These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
1

Osteopontin: an early innate immune marker of Escherichia coli mastitis harbors genetic polymorphisms with possible links with resistance to mastitis  

PubMed Central

Background Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable alleles that support greater resistance to infection, thus reducing antibiotic use. This study aims to identify a key gene in the innate immune response to mastitis, led us to evaluate its genetic association with somatic cell score (SCS), which is an indicator of clinical mastitis, and to evaluate its impact on other traits related to milk production. Results The osteopontin transcript (SPP1) was identified in the somatic cells from cows experimentally infected with Escherichia coli. By selecting bulls with extreme estimated breeding values (EBVs) for SCS, which is an indicator of mammary gland health, four DNA polymorphisms in the SPP1 genomic sequence were found. Statistical analysis revealed that the SNP SPP1c.-1301G>A has an impact on EBV for SCS (P < 0.001) Using an allele substitution model, SPP1c.-1251C>T, SPP1c.-430G>A, and SPP1c.*40A>C have an impact on SCS whereas SPP1c.-1301G>A has an effect on the EBVs for milk yield (second and third lactations), fat and protein percentages (all three lactations). Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (P = 0.012), second (P < 0.001), and third (P < 0.001) lactations. Conclusion This study reports the link between DNA polymorphisms of SPP1, the number of milk immune cells and, potentially, the susceptibility to mastitis. These SNPs were identified by in silico search to be located in transcription factor recognition sites which factors are presumably involved in the Th1 immune response and in the Th2 regulation pathway. Indeed, one SNP abolished the SP1 recognition site, whereas another SNP affected the transcription binding factor IKAROS. All together, these findings support the genetic potential of these variants in terms of selection for the improvement of mastitis resistance in dairy cows. PMID:19765294

Alain, Karin; Karrow, Niel A; Thibault, Catherine; St-Pierre, Jessika; Lessard, Martin; Bissonnette, Nathalie

2009-01-01

2

Genetic Polymorphism in Evolving Population  

E-print Network

We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping diversity in the gene pool under abrupt environmental changes. The model provides reasonable estimates for the proportions of polymorphic and heterozygous loci and for the mutation rate, as observed in nature.

H. Y. Lee; D. Kim; M. Y. Choi

1998-01-09

3

Genetic polymorphisms in Kawasaki disease  

PubMed Central

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. PMID:21892198

Kuo, Ho-chang; Chang, Wei-chiao

2011-01-01

4

Stability of genetic polymorphism in hostparasite interactions  

E-print Network

Stability of genetic polymorphism in host­parasite interactions Aure´lien Tellier* and James K. M. Brown Department of Disease and Stress Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK Allelic

Brown, James

5

Migraine and Genetic Polymorphisms: An Overview  

PubMed Central

The relationship between genetic polymorphisms and migraine as a cause of an increased risk of thrombotic disorders development is still debated In this respect, factor V Leiden, factor V (H1299R), prothrombin G20210A, factor XIII (V34L), ?-fibrinogen, MTHFR (C677T), MTHFR (A1298C), APO E, PAI-1, HPA-1 and ACE I/D seem to play a determinant role in vascular diseases related to migraine. The present review analyzes both the incidence of the above genetic vascular mutations in migraineurs and the most re-cent developments related to genetic polymorphisms and migraine. PMID:22962564

Pizza, Vincenzo; Agresta, Anella; Agresta, Antonio; Lamaida, Eros; Lamaida, Norman; Infante, Francesco; Capasso, Anna

2012-01-01

6

Digoxin pharmacokinetics and MDR1 genetic polymorphisms  

Microsoft Academic Search

Background. The effect of MDR1 C3435T single nucleotide polymorphism (SNP) in exon 26 on digoxin pharmacokinetics has recently been challenged. Objective. To clarify the relationships between MDR1 genetic polymorphisms in exon 26 (C3435T) and 21 (G2677T\\/A) and digoxin pharmacokinetics. Materials and methods. MDR1 genotypes for C3435T and G2677T\\/A SNPs were determined in 32 healthy subjects whose single oral dose digoxin

Cline Verstuyft; Mathias Schwab; Elke Schaeffeler; Reinhold Kerb; Ulrich Brinkmann; Patrice Jaillon; Christian Funck-Brentano; Laurent Becquemont

2003-01-01

7

Genetic polymorphisms linked to susceptibility to malaria  

PubMed Central

The influence of host genetics on susceptibility to Plasmodium falciparum malaria has been extensively studied over the past twenty years. It is now clear that malaria parasites have imposed strong selective forces on the human genome in endemic regions. Different genes have been identified that are associated with different malaria related phenotypes. Factors that promote severity of malaria include parasitaemia, parasite induced inflammation, anaemia and sequestration of parasitized erythrocytes in brain microvasculature. Recent advances in human genome research technologies such as genome-wide association studies (GWAS) and fine genotyping tools have enabled the discovery of several genetic polymorphisms and biomarkers that warrant further study in host-parasite interactions. This review describes and discusses human gene polymorphisms identified thus far that have been shown to be associated with susceptibility or resistance to P. falciparum malaria. Although some polymorphisms play significant roles in susceptibility to malaria, several findings are inconclusive and contradictory and must be considered with caution. The discovery of genetic markers associated with different malaria phenotypes will help elucidate the pathophysiology of malaria and enable development of interventions or cures. Diversity in human populations as well as environmental effects can influence the clinical heterogeneity of malaria, thus warranting further investigations with a goal of developing new interventions, therapies and better management against malaria. PMID:21929748

2011-01-01

8

Genome-wide association study to identify genetic variants present in Japanese patients harboring intracranial aneurysms  

Microsoft Academic Search

An intracranial aneurysm (IA), which results in a subarachnoid hemorrhage with a high mortality on rupture, is a major public health concern. To identify genetic susceptibility loci for IA, we carried out a multistage association study using genome-wide single nucleotide polymorphisms (SNPs) in Japanese casecontrol subjects. In this study, we assessed evidence for association in standard approaches, and additional tests

Koichi Akiyama; Akira Narita; Hirofumi Nakaoka; Tailin Cui; Tomoko Takahashi; Katsuhito Yasuno; Atsushi Tajima; Boris Krischek; Ken Yamamoto; Hidetoshi Kasuya; Akira Hata; Ituro Inoue

2010-01-01

9

Approaches on genetic polymorphism of Cryptococcus species complex.  

PubMed

The Cryptococcus species complex is the significant pathogenic fungi that result in over 1 million cases of cryptococcosis each year in the world. Proper strategy for genetic polymorphism study of the Cryptococcus species complex is crucial to unfold genetic population structure, spread profile and pathogenicity of these pathogenic yeasts worldwide. Currently, an array of approaches, including serotype, PCR fingerprinting, amplified fragment length polymorphisms (AFLP), analysis of DNA sequence, and matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF MS) etc. improved our understanding of genetic diversity or phylogenetic of Cryptococcus species complex. This review synthesizes existing techniques of cryptococcal genetic polymorphism and raises issues that remain to be addressed. PMID:23747878

Li, Meng; Chen, Min; Pan, Weihua

2013-01-01

10

Genetic Polymorphisms and Risk Assessment for Cancer Chemoprevention  

Microsoft Academic Search

Cancer risk carries wide interindividual variation; only a fraction of the population exposed to a known carcinogen develops\\u000a cancer. Genetic susceptibility is both inherited and acquired. Genes that affect cancer susceptibility can be found in those\\u000a controlling behavior, carcinogen metabolism, and cellular response to carcinogen exposure. Genetic traits affect DNA repair,\\u000a cell cycle control, and immune response. Polymorphic genetic variants

Sonia de Assis; Peter G. Shields

11

Genetic Polymorphisms and Sepsis in Premature Neonates  

PubMed Central

Identifying single nucleotide polymorphisms (SNPs) in the genes involved in sepsis may help to clarify the pathophysiology of neonatal sepsis. The aim of this study was to evaluate the relationships between sepsis in pre-term neonates and genes potentially involved in the response to invasion by infectious agents. The study involved 101 pre-term neonates born between June 2008 and May 2012 with a diagnosis of microbiologically confirmed sepsis, 98 pre-term neonates with clinical sepsis and 100 randomly selected, otherwise healthy pre-term neonates born during the study period. During the study, 47 SNPs in 18 candidate genes were genotyped on Guthrie cards using an ABI PRISM 7900 HT Fast real-time and MAssARRAY for nucleic acids instruments. Genotypes CT and TT of rs1143643 (the IL1? gene) and genotype GG of rs2664349GG (the MMP-16 gene) were associated with a significantly increased overall risk of developing sepsis (p?=?0.03, p?=?0.05 and p?=?0.03), whereas genotypes AG of rs4358188 (the BPI gene) and CT of rs1799946 (the DEF?1 gene) were associated with a significantly reduced risk of developing sepsis (p?=?0.05 for both). Among the patients with bacteriologically confirmed sepsis, only genotype GG of rs2664349 (the MMP-16 gene) showed a significant association with an increased risk (p?=?0.02). Genotypes GG of rs2569190 (the CD14 gene) and AT of rs4073 (the IL8 gene) were associated with a significantly increased risk of developing severe sepsis (p?=?0.05 and p?=?0.01). Genotype AG of rs1800629 (the LTA gene) and genotypes CC and CT of rs1341023 (the BPI gene) were associated with a significantly increased risk of developing Gram-negative sepsis (p?=?0.04, p?=?0.04 and p?=?0.03). These results show that genetic variability seems to play a role in sepsis in pre-term neonates by influencing susceptibility to and the severity of the disease, as well as the risk of having disease due to specific pathogens. PMID:25000179

Esposito, Susanna; Zampiero, Alberto; Pugni, Lorenza; Tabano, Silvia; Pelucchi, Claudio; Ghirardi, Beatrice; Terranova, Leonardo; Miozzo, Monica; Mosca, Fabio; Principi, Nicola

2014-01-01

12

Genetics of Color Polymorphism in the Pea Aphid, Acyrthosiphon pisum  

PubMed Central

The genetic basis of color polymorphism is explored in the pea aphid, Acyrthosiphon pisum (Harris) (Homoptera: Sternorrhyncha), in which two color morphs have been described (pink or green). Laboratory crosses and a Mendelian genetic analysis reveal that color polymorphism in pea aphids is determined by a single biallelic locus, which we name colorama, with alleles P and p, pink being dominant to green. The putative genotypes are Pp or PP for pink morphs, and pp for green morphs. This locus is shown to be autosomal. Last, there was no evidence of influence of the direction of the cross on color inheritance, thus showing that cytoplasmic effects and/or maternally-inherited symbionts play no role in the inheritance of color polymorphism in pea aphids. The existence of a simple genetic determinism for color polymorphism in a system in which genetic investigation is possible may facilitate investigations on the physiological and molecular mechanisms of genetically-based color morph variation, and the establishment of a link between this locus and fitness in a range of ecological conditions. PMID:20673119

Caillaud, Marina C.; Losey, John E.

2010-01-01

13

UGT1A9 Genetic Polymorphisms and Raloxifene Pharmacogenetics.  

National Technical Information Service (NTIS)

The goal of this DOD Breast Concept award was to identify and functionally characterize common genetic polymorphisms in the human UDP- glucuronosyltransferase gene, UGT1A9. We had previously determined that UGT1A9, a metabolic enzyme expressed predominant...

R. B. Raftogianis

2003-01-01

14

Phenytoin Toxicity Due to Genetic Polymorphism  

Microsoft Academic Search

IntroductionPatients with traumatic brain injury commonly receive phenytoin for seizure prophylaxis. Due to the non-linear pharmacokinetics\\u000a of phenytoin and narrow therapeutic window, phenytoin concentrations are monitored to ensure efficacy and prevent toxicity.\\u000a Because phenytoin is hepatically metabolized, polymorphisms within cytochrome P450 enzymes can affect phenytoin concentrations.\\u000a \\u000a \\u000a \\u000a MethodsWe report a case of a 53-year-old Asian female admitted to the neuroscience intensive

Lauren K. McCluggage; Stacy A. Voils; Malcolm Ross Bullock

2009-01-01

15

Biochemical genetics of phosphohydrolase polymorphism in Culex pipiens complex.  

PubMed

1. Single 4th-instar larvae were used in the investigation of alkaline phosphohydrolase (APH) variability in Culex pipiens quinequefasciatus. The genetic basis of isozyme variability was determined from genetic crosses performed with isogenic and hybrid strains of mosquitoes. 2. Isozyme electromorphs presented four enzyme activity zones, three monomorphic and one polymorphic, correspondent with four APH gene loci (aph1, aph2, aph3 and aph4). 3. All isozymes migrated anodically, with aph4 isozymes migrating most rapidly. 4. Enzyme polymorphism was evident only at aph4 locus, with three allozymes present. 5. aph4 allozymes are conditioned by multiple, co-dominant alleles transmitted in a Mendelian manner. 6. Differential frequencies and selection for aph4 alleles and genotypes are suggested by data from genetic crosses. PMID:1664307

Igbokwe, E C; Daniels, C M; Braden, P

1991-01-01

16

Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)  

PubMed Central

Background The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary. Methodology/Principal Findings Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 5465% and 4663% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses. Conclusions Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts. PMID:19582155

Kang, Hae Ji; Bennett, Shannon N.; Sumibcay, Laarni; Arai, Satoru; Hope, Andrew G.; Mocz, Gabor; Song, Jin-Won; Cook, Joseph A.; Yanagihara, Richard

2009-01-01

17

[Genetic polymorphism of bluegrass cultivars detected by RAPDs].  

PubMed

Kentucky bluegrass (Poa pratensis L.) is a hardy, persistent forage and turf grass adapted to a wide range of soils and climates. Its ever-increasing adoption in highly cared-for sports fields has attracted the attention of many seed companies. However in the past, the breeding of elite varieties was often hampered by the extreme complexity of the genome. The polymorphism is important for broading the genetic basis and may be exploited for application of heterosis. The genetic relationship of 16 bluegrass cultivars, including 15 accessions Kentucky bluegrass cultivars and 1 entries Canada bluegrass (Poa compressa L.) cultivar from different breeding company were analyzed using 25 RAPD markers. 25 RAPD primers generated 218 bands, of which 196 bands (89.91%) were polymorphism. It showed that the Canada Bluegrass was separated from other Kentucky Bluegrass and genetic polymorphism in the Kentucky Bluegrass cultivars was low, the genetic similarity among the cultivars fell between 66%-98%. Dendrogram obtained using these molecular markers were partly in agreement with their separated morphologic character. Cultivars from the same company were not clustered in one group. PMID:16120587

Ning, Ting-Ting; Zhang, Zai-Jun; Jin, Cheng-Zan; Zhu, Ying-Guo

2005-07-01

18

Disrupted Cell Cycle Control in Cultured Endometrial Cells from Patients with Endometriosis Harboring the Progesterone Receptor Polymorphism PROGINS  

PubMed Central

Presently, little is understood about how endometriosis is established or maintained, or how genetic factors can predispose women to the disease. Because of the crucial role that the progesterone receptor polymorphism PROGINS plays in predisposing women to the development of endometriosis, we hypothesized that this variant may influence critical steps during endometrial cell metabolism that are involved in the pathogenesis of endometriosis. Eutopic endometria were collected from three sources: women with endometriosis who had a single PROGINS allele (from the progesterone receptor gene); women with endometriosis who had the wild-type progesterone receptor allele; and women without endometriosis who had the wild-type allele. Cells prepared from the eutopic endometria of these women were stimulated with both estradiol and progesterone, and then examined for cell proliferation, viability, and apoptosis. The cells from women with endometriosis that carried the PROGINS allele demonstrated increased proliferation, greater viability, and decreased apoptosis following progesterone treatment. In general, these parameters were very different as compared with those of women with endometriosis but without the PROGINS allele and women in the control group. This result indicates there is a reduced level of progesterone responsiveness in women who carry the PROGINS polymorphism. Because progesterone responsiveness is known to be an important characteristic of women with endometriosis, these data support the contention that the PROGINS polymorphism enhances the endometriosis phenotype. PMID:19497994

D'Amora, Paulo; Maciel, Thiago Trovati; Tambellini, Rodrigo; Mori, Marcelo A.; Pesquero, Joao Bosco; Sato, Helio; Girao, Manoel Joao Batista Castello; Guerreiro da Silva, Ismael Dale Cotrim; Schor, Eduardo

2009-01-01

19

EFFECT OF CYTOKINE AND PHARMACOGENOMIC GENETIC POLYMORPHISMS IN TRANSPLANTATION  

PubMed Central

Purpose of review Recent investigations related to the polymorphism of genes that affect drug therapy and the polymorphisms of cytokines and growth factors that control immune responses have been associated with outcomes following solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT). This review will provide a current update on the most recent findings and discuss the challenges for developing individualized therapeutic strategies based on clinical and genetic profiles. Recent Findings Single nucleotide polymorphisms (SNPs) of cytokine genes have been shown to have an impact in vitro or in vivo protein secretion, dividing the individuals into High, Low or Intermediate producers for a given molecule. Many studies have been performed to determine the contribution of single cytokine gene SNPs on SOT or HSCT outcomes and the reported results are still controversial. However, analysis of a combination of several cytokines and/or cytokine receptor polymorphisms adjusted for known clinical risk factors and ethnicity have resulted in significant clinical correlations. Furthermore, associations with gene polymorphisms that affect immunosuppressive drug therapy in solid organ transplantation have also been extensively studied. There is a continuous flow of new information regarding functional SNPs that may affect the immune response to the allograft or to drug therapy and their impact on clinical outcomes have yet to be validated in large cohorts SOT or HSCT Summary Consolidating the information that we have on pharmacogenetics and on cytokine genetics to produce patient-oriented individualized drug regimens is an important challenge in transplantation medicine. Using a multi-variant approach based on genetic profile and other relevant clinical factors a score system may be developed to predict the severity of rejection, infection or other complications associated with transplantation. The ultimate goal of these studies is to improve patient outcome through individualized drug regimens. PMID:18706500

Girnita, Diana M; Burckart, Gilbert; Zeevi, Adriana

2008-01-01

20

Genetic analysis of thiopurine methyltransferase polymorphism in a Japanese population  

Microsoft Academic Search

Thiopurine methyltransferase (TPMT) catalyses the S-methylation of thiopurine drugs such as 6-mercaptopurine, 6-thioguanine, and azathiopurine. Several mutations in the TPMT gene have been identified which correlate with a low activity phenotype. The molecular basis for the genetic polymorphism of TPMT has been established for European Caucasians, African-Americans, Southwest Asians and Chinese, but it remains to be elucidated in Japanese populations.

Masahiro Hiratsuka; Tomoko Inoue; Fumiko Omori; Yasuyuki Agatsuma; Michinao Mizugaki

2000-01-01

21

SLC6A4 polymorphism, population genetics, and psychiatric traits.  

PubMed

5HTTLPR, which is the trivial name for a variable number of tandem repeats (VNTR) polymorphism mapped to the 5' region of the SLC6A4 (serotonin transporter protein) gene, is one of the most studied variants with respect to psychiatric traits. It is also widely studied in the context of intermediate phenotypes such as neuroimaging measures, and gene-by-environment interaction, the latter generally in the context of affective and anxiety phenotypes. In this article, the author discusses the importance of the variant in the context of a population genetics article published in Human Genetics sixteen years ago. PMID:24385047

Gelernter, Joel

2014-04-01

22

High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis  

SciTech Connect

The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

1994-09-01

23

Genetic polymorphisms and associated susceptibility to asthma  

PubMed Central

As complex common diseases, asthma and allergic diseases are caused by the interaction of multiple genetic variants with a variety of environmental factors. Candidate-gene studies have examined the involvement of a very large list of genes in asthma and allergy, demonstrating a role for more than 100 loci. These studies have elucidated several themes in the biology and pathogenesis of these diseases. A small number of genes have been associated with asthma or allergy through traditional linkage analyses. The publication of the first asthma-focused genome-wide association (GWA) study in 2007 has been followed by nearly 30 reports of GWA studies targeting asthma, allergy, or associated phenotypes and quantitative traits. GWA studies have confirmed several candidate genes and have identified new, unsuspected, and occasionally uncharacterized genes as asthma susceptibility loci. Issues of results replication persist, complicating interpretation and making conclusions difficult to draw, and much of the heritability of these diseases remains undiscovered. In the coming years studies of complex diseases like asthma and allergy will probably involve the use of high-throughput next-generation sequencing, which will bring a tremendous influx of new information as well as new problems in dealing with vast datasets. PMID:23637549

March, Michael E; Sleiman, Patrick MA; Hakonarson, Hakon

2013-01-01

24

Genetic polymorphism in the NRF2 gene as a prognosis marker for cancer chemotherapy  

PubMed Central

NF-E2-related factor 2 (NRF2) is a transcription factor that controls the expression of a variety of antioxidant and detoxification genes. Accumulating evidence strongly suggests that NRF2 mediates cancer cell proliferation and drug resistance, as well. Single nucleotide polymorphism (SNP) -617C > A in the anti-oxidant response element-like loci of the human NRF2 gene play a pivotal role in the positive feedback loop of transcriptional activation of the NRF2 gene. Since the SNP (-617A) reportedly decreases the binding affinity to the transcription factors of NRF2/small multiple alignment format (MafK), the homozygous -617A/A allele may attenuate the positive feedback loop of transcriptional activation of the NRF2 gene and reduce the NRF2 protein level. As the consequence, cancer cells are considered to become more sensitive to therapy and less aggressive than cancer cells harboring the -617C (WT) allele. Indeed, Japanese lung cancer patients carrying SNP homozygous alleles (c. -617A/A) exhibited remarkable survival over 1,700 days after surgical operation (log-rank p = 0.021). The genetic polymorphism in the human NRF2 gene is considered as one of prognosis markers for cancer therapy. PMID:25408701

Ishikawa, Toshihisa

2014-01-01

25

Genetic polymorphisms for vascular endothelial growth factor in perinatal complications.  

PubMed

Low birth weight (LBW) infants have increased susceptibility to perinatal complications. An immature and impaired vascular system may possibly participate in these complications. There is evidence that supports the notion that vascular endothelial growth factor (VEGF), which is an essential regulator of embryonic angiogenesis, plays a central role in the pathogenesis of perinatal complications. We aimed to test whether functional genetic polymorphisms of VEGF are associated with the risk of preterm birth or perinatal morbidity. We enrolled 128 LBW infants (< or = 1500 grams). VEGF T-460C, VEGF C-2578A and VEGF G+405C polymorphisms were determined by real-time PCR or PCR-RFLP, respectively. Their genotypes were compared with VEGF genotypes of 200 healthy, term neonates. The prevalence of the VEGF+405 C allele was higher in LBW infants than in healthy, term neonates (OR [95% CI]: 1.29 [1.01-1.65]). Carrier state for the VEGF -2578A allele was an independent risk factor for enterocolitis necrotisans (NEC) (adjusted OR [95% CI]: 2.77 [1.00-7.65]). The carrier state for the VEGF -2578AA genotype was associated with a decreased risk of acute renal failure (ARF) (adjusted OR [95% CI]: 0.2 [0.05-0.78]). These results suggest that VEGF G+405C polymorphism might be associated with a higher risk of preterm birth and that VEGF C-2578A polymorphism may participate in the development of perinatal complications such as NEC and ARF. PMID:17353160

Bnysz, Ilona; Bokodi, Gza; Vsrhelyi, Barna; Treszl, Andrs; Derzbach, Lszl; Szab, Andrs; Tulassay, Tivadar; Vannay, Adm

2006-12-01

26

Interethnic genetic differentiation: GM polymorphism in eastern Senegal.  

PubMed Central

Analysis of GM polymorphism has been performed on 1,806 individuals representing three sympatric ethnic groups--Bedik, Fulani, and Mandenkalu--of eastern Senegal. Haplotype frequencies estimated by maximum likelihood have been used to compute common genetic pools between the three samples and a number of other sub-Saharan African populations. Despite extreme linguistic and sociocultural differentiations and very high levels of endogamy, especially in the Bedik and Niokholo Mandenkalu, the three populations share about 90%-95% of their haplotype frequencies in a system which commonly provides strong genetic differentiations. This supports the view that, despite its importance at a large continental scale level, as it is discussed for a set of populations from many regions of sub-Saharan Africa, sociocultural differentiation usually has little effect on local genetic diversity. PMID:2105642

Blanc, M; Sanchez-Mazas, A; Van Blyenburgh, N H; Sevin, A; Pison, G; Langaney, A

1990-01-01

27

From twins to genetic polymorphisms: behavioral genetic research in poland.  

PubMed

Behavioral genetic research has been conducted at the University of Warsaw for the past 20 years. The work done at the University focuses primarily on the origins of individual differences in temperament and other personality traits. In particular, research is directed toward the traits postulated in the Regulative Theory of Temperament. We also focused on the heritability of socio-political attitudes, risk factors for human health, and post-traumatic stress disorder. The majority of the research that has been carried out is grounded in twin and family studies, although recent work based on molecular techniques has also been developed. This article reviews the most important directions and findings of behavioral genetics research at the University of Warsaw. PMID:25091033

Oniszczenko, W?odzimierz; Dragan, Wojciech ?ukasz

2014-10-01

28

Genetic diversity and chemical polymorphism of some Thymus species.  

PubMed

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 ?ELAK. (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. PMID:23776024

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

2013-06-01

29

Genetic polymorphism of cytochrome P450 as a biomarker of susceptibility to environmental toxicity.  

PubMed Central

Cytochrome P450 (CYP) enzymes are responsible for the metabolism of numerous xenobiotics and endogenous compounds, including the metabolic activation of most environmental toxic chemicals and carcinogens. Both metabolic and genetic polymorphisms have been identified for human CYP enzymes. The association of CYP genetic polymorphism and human cancer risk, and susceptibility to environmental hazards, have received increasing attention. This article briefly reviews the approaches and methods currently used in CYP genetic polymorphism studies. In addition, the current status and perspectives of using CYP genetic polymorphism as a biomarker of individual susceptibility to cancer and environmental toxicity are discussed. PMID:9255558

Hong, J Y; Yang, C S

1997-01-01

30

Destabilizing Protein Polymorphisms in the Genetic Background Direct Phenotypic Expression of Mutant SOD1 Toxicity  

PubMed Central

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. PMID:19266020

Gidalevitz, Tali; Krupinski, Thomas; Garcia, Susana; Morimoto, Richard I.

2009-01-01

31

Genetic susceptibility to eating disorders: associated polymorphisms and pharmacogenetic suggestions.  

PubMed

Anorexia nervosa (AN), bulimia nervosa (BN) and binge-eating disorder (BED) are characterized by abnormal eating behaviors often resulting in dramatic physical consequences for the patients. The etiology of eating disorders (EDs) is currently unknown; however, a strong genetic contribution is likely to be involved. To date, the majority of genetic studies have focused on candidate genes, and polymorphic variants of genes coding for substances likely to be involved in the etiopathogenesis of EDs have been assessed for association with AN, BN, BED and/or ED-related phenotypic traits. Results have been generally inconsistent and cannot be considered conclusive because of several methodological flaws and differences, such as small sample sizes, ethnic heterogeneity of studied populations, lack of statistical correction for multiple testing, adoption of different diagnostic criteria and population stratification. Although, at present, no convincing evidence for associations of candidate genes with EDs has been provided, the 5-HT(2A) receptor gene and the BDNF gene seem to be promising candidates for genetic influences on AN, since polymorphic variants of these genes have been found quite consistently, although not specifically, linked to AN restricting subtype in large sample studies. Moreover, pharmacogenetic investigations have suggested a possible role of some gene polymorphisms in predicting the response to treatment with selective serotonin reuptake inhibitors in BN, but results are still preliminary. The heterogeneity of ED phenotypes is believed to represent the most relevant variable responsible for contradictory and not conclusive results. Future studies should focus on more homogeneous subgroups, either relying on specific ED traits or identifying endophenotypes. This will be useful also for prevention and treatment of EDs. PMID:18855537

Monteleone, Palmiero; Maj, Mario

2008-10-01

32

Proton pump inhibitors, genetic polymorphisms and response to clopidogrel therapy.  

PubMed

Clopidogrel has become part of the mainstay of therapy for acute coronary syndromes and in patients post stenting. Clopidogrel is a pro drug and is metabolised by liver enzymes, particularly CYP2C19, into its active form. A considerable proportion of patients have a poor response to clopidogrel and this may be due to several factors. Genetic polymorphisms involved in clopidogrel's absorption, metabolism and activity at the platelet may interfere with its antiplatelet actions. Further, proton pump inhibitors (PPI) may interfere with clopidogrel's actions by functionally reducing the ability of CYP2C19 to convert clopidogrel to its active metabolite. By attenuating clopidogrel's actions, both polymorphisms and drug interactions may increase the risk of thrombotic events during clopidogrel therapy. This review will explore the current evidence relating to the association between PPIs, genetic polymorphisms and poor response to clopidogrel. Routine genetic testing cannot be recommended for patients receiving dual antiplatelet therapy (DAPT). However, it may have a role for patients with an episode of stent thrombosis, prior to planned high-risk stenting or major bleeding. Regarding concomitant clopidogrel and PPI therapy, it is recommended that only patients with previous gastrointestinal (GI) bleeding or multiple risk factors for GI bleeding should be prescribed gastroprotection. This is due to the uncertainty surrounding the clinical significance of this interaction given the discordant biochemical and clinical data, conflicting results from observational studies and the limitations of the COGENT study. Pantoprazole seems least likely to interact with clopidogrel and most suitable for use in patients receiving DAPT. PMID:21544314

Fernando, H; Dart, A M; Peter, K; Shaw, J A

2011-06-01

33

Random amplified polymorphic DNA analysis of genetically modified organisms.  

PubMed

Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45% similarity from the RAPD. RAPD analysis showed that the maize and soybean samples were clustered differently besides the GMO and non-GMO products. PMID:16860900

Yoke-Kqueen, Cheah; Radu, Son

2006-12-15

34

Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism  

Microsoft Academic Search

We report construction of an initial genetic linkage map for the black tiger shrimp, Penaeus monodon. Mapping was carried out using polymorphic markers derived from 23 Amplified Fragment Length Polymorphism (AFLP) primer pairs. These were analysed on three reference families of known pedigree. A total of 673 polymorphic AFLP loci that conformed to expected Mendelian segregation ratios were scored in

Kate Wilson; Yutao Li; Vicki Whan; Sigrid Lehnert; Keren Byrne; Stephen Moore; Siriporn Pongsomboon; Anchalee Tassanakajon; George Rosenberg; Elizabeth Ballment; Zahra Fayazi; Jennifer Swan; Matthew Kenway; John Benzie

2002-01-01

35

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers  

Microsoft Academic Search

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymor- phism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer com- binations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence

Ranulfo Gonzlez; Richard Wilkerson; Marco Fidel Surez; Felipe Garca; Gerardo Gallego; Heiber Crdenas; Carmen Elisa Posso; Myriam Cristina Duque

2007-01-01

36

A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism  

Microsoft Academic Search

A genetic linkage map of tef was constructed with amplified fragment length polymorphism (AFLP) markers using F5 recombinant inbred lines (RILs) derived by single seed descent from the intraspecific cross of Kaye MurriגFesho. A total\\u000a of 192 EcoRI\\/MseI primer combinations were screened for parental polymorphism. Around three polymorphic fragments per primer combination were\\u000a detected, indicating a low polymorphism level in

G. Bai; H. Tefera; M. Ayele; H. T. Nguyen

1999-01-01

37

Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs  

Microsoft Academic Search

Recently a new class of genetic polymorphism, restriction fragment length polymorphisms (RFLPs), has been uncovered by the use of restriction endonucleases which cleave DNA molecules at specific sites and cloned DNA probes which detect specific homologous DNA fragments. RFLPs promise to be exceedingly numerous and are expected to have genetic characteristics lack of dominance, multiple allelic forms and absence

J. S. Beckmann; M. Soller

1983-01-01

38

Genetic polymorphisms in diabetes: influence on therapy with oral antidiabetics.  

PubMed

Due to new genetic insights, etiologic classification of diabetes is under constant scrutiny. Hundreds, or even thousands, of genes are linked with type 2 diabetes. Three common variants (Lys23 of KCNJ11, Pro12 of PPARG, and the T allele at rs7903146 of TCF7L2) have been shown to be predisposed to type 2 diabetes mellitus across many large studies. Individually, each of these polymorphisms is only moderately predisposed to type 2 diabetes. On the other hand, monogenic forms of diabetes such as MODY and neonatal diabetes are characterized by unique clinical features and the possibility of applying a tailored treatment.Genetic polymorphisms in drug-metabolizing enzymes, transporters, receptors, and other drug targets have been linked to interindividual differences in the efficacy and toxicity of a number of medications. Mutations in genes important in drug absorption, distribution, metabolism and excretion (ADME) play a critical role in pharmacogenetics of diabetes.There are currently five major classes of oral pharmacological agents available to treat type 2 diabetes: sulfonylureas, meglitinides, metformin (a biguanide), thiazolidinediones, and ?-glucosidase inhibitors. Other classes are also mentioned in literature.In this work, different types of genetic mutations (mutations of the gene for glucokinase, HNF 1?, HNF1? and Kir6.2 and SUR1 subunit of KATP channel, PPAR-?, OCT1 and OCT2, cytochromes, direct drug-receptor (KCNJ11), as well as the factors that influence the development of the disease (TCF7L2) and variants of genes that lead to hepatosteatosis caused by thiazolidinediones) and their influence on the response to therapy with oral antidiabetics will be reviewed. PMID:21169132

Glamo?lija, Una; Jevri?-?auevi?, Adlija

2010-12-01

39

Population Genetics Study of Anopheles Darlingi (Diptera: Culicidae) from Colombia Based on Random Amplified Polymorphic DNA-Polymerase Chain Reaction and Amplified Fragment Length Polymorphism Markers.  

National Technical Information Service (NTIS)

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 4...

F. Garcia, G. Gallego, M. F. Suarez, R. Gonzalez, R. Wilkerson

2007-01-01

40

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms  

E-print Network

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms Anne genetic control, respectively, showing that genetic modifiers contribute to persistence. These results-L, Nagarajan M, Veyrieras J-B, Bottin H, Steinmetz LM, et al. (2012) Genetic Modifiers of Chromatin Acetylation

Paris-Sud XI, Université de

41

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster  

SciTech Connect

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.

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

42

Colour polymorphism and correlated characters: genetic mechanisms and evolution.  

PubMed

Colour polymorphisms (CP's) continue to be of interest to evolutionary biologists because of their general tractability, importance in studies of selection and potential role in speciation. Since some of the earliest studies of CP, it has been evident that alternative colour morphs often differ in features other than colour. Here we review the rapidly accumulating evidence concerning the genetic mechanisms underlying correlations between CP and other traits in animals. We find that evidence for genetic correlations is now available for taxonomically diverse systems and that physical linkage and regulatory mechanisms including transcription factors, cis-regulatory elements, and hormone systems provide pathways for the ready accumulation or modification of these correlations. Moreover, physical linkage and regulatory mechanisms may both contribute to genetic correlation in some of the best-studied systems. These results raise the possibility that negative frequency-dependent selection and disruptive selection might often be acting on suites of traits and that the cumulative effects of such selection, as well as correlational selection, may be important to CP persistence and evolution. We consider additional evolutionary implications. We recommend continued efforts to elucidate the mechanisms underlying CP-correlated characters and the more frequent application of comparative approaches, looking at related species that vary in character correlations and patterns of selection. We also recommend efforts to elucidate how frequency-dependent selection may act on suites of characters. PMID:21040047

McKinnon, Jeffrey S; Pierotti, Michele E R

2010-12-01

43

[Genetic polymorphisms commonly influencing efficacy of diverse addictive substances].  

PubMed

Opioids, such as morphine and fentanyl, are widely used as effective analgesics for the treatment of acute and chronic pain. In addition, the opioid system has a key role in the rewarding effects of morphine, ethanol, cocaine and various other drugs. The authors have focused on G-protein-activated inwardly rectifying potassium (GIRK) channel subunits, GIRK2 and GIRK3, that are important molecules in opioid transmission, and found that the single-nucleotide polymorphisms (SNPs) within the GIRK2 and GIRK3 gene regions were significantly associated with postoperative requirements of analgesics including opioids in patients who underwent abdominal surgery and mRNA expression of these genes in postmortem specimens, one of which was also associated with vulnerability to methamphetamine (METH) dependence. Further, by conducting a multistage genome-wide association study (GWAS) in healthy subjects, the authors found that genetic polymorphisms within a linkage disequilibrium block that spans 2q33.3-2q34 were strongly associated with the requirements for postoperative opioid analgesics after painful cosmetic surgery. The C allele of the best candidate SNP, rs2952768, was associated with more analgesic requirements, and consistent results were obtained in patients who underwent abdominal surgery. In addition, carriers of the C allele in this SNP exhibited less vulnerability to severe drug dependence in patients with methamphetamine dependence, alcohol dependence, and eating disorders and a lower 'Reward Dependence score on a personality questionnaire in healthy subjects. Furthermore, the C/C genotype of this SNP was significantly associated with the elevated expression of a neighboring gene, CREB1. The results show that SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. These outcomes provide valuable information for the personalized treatment of pain and drug dependence. PMID:24946391

Nishizawa, Daisuke; Ikeda, Kazutaka

2014-04-01

44

ZRT1 Harbors an Excess of Nonsynonymous Polymorphism and Shows Evidence of Balancing Selection in Saccharomyces cerevisiae  

PubMed Central

Estimates of the fraction of nucleotide substitutions driven by positive selection vary widely across different species. Accounting for different estimates of positive selection has been difficult, in part because selection on polymorphism within a species is known to obscure a signal of positive selection among species. While methods have been developed to control for the confounding effects of negative selection against deleterious polymorphism, the impact of balancing selection on estimates of positive selection has not been assessed. In Saccharomyces cerevisiae, there is no signal of positive selection within protein coding sequences as the ratio of nonsynonymous to synonymous polymorphism is higher than that of divergence. To investigate the impact of balancing selection on estimates of positive selection, we examined five genes with high rates of nonsynonymous polymorphism in S. cerevisiae relative to divergence from S. paradoxus. One of the genes, the high-affinity zinc transporter ZRT1 showed an elevated rate of synonymous polymorphism indicative of balancing selection. The high rate of synonymous polymorphism coincided with nonsynonymous divergence among three haplotype groups, among which we found no detectable differences in ZRT1 function. Our results implicate balancing selection in one of five genes exhibiting a large excess of nonsynonymous polymorphism in yeast. We conclude that balancing selection is a potentially important factor in estimating the frequency of positive selection across the yeast genome. PMID:23550117

Engle, Elizabeth K.; Fay, Justin C.

2013-01-01

45

Acute myeloid leukemia of donor origin after allogeneic stem cell transplantation from a sibling who harbors germline XPD and XRCC3 homozygous polymorphisms  

PubMed Central

A 54-year-old woman was diagnosed with infiltrative ductal breast carcinoma. Two years after treatment, the patient developed an acute myeloid leukemia (AML) which harbored del(11q23) in 8% of the blast cells. The patient was submitted for allogeneic stem cell transplantation (aSCT) from her HLA-compatible sister. Ten months after transplantation, she relapsed with an AML with basophilic maturation characterized by CD45low CD33high, CD117+, CD13-/+, HLA Drhigh, CD123high, and CD203c+ blast cells lacking expression of CD7, CD10, CD34, CD15, CD14, CD56, CD36, CD64, and cytoplasmic tryptase. Karyotype analysis showed the emergence of a new clone with t(2;14) and FISH analysis indicated the presence of MLL gene rearrangement consistent with del(11q23). Interestingly, AML blast cell DNA tested with microsatellite markers showed the same pattern as the donor's, suggesting that this AML emerged from donor cells. Additionally, polymorphisms of the XPA, XPD, XRCC1, XRCC3 and RAD51 DNA repair genes revealed three unfavorable alleles with low DNA repair capacity. In summary, we report the first case of AML involving XPD and XRCC3 polymorphisms from donor origin following allogeneic stem cell transplantation and highlight the potential need for careful analysis of DNA repair gene polymorphisms in selecting candidate donors prior to allogeneic stem cell transplantation. PMID:21951951

2011-01-01

46

Detection of genetic variation with radioactive ligands. III. genetic polymorphism of transcobalamin II in human plasma.  

PubMed Central

We detected genetically determined, electrophoretic variants of vitamin B12 binding proteins, most probably transcobalamin II, in human plasma. Polymorphic variants were observed in all populations tested; the two most common alleles (of at least four detected to date) attain frequencies of greater than 40% in Caucasians and Orientals. The variants are autosomally inherited and are seen as doublets in homozygotes, and four-banded patterns, the sum of two dissimilar homozygote patterns, in heterozygotes. The technique used in this survey, polyacrylamide gel electrophoresis (PAGE) autoradiography of plasma and serum labeled in vitro with 57Co-vitamin B12 is particularly applicable to the study of trace proteins such as the transcobalamins (10(-9)M). Possible functional variation in the TC II allele products is described, and the selective significance of this worldwide polymorphism is considered. Images Fig. 1 Fig. 2 PMID:655167

Daiger, S P; Labowe, M L; Parsons, M; Wang, L; Cavalli-Sforza, L L

1978-01-01

47

Cytokines, their Genetic Polymorphisms, and Outcome after Abdominal Aortic Aneurysm Repair  

Microsoft Academic Search

Background. Excessive cytokine production has been implicated in the development of organ failure. Polymorphic sites in cytokine genes have been shown to affect levels of production in vitro and may influence cytokine production in vivo. The aims of this study were to determine if cytokines or their genetic polymorphisms were related to outcome after abdominal aortic aneurysm (AAA) repair.Methods. A

M. J Bown; T Horsburgh; M. L Nicholson; P. R. F Bell; R. D Sayers

2004-01-01

48

Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines  

Microsoft Academic Search

Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of

W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

1995-01-01

49

Effects of genetic polymorphism of cytochrome P450 enzymes on the pharmacokinetics of benzodiazepines.  

PubMed

Pharmacogenetic studies have shown that several cytochrome P450 (CYP) enzymes exhibit genetic polymorphisms. Several benzodiazepines (BZPs) are metabolized predominantly or partly by polymorphic CYP2C19 and CYP3A4/5. The pharmacokinetics of diazepam, etizolam, quazepam and desmethylclobazam have been shown to be affected by CYP2C19 polymorphism. The CYP3A5 polymorphism has been reported to affect the pharmacokinetics of alprazolam, but its effect on midazolam kinetics has been inconclusive. For etizolam and desmethylclobazam, some data suggest that CYP2C19 deficiency leads to side-effects or toxicity. For the remaining BZPs the clinical significance of the observed pharmacokinetic changes remains unclear. Further studies on the effects of genetic polymorphisms of CYP enzymes on the pharmacokinetics and pharmacodynamics of BZPs are necessary to guide treatment individualization and optimization. PMID:17635335

Fukasawa, T; Suzuki, A; Otani, K

2007-08-01

50

Influence of GSTT1 Genetic Polymorphisms on Arsenic Metabolism  

PubMed Central

SUMMARY A repeated measures study was conducted in Pabna, Bangladesh to investigate factors that influence biomarkers of arsenic exposure. Drinking water arsenic concentrations were measured by inductively-coupled plasma mass spectrometry (ICP-MS) and urinary arsenic species [arsenite (As3), arsenate (As5), monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)] were detected using High Performance Liquid Chromatography (HPLC) and Hydride Generated Atomic Absorption Spectrometry (HGAAS). Linear mixed effects models with random intercepts were used to evaluate the effects of arsenic contaminated drinking water, genetic polymorphisms in glutathione-S-transferase (GSTT1 and GSTM1) on total urinary arsenic, primary methylation index [MMA/(As3+As5)], secondary methylation index (DMA/MMA), and total methylation index [(MMA+DMA)/(As3+As5)]. Drinking water arsenic concentrations were positively associated with total urinary arsenic concentrations and total methylation index. A significant gene-environment interaction was observed between urinary arsenic exposure in drinking water GSTT1 but not GSTM1 where GSTT1 null individuals had a slightly higher excretion rate of arsenic compared to GSTT1 wildtypes after adjusting for other factors. Additionally, individuals with GSTT1 null genotypes had a higher primary methylation index and lower secondary methylation index compared to GSTT1 wildtype after adjusting for other factors. This data suggests that GSTT1 contributes to the observed variability in arsenic metabolism. Since individuals with a higher primary methylation index and lower secondary methylation index are more susceptible to arsenic related disease, these results suggest that GSTT1 null individuals may be more susceptible to arsenic-related toxicity. No significant associations were observed between GSTM1 and any of the arsenic methylation indices. PMID:24511153

Kile, Molly L.; Houseman, E. Andres; Quamruzzaman, Quazi; Rahman, Mahmuder; Mahiuddin, Golam; Mostofa, Golam; Hsueh, Yu-Mei; Christiani, David C.

2014-01-01

51

A genetic polymorphism for tannin production in Lotus corniculatus and its relationship to cyanide polymorphism  

Microsoft Academic Search

A study of 172 unnamed populations and 22 cultivars of Lotus corniculatus showed: (1) that all plants of most strains of both categories contained leaf tannins (total 172 strains); (2) that 6 strains were tannin-negative; and (3) that 16 strains were polymorphic. Because of the small number of tested plants per strain, the above frequency of polymorphism is probably underestimated.

M. D. Ross; W. T. Jones

1983-01-01

52

Amplified Fragment Length Polymorphism Marker-Based Genetic Diversity in Tamarind (Tamarindus indica)  

Microsoft Academic Search

Tamarindus indica, commonly called tamarind, is a medium-sized evergreen tree that gives a high yield. The fruit is commonly used as a spice. Despite its commercial importance in the international market, it has been little explored. The genetic diversity and genetic relatedness of 36 tamarind genotypes were studied using amplified fragment length polymorphism (AFLP) markers. Twelve primer pairs were used

Ali Qaid Ahmed Yahya Algabal; Narayanaswamy Papanna; Luke Simon

2011-01-01

53

The use of genetically engineered cells for assessing CYP2D6-related polymorphic effects  

Microsoft Academic Search

As an example of advanced testing in the field of metabolism in an industrial environment, the introduction of some novel approaches, including the use of genetically engineered cell lines for assessing CYP 2D6-related polymorphic effects is illustrated. In this paper, it is demonstrated that novel in vitro test systems can be developed by using these genetically engineered cell lines for

S Coecke; A Bogni; I Langezaal; A Worth; T Hartung; M Monshouwer

2001-01-01

54

Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms  

Microsoft Academic Search

Genetic linkage maps were constructed for both maize and tomato, utilizing restriction fragment length polymorphisms (RFLPs) as the source of genetic markers. In order to detect these RFLPs, unique DNA sequence clones were prepared from either maize or tomato tissue and hybridized to Southern blots containing restriction enzyme-digested genomic DNA from different homozygous lines. A subsequent comparison of the RFLP

T. Helentjaris; M. Slocum; S. Wright; A. Schaefer; J. Nienhuis

1986-01-01

55

Genetic diversity of fringed brome ( Bromus ciliatus ) as determined by amplified fragment length polymorphism  

Microsoft Academic Search

Fringed brome (Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four

Yong-Bi Fu; Bruce E. Coulman; Yasas S. N. Ferdinandez; Jacques Cayouette; Paul M. Peterson

2005-01-01

56

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

PubMed

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. PMID:23028365

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

2012-09-01

57

Genetic diversity and identification of cymbidium cultivars as measured by random amplified polymorphic DNA (RAPD) markers  

Microsoft Academic Search

DNA from thirty-six cymbidium cultivars was examined using polymerase chain reaction (PCR) to determine the efficiency of\\u000a randomly amplified polymorphic DNA (RAPD) markers in identifying cultivars and determining levels of genetic variability.\\u000a A total of 132 RAPD markers, 78% of which were polymorphic, were produced from 15 10mer arbitrary primers. All the cultivars\\u000a were distinguishable when a number of primers

P. Obara-Okeyo; S. Kako

1998-01-01

58

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

PubMed

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 P450enzymes, N-acetyltransferases, etc.), drug transporters (ATP-binding cassette transporters), and drug targets (tumor necrosis factor-? 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. PMID:25144752

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

2014-11-01

59

Association of Polymorphism Harbored by Tumor Necrosis Factor Alpha Gene and Sex of Calf with Lactation Performance in Cattle  

PubMed Central

In a majority of mammals, male infants have heavier body mass and grow faster than female infants. Accordingly, male offspring nursing requires a much greater maternal energy contribution to lactation. It is possible that the maternal-fetal immunoendocrine dialog plays an important role in female preparation for lactation during pregnancy. Immune system genes are an integral part of gene regulatory networks in lactation and tumor necrosis factor alpha (TNF?) is a proinflammatory cytokine that also plays an important role in normal mammary gland development. The aim of this study was to evaluate the influence of the sex of calf and/or the -824A/G polymorphism in the promoter region of TNF? gene on milk performance traits in Black Pied cattle over the course of lactation. We also studied the allele frequency differences of -824A/G variants across several cattle breeds, which were bred in different climatic conditions. The G allele frequency decreased gradually over the course of lactation events in the Black Pied dairy cattle because of a higher culling rate of cows with the G/G genotype (p<0.001). In contrast to the genotypes A/A and A/G, cows with G/G genotype showed significant variability of milk and milk fat yield subject to sex of delivered calf. Milk yield and milk fat yield were significantly higher in the case of birth of a bull calf than with a heifer calf (p<0.03). The G allele frequency varies from 48% to 58% in Grey Ukrainian and Black Pied cattle to 77% in aboriginal Yakut cattle. Our results suggest that the TNF? -824A/G gene polymorphism may have an influence on the reproductive efforts of cows over the course of lactation events depending on the sex of progeny. Allocation of resources according to sex of the calf allows optimizing the energy cost of lactation. This may be a probable reason for high G allele frequency in Yakut cattle breeding in extreme environmental conditions. Similarly, the dramatic fall in milk production after birth of a heifer calf increases the probability of culling for the cows with the G/G genotype in animal husbandry. PMID:25049721

Yudin, N. S.; Aitnazarov, R. B.; Voevoda, M. I.; Gerlinskaya, L. A.; Moshkin, M. P.

