Enzymes (GSTM1, GSTT1, and GSTP1 and Schizophrenia Risk: A Meta-Analysis

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    Su Kang Kim

    2015-08-01

    Full Text Available The association between polymorphisms of glutathione-related enzyme (GST genes and the risk of schizophrenia has been investigated in many published studies. However, their results were inconclusive. Therefore, we performed a meta-analysis to explore the association between the GSTM1, GSTT1, and GSTP1 polymorphisms and the risk of schizophrenia. Twelve case-control studies were included in this meta-analysis. The odds ratio (OR and 95% confidence interval (95% CI were used to investigate the strength of the association. Our meta-analysis results revealed that GSTM1, GSTT1, and GSTP1 polymorphisms were not related to risk of schizophrenia (p > 0.05 in each model. Further analyses based on ethnicity, GSTM polymorphism showed weak association with schizophrenia in East Asian population (OR = 1.314, 95% CI = 1.025–1.684, p = 0.031. In conclusion, our meta-analysis indicated the GSTM1 polymorphism may be the only genetic risk factor for schizophrenia in East Asian population. However, more meta-analysis with a larger sample size were needed to provide more precise evidence.

  9. Genetic polymorphisms of enzyme proteins and transporters related to methotrexate response and pharmacokinetics in a Japanese population.

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    Hashiguchi, Masayuki; Shimizu, Mikiko; Hakamata, Jun; Tsuru, Tomomi; Tanaka, Takanori; Suzaki, Midori; Miyawaki, Kumika; Chiyoda, Takeshi; Takeuchi, Osamu; Hiratsuka, Jiro; Irie, Shin; Maruyama, Junya; Mochizuki, Mayumi

    2016-01-01

    Methotrexate (MTX) is currently the anchor drug widely used worldwide in the treatment of rheumatoid arthritis (RA). However, the therapeutic response to MTX has been shown to vary widely among individuals, genders and ethnic groups. The reason for this has been not clarified but it is considered to be partially due to several mechanisms in the cellular pathway of MTX including single-nucleotide polymorphisms (SNPs). The purpose of this study was to investigate the allelic frequencies in different ethnic and/or population groups in the 10 polymorphisms of enzyme proteins and transporters related to the MTX response and pharmacokinetics including MTHFR, TYMS, RFC1, FPGS, GGH, ABCB1, ABCC2 and ABCG2 in unrelated healthy Japanese adults and patients with RA. Ten polymorphisms, methylenetetrahydrofolate reductase (MTHFR) 1298, thymidylate synthase (TYMS) 3'-UTR, reduced folate carrier 1 (RFC1) 80 and-43, folypolyglutamyl synthase (FPGS) 1994, γ-glutamyl hydrolase (GGH) 452 and-401, the ABC transporters (ABCB1 3435, ABCC2 IVS23 + 56, ABCG2 914) of enzyme proteins and transporters related to MTX response and pharmacokinetics in 299 unrelated healthy Japanese adults and 159 Japanese patients with RA were investigated to clarify their contributions to individual variations in response and safety to MTX and establish personalized MTX therapy. SNPs were evaluated using real-time polymerase chain reaction (PCR). Comparison of allelic frequencies in our study with other ethnic/population groups of healthy adults and RA patients showed significant differences in 10 polymorphisms among healthy adults and 7 among RA patients. Allelic frequencies of MTHFR 1298 C, FPGS 1994A and ABCB1 3435 T were lower in Japanese than in Caucasian populations and those of ABCC2 IVS23 + 56 C and ABCG2 914A were higher in Japanese than in Caucasian/European populations in both healthy adults and RA patients. Allelic frequencies of MTHFR 1298 C, GGH-401 T, ABCB1 3435 T, and ABCG2 914A

  10. Genetic polymorphisms located in genes related to immune and inflammatory processes are associated with end-stage renal disease: a preliminary study

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    Jimenez-Sousa Ma

    2012-07-01

    Full Text Available Abstract Background Chronic kidney disease progression has been linked to pro-inflammatory cytokines and markers of inflammation. These markers are also elevated in end-stage renal disease (ESRD, which constitutes a serious public health problem. Objective To investigate whether single nucleotide polymorphisms (SNPs located in genes related to immune and inflammatory processes, could be associated with ESRD development. Design and methods A retrospective case-control study was carried out on 276 patients with ESRD and 288 control subjects. Forty-eight SNPs were genotyped via SNPlex platform. Logistic regression was used to assess the relationship between each sigle polymorphism and the development of ESRD. Results Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R gene (OR: 0.66 (95%CI = 0.46-0.95; p = 0.025; overdominant model, rs4586 in chemokine (C-C motif ligand 2 (CCL2 gene (OR: 0.70 (95%CI = 0.54-0.90; p = 0.005; additive model, rs301640 located in an intergenic binding site for signal transducer and activator of transcription 4 (STAT4 (OR: 1.82 (95%CI = 1.17-2.83; p = 0.006; additive model and rs7830 in the nitric oxide synthase 3 (NOS3 gene (OR: 1.31 (95%CI = 1.01-1.71; p = 0.043; additive model. After adjusting for multiple testing, results lost significance. Conclusion Our preliminary data suggest that four genetic polymorphisms located in genes related to inflammation and immune processes could help to predict the risk of developing ESRD.

  11. Genetic polymorphisms in the hypothalamic pathway in relation to subsequent weight change--the DiOGenes study.

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    Huaidong Du

    Full Text Available BACKGROUND: Single nucleotide polymorphisms (SNPs in genes encoding the components involved in the hypothalamic pathway may influence weight gain and dietary factors may modify their effects. AIM: We conducted a case-cohort study to investigate the associations of SNPs in candidate genes with weight change during an average of 6.8 years of follow-up and to examine the potential effect modification by glycemic index (GI and protein intake. METHODS AND FINDINGS: Participants, aged 20-60 years at baseline, came from five European countries. Cases ('weight gainers' were selected from the total eligible cohort (n = 50,293 as those with the greatest unexplained annual weight gain (n = 5,584. A random subcohort (n = 6,566 was drawn with the intention to obtain an equal number of cases and noncases (n = 5,507. We genotyped 134 SNPs that captured all common genetic variation across the 15 candidate genes; 123 met the quality control criteria. Each SNP was tested for association with the risk of being a 'weight gainer' (logistic regression models in the case-noncase data and with weight gain (linear regression models in the random subcohort data. After accounting for multiple testing, none of the SNPs was significantly associated with weight change. Furthermore, we observed no significant effect modification by dietary factors, except for SNP rs7180849 in the neuromedin β gene (NMB. Carriers of the minor allele had a more pronounced weight gain at a higher GI (P = 2 x 10⁻⁷. CONCLUSIONS: We found no evidence of association between SNPs in the studied hypothalamic genes with weight change. The interaction between GI and NMB SNP rs7180849 needs further confirmation.

  12. A comprehensive study of tumor necrosis factor-alpha genetic polymorphisms, its expression in skin and relation to histopathological features in psoriasis

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    Nikhil N Moorchung

    2015-01-01

    Full Text Available Background: Tumor necrosis factor-alpha (TNFα is an important inflammatory mediator in psoriasis and several genetic polymorphisms of this cytokine have been reported. Majority of studies have focused on the increased G- A polymorphism at the -308 position in psoriasis. There has been no comprehensive study evaluating the genetic polymorphisms, TNFα expression in the skin and histopathology. We are undertaking this study to outline TNFα genetic polymorphisms, its skin expression and histopathological correlation to help determine its role at the genetic and protein level. Materials and Methods : 112 patients of psoriasis and 243 healthy controls were included in this prospective study. 5 ml of peripheral blood was collected to study the TNFα genetic polymorphisms by polymerase chain reaction and restriction fragment length polymorphism analysis. Histopathological analysis of biopsies from the 112 patients were done using visual analogue scale and correlated with the findings. 61 of these cases were analyzed for TNFα expression by immunohistochemistry. The results of study were statistically analyzed using SPSS 13.0 statistical package program. Results: A strong association of TNFα -308 G/A polymorphism in psoriasis cases was detected. The A allele of the TNFα -308 G/A polymorphism occurs rarely in the Indian population, however there is an over representation of this allele in psoriatic patients. There was no association seen between TNFα genotype and histopathological severity of psoriasis. Conclusion: The study emphasized the central role of TNFα in the pathogenesis of psoriasis. TNFα genotyping may be helpful in identifying subjects in whom anti-TNFα therapeutic strategies may be tried.

  13. Fc gamma receptor polymorphisms in relation to periodontitis

    NARCIS (Netherlands)

    Loos, BG; Leppers-Van de Straat, FGJ; Van de Winkel, JGJ; Van der Velden, U

    Objectives: Evidence suggests functional relevance for polymorphisms in Fcgamma R in relation to inflammatory and infectious diseases. The present aim was to investigate genetic polymorphisms in three Fcgamma R in relation to susceptibility and severity of periodontitis. Material and Methods: The

  14. Fc gamma receptor polymorphisms in relation to periodontitis

    NARCIS (Netherlands)

    Loos, BG; Leppers-Van de Straat, FGJ; Van de Winkel, JGJ; Van der Velden, U

    2003-01-01

    Objectives: Evidence suggests functional relevance for polymorphisms in Fcgamma R in relation to inflammatory and infectious diseases. The present aim was to investigate genetic polymorphisms in three Fcgamma R in relation to susceptibility and severity of periodontitis. Material and Methods: The st

  15. Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy.

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    Ruixuan Geng

    Full Text Available BACKGROUND: Oxidative stress genes are related to cancer development and treatment response. In this study, we aimed to determine the predictive and prognostic roles of oxidative stress-related genetic polymorphisms in metastatic gastric cancer (MGC patients treated with chemotherapy. METHODS: In this retrospective study, we genotyped nine oxidative stress-related single nucleotide polymorphisms (SNPs in NQO1, SOD2, SOD3, PON1, GSTP1, GSTT1, and NOS3 (rs1800566, rs10517, rs4880, rs1799895, rs662, rs854560, rs1695, rs2266637, rs1799983, respectively in 108 consecutive MGC patients treated with epirubicin, oxaliplatin, and 5-fluorouracil (EOF regimen as the first-line chemotherapy and analyzed the association between the genotypes and the disease control rate (DCR, progression-free survival (PFS, and overall survival (OS. RESULTS: We found that, in addition to a lower pathological grade (p = 0.017, NQO1 rs1800566 CT/TT genotype was an independent predictive factor of poor PFS (hazard ratio [HR] = 1.97, 95% confidence interval [CI] = 1.23-3.16; p = 0.005. PON1 rs662 AA/AG genotype was significantly associated with poor OS (HR = 1.95, 95% CI = 1.07-3.54; p = 0.029. No associations were detected between the nine SNPs and DCR. CONCLUSIONS: NQO1 rs1800566 is an independent predictive factor of PFS for MGC patients treated with EOF chemotherapy, and PON1 rs662 is a noteworthy prognostic factor of OS. Information on oxidative stress-related genetic variants may facilitate optimization of individualized chemotherapy in clinical practice.

  16. Indian studies on genetic polymorphisms and cancer risk

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    A Bag

    2012-01-01

    Full Text Available Genetic influences on cancer development have been extensively investigated during the last decade following publication of human genome sequence. The present review summarizes case-control studies on genetic polymorphisms and cancer risk in Indians. It is observed that the most commonly studied genes in the Indian population included members of phase I and phase II metabolic enzymes. Other than these genes, genetic polymorphisms for cell cycle and apoptosis-related factors, DNA repair enzymes, immune response elements, growth factors, folate metabolizing enzymes, vitamin/hormone receptors, etc., were investigated. Several studies also evidenced a stronger risk for combined genotypes rather than a single polymorphism. Gene-environment interaction was also found to be a determining factor for cancer development in some experiments. Data for single polymorphism and single cancer type, however, was insufficient to validate an association. It appears that much more experiments involving larger sample size, cross-tabulating genetic polymorphisms and environmental factors are required in order to identify genetic markers for different cancers in Indian populations.

  17. The Effect of Genetic Polymorphism upon Antineoplastic Sensitivity

    Institute of Scientific and Technical Information of China (English)

    Jun Liang

    2006-01-01

    In clinical practice, patients undergoing chemotherapy display prominent individual differences, adverse reactions and sensitivity to antineoplastic therapy. Those differences are caused by individual genetic polymorphism of related genes. Genetic variation can induce distinct alterations of drug-metabolizing enzymes, drug transporters, drug targets and DNA repair enzymes and thereby influence the ability of the drugs to reach their target sites. This article reviews in detail the potential interactions mentioned above.

  18. GENETIC ASSOCIATION BETWEEN ARTERIAL STIFFNESS-RELATED GENE POLYMORPHISMS IN BRVO AND CRVO PATIENTS IN A TURKISH POPULATION.

    Science.gov (United States)

    Demir, Selim; Ortak, Hüseyin; Benli, İsmail; Alim, Sait; Bütün, İlknur; Güneş, Alper; Ateş, Ömer

    2015-10-01

    To investigate possible associations between five different single-nucleotide polymorphisms, from genes associated with arterial stiffness and branch retinal vein occlusion (BRVO), or central retinal vein occlusion. A total of 187 patients with retinal vein occlusion (133 with BRVO and 54 with central retinal vein occlusion), and 167 controls, were enrolled in this study. All subjects were screened for hypertension, diabetes, smoking status, body mass index, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, total cholesterol, and very low-density lipoprotein. The genotyping of adiponectin +276 G/T, ACE I/D, AGTR1 A1166C, eNOS E298D, and p22phox -242 C/T polymorphisms was performed using real-time polymerase chain reaction. The percentage of the adiponectin +275 T allele carriers was significantly higher in the BRVO patients (37%) than in the controls (23%, P AGTR1 1166 C allele carriers was significantly higher in the BRVO patients (38%) than in the controls (24%, P AGTR1 1166 C allele carrier status were found to be associated with an increased risk of BRVO (TT vs. GG and TG: odds ratio = 2.278, P = 0.002, 95% confidence interval: 1.370-3.789; CC vs. AA and AC: odds ratio = 1.804, P = 0.025, 95% confidence interval: 1.079-3.017). The genotype distributions or allelic frequencies of ACE I/D, eNOS E298D, and p22phox -242 C/T did not significantly differ between the patients with BRVO and the control subjects. There was no significant difference between the central retinal vein occlusion patients and controls for the genotype or the allele frequency distributions of all evaluated single-nucleotide polymorphisms. Adiponectin +276 G/T and AGTR1 A1166C single-nucleotide polymorphism are likely to be risk factors for BRVO.

  19. Genetic associations of the visfatin G-948T polymorphism with obesity-related metabolic traits in an Iranian population

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    Shaghayegh Haghjooy Javanmard

    2016-01-01

    Full Text Available Background: Obesity is a global public health problem. Visfatin, as an adipocytokine, is coded by a gene known as nicotinamide phosphoribosyltransferase. So far, results were conflicted regarding correlations of visfatin with obesity and metabolic variables. The present study aimed to explore the association between G-948T polymorphism of visfatin gene with obesity and lipid profile in a nationally representative sample of Iranian population. Materials and Methods: In this case–control study, we assessed 129 randomly selected patients with obesity and 182 healthy normal weight controls from participants of Isfahan Healthy Heart Program. Genomic DNA was isolated from peripheral blood cells, and high-resolution melt polymerase chain reaction was performed to explore the presence of G-948T polymorphism. Results: T carriers “GT + TT” were statistically more frequent in the obese patients than the controls (P = 0.013; odds ratio = 1.9, 95% confidence interval = 1.1–3.1. The serum levels of total cholesterol and low-density lipoprotein cholesterol (LDL-C were significantly different between T carriers and GG homozygote genotype (P = 0.03 and 0.02, respectively. Conclusion: We concluded that visfatin G-948T polymorphism was correlated with obesity, total cholesterol, and LDL-C levels in our population.

  20. Genetic associations of the visfatin G-948T polymorphism with obesity-related metabolic traits in an Iranian population.

    Science.gov (United States)

    Javanmard, Shaghayegh Haghjooy; Dehghananzadeh, Raheleh; Rafiee, Laleh; Naji, Hajar; Rezayat, Azadeh; Sarrafzadegan, Nizal

    2016-01-01

    Obesity is a global public health problem. Visfatin, as an adipocytokine, is coded by a gene known as nicotinamide phosphoribosyltransferase. So far, results were conflicted regarding correlations of visfatin with obesity and metabolic variables. The present study aimed to explore the association between G-948T polymorphism of visfatin gene with obesity and lipid profile in a nationally representative sample of Iranian population. In this case-control study, we assessed 129 randomly selected patients with obesity and 182 healthy normal weight controls from participants of Isfahan Healthy Heart Program. Genomic DNA was isolated from peripheral blood cells, and high-resolution melt polymerase chain reaction was performed to explore the presence of G-948T polymorphism. T carriers "GT + TT" were statistically more frequent in the obese patients than the controls (P = 0.013; odds ratio = 1.9, 95% confidence interval = 1.1-3.1). The serum levels of total cholesterol and low-density lipoprotein cholesterol (LDL-C) were significantly different between T carriers and GG homozygote genotype (P = 0.03 and 0.02, respectively). We concluded that visfatin G-948T polymorphism was correlated with obesity, total cholesterol, and LDL-C levels in our population.

  1. Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype.

    Science.gov (United States)

    Etemadi, Arash; Islami, Farhad; Phillips, David H; Godschalk, Roger; Golozar, Asieh; Kamangar, Farin; Malekshah, Akbar Fazel-Tabar; Pourshams, Akram; Elahi, Seerat; Ghojaghi, Farhad; Strickland, Paul T; Taylor, Philip R; Boffetta, Paolo; Abnet, Christian C; Dawsey, Sanford M; Malekzadeh, Reza; van Schooten, Frederik J

    2013-06-15

    Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to xenobiotic metabolism and 12 SNPs in eight DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by32P-postlabeling. Multivariable regression models were compared by Akaike's information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 10(8) nucleotides (mean: 5.8 ± 3.1). DNA adduct level was significantly lower in homozygotes for NAT2 slow alleles and ERCC5 non-risk-allele genotype, and was higher in the MPO homozygote risk-allele genotype. The sum of risk alleles in these genes significantly correlated with the log-adduct level (r = 0.4, p adduct levels. NER capacity was affected by polymorphisms in the MTHFR and ERCC1 genes. Female non-smokers in this population had PAH-related DNA adduct levels three to four times higher than smokers and occupationally-exposed groups in previous studies, with large inter-individual variation which could best be explained by a combination of Phase I genes and NER capacity.

  2. Genetic polymorphisms of leptin and leptin receptor genes in relation with production and reproduction traits in cattle.

    Science.gov (United States)

    Trakovická, Anna; Moravčíková, Nina; Kasarda, Radovan

    2013-01-01

    Leptin and leptin receptor genes are considered as production traits markers in dairy or beef cattle. The aim of this study was to verify the associations of polymorphisms in bovine LEP and LEPR genes with production and reproduction traits in Slovak Spotted and Pinzgau cows. Long-life production was evaluated: milk, protein, and fat yield and reproduction traits: age at first calving, calving interval, days open, and insemination interval. In total, 296 blood samples of Slovak Spotted and 85 hair roots samples of Pinzgau cows were analyzed. In order to detect LEP/Sau3AI (BTA 4, inron 2) and LEPR/T945M (BTA 3, exon 20) genotypes PCR-RFLP method was used. In Slovak Spotted and Pinzgau cows allele frequencies were 0.838/0.162 and 0.694/0.306 for A and B LEP variants, and 0.954/0.046 and 0.912/0.088 for C and T LEPR variants, respectively. For testing the associations between SNPs LEP/Sau3AI and LEPR/T945M and evaluated traits, the General Linear Model procedure in SAS Software was used. Statistical analysis showed that SNP LEP/Sau3AI significantly affected milk, protein and fat yield (Pcattle breeds.

  3. The Role of Genetic Polymorphisms as Related to One-Carbon Metabolism, Vitamin B6, and Gene–Nutrient Interactions in Maintaining Genomic Stability and Cell Viability in Chinese Breast Cancer Patients

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    Xiayu Wu

    2016-06-01

    Full Text Available Folate-mediated one-carbon metabolism (FMOCM is linked to DNA synthesis, methylation, and cell proliferation. Vitamin B6 (B6 is a cofactor, and genetic polymorphisms of related key enzymes, such as serine hydroxymethyltransferase (SHMT, methionine synthase reductase (MTRR, and methionine synthase (MS, in FMOCM may govern the bioavailability of metabolites and play important roles in the maintenance of genomic stability and cell viability (GSACV. To evaluate the influences of B6, genetic polymorphisms of these enzymes, and gene–nutrient interactions on GSACV, we utilized the cytokinesis-block micronucleus assay (CBMN and PCR-restriction fragment length polymorphism (PCR-RFLP techniques in the lymphocytes from female breast cancer cases and controls. GSACV showed a significantly positive correlation with B6 concentration, and 48 nmol/L of B6 was the most suitable concentration for maintaining GSACV in vitro. The GSACV indexes showed significantly different sensitivity to B6 deficiency between cases and controls; the B6 effect on the GSACV variance contribution of each index was significantly higher than that of genetic polymorphisms and the sample state (tumor state. SHMT C1420T mutations may reduce breast cancer susceptibility, whereas MTRR A66G and MS A2756G mutations may increase breast cancer susceptibility. The role of SHMT, MS, and MTRR genotype polymorphisms in GSACV is reduced compared with that of B6. The results appear to suggest that the long-term lack of B6 under these conditions may increase genetic damage and cell injury and that individuals with various genotypes have different sensitivities to B6 deficiency. FMOCM metabolic enzyme gene polymorphism may be related to breast cancer susceptibility to a certain extent due to the effect of other factors such as stress, hormones, cancer therapies, psychological conditions, and diet. Adequate B6 intake may be good for maintaining genome health and preventing breast cancer.

  4. Urinary proteins, vitamin D and genetic polymorphisms as risk factors for febrile urinary tract infection and relation with bacteremia: a case control study.

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    Willize E van der Starre

    Full Text Available Febrile urinary tract infection (UTI is a common bacterial disease that may lead to substantial morbidity and mortality especially among the elderly. Little is known about biomarkers that predict a complicated course. Our aim was to determine the role of certain urinary cytokines or antimicrobial proteins, plasma vitamin D level, and genetic variation in host defense of febrile UTI and its relation with bacteremia.A case-control study. Out of a cohort of consecutive adults with febrile UTI (n = 787 included in a multi-center observational cohort study, 46 cases with bacteremic E.coli UTI and 45 cases with non-bacteremic E.coli UTI were randomly selected and compared to 46 controls. Urinary IL-6, IL-8, LL37, β-defensin 2 and uromodulin as well as plasma 25-hydroxyvitamin D were measured. In 440 controls and 707 UTI patients polymorphisms were genotyped in the genes CXCR1, DEFA4, DEFB1, IL6, IL8, MYD88, UMOD, TIRAP, TLR1, TLR2, TLR5 and TNF.IL-6, IL-8, and LL37 are different between controls and UTI patients, although these proteins do not distinguish between patients with and without bacteremia. While uromodulin did not differ between groups, inability to produce uromodulin is more common in patients with bacteremia. Most participants in the study, including the controls, had insufficient vitamin D and, at least in winter, UTI patients have lower vitamin D than controls. Associations were found between the CC genotype of IL6 SNP rs1800795 and occurrence of bacteremia and between TLR5 SNP rs5744168 and protection from UTI. The rare GG genotype of IL6 SNP rs1800795 was associated with higher β-defensin 2 production.Although no biomarker was able to distinguish between UTI with or without bacteremia, two risk factors for bacteremia were identified. These were inability to produce uromodulin and an IL6 rs1800795 genotype.

  5. Genetic polymorphisms and lipid response to dietary changes in humans

    NARCIS (Netherlands)

    Weggemans, R.M.; Zock, P.L.; Ordovas, J.M.; Ramos-Galluzzi, J.; Katan, M.B.

    2001-01-01

    Previous studies on the effects of genetic polymorphisms on the serum cholesterol response to dietary treatments were often inconsistent and frequently involved small numbers of subjects. We studied the effect of 10 genetic polymorphisms on the responses of serum cholesterol to saturated and trans f

  6. Genetic polymorphisms and metabolism of endocrine disruptors in cancer susceptibility

    Directory of Open Access Journals (Sweden)

    Hatagima Ana

    2002-01-01

    Full Text Available Epidemiological studies have estimated that approximately 80% of all cancers are related to environmental factors. Individual cancer susceptibility can be the result of several host factors, including differences in metabolism, DNA repair, altered expression of tumor suppressor genes and proto-oncogenes, and nutritional status. Xenobiotic metabolism is the principal mechanism for maintaining homeostasis during the body's exposure to xenobiotics. The balance of xenobiotic absorption and elimination rates in metabolism can be important in the prevention of DNA damage by chemical carcinogens. Thus the ability to metabolize and eliminate xenobiotics can be considered one of the body's first protective mechanisms. Variability in individual metabolism has been related to the enzymatic polymorphisms involved in activation and detoxification of chemical carcinogens. This paper is a contemporary literature review on genetic polymorphisms involved in the metabolism of endocrine disruptors potentially related to cancer development.

  7. Genetic polymorphisms and metabolism of endocrine disruptors in cancer susceptibility

    Directory of Open Access Journals (Sweden)

    Ana Hatagima

    2002-04-01

    Full Text Available Epidemiological studies have estimated that approximately 80% of all cancers are related to environmental factors. Individual cancer susceptibility can be the result of several host factors, including differences in metabolism, DNA repair, altered expression of tumor suppressor genes and proto-oncogenes, and nutritional status. Xenobiotic metabolism is the principal mechanism for maintaining homeostasis during the body's exposure to xenobiotics. The balance of xenobiotic absorption and elimination rates in metabolism can be important in the prevention of DNA damage by chemical carcinogens. Thus the ability to metabolize and eliminate xenobiotics can be considered one of the body's first protective mechanisms. Variability in individual metabolism has been related to the enzymatic polymorphisms involved in activation and detoxification of chemical carcinogens. This paper is a contemporary literature review on genetic polymorphisms involved in the metabolism of endocrine disruptors potentially related to cancer development.

  8. Association of Genetic Polymorphisms of Renin–Angiotensin–Aldosterone System-Related Genes with Arterio-Venous Fistula Malfunction in Hemodialysis Patients

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    Yu-Wei Chen

    2016-05-01

    Full Text Available Hemodialysis (HD is the most commonly-used renal replacement therapy for patients with end-stage renal disease worldwide. Arterio-venous fistula (AVF is the vascular access of choice for HD patients with lowest risk of infection and thrombosis. In addition to environmental factors, genetic factors may also contribute to malfunction of AVF. Previous studies have demonstrated the effect of genotype polymorphisms of angiotensin converting enzyme on vascular access malfunction. We conducted a multicenter, cross-sectional study to evaluate the association between genetic polymorphisms of renin-angiotensin-aldosterone system and AVF malfunction. Totally, 577 patients were enrolled. Their mean age was 60 years old and 53% were male. HD patients with AVF malfunction had longer duration of HD (92.5 ± 68.1 vs. 61.2 ± 51.9 months, p < 0.001, lower prevalence of hypertension (44.8% vs. 55.3%, p = 0.025, right-sided (31.8% vs. 18.4%, p = 0.002 and upper arm AVF (26.6% vs. 9.7%, p < 0.001, and higher mean dynamic venous pressure (DVP (147.8 ± 28.3 vs. 139.8 ± 30.0, p = 0.021. In subgroup analysis of different genders, location of AVF and DVP remained significant clinical risk factors of AVF malfunction in univariate and multivariate binary logistic regression in female HD patients. Among male HD patients, univariate binary logistic regression analysis revealed that right-side AVF and upper arm location are two important clinical risk factors. In addition, two single nucleotide polymorphisms (SNPs, rs275653 (Odds ratio 1.90, p = 0.038 and rs1492099 (Odds ratio 2.29, p = 0.017 of angiotensin II receptor 1 (AGTR1, were associated with increased risk of AVF malfunction. After adjustment for age and other clinical factors, minor allele-containing genotype polymorphisms (AA and CA of rs1492099 still remained to be a significant risk factor of AVF malfunction (Odds ratio 3.63, p = 0.005. In conclusion, we demonstrated that rs1492099, a SNP of AGTR1 gene, could

  9. Pharmacogenetic effect of the stromelysin (MMP3) polymorphism on stroke risk in relation to antihypertensive treatment: the genetics of hypertension associated treatment study.

    Science.gov (United States)

    Sherva, Richard; Ford, Charles E; Eckfeldt, John H; Davis, Barry R; Boerwinkle, Eric; Arnett, Donna K

    2011-02-01

    Atherothrombotic diseases including stroke share a common etiology of atherosclerosis, and susceptibility to atherosclerosis has a genetic component. Stromelysin-1 (matrix metalloproteinase-3 [MMP3]) regulates arterial matrix composition and is a candidate gene for atherothrombosis. A common polymorphism of MMP3 alters expression levels and affects atherosclerotic progression and plaque stability. As part of the Genetics of Hypertension Associated Treatment study, ancillary to the Antihypertensive and Lipid Lowering to Prevent Heart Attack Trial, we evaluated the 5A/6A polymorphism in MMP3 to determine its association with stroke and determine whether it modifies clinical outcome response to blood pressure-lowering drugs. The effect of the MMP3 5A/6A polymorphism on stroke rates was examined by using multivariate-adjusted Cox regression models, including a test for interactions between genotype and antihypertensive drug class. Compared with participants treated with chlorthalidone with the 6A/6A genotype, individuals with the 6A/6A genotype randomized to lisinopril had higher stroke rates (hazard ratio=1.32; 95% CI, 1.08 to 1.61; P=0.007) and 5A/6A individuals taking lisinopril had lower stroke rates (hazard ratio(interaction)=0.74; 95% CI, 0.53 to 1.04; P(interaction)=0.08), whereas 5A/5A individuals taking lisinopril had the lowest stroke rate (hazard ratio(interaction)=0.51; 95% CI, 0.31 to 0.85; P(interaction)=0.009). There were no pharmacogenetic differences in stroke rate by genotype in patients taking amlodipine or doxazosin vs chlorthalidone. The MMP3 6A/6A genotype is associated with an increased risk of stroke in hypertensive subjects taking lisinopril compared with patients treated with chlorthalidone, whereas a protective effect was found for 5A/5A individuals treated with lisinopril. Genetic screening for the MMP3 5A/6A genotype might be a useful tool to select optimal antihypertensive therapy if this finding is replicated. Clinical Trial Registration

  10. Genetic Association Study of KCNQ5 Polymorphisms with High Myopia

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    Xuan Liao

    2017-01-01

    Full Text Available Identification of genetic variations related to high myopia may advance our knowledge of the etiopathogenesis of refractive error. This study investigated the role of potassium channel gene (KCNQ5 polymorphisms in high myopia. We performed a case-control study of 1563 unrelated Han Chinese subjects (809 cases of high myopia and 754 emmetropic controls. Five tag single-nucleotide polymorphisms (SNPs of KCNQ5 were genotyped, and association testing with high myopia was conducted using logistic regression analysis adjusted for sex and age to give Pasym values, and multiple comparisons were corrected by permutation test to give Pemp values. All five noncoding SNPs were associated with high myopia. The SNP rs7744813, previously shown to be associated with refractive error and myopia in two GWAS, showed an odds ratio of 0.75 (95% CI 0.63–0.90; Pemp = 0.0058 for the minor allele. The top SNP rs9342979 showed an odds ratio of 0.75 (95% CI 0.64–0.89; Pemp = 0.0045 for the minor allele. Both SNPs are located within enhancer histone marks and DNase-hypersensitive sites. Our data support the involvement of KCNQ5 gene polymorphisms in the genetic susceptibility to high myopia and further exploration of KCNQ5 as a risk factor for high myopia.

  11. Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

    Science.gov (United States)

    Lukoschek, V; Waycott, M; Keogh, J S

    2008-07-01

    Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

  12. Genetics: Polymorphisms, Epigenetics, and Something In Between

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    Keith A. Maggert

    2012-01-01

    Full Text Available At its broadest sense, to say that a phenotype is epigenetic suggests that it occurs without changes in DNA sequence, yet is heritable through cell division and occasionally from one organismal generation to the next. Since gene regulatory changes are oftentimes in response to environmental stimuli and may be retained in descendent cells, there is a growing expectation that one's experiences may have consequence for subsequent generations and thus impact evolution by decoupling a selectable phenotype from its underlying heritable genotype. But the risk of this overbroad use of “epigenetic” is a conflation of genuine cases of heritable non-sequence genetic information with trivial modes of gene regulation. A look at the term “epigenetic” and some problems with its increasing prevalence argues for a more reserved and precise set of defining characteristics. Additionally, questions arising about how we define the “sequence independence” aspect of epigenetic inheritance suggest a form of genome evolution resulting from induced polymorphisms at repeated loci (e.g., the rDNA or heterochromatin.

  13. Genetic Polymorphism and Expression of CXCR4 in Breast Cancer

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    Marina Okuyama Kishima

    2015-01-01

    Full Text Available CXCR4 genetic polymorphisms, as well as their expression level, have been associated with cancer development and prognosis. The present study aimed to investigate the influence of CXCR4 rs2228014 polymorphism on its mRNA and protein expression in breast cancer samples. It was observed that patients presented higher CXCR4 mRNA relative expression (5.7-fold than normal mammary gland, but this expression was not correlated with patients clinicopathological features (nuclear grade, nodal status, ER status, PR status, p53 staining, Ki67 index, and HER-2 status. Moreover, CXCR4 mRNA relative expression also did not differ regarding the presence or absence of T allele (p=0.301. In the immunohistochemical assay, no difference was observed for CXCR4 cytoplasmic protein staining in relation to different genotypes (p=0.757; however, high cytoplasmic CXCR4 staining was verified in invasive breast carcinoma (p<0.01. All in all, the results from present study indicated that rs2228014 genetic variant does not alter CXCR4 mRNA or protein expression. However, this receptor was more expressed in tumor compared to normal tissue, in both RNA and protein levels, suggesting its promising applicability in the general context of mammary carcinogenesis.

  14. Genetic Polymorphism and Expression of CXCR4 in Breast Cancer

    Science.gov (United States)

    Okuyama Kishima, Marina; Brajão de Oliveira, Karen; Ariza, Carolina Batista; de Oliveira, Carlos Eduardo Coral; Losi Guembarovski, Roberta; Banin Hirata, Bruna Karina; de Almeida, Felipe Campos; Vitiello, Glauco Akelinghton Freire; Trugilo, Kleber Paiva; Guembarovski, Alda Fiorina Maria Losi; Jorge Sobrinho, Walter; Campos, Clodoaldo Zago; Watanabe, Maria Angelica Ehara

    2015-01-01

    CXCR4 genetic polymorphisms, as well as their expression level, have been associated with cancer development and prognosis. The present study aimed to investigate the influence of CXCR4 rs2228014 polymorphism on its mRNA and protein expression in breast cancer samples. It was observed that patients presented higher CXCR4 mRNA relative expression (5.7-fold) than normal mammary gland, but this expression was not correlated with patients clinicopathological features (nuclear grade, nodal status, ER status, PR status, p53 staining, Ki67 index, and HER-2 status). Moreover, CXCR4 mRNA relative expression also did not differ regarding the presence or absence of T allele (p = 0.301). In the immunohistochemical assay, no difference was observed for CXCR4 cytoplasmic protein staining in relation to different genotypes (p = 0.757); however, high cytoplasmic CXCR4 staining was verified in invasive breast carcinoma (p < 0.01). All in all, the results from present study indicated that rs2228014 genetic variant does not alter CXCR4 mRNA or protein expression. However, this receptor was more expressed in tumor compared to normal tissue, in both RNA and protein levels, suggesting its promising applicability in the general context of mammary carcinogenesis. PMID:26576337

  15. Genetic polymorphism as a background of animal behavior.

    Science.gov (United States)

    Inoue-Murayama, Miho

    2009-04-01

    Various studies have shown the associations between differences in human behavioral traits and genetic polymorphism of neurotransmitter-related proteins such as receptors, transporters and monoamine oxidase. To clarify the genetic background of animal behavior, corresponding regions in animals have been analyzed. The study has been especially focused on primates, as the evolutionally closest animal to humans, and on dogs, as the socially closest animal to humans. In primates, polymorphisms were discovered between or within species, and the functional effects on neural transmission were found to be different by alleles. Even in apes, the closest species to humans, function was different from that in humans. In dogs, allele distributions of several genes were different among breeds showing different behavioral traits, and genes associated with individual differences in aggressiveness and aptitude of working dogs were surveyed. The survey of behavior-related genes has also been carried out in other mammals such as horses and cetaceans. Genes controlling various behaviors in birds have also been reported. The marker genes for behavior will provide useful information for human evolution, welfare of zoo animals and effective selection of working dogs and industry animals.

  16. Vitamins B2 and B6 and Genetic Polymorphisms Related to One-Carbon Metabolism as Risk Factors for Gastric Adenocarcinoma in the European Prospective Investigation into Cancer and Nutrition

    NARCIS (Netherlands)

    Eussen, Simone J. P. M.; Vollset, Stein Emil; Hustad, Steinar; Midttun, Oivind; Meyer, Klaus; Fredriksen, Ase; Ueland, Per Magne; Jenab, Mazda; Slimani, Nadia; Ferrari, Pietro; Agudo, Antonio; Sala, Nuria; Capella, Gabriel; Del Giudice, Giuseppe; Palli, Domenico; Boeing, Heiner; Weikert, Cornelia; Bueno-de-Mesquita, H. Bas; Buechner, Frederike L.; Carneiro, Fatima; Berrino, Franco; Vineis, Paolo; Tumino, Rosario; Panico, Salvatore; Berglund, Goran; Manjer, Jonas; Stenling, Roger; Hallmans, Goeran; Martinez, Carmen; Arrizola, Larraitz; Barricarte, Aurelio; Navarro, Carmen; Rodriguez, Laudina; Bingham, Sheila; Linseisen, Jakob; Kaaks, Rudolf; Overvad, Kim; Tjonneland, Anne; Peeters, Petra H. M.; Numans, Mattijs E.; Clavel-Chapelon, Francoise; Boutron-Ruault, Marie-Christine; Morois, Sophie; Trichopoulou, Antonia; Lund, Eiliv; Plebani, Mario; Riboli, Elio; Gonzalez, Carlos A.

    2010-01-01

    B vitamins and polymorphisms in genes coding for enzymes involved in one-carbon metabolism may affect DNA synthesis and methylation and thereby be implicated in carcinogenesis. Previous data on vitamins B2 and B6 and genetic polymorphisms other than those involving MTHFR as risk factors for gastric

  17. Vitamins B2 and B6 and genetic polymorphisms related to one-carbon metabolism as risk factors for gastric adenocarcinoma in the European prospective investigation into cancer and nutrition.

    NARCIS (Netherlands)

    Eussen, S.J.; Vollset, S.E.; Hustad, S.; Midttun, O.; Meyer, K.; Fredriksen, A.; Ueland, P.M.; Jenab, M.; Slimani, N.; Ferrari, P.; Agudo, A.; Sala, N.; Capella, G.; Giudice, G. Del; Palli, D.; Boeing, H.; Weikert, C.; Bueno-De-Mesquita, H.B.; Buchner, F.L.; Carneiro, F.; Berrino, F.; Vineis, P.; Tumino, R.; Panico, S.; Berglund, G.; Manjer, J.; Stenling, R.; Hallmans, G.; Martinez, C.; Arrizola, L.; Barricarte, A.; Navarro, C.; Rodriguez, L.; Bingham, S.; Linseisen, J.; Kaaks, R.; Overvad, K.; Tjonneland, A.; Peeters, P.H.M.; Numans, M.E.; Clavel-Chapelon, F.; Boutron-Ruault, M.C.; Morois, S.; Trichopoulou, A.; Lund, E.; Plebani, M.; Riboli, E.; Gonzalez, C.A.

    2010-01-01

    B vitamins and polymorphisms in genes coding for enzymes involved in one-carbon metabolism may affect DNA synthesis and methylation and thereby be implicated in carcinogenesis. Previous data on vitamins B2 and B6 and genetic polymorphisms other than those involving MTHFR as risk factors for gastric

  18. Evaluation of the impact of genetic polymorphisms in glutathione-related genes on the association between methylmercury or n-3 polyunsaturated long chain fatty acids and risk of myocardial infarction: a case-control study

    Directory of Open Access Journals (Sweden)

    Norberg Margareta

    2011-04-01

    Full Text Available Abstract Background The n-3 polyunsaturated fatty acids eicosapentaenoic acid and docosahexaenoic acid, which are present in fish, are protective against myocardial infarction. However, fish also contains methylmercury, which influences the risk of myocardial infarction, possibly by generating oxidative stress. Methylmercury is metabolized by conjugation to glutathione, which facilitates elimination. Glutathione is also an antioxidant. Individuals with certain polymorphisms in glutathione-related genes may tolerate higher exposures to methylmercury, due to faster metabolism and elimination and/or better glutathione-associated antioxidative capacity. They would thus benefit more from the protective agents in fish, such as eicosapentaenoic+docosahexaenoic acid and selenium. The objective for this study was to elucidate whether genetic polymorphisms in glutathione-related genes modify the association between eicosapentaenoic+docosahexaenoic acid or methylmercury and risk of first ever myocardial infarction. Methods Polymorphisms in glutathione-synthesizing (glutamyl-cysteine ligase catalytic subunit, GCLC and glutamyl-cysteine ligase modifier subunit, GCLM or glutathione-conjugating (glutathione S-transferase P, GSTP1 genes were genotyped in 1027 individuals from northern Sweden (458 cases of first-ever myocardial infarction and 569 matched controls. The impact of these polymorphisms on the association between erythrocyte-mercury (proxy for methylmercury and risk of myocardial infarction, as well as between plasma eicosapentaenoic+docosahexaenoic acid and risk of myocardial infarction, was evaluated by conditional logistic regression. The effect of erythrocyte-selenium on risk of myocardial infarction was also taken into consideration. Results There were no strong genetic modifying effects on the association between plasma eicosapentaenoic+docosahexaenoic acid or erythrocyte-mercury and risk of myocardial infarction risk. When eicosapentaenoic

  19. Genetic polymorphisms of immune checkpoint proteins PD-1 and TIM-3 are associated with survival of patients with hepatitis B virus-related hepatocellular carcinoma

    Science.gov (United States)

    Li, Zhu; Li, Na; Li, Fang; Zhou, Zhihua; Sang, Jiao; Jin, Zhao; Liu, Huihui; Han, Qunying; Lv, Yi; Liu, Zhengwen

    2016-01-01

    Programmed cell death protein 1 (PD-1) and T-cell immunoglobulin domain and mucin domain containing molecule 3 (TIM-3) are involved in hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC). This study examined the associations of PD1 and TIM3 polymorphisms with the overall survival (OS) of a prospective cohort of 258 HBV-related HCC patients. Results showed that PD1 +8669 G allele-containing genotypes or TIM3 −1516 genotype GG were significantly associated with longer OS (P < 0.001 and P = 0.001, respectively). In multivariate analysis, PD1 +8669 G allele-containing genotypes and TIM3 −1516 genotype GG were independently associated with longer OS (hazard ratio (HR), 1.835; 95% confidence interval (CI), 1.342–2.509; P < 0.001 and HR, 2.070; 95%CI, 1.428–3.002; P < 0.001, respectively). PD1 +8669 G allele-containing genotypes were significantly associated with longer OS in patients receiving surgical (resection or radiofrequency) treatment, transcatheter arterial chemoembolization (TACE) or supportive and symptomatic treatment. TIM3 −1516 genotype GG was significantly associated with longer OS in TACE patients. In multivariate analysis, PD1 +8669 G allele-containing genotypes were independently associated with longer OS in each treatment population. TIM3 −1516 genotype GG was independently associated with longer OS in patients receiving surgical treatment or TACE. These findings suggest that PD1 +8669 A/G and TIM3 −1516 G/T polymorphisms may affect the prognosis of HBV-related HCC and may be new predictors of prognosis for HCC patients. PMID:27034168

  20. Interleukin 28B genetic polymorphism and hepatitis B virus infection.

    Science.gov (United States)

    Takahashi, Toru

    2014-09-14

    Interleukin (IL) 28B genetic polymorphism is significantly associated with the sustained virological response rate in patients with chronic hepatitis C treated with pegylated interferon-α (PEG-IFN) plus ribavirin and with spontaneous hepatitis C virus clearance. However, a consensus on the relationship between IL28B genetic polymorphism and the favorable outcome of chronic hepatitis B virus infection defined by hepatitis B e antigen seroconversion, and/or hepatitis B surface antigen seroclearance in patients treated with interferon or PEG-IFN has not been reached. Several reports failed to show a positive association, while some studies demonstrated a positive association in certain subject settings. More prospective studies including large cohorts are needed to determine the possible association between IL28B genetic polymorphism and the outcome of interferon or PEG-IFN treatment for chronic hepatitis B.

  1. Specific Reaction Patterns to Distinct Positive Emotional Cues Related to Incentive Motivation in Dependence of the Taq1A-Polymorphism: Molecular Genetic Associations of Early and Late Event-Related Potentials.

    Science.gov (United States)

    Munk, Aisha J L; Wielpuetz, Catrin; Osinsky, Roman; Müller, Erik M; Grant, Phillip; Hennig, Jürgen

    2016-01-01

    Early and late event-related potential (ERP) responses, representing early subconscious and late motivational processes, were recorded for positive emotional words related to 'wanting' and 'liking', in dependence of the dopamine-related Taq1A genotype (ANKK1/DRD2). Research suggests that 'wanting' as opposed to 'liking' is related to dopaminergic processes. Therefore, it was hypothesized that risk allele carriers of the Taq1A polymorphism exhibit late ERP changes in reaction to words representing incentive motivation, i.e. 'wanting' (word categories 'lust' and 'anticipation'), but not to words representing 'liking' ('closeness'). Seventy-two male participants performed an emotional-word Stroop task during EEG recording and were genotyped according to the Taq1A polymorphism of ANKK1/DRD2. Positive emotional words related to anticipation and lust revealed blunted responses in the late positive potential (LPP) in carriers of the A1 allele, an effect absent in response to 'liking'-related words. These differences were not evident in the earlier posterior negativity (EPN). As no differences in dependence of the Taq1A genotype were observed in reaction to 'wanting'- and 'liking'-related words in the EPN, but merely in the LPP, it can be assumed that incentive-motivational stimuli only modify motivation-related ERP responses in carriers of the A1 allele of the Taq1A polymorphism, indicating the role of dopamine in late ERP components. © 2016 S. Karger AG, Basel.

  2. Ecosensitivity and genetic polymorphism of somatic traits in the perinatal development of twins.

    Science.gov (United States)

    Waszak, Małgorzata; Cieślik, Krystyna; Skrzypczak-Zielińska, Marzena; Szalata, Marlena; Wielgus, Karolina; Kempiak, Joanna; Bręborowicz, Grzegorz; Słomski, Ryszard

    2016-04-01

    In view of criticism regarding the usefulness of heritability coefficients, the aim of this study was to analyze separately the information on genetic and environmental variability. Such an approach, based on the normalization of trait's variability for its value, is determined by the coefficients of genetic polymorphism (Pg) and ecosensitivity (De). The studied material included 1263 twin pairs of both sexes (among them 424 pairs of monozygotic twins and 839 pairs of dizygotic twins) born between the 22nd and 41st week of gestation. Variability of six somatic traits was analyzed. The zygosity of same-sex twins was determined based on the polymorphism of DNA from lymphocytes of the umbilical cord blood, obtained at birth. The coefficients of genetic polymorphism and ecosensitivity for analyzed traits of male and female twins born at various months of gestation were calculated. Our study revealed that a contribution of the genetic component predominated over that of the environmental component in determining the phenotypic variability of somatic traits of newborns from twin pregnancies. The genetically determined phenotypic variability in male twins was greater than in the females. The genetic polymorphism and ecosensitivity of somatic traits were relatively stable during the period of fetal ontogeny analyzed in this study. Only in the case of body weight, a slight increase in the genetic contribution of polygenes to the phenotypic variance could be observed with gestational age, along with a slight decrease in the influence of environmental factors. Copyright © 2015 Elsevier GmbH. All rights reserved.

  3. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  4. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    Science.gov (United States)

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  5. [Polymorphism of connexin 40 gene-- a novel genetic marker of the sick sinus node syndrome].

    Science.gov (United States)

    Chernova, A A; Nikulina, S Iu; Shul'man, V A; Kukushkina, T S; Voevoda, M I; Maksimov, V N

    2011-01-01

    In this work we have demonstrated for the first time on the clinico-genetic material association between hereditary sick sinus node syndrome and connexin 40 gene polymorphism. We have revealed that heterozygous variant of connexin 40 gene variant is more frequent among patients with sick sinus node syndrome and their healthy relatives than in persons of control group.

  6. Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection.

    Science.gov (United States)

    Chang, Stewart T; Linderman, Jennifer J; Kirschner, Denise E

    2008-07-01

    Several molecules related to antigen presentation, including gamma interferon (IFN-gamma) and the major histocompatibility complex (MHC), are encoded by polymorphic genes. Some polymorphisms were found to affect susceptibility to tuberculosis (TB) when they were considered singly in epidemiological studies, but how multiple polymorphisms interact to determine susceptibility to TB in an individual remains an open question. We hypothesized that polymorphisms in some genes may counteract or intensify the effects of polymorphisms in other genes. For example, an increase in IFN-gamma expression may counteract the weak binding that a particular MHC variant displays for a peptide from Mycobacterium tuberculosis to establish the same T-cell response as another, more strongly binding MHC variant. To test this hypothesis, we developed a mathematical model of antigen presentation based on experimental data for the known effects of genetic polymorphisms and simulated time courses when multiple polymorphisms were present. We found that polymorphisms in different genes could affect antigen presentation to the same extent and therefore compensate for each other. Furthermore, we defined the conditions under which such relationships could exist. For example, increased IFN-gamma expression compensated for decreased peptide-MHC affinity in the model only above a certain threshold of expression. Below this threshold, changes in IFN-gamma expression were ineffectual compared to changes in peptide-MHC affinity. The finding that polymorphisms exhibit such relationships could explain discrepancies in the epidemiological literature, where some polymorphisms have been inconsistently associated with susceptibility to TB. Furthermore, the model allows polymorphisms to be ranked by effect, providing a new tool for designing association studies.

  7. Relationships of OPG Genetic Polymorphisms with Susceptibility to Cardiovascular Disease: A Meta-Analysis.

    Science.gov (United States)

    Song, De-Hua; Zhou, Peng-Zhen; Xiu, Xiao-Lin; Zhou, Guang-Hui; Sun, Yu-Xia; Song, Chun

    2016-04-12

    BACKGROUND The aim of this meta-analysis was to determine whether genetic polymorphisms in the osteoprotegerin (OPG) gene contribute to increased risk of cardiovascular disease (CVD). MATERIAL AND METHODS Electronic databases were searched carefully without any language restriction. Analyses of data were conducted using STATA software. Odds ratios (OR) and 95% confidence intervals (95%CI) were also calculated. RESULTS Seven clinical case-control studies that enrolled 1170 CVD patients and 1194 healthy subjects were included. The results indicated that OPG gene polymorphism might be closely associated with susceptibility to CVD, especially for rs2073617 T>C and rs2073618 G>C polymorphisms. Ethnicity-stratified analysis indicated that genetic polymorphism in the OPG were closely related with the pathogenesis of CVD among Asians (all P0.05). CONCLUSIONS Our meta-analysis provided quantitative evidence that OPG gene polymorphism may be closely related to an increased risk of CVD, especially for rs2073617 T>C and rs2073618 G>C polymorphisms.

  8. Genetic diversity among sorghum landraces and polymorphism ...

    African Journals Online (AJOL)

    1 Institute of Environment and Agricultural Research (INERA), BP 910 Bobo Dioulasso, ... This investigation was undertaken to study the genetic diversity among local ... resources could develop new and durable production systems. The biological basis of world food security .... Two control panel DNA samples were used in.

  9. Phenotypic evolution from genetic polymorphisms in a radial network architecture

    Directory of Open Access Journals (Sweden)

    Siegel Paul B

    2007-11-01

    Full Text Available Abstract Background The genetic architecture of a quantitative trait influences the phenotypic response to natural or artificial selection. One of the main objectives of genetic mapping studies is to identify the genetic factors underlying complex traits and understand how they contribute to phenotypic expression. Presently, we are good at identifying and locating individual loci with large effects, but there is a void in describing more complex genetic architectures. Although large networks of connected genes have been reported, there is an almost complete lack of information on how polymorphisms in these networks contribute to phenotypic variation and change. To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support. Results A previous study provided evidence that nearly half of the difference in eight-week body weight between two divergently selected lines of chickens was a result of four loci organized in a 'radial' network (one central locus interacting with three 'radial' loci that, in turn, only interacted with the central locus. Here, we study the relationship between phenotypic change and genetic polymorphism in this empirically detected network. We use a model-free approach to study, through individual-based simulations, the dynamic properties of this polymorphic and epistatic genetic architecture. The study provides new insights to how epistasis can modify the selection response, buffer and reveal effects of major loci leading to a progressive release of genetic variation. We also illustrate the difficulty of predicting genetic architecture from observed selection response, and discuss mechanisms that might lead to misleading conclusions on underlying genetic architectures from quantitative trait locus (QTL experiments in selected populations. Conclusion Considering both molecular (QTL and phenotypic (selection

  10. Identification of possible genetic polymorphisms involved in cancer cachexia: a systematic review

    Indian Academy of Sciences (India)

    Benjamin H. L. Tan; James A. Ross; Stein Kaasa; Frank Skorpen; Kenneth C. H. Fearon; European Palliative Care Research Collaborative

    2011-04-01

    Cancer cachexia is a polygenic and complex syndrome. Genetic variations in regulation of the inflammatory response, muscle and fat metabolic pathways, and pathways in appetite regulation are likely to contribute to the susceptibility or resistance to developing cancer cachexia. A systematic search of Medline and EmBase databases, covering 1986–2008 was performed for potential candidate genes/genetic polymorphisms relating to cancer cachexia. Related genes were then identified using pathway functional analysis software. All candidate genes were reviewed for functional polymorphisms or clinically significant polymorphisms associated with cachexia using the OMIM and GeneRIF databases. Genes with variants which had functional or clinical associations with cachexia and replicated in at least one study were entered into pathway analysis software to reveal possible network associations between genes. A total of 184 polymorphisms with functional or clinical relevance to cancer cachexia were identified in 92 candidate genes. Of these, 42 polymorphisms (in 33 genes) were replicated in more than one study with 13 polymorphisms found to influence two or more hallmarks of cachexia (i.e. inflammation, loss of fat mass and/or lean mass and reduced survival). Thirty-three genes were found to be significantly interconnected in two major networks with four genes (ADIPOQ, IL6, NFKB1 and TLR4) interlinking both networks. Selection of candidate genes and polymorphisms is a key element of multigene study design. The present study provides an initial framework to select genes/polymorphisms for further study in cancer cachexia, and to develop their potential as susceptibility biomarkers of developing cachexia.

  11. Cytochrome P450 genetic polymorphisms of Mexican indigenous populations.

    Science.gov (United States)

    Sosa-Macías, Martha; Llerena, Adrián

    2013-01-01

    This review focuses on the genetic polymorphisms of the cytochrome P450 (CYP) genes in Mexican indigenous populations, who are a part of the wide ethnic diversity of this country. These native groups have a particular historical trajectory that is different from the Mexican Mestizos. This variability may be reflected in the frequency distribution of polymorphisms in the CYP genes that encode enzymes involved in the metabolism of drugs and other xenobiotics. Therefore, these polymorphisms may affect drug efficacy and safety in indigenous populations in Mexico. The present study aimed to analyze the prevalence of CYP polymorphisms in indigenous Mexicans and to compare the results with studies in Mexican Mestizos. Because the extrapolation of pharmacogenetic data from Mestizos is not applicable to the majority of indigenous groups, pharmacogenetic studies directed at indigenous populations need to be developed. The Amerindians analyzed in this study showed a low phenotypic (CYP2D6) and genotypic (CYP2D6, CYP2C9) diversity, unlike Mexican Mestizos. The frequency of polymorphisms in the CYP1A1, CYP2C19, CYP2E1, and CYP3A4 genes was more similar among the Amerindians and Mexican Mestizos, with the exception of the CYP1A2 gene, whose *1F variant frequency in Mexican Amerindians was the highest described to date.

  12. CD209 genetic polymorphism and tuberculosis disease.

    Directory of Open Access Journals (Sweden)

    Fredrik O Vannberg

    Full Text Available BACKGROUND: Tuberculosis causes significant morbidity and mortality worldwide, especially in sub-Saharan Africa. DC-SIGN, encoded by CD209, is a receptor capable of binding and internalizing Mycobacterium tuberculosis. Previous studies have reported that the CD209 promoter single nucleotide polymorphism (SNP-336A/G exerts an effect on CD209 expression and is associated with human susceptibility to dengue, HIV-1 and tuberculosis in humans. The present study investigates the role of the CD209 -336A/G variant in susceptibility to tuberculosis in a large sample of individuals from sub-Saharan Africa. METHODS AND FINDINGS: A total of 2,176 individuals enrolled in tuberculosis case-control studies from four sub-Saharan Africa countries were genotyped for the CD209 -336A/G SNP (rs4804803. Significant overall protection against pulmonary tuberculosis was observed with the -336G allele when the study groups were combined (n = 914 controls vs. 1262 cases, Mantel-Haenszel 2 x 2 chi(2 = 7.47, P = 0.006, odds ratio = 0.86, 95%CI 0.77-0.96. In addition, the patients with -336GG were associated with a decreased risk of cavitory tuberculosis, a severe form of tuberculosis disease (n = 557, Pearson's 2x2 chi(2 = 17.34, P = 0.00003, odds ratio = 0.42, 95%CI 0.27-0.65. This direction of association is opposite to a previously observed result in a smaller study of susceptibility to tuberculosis in a South African Coloured population, but entirely in keeping with the previously observed protective effect of the -336G allele. CONCLUSION: This study finds that the CD209 -336G variant allele is associated with significant protection against tuberculosis in individuals from sub-Saharan Africa and, furthermore, cases with -336GG were significantly less likely to develop tuberculosis-induced lung cavitation. Previous in vitro work demonstrated that the promoter variant -336G allele causes down-regulation of CD209 mRNA expression. Our present work suggests that decreased

  13. USF-1 genetic polymorphisms confer a high risk of nonalcoholic fatty liver disease in Chinese population.

    Science.gov (United States)

    Wang, Ying; Wang, Bai-Fang; Tong, Jing; Chang, Bing; Wang, Bing-Yuan

    2015-01-01

    Genetic polymorphisms in upstream transcription factor 1 (USF1) were investigated for their links to increased risk of nonalcoholic fatty liver disease (NAFLD) in Chinese population. Between January 2013 and April 2014, 174 patients with NAFLD in the First Affiliated Hospital of China Medical University were selected for this study. A group of 100 healthy subjects were identified as the control group. The MALDI-TOF-MS, a mass spectrometry based technique, was used to detect USF-1 genetic polymorphisms using PCR amplified DNA products. Furthermore, Automatic Chemistry Analyzer (ACA) was used to determine the clinical indicators. Genotypes, allele frequencies and clinical indicators were measured to assess NAFLD risk in relation to the SNPs. USF-1 rs6427573 genetic polymorphisms were associated with an increased risk of NAFLD (AA vs. GG: OR = 3.16, 95% CI = 1.56-6.43, P = 0.001; GA + AA vs. GG: OR = 1.87, 95% CI = 1.13-3.09, P = 0.015; GG + AA vs. AA: OR = 2.96, 95% CI = 1.49-5.88, P = 0.001; G vs. A: OR = 2.10, 95% CI = 1.43-3.09, P 0.05). Two USF-1 genetic polymorphisms, rs6427573 and rs2516839, may present an increased risk of NAFLD.

  14. Development of an assay to determine single nucleotide polymorphisms in the prion gene for the genetic diagnosis of relative susceptibility to classical scrapie in sheep.

    Science.gov (United States)

    Johnson, Mary Lynn; Evoniuk, Jessica M; Stoltenow, Charles L; O'rourke, Katherine I; Redmer, Dale A

    2007-01-01

    The objective of this study was to develop a reliable Taqman 5' Nuclease Assay for genotyping sheep for scrapie susceptibility. The sheep prion gene contains 2 single nucleotide polymorphisms (SNPs) that may mediate resistance to classical scrapie, one at codon 136, alanine (A) or valine (V), and another at codon 171, arginine (R) or glutamine (Q). The R allele appears to confer resistance to classical scrapie, with the AA(136) RR(171) genotype the most resistant to scrapie and QR(171) only rarely infected in the US sheep population. The Assays by Design protocol was used for development of probes and primers for codon 136 and Primer Express for codon 171. Commercially available kits were used to isolate genomic DNA from blood or muscle. For validation, 70 SNP determinations for each codon were compared to commercial testing with an error rate of less than 1%. Then, 935 samples from blood (n = 818) and muscle (n = 117) were tested for both codons with 928 successful determinations and only 7 samples (scrapie-resistant. This new Taqman 5' Nuclease SNP genotyping assay is accurate, easy to perform, and useful in the study of classical scrapie in sheep and its prevention through selective breeding programs to eliminate highly susceptible animals.

  15. Correlation of M-type phospholipase A2 receptor genetic polymorphism with idiopathic membranous nephropathy

    Institute of Scientific and Technical Information of China (English)

    周广宇

    2013-01-01

    Objective To investigate the correlation of M-typephos pholipase A2receptor(PLA2R) genetic polymorphism in two single nucleotide polymorphisms(SNPs) with idiopathic membranous nephropathy(IMN) of Chinese

  16. Calcium/magnesium intake ratio, but not magnesium intake, interacts with genetic polymorphism in relation to colorectal neoplasia in a two-phase study.

    Science.gov (United States)

    Zhu, Xiangzhu; Shrubsole, Martha J; Ness, Reid M; Hibler, Elizabeth A; Cai, Qiuyin; Long, Jirong; Chen, Zhi; Li, Guoliang; Jiang, Ming; Hou, Lifang; Kabagambe, Edmond K; Zhang, Bing; Smalley, Walter E; Edwards, Todd L; Giovannucci, Edward L; Zheng, Wei; Dai, Qi

    2016-10-01

    Some studies suggest that the calcium to magnesium ratio intakes modify the associations of calcium or magnesium with risk of colorectal adenoma, adenoma recurrence, and cancer. Parathyroid hormone (PTH) plays a key role in the regulation of homeostasis for both calcium and magnesium. We hypothesized that polymorphisms in PTH and 13 other genes may modify the association between the calcium/magnesium intake ratio and colorectal neoplasia risk. We conducted a two-phase study including 1336 cases and 2891 controls from the Tennessee Colorectal Polyp Study. In Phase I, we identified 19 SNPs that significantly interacted with the calcium/magnesium intake ratio in adenoma risk. In Phase II, rs11022858 in PTH was replicated. In combined analysis of phases I and II, we found high calcium/magnesium intake ratio tended to be associated with a reduced risk of colorectal adenoma (P for trend, 0.040) among those who carried the TT genotype in rs11022858. In stratified analyses, calcium intake (≥ 1000 mg/d) was significantly associated with 64% reduced adenoma risk (OR = 0.36 (95% CI : 0.18-0.74)) among those homozygous for the minor allele (TT genotype) (P for trend, 0.012), but not associated with risk in other genotypes (CC/TC). Conversely, we found that highest magnesium intake was significantly associated with 27% reduced risk (OR = 0.73 (95% CI : 0.54-0.97)) of colorectal adenoma (P for trend, 0.026) among those who possessed the CC/TC genotypes, particularly among those with the TC genotype, whereas magnesium intake was not linked to risk among those with the TT genotype. These findings, if confirmed, will help for the development of personalized prevention strategies for colorectal cancer. © 2015 Wiley Periodicals, Inc.

  17. CYTOKINES GENETIC POLYMORPHISM: THE PAST AND THE FUTURE

    Directory of Open Access Journals (Sweden)

    L. V. Puzyryova

    2016-01-01

    Full Text Available The molecular genetics opens the new horizons in modern medicine, especially now when many diseases are given huge value in a type of their prevalence among various groups of population. Extremely high interleukin genes polymorphism degrees are studied well especially genetic polymorphism of tumor necrosis factor. Patients with HIV infection in the territory of Russia cause now the highest degree of mortality that is the most actual and socially significant problem of healthcare. This problems studying attracts many researchers. Works in respect of genetic immunity to a virus and influence of cytokines production on the disease forecast are especially interesting. One of the HIV replication influencing factors are cytokines, some of which, including the tumor necrosis factor and interleukin-6 can promote replication of HIV, raising an expression of virus regulatory genes. During disease progress in parallel of anti-inflammatory cytokines level increase (causing in this case rather ineffective antibodies level increase there is an T-helpers suppression stimulating a strong cellular component. Cytokine network functioning during HIV infection depends on many reasons which the individual variation in cytokine production caused by a number of genetic features, as well as an existence of opportunistic infection. Cytokines polymorphism determination in HIV infected patients is necessary in clinical practice for disease progression forecast to adverse fast transition to AIDS that it is important to consider in a choice of tactics of the supporting therapy of HIV-positive patients. Considering insufficient efficiency of modern methods of treatment, restoration and modulation of cytokines balance will increase anti-virus activity of immune system, influencing the factors blocking replication of a HIV.

