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Genotypic Distribution (genotypic + distribution)
Selected AbstractsAssociation between neuropeptide Y gene and its receptor Y1 gene and methamphetamine dependencePSYCHIATRY AND CLINICAL NEUROSCIENCES, Issue 3 2009Yuko Okahisa md Aims:, Neuropeptide Y (NPY) is a 36-amino acid peptide that is widely distributed in the brain, adrenal medulla, and sympathetic nervous system. Several lines of evidence suggest a possible involvement of the NPY system in the physiological effects of several classes of abused substances including alcohol, phencyclidine, cocaine, and marijuana and in endogenous psychosis. Accordingly, it was hypothesized that the NPY system may also be involved in methamphetamine dependence or psychosis. Methods:, The single nucleotide polymorphisms rs16147 of the NPY gene (,485C>T) and rs7687423 of the NPY receptor Y1 (NPY1R) gene were analyzed in 222 patients with methamphetamine dependence and psychosis and 288 age- and gender-matched controls. Results:, Genotypic distribution of the NPY1R gene showed a significant association with methamphetamine dependence and psychosis (P = 0.04), whereas the NPY gene had no significant association with them. Conclusion:, It is possible that genetic variants of the NPY1R gene affect the NPY-NPY receptor type Y1 signaling system in the brain, which may result in susceptibility to methamphetamine dependence or the development of methamphetamine psychosis, but the present findings need to be confirmed on replication. [source] Isolation and characterization of five dinucleotide microsatellite loci in the sandbar shark, Carcharhinus plumbeusMOLECULAR ECOLOGY RESOURCES, Issue 2 2006D. S. PORTNOY Abstract Five dinucleotide markers were isolated and optimized from a microsatellite-enriched genomic library obtained from the sandbar shark, Carcharhinus plumbeus. Genotypic distributions of all markers were found to be in conformance with the expectations of Hardy,Weinberg equilibrium with four to 39 alleles present per locus. We amplified these loci in two female sharks and their litters. A maternal allele was recovered at each locus in all progeny indicating reliable amplification. More than two paternal alleles were recovered across both litters indicating genetic polyandry. Additionally, these markers were amplified across 10 carcharhiniform species to examine their utility in other studies. [source] Intimately linked or hardly speaking?MOLECULAR ECOLOGY, Issue 3 2001The relationship between genotype, environmental gradients in a Louisiana Iris hybrid population Abstract Several models of hybrid zone evolution predict the same spatial patterns of genotypic distribution whether or not structuring is due to environment-dependent or -independent selection. In this study, we tested for evidence of environment-dependent selection in an Iris fulva×Iris brevicaulis hybrid population by examining the distribution of genotypes in relation to environmental gradients. We selected 201 Louisiana Iris plants from within a known hybrid population (80 m × 80 m) and placed them in four different genotypic classes (I. fulva, I. fulva -like hybrid, I. brevicaulis -like hybrid and I. brevicaulis) based on seven species-specific random amplified polymorphic DNA (RAPD) markers and two chloroplast DNA haplotypes. Environmental variables were then measured. These variables included percentage cover by tree canopy, elevation from the high water mark, soil pH and percentage soil organic matter. Each variable was sampled for all 201 plants. Canonical discriminant analysis (CDA) was used to infer the environmental factors most strongly associated with the different genotypic groups. Slight differences in elevation (,0.5 m to +0.4 m) were important for distinguishing habitat distributions described by CDA, even though there were no statistical differences between mean elevations alone. I. brevicaulis occurred in a broad range of habitats, while I. fulva had a narrower distribution. Of all the possible combinations, I. fulva -like hybrids and I. brevicaulis -like hybrids occurred in the most distinct habitat types relative to one another. Each hybrid class was not significantly different from its closest parent with regard to habitat occupied, but was statistically unique from its more distant parental species. Within the hybrid genotypes, most, but not all, RAPD loci were individually correlated with environmental variables. This study suggests that, at a very fine spatial scale, environment-dependent selection contributed to the genetic structuring of this hybrid zone. [source] Evidence for predominant clones in a cyclically parthenogenetic organism provided by combined demographic and genetic analysesMOLECULAR ECOLOGY, Issue 12 2000L. Haack Abstract Aphids are particularly interesting models in the study of genetic and demographic components of plant adaptation because of their breeding system which combines parthenogenesis and sexual reproduction (i.e. cyclical parthenogenesis), and the frequent emergence of host-adapted races reported in this group. In this paper, patterns of host adaptation were assessed on local populations of the aphid Sitobion avenae by following their demographic and genetic structure in a maize field for two consecutive years. The existence of putative generalist (polyphagous) or specialized (host-adapted) genotypes was also investigated by comparing the genotypic distribution of this aphid on maize and other cultivated