ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes

Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach

Verificação do efeito da ingestão de capim quicuio da Amazônia infestado com Pithomyces chartarum em bubalinos.

bitstream/item/57675/1/CPATU-PA118.pd

Cell-Free Antigens from Paracoccidioides brasiliensis Drive IL-4 Production and Increase the Severity of Paracoccidioidomycosis

The thermally dimorphic fungus Paracoccidioides brasiliensis (Pb) is the causative agent of paracoccidioidomycosis (PCM), one of the most frequent systemic mycosis that affects the rural population in Latin America. PCM is characterized by a chronic inflammatory granulomatous reaction, which is consequence of a Th1-mediated adaptive immune response. In the present study we investigated the mechanisms involved in the immunoregulation triggered after a prior contact with cell-free antigens (CFA) during a murine model of PCM. The results showed that the inoculation of CFA prior to the infection resulted in disorganized granulomatous lesions and increased fungal replication in the lungs, liver and spleen, that paralleled with the higher levels of IL-4 when compared with the control group. The role of IL-4 in facilitating the fungal growth was demonstrated in IL-4-deficient- and neutralizing anti-IL-4 mAb-treated mice. The injection of CFA did not affect the fungal growth in these mice, which, in fact, exhibited a significant diminished amount of fungus in the tissues and smaller granulomas. Considering that in vivo anti-IL-4-application started one week after the CFA-inoculum, it implicates that IL-4-CFA-induced is responsible by the mediation of the observed unresponsiveness. Further, the characterization of CFA indicated that a proteic fraction is required for triggering the immunosuppressive mechanisms, while glycosylation or glycosphingolipids moieties are not. Taken together, our data suggest that the prior contact with soluble Pb antigens leads to severe PCM in an IL-4 dependent manner

A solicitação de opiniões consultivas ao Tribunal Permanente de Revisão do MERCOSUL pelo judiciário brasileiro

O objetivo central do presente trabalho é demonstrar a relevância do instituto da remição da execução, previsto no art. 651 do Código de Processo Civil, para o atual panorama do processo executivo. Por meio do exercício desse direito subjetivo o executado, no procedimento executivo para pagamento de quantia, pode quitar o débito que lhe é cobrado antes de sofrer expropriações em seu patrimônio. Assim, ao passo que satisfaz a obrigação pecuniária devida, a aplicação do instituto propicia a extinção do processo executivo. Inicialmente, fixando as premissas necessárias ao desenvolvimento do tema, discorre-se sobre os sujeitos do processo e suas relações, considerando, notadamente, o modelo teórico liberal que fundamentou o Código de Processo Civil de 1973. Nesse contexto, são traçadas algumas ponderações sobre a perspectiva do processo de execução, o qual também foi concebido sob a mesma linha de pensamento. A seguir, disserta-se sobre o procedimento executivo para pagamento de quantia e sobre todas as características e peculiaridades que permeiam o instituto da remição, como seu conceito, histórico, fundamentos, diferenciando-o dos institutos aparentemente semelhantes, com a finalidade de vislumbrar sua melhor forma de aplicação. Não escapou ao trabalho as alterações legislativas perpetradas ao processo de execução pelas Leis n.º 11.232/2005 e n.º 11.382/06, vez que trouxeram novidades quanto ao tema, seja adaptando-o à nova ordem de expropriação de bens prevista no Código de Processo, seja, como entende parte da doutrina, por trazer novos institutos que poderiam ser qualificados como espécies de remição da execução civil. Em conclusão, trata-se dos aspectos positivos e negativos da aplicação do instituto da remição da execução no atual momento da ciência do Direito Processual, que cada vez mais reserva ao processo a natureza de um instrumento de concretização das garantias constitucionais e de realização da justiça. Palavras-chave: Direito processual civil. Processo executivo. Remição da execução. Direito subjetivo. Leis n.º 11.232/2005 e n.º 11.382/06. Novas espécies de remição

Virulence markers and genetic relationships of Shiga toxin-producing Escherichia coli strains from serogroup O111 isolated from cattle