2013-01-01

60

Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat  

PubMed Central

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2013-01-01

61

Relationships of LDLR genetic polymorphisms with cerebral infarction: a meta-analysis.  

PubMed

This meta-analysis was undertaken to identify the relationships between genetic polymorphisms in the LDLR gene and the risk of cerebral infarction. The Web of Science (1945-2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966-2013), EMBASE (1980-2013), CINAHL (1982-2013) and the Chinese Biomedical Database (CBM) (1982-2013) were searched for relevant articles without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Crude odds ratios (OR) with their corresponding 95% confidence interval (CI) were calculated. Eight case-control studies with a total of 4,655 patients with cerebral infarction and 15,920 healthy control subjects were included in our meta-analysis. Five common polymorphisms in the LDLR gene were evaluated, including rs11669576 A > T, rs1433099 C > T, rs5925 C > T, rs688 C > T, rs1122608 T > G in the LDLR gene. The results of this meta-analysis revealed that cerebral infarction patients had a higher frequency of LDLR genetic polymorphisms than that of healthy controls (allele model: OR 1.17, 95% CI 1.05-1.30, P = 0.004; dominant model: OR 1.18, 95% CI 1.05-1.33, P = 0.007; homozygous model: OR 1.50, 95% CI 1.03-2.16, P = 0.032; respectively), especially for the rs11669576 A > T, rs1433099 C > T and rs5925 C > T polymorphisms. Among different ethnic subgroups, the results demonstrated positive correlations between LDLR genetic polymorphisms and an increased risk of cerebral infarction among both Asians and Caucasians under the allele and dominant models (all P < 0.05). Our findings indicate that LDLR genetic polymorphisms may be strongly involved in the pathogenesis of cerebral infarction, especially the rs11669576 A > T, rs1433099 C > T, rs5925 C > T polymorphisms. PMID:24595448

Yan, Hai-Cheng; Wang, Wei; Dou, Chang-Wu; Tian, Fu-Ming; Qi, Song-Tao

2014-07-01

62

Investigation of the Association between Genetic Polymorphism of Microsomal Epoxide Hydrolase and Primary Brain Tumor Incidence  

PubMed Central

mEH is a critical biotransformation enzyme that catalyzes the conversion of xenobiotic epoxide substrates into more polar diol metabolites: it is also capable of inactivating a large number of structurally different molecules. Two polymorphisms affecting enzyme activity have been described in the exon 3 and 4 of the mEH gene. The hypothesis of this study is that inherent genetic susceptibility to a primary brain tumor is associated with mEH gene polymorphisms. The polymorphisms of the mEH gene were determined with PCR-RFLP techniques and 255 Turkish individuals. Our results indicate that the frequency of the mEH exon 4 polymorphism (in controls) is significantly higher than that of primary brain tumor patients (OR = 1.8, 95% CI = 1.03.4). This report, however, failed to demonstrate a significant association between mEH exon 3 polymorphism and primary brain tumor susceptibility in this population. Analysis of patients by both histological types of primary brain tumor and gene variants showed no association, although analysis of family history of cancer between cases and controls showed a statistically significant association (?2 = 7.0, P = 0.01). Our results marginally support the hypothesis that genetic susceptibility to brain tumors may be associated with mEPHX gene polymorphisms. PMID:24455257

Aydin, Ali; Pinarbasi, Hatice; Gurelik, Mustafa

2013-01-01

63

Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers.  

PubMed

Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701). The accessions with the highest genetic diversity (effective number of alleles, NE = 1.609; Nei's genetic diversity, H = 0.372; Shannon information index, I = 0.556) were from Italy. The richest genetic diversity was revealed in a chicory line (NE = 1.478, H = 0.289, I = 0.443) among the 3 types (line, wild, and cultivar). The chicory genetic structure of 8 geographical groups showed that the genetic differentiation coefficient (GST) was 14.20% and the number of immigrants per generation (Nm) was 3.020. A GST of 6.80% and an Nm of 6.853 were obtained from different types. This observation suggests that these chicory lines, especially those from the Mediterranean region, have potential for providing rich genetic resources for further breeding programs, that the chicory genetic structure among different countries obviously differs with a certain amount of gene flow, and that SRAP markers could be applied to analyze genetic relationships and classifications of Cichorium intybus and C. endivia. PMID:25299087

Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F

2014-01-01

64

Genetic Polymorphisms in VIR Genes among Indian Plasmodium vivax Populations  

PubMed Central

The vir genes are antigenic genes and are considered to be possible vaccine targets. Since India is highly endemic to Plasmodium vivax, we sequenced 5 different vir genes and investigated DNA sequence variations in 93 single-clonal P. vivax isolates. High variability was observed in all the 5 vir genes; the vir 1/9 gene was highly diverged across Indian populations. The patterns of genetic diversity do not follow geographical locations, as geographically distant populations were found to be genetically similar. The results in general present complex genetic diversity patterns in India, requiring further in-depth population genetic and functional studies. PMID:25352708

Gupta, Purva; Pande, Veena; Das, Aparup

2014-01-01

65

Levels of genetic polymorphism: marker loci versus quantitative traits.  

PubMed Central

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species. PMID:9533123

Butlin, R K; Tregenza, T

1998-01-01

66

Genetic association between p53 codon 72 polymorphism and risk of cutaneous squamous cell carcinoma.  

PubMed

This study was designed to obtain a conclusive result about the relevance of p53 codon 72 polymorphism to the risk of cutaneous squamous cell carcinoma (SCC). We performed an updated meta-analysis of 3,792 subjects (1,349 cancer cases and 2,443 controls) to summarize the data available for p53 codon 72 polymorphism and SCC risk. The association was estimated by odds ratios (ORs) with 95% confidence intervals (CIs). The meta-analysis showed no statistical significance for SCC risk associated with any of the genetic models of p53 codon 72 polymorphism. The analyses by ethnic subgroup also failed to produce significant associations. This study suggests that p53 codon 72 polymorphism does not appear to represent a significant susceptibility factor for SCC in Caucasians. PMID:24353089

Liu, Ting; Lei, Zeyuan; Pan, ZhengYing; Chen, Yu; Li, Xiang; Mao, TongChun; He, Qian; Fan, Dongli

2014-04-01

67

Genetic Polymorphism of Thiopurine S-Methyltransferase: Molecular Mechanisms and Clinical Importance  

Microsoft Academic Search

The activity of thiopurine S-methyltransferase (TPMT) is inherited as an autosomal co-dominant trait. In most large world populations studied to date, approximately 10% of the population have intermediate activity due to heterozygosity at the TPMT locus, and about 0.33% is TPMT deficient. TPMT is now one of the most well characterized genetic polymorphisms of drug metabolism, with the genetic basis

Eugene Y. Krynetski; William E. Evans

2000-01-01

68

The origins of extraversion: joint effects of facultative calibration and genetic polymorphism.  

PubMed

The origins of variation in extraversion are largely mysterious. Recent theories and some findings suggest that personality variation can be orchestrated by specific genetic polymorphisms. Few studies, however, have examined an alternative hypothesis that personality traits are facultatively calibrated to variations in other phenotypic features, and none have considered how these distinct processes may interact in personality determination. Since physical strength and physical attractiveness likely predicted the reproductive payoffs of extraverted behavioral strategies over most of human history, it was theorized that extraversion is calibrated to variation in these characteristics. Confirming these predicted patterns, strength and attractiveness together explained a surprisingly large fraction of variance in extraversion across two studies--effects that were independent of variance explained by an androgen receptor gene polymorphism. These novel findings initially support an integrative model wherein facultative calibration and specific genetic polymorphisms operate in concert to determine personality variation. PMID:21307179

Lukaszewski, Aaron W; Roney, James R

2011-03-01

69

Population genetics of the metabolically related Adh, Gpdh and Tpi polymorphisms in Drosophila melanogaster  

E-print Network

génétique du polymorphisme aux loci d'Adh, Gpdh et Tpi chez Drosophila melanogaster. Il. VariationsPopulation genetics of the metabolically related Adh, Gpdh and Tpi polymorphisms in Drosophila melanogaster : II. Temporal and Spatial Variation in an Orchard Population Karen M. NIELSEN A.A. HOFFMANN S

Paris-Sud XI, Université de

70

Pharmacogenetics of acute azathioprine toxicity: Relationship to thiopurine methyltransferase genetic polymorphism  

Microsoft Academic Search

Azathioprine therapy can cause acute myelosuppression. Toxicity is in part caused by the incorporation of azathioprine-derived 6-thioguanine nucleotides (6-TGN) into deoxyribonucleic acid (DNA). The enzyme thiopurine methyltransferase (TPMT) plays an important role in azathioprine catabolism. TPMT activity is controlled by a common genetic polymorphism, and one in 300 subjects has very low enzyme activity. Azathioprine was withdrawn in five study

Lynne Lennard; Jon A Van Loon; Richard M Weinshilboum

1989-01-01

71

Amplified Fragment Length Polymorphism Assessment of Genetic Diversity in Pacific Lampreys  

Microsoft Academic Search

This study is the first to document genetic differences among Pacific lampreys Lampetra tridentata across much of their range. We examined collections of migrating adult Pacific lampreys from the Naka River, Japan; Moose River, Alaska; and six Pacific Northwest locations (North Fork Toutle, Willamette, Deschutes, John Day, Rogue, and Klamath rivers) based on variation at 180 polymorphic loci among the

Binbin Lin; Ziping Zhang; Yilei Wang; Kenneth P. Currens; Adrian Spidle; Yuji Yamazaki; David A. Close

2008-01-01

72

Cystic Fibrosis Locus Defined by a Genetically Linked Polymorphic DNA Marker  

Microsoft Academic Search

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of

Lap-Chee Tsui; Manuel Buchwald; David Barker; Jeffrey C. Braman; Robert Knowlton; James W. Schumm; Hans Eiberg; Jan Mohr; Dara Kennedy; Natasa Plavsic; Martha Zsiga; Danuta Markiewicz; Gita Akots; Valerie Brown; Cynthia Helms; Thomas Gravius; Carol Parker; Kenneth Rediker; Helen Donis-Keller

1985-01-01

73

Genetic Polymorphism in Natural Populations of Avena fatua and A. barbata  

Microsoft Academic Search

IN a previous paper1 estimates of the degree of polymorphism at four marker loci and the between and within-family components of quantitative genetic variation were reported for several natural populations of Avena fatua and A. barbata from a small region of the Central Valley of California. These data indicated that the two species differed markedly in population structure; populations of

D. R. Marshall; S. K. Jain

1969-01-01

74

Genetic polymorphisms in pre-microRNAs and risk of ischemic stroke in a Chinese population.  

PubMed

Ischemic stroke is considered to be a complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. MicroRNAs participated in various physiopathological processes; common single-nucleotide polymorphisms (SNPs) in pre-miRNAs have been shown to be associated with susceptibility to several human diseases. We evaluated the associations of the hsa-mir-196-a2/rs11614913 T/C, hsa-mir-146a/rs2910164 C/G, and hsa-mir-499/rs3746444 A/G polymorphisms in pre-miRNAs with the risk of ischemic stroke in a Chinese population. The three polymorphisms were identified in 296 ischemic stroke patients and 391 healthy controls using polymerase chain reaction-restriction fragment length polymorphism. The frequency of the allele G of hsa-mir-499/rs3746444 A/G showed significant association with ischemic stroke when compared with controls (OR = 1.509, 95%CI = 1.151-1.978, P = 0.003). Increased ischemic stroke risks were associated with rs3746444 A/G genotypes in different genetic model (homozygote comparison: P = 0.045, OR = 2.084, 95%CI = 1.019-4.262; heterozygote comparison: P = 0.024, OR = 1.489, 95%CI = 1.063-2.087; dominant genetic model: P = 0.007, OR = 1.563, 95%CI = 1.135-2.153). Similar results were obtained by adjusted fully risk factors. However, we failed to find any association between the alleles and genotypes of rs2910164 C/G and rs11614913 T/C SNPs and ischemic stroke, respectively (p > 0.05). The present study provided evidence that hsa-mir-499/rs3746444 A/G polymorphism might be associated with a significantly increased risk of ischemic stroke in a Chinese population, indicating that the common genetic polymorphism in pre-microRNAs contributed to the pathogenesis of ischemic stroke. PMID:24178064

Liu, Yun; Ma, Ying; Zhang, Bo; Wang, Shun-Xian; Wang, Xiao-Ming; Yu, Ju-Ming

2014-04-01

75

Harbor lights  

PubMed

Illuminating Life: Selected Papers from Cold Spring Harbor (1903-1969) by J. Witkowski Cold Spring Harbor Laboratory Press (2000) pp. 383 + xvi. ISBN 0-87969-566-8 $25.00 If you are anywhere on the spectrum from frequent Cold Spring Harbor visitor to someone who barely knows that Symposia of that name were until recently published in maroon covers, and if you want to learn more of the history of this remarkable research centre, then this book is for you. At first sight, Illuminating Life looks like a coffee table book, but it is much more than that. Jan Witkowski has assembled a history of the Cold Spring Harbor Laboratories from their inception in 1890 through to 1968, illustrated by a selection of research papers from 1903 to 1969. Each one or two papers is preceded by an interpretative essay and a biographical note on the principal author(s), and the whole is introduced by an informative historical preface. At the end are three obituaries from the literature summarizing the lives of three key players, Davenport, Harris and Demerec. For a book of this size and compass, the essentials can be assimilated remarkably quickly, and at $25 the book is exceptional value for money. First read the preface. Then the essays. These are gems, and at two or three pages each there is no need to postpone them until later! Then dip into a few research papers. Then re-read the preface. Then you will know a lot about Cold Spring Harbor. If you read the obituaries you will know even more. Here are just a few impressions. On p. 364 there is a photograph of one of the early buildings, the James Laboratory. The laboratory was constructed for $12,000 in 1928 for biophysics research (p117). It looks tiny, but in the early years of the Symposia, which were then on biophysical topics, it housed a galaxy of summer visitors including Curtis and Cole (electrophysiology), J. Z. Young (nerve conduction), Davison and Danielli (need one say more?) and many others. If biophysics under Reginald Harris (1924-36) was what made Cold Spring Harbor Quantitative, then the quest for the genetic material and its properties is what has made it most widely famed. The book brings out the seminal contributions of Demerec, both as scientist and as director (1941-60) and of McClintock, Hershey, Cairns (director 1963-8) and others. The chosen research papers include many that are landmarks in science, from maize to bacteria and phage, and generally they are easy to read. They are largely devoid of the ponderous throat-clearing and innumerable citations that are so much a part of scientific literature today. Many examples could be given of such ease of style and freedom from excess verbage, but one will suffice here. 'Aggregation of DNA is often suspected but seldom studied. In phage &lgr; we found a DNA that can form characteristic and stable complexes. A first account of them is given here'. That is the entire introduction in Hershey, A. D., Burgi, E. and Ingraham, L. (1963), Cohesion of DNA molecules isolated from phage &lgr;. Proc. Nat. Acad. Sci. USA 49, 748-755. The paper by de Lucia and Cairns (1969) on 'Isolation of an E. coli strain with a mutation affecting DNA polymerase' is a fitting choice with which to conclude the compilation. In the late 1960s something seemed not quite right about the Kornberg enzyme as the putative engine of replication. Several suspicious inconsistencies were accumulating. How to test these suspicions? Random mutagenesis, a precise and rapid screening assay applicable to thousands of isolates. The rest is history. What of the last thirty years? The spine of the cover says, rather enigmatically, 'Volume 1'; the reviewer could find no statement elsewhere in the book that more is to follow. Perhaps we can look forward to Volume 2. Surely that volume will contain, among many other landmark papers, one called 'An amazing sequence arrangement at the 5 ends of Adenovirus 2 messenger RNA'. PMID:11069757

Maden

2000-12-01

76

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers  

Microsoft Academic Search

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a poly- merase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in

G. Yan; J. Romero-Severson; M. Walton; D. D. CHADEEand; D. W. Severson

1999-01-01

77

PEARL HARBOR  

Microsoft Academic Search

For Pearl Harbor, ILM created vistas of period battleships under attack and CG planes in combat at Pearl Harbor and in other battles. Simulation software was written for the huge billowing smoke from destroyed battleship row and new rigid body software was developed for the destruction of planes and ships. Other developments included: new environmental lighting techniques to enhance the

2001-01-01

78

Safe Harbor  

NSDL National Science Digital Library

Safe Harbor was created as a response to the European Commission's Directive on Data Privacy which was launched in October 1998 and prohibits the transfer of personal data to countries outside of the European Union that do not meet the EU's standards for privacy protection. Because the United States has significantly lower standards for privacy protection, the Directive on Data Privacy would have prohibited many transactions between the US and EU nations. Safe Harbor is a framework of US organizations that have agreed to comply with the Directive. The Safe Harbor Website contains a basic overview of the initiative which explains its history and mission. Safe Harbor documents include privacy principles, an in-depth collection of FAQs, information on how Safe Harbor is enforced, and other documents from both the US and the EU.

79

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

PubMed Central

Introduction Skin changes are among the most visible signs of aging. Skin properties such as hydration, elasticity, and antioxidant capacity play a key role in the skin aging process. Skin aging is a complex process influenced by heritable and environmental factors. Recent studies on twins have revealed that up to 60% of the skin aging variation between individuals can be attributed to genetic factors, while the remaining 40% is due to non-genetic factors. Recent advances in genomics and bioinformatics approaches have led to the association of certain single nucleotide polymorphisms (SNPs) to skin properties. Our aim was to classify individuals based on an ensemble of multiple polymorphisms associated with certain properties of the skin for providing personalized skin care and anti-aging therapies. Methods and results We identified the key proteins and SNPs associated with certain properties of the skin that contribute to skin aging. We selected a set of 13 SNPs in gene coding for these proteins which are potentially associated with skin aging. Finally, we classified a sample of 120 female volunteers into ten clusters exhibiting different skin properties according to their genotypic signature. Conclusion This is the first study that describes the actual frequency of genetic polymorphisms and their distribution in clusters involved in skin aging in a Caucasian population. Individuals can be divided into genetic clusters defined by genotypic variables. These genotypic variables are linked with polymorphisms in one or more genes associated with certain properties of the skin that contribute to a persons perceived age. Therefore, by using this classification, it is possible to characterize human skin care and anti-aging needs on the basis of an individuals genetic signature, thus opening the door to personalized treatments addressed at specific populations. This is part of an ongoing effort towards personalized anti-aging therapies combining genetic signatures with environmental and life style evaluations. PMID:25061327

Naval, Jordi; Alonso, Vicente; Herranz, Miquel Angel

2014-01-01

80

Genetic polymorphism of CYP2C19 & therapeutic response to proton pump inhibitors.  

PubMed

Proton pump inhibitors (PPIs) are extensively metabolized in the liver by CYP2C19, that demonstrates genetic polymorphism with 21 mutant alleles. The subjects can be divided into 2 groups with respect to CYP2C19 phenotypes viz., extensive metabolizers (EMs) and poor metabolizers (PMs) of PPIs. This division results in marked interindividual variations in the pharmacokinetics and pharmacodynamics of PPIs in the population. Intragastric pH values and the plasma concentration of PPIs after oral ingestion were significantly lower in EMs namely normal homozygotes (CYP2C19*1/*1) and heterozygotes (CYP2C19*1/*X) compared to PMs namely mutant homozygotes (CYP2C19*X/*X) where 'X' represents the mutant allele. Hence, association has been found between the genetic polymorphism of CYP2C19 and therapeutic response to PPIs. CYP2C19 polymorphism affected eradication of Helicobacter pylori using diferent PPI based eradication therapies as PM patients demonstrated significantly higher eradication rates compared to EMs. CYP2C19 genetic polymorphism also affects the therapeutic outcome of gastroesophageal reflux disease (GERD), reflux oesophagitis and duodenal ulcers. For optimal therapeutic response with PPIs, CYP2C19 pharmacogenetics should be taken into consideration. This shall help in the prescription of optimal doses of PPIs, thus paving the way for personalized medication. PMID:18765869

Chaudhry, A S; Kochhar, R; Kohli, K K

2008-06-01

81

Polymorphs  

E-print Network

? Lactose (anhydrous; also monohydrate) ? Aspartame (anhydrous; hydrate forms) ? Magnesium stearate (can affect lubrication of tablets) ? Triglycerides (?, ?, ?? forms) 26 Methods for study of polymorphism All of the phenomena mentioned could be used...

Prankerd, Richard

2006-10-26

82

UGT1A9 Genetic Polymorphisms and Raloxifene Pharmacogenetics.  

National Technical Information Service (NTIS)

The goal of this DOD Breast Concept award was to identify and functionally characterize common genetic polymorphisnis in the human UDP- glucuronosyltransferase gene, UGTlA9. We had previously determined that UGTlA9, a metabolic enzyme expressed predominan...

R. B. Raftogianis

2002-01-01

83

Genetic polymorphisms and lung cancer susceptibility: a review  

Microsoft Academic Search

Lung cancer is a major cause of cancer-related death in the developed countries and the overall survival rate has still an extremely poor. Cigarette smoking is an established risk factor for lung cancer although a possible role for genetic susceptibility in the development of lung cancer has been inferred from familial clustering of the disease and segregation analyzes. Everyone may

Chikako Kiyohara; Akiko Otsu; Taro Shirakawa; Sanae Fukuda; Julian M Hopkin

2002-01-01

84

A combination of genetic polymorphisms increases the risk of progressive disease in chronic hepatitis C  

PubMed Central

Background: There is increasing interest in the influence of host genetic factors on hepatic fibrosis, and whether genetic markers can reliably identify subjects at risk of developing severe disease. We hypothesised that hepatitis C virus (HCV) infected subjects with progressive fibrosis, classified using strict criteria based on histology at biopsy in addition to disease duration would be more likely to inherit several genetic polymorphisms associated with disease progression compared with subjects with a low rate of disease progression. Methods: We examined polymorphisms in eight genes that have been reported to have an association with hepatic fibrosis. Results: Associations between polymorphisms in six genes and more rapidly progressing fibrosis were observed, with individual adjusted odds ratios ranging from 2.1 to 4.5. The relationship between rapidly progressing fibrosis and possession of ?3, ?4, or ?5 progression associated alleles was determined and the adjusted odds ratios increased with increasing number of progression associated alleles (9.1, 15.5, and 24.1, respectively). Using logistic regression analysis, a predictive equation was developed and tested using a second cohort of patients with rapidly progressing fibrosis. The predictive equation correctly classified 80% of patients in this second cohort. Conclusions: This approach may allow determination of a genetic profile predictive of rapid disease progression in HCV and identify patients warranting more aggressive therapeutic management. PMID:15994870

Richardson, M; Powell, E; Barrie, H; Clouston, A; Purdie, D; Jonsson, J

2005-01-01

85

Characterization of genetic identities and relationships of Brassica oleracea L. via a random amplified polymorphic DNA assay  

Microsoft Academic Search

Effective conservation and the use of plant genetic resources are essential for future agricultural progress. Critical to this conservation effort is the development of genetic markers which not only distinguish individuals and accessions but also reflect the inherent variation and genetic relationships among collection holdings. We have examined the applicability of the random amplified polymorphic DNA (RAPD) assay for quick,

S. Kresovich; J. G. K. Williams; J. R. McFerson; E. J. Routman; B. A. Schaal

1992-01-01

86

Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The\\u000a AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted.\\u000a Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs)\\u000a for AFLP markers among elite public

Vipa Hongtrakul; Gordon M. Huestis; Steven J. Knapp

1997-01-01

87

Correlations of IFN-? genetic polymorphisms with susceptibility to breast cancer: a meta-analysis.  

PubMed

The meta-analysis was conducted to evaluate the correlations between common genetic polymorphisms in the IFN-? gene and susceptibility to breast cancer. The following electronic databases were searched without language restrictions: MEDLINE (1966 ~ 2013), the Cochrane Library Database (issue 12, 2013), EMBASE (1980 ~ 2013), CINAHL (1982 ~ 2013), Web of Science (1945 ~ 2013), and the Chinese Biomedical Database (CBM) (1982 ~ 2013). Meta-analysis was performed with the use of the STATA statistical software. Odds ratios (OR) with their 95 % confidence intervals (95 % CIs) were calculated. Nine clinical case-control studies met all the inclusion criteria and were included in this meta-analysis. A total of 1,182 breast cancer patients and 1,525 healthy controls were involved in this meta-analysis. Three functional polymorphisms were assessed, including rs2069705 C>T, rs2430561 T>A, and CA repeats 2/X. Our meta-analysis results indicated that IFN-? genetic polymorphisms might be significantly associated with an increased risk of breast cancer (allele model: OR = 1.37, 95 % CI = 1.03 ~ 1.83, P = 0.031; dominant model: OR = 1.55, 95 % CI = 1.01 ~ 2.37, P = 0.046; homozygous model: OR = 2.23, 95 % CI = 1.30 ~ 3.82, P = 0.004; respectively), especially the rs2430561 T>A polymorphism. Subgroup analysis based on ethnicity suggested that genetic polymorphisms in the IFN-? gene were closely correlated with increased breast cancer risk among Asians (allele model: OR = 1.21, 95 % CI = 1.02 ~ 1.58, P = 0.017; dominant model: OR = 3.44, 95 % CI = 2.07 ~ 5.71, P < 0.001; recessive model: OR = 1.58, 95 % CI = 1.06 ~ 2.37, P = 0.025; homozygous model: OR = 1.83, 95 % CI = 1.19 ~ 2.80, P = 0.006; respectively), but not among Caucasians (all P > 0.05). Our meta-analysis supported the hypothesis that IFN-? genetic polymorphisms may contribute to an increased risk of breast cancer, especially the rs2430561 T>A polymorphism among Asians. PMID:25051917

Li, Chun-Jiang; Dai, Yue; Fu, Yan-Jun; Tian, Jia-Ming; Li, Jin-Lun; Lu, Hong-Jun; Duan, Feng; Li, Qing-Wang

2014-07-01

88

Harboring chaos  

E-print Network

Hurricane shelters have become the unknown point of last resort for many coastal communities. Harboring displaced populations during a hurricane and it's chaotic aftermath are no longer seen as a need in a coastal communities ...

Anderson, Jeffrey A. (Jeffrey Arthur)

2007-01-01

89

Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers  

Microsoft Academic Search

Eryngium alpinum L. is an endangered species found across the European Alps. In order to obtain base-line data for the conservation of this species, we investigated levels of genetic diversity within and among 14 populations from the French Alps. We used the amplified fragment length polymorphism (AFLP) technique with three primer pairs and scored a total of 62 unambiguous, polymorphic

M. Gaudeul; P. Taberlet; I. Till-Bottraud

2000-01-01

90

Genetic polymorphism of cytochrome P450s in beagles: possible influence of CYP1A2 deficiency on toxicological evaluations  

Microsoft Academic Search

A number of human cytochrome P450 (CYP) isozymes have been shown to be genetically polymorphic, and extensive pharmaceutical studies have been conducted to characterize the clinical relevance of the polymorphism. Although the beagle is extensively used in the safety assessment studies of new drug candidates and agricultural chemicals, only a limited number of studies have been reported on the significance

H. Kamimura

2006-01-01

91

Skin fibroblast model to study an impaired glutathione synthesis: Consequences of a genetic polymorphism on the proteome  

Microsoft Academic Search

An impaired glutathione (GSH) synthesis was observed in several multifactorial diseases, including schizophrenia and myocardial infarction. Genetic studies revealed an association between schizophrenia and a GAG trinucleotide repeat (TNR) polymorphism in the catalytic subunit (GCLC) of the glutamate cysteine ligase (GCL). Disease-associated genotypes of this polymorphism correlated with a decrease in GCLC protein expression, GCL activity and GSH content. To

Ren Gysin; Irne M. Riederer; Michel Cunod; Beat M. Riederer

2009-01-01

92

[Genetic polymorphisms commonly associated with sensitivity to various addictive substances].  

PubMed

Opioids, such as morphine and fentanyl, are widely used as effective analgesics for the treatment of acute and chronic pain. In addition, the opioid system has a key role in the rewarding effects of morphine, ethanol, cocaine and various other drugs. The authors have focused on G-protein-activated inwardly rectifying potassium (GIRK) channel subunits, GIRK2 and GIRK3, which are important molecules in opioid transmission, and found that the SNPs within the GIRK2 and GIRK3 gene region were significantly associated with postoperative analgesic requirements, one of which was also associated with vulnerability to methamphetamine (METH) dependence. Further, by conducting a multistage genome-wide association study (GWAS) in healthy subjects, the authors found that the rs2952768 single-nucleotide polymorphism (SNP) was strongly associated with the requirements for postoperative opioid analgesics after painful cosmetic surgery and consistent results were obtained in patients who underwent abdominal surgery. In addition, the SNP also showed significant association with vulnerability to severe drug dependence in patients with METH dependence, alcohol dependence, and eating disorders and a lower 'Reward Dependence' score on a personality questionnaire in healthy subjects. These outcomes provide valuable information for the personalized treatment of pain and drug dependence. PMID:25069259

Nishizawa, Daisuke; Ikeda, Kazutaka

2013-11-01

93

Electrophoretic detection of genetic variability among Schistosoma japonicum isolates by sequence-related amplified polymorphism.  

PubMed

In the present study, sequence-related amplification polymorphism (SRAP) was utilized to study the genetic variability among Schistosoma japonicum isolates from different provinces in China, using Schistosoma mansoni from Puerto Rico for comparison. Five out of ten tested SRAP primer combinations displayed significant polymorphisms among S. japonicum isolates from China, namely ME2/EM1, ME4/EM1, ME4/EM6, ME5/EM4 and ME5/EM5. Analysis of the 61 S. japonicum samples from China with five SRAP primer combinations identified a total of 83 reproducible polymorphic fragments. The number of fragments using each primer combination ranged from 14 to 19, with an average of 16 polymorphic bands per primer pair, and the size of fragment ranged approximately from 100 to 1000?bp. Representative-specific SRAP fragments were excised from the gels, and confirmed by PCR amplification of genomic DNA using primers designed and based on the sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair-group method with arithmetic averages (UPGMA) dendrogram was constructed. UPGMA clustering algorithm categorized S. japonicum isolates from China into nine clades and two lineages (representing the mountainous and lake/marshland regions). These results indicate the usefulness of the SRAP technique for revealing genetic variability among S. japonicum isolates from China, and the SRAP technique should be applicable to other living organisms. PMID:21538983

Song, Hui-Qun; Mo, Xi-Hao; Zhao, Guang-Hui; Li, Juan; Zou, Feng-Cai; Liu, Wei; Wu, Xiang-Yun; Lin, Rui-Qing; Weng, Ya-Biao; Zhu, Xing-Quan

2011-06-01

94

Genetic polymorphism of IL-12 p40 gene in immune-mediated disease.  

PubMed

Understanding of the genetic basis of autoimmune diseases is currently incomplete. Cytokine gene polymorphisms warrant consideration as factors explaining variation in the human immune and inflammatory responses and as candidate susceptibility genes for related pathological states. Interleukin 12 (IL-12) is a key regulator of the polarisation of immune responses to T helper 1 or 2 categories and plays a role in autoimmune and infectious diseases. Using a bioinformatic strategy, we aligned cDNA and expressed sequence tag sequences to identify putative polymorphic regions of the IL-12 p40 gene. Position 1188 in the 3' untranslated region (UTR) was polymorphic with the frequency of the common allele around 80% in healthy UK Caucasoids. PCR genotyping of multiple Caucasoid groups and an African group showed significant population variation. In a case-control design, the polymorphism was not associated with rheumatoid arthritis, Felty's syndrome or large granular lymphocyte syndrome with arthritis or multiple sclerosis. A nonsignificant increase in the B allele frequency was observed in the rare large granular lymphocyte syndrome without arthritis (odds ratio 2.02 95% CI 0.95-4.3). This new genetic marker could be useful in anthropological studies and should be investigated in other autoimmune, allergic, inflammatory and infectious diseases. PMID:11196715

Hall, M A; McGlinn, E; Coakley, G; Fisher, S A; Boki, K; Middleton, D; Kaklamani, E; Moutsopoulos, H; Loughran, T P; Ollier, W E; Panayi, G S; Lanchbury, J S

2000-02-01

95

Investigation of Genetic Polymorphisms Related to the Outcome of Radiotherapy for Prostate Cancer Patients  

PubMed Central

The purpose of this study was to evaluate the association between ATM, TP53 and MDM2 polymorphisms in prostate cancer patients and morbidity after radiotherapy. The presence of ATM (rs1801516), TP53 (rs1042522, rs1800371, rs17878362, rs17883323, and rs35117667), and MDM2 (rs2279744) polymorphisms was assessed by direct sequencing of PCR fragments from 48 patients with histologically proven prostate adenocarcinoma and treated with external beam radiation. The side effects were classified according to the Radiation Therapy Oncology Group (RTOG) score. The results showed no association between clinical characteristics and the development of radiation toxicities (P > 0.05). The C>T transition in the position 16273 (intron 3) of TP53 (rs35117667) was significantly associated with the risk of acute skin toxicity (OR: 0.0072, 95% CI 0.00020.227, P = 0.003). The intronic TP53 polymorphism at position 16250 (rs17883323) was associated with chronic urinary toxicity (OR: 0.071, 95%CI 0.0060.784, P = 0.032). No significant associations were found for the remaining polymorphisms (P > 0.05). The results show that clinical characteristics were not determinant on the developing of radiation sensitivity in prostate cancer patients, and intronic TP53 polymorphisms would be associated with increased acute and chronic radiation toxicities. These observations corroborate the importance of investigating the genetic profile to predict adverse side effects in patients undergoing radiotherapy. PMID:24324286

Cintra, Hellen Silva; Pinezi, Juliana Castro Dourado; Machado, Graziella Dias Pinheiro; de Carvalho, Gustavo Moura; Carvalho, Ana Terra Silva; dos Santos, Thalles Eduardo Dias; Marciano, Ricardo Duarte; Soares, Renata de Bastos Ascenco

2013-01-01

96

Polymorphism, Genetic Effect and Association with Egg Production Traits of Chicken Matrix Metalloproteinases 9 Promoter  

PubMed Central

Matrix metalloproteinases (MMP) are key enzymes involved in cell and tissue remodeling during ovarian follicle development and ovulation. The control of MMP9 transcription in ovarian follicles occurs through a core promoter region (?2,400 to ?1,700 bp). The aim of this study was to screen genetic variations in the core promoter region and examine MMP9 transcription regulation and reproduction performance. A single cytosine deletion/insertion polymorphism was found at ?1954 C+/C?. Genetic association analysis indicated significant correlation between the deletion genotype (C?) with total egg numbers at 28 weeks (p = 0.031). Furthermore, luciferase-reporter assay showed the deletion genotype (C?) had significantly lower promoter activity than the insertion genotype (C+) in primary granulosa cells (p<0.01). Therefore, the identified polymorphism could be used for marker-assisted selection to improve chicken laying performance. PMID:25358310

Zhu, Guiyu; Jiang, Yunliang

2014-01-01

97

Polymorphism-screening: genetic testing for predispositionguidance for technology assessment  

Microsoft Academic Search

Health policy is increasingly confronted with the demand for financing genetic testing on inherited susceptibility to disease.\\u000a Tests on polymorphism\\/SNP associated with multicausal and chronic conditions are already offered in private commercial institutions\\u000a or in academic hospitals. The increasing pressure on public health services to offer SNP testing leads to first methodological\\u000a approaches for a generally valid regulatory framework applicable

Claudia Wild

2008-01-01

98

PERMANENT GENETIC RESOURCES: Ten polymorphic microsatellite markers for the pygmy rabbit (Brachylagus idahoensis).  

PubMed

We developed 10 polymorphic microsatellite loci for the pygmy rabbit (Brachylagus idahoensis). Nine of the 10 loci amplified reliably and had a low frequency of null alleles. Number of alleles per locus ranged from four to 12, and observed and expected heterozygosities ranged from 0.26 to 0.89 and from 0.63 to 0.88, respectively. These loci will be useful in determining population genetic structure and assessing patterns of gene flow in the pygmy rabbit. PMID:21585792

Estes-Zumpf, Wendy A; Rachlow, Janet L; Waits, Lisette P

2008-03-01

99

Genetic polymorphism of enzymes involved in xenobiotic metabolism and the risk of lung cancer  

Microsoft Academic Search

Chronic inhalation of cigarette smoke is a major risk factor for the development of lung cancer. It has been suggested that\\u000a genetic susceptibility may contribute to the risk, because only a small portion of smokers develops the disease. Several polymorphisms\\u000a that involve the metabolic activation or detoxification of carcinogens derived from cigarette smoke have been found to be\\u000a associated with

Chikako Kiyohara; Taro Shirakawa; Julian M. Hopkin

2002-01-01

100

Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms  

Microsoft Academic Search

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),

W. Scott Watkins; Alan R. Rogers; Christopher T. Ostler; Steve Wooding; Michael J. Bamshad; Anna-Marie E. Brassington; Marion L. Carroll; Son V. Nguyen; Jerilyn A. Walker; B. V. Ravi Prasad; P. Govinda Reddy; Pradipta K. Das; Mark A. Batzer; Lynn B. Jorde

2003-01-01

101

Genetic effect of CysLTR2 polymorphisms on its mRNA synthesis and stabilization  

Microsoft Academic Search

BACKGROUND: We previously demonstrated that single nucleotide polymorphism (SNP) and haplotypes were associated with aspirin hypersensitivity in asthmatics. We investigated the genetic effects of the SNPs and haplotypes on the expression of the CysLTR2 gene. METHODS: We measured CysLTR2 protein and mRNA expression in EB virus-infected B cell lines from asthmatics having ht1+\\/+ and ht2+\\/+. A gel retardation assay was

Jeong-Ah Shin; Hun Soo Chang; Se-Min Park; An-Soo Jang; Sung Woo Park; Jong Sook Park; Soo-Taek Uh; Gune Il Lim; Taiyoun Rhim; Mi-Kyeong Kim; Inseon S Choi; Il Yup Chung; Byung Lae Park; Hyoung Doo Shin; Choon-Sik Park

2009-01-01

102

Genetic polymorphism of thiopurine methyltransferase and its clinical relevance for childhood acute lymphoblastic leukemia  

Microsoft Academic Search

Thiopurine methyltransferase (TPMT) catalyses the S-methylation of thiopurines, including 6-mercaptopurine and 6-thioguanine. TPMT activity exhibits genetic polymorphism, with about 1\\/300 inheriting TPMT deficiency as an autosomal recessive trait. If treated with standard doses of thiopurines, TPMT-deficient patients accumulate excessive thioguanine nucleotides in hematopoietic tissues, leading to severe hematological toxicity that can be fatal. However, TPMT-deficient patients can be successfully treated

HL McLeod; EY Krynetski; MV Relling; WE Evans

2000-01-01

103

High altitude hypoxia environment changes of the content of RAAS and ACE2 Genetics polymorphisms  

Microsoft Academic Search

Objective To study the function of the rennin- angiotensin-aldoterone system(RAAS) under high altitude hypoxia environment and objective to investigate the effects of high altitude hypoxia on the angiotensin conversion enzyme 2(ACE2) Genetics polymorphisms. Methods Forty male adult Sprague Dawley( SD) rats, under high altitude hypoxia environment were divided randomly into 4 groups: the control group(D group, Xi'an area 5m above

Wenhua Li; Liu Zhong

2011-01-01

104

Genetic diversity in coconut (Cocos nucifera L.) revealed by restriction fragment length polymorphism (RFLP) markers  

Microsoft Academic Search

A study of the genetic diversity in coconut by RFLP analysis was performed in 100 individuals representing 10 Tall and seven\\u000a Dwarf local populations or 'ecotypes' from various geographical origins. Nine cDNA clones from rice, one mitochondrial DNA\\u000a clone (CoxI) and one genomic clone (rDNA) from wheat were used as probe for southern hybridization. The distribution of the\\u000a 40 polymorphic

P. Lebrun; Y. P. N'cho; M. Seguin; L. Grivet; L. Baudouin

1998-01-01

105

Morphological, genetic, and chemical polymorphism of Curcuma kwangsiensis.  

PubMed

Previously, Chinese gajutsu available in Japan was identified, from the chloroplast trnK gene sequence, to be the rhizomes of Curcuma phaeocaulis and two genotypes of C. kwangsiensis. Although we defined the two genotypes, the pl and gl types, on the basis of the nucleotide difference, their external features did not correspond to the two phenotypes described in the literature. In this paper, to investigate the relationship between genotype and phenotype of C. kwangsiensis, a field investigation was carried out in its main cultivation areas of Guangxi Zhuangzu Autonomous Region and Guangdong Province, China, and sequence analysis of the trnK gene and single-nucleotide polymorphism (SNP) analysis of the nuclear 18S rRNA gene were performed on the collected specimens. Four genotypes of C. kwangsiensis were recognized from the combined 18S rRNA gene-trnK gene sequences: homozygote-K(gl)Wtk type, homozygote-K(pl)Ztk type, heterozygote-K(gl)Wtk type, and heterozygote-Ltk type. Among the four genotypes, C. kwangsiensis in a field used for cultivation of gajutsu was of heterozygote-K(gl)Wtk type. Formation of a heterozygote in the 18S rRNA gene might be a result of crossbreeding of C. kwangsiensis with several Curcuma species which had cytosine at nucleotide position 234. GC analysis of the rhizomes revealed that C. kwangsiensis was characterized by camphor and beta-elemene, and by detecting additional components such as curdione and curcumenol Curcuma species involved in the formation of the heterozygote might be speculated upon. PMID:18633691

Komatsu, Katsuko; Sasaki, Yohei; Tanaka, Ken; Kuba, Yoshiaki; Fushimi, Hirotoshi; Cai, Shao-Qing

2008-10-01

106

The genetic polymorphism linked to mate-securing strategies in the male damselfly Mnais costalis Selys (Odonata: Calopterygidae)  

Microsoft Academic Search

Alternative male mate-securing strategies are widespread among animal taxa, but there are few well-documented examples of genetic polymorphisms for them. In the Japanese calopterygid damselfly Mnais costalis, males occur as either orange-winged territorial fighter males, or clear-winged non-territorial sneaker males. It has previously been suggested that this behavioral polymorphism is genetically controlled. However, there was no direct evidence for this.

Yoshitaka Tsubaki

2003-01-01

107

Ethnical disparities of prostate cancer predisposition: genetic polymorphisms in androgen-related genes  

PubMed Central

Prostate cancer (PCa) is the most commonly diagnosed male malignancy and the second biggest cause of cancer death in men of the Western world. Higher incidences of PCa occur in men from North America, Oceania and Western countries, whereas men from Asia and North Africa have a much lower PCa incidence rate. Investigations into this population disparity of PCa incidence, in order to identify potential preventive factors or targets for the therapeutic intervention of PCa, have found differences in both environmental and genetic variations between these populations. Environmental variations include both diet and lifestyle, which vary widely between populations. Evidence that diet comes into play has been shown by men who immigrate from Eastern to Western countries. PCa incidence in these men is higher than men in their native countries. However the number of immigrants developing PCa still doesnt match native black/white men, therefore genetic factors also contribute to PCa risk, which are supported by familial studies. There are a number of genetic polymorphisms that are differentially presented between Western and Eastern men, which are potentially associated with PCa incidence. Androgen and its receptor (AR) play a major role in PCa development and progression. In this study, we focus on genes involved in androgen biosynthesis and metabolism, as well as those associated with AR pathway, whose polymorphisms affect androgen level and biological or physiological functions of androgen. While many of the genetic polymorphisms in this androgen/AR system showed different frequencies between populations, contradictory evidences exist for most of these genes investigated individually as to the true contribution to PCa risk. More accurate measurements of androgen activity within the prostate are required and further studies need to include more African and Asian subjects. As many of these genetic polymorphisms may contribute to different steps in the same biological/physiological function of androgen and AR pathway, an integrated analysis considering the combined effect of all the genetic polymorphisms may be necessary to assess their contribution to PCa initiation and progression. PMID:23593537

Li, Jie; Mercer, Emma; Gou, Xin; Lu, Yong-Jie

2013-01-01

108

The Roles of Genetic Polymorphisms and Human Immunodeficiency Virus Infection in Lipid Metabolism  

PubMed Central

Dyslipidemia has been frequently observed among individuals infected with human immunodeficiency virus type 1 (HIV-1), and factors related to HIV-1, the host, and antiretroviral therapy (ART) are involved in this phenomenon. This study reviews the roles of genetic polymorphisms, HIV-1 infection, and highly active antiretroviral therapy (HAART) in lipid metabolism. Lipid abnormalities can vary according to the HAART regimen, such as those with protease inhibitors (PIs). However, genetic factors may also be involved in dyslipidemia because not all patients receiving the same HAART regimen and with comparable demographic, virological, and immunological characteristics develop variations in the lipid profile. Polymorphisms in a large number of genes are involved in the synthesis of structural proteins, and enzymes related to lipid metabolism account for variations in the lipid profile of each individual. As some genetic polymorphisms may cause dyslipidemia, these allele variants should be investigated in HIV-1-infected patients to identify individuals with an increased risk of developing dyslipidemia during treatment with HAART, particularly during therapy with PIs. This knowledge may guide individualized treatment decisions and lead to the development of new therapeutic targets for the treatment of dyslipidemia in these patients. PMID:24319689

de Almeida, Elaine Regina Delicato; Reiche, Edna Maria Vissoci; Flauzino, Tamires; Watanabe, Maria Angelica Ehara

2013-01-01

109

Relationships of FOXE1 and ATM genetic polymorphisms with papillary thyroid carcinoma risk: a meta-analysis.  

PubMed

We conducted the meta-analysis of all relevant case-control studies aiming to evaluate the relationships of common polymorphisms in forkhead box E1 (FOXE1) and ataxia telangiectasia mutated (ATM) genes to the risk of papillary thyroid carcinoma (PTC). A range of electronic databases were searched without language restrictions: Web of Science (1945 ~ 2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966 ~ 2013), EMBASE (1980 ~ 2013), CINAHL (1982 ~ 2013), and the Chinese Biomedical Database (CBM) (1982 ~ 2013). This meta-analysis was conducted using the STATA 12.0 software. Crude odds ratio (OR) with their 95 % confidence interval (CI) were calculated. Eight case-control studies with 2,085 PTC patients and 10,341 healthy controls were included. Fourteen common polymorphisms were evaluated, including rs3758249 A > G, rs907577 G > A, rs1867277 G > A, rs3021526 C > T, rs1443434 G > T, rs907580 G > A, rs965513 A > G, rs944289 C > T, and rs189037 G > A polymorphisms in the FOXE1 gene and rs373759 G > A, rs4988099 A > G, rs1801516 G > A, rs664677 T > C, and rs609429 G > C polymorphisms in the ATM gene. Our results demonstrated that the FOXE genetic polymorphisms might be closely related to an increased risk of developing PTC under five genetic models (all P < 0.005), especially for rs3758249, rs907577, rs1867277, rs3021526, rs1443434, rs907580, rs704839, rs894673, and rs10119760 polymorphisms. Nevertheless, no positive associations were found between the ATM genetic polymorphisms and the development of PTC (all P > 0.05). The current meta-analysis provided evidence that FOXE1 genetic polymorphisms may contribute to increased PTC risk, especially for rs3758249, rs907577, rs1867277, rs3021526, rs1443434, rs907580, rs704839, rs894673, and rs10119760 polymorphisms. However, the ATM genetic polymorphisms may not be important dominants of susceptibility to PTC. PMID:24756757

Kang, Jie; Deng, Xian-Zhao; Fan, You-Ben; Wu, Bo

2014-07-01

110

Genetic Analysis of 430 Chinese Cynodon dactylon Accessions Using Sequence-Related Amplified Polymorphism Markers.  

PubMed

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260-1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53-0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars. PMID:25338051

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-01-01

111

Genetic Analysis of 430 Chinese Cynodon dactylon Accessions Using Sequence-Related Amplified Polymorphism Markers  

PubMed Central

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 2601800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.530.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars. PMID:25338051

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-01-01

112

The genetic relationship among Iranian ethnic groups: an anthropological view based on HLA class II gene polymorphism.  

PubMed

Highly polymorphic human leukocyte antigen (HLA) genes are considered as useful markers by molecular anthropologists to determine genetic relationship among populations. This review summarizes the results of molecular analyses of HLA class II gene polymorphism in 816 DNA samples from 11 Iranian ethnic groups. The genetic relationship of Iranians to Asians and Europeans has also been reported here. The results of this study revealed a close genetic relationship among Iranian subpopulations which were well separated from other Asian and European populations, however, a genetic similarity was observed among Iranians, Macedonians, Greeks, and Italians. PMID:18979226

Farjadian, Shirin; Ota, Massao; Inoko, Hidetoshi; Ghaderi, Abbas

2009-09-01

113

COMT val158met and 5-HTTLPR genetic polymorphisms moderate executive control in cannabis users.  