  18. Vitamin D receptor genetic polymorphisms and tuberculosis among Chinese Han ethnic group

    Institute of Scientific and Technical Information of China (English)

    CAO Shang; LUO Peng-fei; LI Wei; TANG Wan-qin; CONG Xiao-na; WEI Ping-min

    2012-01-01

    Background In epidemiological studies,tuberculosis (TB) appears intimately with vitamin D insufficiency whereas its relationship with vitamin D receptor (VDR) polymorphism caused by radical difference remains unspecified.This study aimed to investigate the relationship between vitamin D genetic polymorphism and tuberculosis in Han ethnic group.Methods Meta-analysis was adopted in the synthetic quantitative analysis of documents home and abroad on the relationship between vitamin D genetic polymorphisms and tuberculosis,which were openly published during June 2000 to January 2010.Random effect model and fixed effect model analyses were used to calculate the incorporated odds ratio (OR) based on the heterogeneity test data.Results A total of 6 eligible studies were included in this analysis.The Fokl-ff genotype showed a significant marginal association (Fixed effect model:OR 1.91,95% CI 1.44-2.52; Random effect model:OR 1.91,95% CI 0.94-3.88),yet Taql polymorphisms was not significantly related to TB.Conclusion The interaction between FoKI genotype polymorphism and TB observed demonstrates that vitamin D deficiency might exist as a risk factor during the development of TB in Han ethnic group and more evidences needed to validate the conclusion.

  19. Vitamin D receptor genetic polymorphisms and tuberculosis among Chinese Han ethnic group.

    Science.gov (United States)

    Cao, Shang; Luo, Peng-fei; Li, Wei; Tang, Wan-qin; Cong, Xiao-na; Wei, Ping-min

    2012-03-01

    In epidemiological studies, tuberculosis (TB) appears intimately with vitamin D insufficiency whereas its relationship with vitamin D receptor (VDR) polymorphism caused by radical difference remains unspecified. This study aimed to investigate the relationship between vitamin D genetic polymorphism and tuberculosis in Han ethnic group. Meta-analysis was adopted in the synthetic quantitative analysis of documents home and abroad on the relationship between vitamin D genetic polymorphisms and tuberculosis, which were openly published during June 2000 to January 2010. Random effect model and fixed effect model analyses were used to calculate the incorporated odds ratio (OR) based on the heterogeneity test data. A total of 6 eligible studies were included in this analysis. The FokI-ff genotype showed a significant marginal association (Fixed effect model: OR 1.91, 95%CI 1.44-2.52; Random effect model: OR 1.91, 95%CI 0.94-3.88), yet TaqI polymorphisms was not significantly related to TB. The interaction between FoKI genotype polymorphism and TB observed demonstrates that vitamin D deficiency might exist as a risk factor during the development of TB in Han ethnic group and more evidences needed to validate the conclusion.

  20. PTC bitter taste genetic polymorphism, food choices, physical growth in body height and body fat related traits among adolescent girls from Kangra Valley, Himachal Pradesh (India).

    Science.gov (United States)

    Sharma, Krishan; Kaur, Goga Kirandeep

    2014-01-01

    Bitter sensitivity among individuals and ethnic groups is partly due to polymorphic bitter taste receptor genes (TAS2Rs). PTC/PROP bitter taste responsiveness at locus TAS2R38 is a well-established index of individual variation in oral sensation that has been linked with predicting food liking and consumption. Previous studies suggest that the relationship between PTC/PROP and anthropometric traits remains controversial. To explore the role of TAS2R38 locus in taste choices, adolescent growth trend for body height, weight and fat patterning among girls and to evaluate their growth status. Cross-sectional data on 210 girls ranging in age from 11-18 years were collected from Palampur in the Kangra valley of Himachal Pradesh. The proportion of PTC non-tasters was 19.52%. PTC tasters and non-tasters had some differences in their food choices and preferences. More sensitive PTC tasters had a low preference for raw cruciferous vegetables and bitter tasting foods (like bitter gourd) and beverages, while they had higher preference for sweet-tasting foods (p < 0.05). PTC tasters overtook their PTC non-taster counterparts from age 14 through 16 years in having higher mean average skinfold, percentage body fat, fat mass index and fat-free mass index. PTC non-tasters had higher mean stature than tasters through all age groups. PTC tasters had slightly higher mean body weight than tasters at age 11, but in later years the advantage was lost; the total gain among non-tasters through adolescence was higher (78.20%) than tasters (66.92%). PTC thresholds significantly and negatively correlated with body height. TAS2R38 locus seems to have a role in food tastes, choices and preferences. Perceived bitterness of PTC/PROP thresholds were significantly and negatively correlated with body height and fat-free mass. These results, thus, tentatively suggest that the PTC non-taster gene may help in better absorption of calcium than its counter taster allele. Studies on differences in

  1. Polymorphisms in genes involved in neurotransmission in relation to smoking.

    Science.gov (United States)

    Arinami, T; Ishiguro, H; Onaivi, E S

    2000-12-27

    Smoking behavior is influenced by both genetic and environmental factors. The genetic contribution to smoking behavior is at least as great as its contribution to alcoholism. Much progress has been achieved in genomic research related to cigarette-smoking within recent years. Linkage studies indicate that there are several loci linked to smoking, and candidate genes that are related to neurotransmission have been examined. Possible associated genes include cytochrome P450 subfamily polypeptide 6 (CYP2A6), dopamine D(1), D(2), and D(4) receptors, dopamine transporter, and serotonin transporter genes. There are other important candidate genes but studies evaluating the link with smoking have not been reported. These include genes encoding the dopamine D(3) and D(5) receptors, serotonin receptors, tyrosine hydroxylase, trytophan 2,3-dioxygenase, opioid receptors, and cannabinoid receptors. Since smoking-related factors are extremely complex, studies of diverse populations and of many aspects of smoking behavior including initiation, maintenance, cessation, relapse, and influence of environmental factors are needed to identify smoking-associated genes. We now review genetic polymorphisms reported to be involved in neurotransmission in relation to smoking.

  2. Genetic polymorphism of blood proteins in a population of Shetland ponies

    NARCIS (Netherlands)

    Buis, R.C.

    1976-01-01

    Genetic variation of proteins (protein polymorphism) is widespread among many animal species. The biological significance of protein polymorphism has been the subject of many studies. This variation has a supporting function for population genetic studies as a source of genetic markers. In farm anim

  3. Genetic polymorphism of milk protein loci in Argentinian Holstein cattle

    Directory of Open Access Journals (Sweden)

    Bonvillani Adriana Gloria

    2000-01-01

    Full Text Available Some alleles of milk protein loci are associated with superior cheese production characteristics. The genetic polymorphism of the milk protein loci alphas1-casein, beta-casein, k-casein and beta-lactoglobulin was examined in Argentinian Holstein cattle. Samples from 12 herds of four regions of Córdoba were analyzed by starch gel electrophoresis. The chi² test was used to assess whether the populations were in Hardy-Weinberg equilibrium. Genotypic diversity was analyzed by the Shannon-Weaver index. The observed genotypic frequencies were analyzed by Hedrick's genetic identity and the genetic distance of Balakrishnan and Sanghvi. The allelic and genotypic frequencies were similar to those of other Holstein populations. The genotypic frequencies of the alphas1-casein and beta-casein loci were in equilibrium, whereas in some populations the k-casein and beta-lactoglobulin loci were not. According to the Shannon-Weaver index the total genetic diversity within each herd was greater than 96%. The high values of identity agreed with the low genetic distances among populations. We conclude that there is extensive genetic homogeneity in Holstein cattle in Córdoba Province and that it would be feasible to select for B alleles at the k-casein and b-lactoglobulin loci in order to improve the quality of milk available for cheese manufacturing.

  4. Genetic diversity and chemical polymorphism of some Thymus species.

    Science.gov (United States)

    Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

    2013-06-01

    To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ČELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles.

  5. Genetic polymorphisms related to meat traits in purebred and crossbred Nelore cattle Polimorfismos genéticos relacionados às características da carne em bovinos Nelore puros e cruzados

    Directory of Open Access Journals (Sweden)

    Rogério Abdallah Curi

    2009-12-01

    Full Text Available The objective of this work was to estimate the allelic and genotypic frequencies of CAST/XmnI, a calpastatin gene polymorphism, and CAPN530, a calpain 1 large subunit gene polymorphism, in different beef genetic groups (Nelore and Nelore x Bos taurus, and to investigate associations between these polymorphisms and carcass and meat traits. Three hundred animals - comprising 114 Nelore, 67 Angus x Nelore, 44 Rubia Gallega x Nelore, 41 Canchim, 19 Brangus three-way cross and 15 Braunvieh three-way cross- were genotyped by PCR-RFLP and phenotyped for rib-eye area (REA, back-fat thickness (BT, intramuscular fat (IF, shear force (SF and myofibrillar fragmentation index (MFI. The occurrence of the two alleles of the CAST/XmnI and CAPN530 single nucleotide polymorphisms (SNPs in a B. indicus breed, which permitted association studies in purebred and crossbred Nelore cattle, was first shown in the present work. No relationship was found between the CAST or CAPN1 SNPs and growth-related traits (REA or fat deposition (BT and IF, since calpastatin and µ-calpain are not physiologically involved with these traits. Moreover, the association results between genotypes and aged meat tenderness (assessed by SF and MFI showed that these markers are useless in assisted selection for purebred Nelore and their crosses with B. taurus.O presente trabalho objetivou estimar, em bovinos de corte de diferentes grupos genéticos (Nelore e Nelore x Bos taurus, as frequências alélicas e genotípicas dos polimorfismos CAST/XmnI, do gene da calpastatina, e CAPN530, do gene da calpaína, bem como avaliar a ocorrência de associações entre esses polimorfismos e características da carcaça e da carne produzida. Trezentos animais - 114 Nelore, 67 Angus x Nelore, 44 Rubia Galega x Nelore, 41 Canchim, 19 tricross Brangus e 15 tricross Braunvieh - foram genotipados por PCR-RFLP e fenotipados para área de olho de lombo (AOL, cobertura de gordura subcutânea (CGS, gordura

  6. Genetic polymorphism of MMP family and coronary disease susceptibility: a meta-analysis.

    Science.gov (United States)

    Li, Min; Shi, Jingpu; Fu, Lingyu; Wang, Hailong; Zhou, Bo; Wu, Xiaomei

    2012-03-01

    The issue that genetic polymorphism of matrix metalloproteinase (MMP) family is in association with coronary disease is controversial. So we did a meta-analysis to clarify it clearly. We made a literature search of PubMed, the Web of Science, and Cochrane Collaboration's database to identify eligible reports. The methodological quality of each included studies was assessed. We calculated the pooled ORs with their 95%CI for each genetic polymorphism in STATA 11 software. Separate analysis was performed to address the consistency of results across the subgroup with different continents. A total of 39 studies were included, with a sample of 42269 individuals. This meta-analysis provided evidence that genetic polymorphism of MMP1-1607 1G/2G, MMP3-Gly45lys, MMP3-376 G/C, MMP3-1171 5A/6A, MMP9-1562 C/T and MMP9-R279Q have a small to medium effect on incidence of coronary disease. There was no evidence that MMP1-519 A/G, MMP1-340 T/C and MMP2-1306 C/T polymorphism could increase risk of coronary disease. Results from subgroup analysis supported a relation between MMP3-1711 5A allele, MMP9-1562 C allele and coronary disease especially in Asian population. The results provide moderate association between the six common genetic polymorphism of matrix metalloproteinase family and coronary disease. However, the challenge for researcher is identifying separate effect on different races.

  7. Potential for Incorporation of Genetic Polymorphism Data in Human Health Risk Assessment

    Science.gov (United States)

    This overview summarizes several EPA assessment publications evaluating the potential impact of genetic polymorphisms in ten metabolizing enzymes on the variability in enzyme function across ethnically diverse populations.

  8. GENETIC POLYMORPHISM OF STR LOCI IN CHINESE DRUNGS

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Objective:To study the STR polymorphism in Chinese Drungs.Methods:The genetic distributions of 15 STR loci and Amelogenin locus were generated through coamplification,genescan and genotype from 65 Drungs Results:There were 144 STR and 2 Amelogenin alleles in Drung nationality,with their frequencies ranging from 0.0077 to 0.7846,H0.3723-0.8639,DP0.5567-0.9548,EPP0.2738-0.8358,and PIC 0.3461-0.8456,the accumulative DP 0.9999998and EPP 0.9999894,Conclusion:The study founded a basis for the genetic structure of Chinese ethnic groups ,which is useful for the application to anthropology and forensic science.

  9. Genetic polymorphism in pathogenesis of irritable bowel syndrome.

    Science.gov (United States)

    Cheung, Cynthia K Y; Wu, Justin C Y

    2014-12-21

    Irritable bowel syndrome (IBS) is a complex symptom-based disorder without established biomarkers or putative pathophysiology. IBS is a common functional gastrointestinal disorder which is defined as recurrent abdominal pain or discomfort that has at least two of the following symptoms for 3 d per month in the past 3 mo according to ROME III: relief by defecation, onset associated with a change in stool frequency or onset with change in appearance or form of stool. Recent discoveries revealed genetic polymorphisms in specific cytokines and neuropeptides may possibly influence the frequencies and severity of symptoms, as well as the therapeutic responses in treating IBS patients. This review gives new insights on how genetic determinations influence in clinical manifestations, treatment responses and potential biomarkers of IBS.

  10. GENETIC POLYMORPHISM OF STR LOCI IN CHINESE DRUNGS

    Institute of Scientific and Technical Information of China (English)

    赖江华; 郑海波; 朱波峰; 李生斌

    2002-01-01

    Objective To study the STR polymorphism in Chi nese Drungs. Methods The genetic distributions of 15 STR loci a nd Amelogenin locus were generated through coamplification, genescan and genotyp e from 65 Drungs. Results There were 144 STR and 2 Amelogenin alleles in Drung n ationality, with their frequencies ranging from 0.0077 to 0.7846, H 0.3723~0.8 639, DP 0.5567~0.9548, EPP 0.2738~0.8358, and PIC 0.3461~0.8456, the accumul ative DP 0.99999998 and EPP 0.99999894. Conclusion The study f ounded a basis for the genetic structure of Chinese ethnic group s,which is useful for the application to anthropology and forensic science.

  11. Genetic Polymorphisms in Genes Related to Oxidative Stress (GSTP1, GSTM1, GSTT1, CAT, MnSOD, MPO, eNOS) and Survival of Rectal Cancer Patients after Radiotherapy

    National Research Council Canada - National Science Library

    Funke, Silvia; Risch, Angela; Nieters, Alexandra; Hoffmeister, Michael; Stegmaier, Christa; Seiler, Christoph M; Brenner, Hermann; Chang-Claude, Jenny

    2009-01-01

    Radiotherapy exerts part of its antineoplastic effect by generating oxidative stress, therefore genetic variation in oxidative stress-related enzymes may influence survival of rectal cancer patients...

  12. Genetic polymorphism in Taenia solium metacestodes from different Brazilian geographic areas.

    Science.gov (United States)

    Barcelos, Ivanildes Solange da Costa; Souza, Maria Aparecida; Pena, Janethe Deolinda de Oliveira; Machado, Gleyce Alves; Moura, Lísia Gomes Martins de; Costa-Cruz, Julia Maria

    2012-02-01

    The aim of the present study is to investigate genetic polymorphisms in Taenia solium metacestodes from different Brazilian geographical areas and to relate them to antibody recognition in serum samples of neurocysticercosis (NC) patients. Metacestodes were obtained from the Distrito Federal (DF), Bahia, Minas Gerais (MG) and São Paulo (SP) regions of Brazil. Samples of human sera from 49 individuals with NC, 68 individuals with other helminthiasis and 40 healthy volunteers were analysed (157 individuals in total). Antigens were prepared and used in enzyme-linked immunosorbent assay and western blotting assays to detect specific immunoglobulin G antibodies. Genetic distances between metacestode populations were analysed using random amplified polymorphic DNA (RAPD) analysis. Our results show that there was a higher frequency of reactivity in the DF region in the sera from NC patients (p solium metacestodes from different areas in Brazil and the differences in antibody detection in patients with NC were established.

  13. Molecular genetics of Psoriasis (Principles, technology, gene location, genetic polymorphism and gene expression).

    Science.gov (United States)

    Al Robaee, Ahmad A

    2010-11-01

    Psoriasis is a common inflammatory skin disease with an etiology bases on both environmental and genetic factors. As is the case of many autoimmune diseases its real cause remains poorly defined. However, it is known that genetic factors contribute to disease susceptibility. The linkage analysis has been used to identify multiple loci and alleles that confer risk of the disease. Some other studies have focused upon single nucleotide polymorphisms (SNPs) for mapping of probable causal variants. Other studies, using genome-wide analytical techniques, tried to link the disease to copy number variants (CNVs) that are segments of DNA ranging in size from kilobases to megabases that vary in copy number. CNVs represent an important element of genomic polymorphism in humans and harboring dosage-sensitive genes may cause or predispose to a variety of human genetic diseases. The mechanisms giving rise to SNPs and CNVs can be considered as fundamental processes underlying gene duplications, deletions, insertions, inversions and complex combinations of rearrangements. The duplicated genes being the results of 'successful' copies are fixed and maintained in the population. Conversely, many 'unsuccessful' duplicates remain in the genome as pseudogenes. There is another form of genetic variations termed copy-neutral loss of heterozygosity (LOH) with less information about their potential impact on complex diseases. Additional studies would include associated gene expression variations with either SNPs or CNVs. Now many genetic techniques such as PCR, real time PCR, microarray and restriction fragment length analysis are available for detecting genetic polymorphisms, gene mapping and estimation of gene expression. Recently, the scientists have used these tools to define genetic signatures of disease, to understand genetic causes of disease and to characterize the effects of certain drugs on gene expression. This review highlights the principles, technology and applications on

  14. Analysis of the cumulative effect of schizophrenia-related single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Lozano R

    2014-06-01

    Full Text Available Roberto Lozano,1 Reyes Marín,2 Isabel Freire,2 María-Jesús Santacruz,2 Asunción Pascual-García21Pharmacy Department, 2Psychiatry Department, Hospital Real de Nuestra Señora de Gracia, Zaragoza, SpainIt is currently believed that predisposition for schizophrenia stems from the combined effect of multiple common polymorphisms. Thus, no genetic variant is considered to be fully responsible for the disease. For this reason, analysis of the cumulative effect of schizophrenia-related single nucleotide polymorphisms (SNPs could provide information about the genetic mechanisms that underlie susceptibility.

  15. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  16. 不同种源红椿SRAP标记的遗传多样性分析%Genetic Diversity of Toona ciliata from Different Provenances Based on Sequence-Related Amplified Polymorphism ( SRAP) Markers

    Institute of Scientific and Technical Information of China (English)

    李培; 阙青敏; 欧阳昆唏; 李俊成; 湛欣; 朱芹; 张俊杰; 邓小梅; 陈晓阳

    2016-01-01

    果与地理分布格局基本吻合.在红椿保护和管理的过程中,在对原有生境进行保护的同时,要加强人工繁育技术研究,并注意最大限度地保护红椿的遗传多样性.%[Objective]Poor natural regeneration and over-exploitation have resulted in the continual decline of natural forests and trees of Toona ciliata. In depth studies of genetic diversity and structure of T. ciliata of different provenances are particularly important for conservation,utilization of genetic resources,and the development of future breeding programs for the species.[Method]Sequence-related amplified polymorphism ( SRAP) markers were used to investigate genetic diversity of 29 provenances from China and one provenance from Australia of T. ciliata to define the level of genetic diversity and the relationships among different provenances. Samples from China were collected from natural stands. Each provenance was represented by 30 sample trees with a distance of at least 50 m among the sample trees. The Australian provenance was taken from the resources collection nursery of the South China Agricultural University. The POPGENE1. 32 software was used for genetic diversity parameters calculation. The NTSYS-pc2. 1 software was used for cluster analysis based on the matrix of Nei's genetic distances and the degree of genetic relatedness among provenances was assessed by principal coordinates analysis (PCoA) and MANTEL analysis with GenAIEx 6. 5. STRUCTRUE 2. 3 was used to analysis the genetic structure. [Result]A total of 505 polymorphic bands were amplified by 24 pairs of primers. The average value of polymorphism information content (PIC) was 0. 41. The average value of Nei's gene diversity index (H) was 0. 377 0. Shannon's information index (I) within provenances ranged from 0. 157 5 to 0. 467 5,the average value was 0. 556 9 among provenances. The AMOVA indicated that 79. 24% of the total variation was among provenances and 20. 76% was within provenances,revealing that provenance

  17. Genetic polymorphism in Taenia solium metacestodes from different Brazilian geographic areas

    Directory of Open Access Journals (Sweden)

    Ivanildes Solange da Costa Barcelos

    2012-02-01

    Full Text Available The aim of the present study is to investigate genetic polymorphisms in Taenia solium metacestodes from different Brazilian geographical areas and to relate them to antibody recognition in serum samples of neurocysticercosis (NC patients. Metacestodes were obtained from the Distrito Federal (DF, Bahia, Minas Gerais (MG and São Paulo (SP regions of Brazil. Samples of human sera from 49 individuals with NC, 68 individuals with other helminthiasis and 40 healthy volunteers were analysed (157 individuals in total. Antigens were prepared and used in enzyme-linked immunosorbent assay and western blotting assays to detect specific immunoglobulin G antibodies. Genetic distances between metacestode populations were analysed using random amplified polymorphic DNA (RAPD analysis. Our results show that there was a higher frequency of reactivity in the DF region in the sera from NC patients (p < 0.05, while discrimination between active and inactive NC was seen only in extracts from the MG and SP regions (p < 0.05. Using RAPD, the sample from the DF region presented a greater increase compared to the other regions. A relationship between genetic polymorphisms among T. solium metacestodes from different areas in Brazil and the differences in antibody detection in patients with NC were established.

  18. Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji

    Science.gov (United States)

    Talbot, Sandra; Palmer, A.G.; Sage, G.K.; Sonsthagen, Sarah A.; Swem, T.; Brimm, D.J.

    2014-01-01

    We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.

  19. ANALYSIS ON GENETIC POLYMORPHISM OF 6 STR LOCI ON CHROMOSOME 12 IN CHINESE HAN POPULATION

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.

  20. Relationship between genetic polymorphism of cytochrome P450IIE1 and fatty liver

    Institute of Scientific and Technical Information of China (English)

    Yun-Feng Piao; Jing-Tao Li; Yang Shi

    2003-01-01

    AIM: To study the correlation between genetic polymorphism of cytochrome P450IIE1 (CYPIIE1) and fatty liver.METHODS: Peripheral blood mononuclear cells were collected in 56 patients with fatty liver, 26 patients without fatty liver and 20 normal controls. Then PCR-RFLP was used to analyze genetic polymorphism of CYPIIE1 in monocytes on the region of Pst I and Rsa I.RESULTS: The frequency of homozygotic C1 gene in patients with alcoholic fatty liver (28.6 %), obese fatty liver (38.5 %), or diabetic fatty liver (33.3 %) was significantly lower than that of the corresponding patients without fatty liver (100 %, 100 % and 80 % respectively), while the frequency of C2 genes, including C1/C2 and C2/C2, was significantly higher (71.4 %/0 %, 61.5 %/0 %, and 66.7 %/20 %) (P0.05).CONCLUSION: The genetic polymorphism of CYPIIE1 on the position of Pst I and Rsa I is related to the susceptibility of fatty liver. Besides, C2 gene may play a key role in the pathogenesis of fatty liver.

  1. Clopidogrel metabolism related gene polymorphisms in Chinese patients with acute coronary syndrome

    Institute of Scientific and Technical Information of China (English)

    冯广迅

    2013-01-01

    Objective To detect the single nucleotide polymorphisms of clopidogrel metabolism related genes(CYP2C19,ABCB1 and PON1) in Chinese patients with acute coronary syndrome(ACS) by genotype analysis. Methods Genetic analysis was performed in patients admitted to

  2. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers

    DEFF Research Database (Denmark)

    Su, Guosheng; Christensen, Ole Fredslund; Ostersen, Tage;

    2012-01-01

    Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total...... genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition...... of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects...

  3. Genetic polymorphisms in CYP1A1, CYP1B1 and COMT genes in Greenlandic Inuit and Europeans

    OpenAIRE

    Ghisari, Mandana; Long, Manhai; Bonefeld-Jørgensen, Eva Cecilie

    2013-01-01

    Background. The Indigenous Arctic population is of Asian descent, and their genetic background is different from the Caucasian populations. Relatively little is known about the specific genetic polymorphisms in genes involved in the activation and detoxification mechanisms of environmental contaminants in Inuit and its relation to health risk. The Greenlandic Inuit are highly exposed to legacy persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) and organochlorine pes...

  4. Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD.

    Science.gov (United States)

    Sun, Wei; Kechris, Katerina; Jacobson, Sean; Drummond, M Bradley; Hawkins, Gregory A; Yang, Jenny; Chen, Ting-Huei; Quibrera, Pedro Miguel; Anderson, Wayne; Barr, R Graham; Basta, Patricia V; Bleecker, Eugene R; Beaty, Terri; Casaburi, Richard; Castaldi, Peter; Cho, Michael H; Comellas, Alejandro; Crapo, James D; Criner, Gerard; Demeo, Dawn; Christenson, Stephanie A; Couper, David J; Curtis, Jeffrey L; Doerschuk, Claire M; Freeman, Christine M; Gouskova, Natalia A; Han, MeiLan K; Hanania, Nicola A; Hansel, Nadia N; Hersh, Craig P; Hoffman, Eric A; Kaner, Robert J; Kanner, Richard E; Kleerup, Eric C; Lutz, Sharon; Martinez, Fernando J; Meyers, Deborah A; Peters, Stephen P; Regan, Elizabeth A; Rennard, Stephen I; Scholand, Mary Beth; Silverman, Edwin K; Woodruff, Prescott G; O'Neal, Wanda K; Bowler, Russell P

    2016-08-01

    Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10-392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the

  5. Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

    2001-04-16

    For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

  6. Impact of genetic polymorphisms on clinical response to antithrombotics

    Directory of Open Access Journals (Sweden)

    Kena J Lanham

    2010-06-01

    Full Text Available Kena J Lanham1,2, Julie H Oestreich3, Steven P Dunn1,2, Steven R Steinhubl41Pharmacy Services, UK HealthCare, University of Kentucky, Lexington, Kentucky, USA; 2Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA; 3Department of Pharmacy Practice, College of Pharmacy, University of Nebraska, Omaha, Nebraska, USA; 4The Medicines Company, Zurich, Switzerland and The Geisinger Clinic, Danville, Pennsylvania, USAAbstract: Antithrombotic therapy, including anticoagulants as well as antiplatelet drugs, is an important component in the treatment of cardiovascular disease. Variability in response to such medications, of which pharmacogenetic response is a major source, can decrease or enhance the benefits expected. This review is a comprehensive assessment of the literature published to date on the effects of genetic polymorphisms on the actions of a variety of antithrombotic medications, including warfarin, clopidogrel, prasugrel, and aspirin. Literature evaluating surrogate markers in addition to the impact of pharmacogenetics on clinical outcomes has been reviewed. The results of the studies are conflicting as to what degree pharmacogenetics will affect medication management in cardiovascular disease. Additional research is necessary to discover, characterize, and prospectively evaluate genetic and non-genetic factors that impact antithrombotic treatment in order to maximize the effectiveness and limit the harmful effects of these valuable agents.Keywords: aspirin, warfarin, clopidogrel, prasugrel, pharmacogenetic, antithrombotic, antiplatelet

  7. HAS-1 genetic polymorphism in sporadic abdominal aortic aneurysm

    Directory of Open Access Journals (Sweden)

    Alberto Balbarini

    2009-04-01

    Full Text Available The hyaluronan synthase 1 (HAS-1 gene encodes a plasma membrane protein that synthesizes hyaluronan (HA, an extracellular matrix molecule. Accumulating evidence emphasizes the relevance of HA metabolism in an increasing number of processes of clinical interest, including abdominal aortic aneurysm (AAA. The existence of aberrant splicing variants of the HAS-1 gene could partly explain the altered extracellular matrix architecture and influence various biological functions, resulting in progressive arterial wall failure in the development of AAA. In the present study, we assessed the hypothesis that HAS-1 genetic 833A/G polymorphism could be associated with the risk of AAA by performing a case-control association study, involving AAA patients and healthy matched donors.

  8. MicroRNA related polymorphisms and breast cancer risk

    NARCIS (Netherlands)

    S. Khan (Sofia); D. Greco (Dario); K. Michailidou (Kyriaki); R.L. Milne (Roger); T.A. Muranen (Taru); T. Heikkinen (Tuomas); K. Aaltonen (Kirsimari); J. Dennis (Joe); M.K. Bolla (Manjeet); J. Liu (Jianjun); P. Hall (Per); A. Irwanto (Astrid); M.K. Humphreys (Manjeet); J. Li (Jingmei); K. Czene (Kamila); J. Chang-Claude (Jenny); R. Hein (Rebecca); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); O. Fletcher (Olivia); J. Peto (Julian); I. dos Santos Silva (Isabel); N. Johnson (Nichola); L.J. Gibson (Lorna); A. Aitken; J.L. Hopper (John); H. Tsimiklis (Helen); M. Bui (Minh); E. Makalic (Enes); D.F. Schmidt (Daniel); M.C. Southey (Melissa); C. Apicella (Carmel); J. Stone (Jennifer); Q. Waisfisz (Quinten); E.J. Meijers-Heijboer (Hanne); M.A. Adank (Muriel); R.B. van der Luijt (Rob); A. Meindl (Alfons); R.K. Schmutzler (Rita); B. Müller-Myhsok (B.); P. Lichtner (Peter); C. Turnbull (Clare); N. Rahman (Nazneen); S.J. Chanock (Stephen); D. Hunter (David); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); M.K. Schmidt (Marjanka); A. Broeks (Annegien); L.J. van 't Veer (Laura); F.B.L. Hogervorst (Frans); P.A. Fasching (Peter); A. Schrauder (André); A.B. Ekici (Arif); M.W. Beckmann (Matthias); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); J. Benítez (Javier); P.M. Zamora (Pilar M.); J.I.A. Perez (Jose Ignacio Arias); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L.L. March (Loic Le); P.D.P. Pharoah (Paul); A.M. Dunning (Alison); M. Shah (Mitul); R.N. Luben (Robert); J. Brown (Judith); F.J. Couch (Fergus); X. Wang (X.); C. Vachon (Celine); J.E. Olson (Janet); D. Lambrechts (Diether); M. Moisse (Matthieu); R. Paridaens (Robert); M.R. Christiaens (Marie Rose); P. Guénel (Pascal); T. Truong (Thérèse); P. Laurent-Puig (Pierre); C. Mulot (Claire); F. Marme (Frederick); B. Burwinkel (Barbara); A. Schneeweiss (Andreas); C. Sohn (Christof); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); I.L. Andrulis (Irene); J.A. Knight (Julia); S. Tchatchou (Srine); A.-M. Mulligan (Anna-Marie); T. Dörk (Thilo); N.V. Bogdanova (Natalia); N.N. Antonenkova (Natalia); H. Anton-Culver (Hoda); H. Darabi (Hatef); M. Eriksson (Mats); M. García-Closas (Montserrat); J.D. Figueroa (Jonine); J. Lissowska (Jolanta); L.A. Brinton (Louise); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); V. Kristensen (Vessela); S. Slager (Susan); A.E. Tol (Ama E.); C.B. Ambrosone (Christine); D. Yannoukakos (Drakoulis); A. Lindblom (Annika); S. Margolin (Sara); P. Radice (Paolo); P. Peterlongo (Paolo); M. Barile (Monica); P. Mariani (Paolo); M.J. Hooning (Maartje); J.W.M. Martens (John); J. Margriet Collée; A. Jager (Agnes); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska-Bieniek (Katarzyna); K. Durda (Katarzyna); G.G. Giles (Graham); C.A. McLean (Catriona Ann); H. Brauch (Hiltrud); T. Brüning (Thomas); Y.-D. Ko (Yon-Dschun); H.B. The Genica Network (Hermann Brenner); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); A.J. Swerdlow (Anthony ); A. Ashworth (Alan); N. Orr (Nick); M. Jones (Michael); J. Simard (Jacques); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); A. Mannermaa (Arto); U. Hamann (Ute); G. Chenevix-Trench (Georgia); C. Blomqvist (Carl); K. Aittomäki (Kristiina); D.F. Easton (Douglas); H. Nevanlinna (Heli)

    2014-01-01

    textabstractGenetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility

  9. MicroRNA Related Polymorphisms and Breast Cancer Risk

    DEFF Research Database (Denmark)

    Khan, Sofia; Greco, Dario; Michailidou, Kyriaki

    2014-01-01

    Genetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer...

  10. MicroRNA related polymorphisms and breast cancer risk

    NARCIS (Netherlands)

    S. Khan (Sofia); D. Greco (Dario); K. Michailidou (Kyriaki); R.L. Milne (Roger); T.A. Muranen (Taru); T. Heikkinen (Tuomas); K. Aaltonen (Kirsimari); J. Dennis (Joe); M.K. Bolla (Manjeet); J. Liu (Jianjun); P. Hall (Per); A. Irwanto (Astrid); M.K. Humphreys (Manjeet); J. Li (Jingmei); K. Czene (Kamila); J. Chang-Claude (Jenny); R. Hein (Rebecca); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); O. Fletcher (Olivia); J. Peto (Julian); I. dos Santos Silva (Isabel); N. Johnson (Nichola); L.J. Gibson (Lorna); A. Aitken; J.L. Hopper (John); H. Tsimiklis (Helen); M. Bui (Minh); E. Makalic (Enes); D.F. Schmidt (Daniel); M.C. Southey (Melissa); C. Apicella (Carmel); J. Stone (Jennifer); Q. Waisfisz (Quinten); E.J. Meijers-Heijboer (Hanne); M.A. Adank (Muriel); R.B. van der Luijt (Rob); A. Meindl (Alfons); R.K. Schmutzler (Rita); B. Müller-Myhsok (B.); P. Lichtner (Peter); C. Turnbull (Clare); N. Rahman (Nazneen); S.J. Chanock (Stephen); D. Hunter (David); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); M.K. Schmidt (Marjanka); A. Broeks (Annegien); L.J. van 't Veer (Laura); F.B.L. Hogervorst (Frans); P.A. Fasching (Peter); A. Schrauder (André); A.B. Ekici (Arif); M.W. Beckmann (Matthias); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); J. Benítez (Javier); P.M. Zamora (Pilar M.); J.I.A. Perez (Jose Ignacio Arias); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L.L. March (Loic Le); P.D.P. Pharoah (Paul); A.M. Dunning (Alison); M. Shah (Mitul); R.N. Luben (Robert); J. Brown (Judith); F.J. Couch (Fergus); X. Wang (X.); C. Vachon (Celine); J.E. Olson (Janet); D. Lambrechts (Diether); M. Moisse (Matthieu); R. Paridaens (Robert); M.R. Christiaens (Marie Rose); P. Guénel (Pascal); T. Truong (Thérèse); P. Laurent-Puig (Pierre); C. Mulot (Claire); F. Marme (Frederick); B. Burwinkel (Barbara); A. Schneeweiss (Andreas); C. Sohn (Christof); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); I.L. Andrulis (Irene); J.A. Knight (Julia); S. Tchatchou (Srine); A.-M. Mulligan (Anna-Marie); T. Dörk (Thilo); N.V. Bogdanova (Natalia); N.N. Antonenkova (Natalia); H. Anton-Culver (Hoda); H. Darabi (Hatef); M. Eriksson (Mats); M. García-Closas (Montserrat); J.D. Figueroa (Jonine); J. Lissowska (Jolanta); L.A. Brinton (Louise); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); V. Kristensen (Vessela); S. Slager (Susan); A.E. Tol (Ama E.); C.B. Ambrosone (Christine); D. Yannoukakos (Drakoulis); A. Lindblom (Annika); S. Margolin (Sara); P. Radice (Paolo); P. Peterlongo (Paolo); M. Barile (Monica); P. Mariani (Paolo); M.J. Hooning (Maartje); J.W.M. Martens (John); J. Margriet Collée; A. Jager (Agnes); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska-Bieniek (Katarzyna); K. Durda (Katarzyna); G.G. Giles (Graham); C.A. McLean (Catriona Ann); H. Brauch (Hiltrud); T. Brüning (Thomas); Y.-D. Ko (Yon-Dschun); H.B. The Genica Network (Hermann Brenner); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); A.J. Swerdlow (Anthony ); A. Ashworth (Alan); N. Orr (Nick); M. Jones (Michael); J. Simard (Jacques); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); A. Mannermaa (Arto); U. Hamann (Ute); G. Chenevix-Trench (Georgia); C. Blomqvist (Carl); K. Aittomäki (Kristiina); D.F. Easton (Douglas); H. Nevanlinna (Heli)

    2014-01-01

    textabstractGenetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility

  11. Genetic diversity among elite Sorghum lines revealed by restriction fragment length polymorphisms and random amplified polymorphic DNAs.

    Science.gov (United States)

    Vierling, R A; Xiang, Z; Joshi, C P; Gilbert, M L; Nguyen, H T

    1994-02-01

    The genetic diversity of sorghum, as compared to corn, is less well characterized at the genetic and molecular levels despite its worldwide economic importance. The objectives of this study were to: (1) investigate genetic diversity for restriction fragment length polymorphism (RFLPs) and random amplified polymorphic DNAs (RAPDs) in elite sorghum lines, (2) compare similarities based on molecular markers with pedigree relationships, and (3) examine the potential of RFLPs and RAPDs for assigning sorghum lines to the A/B (sterile) and R (restorer) groups. Using four restriction enzymes, polymorphism was detected with 61% of the RFLP probes used, compared to 77% of the random primers. One hundred and sixteen (64%) probe-enzyme combinations yielded multiple-band profiles compared to 98% of the random primers. RFLP profiles generated 290 polymorphic bands compared to 177 polymorphic RAPDs. Pair-wise comparisons of polymorphic RFLPs and RAPDs were used to calculate Nei and Jaccard coefficients. These were employed to generate phenograms using UPGMA and neighborjoining clustering methods. Analysis of RFLP data with Jaccard's coefficient and neighbor-joining clustering produced the phenogram with the closest topology to the known pedigree.

  12. Single strand conformation polymorphism of genomic and EST-SSRs marker and its utility in genetic evaluation of sugarcane.

    Science.gov (United States)

    Kalwade, Sachin B; Devarumath, Rachayya M

    2014-07-01

    Sugarcane is an important crop producing around 75 % of sugar in world and used as first generation biofuel. In present study, the genomic and gene based microsatellite markers were analyzed by low cost Single Strand Confirmation Polymorphism technique for genetic evaluation of 22 selected sugarcane genotypes. Total 16 genomic and 12 Expression Sequence Tag derived markers were able to amplify the selected sugarcane genotypes. Total 138 alleles were amplified of which 99 alleles (72 %) found polymorphic with an average of 4.9 alleles per locus. Microsatellite marker, VCSSR7 and VCSSR 12 showed monomorphic alleles with frequency 7.1 % over the average of 3.5 obtained for polymorphic locus. The level of Polymorphic Information Content (PIC) varied from 0.09 in VCSSR 6 to 0.88 in VCSSR 11 marker respectively with a mean of 0.49. Genomic SSRs showed more polymorphism than EST-SSRs markers on selected sugarcane genotypes whereas, the genetic similarity indices calculated by Jaccard's similarity coefficient varied from 0.55 to 0.81 indicate a high level of genetic similarity among the genotypes that was mainly attributed to intra specific diversity. Hence, the SSR-SSCP technique helped to identify the genetically diverse clones which could be used in crossing program for introgression of sugar and stress related traits in hybrid sugarcane.

  13. Genetic polymorphisms in the DRD2, DRD3, and SLC6A3 gene in elderly patients with delirium.

    NARCIS (Netherlands)

    Munster, B.C. van; Yazdanpanah, M.; Tanck, M.W.T.; Rooij, S.E.J.A. de; Giessen, E. van de; Sijbrands, E.J.G.; Zwinderman, A.H.; Korevaar, J.C.

    2010-01-01

    Dopamine excess appears to be critical in the final common pathway of delirium. The aim of this study was to investigate whether genetic polymorphisms in three dopamine-related genes (the dopamine receptor 2 (DRD2), dopamine receptor 3 (DRD3), and the dopamine transporter (SLC6A3) gene) were associa

  14. Cystathionine β-synthase 844ins68 Genetic Polymorphism in Spontaneous Abortion Susceptibility

    Directory of Open Access Journals (Sweden)

    Radu Anghel POPP

    2011-12-01

    Full Text Available Aim: Genetic polymorphisms in homocysteine-related genes are subject of a large body of research in pregnancy and newborn associated pathologies. The enzyme cystationine β-synthase (CBS is involved in the transsulfuration pathway of homocysteine to cysteine. Our objective was to analyze the association of a common polymorphism exhibited by the CBS gene, 844ins68, with idiopathic spontaneous abortions (SA. Material and Methods: 131 patients with a history of at least one unexplained SA and 135 healthy women with at least one successful pregnancy and no SA were included in a case-control study. Simplex PCR was used to genotype the cases and control volunteers for the CBS 844ins68 polymorphism. Fisher’s exact test was performed to obtain the odds-based parameters describing the relationship between the two variables. Results: The variant allele was encountered with a frequency of 0.08 in the SA group and 0.048 in controls. The dominant model analysis of risk revealed the OR 1.957, 95%CI [0.920, 4.162], Fisher’s p = 0.09. Conclusion: The findings suggest possible effects of this polymorphism in SA risk that did not reach the significance level in this study. Future studies might validate or clarify the association between CBS 844ins68 and idiopathic SA.

  15. Genetic Polymorphisms in Glutathione (GSH- Related Genes Affect the Plasmatic Hg/Whole Blood Hg Partitioning and the Distribution between Inorganic and Methylmercury Levels in Plasma Collected from a Fish-Eating Population

    Directory of Open Access Journals (Sweden)

    Andréia Ávila Soares de Oliveira

    2014-01-01

    Full Text Available This study aims to evaluate the effects of polymorphisms in glutathione (GSH- related genes (GSTM1, GSTT1, GSTP1, GCLM, and GCLC in the distribution of Hg in the blood compartments in humans exposed to methylmercury (MeHg. Subjects (n=88, exposed to MeHg from fish consumption, were enrolled in the study. Hg species in the plasma compartment were determined by LC-ICP-MS, whereas genotyping was performed by PCR assays. Mean total Hg levels in plasma (THgP and whole blood (THgB were 10±4.2 and 37±21, whereas mean evels of plasmatic MeHg (MeHgP, inorganic Hg (IHgP, and HgP/HgB were 4.3±2.9, 5.8±2.3 µg/L, and 0.33±0.15, respectively. GSTM1 and GCLC polymorphisms influence THgP and MeHgP (multivariate analyses, P<0.050. Null homozygotes for GSTM1 showed higher THgP and MeHgP levels compared to subjects with GSTM1 (THgP β=0.22, P=0.035; MeHgP β=0.30, P=0.050 and persons carrying at least one T allele for GCLC had significant higher MeHgP (β=0.59, P=0.046. Also, polymorphic GCLM subjects had lower THgP/THgB than those with the nonvariant genotype. Taken together, data of this study suggest that GSH-related polymorphisms may change the metabolism of MeHg by modifying the distribution of mercury species iin plasma compartment and the HgP/HgB partitioning.

  16. Genetic diversity and prevalence of CCR2-CCR5 gene polymorphisms in the Omani population

    Directory of Open Access Journals (Sweden)

    Samira H. Al-Mahruqi

    2014-01-01

    Full Text Available Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Ocean. In this study, we examined the CCR2-CCR5 haplotypes in Omanis and compared the patterns of genetic diversity with those of other populations. Blood samples were collected from 115 Omani adults and genomic DNA was screened to identify the polymorphic sites in the CCR5 gene and the CCR2V64I mutation. Four minor alleles were common: CCR5-2554T and CCR5-2086G showed frequencies of 49% and 46%, respectively, whereas CCR5-2459A and CCR5-2135C both had a frequency of 36%. These alleles showed moderate levels of heterozygosity, indicating that they were under balancing selection. However, the well-known allele CCR5!32 was relatively rare. Eleven haplotypes were identified, four of which were common: HHC (46%, HHE (20%, HHA (14% and HHF*2 (12%.

  17. Genetic diversity and prevalence of CCR2-CCR5 gene polymorphisms in the Omani population.

    Science.gov (United States)

    Al-Mahruqi, Samira H; Zadjali, Fahad; Beja-Pereira, Albano; Koh, Crystal Y; Balkhair, Abdullah; Al-Jabri, Ali A

    2014-03-01

    Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Ocean. In this study, we examined the CCR2-CCR5 haplotypes in Omanis and compared the patterns of genetic diversity with those of other populations. Blood samples were collected from 115 Omani adults and genomic DNA was screened to identify the polymorphic sites in the CCR5 gene and the CCR2V64I mutation. Four minor alleles were common: CCR5-2554T and CCR5-2086G showed frequencies of 49% and 46%, respectively, whereas CCR5-2459A and CCR5-2135C both had a frequency of 36%. These alleles showed moderate levels of heterozygosity, indicating that they were under balancing selection. However, the well-known allele CCR5Δ32 was relatively rare. Eleven haplotypes were identified, four of which were common: HHC (46%), HHE (20%), HHA (14%) and HHF*2 (12%).

  18. Genetic polymorphisms and cerebrovascular disease in children with sickle cell anemia from Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Isaac Lima da Silva Filho

    2011-06-01

    Full Text Available The aim of the present work was to examine possible genetic risk factors related to the occurrence of cerebrovascular disease (CVD in Brazilian population, the frequency of βS-globin gene haplotypes and co-inheritance with α-thalassemia (-α3.7kb and single nucleotide polymorphism of methylenetetrahydrofolate reductase (MTHFR-C677T, Factor V Leiden (FV-G1691A and prothrombin (PT-G20210A genes in children from Rio de Janeiro. Ninety four children with sickle cell anemia (SCA were included, 24 patients with cerebrovascular involvement and 70 patients without CVD as control group. The mean age of children at the time of the cerebrovascular event was similar to the control group. The frequency of -α3.7kb thalassemia was similar in both groups (p=0.751. Children with Bantu/Atypical βS-globin gene haplotype presented 15 times more chance (OR=15.4 CI 95% 2.9-81.6 of CVD than the other βS-globin gene haplotypes. The C677T polymorphism of MTHFR gene was similar in both groups (p=0.085. No mutation in the FV Leiden or PT genes was found. A large study seems necessary to establish the role of these genetic polymorphisms in Brazilian miscegenated population.

  19. The application and performance of single nucleotide polymorphism (SNP markers for population genetic analyses of Lepidoptera

    Directory of Open Access Journals (Sweden)

    Brad S. Coates

    2011-06-01

    Full Text Available Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of null alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae using next-generation expressed sequence tag (EST data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2% were in Hardy-Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance (AMOVA, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may be the result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant mutation data molecular genetic marker development in non-model species with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need be considered in the interpretation of empirical data.

  20. Renin-angiotensin system genetic polymorphisms and brain white matter lesions in older Australians.

    Science.gov (United States)

    Assareh, Amelia A; Mather, Karen A; Crawford, John D; Wen, Wei; Anstey, Kaarin J; Easteal, Simon; Tan, Xiaoyun; Mack, Holly A; Kwok, John B J; Schofield, Peter R; Sachdev, Perminder S

    2014-09-01

    White matter lesions (WMLs), seen as hyperintensities on T2-weighted magnetic resonance imaging brain scans, are common in the brains of healthy older individuals. They are thought to be related to cerebral small vessel disease and to have a genetic component to their aetiology, and hypertension is thought to be an important risk factor. Genetic polymorphisms in hypertension-related genes may therefore be associated with the formation of WMLs. In this study, a sample of 445 Australians aged 60-65 years was drawn from a larger longitudinal epidemiological study, the Personality and Total Health Through Life Project. The associations of single nucleotide polymorphisms (SNPs) in the genes encoding angiotensinogen (AGT, rs699), angiotensin-converting enzyme (ACE, rs4362), and angiotensin II receptor type 1 (AGTR1, rs5182) with WMLs were examined. No individual SNPs showed a significant association with WMLs for the whole sample. When the cohort was stratified by sex, ACE rs4362 and AGT rs699 showed significant associations with WMLs in men only (P = 0.01 and P = 0.03, respectively), and remained significant after controlling for hypertension. Although the AGTR1 SNP did not show any association with WMLs, the interaction of the AGT rs699 and AGTR1 rs5182 SNPs with WMLs was significant before (P = 0.03) and after adjustment for hypertension (P = 0.045). The results provide evidence for association of polymorphisms in the renin-angiotensin system genes with WMLs, independent of hypertension. Male-only associations with WMLs were found for the AGT rs699 and ACE rs362 polymorphisms. Moreover, for the entire sample an interaction between AGT and AGTR1 rs5182 genotypes on WMLs was observed. © American Journal of Hypertension, Ltd 2014. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Genetic basis of interindividual susceptibility to cancer cachexia: selection of potential candidate gene polymorphisms for association studies.

    Science.gov (United States)

    Johns, N; Tan, B H; MacMillan, M; Solheim, T S; Ross, J A; Baracos, V E; Damaraju, S; Fearon, K C H

    2014-12-01

    Cancer cachexia is a complex and multifactorial disease. Evolving definitions highlight the fact that a diverse range of biological processes contribute to cancer cachexia. Part of the variation in who will and who will not develop cancer cachexia may be genetically determined. As new definitions, classifications and biological targets continue to evolve, there is a need for reappraisal of the literature for future candidate association studies. This review summarizes genes identified or implicated as well as putative candidate genes contributing to cachexia, identified through diverse technology platforms and model systems to further guide association studies. A systematic search covering 1986-2012 was performed for potential candidate genes / genetic polymorphisms relating to cancer cachexia. All candidate genes were reviewed for functional polymorphisms or clinically significant polymorphisms associated with cachexia using the OMIM and GeneRIF databases. Pathway analysis software was used to reveal possible network associations between genes. Functionality of SNPs/genes was explored based on published literature, algorithms for detecting putative deleterious SNPs and interrogating the database for expression of quantitative trait loci (eQTLs). A total of 154 genes associated with cancer cachexia were identified and explored for functional polymorphisms. Of these 154 genes, 119 had a combined total of 281 polymorphisms with functional and/or clinical significance in terms of cachexia associated with them. Of these, 80 polymorphisms (in 51 genes) were replicated in more than one study with 24 polymorphisms found to influence two or more hallmarks of cachexia (i.e., inflammation, loss of fat mass and/or lean mass and reduced survival). Selection of candidate genes and polymorphisms is a key element of multigene study design. The present study provides a contemporary basis to select genes and/or polymorphisms for further association studies in cancer cachexia, and

  2. Genetic basis of interindividual susceptibility to cancer cachexia: selection of potential candidate gene polymorphisms for association studies

    Indian Academy of Sciences (India)

    N. Johns; B. H. Tan; M. Macmillan; T. S. Solheim; J. A. Ross; V. E. Baracos; S. Damaraju; K. C. H. Fearon

    2014-12-01

    Cancer cachexia is a complex and multifactorial disease. Evolving definitions highlight the fact that a diverse range of biological processes contribute to cancer cachexia. Part of the variation in who will and who will not develop cancer cachexia may be genetically determined. As new definitions, classifications and biological targets continue to evolve, there is a need for reappraisal of the literature for future candidate association studies. This review summarizes genes identified or implicated as well as putative candidate genes contributing to cachexia, identified through diverse technology platforms and model systems to further guide association studies. A systematic search covering 1986–2012 was performed for potential candidate genes / genetic polymorphisms relating to cancer cachexia. All candidate genes were reviewed for functional polymorphisms or clinically significant polymorphisms associated with cachexia using the OMIM and GeneRIF databases. Pathway analysis software was used to reveal possible network associations between genes. Functionality of SNPs/genes was explored based on published literature, algorithms for detecting putative deleterious SNPs and interrogating the database for expression of quantitative trait loci (eQTLs). A total of 154 genes associated with cancer cachexia were identified and explored for functional polymorphisms. Of these 154 genes, 119 had a combined total of 281 polymorphisms with functional and/or clinical significance in terms of cachexia associated with them. Of these, 80 polymorphisms (in 51 genes) were replicated in more than one study with 24 polymorphisms found to influence two or more hallmarks of cachexia (i.e., inflammation, loss of fat mass and/or lean mass and reduced survival). Selection of candidate genes and polymorphisms is a key element of multigene study design. The present study provides a contemporary basis to select genes and/or polymorphisms for further association studies in cancer cachexia, and

  3. Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

    Science.gov (United States)

    Cox, Christian L; Chippindale, Paul T

    2014-08-01

    We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

  4. Genetic polymorphisms of the TYMS gene are not associated with congenital cardiac septal defects in a Han Chinese population.

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    Jian-Yuan Zhao

    Full Text Available BACKGROUND: Clinical research indicates that periconceptional administration of folic acid can reduce the occurrence of congenital cardiac septal defects (CCSDs. The vital roles of folate exhibits in three ways: the unique methyl donor for DNA expression regulation, the de novo biosynthesis of purine and pyrimidine for DNA construction, and the serum homocysteine removal. Thymidylate synthase (TYMS is the solo catalysis enzyme for the de novo synthesis of dTMP, which is the essential precursor of DNA biosynthesis and repair process. To examine the role of TYMS in Congenital Cardiac Septal Defects (CCSDs risk, we investigated whether genetic polymorphisms in the TYMS gene associated with the CCSDs in a Han Chinese population. METHOD: Polymorphisms in the noncoding region of TYMS were identified via direct sequencing in 32 unrelated individuals composed of half CCSDs and half control subjects. Nine SNPs and two insertion/deletion polymorphisms were genotyped from two independent case-control studies involving a total of 529 CCSDs patients and 876 healthy control participants. The associations were examined by both single polymorphism and haplotype tests using logistic regression. RESULT: We found that TYMS polymorphisms were not related to the altered CCSDs risk, and even to the changed risk of VSDs subgroup, when tested in both studied groups separately or in combination. In the haplotype analysis, there were no haplotypes significantly associated with risks for CCSDs either. CONCLUSION: Our results show no association between common genetic polymorphisms of the regulatory region of the TYMS gene and CCSDs in the Han Chinese population.

  5. Upper petal lip colour polymorphism in Collinsia heterophylla (Plantaginaceae): genetic basis within a population and its use as a genetic marker

    Indian Academy of Sciences (India)

    Asa Lankinen

    2009-08-01

    Understanding the genetics of a polymorphic trait is important to predict its likely evolution. In Collinsia heterophylla, the upper petal lip colour can be either be white or white with a purple band, while the lower petal lip colour is invariably purple. Because the corolla is only partly polymorphic, the polymorphism can not have evolved due to a mutation where a pigment was lost in the entire plant, which is common in other polymorphic species. In a previous study, high frequency of the purple band was found in populations with darker flowers, indicating possible selection for this trait. In this study, I determined inheritance of the colour polymorphism using two populations (one with only white morph and other with both morphs). I conducted experimental crosses within and between floral morphs to determine whether patterns of segregation in offspring conform to single-gene predictions. Data from F1, F2, F3 and backcross progeny are consistent with a genetic model of one major locus with presence of the band being completely dominant, as indicated in earlier studies using distantly related populations. A novel finding in this study was that the two morphs did not show a difference in seed germination frequency or seedling survival. This trait can thus be valuable as a genetic marker. Even though more thorough ecological data are needed to understand the potential selection pressures on upper petal lip colour in C. heterophylla, its simple inheritance may indicate the possibility of fast evolutionary response to selective forces acting on this trait.

  6. Analysis of polymorphisms and haplotype structure of the human thymidylate synthase genetic region: a tool for pharmacogenetic studies.

    Directory of Open Access Journals (Sweden)

    Soma Ghosh

    Full Text Available 5-Fluorouracil (5FU, a widely used chemotherapeutic drug, inhibits the DNA replicative enzyme, thymidylate synthase (Tyms. Prior studies implicated a VNTR (variable numbers of tandem repeats polymorphism in the 5'-untranslated region (5'-UTR of the TYMS gene as a determinant of Tyms expression in tumors and normal tissues and proposed that these VNTR genotypes could help decide fluoropyrimidine dosing. Clinical associations between 5FU-related toxicity and the TYMS VNTR were reported, however, results were inconsistent, suggesting that additional genetic variation in the TYMS gene might influence Tyms expression. We thus conducted a detailed genetic analysis of this region, defining new polymorphisms in this gene including mononucleotide (poly A:T repeats and novel single nucleotide polymorphisms (SNPs flanking the VNTR in the TYMS genetic region. Our haplotype analysis of this region used data from both established and novel genetic variants and found nine SNP haplotypes accounting for more than 90% of the studied population. We observed non-exclusive relationships between the VNTR and adjacent SNP haplotypes, such that each type of VNTR commonly occurred on several haplotype backgrounds. Our results confirmed the expectation that the VNTR alleles exhibit homoplasy and lack the common ancestry required for a reliable marker of a linked adjacent locus that might govern toxicity. We propose that it may be necessary in a clinical trial to assay multiple types of genetic polymorphisms in the TYMS region to meaningfully model linkage of genetic markers to 5FU-related toxicity. The presence of multiple long (up to 26 nt, polymorphic monothymidine repeats in the promoter region of the sole human thymidylate synthetic enzyme is intriguing.

  7. The prion-related protein (testis-specific) gene (PRNT) is highly polymorphic in Portuguese sheep.

    Science.gov (United States)

    Mesquita, P; Garcia, V; Marques, M R; Santos Silva, F; Oliveira Sousa, M C; Carolino, I; Pimenta, J; Fontes, C M G A; Horta, A E M; Prates, J A M; Pereira, R M

    2016-02-01

    The objective of this study was to search for polymorphisms in the ovine prion-related protein (testis-specific) gene (PRNT). Sampling included 567 sheep from eight Portuguese breeds. The PRNT gene-coding region was analyzed by single-strand conformation polymorphism and sequencing, allowing the identification of the first ovine PRNT polymorphisms, in codons 6, 38, 43 and 48: c.17C>T (p.Ser6Phe, which disrupts a consensus arginine-X-X-serine/threonine motif); c.112G>C (p.Gly38>Arg); c.129T>C and c.144A>G (synonymous) respectively. Polymorphisms in codons 6, 38 and 48 occur simultaneously in 50.6% of the animals, 38.8% presenting as heterozygous. To study the distribution of the polymorphism in codon 43, a restriction fragment length polymorphism analysis was performed. Polymorphic variant c.129C, identified in 89.8% of the animals with 32.8% presented as heterozygous, was considered the wild genotype in Portuguese sheep. Eight different haplotypes which have comparable distribution in all breeds were identified for the PRNT gene. In conclusion, the PRNT coding region is highly polymorphic in sheep, unlike the prion protein 2 dublet gene (PRND), in which we previously found only one synonymous substitution (c.78G>A), in codon 26. The absence or reduced number of PRND heterozygotes (c.78G>A) was significantly associated with three PRNT haplotypes (17C-112G-129T-144A,17CT-112GC-129CT-144AG and 17T-112C-129C-144G), and the only three animals found homozygous at c.78A had the 17C-112G-129C-144A PRNT haplotype. These results constitute evidence of an association between polymorphic variation in PRND and PRNT genes, as has already been observed for PRND and prion protein gene (PRNP). © 2015 Stichting International Foundation for Animal Genetics.

  8. Associations between heat shock protein 70 genetic polymorphisms and calving traits in crossbred Brahman cows

    Science.gov (United States)

    Stressors such as heat, cold, toxins, and oxygen deprivation are known to induce heat shock proteins. Genetic polymorphisms associated with heat shock protein genes have been associated with decreased male and female fertility. Our objectives were to 1) confirm single nucleotide polymorphisms (SNP) ...

  9. Susceptibility to pre-eclampsia is associated with multiple genetic polymorphisms in maternal biotransformation enzymes.

    NARCIS (Netherlands)

    Zusterzeel, P.L.M.; Peters, W.H.M.; Burton, G.J.; Visser, W. de; Roelofs, H.M.J.; Steegers, E.A.P.

    2007-01-01

    BACKGROUND/AIMS: Probably no single gene is responsible for pre-eclampsia, but the disease merely is the result of polymorphisms in several genes in association with environmental factors. We therefore studied the simultaneous occurrence of several genetic polymorphisms in biotransformation enzymes

  10. Genetic polymorphism of metabolic enzymes modifies the risk of chronic solvent-induced encephalopathy

    NARCIS (Netherlands)

    S. Kezic; F. Calkoen; M.A.M. Wenker; J.J.L. Jacobs; M.M. Verberk

    2006-01-01

    In the present study, we investigate whether genetic polymorphism in enzymes involved in the metabolism of organic solvents influences susceptibility to chronic solvent encephalopathy (CSE), which is one of the major effects of long-term exposure to organic solvents. Polymorphisms in the genes encod

  11. KCNJ11: Genetic Polymorphisms and Risk of Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Polin Haghvirdizadeh

    2015-01-01

    Full Text Available Diabetes mellitus (DM is a major worldwide health problem and its prevalence has been rapidly increasing in the last century. It is caused by defects in insulin secretion or insulin action or both, leading to hyperglycemia. Of the various types of DM, type 2 occurs most frequently. Multiple genes and their interactions are involved in the insulin secretion pathway. Insulin secretion is mediated through the ATP-sensitive potassium (KATP channel in pancreatic beta cells. This channel is a heteromeric protein, composed of four inward-rectifier potassium ion channel (Kir6.2 tetramers, which form the pore of the KATP channel, as well as sulfonylurea receptor 1 subunits surrounding the pore. Kir6.2 is encoded by the potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11 gene, a member of the potassium channel genes. Numerous studies have reported the involvement of single nucleotide polymorphisms of the KCNJ11 gene and their interactions in the susceptibility to DM. This review discusses the current evidence for the contribution of common KCNJ11 genetic variants to the development of DM. Future studies should concentrate on understanding the exact role played by these risk variants in the development of DM.

  12. Genetic polymorphisms in catalase and CYP1B1 determine DNA adduct formation by benzo(a)pyrene ex vivo.

    Science.gov (United States)

    Schults, Marten A; Chiu, Roland K; Nagle, Peter W; Wilms, Lonneke C; Kleinjans, Jos C; van Schooten, Frederik J; Godschalk, Roger W

    2013-03-01

    Genetic polymorphisms can partially explain the large inter-individual variation in DNA adduct levels following exposure to polycyclic aromatic hydrocarbons. Effects of genetic polymorphisms on DNA adduct formation are difficult to assess in human studies because exposure misclassification attenuates underlying relationships. Conversely, ex vivo studies offer the advantage of controlled exposure settings, allowing the possibility to better elucidate genotype-phenotype relationships and gene-gene interactions. Therefore, we exposed lymphocytes of 168 non-smoking volunteers ex vivo to the environmental pollutant benzo(a)pyrene (BaP) and BaP-related DNA adducts were quantified. Thirty-four genetic polymorphisms were assessed in genes involved in carcinogen metabolism, oxidative stress and DNA repair. Polymorphisms in catalase (CAT, rs1001179) and cytochrome P450 1B1 (CYP1B1, rs1800440) were significantly associated with DNA adduct levels, especially when combined. Moreover, reverse transcription-polymerase chain reaction (RT-PCR) analysis in a subset of 30 subjects revealed that expression of catalase correlated strongly with expression of CYP1B1 (R = 0.92, P CYP1B1 and how they simultaneously affect BaP-related DNA adduct levels, catalase expression was transiently knocked down in the human lung epithelial cell line A549. Although catalase knockdown did not immediately change CYP1B1 gene expression, recovery of catalase expression 8 h after the knockdown coincided with a 2.2-fold increased expression of CYP1B1 (P polymorphism in the promoter region of CAT may determine the amount and activity of catalase, which may subsequently regulate the expression of CYP1B1. As a result, both genetic polymorphisms modulate DNA adduct levels in lymphocytes by BaP ex vivo.

  13. Genetic polymorphisms and non-small-cell lung cancer: future paradigms

    Energy Technology Data Exchange (ETDEWEB)

    Mello, Ramon Andrade Bezerra de [Serviço de Oncologia Médica, Instituto Português de Oncologia Francisco Gentil, Porto (Portugal); Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro (Portugal)

    2014-07-01

    This article addresses some current issues about genetic polymorphisms studied in the non-small-cell lung cancer translational field. Furthermore, it discusses about new potential biomarkers regarding lung cancer risk and prognosis.

