miRNApath: A database of miRNAs, target genes and metabolic pathways

MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression and hence play important roles in metabolic pathways. Recent studies have evidenced the interrelation of miRNAs with cell proliferation, differentiation, development, and diseases. Since they are involved in gene regulation, they are intrinsically related to metabolic pathways. This leads to questions that are particularly interesting for investigating medical and laboratorial applications. We developed an miRNApath online database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways. There are also internal links that lead to a deeper analysis and cross-links to other databases with more detailed information. miRNApath is being continually updated and is available at http://lgmb.fmrp.usp.br/mirnapath. ©FUNPEC-RP.

Semi-synthetic minimal cells: Biochemical, physical, and technological aspects

The construction of synthetic cells is one of the major goals of bioengineering. The most successful approach consists in the encapsulation of biochemical materials (DNA, RNA, enzymes, etc.) inside lipid vesicles (liposomes), mimicking a cell structure. In this contribution, that also aims at introducing the reader to 'chemical synthetic biology,' we describe the current state of the art of 'semi-synthetic minimal cells' (SSMCs), namely, cell-like structures containing the minimal number of biological compounds that are required to reconstruct a function of interest. We will first describe how the concept of the minimal cell was originated and its relation with the theory of autopoiesis, then we review the most advanced results focused on genetic/metabolic networks inside liposomes. Next, we emphasize that relevance of physical aspects (too often neglected) that impact on the solute entrapment process, and finally we discuss new technological trends in SSMC research that will probably allow their future use in biotechnology. © 2013 Copyright © 2013 Elsevier Inc. All rights reserved.

Reconstruction of molecular networks involved in citokine-induced myotubes atrophy integrating microRNA and mRNA expression

Pós-graduação em Ciências Biológicas (Genética) - IBB

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

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