PubMed

The adverse effects of cannabis use on executive functions are still controversial, fostering the need for novel biomarkers able to unveil individual differences in the cognitive impact of cannabis consumption. Two common genetic polymorphisms have been linked to the neuroadaptive impact of ?9-tetrahydrocannabinol (THC) exposure and to executive functions in animals: the catechol-O-methyltransferase (COMT) gene val158met polymorphism and the SLC6A4 gene 5-HTTLPR polymorphism. We aimed to test if these polymorphisms moderate the harmful effects of cannabis use on executive function in young cannabis users. We recruited 144 participants: 86 cannabis users and 58 non-drug user controls. Both groups were genotyped and matched for genetic makeup, sex, age, education, and IQ. We used a computerized neuropsychological battery to assess different aspects of executive functions: sustained attention (CANTAB Rapid Visual Information Processing Test, RVIP), working memory (N-back), monitoring/shifting (CANTAB ID/ED set shifting), planning (CANTAB Stockings of Cambridge, SOC), and decision-making (Iowa Gambling Task, IGT). We used general linear model-based analyses to test performance differences between cannabis users and controls as a function of genotypes. We found that: (i) daily cannabis use is not associated with executive function deficits; and (ii) COMT val158met and 5-HTTLPR polymorphisms moderate the link between cannabis use and executive performance. Cannabis users carrying the COMT val/val genotype exhibited lower accuracy of sustained attention, associated with a more strict response bias, than val/val non-users. Cannabis users carrying the COMT val allele also committed more monitoring/shifting errors than cannabis users carrying the met/met genotype. Finally, cannabis users carrying the 5-HTTLPR s/s genotype had worse IGT performance than s/s non-users. COMT and SLC6A4 genes moderate the impact of cannabis use on executive functions. PMID:23449176

Verdejo-Garca, Antonio; Fagundo, Ana Beatriz; Cuenca, Aida; Rodriguez, Joan; Cuys, Elisabet; Langohr, Klaus; de Sola Llopis, Susana; Civit, Ester; Farr, Mag; Pea-Casanova, Jordi; de la Torre, Rafael

2013-07-01

114

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

PubMed Central

Background 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. Methods 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. Results 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. Conclusions 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. PMID:22380592

2012-01-01

115

Mycoplasma hominis in Cuban Trichomonas vaginalis isolates: association with parasite genetic polymorphism.  

PubMed

Trichomonas vaginalis can be naturally infected with intracellular Mycoplasma hominis. This bacterial infection may have implications for trichomonal virulence and disease pathogenesis. The objective of the study was to report the presence of M. hominis in Cuban T. vaginalis isolates and to describe the association between the phenotype M. hominis infected with RAPD genetic polymorphism of T. vaginalis. The Random Amplified Polymorphic DNA (RAPD) technique was used to determine genetic differences among 40 isolates of T. vaginalis using a panel of 30 random primers and these genetic data were correlated with the infection of isolates with M. hominis. The trees drawn based on RAPD data showed no relations with metronidazole susceptibility and significantly association with the presence of M. hominis (P=0.043), which demonstrates the existence of concordance between the genetic relatedness and the presence of M. hominis in T. vaginalis isolates. This result could point to a predisposition of T. vaginalis for the bacterial enters and/or survival. PMID:22584035

Fraga, Jorge; Rodrguez, Nadia; Fernndez, Carmen; Mondeja, Brian; Sariego, Idalia; Fernndez-Calienes, Aym; Rojas, Lazara

2012-07-01

116

Random Amplified Polymorphic Markers as Indicator for Genetic Conservation Program in Iranian Pheasant (Phasianus colchicus)  

PubMed Central

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

117

Random amplified polymorphic markers as indicator for genetic conservation program in Iranian pheasant (Phasianus colchicus).  

PubMed

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

118

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers.  

PubMed

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity. PMID:16734682

SanCristobal, M; Chevalet, C; Peleman, J; Heuven, H; Brugmans, B; van Schriek, M; Joosten, R; Rattink, A P; Harlizius, B; Groenen, M A M; Amigues, Y; Boscher, M-Y; Russell, G; Law, A; Davoli, R; Russo, V; Dsauts, C; Alderson, L; Fimland, E; Bagga, M; Delgado, J V; Vega-Pla, J L; Martinez, A M; Ramos, M; Glodek, P; Meyer, J N; Gandini, G; Matassino, D; Siggens, K; Laval, G; Archibald, A; Milan, D; Hammond, K; Cardellino, R; Haley, C; Plastow, G

2006-06-01

119

Typhoid fever and genetic polymorphisms at the natural resistance-associated macrophage protein 1.  

PubMed

Control of Salmonella enterica serovar Typhimurium (S. typhimurium) infection in the mouse model of typhoid fever is critically dependent on the natural resistance-associated macrophage protein 1 (Nramp1). In this study, we examined the role of genetic polymorphisms in the human homologue, NRAMP1, in resistance to typhoid fever in southern Vietnam. Patients with blood-culture-confirmed typhoid fever and healthy control subjects were genotyped for 6 polymorphic markers within and near NRAMP1 on chromosome 2q35. Four single base-pair polymorphisms (274 C/T, 469+14 G/C, 1465-85 G/A, and D543N), a (GT)(n) repeat in the promoter region of NRAMP1 and D2S1471, and a microsatellite marker approximately 130-kb downstream of NRAMP1 were examined. The allelic and genotypic frequencies for each polymorphism were compared in case patients and control subjects. No allelic association was identified between the NRAMP1 alleles and typhoid fever susceptibility. In addition, neither homozygotes nor heterozygotes for any NRAMP1 variants were at increased risk of typhoid fever. PMID:11237848

Dunstan, S J; Ho, V A; Duc, C M; Lanh, M N; Phuong, C X; Luxemburger, C; Wain, J; Dudbridge, F; Peacock, C S; House, D; Parry, C; Hien, T T; Dougan, G; Farrar, J; Blackwell, J M

2001-04-01

120

Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism.  

PubMed

Hypsizygus marmoreus is an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis of H. marmoreus sequences from GenBank database. The genomic DNA extracted from H. marmoreus was amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains of H. marmoreus were classified into two main groups. PMID:25013861

Qiu, Chengshu; Yan, Wenjuan; Deng, Wangqiu; Song, Bin; Li, Taihui

2014-01-01

121

Genetic Diversity Analysis of Hypsizygus marmoreus with Target Region Amplification Polymorphism  

PubMed Central

Hypsizygus marmoreus is an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis of H. marmoreus sequences from GenBank database. The genomic DNA extracted from H. marmoreus was amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains of H. marmoreus were classified into two main groups. PMID:25013861

Qiu, Chengshu; Yan, Wenjuan; Deng, Wangqiu; Song, Bin; Li, Taihui

2014-01-01

122

Transcriptomics and functional genetic polymorphisms as biomarkers of micronutrient function: focus on selenium as an exemplar.  

PubMed

Micronutrients are essential for optimal human health. However, in some cases, raising intake by supplementation has not proven to be beneficial and there is even some evidence that supplementation may increase disease risk, highlighting the importance of assessing the functional status of micronutrients. Techniques such as gene microarrays and single-nucleotide polymorphism analysis have the potential to examine effects of micronutrient intake on patterns of gene expression and inter-individual variation in micronutrient metabolism. Recent genomic research related to selenium (Se) provides examples illustrating how studies of functional single-nucleotide polymorphism and gene expression patterns can reveal novel biomarkers of micronutrient function. Both in vitro and in vivo experiments show that there are functionally relevant polymorphisms in genes encoding glutathione peroxidases 1, 3 and 4, selenoprotein P, selenoprotein S and the 15 kDa selenoprotein. Disease association studies investigating these gene variants have so far been relatively small but an association of a polymorphism in the selenoprotein S gene with colorectal cancer risk has been replicated in two distinct populations. Future disease association studies should examine effects of multiple variants in combination with nutritional status. Gene microarray studies indicate that changes in Se intake alter expression of components of inflammatory, stress response and translation pathways. Our hypothesis is that Se intake and genetic factors have linked effects on stress response, inflammation and apoptotic pathways. Combining such data in a systems biology approach has the potential to identify both biomarkers of micronutrients status and sub-group populations at particular risk. PMID:21557886

Hesketh, John; Mplan, Catherine

2011-05-01

123

Correlation between cystathionine ?-synthase T883C genetic polymorphism and primary hypertension  

PubMed Central

The present study aimed to investigate the correlation between cystathionine ?-synthase (CBS) T833C polymorphisms and primary hypertension. A case-control study was conducted by genotyping the representative variation in 545 hypertensive individuals (aged 49.237.56 years) and 500 normotensive individuals (aged 49.9010.01 years). The T833C genetic polymorphisms of the CBS enzyme were detected in all subjects by amplification refractory mutation system polymerase chain reaction (PCR) analysis. The CBS T833C polymorphism was successfully genotyped in the general population with a sample size of 1,045 (545+500) individuals. The genotypic and allelic frequency distributions of the CBS T833C polymorphism were not significantly different between the hypertensive and normotensive groups (P>0.05). The CC genotype was significantly different (P<0.05) from the CT and TT genotypes in terms of body mass index (BMI), and the levels of triglycerides (TG) and homocysteine (Hcy). Multiple logistic regression analysis revealed that BMI, total cholesterol (TC) level, smoking, plasma Hcy level and a family history of hypertension were the independent risk factors for hypertension in the population studied. The results indicate that the level of plasma Hcy was a risk factor for hypertension in the population studied. However, the mutation of the CBS T833C gene was not concluded to be an important hereditary factor for influencing the level of plasma Hcy. PMID:25120587

ZHANG, YING; WANG, HONG; SUN, HUAN-WEN; CHEN, YU-LAN; OUYANG, JU-YAN; WANG, YU; WANG, LING; ZHANG, XIANG-YANG

2014-01-01

124

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

PubMed Central

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 geneenvironment, genegene, and environmentenvironment interactions. Currently, there is great inconsistency among studies mainly due to differences in genetic background and unique geneenvironment 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. PMID:23776356

Gao, Zhiwei; Rennie, Donna C; Senthilselvan, Ambikaipakan

2010-01-01

125

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

PubMed

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%). PMID:24688285

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

2014-03-01

126

Polymorphisms of interleukin 18 in the genetics of preterm birth and bronchopulmonary dysplasia.  

PubMed

Interleukin 18 (IL-18) is an important cytokine and involved in the pathogenesis and genetics of many diseases. The authors studied two different populations of preterm infants to test whether polymorphisms within IL-18 are in association with prematurity itself or with typical pulmonary disease or measurements seen in preterm infants, such as bronchopulmonary dysplasia, pneumothoraces and application of surfactant, inhalation or mechanical ventilation. Whereas the first population of 228 preterm infants showed strong association of IL-18 with preterm birth (p<0.001), this was not confirmed in the second population of 346 preterm infants. In addition, no association with any lung condition of prematurity was observed. The authors conclude that IL-18 does not play an important role in the genetics of preterm birth nor in the development of bronchopulmonary dysplasia and other lung complications in preterm infants. Caution must be taken in the interpretation of the results of genetic association studies performed in one population. PMID:20971720

Krueger, M; Heinzmann, A; Mailaparambil, B; Hrtel, C; Gpel, W

2011-07-01

127

[Pearl Harbor.  

ERIC Educational Resources Information Center

This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor, and with a

Johnson, Jennifer, Ed.

1992-01-01

128

A Genetic Map of Lettuce (Lactuca sativa L.) With Restriction Fragment Length Polymorphism, Isozyme, Disease Resistance and Morphological Markers  

Microsoft Academic Search

A detailed linkage map of lettuce was constructed using 53 genetic markers including 4 1 restriction fragment length polymorphism (RFLP) loci, five downy mildew resistance genes, four isozyme loci and three morphological markers. The genetic markers were distributed into nine linkage groups and cover 404 cM which may be 25-30% of the lettuce genome. The majority (31 of 34) of

Benoit S. Landry; Rick V. Kesseli; Barry Farrara; Richard W. Michelmore

1987-01-01

129

Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes.  

PubMed Central

We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor necrosis factor (TNF) locus. TNFc is located within the first intron of the TNF-beta gene and has only 2 alleles. TNFa and TNFb are 3.5 kilobases upstream (telomeric) of the TNF-beta gene and have at least 13 and 7 alleles, respectively. TNFa, -b, and -c alleles are in linkage disequilibrium with alleles at other loci within the MHC, including class I, class II, and class III. TNFa, -b, and -c alleles are also associated with extended HLA haplotypes. These TNF polymorphisms will allow a thorough genetic analysis of the involvement of TNF in MHC-linked pathologies. Images PMID:1946393

Jongeneel, C V; Briant, L; Udalova, I A; Sevin, A; Nedospasov, S A; Cambon-Thomsen, A

1991-01-01

130

Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker.  

PubMed

Genetic diversity and interrelationships among 31 lentil genotypes were evaluated using 10 Inter-Simple Sequence Repeat (ISSR) and 10 directed amplification of minisatellite DNA region (DAMD) primers. A total of 43 and 48 polymorphic bands were amplified by ISSR and DAMD markers, respectively. Average polymorphism information content (PIC) for ISSR and DAMD markers were 0.37 and 0.41, respectively. All 31 lentil genotypes could be distinguished by ISSR markers into three groups and by DAMD markers into two groups. Various molecular markers show a different efficiency for evaluating DNA polymorphism in lentil and indicate that the patterns of variation are clearly influenced by the genetic marker used. Comparatively, the genetic diversity of examined lentil genotypes by two different marker techniques (ISSR and DAMD) was high and indicated that ISSR and DAMD are effective and promising marker systems for fingerprinting in lentil and give useful information on its genetic relationships. PMID:25320472

Seyedimoradi, Hiva; Talebi, Reza

2014-10-01

131

CCR5 gene polymorphism is a genetic risk factor for radiographic severity of rheumatoid arthritis.  

PubMed

The chemokine receptor [C-C chemokine receptor 5 (CCR5)] is expressed on diverse immune effecter cells and has been implicated in the pathogenesis of rheumatoid arthritis (RA). This study sought to determine whether single-nucleotide polymorphisms (SNPs) in the CCR5 gene and their haplotypes were associated with susceptibility to and severity of RA. Three hundred fifty-seven patients with RA and 383 healthy unrelated controls were recruited. Using a pyrosequencing assay, we examined four polymorphisms -1118 CTAT(ins) (/del) (rs10577983), 303 A>G (rs1799987), 927 C>T (rs1800024), and 4838 G>T (rs1800874) of the CCR5 gene, which were distributed over the promoter region as well as the 5' and 3' untranslated regions. No significant difference in the genotype, allele, and haplotype frequencies of the four selected SNPs was observed between RA patients and controls. CCR5 polymorphisms of -1118 CTAT(del) (P = 0.012; corrected P = 0.048) and 303 A>G (P = 0.012; corrected P = 0.048) showed a significant association with radiographic severity in a recessive model, and, as a result of multivariate logistic regression analysis, were found to be an independent predictor of radiographic severity. When we separated the erosion score from the total Sharp score, the statistical significance of CCR5 polymorphisms showed an increase; -1118 CTAT(ins) (/del) (P = 0.007; corrected P = 0.028) and 303 A>G (P = 0.007; corrected P = 0.028). Neither SNPs nor haplotypes of the CCR5 gene showed a significant association with joint space narrowing score. These results indicate that genetic polymorphisms of CCR5 are an independent risk factor for radiographic severity denoted by modified Sharp score, particularly joint erosion in RA. PMID:22924548

Han, S W; Sa, K H; Kim, S I; Lee, S I; Park, Y W; Lee, S S; Yoo, W H; Soe, J S; Nam, E J; Lee, J; Park, J Y; Kang, Y M

2012-11-01

132

Genetic Polymorphisms and the Risk of Accelerated Renal Function Decline in Women  

PubMed Central

Background Reduced glomerular filtration rate is an important predictor of cardiovascular disease and death. Genetic polymorphisms, particularly in genes involved in the renin-angiotensin system (RAS), may influence the rate of renal function decline. Methodology/Principal Findings We examined the relation between specific single nucleotide polymorphisms (SNPs), including those in the RAS, apolipoprotein E and alpha-adducin, and renal function decline assessed by estimated glomerular filtration rate (eGFR) over an 11-year period in 2578 Caucasian participants of the Nurses' Health Study. Logistic regression was used to examine the associations between genotype and risk of eGFR decline of ?25%. Results After 11 years between creatinine measurements, the eGFR declined by ?25% in 423 of 2578 (16%) women. The angiotensinogen (AGT) A-20C polymorphism was associated with a higher risk of renal function decline when two risk alleles were present than if one or no alleles were present (CC vs AA and AC) OR 1.83 (95% CI 1.023.26; p?=?0.04). The angiotensin II type 1 receptor (AT1R) A1166C polymorphism was marginally associated with a higher risk of renal function decline when two risk alleles were present (CC vs AA, OR?=?1.41; 95% CI 0.982.01; p?=?0.06). The alpha-adducin G460W polymorphism was associated with a lower risk of renal function decline when any number of risk alleles were present (WG vs GG, OR?=?0.78, 95% CI 0.610.99, p?=?0.04; WW vs GG, OR?=?0.46; 95% CI 0.201.07, p?=?0.07). Linear regression analysis with change in eGFR as the outcome showed a larger decline of 3.5 (95% CI 0.5 to 6.4, p?=?0.02) ml/min/1.73 m2 in AGT A-20C CC homozygotes. No other polymorphisms were significantly associated with renal function decline or absolute change in eGFR over the study period. Conclusions Genetic variants in the angiotensinogen, angiotensin II type 1 receptor and alpha-adducin genes may contribute to loss of renal function in the general female Caucasian population. PMID:19274077

Cooper Worobey, Cynthia; Fisher, Naomi D. L.; Cox, David; Forman, John P.; Curhan, Gary C.

2009-01-01

133

Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam  

PubMed

Moringa oleifera is an important multipurpose tree introduced to Africa from India at the turn of this century. Despite limited knowledge of the levels of genetic diversity and relatedness of introduced populations, their utilization as a source of seed for planting is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for a selective breeding programme, genetic analysis of seven populations was performed using amplified fragment length polymorphism (AFLP) markers. The four pairs of AFLP primers (PstI/MseI) generated a total of 236 amplification products of which 157 (66.5%) were polymorphic between or within populations. Analysis of molecular variance (AMOVA) revealed significant differences between regions and populations, even though outcrossing perennial plants are expected to maintain most variation within populations. A phenetic tree illustrating relationships between populations suggested at least two sources of germplasm introductions of Kenya. The high levels of population differentiation detected suggest that provenance source is an important factor in the conservation and exploitation of M. oleifera genetic resources. PMID:10199008

Muluvi; Sprent; Soranzo; Provan; Odee; Folkard; McNicol; Powell

1999-03-01

134

The Significance of Genetic Polymorphisms within and between Founder Populations of Ceratitis capitata (Wied.) from Argentina  

PubMed Central

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

Basso, Alicia; Martinez, Laura; Manso, Fanny

2009-01-01

135

Closure of a genetic linkage map of human chromosome 7q with centromere and telomere polymorphisms  

SciTech Connect

The authors have constructed a 2.4-cM resolution genetic linkage map for chromosome 7q that is bounded by centromere and telomere polymorphisms and contains 66 loci (88 polymorphic systems), 38 of which are uniquely placed with odds for order of at least 1000:1. Ten genes are included in the map and 11 markers have heterozygosities of at least 70%. This map is the first to incorporate several highly informative markers derived from a telomere YAC clone HTY146 (locus D7S427), including HTY146c3 (HET 92%). The telomere locus markers span at least 200 kb of the 7q terminus and no crossovers within the physical confines of the locus were observed in approximately 240 jointly informative meioses. The sex-equal map length is 158 cM and the largest genetic interval between uniquely localized markers in this map is 11 cM. The female and male map lengths are 181 and 133 cM, respectively. The map is based on the CEPH reference pedigrees and includes over 4000 new genotypes, the previously reported data plus 29 allele systems from the published CEPH version 5 database, and was constructed using the program package CRI-MAP. This genetic linkage map can be considered a baseline map for 7q, and will be useful for defining the extent of chromosome deletions previously reported for breast and prostate cancers, for developing additional genetic maps such as index marker and 1-cM maps, and ultimately for developing a fully integrated genetic and physical map for this chromosome. 63 refs., 4 figs., 1 tab.

Helms, C.; Mishra, S.K.; Burgess, A.K.; Ramachandra, S.; Tierney, C.; Dorsey, D.; Donis-Keller, H. (Washington Univ. School of Medicine, St. Louis, MO (United States)); Riethman, H. (Wistar Institute, Philadelphia, PA (United States))

1992-12-01

136

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

PubMed Central

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 ?PT 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

2010-01-01

137

Association between genetic polymorphisms in the serotonergic system and comorbid personality disorders among patients with first-episode depression.  

PubMed

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. PMID:24344840

Bukh, Jens D; Bock, Camilla; Kessing, Lars V

2014-06-01

138

Relationships between genetic polymorphisms and transcriptional profiles for outcome prediction in anticancer agent treatment.  

PubMed

In the era of personal genomics, predicting the individual response to drug-treatment is a challenge of biomedical research. The aim of this study was to validate whether interaction information between genetic and transcriptional signatures are promising features to predict a drug response. Because drug resistance/susceptibilities result from the complex associations of genetic and transcriptional activities, we predicted the inter-relationships between genetic and transcriptional signatures. With this concept, captured genetic polymorphisms and transcriptional profiles were prepared in cancer samples. By splitting ninety-nine samples into a trial set (n = 30) and a test set (n = 69), the outperformance of relationship-focused model (0.84 of area under the curve in trial set, P = 2.90 x 10??) was presented in the trial set and validated in the test set, respectively. The prediction results of modeling show that considering the relationships between genetic and transcriptional features is an effective approach to determine outcome predictions of drug-treatment. PMID:21189162

Paik, Hyojung; Lee, Eunjung; Lee, Doheon

2010-12-01

139

Genetic polymorphisms of the renin-angiotensin system and the outcome of focal segmental glomerulosclerosis in children  

Microsoft Academic Search

Genetic polymorphisms of the renin-angiotensin system and the outcome of focal segmental glomerulosclerosis in children.BackgroundThe clinical course of primary focal segmental glomerulosclerosis (FSGS) in children is variable, with some patients having a much more rapidly progressing course than others. The purpose of our study was to compare the frequency of three polymorphisms of the renin-angiotensin system (RAS) in children with

Yaacov Frishberg; Rachel Becker-Cohen; David Halle; Elad Feigin; Bella Eisenstein; Raphael Halevy; Danny Lotan; Isam Juabeh; Nathan Ish-Shalom; Daniella Magen; Yigal Shvil; Levana Sinai-Treiman; Alfred Drukker

1998-01-01

140

Association of p53 genetic polymorphism (Arg72Pro) with estrogen receptor positive breast cancer risk in Japanese women  

Microsoft Academic Search

Since it is well established that inactivation of p53 is involved in pathogenesis of breast cancer, it seems to be reasonable to assume that p53 genetic polymorphism at codon 72 (p53Arg72Pro) which affects the function of p53 might have an influence on breast cancer risk. Thus, in the present study, we have studied the association of p53Arg72Pro polymorphism with breast

Chikako Noma; Yasuo Miyoshi; Tetsuya Taguchi; Yasuhiro Tamaki; Shinzaburo Noguchi

2004-01-01

141

Update on the Genetic Polymorphisms of Drug-Metabolizing Enzymes in Antiepileptic Drug Therapy  

PubMed Central

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.

Saruwatari, Junji; Ishitsu, Takateru; Nakagawa, Kazuko

2010-01-01

142

Construction of a Genetic Linkage Map Based on Amplified Fragment Length Polymorphism Markers and Development of Sequence-Tagged Site Markers for Marker-Assisted Selection of the Sporeless Trait in the Oyster Mushroom (Pleurotus eryngii)  

PubMed Central

A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Qul. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection. PMID:22210222

Ueda, Jun; Obatake, Yasushi; Murakami, Shigeyuki; Fukumasa, Yukitaka; Matsumoto, Teruyuki

2012-01-01

143

Construction of a genetic linkage map based on amplified fragment length polymorphism markers and development of sequence-tagged site markers for marker-assisted selection of the sporeless trait in the oyster mushroom (Pleurotus eryngii).  

PubMed

A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Qul. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection. PMID:22210222

Okuda, Yasuhito; Ueda, Jun; Obatake, Yasushi; Murakami, Shigeyuki; Fukumasa, Yukitaka; Matsumoto, Teruyuki

2012-03-01

144

16S rRNA Restriction Fragment Length Polymorphism Analysis of Bacterial Diversity as a Biomarker of Ecological Health in Polluted Sediments from New Bedford Harbor, Massachusetts, USA  

Microsoft Academic Search

A polymerase chain reaction (PCR)-based method was developed to compare bacterial diversity among environmental sites with varying degrees of anthropogenic impact. New Bedford Harbor, MA, a US Environmental Protection Agency-designated Superfund hazardous waste site, was studied to assess changes in bacterial diversity resulting from long-term inputs of organic and inorganic pollutants. Total DNA was extracted from surficial sediments sampled from

Jonathan J. Sorci; Joseph D. Paulauskis; Timothy E. Ford

1999-01-01

145

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean  

PubMed Central

Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364??G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93??JALO EEP558 and DOR364??BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041?cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop. PMID:22734675

2012-01-01

146

Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers.  

PubMed

Sequence-related amplified polymorphism (SRAP), amplified fragment length polymorphism (AFLP), and inter-simple sequence repeat (ISSR) markers were used to estimate the genetic diversity and relationships among Eucommia ulmoides cultivars in China. A total of 240, 192, and 150 DNA fragments were detected by 10 SRAP primer combinations, 10 AFLP primer combinations, and 10 ISSR primers, among which 89.2, 65.1, and 88.0% of the fragments were polymorphic, respectively. Cluster analysis revealed that Qinzhong No. 3, Xiaoyeci, Qinzhong No. 1, and Qinzhong No. 2 formed independent clusters. The other 15 cultivars exhibited two clusters. The results of this study will help in the selection of parents for both genome mapping and crossbreeding purposes. PMID:25366761

Li, Y; Wang, S H; Li, Z Q; Jin, C F; Liu, M H

2014-01-01

147

Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs.  

PubMed

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity. PMID:16740626

Foulley, J-L; van Schriek, M G M; Alderson, L; Amigues, Y; Bagga, M; Boscher, M-Y; Brugmans, B; Cardellino, R; Davoli, R; Delgado, J V; Fimland, E; Gandini, G C; Glodek, P; Groenen, M A M; Hammond, K; Harlizius, B; Heuven, H; Joosten, R; Martinez, A M; Matassino, D; Meyer, J-N; Peleman, J; Ramos, A M; Rattink, A P; Russo, V; Siggens, K W; Vega-Pla, J L; Ollivier, L

2006-01-01

148

UGT1A1 genetic polymorphisms, endogenous estrogen exposure, soy food intake, and endometrial cancer risk.  

PubMed

Estrogen exposures play a critical role in the development of endometrial cancer. Genetic variation in the estrogen metabolism UGT1A1 gene may modify the effect of estrogenic exposures on endometrial cancer risk. We tested this hypothesis in a population-based case-control study of 1,047 endometrial cancer cases and 1,035 controls who completed an in-person interview and were genotyped for the UGT1A1 polymorphisms rs2070959 (A/G), rs887829 (G/A), and rs8175347 (6/7 TA repeats). Estrogen exposure-related factors evaluated include menstrual characteristics, oral contraceptive use, body mass index, waist-hip ratio, and soy food intake. Conditional logistic regression was used to calculate odds ratios and 95% confidence intervals. The homozygote variant genotype (G/G) of the rs2070959 polymorphism was significantly associated with a reduced risk of endometrial cancer (odds ratio, 0.5; 95% confidence interval, 0.3-0.8). No significant associations between endometrial cancer risk and genotype were seen for the rs887829 and rs8175347 polymorphisms. Analysis of the joint effects of genotype and markers of estrogen exposure found the lowest risk of endometrial cancer among those with the homozygous variant genotype of the rs2070959 polymorphism and who were postmenopausal, had low body mass index, and had low soy food intake, although a test for multiplicative interaction was not significant. Taken together, these data suggest that the G/G genotype (rs2070959) in the UGT1A1 gene may decrease the risk of endometrial cancer and that this effect is most evident among women with low levels of endogenous estrogen exposure or with low soy food intake. PMID:18349273

Deming, Sandra L; Zheng, Wei; Xu, Wang-Hong; Cai, Qiuyin; Ruan, Zhixian; Xiang, Yong-Bing; Shu, Xiao-Ou

2008-03-01

149

No association between XRCC1 genetic polymorphisms and differentiated thyroid carcinoma risk: a meta-analysis.  

PubMed

The X-ray repair cross-complementing group 1 (XRCC1) gene belongs to the family of DNA repair genes. Polymorphisms in the XRCC1 gene, Arg399Gln, Arg194Trp and Arg280His, have been reported to have implications in differentiated thyroid carcinoma (DTC) susceptibility, but the results remain conflicting and no meta-analysis has been published. Therefore, we carried out a systematic review of the published epidemiology studies, aiming to assess the relationship between XRCC1 polymorphisms and susceptibility to DTC risk. We selected three databases, PubMed, EMBASE and CNKI, in which to search for published literature. With respect to DTC risk associated with XRCC1, combined odds ratios (ORs) and 95% confidence intervals (CI) were appropriately calculated on the basis of co-dominant, dominant and recessive models. To investigate different effects from specific race, subgroup analyses were carried out in Asian and Caucasian populations. Eight studies meeting the inclusion criteria were eventually selected for Arg399Gln (1,550 cases and 2,692 controls), five studies for Arg194Trp (858 cases and 1,394 controls) and five studies for Arg280His (1,237 cases and 2,267 controls). The combined results of the relevant studies exhibited that no significant associations with DTC risk were demonstrated for polymorphisms in XRCC1 Arg399Gln, Arg194Trp and Arg280His in all genetic models. Stratified analyses in Asian and Caucasian populations showed similar results. This meta-analysis arrives at a conclusion that the XRCC1 (Arg399Gln, Arg194Trp, Arg280His) polymorphisms appear to confer no risk for DTC. PMID:25086624

Li, Cuiping; Xiang, Xue; Zhou, Yang

2014-11-01

150

Methylenetetrahydrofolate reductase genetic polymorphisms and toxicity to 5-FU-based chemoradiation in rectal cancer  

PubMed Central

Background: There is a large degree of variation in tumour response and host toxicities associated with neoadjuvant chemoradiation for rectal cancer patients. We performed a complimentary pharmacogenetic study to investigate germline polymorphisms of genes involved in 5-fluorouracil (5-FU) and irinotecan pathways and their potential association with clinical outcomes and toxicities from neoadjuvant chemoradiation in patients with rectal cancer treated in a prospective genotype-directed study. Methods: The germline DNA of 131 patients was genotyped for 10 variants in TYMS, MTHFR, DPYD, UGT1A1, ABCC1 and SLCO1B1 genes. Ninety-six patients were treated with 5-FU/radiotherapy (RT) and 35 received 5-FU/RT/irinotecan. Relationships between genetic variants and adverse events, tumour response, overall and disease-free survivals were assessed. Results: MTHFR 1298A>C and MTHFR diplotypes (for 677C>T and 1298A>C) were associated with chemoradiation-related toxicity when 5-FU was used alone. MTHFR haplotypes (677C1298C) and diplotypes (CATA and TATA) showed, respectively, a protective and a negative effect on the incidence of severe diarrhoea or mucositis. No association was observed between genetic markers and drug response. Conclusion: MTHFR polymorphisms can potentially predict toxicity in patients treated with 5-FU as a single chemotherapeutic drug. PMID:22045187

Thomas, F; Motsinger-Reif, A A; Hoskins, J M; Dvorak, A; Roy, S; Alyasiri, A; Myerson, R J; Fleshman, J W; Tan, B R; McLeod, H L

2011-01-01

151

Fatal methadone toxicity: potential role of CYP3A4 genetic polymorphism.  

PubMed

Methadone is difficult to administer as a therapeutic agent because of a wide range of interindividual pharmacokinetics, likely due to genetic variability of the CYP450 enzymes responsible for metabolism to its principal metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP). CYP3A4 is one of the primary CYP450 isoforms responsible for the metabolism of methadone to EDDP in humans. The purpose of this study was to evaluate the role of CYP3A4 genetic polymorphisms in accidental methadone fatalities. A study cohort consisting of 136 methadone-only and 92 combined methadone/benzodiazepine fatalities was selected from cases investigated at the West Virginia and Kentucky Offices of the Chief Medical Examiner. Seven single nucleotide polymorphisms (SNPs) were genotyped within the CYP3A4 gene. Observed allelic and genotypic frequencies were compared with expected frequencies obtained from The National Center for Biotechnology Information dbSNP database. SNPs rs2242480 and rs2740574 demonstrated an apparent enrichment within the methadone-only overdose fatalities compared with the control group and the general population. This enrichment was not apparent in the methadone/benzodiazepine cases for these two SNPs. Our findings indicate that there may be two or more SNPs on the CYP3A4 gene that cause or contribute to the methadone poor metabolizer phenotype. PMID:25217544

Richards-Waugh, Lauren L; Primerano, Donald A; Dementieva, Yulia; Kraner, James C; Rankin, Gary O

2014-10-01

152

Impact of genetic polymorphisms on chemotherapy toxicity in childhood acute lymphoblastic leukemia  

PubMed Central

The efficacy of chemotherapy in pediatric acute lymphoblastic leukemia (ALL) patients has significantly increased in the last 20 years; as a result, the focus of research is slowly shifting from trying to increase survival rates to reduce chemotherapy-related toxicity. At the present time, the cornerstone of therapy for ALL is still formed by a reduced number of drugs with a highly toxic profile. In recent years, a number of genetic polymorphisms have been identified that can play a significant role in modifying the pharmacokinetics and pharmacodynamics of these drugs. The best example is that of the TPMT gene, whose genotyping is being incorporated to clinical practice in order to individualize doses of mercaptopurine. However, there are additional genes that are relevant for the metabolism, activity, and/or transport of other chemotherapy drugs that are widely use in ALL, such as methotrexate, cyclophosphamide, vincristine, L-asparaginase, etoposide, cytarabine, or cytotoxic antibiotics. These genes can also be affected by genetic alterations that could therefore have clinical consequences. In this review we will discuss recent data on this field, with special focus on those polymorphisms that could be used in clinical practice to tailor chemotherapy for ALL in order to reduce the occurrence of serious adverse effects. PMID:23189085

Gervasini, Guillermo; Vagace, Jose M.

2012-01-01

153

Genetic and Molecular Basis of QTL of Diabetes in Mouse: Genes and Polymorphisms  

PubMed Central

A systematic study has been conducted of all available reports in PubMed and OMIM (Online Mendelian Inheritance in Man) to examine the genetic and molecular basis of quantitative genetic loci (QTL) of diabetes with the main focus on genes and polymorphisms. The major question is, What can the QTL tell us? Specifically, we want to know whether those genome regions differ from other regions in terms of genes relevant to diabetes. Which genes are within those QTL regions, and, among them, which genes have already been linked to diabetes? whether more polymorphisms have been associated with diabetes in the QTL regions than in the non-QTL regions. Our search revealed a total of 9038 genes from 26 type 1 diabetes QTL, which cover 667,096,006 bp of the mouse genomic sequence. On one hand, a large number of candidate genes are in each of these QTL; on the other hand, we found that some obvious candidate genes of QTL have not yet been investigated. Thus, the comprehensive search of candidate genes for known QTL may provide unexpected benefit for identifying QTL genes for diabetes. PMID:19471607

Gao, Peng; Jiao, Yan; Xiong, Qing; Wang, Cong-Yi; Gerling, Ivan; Gu, Weikuan

2008-01-01

154

Genetic Polymorphisms in the Thioredoxin 2 (TXN2) Gene and Risk for Spina Bifida  

PubMed Central

TXN2 encodes human thioredoxin 2, a small redox protein important in cellular antioxidant defenses, as well as in the regulation of apoptosis. Txn2 knockout mice fail to complete neural tube closure by E10.5 and die in utero. We hypothesized that genetic variation in human TXN2 gene may alter the function of the encoded protein in a manner associated with an increased risk for neural tube defects (NTDs). A DNA re-sequencing effort of the human TXN2 gene was taken. After a variation in the promoter was identified, the transcriptional activity of different alleles was investigated. The possible association between these variations and the risk of spina bifida was further evaluated in a subset of samples obtained from a large population-based case-control study in California in two different ethnicity groups, non-Hispanic white and Hispanic white. We identified a novel promoter insertion polymorphism located 9 base pairs upstream of the transcription start site of exon 1(?9 insertion). The GA, G and GGGA insertions were associated with a marked decrease of transcriptional activity when overexpressed in both U2-OS (an osteosarcoma cell line) and 293 cells (derived from human embryonic kidney). Further analysis revealed that the GA insertion was associated with increased spina bifida risk for Hispanic whites. Our study revealed a novel Ins/Del polymorphism in the human TXN2 gene proximal promoter region that altered the transcriptional activity and is associated with spina bifida risk. This polymorphism may be a genetic modifier of spina bifida risk in this California population. PMID:19165900

Wen, Shu; Lu, Wei; Zhu, Huiping; Yang, Wei; Shaw, Gary M.; Lammer, Edward J.; Islam, Ana; Finnell, Richard H.

2010-01-01

155

Genetic diversity and structure of an estuarine fish ( Fundulus heteroclitus ) indigenous to sites associated with a highly contaminated urban harbor  

Microsoft Academic Search

Intense selection on isolated populations can cause loss of genetic diversity, which if persistent, reduces adaptive potential and increases extinction probability. Phenotypic evidence of inherited tolerance suggests that polychlorinated biphenyls (PCBs), have acted as strong selective agents on populations of a non-migratory fish, Fundulus heteroclitus, indigenous to heavily contaminated sites. To evaluate population genetic structure and test for effects of

Amy M. McMillan; Mark J. Bagley; Suzanne A. Jackson; Diane E. Nacci

2006-01-01

156

Genetic Diversity of Eurycoma longifolia Inferred from Single Nucleotide Polymorphisms1[w  

PubMed Central

Eurycoma longifolia Jack. is a treelet that grows in the forests of Southeast Asia and is widely used throughout the region because of its reported medicinal properties. Widespread harvesting of wild-grown trees has led to rapid thinning of natural populations, causing a potential decrease in genetic diversity among E. longifolia. Suitable genetic markers would be very useful for propagation and breeding programs to support conservation of this species, although no such markers currently exist. To meet this need, we have applied a genome complexity reduction strategy to identify a series of single nucleotide polymorphisms (SNPs) within the genomes of several E. longifolia accessions. We have found that the occurrence of these SNPs reflects the geographic origins of individual plants and can distinguish different natural populations. This work demonstrates the rapid development of molecular genetic markers in species for which little or no genomic sequence information is available. The SNP markers that we have developed in this study will also be useful for identifying genetic fingerprints that correlate with other properties of E. longifolia, such as high regenerability or the appearance of bioactive metabolites. PMID:12644679

Osman, Asiah; Jordan, Barbara; Lessard, Philip A.; Muhammad, Norwati; Haron, M. Rosli; Riffin, Norifiza Mat; Sinskey, Anthony J.; Rha, ChoKyun; Housman, David E.

2003-01-01

157

Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite  

PubMed Central

Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates. PMID:20813140

Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A.; Upcroft, Jacqui; Sullivan, Steven A.; Tachezy, Jan; Carlton, Jane M.

2010-01-01

158

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard ( Brassica juncea ) and its relationship to heterosis  

Microsoft Academic Search

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism

A. Jain; S. Bhatia; S. S. Banga; S. Prakash; M. Lakshmikumaran

1994-01-01

159

Genetic differentiation across the social transition in a socially polymorphic sweat bee, Halictus rubicundus.  

PubMed

Eusociality is widely considered a major evolutionary transition. The socially polymorphic sweat bee Halictus rubicundus, solitary in cooler regions of its Holarctic range and eusocial in warmer parts, is an excellent model organism to address this transition, and specifically the question of whether sociality is associated with a strong barrier to gene flow between phenotypically divergent populations. Mitochondrial DNA (COI) from specimens collected across the British Isles, where both solitary and social phenotypes are represented, displayed limited variation, but placed all specimens in the same European lineage; haplotype network analysis failed to differentiate solitary and social lineages. Microsatellite genetic variability was high and enabled us to quantify genetic differentiation among populations and social phenotypes across Great Britain and Ireland. Results from conceptually different analyses consistently showed greater genetic differentiation between geographically distant populations, independently of their social phenotype, suggesting that the two social forms are not reproductively isolated. A landscape genetic approach revealed significant isolation by distance (Mantel test r = 0.622, P < 0.001). The Irish Sea acts as physical barrier to gene flow (partial Mantel test r = 0.453, P < 0.01), indicating that geography, rather than expression of solitary or social behaviour (partial Mantel test r = -0.238, P = 0.053), had a significant effect on the genetic structure of H. rubicundus across the British Isles. Although we cannot reject the hypothesis of a genetic underpinning to differences in solitary and eusocial phenotypes, our data clearly demonstrate a lack of reproductive isolation between the two social forms. PMID:20666996

Soro, A; Field, J; Bridge, C; Cardinal, S C; Paxton, R J

2010-08-01

160

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.  

PubMed

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. PMID:24958856

Qi, Ji; Chen, Yamao; Copenhaver, Gregory P; Ma, Hong

2014-07-01

161

Frequency of genetic polymorphisms of ADAM33 and their association with allergic rhinitis among Jordanians.  

PubMed

Allergic rhinitis is a chronic inflammatory disease that is assumed to be due to an interaction between different genetic and/or environmental factors. A disintegrin and metalloprotease domain 33 (ADAM33) has been extensively studied as a susceptibility gene in asthma and has been linked to bronchial hyper-responsiveness. In this study, we investigated the association between ADAM33 single nucleotide polymorphisms and the incidence of allergic rhinitis among the Jordanian population. We conducted a case-control association study on 120 adult individuals diagnosed with allergic rhinitis and 128 normal healthy controls. 8 single-nucleotide polymorphisms in ADAM33 were genotyped using PCR-RFLP method. No significant differences in the allelic frequencies of all SNPs tested between AR patients and the control volunteers were found, although S2 C/G SNP showed a tendency toward significance with P=0.06. On the genotype level significant association were found in the following genotypes: T1 AA, T1 AG, T2 GG, T2 AG, T+1 GG, T+1 AG, V4 CG, S2 CC, S2 CG, Q-1AA. Seven haplotypes were present only within AR patients and eight haplotypes were completely absent from the AR patients. Three haplotypes exhibited significant association with AR P ? 0.05, two of them were present only in AR patients. In conclusion, the polymorphisms in the ADAM33 gene are associated with susceptibility to AR in the Jordanian population. Furthermore, the haplotype of the tested SNPs were also associated with the risk of AR. PMID:24035932

Zihlif, Malek; Mahafza, Tareq; Obeidat, Nathir M; Froukh, Tawfiq; Shaban, Mazen; Al-Akhras, Fatima M; Zihlif, Nadwa; Naffa, Randa

2013-12-01

162

Genetic polymorphisms of DNA double-strand break repair pathway genes and glioma susceptibility  

PubMed Central

Background Genetic variations in DNA double-strand break repair genes can influence the ability of a cell to repair damaged DNA and alter an individuals susceptibility to cancer. We studied whether polymorphisms in DNA double-strand break repair genes are associated with an increased risk of glioma development. Methods We genotyped 10 potentially functional single nucleotide polymorphisms (SNPs) in 7 DNA double-strand break repair pathway genes (XRCC3, BRCA2, RAG1, XRCC5, LIG4, XRCC4 and ATM) in a casecontrol study including 384 glioma patients and 384 cancer-free controls in a Chinese Han population. Genotypes were determined using the OpenArray platform. Results In the single-locus analysis there was a significant association between gliomas and the LIG4 rs1805388 (Ex2 +54C>T, Thr9Ile) TT genotype (adjusted OR, 3.27; 95% CI, 1.87-5.71), as well as the TC genotype (adjusted OR, 1.62; 95% CI, 1.20-2.18). We also found that the homozygous variant genotype (GG) of XRCC4 rs1805377 (IVS7-1A>G, splice-site) was associated with a significantly increased risk of gliomas (OR, 1.77; 95% CI, 1.12-2.80). Interestingly, we detected a significant additive and multiplicative interaction effect between the LIG4 rs1805388 and XRCC4 rs1805377 polymorphisms with an increasing risk of gliomas. When we stratified our analysis by smoking status, LIG4 rs1805388 was associated with an increased glioma risk among smokers. Conclusions These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs1805377, alone or in combination, are associated with a risk of gliomas. PMID:23663450

2013-01-01

163

Intraspecific genetic structure of white sucker ( Catostomus commersoni ) in northeastern North America as revealed by mitochondrial DNA polymorphism  

Microsoft Academic Search

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to study the influence of Pleistocene glaciations on the intraspecific genetic structure and distribution of the white sucker (Catostomus commersoni )i n northeastern North America. A total of 312 white sucker from 13 populations, including a population of dwarf ecotypes (Catostomus commersoni utawana), were analysed. An average of 93 fragments

Pascale Lafontaine; Julian J. Dodson

1997-01-01

164

Genetic relatedness among Tunisian plum cultivars by random amplified polymorphic DNA analysis and evaluation of phenotypic characters  

Microsoft Academic Search

Analysis of differentiation among local and introduced plum cultivars using morphological, pomological and RAPD markers revealed considerable genetic diversity. The phenotypic analysis shows that pomological and tree growth traits were permitted to evaluate morphological variability of plum cultivars. Ten arbitrary primers used to assay 27 cultivars revealed 143 RAPD markers. The percentage of polymorphic bands (97.28) and the resolving power

Ben Tamarzizt Hend; Baraket Ghada; Ben Mustapha Sana; Marrakchi Mohamed; Trifi Mokhtar; Salhi-Hannachi Amel

2009-01-01

165

Genetic Variations in Three Interacting Single Nucleotide Polymorphisms and the Risk of Preterm Birth in Black Families  

Microsoft Academic Search

Preterm birth, defined as birth prior to 37 completed weeks gestation, is a serious health concern. Despite advances in health care screening and interventions, the rate of preterm birth in the United States has risen more than 30 percent since 1981. In 2006, Menon and associates reported the first multilocus genetic interaction in three single nucleotide polymorphisms predictive of spontaneous

Margaret Steinbach

2009-01-01

166

Genetic polymorphism of CYP1A1, GSTM1 and GSTT1 genes in Indian oral cancer  

Microsoft Academic Search

Oral cancer ranks first among all cancers in males and is the third most common among females in India. Tobacco-derived carcinogens are involved in the development of oral cancer. Environmentgene interaction in oral carcinogenesis is well demonstrated by phase I and II enzymes that are involved in the metabolism of carcinogens. This study looked at the significance of genetic polymorphisms

T. T Sreelekha; K Ramadas; M Pandey; G Thomas; K. R Nalinakumari; M. R Pillai

2001-01-01

167

A preliminary report on the genetic variation in pointed gourd (Trichosanthes dioica Roxb.) as assessed by random amplified polymorphic DNA.  

PubMed

Pointed gourd (Trichosanthes dioica Roxb.) is an economically important cucurbit and is extensively propagated through vegetative means, viz vine and root cuttings. As the accessions are poorly characterized it is important at the beginning of a breeding programme to discriminate among available genotypes to establish the level of genetic diversity. The genetic diversity of 10 pointed gourd races, referred to as accessions was evaluated. DNA profiling was generated using 10 sequence independent RAPD markers. A total of 58 scorable loci were observed out of which 18 (31.03%) loci were considered polymorphic. Genetic diversity parameters [average and effective number of alleles, Shannon's index, percent polymorphism, Nei's gene diversity, polymorphic information content (PIC)] for RAPD along with UPGMA clustering based on Jaccard's coefficient were estimated. The UPGMA dendogram constructed based on RAPD analysis in 10 pointed gourd accessions were found to be grouped in a single cluster and may represent members of one heterotic group. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd. PMID:24873909

Adhikari, S; Biswas, A; Bandyopadhyay, T K; Ghosh, P D

2014-06-01

168

Genetic Polymorphisms in the Renin-Angiotensin System in High-Altitude and Low-Altitude Native  

E-print Network

to angiotensin I (AT-I), a decapeptide with mild vasoconstrictive properties, by the proteolytic enzyme reninGenetic Polymorphisms in the Renin-Angiotensin System in High-Altitude and Low-Altitude Native loci in genes encoding components of the renin-angiotensin system (RAS) that have alleles associated

Kidd, Kenneth

169

Early-Onset and Late-Onset Depression Are Independent of the Genetic Polymorphism of Apolipoprotein E  

Microsoft Academic Search

The recently shown association between apolipoprotein E (APOE) genotype and depressive illness has been challenged by subsequent studies. However, controversial results may derive from the different diagnostic criteria used for depression and from the small numbers of depressed patients included in the studies. We examined the association between depression and the genetic polymorphism of APOE in a large sample of

Andreas Papassotiropoulos; Metin Bagli; Frank Jessen; Marie Luise Rao; Sibylle G. Schwab; Reinhard Heun

1999-01-01

170

Platinum\\/paclitaxel-based chemotherapy in advanced ovarian carcinoma: glutathione S -transferase genetic polymorphisms as predictive biomarkers of disease outcome  

Microsoft Academic Search

Background. The glutathione S-transferases (GSTs) are a group of multifunctional enzymes that catalyze the conjugation of glutathione with a variety of electrophilic compounds, including cytotoxic agents. A significant percentage of normal individuals exhibit genetic polymorphism with a homozygous deletion (null genotype) of the genes, leading to absence of the enzyme. Methods. In the present study we analyzed GSTM1 and GSTT1

Rui Medeiros; Deolinda Pereira; Nomia Afonso; Carlos Palmeira; Cristina Faleiro; Carlos Afonso-Lopes; Margarida Freitas-Silva; Andr Vasconcelos; Sandra Costa; Teresa Osrio; Carlos Lopes

2003-01-01

171

Effect of genetic polymorphism of GSTM1 and GSTT1 genotypes on cytogenetic biomarkers among coaltar workers  

Microsoft Academic Search

Chromosomal aberrations (CAs) in peripheral blood lymphocytes and micronuclei (MN) in exfoliated buccal cells have been used for decades as cytogenetic biomarkers to investigate genotoxicity among occupationally or environmentally exposed population. In our study, we investigated the association of increased cytogenetic damage with genetic polymorphism in glutathione-S transferase genotypes among occupationally exposed 115 coaltar workers and 105 unexposed controls. We

Anil Kumar; Anita Yadav; Shiv Kumar Giri; Kapil Dev; Sanjeev Kumar Gautam; Ranjan Gupta; Neeraj Aggarwal

2011-01-01

172

Investigating the genetic polymorphism of sheep milk proteins: a useful tool for dairy production.  