  14. Genetic polymorphisms in host antiviral genes: associations with humoral and cellular immunity to measles vaccine.

    Science.gov (United States)

    Haralambieva, Iana H; Ovsyannikova, Inna G; Umlauf, Benjamin J; Vierkant, Robert A; Shane Pankratz, V; Jacobson, Robert M; Poland, Gregory A

    2011-11-08

    Host antiviral genes are important regulators of antiviral immunity and plausible genetic determinants of immune response heterogeneity after vaccination. We genotyped and analyzed 307 common candidate tagSNPs from 12 antiviral genes in a cohort of 745 schoolchildren immunized with two doses of measles-mumps-rubella (MMR) vaccine. Associations between SNPs/haplotypes and measles virus-specific immune outcomes were assessed using linear regression methodologies in Caucasians and African-Americans. Genetic variants within the DDX58/RIG-I gene, including a coding polymorphism (rs3205166/Val800Val), were associated as single-SNPs (p≤0.017; although these SNPs did not remain significant after correction for false discovery rate/FDR) and in haplotype-level analysis, with measles-specific antibody variations in Caucasians (haplotype allele p-value=0.021; haplotype global p-value=0.076). Four DDX58 polymorphisms, in high LD, demonstrated also associations (after correction for FDR) with variations in both measles-specific IFN-γ and IL-2 secretion in Caucasians (p≤0.001, q=0.193). Two intronic OAS1 polymorphisms, including the functional OAS1 SNP rs10774671 (p=0.003), demonstrated evidence of association with a significant allele-dose-related increase in neutralizing antibody levels in African-Americans. Genotype and haplotype-level associations demonstrated the role of ADAR genetic variants, including a non-synonymous SNP (rs2229857/Arg384Lys; p=0.01), in regulating measles virus-specific IFN-γ Elispot responses in Caucasians (haplotype global p-value=0.017). After correction for FDR, 15 single-SNP associations (11 SNPs in Caucasians and 4 SNPs in African-Americans) still remained significant at the q-valuemeasles vaccine in Caucasians and African-Americans.

  15. Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: A meta-analysis

    Directory of Open Access Journals (Sweden)

    Chikako Kiyohara, Kouichi Yoshimasu

    2007-01-01

    Full Text Available Various DNA alterations can be caused by exposure to environmental and endogenous carcinogens. Most of these alterations, if not repaired, can result in genetic instability, mutagenesis and cell death. DNA repair mechanisms are important for maintaining DNA integrity and preventing carcinogenesis. Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. We identified a sufficient number of epidemiologic studies on lung cancer to conduct a meta-analysis for genetic polymorphisms in nucleotide excision repair pathway genes, focusing on xeroderma pigmentosum group A (XPA, excision repair cross complementing group 1 (ERCC1, ERCC2/XPD, ERCC4/XPF and ERCC5/XPG. We found an increased risk of lung cancer among subjects carrying the ERCC2 751Gln/Gln genotype (odds ratio (OR = 1.30, 95% confidence interval (CI = 1.14 - 1.49. We found a protective effect of the XPA 23G/G genotype (OR = 0.75, 95% CI = 0.59 - 0.95. Considering the data available, it can be conjectured that if there is any risk association between a single SNP and lung cancer, the risk fluctuation will probably be minimal. Advances in the identification of new polymorphisms and in high-throughput genotyping techniques will facilitate the analysis of multiple genes in multiple DNA repair pathways. Therefore, it is likely that the defining feature of future epidemiologic studies will be the simultaneous analysis of large samples.

  16. Genetic diversity analysis of salinity related germplasm in cotton

    OpenAIRE

    Lina Zhang; Wuwei Ye; Junjuan Wang; Baoxiang Fan; Delong Wang

    2010-01-01

    In order to study the genetic variation of salinity related cotton germplasm, 47 upland cotton accessions including 23 salinity tolerant materials and 24 salinity sensitive materials were explored using 88 simple sequence repeat (SSR) markers. We detected a total of 338 alleles at 88 SSR loci with an average of 3.841 alleles per locus, 333 of these alleles were detected in salinity tolerant germplasm and 312 alleles in salinity sensitive germplasm. Mean polymorphism information content (PIC),...

  17. A case-control study on proinflammatory genetic polymorphisms on sudden sensorineural hearing loss.

    Science.gov (United States)

    Cadoni, Gabriella; Gaetani, Eleonora; Picciotti, Pasqualina M; Arzani, Dario; Quarta, Miriam; Giannantonio, Sara; Paludetti, Gaetano; Boccia, Stefania

    2015-01-01

    Sudden sensorineural hearing loss (SSNHL) is strictly related to inner ear vascular injuries and recently to some atherosclerotic risk factors. The pathogenic role of inflammatory molecules in atherosclerosis is well established. However, there is little knowledge about the potential role of inflammatory cytokines and adhesion molecules on SSNHL etiology. The aim of this study was to evaluate the role of proinflammatory genetic polymorphisms of the MCP-1 (CCL2), E-selectin, and interleukin (IL)-6 gene in SSNHL patients. We evaluated the frequency and distribution of selected single nucleotide polymorphisms of the MCP-1 (CCL2), E-selectin, and IL-6 gene in 87 SSNHL patients and 107 healthy controls. Our results did not show significant difference between the compared groups for MCP-1 and E-selectin genes, whereas a significant difference was reported for the IL-6 gene (P < .0001). The main finding of our study is that the 174G/G polymorphism (with a wider distribution of wt/wt genotype in SSNHL patients than in the healthy controls) of the IL-6 gene is significantly associated with the risk of SSNHL, which is consistent with a previous finding on serum levels of IL-6 in SSNHL. It is possible that the variant acts as a triggering agent of different lipidemia-related phenotypes. Both the -174G/G polymorphism and elevated IL-6 levels in SSNHL patients could suggest that IL-6 plays a role in the inner ear involvement by atherosclerotic inflammatory events. © 2014 The American Laryngological, Rhinological and Otological Society, Inc.

  18. Association of Environmental Arsenic Exposure, Genetic Polymorphisms of Susceptible Genes, and Skin Cancers in Taiwan

    Directory of Open Access Journals (Sweden)

    Ling-I Hsu

    2015-01-01

    Full Text Available Deficiency in the capability of xenobiotic detoxification and arsenic methylation may be correlated with individual susceptibility to arsenic-related skin cancers. We hypothesized that glutathione S-transferase (GST M1, T1, and P1, reactive oxygen species (ROS related metabolic genes (NQO1, EPHX1, and HO-1, and DNA repair genes (XRCC1, XPD, hOGG1, and ATM together may play a role in arsenic-induced skin carcinogenesis. We conducted a case-control study consisting of 70 pathologically confirmed skin cancer patients and 210 age and gender matched participants with genotyping of 12 selected polymorphisms. The skin cancer risks were estimated by odds ratio (OR and 95% confidence interval (CI using logistic regression. EPHX1 Tyr113His, XPD C156A, and GSTT1 null genotypes were associated with skin cancer risk (OR = 2.99, 95% CI = 1.01–8.83; OR = 2.04, 95% CI = 0.99–4.27; OR = 1.74, 95% CI = 1.00–3.02, resp.. However, none of these polymorphisms showed significant association after considering arsenic exposure status. Individuals carrying three risk polymorphisms of EPHX1 Tyr113His, XPD C156A, and GSTs presented a 400% increased skin cancer risk when compared to those with less than or equal to one polymorphism. In conclusion, GSTs, EPHX1, and XPD are potential genetic factors for arsenic-induced skin cancers. The roles of these genes for arsenic-induced skin carcinogenesis need to be further evaluated.

  19. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis

    Directory of Open Access Journals (Sweden)

    Rabinowicz Pablo D

    2010-01-01

    Full Text Available Abstract Background Castor bean (Ricinus communis is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74% followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

  20. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

    Science.gov (United States)

    2010-01-01

    Background Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p < 0.01). Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity. PMID:20082707

  1. Genetic polymorphism of antioxidant enzymes in eosinophilic and non-eosinophilic nasal polyposis.

    Science.gov (United States)

    Akyigit, Abdulvahap; Keles, Erol; Etem, Ebru Onalan; Ozercan, Ibrahim; Akyol, Hatice; Sakallioglu, Oner; Karlidag, Turgut; Polat, Cahit; Kaygusuz, Irfan; Yalcin, Sinasi

    2017-01-01

    Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease of the paranasal sinuses, and its pathophysiology is not yet precisely known. It is suggested that oxygen free radicals play an important role in the pathogenesis of nasal polyposis. This study aimed to identify genetic polymorphisms of superoxide dismutase (SOD 2), catalase (CAT), and inducible nitric oxide synthase (iNOS) enzymes in eosinophilic CRSwNP and non-eosinophilic CRSwNP patients; the study also aimed to evaluate the effect of genetic polymorphism of antioxidant enzymes on CRSwNP etiopathogenesis. One hundred thirty patients, who received endoscopic sinus surgery due to CRSwNP, and 188 control individuals were included in this study. Nasal polyp tissues were divided into two groups histopathologically as eosinophilic CRSwNP and non-eosinophilic CRSwNP. Venous blood samples were taken from the patient and control groups. Polymorphisms in the Ala16Va1 gene, which is the most common variation of SOD-2 gene, and 21 A/T polymorphisms in catalase gene were evaluated with the restriction fragment length polymorphism method and -277 C/T polymorphism in the iNOS gene was evaluated with the DNA sequencing method. The GG genotype distribution for the (-277) A/G polymorphism in the iNOS gene was a statistically significant difference between eosinophilic CRSwNP and control groups (p  0.05). The TT genotype distribution for the A/T polymorphism in catalase gene at position -21 was statistically significant differences in eosinophilic CRSwNP and control groups (p levels, which are considered effective factors in the pathogenesis of CRSwNP, can occur due to genetic polymorphism of enzymes in the antioxidant system and genetic polymorphism of antioxidant enzymes in eosinophilic CRSwNP patients might contribute to the pathophysiology.

  2. drs (Distantly Related sic) Gene Polymorphisms among emm12-Type Streptococcus pyogenes Isolates

    OpenAIRE

    Brandt, Claudia M.; Haase, Gerhard; Spellerberg, Barbara; Holland, Regina; Lütticken, Rudolf

    2003-01-01

    Twenty-eight emm12-type Streptococcus pyogenes isolates from patients with invasive and noninvasive infections or from asymptomatic carriers were genetically typed. Sequencing of drs (distantly related sic [streptococcal inhibitor of complement]) genes identified two novel alleles and revealed a polymorphism for drs similar to that of sic. No association was observed between the five different drs alleles and the five restriction patterns of the vir regulon for the isolates studied. These dat...

  3. Bovine gene polymorphisms related to fat deposition and meat tenderness

    Directory of Open Access Journals (Sweden)

    Marina R.S. Fortes

    2009-01-01

    Full Text Available Leptin, thyroglobulin and diacylglycerol O-acyltransferase play important roles in fat metabolism. Fat deposition has an influence on meat quality and consumers' choice. The aim of this study was to determine allele and genotype frequencies of polymorphisms of the bovine genes, which encode leptin (LEP, thyroglobulin (TG and diacylglycerol O-acyltransferase (DGAT1. A further objective was to establish the effects of these polymorphisms on meat characteristics. We genotyped 147 animals belonging to the Nelore (Bos indicus, Canchim (5/8 Bos taurus + 3/8 Bos indicus, Rubia Gallega X Nelore (1/2 Bos taurus + 1/2 Bos indicus, Brangus Three-way cross (9/16 Bos taurus + 7/16 Bos indicus and Braunvieh Three-way cross (3/4 Bos taurus + 1/4 Bos indicus breeds. Backfat thickness, total lipids, marbling score, ribeye area and shear force were fitted, using the General Linear Model (GLM procedure of the SAS software. The least square means of genotypes and genetic groups were compared using Tukey's test. Allele frequencies vary among the genetic groups, depending on Bos indicus versus Bos taurus influence. The LEP polymorphism segregates in pure Bos indicus Nelore animals, which is a new finding. The T allele of TG is fixed in Nelore, and DGAT1 segregates in all groups, but the frequency of allele A is lower in Nelore animals. The results showed no association between the genotypes and traits studied, but a genetic group effect on these traits was found. So, the genetic background remains relevant for fat deposition and meat tenderness, but the gene markers developed for Bos taurus may be insufficient for Bos indicus.

  4. [Genetic polymorphisms of X-STR loci in Chinese Yugur ethnic group and its application].

    Science.gov (United States)

    Chen, Yan-Jiong; Chen, Feng; Xin, Na; Zhang, Hong Bo; Zheng, Hai Bo; Yu, Bing; Li, Sheng-Bin; Chen, Teng

    2008-09-01

    To study the genetic polymorphism of nine short tandem repeats (STRs) loci (DXS7130, DXS7132, DXS6804, DXS7423, DXS7424, DXS6789, DXS6799, DXS8378, and HPRTB) on X chromosome in Chinese Yugur ethnic group. The allele and genotype frequency of nine X-STR loci among 120 unrelated individuals (55 female, 65 male) from Yugur ethnic group were analyzed using PCR and followed by polyacrylamide gel electrophoresis and silver staining. The numbers of alleles in the nine X-STR loci were 8, 6, 6, 5, 6, 7, 6, 4, and 6, respectively; the numbers of genotypes in the nine loci were 16, 14, 13, 6, 13, 20, 11, 6, and 12, respectively. The genotype frequencies in females were in accordance with Hardy-Weinberg equilibrium (P>0.05). The nine X-STR loci were relatively abundant in polymorphic information for individual identification, paternity testing and population genetics. A total of 15 haplotypes were detected in DXS7130 and DXS8378 loci, and 55 haplotypes were detected in DXS6789, DXS6799, DXS7424, and DXS6804 loci. The haplotype diversity reached 0.8212 and 0.9947, respectively. Phylogeny tree and cluster analysis based on X-STR allele frequencies in genesis showed that Yugur ethnic group share a close relationship with Mongolian ethnic group and Chinese Han, Tibetan population and far from Hui and Uygur ethnic group, who dwell in the northwest of China.

  5. Functional genetic polymorphisms and female reproductive disorders : Part II-025EFendometriosis

    NARCIS (Netherlands)

    Tempfer, C. B.; Simoni, M.; Destenaves, B.; Fauser, B. C. J. M.

    2009-01-01

    Endometriosis has a strong genetic component, and numerous genetic studies have been reported. We have systematically reviewed these studies and included 114 in our final selection. We found no consistent evidence linking endometriosis with specific polymorphisms in genes encoding inflammatory media

  6. Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.

    Science.gov (United States)

    Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations.

  7. Early Prediction of Sepsis Incidence in Critically Ill Patients Using Specific Genetic Polymorphisms.

    Science.gov (United States)

    David, Vlad Laurentiu; Ercisli, Muhammed Furkan; Rogobete, Alexandru Florin; Boia, Eugen S; Horhat, Razvan; Nitu, Razvan; Diaconu, Mircea M; Pirtea, Laurentiu; Ciuca, Ioana; Horhat, Delia; Horhat, Florin George; Licker, Monica; Popovici, Sonia Elena; Tanasescu, Sonia; Tataru, Calin

    2017-06-01

    Several diagnostic methods for the evaluation and monitoring were used to find out the pro-inflammatory status, as well as incidence of sepsis in critically ill patients. One such recent method is based on investigating the genetic polymorphisms and determining the molecular and genetic links between them, as well as other sepsis-associated pathophysiologies. Identification of genetic polymorphisms in critical patients with sepsis can become a revolutionary method for evaluating and monitoring these patients. Similarly, the complications, as well as the high costs associated with the management of patients with sepsis, can be significantly reduced by early initiation of intensive care.

  8. [Influence of genetic polymorphisms (IL-10/CXCL8/CXCR2/NFκB) on the susceptibility of autoimmune rheumatic diseases].

    Science.gov (United States)

    Salim, Patricia Hartstein; Xavier, Ricardo Machado

    2014-01-01

    The autoimmune rheumatologic disorders mostly have a common genetic path to the autoimmunity. Several genes have been associated with rheumatologic disorders; therefore, we are analyzing just the ones in those containing several evidences of the existence of association with the risk or protection from autoimmune disorder. The nuclear factor kappa beta (NF-kappa B), which regulates the autoimmune and anti-inflammatory responses, is associated with systemic sclerosis (SS), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), just as the CXCR2 e CXCL8 genes. On the other hand, the interleukin-10 (IL-10), which is an anti-inflammatory cytokine, is associated with almost all rheumatologic disorders. In this article, we are reviewing the potential roles of these genes in the immune system and in several rheumatologic disorders. In relation to IL-10, several studies have been carried out, but most of them are controversial - some detected the absence of association, and others found association in different genetic polymorphisms. Conversely, in relation to NF-kappa B, it was studied just in RA and SLE, and no relevant significant analyses were observed. The genetic polymorphisms of the CXCR2 gene were associated with SS, but not with RA e SLE. On the other side, the genetic polymorphisms of the CXCL8 gene are not associated with SS, but with RA. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

  9. Contrasting genetic influence of PON 1 coding gene polymorphisms ...

    African Journals Online (AJOL)

    Nadia Youssef Sadek Morcos

    2015-03-31

    Mar 31, 2015 ... c Toxicity Department, Poison Control Center, Ain Shams Universty Hospital, Egypt ... frequency distribution of PON1 Q192R polymorphism showed a highly ... at position 192, where either glutamine (Q) or arginine (R).

  10. RAGE genetic polymorphisms are associated with risk, chemotherapy response and prognosis in patients with advanced NSCLC.

    Directory of Open Access Journals (Sweden)

    Xiang Wang

    Full Text Available AIM: To explore the association between genetic polymorphisms of the receptor for advanced glycation end-products (RAGE and susceptibility, chemotherapy response rate and prognosis of non-small cell lung cancer (NSCLC. METHOD: This is a prospective study in which 562 patients with NSCLC and 764 healthy controls were enrolled. Three RAGE genetic polymorphisms, namely, -429T/C, -374T/A and 82G/S were genotyped. Platinum-based chemotherapy was given to 432 subjects with advanced inoperable NSCLC and their responses to chemotherapy were evaluated. RESULTS: All the polymorphic genotypes of RAGE polymorphisms were associated with susceptibility for NSCLC. Only the 82G/S polymorphisms denoted a significant difference between responders and non-responders to chemotherapy. The 82SS genotype and 82S allele distribution not only increased the NSCLC risk, but also was associated with a lower chemotherapy response rate and poor prognosis, indicated by overall survival and progression free survival. CONCLUSION: The 82G/S genetic polymorphism of RAGE gene might be used as a genetic marker to screen for patients sensitive to thermotherapy and to predict the prognosis of NSCLC.

  11. Molecular phylogeny of Lathyrus species: insights from sequence-related amplified polymorphism markers.

    Science.gov (United States)

    Marghali, S; Touati, A; Gharbi, M; Sdouga, D; Trifi-Farah, N

    2016-03-31

    Sequence-related amplified polymorphism (SRAP) markers were used to evaluate the intra- and interspecific variation among 40 Lathyrus genotypes (four species) (Fabaceae). Ten SRAP primer combinations resulted in a total of 94 bands, and they exhibited high interspecific variability. The genetic differentiation among Lathyrus, estimated using AMOVA, was highly significant. The results indicated that 58% of the total genetic variation existed among species, and 42% of the differentiation was within species. This was explained by the high level of genome conservation of these species as well as the recent and slow evolution of this genus. These results were confirmed by the topology of the neighbor-joining cladogram and the results of the principal coordinate analysis. Our data support previous results based on seed protein diversity. These results make SRAP markers choice markers for the study of functional polymorphism that is directly related to the transcriptomic data. The SRAP markers used in this study provide an accurate picture of the population structure within Lathyrus germplasm, which is critically important information for the design of genetic diversity and structure analyses. Moreover, further extensive studies are necessary to fully examine other Lathyrus species and tests that adopt the SRAP technique to enrich the Lathyrus library for next-generation sequencing, thus providing a potent protocol for the study of polymorphism.

  12. Typing of bacteriophages by randomly amplified polymorphic DNA (RAPD)-PCR to assess genetic diversity.

    Science.gov (United States)

    Gutiérrez, Diana; Martín-Platero, Antonio M; Rodríguez, Ana; Martínez-Bueno, Manuel; García, Pilar; Martínez, Beatriz

    2011-09-01

    The recent boom in phage therapy and phage biocontrol requires the design of suitable cocktails of genetically different bacteriophages. The current methods for typing phages need significant quantities of purified DNA, may require a priori genetic information and are cost and time consuming. We have evaluated the randomly amplified polymorphic DNA (RAPD)-PCR technique to produce unique and reproducible band patterns from 26 different bacteriophages infecting Staphylococcus epidermidis, Staphylococcus aureus, Lactococcus lactis, Escherichia coli, Streptococcus thermophilus, Bacillus subtilis and Lactobacillus casei bacterial strains. Initially, purified DNA and phage suspensions of seven selected phages were used as a template. The conditions that were found to be optimal 8 μM of 10-mer primers, 3 μM magnesium oxalacetate and 5% dimethyl sulfoxide. The RAPD genomic fingerprints using a phage titer suspension higher than 10(9) PFU mL(-1) were highly reproducible. Clustering by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm correlated largely with genetically different phages infecting the same bacterial species, although closely related phages with a similar DNA restriction pattern were indistinguishable. The results support the use of RAPD-PCR for quick typing of phage isolates and preliminary assessment of their genetic diversity bypassing tedious DNA purification protocols and previous knowledge of their sequence.

  13. Forecast of the Heterosis of Imported Meat Sheep by Genetic Polymorphism of Microsatellite DNA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ying-jie; LIU Yue-qin; SUN Hong-xin; SUN Shao-hua; LI Yu

    2007-01-01

    Forecast of the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA was done in different sheep breeds. The gene frequency, the polymorphism information contents, the number of effective alleles, the heterozygosity, and the genetic distances were studied in four imported meat sheep and Small Tail Han sheep using five microsatellite loci. The crossing effects on the Small Tail Han sheep with four imported meat sheep were tested. The results indicate that there are genetic polymorphisms at five microsatellite loci in five sheep breeds. Five microsatellite loci can be used for genetic diversity evaluation in sheep breeds. The genetic variability of Dorset is the highest, and that of the Small Tail Han sheep is the lowest in the five sheep breeds. The order of heterosis from large to small in four imported meat sheep by the analysis of genetic relationship is White-Suffolk, Black-Suffolk,Dorset, and Texel. This accords with the testing results of actual heterosis. It is feasible to forecast the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA, which will have an important value for sheep breeding in the future.

  14. MicroRNA Related Polymorphisms and Breast Cancer Risk

    Science.gov (United States)

    Khan, Sofia; Greco, Dario; Michailidou, Kyriaki; Milne, Roger L.; Muranen, Taru A.; Heikkinen, Tuomas; Aaltonen, Kirsimari; Dennis, Joe; Bolla, Manjeet K.; Liu, Jianjun; Hall, Per; Irwanto, Astrid; Humphreys, Keith; Li, Jingmei; Czene, Kamila; Chang-Claude, Jenny; Hein, Rebecca; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Fletcher, Olivia; Peto, Julian; dos Santos Silva, Isabel; Johnson, Nichola; Gibson, Lorna; Aitken, Zoe; Hopper, John L.; Tsimiklis, Helen; Bui, Minh; Makalic, Enes; Schmidt, Daniel F.; Southey, Melissa C.; Apicella, Carmel; Stone, Jennifer; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel A.; van der Luijt, Rob B.; Meindl, Alfons; Schmutzler, Rita K.; Müller-Myhsok, Bertram; Lichtner, Peter; Turnbull, Clare; Rahman, Nazneen; Chanock, Stephen J.; Hunter, David J.; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Schmidt, Marjanka K.; Broeks, Annegien; Veer, Laura J. V. a. n't.; Hogervorst, Frans B.; Fasching, Peter A.; Schrauder, Michael G.; Ekici, Arif B.; Beckmann, Matthias W.; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; Benitez, Javier; Zamora, Pilar M.; Perez, Jose I. A.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Pharoah, Paul D. P.; Dunning, Alison M.; Shah, Mitul; Luben, Robert; Brown, Judith; Couch, Fergus J.; Wang, Xianshu; Vachon, Celine; Olson, Janet E.; Lambrechts, Diether; Moisse, Matthieu; Paridaens, Robert; Christiaens, Marie-Rose; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Mulot, Claire; Marme, Frederick; Burwinkel, Barbara; Schneeweiss, Andreas; Sohn, Christof; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Andrulis, Irene L.; Knight, Julia A.; Tchatchou, Sandrine; Mulligan, Anna Marie; Dörk, Thilo; Bogdanova, Natalia V.; Antonenkova, Natalia N.; Anton-Culver, Hoda; Darabi, Hatef; Eriksson, Mikael; Garcia-Closas, Montserrat; Figueroa, Jonine; Lissowska, Jolanta; Brinton, Louise; Devilee, Peter; Tollenaar, Robert A. E. M.; Seynaeve, Caroline; van Asperen, Christi J.; Kristensen, Vessela N.; Slager, Susan; Toland, Amanda E.; Ambrosone, Christine B.; Yannoukakos, Drakoulis; Lindblom, Annika; Margolin, Sara; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Mariani, Paolo; Hooning, Maartje J.; Martens, John W. M.; Collée, J. Margriet; Jager, Agnes; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Giles, Graham G.; McLean, Catriona; Brauch, Hiltrud; Brüning, Thomas; Ko, Yon-Dschun; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Mannermaa, Arto; Hamann, Ute; Chenevix-Trench, Georgia; Blomqvist, Carl; Aittomäki, Kristiina; Easton, Douglas F.; Nevanlinna, Heli

    2014-01-01

    Genetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer. We investigated associations between miRNA related SNPs and breast cancer risk. First we evaluated 2,196 SNPs in a case-control study combining nine genome wide association studies (GWAS). Second, we further investigated 42 SNPs with suggestive evidence for association using 41,785 cases and 41,880 controls from 41 studies included in the Breast Cancer Association Consortium (BCAC). Combining the GWAS and BCAC data within a meta-analysis, we estimated main effects on breast cancer risk as well as risks for estrogen receptor (ER) and age defined subgroups. Five miRNA binding site SNPs associated significantly with breast cancer risk: rs1045494 (odds ratio (OR) 0.92; 95% confidence interval (CI): 0.88–0.96), rs1052532 (OR 0.97; 95% CI: 0.95–0.99), rs10719 (OR 0.97; 95% CI: 0.94–0.99), rs4687554 (OR 0.97; 95% CI: 0.95–0.99, and rs3134615 (OR 1.03; 95% CI: 1.01–1.05) located in the 3′ UTR of CASP8, HDDC3, DROSHA, MUSTN1, and MYCL1, respectively. DROSHA belongs to miRNA machinery genes and has a central role in initial miRNA processing. The remaining genes are involved in different molecular functions, including apoptosis and gene expression regulation. Further studies are warranted to elucidate whether the miRNA binding site SNPs are the causative variants for the observed risk effects. PMID:25390939

  15. MicroRNA related polymorphisms and breast cancer risk.

    Directory of Open Access Journals (Sweden)

    Sofia Khan

    Full Text Available Genetic variations, such as single nucleotide polymorphisms (SNPs in microRNAs (miRNA or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer. We investigated associations between miRNA related SNPs and breast cancer risk. First we evaluated 2,196 SNPs in a case-control study combining nine genome wide association studies (GWAS. Second, we further investigated 42 SNPs with suggestive evidence for association using 41,785 cases and 41,880 controls from 41 studies included in the Breast Cancer Association Consortium (BCAC. Combining the GWAS and BCAC data within a meta-analysis, we estimated main effects on breast cancer risk as well as risks for estrogen receptor (ER and age defined subgroups. Five miRNA binding site SNPs associated significantly with breast cancer risk: rs1045494 (odds ratio (OR 0.92; 95% confidence interval (CI: 0.88-0.96, rs1052532 (OR 0.97; 95% CI: 0.95-0.99, rs10719 (OR 0.97; 95% CI: 0.94-0.99, rs4687554 (OR 0.97; 95% CI: 0.95-0.99, and rs3134615 (OR 1.03; 95% CI: 1.01-1.05 located in the 3' UTR of CASP8, HDDC3, DROSHA, MUSTN1, and MYCL1, respectively. DROSHA belongs to miRNA machinery genes and has a central role in initial miRNA processing. The remaining genes are involved in different molecular functions, including apoptosis and gene expression regulation. Further studies are warranted to elucidate whether the miRNA binding site SNPs are the causative variants for the observed risk effects.

  16. MicroRNA related polymorphisms and breast cancer risk.

    Science.gov (United States)

    Khan, Sofia; Greco, Dario; Michailidou, Kyriaki; Milne, Roger L; Muranen, Taru A; Heikkinen, Tuomas; Aaltonen, Kirsimari; Dennis, Joe; Bolla, Manjeet K; Liu, Jianjun; Hall, Per; Irwanto, Astrid; Humphreys, Keith; Li, Jingmei; Czene, Kamila; Chang-Claude, Jenny; Hein, Rebecca; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Fletcher, Olivia; Peto, Julian; dos Santos Silva, Isabel; Johnson, Nichola; Gibson, Lorna; Aitken, Zoe; Hopper, John L; Tsimiklis, Helen; Bui, Minh; Makalic, Enes; Schmidt, Daniel F; Southey, Melissa C; Apicella, Carmel; Stone, Jennifer; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel A; van der Luijt, Rob B; Meindl, Alfons; Schmutzler, Rita K; Müller-Myhsok, Bertram; Lichtner, Peter; Turnbull, Clare; Rahman, Nazneen; Chanock, Stephen J; Hunter, David J; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Schmidt, Marjanka K; Broeks, Annegien; Van't Veer, Laura J; Hogervorst, Frans B; Fasching, Peter A; Schrauder, Michael G; Ekici, Arif B; Beckmann, Matthias W; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Benitez, Javier; Zamora, Pilar M; Perez, Jose I A; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Pharoah, Paul D P; Dunning, Alison M; Shah, Mitul; Luben, Robert; Brown, Judith; Couch, Fergus J; Wang, Xianshu; Vachon, Celine; Olson, Janet E; Lambrechts, Diether; Moisse, Matthieu; Paridaens, Robert; Christiaens, Marie-Rose; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Mulot, Claire; Marme, Frederick; Burwinkel, Barbara; Schneeweiss, Andreas; Sohn, Christof; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Andrulis, Irene L; Knight, Julia A; Tchatchou, Sandrine; Mulligan, Anna Marie; Dörk, Thilo; Bogdanova, Natalia V; Antonenkova, Natalia N; Anton-Culver, Hoda; Darabi, Hatef; Eriksson, Mikael; Garcia-Closas, Montserrat; Figueroa, Jonine; Lissowska, Jolanta; Brinton, Louise; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline; van Asperen, Christi J; Kristensen, Vessela N; Slager, Susan; Toland, Amanda E; Ambrosone, Christine B; Yannoukakos, Drakoulis; Lindblom, Annika; Margolin, Sara; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Mariani, Paolo; Hooning, Maartje J; Martens, John W M; Collée, J Margriet; Jager, Agnes; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Giles, Graham G; McLean, Catriona; Brauch, Hiltrud; Brüning, Thomas; Ko, Yon-Dschun; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Mannermaa, Arto; Hamann, Ute; Chenevix-Trench, Georgia; Blomqvist, Carl; Aittomäki, Kristiina; Easton, Douglas F; Nevanlinna, Heli

    2014-01-01

    Genetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer. We investigated associations between miRNA related SNPs and breast cancer risk. First we evaluated 2,196 SNPs in a case-control study combining nine genome wide association studies (GWAS). Second, we further investigated 42 SNPs with suggestive evidence for association using 41,785 cases and 41,880 controls from 41 studies included in the Breast Cancer Association Consortium (BCAC). Combining the GWAS and BCAC data within a meta-analysis, we estimated main effects on breast cancer risk as well as risks for estrogen receptor (ER) and age defined subgroups. Five miRNA binding site SNPs associated significantly with breast cancer risk: rs1045494 (odds ratio (OR) 0.92; 95% confidence interval (CI): 0.88-0.96), rs1052532 (OR 0.97; 95% CI: 0.95-0.99), rs10719 (OR 0.97; 95% CI: 0.94-0.99), rs4687554 (OR 0.97; 95% CI: 0.95-0.99, and rs3134615 (OR 1.03; 95% CI: 1.01-1.05) located in the 3' UTR of CASP8, HDDC3, DROSHA, MUSTN1, and MYCL1, respectively. DROSHA belongs to miRNA machinery genes and has a central role in initial miRNA processing. The remaining genes are involved in different molecular functions, including apoptosis and gene expression regulation. Further studies are warranted to elucidate whether the miRNA binding site SNPs are the causative variants for the observed risk effects.

  17. Genetic polymorphisms at the leptin receptor gene in three beef cattle breeds

    Directory of Open Access Journals (Sweden)

    Sabrina E.M. Almeida

    2008-01-01

    Full Text Available The genetic diversity of a single nucleotide polymorphism (SNP at the exon 20 (T945M of the leptin receptor gene (LEPR and of three short tandem repeats (STRs BM7225, BMS694, and BMS2145 linked to LEPR was investigated in three beef cattle herds (Brangus Ibagé, Charolais, and Aberdeen Angus. A cheap and effective new method to analyze the T945M polymorphism in cattle populations was developed and the possible role of these polymorphisms in reproduction and weight gain of postpartum cows was evaluated. High levels of genetic diversity were observed with the average heterozygosity of STRs ranging from 0.71 to 0.81. No significant association was detected between LEPR markers and reproductive parameters or daily weight gain. These negative results suggest that the LEPR gene polymorphisms, at least those herein described, do not influence postpartum cows production.

  18. Music genetics research: Association with musicality of a polymorphism in the AVPR1A gene.

    Science.gov (United States)

    Mariath, Luiza Monteavaro; Silva, Alexandre Mauat da; Kowalski, Thayne Woycinck; Gattino, Gustavo Schulz; Araujo, Gustavo Andrade de; Figueiredo, Felipe Grahl; Tagliani-Ribeiro, Alice; Roman, Tatiana; Vianna, Fernanda Sales Luiz; Schuler-Faccini, Lavínia; Schuch, Jaqueline Bohrer

    2017-01-01

    Musicality is defined as a natural tendency, sensibility, knowledge, or talent to create, perceive, and play music. Musical abilities involve a great range of social and cognitive behaviors, which are influenced by both environmental and genetic factors. Although a number of studies have yielded insights into music genetics research, genes and biological pathways related to these traits are not fully understood. Our hypothesis in the current study is that genes associated with different behaviors could also influence the musical phenotype. Our aim was to investigate whether polymorphisms in six genes (AVPR1A, SLC6A4, ITGB3, COMT, DRD2 and DRD4) related to social and cognitive traits are associated with musicality in a sample of children. Musicality was assessed through an individualized music therapy assessment profile (IMTAP) which has been validated in Brazil to measure musical ability. We show here that the RS1 microsatellite of the AVPR1A gene is nominally associated with musicality, corroborating previous results linking AVPR1A with musical activity. This study is one of the first to investigate musicality in a comprehensive way, and it contributes to better understand the genetic basis underlying musical ability.

  19. Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms.

    Science.gov (United States)

    Abraham, Anne-Laure; Nagarajan, Muniyandi; Veyrieras, Jean-Baptiste; Bottin, Hélène; Steinmetz, Lars M; Yvert, Gaël

    2012-09-01

    Natural populations are known to differ not only in DNA but also in their chromatin-associated epigenetic marks. When such inter-individual epigenomic differences (or "epi-polymorphisms") are observed, their stability is usually not known: they may or may not be reprogrammed over time or upon environmental changes. In addition, their origin may be purely epigenetic, or they may result from regulatory variation encoded in the DNA. Studying epi-polymorphisms requires, therefore, an assessment of their nature and stability. Here we estimate the stability of yeast epi-polymorphisms of chromatin acetylation, and we provide a genome-by-epigenome map of their genetic control. A transient epi-drug treatment was able to reprogram acetylation variation at more than one thousand nucleosomes, whereas a similar amount of variation persisted, distinguishing "labile" from "persistent" epi-polymorphisms. Hundreds of genetic loci underlied acetylation variation at 2,418 nucleosomes either locally (in cis) or distantly (in trans), and this genetic control overlapped only partially with the genetic control of gene expression. Trans-acting regulators were not necessarily associated with genes coding for chromatin modifying enzymes. Strikingly, "labile" and "persistent" epi-polymorphisms were associated with poor and strong genetic control, respectively, showing that genetic modifiers contribute to persistence. These results estimate the amount of natural epigenomic variation that can be lost after transient environmental exposures, and they reveal the complex genetic architecture of the DNA-encoded determinism of chromatin epi-polymorphisms. Our observations provide a basis for the development of population epigenetics.

  20. Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms.

    Directory of Open Access Journals (Sweden)

    Anne-Laure Abraham

    2012-09-01

    Full Text Available Natural populations are known to differ not only in DNA but also in their chromatin-associated epigenetic marks. When such inter-individual epigenomic differences (or "epi-polymorphisms" are observed, their stability is usually not known: they may or may not be reprogrammed over time or upon environmental changes. In addition, their origin may be purely epigenetic, or they may result from regulatory variation encoded in the DNA. Studying epi-polymorphisms requires, therefore, an assessment of their nature and stability. Here we estimate the stability of yeast epi-polymorphisms of chromatin acetylation, and we provide a genome-by-epigenome map of their genetic control. A transient epi-drug treatment was able to reprogram acetylation variation at more than one thousand nucleosomes, whereas a similar amount of variation persisted, distinguishing "labile" from "persistent" epi-polymorphisms. Hundreds of genetic loci underlied acetylation variation at 2,418 nucleosomes either locally (in cis or distantly (in trans, and this genetic control overlapped only partially with the genetic control of gene expression. Trans-acting regulators were not necessarily associated with genes coding for chromatin modifying enzymes. Strikingly, "labile" and "persistent" epi-polymorphisms were associated with poor and strong genetic control, respectively, showing that genetic modifiers contribute to persistence. These results estimate the amount of natural epigenomic variation that can be lost after transient environmental exposures, and they reveal the complex genetic architecture of the DNA-encoded determinism of chromatin epi-polymorphisms. Our observations provide a basis for the development of population epigenetics.

  1. Genetic structure of the polymorphic metrosideros (Myrtaceae complex in the Hwaiian islands using nuclear microsatellite data.

    Directory of Open Access Journals (Sweden)

    Danica T Harbaugh

    Full Text Available BACKGROUND: Five species of Metrosideros (Myrtaceae are recognized in the Hawaiian Islands, including the widespread M. polymorpha, and are characterized by a multitude of distinctive, yet overlapping, habit, ecological, and morphological forms. It remains unclear, despite several previous studies, whether the morphological variation within Hawaiian Metrosideros is due to hybridization, genetic polymorphism, phenotypic plasticity, or some combination of these processes. The Hawaiian Metrosideros complex has become a model system to study ecology and evolution; however this is the first study to use microsatellite data for addressing inter-island patterns of variation from across the Hawaiian Islands. METHODOLOGY/PRINCIPAL FINDINGS: Ten nuclear microsatellite loci were genotyped from 143 individuals of Metrosideros. We took advantage of the bi-parental inheritance and rapid mutation rate of these data to examine the validity of the current taxonomy and to investigate whether Metrosideros plants from the same island are more genetically similar than plants that are morphologically similar. The Bayesian algorithm of the program structure was used to define genetic groups within Hawaiian Metrosideros and the closely related taxon M. collina from the Marquesas and Austral Islands. Several standard and nested AMOVAs were conducted to test whether the genetic diversity is structured geographically or taxonomically. CONCLUSIONS/SIGNIFICANCE: The results suggest that Hawaiian Metrosideros have dynamic gene flow, with genetic and morphological diversity structured not simply by geography or taxonomy, but as a result of parallel evolution on islands following rampant island-island dispersal, in addition to ancient chloroplast capture. Results also suggest that the current taxonomy requires major revisions in order to reflect the genetic structure revealed in the microsatellite data.

  2. Genetic diversity and prevalence of CCR2-CCR5 gene polymorphisms in the Omani population

    OpenAIRE

    2014-01-01

    Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Oc...

  3. Genetic diversity and prevalence of CCR2-CCR5 gene polymorphisms in the Omani population

    OpenAIRE

    2013-01-01

    Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Oc...

  4. Association of AIRE polymorphisms with genetic susceptibility to rheumatoid arthritis in a Chinese population.

    Science.gov (United States)

    Shao, Song; Li, Xing-Rui; Cen, Han; Yin, Zong-Sheng

    2014-04-01

    Recently, genetic polymorphisms within the autoimmune regulator (AIRE) have been implicated in the genetic susceptibility to rheumatoid arthritis (RA) in Japanese and Spanish. The aim of this case-control study involving 232 patients with RA and 313 ethnically matched control subjects was to investigate the association of AIRE rs2075876 and rs760426 polymorphisms with genetic predisposition to RA in a Chinese population. The genotypes of AIRE rs2075876 and rs760426 polymorphisms were determined by SNaPshot assay. A significant difference in the allele frequency of AIRE rs2075876 polymorphism between cases and controls was detected (A versus G, OR 1.33, 95 %CI 1.04-1.69, P = 0.02, P corrected (Bonferroni correction) Pc = 0.04). Significant evidence was found for the association between the minor allele A of AIRE rs2075876 polymorphism and the risk of RA under the recessive model (AA versus AG + GG, P = 7.15 × 10(-3), Pc = 1.43 × 10(-2)). The frequency of the minor allele G of AIRE rs760426 polymorphism was higher in patients compared with controls (47.8 % versus 42.1 %), and this deviation showed a trend towards significant level (P = 0.06, Pc = 0.12). The association between the minor allele G of AIRE rs760426 polymorphism with RA risk under the dominant model and the recessive model revealed that significant evidence was detected under the recessive model (GG versus GA + AA, P = 0.02, Pc = 0.04). Our results indicated that AIRE rs2075876 and rs760426 polymorphisms were involved in the genetic background of RA in the Chinese population.

  5. Genetic polymorphisms in DPF3 associated with risk of breast cancer and lymph node metastases

    Directory of Open Access Journals (Sweden)

    Hoyal Carolyn R

    2005-08-01

    Full Text Available Abstract Background Several studies have identified rare genetic variations responsible for many cases of familial breast cancer but their contribution to total breast cancer incidence is relatively small. More common genetic variations with low penetrance have been postulated to account for a higher proportion of the population risk of breast cancer. Methods and Results In an effort to identify genes that influence non-familial breast cancer risk, we tested over 25,000 single nucleotide polymorphisms (SNPs located within approximately 14,000 genes in a large-scale case-control study in 254 German women with breast cancer and 268 age-matched women without malignant disease. We identified a marker on chromosome 14q24.3-q31.1 that was marginally associated with breast cancer status (OR = 1.5, P = 0.07. Genotypes for this SNP were also significantly associated with indicators of breast cancer severity, including presence of lymph node metastases (P = 0.006 and earlier age of onset (P = 0.01. The association with breast cancer status was replicated in two independent samples (OR = 1.35, P = 0.05. High-density association fine mapping showed that the association spanned about 80 kb of the zinc-finger gene DPF3 (also known as CERD4. One SNP in intron 1 was found to be more strongly associated with breast cancer status in all three sample collections (OR = 1.6, P = 0.003 as well as with increased lymph node metastases (P = 0.01 and tumor size (P = 0.01. Conclusion Polymorphisms in the 5' region of DPF3 were associated with increased risk of breast cancer development, lymph node metastases, age of onset, and tumor size in women of European ancestry. This large-scale association study suggests that genetic variation in DPF3 contributes to breast cancer susceptibility and severity.

  6. Genetic polymorphisms affect efficacy and adverse drug reactions of DMARDs in rheumatoid arthritis.

    Science.gov (United States)

    Zhang, Ling Ling; Yang, Sen; Wei, Wei; Zhang, Xue Jun

    2014-11-01

    Disease-modifying antirheumatic drugs (DMARDs) and biological agents are critical in preventing the severe complications of rheumatoid arthritis (RA). However, the outcome of treatment with these drugs in RA patients is quite variable and unpredictable. Drug-metabolizing enzymes (dihydrofolate reductase, cytochrome P450 enzymes, N-acetyltransferases, etc.), drug transporters (ATP-binding cassette transporters), and drug targets (tumor necrosis factor-α receptors) are coded for by variant alleles. These gene polymorphisms may influence the pharmacokinetics, pharmacodynamics, and side effects of medicines. The cause for differences in efficacy and adverse drug reactions may be genetic variation in drug metabolism among individuals. Polymorphisms in drug transporter genes may change the distribution and excretion of medicines, and the sensitivity of the targets to drugs is strongly influenced by genetic variations. In this article, we review the genetic polymorphisms that affect the efficacy of DMARDs or the occurrence of adverse drug reactions associated with DMARDs in RA.

  7. Genetic polymorphism of serotonin transporter 5-HTTLPR: involvement in smoking behaviour

    Indian Academy of Sciences (India)

    Maria Angelica Ehara Watanabe; Sandra Odebrechet Vargas Nunes; Marla Karine Amarante; Roberta Losi Guembarovski; Julie Massayo Maeda Oda; Kalil William Alves De Lima; Maria Helena Pelegrinelli Fungaro

    2011-04-01

    Data suggest that the serotonin (5-hydroxytryptamine, 5-HT) system is implicated in the pathogenesis of multiple neuropsychiatric disorders and may also be involved in smoking behaviour since nicotine increases brain serotonin secretion. It is known that smoking behaviour is influenced by both genetic and environmental factors. The present review examines the role of the serotonin transporter gene (5-HTT) in smoking behaviour and investigating studies that showed association of 5-HTT gene with smoking. This study discusses a polymorphism which has been investigated by many researchers, as the bi-allelic insertion/deletion polymorphism in the 5′-flanking promoter region (5-HTTLPR). This gene has received considerable attention in attempts to understand the molecular determinants of smoking. Therefore, in the present study, the relationship between genetic polymorphism of serotonin transporter in smoking behaviour is reviewed considering the interactive effect of genetic factors.

  8. MUTYH Gln324His gene polymorphism and genetic susceptibility for lung cancer in a Japanese population

    Directory of Open Access Journals (Sweden)

    Tsutou Akimitsu

    2009-01-01

    Full Text Available Abstract Background Genetic polymorphisms of DNA repair enzymes in the base excision repair (BER pathway, may lead to genetic instability and lung cancer carcinogenesis. We investigated the interactions among the gene polymorphisms in DNA repair genes and lung cancer. Methods We analyzed associations among OGG1 Ser326Cys and MUTYH Gln324His gene polymorphisms in relation to lung cancer risk using PCR-RFLP. The study involved 108 lung cancer patients and 121 non-cancer controls divided into non-smokers, smokers according to pack-years smoked in Japanese. Results The results showed that the MUTYH His/His genotype compared with Gln/Gln genotype showed an increased risk for lung cancer (adjusted odds ratio [OR] 3.03, confidence interval [95%CI], 1.31–7.00, p = 0.010, whereas there was no significant increase for the Gln/His genotype (adjusted OR 1.35, 95%CI 0.70–2.61, p = 0.376. The MUTYH His/His genotype was at a borderline increased risk for both adenocarcinoma and squamous cell carcinoma (adjusted OR 2.50, 95%CI 0.95–6.62, p = 0.065 for adenocarcinoma; adjusted OR 3.20, 95%CI 0.89–11.49, p = 0.075 for squamous cell carcinoma, respectively. However, the OGG1 Ser/Cys or Cys/Cys genotypes compared with the Ser/Ser genotype did not have significantly increased risk for lung cancer, containing either adenocarcinoma or squamous cell carcinoma. The joint effect of tobacco exposure and the MUTYH His/His genotype compared with the Gln/Gln genotype showed a significant association with lung cancer risk in smokers, and there was not significantly increased in non-smokers (adjusted OR 3.82, 95%CI 1.22–12.00, p = 0.022 for smokers; adjusted OR 2.60, 95%CI 0.60–11.25, p = 0.200 for non-smokers, respectively. The effect of tobacco exposure and the OGG1 Ser326Cys showed also no significant risk for lung cancer. Conclusion Our findings suggest that the MUTYH Gln324His polymorphism appear to play an important role in modifying the risk for lung cancer

  9. Genetic polymorphisms of milk epithelial mucin of yaks

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yucai; ZHAO Xingbo; JIN Suyu; PENG Xianwen; BAI Wenlin

    2006-01-01

    Milk epithelial mucin (MUC1) of yaks was separated by SDS-polyacrylamide gel electrophoresis. A total of nine types of MUC1 were revealed in 427 yaks from five yak breeds including Maiwa yak, Jiulong yak, Tianzhu white yak, Qinghai yak and Tibetan yak. The molecular weights of MUC1 are from 163 kD to 208 kD, most of which are larger than those of bovine. Population genetic analysis shows that the gene frequency and genotype frequency of yak MUC1 differ among breeds, with relatively high gene heterozygosity.The five yak breeds studied fall into two groups according to their milk MUC1 gene frequency, suggesting that milk MUC1 exhibits specificities for local yak groups.

  10. Genetic variants in hormone-related genes and risk of breast cancer.

    Directory of Open Access Journals (Sweden)

    Tess Clendenen

    Full Text Available Sex hormones play a key role in the development of breast cancer. Certain polymorphic variants (SNPs and repeat polymorphisms in hormone-related genes are associated with sex hormone levels. However, the relationship observed between these genetic variants and breast cancer risk has been inconsistent. We conducted a case-control study nested within two prospective cohorts to assess the relationship between specific genetic variants in hormone-related genes and breast cancer risk. In total, 1164 cases and 2111 individually-matched controls were included in the study. We did not observe an association between potential functional genetic polymorphisms in the estrogen pathway, SHBG rs6259, ESR1 rs2234693, CYP19 rs10046 and rs4775936, and UGT1A1 rs8175347, or the progesterone pathway, PGR rs1042838, with the risk of breast cancer. Our results suggest that these genetic variants do not have a strong effect on breast cancer risk.

  11. The evolution, maintenance and adaptive function of genetic colour polymorphism in birds.

    Science.gov (United States)

    Roulin, Alexandre

    2004-11-01

    The hypothesis that ornaments can honestly signal quality only if their expression is condition-dependent has dominated the study of the evolution and function of colour traits. Much less interest has been devoted to the adaptive function of colour traits for which the expression is not, or is to a low extent, sensitive to body condition and the environment in which individuals live. The aim of the present paper is to review the current theoretical and empirical knowledge of the evolution, maintenance and adaptive function of colour plumage traits for which the expression is mainly under genetic control. The finding that in many bird species the inheritance of colour morphs follows the laws of Mendel indicates that genetic colour polymorphism is frequent. Polymorphism may have evolved or be maintained because each colour morph facilitates the exploitation of alternative ecological niches as suggested by the observation that individuals are not randomly distributed among habitats with respect to coloration. Consistent with the hypothesis that different colour morphs are linked to alternative strategies is the finding that in a majority of species polymorphism is associated with reproductive parameters, and behavioural, life-history and physiological traits. Experimental studies showed that such covariations can have a genetic basis. These observations suggest that colour polymorphism has an adaptive function. Aviary and field experiments demonstrated that colour polymorphism is used as a criterion in mate-choice decisions and dominance interactions confirming the claim that conspecifics assess each other's colour morphs. The factors favouring the evolution and maintenance of genetic variation in coloration are reviewed, but empirical data are virtually lacking to assess their importance. Although current theory predicts that only condition-dependent traits can signal quality, the present review shows that genetically inherited morphs can reveal the same qualities

  12. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Wong, G K; Hillier, L; Brandstrom, M; Croojmans, R; Ovcharenko, I; Gordon, L; Stubbs, L; Lucas, S; Glavina, T; Kaiser, P; Gunnarsson, U; Webber, C; Overton, I

    2005-02-20

    We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines--contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

  13. [Metabolic bone disease in premature infants and genetic polymorphisms

    NARCIS (Netherlands)

    Funke, S.; Morava, E.; Czako, M.; Vida, G.; Ertl, T.; Kosztolanyi, G.Y.

    2007-01-01

    Metabolic bone disease is an important complication among infants very-low-birth-weight (< 1500 g). In adults, osteoporosis has been shown to be associated with polymorphisms of vitamin D receptor, estrogen receptor, and collagen Ialpha1 receptor genes. AIM: The primary goal of the study was to i

  14. Influence of genetic polymorphisms on bone disease of preterm infants.

    NARCIS (Netherlands)

    Funke, S.; Morava, E.; Czako, M.; Vida, G.; Ertl, T.; Kosztolanyi, G.Y.

    2006-01-01

    Bone disease is an important complication among very low birth weight (VLBW, <1500 g) infants. In adults, osteoporosis is associated with polymorphisms of vitamin D receptor (VDR), estrogen receptor (ER), and collagen Ialpha1 (COLIA1) genes. However, limited information is available regarding the

  15. Risk assessment: the importance of genetic polymorphisms in man

    DEFF Research Database (Denmark)

    Knudsen, Lisbeth E.; Loft, S H; Autrup, H

    2001-01-01

    and increased cancer risk, such results indicate effect modification regarding cancer risk. In risk assessment the safety 'factor' of 10 is generally accepted to allow for variation in individual susceptibility. Reviewing the literature justifies the factor of 10 when considering single polymorphisms. However...... the application in insurance situations is criticised....

  16. Risk assessment: the importance of genetic polymorphisms in man

    DEFF Research Database (Denmark)

    E. Knudsen, Lisbeth; Loft, Steffen; Autrup, Herman

    2001-01-01

    and increased cancer risk, such results indicate effect modification regarding cancer risk. In risk assessment the safety ‘factor’ of 10 is generally accepted to allow for variation in individual susceptibility. Reviewing the literature justifies the factor of 10 when considering single polymorphisms. However...... the application in insurance situations is criticised....

  17. A Simplified Technique for Evaluating Human "CCR5" Genetic Polymorphism

    Science.gov (United States)

    Falteisek, Lukáš; Cerný, Jan; Janštová, Vanda

    2013-01-01

    To involve students in thinking about the problem of AIDS (which is important in the view of nondecreasing infection rates), we established a practical lab using a simplified adaptation of Thomas's (2004) method to determine the polymorphism of HIV co-receptor CCR5 from students' own epithelial cells. CCR5 is a receptor involved in inflammatory…

  18. A Simplified Technique for Evaluating Human "CCR5" Genetic Polymorphism

    Science.gov (United States)

    Falteisek, Lukáš; Cerný, Jan; Janštová, Vanda

    2013-01-01

    To involve students in thinking about the problem of AIDS (which is important in the view of nondecreasing infection rates), we established a practical lab using a simplified adaptation of Thomas's (2004) method to determine the polymorphism of HIV co-receptor CCR5 from students' own epithelial cells. CCR5 is a receptor involved in…

  19. Relationship between genetic polymorphisms of DNA ligase 1 and non-small cell lung cancer susceptibility and radiosensitivity.

    Science.gov (United States)

    Tian, H; He, X; Yin, L; Guo, W J; Xia, Y Y; Jiang, Z X

    2015-06-26

    The aim of this study was to examine the relationship between genetic polymorphisms in DNA ligase 1 (LIG1) and non-small cell lung cancer (NSCLC) susceptibility and radiosensitivity in a Chinese population. This was a case-control study that included 352 NSCLC patients and 448 healthy controls. Polymerase chain reaction-restriction fragment length polymorphism analysis was conducted to detect HaeIII polymorphisms in exon 6 of the LIG1 gene in this popula-tion. This information was used to observe the effects of radiation in pa-tients with different genotypes in order to determine the genotypes as-sociated with radiosensitivity. The CC genotype and C allele frequency were significantly higher in the NSCLC group than in the control group (P = 0.012 and P = 0.023, respectively). The relative risk of experienc-ing NSCLC was 2.55 [95% confidence interval (CI), 1.12-3.98] for CC homozygous patients and 0.87 (95%CI, 0.46-1.88) for AA homozygous patients. Analysis of LIG1 genetic polymorphisms and radiosensitiv-ity of NSCLC patients showed that AA homozygous patients were sig-nificantly more radiosensitive than the control group (AA vs AC, P = 0.014; AA vs CC, P < 0.001; AC vs CC, P = 0.023). Therefore, the LIG1 CC genotype was associated with susceptibility to NSCLC, and the AA genotype demonstrated increased radiosensitivity compared to the AC and CC genotypes.

  20. Optimization of a Reaction System of Sequence Related Amplified Polymorphism and Segregation of Polymorphic Loci in an F2 Population of Rice

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An effective PCR protocol for detecting the sequence related amplified polymorphism (SRAP) in rice was developed.One hundred and ten pairs of SRAP primers were used for segregation analysis in an F2 population derived from a cross between Shennong 606 and Lijiangxintuanheigu.Among the 110 primer pairs,35 pairs generated 143 polymorphic bands with an average of 4.09 polymorphic bands per primer pair,and 24 pairs (16.78%) showed the genetic distortion (P<0.05).Of the 24 primer pairs,12 pairs deviated toward the male parent Shennong 606 and 11 pairs toward the female parent Lijiangxintuanheigu,only one toward heterozygote.It was found that the segregation distortion might be caused by the joint gametic and zygotic effects.

  1. Obesity-related polymorphisms and their associations with the ability to regulate fat oxidation in obese Europeans : the NUGENOB study

    NARCIS (Netherlands)

    Corpeleijn, Eva; Petersen, Liselotte; Holst, Claus; Saris, Wim H; Astrup, Arne; Langin, Dominique; MacDonald, Ian; Martinez, J Alfredo; Oppert, Jean-Michel; Polak, Jan; Pedersen, Oluf; Froguel, Philippe; Arner, Peter; Sørensen, Thorkild I A; Blaak, Ellen E

    Both obesity and insulin resistance have been related to low fat oxidation rates, which may be genetically determined. The association between variation in fat oxidation rates among obese subjects and genotype was studied for 42 common single-nucleotide polymorphisms (SNPs) in 26 candidate genes for

  2. Study of the generated genetic polymorphisms during the photocatalytic elimination of Klebsiella pneumoniae in water.

    Science.gov (United States)

    Venieri, Danae; Fraggedaki, Antonia; Binas, Vassilios; Zachopoulos, Apostolos; Kiriakidis, George; Mantzavinos, Dionissios

    2015-03-01

    Klebsiella pneumoniae is considered to be an emerging pathogen persisting under extreme environmentally stressed conditions. The aim of the present study is the investigation of inactivation rates of this pathogen in water by means of heterogeneous photocatalytic treatment under solar irradiation and the induced genetic variance applying RAPD-PCR as a molecular typing tool. Novel Mn- and Co-doped TiO2 catalysts were assessed in terms of their disinfection efficiency. The reference strain of K. pneumoniae proved to be readily inactivated, since disinfection occurred rapidly (i.e. after only 10 min of treatment) and low levels of bacterial regrowth were recorded in the dark and under natural sunlight. Binary doped titania exhibited the best photocatalytic activity, verifying the synergistic effect induced by composite dopants. Applying RAPD analysis to viable cells after treatment we concluded that increasing the treatment time led to considerable alteration of RAPD profiles and the homology coefficient ranged almost between 35 and 60%. RAPD-PCR proved to be a useful typing molecular tool that under standardized conditions exhibits highly reproducible results. Genetic variation among isolates increased in relation to the period of treatment and prolonged irradiation in each case affected the overall alteration in band patterns. RAPD patterns were highly diverse between treated and untreated isolates when disinfection was performed with the Co-doped titania. The broad spectrum of genetic variance and generated polymorphisms has the potential to increase the already significant virulence of the species.

  3. Role of genetic polymorphisms of ion channels in the pathophysiology of coronary microvascular dysfunction and ischemic heart disease.

    Science.gov (United States)

    Fedele, Francesco; Mancone, Massimo; Chilian, William M; Severino, Paolo; Canali, Emanuele; Logan, Suzanna; De Marchis, Maria Laura; Volterrani, Maurizio; Palmirotta, Raffaele; Guadagni, Fiorella

    2013-11-01

    Conventionally, ischemic heart disease (IHD) is equated with large vessel coronary disease. However, recent evidence has suggested a role of compromised microvascular regulation in the etiology of IHD. Because regulation of coronary blood flow likely involves activity of specific ion channels, and key factors involved in endothelium-dependent dilation, we proposed that genetic anomalies of ion channels or specific endothelial regulators may underlie coronary microvascular disease. We aimed to evaluate the clinical impact of single-nucleotide polymorphisms in genes encoding for ion channels expressed in the coronary vasculature and the possible correlation with IHD resulting from microvascular dysfunction. 242 consecutive patients who were candidates for coronary angiography were enrolled. A prospective, observational, single-center study was conducted, analyzing genetic polymorphisms relative to (1) NOS3 encoding for endothelial nitric oxide synthase (eNOS); (2) ATP2A2 encoding for the Ca²⁺/H⁺-ATPase pump (SERCA); (3) SCN5A encoding for the voltage-dependent Na⁺ channel (Nav1.5); (4) KCNJ8 and KCNJ11 encoding for the Kir6.1 and Kir6.2 subunits of K-ATP channels, respectively; and (5) KCN5A encoding for the voltage-gated K⁺ channel (Kv1.5). No significant associations between clinical IHD manifestations and polymorphisms for SERCA, Kir6.1, and Kv1.5 were observed (p > 0.05), whereas specific polymorphisms detected in eNOS, as well as in Kir6.2 and Nav1.5 were found to be correlated with IHD and microvascular dysfunction. Interestingly, genetic polymorphisms for ion channels seem to have an important clinical impact influencing the susceptibility for microvascular dysfunction and IHD, independent of the presence of classic cardiovascular risk factors.

  4. Common polymorphisms in dopamine-related genes combine to produce a 'schizophrenia-like' prefrontal hypoactivity.

    Science.gov (United States)

    Vercammen, A; Weickert, C S; Skilleter, A J; Lenroot, R; Schofield, P R; Weickert, T W

    2014-02-04

    Individual changes in dopamine-related genes influence prefrontal activity during cognitive-affective processes; however, the extent to which common genetic variations combine to influence prefrontal activity is unknown. We assessed catechol-O-methyltransferase (COMT) Val108/158Met (rs4680) and dopamine D2 receptor (DRD2) G-T (rs2283265) single nucleotide polymorphisms and functional magnetic resonance imaging during an emotional response inhibition test in 43 healthy adults and 27 people with schizophrenia to determine the extent to which COMT Val108/158Met and DRD2 G-T polymorphisms combine to influence prefrontal response to cognitive-affective challenges. We found an increased number of cognitive-deficit risk alleles in these two dopamine-regulating genes predict reduced prefrontal activation during response inhibition in healthy adults, mimicking schizophrenia-like prefrontal hypoactivity. Our study provides evidence that functionally related genes can combine to produce a disease-like endophenotype.

  5. Association between pepsinogen C gene polymorphism and genetic predisposition to gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Hui-Jie Liu; Xiao-Lin Guo; Ming Dong; Lan Wang; Yuan Yuan

    2003-01-01

    AIM: To identify a molecular marker for gastric cancer, andto investigate the relationship between the polymorphismof pepsinogen C (PGC) gene and the genetic predispositionto gastric cancer.METHODS: A total of 289 cases were involved in this study.115 cases came from Shenyang area, a low risk area ofgastric cancer, including 42 unrelated controls and 73 patientswith gastric cancer. 174 cases came from Zhuanghe area, ahigh-risk area of gastric cancer, including 113 unrelatedcontrols, and 61 cases from gastric cancer kindred families.The polymorphism of PGC gene was detected by polymerasechain reaction (PCR) and the relation between the geneticpolymorphism of PGC and gastric cancer was examined.RESULTS: Four alleles, 310bp (allele 1), 400bp (allele 2),450bp (allele 3), and 480bp (allele 4) were detected byPCR. The frequency of allele 1 was higher in patients withgastric cancer than that in controls. Genotypes containinghomogenous allele 1 were significantly more frequent inpatients with gastric cancerthan that in controls (0.33, 0.14,x2=3.86, P<0.05). There was no significant differencebetween the control group of Zhuanghe and the group ofgastric cancer kindred. But the frequency of allele 1 washigher in control group of Zhuanghe area than that in controlgroup of Shenyang area and genotypes containinghomogenous allele 1 were significantly more frequent inthe control group of Zhuanghe area than those in controlgroup of Shenyang area (0.33, 0.14, x2=4.32, P<0.05). Inthe group of gastric cancer kindred the frequency of allele 1was significantly higher than that in control group ofShenyang area (0.5164, 0.3571, x2=4.47, P<0.05).Genotypes containing homogenous allele 1 were significantlymore frequent in the group of gastric cancer kindred thanthose in control group of Shenyang area (0.36, 0.14, x2=4.91,P<0.05).CONCLUSION: These results suggest that there is somerelation between pepsinogen C gene polymorphism andgastric cancer, and the person with

  6. Single-strand conformation polymorphism analysis of genetic variation in Labiostrongylus longispicularis from kangaroos.

    Science.gov (United States)

    Huby-Chilton, F; Beveridge, I; Gasser, R B; Chilton, N B

    2001-06-01

    Single-strand conformation polymorphism (SSCP) analysis was employed to screen for sequence heterogeneity in the second internal transcribed spacer (ITS-2) of ribosomal (r) DNA of Labiostrongylus longispicularis, a parasitic strongylid nematode occuring in some species of kangaroo in different geographical regions of Australia. The results showed that most of the nematodes screened had different SSCP profiles, which were subsequently shown to correspond to polymorphisms and/or an indel in the ITS-2 sequence. These variable sites related mainly to unpaired regions of the predicted secondary structure of the precursor rRNA molecule. SSCP profiles could be used to distinguish L. longispicularis in Macropus robustus robustus (New South Wales) from L. longispicularis in Macropus robustus erubescens and Macropus rufus (South Australia). This difference corresponded to a transversional change in the ITS-2 sequence at alignment position 82. The study demonstrated clearly the effectiveness of SSCP analysis for future large-scale population genetic studies of L. longispicularis in order to test the hypothesis that L. longispicularis from different geographical regions represents multiple sibling species.

