Background: Diabetic nephropathy (DN) is a disorder affecting glomerular function that, histologically, is due to the presence of glomerulosclerosis accompanied with endothelial dysfunction of the ...afferent and efferent renal arterioles. Insulin resistance in diabetic patients is known to be one of the causes of endothelial dysfunction because it increases oxidative stress, and one of the main genes regulating the production pathways of reactive oxygen species is p66Shc. The aim of this study was to evaluate the p66Shc gene expression as a precocious biomarker of renal dysfunction in diabetic patients, using liquids samples of urine sediment and peripheral blood.
Methods: 29 diabetic patients and 37 healthy donors were recruited from the Centro Universitário FMABC outpatient clinic. The RT-gPCR technique was applied to evaluate p66Shc gene expression in urine and peripheral blood samples from diabetic patients, which were compared with healthy donors.
Results: There was no significant expression of p66Shc gene in samples from diabetic patients compared with healthy donors. However, p66Shc expression in the blood samples of diabetics (0.02417±0.078652-ΔCT, n=29) was 3.6 times higher than in healthy participants (0.00689±0.01758, n=37) while in the urine samples, it was 1.48 times higher in diabetics group (0.02761±0.05412-ΔCT) than in CTL group (0.0186±0.02199).
Conclusion: There was no significant p66Shc gene expression in peripheral blood and urine samples of diabetic patients without kidney injury compared with healthy donors, although there is a tendency for this gene to participate in the oxidative imbalance present in diabetes.
Extension of the IsaViz software for the representation of metabolic and regulatory networks Veiga, Diogo Fernando(Departamento de Engenharia Química e Engenharia de Alimentos Grupo de Engenharia Genômica ,Universidade Federal de Santa Catarina Departamento de Informática e Estatística); Cecconello, Pedro de Stege(Universidade Federal de Santa Catarina Departamento de Informática e Estatística); Lucca, José Eduardo de(Universidade Federal de Santa Catarina Departamento de Informática e Estatística) ...
Brazilian archives of biology and technology,
06/2005, Letnik:
48, Številka:
spe
Journal Article
Recenzirano
Odprti dostop
In this work we developed an extension of IsaViz software, a RDF (Resource Description Framework) authoring tool, designed to be a graphical environment to build models of metabolic and regulatory ...networks. This environment, called Metabolic IsaViz, was linked to a genomic library of types and was modeled on the basis of ontologies. Biochemical pathways included data at sequence level (e.g., the amino acid sequence of enzymes), besides kinetic and thermodynamic parameters for the reactions. Models created with Metabolic IsaViz could be exported to pathways simulators through SBML (Systems Biology Markup Language), which allowed to analyze the pathway dynamics of target chemicals.
A determinação de vias metabólicas e regulatórias de microrganismos é essencial para estudos pós-sequenciamento de DNA, com aplicações diretas em várias áreas da biotecnologia, em especial em engenharia metabólica. Neste trabalho desenvolvemos uma extensão do software IsaViz, editor de grafos RDF (Resource Description Framework), com a finalidade de criar um ambiente gráfico para a construção de modelos de vias metabólicas e regulatórias. Este ambiente, o Metabolic IsaViz, foi integrado a uma biblioteca de tipos genômicos, modelada com base em ontologias, sendo que as vias bioquímicas podem incluir dados ao nível de seqüência (como a seqüência de aminoácidos das enzimas), além de parâmetros cinéticos e termodinâmicos. Os modelos criados com o Metabolic IsaViz podem ser exportados para simuladores de vias metabólicas através da linguagem SBML (Systems Biology Markup Language) para análise da formação de metabólitos de interesse.
Gene regulatory networks, or simply gene networks (GNs), have shown to be a promising approach that the bioinformatics community has been developing for studying regulatory mechanisms in biological ...systems. GNs are built from the genome-wide high-throughput gene expression data that are often available from DNA microarray experiments. Conceptually, GNs are (un)directed graphs, where the nodes correspond to the genes and a link between a pair of genes denotes a regulatory interaction that occurs at transcriptional level. In the present study, we had two objectives: 1) to develop a framework for GN reconstruction based on a Bayesian network model that captures direct interactions between genes through nonparametric regression with B-splines, and 2) to demonstrate the potential of GNs in the analysis of expression data of a real biological system, the yeast pheromone response pathway. Our framework also included a number of search schemes to learn the network. We present an intuitive notion of GN theory as well as the detailed mathematical foundations of the model. A comprehensive analysis of the consistency of the model when tested with biological data was done through the analysis of the GNs inferred for the yeast pheromone pathway. Our results agree fairly well with what was expected based on the literature, and we developed some hypotheses about this system. Using this analysis, we intended to provide a guide on how GNs can be effectively used to study transcriptional regulation. We also discussed the limitations of GNs and the future direction of network analysis for genomic data. The software is available upon request.
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