PubMed

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. 2014 Society of Chemical Industry. PMID:24862201

Selvaggi, Maria; Laudadio, Vito; Dario, Cataldo; Tufarelli, Vincenzo

2014-12-01

173

Population genetics of insertion-deletion polymorphisms in South Koreans using Investigator DIPplex kit.  

PubMed

We assessed the applicability of 30 insertion-deletion polymorphisms (INDELs) in forensic use and the level of genetic diversity in South Korea (n=373) using the Investigator DIPplex kit (Qiagen). Allele frequencies, heterozygocities, and forensic efficacy parameters were determined. No deviation from Hardy-Weinberg equilibrium was observed for any of the INDEL markers. A high level of discrimination power was observed (combined power of discrimination: 0.99999999995). The combined match probability value was 2.84 10(-11) and the mean typical paternity indices were 0.878. Furthermore, we found one microvariant allele at HLD93 (rs2307570) that has not been reported. We expect that these 30 loci of INDEL markers will be useful for forensic identification and paternity testing in the South Korean population. PMID:24315593

Seong, Ki Min; Park, Ji Hye; Hyun, Young Se; Kang, Pil Won; Choi, Dong Ho; Han, Myun Soo; Park, Ki Won; Chung, Ki Wha

2014-01-01

174

Genetic polymorphism of 17 Y-STR loci in Han Chinese living in Lanzhou.  

PubMed

The genetic polymorphism across 17 Y-STR loci in a population of Han Chinese in Lanzhou was investigated. Haplotypes and allele frequencies for the 17 Y-chromosomal STRs loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 were determined in 500 healthy unrelated autochthonous males from Lanzhou. The results showed that no shared haplotypes were observed. Gene diversity values ranged from 0.3987 (DYS391) to 0.9740 (DYS385a,b). It was concluded that these loci will be very useful for human identification in forensic cases and paternity tests within the Han Chinese population inhabiting Lanzhou. PMID:24337856

Sun, Hong-bing; Yang, Xin; Ha, Fei; Zhang, Zi-long

2013-12-01

175

The DRD2 C957T polymorphism and the attentional blink--a genetic association study.  

PubMed

The attentional blink phenomenon (AB) describes a transient deficit in temporally selective visual attention regarding the processing of the second of two target stimuli in a rapid serial visual presentation (RSVP) task. The AB is a very prominent paradigm in the Cognitive Neurosciences that has been extensively studied by diverse psychophysiological techniques such as EEG or fMRI. Association studies from molecular genetics are scarce although the high heritability of higher cognitive functioning is proven. Only one seminal study reported an association between AB magnitude and the dopamine receptor D2 (DRD2) C957T polymorphism (Colzato et al., 2011). This functional polymorphism influences striatal D2 receptor binding affinity and thereby the efficacy of dopaminergic neurotransmission which is important for working memory and attentional processes. Colzato et al. (2011) reported that DRD2 C957T T/T-carriers exhibit a significant smaller AB than C-allele carriers. In the present study this influence of the DRD2 SNP on the AB could not be replicated in N=211 healthy participants. However, a significantly larger lag 1 sparing was observed for homozygous T/T-carriers. Moreover, carriers of at least one T-allele showed a significantly poorer performance in the identification of T1. In general, these results support the notion of a role of the dopaminergic system on the AB. However, as our results do not parallel previous findings the exact nature of this influence and its dependence on task parameters will have to be examined in further genetic association studies. PMID:23084608

Felten, Andrea; Montag, Christian; Kranczioch, Cornelia; Markett, Sebastian; Walter, Nora T; Reuter, Martin

2013-08-01

176

Genetic polymorphism of IL28B in hepatitis C-infected haemophilia patients in Israel.  

PubMed

Single-nucleotide polymorphisms (SNPs) near the IL28B gene were identified as major predictors of treatment response (sustained virologic response--SVR) and spontaneous clearance of HCV. Haemophilia patients have the highest prevalence of HCV, and are a unique target for genetic studies. The Israeli population is ethnically heterogeneous; therefore, genetic variability is anticipated. To determine the IL28B haplotypes in HCV-infected haemophilia patients and association with SVR and spontaneous viral clearance. IL28B polymorphism at SNPs rs12979860 and rs8099917 was determined in sera obtained from 130 HCV-infected haemophilia patients. The frequency of the various haplotypes was analysed according to treatment response, spontaneous HCV clearance, viral load and degree of fibrosis. The CC haplotype at SNP rs12979860 was found in 31% of patients, whereas the TT genotype at SNP rs8099917 was detected in 57% of cases. SVR was achieved in 70% of patients carrying the CC haplotype (P = 0.0196 vs. CT/TT), and 50% of the TT genotype at SNP rs8099917 (P = 0.0227 vs. TG/GG). Thirty-five percent of patients carrying the CC haplotype and 26% with the TT genotype at SNP rs8099917 showed spontaneous clearance of HCV infection (P = 0.00262 vs. CT/TT; and P = 0.00371 vs. TG/GG respectively). The C-allele frequency was exceptionally high (71%) in immigrants from the Asian republics of Russia. In HCV-infected haemophilia patients, SVR was more commonly achieved among patients who had the CC (rs12979860) or TT (rs8099917) genotype. Likewise, patients who possess harbour the CC or TT genotypes were more likely to clear HCV infection spontaneously. A unique distribution of the CC genotype was observed in some ethnic groups. PMID:22913807

Maor, Y; Morali, G; Bashari, D; Pnaranda, G; Schapiro, J M; Martinowitz, U; Halfon, P

2013-01-01

177

Genetic Polymorphisms in the Methylenetetrahydrofolate Reductase and Thymidylate Synthase Genes and Risk of Hepatocellular Carcinoma  

PubMed Central

Methylenetetrahydrofolate reductase (MTHFR) and thymidylate synthase (TYMS) are known to play a role in DNA methylation, synthesis, and repair. The genetic mutations in MTHFR and TYMS genes may have influences on their respective enzyme activities. Data on the association studies of the MTHFR and TYMS genetic polymorphisms and risk of hepatocellular carcinoma (HCC) are sparse. MTHFR and TYMS genotypes were determined on 365 HCC cases and 457 healthy control subjects among Hispanic and non-Hispanic whites and African-Americans in Los Angeles County, California, and among Chinese in the city of Nanning, Guangxi, China. Relative to the high-activity genotype, each low-activity genotype of MTHFR was associated with a statistically nonsignificant 30% to 50% reduction in risk of HCC. Relative to the TYMS3?UTR +6/+6 genotype, individuals with 1 or 2 copies of the deletion allele had a statistically significant 50% reduction in risk of HCC. When we examined HCC risk by the total number of mutant alleles in the 3 polymorphic loci of MTHFR/TYMS (range, 0-4), there was a monotonic decrease in risk with increasing number of mutant alleles (P for trend = 0.003). Individuals possessing the maximum number of mutant alleles (i.e., 4) had an odds ratio of 0.46 (95% confidence interval = 0.23-0.93) for HCC compared with those with no or only 1 mutant allele. Conclusion This study supports the hypothesis that reduced MTHFR activity and enhanced TYMS activity, both of which are essential elements in minimizing uracil misincorporation into DNA, may protect against the development of HCC. PMID:17659576

Yuan, Jian-Min; Lu, Shelly C.; Van Den Berg, David; Govindarajan, Sugantha; Zhang, Zhen-Quan; Mato, Jose M.; Yu, Mimi C.

2008-01-01

178

Genetic Diversity of Thottapalayam Virus, a Hantavirus Harbored by the Asian House Shrew (Suncus murinus) in Nepal  

PubMed Central

Despite the recent discovery of genetically divergent hantaviruses in shrews of multiple species in widely separated geographic regions, data are unavailable about the genetic diversity and phylogeography of Thottapalayam virus (TPMV), a hantavirus originally isolated from an Asian house shrew (Suncus murinus) captured in southern India more than four decades ago. To bridge this knowledge gap, the S, M, and L segments of hantavirus RNA were amplified by reverse transcription polymerase chain reaction from archival lung tissues of Asian house shrews captured in Nepal from January to September 1996. Pair-wise alignment and comparison revealed approximately 80% nucleotide and > 94% amino acid sequence similarity to prototype TPMV. Phylogenetic analyses, generated by maximum likelihood and Bayesian methods, showed geographic-specific clustering of TPMV, similar to that observed for rodent- and soricid-borne hantaviruses. These findings confirm that the Asian house shrew is the natural reservoir of TPMV and suggest a long-standing virushost relationship. PMID:21896819

Kang, Hae Ji; Kosoy, Michael Y.; Shrestha, Sanjaya K.; Shrestha, Mrigendra P.; Pavlin, Julie A.; Gibbons, Robert V.; Yanagihara, Richard

2011-01-01

179

Short report: Genetic diversity of Thottapalayam virus, a Hantavirus harbored by the Asian house shrew (Suncus murinus) in Nepal.  

PubMed

Despite the recent discovery of genetically divergent hantaviruses in shrews of multiple species in widely separated geographic regions, data are unavailable about the genetic diversity and phylogeography of Thottapalayam virus (TPMV), a hantavirus originally isolated from an Asian house shrew (Suncus murinus) captured in southern India more than four decades ago. To bridge this knowledge gap, the S, M, and L segments of hantavirus RNA were amplified by reverse transcription polymerase chain reaction from archival lung tissues of Asian house shrews captured in Nepal from January to September 1996. Pair-wise alignment and comparison revealed approximately 80% nucleotide and > 94% amino acid sequence similarity to prototype TPMV. Phylogenetic analyses, generated by maximum likelihood and Bayesian methods, showed geographic-specific clustering of TPMV, similar to that observed for rodent- and soricid-borne hantaviruses. These findings confirm that the Asian house shrew is the natural reservoir of TPMV and suggest a long-standing virus-host relationship. PMID:21896819

Kang, Hae Ji; Kosoy, Michael Y; Shrestha, Sanjaya K; Shrestha, Mrigendra P; Pavlin, Julie A; Gibbons, Robert V; Yanagihara, Richard

2011-09-01

180

Genetic diversity of endangered Polyporus umbellatus from China assessed using a sequence-related amplified polymorphism technique.  

PubMed

Polyporus umbellatus (Pers.) Fries is an endangered medicinal fungus in China with in vivo anticancer activity, but its genetic information is lacking. Eight natural P. umbellatus strains collected from 7 provinces in China were subjected to sequence-related amplified polymorphism markers to estimate the level and pattern of genetic diversity. Forty-nine primer combinations generated 1219 highly reproducible and discernible loci, among which 1023 were polymorphic. The percentage of polymorphism varied from 35.71 to 96.30 with an average of 83.92. Genetic identity among all strains ranged from 0.15 to 0.78 with an average of 0.46. The unweighted pair group method with arithmetic mean dendrogram clustered 8 strains into 3 clusters, and the clustering pattern showed 3 groups. Principal coordinate analysis further indicated that the genetic diversity of P. umbellatus strains was unevenly distributed and instead displayed a clustered distribution pattern. A relatively high level of genetic diversity was maintained in 8 natural P. umbellatus strains, but its abundance might be subjected to environmental heterogeneity, and the population structure of co-evolved Armillaria species may be selected by nature under the specific microenvironment. PMID:23315801

Zhang, Y; Kang, Y; Qin, Y; Zhou, Z; Lei, M; Guo, H

2012-01-01

181

Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum field isolates from Myanmar  

PubMed Central

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. PMID:20478015

2010-01-01

182

Genetic characterization of Okinawan black rats showing coat color polymorphisms of white spotting and melanism.  

PubMed

We examined pelage color variation in wild populations of black rats (the Rattus rattus species complex) in the Yambaru forest area, northern Okinawa Island, Ryukyu Archipelago, Japan. Our field study revealed that 8.7% (38/438) and 0.2% (4/2500) of rats exhibited two types of coat color: white spotting and melanism, respectively. Using 34 representative animals, the phylogeography of the population was inferred using a nuclear gene marker, i.e., sequences (954 bp) of the melanocortin-1 receptor (Mc1r) gene responsible for the melanistic form in black rats. Four sequences from Okinawa were characterized as R. tanezumi, the Asian strain of black rat. Notably, neither of the phenotypic characters of white spotting or melanism was associated with the Mc1r haplotypes. Analysis of mitochondrial cytochrome b (Cytb) sequences (1140 bp) revealed that four haplotypes recovered from Okinawa clustered with the clade of R. tanezumi and differed by one or more bases from haplotypes at other localities in Japan and Asian countries. Thus, both variants may have arisen in the native rat population of Okinawa without interaction with the lineage of R. rattus, which exhibits a worldwide distribution and displays such coat color variants. The Yambaru population of black rats has thus experienced its own evolutionary history in allopatry for a substantial period of time (e.g., 10,000 years), which has preserved valuable genetic polymorphisms and will be useful for assessing the ecological consequences of genetic variation in natural populations. PMID:22531792

Kambe, Yoshikazu; Nakata, Katsushi; Yasuda, Shumpei P; Suzuki, Hitoshi

2012-01-01

183

Genetic association study of mitochondrial polymorphisms in neovascular age-related macular degeneration  

PubMed Central

Purpose Age-related macular degeneration (AMD) is a multifactorial disease involving genetic and environmental factors. Most of the genetic factors identified so far involve the nuclear genome. Recently, two studies in North America and Australia reported an association between advanced AMD and the mitochondrial T2 haplogroup. Our purpose was to assess this association in a large French population. Methods This case control study included 1,224 patients with neovascular AMD and 559 controls with normal fundus. Mitochondrial DNA polymorphisms at and around nucleotides 4917, 11,812, and 14,233 were determined using PCR amplification and direct sequencing of mitochondrial DNA. Results No association was found between the mitochondrial T2 haplogroup and neovascular AMD in the French population: 94/1,152 patients with neovascular AMD had the T2 haplogroup (8.2%) versus 34/482 controls (7.1%; odds ratio=0.9 [0.51.5], p=0.66). Conclusions An association between AMD and the T2 haplogroup, previously described in North American and Australian populations, was not confirmed in a large French population. PMID:23734082

Tilleul, Julien; Richard, Florence; Puche, Nathalie; Zerbib, Jennyfer; Leveziel, Nicolas; Sahel, Jose Alain; Cohen, Salomon Yves; Korobelnik, Jean-Francois; Feingold, Josue; Munnich, Arnold; Kaplan, Josseline; Rozet, Jean-Michel

2013-01-01

184

Genetic polymorphism of Hucul horse population based on 17 microsatellite loci.  

PubMed

Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyped and mean number of alleles per locus was estimated (7.00). Means of observed (Ho) and expected (He) heterozygosity were calculated 0.7288 and 0.7027, respectively. The observed heterozygosity was similar to the results of research on Hucul horse population in another area of Carpathians Mountains. The average polymorphism information content (PIC) for analyses of seventeen microsatellite markers indicates the usefulness of this set of markers for Hucul horse parentage testing. PMID:24432328

Fornal, Agnieszka; Radko, Anna; Piestrzy?ska-Kajtoch, Agata

2013-01-01

185

Genetic imaging of the association of oxytocin receptor gene (OXTR) polymorphisms with positive maternal parenting  

PubMed Central

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 46 years old. Results: In response to child stimuli during functional magnetic resonance imaging (fMRI), hemodynamic responses in brain regions that mediate affect, reward, and social behavior were significantly correlated with observed positive parenting. Furthermore, single nucleotide polymorphisms (SNPs) (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 (OFC), anterior cingulate cortex (ACC), 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. PMID:24550797

Michalska, Kalina J.; Decety, Jean; Liu, Chunyu; Chen, Qi; Martz, Meghan E.; Jacob, Suma; Hipwell, Alison E.; Lee, Steve S.; Chronis-Tuscano, Andrea; Waldman, Irwin D.; Lahey, Benjamin B.

2013-01-01

186

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

PubMed

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. PMID:24668635

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

2014-01-01

187

Genetic polymorphisms and drug interactions leading to clopidogrel resistance: why the Asian population requires special attention.  

PubMed

Ischemic heart disease and stroke are the two leading causes of death worldwide. Antiplatelet therapy plays the most significant role in the management of these cardiovascular and cerebrovascular occlusive events to prevent recurrent ischemic attack. Clopidogrel, an antiplatelet drug, is widely prescribed either alone or in combination with aspirin as dual antiplatelet therapy for the prevention of vascular occlusive events. The antiplatelet response to clopidogrel varies widely. Hyporesponders and nonresponders are likely to have adverse cardiovascular events during follow-up. Some drugs, such as proton pump inhibitors (omeprazole), calcium channel blockers, selective serotonin reuptake inhibitors (nefazadone), coumarin derivatives (phenprocoumon), benzodiazepines, sulfonylurea, erythromycin, and itraconazole, decrease the antiplatelet effect of clopidogrel when administered concomitantly. Decreased response to clopidogrel is common among Asians due to genetic polymorphisms associated with clopidogrel resistance, and it is nearly 70% in some of the Asian communities. It is necessary to study Asian populations, because there are a large number of Asians throughout the world due to increased migration. Current guidelines do not make genetic testing or platelet response testing mandatory prior to clopidogrel prescription. Therefore, it is important for clinicians treating Asian patients to keep in mind the interindividual variability in response to clopidogrel when prescribing the drug. PMID:23110469

Hasan, Md Shariful; Basri, Hamidon Bin; Hin, Lim Poh; Stanslas, Johnson

2013-03-01

188

New associations of the genetic polymorphisms in nicotinic receptor genes with the risk of lung cancer  

PubMed Central

Aims Previous studies revealed association of lung cancer risk with single nucleotide polymorphisms (SNPs) in chromosome 15q25 region containing CHRNA5-CHRNA3-CHRNB4 nicotinic acetylcholine receptor (nAChR) subunit gene cluster. The genetic variations in other lung nAChRs remained unknown. In this study, we perform case-control analysis of CHRNA9 and CHRNA3 genes using 340 non-small cell lung cancer cases and 435 controls. Main methods All exons, 3UTR, intron 1 and parts of other introns surrounding exons 25 of CHRNA9 gene as well as exons 2, 3 of CHRNA3 gene and parts of surrounding intronic regions were sequenced. The study was controlled for gender, age and ethnicity related differences. Each SNP in analyzed groups was assessed by allele frequency, genotype distribution and haplotype analysis. Key findings The case-control analysis revealed that an increased risk is associated with two SNPs in CHRNA9, rs56159866 and rs6819385, and one in CHRNA3, rs8040868. The risk was reduced for three SNPs in CHRNA9, rs55998310, rs56291234, and newly discovered ss410759555, and also in carriers of the haplotype NP_060051.2 containing ancestral N442 variant of ?9. Significance The nonsynonymous substitutions can produce receptors exhibiting unique ligand-binding and downstream signaling characteristics, synonymous as well all intronic SNPs may affect protein production at the transcriptional and/or translational levels, or just manifest association with cancer by genetic linkage to other alleles. Elucidation of the mechanisms by which individual genetic variations in ?9 affect predisposition to lung cancer may lead to development of personalized approaches to cancer prevention and treatment as well as protection against tobacco consumption. PMID:22280835

Chikova, Anna; Bernard, Hans-Ulrich; Shchepotin, Igor B.; Grando, Sergei A.

2012-01-01

189

An association between a NQO1 genetic polymorphism and risk of lung cancer.  

PubMed

NAD(P)H:quinone oxidoreductase (NQO1) is a detoxification enzyme that protects against the regeneration of reactive oxygen species chemically induced by oxidative stress, cytotoxicity, mutagenicity, and carcinogenicity. The protection conferred by NQO1 protein reduces certain environmental carcinogens, such as nitroaromatic compounds, heterocyclic amines, and possible cigarette smoke condensate. The gene coding for NQO1 has a genetic polymorphism (C-->T) at nucleotide position 609 (i.e. amino acid codon 187) of the NQO1 cDNA. This polymorphism was shown to reduce NQO1 enzyme activity, thereby diminishing the protection provided by NQO1. Therefore, we hypothesized that individuals with the variant NQO1 genotype are at higher risk for lung cancer. Using a case-control study, we genotyped the NQO1 variants successfully by PCR-RFLP in 826 lung cancer patients and 826 healthy control subjects matched for age, sex, ethnicity, and smoking status. The frequency of the NQO1 T-allele was statistically significantly different among three ethnic groups (p<0.001). In further analysis of Caucasians, the variant NQO1 genotypes (CT and TT) were associated with a marginally increased lung cancer risk (OR=1.19; 95% CI: 0.95-1.50). The elevated lung cancer risk was only evident in younger individuals (age <62 years old) (OR=1.46; 95% CI: 1.04-2.05), women (OR=1.89; 95% CI: 1.33-2.68), and never smokers (OR=1.80; 95% CI: 1.03-3.13). Furthermore, we found a statistically significant trend in the development of lung cancer at an early age in women with increasing copies of the variant allele (p=0.03). These results suggest that the NQO1 variant genotype may modulate lung cancer risk, especially in younger individuals (age<62), women, and never smokers. PMID:15781212

Saldivar, Salvador J; Wang, Yunfei; Zhao, Hua; Shao, Lina; Lin, Jie; Spitz, Margaret R; Wu, Xifeng

2005-04-01

190

Plasmodium falciparum and Plasmodium vivax specific lactate dehydrogenase: genetic polymorphism study from Indian isolates.  

PubMed

Control and eradication of malaria is hindered by the acquisition of drug resistance by Plasmodium species. This has necessitated a persistent search for novel drugs and more efficient targets. Plasmodium species specific lactate dehydrogenase is one of the potential therapeutic and diagnostic targets, because of its indispensable role in endoerythrocytic stage of the parasite. A target molecule that is highly conserved in the parasite population can be more effectively used in diagnostics and therapeutics, hence, in the present study polymorphism in PfLDH (Plasmodiumfalciparum specific LDH) and PvLDH (Plasmodiumvivax specific LDH) genes was analyzed using PCR-single strand confirmation polymorphism (PCR-SSCP) and sequencing. Forty-six P. falciparum and thirty-five P. vivax samples were screened from different states of India. Our findings have revealed presence of a single PfLDH genotype and six PvLDH genotypes among the studied samples. Interestingly, along with synonymous substitutions, nonsynonymous substitutions were reported to be present for the first time in the PvLDH genotypes. Further, through amino acid sequence alignment and homology modeling studies we observed that the catalytic residues were conserved in all PvLDH genotypes and the nonsynonymous substitutions have not altered the enzyme structure significantly. Evolutionary genetics studies have confirmed that PfLDH and PvLDH loci are under strong purifying selection. Phylogenetic analysis of the pLDH gene sequences revealed that P. falciparum compared to P. vivax, has recent origin. The study therefore supports PfLDH and PvLDH as suitable therapeutic and diagnostic targets as well as phylogenetic markers to understand the genealogy of malaria species. PMID:24953504

Keluskar, Priyadarshan; Singh, Vineeta; Gupta, Purva; Ingle, Sanjay

2014-08-01

191

TAP1 and TAP2 polymorphisms associated with ankylosing spondylitis in genetically homogenous Chinese Han population.  

PubMed

Human leukocyte antigen (HLA)-B27 is strongly associated with the autoimmune disease ankylosing spondylitis (AS). Other autoimmune disease-associated genes, such as transporter associated with antigen processing (TAP) genes, could also influence AS susceptibility. In this study, we investigated the association of TAP1 and TAP2 polymorphisms in genetically homogenous Chinese AS patients. Six TAP1 single nucleotide polymorphisms (SNPs) and three TAP2 SNPs sites were analyzed in B27-positive AS cases, healthy B27-negative controls, and healthy B27-positive controls. In the allele and genotype analysis, the results indicated that TAP1 site 1910 allele G, genotype AG and TAP2 site 1693 genotype AA were associated with increased AS risk in a case-B27 negative control (p < 0.05). In the haplotype analysis, TAP1 SNP haplotype (GGGGGG, TAP1*020101) and TAP1-TAP2 SNP haplotypes (GGGGGG-GGG, TAP1*020101-TAP2*0101, and GGAAGG-GAG, TAP1*0101-TAP2*0102) increased AS risk in case-B27 negative control (p < 0.05). In contrast, TAP1-TAP2 SNP haplotype GGGGGG-GAG (TAP1*020101-TAP2*0102) was less common in cases than in B27-negative controls (p < 0.05). Moreover, TAP1-TAP2 SNP haplotype GGGAGG-GGG (TAP1*0301-TAP2*0101) was less common in cases than in B27-positive controls. The two haplotypes appeared to confer protection in AS (p < 0.05). These results suggest a potential mechanism of altered antigen-peptide selection and transport in AS pathogenesis. PMID:19480848

Feng, Mingliang; Yin, Biao; Shen, Tong; Ma, Qing; Liu, Lidong; Zheng, Jiewei; Zhao, Yulin; Qian, Kaicheng; Liu, Dazhuang

2009-04-01

192

Genetic Role of BDNF Val66Met and 5-HTTLPR Polymorphisms on Depressive Disorder  

PubMed Central

Objective We investigated possible association between depressive disorders and BDNF Val66Met and 5-HTTLPR. Brain derived neurotrophic factor (BDNF) gene and serotonin transporter (SLC6A4) gene are promising candidate genes for depressive disorders. It has been suggested that BDNF promotes the survival and differentiation of serotonergic neurons and that serotonergic transmission exerts powerful control over BDNF gene expression. Methods Final analyses were performed on 186 patients with depressive disorders and 1032 controls. Val66Met polymorphism of BDNF gene and 5-HTTLPR polymorphism of serotonin transporter gene were genotyped and allele and genotypic associations on the diagnosis of depression and age at onset of depression were analyzed. Results The 5-HTTLPR was positively associated with depressive affected status in the total sample and in females (p=0.038 for allelewise, p=0.015 for genotype-wise associations), but, not in males. The BDNF Val66Met showed no association with depression. BDNF Val66Met and 5-HTTLPR alone were not associated with age at onset of depression. Additional analysis on the interaction between BDNF Val66Met and 5-HTTLPR found a significant association with age at onset of depression in the entire patient group. This association was also found in the female but not in the male patient group. None of the positive results survived Bonferroni correction for multiple testing. Conclusion This result suggested that BDNF Val66Met and 5-HTTLPR may contribute to depressive disorders in a complex way and that the genetic effect could differ by gender. Further studies with large number of patients will be necessary. PMID:24843376

Lee, Kyu Young; Jeong, Seong Hoon; Kim, Se Hyun; Ahn, Yong Min; Kim, Yong Sik; Jung, Hee Yeon; Bang, Yang Weon

2014-01-01

193

Characterization of genetic identities and relationships of Brassica oleracea L. via a random amplified polymorphic DNA assay.  

PubMed

Effective conservation and the use of plant genetic resources are essential for future agricultural progress. Critical to this conservation effort is the development of genetic markers which not only distinguish individuals and accessions but also reflect the inherent variation and genetic relationships among collection holdings. We have examined the applicability of the random amplified polymorphic DNA (RAPD) assay for quick, cost-effective, and reliable use in addressing these needs in relation to collection organization and management. Twenty-five decamer oligonucleotide primers were screened individually with a test array composed of individuals representing a range of genetic relationships in Brassica oleracea L. (vegetable and forage cole crops). Over 140 reproducible, polymorphic fragments were generated for study. Each individual of the test array exhibited a unique molecular genotype and composites specific for accessions and botanical varieties could be established. An analysis of similarity based on amplified DNA fragments reflected the known genetic relationships among the selected entries. These results demonstrated that RAPD markers can be of great value in gene bank management for purposes of identification, measurement of variation, and establishment of genetic similarity at the intraspecific level. PMID:24197304

Kresovich, S; Williams, J G; McFerson, J R; Routman, E J; Schaal, B A

1992-11-01

194

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

PubMed

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. PMID:19700859

Lankinen, Asa

2009-08-01

195

What the Genetic Background of Individuals with Asthma and Obesity Can Reveal: Is ?2-Adrenergic Receptor Gene Polymorphism Important?  

PubMed Central

The goal of this review was to evaluate the association of ?2-adrenergic receptor (ADRB2) gene polymorphisms with asthma and obesity. Asthma is the most common pediatric inflammatory disorder. The prevalence, severity, and hospitalization index for asthma have increased markedly in the last several decades. Interestingly, asthma is often diagnosed along with obesity. Genetic factors are essential for both conditions, and some of the candidate pleiotropic genes thought to be involved in the development of these diseases are ADRB2, vitamin D receptor (VDR), leptin (LEP), protein kinase C alpha (PRKCA), and tumor necrosis factor alpha (TNF?). The ADRB2 has been studied in multiple populations and more than 80 polymorphisms, mainly single-nucleotide polymorphisms, have been identified. For nonsynonymous Arg16Gly, Gln27Glu, and Thr164Ile, functional effects have been shown. In vivo, these polymorphisms have been evaluated to determine their association with both obesity and asthma, but the results are inconsistent and depend on the population studied or how the disease was defined. Currently, there are only few reports describing the genetic background for the comorbidity of asthma and obesity. PMID:25276484

2014-01-01

196

Asexual genetic variability in Agavaceae determined with inverse sequence-tagged repeats and amplification fragment length polymorphism analysis  

Microsoft Academic Search

Agaves are succulent monocot plants rich in fibers, sugars and other important compounds. They are also valued as ornamental\\u000a plants and for their ability to grow in poor soils. In the present study, inverse sequence-tagged repeats (ISTR) and amplified\\u000a fragment length polymorphism (AFLP) analysis were used to study genetic diversity in differentAgavaceae plant samples. Comparison of the banding patterns between

Digenes Infante; Sandy Molina; Jhonny R. Demey; Elizabeth Gmez

2006-01-01

197

Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits  

Microsoft Academic Search

An analysis of 11 Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans; Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting

David Comas; Francesc Calafell; Noufissa Benchemsi; Ahmed Helal; Gerard Lefranc; Mark Stoneking; Mark A. Batzer; Jaume Bertranpetit; Antti Sajantila

2000-01-01

198

Genetic control of human apolipoprotein E polymorphism: Comparison of one-and two-dimensional techniques of isoprotein analysis  

Microsoft Academic Search

Genetic polymorphism of human apolipoprotein E (apo E) has previously been demonstrated by one-dimensional isoelectric focusing (Utermann et al. 1977b) and by two-dimensional electrophoresis of apolipoproteins (Zannis et al. 1981), but the relationship between the results obtained by these methods remained unclear. We therefore performed comparative phenotyping by one-dimensional and two-dimensional electrophoresis. Apoproteins from very low-density lipoproteins (apo VLDL) prepared

Gerd Utermann; Armin Steinmetz; Wilfried Weber

1982-01-01

199

Evaluation of the Association between the AC3 Genetic Polymorphisms and Obesity in a Chinese Han Population  

Microsoft Academic Search

BackgroundAC3 is one of adenylyl cyclase isoforms involved in cAMP and insulin signaling pathway. Recent reports have demonstrated that the AC3 genetic polymorphisms are associated with obesity in a Swedish population. AC3 knock out mice exhibit obese when they age. These findings suggest that AC3 plays an important role in the regulation of body weight.Methodology\\/Principal FindingsIn the present study, we

Hairu Wang; Ming Wu; Weiguang Zhu; Jin Shen; Xiaoming Shi; Jie Yang; Qihui Zhao; Chuan Ni; Yaochu Xu; Hongbing Shen; Chong Shen; Harvest F. Gu; Adrian Vella

2010-01-01

200

Polymorphisms G691S\\/S904S of RET as Genetic Modifiers of MEN 2A1  

Microsoft Academic Search

Multiple endocrine neoplasia type 2A (MEN 2A) is associated with specific germ-line missense mutations in the RET proto-oncogene. Only a minor fraction of human disorders are simple monogenic diseases, and the identification of polymorphisms that increase susceptibility, including variations in pathological phenotypes, to human diseases is one of the key problems in medical genetics. To explore this idea, we analyzed

Mercedes Robledo; Laura Gil; Marina Pollan; Arancha Cebrian; Sergio Ru ; Marta Azanedo; Javier Benitez; Javier Menarguez

2003-01-01

201

Genetic polymorphism of RhD-negative associated haplotypes in the Chinese.  

PubMed

The Rh blood group is the most polymorphic human blood group system, and is clinically significant in transfusion medicine. Individuals are classified as Rh-positive and Rh-negative depending on the presence or absence of the D antigen on the red cell surface. The RhD-negative trait could be generated by multiple genetic mechanisms, which have been shown to be ethnic group-dependent. In this study, we evaluated the status of seven RHD-specific exons (exons 3, 4, 5, 6, 7, 9, and 10) and RH intron 4 in 119 Chinese blood donors, using the sequence-specific primers polymerase chain reaction (SSP-PCR). Of the 87 individuals who were RhD-negative, 52 with the ce/ce, ce/cE, or Ce/ce genotype (60%) lacked the above seven RHD exons; 22 with the Ce/Ce or Ce/ce genotype (25%) had all the RHD exons examined; 13 with the Ce/ce genotype (15%) carried at least one RHD exon. Antigen association analysis suggested the existence of a novel class of RhD-negative associated haplotypes in the Chinese, tentatively denoted D(nf)Ce. The D(nf)Ce haplotype consisted of a normal RHCe allele and a nonfunctional RHD gene, which vary depending on the structure of the RHD gene. Among the RhD-negative Chinese, the estimated frequencies of the dce, dCe, and D(nf)Ce haplotypes were 0.7500, 0.0465, and 0.2035, respectively. No statistically significant deviation from Hardy-Weinberg equilibrium was observed using this genetic model. PMID:10944852

Lan, J C; Chen, Q; Wu, D L; Ding, H; Pong, D B; Zhao, T

2000-01-01

202

Genetically determined oxidation polymorphism and drug hepatotoxicity. Study of 51 patients.  

PubMed

The influence of genetically determined oxidation polymorphism on drug hepatotoxicity has been poorly investigated and results are controversial. We studied drug oxidation capacity in 51 patients with hepatitis caused mainly by drugs undergoing oxidative metabolism, using dextromethorphan, a test compound recently proposed as a substitute for debrisoquine. Phenotyping was performed using the metabolic ratio (MR) calculated as MR = 0-10 h urinary output of dextromethorphan/0-10 h urinary output of dextrorphan (the main oxidative metabolite), after oral administration of 40 mg dextromethorphan hydrobromide. Dextromethorphan oxidation capacity was similar in patients and in 103 control subjects as judged by: (a) the prevalence of each phenotype (5.9% versus 3.9% for the poor metabolizer phenotype and 94.1% versus 96.1% for the extensive metabolizer phenotype; (b) the frequency distribution histograms of log metabolic ratio; (c) the mean values of dextromethorphan and dextrorphan urinary outputs and of log metabolic ratio for each phenotype. These results show that hepatotoxicity of several drugs, including amineptine, amodiaquine and Plethoryl, is related neither to an impairment in dextromethorphan oxidation capacity nor to an unusually high capacity to oxidize this drug. PMID:2715619

Larrey, D; Tinel, M; Amouyal, G; Freneaux, E; Berson, A; Fouin-Fortunet, H; Babany, G; Letteron, P; Iglicki, F; Slama, J L

1989-03-01

203

Genetic structure of the genus Lemna L. (Lemnaceae) as revealed by amplified fragment length polymorphism.  

PubMed

Duckweeds (Lemnaceae) are extremely reduced in morphology, which made their taxonomy a challenge for a long time. The amplified fragment length polymorphism (AFLP) marker technique was applied to solve this problem. 84 clones of the genus Lemna were investigated representing all 13 accepted Lemna species. By neighbour-joining (NJ) analysis, 10 out of these 13 species were clearly recognized: L. minor, L. obscura, L. turionifera, L. japonica, L. disperma, L. aequinoctialis, L. perpusilla, L. trisulca, L. tenera, and L. minuta. However, L. valdiviana and L. yungensis could be distinguished neither by NJ cluster analysis nor by structure analysis. Moreover, the 16 analysed clones of L. gibba were assembled into four genetically differentiated groups. Only one of these groups, which includes the standard clones 7107 (G1) and 7741 (G3), represents obviously the "true" L. gibba. At least four of the clones investigated, so far considered as L. gibba (clones 8655a, 9481, 9436b, and Tra05-L), represent evidently close relatives to L. turionifera but do not form turions under any of the conditions tested. Another group of clones (6745, 6751, and 7922) corresponds to putative hybrids and may be identical with L. parodiana, a species not accepted until now because of the difficulties of delineation on morphology alone. In conclusion, AFLP analysis offers a solid base for the identification of Lemna clones, which is particularly important in view of Lemnaceae application in biomonitoring. PMID:20526614

Bog, Manuela; Baumbach, Henryk; Schween, Ulrike; Hellwig, Frank; Landolt, Elias; Appenroth, Klaus-J

2010-08-01

204

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis  

PubMed Central

Newcastle disease and Avian Influenza are considered to be the most dangerous fowl diseases which may cause huge economic losses. Newcastle disease is caused by the enveloped, and single-stranded RNA virus (NDV, APMV-1; belonging to Paramyxoviridae family), which can be further divided into sixteen different genotypes grouped into five pathotypes according to their pathogenicity. It has been reported that low pathogenic virus can greatly increase its pathogenicity even during a single passage. Additionally, due to the widespread use of live vaccines, a mixture of two or more different viruses in one sample can be detected. Hence, there is a great need for establishment of fast, inexpensive, sensitive, and relatively simple diagnostic method for multistrain and quasispecies detection of NDV infection. In this paper we describe a diagnostic method based on RT-PCR followed by a modified version of single-stranded conformational polymorphism analysis using short DNA fragments of gene encoding viral F protein. The method allows for rapid diagnosis of genetic variant emerging from previously stable population which may prevent the spread of the pathogenic viral variant. PMID:24812625

Rabalski, Lukasz; Smietanka, Krzysztof

2014-01-01

205

[Polymorphism in coding region of pig PRDX6 gene and its genetic effects analysis].  

PubMed

PRDX6, a member of antioxidant protein superfamily, plays an important role in oxidative stress, catabolism of lipids and phospholipid lipisomes. Therefore, we used PRDX6 as an important candidate gene for meat quality according to its physiological and biochemical function. Partial coding sequence of porcine PRDX6 was isolated and two potenial SNPs, one at 417 bp (C/T) and the other at 423 bp (A/G), were found in the fourth exon by comparison of the obtained sequence from different pig breeds. In order to explore the relationship between PRDX6 polymorphism and meat quality, genetic variation and trait association of these two SNPs were separately performed in 6 purebred pig population and 247 F2 "Large White x Meishan" resource population by pyrosequencing. The results showed that allele C was predominant in western pig breeds, while allele T was predominant in Chinese indigenous breeds at 417 bp (C/T). This SNP was significantly associated with the intramuscular fat and water moisture (P < 0.05). The A/G mutation at 423 bp was significantly associated with drip water rate, water holding capacity, intramuscular fat, and water moisture (P < 0.05). Allele A was predominant in western pig breeds, while allele G was predominant in Chinese indigenous breeds. These two SNPs were likely to be important markers affecting meat quality traits (especially the muscle tenderness). PMID:22049688

Liu, Yang; Wu, Wang-Jun; Zuo, Bo; Ren, Zhu-Qing; Xiong, Yuan-Zhu

2011-07-01

206

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

PubMed Central

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 chloroplast genome. Melon accessions were classified into three subclusters by cytoplasm type and then into 12 subgroups. Geographical origin and seed size also differed between the three subclusters. Subcluster Ia contained small-seed melon from Southern Africa and South and East Asia and subcluster Ib mainly consisted of large-seed melon from northern Africa, Europe and USA. Melon accessions of subcluster Ic were only found in West, Central and Southern Africa. Our results indicated that European melon groups and Asian melon groups diversified independently and shared the same maternal lineage with northern African large-seed melon and Southern African small-seed melon, respectively. Cultivated melon of subcluster Ic may have been domesticated independently in Africa. The presence of 11 cytoplasm types in Africa strongly supported African origin of cultivated melon and indicated the importance of germplasm from Africa. PMID:23853513

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

207

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

PubMed

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 IFN? 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. PMID:25098560

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

2014-11-01

208

Protein polymorphism and genetic distance in South American cricetid rodents of the genus Calomys.  

PubMed

Allozymic variation in population samples of Calomys laucha, C. musculinus and C. venustus collected simultaneously from the province of Crdoba, Argentina, was analyzed by gel electrophoresis. These three species showed high levels of polymorphism: for C. laucha, the P value was 72.7% and the H value was 0.147 (19 loci); for C. musculinus, P = 61.9% and H = 0.149 (20 loci); for C. venustus, P = 66.7% and H = 0.146 (18 loci). These species are non-fossorial generalists, have a high reproductive rate and live in disturbed habitats. The similarity indices (S) range between 0.613 and 0.681. On the basis of genetic distance, D (between 0.354 and 0.476), divergence time was estimated to be from 6.3 to 8.5 million years (late Miocene). Even admitting some imprecision for this estimate, the remarkable differences at the structural gene level shown by the species analyzed, suggest they had an early origin. PMID:2199323

Gardenal, C N; Garca, B A; Sabattini, M S; Blanco, A

1990-01-01

209

Hyperhomocysteinemia and of Methylenetetrahydrofolate Reductase (C677T) Genetic Polymorphism in Patients with Deep Vein Thrombosis  

PubMed Central

Aim: To determine the concentration of total plasma homocysteine (tHcy) as well as different genotypes of methylenetetrahydrofolate reductase MTHFR (C677T) in healthy subjects and patients with deep vein thrombosis (DVT). Material and methods: The investigation comprised a total of 160 subjects divided in two main groups: 80 healthy subjects (control group) and 80 patients with deep vein thrombosis. Concentration of tHcy was determined by spectrophotometric cyclic enzymatic method and mutation of MTHFR (C677T) gene was examined by polymerase chain reaction according to Schneider. Results: The results obtained for plasma tHcy in the control group were 11.623.43 ?mol/L, while tHcy level was significantly higher in patients with deep vein thrombosis as compared to the control group, 15.193.63 ?mol/L (?<0.001). The analysis of the results has shown that MTHFR (C677T) genetic polymorphism was responsible for mild to moderate hyperhomocysteinemia in the majority of subjects. Conclusion: The level of tHcy in the examined patients was significantly higher in comparison with the control group. Multiple regression analysis has shown that tHcy level in CT and TT genotypes of MTHFR (C677T) was statistically higher in comparison with CC genotype of MTHFR (C677T) in both, the control group and the DVT patients. PMID:24167429

Brezovska-Kavrakova, Julijana; Krstevska, Marija; Bosilkova, Gordana; Alabakovska, Sonja; Panov, Saso; Orovchanec, Nikola

2013-01-01

210

Genetic Diversity of Myanmar and Indonesia Native Chickens Together with Two Jungle Fowl Species by Using 102 Indels Polymorphisms  

PubMed Central

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island. PMID:25049646

Maw, Aye Aye; Shimogiri, Takeshi; Riztyan; Kawabe, Kotaro; Kawamoto, Yasuhiro; Okamoto, Shin

2012-01-01

211

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

PubMed Central

Introduction Recently, testosterone (T) has been shown to be associated with premature ejaculation (PE) symptoms in the literature. Furthermore, studies suggest that the etiology of PE is partly under genetic control. Aim The aim of this study was to reassess findings suggesting an association between testosterone (T) and a key symptom of PE, ejaculation latency time (ELT), as well as exploratively investigating associations between six androgen-related genetic polymorphisms and ELT. Materials and Methods Statistical analyses were performed on a population-based sample of 1,429 Finnish men aged 1845 years (M = 26.9, SD = 4.7). Genotype information was available for 1,3451,429 of these (depending on the polymorphism), and salivary T samples were available from 384 men. Two androgen receptor gene-linked, two 5-alpha-reductase type 2-gene-linked, and two sex hormone-binding globuline gene-linked polymorphisms were genotyped. Main Outcome Measures Ejaculatory function was assessed using self-reported ELT. Results We found no association between salivary T levels and ELT. We found a nominally significant association between a 5-alpha-reductase type 2-gene-linked polymorphism (rs2208532) and ELT, but this association did not remain significant after correction for multiple testing. One single nucleotide polymorphism in the sex hormone-binding globulin gene (rs1799941) moderated (significantly after correction for multiple testing) the association between salivary T and ELT, so that A:A genotype carriers had significantly lower salivary T levels as a function of increasing ELT compared with other genotype groups. 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;2:107114.

Jern, Patrick; Westberg, Lars; Ankarberg-Lindgren, Carina; Johansson, Ada; Gunst, Annika; Sandnabba, N Kenneth; Santtila, Pekka

2014-01-01

212

Genetic variations and polymorphisms in the ezrin gene are associated with age-related cataract  

PubMed Central

Purpose Age-related cataract (ARC) is a complex multifactorial disorder, including genetic and environmental factors. Ezrin (EZR), a member of the ezrin/radixin/moesin (ERM) protein family, plays a crucial role in the development of the lens as a plasma membranecytoskeleton linker. We conducted this study to investigate the role of genetic variations of ezrin and the relationship between single nucleotide polymorphisms (SNPs) in EZR and susceptibility to ARC in a Chinese population. Methods A total of 205 sporadic age-related cataract patients and 218 unrelated random healthy controls participated in our study. Genomic DNA was extracted from peripheral blood leukocytes. All exons of EZR were sequenced after being amplified with polymerase chain reaction. The functional consequences of the mutations were analyzed using PolyPhen2. SNP statistical analysis was performed using SNPstats. Results We found three novel variations in 205 patients. None presented in the 218 controls, including c.441C>G, c.924G>C, and c.1503G>A. PolyPhen2 predicted that the c.924G>C mutation probably had pathogenicity. Compared with the healthy controls, the rs5881286 -/GT genotype and - allele frequencies (p=0.0012; odds ratio [OR]=3.37; 95% confidence interval [CI]=1.706.70; p=3.96e-5; ?2=18.98, respectively), rs2242318 T/C genotype and C allele frequencies (p=0.0045; OR=3.40; 95% CI=1.706.79; p=8.82e-6; ?2=21.86, respectively), and rs144581330 A/G genotype and G allele frequencies (p=0.0472; OR=14.46; 95% CI=1.29162.43; p=0.0244, ?2=6.99, respectively) were higher in the patients with age-related cataract. SNP rs144581330 in exon 2 was also predicted to be probably damaging by PolyPhen2. Haplotype association including the - allele of rs5881286, C allele of rs2242318, and A allele of rs144581330 exhibited significantly higher distribution in the patients with ARC (p=8.0e-4; OR=3.38; 95% CI=1.666.87). Conclusions This study suggests that the genetic variations and SNPs in the gene EZR possibly contribute to the development of age-related cataracts in the Chinese population. PMID:23882136

Lin, Qinghong; Zhou, Nan; Zhang, Na; Zhu, Bidan; Hu, Shanshan; Zhou, Zhou

2013-01-01

213

MicroRNAs related polymorphisms and genetic susceptibility to esophageal squamous cell carcinoma.  

PubMed

Esophageal cancer (EC) is the sixth leading cause of cancer-associated death worldwide and the incidence and mortality in China are the highest. The single nucleotide polymorphisms (SNPs) related to microRNAs could lead to alteration in microRNA expression and contribute to the susceptibility of cancer. To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381 patients with esophageal squamous cell carcinoma (ESCC) and 426 gender, age-matched controls was carried out to investigate the genetic susceptibility of five microRNA-related SNPs (rs2910164 in microRNA-146a, rs11614913 in microRNA-196a-2, rs7813 in GEMIN4, rs1595066 and rs16845990 in ErbB4) as well as the interactions of gene-gene and gene-environment in the development of ESCC. Variant homozygote genotype of rs11614913 in microRNA-196a-2 and rs1595066 in ErbB4 were significantly associated with reduced ESCC risk (ORadjusted: 0.62, 95% CI: 0.39-0.99 and ORadjusted: 0.38, 95% CI: 0.24-0.61). The analysis of haplotypes in ErbB4 gene showed significant increased ESCC risk in Grs1595066Crs16845990 and Grs1595066Trs16845990 haplotypes (ORadjusted: 1.46, 95% CI: 1.08-1.99 and ORadjusted: 1.33, 95% CI: 1.10-1.62), and inversely reduced ESCC risk in Ars1595066Crs16845990 and Ars1595066Trs16845990 haplotypes with OR (95% CI) of 0.75 (0.60-0.94) and 0.65 (0.49-0.86), respectively. These findings suggest that the polymorphisms in the microRNA-related genes may affect susceptibility of ESCC in Chinese Han population and the gene-gene interactions play vital roles in the progression on esophageal cancer. Future studies with larger sample and different ethnic populations are required to support and validate our findings. PMID:24916311

Qu, Yanhong; Qu, Honghong; Luo, Manli; Wang, Peng; Song, Chunhua; Wang, Kaijuan; Zhang, Jianying; Dai, Liping

2014-12-01

214

The Influence of Genetic Polymorphisms on Population Variability in Six Xenobiotic-Metabolizing Enzymes  

Microsoft Academic Search

This review provides variability statistics for polymorphic enzymes that are involved in the metabolism of xenobiotics. Six enzymes were evaluated: cytochrome P-450 (CYP) 2D6, CYP2E1, aldehyde dehydrogenase-2 (ALDH2), paraoxonase (PON1), glutathione transferases (GSTM1, GSTT1, and GSTP1), and N-acetyltransferases (NAT1 and NAT2). The polymorphisms were characterized with respect to (1) number and type of variants, (2) effects of polymorphisms on enzyme

Gary Ginsberg; Susan Smolenski; Patricia Neafsey; Dale Hattis; Katy Walker; Kathryn Z. Guyton; Douglas O. Johns; Babasaheb Sonawane

2009-01-01

215

Trophic polymorphism in a riverine fish: morphological, dietary, and genetic analysis of mountain whitefish  

E-print Network

(Salmonidae: Prosopium williamsoni), which has been hypothesized to exhibit a rare example of reproductively KEYWORDS: Coregonus � Gasterosteus � microsatellite � morphology � Prosopium � resource polymorphism

Whiteley, Andrew

216

The impact of genetics profile (gene polymorphisms) in obese non-PCOS women entering an IVF/ICSI program.  