  7. Molecular genetics of avian proteins. XIII. Protein polymorphism in three species of Australian passerines.

    Science.gov (United States)

    Manwell, C; Baker, C M

    1975-12-01

    An introduced species, the house sparrow (Passer domesticus), and two Australian native species, the welcome swallow (Hirundo tahitica neoxena) and the fairy martin (Petrochelidon ariel), have moderately low levels of protein polymorphism compared with domesticated or semi-wild 'managed' species of birds. Genetically varient proteins in these birds include transferrin, esterase, phosphoglucomutase, NADP-dependent isocitrate dehydrogenases, phosphogluconate dehydrogenase (decarboxylating) and glucose-6-phosphate dehydrogenase. Egg-white protein polymorphism confirms heterogeneity of egg colour, markings and shape, and suggests that approximately 10% of the 'clutches' in house sparrow nests represent infidelity (intraspecific nest parasitism). For the four enzymes capable of supplying reduced NADP for reductive biosyntheses in growth and detoxification, the house sparrow has more heterozygosity (29%) than either the welcome swallow (9-4%) or the fairy martin (2-3%) and the difference is highly significant statistically. The results are discussed in relation to possible biochemical correlates of MacArthur and Wilson's (1967) evolutionary strategies or r or K selection.

  8. Nine genetic polymorphisms associated with power athlete status - A Meta-Analysis.

    Science.gov (United States)

    Weyerstraß, Jan; Stewart, Kelly; Wesselius, Anke; Zeegers, Maurice

    2017-06-21

    In this study the association between genetic polymorphisms and power athlete status with possible interference by race and sex was investigated to identify genetic variants favourable for becoming a power athlete. This meta-analysis included both, case-control and Cohort studies. Databases of PubMed and Web of Science were searched for studies reporting on genetic polymorphisms associated with the status of being a power athlete. Thirty-five articles published between 2008 and 2016 were identified as eligible including a total number of 5834 power athletes and 14,018 controls. A series of meta-analyses were conducted for each of the identified genetic polymorphisms associated with power athlete status. Odds ratios (ORs) based on the allele and genotype frequency with corresponding 95% confidence intervals (95%CI) were calculated per genetic variant. Heterogeneity of the studies was addressed by Chi-square based Q-statistics at 5% significance level and a fixed or random effects model was used in absence or presence of heterogeneity respectively. Stratified analyses were conducted by race and sex to explore potential sources of heterogeneity. Significant associations were found for the genetic polymorphisms in the ACE (rs4363, rs1799752), ACTN3 (rs1815739), AGT (rs699), IL6-174 (rs1800795), MnSOD (rs1799725), NOS3 (rs1799983, rs2070744) and SOD2 (rs4880) genes. Nine genetic polymorphisms have been identified in the meta-analyses to have a significant association with the status of being a power athlete. Nevertheless, more research on the investigated genes needs to be done to draw comprehensive conclusions. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  9. Polymorphism of microsatellite loci in bread wheat (Triticum aestivum L. and related species

    Directory of Open Access Journals (Sweden)

    Kondić-Špika Ankica Đ.

    2016-01-01

    Full Text Available This study analysed polymorphism of 15 microsatellite loci in the col­lection comprising of 40 genotypes of bread wheat (Triticum aestivum L., 32 genotypes belonging to other species within Triticum genus and 3 genotypes from Aegilops genus. The results showed significant differences in the variability of the tested loci in bread wheat and related species. In the collection of bread wheat genotypes, 119 alleles were detected with the average number of 7.9 alleles per locus. In wild and cultivated related species 157 alleles were identified, with the average of 10.5 alleles per locus. All analysed parameters of micro­satellite loci variability (PIC value, gene diversity, heterozygosity, etc. indicated higher level of polymorphism in wild relatives than in the cultivated bread wheat. Analyses of individual genomes indicated that in the bread wheat genetic diversity of the B and D genomes was significantly reduced in relation to the A genome, while the differences in polymorphism between genomes in the wild relatives were significantly lower. The results showed that wild related species can be used as sources for new variability in wheat breeding. [Project of the Serbian Ministry of Education, Science and Technological Development

  10. Genetic determinants of obesity and related vascular diseases.

    Science.gov (United States)

    Winter, Yaroslav; Sankowski, Roman; Back, Tobias

    2013-01-01

    Obesity is one of the major risk factors of vascular diseases, and its prevalence is increasing worldwide. In the past decade, progress has been made in the understanding of genetic determinants of obesity and obesity-associated diseases. Genome-wide association studies identified a number of genetic variants associated with obesity. In addition to common variants, FTO and MC4R, new loci, such as TMEM18, KCTD15, GNPDA2, SH2B1, MTCH2, and NEGR1 have been detected. In the past years, abdominal obesity has been shown to be a more important vascular risk factor than the body mass index. In the context of vascular risk assessment, identification of genetic polymorphisms associated with accumulation of visceral fat is of special importance. Some polymorphisms associated with abdominal obesity, such as variants of gene encoding microsomal triglyceride transfer protein, have been already discovered. In this chapter, we provide a review of genetic determinants of obesity and discuss their role in obesity-related vascular diseases.

  11. Maternal genetic polymorphisms and unexplained recurrent miscarriage: a systematic review and meta-analysis.

    Science.gov (United States)

    Shi, X; Xie, X; Jia, Y; Li, S

    2017-02-01

    The roles of genetic polymorphisms in the pathogenesis of recurrent miscarriage (RM) have been intensively studied. However, the results of these studies were inconsistent, especially when conducted in different populations. Therefore, we performed the current study to systematically review the broad spectrum of genetic polymorphisms that were suspected to be involved in RM, and discussed potential genetic biomarkers of RM. Eligible articles were identified in PubMed, Medline, Embase and CNKI. Odd ratios (ORs) and 95% confidence intervals (CIs) were used to describe the strength of association, and a probability value (p value) of 0.05 or less was considered as statistically significant. A total of 425 eligible articles were included in this systematic review and 369 articles evaluating 124 polymorphisms of 73 genes were meta-analyzed. Significant associations were found between RM and 53 genetic polymorphisms of 37 genes. Our findings suggest that genetic variants of HLA-G, IFNG, TNF, IL-6, IL-10, FII, FV, FXIII, ITGB3, MTR, MTHFR, PAI-1, NOS3, KDR, TP53, VEGFA, CYP17, CYP1A1, CYP2D6, ANXA5, and XCI may serve as biological markers of RM. This study indicates that over-active immunological responses, thrombophilia, abnormal placental function, and disturbance of metabolic regulation may be implicated in the pathogenesis of RM. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Relation between ADIPOQ Gene Polymorphisms and Type 2 Diabetes

    OpenAIRE

    Zhi-Peng Li; Mei Zhang; Jie Gao; Guo-Yan Zhou; Shuang-Qing Li; Zhen-Mei An

    2015-01-01

    Objective: The manuscript investigates the relation between adiponectin gene (ADIPOQ) polymorphisms and type 2 diabetes mellitus (T2DM) in a Chinese population. Methods: We designed a case-control study involving 340 normal glucose tolerant (NGT) subjects and 340 type 2 diabetes patients. Three SNPs (rs182052, rs1501299, and rs7627128) were genotyped by TaqMan methods. Results: We found that rs7627128, rs1501299 and rs182052 were significantly associated with T2DM. Haplotypes analysis indicat...

  13. Combined effect of genetic polymorphisms in phase I and II biotransformation enzymes on head and neck cancer risk

    NARCIS (Netherlands)

    Lacko, M.; Voogd, A.C.; Roelofs, H.M.J.; Morsche, R.H.M. te; Ophuis, M.B.; Peters, W.H.M.; Manni, J.J.

    2013-01-01

    BACKGROUND: Combinations of genetic polymorphisms in biotransformation enzymes might modify the individual risk for head and neck cancer. METHODS: Blood from 432 patients with head and neck cancer and 437 controls was investigated for genetic polymorphisms in 9 different phase I and II biotransforma

  14. Random amplified polymorphic DNA and amplified fragment length polymorphism assessment of genetic variation in Nicaraguan populations of Pinus oocarpa.

    Science.gov (United States)

    Díaz, V; Muñiz, L M; Ferrer, E

    2001-11-01

    Pinus oocarpa is the most widely distributed pine species of Mexico and Central America. The natural populations of Nicaragua have been affected by extensive human activities. As a consequence, their size has been reduced, and there is a serious threat to the development of mature woodland. Knowledge of population structures and the genetic diversity of the species is required for the design of sustainable use and conservation strategies. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic variation among 10 populations from three geographical regions of Nicaragua. Both markers revealed high levels of diversity in these populations. G(ST) values and analyses of molecular variance (AMOVA) found that most variation was within populations but there is still a significant differentiation between populations indicating that the populations sampled cannot be considered a single panmictic unit. The partitions created by AMOVA also showed that there was little differentiation between populations of different regions, although cluster analyses based on RAPDs and AFLPs indicated a closer relationship among most of the populations from a same geographical region. Management of P. oocarpa in Nicaragua should be aimed to maintain the high degree of genetic variation within individual populations that is still observed even in some of these highly degraded populations.

  15. Monitoring low benzene exposure: comparative evaluation of urinary biomarkers, influence of cigarette smoking, and genetic polymorphisms.

    Science.gov (United States)

    Fustinoni, Silvia; Consonni, Dario; Campo, Laura; Buratti, Marina; Colombi, Antonio; Pesatori, Angela C; Bonzini, Matteo; Bertazzi, Pier A; Foà, Vito; Garte, Seymour; Farmer, Peter B; Levy, Leonard S; Pala, Mauro; Valerio, Federico; Fontana, Vincenzo; Desideri, Arianna; Merlo, Domenico F

    2005-09-01

    Benzene is a human carcinogen and an ubiquitous environmental pollutant. Identification of specific and sensitive biological markers is critical for the definition of exposure to low benzene level and the evaluation of the health risk posed by this exposure. This investigation compared urinary trans,trans-muconic acid (t,t-MA), S-phenylmercapturic acid, and benzene (U-benzene) as biomarkers to assess benzene exposure and evaluated the influence of smoking and the genetic polymorphisms CYP2E1 (RsaI and DraI) and NADPH quinone oxidoreductase-1 on these indices. Gas station attendants, urban policemen, bus drivers, and two groups of controls were studied (415 subjects). Median benzene exposure was 61, 22, 21, 9 and 6 microg/m(3), respectively, with higher levels in workers than in controls. U-benzene, but not t,t-MA and S-phenylmercapturic acid, showed an exposure-related increase. All the biomarkers were strongly influenced by cigarette smoking, with values up to 8-fold higher in smokers compared with nonsmokers. Significant correlations of the biomarkers with each other and with urinary cotinine were found. A possible influence of genetic polymorphism of CYP2E1 (RsaI and/or DraI) on t,t-MA and U-benzene in subjects with a variant allele was found. Multiple linear regression analysis correlated the urinary markers with exposure, smoking status, and CYP2E1 (RsaI; R(2) up to 0.55 for U-benzene). In conclusion, in the range of investigated benzene levels (<478 micro/m(3) or <0.15 ppm), smoking may be regarded as the major source of benzene intake; among the study indices, U-benzene is the marker of choice for biomonitoring low-level occupational and environmental benzene exposure.

  16. Genetic Polymorphisms Associated to Folate Transport as Predictors of Increased Risk for Acute Lymphoblastic Leukemia in Mexican Children

    Science.gov (United States)

    Zaruma-Torres, Fausto; Lares-Asseff, Ismael; Lima, Aurea; Reyes-Espinoza, Aarón; Loera-Castañeda, Verónica; Sosa-Macías, Martha; Galaviz-Hernández, Carlos; Arias-Peláez, María C.; Reyes-López, Miguel A.; Quiñones, Luis A.

    2016-01-01

    Acute lymphoblastic leukemia (ALL) is a frequent neoplasia occurring in children. The most commonly used drug for the treatment of ALL is methotrexate (MTX), an anti-folate agent. Previous studies suggest that folate transporters play a role in ALL prognosis and that genetic polymorphism of genes encoding folate transporters may increase the risk of ALL. Therefore, the main goal of this study was to determine the associations among six genetic polymorphisms in four genes related with the folate transporter pathway to determine a relationship with the occurrence of ALL in Mexican children. A case-control study was performed in 73 ALL children and 133 healthy children from Northern and Northwestern Mexico. COL18A1 (rs2274808), SLC19A1 (rs2838956), ABCB1 (rs1045642 and rs1128503), and ABCC5 (rs9838667 and rs3792585). Polymorphisms were assayed through qPCR. Our results showed an increased ALL risk in children carrying CT genotype (OR = 2.55, CI 95% 1.11–5.83, p = 0.0001) and TT genotype (OR = 21.05, CI 95% 5.62–78.87, p < 0.0001) of COL18A1 rs2274808; in SLC19A1 rs2838956 AG carriers (OR = 44.69, CI 95% 10.42–191.63, p = 0.0001); in ABCB1 rs1045642 TT carriers (OR = 13.76, CI 95% 5.94–31.88, p = 0.0001); in ABCC5 rs9838667 AC carriers (OR = 2.61, CI 95% 1.05–6.48, p < 0.05); and in ABCC5 rs3792585 CC carriers (OR = 9.99, CI 95% 3.19–31.28, p = 0.004). Moreover, several combinations of genetic polymorphisms were found to be significantly associated with a risk for ALL. Finally, two combinations of ABCC5 polymorphisms resulted in protection from this neoplasia. In conclusion, certain genetic polymorphisms related to the folate transport pathway, particularly COL18A1 rs2274808, SLC19A1 rs2838956, ABCB1 rs1045642, and ABCC5 rs3792585, were associated with an increased risk for ALL in Mexican children. PMID:27547186

  17. Genetic polymorphisms associated to folate transport as predictors of increased risk for acute lymphoblastic leukemia in Mexican children

    Directory of Open Access Journals (Sweden)

    Fausto Zaruma-Torres

    2016-08-01

    Full Text Available Acute lymphoblastic leukemia (ALL is a frequent neoplasia occurring in children. The most commonly used drug for the treatment of ALL is methotrexate (MTX, an anti-folate agent. Previous studies suggest that folate transporters play a role in ALL prognosis and that genetic polymorphism of genes encoding folate transporters may increase the risk of ALL. Therefore, the main goal of this study was to determine the associations among six genetic polymorphisms in four genes related with the folate transporter pathway to determine a relationship with the occurrence of ALL in Mexican children.A case-control study was performed in 73 ALL children and 133 healthy children from Northern and Northwestern Mexico. COL18A1 (rs2274808, SLC19A1 (rs2838956, ABCB1 (rs1045642 and rs1128503 and ABCC5 (rs9838667 and rs3792585. polymorphisms were assayed through qPCR.Our results showed an increased ALL risk in children carrying CT genotype (OR=2.55, CI 95% 1.11-5.83, p=0.0001 and TT genotype (OR=21.05, CI 95% 5.62-78.87, p<0.0001 of COL18A1 rs2274808; in SLC19A1 rs2838956 AG carriers (OR=44.69, CI 95% 10.42-191.63, p=0.0001; in ABCB1 rs1045642 TT carriers (OR=13.76, CI 95% 5.94-31.88, p=0.0001; in ABCC5 rs9838667 AC carriers (OR=2.61, CI 95% 1.05-6.48, p<0.05; and in ABCC5 rs3792585 CC carriers (OR=9.99, CI 95% 3.19-31.28, p=0.004. Moreover, several combinations of genetic polymorphisms were found to be significantly associated with a risk for ALL. Finally, two combinations of ABCC5 polymorphisms resulted in protection from this neoplasia.In conclusion, certain genetic polymorphisms related to the folate transport pathway, particularly COL18A1 rs2274808, SLC19A1 rs2838956, ABCB1 rs1045642 and ABCC5 rs3792585, were associated with an increased risk for ALL in Mexican children.

  18. Gene polymorphisms related to angiogenesis, inflammation and thrombosis that influence risk for oral cancer.

    Science.gov (United States)

    Vairaktaris, E; Serefoglou, Z; Avgoustidis, D; Yapijakis, C; Critselis, E; Vylliotis, A; Spyridonidou, S; Derka, S; Vassiliou, S; Nkenke, E; Patsouris, E

    2009-03-01

    Genetic association studies have implicated functional DNA polymorphisms in genes encoding factors related to angiogenesis, inflammation and thrombosis with increased risk for oral squamous cell carcinoma (OSCC). This study examines possible interactions between nine such genotype polymorphisms and their combinatory effect in assessing the OSCC risk in a European population. OSCC cases (N=162) and healthy controls (N=168) of comparable age, gender, and ethnicity (Greeks and Germans) were studied. Multivariate logistic regression models were constructed in order to assess the contribution of homozygous or heterozygous variant genotypes of polymorphisms MMP-1 (-1607 1G/2G), MMP-3 (-1171 5A/6A), MMP-9 (-1562C/T), TIMP-2 (-418C/G), VEGF (+936C/T), GPI-alpha (+807C/T), PAI-1 (4G/5G), ACE (intron 16D/I) and TAFI (+325C/T) upon overall, early and advanced stages of OSCC. Four out of nine polymorphisms affecting PAI-1, MMP-9, TIMP-2 and ACE expression contributed significantly in OSCC prediction in the various logistic regression models. Based on these findings and previous reports, possible interactions of the implicated factors leading to OSCC development, as well as an algorithm of risk estimation are discussed.

  19. Relationship between genetic polymorphisms in the DRD5 gene and paranoid schizophrenia in northern Han Chinese.

    Science.gov (United States)

    Zhao, Y; Ding, M; Pang, H; Xu, X M; Wang, B J

    2014-03-12

    Dopamine (DA) has been implicated in the pathophysiol-ogy of several psychiatric disorders, including schizophrenia. Thus, genes related to the dopaminergic (DAergic) system are good candidate genes for schizophrenia. One of receptors of the DA receptor system is dopa-mine receptor 5 (DRD5). Single nucleotide polymorphisms (SNPs) in the regulatory regions of DRD5 gene may affect gene expression, influence biosynthesis of DA and underlie various neuropsychiatric disorders re-lated to DA dysfunction. The present study explored the association of SNPs within the DRD5 gene with paranoid schizophrenia in Han Chinese. A total of 176 patients with schizophrenia and 206 healthy controls were genotyped for four DRD5 SNPs (rs77434921, rs2076907, rs6283, and rs1800762). Significant group differences were observed in the allele and genotype frequencies of rs77434921 and rs1800762 and in the frequen-cies of GC haplotypes corresponding to rs77434921-rs1800762. Our find-ings suggest that common genetic variations of DRD5 are likely to con-tribute to genetic susceptibility to paranoid schizophrenia in Han Chinese. Further studies in larger samples are needed to replicate this association.

  20. Morphological and sequence-related amplified polymorphism-based molecular diversity of local and exotic wheat genotypes.

    Science.gov (United States)

    Abdelkhalik, S M; Salem, A K M; Abdelaziz, A R; Ammar, M H

    2016-04-28

    Assessing genetic diversity is a prerequisite for the genetic improvement of wheat. Molecular markers offer accurate and reproducible means for assessing genetic diversity. Field performance and sequence-related amplified polymorphism (SRAP)-based assessment of molecular diversity was carried out on a set of 10 local and introduced bread wheat (Triticum sativum L.) genotypes grown in the middle arid region of Saudi Arabia. The results revealed highly significant differences among the studied phenological traits and revealed a significant amount of genetic diversity across the tested genotypes. The overall performance revealed the superiority of KSU 102 in terms of yield and its components, with a yield potential of 8.7 tons/ha. Highly significant and positive correlations were observed among grain yield and biological yield, and also, spike length and spike weight. Thirteen SRAP primer combinations successfully amplified 954 fragments. The total number of genetic loci analyzed was 312. The overall polymorphism ratio was 99.67%, ranging from 98 to 100%. The polymorphic information content values ranged from 0.67 for ME11 x EM5 to 0.97 for ME9 x EM4 and ME11 x EM6, respectively. The wheat genotypes were clustered based on their genetic constitution and origin. The results demonstrate the power of SRAP primers for detecting molecular diversity and for varietal discrimination. The results show that high levels of genetic diversity exist, and suggest the potential of the tested materials for wheat crop improvement in the arid central region of Saudi Arabia.

  1. Functional characterization of genetic polymorphisms identified in the promoter region of the bovine PEPS gene.

    Science.gov (United States)

    Ju, Zhihua; Zheng, Xue; Huang, Jinming; Qi, Chao; Zhang, Yan; Li, Jianbin; Zhong, Jifeng; Wang, Changfa

    2012-06-01

    Peptidase S (PEPS) is a metallopeptidase that cleaves N-terminal residues from proteins and peptides. PEPS is used as a cell maintenance enzyme with critical roles in peptide turnover. The promoter region located upstream of the initiation site plays an important role in regulating gene expression. Polymorphism in the promoter region can alter gene expression and lead to biological changes. In the current study, polymorphisms in the promoter region of the PEPS gene were investigated. Polymerase chain reaction (PCR)-restriction fragment length polymorphism and DNA sequencing methods were used to screen sequence variations in the promoter region of DNA samples from 743 Chinese Holstein cattle. Two polymorphisms (g. -534 T>C and g. -2545 G>A) were identified and eight haplotypes were classified by haplotype analysis. The two genetic polymorphisms and haplotypes were associated with fat percentage and somatic cell score in Chinese Holstein cattle. The results of real-time PCR showed that cow kidneys exhibit the highest PEPS expression level. Moreover, bioinformatics analysis predicted that the single-nucleotide polymorphism g. -534 T>C is located in the core promoter region and in the transcription factor binding sites. The promoter activities of the polymorphism of -543 T>C were measured by luciferase assay in the human kidney epithelial cell line 293T. Transcriptional activity is significantly lower in cell lines transfected with the reporter construct containing 2.5 kb upstream fragments with -543 C than in those with wild-type -543 T. The results indicated that genetic variation at locus -543 influences PEPS promoter activity. The genetic variation in the promoter region of PEPS gene may regulate PEPS gene transcription and might have consequences at a regulatory level.

  2. Genetic Association between Akt1 Polymorphisms and Alzheimer's Disease in a Japanese Population

    Directory of Open Access Journals (Sweden)

    Nobuto Shibata

    2011-01-01

    Full Text Available A recent paper reported that Aβ oligomer causes neuronal cell death through the phosphatidylinositol-3-OH kinase (PI3K-Akt-mTOR signaling pathway. Intraneuronal Aβ, a main pathological finding of Alzheimer's disease (AD, is also known as inhibiting activation of Akt. This study aims to investigate whether single nucleotide polymorphisms (SNPs of the Akt1 gene are associated with AD. SNPs genotyped using TaqMan technology was analyzed using a case-control study design. Our case-control dataset consisted of 180 AD patients and 130 age-matched controls. Although two SNPs showed superficial positive, Hardy-Weinberg equilibrium (HWE tests, and linkage disequilibrium (LD analyses suggested that genetic regions of the gene are highly polymorphic. We failed to detect any synergetic association among Akt1 polymorphisms, Apolipoprotein E (APO E, and AD. Further genetic studies are needed to clarify the relationship between the Akt1 and AD.

  3. Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.

    Science.gov (United States)

    Mattagajasingh, Ilwola; Mukherjee, Arup Kumar; Das, Premananda

    2006-01-01

    Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.

  4. Influence of ethnicity on the distribution of genetic polymorphisms associated with risk of chronic liver disease in South American populations.

    Science.gov (United States)

    Pontoriero, Ana Cecilia; Trinks, Julieta; Hulaniuk, María Laura; Caputo, Mariela; Fortuny, Lisandro; Pratx, Leandro Burgos; Frías, Analía; Torres, Oscar; Nuñez, Félix; Gadano, Adrián; Argibay, Pablo; Corach, Daniel; Flichman, Diego

    2015-07-29

    The global burden of chronic liver disease is rising. Besides environmental, behavioral, viral and metabolic factors, genetic polymorphisms in patatin-like phospholipase-3 (PNPLA3) and vitamin D receptor (VDR) genes have been related to the development of chronic liver disease and progression towards liver cancer. Although their prevalence differs remarkably among ethnic groups, the frequency of these polymorphisms in South American populations -whose genetic background is highly admixed- has been poorly studied. Hence, the aim of this study was to characterize polymorphisms related to chronic liver disease and their association with the genetic ancestry of South American populations. DNA samples from 258 healthy unrelated male volunteers were analyzed. The frequencies of G and C alleles of rs738409 polymorphism (PNPLA3 gene) were 74 % and 26 %, respectively; whereas the bAt (CCA) haplotype (VDR gene) was observed in 32.5 % of the samples. The GG genotype of PNPLA3 rs738409 and the bAt (CCA) haplotype -associated with an increased risk of chronic liver disease and progression towards liver cancer- were significantly more frequent among samples exhibiting maternal and paternal Native American haplogroups (63.7 % and 64.6 %), intermediate among admixed samples (45.1 % and 44.9 %; p = 0.03) and the lowest for Non-native American ancestry (30.1 % and 29.6 %; p = 0.001 and p = 0.0008). These results suggest that individuals with Native American ancestry might have a high risk of chronic liver disorders and cancer. Furthermore, these data not only support the molecular evaluation of ancestry in multi-ethnic population studies, but also suggest that the characterization of these variants in South American populations may be useful for establishing public health policies aimed at high risk ethnic communities.

  5. New exome data question the pathogenicity of genetic variants previously associated with catecholaminergic polymorphic ventricular tachycardia

    DEFF Research Database (Denmark)

    Jabbari, Javad; Jabbari, Reza; Nielsen, Morten Wagner

    2013-01-01

    Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a lethal, rare hereditary disease with an estimated prevalence of 1:10 000. The genetic variants that cause CPVT are usually highly penetrant. To date, about 189 variants in 5 genes (RYR2, CASQ2, CALM1, TRND, and KCNJ2) have been...

  6. Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Atabay, H.I.; Amisu, K.O.

    2004-01-01

    Aims: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. Methods and Results: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and Nor...

  7. No interactions between genetic polymorphisms and stressful life events on outcome of antidepressant treatment

    DEFF Research Database (Denmark)

    Bukh, Jens Drachmann; Bock, Camilla; Vinberg, Maj;

    2009-01-01

    in the genes encoding the serotonin transporter, brain derived neurotrophic factor, catechol-O-methyltransferase, angiotensin converting enzyme, tryptophan hydroxylase, and the serotonin receptors 1A, 2A, and 2C. We found no evidence that the effects of the genetic polymorphisms on treatment outcome were...

  8. Genetic diversity among Bacillus anthracis, Bacillus cereus and Bacillus thuringiensis strains using repetitive element polymorphism-PCR.

    Science.gov (United States)

    Brumlik, Michael J; Bielawska-Drózd, Agata; Zakowska, Dorota; Liang, Xudong; Spalletta, Ronald A; Patra, Guy; Delvecchio, Vito G

    2004-01-01

    Repetitive element polymorphism-PCR (REP-PCR) is one of the tools that has been used to elucidate genetic diversity of related microorganisms. Using the MB1 primer, REP-PCR fingerprints from 110 Bacillus strains within the "B. cereus group" have identified eighteen distinct categories, while other more distantly related bacterial species fell within six additional categories. All Bacillus anthracis strains tested were found to be monomorphic by fluorophore-enhanced REP-PCR (FERP) fingerprinting using the MB1 primer. In contrast, other non- B. anthracis isolates displayed a high degree of polymorphism. Dendrogramic analysis revealed that the non- B. anthracis strains possessing the Ba813 chromosomal marker were divided into two clusters. One of the clusters shared identity with the B. cereus strains examined.

  9. Impact of genetic polymorphisms on paediatric atopic dermatitis.

    Science.gov (United States)

    Esposito, Susanna; Patria, Maria Francesca; Spena, Silvia; Codecà, Claudio; Tagliabue, Claudia; Zampiero, Alberto; Lelii, Mara; Montinaro, Valentina; Pelucchi, Claudio; Principi, Nicola

    2015-09-01

    In order to investigate whether polymorphisms of genes encoding some factors of innate and adaptive immunity play a role in the development of, or protection against atopic dermatitis (AD) and condition its severity, we genotyped 33 candidate genes and 47 single nucleotide polymorphisms (SNPs) using Custom TaqMan Array Microfluidic Cards and an ABI 7900HT analyser (Applied Biosystems, Foster City, CA, USA). The study involved 104 children with AD (29 with mild-to-moderate and 75 with severe disease; 42 girls; mean age ± SD, 5.8 ± 3.3 years) and 119 healthy controls (49 girls; mean age, 4.8 ± 3.0 years). IL10-rs1800872T, TG and MBL2-rs500737AG were all significantly more frequent among the children with AD (P = 0.015, P = 0.004 and P = 0.030), whereas IL10-rs1800896C and TC were more frequent in those without AD (P = 0.028 and P = 0.032). The VEGFA-rs2146326A and CTLA4-rs3087243AG SNPs were significantly more frequent in the children with mild/moderate AD than in those with severe AD (P = 0.048 andP = 0.036). IL10-rs1800872T and TG were significantly more frequent in the children with AD and other allergic diseases than in the controls (P = 0.014 and P = 0.007), whereas IL10-rs1800896TC and C were more frequent in the controls than in the children with AD and other allergic diseases (P = 0.0055 and P = 0.0034). These findings show that some of the polymorphisms involved in the immune response are also involved in some aspects of the development and course of AD and, although not conclusive, support the immunological hypothesis of the origin of the inflammatory lesions.

  10. DNA Repair Gene Polymorphisms in Relation to Non-Small Cell Lung Cancer Survival

    Directory of Open Access Journals (Sweden)

    Yuliang Su

    2015-07-01

    Full Text Available Background: Single nucleotide polymorphisms (SNPs in the DNA repair genes are suspected to be related to the survival of lung cancer patients due to their possible influence on DNA repair capacity (DRC. However, the study results are inconsistent. Methods: A follow-up study of 610 non-small cell lung cancer (NSCLC patients was conducted to investigate genetic polymorphisms associated with the DNA repair genes in relation to NSCLC survival; 6 SNPs were genotyped, including XRCC1 (rs25487 G>A, hOGG1 (rs1052133 C>G, MUTYH (rs3219489 G>C, XPA (rs1800975 G>A, ERCC2 (rs1799793 G>A and XRCC3 (rs861539 C>T. Kaplan-Meier survival curve and Cox proportional hazards regression analyses were performed. SNP-SNP interaction was also examined using the survival tree analysis. Results: Advanced disease stage and older age at diagnosis were associated with poor prognosis of NSCLC. Patients with the variant ‘G' allele of hOGG1 rs1052133 had poor overall survival compared with those with the homozygous wild ‘CC' genotype, especially in female patients, adenocarcinoma histology, early stage, light smokers and without family history of cancer. For never smoking female lung cancer patients, individuals carrying homozygous variant ‘AA' genotype of XPA had shorter survival time compared to those with wild ‘G' alleles. Furthermore, females carrying homozygous variant XPA and hOGG1 genotypes simultaneously had 2.78-fold increased risk for death. Among all 6 polymorphisms, the homozygous variant ‘AA' of XPA carriers had poor prognosis compared to the carriers of wild ‘G' alleles of XPA together with other base excision repair (BER polymorphisms. Conclusions: Besides disease stage and age, the study found DNA repair gene polymorphisms were associated with lung cancer survival.

  11. Polymorphic microsatellite markers for genetic studies of African ...

    African Journals Online (AJOL)

    Administrator

    2011-09-26

    Sep 26, 2011 ... often defined by high diversity of wildlife and seasonal ungulates migrations. The ecosystem ..... The molecular toolbox: genetic techniques in wildlife ecology and management. J. ... for European roe deer. Mol. Ecol. Notes, 3: ...

  12. Genetic characterization of Lithuanian honeybee lines based on ISSR polymorphism

    OpenAIRE

    Ceksteryte, Violeta; Paplauskiene, Vanda; Tamasauskiene, Diana; Pasakinskiene, Izolda; Mazeikiene, Ingrida

    2012-01-01

    International audience; This study presents the first results from the selection and evaluation of inter-simple sequence repeat markers for the genetic assessment of honeybee lines developed in Lithuania and introduced subspecies. Two Lithuania-bred lines of Apis mellifera carnica were compared to those introduced from Czech Republic and Slovenia and also to a subspecies introduced from the Caucasus (Apis mellifera caucasica) and local Buckfast hybrids. The genetic constitution was assayed wi...

  13. Glutathione S-Transferase P1 (GSTP1 gene polymorphism increases age-related susceptibility to hepatocellular carcinoma

    Directory of Open Access Journals (Sweden)

    Kuo Wu-Hsien

    2010-03-01

    Full Text Available Abstract Background Hepatocellular carcinoma (HCC is one of the most frequent malignant neoplasms in the world. Genetic polymorphism has been reported to be a factor increasing the risk of HCC. Phase II enzymes such as glutathione s-transferases (GSTP1, GSTA1 play important roles in protecting cells against damage induced by carcinogens. The aim of this study was to estimate the relationship of the GSTP1 and GSTA1 gene polymorphisms to HCC risk and clinico-pathological status. Methods Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP was used to measure GSTP1 (A→G and GSTA1 (C→T gene polymorphisms in 386 healthy controls and 177 patients with HCC. Results Neither gene polymorphism was associated with the clinico-pathological status of HCC and serum expression of liver-related clinico-pathological markers. No association between the GSTA1 gene polymorphism and HCC susceptibility was found. However, in the younger group, aged ≤ 57 years, individuals with AG or GG alleles of GSTP1 had a 2.18-fold (95%CI = 1.09-4.36; p = 0.02 and 5.64-fold (95%CI = 1.02-31.18; p = 0.04 risk, respectively, of developing HCC compared to individuals with AA alleles, after adjusting for other confounders. Conclusion AG and GG alleles of GSTP1 gene polymorphisms may be considered as factors increasing the susceptibility to and risk of HCC in Taiwanese aged ≤ 57 years.

  14. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  15. drs (Distantly Related sic) Gene Polymorphisms among emm12-Type Streptococcus pyogenes Isolates

    Science.gov (United States)

    Brandt, Claudia M.; Haase, Gerhard; Spellerberg, Barbara; Holland, Regina; Lütticken, Rudolf

    2003-01-01

    Twenty-eight emm12-type Streptococcus pyogenes isolates from patients with invasive and noninvasive infections or from asymptomatic carriers were genetically typed. Sequencing of drs (distantly related sic [streptococcal inhibitor of complement]) genes identified two novel alleles and revealed a polymorphism for drs similar to that of sic. No association was observed between the five different drs alleles and the five restriction patterns of the vir regulon for the isolates studied. These data suggest that drs sequencing may be useful for further differentiation of S. pyogenes isolates with emm12 and identical vir regulon restriction patterns. PMID:12682191

  16. Genetic Polymorphisms Analysis of Pharmacogenomic VIP Variants in Miao Ethnic Group of Southwest China.

    Science.gov (United States)

    Jin, Tianbo; Aikemu, Ainiwaer; Zhang, Mingxi; Geng, Tingting; Feng, Tian; Kang, Longli; Luo, Man Lin

    2015-12-03

    BACKGROUND Genetic polymorphisms have a potential clinical role in determining both inter-individual and inter-ethnic differences in drug efficacy, but we have not found any pharmacogenomics information regarding minorities, such as the Miao ethnic group. Our study aimed to screen numbers of the Miao ethnic group for genotype frequencies of VIP variants and to determine differences between the Miao and other human populations worldwide. MATERIAL AND METHODS In this study, we genotyped 66 Very Important Pharmacogene (VIP) variants selected from PharmGKB in 98 unrelated, healthy Miao individuals from the Guizhou province and compared our data with 12 other populations, including 11 populations from the HapMap data set and Xi'an Han Chinese. RESULTS Using the χ2 test, we found that the allele frequencies of the VDR rs1544410 and VKORC1 (rs9934438) variants in the Miao population are quite different from that in other ethnic groups. Furthermore, we found that genotype frequencies of rs1801133 (MTHFR) in the 13 selected populations are significantly different. Population structure and F-statistics (Fst) analysis show that the genetic background of the Miao is relatively close to that of Chinese in metropolitan Denver, CO, USA (CHD). CONCLUSIONS Our results help complete the information provided by the pharmacogenomics database of the Miao ethnic group and provide a theoretical basis for safer drug administration, which may be useful for diagnosing and treating diseases in this population.

  17. The Analysis of Genetic Polymorphism. The Relationship between Interleukin – 4 Polymorphisms and Intraepithelial Cervical Neoplasia

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    Florin STAMATIAN

    2010-09-01

    Full Text Available Objectives: Interleukin 4 plays a critical role in T helper 2 responses to HPV infection and angiogenesis. The present study aim to study the association between the IL4 promoter polymorphism – 590 C>T, respectively VNTR intron 2 polymorphism and cervical intraepithelial neoplasia. Material and method: We have realized a prospective case controls study that included 128 cases of intraepithelial neoplasia positive for HPV HR testing and 111 controls negative for intraepithelial lesion and also negative for HPV HR. Clinical examination was performed on each patient; blood and cervical sample were obtained. Cervical probes were analyzed regarding cytology and HPV HR testing. From peripheral blood DNA sample was obtain followed by genotype analysis for IL4 -590 C>T using PCR RFLP, respectively IL4 70 bp VNTR determined by PCR. Results: The absolute frequency of genotypes for IL4 -590 C>T was T/T-5, C/T-42, C/C-81 in the cases group respectively T/T-2, C/T-32, C/C-77 in the control group. The chi-square test had a value of 0.983 (p=0.321 while considering the presence of a minimum one single variant allele as a risk factor for cervical cancer, respectively 0.926 (p=0.336 for homozygous variant genotype. Odds ratio was 0.761 (95%CI [0.443-1.306] while considering C/T+T/T respectively 2R/3R, 2R/2R as a risk factor, and 0.451 (95%CI 95% [0.086-2.374] - TT respectively 2R/2R as a risk factor. Conclusion: No linear statistical significant association has been found between IL4 polymorphism and cervical neoplasia (p = 0.322.

  18. Application of restriction site amplified polymorphism (RSAP) to genetic diversity in Saccharina japonica

    Institute of Scientific and Technical Information of China (English)

    ZHAO Cui; LIU Cui; LI Wei; CHI Shan; FENG Rongfang; LIU Tao

    2013-01-01

    Restriction site amplified polymorphism (RSAP) was used,for the first time,to analyze the genetic structure and diversity of four,mainly cultivated,varieties of the brown alga,Saccharinajaponica.Eighty-eight samples from varieties "Rongfu","Fujian","Ailunwan" and "Shengchanzhong" were used for the genetic analyses.One hundred and ninety-eight bands were obtained using eight combinations of primers.One hundred and ninety-one (96.46%) were polymorphic bands.Nei's genetic diversity was 0.360,and the coefficient of genetic differentiation was 0.357.No inbreeding-type recession was found in the four brown alga varieties and the results of the "Ailunwan" variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program.Genetic diversity and cluster analyses results were consistent with these genetic relationships.The results show the RSAP method is suitable for genetic analysis.Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.

  19. Genetic polymorphism of β-fibrinogen gene-455G/A can contribute to the risk of ischemic stroke.

    Science.gov (United States)

    Gu, Lian; Wu, Guangliang; Su, Li; Yan, Yan; Long, Jianxiong; Tan, Jinjing; Liang, Baoyun; Guo, Xiaojing; Huang, Guihua

    2014-02-01

    Many studies have investigated the association between the β-fibrinogen gene-455G/A (FGβ-455G/A) polymorphism and the risk of ischemic stroke. However, these evidences were inadequate to provide stronger conclusions because most studies were generally small. To shed light on these inconclusive findings, we conducted a large sample size meta-analysis of studies relating to the FGβ-455G/A polymorphism and the risk of ischemic stroke. Odds ratios with a 95 % confidence interval were used to investigate the association between FGβ-455G/A polymorphism and ischemic stroke. Publication bias was tested by Egger's test and funnel plot. Inconsistency index and Cochran's Q statistic were used to check heterogeneity. Cumulative and recursive cumulative meta-analyses were performed to provide a framework for updating a genetic effect from all of the included studies. Twenty-six independent publications with 4,070 cases and 4,649 controls were included in this meta-analysis. Results showed that the β-fibrinogen-455G/A polymorphism was significantly associated with the risk of ischemic stroke. The FGβ-455G/A polymorphism was found to be a risk factor for ischemic stroke in Asians and adults, while association was not observed for Caucasians and juveniles based on the small size and it may be necessary to conduct larger studies on them to investigate the association in the future. The cumulative meta-analysis indicated a decline from 1998 to 2003, and the results remained stable during the period 2004-2012. The results indicate that FGβ-455G/A polymorphism may be a susceptible predictor of ischemic stroke. More studies are needed to elucidate the relationship further.

  20. Are "functionally related polymorphisms" of renin-angiotensin-aldosterone system gene polymorphisms associated with hypertension?

    NARCIS (Netherlands)

    Hahntow, I.N.; Mairuhu, G.; Valkengoed, I.G.M.; Koopmans, R.P.; Michel, M.C.

    2010-01-01

    ABSTRACT: BACKGROUND: Genotype-phenotype association studies are typically based upon polymorphisms or haplotypes comprised of multiple polymorphisms within a single gene. It has been proposed that combinations of polymorphisms in distinct genes, which functionally impact the same phenotype, may hav

  1. Genetic polymorphisms in biotransformation enzymes for benzo[a]pyrene and related levels of benzo[a]pyrene-7,8-diol-9,10-epoxide-DNA adducts in Goeckerman therapy.

    Science.gov (United States)

    Beranek, Martin; Fiala, Zdenek; Kremlacek, Jan; Andrys, Ctirad; Hamakova, Kvetoslava; Chmelarova, Marcela; Palicka, Vladimir; Borska, Lenka

    2016-07-25

    Goeckerman therapy (GT) for psoriasis combines the therapeutic effect of crude coal tar (CCT) and ultraviolet radiation (UVR). CCT contains polycyclic aromatic hydrocarbons, some of which can form DNA adducts that may induce mutations and contribute to carcinogenesis. The aim of our work was to evaluate the relationship between concentrations of benzo[a]pyrene-7,8-diol-9,10-epoxide-DNA adducts (BPDE-DNA adducts) and rs4646903 (CYP1A1 gene), rs1048943 (CYP1A1), rs1056836 (CYP1B1), rs1051740 (EPHX1), rs2234922 (EPHX1) and rs8175347 (UGT1A1) polymorphic sites, and GSTM1 null polymorphism in 46 patients with chronic stable plaque psoriasis who underwent GT. The level of BPDE-DNA adducts was determined using the OxiSelect BPDE-DNA Adduct ELISA Kit. Polymerase chain reaction (PCR) and restriction fragment length polymorphism analysis (rs4646903, rs1048943, rs1051740, and rs2234922), fragment analysis (rs8175347), real-time PCR (rs1056836), and digital droplet PCR polymorphism (GSTM1) were used. CYP1B1*1/*1 wild-type subjects and CYP1B1*3/*1 heterozygotes for rs1056836 formed significantly higher amounts of BPDE-DNA adducts than CYP1B1*3/*3 homozygotes (p=0.031 and p=0.005, respectively). Regarding rs1051740, individuals with EPHX1*3/*1 heterozygosity revealed fewer adducts than EPHX1*1/*1 wild-type subjects (p=0.026). Our data suggest that CYP1B1/EPHX1 genotyping could help to predict the risk of DNA damage and to optimize doses of coal tar and UVR exposure in psoriatic patients in whom GT was applied.

  2. Genetic studies of the Macushi and Wapishana indians. I. Rare genetic variants and a private polymorphism of esterase A

    Energy Technology Data Exchange (ETDEWEB)

    Neel, J.V. (Univ. of Michigan, Ann Arbor); Tanis, R.J.; Migliazza, E.C.; Spielman, R.S.; Salzano, F.; Oliver, W.J.; Morrow, M.; Bachofer, S.

    1977-01-01

    Blood samples from 509 Macushi and 623 Wapishana Amerindians of Northern Brazil and Southern Guyana have been analyzed with reference to the occurrence of rare variants and genetic polymorphisms of the following 25 systems: Erythrocyte enzymes: acid phosphatase-1, adenosine deaminase, adenylate kinase-k, carbonic anhydrase-1, carbonic anhydrase-2, esterase A/sub 1/,/sub 2/,/sub 3/, esterase D, galactose-1-phosphate uridyltransferase, isocitrate dehydrogenase, lactate dehydrogenase, malate dehydrogenase, nucleoside phosphorylase, peptidase A, peptidase B, phosphoglucomutase 1, phosphoglucomutase 2, phosphogluconate dehydrogenase, phosphohexoseisomerase, trisephosphate isomerase and Serum proteins: albumin, ceruloplasmin, haptoglobin, hemoglobin A, hemoglobin A/sub 2/ and transferrin. Fifteen different rare variants were detected, involving 11 of these systems. In addition, a previously undescribed variant of ESA/sub 1/,/sub 2/,/sub 3/ which achieves polymorphic proportions in both these tribes is described. Excluding this variant, the frequency of rare variants is 1.1/1000 in 12,510 determinations in the Macushi and 4.7/1000 in 15,396 determinations in the Wapishana. The ESA/sub 1/,/sub 2/,/sub 3/ polymorphism was not observed in 382 Makiritare, 232 Yanomama, 146 Piaroa, 404 Cayapo, 190 Kraho and 112 Moro. Irregularities in the intratribal distribution of this polymorphism in the Macushi and Wapishana render a decision as to the tribe of origin impossible at present. Gene frequencies are also given for previously described polymorphisms of 5 systems: haptoglobin, phosphoglucomutase 1, erythrocyte acid phosphatase, esterase D, and galactose-1-phosphate-uridyl-transferase.

  3. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    Science.gov (United States)

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  4. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  5. Exploiting the extraordinary genetic polymorphism of ciona for developmental genetics with whole genome sequencing.

    Science.gov (United States)

    Abdul-Wajid, Sarah; Veeman, Michael T; Chiba, Shota; Turner, Thomas L; Smith, William C

    2014-05-01

    Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca(2+) channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.

  6. ORAI1 genetic polymorphisms associated with the susceptibility of atopic dermatitis in Japanese and Taiwanese populations.

    Science.gov (United States)

    Chang, Wei-Chiao; Lee, Chih-Hung; Hirota, Tomomitsu; Wang, Li-Fang; Doi, Satoru; Miyatake, Akihiko; Enomoto, Tadao; Tomita, Kaori; Sakashita, Masafumi; Yamada, Takechiyo; Fujieda, Shigeharu; Ebe, Koji; Saeki, Hidehisa; Takeuchi, Satoshi; Furue, Masutaka; Chen, Wei-Chiao; Chiu, Yi-Ching; Chang, Wei Pin; Hong, Chien-Hui; Hsi, Edward; Juo, Suh-Hang Hank; Yu, Hsin-Su; Nakamura, Yusuke; Tamari, Mayumi

    2012-01-01

    Atopic dermatitis is a chronic inflammatory skin disease. Multiple genetic and environmental factors are thought to be responsible for susceptibility to AD. In this study, we collected 2,478 DNA samples including 209 AD patients and 729 control subjects from Taiwanese population and 513 AD patients and 1027 control subject from Japanese population for sequencing and genotyping ORAI1. A total of 14 genetic variants including 3 novel single-nucleotide polymorphisms (SNPs) in the ORAI1 gene were identified. Our results indicated that a non-synonymous SNP (rs3741596, Ser218Gly) associated with the susceptibility of AD in the Japanese population but not in the Taiwanese population. However, there is another SNP of ORAI1 (rs3741595) associated with the risk of AD in the Taiwanese population but not in the Japanese population. Taken together, our results indicated that genetic polymorphisms of ORAI1 are very likely to be involved in the susceptibility of AD.

  7. ORAI1 genetic polymorphisms associated with the susceptibility of atopic dermatitis in Japanese and Taiwanese populations.

    Directory of Open Access Journals (Sweden)

    Wei-Chiao Chang

    Full Text Available Atopic dermatitis is a chronic inflammatory skin disease. Multiple genetic and environmental factors are thought to be responsible for susceptibility to AD. In this study, we collected 2,478 DNA samples including 209 AD patients and 729 control subjects from Taiwanese population and 513 AD patients and 1027 control subject from Japanese population for sequencing and genotyping ORAI1. A total of 14 genetic variants including 3 novel single-nucleotide polymorphisms (SNPs in the ORAI1 gene were identified. Our results indicated that a non-synonymous SNP (rs3741596, Ser218Gly associated with the susceptibility of AD in the Japanese population but not in the Taiwanese population. However, there is another SNP of ORAI1 (rs3741595 associated with the risk of AD in the Taiwanese population but not in the Japanese population. Taken together, our results indicated that genetic polymorphisms of ORAI1 are very likely to be involved in the susceptibility of AD.

  8. Polymorphism, genetic exchange and intragenic recombination of the aureolysin gene among Staphylococcus aureus strains

    Directory of Open Access Journals (Sweden)

    Kowal Julia

    2008-07-01

    Full Text Available Abstract Background Staphylococcus aureus expresses several proteases, which are thought to contribute to the virulence of this bacterium. Here we focus on aureolysin, the major thermolysin-like metalloprotease. Despite the importance of aureolysin in the physiology and pathogenesis of S. aureus, relatively little information was so far available concerning the aur gene diversity and mobility within and between the major subdivisions of the S. aureus population. Therefore, an epidemiologically and genetically diverse collection of S. aureus strains was used to determine the range of aureolysin (aur gene polymorphism. Results Sequence analyses support the conclusion that the aur gene occurs in two distinct types of related sequences. The aur gene was much more polymorphic but, at the same time, showed higher purifying selection than genes utilized for multilocus sequence typing (MLST. Gene trees constructed from aur and concatenated MLST genes revealed several putative assortative recombination events (i.e. entire aur gene exchanges between divergent lineages of S. aureus. Evidence for intragenic recombination events (i.e. exchanges of internal aur segments across aur genes was also found. The biochemical properties and substrate specificity of the two types of aureolysin purified to homogeneity were studied, revealing minor differences in their affinity to low molecular weight synthetic substrates. Conclusion Although numerous nucleotide differences were identified between the aur alleles studied, our findings showed that a strong purifying selection is acting on the aur gene. Moreover, our study distinguishes between homologous exchanges of the entire aur gene (assortative recombination between divergent S. aureus lineages and recombination events within aur genes.

  9. TP53 Polymorphisms allow for genetic sub-grouping of the canine transmissible venereal tumor

    Science.gov (United States)

    Sánchez-Servín, Abel; Córdova-Alarcon, Emilio; Fajardo, Raúl

    2009-01-01

    The canine transmissible venereal tumor (CTVT) is found mainly in dogs' sexual organs. Currently, it is widely accepted that all samples of CTVT show similar histopathological characteristics and share common genetic alterations. Despite the common genetic origin of CTVT, mutations in the P53 gene have been reported. In this study, we proposed that tumor samples can be genetically grouped using this gene. The presence of different subgroups of CTVT was determined in Mexican dogs using the TP53 gene sequence in CTVT samples. Four new polymorphisms were found and therefore, the CTVT samples were classified in five subgroups. PMID:19934603

  10. Genetic Polymorphism of Secretoglobin SCGB1A1 and Development of Lung Pathology in Children

    Directory of Open Access Journals (Sweden)

    N.K. Malaya

    2014-03-01

    Full Text Available The purpose of investigation — to study of A(38G genetic polymorphism of the first exon of secretoglobin SCGB1A1 in Crimean children and to identify the possible correlation between the degree of polymorphism and development of lung pathology (bronchial asthma and recurrent bronchitis. There were investigated DNA samples from children with bronchial asthma (75 persons, recurrent bronchitis (19 persons and healthy children (20 persons aged from 6 to 16 years. The genetic polymorphism was determined by polymerase chain reaction with method of allele discrimination with registration the results by electrophoresis. Frequency of allele combinations of genetic variants of studied polymorphism was different in patients with bronchial asthma, recurrent bronchitis and in control group. Thus, among patients with bronchial asthma the frequency of homozygous allele AA carriers is lower, and among patients with recurrent bronchitis it is higher then in control group. Contrary, the frequency of AG heterozygotes was higher among patients with bronchial asthma then in patients with recurrent bronchitis and in control group. Also the frequency of AG heterozygotes in patients with recurrent bronchitis is much lower than homozygotes. The obtained results can be used for prognostic purpose to evaluate the prospects of the obstructive syndrome development.

  11. Genetic polymorphism and immune response to tuberculosis in indigenous populations: a brief review

    Directory of Open Access Journals (Sweden)

    Renata Maronna Praça Longhi

    Full Text Available We systematically reviewed studies of the immune response to tuberculosis and the genetic polymorphisms associated with Th1-or Th2-mediated cytokine expression in indigenous populations. A bibliographic search was performed on the Medline and ISI databases and included studies published between January 1980 and October 2011. The search terms were tuberculosis, American Indians, Amerindian, indigenous, Indians, native people, aboriginal, immun*, host immune, immune response, cytokine*, polymorphism*, and gene. Regardless of their design, studies that evaluated immunoglobulin, cytokine levels and genetic polymorphisms that altered cytokine expression were included. Thirteen studies met the inclusion criteria. The majority of studies were performed in Latin America, and five investigated the Warao ethnic group of Venezuela. Most of the investigations indirectly evaluated the immune response. Higher anergy to the tuberculin skin test, higher IgG4 and IgM levels, higher IL-5 production and lower TNF-a, IL-12p40 and IFN-I production were found in the indigenous populations. The studies also reported a predominantly Th2-type response in these populations and a possibly higher susceptibility to tuberculosis. A better understanding of the relevant genetic polymorphisms and their role in immune regulation would help to clarify the immunogenetic mechanisms of TB infection in these populations. This information would be useful for identifying new treatments and preventing infection and progression to active disease.

  12. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    Science.gov (United States)

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-07-22

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

  13. Association of symptoms and severity of rift valley fever with genetic polymorphisms in human innate immune pathways.

    Directory of Open Access Journals (Sweden)

    Amy G Hise

    2015-03-01

    -associated clinical outcomes. Studies of these and related genetic polymorphisms are warranted to advance understanding of RVF pathogenesis.

  14. Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms.

    Directory of Open Access Journals (Sweden)

    John E Bowers

    Full Text Available The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences targeting 86,023 unigenes from sunflower (Helianthus annuus L. and related species to test for single-feature polymorphisms (SFPs in a recombinant inbred line (RIL mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801. We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.

  15. RESEARCH OF GENETIC POLYMORPHISM OF 5-HTT IN CHILDHOOD AUTISM

    Institute of Scientific and Technical Information of China (English)

    Sun Xiaomian; Li Yamei; Zheng Chongxun

    2006-01-01

    Objective To reveal the relationship between the 5-HTTLPR and the Chinese Han nationality children with CA, compared the distribution of the 5-HTTLPR between the Han Chinese children with CA and healthy Han Chinese children ,and analyzed the association between the 5-HTTLPR and clinical symptoms of the Han Chinese children with CA. Methods Genomic DNAs of fifty subjects including 25 autistic children and 25 controls were extracted from blood samples. PCR amplification using Oligonucleotide primers flanking 5-HTTLPR was performed. Results ① Three kinds of alleles including the S (short) allele, the L (long) allele and the VL allele were found , and the 5-HTTLPR genotypes shown were S/S, L/L, S/L and L/VL. ② Allele frequencies did not differ significantly in patient groups in comparison with the control sample. No significant difference was identified between the observed 5-HTTLPR genotype distribution of the patient groups and control group. ③ The distribution of homozygous and heterozygous subjects between the two groups differed significantly. ④ The genotypes of the 5-HTTLPR polymorphism correlated significantly with the Body Movement Factor. ⑤ The allele frequency of healthy Han Chinese population and that of healthy Japanese population were similar. The frequency of S allele in not only autistic subjects but also healthy children in this study was considerably more than that in Caucasians and the frequency of L allele in our subjects decreased correspondingly. Conclusion ① A significant difference in the allele frequency between the Han Chinese and Caucasian populations was found. ② The genotypes of the 5-HTTLPR polymorphism correlated significantly with the Body Movement Factor of the patients. ③ The homozygote and the L allele were positively relevant to CA and they might be the risk factors of CA. The heterozygote and the S allele were negatively relevant to CA and they might be the protective factors of CA.

  16. Genetic polymorphisms in CYP1A1, CYP1B1 and COMT genes in Greenlandic Inuit and Europeans

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    Mandana Ghisari

    2013-06-01

    Full Text Available Background. The Indigenous Arctic population is of Asian descent, and their genetic background is different from the Caucasian populations. Relatively little is known about the specific genetic polymorphisms in genes involved in the activation and detoxification mechanisms of environmental contaminants in Inuit and its relation to health risk. The Greenlandic Inuit are highly exposed to legacy persistent organic pollutants (POPs such as polychlorinated biphenyls (PCBs and organochlorine pesticides (OCPs, and an elucidation of gene–environment interactions in relation to health risks is needed. Objectives. The aim of this study was to determine and compare the genotype and allele frequencies of the cytochrome P450 CYP1A1 Ile462Val (rs1048943, CYP1B1 Leu432Val (rs1056836 and catechol-O-methyltransferase COMT Val158Met (rs4680 in Greenlandic Inuit (n=254 and Europeans (n=262 and explore the possible relation between the genotypes and serum levels of POPs. Results. The genotype and allele frequency distributions of the three genetic polymorphisms differed significantly between the Inuit and Europeans. For Inuit, the genotype distribution was more similar to those reported for Asian populations. We observed a significant difference in serum polychlorinated biphenyl (CB-153 and the pesticide 1,1-dichloro-2,2-bis(p-chlorophenyl-ethylene (p,p′-DDE levels between Inuit and Europeans, and for Inuit also associations between the POP levels and genotypes for CYP1A1, CYP1B1 and COMT. Conclusion. Our data provide new information on gene polymorphisms in Greenlandic Inuit that might support evaluation of susceptibility to environmental contaminants and warrant further studies.

  17. Impact of genetic polymorphisms of four cytokine genes on treatment ...

    African Journals Online (AJOL)

    Manar Obada

    2016-04-25

    Apr 25, 2016 ... genes on treatment induced viral clearance in HCV infected Egyptian .... shown to influence TNF-a expression [11]. Interferon gamma ... has been carried out in accordance with The Code of Ethics of the World ... Molecular testing. Genomic DNA ..... Our findings could be explained on the basis that genetic.

  18. [A feasibility analysis on individualized acupuncture treatment of irritable bowel syndrome under help of genetic polymorphism technique].

    Science.gov (United States)

    Wu, Xiao-Liang; Sun, Jian-Hua; Liu, Lan-Ying; Fu, Hai-Yang; Jiao, Dai-Yan; Shu, Yan-Ye; Chen, Dong; Liu, Cheng-Yong; Zhan, Dao-Wei; Zhang, Wei

    2014-06-01

    Along with the application of genetic polymorphism techniques to individualized treatment of clinical disorders, the screening of polymorphisms markers of serotonin (5-HT) transporter (SERT) is a hot-spot of researches on irritable bowel syndrome (IBS). In the present paper, the authors introduce 1) optimized schemes of diagnosis and treatment of IBS on the basis of syndrome-differentiation for acupuncture in combination with Chinese herbal medicines, and application of 5-HT transporter polymorphism, 2) application of genetic polymorphism to researches on IBS, and 3) feasibility of genetic polymorphism techniques for guiding individualized treatment of IBS. Up to now, serotonin transporter length polymorphic region (5-HTTLPR), serotonin transporter intron 2 variable number of tandem repeat (Stin 2 VNTR) and single nucleotide polymorphism rs 25531 in the long allele of the 5-HTTLPR have been identified. On the basis of the treatment of IBS, we need establishing a set of guide lines for the individualized acupuncture treatment. The genotyping methods for genetic polymorphism should be widely used in this research field. 5-HT TLPR/ Stin 2 VNTR/rs 25531 polymorphisms would have a bright future in the field of IBS research and treatment.

  19. Short communication: Development of a new polymorphic genetic marker in Araucaria araucana (Mol) K. Koch

    Energy Technology Data Exchange (ETDEWEB)

    Drake, F.; Martin, M. A.; Alvarez, A.; Molina, J. R.; Alvarez, J. B.; Herrera, M. A.; Martin, L. M.

    2012-11-01

    Seed storage proteins have been used as genetic marker in forest species to evaluate genetic variability, demonstrating its effectiveness both in conifers and broad-leaved. In conifers, megagametophyte storage proteins are particularly useful because of their haploid nature. The aim of this study was to determine whether these proteins could be used as a new marker of genetic diversity in Araucaria araucana, one of the oldest conifers of South America and a representative symbol of Chilean forest biodiversity. For this, megagametophytes from two A. araucana populations were assessed to identify polymorphic bands and to obtain a preliminary estimation of the genetic diversity. The results revealed that globulin is the best fraction for measuring the variability in the species, due to their high level of variation (20 identified bands, 11 of them polymorphic). Both populations showed high genetic diversity, with more than 92% of the variation within populations. The study highlighted that these proteins can be used to measure the genetic diversity in A. araucana, providing good information to ensure the preservation of the species genetic resources. (Author) 29 refs.

  20. Polymorphisms in the genes related to angiogenesis are associated with uterine cervical cancer.

    Science.gov (United States)

    Ramos-Flores, Christian; Romero-Gutiérrez, Teresa; Delgado-Enciso, Iván; Maldonado, Gabriela Enríquez; Plascencia, Víctor Montaño; Vazquez-Vuelvas, Oscar F; Quintero-Ramos, Antonio; Mejía, Roberto Chaparro; Espinoza-Gomez, Francisco; Baltazar-Rodriguez, Luz M; Valdez-Velazquez, Laura L

    2013-09-01

    The expression of plasminogen activator inhibitor type 1 (PAI-1), vascular endothelial growth factor (VEGF), and transforming growth factor β1 (TGF-β1) participates in the angiogenesis of several cancer types. The goal of this study was to investigate polymorphisms in genes related to angiogenesis (PAI-1-675 4G/5G, VEGF C936T, and TGF-β1 G-800A) to evaluate the risk for developing uterine cervical cancer (UCC). In a case-control study, 100 healthy subjects and 100 patients with UCC from Mexico were included. We determined the genetic profile of the polymorphic markers, which were evaluated by polymerase chain reaction using a sequence-specific primer. There was no statistical difference in the allele distribution from the intergroup comparisons of PAI-1 675 4G/5G and VEGF C936T data; however, a significant difference was observed within TGF-β1 G-800A. The linkage disequilibrium analysis revealed that PAI-1 -675 4G and TGF-β1 -800A pair-haplotype was in strong linkage disequilibrium with a significantly increased risk (odds ratio, 3.44; 95% confidence interval, 1.66-7.25) to UCC. The polymorphisms in the genes related to angiogenesis -675 4G/5G PAI-1 and G-800A TGF-β1, segregated solely or combined, might contribute to the increased susceptibility to UCC in a Mexican population.

  1. Genetic Polymorphism of the Serotonin Transporter Gene, SLC6A4 rs16965628, Is Associated with Obsessive Compulsive Disorder.

    Science.gov (United States)

    Cengiz, Mujgan; Okutan, Saide Nur; Bayoglu, Burcu; Sakalli Kani, Ayse; Bayar, Reha; Kocabasoglu, Nese

    2015-05-01

    Obsessive compulsive disorder (OCD) is a psychiatric disorder characterized by obsessive ideas and compulsive behaviors. Genetic studies have centered on candidate genes involved in OCD etiology related to serotonergic and dopaminergic systems. In this study, the relationship between cathechol-O-methyltransferase (COMT) -287A/G (rs2097063), serotonin transporters 5-HTTLPR I/D, and SLC6A4 rs16965628 polymorphisms in 80 OCD patients and 100 healthy controls was determined. Patients and controls were genotyped for COMT rs2097063 and SLC6A4 rs16965628 polymorphisms by real-time polymerase chain reaction (PCR). The 5-HTTLPR I/D polymorphism was genotyped using PCR and agarose gel electrophoresis. Severity of symptoms was checked with a Yale-Brown Obsession Compulsion Scale (Y-BOCS). When the OCD group and controls were compared, no significant difference was found between COMT -287A/G (rs2097063), 5-HTTLPR I/D polymorphisms, and OCD. However, a significant difference was found between 5-HTT rs16965628 polymorphism and OCD (p=0.025, OR=3.43, 95% CI 1.41-10.35). In addition, the G allele frequency was found to be higher for rs16965628 in the OCD group. No significant difference was observed between COMT -287A/G (rs2097063), SLC6A4 rs16965628, and 5-HTTLPR I/D polymorphisms and Y-BOCS scores (p>0.05). There was also lack of correlation between Yale-Brown scores and gender of OCD patients. On the other hand, combined genotypes of SLC6A4 rs16965628 GG+GC were found to be risk factors for OCD development (p=0.02, OR=3.464; 95% CI 1.214-9.883) in logistic regression analysis adjusted for age and gender. Our findings suggest that subjects carrying the G allele of rs16965628 have genetic susceptibility to OCD. These data are the first to suggest that polymorphism in serotonin transporter (rs16965628) is associated with the development of OCD in the Turkish population.