host plants, using five microsatellite loci. Although population dynamics revealed strong variation in aphid abundance during the colonization period on maize, two genotypes identified at seven additional microsatellite loci were predominant and exhibited stable frequencies over cropping season and between years. Based on present and earlier studies, these two prevalent genotypes were shown to survive on different host plants other than maize, to colonize large geographical zones and to persist parthenogenetically for several years. All these data strongly suggest that these two genotypes are asexual generalist clones that could have been favoured by agricultural practices encountered in western Europe. Besides these two clones, a continual replacement of rare genotypes was observed on maize in both years. Hypotheses involving selection via aphid,plant interactions and natural enemies were proposed for explaining the disappearance of these genotypes on maize. [source] Distribution of Porphyromonas gingivalis fimA genotypes in cardiovascular specimens from Japanese patientsMOLECULAR ORAL MICROBIOLOGY, Issue 2 2008K. Nakano Introduction:,Porphyromonas gingivalis, a major periodontal pathogen, is gaining increasing attention for its possible association with cardiovascular diseases. Its fimbriae are classified into six genotypes (types I,V and Ib) based on the diversity of the fimA genes encoding the fimbrial subunits. In this study, fimA genotypic distribution was analyzed in P. gingivalis -infected cardiovascular specimens. Methods:, A total of 112 heart valves and 80 atheromatous plaque specimens were collected from patients undergoing cardiovascular surgery, as well as 56 dental plaque specimens. Bacterial DNA was extracted from each, and polymerase chain reaction analysis was carried out with a P. gingivalis -specific set of primers. P. gingivalis- positive specimens were further analyzed to discriminate the fimA genotype using polymerase chain reaction with fimA type-specific primer sets. Results:,P. gingivalis was detected in 10.4% of the cardiovascular specimens and 50.0% of the dental plaque samples. In the latter, type II was most frequently detected (35.7%), followed by types I (28.6%) and IV (21.4%), while types IV and II were detected with considerable frequencies of 45.0% and 30.0%, respectively, in the cardiovascular specimens. In contrast, the occurrence of type I was limited (5.0%) in the cardiovascular specimens. Conclusion:, These results suggest that specific fimA genotypic clones, which are reportedly associated with periodontitis, are also frequently harbored in cardiovascular specimens, indicating the possible involvement of type II and IV clones in the initiation and progression of cardiovascular diseases. [source] Relationship between SP1 polymorphism and osteoporosis in ,-thalassemia major patientsPEDIATRICS INTERNATIONAL, Issue 4 2008Ozlem Guzeloglu-Kayisli Abstract Background: ,-Thalassemia is an autosomal recessive disease characterized by defective ,-globin chain production. Osteoporosis is an important cause of morbidity in patients with ,-thalassemia major. The pathogenesis of reduced bone mineral density (BMD) is multifactorial. A range of genetics factors have been implicated in other populations of patients with osteoporosis. Polymorphism at the Sp1 binding site of the collagen type I A1 (COLIA1) gene is thought to be an important factor in the development of osteoporosis. Methods: Alleles S and s, detected by presence of a G or T nucleotide, respectively in a regulatory site of the COLIA1 gene were investigated in 37 ,-thalassemia major patients with osteoporosis and 92 controls without osteoporosis or osteopenia using polymerase chain reaction,restriction fragment length polymorphism. Results: Fifteen and nine ,-thalassemia major patients displayed SS and Ss genotypes, respectively, whereas 13 were found to have an ss genotype. The mean BMD of the ,-thalassemia major patients with ss genotype was similar to those with the Ss and SS genotypes. In the control group, 77 and 15 subjects had SS and Ss genotypes, respectively, with no ss genotype. Allelic and genotypic distribution in patients were significantly different from controls. Conclusion: Determining base substitutions at the Sp1 binding site on the COLIA1 gene in early years may be important in preventing osteoporosis in children with ,-thalassemia major. [source] Association study of 5,-UTR polymorphisms of the human dopamine transporter gene with manic depressionBIPOLAR DISORDERS, Issue 5p1 2006Gerald Stöber Objectives:, To determine the degree of association of five single nucleotide polymorphisms at the 5,-untranslated region (5,-UTR) of the human dopamine transporter gene (hSLC6A3; hDAT1) in bipolar affective disorder. Methods:, In a case,control design study, the polymorphisms were genotyped for allelic and genotypic distribution between 105 index cases (50 males) with bipolar affective disorder according to DSM IV and 199 unaffected control subjects (120 males). Results:, At the 5,-UTR locus of hSLC6A3, no significant allelic or genotypic differences were observed between index cases and controls. However, distinct 5-locus genotypes accumulated in subjects with bipolar affective disorder compared to control subjects (p = 0.029, odds ratio 1.84, 95% confidence interval 1.12,3.02). Conclusions:, In conclusion, our data do not provide evidence for a major role of the 5,-UTR of the dopamine transporter gene in bipolar