High Density Of Polymorphisms Research Articles

DNA Sequence Dimorphisms in Populations of the Clubroot Pathogen Plasmodiophora brassicae.

To develop genetic markers for differentiation between pathotypes of the clubroot pathogen Plasmodiophora brassicae, DNA polymorphisms of 85 P. brassicae genes were investigated by comparing the sequences of these genes from published expressed sequence tag libraries to their sequences in the two released whole genomes. A significant portion of the identified sequence differences across all polymorphic genes are between an isolate from New Zealand and the two whole-genome sequenced isolates. Four genes with a high density of polymorphisms were selected and their partial sequences were amplified by polymerase chain reaction (PCR) from the old pathotypes 2, 3, 5, 6, and 8 (based on the Williams differential set) and the new virulent populations 3-like and 5-like. On the sequences of two of the four genes, the old pathotypes are all identical to the two whole-genome sequenced isolates and all of the new virulent populations are identical to the New Zealand isolate. Based on the dimorphism on the sequence of these two genes, an RNase H-dependent PCR protocol was developed. This protocol was demonstrated to be useful for virulent pathotype identification and may also be used to study the population dynamics of P. brassicae and the in planta interaction of different pathotypes.

Unstructural biology of the Dengue virus proteins.

In this study, we used a wide spectrum of bioinformatics techniques to evaluate the extent of intrinsic disorder in the complete proteomes of genotypes of four human dengue virus (DENV), to analyze the peculiarities of disorder distribution within individual DENV proteins, and to establish potential roles for the structural disorder with respect to their functions. We show that several proteins (ER, E, 1, 2A and 4A) are predicted to be mostly ordered, whereas four proteins (C, 2k, NS3 and NS5) are expected to have high disorder levels. The profiles of disorder propensities are similar across the four genotypes, except for the NS5 protein. Cleavage sites are depleted in polymorphic sites, and have a high propensity for disorder, especially relative to neighboring residues. Disordered regions are highly polymorphic in type 1 DENV but have a relatively low number of polymorphic sites in the type 4 virus. There is a high density of polymorphisms in proteins 2A and 4A, which are depleted in disorder. Thus, a high density of polymorphism is not unique to disordered regions. Analysis of disorder/function association showed that the predominant function of the disordered regions in the DENV proteins is protein-protein interaction and binding of nucleic acids, metals and other small molecules. These regions are also associated with phosphorylation, which may regulate their function.

No role for estrogen receptor 1 gene intron 1 Pvu II and exon 4 C325G polymorphisms in migraine susceptibility

BackgroundWe have previously reported an association between the estrogen receptor 1 (ESR1) gene exon 8 G594A polymorphism and migraine susceptibility in two independent Australian cohorts. In this paper we report results of analysis of two further single nucleotide polymorphisms (SNPs) in the ESR1 gene in the same study group, the T/C Pvu II SNP in intron 1 and the C325G SNP in exon 4, as well as results of linkage disequilibrium (LD) analysis on these markers.MethodsWe investigated these variants by case-control association analysis in a cohort of 240 migraineurs and 240 matched controls. The SNPs were genotyped using specific restriction enzyme assays. Results were analysed using contingency table methods incorporating the chi-squared statistic. LD results are presented as D' statistics with associated P values.ResultsWe found no evidence for association of the Pvu II T/C polymorphism and the C325G polymorphism and migraine susceptibility and no evidence for LD between these two SNPs and the previously implicated exon 8 G594A marker.ConclusionWe have found no role for the polymorphisms in intron 1 and exon 4 with migraine susceptibility. To further investigate our previously implicated exon 8 marker, we suggest the need for studies with a high density of polymorphisms be undertaken, with particular focus on markers in LD with the exon 8 marker.