  2. Prediction formulas for individual opioid analgesic requirements based on genetic polymorphism analyses.

    Directory of Open Access Journals (Sweden)

    Kaori Yoshida

    Full Text Available The analgesic efficacy of opioids is well known to vary widely among individuals, and various factors related to individual differences in opioid sensitivity have been identified. However, a prediction model to calculate appropriate opioid analgesic requirements has not yet been established. The present study sought to construct prediction formulas for individual opioid analgesic requirements based on genetic polymorphisms and clinical data from patients who underwent cosmetic orthognathic surgery and validate the utility of the prediction formulas in patients who underwent major open abdominal surgery.To construct the prediction formulas, we performed multiple linear regression analyses using data from subjects who underwent cosmetic orthognathic surgery. The dependent variable was 24-h postoperative or perioperative fentanyl use, and the independent variables were age, gender, height, weight, pain perception latencies (PPL, and genotype data of five single-nucleotide polymorphisms (SNPs. To examine the utility of the prediction formulas, we performed simple linear regression analyses using subjects who underwent major open abdominal surgery. Actual 24-h postoperative or perioperative analgesic use and the predicted values that were calculated using the multiple regression equations were incorporated as dependent and independent variables, respectively.Multiple linear regression analyses showed that the four SNPs, PPL, and weight were retained as independent predictors of 24-h postoperative fentanyl use (R² = 0.145, P = 5.66 × 10⁻¹⁰ and the two SNPs and weight were retained as independent predictors of perioperative fentanyl use (R² = 0.185, P = 1.99 × 10⁻¹⁵. Simple linear regression analyses showed that the predicted values were retained as an independent predictor of actual 24-h postoperative analgesic use (R² = 0.033, P = 0.030 and perioperative analgesic use (R² = 0.100, P = 1.09 × 10⁻⁴, respectively.We constructed

  3. Morph-specific genetic and environmental variation in innate and acquired immune response in a color polymorphic raptor.

    Science.gov (United States)

    Gangoso, Laura; Roulin, Alexandre; Ducrest, Anne-Lyse; Grande, Juan Manuel; Figuerola, Jordi

    2015-08-01

    Genetic color polymorphism is widespread in nature. There is an increasing interest in understanding the adaptive value of heritable color variation and trade-off resolution by differently colored individuals. Melanin-based pigmentation is often associated with variation in many different life history traits. These associations have recently been suggested to be the outcome of pleiotropic effects of the melanocortin system. Although pharmacological research supports that MC1R, a gene with a major role in vertebrate pigmentation, has important immunomodulatory effects, evidence regarding pleiotropy at MC1R in natural populations is still under debate. We experimentally assessed whether MC1R-based pigmentation covaries with both inflammatory and humoral immune responses in the color polymorphic Eleonora's falcon. By means of a cross-fostering experiment, we disentangled potential genetic effects from environmental effects on the covariation between coloration and immunity. Variation in both immune responses was primarily due to genetic factors via the nestlings' MC1R-related color genotype/phenotype, although environmental effects via the color morph of the foster father also had an influence. Overall, dark nestlings had lower immune responses than pale ones. The effect of the color morph of the foster father was also high, but in the opposite direction, and nestlings raised by dark eumelanic foster fathers had higher immune responses than those raised by pale foster fathers. Although we cannot completely discard alternative explanations, our results suggest that MC1R might influence immunity in this species. Morph-specific variation in immunity as well as pathogen pressure may therefore contribute to the long-term maintenance of genetic color polymorphism in natural populations.

  4. Genetic polymorphism of adult reindeer coat colour in a herding cooperative in Finnish Lapland

    Directory of Open Access Journals (Sweden)

    Jean J. Lauvergne

    2011-04-01

    Full Text Available In a random sample of 188 adult reindeer belonging to a reindeer herding cooperative in Finnish Lapland, the following coat colour mutants were identified: Abf at the locus Agouti (A, kalppinokka (WNk at the locus White Nose (WN and white at the locus W (White. Coefficients of coat colour phenotypic polymorphism K were estimated, in order to quantify this genetic polymorphism. Estimations of K were 12.8% for the locus A (Agouti, 5.1% for the locus WN (White Nose, and 7.5% for the locus W (White. This polymorphism results probably from a change in fitness coefficient of genotypes carrying colour mutants following domestication in a random mating context which has not yet been proved.

  5. Stratification for smoking in case-cohort studies of genetic polymorphisms and lung cancer

    DEFF Research Database (Denmark)

    Sørensen, Mette; López, Ana García; Andersen, Per Kragh;

    2009-01-01

    The risk estimates obtained in studies of genetic polymorphisms and lung cancer differ markedly between studies, which might be due to chance or differences in study design, in particular the stratification/match of comparison group. The effect of different strategies for stratification...... and adjustment for smoking on the estimated effect of polymorphisms on lung cancer risk was explored in the case-cohort design. We used an empirical and a statistical simulation approach. The stratification strategies were: no smoking stratification, stratification for smoking status and stratification...... with smoking. In the empirical approach the risk estimates of the investigated polymorphisms differed between the three different stratification strategies. Simulated data with neither stratification nor adjustment for smoking resulted in low biases and narrow confidence intervals (CI) in the absence...

  6. Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair

    Science.gov (United States)

    Sterpone, Silvia; Cozzi, Renata

    2010-01-01

    It is well known that ionizing radiation (IR) can damage DNA through a direct action, producing single- and double-strand breaks on DNA double helix, as well as an indirect effect by generating oxygen reactive species in the cells. Mammals have evolved several and distinct DNA repair pathways in order to maintain genomic stability and avoid tumour cell transformation. This review reports important data showing a huge interindividual variability on sensitivity to IR and in susceptibility to developing cancer; this variability is principally represented by genetic polymorphisms, that is, DNA repair gene polymorphisms. In particular we have focussed on single nucleotide polymorphisms (SNPs) of XRCC1, a gene that encodes for a scaffold protein involved basically in Base Excision Repair (BER). In this paper we have reported and presented recent studies that show an influence of XRCC1 variants on DNA repair capacity and susceptibility to breast cancer. PMID:20798883

  7. Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair

    Directory of Open Access Journals (Sweden)

    Silvia Sterpone

    2010-01-01

    Full Text Available It is well known that ionizing radiation (IR can damage DNA through a direct action, producing single- and double-strand breaks on DNA double helix, as well as an indirect effect by generating oxygen reactive species in the cells. Mammals have evolved several and distinct DNA repair pathways in order to maintain genomic stability and avoid tumour cell transformation. This review reports important data showing a huge interindividual variability on sensitivity to IR and in susceptibility to developing cancer; this variability is principally represented by genetic polymorphisms, that is, DNA repair gene polymorphisms. In particular we have focussed on single nucleotide polymorphisms (SNPs of XRCC1, a gene that encodes for a scaffold protein involved basically in Base Excision Repair (BER. In this paper we have reported and presented recent studies that show an influence of XRCC1 variants on DNA repair capacity and susceptibility to breast cancer.

  8. The association between hepatitis C virus infection, genetic polymorphisms of oxidative stress genes and B-cell non-Hodgkin's lymphoma risk in Egypt.

    Science.gov (United States)

    Farawela, Hala; Khorshied, Mervat; Shaheen, Iman; Gouda, Heba; Nasef, Aya; Abulata, Nelly; Mahmoud, Hebat-Allah; Zawam, Hamdy M; Mousa, Somaia M

    2012-08-01

    Hepatitis C virus (HCV) has been postulated to be an etiological agent for lymphoid malignancies. Polymorphisms in oxidative stress genes as; superoxide dismutase (SOD2), glutathione peroxidase (GPX1), catalase (CAT), myeloperoxidase (MPO) and nitric oxide synthase (NOS2) may influence non-Hodgkin's lymphoma (NHL) risk. HCV screening and polymorphisms in these five genes coding for antioxidant enzymes were studied in 100 Egyptian patients with B cell-NHL and 100 controls to clarify the association between HCV infection, oxidative stress genes polymorphisms and B cell-NHL risk. A significantly higher prevalence of HCV infection was detected among NHL patients relative to controls and this carried a 14-fold increased NHL risk (odds ratio (OR)=14.3, 95% confidence interval (CI)=5.4-38.3, pEgypt. Polymorphisms in GPX1 and MPO genes may influence NHL risk in HCV infected Egyptian patients. Larger scale studies are warranted to establish this genetic susceptibility for NHL.

  9. Genetic polymorphisms: impact on the risk of fetal alcohol spectrum disorders.

    Science.gov (United States)

    Warren, Kenneth R; Li, Ting-Kai

    2005-04-01

    Clinical reports on monozygotic and dizygotic twins provided the initial evidence for the involvement of genetic factors in risk vulnerability for fetal alcohol spectrum disorders (FASD) including fetal alcohol syndrome (FAS). Research with selectively bred and inbred rodents, genetic crosses of these lines and strains, and embryo culture studies have further clarified the role of both maternal and fetal genetics in the development of FASD. Research to identify specific polymorphisms contributing to FASD is still at an early stage. To date, polymorphisms of only one of the genes for the alcohol dehydrogenase enzyme family, the ADH1B, have been demonstrated to contribute to FASD vulnerability. In comparison with ADH1B*1, both maternal and fetal ADH1B*2 have been shown to reduce risk for FAS in a mixed ancestry South African population. ADH1B*3 appears to afford protection for FASD outcomes in African-American populations. Other candidate genes should be examined with respect to FASD risk, including those for the enzymes of serotonin metabolism, in particular the serotonin transporter. By its very nature, alcohol teratogenesis is the expression of the interaction of genes with environment. The study of genetic factors in FASD falls within the new field of ecogenetics. Understanding of the array of genetic factors in FASD will be enhanced by future genetic investigations, including case-control, family association, and linkage studies.

  10. RELATIONSHIP OF HOMOCYSTEINE AND GENE POLYMORPHISMS OF ITS RELATED METABOLIC ENZYMES WITH ALZHEIMER'S DISEASE

    Institute of Scientific and Technical Information of China (English)

    Ying-dong Zhang; Xiao-yan Ke; Wei Shen; Yang Liu

    2005-01-01

    Objective To investigate the relationship of plasma homocysteine (Hcy) levels and the gene polymorphisms of N5,N10-methylenetetrahydrofolate reductase (MTHFR), cystathionine 3-synthase (CBS) with Alzheimer's disease (AD).Methods Plasma Hcy levels were measured by means of high voltage capillary electrophoresis with ultra-violet detection, the polymorphisms of C677T in exon 4 of MTHFR gene and 844ins68 in exon 8 of CBS gene were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 105 AD patients and 102 non-AD controls. All controls were excluded from cardiocerebrovascular disorders and other diseases.Results The plasma Hcy level in AD patients (16.04 ± 3.84 μmol/L) was significantly higher than that in the controls (11.94±3.87 μmol/L, P<0.001). There were no significant differences of the genotype and allele frequencies of MTHFR C677T mutation and CBS 844ins68 mutation between the patients and controls. However, the T allele of MTHFR gene was found to relate with the plasma Hcy level increase in all subjects.Conclusion The elevated plasma Hcy level in AD patients is probably involved in the pathogenesis of AD, which may be due to the environmental factor rather than genetic factors of the mutations of MTHFR and CBS.

  11. Sequence-Related Amplified Polymorphism (SRAP Markers: A Potential Resource for Studies in Plant Molecular Biology

    Directory of Open Access Journals (Sweden)

    Daniel W. H. Robarts

    2014-07-01

    Full Text Available In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR, random-amplified polymorphic DNA (RAPD, and amplified fragment length polymorphism (AFLP to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use. highly variable marker with inherent biological significance.

  12. [Clinical variations of chronic generalized periodontitis, genetic polymorphism and systemic production of inflammatory cytokines].

    Science.gov (United States)

    Grigorovich, E Sh; Pomorgailo, E G; Khomutova, E Yu; Stepanov, S S

    2015-01-01

    Carriage of polymorphic alleles of genes of cytokines-interleukines IL-1β, IL-1RN, TNFα, IL-4 can be a specific feature of chronic periodontitis patients. Genetic tests can be used to predict the course of the disease at its early manifestations. Objective: To establish the relationship of clinical manifestations of periodontal disease, inflammatory cytokines gene polymorphism and systemic levels of cytokine production. Periodontal tissue assessment and cone-beam computed tomography (CBCT) were performed in 150 periodontitis patients. A molecular--genetic testing for the presence of polymorphic alleles of genes IL-1β -511 C>T and +3953 C>T, IL-1RN (VNTR intron 2), IL-4 (VNTR intron 3), TNFα-308 G>A; content determined IL-1β, TNFα, IL-4 in peripheral blood was carried out in 150 patients with periodontitis and 150 healthy donors. Based on the analysis of the speed and nature of the supporting bone resorption and clinical manifestations patients are divided in "aggressive", "moderately progressive" and "slowly progressive" periodontits course groups. Disease severity was associated with distribution of genotypes and alleles of polymorphic genes cytokine IL-1RN (VNTR intron 2), TNFα-308 G>A and IL-4 (VNTR intron 3); haplotype IL-1β-511 TIL-1β +3953 T/IL-1RN 2R. There was no statistically significant difference in systemic level of IL-1β, TNFα and IL-4 between periodontitis groups but the donor level of cytokines was 2-4 times less.

  13. Role of common sarcomeric gene polymorphisms in genetic susceptibility to left ventricular dysfunction

    Indian Academy of Sciences (India)

    SURENDRA KUMAR; AVSHESH MISHRA; ANSHIKA SRIVASTAVA; MANSI BHATT; N. GARG; S. K. AGARWAL; SHANTANU PANDE; BALRAJ MITTAL

    2016-06-01

    Mutations in sarcomeric genes are common genetic cause of cardiomyopathies. An intronic 25-bp deletion in cardiac myosin binding protein C (MYBPC3) at 3' region is associated with dilated and hypertrophic cardiomyopathies in Southeast Asia. However, the frequency of sarcomeric gene polymorphisms and associated clinical presentation have not been established with left ventricular dysfunction (LVD). Therefore, the aim of the present study was to explore the association of MYBPC3 25-bp deletion, titin (TTN) 18 bp I/D, troponin T type 2 (TNNT2) 5 bp I/D and myospryn K2906N polymorphisms with LVD. This study includes 988 consecutive patients with angiographically confirmed coronary artery disease (CAD) and 300 healthy controls. Among the 988 CAD patients, 253 with reduced left ventricle ejection fraction (LVEF≤45%) were categorized as LVD. MYBPC3 25-bp deletion,TTN 18 bp I/D and TNNT25 bp I/D polymorphisms were determined by direct polymerase chain reaction method, while myospryn K2906N polymorphism by TaqMan assay. Our results showed that MYBPC3 25-bpdeletion polymorphism was significantly associated with elevated risk of LVD (LVEF <45) (healthy controls versus LVD: OR= 3.85,P<0.001; and nonLVD versus LVD: OR=1.65,P=0.035), while TTN 18 bp I/D, TNNT25bpI/Dand myospryn K2906N polymorphisms did not show any significant association with LVD. The results also showed that MYBPC3 25-bp deletion polymorphism was significantly associated with other parameters of LV remodelling, i.e. LV dimensions (LV end diastole dimension, LVEDD: P= 0.037 and LV end systolic dimension, LVESD: P= 0.032).Our data suggests that MYBPC3 25-bp deletion may play significant role in conferring LVD as well as CAD risk in north Indian population

  14. Pilot Study on Genetic Polymorphisms CYP1A2*1F on Asthma Patients and Nonasthma in Indonesia

    Directory of Open Access Journals (Sweden)

    Doddy de Queljoe

    2015-03-01

    Full Text Available Genetic polymorphisms of CYP1A2 is related to the theophylline metabolism that may affect drug levels in the blood, which can also affect incidence of adverse drug reaction (ADR and clinical outcomes of asthma therapy. The frequency of CYP1A2 polymorphism is known to vary among ethnic. Allegedly the Indonesian population has high frequency of gene variants of CYP1A2*1F. This study aims to determine the profile of CYP1A2*1F gene polymorphism in a sample of nonasthma and asthma in Indonesia with other populations based on the literature. Data were taken on January–June 2014. Blood samples were obtained from 29 nonasthma samples and 16 patients with asthma. After extraction of genomic DNA, CYP1A2*1F gene polymorphisms determined by PCR-RFLP. The results of this study indicate that the CYP1A2*1F gene polymorphism in nonasthma samples was 10.35% (3/29 for C/C, 37.93% (11/29 for the C/A, and 51.72% (15/29 for A/A. The asthmatics genotype have a frequency distribution of C/A genotype of 81.25% (13/16 and A/A of 18.75% (3/16. There was no significant difference (p=0.276 allele frequencies between samples of nonasthma and asthma patients. The frequency of CYP1A2*1F gene in Indonesian population is higher than the population of Egypt, Japan, and UK, but lower compared to Malaysia. It can be concluded that there is no difference in frequency.

  15. Expression of ICAM1 and VCAM1 Serum Levels in Rheumatoid Arthritis Clinical Activity. Association with Genetic Polymorphisms

    Directory of Open Access Journals (Sweden)

    Rosa Elena Navarro-Hernández

    2009-01-01

    Full Text Available To investigate the association of sICAM-1 and sVCAM-1 with ICAM1 721G>A and VCAM1 1238G>C polymorphisms and rheumatoid arthritis (RA clinical activity, sixty RA patients and 60 healthy non-related subjects (HS matched for age and sex were recruited. Soluble adhesion molecules were determined by ELISA technique. Rheumatoid factor (RF, C reactive protein (CRP and the erythrocyte sedimentation rate (ESR were measured by routine methods. Disability and clinical activity was measured with Spanish-HAQ-DI and DAS28 scores, respectively. The ICAM1 and VCAM1 polymorphism were identified using the PCR-RFLP procedure. Inter-group comparison showed increased levels of sICAM-1 and sVCAM-1 in RA patients (284 and 481 ng/mL versus HS (132 and 280 ng/mL; in the RA group, significant correlations between sVCAM-1 and RF (r = 0.402, ESR (r = 0.426, Spanish-HAQ-DI (r = 0.276, and DAS28 (r = 0.342 were found, whereas sICAM-1 only correlated with RF (r = 0.445. In RA patients, a significant association with the 721A allele of ICAM1 polymorphism (p = 0.04, was found. In addition, the allele impact (G/A + A/A of this polymorphism was confirmed, (p = 0.038, OR = 2.3, C.I. 1.1–5.0. sVCAM-1 and sICAM-1 serum levels reflected the clinical status in RA, independently of the ICAM1 and VCAM1 polymorphism. However, the ICAM1 721A allele could be a genetic marker to RA susceptibility.

  16. Effect of Bcl-2 rs956572 polymorphism on age-related gray matter volume changes.

    Directory of Open Access Journals (Sweden)

    Mu-En Liu

    Full Text Available The anti-apoptotic protein B-cell CLL/lymphoma 2 (Bcl-2 gene is a major regulator of neural plasticity and cellular resilience. Recently, the Bcl-2 rs956572 single nucleotide polymorphism was proposed to be a functional allelic variant that modulates cellular vulnerability to apoptosis. Our cross-sectional study investigated the genetic effect of this Bcl-2 polymorphism on age-related decreases in gray matter (GM volume across the adult lifespan. Our sample comprised 330 healthy volunteers (191 male, 139 female with a mean age of 56.2±22.0 years (range: 21-92. Magnetic resonance imaging and genotyping of the Bcl-2 rs956572 were performed for each participant. The differences in regional GM volumes between G homozygotes and A-allele carriers were tested using optimized voxel-based morphometry. The association between the Bcl-2 rs956572 polymorphism and age was a predictor of regional GM volumes in the right cerebellum, bilateral lingual gyrus, right middle temporal gyrus, and right parahippocampal gyrus. We found that the volume of these five regions decreased with increasing age (all P<.001. Moreover, the downward slope was steeper among the Bcl-2 rs956572 A-allele carriers than in the G-homozygous participants. Our data provide convergent evidence for the genetic effect of the Bcl-2 functional allelic variant in brain aging. The rs956572 G-allele, which is associated with significantly higher Bcl-2 protein expression and diminished cellular sensitivity to stress-induced apoptosis, conferred a protective effect against age-related changes in brain GM volume, particularly in the cerebellum.

  17. Spina bifida and genetic factors related to myo-inositol, glucose, and zinc.

    NARCIS (Netherlands)

    Groenen, P.; Klootwijk, E.D.; Schijvenaars, M.M.V.A.P.; Straatman, H.M.P.M.; Mariman, E.C.M.; Franke, B.; Steegers-Theunissen, R.P.M.

    2004-01-01

    BACKGROUND: Myo-inositol, glucose and zinc and related genetic factors are suggested to be implicated in the etiology of spina bifida. We investigated the biochemical concentrations of these nutrients and polymorphisms in the myo-inositol transporter SLC5A11, myo-inositol synthase ISYNA1, and zinc

  18. Genetic association analysis between polymorphisms of HAIRY-AND-ENHANCER-OF SPLIT-7 and congenital scoliosis

    OpenAIRE

    Gu, Zuchao; Qiu, Guixing; Zhang, Yu

    2015-01-01

    Objective: We explored the association between genetic polymorphisms of HAIRY-AND-ENHANCER-OF-SPLIT-7 (HES7) and congenital scoliosis (CS) in 246 cases of congenital scoliosis and non-congenital controls, in which the age and sex were fully matched. All participants were Chinese Han population. Methods: The genome DNA was extracted from peripheral blood sample. Two SNPs were defined for HES7 using NCBI database. The genotypes of two SNPs were determined by SNP stream UHT Genotyping System. Re...

  19. Diversification and genetic differentiation of cultivated melon inferred from sequence polymorphism in the chloroplast genome

    OpenAIRE

    Tanaka, Katsunori; Akashi, Yukari; FUKUNAGA, Kenji; Yamamoto, Tatsuya; Aierken, Yasheng; Nishida, Hidetaka; Long, Chun Lin; Yoshino, Hiromichi; Sato, Yo-Ichiro; KATO, Kenji

    2013-01-01

    Molecular analysis encouraged discovery of genetic diversity and relationships of cultivated melon (Cucumis melo L.). We sequenced nine inter- and intra-genic regions of the chloroplast genome, about 5500 bp, using 60 melon accessions and six reference accessions of wild species of Cucumis to show intra-specific variation of the chloroplast genome. Sequence polymorphisms were detected among melon accessions and other Cucumis species, indicating intra-specific diversification of the chloroplas...

  20. Applicability of genetic polymorphism analysis for the diagnosis of Angelman syndrome and the correlation between language difficulties and disease phenotype

    National Research Council Canada - National Science Library

    Wang, K; Li, Y T; Hou, M

    2016-01-01

    ...% of patients with AS. The aim of this study was to validate the clinical features and genetic polymorphisms of AS, and to discuss the relationship between functional language lateralization and the arcuate fasciculus...

  1. Combined effects of antioxidant vitamin and NOS3 genetic polymorphisms on breast cancer risk in women.

    Science.gov (United States)

    Lee, Sang-Ah; Lee, Kyoung-Mu; Yoo, Keun-Young; Noh, Dong-Young; Ahn, Sei-Hyun; Kang, Daehee

    2012-02-01

    It is becoming increasingly clear that there is wide heterogeneity in genetic predisposition to breast cancer and that breast cancer risk is determined by interactive effect between genetic and environmental factors. We investigated the combined effects of antioxidant vitamin intake and NOS3 genetic polymorphisms on breast cancer risk in a Korean population (Seoul Breast Cancer Study). Histologically confirmed breast cancer cases (n = 512) and age, menopause status-matched controls (n = 512) with no present or previous history of cancer were recruited from several teaching hospitals in Seoul during 2001-2003. Two genetic polymorphisms of NOS3 (298G > T and -786 T > C) were assessed by single base extension assays. No overall association between the individual NOS3 genotypes or diplotypes and breast cancer risk was found, although the difference between cases and controls in the frequency of the NOS3 894 G > T polymorphism showed borderline significance (OR = 0.74, 95% CI = 0.52-1.06). There was no significant difference in energy intake or the intake of antioxidant vitamins between cases and controls, with the exception of vitamin E (OR = 0.49 lowest vs. highest quartile, P(trend) NOS3 -786 T > C or 894 G > T genetic polymorphisms on breast cancer risk. Although a multiplicative interaction was not observed, the protective effect of β-carotene intake on breast cancer risk was observed predominantly in individuals with the TG:TG diplotype of NOS3 (OR = 0.68) but not observed with others diplotype. An inverse association between vitamin E intake and breast cancer risk was observed for individuals with the NOS3 786 TC + TT genotype and the NOS3 894 GG genotype. In addition, folic acid had a protective effect in the NOS3 786 TT and NOS3 894 GT + TT genotype. Our results suggest that intake of antioxidant vitamins might modify the association between genetic polymorphisms of NOS3 and breast cancer risk. Copyright © 2011 Elsevier Ltd and

  2. Analysis of genetic diversity for wild and captive green peafowl populations by random amplified polymorphic DNA technique

    Institute of Scientific and Technical Information of China (English)

    KEYa-yong; CHANGHong; ZHANGGuo-ping

    2004-01-01

    The genetic diversity of the populations for 14 wild green peafowls (Pavo muticus) and 18 captive green peafowls was investigated by using the technology of random amplified polymorphic DNA (RAPD). Totally 161 and 166 amplified bands were obtained by using 23 arbitrary primers to amplify the genomic DNA of wild and captive green peafowls respectively. The results showed that the average relative genetic distance of the wild and captive green peafowls populations was 0.0555 and 0.1355, respectively, and difference of the average relative genetic distances between the two populations was 0.1635. The Shannon diversity index for the wild and captive green peafowl populations was 0.4348 and 1.0163, respectively, which means that there exists significant difference in genetic diversity between the two populations, and the genetic diversity of wild green peafowl was low. The two populations originated from two different families according to analysis by the UPGMA method. This research can provide the theoretical basis for supervising genealogies management of peafowl populations.

  3. Genetic polymorphism of β-lactoglobulin and κ-casein of cattle breeds in Croatia

    Directory of Open Access Journals (Sweden)

    Ante Ivanković

    2011-12-01

    Full Text Available Profitable milk production respects the interests of producers, processing industries, consumer requirements and welfare of animals. Development of new methods of direct gene analysis responsible for milk proteins polymorphism provide new tools to raise the profitability of milk production and dairy products through implementation of breed genetic profile in breeding program. Because of necessity to determinate genetic profiles of cattle breeds in Croatia using new analytical methods, the ratio of dominant allelic polymorphic variants of beta-lactoglobulin (β-Lg and kappa-casein (κ-CN is defined. The share of beta-lactoglobulin B variant is dominant in all investigated cattle breeds (>52.9 %. Kappa- casein allelic variant A is dominant in selected cattle breeds (60.7-76.4 %, while the share of B variant is significantly more presented in autochthonous cattle breeds (48.2-84.1 %. Knowledge about genetic profile of breeds due to studied polymorphic variants of milk proteins is useful in further breeding development and economic reaffirmation of cattle breeds, especially autochthonous ones.

  4. Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism

    Directory of Open Access Journals (Sweden)

    Sukhjiwan Kaur

    2014-01-01

    Full Text Available Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L. genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA, deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain.

  5. Study of the association between ITPKC genetic polymorphisms and calcium nephrolithiasis.

    Science.gov (United States)

    Kan, Wei-Chih; Chou, Yii-Her; Chiu, Siou-Jin; Hsu, Yu-Wen; Lu, Hsing-Fang; Hsu, Wenli; Chang, Wei-Chiao

    2014-01-01

    Nephrolithiasis is a multifactorial disease caused by environmental, hormonal, and genetic factors. Genetic polymorphisms of ORAI1, which codes for the main subunit of the store-operated calcium (SOC) channel, were reported to be associated with the risk and recurrence of calcium nephrolithiasis. Inositol 1,4,5-trisphosphate (IP3) 3-kinase C (ITPKC) is a negative regulator of the SOC channel-mediated signaling pathway. We investigated the association between calcium containing nephrolithiasis and genetic variants of ITPKC gene in Taiwanese patients. 365 patients were recruited in this study. Eight tagging single nucleotide polymorphisms of ITPKC were selected for genotyping. ITPKC genotypes were determined by TaqMan assay. ITPKC plasmids were transfected into cells to evaluate the intracellular calcium mobilization. Our results indicated that rs2607420 CC genotype in the intron region of the ITPKC gene is associated with a lower eGFR by both Modification of Diet in Renal Diseases (P = 0.0405) and Cockcroft-Gault (P = 0.0215) equations in patients with calcium nephrolithiasis. Our results identify a novel polymorphism for renal function and highlight the importance of ITPKC as a key molecule to regulate calcium signaling.

  6. Study of the Association between ITPKC Genetic Polymorphisms and Calcium Nephrolithiasis

    Directory of Open Access Journals (Sweden)

    Wei-Chih Kan

    2014-01-01

    Full Text Available Nephrolithiasis is a multifactorial disease caused by environmental, hormonal, and genetic factors. Genetic polymorphisms of ORAI1, which codes for the main subunit of the store-operated calcium (SOC channel, were reported to be associated with the risk and recurrence of calcium nephrolithiasis. Inositol 1,4,5-trisphosphate (IP3 3-kinase C (ITPKC is a negative regulator of the SOC channel-mediated signaling pathway. We investigated the association between calcium containing nephrolithiasis and genetic variants of ITPKC gene in Taiwanese patients. 365 patients were recruited in this study. Eight tagging single nucleotide polymorphisms of ITPKC were selected for genotyping. ITPKC genotypes were determined by TaqMan assay. ITPKC plasmids were transfected into cells to evaluate the intracellular calcium mobilization. Our results indicated that rs2607420 CC genotype in the intron region of the ITPKC gene is associated with a lower eGFR by both Modification of Diet in Renal Diseases (P=0.0405 and Cockcroft-Gault (P=0.0215 equations in patients with calcium nephrolithiasis. Our results identify a novel polymorphism for renal function and highlight the importance of ITPKC as a key molecule to regulate calcium signaling.

  7. Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer in Women

    Science.gov (United States)

    ... Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-related Cancer in Women The U.S. Preventive Services ... Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-related Cancer in Women. This final recommendation statement ...

  8. Environmental Exposures, Genetic Polymorphisms and p53 Mutational Spectra in a Case-Control Study of Breast Cancer

    Science.gov (United States)

    1999-01-01

    Tyrosine hydroxylase converts (n = 315) who reported smoking at least 5 cigarettes a phenylalanine to dopamine and is a rate limiting day for at least I...180 APPENDIX R - Lack of association of tyrosine hydroxylase genetic polymorphism with cigarette sm oking...Shields, P. G., Main, D., Audrain, J., Roth, J., Boyd, N. R. and Caporaso, N. E.: Lack of association of tyrosine hydroxylase genetic polymorphism with

  9. Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP Markers in Vicia faba L.

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    Salem S. Alghamdi

    2012-12-01

    Full Text Available Sequence-related amplified polymorphism (SRAP markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L. genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments, of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding.

  10. Genetic Architecture of Domestication-Related Traits in Maize.

    Science.gov (United States)

    Xue, Shang; Bradbury, Peter J; Casstevens, Terry; Holland, James B

    2016-09-01

    Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domestication-related traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.

  11. Genetic polymorphisms associated with rubella virus-specific cellular immunity following MMR vaccination.

    Science.gov (United States)

    Kennedy, Richard B; Ovsyannikova, Inna G; Haralambieva, Iana H; Lambert, Nathaniel D; Pankratz, V Shane; Poland, Gregory A

    2014-11-01

    Rubella virus causes a relatively benign disease in most cases, although infection during pregnancy can result in serious birth defects. An effective vaccine has been available since the early 1970s and outbreaks typically do not occur among highly vaccinated (≥2 doses) populations. Nevertheless, considerable inter-individual variation in immune response to rubella immunization does exist, with single-dose seroconversion rates ~95 %. Understanding the mechanisms behind this variability may provide important insights into rubella immunity. In the current study, we examined associations between single nucleotide polymorphisms (SNPs) in selected cytokine, cytokine receptor, and innate/antiviral genes and immune responses following rubella vaccination in order to understand genetic influences on vaccine response. Our approach consisted of a discovery cohort of 887 subjects aged 11-22 at the time of enrollment and a replication cohort of 542 older adolescents and young adults (age 18-40). Our data indicate that SNPs near the butyrophilin genes (BTN3A3/BTN2A1) and cytokine receptors (IL10RB/IFNAR1) are associated with variations in IFNγ secretion and that multiple SNPs in the PVR gene, as well as SNPs located in the ADAR gene, exhibit significant associations with rubella virus-specific IL-6 secretion. This information may be useful, not only in furthering our understanding immune responses to rubella vaccine, but also in identifying key pathways for targeted adjuvant use to boost immunity in those with weak or absent immunity following vaccination.

  12. Correlations between BDNF genetic polymorphism and postpartum depression in cesarean section parturient

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    Ying-yong ZHOU

    2017-08-01

    Full Text Available Objective To study the correlations between the genetic polymorphism of brain-derived neurotrophic factor (BDNF and the postpartum depression (PPD in cesarean section parturient. Methods Three hundred and sixty parturients, who underwent cesarean section under spinal anesthesia from Feb. 2014 to Feb. 2015 in Third Xiangya Hospital of Central South University or Hunan Maternal and Child Health Hospital, were selected as subjects. The general information of parturients was recorded and Edinburgh Postnatal Depression Scale (EPDS was used to evaluate the depression condition of parturients at the prenatal 1 day and the 42th day postpartum, and with a cut-off point of 12/13 for identifying PPD. The genotypes of BDNF gene locus G712A, rs56164415, rs11030100, rs11030101 and rs6265 were measured by Sequenom® Mass Array SNP. Finally, the correlations of PPD to different genotypes and general information of parturients were statistically analyzed. Results The incidence of PPD among the selected subjects was 7.2%. Pregnancy mental stress, poor pregnancy mood, perinatal elevated monocyte count, prenatal depression mood and BDNF gene locus rs6265 mutation all could affect the incidence of PPD in cesarean section parturients (P0.05, and their haploid forms were not related to PPD also. Conclusion BDNF rs6265CC genotype, pregnancy mental stress, poor pregnancy mood, perinatal elevated monocyte count and prenatal depression mood are the risk factors for postpartum depression. DOI: 10.11855/j.issn.0577-7402.2017.06.11

  13. Genetic influences on insight problem solving: the role of catechol-O-methyltransferase (COMT) gene polymorphisms.

    Science.gov (United States)

    Jiang, Weili; Shang, Siyuan; Su, Yanjie

    2015-01-01

    People may experience an "aha" moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-O-methyltransferase (COMT) gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving.

  14. Genetic influences on insight problem solving: The role of catechol-o-methyltransferase (COMT gene polymorphisms

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    Weili eJiang

    2015-10-01

    Full Text Available People may experience an aha moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-o-methyltransferase (COMT gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving.

  15. Genetic polymorphism of the phospholipase C epsilon 1 gene and risk of gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Liu Xinyang; Zhang Xiaowei; Wang Zhichao; Chang Jinjia; Wu Zheng; Zhang Zhe; Wang Shanshan

    2014-01-01

    Background The pathogenesis of gastric cancer (GC) involves environmental and genetic factors.Recently,two genome-wide association studies found that phospholipase C epsilon 1 (PLCE1) polymorphisms might be related to GC risk,and several studies further validated this finding.However,these studies yielded inconsistent results.Methods A comprehensive database search was performed to identify eligible studies.Odds ratios with 95% confidence intervals were calculated to assess the strength of the association between PLCE1 rs2274223,rs753724,and rs11187842 and risk of GC.Subgroup analyses,publication bias,and sensitivity analyses were also conducted.Results Eleven studies (12 cohorts) were included in the meta-analysis.Based on 13 676 cases and 23 569 controls,a significant association between PLCE1 rs2274223 and GC risk was detected under various genotypic models.In the subgroup analyses,the association was significant for cardia GC,but weak for non-cardia GC.The association under the heterozygote model was detected for PLCE1 rs753724 and rs11187842 based on three studies involving 2768 cases and 3890 controls.Conclusions Our findings demonstrate that the presence of the G allele at rs2274223 of the PLCE1 gene may contribute to susceptibility to GC,especially cardia GC.PLCE1 rs753724 and rs11187842 are associated with GC risk under the heterozygote model.Further well-designed large studies are warranted to validate these findings.

  16. Use of latent class models to accommodate inter-laboratory variation in assessing genetic polymorphisms associated with disease risk

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    Walter Stephen D

    2008-08-01

    Full Text Available Abstract Background Researchers wanting to study the association of genetic factors with disease may encounter variability in the laboratory methods used to establish genotypes or other traits. Such variability leads to uncertainty in determining the strength of a genotype as a risk factor. This problem is illustrated using data from a case-control study of cervical cancer in which some subjects were independently assessed by different laboratories for the presence of a genetic polymorphism. Inter-laboratory agreement was only moderate, which led to a very wide range of empirical odds ratios (ORs with the disease, depending on how disagreements were treated. This paper illustrates the use of latent class models (LCMs and to estimate OR while taking laboratory accuracy into account. Possible LCMs are characterised in terms of the number of laboratory measurements available, and if their error rates are assumed to be differential or non-differential by disease status and/or laboratory. Results The LCM results give maximum likelihood estimates of laboratory accuracy rates and the OR of the genetic variable and disease, and avoid the ambiguities of the empirical results. Having allowed for possible measurement error in the expure, the LCM estimates of exposure – disease associations are typically stronger than their empirical equivalents. Also the LCM estimates exploit all the available data, and hence have relatively low standard errors. Conclusion Our approach provides a way to evaluate the association of a polymorphism with disease, while taking laboratory measurement error into account. Ambiguities in the empirical data arising from disagreements between laboratories are avoided, and the estimated polymorphism-disease association is typically enhanced.

  17. Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14.

    Science.gov (United States)

    Edenberg, Howard J; Bierut, Laura J; Boyce, Paul; Cao, Manqiu; Cawley, Simon; Chiles, Richard; Doheny, Kimberly F; Hansen, Mark; Hinrichs, Tony; Jones, Kevin; Kelleher, Mark; Kennedy, Giulia C; Liu, Guoying; Marcus, Gregory; McBride, Celeste; Murray, Sarah Shaw; Oliphant, Arnold; Pettengill, James; Porjesz, Bernice; Pugh, Elizabeth W; Rice, John P; Rubano, Todd; Shannon, Stu; Steeke, Rhoberta; Tischfield, Jay A; Tsai, Ya Yu; Zhang, Chun; Begleiter, Henri

    2005-12-30

    The data provided to the Genetic Analysis Workshop 14 (GAW 14) was the result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from The Center for Inherited Disease Research (CIDR) and the organizers of GAW 14, Jean MacCluer and Laura Almasy. The DNA, phenotypic characterization, and microsatellite genomic survey were provided by the Collaborative Study on the Genetics of Alcoholism (COGA), a nine-site national collaboration funded by the National Institute of Alcohol and Alcoholism (NIAAA) and the National Institute of Drug Abuse (NIDA) with the overarching goal of identifying and characterizing genes that affect the susceptibility to develop alcohol dependence and related phenotypes. CIDR, Affymetrix, and Illumina provided single-nucleotide polymorphism genotyping of a large subset of the COGA subjects. This article briefly describes the dataset that was provided.

  18. Effect of serotonin-related gene polymorphisms on pathogenesis and treatment response in Korean schizophrenic patients.

    Science.gov (United States)

    Kim, Yong-Ku; Yoon, Ho-Kyoung

    2011-09-01

    Serotonin has been implicated in the pathophysiology of several psychiatric disorders including schizophrenia. Serotonergic system-related genes may be good candidates in investigating the genetic basis of schizophrenia. We aimed to investigate the associations of HTR1A C-1019G, HTR2A-1438A/G, TPH1 218A/C, and TPH2-703G/T variants with schizophrenia. A total of 202 patients with schizophrenia and 165 normal controls were genotyped for HTR1A C-1019G, HTR2A-1438A/G, TPH1 218A/C, and TPH2-703G/T single nucleotide polymorphisms (SNPs). In order to assess the severity of a patient's psychiatric symptoms, the brief psychiatric rating scale (BPRS), the positive and negative symptom scale (PANSS), and the Calgary depression scale for Schizophrenia (CDSS) were administered. Genotype and allele frequencies were compared between groups via χ(2) statistics. Associations between the genotypes of candidate SNPs with the severity of symptoms were examined with ANOVA by comparing the mean scores of BPRS, PANSS, and CDSS according to genotype. No significant differences in the genotype distributions and allele frequencies of four SNPs were found between patients with schizophrenia and normal controls. There was a trend towards association of HTR1A C-1019G polymorphism with negative symptom. Negative symptom score of PANSS was lower in the patients with CC genotype than in the G allele carriers. These results suggested that C allele might be associated with lesser negative symptom. More studies are needed to confirm these findings. In the future, we plan to study the associations between schizophrenia and other genetic polymorphisms.

  19. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

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    Yuichi Nakajima

    Full Text Available The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts. We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L and 44 were mt-Short (mt-S. Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs among the 53 mt-L colonies (NMLL/N = 0.189, and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159. Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001. Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

  20. Glucocorticoid-related genetic susceptibility for Alzheimer's disease.

    Science.gov (United States)

    de Quervain, Dominique J-F; Poirier, Raphael; Wollmer, M Axel; Grimaldi, Luigi M E; Tsolaki, Magdalini; Streffer, Johannes R; Hock, Christoph; Nitsch, Roger M; Mohajeri, M Hasan; Papassotiropoulos, Andreas

    2004-01-01

    Because glucocorticoid excess increases neuronal vulnerability, genetic variations in the glucocorticoid system may be related to the risk for Alzheimer's disease (AD). We analyzed single-nucleotide polymorphisms in 10 glucocorticoid-related genes in a population of 814 AD patients and unrelated control subjects. Set-association analysis revealed that a rare haplotype in the 5' regulatory region of the gene encoding 11beta-hydroxysteroid dehydrogenase type 1 (HSD11B1) was associated with a 6-fold increased risk for sporadic AD. Results of a reporter-gene assay indicated that the rare risk-associated haplotype altered HSD11B1 transcription. HSD11B1 controls tissue levels of biologically active glucocorticoids and thereby influences neuronal vulnerability. Our results indicate that a functional variation in the glucocorticoid system increases the risk for AD, which may have important implications for the diagnosis and treatment of this disease.

  1. Genetic Architecture of Plasma Adiponectin Overlaps With the Genetics of Metabolic Syndrome–Related Traits

    Science.gov (United States)

    Henneman, Peter; Aulchenko, Yurii S.; Frants, Rune R.; Zorkoltseva, Irina V.; Zillikens, M. Carola; Frolich, Marijke; Oostra, Ben A.; van Dijk, Ko Willems; van Duijn, Cornelia M.

    2010-01-01

    OBJECTIVE Adiponectin, a hormone secreted by adipose tissue, is of particular interest in metabolic syndrome, because it is inversely correlated with obesity and insulin sensitivity. However, it is not known to what extent the genetics of plasma adiponectin and the genetics of obesity and insulin sensitivity are interrelated. We aimed to evaluate the heritability of plasma adiponectin and its genetic correlation with the metabolic syndrome and metabolic syndrome–related traits and the association between these traits and 10 ADIPOQ single nucleotide polymorphisms (SNPs). RESEARCH DESIGN AND METHODS We made use of a family-based population, the Erasmus Rucphen Family study (1,258 women and 967 men). Heritability analysis was performed using a polygenic model. Genetic correlations were estimated using bivariate heritability analyses. Genetic association analysis was performed using a mixed model. RESULTS Plasma adiponectin showed a heritability of 55.1%. Genetic correlations between plasma adiponectin HDL cholesterol and plasma insulin ranged from 15 to 24% but were not significant for fasting glucose, triglycerides, blood pressure, homeostasis model assessment of insulin resistance (HOMA-IR), and C-reactive protein. A significant association with plasma adiponectin was found for ADIPOQ variants rs17300539 and rs182052. A nominally significant association was found with plasma insulin and HOMA-IR and ADIPOQ variant rs17300539 after adjustment for plasma adiponectin. CONCLUSIONS The significant genetic correlation between plasma adiponectin and HDL cholesterol and plasma insulin should be taken into account in the interpretation of genome-wide association studies. Association of ADIPOQ SNPs with plasma adiponectin was replicated, and we showed association between one ADIPOQ SNP and plasma insulin and HOMA-IR. PMID:20067957

  2. Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates.

    Science.gov (United States)

    Ju, Hye-Lim; Kang, Jung-Mi; Moon, Sung-Ung; Kim, Jung-Yeon; Lee, Hyeong-Woo; Lin, Khin; Sohn, Woon-Mok; Lee, Jin-Soo; Kim, Tong-Soo; Na, Byoung-Kuk

    2012-03-01

    Plasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed. Fifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs. Thirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII. PvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine.

  3. Genetic polymorphisms in peroxisome proliferator-activated receptor delta associated with obesity.

    Science.gov (United States)

    Shin, Hyoung Doo; Park, Byung Lae; Kim, Lyoung Hyo; Jung, Hye Seung; Cho, Young Min; Moon, Min Kyong; Park, Young Joo; Lee, Hong Kyu; Park, Kyong Soo

    2004-03-01

    Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors regulating the expression of genes involved in lipid and glucose metabolism. Three different PPARs, PPAR-alpha, -gamma, and -delta, have been characterized, and they are distinguished from each other by tissue distribution and cell activation. All PPARs are, to different extents, activated by fatty acids and derivatives. Recently, it has been shown that PPAR-delta serves as a widespread regulator of fat burning, suggesting that it might be a potential target in the treatment of obesity and type 2 diabetes. In an effort to identify polymorphic markers in potential candidate genes for type 2 diabetes, we have sequenced PPAR-delta, including -1,500 bp of the 5' flanking region. Nine polymorphisms were identified in PPAR-delta: four in the intron, one in the 5' untranslated region (UTR), and four in the 3' UTR. Among identified polymorphisms, five common sites, including c.-13454G>T, c.-87T>C, c.2022+12G>A, c.2629T>C, and c.2806C>G, were genotyped in subjects with type 2 diabetes and normal control subjects (n = 702). The genetic associations with the risk of type 2 diabetes and metabolic phenotype were analyzed. No significant associations with the risk of type 2 diabetes were detected. However, several positive associations of PPAR-delta polymorphisms with fasting plasma glucose and BMI were detected in nondiabetic control subjects. The genetic information about PPAR-delta from this study would be useful for further genetic study of obesity, diabetes, and other metabolic diseases.

  4. The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the repeatability of evolution.

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    Carrie A Wu

    Full Text Available A long-standing question in evolutionary biology asks whether the genetic changes contributing to phenotypic evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within a population of Mimulus lewisii. To determine whether these types of changes are predictable, we combined this information with data from other species to investigate whether the spectrum of mutations affecting flower color transitions differs based on the evolutionary time-scale since divergence. We used classic genetic techniques, along with gene expression and population genetic approaches, to identify the putative, loss-of-function mutation that generates rare, white flowers instead of the common, pink color in M. lewisii. We found that a frameshift mutation in an anthocyanin pathway gene is responsible for the white-flowered polymorphism found in this population of M. lewisii. Comparison of our results with data from other species reveals a broader spectrum of flower color mutations segregating within populations relative to those that fix between populations. These results suggest that the genetic basis of fixed differences in flower color may be predictable, but that for segregating variation is not.

  5. A genetic linkage map for Tribolium confusum based on random amplified polymorphic DNAs and recombinant inbred lines.

    Science.gov (United States)

    Yezerski, A; Stevens, L; Ametrano, J

    2003-10-01

    Tribolium beetles provide an excellent and easily manipulated model system for the study of genetics. However, despite significant increases in the availability of molecular markers for the study of genetics in recent years, a significant genetic linkage map for these beetles remains undeveloped. We present the first molecular genetic linkage map for Tribolium confusum using random amplified polymorphic DNA markers. The linkage map contains 137 loci mapped on to eight linkage groups totaling 968.5 cM.

  6. Inference of distant genetic relations in humans using "1000 genomes".

    Science.gov (United States)

    Al-Khudhair, Ahmed; Qiu, Shuhao; Wyse, Meghan; Chowdhury, Shilpi; Cheng, Xi; Bekbolsynov, Dulat; Saha-Mandal, Arnab; Dutta, Rajib; Fedorova, Larisa; Fedorov, Alexei

    2015-01-07

    Nucleotide sequence differences on the whole-genome scale have been computed for 1,092 people from 14 populations publicly available by the 1000 Genomes Project. Total number of differences in genetic variants between 96,464 human pairs has been calculated. The distributions of these differences for individuals within European, Asian, or African origin were characterized by narrow unimodal peaks with mean values of 3.8, 3.5, and 5.1 million, respectively, and standard deviations of 0.1-0.03 million. The total numbers of genomic differences between pairs of all known relatives were found to be significantly lower than their respective population means and in reverse proportion to the distance of their consanguinity. By counting the total number of genomic differences it is possible to infer familial relations for people that share down to 6% of common loci identical-by-descent. Detection of familial relations can be radically improved when only very rare genetic variants are taken into account. Counting of total number of shared very rare single nucleotide polymorphisms (SNPs) from whole-genome sequences allows establishing distant familial relations for persons with eighth and ninth degrees of relationship. Using this analysis we predicted 271 distant familial pairwise relations among 1,092 individuals that have not been declared by 1000 Genomes Project. Particularly, among 89 British and 97 Chinese individuals we found three British-Chinese pairs with distant genetic relationships. Individuals from these pairs share identical-by-descent DNA fragments that represent 0.001%, 0.004%, and 0.01% of their genomes. With affordable whole-genome sequencing techniques, very rare SNPs should become important genetic markers for familial relationships and population stratification. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Genetic variability of Amorphophallus muelleri Blume in Java based on Random Amplified Polymorphic DNA

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    DIYAH MARTANTI

    2008-10-01

    Full Text Available Amorphophallus muelleri Blume (Araceae is valued for its glucomanan content for use in food industry (healthy diet food, paper industry, pharmacy and cosmetics. The species is triploid (2n=3x=39 and the seed is developed apomictically. The present research is aimed to identify genetic variability of six population of A. muelleri from Java (consisted of 50 accessions using random amplified polymorphic DNA (RAPD. The six populations of the species are: East Java: (1 Silo-Jember, (2 Saradan-Madiun, (3 IPB (cultivated, from Saradan-Madiun, (4 Panti-Jember, (5 Probolinggo; and Central Java: (6 Cilacap. The results showed that five RAPD primers generated 42 scorable bands of which 29 (69.05% were polymorphic. Size of the bands varied from 300bp to 1.5kbp. The 50 accessions of A. muelleri were divided into two main clusters, some of them were grouped based on their populations, and some others were not. The range of individual genetic dissimilarity was from 0.02 to 0.36. The results showed that among six populations investigated, Saradan population showed the highest levels of genetic variation with mean values of na = 1.500+ 0.5061, ne = 1.3174 + 0.3841, PLP = 50% and He = 0, 0.1832+0.2054, whereas Silo-Jember population showed the lowest levels of genetic variation with mean values na = 1.2619+ 0.4450, ne = 1.1890 + 0.3507, PLP = 26.19% and He = 0.1048+0.1887. Efforts to conserve, domesticate, cultivate and improve genetically should be based on the genetic properties of each population and individual within population, especially Saradan population which has the highest levels of genetic variation, need more attention for its conservation.

  8. Brassica, biotransformation and cancer risk: genetic polymorphisms alter the preventive effects of cruciferous vegetables.

    Science.gov (United States)

    Lampe, Johanna W; Peterson, Sabrina

    2002-10-01

    The chemoprotective effect of cruciferous vegetables is due to their high glucosinolate content and the capacity of glucosinolate metabolites, such as isothiocyanates (ITC) and indoles, to modulate biotransformation enzyme systems (e.g., cytochromes P450 and conjugating enzymes). Data from molecular epidemiologic studies suggest that genetic and associated functional variations in biotransformation enzymes, particularly glutathione S-transferase (GST)M1 and GSTT1, which metabolize ITC, alter cancer risk in response to cruciferous vegetable exposure. Moreover, genetic polymorphisms in receptors and transcription factors that interact with these compounds may further contribute to variation in response to cruciferous vegetable intake. This review outlines the metabolism and mechanisms of action of cruciferous vegetable constituents, discusses the recent human studies testing effects of cruciferous vegetables on biotransformation systems and summarizes the epidemiologic and experimental evidence for an effect of genetic polymorphisms in these enzymes on response to cruciferous vegetable intake. Taken together, genetic differences in biotransformation enzymes and the factors that regulate them, as well as variation in glucosinolate content of cruciferous vegetables and the methods used to prepare these foods underscore the multiple layers of complexity that affect the study of gene-diet interactions and cancer risk in humans.

  9. Genetic polymorphism of 30 autosomal InDel loci in Chinese Uygur population residing in Xinjiang

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    Ru-feng BAI

    2014-10-01

    Full Text Available Objective To investigate the genetic data of 30 insertion deletion polymorphism (InDel loci included in Investigator® DIPplex in Uygur population from Xinjiang, and evaluate its application in forensic medicine. Methods Allele frequencies, population genetics parameters of the 30 InDels were determined in 223 unrelated Uygur individuals with Investigator® DIPplex, and they were statistically analyzed and compared with available data of other populations of different races from different regions. Results After Bonferroni's correction, there were no significant departure from Hardy-Weinberg equilibrium or linkage disequilibrium between the loci. The average heterozygosity (Ho was 0.468 6, the mean discrimination power (DP was 0.609 5, and the total probability of discrimination power (TDP reached 0.999 999 999 995. The cumulative probability of exclusion was 0.995 478 in trio cases (CPEtrio and 0.972 007 in duo cases (CPEduo. The genetic distance between Uygur and Kazakh was closer than those between Uygur and other populations, such as African American. Conclusion Multiplex detection of the 30 InDel loci revealed a moderately high polymorphic genetic distribution in Chinese Uygur population residing in Xinjiang, demonstrating that the Investigator® DIPplex kit can be used as a supplementary tool for human identity tests, especially in challenging DNA cases. DOI: 10.11855/j.issn.0577-7402.2014.10.10

  10. GENETIC POLYMORPHISM OF SIX Y CHROMOSOMAL STR IN CHINESE HUI ETHNIC GROUP

    Institute of Scientific and Technical Information of China (English)

    Zhu Bofeng; Lü Guiping; Yao Guifa; Zhu Jun; Dong Hongwang; Sun Qingdong; Huang Lei; Liu Yao

    2005-01-01

    Objective To study genetic polymorphism of 6 Y chromosomal STR in Hui ethnic group living in Ningxia Hui ethnic autonomous region, in order to evaluate their usefulness in forensic science and enrich the Chinese genetic information resources. Methods We investigated 101 unrelated, healthy, male individuals of Hui ethnic group and studied their allelic frequency distribution and haplotype diversity of 6 Y chromosomal STR. Primer for each loci was labeled with the fluorescent by FAM (blue) or TAMRA(yellow). The data of Hui ethnic group were generated co-amplification, GeneScan, genotype, and genetic distribution analysis. Results 31 alleles and 43 phenotype(DYS385) were detected, with the frequencies ranging from 0.0099-0.7129. Out of a total of 101 individuals, 96 showed different haplotypes; 91 were unique; 5 were found 2 times. The haplotype diversity for 6 Y-STR loci was 0.9990. Conclusion The date obtained can be valuable for individual identification, paternity testing in forensic fields and for population genetics because of 6 Y-STR loci high polymorphism.

  11. Genetic diversity among Puntius sophore complex using restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Smitha Balaraj

    2012-08-01

    Full Text Available Restriction fragment length polymorphism (RFLP analysis of genomic DNA was employed to characterize species of Puntius sophore complex, a benthopelagic freshwater fish species. Samples of five species of Puntius viz, Puntius sophore, Puntius amphibius, Puntius chola, Puntius bimaculatus and Puntius dorsalis from the East-flowing Tamiraparani and Kuzhithurai and West-flowing Tamiraparani river basins (Western Ghats were analyzed. The restriction enzyme employed (Hind III generated species-specific DNA patterns for each of the five species. DNA exhibited considerable polymorphism among species. All samples showed relatively high values of diversity. The relation between species is discussed.

  12. Association of OGG1 and MTHFR polymorphisms with age-related cataract: A systematic review and meta-analysis

    Science.gov (United States)

    Liu, Yizhi

    2017-01-01

    Purpose To discern and confirm genetic biomarkers that help identify populations at high risk for age-related cataract (ARC). Methods A literature search was performed in the PubMed, Web of Science and China National Knowledge Internet databases for genetic association studies published before June 26, 2016 regarding ARC susceptibility. All genetic polymorphisms reported were systematically reviewed, followed by extraction of candidate genes/loci with sufficient genotype data in ≥3 studies for the meta-analysis. A random/fixed-effects model was used to calculate the pooled odds ratios and 95% confidence intervals to evaluate the associations considering multiple genetic models. Sensitivity analysis was also performed. Results A total of 144 polymorphisms in 36 genes were reported in the 61 previous genetic association studies. Thereby, three polymorphisms of two genes (8-oxoguanine DNA glycosylase-1 [OGG1]; methylenetetrahydrofolate reductase NADPH [MTHFR]) in eight studies were included in the meta-analysis. Regarding the OGG1-rs1052133, the GG (OR = 1.925; 95%CI, 1.181–3.136; p = 0.009) and CG (OR = 1.384; 95%CI, 1.171–1.636; p<0.001) genotypes indicated higher risk of ARC. For the MTHFR gene, the CC+TT genotype of rs1801133 might be protective (OR, 0.838; 95%CI, 0.710–0.989; p = 0.036), whereas the AA+CC genotype of rs1801131 indicated increased risk for the mixed subtype (OR = 1.517; 95%CI, 1.113–2.067; p = 0.008). Conclusions Polymorphisms of OGG1 and MTHFR genes are associated with ARC susceptibility and may help identify populations at high risk for ARC. PMID:28253266

  13. Genetic polymorphisms in the carbonic anhydrase VI gene and dental caries susceptibility.

    Science.gov (United States)

    Li, Z-Q; Hu, X-P; Zhou, J-Y; Xie, X-D; Zhang, J-M

    2015-06-01

    We investigated the role of 7 single nucleotide polymorphisms in the carbonic anhydrase (CA) VI gene (rs2274328, rs17032907, rs11576766, rs2274333, rs10864376, rs3765964, and rs6680186) and the possible association between these polymorphisms and dental caries susceptibility in a Northwestern Chinese population. We collected samples from 164 high caries experience and 191 very low caries experience and conducted a case-control study according to the number of decayed, missing, and filled teeth index and genotyped the 7 polymorphisms using a 384-well plate format with the Sequenom MassARRAY platform. Individuals carrying the rs17032907 TT genotype were more likely to have an increased risk of dental caries compared with carriers of the C/C genotype in the co-dominant model, with an odds ratio (95% confidence interval) of 2.144 (1.096-4.195). We also found that the haplotype (ACA) (rs2274328, rs17032907 and rs11576766) was associated with a low number of decayed, missing, and filled teeth index with an odds ratio (95% confidence interval) of 0.635 (0.440-0.918). However, we found no association between dental caries susceptibility and the rs2274328, rs11576766, rs2274333, rs10864376, rs3765964, and rs6680186 polymorphisms and other haplotypes. The rs17032907 genetic variant and the haplotype (ACA) of CA VI may be associated with dental caries susceptibility.

  14. The impact of a TSH receptor gene polymorphism on thyroid-related phenotypes in a healthy Danish twin population

    DEFF Research Database (Denmark)

    Hansen, P.S.; Deure, W.M. van der; Peeters, R.P.;

    2007-01-01

    OBJECTIVES: The Asp727Glu polymorphism in the TSH receptor (TSHR) gene is associated with serum TSH levels. However, the proportion of genetic variation accounted for by this polymorphism is unknown. In this study, we (1) examined the association of the Asp727Glu polymorphism with thyroid size...

  15. Analysis of Genetic Diversity and Relationships in a Tunisian Fig (Ficus carica) Germplasm Collection by Random Amplified Microsatellite Polymorphisms

    Institute of Scientific and Technical Information of China (English)

    Khaled Chatti; Olfa Saddoud; Amel Salhi-Hannachi; Messaoud Mars; Mohamed Marrakchi; Mokhtar Trifi

    2007-01-01

    The random amplified mirosatellite polymorphism method was performed in a set of Tunisian fig landraces using eighteen primer combinations. Atotal of sixty three random amplified microsatellite polymorphism (RAMPO) markers were scored and used either to assess the genetic diversity in these cultivars or to detect cases of mislabeling. Opportunely, data proved that the designed procedure constitutes an attractive and fast method with low costs and prevents radio exposure. As a result, we have identified the primer combinations that are the most efficient to detect genetic polymorphism in this crop. Therefore, the derived unweighted pair-group method with arithmetic averages (UPGMA) dendrogram illustrates the genetic divergence among the landraces studied and exhibits a typically continuous variation. Moreover, no evident correlation between the sexes of trees was observed. In addition, using these markers, discrimination between landraces has been achieved. Thus, random amplified mirosatellite polymorphism is proved to be powerful for characterizing the local fig germplasm.

  16. Genetic polymorphism of human glutathione S-transferase A1 gene in mainland Chinese and its association with phenotype

    Institute of Scientific and Technical Information of China (English)

    JiePING; HuiWANG

    2005-01-01

    AIM Human glutathione S-transferase A1 (GSTA1) is an important phase Ⅱ metabolizing enzyme involved in the metabolism of many therapeutic drugs and is responsible for the metabolic detoxification of numerous promutagens and procarcinogens. The genetic polymorphism of GSTA1 has important implications for drug efficacy and cancer susceptibility. In this study, we determined the distribution of GSTA1 genetic polymorphism in Mainland Chinese. And we also investigated whether there exists the potential phenotype alterations caused by the genetic polymorphism in human. METHODS Genomic DNA was ex-tracted from peripheral blood of 140 Chinese people and 16 liver tissues obtained from non-liverish patients who underwent partial hepatectomy. And then the genotypes of human GSTA1 gene were analyzed by polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP).

  17. Association of the Genetic Polymorphisms RRM1 -756T>C and -269C>A With Cervical Neoplasia.

    Science.gov (United States)

    Chang, Ching-Wen; Yang, Shun-Fa; Wang, Po-Hui; Chang, Hsiu-Ju; Liu, Wen-Chi; Tsai, Hsiu-Ting

    2016-10-01

    Cervical neoplasia is one of the most prevalent malignant neoplasms worldwide. Ribonucleotide reductase 1 (RRM1) is thought to play an essential role in modulating the development and progression of cervical neoplasia. Two novel genetic polymorphisms, RRM1 -756T>C and -269 C>A, are significantly correlated with RRM1 expression. Some epidemiological studies have demonstrated that genetic variants play a crucial role in susceptibility to cervical cancer. The present study aimed to identify the genetic polymorphisms RRM1 -756T>C and -269 C>A in patients with cervical neoplasia and healthy controls. In total, 493 subjects, comprising 324 healthy controls and 169 patients with cervical neoplasia, were enrolled for this study. The allelic discrimination of the RRM1 -756T>C (rs11030918) and -269C>A (rs12806698) polymorphisms was assessed using the ABI StepOne™ real-time polymerase chain reaction system and analyzed using Software Design Specification (SDS), Version 3.0, software with TaqMan assays. The risk of cervical cancer was examined, revealing adjusted odds ratios and 95% confidence intervals of 1.25 [0.51, 3.08] and 1.09 [0.43, 2.78] for individuals with CC alleles of RRM1 -756T>C and for individuals with AA alleles of RRM1 -269C>A genetic polymorphisms, respectively, compared to individuals with wild-type RRM1 genetic polymorphisms. No significant genetic interaction effect was observed in susceptibility to cervical neoplasia, and no association was found between genetic polymorphisms and clinical statuses of invasive cervical cancer. The genetic polymorphisms RRM1 -756T>C and -269C>A may not be a factor for susceptibility to cervical neoplasia.