PubMed

Data concerning the effects of increased body mass index (BMI) on ovarian and pregnancy outcome are rich, but the results are rather controversial. Regarding pharmacogenetics, gene polymorphisms of hormonal receptor genes, such as Estrogen Receptor alpha (ESR1), Estrogen Receptor beta (ESR2) and FSH receptor (FSHR) genes, are associated with ovarian stimulation and pregnancy outcome and may constitute a useful tool for ART experts for the prediction of this outcome. The aim of this study is to track differences in the distribution of gene polymorphisms among obese non-PCOS and non-obese patients concerning three distinct genes which are involved in the ovarian stimulation mechanism: PvuII polymorphism of ESR1 gene, RsaI polymorphism of ESR2 gene and Ser680Asn variation of FSHR gene, using restriction fragment length polymorphism analysis and real-time polymerase chain reaction. A total of 151 normally ovulating female patients underwent IVF or ICSI. Interestingly, the pregnancy rate in the BMI?30 kg/m group was higher in a statistically significant way (40.9% versus 17.8%, p=0.023). The obese patients of this study were in need of increased total FSH dose in order to achieve a satisfactory oocyte number (p<0.001) and needed more days of stimulation (p=0.002), but also presented lower basal FSH levels (p=0.032), which may explain, to an extend, the better pregnancy outcome. Concerning the polymorphisms of ESR1, ESR2 and FSHR genes, we did not observe differences in the genotype distribution when we compared the obese non-PCOS population with the non-obese population. Thus, obesity does not constitute an additional indication to perform a genetic analysis before entering an IVF/ICSI program. PMID:23614677

Anagnostou, Elli; Drakakis, Petros; Marinopoulos, Spyridon; Mavrogianni, Despina; Loutradis, Dimitrios

2013-07-01

217

Several genetic polymorphisms interact with overweight/obesity to influence serum lipid levels  

PubMed Central

Background Information about the interactions of single nucleotide polymorphisms (SNPs) and overweight/obesity on serum lipid profiles is still scarce. The present study was undertaken to detect ten SNPs and their interactions with overweight/obesity on serum lipid levels. Methods A total of 978 normal weight and 751 overweight/obese subjects of Bai Ku Yao were randomly selected from our previous stratified randomized cluster samples. Normal weight, overweight and obesity were defined as a body mass index (BMI) < 24, 2428, and > 28 kg/m2; respectively. Serum total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein (Apo) A1 and ApoB levels were measured. Genotyping of ATP-binding cassette transporter A1 (ABCA-1) V825I, acyl-CoA:cholesterol acyltransferase-1 (ACAT-1) rs1044925, low density lipoprotein receptor (LDL-R) AvaII, hepatic lipase gene (LIPC) -250G>A, endothelial lipase gene (LIPG) 584C>T, methylenetetrahydrofolate reductase (MTHFR) 677C>T, the E3 ubiquitin ligase myosin regulatory light chain-interacting protein (MYLIP) rs3757354, proprotein convertase subtilisin-like kexin type 9 (PCSK9) E670G, peroxisome proliferator-activated receptor delta (PPARD) +294T>C, and Scavenger receptor class B type 1 (SCARB1) rs5888 was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. The interactions were detected by factorial design covariance analysis. Results The genotypic and allelic frequencies of LIPC and PCSK9 were different between normal weight and overweight/obese subjects, the genotypic frequency of LIPG and allelic frequency of MYLIP were also different between normal weight and overweight/obese subjects (P < 0.05-0.001). The levels of TC, ApoA1 (ABCA-1); TC, LDL-C, ApoA1, ApoB and ApoA1/ApoB (LIPC); TG, HDL-C, and ApoA1 (LIPG); TC, HDL-C, LDL-C, ApoA1 and ApoB (MTHFR); HDL-C and ApoA1 (MYLIP) in normal weight subjects were different among the genotypes (P < 0.01-0.001). The levels of LDL-C, ApoB and ApoA1/ApoB (ABCA-1); HDL-C, ApoA1, ApoB and ApoA1/ApoB (LIPC); TC, HDL-C, ApoA1 and ApoB (LIPG); TC, TG, HDL-C, LDL-C, ApoA1 and ApoB (MTHFR); TC, TG and ApoB (MYLIP); TG (PCSK9); TG, ApoA1 and ApoB (PPARD); and TC, HDL-C, LDL-C, ApoA1 and ApoB (SCARB1) in overweight/obese subjects were different among the genotypes (P < 0.01-0.001). The SNPs of ABCA-1 (LDL-C and ApoA1/ApoB); LIPC (TC, LDL-C, ApoA1 and ApoB); LIPG (ApoB); MTHFR (TC, TG and LDL-C); MYLIP (TC and TG); PCSK9 (TG, HDL-C, ApoB and ApoA1/ApoB); PPARD (TG and ApoA1/ApoB); and SCARB1 (TG, ApoA1 and ApoB) interacted with overweight/obesity to influence serum lipid levels (P < 0.05-0.001). Conclusions The differences in serum lipid levels between normal weight and overweight/obese subjects might partly result from different genetic polymorphisms and the interactions between several SNPs and overweight/obesity. PMID:23039238

2012-01-01

218

Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)  

PubMed Central

Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

Holtgrawe, Daniela; Sorensen, Thomas Rosleff; Viehover, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

2014-01-01

219

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers  

PubMed Central

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3? untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3? UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, Stella was separated from Compact Stella. This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3? UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

220

Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.  

PubMed

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez I Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font I Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

221

Genetic Dissection of New Genotypes of Drumstick Tree (Moringa oleifera Lam.) Using Random Amplified Polymorphic DNA Marker  

PubMed Central

The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20 Moringa oleifera were carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twenty M. oleifera genotypes from various origins were collected and germinated and raised in nursery before transplanting to the field at University Agricultural Park (TPU). Genetic diversity parameter, such as Shannon's information index and expected heterozygosity, revealed the presence of high genetic divergence with value of 1.80 and 0.13 for Malaysian population and 0.30 and 0.19 for the international population, respectively. Mean of Nei's gene diversity index for the two populations was estimated to be 0.20. In addition, a dendrogram constructed, using UPGMA cluster analysis based on Nei's genetic distance, grouped the twenty M. oleifera into five distinct clusters. The study revealed a great extent of variation which is essential for successful breeding and improvement program. From this study, M. oleifera genotypes of wide genetic origin, such as T-01, T-06, M-01, and M-02, are recommended to be used as parent in future breeding program. PMID:23862149

Rufai, Shamsuddeen; Hanafi, M. M.; Rafii, M. Y.; Ahmad, S.; Arolu, I. W.; Ferdous, Jannatul

2013-01-01

222

Population genetics of four PKLR intragenic polymorphisms in Portugal and So Tom e Prncipe (Gulf of Guinea).  

PubMed

Four intragenic PKLR polymorphisms [1705A/C, 1738C/T. T10/19, and (ATT)n microsatellite] were studied in normal population samples of Central Portugal and So Tom e Prncipe, a small archipelago located in the Gulf of Guinea, West Africa. For all loci, the observed genotype distributions do not deviate from Hardy-Weinberg equilibrium. The allele frequencies found in the Portuguese population are similar to those previously described in Caucasian populations. Mother-child pair analysis for the (ATT)n microsatellite does not show deviations to the Mendelian rules. In So Tom e Prncipe the biallelic polymorphisms 1705A/C, 1738C/T, and T10/19 presented inverse allelic frequencies when compared with the Portuguese population. Two new alleles were found at the (ATT)n microsatellite. Significant statistical differences were found between both populations. The results showed that So Tomeans had higher haplotype diversity and lower linkage disequilibrium among the polymorphic sites. The PKLR intragenic polymorphisms, commonly used in haplotype analysis with the gene mutations in PK-deficient patients, can thus be successfully employed in anthropological genetics. PMID:11459427

Manco, L; Oliveira, A L; Gomes, C; Granjo, A; de Jesus Trovoada, M; Ribeiro, M L; Abade, A; Amorim, A

2001-06-01

223

MTLRP genetic polymorphism (214C>A) was associated with Type 2 diabetes in Caucasian population: a meta-analysis  

PubMed Central

Background Previous studies reported the relation between MTLRP genetic polymorphism and type 2 diabetes, however, the conclusion were conflicting. In the present study, we performed a meta-analysis to reveal this association. Methods Literature retrieval, selection and assessment, data extraction, and meta-analyses were performed according to the RevMan 5.0 guidelines. In the meta-analysis, we utilized random-effect model or fixed-effect model to pool the Odds ratio (OR) according to the test of heterogeneity. Results A total of nine casecontrol studies included 4460 type 2 diabetes patients and 4114 healthy control subjects were analyzed. We did not found association between the MTLRP polymorphism and type 2 diabetes risk in the overall population (CC vs CA?+?AA: OR?=?1.02; 95% CI: 0.89-1.17, P?=?0.77; A vs C: OR?=?1.02; 95% CI: 0.84-0.96, P?=?0.62). However, in subgroup analyses stratified by ethnicity, we found significant association of MTLRP polymorphism with type 2 diabetes in Caucasians (CC vs CA?+?AA: OR?=?1.27; 95% CI: 1.02-1.57, P?=?0.03; A vs C: OR?=?0.74, 95% CI: 0.600.91, P?=?0.005). Conclusion The MTLRP polymorphism was associated with type 2 diabetes in Caucasians. PMID:25095788

2014-01-01

224

Genetic Analysis and Discrimination of Sweet Cherry Cultivars and Selections Using Amplified Fragment Length Polymorphism Fingerprints  

Microsoft Academic Search

Amplified fragment length polymorphisms (AFLPs) were used to analyze the relationships between sweet cherry (Prunus avium L.) cultivars and selections from the breeding program at the Pacific Agri-Food Research Centre in Summerland, Canada. Six pairs of preselected primers were used for the analysis of a total of 67 cultivars and selections. Scoring the absence and presence of 118 polymorphic DNA

Lili Zhou; Frank Kappel; Cheryl Hampson; Paul A. Wiersma; Guus Bakkeren

225

Genetic Load in Natural Populations: Is It Compatible with the Hypothesis That Many Polymorphisms Are Maintained by Natural Selection?  

PubMed Central

Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster. PMID:4213125

Tracey, Martin L.; Ayala, Francisco J.

1974-01-01

226

Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids  

PubMed Central

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium II 8K array. We then evaluated this apple and pear Infinium II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (Old HomeבLouise Bon Jersey) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality. PMID:24155917

Troggio, Michela; Malnoy, Mickael; Velasco, Riccardo; Fontana, Paolo; Won, KyungHo; Durel, Charles-Eric; Perchepied, Laure; Schaffer, Robert; Wiedow, Claudia; Bus, Vincent; Brewer, Lester; Gardiner, Susan E.; Crowhurst, Ross N.; Chagne, David

2013-01-01

227

avpr1a length polymorphism is not associated with either social or genetic monogamy in free-living prairie voles.  

PubMed

Recent discoveries of single-gene influences on social behaviour have generated a great deal of interest in the proximate mechanisms underlying the expression of complex behaviours. Length polymorphism in a microsatellite in the regulatory region of the gene encoding the vasopressin 1a receptor (avpr1a) has been associated with both inter- and intra-specific variation in socially monogamous behaviour in voles (genus Microtus) under laboratory conditions. Here, we evaluate the relationship between avpr1a length polymorphism and social associations, genetic monogamy, and reproductive success in free-living prairie vole (M. ochrogaster) populations. We found no evidence of a relationship between avpr1a microsatellite length and any of our correlates of either social or genetic monogamy in the field. Our results, especially when taken in conjunction with those of recent experimental studies in semi-natural enclosures, suggest that avpr1a polymorphism is unlikely to have been a major influence in the evolution or maintenance of social monogamy in prairie voles under natural conditions. PMID:21442019

Mabry, Karen E; Streatfeild, Craig A; Keane, Brian; Solomon, Nancy G

2011-01-01

228

CHARLOTTE HARBOR IR, 2002  

EPA Science Inventory

The 2002 Charlotte Harbor Implementation Review (IR) summarizes the progress and challenges ahead for the Charlotte Harbor National Estuary Program (CHNEP). The implementation review report requires seven components: Status of CCMP implementation (programmatic progress); Environm...

229

Genetic polymorphism of dopamine D2 receptors in Parkinson's disease and interactions with cigarette smoking and MAO-B intron 13 polymorphism  

PubMed Central

Genetic polymorphisms of dopamine D2 receptors (DRD2) may be susceptibility factors for Parkinson's disease due to their influence on dopamine response and association with cigarette smoking, which is inversely related to risk of Parkinson's disease. Relations of TaqIA and TaqIB DRD2 genotypes with Parkinson's disease were investigated and tested for interactive effects with smoking and the monoamine oxidase B (MAO-B) intron 13 polymorphism previously found to be related to smoking. Study subjects were 152 cases of idiopathic Parkinson's disease and 231 controls. The smoking history of all genotyped subjects was known. Subjects of genotype B12 were more frequent among cases than controls (27% and 23.8%, respectively), and were more frequent among "ever smokers" than "never smokers", among controls (27.8% and 17.2%, respectively), although these associations were not statistically significant. Neither TaqIA or TaqIB genotypes modified the inverse relation of smoking and Parkinson's disease. When genotypes for DRD2 were considered in combination with genotypes for intron 13 of MAO-B, genotype combinations with high risk of Parkinson's disease were found; although the MAO-B/DRD2 interaction did not reach statistical significance after Bonferroni correction for multiple comparisons, these results are suggestive of a possible synergism between MAOB and DRD2 genes with respect to Parkinson's disease.?? PMID:10990520

Costa-Mallen, P.; Costa, L.; Smith-Weller, T.; Franklin, G.; Swanson, P.; Checkoway, H.

2000-01-01

230

Genetic polymorphisms in vitamin D receptor VDR/RXRA influence the likelihood of colon adenoma recurrence.  

PubMed

Low circulating levels of vitamin D affect colorectal cancer risk. The biological actions of the hormonal form of vitamin D, 1,25(OH)(2)D(3), are mediated by the vitamin D receptor (VDR), which heterodimerizes with retinoid X receptors (RXR). Using a single nucleotide polymorphism (SNP) tagging approach, we assessed the association between genetic variations in RXRA and VDR and odds of recurrent (metachronous) colorectal neoplasia in a pooled population of two studies. A total of 32 tag SNPs in RXRA and 42 in VDR were analyzed in 1,439 participants. A gene-level association was observed for RXRA and any (P = 0.04) or proximal (P = 0.03) metachronous neoplasia. No gene-level associations were observed for VDR, nor was any single SNP in VDR related to any metachronous adenoma after correction for multiple comparisons. In contrast, the association between RXRA SNP rs7861779 and proximal metachronous neoplasia was of borderline statistical significance [odds ratio (OR), 0.68; 95% confidence interval (95% CI), 0.53-0.86; unadjusted P = 0.001; adjusted P = 0.06], including when observed independently in each individual study. Haplotypes within linkage blocks of RXRA support an approximately 30% reduction in odds of metachronous neoplasia arising in the proximal colon among carriers of specific haplotypes, which was strongest (OR(proximal), 0.67; 95% CI, 0.52-0.86) for carriers of a CGGGCA haplotype (rs1805352, rs3132297, rs3132296, rs3118529, rs3118536, and rs7861779). Our results indicate that allelic variation in RXRA affects metachronous colorectal neoplasia, perhaps of particular importance in the development of proximal lesions. PMID:20145122

Egan, Jan B; Thompson, Patricia A; Ashbeck, Erin L; Conti, David V; Duggan, David; Hibler, Elizabeth; Jurutka, Peter W; Leroy, Elizabeth C; Martnez, Mara Elena; Mount, David; Jacobs, Elizabeth T

2010-02-15

231

Common genetic polymorphisms in the ABCB1 gene are associated with risk of major depressive disorder in male Portuguese individuals.  

PubMed

Major depressive disorder (MDD) is a highly prevalent disorder, which has been associated with an abnormal response of the hypothalamus-pituitary-adrenal (HPA) axis. Reports have argued that an abnormal HPA axis response can be due to an altered P-Glycoprotein (P-GP) function. This argument suggests that genetic polymorphisms in ABCB1 may have an effect on the HPA axis activity; however, it is still not clear if this influences the risk of MDD. Our study aims to evaluate the effect of ABCB1 C1236T, G2677TA and C3435T genetic polymorphisms on MDD risk in a subset of Portuguese patients. DNA samples from 80 MDD patients and 160 control subjects were genotyped using TaqMan SNP Genotyping assays. A significant protection for MDD males carrying the T allele was observed (C1236T: odds ratio (OR)=0.360, 95% confidence interval [CI]: [0.140-0.950], p=0.022; C3435T: OR=0.306, 95% CI: [0.096-0.980], p=0.042; and G2677TA: OR=0.300, 95% CI: [0.100-0.870], p=0.013). Male Portuguese individuals carrying the 1236T/2677T/3435T haplotype had nearly 70% less risk of developing MDD (OR=0.313, 95% CI: [0.118-0.832], p=0.016, FDR p=0.032). No significant differences were observed regarding the overall subjects. Our results suggest that genetic variability of the ABCB1 is associated with MDD development in male Portuguese patients. To the best of our knowledge, this is the first report in Caucasian samples to analyze the effect of these ABCB1 genetic polymorphisms on MDD risk. PMID:24200053

Santos, Marlene; Carvalho, Serafim; Lima, Lus; Nogueira, Augusto; Assis, Joana; Mota-Pereira, Jorge; Pimentel, Paulo; Maia, Dulce; Correia, Diana; Gomes, Sofia; Cruz, Agostinho; Medeiros, Rui

2014-01-01

232

Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.  

PubMed

Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature. PMID:24558460

Ophir, Ron; Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Sharabi Schwager, Michal; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Holland, Doron

2014-01-01

233

Genetic Diversity Among Populations of Red Palm Weevil, Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae), Determined by Random Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR)  

Microsoft Academic Search

This study reports the genetic variations between populations of the red palm weevil, Rhynchophorus ferrugineus in the UAE area. To test if the red palm weevil population in the UAE belongs to the same genetic group; the randomly amplified polymorphic DNA (RAPD) technique was used to assay seven populations of the insect from different locations. RAPD primer pairs detected a

G. G. GADELHAK; M. R. ENAN

234

Genetic variation in populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences  

Microsoft Academic Search

Intraspecific genetic variation in two species of calliphorid blowfly, Lucilia sericata and Lucilia cuprina, was studied by random amplified polymorphic DNA (RAPD) analysis and mitochondrial DNA (mtDNA) sequencing. These species are economically important facultative ectoparasites of sheep. Numerical analysis of RAPD fragment data was used to investigate genetic variation in L. sericata across Europe and in both L. sericata and

Jamie Stevens; Richard Wall

1997-01-01

235

Genetic variation in genes associated with arsenic metabolism: glutathione S-transferase omega 1-1 and purine nucleoside phosphorylase polymorphisms in European and indigenous Americans.  

PubMed Central

Individual variability in human arsenic metabolism has been reported frequently in the literature. This variability could be an underlying determinant of individual susceptibility to arsenic-induced disease in humans. Recent analysis revealing familial aggregation of arsenic metabolic profiles suggests that genetic factors could underlie interindividual variation in arsenic metabolism. We screened two genes responsible for arsenic metabolism, human purine nucleoside phosphorylase (hNP), which functions as an arsenate reductase converting arsenate to arsenite, and human glutathione S-transferase omega 1-1 (hGSTO1-1), which functions as a monomethylarsonic acid (MMA) reductase, converting MMA(V) to MMA(III), to develop a comprehensive catalog of commonly occurring genetic polymorphisms in these genes. This catalog was generated by DNA sequencing of 22 individuals of European ancestry (EA) and 24 individuals of indigenous American (IA) ancestry. In (Italic)hNP(/Italic), 48 polymorphic sites were observed, including 6 that occurred in exons, of which 1 was nonsynonymous (G51S). One intronic polymorphism occurred in a known enhancer region. In hGSTO1-1, 33 polymorphisms were observed. Six polymorphisms occurred in exons, of which 4 were nonsynonymous. In contrast to hNP, in which the IA group was more polymorphic than the EA group, in hGSTO1-1 the EA group was more polymorphic than the IA group, which had only 1 polymorphism with a frequency > 10%. Populations representing genetic admixture between the EA and IA groups, such as Mexican Hispanics, could vary in the extent of polymorphism in these genes based upon the extent of admixture. These data provide a framework in which to conduct genetic association studies of these two genes in relevant populations, thereby allowing hNP and hGSTO1-1 to be evaluated as potential susceptibility genes in human arsenicism. PMID:12928150

Yu, Lizhi; Kalla, Kelly; Guthrie, Erin; Vidrine, Amy; Klimecki, Walter T

2003-01-01

236

Genetic Diversity of Pinus Roxburghii Sarg. Collected from Different Himalayan Regions of India Assessed by Random Amplified Polymorphic DNA Analysis  

PubMed Central

Present study was aimed at molecular genetic fingerprint profile of 15 genotypes of three populations of Pinus roxburghii Sarg. from Himalayan regions of India using random amplified polymorphic DNA (RAPD) based markers. Needles of Pinus roxburghii Sarg. were collected from Dharamshala, Himachal Pradesh (HP), Nainital, Uttarakhand (UK) and Darjeeling, West Bengal (WB) regions of India. The samples were subjected to DNA extraction and RAPD analysis using oligonucleotide purification cartridge (OPC) primers. Out of 15 primers tested, nine primers gave scorable bands. Altogether 48 bands were obtained, out of which 43 were found to be polymorphic. Number of amplified fragments with RAPD primers ranged from four to eight with the size of amplicon ranging from 500 to 7,000bp. Investigation of natural diversity at intraspecies level was performed with 15 genotypes. Forty-eight amplification products were scored by RAPD and showed 89.58% polymorphism with a mean intrapopulation genetic diversity (Hpop) of 0.2754. A significant inter- and intrapopulation diversity was observed, with the percentage of polymorphic loci (Pp) ranging from 50.09 to 70.83%, Shannon's information index (I) from 0.3262 to 0.4689 and Nei's gene diversity (h) from 0.2032 to 0.3335 with mean Nei's gene diversity 0.377 and the overall estimate of gene flow being (Nm) 1.3555. Unweighted pair-group method with arithmetic average (UPGMA) analysis based Dendrogram showed single cluster. The variation amongst the samples of the three ecological regions can be attributed to varied climatic conditions and may help in conservation/future cultivation of these species. PMID:24403729

Sinha, Dwaipayan; Singh, Jyotsna; Tandon, P. K.; Kakkar, Poonam

2013-01-01

237

Blood pressure and urinary sodium excretion in relation to 16 genetic polymorphisms in the natriuretic peptide system in Chinese.  

PubMed

We systematically investigated the association between single nucleotide polymorphisms (SNPs) in the natriuretic peptide system (NPPA, NPPB, NPPC, NPRA, NPRC, and Corin genes) and blood pressure in a Chinese population. The study population was recruited from a mountainous area 500 km south of Shanghai from 2003 to 2009. Using the ABI SNapShot method, we first genotyped 951 subjects enrolled in 2005 for 16 SNPs and then the remaining 1355 subjects as validation for 5 SNPs selected from the primary study. Overall, the association of the studied genetic polymorphisms with blood pressure and urinary excretion of cations was weak or non-significant. However, in the primary study, there was significant (Pint=0.003) interaction between the rs198358 polymorphism and age in relation to diastolic blood pressure. After adjustment for covariates, diastolic blood pressure was significantly higher in the G allele carriers than AA homozygotes in 176 subjects aged 60 years or older (77.81.72 vs 73.91.54 mmHg, P=0.001). In the primary combined with validation studies, this interaction remained statistically significant (Pint=0.02). The odds ratio of hypertension for carrying the G allele versus AA homozygotes was 1.25 (95% CI: 1.03-1.52; P=0.03) in all subjects, and 0.85 (0.51-1.41; P=0.53), 1.30 (0.98-1.73; P=0.06), and 1.45 (0.95-2.22; P=0.08) in the subjects younger than 40 years, 40-59 years, and 60 years or older, respectively. Some of the genetic polymorphisms in the natriuretic peptide system might be associated with blood pressure. However, not only the size, but also the direction of the association may change with age. PMID:24954621

Hu, Bang-Chuan; Li, Yan; Liu, Ming; Li, Li-Hua; Sheng, Chang-Sheng; Zhang, Yi; Wang, Ji-Guang

2014-09-29

238

Effect of genetic polymorphisms of MnSOD and MPO on the relationship between PAH exposure and oxidative DNA damage.  

PubMed

To investigate the effect of genetic polymorphisms on the oxidative damage caused by PAH exposure, we measured urinary 1-hydroxypyrene (1-OHP) and 8-hydroxydeoxyguanosine (8-OHdG) levels to determine exposure and oxidative injury in university students. After examining myeloperoxidase (MPO) and manganese superoxide dismutase (MnSOD) genotypes by PCR and RFLP, we evaluated the effects of these polymorphisms on the relationship between the urinary levels of 1-OHP and 8-OHdG. No significant relation was observed between log 1-OHP and 8-OHdG concentrations in the whole study group (p=0.182), or between urinary 8-OHdG levels and polymorphisms of MnSOD or MPO (p=0.539 and 0.993, respectively). However, significant differences of regression coefficient were found for the relation between urinary log 1-OHP and urinary 8-OHdG concentrations in the presence of different MnSOD or MPO genotypes by multiple regression after controlling for age, sex, body mass index, cotinine, and smoking. In those with the MnSOD Val/Ala or Ala/Ala genotypes this regression coefficient was 1.480 (p=0.040), whereas for the MnSOD Val/Val genotype it was 0.088 (p=0.859). The higher regression coefficient was obtained for the subject group with the MnSOD Val/Ala or Ala/Ala genotype in combination with the MPO G/G genotype (p=0.012). We suggest that the oxidative injury caused by PAH exposure is modulated by genetic polymorphisms such as MnSOD and MPO. PMID:16084535

Park, So-Yeon; Lee, Kyoung-Ho; Kang, Daehee; Lee, Kwan-Hee; Ha, Eun-Hee; Hong, Yun-Chul

2006-01-29

239

First Insights into the Genetic Diversity of the Pinewood Nematode in Its Native Area Using New Polymorphic Microsatellite Loci  

PubMed Central

The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed. PMID:23554990

Mallez, Sophie; Castagnone, Chantal; Espada, Margarida; Vieira, Paulo; Eisenback, Jonathan D.; Mota, Manuel; Guillemaud, Thomas; Castagnone-Sereno, Philippe

2013-01-01

240

HLA-DR polymorphism in a Senegalese Mandenka population: DNA oligotyping and population genetics of DRB1 specificities.  

PubMed Central

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1*1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequent specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52b (DRB3*02) represents as much as 80.7% of all DR52 haplotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the Mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes. PMID:1496990

Tiercy, J M; Sanchez-Mazas, A; Excoffier, L; Shi-Isaac, X; Jeannet, M; Mach, B; Langaney, A

1992-01-01

241

Genetic Polymorphism and Molecular Epidemiology of Leishmania (Viannia) braziliensis from Different Hosts and Geographic Areas in Brazil  

PubMed Central

Numerical zymotaxonomy and variability of the internal transcribed spacers (ITS) between the small and large subunits of the rRNA genes were used to examine strain variation and relationships in natural populations of Leishmania (Viannia) braziliensis. A total of 101 strains from distinct hosts and Brazilian geographic regions were assigned to 15 zymodemes clustered in two major genetic groups. The great number of isolates (48.5%) placed in zymodeme IOC/Z-27 were collected on the Atlantic coast. The high molecular diversity found in populations in the Amazon Basin was related to the great number of sandfly vector(s) in that region. The results of the restriction fragment length polymorphism analysis of the ITS depicted considerable intraspecific variation. Genotypic groups A, B, and C contained 39, 40, and 22 isolates, which were divided into 16, 10, and 15 genotypes, respectively. The genetic polymorphism observed demonstrates the degree of diversity of L. (V.) braziliensis strains from different regions where they are endemic. The results reinforce the clonal theory for Leishmania parasites showing the genetic diversity of this pathogen and an association of L. (V.) braziliensis genotypes with specific transmission cycles, probably reflecting an adaptation of different clones to the vector species involved. PMID:12843052

Cupolillo, Elisa; Brahim, Lcia Regina; Toaldo, Cristiane B.; de Oliveira-Neto, Manoel Paes; de Brito, Maria Edileuza Felinto; Falqueto, Aloisio; de Farias Naiff, Maricleide; GrimaldiJr., Gabriel

2003-01-01

242

Genetic polymorphism at an odorant receptor gene (Or39) among mosquitoes of the Anopheles gambiae complex in Senegal (West Africa)  

PubMed Central

Background Olfaction plays a significant role in insect behavior during critical steps of their life-cycle, such as host-seeking during foraging or the search for a mate. Here, we explored genetic polymorphism within and divergence between sibling species of the African malaria mosquito, Anopheles gambiae sensu lato in the gene sequence and encoded peptides of an odorant receptor, Or39. This study included sympatric specimens of An. gambiae sensu stricto, An. coluzzii and An. arabiensis sampled together in the village of Dielmo, Senegal. Results A 1,601bp genomic sequence composed of 6 exons and 5 introns was obtained for Or39 from 68 mosquitoes in each of the 3 species. DNA sequence analysis revealed a high level of molecular polymorphism (??=?0.0154; Haplotype diversity?=?0.867) and high overall genetic differentiation between taxa (Fst?>?0.92, P?polymorphisms in An. gambiae and An. arabiensis as well as species-specific mutations also occurred in the first extracellular domain. Conclusions Although obtained from a limited number of specimens, our results point towards genetic differences between cryptic species within the An. gambiae complex in a gene of biological relevance that might be of evolutionary significance when exposed to disruptive selective forces. PMID:24886539

2014-01-01

243

Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii.  

PubMed

The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ?11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N6717XNL) to the microarray showed that the array had a high call rate (?97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes. PMID:24685548

Nair, Sethu C; Pattaradilokrat, Sittiporn; Zilversmit, Martine M; Dommer, Jennifer; Nagarajan, Vijayaraj; Stephens, Melissa T; Xiao, Wenming; Tan, John C; Su, Xin-Zhuan

2014-01-01

244

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh  

PubMed Central

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.420.14 in zebu to 0.1480.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies. PMID:25178287

Uzzaman, Md. Rasel; Edea, Zewdu; Bhuiyan, Md. Shamsul Alam; Walker, Jeremy; Bhuiyan, A. K. F. H.; Kim, Kwan-Suk

2014-01-01

245

Genetic Polymorphisms of Hypoxia-Inducible Factor1 Alpha and Cardiovascular Disease in Hemodialysis Patients  

Microsoft Academic Search

Background: Hemodialysis patients are prone to ischemic events potentially aggravated by hypoxia. The key player in adaptation to hypoxia is hypoxia-inducible factor-1 alpha (HIF-1?). Therefore, we investigated the association of HIF-1? polymorphisms with ischemia\\/hypoxia-related events in hemodialysis patients. Methods: Patients on maintenance hemodialysis were enrolled from 4 training hospitals in Korea. Seven single nucleotide polymorphisms (SNP) of HIF-1? were genotyped.

Zhen Lon Zheng; Young-Hwan Hwang; Seong Kyun Kim; Sejoong Kim; Min Jung Son; Han Ro; Su-Ah Sung; Hyun Hee Lee; Woo Kyung Chung; Kwon Wook Joo; Jaeseok Yang

2009-01-01

246

Human Population Genetic Structure and Diversity Inferred from Polymorphic L1(LINE1) and Alu Insertions  

Microsoft Academic Search

Background\\/Aims: The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure. Methods: We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations

D. J. Witherspoon; E. E. Marchani; W. S. Watkins; C. T. Ostler; S. P. Wooding; B. A. Anders; J. D. Fowlkes; S. Boissinot; A. V. Furano; D. A. Ray; A. R. Rogers; M. A. Batzer; L. B. Jorde

2006-01-01

247

CYP17 genetic polymorphism in endometrial cancer: are only steroids involved?  

Microsoft Academic Search

Initiation and\\/or promotion of endometrial cancer is known to be associated with estrogen and androgen (androstenedione) excess as well as with hyperinsulinemia\\/insulin resistance. It is possible that some allelic polymorphisms of the genes involved in steroidogenesis or steroid metabolism contribute to endometrial cancer susceptibility. We evaluated here the role of CYP17 biallelic (MspAI) polymorphism in 114 endometrial cancer patients compared

Lev M Berstein; Evgeny N Imyanitov; Vera B Gamajunova; Anatolij Ju Kovalevskij; Ekatherina Sh Kuligina; Evgeniya V Belogubova; Konstantin G Buslov; Maria B Karpova; Alexandr V Togo; Oleg N Volkov; Irina G Kovalenko

2002-01-01

248

Genetic Polymorphisms of Angiotensinogen and Essential Hypertension in a Tibetan Population  

Microsoft Academic Search

The human angiotensinogen gene (AGT) is a promising candidate for an essential hypertension-susceptibility gene. We aimed to explore the single-locus, haplotype and epistasis patterns of three polymorphisms of AGT (A?20C, A?6G and M235T) and their relation to the risk of essential hypertension in a Tibetan population. The three polymorphisms were genotyped in 333 essential hypertension patients and 235 healthy controls

Wenquan Niu; Yue Qi; Weijun Cen; Chaoying Cui; Ciren Zhuoma; Dan Cai; Wenyu Zhou; Changchun Qiu

2007-01-01

249

Analysis of phenotypic and genetic polymorphism among accessions of saltgrass ( Distichlis spicata )  

Microsoft Academic Search

Morphological and genetic analyses were applied on 37 saltgrass (Distichlis spicata) accessions collected from distant locations throughout the American continent in order to: 1) develop and identify morphologic and genetic profiles for the saltgrass genotypes; 2) characterize the genetic distance among saltgrass accessions within the given germplasm collection; and 3) identify a possible linkage between patterns of genetic and eco-geographical

Assael Ram; Michele Zaccai; Dov Pasternak; Amnon Bustan

2004-01-01

250

Genetic characterization of Phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial DNA.  

PubMed

A new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in DNA sequences was developed and applied to the study of the plant pathogen Phytophthora nicotianae. Two regions flanked by genes trnY and rns and trnW and cox2 were identified by comparing the whole mitochondrial genomes of Phytophthora infestans, Phytophthora ramorum, and Phytophthora sojae and amplified using primers designed from the flanking conserved genes. These regions were sequenced from 51 isolatesof P. nicotianae of both A1 and A2 mating type recovered from different hosts and geographic regions. Amplicon length varied from 429bp to 443bp (trnY/rns) and 322bp to 373bp (trnW/cox2) with intraspecific variation due to single nucleotide polymorphisms and indels. Seventeen, seven and 20 different haplotypes were detected by individually analyzing regions trnY-rns, trnW-cox2 and the combined data set of sequences from both regions, respectively. Phylogenetic analysis inferred with three different methods enabledthe grouping of isolates in five clades, each containing different mitochondrial haplotypes and revealed diversity in the mitochondrial genome of P. nicotianae. The majority of isolates from citrus grouped in a single clade indicating either movement of isolates on planting stock or an association of particular isolates with this host. Phylogenetic groups were not correlated with the radial growth rate of the isolates or the rapidity of appleflesh colonization. The method developed in the present study represents an innovative molecular tool for the characterization of natural populations of P. nicotianae and should be easily expanded to other species of Phytophthora as well as other plant pathogens. It can be used to track specific haplotypes and, thanks to its high genetic resolution, it could be standardized and applied in a DNA barcoding like strategy for the precise identification of sub-specific taxa. Compared to alternative molecular methods, a major advantage is that results are unbiased (a list of nucleotides) and highly reproducible, thus enabling the comparisonof data from different laboratories and time periods. Furthermore, the method could be further enhanced by the identification of additional variable mitochondrial and/or nuclear genomic regions. PMID:21530925

Mammella, Marco Antonio; Cacciola, Santa Olga; Martin, Frank; Schena, Leonardo

2011-01-01

251

Genetic Risk Assessment of Type 2 Diabetes-Associated Polymorphisms in African Americans  

PubMed Central

OBJECTIVE Multiple single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D) susceptibility have been identified in predominantly European-derived populations. These SNPs have not been extensively investigated for individual and cumulative effects on T2D risk in African Americans. RESEARCH DESIGN AND METHODS Seventeen index T2D risk variants were genotyped in 2,652 African American case subjects with T2D and 1,393 nondiabetic control subjects. Individual SNPs and cumulative risk allele loads were assessed for association with risk for T2D. Cumulative risk was assessed by counting risk alleles and evaluating the difference in cumulative risk scores between case subjects and control subjects. A second analysis weighted risk scores (ln [OR]) based on previously reported European-derived effect sizes. RESULTS Frequencies of risk alleles ranged from 8.6 to 99.9%. Eleven SNPs had ORs >1, and 5 from ADAMTS9, WFS1, CDKAL1, JAZF1, and TCF7L2 trended or had nominally significant evidence of T2D association (P < 0.05). Individuals carried between 13 and 29 risk alleles. Association was observed between T2D and increase in risk allele load (unweighted OR 1.04 [95% CI 1.011.08], P = 0.010; weighted 1.06 [1.031.10], P = 8.10 10?5). When TCF7L2 SNP rs7903146 was included as a covariate, the risk score was no longer associated with T2D in either model (unweighted 1.02 [0.981.05], P = 0.33; weighted 1.02 [0.981.06], P = 0.40). CONCLUSIONS The trend of increase in risk for T2D with increasing risk allele load is similar to observations in European-derived populations; however, these analyses indicate that T2D genetic risk is primarily mediated through the effect of TCF7L2 in African Americans. PMID:22275441

Cooke, Jessica N.; Ng, Maggie C.Y.; Palmer, Nicholette D.; An, S. Sandy; Hester, Jessica M.; Freedman, Barry I.; Langefeld, Carl D.; Bowden, Donald W.

2012-01-01

252

MTHFR/p53 polymorphisms as genetic factors for cervical intraepithelial neoplasia and cervical cancer in HPV-infected Mexican women.  

PubMed

We performed a case-control association study to evaluate the association between common polymorphisms in MTHFR (C677T and A1298C) and the Arg72Pro polymorphism in the p53 gene and the risk for cervical intraepithelial neoplasia (CIN) or invasive cervical cancer (ICC) in Mexican HPV-infected women. We included 131 women with diagnosis of CIN grade I-II and 78 with CIN III or ICC; as controls we also included 274 women with normal Pap smear and negative HPV test. Genotyping for MTHFR and p53 polymorphisms was performed by PCR-RFPLs. HPV was tested by Hybrid Capture II. Odds ratios and 95% confidence intervals were estimated. Genotype frequencies for the 3 studied polymorphisms were distributed according to the Hardy-Weinberg equilibrium. The A1298C-MTHFR polymorphism showed significant differences for the heterozygous AC genotype and the C allele, whereas the AA genotype and A allele resulted to be genetic risk factors for CIN or ICC (p<0.03). The Arg72Pro-p53 polymorphism showed for the genotypes Arg/Pro and Pro/Pro, and for the Pro allele, a significant association only to the risk for CIN (p<0.03). The MTHFR/p53 interaction showed that the genotype combinations AA/ArgArg and AA/ArgPro were associated, respectively, to the risk of ICC and CIN (p<0.05). This study suggests that the A1298C-MTHFR polymorphism contributes to the genetic risk for both CIN and ICC, whereas the Arg72Pro-p53 polymorphism only contributes to the risk for CIN. The MTHFR/p53 genetic combinations AA/ArgArg and AA/ArgPro are associated genetic risk factors for ICC and CIN in Mexican HPV-infected women. PMID:24474455

Gonzlez-Herrera, Lizbeth; Rodrguez-Morales, Patricia; Gonza Lez-Losa, Mara Del Refugio; Prez-Mendoza, Gerardo; Canul-Canch, Jaqueline; Rosado-Lpez, Ivn; Cetina, Thelma Canto de

2014-01-01

253

The 894G>T endothelial nitric oxide synthase genetic polymorphism affects hemodynamic responses to mental stress performed before and after exercise  

Microsoft Academic Search

Nitric oxide is the primary mediator of vasodilation during mental stress. Since genetic polymorphisms in the nitric oxide\\u000a synthase (eNOS) gene seem to impair the production of NO, this study aimed to evaluate the effect of an exercise bout on hemodynamic\\u000a responses to mental stress in subjects with the 894G>T polymorphism of eNOS. Subjects without (wild-type group; n=16) or with

Natlia Galito Rocha; Fabricia Junqueira Neves; Bruno Moreira Silva; Allan Robson Kluser Sales; Antonio Claudio Nbrega

254

Genetic diversity in potato field populations of Thanatephorus cucumeris AG-3, revealed by ITS polymorphism and RAPD markers.  

PubMed

DNA sequence analysis of the internal transcribed spacer region 1 (ITS1) and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability in relation to agronomic and regional factors among 60 isolates of Thanatephorus cucumeris (anamorph Rhizoctonia solani) collected from lesions on potato stems or sclerotia of potato tubers. Based on comparative sequence analysis it was shown that all isolates belonged to anastomosis group 3 subgroup Potato Type (AG-3 PT). ITS1 sequence polymorphisms were found within 45 of the 60 isolates showing that different types of the ITS-region are present in individual isolates. Cloning and sequence analysis of the ITS1 region from three selected isolates with sequence polymorphism showed that two different ITS1-types were present in each isolate. RAPD analysis identified 51 RAPD-phenotypes among the 60 investigated isolates indicating a high level of diversity within the subgroup AG-3 PT. Putative clonal isolates with identical RAPD- and ITS1-types were identified within fields, and in one case the same phenotype was found in two different fields separated by several hundred kilometers. Population subdivision analysis based on phenotypic as well as genotypic diversities showed differentiation among populations from different fields when isolates were sampled from tubers, indicating restricted gene flow among soil populations. Low differentiation was seen among field populations sampled from stems, indicating that gene flow is taking place. The population structure was not influenced by the previous crop in the rotation nor by the two cultivars 'Sava' and 'Bintje'. PMID:15000234

Justesen, Annemarie Fejer; Yohalem, David; Bay, Anne; Nicolaisen, Mogens

2003-11-01

255

Association Between Genetic Polymorphisms in the ADAM33 Gene and Asthma Risk: A Meta-Analysis.  

PubMed

The aim of this study was to evaluate the associations between the rs3918396 G>A and rs528557 C>G polymorphisms in the disinterring and metalloproteinase domain 33 (ADAM33) gene and asthma risk. We searched CISCOM, CINAHL, Web of Science, PubMed, Google Scholar, EBSCO, Cochrane Library, and CBM databases from inception through August 1st, 2013 without language restrictions. Meta-analysis was performed using the STATA 12.0 software. Crude odds ratios (ORs) with their 95% confidence intervals (95% CI) were calculated. Thirteen case-control studies were included with a total of 7104 asthma patients and 8172 healthy controls. Our meta-analysis results revealed that ADAM33 rs528557 C>G polymorphism was associated with an increased risk of asthma (all p<0.05). However, we found no correlation between the ADAM33 rs3918396 G>A polymorphism and asthma risk (all p>0.05). Subgroup analysis by ethnicity indicated that the ADAM33 rs528557 C>G polymorphism might be strongly associated with an increased risk of asthma among both Caucasian and Asian populations (All p<0.05). No significant association was found between the ADAM33 rs3918396 G>A polymorphism and the risk of asthma among the studied ethnicities (All p>0.05). The present meta-analysis suggests that the ADAM33 rs528557 C>G polymorphism may contribute to susceptibility to asthma. Thus, the ADAM33 rs528557 C>G polymorphism may be utilized as a biomarker for early diagnosis of asthma. PMID:25068505

Liu, Yu; Wang, Zhi-He; Zhen, Wei; Lu, Si-Jing; Liu, Zhong; Zou, Ling-Yun; Xu, Jin-Jiang

2014-11-01

256

Association of Four Genetic Polymorphisms of AGER and Its Circulating Forms with Coronary Artery Disease: A Meta-Analysis  

PubMed Central

Background Considerable efforts have been devoted to evaluating the association of the receptor for advanced glycation end-products (gene AGER and protein: RAGE) genetic variants to coronary artery disease (CAD); the results, however, are often irreproducible. To generate more information, we sought to explore four common polymorphisms of AGER and its circulating forms associated with the risk of CAD via a meta-analysis. Methodology/Principal Findings Articles were identified by searching PubMed, EMBASE, Wanfang and CNKI databases before March 2013. Qualified articles had case-control designs and investigated AGER four polymorphisms (T-429C, T-374A, Gly82Ser, G1704A) or circulating soluble RAGE (sRAGE) or endogenous secretory RAGE (esRAGE) levels associated with CAD. Twenty-seven articles involving 39 independent groups fulfilled the predefined criteria. Overall, no significance was observed for all examined polymorphisms under allelic and dominant models. When restricting groups to CAD patients with diabetes mellitus or renal disease, deviations of risk estimates from the unity were stronger than overall estimates for all polymorphisms except for G1704A due to limited available studies. For example, under dominant model, having -429C allele increased the odds of developing CAD in diabetic patients by 1.22-fold (95% confidence interval (95% CI) 0.991.51; P?=?0.06; I2?=?6.7%) compared with that of overall estimate of 1.15-fold (95% CI: 0.971.36; P?=?0.111; I2?=?18.0%). Circulating sRAGE levels were non-significantly lower in CAD patients than in controls, whereas this reduction was totally and significantly reversed in CAD patients with diabetes mellitus (weighted mean difference: 185.71 pg/ml; 95% CI: 106.82 to 264.61 pg/ml). Circulating esRAGE levels were remarkably lower in CAD patients, as well as in subgroups with or without diabetes mellitus and without renal disease. Conclusions Our findings demonstrated that association of AGER genetic polymorphisms with CAD was potentiated in patients with diabetes mellitus or renal disease. Practically, circulating esRAGE might be a powerful negative predictor for the development of CAD. PMID:23894685

Li, Xiaobo; Li, Yuqiong; Chu, Shaoli; Zhu, Dingliang; Shen, Weifeng; Lin, Jinxiu; Niu, Wenquan

2013-01-01

257

Relationships of glycoproteins IIb-IIIa and Ib content with mean platelet volume and their genetic polymorphisms.  

