Learning HMMs for nucleotide sequences from amino acid alignments

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

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System

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

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.

Curvas de crescimento do fruto de cafeeiro cv. Obatã IAC 1669-20 em diferentes alinhamentos de plantio

The growth of the coffee fruit is highly dependent on physiological and environmental factors. Environmental factors that most influence the yield of coffee during the critical growth stages are the minimum and maximum temperatures of air, which are affected by solar radiation and depend on the apparent path of the sun. This research work correlated dry mass versus fresh mass, and, fresh and dry mass as function of days after flowering of fruit coffee cv. Obata IAC 1669-20 planted in three different alignments based on the apparent trajectory of the sun, in Jaboticabal, SP. The planting was aligned according to the apparent path of the sun. There were three treatments with four replications, a total of twelve plots, each plot with one hundred plants of coffee, each treatment corresponded to an alignment of planting. The three alignments used showed no differences with respect the average fresh and dry mass. The growth rate of fruit, in fresh weight, was higher in the exponential phase, and in dry mass was higher in the linear stage. The dry weight (DW) can be estimated from the fresh weight (FW) using the model: DW = A1*exp(FW/t1). The sigmoidal model that represents the fruit growth in of coffee plants in fresh and/or dry mass in terms of days after flowering (DAF) was: FW(DW) = A2+[(A1-A2)/(1+exp(DAF-x0)/dx)].

Relações radiométricas no terço superior da copa de cafeeiro

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

A Monte Carlo Revisiting of N-Methylformamide and Acetone

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

Cupin: A candidate molecular structure for the Nep1-like protein family

Background: NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known.Results: We predict a 3d-structure for the beta-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position.Conclusion: We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the 3d-structure, we are proposing some possible functions for the NLPs.

14-3-3: Defense and regulatory proteins coding by Eucalyptus genome

The data mining of Eucalyptus ESTs genome finds four clusters (EGCEST2257E11.g, EGBGRT3213F11.g, and EGCCFB1223H11.g) from highly conservative 14-3-3 protein family which modulates a wide variety of cellular processes. Multiple alignments were built from twenty four sequences of 14-3-3 proteins searched into the GenBank databases and into the four pools of Eucalyptus genome programs. The alignment has shown two regions highly conservative on the sequences corresponding to the motifs of protein phosphorylation and nine highly conservative regions on the sequence corresponding to the linkage regions of alpha helices structure based on three dimensional of dimer functional structure. The differences of amino acid into the structural and functional domains of 14-3-3 plant protein were identified and can explain the functional diversity of different isoforms. The phylogenic protein trees were built by the maximum parsimony and neighborjoining procedures of Clustal X alignments and PAUP software for phylogenic analysis.

Variabilidade genética de Sugarcane mosaic virus, causando mosaico em milho no Brasil

O objetivo deste trabalho foi caracterizar biológica e molecularmente três isolados de Sugarcane mosaic virus (SCMV) de lavouras de milho, analisá-los filogeneticamente e discriminar polimorfismos do genoma. Plantas com sintomas de mosaico e nanismo foram coletadas em lavouras de milho, no Estado de São Paulo e no Município de Rio Verde, GO, e seus extratos foliares foram inoculados em plantas indicadoras e submetidos à análise sorológica com antissoros contra o SCMV, contra o Maize dwarf mosaic virus (MDMV) e contra o Johnsongrass mosaic virus (JGMV). Mudas de sorgo 'Rio' e 'TX 2786' apresentaram sintomas de mosaico após a inoculação dos três isolados, e o DAS-ELISA confirmou a infecção pelo SCMV. O RNA total foi extraído e usado para amplificação por transcriptase reversa seguida de reação em cadeia de polimerase (RT-PCR). Fragmentos específicos foram amplificados, submetidos à análise por polimorfismo de comprimento de fragmento de restrição (RFLP) e sequenciados. Foi possível discriminar os genótipos de SCMV isolados de milho de outros isolados brasileiros do vírus. Alinhamentos múltiplos e análises dos perfis filogenéticos corroboram esses dados e mostram diversidade nas sequências de nucleotídeos que codificam para a proteína capsidial, o que explica o agrupamento separado desses isolados e sugere sua classificação como estirpes distintas, em lugar de simples isolados geográficos.

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

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

Molecular characterisation and evolutionary relationships of a potyvirus infecting Crotalaria in Brazil - Brief report

The 3' terminal genomic region of a potyvirus causing mosaic disease in several Crotalaria species has been cloned and sequenced. Comparisons of the nucleotide and deduced amino acid (aa) sequences of the cloned cDNA with those from other potyviruses show that the Crotalaria-infecting virus (designated Crotalaria mosaic virus; CrMV) is closely related to Cowpea aphid-borne mosaic virus (CABMV). Maximum identity (95.4%) at the coat protein (CP) aa level was observed between CrMV and a Brazilian strain of CABMV. Phylogenetic analyses derived from the sequence alignments of the CP and 3' untranslated region confirmed the identification of CrMV as a strain of CABMV and the name CABMV-Cr is suggested.

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Perfil longitudinal e a aplicação do índice de gradiente (RDE) no rio dos Patos, bacia hidrográfica do rio Ivaí, PR

This paper presents the results of the longitudinal profile analysis and the application of gradient index (RDE) in the Patos River, a tributary of the Ivaí River basin, PR. The goal is identify and quantify the anomalous zones along river course concerning their genesis - activity neotectonic or/and lithological imposition. The Patos River has a length of 127 km and a relief amplitude of 660 m, The occurrence of an important knickpoint in the middle course the Patos River can be divided into two stretches. Of the 22 sections measured, 10 were considered anomalous, distributed in both upper and lower course. In the upper course, over a basaltic bedrock of the Serra Geral Formation the RDE values are lower than those in the lower course, where river flows over sedimentary rocks of the Terezina Formation. The 2 nd order anomalies are related to lithological changes, relief alignments and channel confluences - as in the case of São João River. The 1st order anomalies are linked to differences in rock resistance associated with structural control, which provides the formation of waterfalls.

Análise molecular em morcegos do gênero Artibeus Leach, 1821 (Chiroptera, Phyllostomidae) a partir de espécimes depositados em coleção científica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Paralelização da ferramenta de alinhamento de sequências MUSCLE para um ambiente distribuído

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