  18. Allergic rhinitis and genetic components: focus on Toll-like receptors (TLRs gene polymorphism

    Directory of Open Access Journals (Sweden)

    Zhiwei Gao

    2010-11-01

    Full Text Available Zhiwei Gao1, Donna C Rennie2, Ambikaipakan Senthilselvan11Department of Public Health Sciences, School of Public Health, University of Alberta, Edmonton, Alberta, Canada; 2College of Nursing and Canadian Centre for Health and Agricultural Safety, University of Saskatchewan, Saskatoon, Saskatchewan, CanadaAbstract: Allergic rhinitis represents a global health issue affecting 10% to 25% of the population worldwide. Over the years, studies have found that allergic diseases, including allergic rhinitis, are associated with immunological responses to antigens driven by a Th2-mediated immune response. Because Toll-like receptors (TLRs are involved in both innate and adaptive immune responses to a broad variety of antigens, the association between polymorphisms of TLRs and allergic diseases has been the focus in many animal and human studies. Although the etiology of allergic rhinitis is still unknown, extensive research over the years has confirmed that the underlying causes of allergic diseases are due to many genetic and environmental factors, along with the interactions among them, which include gene–environment, gene–gene, and environment–environment interactions. Currently, there is great inconsistency among studies mainly due to differences in genetic background and unique gene–environment interactions. This paper reviews studies focusing on the association between TLR polymorphisms and allergic diseases, including allergic rhinitis, which would help researchers better understand the role of TLR polymorphisms in the development of allergic rhinitis, and ultimately lead to more efficient therapeutic interventions being developed.Keywords: allergic rhinitis, allergic diseases, Toll-like receptors

  19. Meta-analysis of tau genetic polymorphism and sporadic progressive supranuclear palsy susceptibility

    Institute of Scientific and Technical Information of China (English)

    Hai Yuan; Xiuyan Yang; Hanlin Kang; Ying Cheng; Huiming Ren; Xiaotong Wang

    2011-01-01

    OBJECTIVE: To quantitatively evaluate the association between tau genetic polymorphism (H, and H2) and susceptibility to sporadic progressive supranuclear palsy (PSP).DATA SOURCES: Relevant Medical Subject Heading terms and text words were used to identify articles from MEDLINE (1966/2010 07), EMBASE (1984/2010-07), and Chinese National Knowledge Infrastructure (1979/2010), as well as references of the retrieved articles.STUDY SELECTION: The selected articles met the following criteria: sporadic PSP case group and healthy control group, as well as genotype frequency (H,/H, and H,/H2+H2/H2) in cases and controls.Genotype distribution in the control groups was tested using the Hardy-Weinberg Equilibrium (HWE).Articles irrelevant to HWE were excluded, and a forest plot was performed to combine all selected articles with Review Manager (Version 5.0).MAIN OUTCOME MEASURES: The summary odds ratios and corresponding 95% confidence intervals (95%Cl)for tau polymorphism (H,/H, and H,/H2+H2/H2) between sporadic PSP case and healthy control groups were estimated using the fixed effects model to assess whether tau genetic polymorphism is associated with sporadic PSP susceptibility.RESULTS: According to inclusion and exclusion criteria, a total of 16 articles, which included 1 337 sporadic PSP cases and 2 073 controls, were used in the study.Two articles were excluded because of deviation from HWE in the control groups.The combined result, based on all studies,showed a significant difference in genotype distribution between cases and controls: H,H, vs.H,H2 +H2H2 (odds ratio (OR)=4.98, 95%Cl: 3.97-6.23, P < 0.01).Stratifying for geographic distribution of PSP, sporadic PSP cases exhibited a significantly higher frequency of H,H, genotypes than controls in the United States (OR=4.07, 95%CF.3.16-5.25, P < 0.01) and Europe (OR=8.60,95%C1.5.05-14.64, P < 0.01).CONCLUSION: Tau genetic polymorphism is associated with sporadic PSP susceptibility, and geographic distribution might

  20. Expression of STK39 in peripheral blood of hypertension patients and the relationship between its genetic polymorphism and blood pressure.

    Science.gov (United States)

    Li, B; Yang, M; Liu, J W

    2015-01-01

    This study investigated the STK39 expression in peripheral blood of hypertension patients and the relation between its genetic polymorphism and blood pressure. The observation group comprised of 42 primary hypertension patients admitted to our hospital, and the control group comprised of 30 healthy individuals who underwent physical examination in our hospital during the same period. Fasting venous blood was collected from both groups in the morning to determine the STK39 mRNA and protein levels in peripheral blood using quantitative real-time PCR and western blot. STK39 gene SNP (rs6433027) was sequenced using PCR and its genetic variation was analyzed. The relationship between STK39 protein level, genetic variation, and diastolic and systolic blood pressure was also analyzed. The observation group showed increased STK39 mRNA and protein levels in peripheral blood compared to the control group, and the difference was statistically significant (P blood pressure (P blood pressure (P hypertension patients with genetic variation, which is related to the blood pressure.

  1. Effect of genetic polymorphisms in the folate pathway on methotrexate therapy in rheumatic diseases.

    Science.gov (United States)

    Stamp, Lisa K; Roberts, Rebecca L

    2011-10-01

    Methotrexate (MTX) is the first-line treatment for rheumatoid arthritis and is frequently used in the management of other forms of inflammatory arthritis. It is currently challenging to predict which patients will achieve adequate disease control and which patients will develop adverse effects while taking MTX. As an analog of dihydrofolic acid, MTX enters cells through the reduced folate carrier-1 protein, and is polyglutamated. MTX polyglutamates inhibit key enzymes in the folate pathway to produce an anti-inflammatory effect. It has been suggested that genetic polymorphisms in the folate pathway may influence intracellular folate and MTX polyglutamates pools, and thus MTX response. However, studies to identify genetic predictors have yielded inconclusive results. Nonreplication across studies has been attributed to insufficient statistical power as well as pharmacological and clinical confounders. Prospective studies, standardizing the definitions of response and toxicity, and application of genome-wide approaches may advance the search for genetic predictors of MTX response.

  2. Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Xian; Wen-Ming Cong; Shu-Hui Zhang; Meng-Chao Wu

    2005-01-01

    AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments.METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD)with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated,purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data.RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size,histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene.CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcinogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis.

  3. Genetic variation in hemp and marijuana (Cannabis sativa L.) according to amplified fragment length polymorphisms.

    Science.gov (United States)

    Datwyler, Shannon L; Weiblen, George D

    2006-03-01

    Cannabis sativa L. (Cannabaceae) is one of the earliest known cultivated plants and is important in the global economy today as a licit and an illicit crop. Molecular markers distinguishing licit and illicit cultivars have forensic utility, but no direct comparison of hemp and marijuana amplified fragment length polymorphism (AFLP) has been made to date. Genetic variation was surveyed in three populations of fiber hemp and a potent cultivar of marijuana using AFLP markers. Ten primer pairs yielded 1206 bands, of which 88% were polymorphic. Eighteen bands represented fixed differences between all fiber populations and the drug cultivar. These markers have practical utility for (1) establishing conspiracy in the cultivation and distribution of marijuana, (2) identifying geographic sources of seized drugs, and (3) discriminating illegal, potent marijuana cultivars from hemp where the cultivation of industrial hemp is permitted.

  4. PRELIMINARY REPORT ON THE PUTATIVE ASSOCIATION OF IL10 -3575 T/A GENETIC POLYMORPHISM WITH MALARIA SYMPTOMS.

    Science.gov (United States)

    Domingues, Wilson; Kanunfre, Kelly Aparecida; Rodrigues, Jonatas Cristian; Teixeira, Leandro Emidio; Yamamoto, Lidia; Okay, Thelma Suely

    2016-01-01

    Only a small percentage of individuals living in endemic areas develop severe malaria suggesting that host genetic factors may play a key role. This study has determined the frequency of single nucleotide polymorphisms (SNPs) in some pro and anti-inflammatory cytokine gene sequences: IL6 (-174; rs1800795), IL12p40 (+1188; rs3212227), IL4 (+33; rs2070874), IL10 (-3575; rs1800890) and TGFb1 (+869; rs1800470), by means of PCR-RFLP. Blood samples were collected from 104 symptomatic and 37 asymptomatic subjects. Laboratory diagnosis was assessed by the thick blood smear test and nested-PCR. No association was found between IL6 (-174), IL12p40 (+1188), IL4 (+33), IL10 (- 3575), TGFb1 (+869) SNPs and malaria symptoms. However, regarding the IL10 -3575 T/A SNP, there were significantly more AA and AT subjects, carrying the polymorphic allele A, in the symptomatic group (c2 = 4.54, p = 0.01, OR = 0.40 [95% CI - 0.17- 0.94]). When the analysis was performed by allele, the frequency of the polymorphic allele A was also significantly higher in the symptomatic group (c2 = 4.50, p = 0.01, OR = 0.45 [95% CI - 0.21-0.95]). In conclusion, this study has suggested the possibility that the IL10 - 3575 T/A SNP might be associated with the presence and maintenance of malaria symptoms in individuals living in endemic areas. Taking into account that this polymorphism is related to decreased IL10 production, a possible role of this SNP in the pathophysiology of malaria is also suggested, but replication studies with a higher number of patients and evaluation of IL10 levels are needed for confirmation.

  5. XRCC7 rs#7003908 Polymorphism and Helicobacter pylori Infection-Related Gastric Antrum Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Chao Wang

    2013-01-01

    Full Text Available The X-ray repair cross-complementing group 7 (XRCC7 plays a key role in DNA repair that protects against genetic instability and carcinogenesis. To determine whether XRCC7 rs#7003908 polymorphism (XRCC7P is associated with Helicobacter pylori (H. pylori infection-related gastric antrum adenocarcinoma (GAA risk, we conducted a hospital-based case-control study, including 642 patients with pathologically confirmed GAA and 927 individually matched controls without any evidence of tumours or precancerous lesions, among Guangxi population. Increased risks of GAA were observed for individuals with cagA positive (odds ratio (OR 6.38; 95% confidence interval (CI 5.03–8.09. We also found that these individuals with the genotypes of XRCC7 rs#7003908 G alleles (XRCC7-TG or -GG featured increasing risk of GAA (ORs 2.80 and 5.13, resp., compared with the homozygote of XRCC7 rs#7003908 T alleles (XRCC7-TT. GAA risk, moreover, did appear to differ more significantly among individuals featuring cagA-positive status, whose adjusted ORs (95% CIs were 15.74 (10.89–22.77 for XRCC7-TG and 38.49 (22.82–64.93 for XRCC7-GG, respectively. Additionally, this polymorphism multiplicatively interacted with XRCC3 codon 241 polymorphism with respect to HCC risk (ORinteraction=1.49. These results suggest that XRCC7P may be associated with the risk of Guangxiese GAA related to cagA.

  6. MTHFR genetic polymorphism as a risk factor in Egyptian mothers with Down syndrome children.

    Science.gov (United States)

    Meguid, Nagwa A; Dardir, Ahmed A; Khass, Mohamed; Hossieny, Lamia El; Ezzat, Afaf; El Awady, Mostafa K

    2008-01-01

    Recent reports linking Down syndrome (DS) to maternal polymorphisms at the methylenetetrahydrofolate reductase (MTHFR) gene locus have generated great interest among investigators in the field. The present study aimed at evaluation of MTHFR 677C/T and 1298A/C polymorphisms in the MTHFR gene as maternal risk factors for DS. Forty two mothers of proven DS outcomes and forty eight control mothers with normal offspring were included. Complete medical and nutritional histories for all mothers were taken with special emphasis on folate intake. Folic acid intake from food or vitamin supplements was significantly low (below the Recommended Daily Allowance) in the group of case mothers compared to control mothers. Frequencies of MTHFR 677T and MTHFR 1298C alleles were significantly higher among case mothers (32.1% and 57.1%, respectively) compared to control mothers (18.7% and 32.3%, respectively). Heterozygous and homozygous genotype frequencies of MTHFR at position 677 (CT and TT) were higher among case mothers than controls (40.5% versus 25% and 11.9% versus 6.2%, respectively) with an odds ratio of 2.34 (95% confidence interval [CI] 0.93-5.89) and 2.75 (95% CI 0.95-12.77), respectively. Interestingly, the homozygous genotype frequency (CC) at position 1298 was significantly higher in case mothers than in controls (33.3% versus 2.1% respectively) with an odds ratio of 31.5 (95% CI 3.51 to 282.33) indicating that this polymorphism may have more genetic impact than 677 polymorphism. Heterozygous genotype (AC) did not show significant difference between the two groups. We here report on the first pilot study of the possible genetic association between DS and MTHFR 1298A/C genotypes among Egyptians. Further extended studies are recommended to confirm the present work.

  7. MTHFR Genetic Polymorphism As a Risk Factor in Egyptian Mothers with Down Syndrome Children

    Directory of Open Access Journals (Sweden)

    Nagwa A. Meguid

    2008-01-01

    Full Text Available Recent reports linking Down syndrome (DS to maternal polymorphisms at the methylenetetrahydrofolate reductase (MTHFR gene locus have generated great interest among investigators in the field. The present study aimed at evaluation of MTHFR 677C/T and 1298A/C polymorphisms in the MTHFR gene as maternal risk factors for DS. Forty two mothers of proven DS outcomes and forty eight control mothers with normal offspring were included. Complete medical and nutritional histories for all mothers were taken with special emphasis on folate intake. Folic acid intake from food or vitamin supplements was significantly low (below the Recommended Daily Allowance in the group of case mothers compared to control mothers. Frequencies of MTHFR 677T and MTHFR 1298C alleles were significantly higher among case mothers (32.1% and 57.1%, respectively compared to control mothers (18.7% and 32.3%, respectively. Heterozygous and homozygous genotype frequencies of MTHFR at position 677 (CT and TT were higher among case mothers than controls (40.5% versus 25% and 11.9% versus 6.2%, respectively with an odds ratio of 2.34 (95% confidence interval [CI] 0.93–5.89 and 2.75 (95% CI 0.95–12.77, respectively. Interestingly, the homozygous genotype frequency (CC at position 1298 was significantly higher in case mothers than in controls (33.3% versus 2.1% respectively with an odds ratio of 31.5 (95% CI 3.51 to 282.33 indicating that this polymorphism may have more genetic impact than 677 polymorphism. Heterozygous genotype (AC did not show significant difference between the two groups. We here report on the first pilot study of the possible genetic association between DS and MTHFR 1298A/C genotypes among Egyptians. Further extended studies are recommended to confirm the present work.

  8. Distribution of genetic polymorphism of aldehyde dehydrogenase-2 (ALDH2 in Indonesian subjects

    Directory of Open Access Journals (Sweden)

    Septelia I. Wanandi

    2002-09-01

    Full Text Available Aldehyde dehydrogenase (ALDH plays a pivotal role in the alcohol metabolism. Decreased activity of ALDH enzyme has more influence on the hypersensitivity to alcohol than of alcohol dehydrogenase. ALDH enzyme exists in several isozymes. Among these isozymes, ALDH2 is a major isozyme that has a very high affinity for acetaldehyde. Recent studies suggested that the deficiency of ALDH2 may be inherited. Functional polymorphism of ALDH2 gene has been observed in a nucleotide of the 487th codon. In the atypical gene, this codon consists of AAA nucleotides for lysine, instead of GAA for glutamic acid in the wild type gene. In this study, we have analyzed the genetic polymorphism of ALDH2 gene among 100 Indonesian students using genomic DNA extracted from hair roots. Polymerase chain reaction (PCR and restriction fragment length polymorphism (RFLP methods were performed for this purpose. Three oligonucleotide primers were designed for two steps PCR. The reverse primer R was intentionally constructed not to be 100% complementary to the template strand, to generate a restriction site for Eco RI within the variable nucleotide in the PCR product of ALDH2 gene. This study indicates that 70 subjects (70% have wild type, 29 (29% atypical heterozygote and only 1 (1% atypical homozygote ALDH2 alleles. Conclusively, the atypical ALDH2 allele frequency in Indonesians (31/200 is higher than in Caucasoids (only about 5-10%, but less than in Mongoloids (40-50%. This may be due to the diverse ethnics of Indonesian population. (Med J Indones 2002; 11: 135-42 Keywords: alcohol hypersensitivity, genetic polymorphism, aldehyde dehydrogenase-2 (ALDH2 gene

  9. Genetic polymorphisms in metabolizing enzymes modify the association between Smoking and Inflammatory Bowel Diseases

    Science.gov (United States)

    Ananthakrishnan, Ashwin N; Nguyen, Deanna D; Sauk, Jenny; Yajnik, Vijay; Xavier, Ramnik J

    2014-01-01

    Introduction Cigarette smoking is a well established environmental risk factor for Crohn's disease (CD) and ulcerative colitis (UC). The exact mechanism of its effect remains unexplained. Genetic polymorphisms in metabolizing enzymes may influence susceptibility to the effect of smoking and shed light on its mechanism of action. Methods We utilized a prospective cohort of patients with CD, UC, and healthy controls. Smoking status was defined as current, former, or never smoking. Patients were genotyped for polymorphisms in CYP2A6, glutathione transferase enzymes (GSTP1 and GSTM1), NAD(P)H quinone oxidoreductase (NQO), and Heme Oxygenase 1 using a Sequenom platform. Multivariate logistic regression models with CD or UC as the outcome, stratified by genotype were developed and interaction p-values calculated. Results Our study included 634 patients with CD, 401 with UC, and 337 healthy controls. Ever smokers had an increased risk of CD (OR 3.88, 95% CI 2.35 – 6.39) compared to non-smokers among patients with AG/AA genotypes at CYP2A6. However, ever smoking was not associated with CD among patients with the AA genotype (pinteraction 0.001). Former smoking was associated with an increased risk for UC only in the presence of GG/AG genotypes for GSTP1, but not in those with the AA genotype (Pinteraction 0.012). Polymorphisms at the NQO and HMOX loci did not demonstrate a statistically significant interaction with smoking and risk of CD or UC. Conclusion Genetic polymorphisms in metabolizing enzymes may influence the association between smoking and CD and UC. Further studies of gene-environment interaction in IBD are warranted. PMID:24651583

  10. Genetic polymorphisms in metabolizing enzymes modifying the association between smoking and inflammatory bowel diseases.

    Science.gov (United States)

    Ananthakrishnan, Ashwin N; Nguyen, Deanna D; Sauk, Jenny; Yajnik, Vijay; Xavier, Ramnik J

    2014-05-01

    Cigarette smoking is a well-established environmental risk factor for Crohn's disease (CD) and ulcerative colitis (UC). The exact mechanism of its effect remains unexplained. Genetic polymorphisms in metabolizing enzymes may influence susceptibility to the effect of smoking and shed light on its mechanism of action. We used a prospective cohort of patients with CD, UC, and healthy controls. Smoking status was defined as current, former, or never smoking. Patients were genotyped for polymorphisms in CYP2A6, glutathione transferase enzymes (GSTP1 and GSTM1), NAD(P)H quinone oxidoreductase (NQO), and heme oxygenase 1 using a Sequenom platform. Multivariate logistic regression models with CD or UC as the outcome, stratified by genotype, were developed and interaction P-values calculated. Our study included 634 patients with CD, 401 with UC, and 337 healthy controls. Ever smokers had an increased risk of CD (odds ratio = 3.88, 95% confidence interval = 2.35-6.39) compared with nonsmokers among patients with AG/AA genotypes at CYP2A6. However, ever smoking was not associated with CD among patients with the AA genotype (Pinteraction = 0.001). Former smoking was associated with an increased risk for UC only in the presence of GG/AG genotypes for GSTP1 but not in those with the AA genotype (Pinteraction = 0.012). Polymorphisms at the NQO and HMOX loci did not demonstrate a statistically significant interaction with smoking and risk of CD or UC. Genetic polymorphisms in metabolizing enzymes may influence the association between smoking and CD and UC. Further studies of gene-environment interaction in inflammatory bowel disease are warranted.

  11. Genetic polymorphisms in non-alcoholic fatty liver disease in obese Egyptian children

    Directory of Open Access Journals (Sweden)

    Nehal M El-Koofy

    2011-01-01

    Full Text Available Background/Aim : Polymorphisms in the promoter of microsomal triglyceride transfer protein (MTP lead to decreased MTP transcription, less export of triglyceride from hepatocytes, and greater intracellular triglyceride accumulation. Therefore, functional polymorphisms in MTP may be involved in determining susceptibility to nonalcoholic steatohepatitis (NASH. The aim of this study is to examine the effect of some genetic influences among a group of obese Egyptian children. Patients and Methods: A cross-sectional study was conducted on 76 overweight and obese children presenting to the Pediatric Endocrinology Unit, Cairo University Children′s Hospital, Egypt, as well as on 20 healthy controls. Anthropometric measurements were taken for all the patients and they underwent clinical examination, ultrasonographic examination of the liver, and liver biopsy when appropriate. Liver functions, blood glucose, serum insulin, C-peptide, and lipid profile were assessed and HOMA-IR calculated. Blood samples from biopsy-proven NASH patients and controls were analyzed by polymerase chain reaction (PCR and restriction fragment length polymorphism for the −493 G/T polymorphism in the promoter of MTP and the 1183 T/C polymorphism in the mitochondrial targeting sequence of manganese superoxide dismutase (MnSOD. Results : Eight had biopsy-proven simple steatosis and 7 had NASH. NASH patients had a much higher incidence of the MTP G/G genotype (P = 0.002, CI: 2.9-392 compared with the controls. NASH patients also had a 100% prevalence of the MnSOD T/T genotype. Conclusion: Certain genotypes in MTP and MnSOD are significantly more prevalent among obese children with NASH and may be responsible for such a phenotype.

  12. Genetic polymorphisms in non-alcoholic fatty liver disease in obese Egyptian children.

    Science.gov (United States)

    El-Koofy, Nehal M; El-Karaksy, Hanaa M; Mandour, Iman M; Anwar, Ghada M; El-Raziky, Mona S; El-Hennawy, Ahmad M

    2011-01-01

    Polymorphisms in the promoter of microsomal triglyceride transfer protein (MTP) lead to decreased MTP transcription, less export of triglyceride from hepatocytes, and greater intracellular triglyceride accumulation. Therefore, functional polymorphisms in MTP may be involved in determining susceptibility to nonalcoholic steatohepatitis (NASH). The aim of this study is to examine the effect of some genetic influences among a group of obese Egyptian children. A cross-sectional study was conducted on 76 overweight and obese children presenting to the Pediatric Endocrinology Unit, Cairo University Children's Hospital, Egypt, as well as on 20 healthy controls. Anthropometric measurements were taken for all the patients and they underwent clinical examination, ultrasonographic examination of the liver, and liver biopsy when appropriate. Liver functions, blood glucose, serum insulin, C-peptide, and lipid profile were assessed and HOMA-IR calculated. Blood samples from biopsy-proven NASH patients and controls were analyzed by polymerase chain reaction (PCR) and restriction fragment length polymorphism for the -493 G/T polymorphism in the promoter of MTP and the 1183 T/C polymorphism in the mitochondrial targeting sequence of manganese superoxide dismutase (MnSOD). Eight had biopsy-proven simple steatosis and 7 had NASH. NASH patients had a much higher incidence of the MTP G/G genotype (P = 0.002, CI: 2.9-392) compared with the controls. NASH patients also had a 100% prevalence of the MnSOD T/T genotype. Certain genotypes in MTP and MnSOD are significantly more prevalent among obese children with NASH and may be responsible for such a phenotype.

  13. Renin–angiotensin–aldosterone system related gene polymorphisms and urinary total arsenic is related to chronic kidney disease

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Wei-Jen [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Huang, Ya-Li [Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Shiue, Horng-Sheng [Department of Chinese Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan (China); Chen, Tzen-Wen [Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan (China); Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Lin, Yuh-Feng [Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, New Taipei, Taiwan (China); Huang, Chao-Yuan [Department of Urology, National Taiwan University Hospital, College of Medicine National Taiwan University, Taipei, Taiwan (China); Lin, Ying-Chin [Department of Family Medicine, Shung Ho Hospital, Taipei Medical University, New Taipei, Taiwan (China); Department of Health Examination, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan (China); Division of Family Medicine, School of Medicine, Taipei Medical University, Taipei, Taiwan (China); Han, Bor-Cheng [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Hsueh, Yu-Mei, E-mail: ymhsueh@tmu.edu.tw [School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan (China); Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan (China)

    2014-09-01

    A recent study demonstrated that an increased risk of chronic kidney disease (CKD) was associated with high urinary total arsenic levels. However, whether genomic instability is related to CKD remains unclear. An association between CKD and genetic polymorphisms of regulation enzymes of the renin–angiotensin–aldosterone system (RAAS), such as angiotensin-converting enzyme (ACE), angiotensinogen (AGT), angiotensin II type I receptor (AT1R), and aldosterone synthase (CYP11B2) has not been shown. The aim of the present study was to investigate the relationship between arsenic, genetic polymorphisms of RAAS enzymes and CKD. A total of 233 patients and 449 age- and gender-matched controls were recruited from the Taipei Medical University Hospital, Taipei Municipal Wan Fang Hospital and the Shin Kong Wu Ho-Su Memorial Hospital. Concentrations of urinary arsenic were determined by a high-performance liquid chromatography-linked hydride generator, and atomic absorption spectrometry. Polymorphisms of ACE(I/D), AGT(A[− 20]C), (T174M), (M235T), AT1R(A1166C) and CYP11B2(C[− 344]T) were examined by polymerase chain reaction and restriction fragment length polymorphism. Subjects carrying the CYP11B2 TT genotype had a higher odds ratio (OR), 1.39 (0.96–2.01), of CKD; while those with the AGT(A[− 20]C) CC genotype had an inverse OR of CKD (0.20 (0.05–0.81)), and a high-risk genotype was defined as A/A + A/C for AGT(A[− 20C]) and T/T for CYP11B2(C[− 344]T). The trend test showed a higher OR for CKD in patients who had either high urinary total arsenic levels or carried the high-risk genotype, or both, compared to patients with low urinary total arsenic levels, who carried the low-risk genotype, and could also be affected by the hypertension or diabetes status. - Highlights: • AGT(− 20 C) and CYP11B2(− 344 T) genotypes were significantly associated with CKD. • Combined effect of high-risk genotypes and high urinary total arsenic on OR of CKD. • Combined

  14. ACE Insertion/Deletion Polymorphism and Diabetic Nephropathy: Clinical Implications of Genetic Information

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    Sung-Kyu Ha

    2014-01-01

    Full Text Available Approximately 20–40% of diabetic patients develop nephropathy which is the leading cause of ESRD in developed countries. The ACE I/D polymorphism is thought to be a marker for functional polymorphism which regulates circulating and tissue ACE activity. While the initial study found a protective effect of the II genotype on the development of nephropathy in IDDM patients, subsequent studies have addressed the role of ACE I/D polymorphism in the development and progression of diabetic nephropathy. RAAS blockers are the first line drugs for the treatment hypertension associated with diabetes and have been widely used in everyday clinical practice for the purpose of reducing proteinuria in patients with various renal diseases. However, the antiproteinuric effect of RAAS blockers is variable and the percentage of reducing proteinuria is in the range of 20–80%. The antiproteinuric effect of RAAS blockers may be related to a number of factors: the type or the dose of RAAS blockers, the duration of therapy, the level of sodium intake, and the type of patient’s ACE I/D genotype. Besides the nongenetic factors, drug responses, can be influenced by ACE gene polymorphism. In this review, we discuss the relationship between ACE I/D polymorphism and diabetic nephropathy and therapeutic response of RAAS blockers.

  15. Association of genetic polymorphisms in ADH and ALDH2 with risk of coronary artery disease and myocardial infarction: a meta-analysis.

    Science.gov (United States)

    Han, Hongguang; Wang, Huishan; Yin, Zongtao; Jiang, Hui; Fang, Minhua; Han, Jingsong

    2013-09-10

    Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) are the major enzymes responsible for alcohol metabolism in humans. Emerging evidences have shown that functional polymorphisms in ADH and ALDH genes might play a critical role in increasing coronary artery disease (CAD) and myocardial infarction (MI) risks; however, individually published studies showed inconclusive results. The aim of this meta-analysis is to evaluate the associations between the genetic polymorphisms of ADH and ALDH genes with susceptibility to CAD and MI. A literature search was conducted on PubMed, Embase, Web of Science and Chinese BioMedical databases from inception through December 1st, 2012. Crude relative risks (RRs) with 95% confidence intervals (CIs) were calculated. Twelve case-control studies were included with a total of 9616 subjects, including 2053 CAD patients, 1436 MI patients, and 6127 healthy controls. Meta-analysis showed that mutant genotypes (GA+AA) of the rs671 polymorphism in the ALDH2 gene were associated with increased risk of both CAD and MI (CAD: RR=1.20, 95%CI: 1.03-1.40, P=0.021; MI: RR=1.32, 95%CI: 1.11-1.57, P=0.002). However, there were no significant associations of ADH genetic polymorphisms to CAD and MI risks (CAD: RR=0.92, 95%CI: 0.73-1.15, P=0.445; MI: RR=0.93, 95%CI: 0.84-1.03, P=0.148). In conclusion, this meta-analysis provides strong evidence that ALDH2 rs671 polymorphism may be associated with increased risks of CAD and MI. However, further studies are still needed to accurately determine whether ADH genetic polymorphisms are associated with susceptibility to CAD and MI.

  16. Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

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    Staud Roland

    2009-08-01

    Full Text Available Abstract Single nucleotide polymorphisms (SNPs represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T, OPRKA843G (with alleles A and G, and OPRKC846T (with alleles C and T, at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited (p = 0.008. With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

  17. Genetic differentiation among sexually compatible relatives of Brassica napus L.

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    Pipan Barbara

    2013-01-01

    Full Text Available Analysis of gene flow between Brassica napus L. and its sexually compatible relatives that could be found in the wild in Slovenia was performed by microsatellite analysis using fifteen selected primer pairs. Genotypes included in the study were obtained from the field survey of sexually compatible relatives of B. napus in natural habitats around Slovenia and from reference collections. Two different wild species of all the presented sexually compatible relatives of B. napus were found in Slovenia, B. rapa and Sinapis arvensis. The reference genotypes included varieties and wild forms from internal collections as marketable seeds or from gene banks. Reference genotypes were represented by the following species and subspecies: B. napus ssp. napobrassica, B. napus ssp. napus, B. nigra, B. oleracea, B. rapa ssp. oleifera, Diplotaxis muralis; D. tenuifolia, Raphanus raphanistrum, R. sativus, R. sativus var. oleiformis, Rapistrum rugosum, S. alba and S. arvensis. Estimation of gene flow described by average number of migrants was 0.72 followed by 0.20 migrants. Due to the observed gene migrations, genetic drift and selection, Hardy-Weinberg equilibrium was not met. The mean number of alleles over all loci was 16.9, the average polymorphic information content was 0.43. We found four highly divergent and polymorphic loci (Na12-C08, Na10-A08, Ni3-G04b and BRMS-050 at statistically significant level (p<0.05 of gene flow detected. Over all gene diversity intra-individual among populations (0.55 was lower than inter-individual among population (0.77. The results of genetic linkages based standard genetic distance and unweighted pair group method with arithmetic mean clustering method, generally divided the genotypes in three divergent groups. Similar results were obtained by principal coordinate analysis where three main groups were constructed according to three factors. A real number of genetic clusters demonstrated a clear separation between populations

  18. Association between SERPING1 rs2511989 polymorphism and age-related macular degeneration: Meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Yi; Dong; Ze-Dong; Li; Xin-Yu; Fang; Xue-Feng; Shi; Song; Chen; Xin; Tang

    2015-01-01

    AIM: To investigate the association between SERPING1rs2511989(G>A) polymorphism and age-related macular degeneration(AMD).METHODS: A number of electronic databases(up to July 15, 2014) were searched independently by two investigators. A Meta-analysis was performed on the association between SERPING1 rs2511989 polymorphism and AMD. Pooled odds ratios(ORs) with 95% confidence intervals(CIs) were estimated.RESULTS: Eight studies with 16 cohorts consisting of9163 cases and 6813 controls were included in this Metaanalysis. There was no significant association between rs2511989 polymorphism and AMD under all genetic models in overall estimates(A vs G: OR= 0.938, 95%CI =0.858-1.025; AA vs GG:OR =0.871, 95% CI =0.719-1.056;AG vs GG: OR =0.944, 95% CI =0.845-1.054; AA +AG vs GG: OR =0.927, 95% CI =0.823-1.044; AA vs AG +GG:OR =0.890, 95% CI =0.780-1.034). Cumulative Meta-analyses also showed a trend of no association between rs2511989 polymorphism and AMD as information accumulated by year. Subgroup analysis and Meta-regression analysis indicated that age-matching status was the main source of heterogeneity. Sensitivity analysis found the results in overall comparisons and subgroup comparisons of white subjects under the allele model were found to have significantly statistical differences after studies deviating from Hardy-Weinberg equilibrium(HWE) were excluded(overall: OR=0.918, 95%CI = 0.844-0.999, P =0.049; whites: OR =0.901, 95% CI =0.817-0.994, P =0.038). However, the results were notsufficiently robust for further sensitivity analysis and statistical differences disappeared on applying Bonferroni correction(with a significance level set at 0.05/25).CONCLUSION: This Meta-analysis indicates that SERPING1 rs2511989 polymorphism and AMD tend to have no association with each other. Age matching status is a big confounding factor, and more studies with subtle designs are warranted in future.

  19. Association between SERPING1 rs2511989 polymorphism and age-related macular degeneration: Meta-analysis

    Directory of Open Access Journals (Sweden)

    Yi Dong

    2015-04-01

    Full Text Available AIM: To investigate the association between SERPING1 rs2511989 (G>A polymorphism and age-related macular degeneration (AMD. METHODS: A number of electronic databases (up to July 15, 2014 were searched independently by two investigators. A Meta-analysis was performed on the association between SERPING1 rs2511989 polymorphism and AMD. Pooled odds ratios (ORs with 95% confidence intervals (CIs were estimated. RESULTS: Eight studies with 16 cohorts consisting of 9163 cases and 6813 controls were included in this Meta-analysis. There was no significant association between rs2511989 polymorphism and AMD under all genetic models in overall estimates (A vs G: OR= 0.938, 95%CI =0.858-1.025; AA vs GG:OR =0.871, 95%CI =0.719-1.056; AG vs GG: OR =0.944, 95%CI =0.845-1.054; AA+AG vs GG: OR =0.927, 95% CI =0.823-1.044; AA vs AG+GG: OR =0.890, 95%CI =0.780-1.034. Cumulative Meta-analyses also showed a trend of no association between rs2511989 polymorphism and AMD as information accumulated by year. Subgroup analysis and Meta-regression analysis indicated that age-matching status was the main source of heterogeneity. Sensitivity analysis found the results in overall comparisons and subgroup comparisons of white subjects under the allele model were found to have significantly statistical differences after studies deviating from Hardy-Weinberg equilibrium (HWE were excluded (overall: OR=0.918, 95%CI = 0.844-0.999, P =0.049; whites: OR =0.901, 95%CI = 0.817-0.994, P =0.038. However, the results were not sufficiently robust for further sensitivity analysis and statistical differences disappeared on applying Bonferroni correction (with a significance level set at 0.05/25. CONCLUSION: This Meta-analysis indicates that SERPING1 rs2511989 polymorphism and AMD tend to have no association with each other. Age matching status is a big confounding factor, and more studies with subtle designs are warranted in future.

  20. Bone mineral density-associated polymorphisms are associated with obesity-related traits in Korean adults in a sex-dependent manner.

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    Seongwon Cha

    Full Text Available Obesity and osteoporosis share common physiological factors, including the presence of atherosclerosis, a risk factor for cardiometabolic disease, as well as a common progenitor that differentiates into both adipocytes and osteoblasts. Among the 23 polymorphisms associated with bone mineral density (BMD in recent genome-wide association studies (GWASs, an Osterix polymorphism has been identified and associated with childhood obesity in girls. Therefore, we focused on elucidating polymorphisms associated with adulthood obesity in a sex-dependent manner among the previously published BMD-associated polymorphisms from GWASs. We performed 2 screenings of 18 BMD-associated polymorphisms for obesity-related traits in 2,362 adults aged >20 years. We excluded 13 polymorphisms showing deviations from Hardy-Weinberg equilibrium or no association with obesity-related traits (body mass index, waist circumference (WC, and waist-to-hip ratio. Among 5 selected polymorphisms (rs9594738 of RANKL, rs17066364 of NUFIP1, rs7227401 of OSBPL1A, and rs1856057 and rs2982573 of ESR1 analyzed, 2 polymorphisms (rs9594738 and rs17066364 were associated with obesity-related traits. We found sex-dependent associations such that the 4 polymorphisms (excluding rs9594738 of RANKL were associated with abdominal traits such as WC and waist-to-hip ratio only in men. In addition, when the combined genetic risk score (GRS for WC increase was calculated with 4 SNPs (rs9594738, rs17066364, rs7227401, and rs1856057 exhibiting similar trends for both sexes, the magnitude of the GRS effect for the WC increase was larger in men than in women (effect size = 0.856 cm, P = 0.0000452 for men; effect size = 0.598 cm, P = 0.00228 for women. In summary, we found 4 polymorphisms, previously related to osteoporosis, to be associated to obesity-related traits in a sex-dependent manner in Korean adults, particularly in men.

  1. Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms.

    Science.gov (United States)

    Hulbert, S H; Ilott, T W; Legg, E J; Lincoln, S E; Lander, E S; Michelmore, R W

    1988-12-01

    Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.

  2. Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers.

    Science.gov (United States)

    Batley, Jacqueline; Jewell, Erica; Edwards, David

    2007-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

  3. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes

    OpenAIRE

    Kumar, Pankaj; Chaitanya, Pasumarthy S.; Nagarajaram, Hampapathalu A

    2010-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1–6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in s...

  4. Genetic study of the population of Tenerife (Canary Islands, Spain): protein markers and review of classical polymorphisms.

    Science.gov (United States)

    Moral, P; Esteban, E; Vives, S; Valveny, N; Toja, D I; Gonzalez-Reimers, E

    1997-03-01

    Data on six protein polymorphisms (19 alleles) from the human population of Tenerife are presented and discussed along with other classical markers in relation to the origin of the Canarians. Genetic influences from three population groups were considered: the Iberians, and the Berbers and non-Berbers (Arabs) from north Africa. The systems examined show the Tenerife population lies within the limits of variation described for various Iberian groups, with a slight tendency towards the characteristics of north African populations. When blood groups, red cell enzymes and serum protein data were considered, the similarity of the Canary population to Iberians seems strengthened (70% estimated contribution of Iberian peninsula genes to the present-day Canarian pool), while some relation with north African groups is shown. Genetic distances between Canarians and Arabs and Canarians and Berbers are lower than those between the two north African groups, indicating a relative and comparable contribution of each to the present-day gene pool of the Canarian population. The Arab contribution could be attributable to the slaves who were introduced to these islands after the conquest in the 15th century, while the Berber contribution could be the remnants of the extinct aboriginal peoples of the islands (Guanches) or a more recent immigration due to slavery. Genetic data do not allow us to distinguish between these two possibilities.

  5. Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population.

    Science.gov (United States)

    Pombar-Gomez, Maria; Lopez-Lopez, Elixabet; Martin-Guerrero, Idoia; Garcia-Orad Carles, Africa; de Pancorbo, Marian M

    2015-05-01

    Single nucleotide polymorphisms (SNPs) are an interesting option to facilitate the analysis of highly degraded DNA by allowing the reduction of the size of the DNA amplicons. The SNPforID 52-plex panel is a clear example of the use of non-coding SNPs in forensic genetics. However, nonstop advances in studies of genetic polymorphisms are leading to the discovery of new associations between SNPs and diseases. The aim of this study was to perform a comprehensive review of the state of association between the 52 SNPs in the 52-plex panel and diseases or other traits related to their treatment, such as drug response characters. In order to achieve this goal, we have conducted a bioinformatic search for each SNP included in the panel and the SNPs in linkage disequilibrium (LD) with them in the European population (r (2)  > 0.8). A total of 424 SNPs (52 in the panel and 372 in LD) were investigated in PubMed, Scopus, and dbSNP databases. Our results show that three SNPs in the SNPforID 52-plex panel (rs2107612, rs1979255, rs1463729) have been associated with diseases such as hypertension or macular degeneration, as well as drug response. Similarly, three out of the 372 SNPs in LD (rs2107614, r (2)  = 0.859; rs765250, r (2)  = 0.858; rs11064560, r (2)  = 0,887) are also associated with various pathologies. In view of these results, we propose the need for a periodic review of the SNPs used in forensic genetics in order to keep their associations with diseases or related phenotypes updated and to evaluate their continuity in forensic panels for avoiding legal and ethical conflicts.

  6. Role of Genetic Polymorphisms in NFKB-Mediated Inflammatory Pathways in Response to Primary Chemoradiation Therapy for Rectal Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Dzhugashvili, Maia [Department of Hematology and Medical Oncology, University Hospital Morales Meseguer, Murcia (Spain); Department of Radiation Oncology, Madrid Oncology Institute (Group IMO), Murcia (Spain); Luengo-Gil, Ginés; García, Teresa; González-Conejero, Rocío [Department of Hematology and Medical Oncology, University Hospital Morales Meseguer, Murcia (Spain); Conesa-Zamora, Pablo [Department of Pathology, University Hospital Santa Lucía, Cartagena (Spain); Escolar, Pedro Pablo [Department of Radiation Oncology, University Hospital Santa Lucía, Cartagena (Spain); Calvo, Felipe [Department of Radiation Oncology, University General Hospital Gregorio Marañón, Madrid (Spain); Vicente, Vicente [Department of Hematology and Medical Oncology, University Hospital Morales Meseguer, Murcia (Spain); Ayala de la Peña, Francisco, E-mail: frayala@um.es [Department of Hematology and Medical Oncology, University Hospital Morales Meseguer, Murcia (Spain)

    2014-11-01

    Purpose: To investigate whether polymorphisms of genes related to inflammation are associated with pathologic response (primary endpoint) in patients with rectal cancer treated with primary chemoradiation therapy (PCRT). Methods and Materials: Genomic DNA of 159 patients with locally advanced rectal cancer treated with PCRT was genotyped for polymorphisms rs28362491 (NFKB1), rs1213266/rs5789 (PTGS1), rs5275 (PTGS2), and rs16944/rs1143627 (IL1B) using TaqMan single nucleotide polymorphism genotyping assays. The association between each genotype and pathologic response (poor response vs complete or partial response) was analyzed using logistic regression models. Results: The NFKB1 DEL/DEL genotype was associated with pathologic response (odds ratio [OR], 6.39; 95% confidence interval [CI], 0.78-52.65; P=.03) after PCRT. No statistically significant associations between other polymorphisms and response to PCRT were observed. Patients with the NFKB1 DEL/DEL genotype showed a trend for longer disease-free survival (log-rank test, P=.096) and overall survival (P=.049), which was not significant in a multivariate analysis that included pathologic response. Analysis for 6 polymorphisms showed that patients carrying the haplotype rs28362491-DEL/rs1143627-A/rs1213266-G/rs5789-C/rs5275-A/rs16944-G (13.7% of cases) had a higher response rate to PCRT (OR, 8.86; 95% CI, 1.21-64.98; P=.034) than the reference group (rs28362491-INS/rs1143627-A/rs1213266-G/rs5789-C/rs5275-A/rs16944-G). Clinically significant (grade ≥2) acute organ toxicity was also more frequent in patients with that same haplotype (OR, 4.12; 95% CI, 1.11-15.36; P=.037). Conclusions: Our results suggest that genetic variation in NFKB-related inflammatory pathways might influence sensitivity to primary chemoradiation for rectal cancer. If confirmed, an inflammation-related radiogenetic profile might be used to select patients with rectal cancer for preoperative combined-modality treatment.

  7. Genetic variation in Opisthorchis viverrini (Trematoda: Opisthorchiidae) from northeast Thailand and Laos PDR based on random amplified polymorphic DNA analyses

    Science.gov (United States)

    Chilton, Neil B.; Andrews, Ross H.

    2007-01-01

    Genetic variation in Opisthorchis viverrini adults originating from different locations in northeast Thailand and Laos, People’s Democratic Republic (PDR), was examined using random amplified polymorphic DNA (RAPD) analyses. In an initial analysis, the genomic DNA of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among O. viverrini specimens was detected reliably for only four primers. A more detailed RAPD analysis using these four primers was conducted on ten individuals from nine localities. Considerable genetic variation was detected among O. viverrini from different geographical areas and among some individuals from the same collecting locality. Comparison of the RAPD profiles revealed that O. viverrini adults from Laos PDR were genetically distinct from those from northeast Thailand. The taxonomic significance of this finding needs to be explored in more detail. The RAPD markers established in the present study provide opportunities to examine the biology and epidemiology of O. viverrini and fish-borne trematodes within the region. Additionally, application of these markers in such studies could have important implications in relation to the prevalence of cholangiocarcinoma in different regions of Asia. PMID:17016722

  8. Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

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    Arehart Eric

    2009-03-01

    Full Text Available Abstract Background The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation. Results We modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR approach. MDR was originally developed to detect synergistic interactions between multiple SNPs that are predictive of disease susceptibility. We initially assembled data from the Broad Institute as a pilot test for the hypothesis that flanking region patterns associate with mutagenesis (n = 2194. We then confirmed and expanded our inquiry with human SNPs within coding regions and their flanking sequences collected from the National Center for Biotechnology Information (NCBI database (n = 29967 and a control set of sequences (coding region not associated with SNP sites randomly selected from the NCBI database (n = 29967. We discovered seven flanking region pattern associations in the Broad dataset which reached a minimum significance level of p ≤ 0.05. Significant models (p Conclusion The present study represents the first use of this computational methodology for modeling nonlinear patterns in molecular genetics. MDR was able to identify distinct nucleotide patterning around sites of mutations dependent upon the observed nucleotide change. We discovered one flanking region set that included five nucleotides clustered around a specific type of SNP site. Based on the strongly associated patterns identified in

  9. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    Directory of Open Access Journals (Sweden)

    Pooja H. Gupta

    2015-05-01

    Full Text Available Aim: An attempt has been made to study the toll-like receptors 4 (TLR4 gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR, respectively from Kankrej (22 and Triple cross (24 cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p˂0.05. Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05. Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

  10. The significance of genetic polymorphisms within and between founder populations of Ceratitis capitata (Wied. from Argentina.

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    Alicia Basso

    Full Text Available BACKGROUND: The Mediterranean fruit fly Ceratitis Capitata (DIPTERA: Tephritidae is a major agricultural pest in Argentina. One main cause for the success of non-contaminant control programs based on genetic strategies is compatibility between natural and laboratory germplasms. A comprehensive characterization of the fruit fly based on genetic studies and compatibility analysis was undertaken on two founder populations from the provinces of Buenos Aires and Mendoza, used in pioneering sterile male technique control programmes in our country. The locations are 1,000 km apart from each other. METHODOLOGY/PRINCIPAL FINDINGS: We compared the genetic composition of both populations based on cytological, physiological and morphological characterization. Compatibility studies were performed in order to determine the presence of isolation barriers. Results indicate that the Buenos Aires germplasm described previously is partially different from that of the Mendoza population. Both laboratory colonies are a reservoir of mutational and cytological polymorphisms. Some sexual chromosome variants such as the XL and the YL resulting from attachment of a B-chromosome to the X-chromosome or Y-chromosome behave as a lethal sex-linked factor. Our results also show incompatibility between both germplasms and pre-zygotic isolation barriers between them. Our evidence is consistent with the fact that polymorphisms are responsible for the lack of compatibility. CONCLUSIONS: The genetic control mechanism should be directly produced in the germplasm of the target population in order to favour mating conditions. This is an additional requirement for the biological as well as economic success of control programs based on genetic strategies such as the sterile insect technique. The analysis of representative samples also revealed natural auto-control mechanisms which could be used in modifying pest population dynamics.

  11. The Significance of Genetic Polymorphisms within and between Founder Populations of Ceratitis capitata (Wied.) from Argentina

    Science.gov (United States)

    Basso, Alicia; Martinez, Laura; Manso, Fanny

    2009-01-01

    Background The Mediterranean fruit fly Ceratitis Capitata (DIPTERA: Tephritidae) is a major agricultural pest in Argentina. One main cause for the success of non-contaminant control programs based on genetic strategies is compatibility between natural and laboratory germplasms. A comprehensive characterization of the fruit fly based on genetic studies and compatibility analysis was undertaken on two founder populations from the provinces of Buenos Aires and Mendoza, used in pioneering sterile male technique control programmes in our country. The locations are 1,000 km apart from each other. Methodology/Principal Findings We compared the genetic composition of both populations based on cytological, physiological and morphological characterization. Compatibility studies were performed in order to determine the presence of isolation barriers. Results indicate that the Buenos Aires germplasm described previously is partially different from that of the Mendoza population. Both laboratory colonies are a reservoir of mutational and cytological polymorphisms. Some sexual chromosome variants such as the XL and the YL resulting from attachment of a B-chromosome to the X-chromosome or Y-chromosome behave as a lethal sex-linked factor. Our results also show incompatibility between both germplasms and pre-zygotic isolation barriers between them. Our evidence is consistent with the fact that polymorphisms are responsible for the lack of compatibility. Conclusions The genetic control mechanism should be directly produced in the germplasm of the target population in order to favour mating conditions. This is an additional requirement for the biological as well as economic success of control programs based on genetic strategies such as the sterile insect technique. The analysis of representative samples also revealed natural auto-control mechanisms which could be used in modifying pest population dynamics. PMID:19252742

  12. Genetic analysis of Trichinella populations by 'cold' single-strand conformation polymorphism analysis.

    Science.gov (United States)

    Gasser, Robin B; Hu, Min; El-Osta, Youssef Abs; Zarlenga, Dante S; Pozio, Edoardo

    2005-09-05

    A non-isotopic single-strand conformation polymorphism ('cold' SSCP) technique has been assessed for the analysis of sequence variability in the expansion segment 5 (ES5) of domain IV and the D3 domain of nuclear ribosomal DNA within and/or among isolates and individual muscle (first-stage) larvae representing all currently recognized species/genotypes of Trichinella. Data are consistent with the ability of cold SSCP to identify intra-specific as well as inter-specific variability among Trichinella genotypes. The cold SSCP approach should be applicable to a range of other genetic markers for comparative studies of Trichinella populations globally.

  13. Development of polymorphic microsatellite loci for conservation genetic studies of the coral reef fish Centropyge bicolor.

    Science.gov (United States)

    Herrera, M; Saenz-Agudelo, P; Nanninga, G B; Berumen, M L

    2015-09-01

    A total of 23 novel polymorphic microsatellite marker loci were developed for the angelfish Centropyge bicolor through 454 sequencing, and further tested on two spatially separated populations (90 individuals each) from Kimbe Bay in Papua New Guinea. The mean ± s.e. number of alleles per locus was 14·65 ± 1·05, and mean ± s.e. observed (HO ) and expected (HE ) heterozygosity frequencies were 0·676 ± 0·021 and 0·749 ± 0·018, respectively. The markers reported here constitute the first specific set for this genus and will be useful for future conservation genetic studies in the Indo-Pacific region.

  14. Associations between period 3 gene polymorphisms and sleep- /chronotype-related variables in patients with late-life insomnia.

    Science.gov (United States)

    Mansour, Hader A; Wood, Joel; Chowdari, Kodavali V; Tumuluru, Divya; Bamne, Mikhil; Monk, Timothy H; Hall, Martica H; Buysse, Daniel J; Nimgaonkar, Vishwajit L

    2017-02-27

    A variable number tandem repeat polymorphism (VNTR) in the period 3 (PER3) gene has been associated with heritable sleep and circadian variables, including self-rated chronotypes, polysomnographic (PSG) variables, insomnia and circadian sleep-wake disorders. This report describes novel molecular and clinical analyses of PER3 VNTR polymorphisms to better define their functional consequences. As the PER3 VNTR is located in the exonic (protein coding) region of PER3, we initially investigated whether both alleles (variants) are transcribed into messenger RNA in human fibroblasts. The VNTR showed bi-allelic gene expression. We next investigated genetic associations in relation to clinical variables in 274 older adult Caucasian individuals. Independent variables included genotypes for the PER3 VNTR as well as a representative set of single nucleotide polymorphisms (SNPs) that tag common variants at the PER3 locus (linkage disequilibrium (LD) between genetic variants variables analyzed individually in prior analyses, dependent measures included PSG total sleep time and sleep latency, self-rated chronotype, estimated with the Composite Scale (CS), and lifestyle regularity, estimated using the social rhythm metric (SRM). Initially, genetic polymorphisms were individually analyzed in relation to each outcome variable using analysis of variance (ANOVA). Nominally significant associations were further tested using regression analyses that incorporated individual ANOVA-associated DNA variants as potential predictors and each of the selected sleep/circadian variables as outcomes. The covariates included age, gender, body mass index and an index of medical co-morbidity. Significant genetic associations with the VNTR were not detected with the sleep or circadian variables. Nominally significant associations were detected between SNP rs1012477 and CS scores (p = 0.003) and between rs10462021 and SRM (p = 0.047); rs11579477 and average delta power (p = 0.043) (analyses uncorrected

  15. 广西人群DNA修复基因XRCC3多态性与肝细胞癌遗传易感性关联分析%Association of the Thr241Met polymorphism of DNA repair gene XRCC3 with genetic susceptibility to AFB1-related hepatocellular carcinoma in Guangxi population

    Institute of Scientific and Technical Information of China (English)

    龙喜带; 马韵; 邓卓霖; 黄永秩; 韦妮波

    2008-01-01

    Objective To explore the association of the Thr241Met polymorphism of X-my cross-complementing group 3(xRcc3) gene with genetic susceptibility to aflatoxin B1(AFBl)-related hepatocellular carcinoma(HCC)in Guangxi population.Methods We conducted a hospital-based case-control study,including 257 HCC cascs and 711 controls without cancels or liver diseases.The XRCC3 Thr241Met polymorphism was analyzed by PCR.Results The XRCC3 genotypes XRCC3.Thr/Met or XRCC3-Met/Met were related with an elevated risk of HCC.The risk of HCC was associated with the number of mutant Met copies(adjusted OR were 2.20 and 8.56 for XRCC3.Thr/Met and Met/Met,respectively);moreover,there seemed tO be combined effects for HCC risk between the variant genotypes and AFBl DNA adduct levels from peripheral blood leukocytes(adjusted OR was 2.34 to 20.44,P<0.01).Conclusion These results suggested that XRCC3 polymorphism may be associated with the risk of AFBl-related HCC among the Guansxipopulation,and interacts with AFBl exposure in the development of HCC induced by AFBl.%目的 探讨DNA修复基因X线修复交叉互补因子3(X-ray cross-complementing group 3,XRCC3)基因Thr241Met多态性与黄曲霉毒素B1(aflatoxin B1,AFB1)相关性肝细胞癌(hepatocellular carcinoma,HCC)遗传易感性的相关性.方法 应用PCR技术对AFB1高污染区广西地区257例HCC患者和711名对照人群的XRCC3基因多态性进行检测,进行的病例对照研究.结果 (1)XRCC3 3种基因型(Thr/Thr、Thr/Met、Met/Met)中带有Met者与HCC的易感性相关,且这种相关性与Met数量呈正相关(校正风险值OR分别为2.20和8.56);(2)XRCC3突变基因型多态与血白细胞AFB1-DNA加合物水平在HCC发生过程中存在协同作用(校正OR:2.34~20.44,P<0.01).结论 XRCC3多态性与HCC易感性相关,且这种多态性与AFB1暴露水平在HCC发生中存在协同作用.

  16. Isolation and characterization of novel polymorphic microsatellite markers for the white stork, Ciconia ciconia: applications in individual–based and population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Feldman Turjeman, S.; Centeno-Cuadros, A.; Nathan, R.

    2016-07-01

    The white stork, Ciconia ciconia, is a model species for studies of bird migration and behavior, but previously published genetic markers are not informative enough to perform individual–based genetic studies. Following discovery using next generation sequencing, 11 polymorphic markers were selected and tested in samples from two study sites. The number of alleles per locus ranged from 2–10 with an average of 5.3. The mean observed and expected heterozygosities were 0.519 and 0.565 respectively. PID was adequately sensitive for population– and individual–based genetics studies. There was no significant evidence of allelic drop–out, null alleles, or other errors; one sample site deviated from Hardy–Weinberg equilibrium for two loci, but no loci deviated in both samples, suggesting utility of these markers. These markers can be used to answer a range of ecological questions including those related to genetic diversity, degree of natal philopatry, and genetic mating strategies. (Author)

  17. EPHA2 Polymorphisms and Age-Related Cataract in India

    Science.gov (United States)

    Sundaresan, Periasamy; Ravindran, Ravilla D.; Vashist, Praveen; Shanker, Ashwini; Nitsch, Dorothea; Talwar, Badrinath; Maraini, Giovanni; Camparini, Monica; Nonyane, Bareng Aletta S.; Smeeth, Liam; Chakravarthy, Usha; Hejtmancik, James F.; Fletcher, Astrid E.

    2012-01-01

    Objective We investigated whether previously reported single nucleotide polymorphisms (SNPs) of EPHA2 in European studies are associated with cataract in India. Methods We carried out a population-based genetic association study. We enumerated randomly sampled villages in two areas of north and south India to identify people aged 40 and over. Participants attended a clinical examination including lens photography and provided a blood sample for genotyping. Lens images were graded by the Lens Opacification Classification System (LOCS III). Cataract was defined as a LOCS III grade of nuclear ≥4, cortical ≥3, posterior sub-capsular (PSC) ≥2, or dense opacities or aphakia/pseudophakia in either eye. We genotyped SNPs rs3754334, rs7543472 and rs11260867 on genomic DNA extracted from peripheral blood leukocytes using TaqMan assays in an ABI 7900 real-time PCR. We used logistic regression with robust standard errors to examine the association between cataract and the EPHA2 SNPs, adjusting for age, sex and location. Results 7418 participants had data on at least one of the SNPs investigated. Genotype frequencies of controls were in Hardy-Weinberg Equilibrium (p>0.05). There was no association of rs3754334 with cataract or type of cataract. Minor allele homozygous genotypes of rs7543472 and rs11260867 compared to the major homozygote genotype were associated with cortical cataract, Odds ratio (OR) = 1.8, 95% Confidence Interval (CI) (1.1, 3.1) p = 0.03 and 2.9 (1.2, 7.1) p = 0.01 respectively, and with PSC cataract, OR = 1.5 (1.1, 2.2) p = 0.02 and 1.8 (0.9, 3.6) p = 0.07 respectively. There was no consistent association of SNPs with nuclear cataract or a combined variable of any type of cataract including operated cataract. Conclusions Our results in the Indian population agree with previous studies of the association of EPHA2 variants with cortical cataracts. We report new findings for the association with PSC which is particularly prevalent

  18. EPHA2 polymorphisms and age-related cataract in India.

    Directory of Open Access Journals (Sweden)

    Periasamy Sundaresan

    Full Text Available OBJECTIVE: We investigated whether previously reported single nucleotide polymorphisms (SNPs of EPHA2 in European studies are associated with cataract in India. METHODS: We carried out a population-based genetic association study. We enumerated randomly sampled villages in two areas of north and south India to identify people aged 40 and over. Participants attended a clinical examination including lens photography and provided a blood sample for genotyping. Lens images were graded by the Lens Opacification Classification System (LOCS III. Cataract was defined as a LOCS III grade of nuclear ≥4, cortical ≥3, posterior sub-capsular (PSC ≥2, or dense opacities or aphakia/pseudophakia in either eye. We genotyped SNPs rs3754334, rs7543472 and rs11260867 on genomic DNA extracted from peripheral blood leukocytes using TaqMan assays in an ABI 7900 real-time PCR. We used logistic regression with robust standard errors to examine the association between cataract and the EPHA2 SNPs, adjusting for age, sex and location. RESULTS: 7418 participants had data on at least one of the SNPs investigated. Genotype frequencies of controls were in Hardy-Weinberg Equilibrium (p>0.05. There was no association of rs3754334 with cataract or type of cataract. Minor allele homozygous genotypes of rs7543472 and rs11260867 compared to the major homozygote genotype were associated with cortical cataract, Odds ratio (OR = 1.8, 95% Confidence Interval (CI (1.1, 3.1 p = 0.03 and 2.9 (1.2, 7.1 p = 0.01 respectively, and with PSC cataract, OR = 1.5 (1.1, 2.2 p = 0.02 and 1.8 (0.9, 3.6 p = 0.07 respectively. There was no consistent association of SNPs with nuclear cataract or a combined variable of any type of cataract including operated cataract. CONCLUSIONS: Our results in the Indian population agree with previous studies of the association of EPHA2 variants with cortical cataracts. We report new findings for the association with PSC which is

  19. Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species.

    Science.gov (United States)

    Kanzi, Aquillah Mumo; Wingfield, Brenda Diana; Steenkamp, Emma Theodora; Naidoo, Sanushka; van der Merwe, Nicolaas Albertus

    2016-01-01

    In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.

  20. Association of the XRCC1 c.1178G>A genetic polymorphism with lung cancer risk in Chinese.

    Science.gov (United States)

    Wang, Lei; Lin, Yong; Qi, Cong-Cong; Sheng, Bao-Wei; Fu, Tian

    2014-01-01

    The X-ray repair cross-complementing group 1 protein (XRCC1) plays important roles in the DNA base excision repair pathway which may influence the development of lung cancer. This study aimed to evaluate the potential association of the XRCC1 c.1178G>A genetic polymorphism with lung cancer risk. The created restriction site-polymerase chain reaction (CRS-PCR) and DNA sequencing methods were utilized to evaluate the XRCC1 c.1178G>A genetic polymorphism among 376 lung cancer patients and 379 controls. Associations between the genetic polymorphism and lung cancer risk were determined with an unconditional logistic regression model. Our data suggested that the distribution of allele and genotype in lung cancer patients was significantly different from that of controls. The XRCC1 c.1178G>A genetic polymorphism was associated with an increased risk of lung cancer (AA vs GG: OR=2.91, 95%CI 1.70-4.98, pA genetic polymorphism is statistically associated with lung cancer risk in the Chinese population.

  1. Investigation on XRCC1 genetic polymorphism and its relationship with breast cancer risk factors in Chinese women.

    Science.gov (United States)

    Zheng, Luming; Yang, Feng; Zhang, Xukui; Zhu, Jian; Zhou, Pen; Yu, Fang; Hou, Lei; Zhao, Guowei; He, Qingqing; Wang, Baocheng

    2013-12-01

    Breast cancer (BC) remains one of the most common cancers among women. The human X-ray repair cross-complementing 1 (XRCC1) gene plays key roles in base excision repair, and genetic polymorphisms of XRCC1 may be associated with the susceptibility to BC. This study aimed to evaluate the relationship between the XRCC1 genetic polymorphisms and BC susceptibility. A total of 354 BC patients and 366 cancer-free controls were enrolled in this study. Data about the risk factors of BC were collected using questionnaires. The XRCC1 genetic polymorphism was determined using created restriction site-polymerase chain reaction (CRS-PCR) and DNA sequencing methods. No significant differences in the allelic and genotypic frequencies of c.1804C>A genetic polymorphism were detected between cases and controls. The distributions of BC patients' risk factors were not significantly different between CC, CA, and AA genotypes. These findings indicate that the c.1804C>A genetic polymorphism of XRCC1 gene is not significantly associated with BC susceptibility in the Chinese women.

  2. Associations between KCNJ6 (GIRK2) gene polymorphisms and pain-related phenotypes.

    Science.gov (United States)

    Bruehl, Stephen; Denton, Jerod S; Lonergan, Daniel; Koran, Mary Ellen; Chont, Melissa; Sobey, Christopher; Fernando, Shanik; Bush, William S; Mishra, Puneet; Thornton-Wells, Tricia A

    2013-12-01

    G-protein coupled inwardly rectifying potassium (GIRK) channels are effectors determining degree of analgesia experienced upon opioid receptor activation by endogenous and exogenous opioids. The impact of GIRK-related genetic variation on human pain responses has received little research attention. We used a tag single nucleotide polymorphism (SNP) approach to comprehensively examine pain-related effects of KCNJ3 (GIRK1) and KCNJ6 (GIRK2) gene variation. Forty-one KCNJ3 and 69 KCNJ6 tag SNPs were selected, capturing the known variability in each gene. The primary sample included 311 white patients undergoing total knee arthroplasty in whom postsurgical oral opioid analgesic medication order data were available. Primary sample findings were then replicated in an independent white sample of 63 healthy pain-free individuals and 75 individuals with chronic low back pain (CLBP) who provided data regarding laboratory acute pain responsiveness (ischemic task) and chronic pain intensity and unpleasantness (CLBP only). Univariate quantitative trait analyses in the primary sample revealed that 8 KCNJ6 SNPs were significantly associated with the medication order phenotype (P KCNJ6 gene (gene set-based analysis) just failed to reach significance (P = .054). No significant KCNJ3 effects were observed. A continuous GIRK Related Risk Score (GRRS) was derived in the primary sample to summarize each individual's number of KCNJ6 "pain risk" alleles. This GRRS was applied to the replication sample, which revealed significant associations (P KCNJ6 genetic variation on pain outcomes is warranted.

  3. Age-related decline in brain resources modulates genetic effects on cognitive functioning

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    Ulman Lindenberger

    2008-12-01

    Full Text Available Individual differences in cognitive performance increase from early to late adulthood, likely reflecting influences of a multitude of factors. We hypothesize that losses in neurochemical and anatomical brain resources in normal aging modulate the effects of common genetic variations on cognitive functioning. Our hypothesis is based on the assumption that the function relating brain resources to cognition is nonlinear, so that genetic differences exert increasingly large effects on cognition as resources recede from high to medium levels in the course of aging.Direct empirical support for this hypothesis comes from a study by Nagel et al. (2008, who reported that the effects of the Catechol-O-Methyltransferase (COMT gene on cognitive performance are magnified in old age and interacted with the Brain-Derived Neurotrophic Factor (BDNF gene. We conclude that common genetic polymorphisms contribute to the increasing heterogeneity of cognitive functioning in old age. Extensions of the hypothesis to other polymorphisms are discussed.

  4. Age-Related Decline in Brain Resources Modulates Genetic Effects on Cognitive Functioning

    Science.gov (United States)

    Lindenberger, Ulman; Nagel, Irene E.; Chicherio, Christian; Li, Shu-Chen; Heekeren, Hauke R.; Bäckman, Lars

    2008-01-01

    Individual differences in cognitive performance increase from early to late adulthood, likely reflecting influences of a multitude of factors. We hypothesize that losses in neurochemical and anatomical brain resources in normal aging modulate the effects of common genetic variations on cognitive functioning. Our hypothesis is based on the assumption that the function relating brain resources to cognition is nonlinear, so that genetic differences exert increasingly large effects on cognition as resources recede from high to medium levels in the course of aging. Direct empirical support for this hypothesis comes from a study by Nagel et al. (2008), who reported that the effects of the Catechol-O-Methyltransferase (COMT) gene on cognitive performance are magnified in old age and interacted with the Brain-Derived Neurotrophic Factor (BDNF) gene. We conclude that common genetic polymorphisms contribute to the increasing heterogeneity of cognitive functioning in old age. Extensions of the hypothesis to other polymorphisms are discussed. (150 of 150 words) PMID:19225597

  5. Association between genetic polymorphisms in the serotonergic system and comorbid personality disorders among patients with first-episode depression.