PubMed

Quantity of platelet adhesion molecules significantly varies in normal donors and cardiovascular patients and might be affected by platelet size and genetic variations. In this study, we assessed relationships of the content of glycoprotein (GP) IIb-IIIa and GPIb with mean platelet volume (MPV) and their genetic polymorphisms. MPV and GPIIb-IIIa and GPIb numbers were measured in 116 patients with acute coronary syndrome (ACS) at days 1, 3-5 and 8-12 after disease onset and in 32 healthy volunteers. GPIIb-IIIa and GPIb allelic variants were determined in ACS patients. Strong interactions of GPIIb-IIIa and GPIb numbers and MPV were observed in ACS patients and healthy volunteers. In patients, coefficients of correlation (r) were 0.642 and 0.510 (analysis of individual mean values) and in volunteers - 0.594 and 0.508 for GPIIb-IIIa and GPIb, respectively (everywhere P?genetic polymorphisms [GPIIIa Leu33Pro, GPIb? Thr145Met and GPIb? (-5)T/C (Kozak)] determined in ACS patients had no significant impact on their expression. Modest correlation was revealed between MPV and plasma thrombopoietin (TPO) measured at the first day of ACS (r?=?0.279, P?=?0.005). The data obtained indicated that GPIIb-IIIa and GPIb levels are mainly affected by platelet size (MPV) but not by their genetic variations. In some ACS patients, production of large platelets with high GPIIb-IIIa and GPIb contents might be stimulated by elevated TPO. PMID:23941967

Khaspekova, Svetlana G; Zyuryaev, Ilia T; Yakushkin, Vladimir V; Sirotkina, Olga V; Zaytseva, Natalia O; Ruda, Mikhail Y; Panteleev, Mikhail A; Mazurov, Alexey V

2014-03-01

258

A Functional TNFAIP2 3'-UTR rs8126 Genetic Polymorphism Contributes to Risk of Esophageal Squamous Cell Carcinoma  

PubMed Central

Background Accumulated evidences demonstrated that single nucleotide polymorphisms (SNPs) in mRNA 3'-untranslated region (3'-UTR) may impact microRNAs (miRNAs)-mediated expression regulation of oncogenes and tumor suppressors. There is a TNFAIP2 3'-UTR rs8126 T>C genetic variant which has been proved to be associated with head and neck cancer susceptibility. This SNP could disturb binding of miR-184 with TNFAIP2 mRNA and influence TNFAIP2 regulation. However, it is still unclear how this polymorphism is involved in development of esophageal squamous cell carcinoma (ESCC). Therefore, we hypothesized that the functional TNFAIP2 rs8126 SNP may affect TNFAIP2 expression and, thus, ESCC risk. Methods We investigated the association between the TNFAIP2 rs8126 variant and ESCC risk as well as the functional relevance on TNFAIP2 expression in vivo. Genotypes were determined in a case-control set consisted of 588 ESCC patients and 600 controls. The allele-specific regulation on TNFAIP2 expression by the rs8126 SNP was examined in normal and cancerous tissue specimens of esophagus. Results We found that individuals carrying the rs8126 CC or CT genotype had an OR of 1.89 (95%CI ?=?1.232.85, P?=?0.003) or 1.38 (95%CI ?=?1.051.73, P?=?0.017) for developing ESCC in Chinese compared with individual carrying the TT genotype. Carriers of the rs8126 CC and CT genotypes had significantly lower TNFAIP2 mRNA levels than those with the TT genotypes in normal esophagus tissues (P<0.05). Conclusions Our data demonstrate that functional TNFAIP2 rs8126 genetic variant is a ESCC susceptibility SNP. These results support the hypothesis that genetic variants interrupting miRNA-mediated gene regulation might be important genetic modifiers of cancer risk. PMID:25383966

Zhang, Jian; Yu, Hongchen; Zhang, Yi; Zhang, Xiaoshi; Zheng, Guixin; Gao, Yang; Wang, Chuanxin; Zhou, Liqing

2014-01-01

259

Genetic Polymorphisms in CYP2E1: Association with Schizophrenia Susceptibility and Risperidone Response in the Chinese Han Population  

PubMed Central

Background CYP2E1 is a member of the cytochrome P450 superfamily, which is involved in the metabolism and activation of both endobiotics and xenobiotics. The genetic polymorphisms of CYP2E1 gene (Chromosome 10q26.3, Accession Number NC_000010.10) are reported to be related to the development of several mental diseases and to be involved in the clinical efficacy of some psychiatric medications. We investigated the possible association of CYP2E1 polymorphisms with susceptibility to schizophrenia in the Chinese Han Population as well as the relationship with response to risperidone in schizophrenia patients. Methods In a case-control study, we identified 11 polymorphisms in the 5' flanking region of CYP2E1 in 228 schizophrenia patients and 384 healthy controls of Chinese Han origin. From among the cases, we chose 130 patients who had undergone 8 weeks of risperidone monotherapy to examine the relationship between their response to risperidone and CYP2E1 polymorphisms. Clinical efficacy was assessed using the Brief Psychiatric Rating Scale (BPRS). Results Statistically significant differences in allele or genotype frequencies were found between cases and controls at rs8192766 (genotype p?=?0.0048, permutation p?=?0.0483) and rs2070673 (allele: p?=?0.0018, permutation p?=?0.0199, OR?=?1.4528 95%CI?=?1.14871.8374; genotype: p?=?0.0020, permutation p?=?0.0225). In addition, a GTCAC haplotype containing 5 SNPs (rs3813867, rs2031920, rs2031921, rs3813870 and rs2031922) was observed to be significantly associated with schizophrenia (p?=?7.47E-12, permutation p<0.0001). However, no association was found between CYP2E1 polymorphisms/haplotypes and risperidone response. Conclusions Our results suggest that CYP2E1 may be a potential risk gene for schizophrenia in the Chinese Han population. However, polymorphisms of the CYP2E1 gene may not contribute significantly to individual differences in the therapeutic efficacy of risperidone. Further studies in larger groups are warranted to confirm our results. PMID:22606226

Wei, Zhiyun; Shen, Lu; Xiong, Yuyu; Wu, Xi; Niu, Jiamin; Han, Xia; Tian, Zhengan; Yang, Lun; Feng, Guoyin; He, Lin; Qin, Shengying

2012-01-01

260

Genetic Polymorphisms Influence the Ovarian Response to rFSH Stimulation in Patients Undergoing In Vitro Fertilization Programs with ICSI  

PubMed Central

Introduction Obtaining an adequate number of high-quality oocytes is a major challenge in controlled ovarian hyperstimulation (COH). To date, a range of hormonal and clinical parameters have been used to optimize COH but none have significant predictive value. This variability could be due to the genetic predispositions of single-nucleotide polymorphisms (SNPs). Here, we assessed the individual and combined impacts of thirteen SNPs that reportedly influence the outcome of in vitro fertilisation (IVF) on the ovarian response to rFSH stimulation for patients undergoing intracytoplasmic sperm injection program (ICSI). Results Univariate analysis revealed that only FSHR, ESR2 and p53 SNPs influenced the number of mature oocytes. The association was statistically significant for FSHR (p=0.0047) and ESR2 (0.0017) in the overall study population and for FSHR (p=0.0009) and p53 (p=0.0048) in subgroup that was more homogeneous in terms of clinical variables. After Bonferroni correction and a multivariate analysis, only the differences for FSHR and ESR2 polymorphisms were still statistically significant. In a multilocus analysis, only the FSHR and AMH SNP combination significantly influenced oocyte numbers in both population (p<0.01). Discussion We confirmed the impact of FSHR and ESR2 polymorphisms on the IVF outcome. Furthermore, we showed for the first time that a p53 polymorphism (which is already known to impact embryo implantation) could influence the ovarian response. However, given that this result lost its statistical significance after multivariate analysis, more data are needed to draw firm conclusions. Only the FSHR and AMH polymorphism combination appears to influence mature oocyte numbers but this finding also needs to be confirmed. Materials and Methods A 13 gene polymorphisms: FSHR(Asn680Ser), p53(Arg72Pro), AMH(Ile49Ser), ESR2(+1730G>A), ESR1(?397T>C), BMP15(?9C>G), MTHFR1(677C>T), MTHFR2(1298A>C), HLA-G(?725C>G), VEGF(+405G>C), TNF?(?308A>G), AMHR(?482 A>G), PAI-1 (4 G/5 G), multiplex PCR assay was designed to genotype women undergoing ICSI program. We analyzed the overall study population (n=427) and a subgroup with homogeneous characteristics (n=112). PMID:22701696

Boudjenah, Radia; Molina-Gomes, Denise; Torre, Antoine; Bergere, Marianne; Bailly, Marc; Boitrelle, Florence; Taieb, Stephane; Wainer, Robert; Benahmed, Mohamed; de Mazancourt, Philippe; Selva, Jacqueline; Vialard, Francois

2012-01-01

261

Conservation genetics of bush mango from central/west Africa: implications from random amplified polymorphic DNA analysis.  

PubMed

Genetic variation was assessed in the two bush mango species, Irvingia gabonensis and I. wombolu, valuable multipurpose fruit trees from central and west Africa that are currently undergoing domestication. A total of 130 individuals sampled from Cameroon, Nigeria and Gabon were analysed using 74 random amplified polymorphic DNAs (RAPDs). Significant genetic integrity was found in the two morphologically similar species (among-species analysis of molecular variance [AMOVA] variance component 25.8%, P < 0.001), with no evidence of hybridization, even between individuals from areas of sympatry where hybridization was considered probable. Results suggest that large-scale transplantation of either species into new habitats will probably not lead to genetic introgression from or into the other species. Therefore, subsequent cultivation of the two species should not be hindered by this consideration, although further studies on the potential for hybridization/introgression between these species would be prudent. Significant genetic differentiation of both species (among-countries within species, nested AMOVA variance component 9.8%, P < 0.001) was observed over the sampled regions, and genetic similarity of samples decreased significantly with increasing geographical distance, according to number of alleles in common (NAC) analysis. 'Hot spots' of genetic diversity were found clustered in southern Nigeria and southern Cameroon for I. wombolu, and in southern Nigeria, southern Cameroon and central Gabon for I. gabonensis. The possible reasons for this distribution of genetic variation are discussed, but it may reflect evolutionary history, as these populations occur in areas of postulated Pleistocene refugia. The application of these results to domestication programmes and, in the light of extensive deforestation in the region, conservation approaches, is discussed. PMID:10886647

Lowe, A J; Gillies, A C; Wilson, J; Dawson, I K

2000-07-01

262

New genetic variants in the CCR5 gene and the distribution of known polymorphisms in Omani population.  

PubMed

C-C motif chemokine receptor-5 (CCR5) is a pro-inflammatory receptor that binds to chemokines and facilitates the entry of the R5 strain of HIV-1. A number of polymorphisms were identified within the promoter and coding regions of the CCR5 gene, some of which have been found to affect the protein expression and thus receptor function. Although several CCR5 polymorphisms were shown to vary widely in their distribution among different ethnic populations, there has been no study addressing the potential variants of the CCR5 gene in the Omani population. The aim of this study was to identify the polymorphic sites that exist within the CCR5 gene in Omanis. Blood samples were collected from 89 Omani adult individuals, and genomic DNA was amplified by polymerase chain reaction and sequenced to identify the polymorphic sites. The distribution of the detected variants was examined and compared with the previously published data. Four new indels were detected of 32 variable positions, -2973A/-, -2894A/-, -2827TA/- and -2769T/-, and all were located in the 5'UTR. Furthermore, two new mutations, -2248G/A and +658A/G, were observed for the first time; the -2248G/A was detected in the intron 1 region in one subject and +658A/G in the coding region of the CCR5 in another subject. In silico analysis showed that the novel variations in the 5'UTR may have effects on the transcription factor binding sites. Therefore, this study demonstrates the presence of two new SNPs and four novel indels in the CCR5 gene in the Omani population. Our findings support the wide spectrum of genetic diversity reported within the CCR5 gene region among different ethnic groups. PMID:23953748

Al-Mahruqi, S H; Zadjali, F; Koh, C Y; Balkhair, A; Said, E A; Al-Balushi, M S; Hasson, S S; Al-Jabri, A A

2014-02-01

263

Genetic Polymorphisms of XRCC1 and Leukemia Risk: A Meta-Analysis of 19 Case-Control Studies  

PubMed Central

Objective Three common X-ray repair cross-complementing groups 1 (XRCC1) polymorphisms, Arg399Gln, Arg194Trp, and Arg280His, have been reported to be implicated in the development of leukemia. However, previous results from different studies were inconsistent. Consequently, we performed a meta-analysis in order to accurately evaluate the association between XRCC1 Arg399Gln, Arg194Trp, and Arg280His polymorphisms and leukemia risk. Methods Through computerized searching of PubMed, ISI Web of Knowledge, Cochrane, EBSCO, and OpenGrey databases, and manually searching relevant references, a total of 19 studies with 3387 cases and 6168 controls for Arg399Gln (G>A) polymorphism, 12 studies with 2043 cases and 4550 controls for Arg194Trp (C>T), and 6 studies with 1445 cases and 1905 controls for Arg280His (G>A) were collected to perform meta-analysis and stratified analysis to explore the associations between these variants and leukemia susceptibility. Based on three genetic models, the codominant model, dominant model and recessive model, odds ratios (ORs) as well as their 95% confidence intervals (CIs) were used to evaluate the association strength between XRCC1 genotypes and leukemia risk. Results With respect to overall leukemia susceptibility, no association was detected. In stratified analyses by tumor type, Arg399Gln was associated with higher acute lymphoblastic leukemia (ALL) risk (AA vs. GG, OR ?=? 1.50, 95% CI: 1.11-2.02; AA+GA vs. GG, OR ?=? 1.35, 95% CI: 1.02-1.78). Additionally, Arg399Gln, Arg194Trp, and Arg280His may influence the susceptibilities of some leukemia type and race populations. Conclusion This meta-analysis indicates these three polymorphisms of XRCC1 do not associate with overall leukemia risks but could be associated with the risks for some specific subgroups. PMID:24363792

Zhang, Haijun; Liu, Hang; Jiang, Gaofeng

2013-01-01

264

FOLFIRI and Bevacizumab in first-line treatment for colorectal cancer patients: safety, efficacy and genetic polymorphisms  

PubMed Central

Background Over 50% of colorectal cancer (CRC) patients develop metastases. The aim of this study was to evaluate efficacy and tolerance of first-line FOLFIRI?+?bevacizumab (B) treatment for metastatic CRC, and to assess genetic polymorphisms as potential markers. Methods Adult patients with histologically-proven, non-resectable metastatic CRC and ECOG???2 were included. 14-day cycles consisted of bevacizumab (5mg/kg), irinotecan (180mg/m2), bolus FU (400mg/m2) and leucovorin (400mg/m2), followed by 46-hour FU infusions (2400mg/m2). Primary endpoint was response rate according to RECIST criteria. Secondary endpoints were overall (OS) and progression-free (PFS) survivals, response duration, and toxicity. Associations between clinical data, UGT1A1, thymidylate synthase, VEGFA polymorphisms and PFS, OS and toxicity were analyzed. Results Sixty-two patients were enrolled (median age 68y). 59/62 patients were eligible and evaluable for response at 6months: 28 showed partial response (47.5%; 95% CI; 34.3-60.9), 20 stable disease (33.9%) and 11 progression (18.6%). Grade 3/4 toxicities were as follows: neutropenia 16.1%; diarrhea 11.3%; nausea-vomiting 1.6%. Median response duration was 9.5months (range 2.7-20); median PFS 10.3months (range 8.8-11.7); and median OS 25.7months (range 20.2-29.7). 11/59 initially unresectable patients were resectable after treatment. VEGFA polymorphism (rs25648) was associated with better OS (HR: 3.61; 95% CI: 1.57-8.30). Conclusions FOLFIRI?+?bevacizumab is active with good response rate, long median OS, and a good safety profile. A VEGFA polymorphism might have a prognostic value in this malignancy. Trial registration Clinicaltrials.gov: NCT00467142 (registration date: April 25, 2007) PMID:24758527

2014-01-01

265

Population genetics of 30 insertion-deletion polymorphisms in two Chinese populations using Qiagen Investigator DIPplex kit.  

PubMed

Insertion-deletion polymorphisms (INDELs) are short length diallelic polymorphisms caused by the insertion or deletion of several bases. INDEL markers can serve as useful supplementary or stand-alone assays for human identification. The Qiagen Investigator() DIPplex kit multiplexes 30 autosomal INDELs plus amelogenin for forensic use. The objective of this study was to estimate genetic diversity of 30 INDEL markers in the Han (the largest ethnic group of China, n=565) and She population (almost the smallest ethnic group of China, n=119), and to evaluate their usefulness in forensic genetics. In the Han and She, the mean observed heterozygosity values were 0.4133 and 0.3896, and the combined matching probability values were 1.8010(-11) and 3.1710(-11), respectively. Furthermore, the allele frequencies for each locus were compared with those in other reported Chinese subpopulations, and the forensic efficacy was compared between this kit and in-house developed INDEL assay. This study demonstrates that the Investigator() DIPplex kit can be used as a supplementary tool for human identity testing in China. PMID:24780854

Wang, Zheng; Zhang, Suhua; Zhao, Shumin; Hu, Zhen; Sun, Kuan; Li, Chengtao

2014-07-01

266

BAT2 and BAT3 polymorphisms as novel genetic risk factors for rejection after HLA-related SCT.  

PubMed

The genetic background of donor and recipient is an important factor determining the outcome of allogeneic hematopoietic SCT (allo-HSCT). We applied whole-genome analysis to investigate genetic variants-other than HLA class I and II-associated with negative outcome after HLA-identical sibling allo-HSCT in a cohort of 110 ?-Thalassemic patients. We identified two single-nucleotide polymorphisms (SNPs) in BAT2 (A/G) and BAT3 (T/C) genes, SNP rs11538264 and SNP rs10484558, both located in the HLA class III region, in strong linkage disequilibrium between each other (R(2)=0.92). When considered as single SNP, none of them reached a significant association with graft rejection (nominal P<0.00001 for BAT2 SNP rs11538264, and P<0.0001 for BAT3 SNP rs10484558), whereas the BAT2/BAT3 A/C haplotype was present at significantly higher frequency in patients who rejected as compared to those with functional graft (30.0% vs 2.6%, nominal P=1.15 10(-8); and adjusted P=0.0071). The BAT2/BAT3 polymorphisms and specifically the A/C haplotype may represent a novel immunogenetic factor associated with graft rejection in patients undergoing allo-HSCT. PMID:25111513

Piras, I S; Angius, A; Andreani, M; Testi, M; Lucarelli, G; Floris, M; Marktel, S; Ciceri, F; Nasa, G La; Fleischhauer, K; Roncarolo, M G; Bulfone, A; Gregori, S; Bacchetta, R

2014-11-01

267

Role of genetic polymorphism of human plasma paraoxonase/arylesterase in hydrolysis of the insecticide metabolites chlorpyrifos oxon and paraoxon.  

PubMed Central

Plasma paraoxonase is a polymorphic enzyme that hydrolyzes paraoxon, the neurotoxic, active metabolite of the insecticide parathion. This enzyme is specified by at least two alleles with frequencies of about .7 and .3 among Caucasoid populations. A specific assay was developed that measured the activity of human plasma paraoxonase without interference from serum albumin which contributes significantly to the hydrolytic breakdown of paraoxon at the high pH values used in many previous assays. There was an 11-fold variation in paraoxonase activities, and the population distribution was at least bimodal. However, this specific assay did not improve the discrimination between the three genetic classes: (1) homozygotes for the low-activity allele, (2) heterozygotes, and (3) homozygotes for the high-activity allele. Chlorpyrifos oxon--the neurotoxic metabolite of the organophosphorus insecticide chlorpyrifos (Dursban)--was hydrolyzed by the same plasma fraction that hydrolyzed paraoxon. There was only four- to fivefold variability in enzyme activity, and the population distribution was unimodal. Homozygotes for low paraoxonase activity ranged over almost the entire spectrum of chlorpyrifos oxonase activity. Possible differences in susceptibility to chlorpyrifos toxicity therefore are unlikely to be predicted by the paraoxonase genotype alone. The ratio of paraoxonase over that of chlorpyrifos oxonase provided an excellent method for genetic typing of the paraoxonase polymorphism, as did the substitution of phenylacetate for chlorpyrifos as the substrate. PMID:2458038

Furlong, C E; Richter, R J; Seidel, S L; Motulsky, A G

1988-01-01

268

Genetic characterization of Fusarium graminearum and F. culmorum isolates from Turkey by using random-amplified polymorphic DNA.  

PubMed

Five Fusarium graminearum and 12 F. culmorum isolates, primarily pathogenic species of Fusarium head blight, were obtained from naturally infected wheat from various agro-ecological regions of Turkey. Genotyping of the isolates was carried out using random-amplified polymorphic DNA (RAPD). Sixty-five 10-mer oligonucleotide primers were used to amplify the RAPD markers. Among them, 50 primers produced strong and reproducible DNA amplicons. The remaining primers generated either insufficient or no amplification patterns. In total, 1200 fragments were scored, 311 of which were determined to be polymorphic and unique to the isolates. The produced RAPD markers ranged from 0.2 to 5 kb. The mean genetic similarity values of the F. graminearum and F. culmorum isolates were 61.5 and 65%, respectively. The similarity coefficient was 43 to 76.1% among F. graminearum isolates and 49 to 81.1% among F. culmorum isolates. Genetically, the most similar F. graminearum isolates were F6 and F7 (76.1%), which originated from the same agro-ecological region (Sakarya). The most similar F. culmorum isolates were F20 and F21 (81.1%), which were from different geographic regions (Bilecik and Uşak, respectively). Moreover, interspecific variation between the two species was determined to be 86.3 to 93.3%. Cluster analysis generated two branched groups, each containing isolates of one species, except F13 of F. culmorum. The sequencing of stable and reproducible monomorphic and polymorphic RAPD markers indicated that the Fusarium genome shared high similarity (105-625 bit scores) with the genomes of other organisms as well as with the F. graminearum reference genome. PMID:23661459

Yrk, E; Albayrak, G

2013-01-01

269

HarborTides.com  

NSDL National Science Digital Library

HarborTides.com is a neat, user-friendly facility for tide information for over 2,500 harbors in the US (and Bermuda). Users may browse by state or search by zip code for information on high and low tides, sunrise and sunset, and longitude and latitude for every harbor. After filling out a form for free membership, users can also print out monthly tide tables.

270

Relationships Between CETP Genetic Polymorphisms and Alzheimer's Disease Risk: A Meta-Analysis.  

PubMed

This meta-analysis was performed to evaluate the relationships between single-nucleotide polymorphisms in the CETP gene and the risk of Alzheimer's disease (AD). The PubMed, CISCOM, CINAHL, Web of Science, Google Scholar, EBSCO, Cochrane Library, and CBM databases were searched from inception through October 1, 2013, without language restrictions. Nine case-control studies with a total of 2172 AD patients and 8017 healthy controls were involved in this meta-analysis. Two common polymorphisms (rs708272 T>C and rs5882?A>G) in the CETP gene were assessed. Our meta-analysis results showed that CETP rs5882?A>G polymorphism might increase the risk of AD (A allele vs. G allele: odds ratio [OR]=1.11, 95% confidence interval [95% CI]=1.02-1.21, p=0.014; AA+AG vs. GG: OR=1.28, 95% CI=1.07-1.52, p=0.006; AA vs. GG: OR=1.32, 95% CI=1.10-1.70, p=0.003; AA vs. AG: OR=1.25, 95% CI=1.03-1.50, p=0.020; respectively). However, we found no correlations of CETP rs708272 T>C polymorphism with AD risk (all p>0.05). Subgroup analysis by ethnicity suggested positive associations between CETP rs5882?A>G polymorphism and an increased risk of AD among Caucasians (A allele vs. G allele: OR=1.10, 95% CI=1.01-1.21, p=0.014; AA+AG vs. GG: OR=1.34, 95% CI=1.06-1.69, p=0.015; AA vs. GG: OR=1.35, 95% CI=1.07-1.70, p=0.011; respectively), but not among Asians (all p>0.05). No associations were found between CETP rs708272 T>C polymorphism and AD risk among both Asians and Caucasians (all p>0.05). Our findings provide empirical evidence that CETP rs5882?A>G polymorphism may contribute to susceptibility to AD, especially among Caucasians. However, CETP rs708272 T>C polymorphism does not seem to be an important determinant in the pathogenesis of AD. PMID:25105518

Chen, Jing-Jiong; Li, Yu-Mei; Zou, Wen-Ying; Fu, Jian-Liang

2014-11-01

271

Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae).  

PubMed

We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (2-10 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and F(ST) value showed weak genetic structuring (F(ST) = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species. PMID:22481877

de Castro E Souza, Andiara Silos Moraes; Mio, Carolina Isabel; Del Lama, Silvia Nassif

2012-01-01

272

Amplified fragment length polymorphism used to investigate genetic variability of the stable fly (Diptera: Muscidae) across North America.  

PubMed

The stable fly, Stomoxys calcitrans (L.), is a cosmopolitan pest of livestock and humans. The pestiferous nature and painful bite cause stress to cattle and other animals. The stress and resulting avoidance behaviors manifest as reductions in weight gain or milk production in cattle; estimated annual economic loss in the United States exceeds US$2 billion. Understanding the population genetics of stable flies could provide information on their population dynamics, origins of outbreaks, and geographical patterns of insecticide resistance, resulting in a tactical advantage for developing management strategies. Previous studies, mostly on a local scale, reported a high level of gene flow between locations. Here, we report results wherein amplified fragment length polymorphism was used to determine genetic diversity of stable fly samples consisting of 11-40 individuals from 12 locations representing the United States, Canada, and Panama. The Analysis of Molecular Variance showed that the majority of genetic diversity was within groups; very little was among groups. The F(ST) and G(ST) values were low (< 0.4), Nm values high (> 1.0). The tests of neutrality suggested population expansion, and no genetic differentiation was found between locations. These results show that stable flies have a high level of gene flow on a continental scale, with limited isolation owing to distance or geographical barriers. PMID:24180107

Kneeland, K M; Skoda, S R; Foster, J E

2013-09-01

273

Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae)  

PubMed Central

We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (210 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and FST value showed weak genetic structuring (FST = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species. PMID:22481877

de Castro e Souza, Andiara Silos Moraes; Mio, Carolina Isabel; Del Lama, Silvia Nassif

2012-01-01

274

Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans  

PubMed Central

Background Candidate gene studies on the basis of biological hypotheses have been a practical approach to identify relevant genetic variation in complex traits. Based on previous reports and the roles in pain pathways, we have examined the effects of variations of loci in the genes of monoamine neurotransmitter systems including metabolizing enzymes, receptors and transporters on acute clinical pain responses in humans. Results Variations in the catecholamine metabolizing enzyme genes (MAOA and COMT) showed significant associations with the maximum post-operative pain rating while the serotonin transporter gene (SLC6A4) showed association with the onset time of post-operative pain. Analgesic onset time after medication was significantly associated with the norepinephrine transporter gene (SLC6A2). However, the association between COMT genetic variation and pain sensitivity in our study differ from previous studies with small sample sizes, population stratification and pain phenotype derived from combining different types of pain stimuli. Correcting for multiple comparisons did not sustain these genetic associations between monoamine neurotransmitter systems and pain sensitivity even in this large and homogeneous sample. Conclusion These results suggest that the previously reported associations between genetic polymorphisms in the monoamine neurotransmitter systems and the interindividual variability in pain responses cannot be replicated in a clinically relevant pain phenotype. PMID:16848906

Kim, Hyungsuk; Lee, Hyewon; Rowan, Janet; Brahim, Jaime; Dionne, Raymond A

2006-01-01

275

Investigation of genetic polymorphisms and smoking in a bladder cancer casecontrol study in Argentina  

E-print Network

: the T variant at nucleotide 677 (MTHFR C677T) and the C variant at nucleotide 1298 (MTHFR A1298C). Variant C677T investigated the role of glutathione S-transferase (GST) enzymes (M1, T1), methylenetetrahydrofolate (MTHFR conferred the highest risks. The MTHFR 677 CT and TT polymorphisms appeared protective against bladder

California at Berkeley, University of

276

Genetic variability in the species Rhizopus stolonifer , assessed by random amplified polymorphic DNA analysis  

Microsoft Academic Search

Rhizopus stolonifer is an important post-harvest pathogenic fungus. Recent taxonomic findings based on morphological and growth characteristics led to a dramatic reduction in the number of accepted species within the genus. The aim of this study was to examine this situation with molecular markers. Twenty-nine R. stolonifer strains isolated from various locations and substrates were characterized by random amplified polymorphic

Csaba Vgvlgyi; Henrietta Heinrich; Klra cs; Tams Papp

2004-01-01

277

Reproductive biology of Geranium sessiliflorum. II. The genetics and morph frequencies of the leaf colour polymorphism  

Microsoft Academic Search

In New Zealand three leaf colour morphs of Geranium sessiliflorum are found: brown, green, and intermediate olive. This polymorphism was investigated using controlled crosses between plants of the different colours, selfs, and harvesting of seeds produced after open pollination in the field and in cultivated plants. The leaf colour trimorphism is considered to be determined by one locus with two

M. Philipp

1987-01-01

278

An insight into the genetic polymorphism among European populations of Lactuca serriola assessed by AFLP  

Microsoft Academic Search

Prickly lettuce (Lactuca serriola) is world-wide distributed and very variable species generally considered as a progenitor of the cultivated lettuce (Lactuca sativa). Altogether, 50 populations of L. serriola were characterized by means of amplified fragment length polymorphism (AFLP) and by isozyme analysis. Relationships among individuals and populations were examined by applying the unweighted pair-group method with the arithmetic averages (UPGMA)

Ale Lebeda; Miloslav Kitner; Marta Dziechciarkov; Ivana Dolealov; Eva K?stkov; Pim Lindhout

2009-01-01

279

Genetic polymorphism of APE1 rs1130409 can contribute to the risk of lung cancer.  

PubMed

Accumulative evidence suggests that polymorphism in the APE1 gene may have association with the etiology of lung cancer by modulating DNA repair capacity. Many studies have evaluated the association with great discrepancies in the results. The present meta-analysis was undertaken to clarify the effects of this polymorphism on lung cancer. A meta-analysis of 15 studies with 4,932 lung cancer patients and 6,555 cancer-free controls was conducted to evaluate the strength of the association using odds ratios (ORs) with 95 % confidence intervals (CIs). Overall, no significant association was found between APE1 polymorphism and lung cancer risk. We also did not observe any statistical evidence of modified lung cancer risk either in smokes or in nonsmokers. In the stratified analysis by ethnicity, however, it was found that the Glu/Clu genotype carriers had 1.16-fold higher risk of suffering lung cancer compared with the carriers of Arg/Glu + Arg/Arg genotypes in Asian population (OR = 1.16, 95 % CI = 1.01-1.32, P = 0.242). This meta-analysis provides statistical evidence for a potential association between APE1 polymorphism and an increased risk of lung cancer in Asian population. PMID:24705777

Jin, Feng; Qian, Chengyuan; Qing, Yi; Zhang, Zhimin; Wang, Ge; Shan, Jinlu; Dai, Nan; Li, Zheng; Wang, Dong

2014-07-01

280

Intersimple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton  

Microsoft Academic Search

We studied the applicability of intersimple sequence repeat (ISSR) polymorphism in cotton. We found that: (i) the resolving power of agarose gels is poor relative to that provided by sequencing gels; (ii) fluorescent labelling of ISSR amplification primers produced numerous scorable bands; (iii) primer mixing (double priming) generated more bands than the sum of fragments resulting from two single primers,

Bao Liu; Jonathan F. Wendel

2001-01-01

281

[Identification of genetic polymorphisms associated with overweight in athletes of winter sports].  

PubMed

The identification of polymorphisms rs9939609 gene FTO, Trp64Arg ADRB3 and gene -866G> A UCP2 gene using multiplex allele-specific PCR hybridization-fluorescence detection in real time has been carried out in highly skilled athletes under the age of 30 years engaged in biathlon (n = 25) and bobsleigh (n = 28). The data on the frequency of allele risk of obesity has been obtained. The study of polymorphism rs9939609 of the FTO gene in biathletes found that 30% of them are carriers of the risk allele of obesity (A). Among the bobsledder the frequency of allele A is slightly higher than in European populations and is 55.4%. The study of gene polymorphism Trp64Arg ADRB3 shored that the frequency of risk allele of obesity 64Arg in biathletes (14%) was slightly higher than in the European population and biathletes (5.4%). The results of the identification of polymorphism -866G> A gene UCP2 in biathletes and bobsledders, found the incidence of obesity risk allele, respectively, 52 and 58.7%. PMID:24741957

Sorokina, E Iu; Solntseva, T N; Radzhabkadiev, R M; Samo?lov, A S

2013-01-01

282

Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers.  

PubMed

The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a atisfactory agreement with increased tolerance to environmental stress conditions of winter rape. PMID:24840830

Amosova, Alexandra V; Zemtsova, Lyudmila V; Grushetskaya, Zoya E; Samatadze, Tatiana E; Mozgova, Galina V; Pilyuk, Yadviga E; Volovik, Valentina T; Melnikova, Natalia V; Zelenin, Alexandr V; Lemesh, Valentina A; Muravenko, Olga V

2014-04-01

283

Genetic fingerprinting of Theobroma clones using randomly amplified polymorphic DNA markers  

Microsoft Academic Search

Randomly amplified polymorphic DNA (RAPD) markers have been used to characterise cocoa clones representing the three main cultivated subpopulations: Criollo, Forastero and Trinitario. The use of single primers of arbitrary nucleotide sequence resulted in the selective amplification of DNA fragments which were unique to the individual cocoa clones studied. The use of a single primer allowed each of the clones

J. Wilde; R. Waugh; W. Powell

1992-01-01

284

Manganese Superoxide Dismutase (MnSOD) Genetic Polymorphisms, Dietary Antioxidants, and Risk of Breast Cancer 1  

Microsoft Academic Search

Oxidative stress, resulting from the imbalance between prooxidant and antioxidant states, damages DNA, proteins, cell membranes, and mito- chondria and seems to play a role in human breast carcinogenesis. Dietary sources of antioxidants (chemical) and endogenous antioxidants (enzymat- ic), including the polymorphic manganese superoxide dismutase (Mn- SOD), can act to reduce the load of oxidative stress. We hypothesized that the

Christine B. Ambrosone; Jo L. Freudenheim; Patricia A. Thompson; Elise Bowman; John E. Vena; James R. Marshall; Saxon Graham; Rosemary Laughlin; Takuma Nemoto; Peter G. Shields

1999-01-01

285

Efficient Genetic Mapping of Single Nucleotide Polymorphisms Based Upon DNA Mismatch Digestion  

Microsoft Academic Search

A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest heteroduplex DNA and hence identify heterozygous single nucleotide polymorphism (SNP) sites in PCR products. Here we show this method can be used to map specific genes with relative simplicity and low cost. A particular nucleotide substitution does not need to be identified, and in

Dainis Rungis; Britta Hamberger; Yanik Berube ; Jennifer Wilkin; Jrg Bohlmann; Kermit Ritland

2005-01-01

286

Genetic variation and phenotypic plasticity in a trophically polymorphic population of pumpkinseed sunfish ( Lepomis gibbosus )  

Microsoft Academic Search

Summary Adaptive variation can exist at a variety of scales in biological systems, including among species, among local populations of a single species and among individuals within a single population. Trophic or resource polymorphisms in fishes are a good example of the lowest level of this hierarchy. In lakes without bluegill sunfish (Lepomis macrochirus), pumpkinseed sunfish (Lepomis gibbosus) can be

Beren W. Robinson; David Sloan Wilson

1996-01-01

287

An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (St John)] using amplified fragment length polymorphism (AFLP) markers.  

PubMed

Amplified fragment length polymorphisms (AFLPs) were used to characterize the genetic diversity within and among natural populations of Sticherus flabellatus. Eight populations within the Sydney region of New South Wales, Australia were surveyed using 11 primer combinations. A total of 1108 reproducible bands were detected of which 469 (42%) were polymorphic. FST estimates averaged over all polymorphic loci indicated that significant genomic differentiation occurs among populations (average = 0.783). Genetic diversity within populations was assessed according to average heterozygosity (H) and percentage polymorphic loci (P) per population. Within-population diversity ranged from H = 0.12 and P = 33.69 to H = 0.04 and P = 15.99. Analysis of genetic similarity among populations suggested that the eight populations studied fall into two groups of four populations, based on population size and the condition of the habitat. Phenetic analysis (AMOVA) indicated that genetic variation is greater among populations (74.34%) than within populations (25.66%). These findings suggest that the breeding system of S. flabellatus is predominantly inbreeding, with genetic diversity maintained by occasional outcrossing in larger populations. The results presented in this study could provide evidence to support the proposal to protect natural stands of S. flabellatus, which has implications for the Australian horticulture industry. PMID:10792700

Keiper, F J; McConchie, R

2000-05-01

288

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers  

USGS Publications Warehouse

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

Meece, J. K.; Anderson, J. L.; Fisher, M. C.; Henk, D. A.; Sloss, B. L.; Reed, K. D.

2011-01-01

289

Adaptive Color Polymorphism and Unusually High Local Genetic Diversity in the Side-Blotched Lizard, Uta stansburiana  

PubMed Central

Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation. PMID:23133520

Micheletti, Steven; Parra, Eliseo; Routman, Eric J.

2012-01-01

290

Genetic Heterogeneity of Borrelia burgdorferi Sensu Lato in the Southern United States Based on Restriction Fragment Length Polymorphism and Sequence Analysis  

PubMed Central

Fifty-six strains of Borrelia burgdorferi sensu lato, isolated from ticks and vertebrate animals in Missouri, South Carolina, Georgia, Florida, and Texas, were identified and characterized by PCR-restriction fragment length polymorphism (RFLP) analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons. A total of 241 to 258 bp of intergenic spacers between tandemly duplicated rrf (5S) and rrl (23S) was amplified by PCR. MseI and DraI restriction fragment polymorphisms were used to analyze these strains. PCR-RFLP analysis results indicated that the strains represented at least three genospecies and 10 different restriction patterns. Most of the strains isolated from the tick Ixodes dentatus in Missouri and Georgia belonged to the genospecies Borrelia andersonii. Excluding the I. dentatus strains, most southern strains, isolated from the ticks Ixodes scapularis and Ixodes affinis, the cotton rat (Sigmodon hispidus), and cotton mouse (Peromyscus gossypinus) in Georgia and Florida, belonged to Borrelia burgdorferi sensu stricto. Seven strains, isolated from Ixodes minor, the wood rat (Neotoma floridana), the cotton rat, and the cotton mouse in South Carolina and Florida, belonged to Borrelia bissettii. Two strains, MI-8 from Florida and TXW-1 from Texas, exhibited MseI and DraI restriction patterns different from those of previously reported genospecies. Eight Missouri tick strains (MOK-3a group) had MseI patterns similar to that of B. andersonii reference strain 21038 but had a DraI restriction site in the spacer. Strain SCGT-8a had DraI restriction patterns identical to that of strain 25015 (B. bissettii) but differed from strain 25015 in its MseI restriction pattern. Strain AI-1 had the same DraI pattern as other southern strains in the B. bissettii genospecies but had a distinct MseI profile. The taxonomic status of these atypical strains needs to be further evaluated. To clarify the taxonomic positions of these atypical Borrelia strains, the complete sequences of rrf-rrl intergenic spacers from 20 southeastern and Missouri strains were determined. The evolutionary and phylogenetic relationships of these strains were compared with those of the described genospecies in the B. burgdorferi sensu lato species complex. The 20 strains clustered into five separate lineages on the basis of sequence analysis. MI-8 and TXW-1 appeared to belong to two different undescribed genospecies, although TXW-1 was closely related to Borrelia garinii. The MOK-3a group separated into a distinct deep branch in the B. andersonii lineage. PCR-RFLP analysis results and the results of sequence analyses of the rrf-rrl intergenic spacer confirm that greater genetic heterogeneity exists among B. burgdorferi sensu lato strains isolated from the southern United States than among strains isolated from the northern United States. The B. andersonii genospecies and its MOK-3a subgroup are associated with the I. dentatus-cottontail rabbit enzootic cycle, but I. scapularis was also found to harbor a strain of this genospecies. Strains that appear to be B. bissettii in our study were isolated from I. minor and the cotton mouse, cotton rat, and wood rat. The B. burgdorferi sensu stricto strains from the south are genetically and phenotypically similar to the B31 reference strain. PMID:11427560

Lin, T.; Oliver, J. H.; Gao, L.; Kollars, T. M.; Clark, K. L.

2001-01-01

291

HLA-DR polymorphism in a senegalese mandenka population: DNA oligotyping and population genetics of DRB1 specificities  

SciTech Connect

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1[sup *]1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequency specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52B (DRB3[sup *]02) represents as much as 80.7% of all DR52 halotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes. 91 refs., 5 figs., 5 tabs.

Tiercy, J.M.; Shi-Isaac, X.; Jeannet, M.; Sanchez-Mazas, A.; Langaney, A.; Mach, B.; Excoffier, L.

1992-09-01

292

Genetic Polymorphisms of CCL22 and CCR4 in Patients with Lung Cancer  

PubMed Central

Background: An association between lung cancer and chemokines has been advocated in the recent years. This study aims at investigating the association between lung cancer and 16C/A single nucleotide polymorphism (SNP) (rs. 4359426) in C-C motif chemokine 22 (CCL22) as well as C1014T SNP (rs. 2228428) in C-C chemokine receptor type 4 (CCR4), which serves as the receptor for CCL22. Methods: Genotyping was performed in 148 lung cancer patients and 148 normal controls using Polymerase Chain Reaction-Restriction-Fragment Length Polymorphism (PCR-RFLP). The data were verified by direct automated sequencing. Results: Frequencies of CC, CA and AA genotypes of 16C/A SNP in CCL22 gene were 112 (75.7%), 33 (22.3%) and 3 (2.0%) in patients, and 119 (80.4%), 24 (16.2%) and 5 (3.4%) in controls respectively. No significant differences were observed in genotype frequencies at this position between cases and controls (P=0.34). Moreover, there was no significant association between CCL22 polymorphism and types of lung cancer in patients. The distribution of CC, CT and TT genotypes of C1014T SNP in CCR4 gene, was 76 (51.4%), 60 (40.5%) and 12 (8.1%) in patients, and 80 (54.1%), 49 (33.1%) and 19 (12.8%) in controls respectively. No statistically significant differences were observed in genotypes frequencies of CCR4 gene between patients and controls (P=0.24). The genotype inherited by patients observed not to be associated with the type of lung cancer (P>0.05). Conclusion: Results reveal that CCL22 gene polymorphism at position 16C/A and CCR4 gene polymorphism at position C1014T, appear not to be associated with susceptibility to lung cancer. PMID:25031489

Erfani, Nasrollah; Nedaei Ahmadi, Ahmadi-Sina; Ghayumi, Mohammad Ali; Mojtahedi, Zahra

2014-01-01

293

Natural Genetic Variation Caused by Transposable Elements in Humans  

PubMed Central

Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 2535% of ?2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation. PMID:15514065

Bennett, E. Andrew; Coleman, Laura E.; Tsui, Circe; Pittard, W. Stephen; Devine, Scott E.

2004-01-01

294

[The importance of examining genetic polymorphism of drug oxidation in psychiatry].  

PubMed

The paper describes: 1. Drug oxidation process. 2. Cytochrome P-450 Isozymes. 3. Genetic polimorphism of drug oxidation. 4. Spartein test. Metabolic ratio, extensive and poor metabolizers. 5. Cytochrom P-450 and drug metabolism. 6. Inhibition of drug oxidation process and inhibitors of CYP450. 7. Influence of CYP450 genetic polimorphism on development of diseases. 8. Clinical value of examining the genetic polimorphism of drug oxidation in psychiatry. PMID:7878153

Besz?ej, J A; Kiejna, A

1995-01-01

295

Inhibition of ADP-induced platelet aggregation by clopidogrel is related to CYP2C19 genetic polymorphisms.  

PubMed

1. Clopidogrel is one of the most important antithrombotic drugs but has different efficacies in different populations. The aim of the present study was to evaluate the contribution of CYP2C19 genetic polymorphisms to the inhibition of ADP-induced platelet aggregation by clopidogrel in healthy Chinese volunteers. 2. Eighteen healthy male volunteers (six CYP2C19*1/CYP2C19*1, six CYP2C19*1/CYP2C19*2and*3 and six CYP2C19*2/CYP2C19*2and*3) were enrolled in the study. Each subject took 300 mg clopidogrel on the first day and then 75 mg once daily for 2 consecutive days. Blood samples were taken to measure ADP-induced platelet aggregation at baseline and 4, 24 and 72 h after administration of the first dose of clopidogrel. 3. There were significant decrease in 2 and 5 micromol/L ADP-induced platelet aggregation at 4, 24 and 72 h after clopidogrel among the three CYP2C19 genotypes compared with baseline (P < 0.001). The change in 5 micromol/L ADP-induced platelet aggregation in subjects with the CYP2C19*1/CYP2C19*1 genotype was greater than that in subjects with the CYP2C19*2/CYP2C19*2and*3 genotype at 4 h (49.0 +/- 15.5 vs 29.7 +/- 17.4%, respectively; P = 0.029), 24 h (48.7 +/- 20.5 vs 25.0 +/- 17.6%, respectively; P = 0.035) and 72 h (45.5 +/- 15.2 vs 26.5 +/- 15.8%, respectively; P = 0.030) after clopidogrel administration. 4. In conclusion, CYP2C19*2 and CYP2C19*3 genetic polymorphisms reduced clopidogrel inhibition of ADP-induced platelet aggregation, with the degree of inhition dependent on the genetic polymorphism present. PMID:18346178

Chen, Bi-Lian; Zhang, Wei; Li, Qing; Li, Ya-Lin; He, Yi-Jing; Fan, Lan; Wang, Lian-Sheng; Liu, Zhao-Qian; Zhou, Hong-Hao

2008-08-01

296

A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.  

PubMed

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly. PMID:22384381

Yu, John Z; Kohel, Russell J; Fang, David D; Cho, Jaemin; Van Deynze, Allen; Ulloa, Mauricio; Hoffman, Steven M; Pepper, Alan E; Stelly, David M; Jenkins, Johnie N; Saha, Sukumar; Kumpatla, Siva P; Shah, Manali R; Hugie, William V; Percy, Richard G

2012-01-01

297

Genetic structure of the genus Lemna L. (Lemnaceae) as revealed by amplified fragment length polymorphism  

Microsoft Academic Search

Duckweeds (Lemnaceae) are extremely reduced in morphology, which made their taxonomy a challenge for a long time. The amplified\\u000a fragment length polymorphism (AFLP) marker technique was applied to solve this problem. 84 clones of the genus Lemna were investigated representing all 13 accepted Lemna species. By neighbour-joining (NJ) analysis, 10 out of these 13 species were clearly recognized: L. minor,

Manuela Bog; Henryk Baumbach; Ulrike Schween; Frank Hellwig; Elias Landolt; Klaus-J. Appenroth

2010-01-01

298

African-Derived Genetic Polymorphisms in TNFAIP3 Mediate Risk for Autoimmunity  

PubMed Central

The TNF ?-induced protein 3 (TNFAIP3) is an ubiquitin-modifying enzyme and an essential negative regulator of inflammation. Genome-wide association studies have implicated the TNFAIP3 locus in susceptibility to autoimmune disorders in European cohorts, including rheumatoid arthritis, coronary artery disease, psoriasis, celiac disease, type 1 diabetes, inflammatory bowel disease, and systemic lupus erythematosus (SLE). There are two nonsynonymous coding polymorphisms in the deubiquitinating (DUB) domain of TNFAIP3: F127C, which is in high-linkage disequilibrium with reported SLE-risk variants, and A125V, which has not been previously studied. We conducted a casecontrol study in African-American SLE patients using these coding variants, along with tagging polymorphisms in TNFAIP3, and identified a novel African-derived risk haplotype that is distinct from previously reported risk variants (odds ratio = 1.6, p = 0.006). In addition, a rare protective haplotype was defined by A125V (odds ratio = 0.31, p = 0.027). Although A125V was associated with protection from SLE, surprisingly the same allele was associated with increased risk of inflammatory bowel disease. We tested the functional activity of nonsynonymous coding polymorphisms within TNFAIP3, and found that the A125V coding-change variant alters the DUB activity of the protein. Finally, we used computer modeling to depict how the A125V amino acid change in TNFAIP3 may affect the three-dimensional structure of the DUB domain to a greater extent than F127C. This is the first report of an association between TNFAIP3 polymorphisms and autoimmunity in African-Americans. PMID:20483768

Lodolce, James P.; Kolodziej, Lauren E.; Rhee, Lesley; Kariuki, Silvia N.; Franek, Beverly S.; McGreal, Nancy M.; Logsdon, Mark F.; Bartulis, Sarah J.; Perera, Minoli A.; Ellis, Nathan A.; Adams, Erin J.; Hanauer, Stephen B.; Jolly, Meenakshi; Niewold, Timothy B.; Boone, David L.

2012-01-01

299

Association of FGFR4 genetic polymorphisms with prostate cancer risk and prognosis  

Microsoft Academic Search

The fibroblast growth factor receptor 4 (FGFR4) is thought to be involved in many critical cellular processes and has been associated with prostate cancer risk. Four single nucleotide polymorphisms (SNPs) within or near FGFR4 were analyzed in a population-based study of 1458 prostate cancer patients and 1352 age-matched controls. We found no evidence to suggest that any of the FGFR4

L M FitzGerald; E Karlins; D M Karyadi; E M Kwon; J S Koopmeiners; J L Stanford; E A Ostrander; EA Ostrander

2009-01-01

300

Genetic association of an alpha2-macroglobulin (Val1000lle) polymorphism and Alzheimer's disease  

Microsoft Academic Search

?2-Macroglobulin (A2M) is a proteinase inhibitor found in association with senile plaques (SP) in Alzheimer's disease (AD). A2M has been implicated biochemically in binding and degradation of the amyloid ? (A?) protein which accumulates in SP. We studied the relationship between Alzheimer's disease and a common A2M polymorphism, Val1000 (GTC)\\/Ile1000 (ATC), which occurs near the thiolester active site of the

A. Liao; R. M. Nitsch; S. M. Greenberg; U. Finckh; D. Blacker; M. Albert; G. W. Rebeck; T. Gomez-Isla; A. Clatworthy; G. Binetti; C. Hock; T. Mueller-Thomsen; U. Mann; K. Zuchowski; U. Beisiegel; H. Staehelin; J. H. Growdon; R. E. Tanzi; B. T. Hyman

1998-01-01

301

A non-radioactive method for mapping restriction fragment length polymorphic genetic markers in Anopheles gambiae.  

PubMed

A non-radioactive method for in situ hybridisation of Restriction Fragment Length Polymorphic (RFLP) markers to the polytene chromosome of Anopheles gambiae, the important malaria vector, which yielded good readable quality of chromosomal bands is reported. The methodology adopted was a Biotin-Streptavidin-Alkaline Phosphatase system which yielded fluorescent signals when stained with dyes such as Nitro Blue Tetrazolium and Bromo Chloro Indolyl Phosphate. PMID:10783765

Kumar, N P

1999-10-01

302

Genetic polymorphisms of the DNA repair gene MPG may be associated with susceptibility to rheumatoid arthritis  

Microsoft Academic Search

Rheumatoid arthritis (RA) is a chronic autoimmune disease and can lead to deformities and severe disabilities, due to irreversible\\u000a damage of tendons, joints, and bones. A previous study indicated that a DNA repair system was involved in the development\\u000a of RA. In this study, we investigated the association of four N-methylpurine-DNA glycosylase (MPG) gene polymorphisms (rs3176364, rs710079, rs2858056, and rs2541632)

S. Y. Chen; L. Wan; C. M. Huang; Y. C. Huang; J. J. C. Sheu; Y. J. Lin; S. P. Liu; Y. C. Lan; C. H. Lai; C. W. Lin; C. H. Tsai; F. J. Tsai

2010-01-01

303

Resistance/susceptibility to lethal Sendai virus infection genetically linked to a mucociliary transport polymorphism.  

