Laboratorio Of Bioinformatica Aplicada

Campinas, Brazil

Laboratorio Of Bioinformatica Aplicada

Campinas, Brazil

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Bitar M.,Federal University of Minas Gerais | Pereira Lobo F.,Laboratorio Of Bioinformatica Aplicada | Paula Peconick A.,Federal University of Lavras | Grynberg P.,Federal University of Minas Gerais | And 7 more authors.
Memorias do Instituto Oswaldo Cruz | Year: 2013

Schistosomiasis is a major neglected tropical disease caused by trematodes from the genus Schistosoma. Because schistosomes exhibit a complex life cycle and numerous mechanisms for regulating gene expression, it is believed that spliced leader (SL) trans-splicing could play an important role in the biology of these parasites. The purpose of this study was to investigate the function of trans-splicing in Schistosoma mansoni through analysis of genes that may be regulated by this mechanism and via silencing SL-containing transcripts through RNA interference. Here, we report our analysis of SL transcript-enriched cDNA libraries from different S. mansoni life stages. Our results show that the trans-splicing mechanism is apparently not associated with specific genes, subcellular localisations or life stages. In cross-species comparisons, even though the sets of genes that are subject to SL trans-splicing regulation appear to differ between organisms, several commonly shared orthologues were observed. Knockdown of trans-spliced transcripts in sporocysts resulted in a systemic reduction of the expression levels of all tested trans-spliced transcripts; however, the only phenotypic effect observed was diminished larval size. Further studies involving the findings from this work will provide new insights into the role of trans-splicing in the biology of S. mansoni and other organisms. All Expressed Sequence Tags generated in this study were submitted to dbEST as five different libraries. The accessions for each library and for the individual sequences are as follows: (i) adult worms of mixed sexes (LIBEST_027999: JZ139310 - JZ139779), (ii) female adult worms (LIBEST_028000: JZ139780 - JZ140379), (iii) male adult worms (LIBEST_028001: JZ140380 - JZ141002), (iv) eggs (LIBEST_028002: JZ141003 - JZ141497) and (v) schistosomula (LIBEST_028003: JZ141498 - JZ141974).

Ghelfi A.,Federal University of Amazonas | Gaziola S.A.,University of Sao Paulo | Cia M.C.,University of Sao Paulo | Kuser-Falcao P.R.,Laboratorio Of Bioinformatica Aplicada | Azevedo R.A.,University of Sao Paulo
Annals of Applied Biology | Year: 2011

Sugarcane yield and quality are affected by a number of biotic and abiotic stresses. In response to such stresses, plants may increase the activities of some enzymes such as glutathione transferase (GST), which are involved in the detoxification of xenobiotics. Thus, a sugarcane GST was modelled and molecular docked using the program LIGIN to investigate the contributions of the active site residues towards the binding of reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB). As a result, W13 and I119 were identified as key residues for the specificity of sugarcane GSTF1 (SoGSTF1) towards CDNB. To obtain a better understanding of the catalytic specificity of sugarcane GST (SoGSTF1), two mutants were designed, W13L and I119F. Tertiary structure models and the same docking procedure were performed to explain the interactions between sugarcane GSTs with GSH and CDNB. An electron-sharing network for GSH interaction was also proposed. The SoGSTF1 and the mutated gene constructions were cloned and expressed in Escherichia coli and the expressed protein purified. Kinetic analyses revealed different Km values not only for CDNB, but also for GSH. The Km values were 0.2, 1.3 and 0.3 mM for GSH, and 0.9, 1.2 and 0.5 mM for CDNB, for the wild type, W13L mutant and I119F mutant, respectively. The Vmax values were 297.6, 224.5 and 171.8 μmol min-1 mg-1 protein for GSH, and 372.3, 170.6 and 160.4 μmol min-1 mg-1 protein for CDNB. © 2011 Association of Applied Biologists.

Faria L.C.B.,University of Campinas | Rocha A.S.L.,University of Campinas | Kleinschmidt J.H.,Federal University of ABC | Silva-Filho M.C.,University of Sao Paulo | And 4 more authors.
PLoS ONE | Year: 2012

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction. © 2012 Faria et al.

Vinecky F.,University of Brasilia | da Silva F.R.,Laboratorio Of Bioinformatica Aplicada | Andrade A.C.,Laboratorio Of Genetica Molecular Lgm
Coffee Science | Year: 2012

Brazil is the largest producer and exporter of coffee and coffee production is a major source of income for small farmers. Drought, which has become increasingly intense over the years, affects the production of these farmers, as it reduces productivity and can even cause entire crop loss. Aiming at the development of drought tolerant crops, several research groups are currently studying the genetic factors involved in plant responses to drought. The construction and sequencing of EST libraries (Expressed Sequence Tags) is a quick and effective way to obtain information about most expressed genes. The functional genome of coffee made available by cDNA sequencing (ESTs), allowed the construction of a large EST database of three different Coffea species. The Coffee EST Database provides a rich source of information for genetic and physiological studies of coffee plants. The goal of this study was to identify genes potentially involved in the response of coffee plants to water stress by means of an (in silico) analysis of available ESTs of the coffee genome database. The methodology was based on in silico comparisons between EST data from libraries SH2 (Coffea arabica) and SH3 (Coffea canephora), with the aid of bioinformatics tools available at the Coffee Genome Database. With the methodology used, several candidate genes have been identified and may be subject to further experimental studies aiming at the establishment of a breeding program based on marker assisted selection for quick development of drought tolerant varieties of coffee.

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