    Science.gov (United States)

    Bukh, Jens D; Bock, Camilla; Kessing, Lars V

    2014-06-01

    Studies on the association between genetic polymorphisms and personality disorders have provided inconsistent results. Using the "enriched sample method," the authors of the present study aimed to assess the association between polymorphisms in the serotonergic transmitter system and comorbid personality disorders in patients recently diagnosed with first-episode depression. A total of 290 participants were systematically recruited via the Danish Psychiatric Central Research Register. Diagnoses of personality disorders were assessed by a SCID-II interview, and polymorphisms in the genes encoding the serotonin transporter, serotonin receptors 1A, 2A, 2C, and tryptophan hydroxylase 1 were genotyped. The authors found a significant effect of the length polymorphism in the serotonin transporter gene (5-HTTLPR) on cluster B personality disorder (mainly borderline disorder), but no influence on cluster C personality disorder, and no associations between other polymorphisms and personality disorders. The study adds evidence to the effect of the serotonin transporter gene specifically on cluster B personality disorders.

  6. Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

    Directory of Open Access Journals (Sweden)

    Huygens Flavia

    2007-08-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. Results The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. Conclusion Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.

  7. Genetic Association of NPY Gene Polymorphisms with Dampness-Phlegm Pattern in Korean Stroke Patients

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    Mi Mi Ko

    2012-01-01

    Full Text Available Neuropeptide Y (NPY, which is widely expressed in both the central and peripheral nervous systems, has an important role in a variety of biological fields. In this study, we analyzed the distribution of NPY polymorphisms in dampness-phlegm pattern and non-dampness-phlegm pattern in elderly Korean subjects with cerebral infarction (CI. A total of 1.097 subjects (498 normal subjects and 599 CI patients, including 198 with dampness-phlegm pattern and 401 with non-dampness-phlegm pattern participated in this study. Genotyping for five SNPs (G-1484A, C-1471T, C-399T, A1201G, and C5325T was conducted by primer extension. The results were statistically analyzed for genetic association of NPY-polymorphisms with normal versus dampness-phlegm pattern or non-dampness-phlegm pattern subjects. Among the five SNPs tested, the T allele of C-399T has a negative association with the dampness-phlegm pattern and is marked by a decrease in serum cholesterol levels. Furthermore, serum cholesterol levels were significantly higher in dampness-phlegm pattern patients than in non-dampness-phlegm pattern patients.In this study, for the first time, the association of NPY polymorphisms with pattern identification (PI of traditional Korean medicine (TKM was analyzed in a large CI patient population.

  8. Genetic polymorphisms in the serotonergic system are associated with circadian manifestations of bruxism.

    Science.gov (United States)

    Oporto, G H; Bornhardt, T; Iturriaga, V; Salazar, L A

    2016-11-01

    Bruxism (BRX) is a condition of great interest for researchers and clinicians in dental and medical areas. BRX has two circadian manifestations; it can occur during sleep (sleep bruxism, SB) or during wakefulness (awake bruxism, WB). However, it can be suffered together. Recent investigations suggest that central nervous system neurotransmitters and their genes could be involved in the genesis of BRX. Serotonin is responsible for the circadian rhythm, maintaining arousal, regulating stress response, muscle tone and breathing. Thus, serotonin could be associated with BRX pathogenesis. The aim of this work was to evaluate the frequency of genetic polymorphisms in the genes HTR1A (rs6295), HTR2A (rs1923884, rs4941573, rs6313, rs2770304), HTR2C (rs17260565) and SLC6A4 (rs63749047) in subjects undergoing BRX treatment. Patients included were classified according to their diagnosis in awake bruxism (61 patients), sleep bruxism (26 patients) and both (43 patients). The control group included 59 healthy patients with no signs of BRX. Data showed significant differences in allelic frequencies for the HTR2A rs2770304 polymorphism, where the C allele was associated with increased risk of SB (odds ratio = 2·13, 95% confidence interval: 1·08-4·21, P = 0·03). Our results suggest that polymorphisms in serotonergic pathways are involved in sleep bruxism. Further research is needed to clarify and increase the current understanding of BRX physiopathology.

  9. New views on the selection acting on genetic polymorphism in central metabolic genes.

    Science.gov (United States)

    Eanes, Walter F

    2017-02-01

    Studies of the polymorphism of central metabolic genes as a source of fitness variation in natural populations date back to the discovery of allozymes in the 1960s. The unique features of these genes and their enzymes and our knowledge base greatly facilitates the systems-level study of this group. The expectation that pathway flux control is central to understanding the molecular evolution of genes is discussed, as well as studies that attempt to place gene-specific molecular evolution and polymorphism into a context of pathway and network architecture. There is an increasingly complex picture of the metabolic genes assuming additional roles beyond their textbook anabolic and catabolic reactions. In particular, this review emphasizes the potential role of these genes as part of the energy-sensing machinery. It is underscored that the concentrations of key cellular metabolites are the reflections of cellular energy status and nutritional input. These metabolites are the top-down signaling messengers that set signaling through signaling pathways that are involved in energy economy. I propose that the polymorphisms in central metabolic genes shift metabolite concentrations and in that fashion act as genetic modifiers of the energy-state coupling to the transcriptional networks that affect physiological trade-offs with significant fitness consequences. © 2016 New York Academy of Sciences.

  10. NIG_MoG: a mouse genome navigator for exploring intersubspecific genetic polymorphisms.

    Science.gov (United States)

    Takada, Toyoyuki; Yoshiki, Atsushi; Obata, Yuichi; Yamazaki, Yukiko; Shiroishi, Toshihiko

    2015-08-01

    The National Institute of Genetics Mouse Genome database (NIG_MoG; http://molossinus.lab.nig.ac.jp/msmdb/) primarily comprises the whole-genome sequence data of two inbred mouse strains, MSM/Ms and JF1/Ms. These strains were established at NIG and originated from the Japanese subspecies Mus musculus molossinus. NIG_MoG provides visualized genome polymorphism information, browsing single-nucleotide polymorphisms and short insertions and deletions in the genomes of MSM/Ms and JF1/Ms with respect to C57BL/6J (whose genome is predominantly derived from the West European subspecies M. m. domesticus). This allows users, especially wet-lab biologists, to intuitively recognize intersubspecific genome divergence in these mouse strains using visual data. The database also supports the in silico screening of bacterial artificial chromosome (BAC) clones that contain genomic DNA from MSM/Ms and the standard classical laboratory strain C57BL/6N. NIG_MoG is thus a valuable navigator for exploring mouse genome polymorphisms and BAC clones that are useful for studies of gene function and regulation based on intersubspecific genome divergence.

  11. Update on the Genetic Polymorphisms of Drug-Metabolizing Enzymes in Antiepileptic Drug Therapy

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    Junji Saruwatari

    2010-08-01

    Full Text Available Genetic polymorphisms in the genes that encode drug-metabolizing enzymes are implicated in the inter-individual variability in the pharmacokinetics and pharmaco-dynamics of antiepileptic drugs (AEDs. However, the clinical impact of these polymorphisms on AED therapy still remains controversial. The defective alleles of cytochrome P450 (CYP 2C9 and/or CYP2C19 could affect not only the pharmacokinetics, but also the pharmacodynamics of phenytoin therapy. CYP2C19 deficient genotypes were associated with the higher serum concentration of an active metabolite of clobazam, N-desmethylclobazam, and with the higher clinical efficacy of clobazam therapy than the other CYP2C19 genotypes. The defective alleles of CYP2C9 and/or CYP2C19 were also found to have clinically significant effects on the inter-individual variabilities in the population pharmacokinetics of phenobarbital, valproic acid and zonisamide. EPHX1 polymorphisms may be associated with the pharmacokinetics of carbamazepine and the risk of phenytoin-induced congenital malformations. Similarly, the UDP-glucuronosyltransferase 2B7 genotype may affect the pharmacokinetics of lamotrigine. Gluthatione S-transferase null genotypes are implicated in an increased risk of hepatotoxicity caused by carbamazepine and valproic acid. This article summarizes the state of research on the effects of mutations of drug-metabolizing enzymes on the pharmacokinetics and pharmacodynamics of AED therapies. Future directions for the dose-adjustment of AED are discussed.

  12. Basic Concepts in Molecular Biology Related to Genetics and Epigenetics.

    Science.gov (United States)

    Corella, Dolores; Ordovas, Jose M

    2017-09-01

    The observation that "one size does not fit all" for the prevention and treatment of cardiovascular disease, among other diseases, has driven the concept of precision medicine. The goal of precision medicine is to provide the best-targeted interventions tailored to an individual's genome. The human genome is composed of billions of sequence arrangements containing a code that controls how genes are expressed. This code depends on other nonstatic regulators that surround the DNA and constitute the epigenome. Moreover, environmental factors also play an important role in this complex regulation. This review provides a general perspective on the basic concepts of molecular biology related to genetics and epigenetics and a glossary of key terms. Several examples are given of polymorphisms and genetic risk scores related to cardiovascular risk. Likewise, an overview is presented of the main epigenetic regulators, including DNA methylation, methylcytosine-phosphate-guanine-binding proteins, histone modifications, other histone regulations, micro-RNA effects, and additional emerging regulators. One of the greatest challenges is to understand how environmental factors (diet, physical activity, smoking, etc.) could alter the epigenome, resulting in healthy or unhealthy cardiovascular phenotypes. We discuss some gene-environment interactions and provide a methodological overview. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  13. ARID5B Genetic Polymorphisms Contribute to Racial Disparities in the Incidence and Treatment Outcome of Childhood Acute Lymphoblastic Leukemia

    Science.gov (United States)

    Xu, Heng; Cheng, Cheng; Devidas, Meenakshi; Pei, Deqing; Fan, Yiping; Yang, Wenjian; Neale, Geoff; Scheet, Paul; Burchard, Esteban G.; Torgerson, Dara G.; Eng, Celeste; Dean, Michael; Antillon, Frederico; Winick, Naomi J.; Martin, Paul L.; Willman, Cheryl L.; Camitta, Bruce M.; Reaman, Gregory H.; Carroll, William L.; Loh, Mignon; Evans, William E.; Pui, Ching-Hon; Hunger, Stephen P.; Relling, Mary V.; Yang, Jun J.

    2012-01-01

    Purpose Recent genome-wide screens have identified genetic variations in ARID5B associated with susceptibility to childhood acute lymphoblastic leukemia (ALL). We sought to determine the contribution of ARID5B single nucleotide polymorphisms (SNPs) to racial disparities in ALL susceptibility and treatment outcome. Patients and Methods We compared the association between ARID5B SNP genotype and ALL susceptibility in whites (> 95% European genetic ancestry; 978 cases and 1,046 controls) versus in Hispanics (> 10% Native American ancestry; 330 cases and 541 controls). We determined the relationships between ARID5B SNP genotype and ALL relapse risk in 1,605 children treated on the Children's Oncology Group (COG) P9904/9905 clinical trials. Results Among 49 ARID5B SNPs interrogated, 10 were significantly associated with ALL susceptibility in both whites and Hispanics (P < .05), with risk alleles consistently more frequent in Hispanics than in whites. rs10821936 exhibited the most significant association in both races (P = 8.4 × 10−20 in whites; P = 1 × 10−6 in Hispanics), and genotype at this SNP was highly correlated with local Native American genetic ancestry (P = 1.8 × 10−8). Multivariate analyses in Hispanics identified an additional SNP associated with ALL susceptibility independent of rs10821936. Eight ARID5B SNPs were associated with both ALL susceptibility and relapse hazard; the alleles related to higher ALL incidence were always linked to poorer treatment outcome and were more frequent in Hispanics. Conclusion ARID5B polymorphisms are important determinants of childhood ALL susceptibility and treatment outcome, and they contribute to racial disparities in this disease. PMID:22291082

  14. BETA-ADRENORECEPTORS GENETIC POLYMORPHISM CONNECTION WITH BETA-BLOKER THERAPY EFFICACY IN PATIENTS WITH CARDIOVASCULAR DISORDERS

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    A.A. Svistunov

    2009-03-01

    Full Text Available At present it is obvious that genetic peculiarities of patients are the major reason for individual differences in pharmacological responses to (β-adrenoblockers. Furthermore ADRB1 gene polymorphism is responsible for the efficiency of (β-adrenoblockers. Thus, a real prospect exists for an individualized approach to administration of (β-adrenoblockers and selection of dosage based on patient’s genotype, which must undoubtedly increase efficiency of the administered therapy. Reviewfocuses on gene polymorphism responsible for (β-adrenoblockers pharmacodynamics and on the clinical significance of the polymorphism detection to individualize drug therapy based on patient’s genotype.

  15. Genetic association of cytokines polymorphisms with autoimmune hepatitis and primary biliary cirrhosis in the Chinese

    Institute of Scientific and Technical Information of China (English)

    Lie-Ying Fan; Xiao-Qing Tu; Ye Zhu; Thomas Pfeiffer; Ralph Feltens; Winfried Stoecker; Ren-Qian Zhong

    2005-01-01

    AIM: To characterize gene polymorphism of several cytokine gene in-patients with AIH and PBC and to analyze the difference of the polymorphism distribution between Chinese patients and healthy controls.METHODS: The study population consisted of 62 patients with AIH, and 77 patients with PBC. The genetic profile of four cytokines was analyzed by restriction fragmentlength polymorphism after specific PCR amplification (PCR-RFLP) or sequence-specific primers PCR (SSP-PCR). The analyzed gene polymorphism included interleukin-1 (IL-1) (at position +3 953 and IL-1RN intron 2), IL-6 (atposition -174), IL-10 promoter (at position -1 082, -819, and -592). The control group consisted of 160 healthyblood donors.RESULTS: The majority of Chinese people including patients and healthy controls exhibited IL-1B 1,1genotype, and there was no significant difference in AIH, PBC patients and controls. There were highly statistically significant differences in the distribution of the IL-1RN gene polymorphism between the patients with PBCcompared with controls. The frequency of IL-1RN 1,1was significantly higher (90.9% vs 79.4%, P = 0.03)and the frequency of IL-1RN 1,2 was significantly lower in PBC patients (6.5% vs 17.5%, P = 0.01). No statistical difference was observed between AIH patients and controls. All of the 160 healthy controls and 62 cases of AIH patients exhibited IL-6-174GG genotype, and there were four cases, which expressed IL-6-174GC genotype in 77 cases of PBC patients. The frequency of IL-6-174GC was markedly significantly higher in PBC patients compared with controls (5.2% vs 0%, P = 0.004). No statistically significant difference was found in the distribution of IL-10 promoter genotype in AIH and PBC patients compared with controls. CONCLUSION: The polymorphisms of IL-1RN and IL-6 -174G/C appear to be associated with PBC in Chinese patients.

  16. VEGF Genetic Polymorphisms May Contribute to the Risk of Diabetic Nephropathy in Patients with Diabetes Mellitus: A Meta-Analysis

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    Li Sun

    2014-01-01

    Full Text Available Objective. This meta-analysis aimed to investigate a comprehensive and reliable conclusion on the correlations of single nucleotide polymorphisms (SNPs in the vascular endothelial growth factor (VEGF gene with the risk of diabetic nephropathy (DN in patients with diabetes mellitus (DM. Methods. We screened PubMed, Embase, Web of Science, Cochrane Library, CISCOM, CINAHL, Google Scholar, CBM, and CNKI databases for those relevant studies that investigated the association of 14,945 subjects with clinicopathological parameters in gastric cancer. Results. Eleven case-control studies that met all inclusion criteria were included in this meta-analysis. A total of 14,945 subjects were involved, including 3,049 DN patients and 11,896 DM patients. Our meta-analysis results revealed that VEGF rs2010963 and rs3025039 polymorphisms might contribute to the risk of DN in DM patients. Ethnicity-stratified analysis suggested that VEGF genetic polymorphisms were associated with an increased risk of DN among Asians. However, we found no correlations of VEGF genetic polymorphisms with susceptibility to DN among Caucasians. Conclusion. Our findings suggest that VEGF rs2010963 and rs3025039 polymorphisms may contribute to the risk of DN in DM patients, especially among Asians. Thus, VEGF genetic polymorphisms could be useful biomarkers for early diagnosis of DN in DM patients.

  17. GENETIC POLYMORPHISM OF CYTOCHROMES P450 2C9 AND 2C19 IN SLOVENIAN POPULATION

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    Darja Herman

    2003-06-01

    Full Text Available Background. Cytochrome P450 2C9 (CYP2C9 and 2C19 (CYP2C19 participate in metabolism of many clinically important drugs. Genetic polymorphisms of the CYP2C9 and CYP2C19 genes are described which may affect drug treatment. The aim of this study was to determine the frequencies of polymorphic CYP2C9 and CYP2C19 alleles in Slovenian population in order to estimate the proportion of the population that might experience adverse drug reaction.Methods. The polymorphism of CYP2C9 and CYP2C19 was analysed by a genotyping technique, based on polymerase chain reaction (PCR followed by restriction enzyme analysis. DNA samples from 129 unrelated healthy subjects were obtained from the Blood Transfusion Centre of Slovenia and University Children’s Hospital in Ljubljana.Results. In the analysed group of samples one-third of individuals carried at least one of the defective CYP2C9 alleles while among them 3.2% of individuals had both alleles affected. The frequencies of CYP2C9*2 and CYP2C9*3 were 0.122 and 0.063, respectively. Almost one-third of Slovenian individuals analysed carried at least one of the CYP2C19 polymorphic allele. The frequencies of CYP2C19*2 and CYP2C19*3 were 0.159 and 0.004, respectively.Conclusions. The results of our study indicate that approximately one-third of the patients from Slovenian population may require either adjustments of dose or increased monitoring when initiating treatment with CYP2C9 and CYP2C19 substrates having a narrow therapeutic index. High risk of adverse drug reaction may be expected in 1–3% of eventual patients.

  18. A Genetic Polymorphism in RBP4 Is Associated with Coronary Artery Disease

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    Ke Wan

    2014-12-01

    Full Text Available Insulin resistance and obesity is influenced by the retinol binding protein 4 (RBP4 adipokine. This study aims to determine if genetic polymorphisms in RBP4 are associated with the risk of coronary artery disease (CAD in Chinese patients. RBP4 polymorphisms were analyzed by high resolution melting (HRM analysis in a case-control study of 392 unrelated CAD patients and 368 controls from China. The Gensini score was used to determine the severity of CAD. The genotypic and allelic frequencies of RBP4 single-nucleotide polymorphisms were evaluated for associations with CAD and severity of disease. The A allele frequency was significantly higher in CAD case groups compared to control groups (16.7% vs. 8.8% at the RBP4 rs7094671 locus. Compared to the G allele, this allele was associated with a higher risk of CAD (OR = 2.07 (1.50–2.84. Polymorphisms at rs7094671 were found to associate with CAD using either a dominant or recessive model (OR, 95% CI: 1.97, 1.38–2.81; 3.81, 1.53–9.51, respectively. Adjusting for sex, history of smoking, serum TC, TG, LDL-c, and HDL-c, the risk of CAD for carriers remained significantly higher in both dominant and recessive models (OR, 95% CI: 1.68, 1.12–2.51; 2.74, 1.00–7.52, respectively. However, this SNP was not significantly associated with severity of CAD using angiographic scores in multivariable linear regression models (p = 0.373. The RBP4 rs7094671 SNP is associated with CAD; however, our results do not indicate that this locus is associated with clinical severity of CAD or the extent of coronary lesions.

  19. Polymorphism of caprine milk alphas1-casein in relation to performance of four Polish goat breeds.

    Science.gov (United States)

    Barłowska, J; Litwińczuk, Z; Kedzierska-Matysek, M; Litwińczuk, A

    2007-01-01

    Polymorphism of goat milk alphas1-casein was determined and potential relations between genetic variants of this protein fraction and goat performance were evaluated. The investigations were performed on 598 goats assigned to of 4 breed groups (White improved 254 units, Coloured improved--124, White non-improved--146 and Coloured non-improved--74). For each goat, alphas1-casein polymorphism was determined in polyacrylamide gel by the PAGE-SDS method and percentage of milk alphas1-casein and gene frequency established. There was evaluated goat performance at successive lactations. In the goat population investigated, AA, AB, BB, AE, BE and EE alphas1-casein genotypes were identified. In all four breeds, alphas1-casein genotype EE clearly predominated (27.2-39.2%), recognized as "medium" and its share was higher in the groups of non-improved goats. It was conditioned by high frequency of gene E alphas1-casein (0.419-0.622). Generally, EE genotype percentage was higher in the non-improved goat groups. The improved goats, though, obtained higher productivity in each of the lactation studied. Analysis of relationships between alphas1-casein genetic variants and goats performance confirmed a significant influence on milk, protein and fat yields only in the Coloured improved goat group. There was revealed a more general tendency indicating a significant impact of "strong" alphas1-casein genotypes on a concentration of basic milk components, i.e. fat and protein, especially casein. In a group of goats producing milk of the highest casein content (over 2.4%) and protein (over 3.0%), the animals showing "strong" alphas1-casein variants dominated (85 and 70 %).

  20. The combined impact of metabolic gene polymorphisms on elite endurance athlete status and related phenotypes.

    Science.gov (United States)

    Ahmetov, Ildus I; Williams, Alun G; Popov, Daniil V; Lyubaeva, Ekaterina V; Hakimullina, Albina M; Fedotovskaya, Olga N; Mozhayskaya, Irina A; Vinogradova, Olga L; Astratenkova, Irina V; Montgomery, Hugh E; Rogozkin, Viktor A

    2009-12-01

    Endurance performance is a complex phenotype subject to the influence of both environmental and genetic factors. Although the last decade has seen a variety of specific genetic factors proposed, many in metabolic pathways, each is likely to make a limited contribution to an 'elite' phenotype: it seems more likely that such status depends on the simultaneous presence of multiple such variants. The aim of the study was to investigate individually and in combination the association of common metabolic gene polymorphisms with endurance athlete status, the proportion of slow-twitch muscle fibers and maximal oxygen consumption. A total of 1,423 Russian athletes and 1,132 controls were genotyped for 15 gene polymorphisms, of which most were previously reported to be associated with athlete status or related intermediate phenotypes. Muscle fiber composition of m. vastus lateralis in 45 healthy men was determined by immunohistochemistry. Maximal oxygen consumption of 50 male rowers of national competitive standard was determined during an incremental test to exhaustion on a rowing ergometer. Ten 'endurance alleles' (NFATC4 Gly160, PPARA rs4253778 G, PPARD rs2016520 C, PPARGC1A Gly482, PPARGC1B 203Pro, PPP3R1 promoter 5I, TFAM 12Thr, UCP2 55Val, UCP3 rs1800849 T and VEGFA rs2010963 C) were first identified showing discrete associations with elite endurance athlete status. Next, to assess the combined impact of all 10 gene polymorphisms, all athletes were classified according to the number of 'endurance' alleles they possessed. The proportion of subjects with a high (≥9) number of 'endurance' alleles was greater in the best endurance athletes compared with controls (85.7 vs. 37.8%, P = 7.6 × 10(-6)). The number of 'endurance' alleles was shown to be positively correlated (r = 0.50; P = 4.0 × 10(-4)) with the proportion of fatigue-resistant slow-twitch fibers, and with maximal oxygen consumption (r = 0.46; P = 7.0 × 10(-4)). These data suggest that the likelihood of

  1. Investigating the genetic basis of theory of mind (ToM: the role of catechol-O-methyltransferase (COMT gene polymorphisms.

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    Haiwei Xia

    Full Text Available The ability to deduce other persons' mental states and emotions which has been termed 'theory of mind (ToM' is highly heritable. First molecular genetic studies focused on some dopamine-related genes, while the genetic basis underlying different components of ToM (affective ToM and cognitive ToM remain unknown. The current study tested 7 candidate polymorphisms (rs4680, rs4633, rs2020917, rs2239393, rs737865, rs174699 and rs59938883 on the catechol-O-methyltransferase (COMT gene. We investigated how these polymorphisms relate to different components of ToM. 101 adults participated in our study; all were genetically unrelated, non-clinical and healthy Chinese subjects. Different ToM tasks were applied to detect their theory of mind ability. The results showed that the COMT gene rs2020917 and rs737865 SNPs were associated with cognitive ToM performance, while the COMT gene rs5993883 SNP was related to affective ToM, in which a significant gender-genotype interaction was found (p = 0.039. Our results highlighted the contribution of DA-related COMT gene on ToM performance. Moreover, we found out that the different SNP at the same gene relates to the discriminative aspect of ToM. Our research provides some preliminary evidence to the genetic basis of theory of mind which still awaits further studies.

  2. Investigating the genetic basis of theory of mind (ToM): the role of catechol-O-methyltransferase (COMT) gene polymorphisms.

    Science.gov (United States)

    Xia, Haiwei; Wu, Nan; Su, Yanjie

    2012-01-01

    The ability to deduce other persons' mental states and emotions which has been termed 'theory of mind (ToM)' is highly heritable. First molecular genetic studies focused on some dopamine-related genes, while the genetic basis underlying different components of ToM (affective ToM and cognitive ToM) remain unknown. The current study tested 7 candidate polymorphisms (rs4680, rs4633, rs2020917, rs2239393, rs737865, rs174699 and rs59938883) on the catechol-O-methyltransferase (COMT) gene. We investigated how these polymorphisms relate to different components of ToM. 101 adults participated in our study; all were genetically unrelated, non-clinical and healthy Chinese subjects. Different ToM tasks were applied to detect their theory of mind ability. The results showed that the COMT gene rs2020917 and rs737865 SNPs were associated with cognitive ToM performance, while the COMT gene rs5993883 SNP was related to affective ToM, in which a significant gender-genotype interaction was found (p = 0.039). Our results highlighted the contribution of DA-related COMT gene on ToM performance. Moreover, we found out that the different SNP at the same gene relates to the discriminative aspect of ToM. Our research provides some preliminary evidence to the genetic basis of theory of mind which still awaits further studies.

  3. Genetic variation of polymorphic NOS STR locus in ten Indian population groups.

    Science.gov (United States)

    Shazia, A; Nithya, P; Seshadri, M

    2009-02-01

    The genotyping of 313 random individuals belonging to ten different population groups from three different states of India was performed for polymorphic pentanucleotide repeat present in the 5'-flanking region of nitric oxide synthase gene (NOS2A) to study the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Likelihood ratio tests showed that all the ten populations for this locus were in Hardy Weinberg equilibrium. Eleven different alleles ranging from 7 repeat to 17 repeats and 46 different genotypes were observed. The observed and the expected heterozygosity ranged from 0.72-0.94 and 0.84-0.89, respectively. The discriminating power of this locus is > or = 0.86 and the polymorphism information content of this locus in ten population groups ranged from 0.80 to 0.85. High PIC, PD and PE value of this STR showed this marker to be informative and can be used for DNA typing and population studies. The eight populations from Kerala showed a lower GST value of 0.016 compared to the GST of ten populations (G(ST) = 0.019), thereby showing that the populations from the same state showed higher genetic proximity probably due to linguistic and geographical proximity between them.

  4. Genetic polymorphism of six DNA loci in six population groups of India.

    Science.gov (United States)

    Ahmad, Shazia; Seshadri, M

    2007-08-01

    The genetic profile based on autosomal markers, four microsatellite DNA markers (D8S315, FES, D8S592, and D2S1328) and two minisatellite DNA markers (TPMT and PDGFA), were analyzed in six endogamous populations to examine the effect of geographic and linguistic affiliation on the genetic affinities among the groups. The six populations are from three different states of India and are linguistically different. Marathas from western India speak Marathi, an Indo-European language. Arayas, Muslims, Ezhavas, and Nairs from Kerala state of South India speak Malayalam, and Iyers from Tamil Nadu state speak Tamil. Genomic DNA was extracted from peripheral blood samples of random, normal, healthy individuals. Locus-specific PCR amplification was carried out, followed by electrophoresis of the amplicons and genotyping. All the loci were highly polymorphic and followed Hardy-Weinberg equilibrium, except for loci D8S315 and PDGFA in Iyers and Marathas, respectively. All six loci had high heterozygosity (average heterozygosity ranged from 0.73 to 0.76) and high polymorphism information content (0.57-0.90). The extent of gene differentiation among the six populations (G(ST) = 0.030) was greater than that for four Kerala populations (G(ST) = 0.011), suggesting proximity between the four Kerala populations. This result conforms with the cultural and linguistic background of the populations. The extent of diversity found among the populations probably resulted from the strict endogamous practices that they follow.

  5. Optimization of random amplified polymorphic DNA techniques for use in genetic studies of Cuban Triatominae.

    Science.gov (United States)

    Fraga, Jorge; Rodriguez, Jinnay; Fuentes, Omar; Fernandez-Calienes, Aymé; Castex, Mayda

    2005-01-01

    Random amplified polymorphic DNA (RAPD) technique is a simple and reliable method to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of assay. In this study, we analyzed the effect of changing the concentration of primer, magnesium chloride, template DNA and Taq DNA polymerase with the objective of determining their optimum concentration for the standardization of RAPD technique for genetic studies of Cuban Triatominae. Reproducible amplification patterns were obtained using 5 pmoL of primer, 2.5 mM of MgCl2, 25 ng of template DNA and 2 U of Taq DNA polymerase in 25 microL of the reaction. A panel of five random primers was used to evaluate the genetic variability of T. flavida. Three of these (OPA-1, OPA-2 and OPA-4) generated reproducible and distinguishable fingerprinting patterns of Triatominae. Numerical analysis of 52 RAPD amplified bands generated for all five primers was carried out with unweighted pair group method analysis (UPGMA). Jaccard's Similarity Coefficient data were used to construct a dendrogram. Two groups could be distinguished by RAPD data and these groups coincided with geographic origin, i.e. the populations captured in areas from east and west of Guanahacabibes, Pinar del Río. T. flavida present low interpopulation variability that could result in greater susceptibility to pesticides in control programs. The RAPD protocol and the selected primers are useful for molecular characterization of Cuban Triatominae.

  6. Genetic polymorphism at 15 STR loci among three important subpopulation of Bihar, India.

    Science.gov (United States)

    Ashma, R; Kashyap, V K

    2002-11-05

    Genotype polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in three genetically important minor caste groups (Yadav, Kurmi and Baniya) of Bihar, a eastern state of India to evaluate their significance in human identification and population genetics study. The selected communities practice endogamy. Despite of same geographical area, the physical features of Yadavs and Baniyas resemble North Indian Indo-Caucasoids whereas Kurmis resemble more to Indo-Austroloids. Among the chosen 15 loci, two are penta-nucleotide repeat: Penta-D and Penta-E, and 13 are tetra-nucleotide repeat: vWA D8S1179, TPOX, FGA, D5S818, D13S317, D7S820, D16S539, D3S1358, THO1, CSF1PO, D21S11, D18S51 and are validated for other population of India and world for forensic testing and human population study. Thirteen of these STR loci are present in the combined DNA index system (CODIS) [J. Forensic Sci. 44 (1999) 1277] and world-wide data is available.

  7. Genetic Association Analysis of Dopamine DRD3 Ser9Gly Polymorphism and Schizophrenia in Malay Population

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    SF Tee

    2011-06-01

    Full Text Available "nBackground: Molecular components of the dopamine receptor (DRD3 play an important role in the pathophysiology of schizophrenia (SCZ. Previous studies have demonstrated an association between the DRD3 Ser9Gly polymorphism and SCZ but the results have been inconclusive. "nMethod: In this study, we investigated this controversial association between the Ser9Gly (A/G polymorphism and SCZ using Malay cases-control (261 cases/157 controls samples. PCR-RFLP was performed to genotype the distribu­tion of the DRD3 Ser9Gly polymorphism."nResults: Both healthy control and SCHZ patient groups were in of Hardy-Weinberg equilibrium for the analyzed ge­netic variability. There was a significant association between the genotype distribution DRD3 polymorphisms and SCZ (χ2= 9.359; df= 2; P= 0.009."nConclusion: We believe that further studies are required to examine the association between others dopamine-related genes and the behavioral phenotypes of SCZ.  

  8. Phosphodiesterase 4 D Gene Polymorphism in Relation to Intracranial and Extracranial Atherosclerosis in Ischemic Stroke

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    Jayantee Kalita

    2011-01-01

    Full Text Available In ischemic stroke, extracranial MR angiography (ECMRA is more frequently abnormal in Caucasians and intracranial (ICMRA in Asians which may have a genetic basis. We report phosphodiesterase (PDE4D gene polymorphism and its correlation with MRA findings in patients with ischemic stroke.

  9. Candidate human genetic polymorphisms and severe malaria in a Tanzanian population.

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    Alphaxard Manjurano

    Full Text Available Human genetic background strongly influences susceptibility to malaria infection and progression to severe disease and death. Classical genetic studies identified haemoglobinopathies and erythrocyte-associated polymorphisms, as protective against severe disease. High throughput genotyping by mass spectrometry allows multiple single nucleotide polymorphisms (SNPs to be examined simultaneously. We compared the prevalence of 65 human SNP's, previously associated with altered risk of malaria, between Tanzanian children with and without severe malaria. Five hundred children, aged 1-10 years, with severe malaria were recruited from those admitted to hospital in Muheza, Tanzania and compared with matched controls. Genotyping was performed by Sequenom MassArray, and conventional PCR was used to detect deletions in the alpha-thalassaemia gene. SNPs in two X-linked genes were associated with altered risk of severe malaria in females but not in males: heterozygosity for one or other of two SNPs in the G6PD gene was associated with protection from all forms of severe disease whilst two SNPs in the gene encoding CD40L were associated with respiratory distress. A SNP in the adenyl cyclase 9 (ADCY9 gene was associated with protection from acidosis whilst a polymorphism in the IL-1α gene (IL1A was associated with an increased risk of acidosis. SNPs in the genes encoding IL-13 and reticulon-3 (RTN3 were associated with increased risk of cerebral malaria. This study confirms previously known genetic associations with protection from severe malaria (HbS, G6PD. It identifies two X-linked genes associated with altered risk of severe malaria in females, identifies mutations in ADCY9, IL1A and CD40L as being associated with altered risk of severe respiratory distress and acidosis, both of which are characterised by high serum lactate levels, and also identifies novel genetic associations with severe malaria (TRIM5 and cerebral malaria(IL-13 and RTN3. Further studies

  10. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

    Science.gov (United States)

    Watkins, W Scott; Rogers, Alan R; Ostler, Christopher T; Wooding, Steve; Bamshad, Michael J; Brassington, Anna-Marie E; Carroll, Marion L; Nguyen, Son V; Walker, Jerilyn A; Prasad, B V Ravi; Reddy, P Govinda; Das, Pradipta K; Batzer, Mark A; Jorde, Lynn B

    2003-07-01

    We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

  11. High genetic polymorphism of relapsing P. vivax isolates in northwest Colombia.

    Science.gov (United States)

    Restrepo, Eliana; Imwong, Mallika; Rojas, Winston; Carmona-Fonseca, Jaime; Maestre, Amanda

    2011-07-01

    Genetic diversity of Plasmodium populations has been more extensively documented in Colombia for Plasmodium falciparum than for Plasmodium vivax. Recently, highly variable microsatellite markers have been described and used in population-level studies of genetic variation of P. vivax throughout the world. We applied this approach to understand the genetic structure of P. vivax populations and to identify recurrence-associated haplotypes. In this, three microsatellite markers of P. vivax were amplified and the combined size of the fragments was used to establish genotypes. Patients from an ongoing treatment efficacy trial who were kept either in endemic or non-endemic regions in the northwest of Colombia were included in the study. In total 58 paired clinical isolates, were amplified. A total of 54 haplotypes were observed among the two regions. Some haplotypes were exclusive to the endemic region where the highest degree of polymorphism was detected. In addition, we confirmed the different genotypes of recurrent-relapsing and primary infection isolates suggesting the activation of heterologous hypnozoite populations. We conclude that analysis of the three microsatellites is a valuable tool to establish the genetic characteristics of P. vivax populations in Colombia.

  12. Genetic Polymorphism of Aedes albopictus Population Inferred From ND5 Gene Variabilities In Subang Jaya, Malaysia.

    Science.gov (United States)

    Adilah-Amrannudin, Nurul; Hamsidi, Mayamin; Ismail, Nurul-Ain; Ismail, Rodziah; Dom, Nazri Che; Ahmad, Abu Hassan; Mastuki, Mohd Fahmi; Basri, Tengku Shahrul Anuar Tengku Ahmad; Khalid, Adira; Muslim, Mohammad; Daud, Nurul Amalina Ahmad; Camalxaman, Siti Nazrina

    2016-12-01

    This study was performed to establish the genetic variability of Aedes albopictus within Subang Jaya, Selangor, Malaysia, by using the nicotinamide adenine dinucleotide dehydrogenase 5 subunit (ND5) mitochondrial DNA (mtDNA) marker. A total of 90 samples were collected from 9 localities within an area of the Subang Jaya Municipality. Genetic variability was determined through the amplification and sequencing of a fragment of the ND5 gene. Eight distinct mtDNA haplotypes were identified. The evolutionary relationship of the local haplotypes alongside 28 reference strains was used to construct a phylogram, the analysis of which revealed low genetic differentiation in terms of both nucleotide and haplotype diversity. Bayesian method was used to infer the phylogenetic tree, revealing a unique relationship between local isolates. The study corroborates the reliability of ND5 to identify distinct lineages for polymorphism-based studies and supplements the existing body of knowledge regarding its genetic diversity. This in turn could potentially aid existing vector control strategies to help mitigate the risk and spread of the dengue virus.

  13. High genetic polymorphism of relapsing P. vivax isolates in northwest Colombia

    Science.gov (United States)

    Restrepo, Eliana; Imwong, Mallika; Rojas, Winston; Carmona-Fonseca, Jaime; Maestre, Amanda

    2011-01-01

    Genetic diversity of Plasmodium populations has been more extensively documented in Colombia for Plasmodium falciparum than for Plasmodium vivax. Recently, highly variable microsatellite markers have been described and used in population-level studies of genetic variation of P. vivax throughout the world. We applied this approach to understand the genetic structure of P. vivax populations and to identify recurrence-associated haplotypes. In this, three microsatellite markers of P. vivax were amplified and the combined size of the fragments was used to establish genotypes. Patients from an ongoing treatment efficacy trial who were kept either in endemic or non-endemic regions in the northwest of Colombia were included in the study. In total 58 paired clinical isolates, were amplified. A total of 54 haplotypes were observed among the two regions. Some haplotypes were exclusive to the endemic region where the highest degree of polymorphism was detected. In addition, we confirmed the different genotypes of recurrent-relapsing and primary infection isolates suggesting the activation of heterologous hypnozoite populations. We conclude that analysis of the three microsatellites is a valuable tool to establish the genetic characteristics of P. vivax populations in Colombia. PMID:21497586

  14. Correlation between genetic HLA class I and II polymorphisms and anthropological aspects in the Chaouya population from Morocco (Arabic speaking).

    Science.gov (United States)

    Canossi, A; Piancatelli, D; Aureli, A; Oumhani, K; Ozzella, G; Del Beato, T; Liberatore, G; El Aouad, R; Adorno, D

    2010-09-01

    The aim of this study was to provide genetic and anthropological information on the Chaouya (CH), an Arabic-speaking population living in West Morocco, Atlantic coast (Settat). In 98 unrelated healthy CH volunteers, we first investigated the human leukocyte antigen (HLA) class I and II allele polymorphisms using a sequence-based typing method and examined haplotypes and relatedness of this group to other African and Mediterranean populations. The study showed the close relatedness with Tunisian population and other North Africans, together with a strong influence of various immigrations, mainly Spaniards, French, and Portuguese, as expected. Nevertheless, analysis of class II allele frequencies (afs) showed that Oromo and Amhara Ethiopian groups cluster together with the Berbers and other North Africans, confirming the relationship between these populations (Afro-Asiatic linguistic group, Hamites). South and sub-Saharan Africans cluster separately at a great distance from CH, except the sub-Saharan Bantu population from Congo Kinshasa, which shows a relatively close genetic relationship ascribable to the effect of a diversifying selection. On the other hand, considering HLA class I afs analyses, it was noteworthy that CH grouped together with sub-Saharans, showing a close genetic distance mainly with Ugandas and Kenians Luo.

  15. Genetic polymorphism of mitochondrial DNA HVS-I and HVS-Ⅱ of Chinese Tu ethnic minority group

    Institute of Scientific and Technical Information of China (English)

    Feng Chen; Yajun Deng; Yonghui Dang; BO Zhang; Haofang Mu; Xiaoguang Yu; Lin Li; Chunxia Yan; Teng Chen

    2008-01-01

    We analyzed the two hypervariable segments HVS-Ⅰ and HVS-Ⅱ of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes.Comparing with Anderson sequence,79 polymorphic loci in HVS-Ⅰ and 40 in HVS-Ⅱ were found in Chi-nese Tu ethnic minority group mtDNA sequences,and 90 and 64 haplotypes were then defined.Haplotype diversity and the mean pair-wise differences were 0.9903:±0.0013 and 5.7785 in HVS-Ⅰ,and 0.9777±0.0013 and 3.5819 in HVS-Ⅱ,respectively.By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-Ⅰ,we defined some new types of sequence variations.We also compared the relationship between Tu population and other populations using mtDNA HVS-Ⅰ sequences.According to Rst genetic distances,the phylogenetic tree showed that the Tu population,the Xi'an Han population,the Chinese Korean,and the Mongol ethnic group were in a clade.This indicated a close genetic relationship between them.There were far relations between the Tu population and other Chinese southern Han populations,Siberian,European,African,and other foreign populations.The results suggest that Tu population has a multi-origin and has also merged with other local populations.

  16. Peroxisome Proliferator-Activated Receptor Genetic Polymorphisms and Nonalcoholic Fatty Liver Disease: Any Role in Disease Susceptibility?

    Directory of Open Access Journals (Sweden)

    Paola Dongiovanni

    2013-01-01

    Full Text Available Nonalcoholic fatty liver disease (NAFLD defines a wide spectrum of liver diseases that extend from simple steatosis, that is, increased hepatic lipid content, to nonalcoholic steatohepatitis (NASH, a condition that may progress to cirrhosis with its associated complications. Nuclear hormone receptors act as intracellular lipid sensors that coordinate genetic networks regulating lipid metabolism and energy utilization. This family of transcription factors, in particular peroxisome proliferator-activated receptors (PPARs, represents attractive drug targets for the management of NAFLD and NASH, as well as related conditions such as type 2 diabetes and the metabolic syndrome. The impact on the regulation of lipid metabolism observed for PPARs has led to the hypothesis that genetic variants within the human PPARs genes may be associated with human disease such as NAFLD, the metabolic syndrome, and/or coronary heart disease. Here we review the available evidence on the association between PPARs genetic polymorphism and the susceptibility to NAFLD and NASH, and we provide a meta-analysis of the available evidence. The impact of PPAR variants on the susceptibility to NASH in specific subgroup of patients, and in particular on the response to therapies, especially those targeting PPARs, represents promising new areas of investigation.

  17. Peroxisome Proliferator-Activated Receptor Genetic Polymorphisms and Nonalcoholic Fatty Liver Disease: Any Role in Disease Susceptibility?

    Science.gov (United States)

    Dongiovanni, Paola; Valenti, Luca

    2013-01-01

    Nonalcoholic fatty liver disease (NAFLD) defines a wide spectrum of liver diseases that extend from simple steatosis, that is, increased hepatic lipid content, to nonalcoholic steatohepatitis (NASH), a condition that may progress to cirrhosis with its associated complications. Nuclear hormone receptors act as intracellular lipid sensors that coordinate genetic networks regulating lipid metabolism and energy utilization. This family of transcription factors, in particular peroxisome proliferator-activated receptors (PPARs), represents attractive drug targets for the management of NAFLD and NASH, as well as related conditions such as type 2 diabetes and the metabolic syndrome. The impact on the regulation of lipid metabolism observed for PPARs has led to the hypothesis that genetic variants within the human PPARs genes may be associated with human disease such as NAFLD, the metabolic syndrome, and/or coronary heart disease. Here we review the available evidence on the association between PPARs genetic polymorphism and the susceptibility to NAFLD and NASH, and we provide a meta-analysis of the available evidence. The impact of PPAR variants on the susceptibility to NASH in specific subgroup of patients, and in particular on the response to therapies, especially those targeting PPARs, represents promising new areas of investigation. PMID:23431284

  18. Genetic polymorphisms of estrogen receptor alpha and catechol-O-methyltransferase genes in Turkish patients with familial prostate carcinoma

    Directory of Open Access Journals (Sweden)

    Ayfer Pazarbasi

    2013-01-01

    Full Text Available Objectives: Estrogen is one of the most crucial hormones participating in the proliferation and carcinogenesis of the prostate glands. Genetic polymorphisms in the estrogen metabolism pathway might be involved in the risk of prostate carcinoma development. We evaluated the association between genetic polymorphisms in estrogen receptor alpha (ESR1 and catechol-O-methyltransferase (COMT genes and the risk of developing familial prostate carcinoma. Materials and Methods: In this study, 34 cases with prostate carcinoma whose first-degree relatives had prostate carcinoma and 30 healthy age-matched male controls were enrolled. The genotypes of ESR1 and COMT genes were analyzed employing polymerase chain reaction-restriction fragment length polymorphism method. 34 cases with prostate carcinoma, whose first degree relatives had prostate carcinoma and 14 age-matched male controls were enrolled to analyze the genotype of these two genes. Results: Among control patients, the ESR1 PvuII genotypes of C/C, C/T and T/T were observed in 37%, 26% and 37%, respectively, whereas the C/C, C/T and T/T genotypes were observed in 18%, 41% and 41% of case patients, respectively. Among controls, the ESR1 PvuII allele frequencies of C and T were equally observed, whereas the C and T allele frequencies were observed in 38% and 62% of patients, respectively. Among ESR1 PvuII genotypes there were not any significant difference in terms of genotype (P = 0.199 and allele (P = 0.181 frequencies . Among controls, the ESR1 XbaI genotypes of G/G, G/A and A/A were observed in 33%, 37% and 33%, respectively, whereas the G/G, G/A and A/A genotypes were observed in 12%, 47% and 41% of patients, respectively. Among controls, the ESR1 XbaI allele frequencies of A and G were observed equally, respectively, whereas the A and G frequencies were observed in 65% and 35% of patients, respectively. Among ESR1 Χ baI, there was not any significant difference in terms of genotype (P = 0.111 and

  19. The associations between two vital GSTs genetic polymorphisms and lung cancer risk in the Chinese population: evidence from 71 studies.

    Directory of Open Access Journals (Sweden)

    Kui Liu

    Full Text Available BACKGROUND: The genetic polymorphisms of glutathione S-transferase (GSTs have been suspected to be related to the development of lung cancer while the current results are conflicting, especially in the Chinese population. METHODS: Data on genetic polymorphisms of glutathione S-transferase Mu 1 (GSTM1 from 68 studies, glutathione S-transferase theta 1 (GSTT1 from 17 studies and GSTM1-GSTT1 from 8 studies in the Chinese population were reanalyzed on their association with lung cancer risk. Odds ratios (OR were pooled using forest plots. 9 subgroups were all or partly performed in the subgroup analyses. The Galbraith plot was used to identify the heterogeneous records. Potential publication biases were detected by Begg's and Egger's tests. RESULTS: 71 eligible studies were identified after screening of 1608 articles. The increased association between two vital GSTs genetic polymorphisms and lung cancer risk was detected by random-effects model based on a comparable heterogeneity. Subgroup analysis showed a significant relationship between squamous carcinoma (SC, adenocarcinoma (AC or small cell lung carcinoma (SCLC and GSTM1 null genotype, as well as SC or AC and GSTT1 null genotype. Additionally, smokers with GSTM1 null genotype had a higher lung cancer risk than non-smokers. Our cumulative meta-analysis demonstrated a stable and reliable result of the relationship between GSTM1 null genotype and lung cancer risk. After the possible heterogeneous articles were omitted, the adjusted risk of GSTs and lung cancer susceptibility increased (fixed-effects model: ORGSTM1 = 1.23, 95% CI: 1.19 to 1.27, P<0.001; ORGSTT1 = 1.18, 95% CI: 1.10 to 1.26, P<0.001; ORGSTM1-GSTT1 = 1.33, 95% CI: 1.10 to 1.61, P = 0.004. CONCLUSIONS: An increased risk of lung cancer with GSTM1 and GSTT1 null genotype, especially with dual null genotype, was found in the Chinese population. In addition, special histopathological classification of lung cancers and a

  20. Genetic polymorphism at codon 546 of the human RAD17 contributes to the risk for esophageal squamous cell carcinoma

    Science.gov (United States)

    Yasuda, Yukiko; Sakai, Akiko; Ito, Sachio; Mita, Yuichiro; Sonoyama, Takayuki; Tanabe, Shunsuke; Shirakawa, Yasuhiro; Naomoto, Yoshio; Katayama, Hiroshi; Shimizu, Kenji

    2016-01-01

    Human RAD17, a human homolog of the Schizosaccharomyces pombe cell cycle checkpoint gene RAD17, plays a significant role in activating checkpoint signals in response to DNA damage. We evaluated the association of hRAD17 Leu546Arg (rs1045051), a missense single nucleotide polymorphism, with the risk of esophageal squamous cell carcinoma in relation to smoking and alcohol consumption history in 154 esophageal squamous cell carcinoma male patients and 695 cancer-free male controls by a case-control study conducted in Japan. The results showed that the hRAD17 Arg/Arg genotype compared to the Leu/Leu and Leu/Arg genotypes was significantly associated with the risk of the esophageal squamous cell carcinoma with an adjusted odds ratios of 2.22 (95% CI: 1.19-4.16 P=0.013). In stratified studies, the risk of esophageal squamous cell carcinoma was markedly higher in light drinkers (less than 23 g ethanol/day) with the Arg/Arg genotype than in heavy drinkers (excess of 23 g ethanol/day) with the Arg/Arg genotype (OR=2.83, 95% CI: 1.05-7.61, P=0.04). We concluded that the genetic variant of hRAD17 Leu546Arg polymorphism exerts a significant effect on esophageal squamous cell carcinoma risk among Japanese men. PMID:27186329

  1. Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

    Directory of Open Access Journals (Sweden)

    Manish Roorkiwal

    2013-07-01

    Full Text Available Single nucleotide polymorphisms (SNPs are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, high-throughput SNP genotyping platforms (e.g., iScan or Infinium may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea ( L. and pigeonpea ( L.. Two sets of SNPs, one each for chickpea (96 SNPs and pigeonpea (48 SNPs, were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.

  2. Association between Genetic Polymorphism in the Swine Leukocyte Antigen-DRA Gene and Piglet Diarrhea in Three Chinese Pig Breeds.

    Science.gov (United States)

    Yang, Q L; Zhao, S G; Wang, D W; Feng, Y; Jiang, T T; Huang, X Y; Gun, S B

    2014-09-01

    The swine leukocyte antigen (SLA)-DRA locus is noteworthy among other SLA class II loci for its limited variation and has not been investigated in depth. This study was investigated to detect polymorphisms of four exons of SLA-DRA gene and its association with piglet diarrhea in Landrace, Large White and Duroc pigs. No polymorphisms were detected in exon 3, while 2 SNPs (c.178G>A and c.211T>C), 2 SNPs (c.3093A>C and c.3104C>T) and 5 SNPs (c.4167A>G, c.4184A>G, c.4194A>G, c.4246A>G and c.4293G>A) were detected in exon 1, exon 2 and exon 4 respectively, and 1 SNP (c.4081T>C) in intron 3. Statistical results showed that genotype had significant effect on piglet diarrhea, individuals with genotype BC had a higher diarrhea score when compared with the genotypes AA, AB, AC and CC. Futhermore, genotype AC had a higher diarrhea score than the genotype CC in exon 1 (ppiglet diarrhea appeared that Hap2, 5, 8, 10, and 14 may be the susceptible haplotypes and Hap9 may be the resistant haplotype to piglet diarrhea. The genetic variations identified of the SLA-DRA gene may potentially be functional mutations related to piglet diarrhea.

  3. Study on Insulin Resistance and Genetic Polymorphisms in Essential Hypertension Patients of Two Different Kinds of TCM Constitution

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To investigate the relationship of insulin resistance and the polymorphisms of insulin receptor-related genes in essential hypertension patients of two different kinds of TCM constitution. Methods: Oral glucose tolerance test (OGTT) and insulin release test (InRT) were conducted in 217 essential hypertensive patients of either sluggish meticulous (SM) constitution (139 cases) or prosperous impetuous (PI) constitution (78 cases), and the polymorphism of three genes,including insulin-like growth factor-1 receptor (IGF-1R), insulin receptor substrate-1 (IRS-1) and 2 (IRS-2) genes were detected. Results: (1) OGTT, InRT and insulin resistance index (Homa-IR) were higher and insulin sensitive index (ISI) was lower in the patients of SM constitution than those in patients of PI constitution. (2) Significant difference of ISI and Homa-IR was shown in patients of both constitutions with genotype G of the 3 genes. Conclusion: Decrease of insulin sensitivity and increase of insulin resistance are more obvious in hypertensive patients with genotype G of the 3 genes of SM constitution than in those of PI constitution. Therefore, the difference in constitution might be one of the genetic characteristics for insulin resistance in hypertensive patients.

  4. Genetic Diversity among Clinical Isolates of Candida glabrata Analyzed by Randomly Amplified Polymorphic DNA and Multilocus Enzyme Electrophoresis Analyses

    Science.gov (United States)

    Boldo, Xavier M.; Villa-Tanaca, Lourdes; Zúñiga, Gerardo; Hernández-Rodríguez, César

    2003-01-01

    The genetic diversity of 47 clinical and reference strains of Candida glabrata from several geographical origins and diverse clinical disorders, with different antifungal susceptibilities, as well as their genetic relationships were studied through multilocus enzyme electrophoresis (MLEE) and randomly amplified polymorphic DNA (RAPD) techniques. The genetic diversity estimated for 11 MLEE loci measured as average heterozygosity (h) was 0.055. A high level of genetic relatedness among isolates was established by cluster analysis. Forty-nine RAPD markers were analyzed, and the average genetic diversity among isolates, estimated by Shannon's index (Ho), was 0.372. The ΦST values estimated through an analysis of molecular variance to assess genetic differentiation among isolates revealed no genetic differentiation among them. Our results revealed very low genetic diversity among isolates, a lack of differentiation, and no association with their geographic origin and the clinical characteristics. PMID:14532225

  5. Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds

    DEFF Research Database (Denmark)

    Strønen, Astrid Vik; Salmela, Elina; Baldursdottir, Birna K.

    2017-01-01

    Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only......: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic...... structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds...

  6. Methylenetetrahydrofolate reductase gene C677T polymorphism and breast cancer risk: Evidence for genetic susceptibility.

    Science.gov (United States)

    Kumar, Pradeep; Yadav, Upendra; Rai, Vandana

    2015-12-01

    There are several evidences supporting the role of 5-10 methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms in breast cancer (BC). Case control association studies on breast cancer have been repeatedly performed over the last two decades, but results are inconsistent. We performed a meta-analysis to confirm the association between MTHFR C677T polymorphism and BC risk. The articles were retrieved by searching the PubMed, Google Scholar, and Springer Link databases. Crude odds ratios (OR) with 95% confidence intervals (CIs) was used to assess the strength of association between C677T polymorphism and BC. Publication bias was assessed by Egger's and Begg-Mazumdar tests. Meta-analysis was performed with Open Meta Analyst. Total 75 studies with 31,315 cases and 35, 608 controls were found suitable for the inclusion in the present meta-analysis. The results of meta-analysis suggested that there were moderate significant association between C677T polymorphism and BC risk using overall comparisons in five genetic models (T vs. C: OR = 1.08, 95% CI = 1.03-1.13, p = < 0.001; TT + CT vs. CC: OR = 1.06, 95% CI = 1.02-1.09, p = < 0.001; TT vs. CC: OR = 1.17, 95% CI = 1.06-1.28, p = 0.001; CT vs. CC OR = 1.05, 95% CI = 1.01-1.08, p = 0.005; TT vs. CT + CC: OR = 1.12, 95% CI = 1.03-1.22, p = 0.005). In conclusion, results of present meta-analysis showed modest association between MTHFR C677T polymorphism with breast cancer in total studies. However, sub-group analysis results based on ethnicity showed strong significant association between TT genotype and breast cancer (TT vs. CC; OR°=°1.26; 95% CI: 1.06-1.51; p = 0.009) in Asian population but in Caucasian population such association was not observed (TT vs. CC; OR°=°1.08; 95% CI: 0.99-1.14; p = 0.05).

  7. Common genetic variability in ESR1 and EGF in relation to endometrial cancer risk and survival

    OpenAIRE

    Einarsdóttir, K; Darabi, H; Czene, K.; Li, Y; Low, Y.L.; Y. Q. Li; Bonnard, C.; Wedrén, S.; Liu, E. T.; Hall, P; Liu, J; Humphreys, K.

    2009-01-01

    We investigated common genetic variation in the entire ESR1 and EGF genes in relation to endometrial cancer risk, myometrial invasion and endometrial cancer survival. We genotyped a dense set of single-nucleotide polymorphisms (SNPs) in both genes and selected haplotype tagging SNPs (tagSNPs). The tagSNPs were genotyped in 713 Swedish endometrial cancer cases and 1567 population controls and the results incorporated into logistic regression and Cox proportional hazards models. We found five a...

  8. Genetic Relation Analysis on Ramie [Boehmeria nivea (L.) Gaud.] Inbred Lines by SRAP Markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The objective of this article is to reveal the variations of ramie inbred lines in DNA level and discuss their molecular background to provide a theoretical basis for ramie cross breeding. In the present study, the genetic relationships among 33 inbred line accessions and two wild types that originated from China and Brazil were estimated using sequence-related amplified polymorphism (SRAP) markers. The results showed that 33 out of 81 primer combinations turned out to be polymorphic and 332 polymorphism bands were obtained. On the basis of the appearance of the markers, the genetic relationships were analyzed using unweighted pair-group method of arithmetic average cluster analysis (UPGMA), and the genetic Jaccard similarity coefficients were calculated. The inbred-lines originating from China and Brazil formed a cluster suggesting a possibility that the Brazilian cultivars could have developed from cultivars introduced from China. Within ramie inbred-lines, the groupings also indicated that the greatest genetic relationship among cultivars was correlated to the region of origin of cultivars. The results provided the evidence that SRAP was an efficient approach, suitable for taxonomic analysis of ramie inbred lines. To the authors' knowledge, this is the first application of SRAP marker on the systematics of ramie inbred lines.

  9. Interleukin-16 Gene Polymorphisms Are Considerable Host Genetic Factors for Patients’ Susceptibility to Chronic Hepatitis B Infection

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    Sara Romani

    2014-01-01

    Full Text Available Host genetic background is known as an important factor in patients’ susceptibility to infectious diseases such as viral hepatitis. The aim of this study was to determine the effect of genetic polymorphisms of interleukin-16 (IL-16 cytokine on susceptibility of hepatitis B virus (HBV infected patients to develop chronic HBV infection. Genotyping was conducted using PCR followed by enzymatic digestion and RFLP (restriction fragment length polymorphism analysis. We genotyped three single nucleotide polymorphisms (SNPs in the Il-16 gene (rs11556218 T>G, rs4778889 T>C, and rs4072111 C>T to test for relationship between variation at these loci and patients’ susceptibility to chronic HBV infection. Allele frequency of Il-16 gene rs4072111 and rs11556218 was significantly different between chronic HBV patients and healthy blood donors. Genotype frequency of rs4778889 polymorphism of Il-16 gene was significantly different when chronic HBV patients and HBV clearance subjects were compared. Our results showed that Il-16 gene polymorphisms are considerable host genetic factors when we chase biomarkers for prognosis of HBV infected patients.

  10. Genetic diversity in somatic mutants of grape (Vitis vinifera) cultivar Italia based on random amplified polymorphic DNA.

    Science.gov (United States)

    Maia, S H Z; Mangolin, C A; Collet, S A O; Machado, M F P S

    2009-01-13

    Random amplified polymorphic DNA (RAPD) markers were used to detect polymorphism and to examine relationships among four table grape clones from northwestern Paraná, in southern Brazil. The 10 primers used for RAPD fingerprints generated 126 reproducible fragments, of which 63, 68, 76, and 72 were polymorphic in cultivars Italia, Rubi, Benitaka, and Brasil, respectively. Among the primers, OPP-08 generated the highest number of fragments, whereas OPE-15 was the most efficient for discriminating polymorphic fragments. The distribution of the clones by cluster analysis indicated that there were no differences in RAPD markers between the colored mutant and the original clone (cultivar Italia), supporting the hypothesis that the non-colored and the colored mutant are the same cultivar. However, we found high levels of polymorphism within and between the cultivars Italia, Rubi, Benitaka, and Brasil (65.1%), contrary to a previous hypothesis that the four clones are genetically uniform. This confirmed our expectation of genetic variation among the clones and within each clone. We conclude that the primers are useful for analyzing the development of the genetic diversity within each of these clones.

  11. Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

    Directory of Open Access Journals (Sweden)

    Nemoda Zsofia

    2011-12-01

    Full Text Available Abstract Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP in the catechol-0-methyltransferase gene (COMT rs4680 and one representative variable number of tandem repeats (VNTR in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days, repeated freeze-thaw cycles (up to 6 cycles, and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using

  12. Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

    Science.gov (United States)

    2011-01-01

    Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP) in the catechol-0-methyltransferase gene (COMT rs4680) and one representative variable number of tandem repeats (VNTR) in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region) were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days), repeated freeze-thaw cycles (up to 6 cycles), and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using 10 ng of DNA per

  13. Genetic polymorphism for IFNγ +874T/A in patients with acute toxoplasmosis

    Directory of Open Access Journals (Sweden)

    Elizabeth de Souza Neves

    2012-12-01

    Full Text Available INTRODUCTION: A single nucleotide polymorphism (SNP in the gene encoding gamma interferon influences its production and is associated with severity of infectious diseases. This study aimed to evaluate the association of IFNγ+874T/A SNP with duration of disease, morbidity, and development of retinochoroiditis in acute toxoplasmosis. METHODS: A case-control study was conducted among 30 patients and 90 controls. RESULTS: Although statistical associations were not confirmed, A-allele was more common among retinochoroiditis cases and prolonged illness, while T-allele was more frequent in severe disease. CONCLUSIONS: Despite few cases, the results could indicate a relation between IFNγ+874T/A single nucleotide polymorphism and clinical manifestations of toxoplasmosis.

  14. The impact of a TSH receptor gene polymorphism on thyroid-related phenotypes in a healthy Danish twin population

    DEFF Research Database (Denmark)

    Hansen, Pia Skov; van der Deure, Wendy M; Peeters, Robin P;

    2007-01-01

    OBJECTIVES: The Asp727Glu polymorphism in the TSH receptor (TSHR) gene is associated with serum TSH levels. However, the proportion of genetic variation accounted for by this polymorphism is unknown. In this study, we (1) examined the association of the Asp727Glu polymorphism with thyroid size......, serum levels of TSH, thyroid hormones, and thyroid antibodies in 1241 healthy Danish twin individuals and (2) assessed the contribution of the polymorphism to the trait variation and the genetic variance. MEASUREMENTS: The effect of the genotype on the traits (mean +/- SD) was established; associations...... between the TSHR-Asp727Glu polymorphism and measures of thyroid homeostasis were assessed and the effect of the polymorphism on the trait's phenotypic variability was quantified by incorporating the genotype information in structural equation modelling. RESULTS: The genotype distribution was Asp/Asp 84...

  15. Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.

    Science.gov (United States)

    Qi, Ji; Chen, Yamao; Copenhaver, Gregory P; Ma, Hong

    2014-07-08

    DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.

  16. Association Between Genetic Polymorphisms in the Serotonergic System and Comorbid Personality Disorders Among Patients with First-Episode Depression

    DEFF Research Database (Denmark)

    Bukh, Jens D; Bock, Camilla; Kessing, Lars V

    2014-01-01

    the serotonin transporter, serotonin receptors 1A, 2A, 2C, and tryptophan hydroxylase 1 were genotyped. The authors found a significant effect of the length polymorphism in the serotonin transporter gene (5-HTTLPR) on cluster B personality disorder (mainly borderline disorder), but no influence on cluster C......Studies on the association between genetic polymorphisms and personality disorders have provided inconsistent results. Using the "enriched sample method," the authors of the present study aimed to assess the association between polymorphisms in the serotonergic transmitter system and comorbid...... personality disorders in patients recently diagnosed with first-episode depression. A total of 290 participants were systematically recruited via the Danish Psychiatric Central Research Register. Diagnoses of personality disorders were assessed by a SCID-II interview, and polymorphisms in the genes encoding...