PubMed Central

Linkage was tested between a mucociliary transport polymorphism and resistance/susceptibility to lethal Sendai virus infection in segregant hybrid mice of C57BL/6J and DBA/2J parents. The distribution of paired phenotypes for tracheal mucociliary transport rates and susceptibility to lethal Sendai virus infection in 171 F1 X DBA/2J mice showed strong interaction of the parental phenotypes. PMID:3033294

Brownstein, D G

1987-01-01

304

Functional genetic polymorphisms and female reproductive disorders: Part I: polycystic ovary syndrome and ovarian response  

PubMed Central

BACKGROUND The identification of polymorphisms associated with a disease can help to elucidate its pathogenesis, and this knowledge can be used to improve prognosis for women with a particular disorder, such as polycystic ovary syndrome (PCOS). Since an altered response to ovarian stimulation is also a characteristic of the disease, further knowledge about its aetiology could help in defining the parameters that determine the response of an individual to ovarian stimulation. METHODS PubMed and EMBASE databases were systematically searched for gene association studies published until the end of August 2007, using search criteria relevant to PCOS and ovarian response to stimulation. Data from additional papers identified through hand searches were also included; 139 publications were reviewed. RESULTS Several genes involved in ovarian function and metabolism are associated with increased susceptibility to PCOS, but none is strong enough to correlate alone with susceptibility to the disease, or response to therapy. A single-nucleotide polymorphism in exon 10 of the FSH receptor (FSHR) gene, FSHR p.N680S, was consistently identified as having a significant association with ovarian response to FSH. CONCLUSIONS No consistent association between gene polymorphism and PCOS could be identified. The FSHR gene may play a significant role in the success of ovarian stimulation, and can be used as a marker to predict differences in FSHR function and ovarian response to FSH. Genotyping the FSHR p.N680S polymorphism may provide a means of identifying a population of poor responders before in vitro fertilization procedures are initiated. PMID:18603647

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

2008-01-01

305

Combined glutathione-S-transferase M1 and T1 genetic polymorphism and tacrine hepatotoxicity  

Microsoft Academic Search

Background: Glutathione conjugation of tacrine reactive metabolites depends in part on the activity of glutathione-S -transferases (GST), of which two isozymes (GST M1 and GST T1) are polymorphically expressed.Objective and Methods: To determine whether GST M1, GST T1, and the combined GST M1 and GST T1 null genotypes predict individual susceptibility to tacrine hepatotoxicity, 141 patients with mild to moderate

Tabassome Simon; Laurent Becquemont; Murielle Mary-Krause; Isabelle de Waziers; Philippe Beaune; Christian Funck-Brentano; Patrice Jaillon

2000-01-01

306

Distribution of genetic polymorphisms of genes encoding drug metabolizing enzymes & drug transporters - a review with Indian perspective  

PubMed Central

Phase I and II drug metabolizing enzymes (DME) and drug transporters are involved in the absorption, distribution, metabolism as well as elimination of many therapeutic agents, toxins and various pollutants. Presence of genetic polymorphisms in genes encoding these proteins has been associated with marked inter-individual variability in their activity that could result in variation in drug response, toxicity as well as in disease predisposition. The emergent field pharmacogenetics and pharmacogenomics (PGx) is a promising discipline, as it predicts disease risk, selection of proper medication with regard to response and toxicity, and appropriate drug dosage guidance based on an individual's genetic make-up. Consequently, genetic variations are essential to understand the ethnic differences in disease occurrence, development, prognosis, therapeutic response and toxicity. For that reason, it is necessary to establish the normative frequency of these genes in a particular population before unraveling the genotype-phenotype associations. Although a fair amount of allele frequency data are available in Indian populations, the existing pharmacogenetic data have not been compiled into a database. This review was intended to compile the normative frequency distribution of the variants of genes encoding DMEs (CYP450s, TPMT, GSTs, COMT, SULT1A1, NAT2 and UGTs) and transporter proteins (MDR1, OCT1 and SLCO1B1) with Indian perspective. PMID:24604039

Umamaheswaran, Gurusamy; Kumar, Dhakchinamoorthi Krishna; Adithan, Chandrasekaran

2014-01-01

307

Association of RET Genetic Polymorphisms and Haplotypes with Papillary Thyroid Carcinoma in the Portuguese Population: A Case-Control Study  

PubMed Central

Thyroid cancer has a multifactorial aetiology resulting from the interaction of genetic and environmental factors. Several low penetrance susceptibility genes have been identified but their effects often vary between different populations. Somatic point mutations and translocations of the REarranged during Transfection (RET) proto-oncogene are frequently found in thyroid cancer. The aim of this case-control study was to determine the effect of four well known RET single nucleotide polymorphisms (SNPs) on the risk for differentiated thyroid carcinoma. A total of 545 Portuguese patients and 543 controls were genotyped by PCR and restriction enzyme analysis, for the following SNPs: G691S (exon 11, rs1799939 G/A), L769L (exon 13, rs1800861 T/G), S836S (exon 14, rs1800862 C/T), and S904S (exon 15, rs1800863 C/G). The minor allele of S836S was overrepresented in patients with papillary thyroid carcinoma (PTC) when compared to controls (OR 1.57; 95% CI 1.052.35; p?=?0.026). The GGTC haplotype was also overrepresented in PTC (OR 2.51; 95% CI 1.075.91; p?=?0.029). No associations were found in follicular thyroid carcinoma (FTC). Multivariate logistic regression analysis showed no differences regarding gender, age at diagnosis, lymph node or distant metastasis. However, a near significant overrepresentation of the minor alleles of G691S and S904S was found in patients with tumours greater than 10 mm of diameter at diagnosis. These data suggest that the RET S836S polymorphism in exon 14 and the GGTC haplotype are risk factors for PTC, but not FTC, and that the G691S/S904S polymorphisms might be associated with tumour behaviour. PMID:25330015

Santos, Marina; Azevedo, Teresa; Martins, Teresa; Rodrigues, Fernando J.; Lemos, Manuel C.

2014-01-01

308

Role of 5-HTTLPR Polymorphism in the Development of the Inward/Outward Personality Organization: A Genetic Association Study  

PubMed Central

Reciprocity with primary caregivers affects subjects' adaptive abilities toward the construction of the most useful personal meaning organization (PMO) with respect to their developmental environment. Within cognitive theory the post-rationalist approach has outlined two basic categories of identity construction and of regulation of cognitive and emotional processes: the Outward and the Inward PMO. The presence of different, consistent clinical patterns in Inward and Outward subjects is paralleled by differences in cerebral activation during emotional tasks on fMRI and by different expression of some polymorphisms in serotonin pathways. Since several lines of evidence support a role for the 5-HTTLPR polymorphism in mediating individual susceptibility to environmental emotional stimuli, this study was conducted to investigate its influence in the development of the Inward/Outward PMO. PMO was assessed and the 5-HTTLPR polymorphism investigated in 124 healthy subjects who were subdivided into an Inward (n?=?52) and an Outward (n?=?72) group. Case-control comparisons of short allele (S) frequencies showed significant differences between Inwards and Outwards (p?=?0.036, ?2 test; p?=?0.026, exact test). Genotype frequencies were not significantly different although values slightly exceeded p?0.05 (p?=?0.056, ?2 test; p?=?0.059, exact test). Analysis of the 5-HTTLPR genotypes according to the recessive inheritance model showed that the S/S genotype increased the likelihood of developing an Outward PMO (p?=?0.0178, ?2 test; p?=?0.0143, exact test; OR?=?3.43, CI (95%)?=?1.1889.925). A logistic regression analysis confirmed the association between short allele and S/S genotypes with the Outward PMO also when gender and age were considered. However none of the differences remained significant after correction for multiple testing, even though using the recessive model they approach significance. Overall our data seem to suggest a putative genetic basis for interindividual differences in PMO development. PMID:24358153

Nardi, Bernardo; Marini, Alessandra; Turchi, Chiara; Arimatea, Emidio; Tagliabracci, Adriano; Bellantuono, Cesario

2013-01-01

309

Role of 5-HTTLPR polymorphism in the development of the inward/outward personality organization: a genetic association study.  

PubMed

Reciprocity with primary caregivers affects subjects' adaptive abilities toward the construction of the most useful personal meaning organization (PMO) with respect to their developmental environment. Within cognitive theory the post-rationalist approach has outlined two basic categories of identity construction and of regulation of cognitive and emotional processes: the Outward and the Inward PMO. The presence of different, consistent clinical patterns in Inward and Outward subjects is paralleled by differences in cerebral activation during emotional tasks on fMRI and by different expression of some polymorphisms in serotonin pathways. Since several lines of evidence support a role for the 5-HTTLPR polymorphism in mediating individual susceptibility to environmental emotional stimuli, this study was conducted to investigate its influence in the development of the Inward/Outward PMO. PMO was assessed and the 5-HTTLPR polymorphism investigated in 124 healthy subjects who were subdivided into an Inward (n = 52) and an Outward (n = 72) group. Case-control comparisons of short allele (S) frequencies showed significant differences between Inwards and Outwards (p = 0.036, ?2 test; p = 0.026, exact test). Genotype frequencies were not significantly different although values slightly exceeded p ? 0.05 (p = 0.056, ?2 test; p = 0.059, exact test). Analysis of the 5-HTTLPR genotypes according to the recessive inheritance model showed that the S/S genotype increased the likelihood of developing an Outward PMO (p = 0.0178, ?2 test; p = 0.0143, exact test; OR = 3.43, CI (95%) = 1.188-9.925). A logistic regression analysis confirmed the association between short allele and S/S genotypes with the Outward PMO also when gender and age were considered. However none of the differences remained significant after correction for multiple testing, even though using the recessive model they approach significance. Overall our data seem to suggest a putative genetic basis for interindividual differences in PMO development. PMID:24358153

Nardi, Bernardo; Marini, Alessandra; Turchi, Chiara; Arimatea, Emidio; Tagliabracci, Adriano; Bellantuono, Cesario

2013-01-01

310

Presence and genetic polymorphism of an epithelial mucin in milk of the goat (Capra hircus).  

PubMed

1. Analysis of individual samples of goat's milk by SDS-PAGE confirmed that they contain a polymorphic, high molecular weight (M(r) greater than 205 kDa) glycoprotein. 2. On SDS-gels, the polymorphism takes the form of two bands of variable mobility which usually stain with equal intensity. This polymorphism resembles that detected in milk mucins of other species and is best explained by an expression of codominant genes containing variable numbers of a tandemly repeated 60-base segment. 3. Analysis of milk fractions provided evidence that the goat mucin is exclusively a membrane protein, and that it can be purified from other fat globule proteins by gel filtration and peanut lectin affinity chromatography. 4. Among proteins in the goat milk fat globule, the mucin appears to be a strong immunogen but the resulting antibodies applied to Western blots only stained the cow's milk mucin mildly and the guinea pig and human milk mucins not at all. PMID:1451438

Campana, W M; Josephson, R V; Patton, S

1992-09-01

311

Polymorphism and genetic mapping of the human oxytocin receptor gene on chromosome 3  

SciTech Connect

Centrally administered oxytocin has been reported to facilitate affiliative and social behaviors, in functional harmony with its well-known peripheral effects on uterine contraction and milk ejection. The biological effects of oxytocin could be perturbed by mutations occurring in the sequence of the oxytocin receptor gene, and it would be of interest to establish the position of this gene on the human linkage map. Therefore we identified a polymorphism at the human oxytocin receptor gene. A portion of the 3{prime} untranslated region containing a 30 bp CA repeat was amplified by polymerase chain reaction (PCR), revealing a polymorphism with two alleles occurring with frequencies of 0.77 and 0.23 in a sample of Caucasian CEPH parents (n = 70). The CA repeat polymorphism we detected was used to map the human oxytocin receptor to chromosome 3p25-3p26, in a region which contains several important genes, including loci for Von Hippel-Lindau disease (VHL) and renal cell carcinoma. 53 refs., 2 figs., 1 tab.

Michelini, S.; Urbanek, M.; Goldman, D. [National Institute of Health-National Institute of Alcohol Abuse and Alcoholism, Rockville, MD (United States)] [and others

1995-06-19

312

A Genetic Polymorphism of the Endogenous Opioid Dynorphin Modulates Monetary Reward Anticipation in the Corticostriatal Loop  

PubMed Central

The dynorphin/?-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. PMID:24587148

Votinov, Mikhail; Pripfl, Juergen; Windischberger, Christian; Kalcher, Klaudius; Zimprich, Alexander; Zimprich, Fritz; Moser, Ewald

2014-01-01

313

Genetic polymorphism of the ? 2-adrenergic receptor is associated with increased platelet aggregation, baroreceptor sensitivity, and salt excretion in normotensive humans  

Microsoft Academic Search

It is likely that a number of independent heritable traits, each encoded by a singular gene, contribute to pathologic elevations in blood pressure in humans. Genetic polymorphisms of individual genes may result in intermediate phenotypes which, by themselves, do not raise blood pressure, but, coupled with environmental or epistatic forces, contribute to the prevalence of human hypertension. The gene for

Kalev Freeman; Stephen Farrow; Alvin Schmaier; Robert Freedman; Tony Schork; Warren Lockette

1995-01-01

314

Enhanced Proteolysis of Thiopurine S-methyltransferase (TPMT) Encoded by Mutant Alleles in Humans (TPMT*3A, TPMT*2): Mechanisms for the Genetic Polymorphism of TPMT Activity  

Microsoft Academic Search

TPMT is a cytosolic enzyme that catalyzes the S-methylation of aromatic and heterocyclic sulfhydryl compounds, including medications such as mercaptopurine and thioguanine. TPMT activity exhibits autosomal codominant genetic polymorphism, and patients inheriting TPMT deficiency are at high risk of potentially fatal hematopoietic toxicity. The most prevalent mutant alleles associated with TPMT deficiency in humans have been cloned and characterized (TPMT*2

Hung-Liang Tai; Eugene Y. Krynetski; Erin G. Schuetz; Yuri Yanishevski; William E. Evans

1997-01-01

315

A DNA Science research and training programme for Secondary School and Junior College teachers and students on genetic polymorphisms in human, animals and plants in Singapore  

Microsoft Academic Search

The objective of this project is to train teachers and students to be competent in the principles and practice of DNA science by working on genetic polymorphisms of humans, animals and plants in Singapore. MOE has provided JC and Secondary Schools in Singapore the life sciences research facilities and equipment which cost millions of dollar s. This project is therefore

Koh CL; Chin HLC; Lum SKY; Tan J; Ang DTJ

316

Genetic Epidemiology 18:331340 (2000) ApoE Polymorphism Accounts for Only Part of the Genetic Variation in Quantitative ApoE Levels  

E-print Network

ApoE levels and chromosome 19 ApoE polymorphisms were measured in a sample of 156 Dutch families. Each pedigree consisted of parents aged 3565 years and their twin offspring aged 1421 years. A significant effect of the chromosome 19 apoE locus on quantitative plasma levels of apolipoprotein E was observed. The ApoE polymorphism explained 16 % of the variance in ApoE levels. Tests of association of ApoE levels with the apoC1 locus, which is in complete linkage disequilibrium with the ApoE locus, also showed a significant effect, although the variance explained by ApoC1 was only 1%. Examination of the covariance between twins classified according to allele sharing indicates that the association is not due to population stratification, but to a genuine effect of the ApoE locus on levels. However, the ApoE locus accounts for only one-fourth of the genetic variation

M. C. Neale; P. De Knijff; L. M. Havekes; D. I. Boomsma

1999-01-01

317

Effect of Genetic Polymorphisms on the Development of Secondary Failure to Sulfonylurea in Egyptian Patients with Type 2 Diabetes  

PubMed Central

Objective: This study investigated the possibility that genetic factors, such as polymorphism of K inward rectifier subunit (Kir6.2), E23K, and Arg972 polymorphism of insulin receptor sub-strate-1 (IRS-1), may predispose patients to sulfonylurea failure. Methods: A total of 100 unrelated Egyptian patients with type 2 diabetes were recruited. They were divided into two equal groups: group I consisted of patients with secondary failure to sulfonylurea (hemoglobin A1c ? 8% despite sulfonylurea therapy) while group II consisted of patients whose condition was controlled with oral therapy. Results: Of all the patients, 45% and 14% were carriers of the K allele and Arg972 variants respectively. The frequency of the K allele was 34% among patients with diabetes that was controlled with oral therapy and 56% among patients with secondary failure to sulfonylurea. The frequency of the Arg972 IRS-1 variant was 6% among patients with diabetes controlled with oral therapy and 22% among patients with secondary failure. Conclusion: The E23K variant of the Kir6.2 gene and Arg972 IRS-1 variants are associated with increased risk for secondary failure to sulfonylurea. PMID:23148181

El-sisi, Alaa E.; Hegazy, Sahar K.; Metwally, Shereen S.; Wafa, Alaa M.; Dawood, Naglaa A.

2011-01-01

318

Genetic analysis of the 3' untranslated region of the bovine SLC11A1 gene reveals novel polymorphisms.  

PubMed

Polymorphisms in microsatellites at the 3' untranslated region (3'UTR) of the SLC11A1 (solute carrier family 11 member A1) gene have been associated with natural resistance to Brucella abortus and Mycobacterium bovis infection in livestock species. Here, we carried out an individual genetic analysis of the two microsatellites present at the 3'UTR SLC11A1 gene in 254 Bos taurus purebred, 125 B. indicus purebred and 54 B. taurus B. indicus crossbred cattle. The genotyping by capillary electrophoresis showed the presence of four alleles (157, 159, 161 and 163) for the first microsatellite (MS1) and six alleles (175, 177, 179, 181, 183 and 185) for the second microsatellite (MS2). The alleles 159 and 175 were the most frequent in all breeds analyzed. B. taurus showed the most homogeneous haplotype and genotype for both microsatellites, whereas B. indicus showed the most heterogeneous haplotype and genotype. Two novel variants (alleles 161 and 163) within the MS1 are reported as well as novel variants in MS2 in Holstein breed. The knowledge of the polymorphisms distribution in both microsatellites at the 3'UTR of the SLC11A1 gene in cattle breeds is useful for future experimental design to evaluate the association between reported genotypes and natural resistance to pathogens infection. PMID:23065223

Hasenauer, F C; Caffaro, M E; Czibener, C; Comerci, D; Poli, M A; Rossetti, C A

2013-01-01

319

RET and PHOX2B Genetic Polymorphisms and Hirschsprung's Disease Susceptibility: A Meta-Analysis  

PubMed Central

Background Many publications have evaluated the correlation between RET, PHOX2B polymorphisms and Hirschsprung's disease with conflicting results. We performed this meta-analysis to clarify the association of RET, PHOX2B polymorphisms with HSCR. Methods We searched Pubmed, Elsevier Science Direct, China National Knowledge Infrastructure database, Chinese Biomedical database, Google scholar. The combined odds ratio (OR) with 95% CI was calculated to estimate the strength of the association. Heterogeneity and publication bias were also assessed. Results In total, 16 studies concerning RET and 4 studies concerning PHOX2B were included in the meta-analysis. The effects of five polymorphisms of RET (rs1800858, rs1800860, rs1800861, rs10900297, rs2435357) and one polymorphism (rs28647582) of PHOX2B were evaluated. We found a significant correlation between RET polymorphisms and HSCR. For rs1800858, the overall ORs (95% CI) of the A versus G, AA versus GG, AA/AG versus GG and AA versus GG/AG were 3.81 (2.286.35); 8.36 (3.4520.25); 3.59 (1.837.02); and 6.60 (3.6611.89). For rs1800861, the comparison of subjects in the G versus T, GG versus TT, GG/TG versus TT and GG versus TT/TG were 2.85(1.814.47); 5.38(2.6810.80); 3.07(2.174.34) and 4.14(1.849.30) respectively. For rs10900297, the comparison results showed statistically significant. (ORC versus A?=?5.05,95%CI?=?4.166.13; ORCC versus AA?=?9.73, 95%CI?=?5.9415.94; ORCC/AC versus AA?=?5.31, 95%CI?=?3.276.82; ORCC versus AC/AA?=?7.06,95%CI?=?5.608.91.) But, for rs1800860, the GG/GA versus AA did not reach statistical association (OR?=?3.77, 95% CI?=?0.9415.07) and the G versus A, GG versus AA, GG versus GA/AA were 2.23 (1.603.11);4.56 (1.1418.27); 2.38 (1.663.43) respectively. For rs2435357, the T versus C, TT versus CC, TT/TC versus CC and TT versus CC/TC were 4.53 (3.276.27); 11.44 (5.6723.10); 4.04 (2.925.57), and 9.01(5.2515.46).The single polymorphism of PHOX2B gene wasn't related to the risk for HSCR. Conclusions This meta-analysis shows a significant association between RET polymorphisms and HSCR. PMID:24651702

Yuan, Xu; Ren, Ling-ling; Shen, Juan; Zhang, Hai-yan

2014-01-01

320

Polymorphic populations of Dactylorhiza incarnata s.l. (Orchidaceae) on the Baltic island of Gotland: morphology, habitat preference and genetic differentiation  

PubMed Central

Background and Aims Organisms may be polymorphic within natural populations, but often the significance and genetic background to such polymorphism is not known. To understand the colour polymorphism expressed in the diploid marsh-orchids Dactylorhiza incarnata, morphological, habitat and genetic differentiation was studied in mixed populations on the island of Gotland, supplemented with genetic marker data from adjacent areas. Methods A total of 398 accessions was investigated for plastid haplotype and three nuclear microsatellites. Morphometric data and vegetation data were obtained from a subset of 104 plants. Key Results No clear pattern of habitat differentiation was found among the colour morphs. Within sites, the yellow-flowered morph (ochroleuca) was slightly larger than the others in some flower characters, whereas the purple-flowered morph with spotted leaves (cruenta) was on average smaller. However, populations of the same colour morph differed considerably between sites, and there was also considerable overlap between morphs. Morphs were often genetically differentiated but imperfectly separated within sites. Most populations were characterized by significant levels of inbreeding. The ochroleuca morph constitutes a coherent, highly homozygous sublineage, although introgression from purple-flowered morphs occurs at some sites. The cruenta morph was genetically variable, although Gotland populations formed a coherent group. Purple-flowered plants with unspotted leaves (incarnata in the strict sense) were even more variable and spanned the entire genetic diversity seen in the other morphs. Conclusions Colour polymorphism in D. incarnata is maintained by inbreeding, but possibly also by other ecological factors. The yellow-flowered morph may best be recognized as a variety of D. incarnata, var. ochroleuca, and the lack of anthocyanins is probably due to a particular recessive allele in homozygous form. Presence of spotted leaves is an uncertain taxonomic character, and genetic differentiation within D. incarnata would be better described by other morphological characters such as leaf shape and stature and size and shape of lip and spur. PMID:19458026

Hedren, Mikael; Nordstrom, Sofie

2009-01-01

321

Genetic polymorphisms in VDR, ESR1 and ESR2 genes may contribute to susceptibility to Parkinson's disease: a meta-analysis.  

PubMed

We conducted this meta-analysis of relevant case-control studies to investigate the relationships between genetic polymorphisms in VDR, ESR1 and ESR2 genes to the susceptibility of Parkinson's disease (PD). A search on electronic databases without any language restrictions was conducted: MEDLINE (1966-2013), the Cochrane Library Database (Issue 12, 2013), EMBASE (1980-2013), CINAHL (1982-2013), Web of Science (1945-2013) and the Chinese Biomedical Database (1982-2013). Meta-analysis was performed using the STATA statistical software. Crude odds ratio (OR) with their 95% confidence interval (95% CI) was calculated. Fourteen case-control studies with a total of 3,689 PD patients and 4,627 healthy subjects were included in our meta-analysis. The results of our meta-analysis demonstrated that the VDR genetic polymorphisms might be closely related to increased risks of PD (allele model: OR = 1.18, 95% CI 1.09-1.29, P < 0.001; dominant model: OR = 1.37, 95% CI 1.16-1.63, P < 0.001; respectively), especially for the polymorphisms rs7976091 and rs10735810. Our findings also illustrated that ESR1 genetic polymorphisms might increase the risk of PD (allele model: OR = 1.56, 95% CI 1.17-2.07, P = 0.002; recessive model: OR = 1.93, 95 % CI 1.33-2.80, P < 0.001; homozygous model: OR = 1.35, 95% CI 1.02-1.79, P = 0.038; heterozygous model: OR = 2.04, 95% CI 1.36-3.07, P = 0.001; respectively), especially for the polymorphisms rs2234693 and rs9340799. Furthermore, we found significant correlations of ESR2 genetic polymorphisms with the risk of PD (allele model: OR = 1.78, 95% CI 1.19-2.67, P = 0.005; recessive model: OR = 1.93, 95% CI 1.15-3.27, P = 0.014; homozygous model: OR = 1.77, 95% CI 1.09-2.89, P = 0.022; heterozygous model: OR = 1.88, 95% CI 1.08-3.27, P = 0.025; respectively), especially for the rs1256049 polymorphism. Our meta-analysis suggests that genetic polymorphisms in VDR, ESR1 and ESR2 genes may contribute to increased risks for PD. PMID:24595449

Gao, Zhan; Fu, Hong-Juan; Xue, Ju-Jun; Wu, Zhi-Xuan; Zhao, Li-Bo

2014-07-01

322

Prevalence of topoisomerase I genetic mutations and UGT1A1 polymorphisms associated with irinotecan in individuals of Asian descent  

PubMed Central

Topoisomerase I (TOP-I) mutations have been shown to be correlated to irinotecan resistance in vitro. However, the prevalence of TOP-I germline mutations has yet to be systematically elucidated. On the other hand, polymorphisms of UGT1A1 have been shown to be associated with CPT-11 toxicity in clinical situations. The primary aim of this study was to investigate the prevalence of mutations in the TOP-I exons associated with CPT-11 resistance, including untreated cancer tissue. A secondary aim was to confirm the less frequent UGT1A1*28 and more frequent UGT1A1*6 in individuals of Asian descent compared to Caucasians and individuals of African descent. The prevalence of 5 reported TOP-I mutations in exons was investigated in volunteers (n=236) using DNA sequencing of the PCR products. The prevalence of TOP-I mutations in untreated lung cancer tissues (n=16) was also investigated. Additionally, 3 UGT1A1 polymorphisms, UGT1A1*6, *27 and *28, were investigated in volunteers (n=126). There were no mutations of TOP-I in any of the 236subjects or in the untreated lung tissues. Among 128subjects, the distribution of homozygous polymorphisms of UGT1A1 was: UGT1A1*28 in 3 (2.4%) and UGT1A1*6 in 4 (3.2%) subjects, and co-occurrence of heterozygous polymorphisms for both UGT1A1*6 and UGT1A1*28 in 4 (3.2%) subjects, and for UGT1A1*27 and UGT1A1*28 in 1 subject (0.8%). The Hardy-Weinberg deviation test showed there was no significant deviation from the equilibrium, and the association analysis indicated no significant linkage between UGT1A1*6 and UGT1A1*28. In conclusion, TOP-I genetic mutations correlated to CPT-11 resistance were not detected in any of the subjects and untreated lung cancer tissues. Less frequent UGT1A1*28 and more frequent UGT1A1*6 were confirmed in East Asian individuals compared to Caucasians and individuals of African descent. Linkage disequilibrium was not detected between UGT1A1*6 and UGT1A1*28. PMID:22866151

Fukui, Tomoya; Mitsufuji, Hisashi; Kubota, Masaru; Inaoka, Hidenori; Hirose, Minoru; Iwabuchi, Keiichi; Masuda, Noriyuki; Kobayashi, Hirosuke

2011-01-01

323

Genetic diversity of Brucella abortus isolates as determined by amplified fragment length polymorphism (AFLP) analysis  

E-print Network

with the powerful Bionumerics software package to determine the genetic relationships between B. abortus field isolates, collected from infections in wild herds of elk and bison to achieve a better understanding of the molecular diversity and evolution of B. abortus...

Bliss, Katherine Ann

2013-02-22

324

Apolipoprotein E genetic polymorphism, serum lipoprotein levels and breast cancer risk: A case-control study  

PubMed Central

The purpose of this study was to evaluate the association between apolipoprotein E (APOE) allelic frequency, serum lipoproteins and breast cancer (BC). We conducted a nested case-control study within a cohort including 47 cases and 165 controls. Polymerase chain reaction-restriction fragment length polymorphism analyses of the APOE polymorphism were performed. In general, participants with the genotype including alleles e2 and e3 tended to have lower serum triglycerides, total cholesterol and low-density lipoprotein cholesterol levels and higher high-density lipoprotein (HDL) cholesterol levels compared to participants homozygous for the e3 allele and participants heterozygous for the e3 and e4 alleles, respectively. BC patients exhibited higher mean levels of total serum cholesterol (P=0.070), dietary fat intake (P=0.020) and dietary cholesterol intake (P=0.017) compared to control subjects. The allelic distribution between the two groups revealed that the presence of the e2 allele was positively associated with the absence of BC, whereas the e4 allele was positively associated with the BC case group (P=0.019). The distribution of the APOE genotypes was not significantly different between cases and controls (P=0.172). The concomitant presence of the e2 and e4 alleles was positively associated with the absence of BC and e4/e4 homozygosity was positively associated with BC (P=0.021). Our findings suggested that APOE polymorphism plays an important role in the development of BC, particularly when associated with higher serum triglyceride levels.

CIBEIRA, GABRIELA HERRMANN; GIACOMAZZI, JULIANA; AGUIAR, ERNESTINA; SCHNEIDER, SILVANA; ETTRICH, BETINA; DE SOUZA, CAROLINE ISOPPO; CAMEY, SUZI; CALEFFI, MAIRA; WEBER, BERNARDETE; ASHTON-PROLLA, PATRICIA; MORIGUCHI, EMILIO HIDEYUKI

2014-01-01

325

Genetic analysis of the ELOVL6 gene polymorphism associated with type 2 diabetes mellitus  

PubMed Central

Recent animal studies have indicated that overexpression of the elongation of long-chain fatty acids family member 6 (Elovl6) gene can cause insulin resistance and ?-cell dysfunction. These are the major factors involved in the development of type 2 diabetes mellitus (T2DM). To identify the relationship between single nucleotide polymorphisms (SNP) of ELOVL6 and T2DM pathogenesis, we conducted a case-control study of 610 Han Chinese individuals (328 newly diagnosed T2DM and 282 healthy subjects). Insulin resistance and islet first-phase secretion function were evaluated by assessment of insulin resistance in a homeostasis model (HOMA-IR) and an arginine stimulation test. Three SNPs of the ELOVL6 gene were genotyped with polymerase chain reaction-restriction fragment length polymorphism, with DNA sequencing used to confirm the results. Only genotypes TT and CT of the ELOVL6 SNP rs12504538 were detected in the samples. Genotype CC was not observed. The T2DM group had a higher frequency of the C allele and the CT genotype than the control group. Subjects with the CT genotype had higher HOMA-IR values than those with the TT genotype. In addition, no statistical significance was observed between the genotype and allele frequencies of the control and T2DM groups for SNPs rs17041272 and rs6824447. The study indicated that the ELOVL6 gene polymorphism rs12504538 is associated with an increased risk of T2DM, because it causes an increase in insulin resistance. PMID:23903678

Liu, Y.; Wang, F.; Yu, X.L.; Miao, Z.M.; Wang, Z.C.; Chen, Y.; Wang, Y.G.

2013-01-01

326

Genetic Polymorphism of Lactoglobulin in Native Sheep from the Island of Pag  

Microsoft Academic Search

Summary Milk samples from 248 Pag ewes, belonging to 14 different flocks and located through the Pag Island (Croatia), were analyzed by isoelectrofocusing and PCR-RFLP. Two genetic variants (A and B) and three genotypes (AA, AB and BB) of -lactoglobulin have been identified. According to the allele frequency (A=0.48, B=0.52) and occurrence of genetic variants, the Pag breed is similar

Vlatka Cubric-Curik; Maria Feligini; Jasmina Lukac-Havranek; Ino Curik; Giuseppe Enne

327

Genetic polymorphisms in the oxidative stress pathway and susceptibility to non-Hodgkin lymphoma  

Microsoft Academic Search

Oxidative damage caused by reactive oxygen species (ROS) and other free radicals is involved in a number of pathological conditions\\u000a including cancer. In a population-based case-control study of non-Hodgkin lymphoma (NHL) (n=518 cases, 597 controls) among women in Connecticut, we analyzed one or more single nucleotide polymorphisms (SNPs) in\\u000a ten candidate genes (AKR1A1, AKR1C1, AKR1C3, CYBA, GPX1, MPO, NOS2A, NOS3,

Qing Lan; Tongzhang Zheng; Min Shen; Yawei Zhang; Sophia S. Wang; Shelia H. Zahm; Theodore R. Holford; Brian Leaderer; Peter Boyle; Stephen Chanock

2007-01-01

328

Toward autonomous harbor surveillance  

E-print Network

In this thesis we address the problem of drift-free navigation for underwater vehicles performing harbor surveillance and ship hull inspection. Maintaining accurate localization for the duration of a mission is important ...

Johannsson, Hordur

2010-01-01

329

Genetic polymorphisms for drug metabolism (CYP2D6) and tardive dyskinesia in schizophrenia.  

PubMed

In the present study, the occurrence of tardive dyskinesia (TD) in chronic schizophrenia patients was investigated in relation to pharmacogenetic polymorphisms. It is known that the metabolism of important neuroleptic drugs is influenced by polymorphisms of the CYP2D6 gene, which encodes the cytochrome P450 enzyme debrisoquine/spartein hydroxylase. Forty-five patients meeting the DSM IV criteria for schizophrenia, chronic course, were recruited. The patients were examined for the mutations CYP2D6*3, CYP2D6*4 and CYP2D6*5. The CYP2D6 genotype distribution in the patient group did not differ from that in healthy Caucasian populations. Tardive dyskinesia was found in 26 patients (57.8%). When comparing patients without CYP2D6 mutations with patients heterozygous for one mutation, we found a higher incidence of TD in the latter (81.3% vs. 46.4%, p = 0.031, multiple regression analysis), which demonstrates a significant influence of the CYP2D6 genotype of the manifestation of TD. As slight differences in the metabolism of drugs in patients heterozygous for CYP2D6 mutations and patients without such mutations are known, we conclude that heterozygous carriers of 2D6 mutated alleles may show an increased susceptibility to developing TD. PMID:9713905

Kapitany, T; Meszaros, K; Lenzinger, E; Schindler, S D; Barnas, C; Fuchs, K; Sieghart, W; Aschauer, H N; Kasper, S

1998-07-27

330

Increased prevalence of MnSOD genetic polymorphism in endurance and power athletes.  

PubMed

The purpose of the current study was to determine the frequency distribution of manganese superoxide dismutase (MnSOD) Val-9Ala polymorphism (rs1799725) among 195 trained endurance and power athletes and 240 healthy controls. Genomic DNA was extracted using a standard protocol. Genotyping of the MnSOD Val-9Ala polymorphism was performed using polymerase chain reaction (PCR). Results showed a higher proportion of the Val/Ala and Ala/Ala genotype, and a lower proportion of Val/Val genotype, in the athletes group compared with that of the controls. The Ala allele frequency was significantly higher (p < 0.001) in the athletes group (46%) compared with that in the control (29%). Interestingly, there was no difference between the endurance and power athletes. In addition, the frequency of Ala/Ala genotype was significantly higher (p < 0.05) among top (international and Olympic-level) athletes (29%) compared with that among national-level endurance and power athletes (17%). We conclude that 1) the Ala allele is more frequent in athletes than in controls; and 2) the higher frequency of the Ala allele was noted in both endurance and power athletes compared with that in controls, suggesting that the positive association between the Ala allele and athletic performance may be related to ROS-related angiogenesis, mitochondrial biosynthesis, and muscle hypertrophy, and not to MnSOD aerobic properties. PMID:23991909

Ben-Zaken, S; Eliakim, A; Nemet, D; Kassem, E; Meckel, Y

2013-12-01

331

Genetic diversity of the edible mushroom Pleurotus sp. by amplified fragment length polymorphism.  

PubMed

Pleurotus strains are the most important fungi used in the agricultural industry. The exact characterization and identification of Pleurotus species is fundamental for correct identification of the individuals and exploiting their full potential in food industry. The amplified fragment length polymorphism (AFLP) method was applied for genomic fingerprinting of 21 Pleurotus isolates of Asian and European origin. Using one PstI restriction endonuclease and four selective primers in an AFLP assay, 371 DNA fragments were generated, including 308 polymorphic bands. The AFLP profiles were found to be highly specific for each strain and they unambiguously distinguished 21 Pleurotus sp. fungi. The coefficient of Jaccard's genome profile similarity between the analyzed strains ranged from 0.0 (Pleurotus sp. I vs. P. sajor-caju 237 and P. eryngii 238) to 0.750 (P. ostreatus 246 vs. P. ostreatus 248), and the average was 0.378. The AFLP-based dendrogram generated by the UPGMA method grouped all the Pleurotus fungi studied into two major clusters and one independent lineage located on the outskirt of the tree occupied by naturally growing Pleurotus species strain I. The results of the present study suggest the possible applicability of the AFLP-PstI method in effective identification and molecular characterization of Pleurotus sp. strains. PMID:22767319

Pawlik, Anna; Janusz, Grzegorz; Koszerny, Joanna; Ma?ek, Wanda; Rogalski, Jerzy

2012-10-01

332

Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus).  

PubMed

Genetic analyses of bird subspecies designated as conservation units can address whether they represent units with independent evolutionary histories and provide insights into the evolutionary processes that determine the degree to which they are genetically distinct. Here we use mitochondrial DNA control region sequence and six microsatellite DNA loci to examine phylogeographical structure and genetic differentiation among five North American grasshopper sparrow (Ammodramus savannarum) populations representing three subspecies, including a population of the endangered Florida subspecies (A. s. floridanus). This federally listed taxon is of particular interest because it differs phenotypically from other subspecies in plumage and behaviour and has also undergone a drastic decline in population size over the past century. Despite this designation, we observed no phylogeographical structure among populations in either marker: mtDNA haplotypes and microsatellite genotypes from floridanus samples did not form clades that were phylogenetically distinct from variants found in other subspecies. However, there was low but significant differentiation between Florida and all other populations combined in both mtDNA (FST = 0.069) and in one measure of microsatellite differentiation (theta = 0.016), while the non-Florida populations were not different from each other. Based on analyses of mtDNA variation using a coalescent-based model, the effective sizes of these populations are large (approximately 80,000 females) and they have only recently diverged from each other (< 26,000 ybp). These populations are probably far from genetic equilibrium and therefore the lack of phylogenetic distinctiveness of the floridanus subspecies and minimal genetic differentiation is due most probably to retained ancestral polymorphism. Finally, levels of variation in Florida were similar to other populations supporting the idea that the drastic reduction in population size which has occurred within the last 100 years has not yet had an impact on levels of variation in floridanus. We argue that despite the lack of phylogenetic distinctiveness of floridanus genotypes the observed genetic differentiation and previously documented phenotypic differences justify continued designation of this subspecies as a protected population segment. PMID:12753205

Bulgin, Natalie L; Gibbs, H Lisle; Vickery, Peter; Baker, Allan J

2003-04-01

333

Allozyme analysis of genetic variation and polymorphism in Eubothrium salvelini and E. crassum (Cestoda: Pseudophyllidea) from alpine lakes.  

PubMed

The genetic structure of the most abundant species in the genus Eubothrium, E. crassum and E. salvelini, was studied by allozyme analysis in order to provide a consistent diagnosis for these morphologically similar species, as well as to assess their genetic relatedness. The proportion of fixed allelic differences (56.3%, 9 of 16 loci) between the species falls within the range accepted for valid species. A strict host specificity of E. crassum and E. salvelini for their typical host (lake trout, Arctic charr, respectively) was found in the French localities examined (Lake Annecy, Lake Bourget). For E. salvelini, polymorphism with the established allelic profile was found in the acid phosphatase (ACP) system. No significant deviation from the Hardy-Weinberg equilibrium expectations for ACP were found in either of the E. salvelini populations, which suggests predominantly cross-fertilization of these hermaphrodites. Analysis of the standardized variance in allelic frequencies demonstrated almost no among population differentiation (estimator theta of Fst = -0.03) between E. salvelini populations. PMID:15175878

Snbel, Viliam; Hanzelov, Vladimra; Scholz, Toms; Gerdeaux, Daniel; Cabaret, Jacques

2004-07-01

334

Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms.  

PubMed

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication. PMID:22101929

Gong, Li; Paris, Harry S; Nee, Michael H; Stift, Gertraud; Pachner, Martin; Vollmann, Johann; Lelley, Tamas

2012-03-01

335

AFLP Polymorphisms Allow High Resolution Genetic Analysis of American Tegumentary Leishmaniasis Agents Circulating in Panama and Other Members of the Leishmania Genus  

PubMed Central

American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP), a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at both intra and inter-specific levels. PMID:24039881

Restrepo, Carlos M.; De La Guardia, Carolina; Sousa, Octavio E.; Calzada, Jose E.; Fernandez, Patricia L.; Lleonart, Ricardo

2013-01-01

336

Genetic differentiation of southeast Baltic populations of sea trout inferred from single nucleotide polymorphisms.  

PubMed

Sea trout (Salmo trutta m. trutta) is a migratory form of brown trout common in the Baltic Sea. Nine populations from the southeast Baltic (Poland; Lithuania; Denmark, Bornholm; Estonia and Russia) were genotyped using iPLEX Gold technology (Sequenom) with 62 informative SNPs. A diagnostic panel of 23 SNPs was applied to estimate genetic differentiation and assess the population structure of Baltic sea trout. The highest level of pairwise FST differences was observed between the Russian (East Gulf of Finland) and Polish (Baltic main basin) populations. The lowest differences were between the two Polish and the Polish and Lithuanian populations. A genetic similarity was noted between the Estonian Riguldi River and Danish Bornholm populations, and this finding was supported by a Bayesian and factorial correspondence analysis. Diversity within populations was highest for populations from Estonia and lowest for the Lithuanian population. Genetic structure analysis indicated that individuals from the nine populations were clustered into four groups. PMID:24236931

Po?wierz-Kotus, A; Berna?, R; D?bowski, P; Kent, M P; Lien, S; Kesler, M; Titov, S; Leli?na, E; Jespersen, H; Drywa, A; Wenne, R

2014-02-01

337

Genetic incompatibility drives sex allocation and maternal investment in a polymorphic finch.  

PubMed

Genetic compatibility may drive individual mate choice decisions because of predictable fitness effects associated with breeding with incompatible partners. In Gouldian finches (Erythrura gouldiae), females paired with genetically incompatible males of alternative color morphs overproduce sons, presumably to reduce investment in inviable daughters. We also observed a reduced overall investment in clutch size, egg size, and care to offspring resulting from incompatible matings. Within-female experimental pairings demonstrate that female birds have the ability to adaptively adjust the sex of their eggs and allocate resources on the basis of partner quality. Female Gouldian finches thus make cumulative strategic allocation decisions to minimize the costs of poor-quality pairings when faced with a genetically incompatible partner. PMID:19299618

Pryke, Sarah R; Griffith, Simon C

2009-03-20

338

Genetic polymorphism of 11 Y-chromosomal STR loci in Yunnan Han Chinese.  

PubMed

Allele frequencies and haplotypes of 11 Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 ab, DYS438, DYS439 and DYS437 were determined in 320 unrelated Yunnan Han Chinese males. A total of 293 haplotypes were identified, of which 268 were unique, 23 were shared in two individuals, and 2 were shared in three individuals. The allele diversity values for each locus ranged from 0.4087 (DYS438) to 0.9701 (DYS385). The allele observed haplotypes diversity value was 0.9994. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications. PMID:20129460

Yanmei, Yang; Tao, Gu; Yubao, Zeng; Chunjie, Xiao; Bifeng, Chen; Shi, Luo; Bingying, Xu; Qiang, Jing; Qinyong, Zhuang; Wen, Zhang; Shengjun, Luo; Shengjie, Nie

2010-02-01

339

Genetic polymorphisms in glutathione S-transferase (GST) superfamily and arsenic metabolism in residents of the Red River Delta, Vietnam  

SciTech Connect

To elucidate the role of genetic factors in arsenic metabolism, we investigated associations of genetic polymorphisms in the members of glutathione S-transferase (GST) superfamily with the arsenic concentrations in hair and urine, and urinary arsenic profile in residents in the Red River Delta, Vietnam. Genotyping was conducted for GST omega1 (GSTO1) Ala140Asp, Glu155del, Glu208Lys, Thr217Asn, and Ala236Val, GST omega2 (GSTO2) Asn142Asp, GST pi1 (GSTP1) Ile105Val, GST mu1 (GSTM1) wild/null, and GST theta1 (GSTT1) wild/null. There were no mutation alleles for GSTO1 Glu208Lys, Thr217Asn, and Ala236Val in this population. GSTO1 Glu155del hetero type showed higher urinary concentration of As{sup V} than the wild homo type. Higher percentage of DMA{sup V} in urine of GSTM1 wild type was observed compared with that of the null type. Strong correlations between GSTP1 Ile105Val and arsenic exposure level and profile were observed in this study. Especially, heterozygote of GSTP1 Ile105Val had a higher metabolic capacity from inorganic arsenic to monomethyl arsenic, while the opposite trend was observed for ability of metabolism from As{sup V} to As{sup III}. Furthermore, other factors including sex, age, body mass index, arsenic level in drinking water, and genotypes of As (+ 3 oxidation state) methyltransferase (AS3MT) were also significantly co-associated with arsenic level and profile in the Vietnamese. To our knowledge, this is the first study indicating the associations of genetic factors of GST superfamily with arsenic metabolism in a Vietnamese population.

