p22phox C242T SNP inhibits inflammatory oxidative damage to endothelial cells and vessels

Background— T NADPH oxidase, by generating reactive oxygen species, is involved in the pathophysiology of many cardiovascular diseases and represents a therapeutic target for the development of novel drugs. A single-nucleotide polymorphism (SNP) C242T of the p22phox subunit of NADPH oxidase has been reported to be negatively associated with coronary heart disease (CHD) and may predict disease prevalence. However, the underlying mechanisms remain unknown. Methods and Results— Using computer molecular modelling we discovered that C242T SNP causes significant structural changes in the extracellular loop of p22phox and reduces its interaction stability with Nox2 subunit. Gene transfection of human pulmonary microvascular endothelial cells showed that C242T p22phox reduced significantly Nox2 expression but had no significant effect on basal endothelial O2.- production or the expression of Nox1 and Nox4. When cells were stimulated with TNFα (or high glucose), C242T p22phox inhibited significantly TNFα-induced Nox2 maturation, O2.- production, MAPK and NFκB activation and inflammation (all p<0.05). These C242T effects were further confirmed using p22phox shRNA engineered HeLa cells and Nox2-/- coronary microvascular endothelial cells. Clinical significance was investigated using saphenous vein segments from non CHD subjects after phlebectomies. TT (C242T) allele was common (prevalence of ~22%) and compared to CC, veins bearing TT allele had significantly lower levels of Nox2 expression and O2.- generation in response to high glucose challenge. Conclusions— C242T SNP causes p22phox structural changes that inhibit endothelial Nox2 activation and oxidative response to TNFα or high glucose stimulation. C242T SNP may represent a natural protective mechanism against inflammatory cardiovascular diseases.

Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Association of CSSM066 and ILSTS011 microsatellite markers and thyroglobulin gene SNP with backfat in Canchim cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. © 2013 Petersen et al.

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Valor prognóstico do SNP TP53 ARG72PRO na susceptibilidade ao desenvolvimento e na sobrevida de pacientes brasileiros com meduloblastoma

O Meduloblastoma é a neoplasia encefálica mais comum na infância, correspondendo a taxas de 16 a 25% de todos os tumores encefálicos em menores de 19 anos e 30-40% de todos os tumores da fossa posterior. Para investigar o papel do polimorfismo de base única (SNP) TP53 Arg72Pro sobre o risco de desenvolvimento, prognóstico e resposta a terapêutica adjuvante em Meduloblastoma, foi realizado um estudo caso-controle com 122 pacientes e 122 controles saudáveis do Brasil. Em comparação com Arg/Arg, que é o genótipo mais comum na população em estudo, tanto o genótipo Arg/Pro e Pro/Pro não influenciaram o risco de desenvolvimento de Meduloblastoma (OR = 1,36 e P = 0,339 para o genótipo Arg/Pro; OR = 1,50 e P = 0,389 para o genótipo Pro/Pro). Com relação ao prognóstico, a sobrevida livre de doença não foi significativamente diferente entre os genótipos SNP TP53 Arg72Pro (P> 0,05), porém o genótipo menos freqüente, Pro/Pro, foi associado a uma menor sobrevida global dos pacientes com Meduloblastoma (P = 0,021 ). Estes dados sugerem que embora não haja nenhuma associação entre o SNP TP53 Arg72Pro e o risco de desenvolvimento de Meduloblastoma, o genótipo Pro/Pro está associado a uma menor sobrevida global dos pacientes submetidos a terapia adjuvante. No entanto, devido à composição interétnica da população brasileira, futuros estudos envolvendo populações maiores e de outras partes do mundo serão essenciais para uma conclusão definitiva da função do SNP TP53 Arg72Pro.

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Influência do SNP T3801C CYP1A1 sobre os níveis de danos oxidativos no DNA de células da mucosa gástrica de pacientes infectados pelo H. Pylori

Helicobacter pylori (H. pylori) is a common gastric pathogen that has infected more than 50% of the population of the world and it has been associated with chronic gastritis, gastric ulcers, duodenal ulcer, and gastric cancer. Although, almost all infected people develop gastritis, there is a variety of clinical outcomes, and only a minority (<1%) of infected individuals develop gastric cancer. There are evidences which suggest that the chronic inflammatory reaction caused by the bacterial infection may be involved in the production of reactive oxygen species or reactive nitrogen species. It may lead to DNA damage, which together with the cellular response could lead to gene mutations, chromosomal aberrations characterizing genomic instability that may represent the early step in gastric carcinogenesis. The extent and severity of gastric mucosal inflammation, as well as the clinical outcome of the infection, depend on a number of factors, including the host genetic susceptibility such SNP T3801 CYP1A1, immune response, age at which the infection was acquired, environmental factors, especially dietary and bacterial virulence factors. Due to the risk of developing gastric cancer in humans infected by H. pylori, we used the Comet Assay to investigate the influence of the SNP T3801C CYP1A1 on levels of oxidative DNA damage in gastric epithelial cells. The study was conducted with biopsies from the gastric antrum and corpus of 103 H. pylori-infected patients and 24 uninfected control patients. Genotype of SNP T3801C CYP1A1 was determined by PCR-RFLP and DNA damage levels were measured in gastric mucosal cells from antrum and corpus by the Comet assay. Levels of DNA damage in gastric mucosa cells from antrum and corpus of H. pylori-infected patients with mild, moderate, severe gastritis, and gastric cancer were significantly higher compared to uninfected normal mucosa cells. However, levels... (Complete abstract click electronic access below)

Avaliação da autozigosidade em vacas Nelore (Bos indicus) através de genótipos SNP de alta densidade

Pós-graduação em Medicina Veterinária - FCAV