Shiga toxin-producing Escherichia coli (STEC) strains isolated from healthy cattle (O111:NM, seven strains; O111:H8, three strains) in Brazil were studied and compared to previously characterized human strains in regard to their phenotypic and genotypic characteristics to evaluate their pathogenic potential. Most bovine STEC O111 strains were isolated from dairy calves, and strains with genotypes stx1 alone and stx1/stx2 (variant stx2) occurred in different regions. Irrespective of the stx genotype, all strains were positive for eae theta, alpha variants of tir, espA and espB, and for ler, qseA, iha, astA and efa1 genes. Only one strain was negative for EHEC-hlyA and all strains were negative for iha, saa and esPP genes and for EAF and bfpA, genetic markers of EPEC. Except for the presence of stx2, bovine strains showed the same profile of putative virulence genes found among the human strains. Similar biochemical behavior was identified among the strains analysed. Two bovine STEC strains produced the localized adherence (LA) phenotype in 6-h tests with Caco-2 (human enterocyte) cells. Intimate attachment (judged by the FAS test) was found in 9 out of 10 bovine strains as it was observed for the human STEC strains. RAPD-PCR analysis showed two distinct RAPD groups among the STEC O111 strains examined. Despite the relative low frequency of STEC O111 strains recovered from cattle no differences in their pathogenic potential were observed compared to some strains isolated from human diarrhea, suggesting that healthy cattle may be a potential source of infection for humans in Brazil. (c) 2006 Elsevier B.V. All rights reserved.Univ Estado Rio de Janeiro, Dept Microbiol Imunol & Parasitol, BR-20551030 Rio de Janeiro, BrazilUniv Fed Fluminense, Dept Bromatol, BR-24241000 Niteroi, RJ, BrazilUniv Fed Fluminense, Dept Microbiol & Parasitol, BR-24210130 Niteroi, RJ, BrazilUniv Fed Rio Grande Sul, Dept Patol Clin Vet, BR-91540000 Porto Alegre, RS, BrazilInst Adolfo Lutz Registro, Setor Enterobacterias, BR-01246902 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilWeb of Scienc

Study of Blood Porphyrin Spectral Profile for Diagnosis of Chronic Renal Failure

The progression to end-stage renal failure is independent of the initial pathogenic mechanism. Metabolic acidosis is a common consequence of chronic renal failure that results from inadequate ammonium excretion and decreased tubular bicarbonate reabsorption. Protoporphyrin IX (PpIX) is the immediate metabolic precursor of the heme molecule. the purpose of this study was to evaluate the levels of erythrocytes protoporphyrin IX at an animal model during progressive renal disease. A total of 36 eight-week-old male Wistar rats were divided into six groups: Normal, 4 and 8 weeks after 5/6 nephrectomy (NX). Renal function was evaluated by creatinine clearance and plasma creatinine levels. the autofluorescence of erythrocytes porphyrin of healthy and NX rats was analyzed using fluorescence spectroscopy. Emission spectra were obtained by exciting the samples at 405 nm. Significant differences between normal and NX rats autofluorescence shape occurred in the 600-700 nm spectral region. A correlation was observed between emission band intensity at 635 nm and progression of renal disease.IPEN CNEN SP, São Paulo, BrazilUniv São Paulo, Inst Fis, BR-01498 São Paulo, BrazilUNIFESP EPM, Disciplina Nefrol, Dept Med, São Paulo, BrazilUNIFESP EPM, Disciplina Nefrol, Dept Med, São Paulo, BrazilWeb of Scienc

Comparative Estimates of Crude and Effective Coverage of Measles Immunization in Low-Resource Settings: Findings from Salud Mesoamérica 2015.

Timely and accurate measurement of population protection against measles is critical for decision-making and prevention of outbreaks. However, little is known about how survey-based estimates of immunization (crude coverage) compare to the seroprevalence of antibodies (effective coverage), particularly in low-resource settings. In poor areas of Mexico and Nicaragua, we used household surveys to gather information on measles immunization from child health cards and caregiver recall. We also collected dried blood spots (DBS) from children aged 12 to 23 months to compare crude and effective coverage of measles immunization. We used survey-weighted logistic regression to identify individual, maternal, household, community, and health facility characteristics that predict gaps between crude coverage and effective coverage. We found that crude coverage was significantly higher than effective coverage (83% versus 68% in Mexico; 85% versus 50% in Nicaragua). A large proportion of children (19% in Mexico; 43% in Nicaragua) had health card documentation of measles immunization but lacked antibodies. These discrepancies varied from 0% to 100% across municipalities in each country. In multivariate analyses, card-positive children in Mexico were more likely to lack antibodies if they resided in urban areas or the jurisdiction of De Los Llanos. In contrast, card-positive children in Nicaragua were more likely to lack antibodies if they resided in rural areas or the North Atlantic region, had low weight-for-age, or attended health facilities with a greater number of refrigerators. Findings highlight that reliance on child health cards to measure population protection against measles is unwise. We call for the evaluation of immunization programs using serological methods, especially in poor areas where the cold chain is likely to be compromised. Identification of within-country variation in effective coverage of measles immunization will allow researchers and public health professionals to address challenges in current immunization programs