Agusa, Tetsuro [Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan); Iwata, Hisato, E-mail: iwatah@agr.ehime-u.ac.j [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan); Fujihara, Junko [Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Kunito, Takashi [Department of Environmental Sciences, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621 (Japan); Takeshita, Haruo [Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Tu Binh Minh; Pham Thi Kim Trang; Pham Hung Viet [Center for Environmental Technology and Sustainable Development (CETASD), Hanoi University of Science, Vietnam National University, T3 Building, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi (Viet Nam); Tanabe, Shinsuke [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan)

2010-02-01

340

A Second Genetic Polymorphism in Methylenetetrahydrofolate Reductase (MTHFR) Associated with Decreased Enzyme Activity  

Microsoft Academic Search

A common mutation in methylenetetrahydrofolate reductase (MTHFR), C677T, results in a thermolabile variant with reduced activity. Homozygous mutant individuals (approximately 10% of North Americans) are predisposed to mild hyperhomocysteinemia, when their folate status is low. This geneticnutrient interactive effect is believed to increase the risk for neural tube defects and vascular disease. In this communication, we characterize a second common

Ilan Weisberg; Pamela Tran; Benedicte Christensen; Sahar Sibani; Rima Rozen

1998-01-01

341

Colon tumor mutations and epigenetic changes associated with genetic polymorphism: Insight into disease pathways  

Microsoft Academic Search

Variation in genes associated with serum levels of proteins may be useful for examining specific disease pathways. Using data from a large study of colon cancer, we examine genetic variants in insulin, inflammation, estrogen, metabolizing enzymes, and energy homeostasis genes to explore associations with microsatellite instability (MSI), CpG Island methylator phenotype (CIMP), mutations of p53 in exons 5 through 8,

Martha L. Slattery; Roger K. Wolff; Karen Curtin; Frank Fitzpatrick; Jennifer Herrick; John D. Potter; Bette J. Caan; Wade S. Samowitz

2009-01-01

342

Genetic Polymorphisms in Organic Cation Transporter 1 (OCT1) in Chinese and Japanese Populations Exhibit Altered  

E-print Network

- betic drug metformin. Genetic variants in OCT1 have been identified largely in European populations. Metformin is in- creasingly being used in Asian populations where the incidence of type 2 diabetes (T2D in Chinese and Japanese pop- ulations may affect the differential response to metformin. Introduction

Sali, Andrej

343

Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam  

Microsoft Academic Search

Moringa oleifera is an important multipurpose tree introduced to Africa from India at the turn of this century. Despite limited knowledge of the levels of genetic diversity and relatedness of introduced populations, their utilization as a source of seed for planting is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for a selective

G. M. MULUVI; J. I. SPRENT; N. SORANZO; J. PROVAN; D. ODEE; G. FOLKARD; J. W. McNICOL; W. POWELL

1999-01-01

344

Genetic polymorphism in nine clones of a parthenogenetic collembolan used in ecotoxicological testing  

Microsoft Academic Search

Ecotoxicological tests are increasingly being used to evaluate the toxicity of a substance or mixture of substances towards soil fauna. One of these uses the parthenogenetic collembolan Folsomia candida to test for soil contamination, and this has been standardised in Europe. However, in such studies, it is important to know whether different laboratories use genetically close clones.In this study, nine

P Chenon; A Rousset; Y Crouau

2000-01-01

345

Population biology of avena. VI. The role of genetic polymorphisms in the outcome of interspecific competition  

Microsoft Academic Search

Three different series of population samples of two Avena species cooccurring in California were grown for an analysis of the role of genetic variation in interspecies competition: I, samples from mixed fatua-barbata sites in nature, grown in mixed stands; II, samples from pure sites and grown in pure stands, and III, the same sites as in II but grown in

B. Yazdi-Samadi; K. K. Wu; S. K. Jain

1978-01-01

346

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms  

PubMed Central

Background Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. Results We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data. Conclusion Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions. PMID:19077280

Watkins, WS; Thara, R; Mowry, BJ; Zhang, Y; Witherspoon, DJ; Tolpinrud, W; Bamshad, MJ; Tirupati, S; Padmavati, R; Smith, H; Nancarrow, D; Filippich, C; Jorde, LB

2008-01-01

347

C-reactive protein polymorphisms and genetic susceptibility to ischemic stroke and hemorrhagic stroke in the Chinese Han population  

PubMed Central

Aim: The inflammatory marker C-reactive protein (CRP) has been strongly correlated with the risk of cardiovascular disease. Some single-nucleotide polymorphisms (SNPs) have been reported to be associated with serum CRP levels. In this study, we assessed the genetic association between SNPs within the CRP gene and ischemic and hemorrhagic stroke in the Han Chinese population. Methods: This study comprises 564 ischemic stroke patients, 220 hemorrhagic stroke patients and 564 controls from the ethnic Han Chinese population in Wuhan. Four CRP SNPs, ?757A>G (rs3093059), ?717A>G (rs2794521), ?286C>T>A (rs3091244) and +2147C>T (rs1205), were genotyped from patients using TaqMan assays. Results: The A allele frequency for the ?717A>G polymorphism was significant higher in controls than in ischemic stroke patients (P=0.037), after adjustment for traditional risk factors (odds ratio 0.28; 95% CI 0.120.65; P=0.003), suggesting a protective effect for this allele against ischemic stroke. Haplotype analysis showed that the H3 (G-C-C) haplotype conferred a significantly increased risk of ischemic stroke (odds ratio 1.052, 95% CI 1.0011.106: P=0.047). Neither CRP genotypes nor haplotypes showed an association with hemorrhagic stroke. However, the frequency for haplotype H5 (A-T-C) was significantly higher in ischemic stroke than hemorrhagic stroke patients (P=0.0003). Conclusion: These data suggest that the CRP gene ?717A allele confers a protective effect against ischemic stroke. Furthermore, the H3 haplotype (G-C-C) is an independent risk marker for ischemic stroke, whereas the H5 haplotype (A-T-C) can be used as a prognostic marker of hemorrhagic stroke. PMID:19262552

Wang, Qi; Ding, Hu; Tang, Jia-rong; Zhang, Lan; Xu, Yu-jun; Yan, Jiang-tao; Wang, Wei; Hui, Ru-tai; Wang, Cong-yi; Wang, Dao-wen

2009-01-01

348

Genetic Association Study of TNFAIP3, IFIH1, IRF5 Polymorphisms with Polymyositis/Dermatomyositis in Chinese Han Population  

PubMed Central

Background Single-nucleotide polymorphisms (SNPs) in the TNFAIP3, IFIH1, and IRF5 genes have been associated with several auto-inflammation diseases, while the susceptibility between these genes and idiopathic inflammatory myopathies (IIMs) were not reported. This study aimed to investigate whether TNFAIP3, IFIH1, and IRF5 gene polymorphisms confer susceptibility for the IIMs in Chinese Han population. Methods A large casecontrol study of Chinese subjects with polymyositis (PM) (n?=?298) and dermatomyositis (DM) (n?=?530) was accomplished. 968 healthy and ethnically matched controls were available for comparison. Six SNPs in the TNFAIP3 region (rs2230926 and rs5029939), the IFIH1 gene (rs1990760 and rs3747517) and the IRF5 region (rs4728142 and rs729302) were assessed and genotyped using the Sequenom MassArray iPLEX platform. Results Our study indicated a strong allele association was observed in PM/DM and PM patients for rs2230926 (OR: 1.61, 95%CI: 1.202.16, Pc?=?7.510?3; OR: 1.88, 95%CI: 1.302.74, Pc?=?4.010?3, respectively) and rs5029939 (OR: 1.64, 95%CI: 1.212.21, Pc?=?6.010?3; OR: 1.88, 95%CI: 1.282.76, Pc?=?5.510?3,respectively). And rs2230926 and rs5029939 were significantly associated with interstitial lung disease (ILD) in PM/DM and PM patients (Pc?=?0.04 and Pc?=?0.016; Pc?=?0.02 and Pc?=?0.03, respectively). In addition, rs4728142 allele and genotype had significant association with PM/DM patients (Pc?=?0.026 and Pc?=?0.048, respectively). Further analysis with three logistic regression genetic models revealed statistically significant difference in the genotypic distribution in the PM/DM, PM or DM patients when the additive and dominant models were used. Conclusions This was the first study to reveal TNFAIP3 and IRF5 polymorphisms were associated with PM/DM patients or these patients with ILD, indicating that TNFAIP3 and IRF5 might be the susceptibility gene for PM/DM patients in Chinese Han population. PMID:25337792

Li, Yuan; Li, Ping; Sun, Fei; Zheng, Wenjie; Wu, Qingjun; Wu, Chanyuan; Deng, Chuiwen; Zhang, Fengchun; Li, Yongzhe

2014-01-01

349

Genetic Characterization and Relatedness among Cherry Cultivars in a Germplasm Bank by Randomly Amplified Polymorphic DNA Analysis  

Microsoft Academic Search

SUMMARY Random amplified polymorphic DNA (RAPD) analysis was performed on 38 cultivars of cherry (Prunus avium L.) grown in the Jerte Valley, Cceres, Spain. Thirty five selected decamer primers produced 69 reproducible polymorphic amplification products. The degree of polymorphism detected made possible the identification of all the cultivars by combining the RAPD banding patterns of only seven primers: OPK-08, OPQ-14,

Jesus MORENO; Isabel TRUJILLO

350

Study of individual and sex genetic diversity among each genus and between two genera of Chrysopa and Chrysoperla (Neuroptera, Chrysopidae) based on RAPD-PCR polymorphism.  

PubMed

RAPD (random amplification of polymorphic DNA) was used to distinguish the genetic diversities between two genera of Chrysopa and Chrysoperla (Neuroptera, Chrysopidae). Sixty specimens were collected in different places in Kermanshah, west of Iran. The wing venation was used for identification of each type of two genera, and the gender was determined by study of external genitalia. 20 random primers were used for polymerase chain reaction. Then, the electrophoresis was used for separation of the PCR products on agarose gel. 294 bands were amplified, which 235 bands were polymorph and others (59s) determined as monomorph. The electrophoresis results showed that the primers OPA02 with 19 bands and OPA03 with 8 bands successively amplified the maximum and minimum of bands among the applied primers. The results showed that there are maximum of genetic diversity and minimum of genetic similarity between Chrysopa male (Chrysopa-M) and Chrysoperla female)Chrysoperla-F) population, in contrast, there are maximum of genetic similarity and minimum of genetic diversity between Chrysoperla-M and Chrysoperla-F, and Chrysopa-M and Chrysopa-F. There are also more genetic similarities, between males and females of Chrysopa and Chrysoperla, than between male of Chrysopa with female of Chrysoperla or vice versa. PMID:22729908

Mirmoayedi, Alinaghi; Kahrizi, Danial; Ebadi, Ali Akbar; Yari, Kheirollah; Mohammadi, Mehdi

2012-09-01

351

TGFB1 genetic polymorphisms and coronary heart disease risk: a meta-analysis  

PubMed Central

Background Genetic variations in TGFB1 gene have been studied in relation to coronary heart disease (CHD) risk, but the results were inconsistent. Methods We performed a systematic review of published studies on the potential role of TGFB1 genetic variation in CHD risk. Articles that reported the association of TGFB1 genetic variants with CHD as primary outcome were searched via Medline and HuGE Navigator through July 2011. The reference lists from included articles were also reviewed. Results Data were available from 4 studies involving 1777 cases and 7172 controls for rs1800468, 7 studies involving 5935 cases and 10677 controls for rs1800469, 7 studies involving 6634 cases and 9620 controls for rs1982073, 5 studies involving 5452 cases and 9999 controls for rs1800471, and 4 studies involving 5143 cases and 4229 controls for rs1800472. The pooled odds ratios (ORs) for CHD among minor T allele carriers of rs1800469, minor C allele carriers of rs1982073, and minor C allele carriers of rs1800471 versus homozygous major allele carriers was 1.14 (95% confidence interval [CI]: 1.05-1.24), 1.18 (95% CI: 1.04-1.35), and 1.16 (95% CI: 1.02-1.32), respectively. No substantial heterogeneity for ORs was detected among the included Caucasian populations for all SNPs. However, for rs1800471, the statistical significance disappeared after adjusting for potential publication bias. No significant association was found between rs1800468 and rs1800472 variants and CHD risk. Conclusion Minor allele carriers of two genetic variants (rs1800469 and rs1982073) in TGFB1 have a 15% increased risk of CHD. PMID:22607024

2012-01-01

352

Genetic Association of a Cystatin C Gene Polymorphism With Late-Onset Alzheimer Disease  

Microsoft Academic Search

Objective: To determine whether the cystatin C gene (CST3) is genetically associated with late-onset Alzhei- mer disease (AD). Design: A case-control study with 2 independent study populations of patients with AD and age-matched, cog- nitively normal control subjects. Setting: The Alzheimer's Disease Research Unit at the University Hospital Hamburg-Eppendorf, Hamburg, Ger- many, for the initial study (n=260). For the indepen-

Ulrich Finckh; Heinz von der Kammer; Joachim Velden; Tiana Michel; Barbara Andresen; Amy Deng; Jun Zhang; Tomas Muller-Thomsen; Kathrin Zuchowski; Gunnar Menzer; Ulrike Mann; Andreas Papassotiropoulos; Reinhard Heun; Jan Zurdel; Frederik Holst; Luisa Benussi; Gabriela Stoppe; Jochen Reiss; Andre R. Miserez; Hannes B. Staehelin; G. William Rebeck; Bradley T. Hyman; Giuliano Binetti; Christoph Hock; John H. Growdon; Roger M. Nitsch

2000-01-01

353

Genetic polymorphism of the adenosine A2A receptor is associated with habitual caffeine consumption13  

Microsoft Academic Search

Background:Caffeineisthemostwidelyconsumedstimulantinthe world, and individual differences in response to its stimulating ef- fects may explain some of the variability in caffeine consumption within a population. Objective: We examined whether genetic variability in caffeine metabolism (cytochrome P450 1A2 (CYP1A2) 163A3C) or the main target of caffeine action in the nervous system (adenosine A2A receptor (ADORA2A) 1083C3T) is associated with habitual caf- feine

Marilyn C Cornelis; Ahmed El-Sohemy; Hannia Campos

354

Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population.  

PubMed

In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vu?eti?". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA() cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies. PMID:21279707

Grkovi?, Branka; Mri?, Gordan; Polaek, Ozren; Vrdoljak, Andro; Merka, Sinia; An?elinovi?, Simun

2011-06-01

355

Common genetic polymorphisms modify the effect of smoking on absolute risk of bladder cancer  

PubMed Central

Bladder cancer results from the combined effects of environmental and genetic factors, smoking being the strongest risk factor. Evaluating absolute risks resulting from the joint effects of smoking and genetic factors is critical to evaluate the public health relevance of genetic information. Analyses included up to 3,942 cases and 5,680 controls of European background in seven studies. We tested for multiplicative and additive interactions between smoking and 12 susceptibility loci, individually and combined as a polygenic risk score (PRS). Thirty-year absolute risks and risk differences by levels of the PRS were estimated for US-males aged 50-years. Six out of 12 variants showed significant additive gene-environment interactions, most notably NAT2 (P=710-4) and UGT1A6 (P=810-4). The 30-year absolute risk of bladder cancer in US males was 6.2% for all current smokers. This risk ranged from 2.9% for current smokers in the lowest quartile of the PRS to 9.9% for current smokers in the upper quartile. Risk difference estimates indicated that 8,200 cases would be prevented if elimination of smoking occurred in 100,000 men in the upper PRS quartile, compared to 2,000 cases prevented by a similar effort in the lowest PRS quartile (P-additive =110-4). The impact of eliminating smoking the on number of bladder cancer cases prevented is larger for individuals at higher than lower genetic risk. Our findings could have implications for targeted prevention strategies. However, other smoking-related diseases, as well as practical and ethical considerations, need to be considered before any recommendations could be made. PMID:23536561

Garcia-Closas, Montserrat; Rothman, Nathaniel; Figueroa, Jonine D.; Prokunina-Olsson, Ludmila; Han, Summer S.; Baris, Dalsu; Jacobs, Eric J; Malats, Nuria; De Vivo, Immaculata; Albanes, Demetrius; Purdue, Mark P; Sharma, Sapna; Fu, Yi-Ping; Kogevinas, Manolis; Wang, Zhaoming; Tang, Wei; Tardon, Adonina; Serra, Consol; Carrato, Alfredo; Garcia-Closas, Reina; Lloreta, Josep; Johnson, Alison; Schwenn, Molly; Karagas, Margaret R; Schned, Alan; Andriole, Gerald; Grubb, Robert; Black, Amanda; Gapstur, Susan M; Thun, Michael; Diver, W Ryan; Weinstein, Stephanie J; Virtamo, Jarmo; Hunter, David J; Caporaso, Neil; Landi, Maria Teresa; Hutchinson, Amy; Burdett, Laurie; Jacobs, Kevin B; Yeager, Meredith; Fraumeni, Joseph F; Chanock, Stephen J; Silverman, Debra T; Chatterjee, Nilanjan

2013-01-01

356

Genetic polymorphisms in 12 autosomal STRs in a Shanghai Han population from China.  

PubMed

In this study, a total of 484 unrelated healthy individuals and 359 two-generation families in the Han population in Shanghai, China were successfully analyzed with the Investigator HDplex Kit (Qiagen, Hilden, Germany). Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (p > 0.05) for the 12 autosomal STRs included in this kit. A total of 173 alleles were detected in 12 autosomal STR loci; the largest number of alleles (32) was detected for the SE33 locus. The combined power of discrimination was 0.99999999992. The combined mean exclusion chance in duo cases was 0.99982, whereas the combined mean exclusion chance in trio cases was 0.9999986. The average mutation rate across all loci was 0.0023 (95% confidence intervals: 0.0013-0.0039). These results suggest that the 12 autosomal STR loci can provide highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China. PMID:23192632

Zhang, Suhua; Zhang, Zheren; Zhao, Shumin; Zhao, Zhenmin; Li, Chengtao

2013-02-01

357

Genetic polymorphisms of 12 X-STR for forensic purposes in Shanghai Han population from China.  

PubMed

X-chromosomal short tandem repeats (X-STR) loci are used for forensic practice in recent years in some complex kinship cases. The commercially available kit of Investigator Argus X-12 (Qiagen, Hilden, Germany) makes it possible to examine the markers of DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101 and DXS10146-DXS10134-DXS7423, which belong to four linkage groups of X-chromosome. In this study, a total of 309 unrelated individuals (200 males and 109 females) from Shanghai Han population were successfully analyzed with this kit. Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (P>0.05) for all of the 12 X-STR loci in the Shanghai Han population. Linkage disequilibrium tests were performed for all pairs of loci by the Arlequin v3.1 software and only DXS10103-DXS10101 remained significant after adjustment for multiple testing (P<0.05/66). The combined power of discrimination in males (CDP(M)) was 0.999999996 while in females (CDP(F)) was 0.999999999999995, and the combined mean exclusion chance in duo cases (CMEC(D)) was 0.999998 while in trio cases (CMEC(T)) was 0.999999986. The results suggest that the twelve X-STR loci may provide high polymorphic information for paternity testing and forensic identification in Chinese Han population from Shanghai. PMID:22189544

Zhang, Suhua; Zhao, Shumin; Zhu, Ruxin; Li, Chengtao

2012-05-01

358

Genetic Identification of the Main Opportunistic Mucorales by PCR-Restriction Fragment Length Polymorphism  

PubMed Central

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera Absidia, Mucor, Rhizopus, and Rhizomucor, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis. PMID:16517858

Machouart, M.; Larch, J.; Burton, K.; Collomb, J.; Maurer, P.; Cintrat, A.; Biava, M. F.; Greciano, S.; Kuijpers, A. F. A.; Contet-Audonneau, N.; de Hoog, G. S.; Grard, A.; Fortier, B.

2006-01-01

359

Molecular analysis of common polymorphisms within the human Tyrosinase locus and genetic association with pigmentation traits.  

PubMed

We have compared the melanogenic activities of cultured melanocytes carrying two common TYR alleles as homozygous 192S-402R wild-type, heterozygous and homozygous variant. This includes assays of TYR protein, DOPAoxidase activity, glycosylation and temperature sensitivity of protein and DOPAoxidase levels. Homozygous wild-type strains on average had higher levels of TYR protein and enzyme activity than other genotypes. Homozygous 402Q/Q melanocytes produced significantly less TYR protein, displayed altered trafficking and glycosylation, with reduced DOPAoxidase. However, near wild-type TYR activity levels could be recovered at lower growth temperature. In a sample population from Southeast Queensland, these two polymorphisms were present on four TYR haplotypes, designated as WT 192S-402R, 192Y-402R and 192S-402Q with a double-variant 192Y-402Q of low frequency at 1.9%. Based on cell culture findings and haplotype associations, we have used an additive model to assess the penetrance of the ten possible TYR genotypes derived from the combination of these haplotypes. PMID:24739399

Jagirdar, Kasturee; Smit, Darren J; Ainger, Stephen A; Lee, Katie J; Brown, Darren L; Chapman, Brett; Zhen Zhao, Zhen; Montgomery, Grant W; Martin, Nicholas G; Stow, Jennifer L; Duffy, David L; Sturm, Richard A

2014-07-01

360

Association analysis of genetic polymorphisms and potential interaction of the osteocalcin (BGP) and ER-? genes with body mass index (BMI) in premenopausal Chinese women  

PubMed Central

Aim: To investigate whether estrogen receptor ? (ER-?) PvuII and osteocalcin (also known as bone Gla protein, or BGP) HindIII genetic polymorphisms and their potential interactions are associated with body mass index (BMI) variation. Methods: Data on BMI and ER-? PvuII and BGP HindIII genotypes were obtained from 328 healthy premenopausal Chinese women in east China. The study subjects were unrelated, at least 21 years old (mean age of 33.25.9 years), and had an average BMI of 21.582.59. All subjects were genotyped at the ER-? PvuII and BGP HindIII loci using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). Results: The BGP HindIII genotypes were significantly associated with BMI (P=0.003). Carriers of the HH and Hh genotypes had approximately 2.73% and 1.27% higher BMI than those of the hh genotype, respectively. In contrast, the ER-? PvuII polymorphism was not significantly associated with BMI (P=0.454). In addition, there was no evidence of potential interactions between the ER-? and BGP genes in our subjects (P?0.013). Conclusion: The HindIII polymorphism of the BGP gene, but not the PvuII polymorphism of the ER-? gene or their potential interaction, was associated with BMI in premenopausal Chinese women. PMID:20305683

Xu, Hong; Xiao, Wen; Luo, Dan; Liu, Yong-ming; Zou, Lin; Kuang, Hai-bin

2010-01-01

361

Genetic polymorphisms and haplotypes of por, encoding cytochrome p450 oxidoreductase, in a Japanese population.  

PubMed

Cytochrome P450 oxidoreductase (POR) transfers electrons from NADPH to all microsomal cytochrome P450 (CYP) enzymes and is necessary for microsomal CYP activities. In this study, to find genetic variations and to elucidate the haplotype structures of POR, we comprehensively screened the genetic variations in the 5'-flanking region, all the exons and their flanking introns of POR for 235 Japanese subjects. Seventy-five genetic variations including 26 novel ones were found: 7 were in the 5'-flanking region, 2 in the 5'-untranslated region (5'-UTR, non-coding exon 1), 16 in the coding exons (10 nonsynonymous and 6 synonymous), 45 in the introns, 4 in the 3'-UTR and 1 in the 3'-flanking region. Of these, 4 novel nonsynonymous variations, 86C>T (T29M), 1648C>T (R550W), 1708C>T (R570C) and 1975G>A (A659T), were detected with allele frequencies of 0.002. We also detected known nonsynonymous SNPs 683C>T (P228L), 1237G>A (G413S), 1453G>A (A485T), 1508C>T (A503V), 1510G>A (G504R) and 1738G>C (E580Q) with frequencies of 0.002, 0.009, 0.002, 0.434, 0.002 and 0.002, respectively. Based on the linkage disequilibrium (LD) profiles, the analyzed region could be divided into two LD blocks. For Blocks 1 and 2, 14 and 46 haplotypes were inferred, respectively, and 2 and 6 common haplotypes found in more than 0.03 frequencies accounted for more than 81% of the inferred haplotypes. This study provides fundamental and useful information for the pharmacogenetic studies of drugs metabolized by CYPs in the Japanese population. PMID:21084761

Saito, Yoshiro; Yamamoto, Noboru; Katori, Noriko; Maekawa, Keiko; Fukushima-Uesaka, Hiromi; Sugimoto, Daisuke; Kurose, Kouichi; Sai, Kimie; Kaniwa, Nahoko; Sawada, Jun-Ichi; Kunitoh, Hideo; Ohe, Yuichiro; Yoshida, Teruhiko; Matsumura, Yasuhiro; Saijo, Nagahiro; Okuda, Haruhiro; Tamura, Tomohide

2011-01-01

362

PERMANENT GENETIC RESOURCES: Polymorphic microsatellite loci for Diachasma alloeum (Hymenoptera: Braconidae).  

PubMed

Here, we report the isolation of 21 novel primers for amplification of microsatellite loci in Diachasma alloeum (Hymenoptera: Braconidae). Diachasma alloeum is a larval parasitoid of the apple maggot fly (Rhagoletis pomonella), which is an economically significant agricultural pest species and a textbook example of sympatric speciation via host-plant shifting. These microsatellite markers will prove useful both for assessing genetic relationships between different host-associated populations of D. alloeum, as well as for future R. pomonella biological control programmes. We also report the cross-species amplification of several loci for Diachasmimorpha mellea and Diachasma ferrugineum, parasitoids of R. pomonella and R. cingulata, respectively. PMID:21585796

Forbes, Andrew A; Powell, Thomas H Q; Lobo, Neil F; Noor, Mohamed A F; Feder, Jeffrey L

2008-03-01

363

Effect of Genetic Polymorphism of OATP-C (SLCO1B1) on Lipid-Lowering Response to HMG-CoA Reductase Inhibitors  

Microsoft Academic Search

Summary: The eect of genetic polymorphism of human organic anion transporting polypeptide C (OATP-C) on the lipid-lowering response to 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase inhibitors was assessed. A retrospective study was conducted on 66 patients who underwent treatment of hyperlipidemia with HMG-CoA reductase inhibitors in a municipal hospital in a community-based cohort of Ehime prefecture in the southern part of Japan. Plasma

Rieko TACHIBANA-IIMORI; Yasuharu TABARA; Hiroyuki KUSUHARA; Katsuhiko KOHARA; Ryuichi KAWAMOTO; Jun NAKURA; Katsushi TOKUNAGA; Ikuko KONDO; Yuichi SUGIYAMA; Tetsuro MIKI

2004-01-01

364

Warfarin Pharmacogenetics: Polymorphisms of the CYP2C9, CYP4F2 , and VKORC1 loci in a genetically admixed Omani Population  

Microsoft Academic Search

This is the first study to evaluate the spectrum and prevalence of dose-predictive genetic polymorphisms of the CYP2C9, CYP4F2 and VKORC1 loci together, in a geographically defined, ethnically admixed healthy adult Omani population sharing common lifestyle\\/environmental factors. Since the present-day Omani population is the result of an admixture of Caucasian, African and Asian ancestries, we compared the pharmacoge- netic profile

Anil V. Pathare; Shoaib Al Zadjali; Rhea Misquith; Salam S. Alkindi; Vinodh Panjwani; Claudine Lapoumeroulie; Sahaya Pravin; Andras Paldi; Rajagopal Krishnamoorthy

2012-01-01

365

Prospective Study of Coronary Heart Disease Incidence in Relation to Fasting Total Homocysteine, Related Genetic Polymorphisms, and B Vitamins The Atherosclerosis Risk in Communities (ARIC) Study  

Microsoft Academic Search

BackgroundElevated plasma total homocysteine (tHcy), low B-vitamin intake, and genetic polymorphisms related to tHcy metabolism may play roles in coronary heart disease (CHD). More prospective studies are needed. Methods and ResultsWe used a prospective case-cohort design to determine whether tHcy-related factors are associated with incidence of CHD over an average of 3.3 years of follow-up in a biracial sample of

Aaron R. Folsom; F. Javier Nieto; Paul G. McGovern; Michael Y. Tsai; M. ReneMalinow; John H. Eckfeldt; David L. Hess; C. E. Davis

366

Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard  

Microsoft Academic Search

A multiplex assay with 49 autosomal single nucleotide polymorphisms (SNPs) developed for human identification was validated for forensic genetic casework and accredited according to the ISO 17025 standard. The multiplex assay was based on the SNPforID 52plex SNP assay [J.J. Sanchez, C. Phillips, C. Brsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe-Court, P.M.

Claus Brsting; Eszter Rockenbauer; Niels Morling

2009-01-01

367

Association analyses between the genetic polymorphisms of HNF4A and FOXO1 genes and Chinese Han patients with type 2 diabetes  

Microsoft Academic Search

The hepatocyte nuclear factor 4-alpha (HNF4A) and human forkhead box O1 (FOXO1) genes have been discovered to be associated with type 2 diabetes (T2D) in different populations. This study aimed to evaluate\\u000a the association between HNF4A and FOXO1 genetic polymorphisms and type 2 diabetes in the Chinese Han population. Five hundred and seventy-seven patients with type\\u000a 2 diabetes and 462

Tianjie Li; Xiaopan Wu; Xilin Zhu; Jingyun Li; Liping Pan; Pengtao Li; Zhenhui Xin; Ying Liu

2011-01-01

368

Association of polymorphisms MTHFR C677T and A1298C with risk of colorectal cancer, genetic and epigenetic characteristic of tumors, and response to chemotherapy  

Microsoft Academic Search

Background and aimsThe enzyme MTHFR plays an important role in folate metabolism, and folate is implicated in carcinogenesis due to its role in DNA methylation,\\u000a repair, and synthesis. We analyze the relationship of MTHFR C677T and A1298C polymorphisms with biological, clinicopathological, genetic and epigenetic features of tumors, and the patient\\u000a outcome after treatment with 5-FU-based chemotherapy to determine the contribution

Antonia M. Fernndez-Peralta; Lydia Daimiel; Nargisse Nejda; Daniel Iglesias; Vicente Medina Arana; Juan J. Gonzlez-Aguilera

2010-01-01

369

Evidence for genetic epistasis in human insulin resistance: the combined effect of PC1 (K121Q) and PPAR?2 (P12A) polymorphisms  

Microsoft Academic Search

Insulin resistance is believed to be under the control of several genes often interacting each other. However, whether genetic epistasis does in fact modulate human insulin sensitivity is unknown. In 338 healthy unrelated subjects from Sicily, all nondiabetic and not morbidly obese, we investigated whether two gene polymorphisms previously associated with insulin resistance (namely PC-1 K121Q and PPAR?2 P12A) affect

R. Baratta; R. Di Paola; D. Spampinato; G. Fini; A. Marucci; A. Coco; R. Vigneri; L. Frittitta; V. Trischitta

2003-01-01

370

Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers.  

PubMed

Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species. PMID:16714575

Elsheikha, H M; Schott, H C; Mansfield, L S

2006-06-01

371

Histo-Blood Group Gene Polymorphisms as Potential Genetic Modifiers of Infection and Cystic Fibrosis Lung Disease Severity  

PubMed Central

Background The pulmonary phenotype in cystic fibrosis (CF) is variable; thus, environmental and genetic factors likely contribute to clinical heterogeneity. We hypothesized that genetically determined ABO histo-blood group antigen (ABH) differences in glycosylation may lead to differences in microbial binding by airway mucus, and thus predispose to early lung infection and more severe lung disease in a subset of patients with CF. Methods and Principal Findings Clinical information and DNA was collected on >800 patients with the ?F508/?F508 genotype. Patients in the most severe and mildest quartiles for lung phenotype were enrolled. Blood samples underwent lymphocyte transformation and DNA extraction using standard methods. PCR and sequencing were performed using standard techniques to identify the 9 SNPs required to determine ABO blood type, and to identify the four SNPs that account for 9095% of Lewis status in Caucasians. Allele identification of the one nonsynonymous SNP in FUT2 that accounts for >95% of the incidence of nonsecretor phenotype in Caucasians was completed using an ABI Taqman assay. The overall prevalence of ABO types, and of FUT2 (secretor) and FUT 3 (Lewis) alleles was consistent with that found in the Caucasian population. There was no difference in distribution of ABH type in the severe versus mild patients, or the age of onset of Pseudomonas aeruginosa infection in the severe or mild groups. Multivariate analyses of other clinical phenotypes, including gender, asthma, and meconium ileus demonstrated no differences between groups based on ABH type. Conclusions and Significance Polymorphisms in the genes encoding ABO blood type, secretor or Lewis genotypes were not shown to associate with severity of CF lung disease, or age of onset of P. aeruginosa infection, nor was there any association with other clinical phenotypes in a group of 808 patients homozygous for the ?F508 mutation. PMID:19169360

Taylor-Cousar, Jennifer L.; Zariwala, Maimoona A.; Burch, Lauranell H.; Pace, Rhonda G.; Drumm, Mitchell L.; Calloway, Hollin; Fan, Haiying; Weston, Brent W.; Wright, Fred A.; Knowles, Michael R.

2009-01-01

372

Genetic polymorphisms in AS3MT and arsenic metabolism in residents of the Red River Delta, Vietnam  

SciTech Connect

To elucidate the role of genetic factors in arsenic (As) metabolism, we studied associations of single nucleotide polymorphisms (SNPs) in As (+ 3 oxidation state) methyltransferase (AS3MT) with the As concentrations in hair and urine, and urinary As profile in residents in the Red River Delta, Vietnam. Concentrations of total As in groundwater were 0.7-502 {mu}g/l. Total As levels in groundwater drastically decreased by using sand filter, indicating that the filter could be effective to remove As from raw groundwater. Concentrations of inorganic As (IAs) in urine and total As in hair of males were higher than those of females. A significant positive correlation between monomethylarsonic acid (MMA)/IAs and age in females indicates that older females have higher methylation capacity from IAs to MMA. Body mass index negatively correlated with urinary As concentrations in males. Homozygote for SNPs 4602AA, 35991GG, and 37853GG, which showed strong linkage disequilibrium (LD), had higher percentage (%) of dimethylarsinic acid (DMA) in urine. SNPs 4740 and 12590 had strong LD and associated with urinary %DMA. Although SNPs 6144, 12390, 14215, and 35587 comprised LD cluster, homozygotes in SNPs 12390GG and 35587CC had lower DMA/MMA in urine, suggesting low methylation capacity from MMA to DMA in homo types for these SNPs. SNPs 5913 and 8973 correlated with %MMA and %DMA, respectively. Heterozygote for SNP 14458TC had higher MMA/IAs in urine than TT homozygote, indicating that the heterozygote may have stronger methylation ability of IAs. To our knowledge, this is the first study on the association of genetic factors with As metabolism in Vietnamese.

Agusa, Tetsuro [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan); Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Iwata, Hisato [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan)], E-mail: iwatah@agr.ehime-u.ac.jp; Fujihara, Junko [Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Kunito, Takashi [Department of Environmental Sciences, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621 (Japan); Takeshita, Haruo [Department of Legal Medicine, Shimane University Faculty of Medicine, Enya 89-1, Izumo 693-8501 (Japan); Minh, Tu Binh [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan); Center for Environmental Technology and Sustainable Development (CETASD), Hanoi University of Science, Vietnam National University, T3 Building, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi (Viet Nam); Trang, Pham Thi Kim; Viet, Pham Hung [Center for Environmental Technology and Sustainable Development (CETASD), Hanoi University of Science, Vietnam National University, T3 Building, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi (Viet Nam); Tanabe, Shinsuke [Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan)

2009-04-15

373

Genetic Polymorphism of Interleukin-18 Gene Promoter Region in Rheumatoid Arthritis Patients from Southern India  

PubMed Central

Background: Interleukin-18 (IL-18) is a pro inflammatory cytokine which plays a key role in the acute and chronic inflammatory phases of Rheumatoid Arthritis (RA). The Single Nucleotide Polymorphisms (SNPs) of IL-18 gene promoter region at positions -137 and -607, are postulated to be associated with RA. To test this, this study aimed to identify the association between these SNPs of the IL-18 gene promoter region of RA in south Indian patients. Materials and Methods: This study was carried on 190 subjects among which 90 were RA patients and 100 were age and sex matched controls. Genomic DNA was extracted by Salting out method. IL 18 gene promotor region SNPs, IL 18 - 607 and IL 18 -137 were amplified by using sequence specific primers. The amplified products of different samples were separated by using a 1.5% agarose gel, stained with ethidium bromide and photographed. All statistical analyses were carried out by using SYSTAT 12 software. Results: At position 607, the frequencies of C allele, CC genotype, A allele and AA genotype were found to be significantly higher in patients and controls respectively and there was no significant difference in CA genotype. At position 137, there was no significant difference between the two groups with regard to G and C allelles but there was a significant increase in GG genotype of patients and CC genotype of controls. There was no association between duration of morning stiffness, rheumatoid factor positivity or negativity, age of onset and gender with distribution of genotypes and alleles. Conclusion: C allele, CC genotype at position-607 and GG genotype at position-137 are risk factors and A allele, AA genotype at position-607 and CC genotype at position-137 have protective effect for RA. PMID:25121046

Polipalli, Sunil Kumar; Karra, Vijay Kumar; Puppala, Madhavi; Pandey, Sanjeev Kumar; Kapoor, Seema; Kumar, Ashok; Godi, Sudhakar

2014-01-01

374

Genetic polymorphisms of ADH2 and ALDH2 association with esophageal cancer risk in southwest China  

PubMed Central

AIM: To evaluate the impact of alcohol dehydrogenase 2 (ADH2) and aldehyde dehydrogenase 2 (ALDH2) polymorphisms on esophageal cancer risk. METHODS: One hundred and ninety-one esophageal cancer patients and 198 healthy controls from Yanting County were enrolled in this study. ADH2 and ALDH2 genotypes were examined by polymerase-chain-reaction with the confronting-two-pair-primer (PCR-CTPP) method. Unconditional logistic regression was used to calculate the odds ratios (OR) and 95% confidence interval (95% CI). RESULTS: Both ADH2*1 allele and ALDH2*1/*2 allele showed an increased risk of developing esophageal cancer. The adjusted OR (95% CI) for ADH2*1 allele compared with ADH2*2/*2 was 1.65 (95% CI = 1.02-2.68) and 1.67 (95% CI = 1.02-2.72) for ALDH2*1/*2 compared with ALDH2*1/*1. A significant interaction between ALDH2 and drinking was detected regarding esophageal cancer risk, the OR was 1.83 (95% CI = 1.13-2.95). Furthermore, when compared with ADH2*2/*2 and ALDH2*1/*1 carriers, ADH2*1 and ALDH2*2 carriers showed an elevated risk of developing esophageal cancer among non-alcohol drinkers (OR = 2.46, 95% CI = 0.98-6.14), and a significantly elevated risk of developing esophageal cancer among alcohol drinkers among alcohol drinkers (OR = 9.86, 95% CI = 3.10-31.38). CONCLUSION: ADH2 and ALDH2 genotypes are associated with esophageal cancer risk. ADH2*1 allele and ALDH2*2 allele carriers have a much higher risk of developing esophageal cancer, especially among alcohol drinkers. PMID:17963305

Yang, Shu-Juan; Wang, Hua-Yu; Li, Xiao-Qing; Du, Hui-Zhang; Zheng, Can-Jie; Chen, Huai-Gong; Mu, Xiao-Yan; Yang, Chun-Xia

2007-01-01

375

Genetic variation in the endothelin system: do polymorphisms affect the therapeutic strategies?  

PubMed

Endothelin-1 (ET-1) exerts multiple biological effects, including vasoconstriction and the stimulation of cell proliferation in tissues both within and outside of the cardiovascular system. ET-1 is synthesized by ET-converting enzymes (ECE), chymases (CMAs), and non-ECE metalloproteases through a process regulated in an autocrine fashion in vascular and nonvascular cells. ET-1 acts through the activation of G(i)protein-coupled receptors. ET(A) receptors mediate vasoconstriction and cell proliferation, whereas ET(B) receptors are important for aldosterone secretion, endothelial cell (EC) migration, the release of nitric oxide (NO) and prostacyclin, the clearance of ET-1, and the inhibition of ECE-1. ET is activated in scleroderma, hypertension, atherosclerosis, restenosis, heart failure, idiopathic cardiomyopathy, and renal failure. Tissue concentrations more reliably reflect the activation of the ET system because of the predominantly abluminal secretion of the peptide. Experimental studies and clinical trials have demonstrated that ET-1 plays a major role in normal cardiovascular homeostasis and in the functional and structural changes observed in arterial and pulmonary hypertension, glomerulosclerosis, atherosclerosis, and heart failure. Accordingly, ET antagonists are promising new agents in the treatment of cardiovascular diseases. Single nucleotide polymorphisms (SNPs) of the genes of preproET-1, ECE-1, CMA, ET(A) and ET(B) receptors have been identified and can be important for their functional regulation. However, for most of them the association with disease conditions and the evidence for a functional role remain controversial. Thus, even though ET antagonists are being used for the treatment of pulmonary hypertension, there is no convincing evidence for a role of SNPs in affecting the therapeutic strategies. PMID:16855133

Rossi, Gian Paolo; Pitter, Gisella

2006-06-01

376

Genetic Association of Objective Sleep Phenotypes with a Functional Polymorphism in the Neuropeptide S Receptor Gene  

PubMed Central

Background The neuropeptide S receptor (NPSR1) and its ligand neuropeptide S (NPS) have received increased attention in the last few years, as both establish a previously unknown system of neuromodulation. Animal research studies have suggested that NPS may be involved in arousal/wakefulness and may also have a crucial role in sleep regulation. The single nucleotide polymorphism (SNP) rs324981 in NPSR1 has begun to shed light on a function of the NPS-system in human sleep regulation. Due to an amino acid exchange, the T-allele leads to an increased sensitivity of the NPSR1. In the only genome-wide association study to date on circadian sleep parameters in humans, an association was found between rs324981 and regular bedtime. However, the sleep parameters in this study were only measured by self-rating. Therefore, our study aimed to replicate these findings using an objective measure of sleep. Methods The study included n?=?393 white subjects (6279 years) who participated in an actigraphic assessment for determining sleep duration, rest duration, sleep onset, rest onset and sleep onset latency. Genotyping of the SNP rs324981 was performed using the TaqMan OpenArray System. Results The genotype at rs324981 was not significantly associated with rest onset (bedtime) or sleep onset (p?=?.146 and p?=?.199, respectively). However, the SNP showed a significant effect on sleep- and rest duration (p?=?.007 and p?=?.003, respectively). Subjects that were homozygous for the minor T-allele had a significantly decreased sleep- and rest duration compared to A-allele carriers. Conclusion The results of this study indicate that the sleep pattern in humans is influenced by the NPS-system. However, the previously reported association between bedtime and rs324981 could not be confirmed. The current finding of decreased sleep duration in T/T allele carriers is in accordance with studies in rodents reporting similar results after NPS application. PMID:24896296

Spada, Janek; Sander, Christian; Burkhardt, Ralph; Hantzsch, Madlen; Mergl, Roland; Scholz, Markus; Hegerl, Ulrich; Hensch, Tilman

2014-01-01

377

Interactions between adiposity and genetic polymorphisms on the risk of psoriasis  

PubMed Central

Background Adiposity is a known risk factor for psoriasis. Genome-wide association studies have identified a number of genes associated with risk of psoriasis while the evidence on gene-environment interactions in psoriasis is very sparse. Objective To investigate the effect modification by obesity measures on the association between SNPs from published GWAS and risk of psoriasis. Methods Our psoriasis GWAS dataset comprised 9,194 participants, including 337 individuals with psoriasis and 8,857 controls from six GWAS, nested within the Nurses Health Study (NHS), NHS II, and Health Professionals Follow-up Study. Clinician-diagnosed psoriasis was ascertained with high validity. For stratified analyses, BMI was dichotomized at 25, and waist circumference was dichotomized at 30 (women) and 36 inches (men), while WHR was dichotomized at 0.8 (women) and 1.0 (men). Results 41 out of 44 previously GWAS reported SNPS were included in our GWAS datasets. After excluding those with high linkage disequilibrium, 33 remained in the analysis. There were significant interactions between BMI and two SNPs in the IL12B (rs3212227) and IL23R genes (rs7530511). Further analysis of these two SNPs indicated interactions between rs3212227 and waist circumference or WHR (Pint<0.05), but not for rs7530511. These observations were confirmed among participants without type 2 diabetes or coronary heart disease. The interactions remained after simultaneously adjusting for BMI as a continuous variable. In addition, we did not observe significant main effect for rs7530511. Conclusions The association between a polymorphism in IL12B and psoriasis risk may be modified by measures of overall and central adiposity. PMID:22897389

Li, W-Q.; Han, J-L.; Zhang, M-F.; Qureshi, A.A.

2014-01-01

378

The Cayapa Indians of Ecuador: a population study of seven protein genetic polymorphisms.  

PubMed

The Cayapa Indians are a population of 3600 individuals living in Ecuador, along the Cayapas River and its tributaries. They are thought to have migrated from the Andes, north of Quito, and settled in the Cayapas area five centuries ago as a consequence of Inca expansion and of the Spanish conquest. In order to study the genetic structure of the Cayapa and their relationships with other native American peoples, and to enquire on the possibility of admixture from nearby Black communities, we have investigated a sample of 139 individuals for seven plasma genetic markers (F13A, F13B, ORM1, AHSG, C6, C7 and APOC2) by isoelectric focusing and immunoblotting. The following gene frequencies have been found: F13A*1 = 0.824, F13A*2 = 0.176; F13B*1 = 0.126, F13B*3 = 0.874; ORM1*1 = 0.554, ORM1*2 = 0.446; AHSG*1 = 0.275, AHSG*2 = 0.725; C6*A = 0.131, C6*B = 0.814, C6*A21 = 0.055; C7*1 = 1.000; APOC2*1 = 1.000. The findings confirm, whenever the comparison was possible, quite a good resemblance of the Cayapa with other Native American populations. PMID:8147578

Scacchi, R; Corbo, R M; Rickards, O; De Stefano, G F

1994-01-01

379

Genetic Polymorphisms of 17 Y-chromosomal Short Tandem Repeat Loci in Atayal Population of Taiwan  

PubMed Central

Aim To define the Y-chromosomal genetic structure in a sample of Atayal men from Taiwan. Methods Buccal swab samples were collected from 170 unrelated healthy male volunteers from Taiwanese aboriginal Atayal population. Genomic DNA was extracted and 17 Y chromosome-specific short tandem repeat loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438, and DYS448) were analyzed using the AmpFlSTR Yfiler Polymerase Chain Reaction Amplification Kit. Results A total of 99 different haplotypes were identified, 69 (69.7%) of which were unique. Total haplotype diversity was 0.9887. The most common haplotype was shared by 9 individuals in the study sample. Gene diversities ranged from 0.0574 for DYS438 to 0.6749 for DYS456. Conclusion Our results will help provide the molecular genetic evidence for human settlement of the Pacific. PMID:19480026

Wu, Fang-Chin; Ho, Chin-Wen; Pu, Chang-En; Hu, Kuang-Yu; Liu, David Hwang

2009-01-01

380

A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids.  

PubMed

A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.. PMID:21931529

Boto, Luis; Cunha, Carina; Doadrio, Ignacio

2011-07-01

381

A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids  

PubMed Central

A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.. PMID:21931529

Boto, Luis; Cunha, Carina; Doadrio, Ignacio

2011-01-01

382

Monitoring of the genetic structure of natural populations: change of the effective population size and inversion polymorphism in Drosophila subobscura.  

PubMed

We analyzed changes in the genetic structure and effective population size of two ecologically distinct populations of Drosophila subobscura over several years. Population sizes of D. subobscura in beech and oak wood habitats for a period of 6 years were estimated by the capture-mark-release-recapture method. Inversion polymorphism parameters were also assessed in the same populations for a period of 3 years. Significant differences in the numbers of individuals were observed between sexes. This affected the effective population sizes between particular years. The ratio of the effective size over the cenzus dropped significantly in beech wood in 2 years. Although overall heterozygosity remained unchanged during the years in both habitats, frequencies of gene arrangements on five chromosomes show variability. After the bottleneck, some complex chromosomal arrangements appeared for the first time in both populations. Standard gene arrangements of chromosome A increased in frequency over the years in each habitat, while the complex arrangements remain rather stable and specific for each population. The results obtained indicate that the population structure may significantly change if the effective size of D. subobscura population is reduced, which is mostly related to microclimatic changes in habitats. Based on the results to date, monitoring of microevolutionary changes by using D. subobscura and its relatives seems a promising way to study the effects of global climate changes. PMID:17668277

Stamenkovic-Radak, Marina; Rasic, Gordana; Savic, Tatjana; Kalajdzic, Predrag; Kurbalija, Zorana; Kenig, Bojan; Andjelkovic, Marko

2008-05-01

383

Comprehensive genetic analysis of cytarabine sensitivity in a cell-based model identifies polymorphisms associated with outcome in AML patients  

PubMed Central

A whole-genome approach was used to investigate the genetic determinants of cytarabine-induced cytotoxicity. We performed a meta-analysis of genome-wide association studies involving 523 lymphoblastoid cell lines (LCLs) from individuals of European, African, Asian, and African American ancestry. Several of the highest-ranked single-nucleotide polymorphisms (SNPs) were within the mutated in colorectal cancers (MCC) gene. MCC expression was induced by cytarabine treatment from 1.7- to 26.6-fold in LCLs. A total of 33 SNPs ranked at the top of the meta-analysis (P < 10?5) were successfully tested in a clinical trial of patients randomized to receive low-dose or high-dose cytarabine plus daunorubicin and etoposide; of these, 18 showed association (P < .05) with either cytarabine 50% inhibitory concentration in leukemia cells or clinical response parameters (minimal residual disease, overall survival (OS), and treatment-related mortality). This count (n = 18) was significantly greater than expected by chance (P = .016). For rs1203633, LCLs with AA genotype were more sensitive to cytarabine-induced cytotoxicity (P = 1.31 10?6) and AA (vs GA or GG) genotype was associated with poorer OS (P = .015), likely as a result of greater treatment-related mortality (P = .0037) in patients with acute myeloid leukemia (AML). This multicenter AML02 study trial was registered at www.clinicaltrials.gov as #NCT00136084. PMID:23538338

Gamazon, Eric R.; Lamba, Jatinder K.; Pounds, Stanley; Stark, Amy L.; Wheeler, Heather E.; Cao, Xueyuan; Im, Hae K.; Mitra, Amit K.; Rubnitz, Jeffrey E.; Ribeiro, Raul C.; Raimondi, Susana; Campana, Dario; Crews, Kristine R.; Wong, Shan S.; Welsh, Marleen; Hulur, Imge; Gorsic, Lidija; Hartford, Christine M.; Zhang, Wei; Cox, Nancy J.; Dolan, M. Eileen

2013-01-01

384

Genetic polymorphisms of 15 STR loci within Turkish student population living in Sarajevo, Bosnia and Herzegovina.  

PubMed

Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were calculated from the referent sample of 100 unrelated individuals of both sexes from Turkish student population living in Sarajevo, Bosnia and Herzegovina. Buccal swab, as a source of DNA, was collected from the volunteers from whom the informed consent form was obtained. DNA extraction was performed using QIAamp DNA Micro kit by Qiagen. DNA template ranging from 0.5 to 2 ng was used to amplify 15 STR loci by PCR multiplex amplification which was performed by using the PowerPlex 16 kit (Promega Corp., Madison, WI, USA) according to the manufacturer's protocol. The amplifications were carried out in a PE Gene Amp PCR System thermal cycler (Applied Biosystems) and capillary electrophoresis was carried out in an ABI PRISM 310 Genetic Analyzer (Applied Biosystems) in accordance with the manufacturer's recommendations. The frequency of each locus was calculated from the numbers of each observed genotype. Deviation from Hardy-Weinberg equilibrium and observed heterozygosity were calculated. Data were analyzed by using Microsoft Excel workbook template--Powerstats V12 and the power of discrimination (PD), power of exclusion (PE), as well as other population genetic indices for the 15 STR loci were calculated. Obtained results contribute to existing Turkish DNA database, as well as insight of differences and similarities in comparison to population of Bosnia and Herzegovina. In addition, 13 autosomal STR loci frequencies (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSFIPO, Penta D, VWA, D8S1 179, TPOX, and FGA) were studied in 15 different worldwide populations (Turkish, Bosnian, Croatian, Serbian, Montenegrin, Macedonian, Albanian, Kosovan, Greek, Russian, Japanese, Korean, Lithuanian, Iraqi, Belarusian). For the proof of corresponding data, two different Turkish population STR data obtained from previously published articles were compared with our data and this showed that our data correspond to these 2 previously published data. Further, STR allele frequency data for 13 loci for each population were obtained from previous scientific articles and the allele frequencies and genetic diversity among the 15 sample populations were compared. In addition, even though the populations are from different nationalities, the STR data are similar among the geographically close populations. The phylogenetic tree established among worldwide populations and genetic distance values show a great affinity among the 15populations. Our data is useful for anthropological and further comparative genetic</