Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology

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

Fungos endofíticos: Uma fonte inexplorada e sustentável de novos e bioativos produtos naturais

Endophytic fungi are a rich source of new and biologically active natural products. They colonize a relatively unexplored ecological habitat and their secondary metabolism is particularly active, presumably due to metabolic interactions with their hosts. In the course of our continuing investigations for new and bioactive compounds from endophytic fungi from brazilian flora Alibertia macrophylla, Caseria sylvestris, Ocotea corymbosa, Cassia spectabilis, Piper aduncum, Cryptocaria mandioccana, Xylopia aromatica and Palicourea marcgravii were investigated. Forty two natural products were isolated and their structures were established on the basis of comprehensive spectral analysis, mainly using 1D and 2D NMR experiments. The compounds were tested in their antifungal, antioxidant, anticholinesterasic and anticancer activities.

Potencial biotecnológico de linhagens mutantes de Bradyrhizobium elkanii caracterizado por PCR quantitativo em tempo real

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Highlights in pathogenic fungal biofilms

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

Determinação de genes mórbidos e drogáveis a partir da construção e análise da rede integrada de interações moleculares entre genes humanos

The discovering process of new morbid genes and new target proteins for drugs have been shown to be very costly and laborious. Having in view cutting costs and speeding up this process, we propose, in this work, a new method to determine the gene druggability score and morbidity score, the probabilities of the protein encoded by the gene have the characteristics that make it a new target for drugs and in case of an alteration in that gene, we observed a phenotype that characterizes a genetic based illness. To determine these characteristics, we built, analyzed and determined the characteristics of the topology of the integrated molecular interactions network among human genes containing physical interactions between proteins, metabolic interactions and interactions of transcriptional regulation, and included other data such as level of gene transcription and cellular localization of the protein encoded by the gene. We tested our model in training sets and achieved results equal or better than the ones achieved by similar methods in the literature. Finally, with the purpose of investigating whether the assigned scores resembles the potential druggabilities and morbities of the previously unclassi ed genes, we looked for evidences in biomedical literature supporting the potential druggability and morbidity status of genes with the 10 highest scores. We found clear evidences for 73% and 90% of potential druggable and morbid genes respectively

Determinação de comunidades em redes biológicas integradas

To understand how biological phenomena emerge, the nonlinear interactions among the components envolved in these and the correspondent connected elements, like genes, proteins, etc., can be represented by a mathematical object called graph or network, where interacting elements are represented by edges connecting pairs of nodes. The analysis of various graph-related properties of biological networks has revealed many clues about biological processes. Among these properties, the community structure, i.e. groups of nodes densely connected among themselves, but sparsely connected to other groups, are important for identifying separable functional modules within biological systems for the comprehension of the high-level organization of the cell. Communities' detection can be performed by many algorithms, but most of them are based on the density of interactions among nodes of the same community. So far, the detection and analysis of network communities in biological networks have only been pursued for networks composed by one type of interaction (e.g. protein-protein interactions or metabolic interactions). Since a real biological network is simultaneously composed by protein-protein, metabolic and transcriptional regulatory interactions, it would be interesting to investigate how communities are organized in this type of network. For this purpose, we detected the communities in an integrated biological network of the Escherichia coli and Saccharomyces cerevisiae by using the Clique Percolation Method and we veri ed, by calculating the frequency of each type of interaction and its related entropy, if components of communities... (Complete abstract click electronic access below)

Dietary restriction and fibre supplementation: Oxidative stress and metabolic shifting for cardiac health

Dietary modification ought to be the first line of strategy in prevention of the development of cardiac disease. The purpose of this study was to investigate whether dietary restriction, dietary-fibre-enriched diet, and their interactions might affect antioxidant capacity and oxidative stress in cardiac tissue. Male Wistar rats (180-200 g; n = 10) were divided into four groups: control ad libitum diet (C), 50% restricted diet (DR), fed with fibre-enriched diet (F), and 50% restricted fibre-enriched diet (DR-F). After 35 days of the treatments, F, DR, and DR-F rats showed low cholesterol, LDL-cholesterol, and triacylglycerol, and high HDL-cholesterol in serum. The DR, DR-F, and F groups had decreased myocardial lipoperoxide and lipid hydroperoxide. The DR-F and F treatments increased superoxide dismutase and glutatione peroxidase (GSH-Px). The DR treatment increased GSH-Px and catalase activities. Dietary fibre beneficial effects were related to metabolic alterations. The F and DR-F groups showed high cardiac glycogen and low lactate dehydrogenase/citrate synthase ratios, indicating diminished anaerobic and elevated aerobic myocardial metabolism in these animals. There was no synergistic effect between dietary restriction and dietary fibre addition, since no differences were observed in markers of oxidative stress in the F and DR-F groups. Dietary fibre supplementation, rather than energy intake and dietary restriction, appears to be the main process retarding oxidative stress in cardiac tissue.

The multifaceted roles of metabolic enzymes in the Paracoccidioides species complex

Paracoccidioides species are dimorphic fungi and are the etiologic agents of paracoccidioidomycosis, which is a serious disease that involves multiple organs. The many tissues colonized by this fungus suggest a variety of surface molecules involved in adhesion. A surprising finding is that most enzymes in the glycolytic pathway, tricarboxylic acid (TCA) cycle and glyoxylate cycle in Paracoccidioides spp. have adhesive properties that aid in interacting with the host extracellular matrix and thus act as 'moonlighting'proteins. Moonlighting proteins have multiple functions, which adds a dimension to cellular complexity and benefit cells in several ways. This phenomenon occurs in both eukaryotes and prokaryotes. For example, moonlighting proteins from the glycolytic pathway or TCA cycle can play a role in bacterial pathogenesis by either acting as proteins secreted in a conventional pathway and/or as cell surface components that facilitate adhesion or adherence. This review outlines the multifunctionality exhibited by many Paracoccidioides spp. enzymes, including aconitase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, isocitratelyase, malatesynthase, triose phosphate isomerase, fumarase, and enolase. We discuss the roles that moonlighting activities play in the virulence characteristics of this fungus and several other human pathogens during their interactions with the host.

Metabolomic evaluation of interactions in rhizosphere between Senna spectabilis and associated microorganisms

Pós-graduação em Química - IQ