  17. AT1 Receptor Gene Polymorphisms in relation to Postprandial Lipemia

    Directory of Open Access Journals (Sweden)

    B. Klop

    2012-01-01

    Full Text Available Background. Recent data suggest that the renin-angiotensin system may be involved in triglyceride (TG metabolism. We explored the effect of the common A1166C and C573T polymorphisms of the angiotensin II type 1 receptor (AT1R gene on postprandial lipemia. Methods. Eighty-two subjects measured daytime capillary TG, and postprandial lipemia was estimated as incremental area under the TG curve. The C573T and A1166C polymorphisms of the AT1R gene were determined. Results. Postprandial lipemia was significantly higher in homozygous carriers of the 1166-C allele (9.39±8.36 mM*h/L compared to homozygous carriers of the 1166-A allele (2.02±6.20 mM*h/L (P<0.05. Postprandial lipemia was similar for the different C573T polymorphisms. Conclusion. The 1166-C allele of the AT1R gene seems to be associated with increased postprandial lipemia. These data confirm the earlier described relationships between the renin-angiotensin axis and triglyceride metabolism.

  18. APOA2 Polymorphism in Relation to Obesity and Lipid Metabolism

    Directory of Open Access Journals (Sweden)

    Moushira Erfan Zaki

    2013-01-01

    Full Text Available Objectives. This study aims to analysis the relationship between c.-492T>C polymorphism in APOA2 gene and the risk for obesity in a sample of Egyptian adolescents and investigates its effect on body fat distribution and lipid metabolism. Material and Methods. A descriptive, cross-sectional study was conducted on 303 adolescents. They were 196 obese and 107 nonobese, aged 16–19 years old. Variables examined included body mass index (BMI, waist circumference (WC, waist to hip ratio (WHR, systolic and diastolic blood pressure (BP, body fat percentage (BF%, abdominal visceral fat layer, and dietary intake. Abdominal visceral fat thickness was determined by ultrasonography. The polymorphism in the APOA2 c.-492T>C was analyzed by PCR amplification. Results. Genotype frequencies were in Hardy-Weinberg equilibrium. The frequency of the mutant C allele was significantly higher in obese cases compared to nonobese. After multivariate adjustment, waist, BF% and visceral adipose layer, food consumption, and HDL-C were significantly higher in homozygous allele CC carriers than TT+TC carriers. Conclusions. Homozygous individuals for the C allele had higher obesity risk than carriers of the T allele and had elevated levels of visceral adipose tissue and serum HDL-C. Moreover, the study shows association between the APOA2 c.-492T>C polymorphism and food consumption.

  19. Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity.

    Directory of Open Access Journals (Sweden)

    Tali Gidalevitz

    2009-03-01

    Full Text Available Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles.

  20. [Genetic polymorphism of steroidogenic enzymes and steroid receptor level in tumors of the reproductive system].

    Science.gov (United States)

    Berstein, L M; Zimarina, T S; Tsyrlina, E V; Kovalevskiĭ, A Iu; Imianitov, E N

    2004-01-01

    The strategy of therapy and prognosis of reproductive system neoplasia generally depend on the steroid receptor status of tumor. The causes of formation of steroid receptor-free tumors are to be investigated. The genetic polymorphism of CYP19 (aromatase), CYP17 (17-hydroxylase; 17,20-lyase), CYP1B1 (4-estrogen hydroxylase) and COMT (catechol-O-methyl transferase) was studied in a total of 254 patients with breast and endometrial cancer, with particular reference to the association of certain polymorphisms and receptor status of tumor. It was found that the lack of estrogen receptor (ER) in breast tumor was due to a deficit in the A3A6 allele (p(0.01), while the absence of progesterone receptors was associated with a lower incidence of the A1A1 and A1A2 variants (p = 0.022) of tetranucleotide repeats in the CYP19 gene. In the same patients, receptor-negative tumors occurred more often (p = 0.032) than in combinations of higher level of 4-hydroxylase estradiol of S-allele in position 48 (Gly/Arg) of the CYP1B1 gene. Moreover, endometrial carcinoma patients tended to reveal (p = 0.058) an increased ratio of A6A7-CYP19 to allele A1-containing variant. No other distinctions between R(+) and R(-) tumors were identified. It is suggested that peculiar polymorphisms of steroidogenic enzymes may moderately influence the genesis of R(-) neoplasms which may be associated with either the rate of estrogen biosynthesis or, as in the case of CYP1B1, with formation of genotoxic derivatives of estrogens. The latter point is to be investigated further.

  1. Genetic susceptibility to chronic otitis media with effusion: candidate gene single nucleotide polymorphisms.

    Science.gov (United States)

    MacArthur, Carol J; Wilmot, Beth; Wang, Linda; Schuller, Michael; Lighthall, Jessyka; Trune, Dennis

    2014-05-01

    The genetic factors leading to a predisposition to otitis media are not well understood. The objective of the current study was to develop a tag-single nucleotide polymorphism (SNP) panel to determine if there is an association between candidate gene polymorphisms and the development of chronic otitis media with effusion. A 1:1 case/control design of 100 cases and 100 controls was used. The study was limited to the chronic otitis media with effusion phenotype to increase the population homogeneity. A panel of 192 tag-SNPs was selected. Saliva for DNA extraction was collected from 100 chronic otitis media with effusion cases and 100 controls. After quality control, 100 case and 79 control samples were available for hybridization. Genomic DNA from each subject was hybridized to the SNP probes, and genotypes were generated. Quality control across all samples and SNPs reduced the final SNPs used for analysis to 170. Each SNP was then analyzed for statistical association with chronic otitis media with effusion. Eight SNPs from four genes had an unadjusted P value of otitis media with effusion phenotype (TLR4, MUC5B, SMAD2, SMAD4); five of these polymorphisms were in the TLR4 gene. Even though these results need to be replicated in a novel population, the presence of five SNPs in the TLR4 gene having association with chronic otitis media with effusion in our study population lends evidence for the possible role of this gene in the susceptibility to otitis media. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  2. Evaluation and Genetic Polymorphism studies of Jatropha (Jatropha curcus for Water Stress Tolerance

    Directory of Open Access Journals (Sweden)

    Borse Tushar

    2010-05-01

    Full Text Available Jatropha (Jatropha curcus is an alternative resource for biodiesel. To boost the rural economy in sustainable manner it is estimated that 30 Million hector plantation may replace current use of fossil fuel. Although Jatropha has an inbuilt ability to grow under water limited conditions, scanty information is available about natural genetic variation for water stress tolerance. Three local genotypes from Pune district were collected and initially screened by imparting artificial stress using PEG – 6000. Seedlings were subjected to increasing concentration of PEG – 6000 (30, 60, 90, 120 and 150 gm/l to study effect on growth parameters.The root growth, number of secondary roots, true leaf expansion at morphological level and palisade mesophyll height, xylem vessel expansion at anatomical level showed drastic negative impact as compared to control. It is worth to note that local germplasm performance was categorized into susceptible group as compared to tolerant genotype [Chattisgadh Selection] indicating need for genetic improvement. These genotypes were further studied at molecular level with RAPD and ISSR markers to amplify genetic variation. Polymorphic bands from Chattisgadh selection genotype are being evaluated for their usefulness as markers for water stress tolerance.

  3. Cathepsin D (C224T) polymorphism in sporadic and genetic Creutzfeldt-Jakob disease.

    Science.gov (United States)

    Kovacs, Gabor G; Sanchez-Juan, Pascual; Ströbel, Thomas; Schuur, Maaike; Poleggi, Anna; Nocentini, Sara; Giannattasio, Claudia; Belay, Girma; Bishop, Matthew; Capellari, Sabina; Parchi, Piero; Gelpi, Ellen; Gal, Aniko; Bakos, Agnes; Molnar, Maria J; Heinemann, Uta; Zerr, Inga; Knight, Richard S G; Mitrova, Eva; van Duijn, Cornelia; Budka, Herbert

    2010-01-01

    Accumulation of cathepsin D immunoreactive lysosomes correlates with tissue pathology in sporadic Creutzfeldt-Jakob disease (CJD) brains. The C-to-T transition within exon 2 of the cathepsin D (CTSD) gene is associated with altered enzymatic activity. Possession of the TT genotype is a risk factor for variant CJD. To verify the association between the CTSD position 224T allele and the risk for and survival in sporadic and genetic CJD, we genotyped 540 sporadic, 101 genetic CJD, and 723 control individuals. Genotype data and duration of illness were compared using multiple logistic regression and Kruskal-Wallis test. Multivariate survival analysis was performed using Cox's regression model. The distribution of CTSD position 224 alleles was approximately the same in all groups. We observed a trend for shorter survival in sporadic CJD patients harboring the T allele at position 224 of the CTSD gene in particular in sporadic CJD patients with the prion protein gene position 129 MM genotype. We conclude that the CTSD position 224 polymorphism alone is not a significant risk or disease-modifying factor in sporadic or genetic CJD.

  4. Genetic polymorphisms at TIMP3 are associated with survival of adenocarcinoma of the gastroesophageal junction.

    Directory of Open Access Journals (Sweden)

    Morteza Bashash

    Full Text Available The poor survival of adenocarcinomas of the gastroesophageal junction (GEJ makes them clinically important. Discovery of host genetic factors that affect outcome may guide more individualized treatment. This study tests whether constitutional genetic variants in matrix metalloproteinases (MMP and tissue inhibitors of metalloproteinases (TIMP genes are associated with outcome of GEJ adenocarcinoma. Single nucleotide polymorphisms (SNPs at four TIMP (TIMP1-4 and three MMP genes (MMP2, MMP7 and MMP9 were genotyped in DNA samples from a prospective cohort of patients with primary adenocarcinoma of the GEJ admitted to the British Columbia Cancer Agency. Cox proportional hazards regression, with adjustment for patient, disease and treatment variables, was used to estimate the association of SNPs with survival. Genotypes for 85 samples and 48 SNPs were analyzed. Four SNPs across TIMP3, (rs130274, rs715572, rs1962223 and rs5754312 were associated with survival. Interaction analyses revealed that the survival associations with rs715572 and rs5754312 are specific and significant for 5FU+cisplatin treated patients. Sanger sequencing of the TIMP3 coding and promoter regions revealed an additional SNP, rs9862, also associated with survival. TIMP3 genetic variants are associated with survival and may be potentially useful in optimizing treatment strategies for individual patients.

  5. Genetic change in the polynesian population of Easter Island: evidence from Alu insertion polymorphisms.

    Science.gov (United States)

    González-Pérez, E; Esteban, E; Via, M; García-Moro, C; Hernández, M; Moral, P

    2006-11-01

    The origin of Pacific islanders is still an open issue in human population genetics. To address this topic we analyzed a set of 18 Alu insertion polymorphisms in a total of 176 chromosomes from native Easter Island inhabitants (Rapanui). Available genealogical records allowed us to subdivide the total island sample into two groups, representative of the native population living in the island around 1900, and another formed by individuals with some ancestors of non-Rapanui origin. Significant genetic differentiation was found between these groups, allowing us to make some biodemographic and historical inferences about the origin and evolution of this geographically isolated island population. Our data are consistent with equivalent and recent contributions from Amerindian and European migrants to the 1900s Rapanui population, with an accelerated increase in the European gene flow during the 20(th) century, especially since the 1960s. Comparative analysis of our results with other available Alu variation data on neighbouring populations supports the "Voyaging Corridor" model of Polynesian human settlement, which indicates that pre-Polynesians are mainly derived from Southeast Asian and Wallacean populations rather than from Taiwan or the Philippines. This study underlines the importance of sampling and taking into account historical information in genetic studies to unravel the recent evolution of human populations.

  6. Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice.

    Science.gov (United States)

    Janecka, Magdalena; Marzi, Sarah J; Parsons, Michael J; Liu, Lin; Paya-Cano, Jose L; Smith, Rebecca G; Fernandes, Cathy; Schalkwyk, Leonard C

    2017-02-01

    Although the search for quantitative trait loci for behaviour remains a considerable challenge, the complicated genetic architecture of quantitative traits is beginning to be understood. The current project utilised heterogeneous stock (HS) male mice (n = 580) to investigate the genetic basis for brain weights, activity, anxiety and cognitive phenotypes. We identified 126 single nucleotide polymorphisms (SNPs) in genes involved in regulation of neurotransmitter systems, nerve growth/death and gene expression, and subsequently investigated their associations with changes in behaviour and/or brain weights in our sample. We found significant associations between four SNP-phenotype pairs, after controlling for multiple testing. Specificity protein 2 (Sp2, rs3708840), tryptophan hydroxylase 1 (Tph1, rs262731280) and serotonin receptor 3A (Htr3a, rs50670893) were associated with activity/anxiety behaviours, and microtubule-associated protein 2 (Map2, rs13475902) was associated with cognitive performance. All these genes except for Tph1 were expressed in the brain above the array median, and remained significantly associated with relevant behaviours after controlling for the family structure. Additionally, we found evidence for a correlation between Htr3a expression and activity. We discuss our findings in the light of the advantages and limitations of currently available mouse genetic tools, suggesting further directions for association studies in rodents.

  7. The genetic polymorphism ofPlasmodium vivax genes in endemic regions of Thailand

    Institute of Scientific and Technical Information of China (English)

    Varakorn Kosaisavee; Ian Hastings; Alister Craig; Usa Lek-Uthai

    2011-01-01

    Objective:To investigate the genetic polymorphism ofPlasmodium vivax (P. vivax)PvCSP andPvMSP1 genes from field isolates at four endemic regions (North, East, West and South) of Thailand.Methods:The152P. vivax infected cases from dried blood spots wereDNA extracted and confirmed by species-specific primer sets using multiplexPCR method.PvMSP1 fragments F2 andF3; PvCSPwere genotyped usingRFLP-PCR method.Results: Totally amplified DNA which was multiple genotypes for PvMSP1 F2 andPvMSP1 F3 were12.50% and8.55%, respectively while PvCSP was3.95%. The overall frequency of multiple genotypes was25%. There were 12 allele types ofPvMSP1 F2 using AluI enzyme digestion and 8 size variations were found in PvMSP1 F3. The isolates from western region was highly genetic diverse when compare among all isolates. The predominant variant type of PvCSP gene wasVK210 type.Conclusions:The multiple genotypes are common found in Thailand and it might hide the real genotype.PvCSP does not have extensive genetic diversity in this study. However, PvMSP1marker due to multiple genotypes is difficult to be analyzed. The multiple genotypes findings might stem from population migration and vector species findings.

  8. Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes.

    Science.gov (United States)

    Gasser, R B; Chilton, N B

    2001-11-22

    The analysis of genetic variation in parasitic nematodes has important implications for studying aspects of taxonomy, diagnosis, population genetics, drug resistance and molecular evolution. This article highlights some applications of PCR-based single-strand conformation polymorphism (SSCP) for the analysis of sequence variation in individual parasites (and their populations) to address some of these areas. It also describes the principles and advantages of SSCP, and provides some examples for future applications in parasitology.

  9. Polymorphisms of GSTM1 and CYP1A1 genes and their genetic susceptibility to prostate cancer in Chinese men

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Background Variation in prostate cancer incidence between different racial groups has been well documented,for which genetic polymorphisms are hypothesized to be an explanation.We evaluated the association between polymorphisms in the cytochrome P-450 CYP1A1(CYP1A1)and glutathione S-transferase M1(GSTM1)genes and genetic susceptibility to prostate cancer in Chinese men.Methods Two hundred and eight prostate cancer patients and 230 age matched controls were enrolled in this study.All DNA samples from peripheral blood lymphocytes were genotyped for common genetic polymorphisms of the CYP1A1 and GSTM1 genes using the oligonucleotide microarray(DNA chip)technique and the polymorphism results confirmed by sequencing.The different polymorphisms in prostate cancer patients were also analyzed according to age at diagnosis,prostate specific antigen level,cancer stage and grade(Gleason score).Results The prevalence of the GSTM1(0/0)genotype was significantly higher in prostate cancer patients(58.2%)than in controls(41.7%,P<0.05).Further analysis demonstrated that the prostate cancer patients with a GSTM1(0/0)genotype were younger than those with the GSTM1(+/+)genotype(P=0.024).No significant differences in the frequency distributions of CYP1A1 polymorphisms were observed between prostate cancer patients and controls.Conclusion GSTM1(0/0)gene polymorphism may be linked to prostate cancer risk and early age of onset in Chinese.

  10. Investigating the genetic polymorphism of sheep milk proteins: a useful tool for dairy production.

    Science.gov (United States)

    Selvaggi, Maria; Laudadio, Vito; Dario, Cataldo; Tufarelli, Vincenzo

    2014-12-01

    Sheep is the second most important dairy species after cow worldwide, and especially in the Mediterranean and Middle East regions. In some countries, the difficult environmental conditions require a peculiar adaptation and, in these contexts, sheep are able to provide higher quality protein than cattle. In the least-developed countries, the amount of dairy sheep and ovine milk production is progressively increasing. In order to improve dairy productions, in particular those with local connotations, it is necessary to obtain in-depth information regarding milk quality and rheological properties. The genetic polymorphisms of milk proteins are often associated with quantitative and qualitative parameters in milk and are potential candidate markers that should be included in breeding strategies similar to those already available for cattle. Due to the current and growing interest in this topic and considering the large amount of new information, the aim of this study was to review the literature on sheep milk protein polymorphisms with a particular emphasis on recent findings in order to give scientists useful support. Moreover, the effects of different protein variants on milk yield and composition are discussed.

  11. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation.

    Science.gov (United States)

    Gasser, Robin B; Hu, Min; Chilton, Neil B; Campbell, Bronwyn E; Jex, Aaron J; Otranto, Domenico; Cafarchia, Claudia; Beveridge, Ian; Zhu, Xingquan

    2006-01-01

    The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for amplicon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.

  12. Transferrin gene polymorphisms and population genetic studies of Atlantic cod (Gadus morhua)

    Institute of Scientific and Technical Information of China (English)

    Berhan Asmamaw

    2016-01-01

    Objective:To detect single nucleotide polymorphisms (SNPs) in the cod transferrin gene by comparing the sequences from Norwegian (North East Atlantic Ocean) and Canadian (North West Atlantic Ocean) specimen, and to quantify the genetic variation and differentiation in East and West Atlantic cod populations. Methods:cDNA sequences between individuals of Canadian (North West Atlantic Ocean) and Norwegian (North East Atlantic Ocean) origin were aligned. Allele frequencies of theSNPs were used to discriminate the different Atlantic cod populations in West/East Atlantic Ocean, and the Baltic Sea. Results: The sequence alignment detected19SNPs, of which 18 of them resulted in amino acid changes in the transferrin protein. Nonsynonymous to synonymous site substitution ratio (dn/ds) was by far greater than 1 providing an evidence for the existence of positive selection. The West Atlantic cod populations showed high values of heterozygosity and the Baltic populations were found to be inbred. Conclusions: This study identified and indicated transferrin gene polymorphisms that can be used for population differentiations.

  13. Genetic Association of PTPN22 Polymorphisms with Autoimmune Hepatitis and Primary Biliary Cholangitis in Japan

    Science.gov (United States)

    Umemura, Takeji; Joshita, Satoru; Yamazaki, Tomoo; Komatsu, Michiharu; Katsuyama, Yoshihiko; Yoshizawa, Kaname; Tanaka, Eiji; Ota, Masao

    2016-01-01

    Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are liver-specific autoimmune conditions that are characterized by chronic hepatic damage and often lead to cirrhosis and hepatic failure. Specifically, the protein tyrosine phosphatase N22 (PTPN22) gene encodes the lymphoid protein tyrosine phosphatase, which acts as a negative regulator of T-cell receptor signaling. A missense single nucleotide polymorphism (SNP) (rs2476601) in PTPN22 has been linked to numerous autoimmune diseases in Caucasians. In the present series, nine SNPs in the PTPN22 gene were analyzed in 166 patients with AIH, 262 patients with PBC, and 322 healthy controls in the Japanese population using TaqMan assays. Although the functional rs3996649 and rs2476601 were non-polymorphic in all subject groups, the frequencies of the minor alleles at rs1217412, rs1217388, rs1217407, and rs2488458 were significantly decreased in AIH patients as compared with controls (all Pc < 0.05). There were no significant relationships with PTPN22 SNPs in PBC patients. Interestingly, the AAGTCCC haplotype was significantly associated with resistance to both AIH (odds ratio [OR] = 0.58, P = 0.0067) and PBC (OR = 0.58, P = 0.0048). SNPs in the PTPN22 gene may therefore play key roles in the genetic resistance to autoimmune liver disease in the Japanese. PMID:27406031

  14. [Genetic polymorphism of clones and their seed progeny in the scotch pine clone plantation].

    Science.gov (United States)

    Korshikov, I I; Demkovich, A E

    2010-01-01

    Genetic variation at 12 allozyme loci (10 of them being polymorphic ones) has been studied in the archive-clone plantation of 23 Pinus sylvestris plus-trees and their seed progeny in the south-east of Ukraine. More than a half of clones had 4-8 heterozygous loci, whereas their seed progeny was marked by a lower variation than maternal trees. Seed progeny was obtained at a high outcrossing rate (t(m) = 95%). The clone progeny was characterized by a high percentage of abnormal allele segregation in megagametophytes. There was also a high frequency of significant deviation in distribution of seed embryo genotypes from the theoretically expected one according to the Hardy-Weinberg law.

  15. Possible genetic basis of pederin polymorphism in rove beetles (Paederus riparius).

    Science.gov (United States)

    Kellner, R L

    2000-01-01

    In Paederus riparius, (+) females able to biosynthesize the unique hemolymph toxin pederin and (-) females lacking this ability co-occur in natural populations. Larvae descended from both types of females were reared in the laboratory and the imagoes were crossed in order to get information about a possible genetic basis of this polymorphism. The daughters of (+) mothers become (+) females or (-) females, while the progeny of (-) mothers comprises only (-) females. This suggests a matrilineal trait because pederin biosynthesis cannot be inherited from the father. The rather stable proportion of nearly 90% (+) females in collected females is not maintained, however, when the beetles are reared in the laboratory. This observation is discussed with regard to artificial rearing conditions, where individuals are kept separate and cannot prey on conspecifics.

  16. Development of polymorphic microsatellite loci for conservation genetic studies of the coral reef fish Centropyge bicolor

    KAUST Repository

    Herrera, M.

    2015-08-14

    A total of 23 novel polymorphic microsatellite marker loci were developed for the angelfish Centropyge bicolor through 454 sequencing, and further tested on two spatially separated populations (90 individuals each) from Kimbe Bay in Papua New Guinea. The mean ± s.e. number of alleles per locus was 14·65 ± 1·05, and mean ± s.e. observed (HO) and expected (HE) heterozygosity frequencies were 0·676 ± 0·021 and 0·749 ± 0·018, respectively. The markers reported here constitute the first specific set for this genus and will be useful for future conservation genetic studies in the Indo-Pacific region. © 2015 The Fisheries Society of the British Isles.

  17. Effect of SULT1A1 and NAT2 genetic polymorphism on the association between cigarette smoking and colorectal adenomas

    NARCIS (Netherlands)

    Tiemersma, E.W.; Bunschoten, J.E.; Kok, F.J.; Glatt, H.; Boer, van S.Y.; Kampman, E.

    2004-01-01

    Cigarette smoke contains polycyclic hydrocarbons and arylamines that may both be activated by sulfotransferase, encoded by SULT1A1. A genetic polymorphism leads to an Arg213His substitution, thereby decreasing enzyme activity and stability and might thus modify the association between smoking and

  18. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm

    Science.gov (United States)

    Utilization of crop diversity held in genebanks is dependent on knowledge of useful traits including those identified genotypically. Target region amplification polymorphism (TRAP) markers were used to evaluate the genetic diversity and relationship among a sample of 263 chickpea landrace germplasm ...

  19. Genetic architecture of domestication-related traits in maize

    Science.gov (United States)

    Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genet...

  20. Association of genetic polymorphism of glutathione S-transferase (GSTM1, GSTT1, GSTP1) with bladder cancer susceptibility.

    Science.gov (United States)

    Safarinejad, Mohammad Reza; Safarinejad, Saba; Shafiei, Nayyer; Safarinejad, Shiva

    2013-10-01

    The glutathione-S-transferases (GSTs) comprise a class of enzymes that detoxify carcinogenic compounds by conjugating glutathione to facilitate their removal. Polymorphisms in GSTM1, GSTT1, and GSTP1 genes have been related to risk for bladder cancer. Studies focusing on GSTs gene variants relationship with the risk of bladder cancer have produced conflicting and inconsistent results. We examine the association between genetic polymorphism of glutathione S-transferase P1, GSTM1, GSTT1 genes and development of bladder transitional cell carcinoma (TCC). The study population consisted of 166 histologically confirmed male bladder TCC cases and 332 healthy male controls. Genotyping was done using the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method and also investigated combined gene interactions. The GSTP1 Val/Val genotype was significantly associated with bladder cancer (OR = 4.32, 95% CI: 2.64-6.34), whereas the association observed for GSTM1 null (OR = 1.32, 95% CI: 0.82-2.62; P = 0.67) and GSTT1 null genotype (OR = 1.18, 95% CI: 0.79-1.67; P = 0.74) did not reach statistical significance. There was a significant multiple interaction between GSTM1, GSTT1, and GSTP1 genotypes in risk of bladder cancer (P for interaction = 0.02). The risk associated with the concurrent presence of GSTM1 positive and GSTP1 Ile/Val or Val/Val (OR = 3.71, 95% CI: 2.34-5.54) and GSTT1 positive and GSTP1 Ile/Val or Val/Val (OR = 2.66, 95% CI: 1.54-4.72) was statistically significant. Patients carrying GSTP1 Val/Val genotype were at increased risk for developing high-grade (OR = 7.68, 95% CI: 4.73-19.25) and muscle invasive (OR = 10.67, 95% CI: 6.34-21.75) bladder cancer. High risk for bladder TCC also was observed with respect to combined GSTT1 null/GSTP1 Ile/Val or Val/Val (OR = 4.76, 95% CI: 2.68-18.72) and GSTM1 null/GSTT1 null/GSTP1 Ile/Val or Val/Val (OR = 6.42, 95% CI: 4.76-14.72) genotype variant. This study suggests that the GSTP1 polymorphism

  1. Melanin-concentrating hormone receptor 1 polymorphisms are associated with components of energy balance in the Complex Diseases in the Newfoundland Population: Environment and Genetics (CODING) study.

    Science.gov (United States)

    Fontaine-Bisson, Bénédicte; Thorburn, James; Gregory, Anne; Zhang, Hongwei; Sun, Guang

    2014-02-01

    The melanin-concentrating hormone receptor 1 (MCHR1) is a G protein-coupled receptor that regulates energy balance and body composition in animal models. Inconsistent effects of MCHR1 polymorphisms on energy homeostasis in humans may partly be attributable to environmental factors. We examined the effect of 4 single nucleotide polymorphisms (rs133073, rs133074, rs9611386, and rs882111) in the MCHR1 gene on body composition as well as energy-related lifestyle factors (diet and physical activity). We also examined the effect of gene-lifestyle interactions on body composition. A total of 1153 participants (248 men and 905 women) from the cross-sectional Complex Diseases in the Newfoundland Population: Environment and Genetics (CODING) study were genotyped by using probe-based chemistry validated assays. Diet and physical activity were estimated by using validated frequency questionnaires, and body composition was assessed by using dual-energy X-ray absorptiometry. Three polymorphisms (rs9611386, rs882111, and rs133073) were associated with differences in body-composition measurements (all P energy intakes (P = 0.02). A similar interaction was shown with rs882111 (P = 0.02). Interactions were also observed between each of these polymorphisms (rs9611386, rs882111, and rs133073) and physical activity score on body-composition measurements (all P gene are associated with differences in body composition and interact with physiologic and energy-related lifestyle factors.

  2. A genetic polymorphism of the endogenous opioid dynorphin modulates monetary reward anticipation in the corticostriatal loop.

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    Mikhail Votinov

    Full Text Available The dynorphin/κ-opioid receptor (KOP-R system has been shown to play a role in different types of behavior regulation, including reward-related behavior and drug craving. It has been shown that alleles with 3 or 4 repeats (HH genotype of the variable nucleotide tandem repeat (68-bp VNTR functional polymorphism of the prodynorphin (PDYN gene are associated with higher levels of dynorphin peptides than alleles with 1 or 2 repeats (LL genotype. We used fMRI on N = 71 prescreened healthy participants to investigate the effect of this polymorphism on cerebral activation in the limbic-corticostriatal loop during reward anticipation. Individuals with the HH genotype showed higher activation than those with the LL genotype in the medial orbitofrontal cortex (mOFC when anticipating a possible monetary reward. In addition, the HH genotype showed stronger functional coupling (as assessed by effective connectivity analyses of mOFC with VMPFC, subgenual anterior cingulate cortex, and ventral striatum during reward anticipation. This hints at a larger sensitivity for upcoming rewards in individuals with the HH genotype, resulting in a higher motivation to attain these rewards. These findings provide first evidence in humans that the PDYN polymorphism modulates neural processes associated with the anticipation of rewards, which ultimately may help to explain differences between genotypes with respect to addiction and drug abuse.

  3. Genetic Polymorphisms in Vitamin D Metabolism and Signaling Genes and Risk of Breast Cancer: A Nested Case-Control Study.

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    Tess V Clendenen

    Full Text Available Genetic polymorphisms in vitamin D metabolism and signaling genes have been inconsistently associated with risk of breast cancer, though few studies have examined SNPs in vitamin D-related genes other than the vitamin D receptor (VDR gene and particularly have not examined the association with the retinoid X receptor alpha (RXRA gene which may be a key vitamin D pathway gene. We conducted a nested case-control study of 734 cases and 1435 individually matched controls from a population-based prospective cohort study, the Northern Sweden Mammary Screening Cohort. Tag and functional SNPs were genotyped for the VDR, cytochrome p450 24A1 (CYP24A1, and RXRA genes. We also genotyped specific SNPs in four other genes related to vitamin D metabolism and signaling (GC/VDBP, CYP2R1, DHCR7, and CYP27B1. SNPs in the CYP2R1, DHCR7, and VDBP gene regions that were associated with circulating 25(OHD concentration in GWAS were also associated with plasma 25(OHD in our study (p-trend <0.005. After taking into account the false discovery rate, these SNPs were not significantly associated with breast cancer risk, nor were any of the other SNPs or haplotypes in VDR, RXRA, and CYP24A1. We observed no statistically significant associations between polymorphisms or haplotypes in key vitamin D-related genes and risk of breast cancer. These results, combined with the observation in this cohort and most other prospective studies of no association of circulating 25(OHD with breast cancer risk, do not support an association between vitamin D and breast cancer risk.

  4. A new polymorphic and multicopy MHC gene family related to nonmammalian class I

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    Leelayuwat, C.; Degli-Esposti, M.A.; Abraham, L.J. [Univ. of Western Australia, Perth (Australia); Townend, D.C. [Sir Charles Gairdner Hospital, Perth (Australia); Dawkins, R.L. [Royal Perth Hospital, Perth (Australia)]|[Univ. of Western Australia, Perth (Australia)]|[Sir Charles Gairdner Hospital, Perth (Australia)

    1994-12-31

    The authors have used genomic analysis to characterize a region of the central major histocompatibility complex (MHC) spanning {approximately} 300 kilobases (kb) between TNF and HLA-B. This region has been suggested to carry genetic factors relevant to the development of autoimmune diseases such as myasthenia gravis (MG) and insulin dependent diabetes mellitus (IDDM). Genomic sequence was analyzed for coding potential, using two neural network programs, GRAIL and GeneParser. A genomic probe, JAB, containing putative coding sequences (PERB11) located 60 kb centromeric of HLA-B, was used for northern analysis of human tissues. Multiple transcripts were detected. Southern analysis of genomic DNA and overlapping YAC clones, covering the region from BAT1 to HLA-F, indicated that there are at least five copies of PERB11, four of which are located within this region of the MHC. The partial cDNA sequence of PERB11 was obtained from poly-A RNA derived from skeletal muscle. The putative amino acid sequence of PERB11 shares {approximately} 30% identity to MHC class I molecules from various species, including reptiles, chickens, and frogs, as well as to other MHC class I-like molecules, such as the IgG FcR of the mouse and rat and the human Zn-{alpha}2-glycoprotein. From direct comparison of amino acid sequences, it is concluded that PERB11 is a distinct molecule more closely related to nonmammalian than known mammalian MHC class I molecules. Genomic sequence analysis of PERB11 from five MHC ancestral haplotypes (AH) indicated that the gene is polymorphic at both DNA and protein level. The results suggest that the authors have identified a novel polymorphic gene family with multiple copies within the MHC. 48 refs., 10 figs., 2 tabs.

  5. Genetic Variation and the Risk of Haloperidol-Related Parkinsonism in Elderly Patients A Candidate Gene Approach

    NARCIS (Netherlands)

    Knol, Wilma; van Marum, Rob J.; Jansen, Paul A. F.; Strengman, Eric; Al Hadithy, Asmar F. Y.; Wilffert, Bob; Schobben, Alfred F. A. M.; Ophoff, Roel A.; Egberts, Toine C. G.

    2013-01-01

    Factors that influence the variation in occurrence of antipsychotic-related parkinsonism in elderly have not been well elucidated. The aim of this study was to investigate whether previous identified and studied genetic polymorphisms at DRD2, ANKK1, DRD3, HTR2A, HTR2C, RGS2, COMT, and BDNF genes are

  6. Genetic polymorphisms of ADH1B, ADH1C and ALDH2 in Turkish alcoholics: lack of association with alcoholism and alcoholic cirrhosis.

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    Vatansever, Sezgin; Tekin, Fatih; Salman, Esin; Altintoprak, Ender; Coskunol, Hakan; Akarca, Ulus Salih

    2015-05-17

    No data exists regarding the alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) gene polymorphisms in Turkish alcoholic cirrhotics. We studied the polymorphisms of ADH1B, ADH1C and ALDH2 genes in alcoholic cirrhotics and compared the results with non-cirrhotic alcoholics and healthy volunteers. Overall, 237 subjects were included for the study: 156 alcoholic patients (78 cirrhotics, 78 non-cirrhotic alcoholics) and 81 healthy volunteers. Three different single-nucleotide-polymorphism genotyping methods were used. ADH1C genotyping was performed using a polymerase chain reaction-restriction fragment length polymorphism method. The identified ADH1C genotypes were named according to the presence or absence of the enzyme restriction sites. ADH1B (Arg47Hys) genotyping was performed using the allele specific primer extension method, and ALDH2 (Glu487Lys) genotyping was performed by a multiplex polymerase chain reaction using two allele-specific primer pairs. For ADH1B, the frequency of allele *1 in the cirrhotics, non-cirrhotic alcoholics and healthy volunteers was 97.4%, 94.9% and 99.4%, respectively. For ADH1C, the frequency of allele *1 in the cirrhotics, non-cirrhotic alcoholics and healthy volunteers was 47%, 36.3% and 45%, respectively. There was no statistical difference between the groups for ADH1B and ADH1C (p>0.05). All alcoholic and non-alcoholic subjects (100%) had the allele *1 for ALDH2. The obtained results for ADH1B, ADH1C, and ALDH gene polymorphisms in the present study are similar to the results of Caucasian studies. ADH1B and ADH1C genetic variations are not related to the development of alcoholism or susceptibility to alcoholic cirrhosis. ALDH2 gene has no genetic variation in the Turkish population.

  7. Genetic polymorphisms of ADH1B, ADH1C and ALDH2 in Turkish alcoholics: lack of association with alcoholism and alcoholic cirrhosis

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    Sezgin Vatansever

    2015-05-01

    Full Text Available No data exists regarding the alcohol dehydrogenase (ADH and aldehyde dehydrogenase (ALDH gene polymorphisms in Turkish alcoholic cirrhotics. We studied the polymorphisms of ADH1B, ADH1C and ALDH2 genes in alcoholic cirrhotics and compared the results with non-cirrhotic alcoholics and healthy volunteers. Overall, 237 subjects were included for the study: 156 alcoholic patients (78 cirrhotics, 78 non-cirrhotic alcoholics and 81 healthy volunteers. Three different single-nucleotide-polymorphism genotyping methods were used. ADH1C genotyping was performed using a polymerase chain reaction-restriction fragment length polymorphism method. The identified ADH1C genotypes were named according to the presence or absence of the enzyme restriction sites. ADH1B (Arg47Hys genotyping was performed using the allele specific primer extension method, and ALDH2 (Glu487Lys genotyping was performed by a multiplex polymerase chain reaction using two allele-specific primer pairs. For ADH1B, the frequency of allele *1 in the cirrhotics, non-cirrhotic alcoholics and healthy volunteers was 97.4%, 94.9% and 99.4%, respectively. For ADH1C, the frequency of allele *1 in the cirrhotics, non-cirrhotic alcoholics and healthy volunteers was 47%, 36.3% and 45%, respectively. There was no statistical difference between the groups for ADH1B and ADH1C (p>0.05. All alcoholic and non-alcoholic subjects (100% had the allele *1 for ALDH2. The obtained results for ADH1B, ADH1C, and ALDH gene polymorphisms in the present study are similar to the results of Caucasian studies. ADH1B and ADH1C genetic variations are not related to the development of alcoholism or susceptibility to alcoholic cirrhosis. ALDH2 gene has no genetic variation in the Turkish population.

  8. Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites.

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    Kumar, Awanish; Misra, Pragya; Dube, Anuradha

    2013-02-01

    With the advent of polymerase chain reaction (PCR), genetic markers are now accessible for all organisms, including parasites. Amplified fragment length polymorphism (AFLP) is a PCR-based marker for the rapid screening of genetic diversity and intraspecific variation. It is a potent fingerprinting technique for genomic DNAs of any origin or complexity and rapidly generates a number of highly replicable markers that allow high-resolution genotyping. AFLPs are convenient and reliable in comparison to other markers like random amplified polymorphic DNA, restriction fragment length polymorphism, and simple sequence repeat in terms of time and cost efficiency, reproducibility, and resolution as it does not require template DNA sequencing. In addition, AFLP essentially probes the entire genome at random, without prior sequence knowledge. So, AFLP markers have emerged as an advance type of genetic marker with broad application in genomic mapping, population genetics, and DNA fingerprinting and are ideally suited as screening tool for molecular markers linked with biological and clinical traits. This review describes the AFLP procedure and its applications and overview in the fingerprinting of a genome, which has been currently used in parasite genome research. We outline the AFLP procedure adapted for Leishmania genome study and discuss the benefits of AFLPs for assessing genetic variation and genome mapping over other existing molecular techniques. We highlight the possible use of AFLPs as genetic markers with its broad application in parasitological research because it allows random screening of the entire genome for linkage with genetic and clinical properties of the parasite. In this review, we have taken a pragmatic approach on the study of AFLP for genome mapping and polymorphism in protozoan parasites and conclude that AFLP is a very useful tool.

  9. Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti

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    Streit Thomas G

    2009-12-01

    Full Text Available Abstract Background Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti. Results From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51% of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75. Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545. Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed. Conclusion Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient

  10. Identification of a genetic marker associated with the resistance to Schistosoma mansoni infection using random amplified polymorphic DNA analysis

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    Abdel-Hamid Z Abdel-Hamid

    2006-12-01

    Full Text Available In schistosomiasis, the host/parasite interaction remains not completely understood. Many questions related to the susceptibility of snails to infection by respective trematode still remain unanswered. The control of schistosomiasis requires a good understanding of the host/parasite association. In this work, the susceptibility/resistance to Schistosoma mansoni infection within Biomphalaria alexandrina snails were studied starting one month post infection and continuing thereafter weekly up to 10 weeks after miracidia exposure. Genetic variations between susceptible and resistant strains to Schistosoma infection within B. alexandrina snails using random amplified polymorphic DNA analysis technique were also carried out. The results showed that 39.8% of the examined field snails were resistant, while 60.2% of these snails showed high infection rates.In the resistant genotype snails, OPA-02 primer produced a major low molecular weight marker 430 bp. Among the two snail strains there were interpopulational variations, while the individual specimens from the same snail strain, either susceptible or resistant, record semi-identical genetic bands. Also, the resistant character was ascendant in contrast to a decline in the susceptibility of snails from one generation to the next.

  11. Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP).

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    Ni, Xiaowei; Huang, Yelin; Wu, Lin; Zhou, Renchao; Deng, Shulin; Wu, Darong; Wang, Bosun; Su, Guohua; Tang, Tian; Shi, Suhua

    2006-05-01

    Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, H (E) = 0.220, I (S) = 0.321), and at species level (P = 85.6% of markers polymorphic, H (E) = 0.339, I (S) = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei's genetic diversity analysis (G (st)=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.

  12. Color-Biased Dispersal Inferred by Fine-Scale Genetic Spatial Autocorrelation in a Color Polymorphic Salamander.

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    Grant, Alexa H; Liebgold, Eric B

    2017-07-01

    Behavioral traits can be influenced by predation rates of color morphs, potentially leading to reduced boldness or increased escape behaviors in one color morph. The red-backed salamander, Plethodon cinereus, is a small terrestrial salamander whose color morphs have different diets and select different microhabitats, but little is known about potential differences in dispersal behaviors. We used fine-scale genetic spatial autocorrelation to examine 122 P. cinereus in a color-polymorphic population at 10 microsatellite loci in order to generate estimates of spatial genetic structure for each color morph. Differences in spatial genetic structure have been used extensively to infer within-population sex-biased dispersal but have never been used to test for dispersal differences between other groups within populations such as color morphs. We found evidence for color-biased dispersal, but not sex-biased dispersal. Striped salamanders had significant positive genetic structure in the shortest distance classes indicating philopatry. In contrast, unstriped salamanders showed a lack of spatial genetic structure at shorter distances and higher than expected genetic similarity at further distances, as expected if they are dispersing from their natal site. These results show that genetic methods typically used for sex-biased dispersal can be used to investigate differences in dispersal between morphs that vary discretely in polymorphic populations, such as color morphs. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Peroxisome proliferator-activated receptor (PPAR) delta genetic polymorphism and its association with insulin resistance index and fasting plasma glucose concentrations in Chinese subjects.

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    Hu, C; Jia, W; Fang, Q; Zhang, R; Wang, C; Lu, J; Xiang, K

    2006-12-01

    Previous studies have shown that the peroxisome proliferator-activated receptor delta (PPARD) genetic polymorphism affects cholesterol metabolism in Whites. This association was not observed in a Korean population in a separate study, but this study showed a link between the PPARD polymorphism and body weight and fasting plasma glucose. The purpose of this study was to determine whether polymorphisms of PPARD influence glucose and cholesterol metabolism in Chinese subjects. We investigated the association between the polymorphism (-87T/C) of the human PPARD gene and phenotypes related to body weight, insulin sensitivity, glucose and lipid metabolism in Chinese subjects. Unrelated Chinese subjects (n = 663) in Shanghai were studied; 287 had newly diagnosed Type 2 diabetes mellitus and 376 were non-diabetic control subjects over 40 years old. Clinical parameters were collected and genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism. In normal glucose tolerant (NGT) subjects, the C allele carriers had higher fasting plasma glucose concentrations (P = 0.0078) and a lower insulin sensitivity index (ISI) (P = 0.0365). The C allele carriers also showed higher concentrations of low-density lipoprotein cholesterol (P = 0.0261) and percentage of body fat (P = 0.0357). There was a trend towards higher visceral adiposity in C allele carriers, but the difference was not significant (P = 0.0830). In diabetes patients, similar results were detected for plasma glucose concentrations (fasting plasma glucose P polymorphism is associated with higher fasting plasma glucose concentrations in both NGT and diabetic subjects, largely due to impaired insulin sensitivity.

  14. Associations between single nucleotide polymorphisms in iron-related genes and iron status in multiethnic populations.

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    Christine E McLaren

    Full Text Available The existence of multiple inherited disorders of iron metabolism suggests genetic contributions to iron deficiency. We previously performed a genome-wide association study of iron-related single nucleotide polymorphisms (SNPs using DNA from white men aged ≥ 25 y and women ≥ 50 y in the Hemochromatosis and Iron Overload Screening (HEIRS Study with serum ferritin (SF ≤ 12 µg/L (cases and controls (SF >100 µg/L in men, SF >50 µg/L in women. We report a follow-up study of white, African-American, Hispanic, and Asian HEIRS participants, analyzed for association between SNPs and eight iron-related outcomes. Three chromosomal regions showed association across multiple populations, including SNPs in the TF and TMPRSS6 genes, and on chromosome 18q21. A novel SNP rs1421312 in TMPRSS6 was associated with serum iron in whites (p = 3.7 × 10(-6 and replicated in African Americans (p = 0.0012.Twenty SNPs in the TF gene region were associated with total iron-binding capacity in whites (p<4.4 × 10(-5; six SNPs replicated in other ethnicities (p<0.01. SNP rs10904850 in the CUBN gene on 10p13 was associated with serum iron in African Americans (P = 1.0 × 10(-5. These results confirm known associations with iron measures and give unique evidence of their role in different ethnicities, suggesting origins in a common founder.

  15. Genetic Polymorphisms of Alcohol Dehydrogenase and Aldehyde Dehydrogenase: Alcohol Use and Type 2 Diabetes in Japanese Men

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    Guang Yin

    2011-01-01

    Full Text Available This study investigated the association of ADH1B (rs1229984 and ALDH2 (rs671 polymorphisms with glucose tolerance status, as determined by a 75-g oral glucose tolerance test, and effect modification of these polymorphisms on the association between alcohol consumption and glucose intolerance in male officials of the Self-Defense Forces. The study subjects included 1520 men with normal glucose tolerance, 553 with prediabetic condition (impaired fasting glucose and impaired glucose tolerance, and 235 men with type 2 diabetes. There was an evident interaction between alcohol consumption and ADH1B polymorphism in relation to type 2 diabetes (interaction P=.03. The ALDH24∗87Lys allele was associated with a decreased prevalence odds of type 2 diabetes regardless of alcohol consumption. In conclusion, the ADH1B polymorphism modified the association between alcohol consumption and type 2 diabetes. A positive association between alcohol consumption and type 2 diabetes was confounded by ALDH2 polymorphism.

  16. Association of BCL2-938C>A genetic polymorphism with glioma risk in Chinese Han population.

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    Li, Wei; Qian, Chunfa; Wang, Linxiong; Teng, Hong; Zhang, Li

    2014-03-01

    Glioma is the most common type of primary brain malignancy in adults. The anti-apoptotic protein B-cell lymphoma 2 (BCL2) has been implicated in the pathogenesis of glioma. This study aimed to evaluate the potential association between BCL2-938C>A genetic polymorphism and glioma susceptibility. This case-control study was conducted in Chinese Han populations consisting of 248 glioma cases and 252 cancer-free controls. The BCL2-938C>A genetic polymorphism was detected by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and verified using DNA sequencing methods. Our data suggested that the genotype/allele of BCL2-938C>A polymorphism were statistically associated with the increased risk of glioma where the risk of glioma for genotype AA or allele A is significantly higher than wild genotype CC (odds ratio (OR) = 2.23, 95% confidence interval (CI) 1.21-4.10, p = 0.009) or allele C (OR = 1.39, 95% CI 1.06-1.82, p = 0.016), respectively. In addition, the BCL2-938AA genotype was significantly more common in patients with glioblastoma and in patients with grade IV glioma. Our findings indicate that the BCL2-938C>A polymorphism is associated with the susceptibility to glioma in Chinese Han populations and might be used as molecular markers for evaluating glioma risk.

  17. Analysis of the Genetic Structure of Sclerotinia sclerotiorum (Lib.) de Bary Populations from Different Regions and Host Plants by Random Amplified Polymorphic DNA Markers

    Institute of Scientific and Technical Information of China (English)

    Jun-Ming SUN; Witold IRZYKOWSKI; Malgorzata JEDRYCZKA; Fen-Xia HAN

    2005-01-01

    The genetic diversity and genetic structure of a population of isolates of Sclerotinia sclerotiorum (Lib.) de Bary from different regions and host plants were investigated using the random amplified polymorphic DNA (RAPD) method with 20 random decamer primer pairs in order to provide some information on the phylogenetic taxa and breeding for resistance to sclerotinia stem rot. A minimum of three and a maximum of 15 unambiguously amplified bands were generated, furnishing a total of 170 bands ranging in size from 100to 3 200 bp, corresponding to an average of 8.5 bands per primer pair. One hundred and four of these 170bands (61.2%) were polymorphic, the percentage of polymorphic bands for each primer pair ranging from 0.0% to 86.7%. The genetic relationships among the isolates, based on the results of RAPD analysis, were examined. The genetic similarity of all selected isolates was quite high. At the species level, the genetic diversity estimated by Nei's gene diversity (h) was 0.197 and S hannon's index of diversity (I) was 0.300. The unweighted pair-group mean analysis (UPGMA) cluster analysis showed that most isolates from the same regions were grouped in the same cluster or a close cluster. The population of isolates from Hefei (Anhui Province, China) was more uniform and relatively distant to other populations. The Canadian population collected from carrot (Daucus carota var. sativa DC.) was relatively close to the Polish population collected from oilseed rape (Brassica napus L.) plants. There was no relationship between isolates from the same host plants. An analysis of molecular variance (AMOVA) revealed that the percentage of variance attributable to variation among and within populations was 50.62% and 49.38%, respectively. When accessions from China, Europe, and Canada were treated as three separate groups, the variance components among groups,among populations within groups, and within populations were -0.96%, 51.48%, and 49.47%, respectively.The genetic

  18. The -351A>G genetic polymorphism in the estrogen receptor alpha gene and risk of endometriosis: a case-control study

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    Reihaneh Asadi

    2015-03-01

    Conclusion: The results do not support the previous findings of an association between -351A>G genetic polymorphism in ESR1 gene and endometriosis. Therefore, comprehensive genetic approaches including linkage analyses and family-based tests, together with a number of replication studies with large sample size, are needed to make conclusive claims about the role of this genetic polymorphism in susceptibility to endometriosis.

  19. [Genetic polymorphism of FIBRA,DHFRP2 and ACTBP2 and their forensic application in Yunnan Han population].

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    Jing, Qiang; Nie, Sheng-Jie

    2002-09-01

    To investigate the genetic polymorphism of FIBRA,DHFRP2 and ACTBP2 in Yunnan Han population as well as their application in forensic science, EDTA-blood specimens were collected from 200 healthy individuals. The DNA were extracted either by the Chloro form, phenol method or by the Chelex-100 method. The PCR products were analyzed by PAG vertical electrophoresis,following by silver staining. All gene frequencies, discrimination power (DP), exclusion of paternity probability (EPP), heterozygosity (H),polymorphisms information content (PIC),matching probability (PM) as well as the Hardy-Weinberg test were calculated. The obtained data are beneficial in the understanding of population genetics of the three STR loci in Yunnan Han population and the results suggest that these loci are valuable genetic markers for paternity testing and personal identification in forensic science practice.

  20. Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum field isolates from Myanmar.

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    Kang, Jung-Mi; Moon, Sung-Ung; Kim, Jung-Yeon; Cho, Shin-Hyeong; Lin, Khin; Sohn, Woon-Mok; Kim, Tong-Soo; Na, Byoung-Kuk

    2010-05-17

    Merozoite surface protein-1 (MSP-1) and MSP-2 of Plasmodium falciparum are potential vaccine candidate antigens for malaria vaccine development. However, extensive genetic polymorphism of the antigens in field isolates of P. falciparum represents a major obstacle for the development of an effective vaccine. In this study, genetic polymorphism of MSP-1 and MSP-2 among P. falciparum field isolates from Myanmar was analysed. A total of 63 P. falciparum infected blood samples, which were collected from patients attending a regional hospital in Mandalay Division, Myanmar, were used in this study. The regions flanking the highly polymorphic characters, block 2 for MSP-1 and block 3 for MSP-2, were genotyped by allele-specific nested-PCR to analyse the population diversity of the parasite. Sequence analysis of the polymorphic regions of MSP-1 and MSP-2 was also conducted to identify allelic diversity in the parasite population. Diverse allelic polymorphism of MSP-1 and MSP-2 was identified in P. falciparum isolates from Myanmar and most of the infections were determined to be mixed infections. Sequence analysis of MSP-1 block 2 revealed that 14 different alleles for MSP-1 (5 for K1 type and 9 for MAD20 type) were identified. For MSP-2 block 3, a total of 22 alleles (7 for FC27 type and 15 for 3D7 type) were identified. Extensive genetic polymorphism with diverse allele types was identified in MSP-1 and MSP-2 in P. falciparum field isolates from Myanmar. A high level of mixed infections was also observed, as was a high degree of multiplicity of infection.

  1. Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum field isolates from Myanmar

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    Kim Tong-Soo

    2010-05-01

    Full Text Available Abstract Background Merozoite surface protein-1 (MSP-1 and MSP-2 of Plasmodium falciparum are potential vaccine candidate antigens for malaria vaccine development. However, extensive genetic polymorphism of the antigens in field isolates of P. falciparum represents a major obstacle for the development of an effective vaccine. In this study, genetic polymorphism of MSP-1 and MSP-2 among P. falciparum field isolates from Myanmar was analysed. Methods A total of 63 P. falciparum infected blood samples, which were collected from patients attending a regional hospital in Mandalay Division, Myanmar, were used in this study. The regions flanking the highly polymorphic characters, block 2 for MSP-1 and block 3 for MSP-2, were genotyped by allele-specific nested-PCR to analyse the population diversity of the parasite. Sequence analysis of the polymorphic regions of MSP-1 and MSP-2 was also conducted to identify allelic diversity in the parasite population. Results Diverse allelic polymorphism of MSP-1 and MSP-2 was identified in P. falciparum isolates from Myanmar and most of the infections were determined to be mixed infections. Sequence analysis of MSP-1 block 2 revealed that 14 different alleles for MSP-1 (5 for K1 type and 9 for MAD20 type were identified. For MSP-2 block 3, a total of 22 alleles (7 for FC27 type and 15 for 3D7 type were identified. Conclusion Extensive genetic polymorphism with diverse allele types was identified in MSP-1 and MSP-2 in P. falciparum field isolates from Myanmar. A high level of mixed infections was also observed, as was a high degree of multiplicity of infection.

  2. Structuring the genetic heterogeneity of the Basque population: a view from classical polymorphisms.

    Science.gov (United States)

    Manzano, C; de, la Rúa C; Iriondo, M; Mazón, L I; Vicario, A; Aguirre, A

    2002-02-01

    In this study we analyze 18 classical polymorphisms (ABO, Rh, MNSs, Lewis, P, Duffy, Kell, ADA, ESD, PGM1, PGD, AK1, ACP1, GLO1, HP, GC, TF, and PI) in over 2000 autochthonous individuals from 14 natural districts in three provinces of the Basque Country (Alava, Guipuzcoa, and Biscay). Heterogeneity analysis via the chi2 test and a calculation of F(ST) indicate that there is significant genetic heterogeneity between the Basque districts. The R matrix informs us that this heterogeneity is not significantly concentrated in a single district or in the districts of a single province, but is rather distributed among several districts belonging to the three provinces analyzed. We undertake to assess the influence of various historical, geographical, and cultural factors on the genetic structure of the Basque population. Analysis suggests that allele distribution is geographically patterned in the Basque Country. The gradient distributions observed in the case of some alleles (ABO*O, RH*cDE, RH*cde, MNS*MS, and ACP1*C) on the basis of Moran's autocorrelation coefficient I, along with the influence of the two main travel routes through the Basque Country (western route through Bilbao and eastern route through Vitoria), suggest that the gene flow tends toward the coast. As regards other factors considered (administrative division, repopulation processes, linguistic heterogeneity, and north vs. south cultural heterogeneity), we detected only a certain influence exerted by an old tribal differentiation (2000 B.P.), which would diminish with the passage of time.

  3. Analysis of large brain MRI databases for investigating the relationships between brain, cognitive, and genetic polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Mazoyer, B

    2006-07-01

    A major challenge for the years to come is the understanding of the brain-behaviour relationships, and in particular the investigation and quantification of the impact of genetic polymorphism on these relationships. In this framework, a promising experimental approach, which we will refer to as neuro-epidemiologic imaging, consists in acquiring multimodal (brain images, psychometric an d sociological data, genotypes) data in large (several hundreds or thousands ) cohorts of subjects. Processing of such large databases requires on first place the conception and implementation of automated 'pipelines', including image registration, spatial normalisation tissue segmentation, and multivariate statistical analysis. Given the number of images and data to be processed, such pipelines must be both fully automated and robust enough to be able to handle multi-center MRI data, e.g. having inhomogeneous characteristics in terms of resolution and contrast. This approach will be illustrated using two databases collected in aged healthy subjects, searching for the impact of genetic and environmental on two markers of brain aging, namely white matter hyper-signals, and grey matter atrophy. (author)

  4. Genetic polymorphism of 14 non-CODIS STR loci for forensic use in southeast China population.

    Science.gov (United States)

    Shi, Meisen; Yu, Xiaojun; Bai, Rufeng; Shu, Xiji; Zhu, Guanghui; Lv, Junyao; Tu, Youhua

    2008-01-15

    We investigated 14 polymorphic STR loci (D1S2142, D2S1360, D3S1545, D7S1517, D10S2325, D12S391, D13S1492, D14S306, D15S659, D16S3253, D18S1270, D19S253, D20S470, D21S1437) which are not included in the standard sets of forensic loci (CODIS) in a sample of 216 unrelated healthy southeast Chinese individuals. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. The accumulated powers of discrimination and power of exclusion for the 14 loci were 99.9999999999 and 99.999998%, respectively. No linkage was observed between the 14 loci and the traditional set of STR markers included in commercially available kits (the AmpFLSTR IdentifilerTM 15 System loci). We thus considered the studied 14 STRs are informative and when necessary, can be used as the candidate genetic markers in the study and application in genetics and forensic practice.

  5. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

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    Mark McMullan

    Full Text Available The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC of guppies (Poecilia reticulata to study the turnover rate of alleles (temporal genetic differentiation, G'(ST. Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1 overdominant selection, (2 fluctuating population size within a metapopulation, and (3 the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST outlier analysis may obscure the signal of selection.

  6. Genetic Imaging of the Association of Oxytocin Receptor Gene (OXTR Polymorphisms with Positive Maternal Parenting

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    Kalina J. Michalska

    2014-02-01

    Full Text Available Background: Well-validated models of maternal behavior in small-brain mammals posit a central role of oxytocin in parenting, by reducing stress and enhancing the reward value of social interactions with offspring. In contrast, human studies are only beginning to gain insights into how oxytocin modulates maternal behavior and affiliation. Methods: To explore associations between oxytocin receptor genes and maternal parenting behavior in humans, we conducted a genetic imaging study of women selected to exhibit a wide range of observed parenting when their children were 4-6 years old. Results: In response to child stimuli during functional magnetic resonance imaging, hemodynamic responses in brain regions that mediate affect, reward, and social behavior were significantly correlated with observed positive parenting. Furthermore, single nucleotide polymorphisms (rs53576 and rs1042778 in the gene encoding the oxytocin receptor were significantly associated with both positive parenting and hemodynamic responses to child stimuli in orbitofrontal cortex, anterior cingulate cortex and hippocampus. Conclusions: These findings contribute to the emerging literature on the role of oxytocin in human social behavior and support the feasibility of tracing biological pathways from genes to neural regions to positive maternal parenting behaviors in humans using genetic imaging methods.

  7. Molecular genetics of cystinuria: Identification of four new mutations and seven polymorphisms, and evidence for genetic heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Gasparini, P.; Bisceglia, L.; Notarangelo, A. [Servizio di Genetica Medica, San Giovanni Rotondo (Italy)] [and others

    1995-10-01

    A cystinuria disease gene (rBAT) has been recently identified, and some mutations causing the disease have been described. The frequency of these mutations has been investigated in a large sample of 51 Italian and Spanish cystinuric patients. In addition, to identify new mutated alleles, genomic DNA has been analyzed by an accurate and sensitive method able to detect nucleotide changes. Because of the lack of information available on the genomic structure of rBAT gene, the study was carried out using the sequence data so far obtained by us. More than 70% of the entire coding sequence and 8 intron-exon boundaries have been analyzed. Four new mutations and seven intragenic polymorphisms have been detected. All mutations so far identified in rBAT belong only to cystinuria type I alleles, accounting for {approximately} 44% of all type I cystinuric chromosomes. Mutation M467T is the most common mutated allele in the Italian and Spanish populations. After analysis of 70% of the rBAT coding region, we have detected normal sequences in cystinuria type II and type III chromosomes. The presence of rBAT mutated alleles only in type I chromosomes of homozygous (type I/I) and heterozygous (type I/III) patients provides evidence for genetic heterogeneity where rBAT would be responsible only for type I cystinuria and suggests a complementation mechanism to explain the intermediate type I/type III phenotype. 25 refs., 1 fig., 3 tabs.

  8. A genetic polymorphism evolving in parallel in two cell compartments and in two clades

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    Watt Ward B

    2013-01-01

    Full Text Available Abstract Background The enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae. PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions. Results PEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5′, exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ↔ Ser, Asp 503 ↔ Glu, and Ile 629 ↔ Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another′s sites which are distant in PEPCK′s structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms′ cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001 ≤ P ≤ 0.006 under differing scenarios. Conclusion Our results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes′ effects

  9. Polymorphisms of estrogen metabolism-related genes ESR1 , UGT2B17 , and UGT1A1 are not associated with osteoporosis in artificial menopausal Japanese women

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    Megumi Yokota

    2015-09-01

    Full Text Available Introduction : Bilateral salpingo-oophorectomy (BSO is a risk factor for osteoporosis. Previous studies have reported an association between genetic polymorphisms and the risk of developing osteoporosis. However, the relationship between osteoporosis and genetic polymorphisms in Japanese women treated with BSO is not well understood. To improve the quality of life for post-BSO patients, it is important to determine the genetic factors that influence their risk for osteoporosis. The aim of this study was to investigate the association between gene variations of estrogen metabolism-related genes and osteoporosis in surgically menopausal patients, which may improve the quality of life for surgically menopausal patients. Material and methods : This study included 203 menopausal women treated with BSO because of gynecologic disorders. One hundred and twenty-six women with artificial (surgical menopause, who had undergone BSO in the premenopausal period, were compared with 77 women with natural menopause, who had undergone BSO in the postmenopausal period. The women were tested for bone mineral density to diagnose osteoporosis. Polymorphisms of estrogen receptor 1 ( ESR1 and UDP-glucuronosyl transferase (UGT genes UGT2B17 and UGT1A1 were analyzed, and their association with bone mass and osteoporosis was statistically evaluated. Results : No significant association was found between osteoporosis and polymorphisms in ESR1 , UGT2B17 , or UGT1A1 in both groups, suggesting that BSO might be a more significant physiological factor in influencing bone mass density compared to genetic variations. Conclusions : These results suggest that the ESR1 , UGT2B17 , and UGT1A1 polymorphisms are not genetic factors affecting osteoporosis in postmenopausal Japanese women.

  10. Genetic variations of Lansium domesticum Corr. accessions from Java, Sumatra and Ceram based on Random Amplified Polymorphic DNA fingerprints

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    KUSUMADEWI SRI YULITA

    2011-07-01

    Full Text Available Yulita KS (2011 Genetic variations of Lansium domesticum Corr. accessions from Java, Bengkulu and Ceram based on Random Amplified Polymorphic DNA fingerprints. Biodiversitas 12: 125-130. Duku (Lansium domesticum Corr. is one of popular tropical fruits in SE Asia. The spesies has three varieties, known as duku, langsat and kokosan; and duku is the most popular one for being the sweetiest fruit. Indonesia has several local varieties of duku, such as duku Condet, duku Sumber and duku Palembang. This present study aimed to assess genetic diversity of 47 accessions of duku from Java, Sumatra, and Ceram based on RAPD fingerprints. Ten RAPD’s primers were initially screened and five were selected for the analysis. These five primers (OPA 7, 13, 18, OPB 7, and OPN 12 generated 53 scorable bands with an average of 10.6 polymorphic fragment per primer. Percentage of polymorphism ranged from 16.89% (OPA 7 and OPN 12 to 24.54% (OPB 7 with an average of 20.16% polymorphism. OPB 7 at 450 bp was exclusively possessed by accession 20 (Java, OPA 18 at 500 bp was by accession 6 (Java, 550 bp by 3 clones from Bengkulu. While OPN 12 at 300 bp and OPA 13 at 450 bp were shared among the accessions. Clustering analysis was performed based on RAPD profiles using the UPGMA method. The range of genetic similarity value among accessions was 0.02-0.65 suggesting high variation of gene pool existed among accessions.

  11. The uses of AFLP for detecting DNA polymorphism, genotype identification and genetic diversity between yeasts isolated from Mexican agave-distilled beverages and from grape musts.

    Science.gov (United States)

    Flores Berrios, E P; Alba González, J F; Arrizon Gaviño, J P; Romano, P; Capece, A; Gschaedler Mathis, A

    2005-01-01

    The objectives were to determine the variability and to compare the genetic diversity obtained using amplified fragment length polymorphism (AFLP) markers in analyses of wine, tequila, mezcal, sotol and raicilla yeasts. A molecular characterization of yeasts isolated from Mexican agave musts, has been performed by AFLP marker analysis, using reference wine strains from Italian and South African regions. A direct co-relation between genetic profile, origin and fermentation process of strains was found especially in strains isolated from agave must. In addition, unique molecular markers were obtained for all the strains using six combination primers, confirming the discriminatory power of AFLP markers. This is the first report of molecular characterization between yeasts isolated from different Mexican traditional agave-distilled beverages, which shows high