affective disorder. A minor contribution of distinct genotypes may be possible and warrants replication in extended samples. [source] Association of vitamin-D receptor (Fok-I) gene polymorphism with bladder cancer in an Indian populationBJU INTERNATIONAL, Issue 4 2007Rama D. Mittal OBJECTIVE To explore the association of vitamin-D receptor (VDR) genotypes and haplotypes (variants at the Fok-I, and Taq-I sites) with the risk of bladder cancer, as vitamin D is antiproliferative and reported to induce apoptosis in human bladder tumour cells in vitro. PATIENTS, SUBJECTS AND METHODS A case-control study using polymerase chain reaction-restriction fragment length polymorphism was conducted in 130 patients with bladder cancer and 346 normal healthy individuals in a north Indian population. Patients were also categorized according to grade and stage of tumour. RESULTS There was a significant difference in genotype and allelic distribution of VDR (Fok-I) polymorphism in the patients (P = 0.033 and = 0.017, respectively). The FF genotype was associated with twice the risk for bladder cancer (odds ratio 2.042, 95% confidence interval, CI, 0.803,5.193). There was no significant difference in genotypic distribution or allelic frequencies of the VDR (Taq-I) polymorphism (P = 0.477 and 0.230) when compared with the controls. The stage and grade of the bladder tumours had no association with VDR (Fok-I and Taq-I) genotypes. There was a significant difference in the frequency distribution of the haplotypes FT and fT (P < 0.001); these haplotypes had a protective effect in the control group (odds ratio 0.167, 95% CI 0.096,0.291, and 0.079, 0.038,0.164). CONCLUSION These data suggest that VDR (Fok-I) polymorphism is associated with the risk of bladder cancer. Further, the results for the haplotype FT and fT indicate that patients with this haplotype have a lower risk of developing bladder cancer than those with other haplotypes. [source] Molecular analysis of HumDN1 VNTR polymorphism of the human deoxyribonuclease I in systemic lupus erythematosusINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2010Suad AlFadhli Summary Deoxyribonuclease I (DNASE1) may be responsible for the removal of DNA from nuclear antigens at sites of high cell turnover, thus preventing the onset of systemic lupus erythematosus (SLE). The purpose of this study was to screen DNASE1 gene for mutations that may have an effect on susceptibility to develop SLE. DNA was extracted from 76 Kuwaiti SLE patients and 92 race-matched controls. PCR-direct sequencing was used to screen DNASE1 promoter, coding sequence and exon,intron boundaries for mutation. Association of genomic variations was assessed using a Chi-square test. Molecular analysis of the DNASE1 gene did not reveal any mutation. However, a 56-bp repeat was detected in intron4 which was previously reported and named HumDN1. The allelic and genotypic distributions of the HumDN1 VNTR were compared between SLE patients and healthy subjects. Alleles were denoted as 2, 3, 4, 5 and 6 corresponding to the number of repeats of the 56 bp unit. Alleles 4, 5, and 6 showed significant association with SLE. Allele 5 showed the highest association [,2 = 32.57; P , 0.001; OR = 4.16; 95% CI: (2.55,6.79)]. Association of allele 5 was also found at the genotypic level, where genotype 5/5 is more prevalent in SLE subjects as compared with controls (17% versus 9%). We report a significant association of HumDN1 VNTR polymorphism in DNASE1 gene with SLE. Further functional assays needed to assess the effect of this VNTR on DNASE1 activity and its association with SLE. [source] Correlation of polymorphism of MTHFRs and RFC-1 genes with neural tube defects in ChinaBIRTH DEFECTS RESEARCH, Issue 1 2008Yali Shang Abstract BACKGROUND: Maternal periconceptional supplementation of folate reduces the incidence of neonatal Neural Tube Defects, indicating that changes in folate metabolism play a role in formation of NTDs. The mutations on two genes involved in folate metabolism, the C677 of the MTHFR gene and the RFC-1(A80G) gene are potential risk factors of NTDs. METHODS: In this study, we analyzed the genotypic distributions and allele frequencies of MTHFR C677T and RFC-1 A80G polymorphisms in DNA samples from mothers with at least one previous child with NTDs (the NTD group) and controls. RESULTS: Our results indicated that there was a significant difference in the genotype and allele frequencies of RFC-1 80A,G between the NTD group and controls (p = .008 and p = .017, respectively). There was, however, no significant difference in the genotype and allele frequencies of the MTHFR 677C,T polymorphism between the NTD group and controls. The NTD group was further separated into the upper and lower types by location of abnormalities. The frequency of RFC-1 80A/G and 80G/G was significantly higher in the upper group than the control (p = .009 and p = .005, respectively). The frequency of G-alleles was also significantly higher in the upper group than the control (OR 2.42; p = .006; 95% CI: 1.28,4.58). For the MTHFR C677 gene, the frequency of T-alleles was significantly lower in the lower defect type than the control group (OR 0.32; p = .027; 95% CI: 0.11,0.9). CONCLUSIONS: These results suggest that in the Shanxi population RFC-1 polymorphisms may play a role in NTD risk, whereas the impact of MTHFR C677T polymorphisms requires further clarification. Birth Defects Research (Part A) 2008. © 2007 Wiley-Liss, Inc. [source] | |||||||||||||