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Genotypic Level (genotypic + level)
Selected AbstractsEVIDENCE FOR NEGATIVE FREQUENCY-DEPENDENT SELECTION DURING EXPERIMENTAL COEVOLUTION OF A FRESHWATER SNAIL AND A STERILIZING TREMATODEEVOLUTION, Issue 9 2009Britt Koskella Host,parasite coevolution is often suggested as a mechanism for maintaining genetic diversity, but finding direct evidence has proven difficult. In the present study, we examine the process of coevolution using a freshwater New Zealand snail (Potamopyrgus antipodarum) and its common parasite (the sterilizing trematode, Microphallus sp.) Specifically, we test for changes in genotypic composition of clonal host populations in experimental populations evolving either with or without parasites for six generations. As predicted under the Red Queen model of coevolution, the initially most common host genotype decreased in frequency in the presence, but not the absence, of parasitism. Furthermore, the initially most common host genotype became more susceptible to infection by the coevolving parasite populations over the course of the experiment. These results are consistent with parasite-meditated selection leading to a rare advantage, and they indicate rapid coevolution at the genotypic level between a host and its parasite. [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] EMK: A Novel Program for Family-Based Allelic and Genotypic Association Tests on Quantitative TraitsANNALS OF HUMAN GENETICS, Issue 3 2008Y. W. Li Summary The QTDT program is a widely-used program for analyzing quantitative trait data, but the methods mainly test allelic association. Since the genotype of a marker is a direct observation for an individual, it is of interest to assess association at the genotypic level. In this study, we extended the allele-based association method developed by Monks and Kaplan (MK method) to genotype-based association tests for quantitative traits. We implemented a novel extended MK (EMK) program that can perform both allele- and genotype- based association tests in any pedigree structure. To evaluate the performance of EMK, we utilized simulated pedigree data and real data from our previous report of GSTO1 and GSTO2 genes in Alzheimer disease (AD). Both allele- and genotype-based EMK methods (allele-EMK and geno-EMK) showed correct type I error for various pedigree structures and admixture populations. The geno-EMK method showed comparable power to the allele-EMK test. By treating age-at-onset (AAO) as a quantitative trait, the EMK program was able to detect significant associations for rs4925 in GSTO1 (P= 0.006 for allele-EMK and P= 0.009 for geno-EMK), and rs2297235 in GSTO2 (P= 0.005 for allele-EMK and P= 0.009 for geno-EMK), which are consistent with our previous findings. [source] A Functional Polymorphism in the Promoter Region of the Tryptophan Hydroxylase Gene Is Associated With Alcohol Dependence in One Aboriginal Group in TaiwanALCOHOLISM, Issue 1 2005H Sunny Sun Background: Polymorphisms within intron 7 of the tryptophan hydroxylase (TPH1) gene were found to be associated with alcohol dependence in different ethnic groups, including the aboriginal Bunun group in Taiwan. This study aimed to identify genetic variants at the TPH1 locus and to examine their associations with alcoholism. We hypothesized that the polymorphism of TPH1 gene is functional and influences the human circadian rhythm to contribute to the pathophysiology of alcohol dependence. Methods: DNA from the Taiwanese Han and Bunun was subjected to sequence for screening genetic variation in the coding and promoter regions of the TPH1 locus. Polymorphisms among individuals with alcohol dependence and control subjects in two ethnic groups in Taiwan were investigated. Results: Three variants in the TPH1 promoter region were identified, and the markers are in complete linkage disequilibrium in both populations. Positive associations at both allelic and genotypic levels were obtained between case and control groups in the Bunun. Expression studies demonstrated that the variants indeed affected reporter gene activity in human choriocarcinoma and colon adenocarcinoma cell lines. Conclusions: Polymorphisms in the promoter region may influence the function of the TPH1 gene and further influence the proclivity of alcohol dependence in one ethnic group in Taiwan. The associations between TPH1 genotypes and alcoholism may deserve further investigation. [source] | |||||||||||||