Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

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

Short-term movement and retreat sites of Leptodactylus labyrinthicus (Anura : Leptodactylidae) during the breeding season: A spool-and-line tracking study

Capture/recapture studies significantly increase our knowledge of the natural history of anuran amphibians. Many different methods have been employed in these studies, but a number of new techniques still require experimental validation. During two reproductive seasons in a Cerrado remnant in southeastern Brazil, we investigated the movement patterns and habitat use of the pepper frog, Leptodactylus labyrinthicus, using a spool-and-line device. This low-cost device did not appear to interfere with the activities of the frogs and allowed for constant monitoring, showing precise routes of movement and great predictability of relocations. Both sexes were active at night. During the day, males and females made use of retreat sites under vegetation or in burrows constructed by small- and medium-sized mammals. Males and females did not use standardized routes; there were no significant differences between their movements, and movements were not correlated with body size or environmental conditions. Individuals are able to move further than 100 m per day, a characteristic that may enable this species to colonize or recolonize open areas.

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Background: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.Results: PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/similar to primer.Conclusion: PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.

The Development of a Universal In Silico Predictor of Protein-Protein Interactions

Protein-protein interactions (PPIs) are essential for understanding the function of biological systems and have been characterized using a vast array of experimental techniques. These techniques detect only a small proportion of all PPIs and are labor intensive and time consuming. Therefore, the development of computational methods capable of predicting PPIs accelerates the pace of discovery of new interactions. This paper reports a machine learning-based prediction model, the Universal In Silico Predictor of Protein-Protein Interactions (UNISPPI), which is a decision tree model that can reliably predict PPIs for all species (including proteins from parasite-host associations) using only 20 combinations of amino acids frequencies from interacting and non-interacting proteins as learning features. UNISPPI was able to correctly classify 79.4% and 72.6% of experimentally supported interactions and non-interacting protein pairs, respectively, from an independent test set. Moreover, UNISPPI suggests that the frequencies of the amino acids asparagine, cysteine and isoleucine are important features for distinguishing between interacting and non-interacting protein pairs. We envisage that UNISPPI can be a useful tool for prioritizing interactions for experimental validation. © 2013 Valente et al.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

Análise teórica de uma nova técnica de processamento de sinais interferométricos baseada na modulação triangular da fase óptica

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Algoritmos para geração de referências, inicialização e proteção de um condicionador unificado de qualidade de energia

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Diagnose de trincas em sistemas rotativos, utilizando modelos de falhas através da metodologia dos observadores de estados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise dinâmica do amortecimento em estruturas compostas com material viscoelástico

Pós-graduação em Engenharia Mecânica - FEB

Geração e otimização de trajetórias de um manipulador robótico utilizando algoritmos genéticos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Simulação numérica do escoamento em difusores radiais com discos frontais fixos e móveis

Pós-graduação em Engenharia Mecânica - FEIS

Load analyser using conservative power theory

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

Redes dinâmicas de sensores sem fio ZigBee para aplicações de monitoramento e controle

Pós-graduação em Engenharia Elétrica - FEB

Dissecting Phaseolus vulgaris Innate Immune System against Colletotrichum lindemuthianum Infection

Background: The genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus. Methodology and Principal Findings: As the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling. Conclusions/Significance: We have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Motion-based wave estimation: Small-scale tests with a crane-barge model

This paper provides additional validation to the problem of estimating wave spectra based on the first-order motions of a moored vessel. Prior investigations conducted by the authors have attested that even a large-volume ship, such as an FPSO unit, could be adopted for on-board estimation of the wave field. The obvious limitation of the methodology concerns filtering of high-frequency wave components, for which the vessel has no significant response. As a result, the estimation range is directly dependent on the characteristics of the vessel response. In order to extend this analysis, further small-scale tests were performed with a model of a pipe-laying crane-barge. When compared to the FPSO case, the results attest that a broader range of typical sea states can be accurately estimated, including crossed-sea states with low peak periods. (C) 2012 Elsevier Ltd. All rights reserved.