Molecular and serological detection of tick-borne pathogens in dogs from an area endemic for Leishmania infantum in Mato Grosso do Sul, Brazil

Patógenos transmitidos por carrapatos atingem uma variedade de hospedeiros vertebrados. Para identificar os agentes patogênicos transmitidos por carrapatos entre cães soropositivos para Leishmania infantum no município Campo Grande-MS, foi realizado um estudo sorológico e molecular para a detecção de Ehrlichia canis, Anaplasma platys e Babesia vogeli em 60 amostras de soro e baço, respectivamente. Adicionalmente, foi realizado o diagnóstico confirmatório de L. infantum por meio de técnicas sorológicas e moleculares. Também foi realizado o alinhamento e análise filogenética das sequências para indicar a identidade das espécies de parasitas que infectam esses animais. Anticorpos IgG anti-Ehrlichia spp., anti-B. vogeli e anti-L. infantum foram detectados em 39 (65%), 49 (81,6%) e 60 (100%) dos cães amostrados, respectivamente. Vinte e sete (45%), cinquenta e quatro (90%), cinquenta e três (88,3%), dois (3,3%) e um (1,6%) cães mostraram-se positivos na PCR para E. canis, Leishmania spp., Leishmania donovani complex, Babesia sp. e Anaplasma sp., respectivamente. Após o seqüenciamento, os amplicons mostraram 99% de similaridade com isolados de E. canis, B. vogeli e A. platys e Leishmania chagasi. Os resultados deste estudo indicaram que os cães soropositivos para L. infantum de Campo Grande, MS, são expostos a vários agentes transmitidos por carrapatos, e, portanto, devem ser incluídos no diagnóstico diferencial em cães com suspeita clínica de leishmaniose.

Improvements in the score matrix calculation method using parallel score estimating algorithm

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.

Uma proposta de sequência didática para o ensino de Programação Linear no Ensino Médio

Pós-graduação em Matemática em Rede Nacional - IBILCE

Improvements in the sensibility of MSA-GA tool using COFFEE objective function

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

The Mycobacterium leprae hsp65 displays proteolytic activity. Mutagenesis studies indicate that the M. leprae hsp65 Proteolytic activity is catalytically related to the HslVU protease?

The present study reports, for the first time, that the recombinant hsp65 from Mycobacterium leprae (chaperonin 2) displays a proteolytic activity toward oligopeptides. The M. leprae hsp65 proteolytic activity revealed a trypsin-like specificity toward quenched fluorescence peptides derived from dynorphins. When other peptide substrates were used (β-endorphin, neurotensin, and angiotensin I), the predominant peptide bond cleavages also involved basic amino acids in P 1, although, to a minor extent, the hydrolysis involving hydrophobic and neutral amino acids (G and F) was also observed. The amino acid sequence alignment of the M. leprae hsp65 with Escherichia coli Hs1VU protease suggested two putative threonine catalytic groups, one in the N-domain (T 136, K 168, and Y 264) and the other in the C-domain (T 375, K 409, and S 502). Mutagenesis studies showed that the replacement of K 409 by A caused a complete loss of the proteolytic activity, whereas the mutation of K 168 to A resulted in a 25% loss. These results strongly suggest that the amino acid residues T 375, K 409, and S 502 at the C-domain form the catalytic group that carries out the main proteolytic activity of the M. leprae hsp65. The possible pathophysiological implications of the proteolytic activity of the M. leprae hsp65 are now under investigation in our laboratory.

Técnicas de otimização em alinhamentos múltiplos de sequência via Cadeias de Markov

Pós-graduação em Ciência da Computação - IBILCE

Short Comments on an Energy Pumping Levels in a MEMS Gyroscope Vibrating Problem, by Using of an Global and Local Optimal Linear Control Design

This paper deals with an energy pumping that occurs in a (MEMS) Gyroscope nonlinear dynamical system, modeled with a proof mass constrained to move in a plane with two resonant modes, which are nominally orthogonal. The two modes are ideally coupled only by the rotation of the gyro about the plane's normal vector. We also developed a linear optimal control design for reducing the oscillatory movement of the nonlinear systems to a stable point.

Joint rolling-horizon scheduling of materials processing and lot-sizing with sequence-dependent setups

A lot sizing and scheduling problem from a foundry is considered in which key materials are produced and then transformed into many products on a single machine. A mixed integer programming (MIP) model is developed, taking into account sequence-dependent setup costs and times, and then adapted for rolling horizon use. A relax-and-fix (RF) solution heuristic is proposed and computationally tested against a high-performance MIP solver. Three variants of local search are also developed to improve the RF method and tested. Finally the solutions are compared with those currently practiced at the foundry.

A modified Primal-Dual Logarithmic-Barrier Method for solving the Optimal Power Flow problem with discrete and continuous control variables

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

Hybrid evolutionary algorithm for the Capacitated Centered Clustering Problem

The Capacitated Centered Clustering Problem (CCCP) consists of defining a set of p groups with minimum dissimilarity on a network with n points. Demand values are associated with each point and each group has a demand capacity. The problem is well known to be NP-hard and has many practical applications. In this paper, the hybrid method Clustering Search (CS) is implemented to solve the CCCP. This method identifies promising regions of the search space by generating solutions with a metaheuristic, such as Genetic Algorithm, and clustering them into clusters that are then explored further with local search heuristics. Computational results considering instances available in the literature are presented to demonstrate the efficacy of CS. (C) 2010 Elsevier Ltd. All rights reserved.

Multi Objective Evolutionary Algorithm Applied to the Optimal Power Flow Problem

This work presents the application of a multiobjective evolutionary algorithm (MOEA) for optimal power flow (OPF) solution. The OPF is modeled as a constrained nonlinear optimization problem, non-convex of large-scale, with continuous and discrete variables. The violated inequality constraints are treated as objective function of the problem. This strategy allows attending the physical and operational restrictions without compromise the quality of the found solutions. The developed MOEA is based on the theory of Pareto and employs a diversity-preserving mechanism to overcome the premature convergence of algorithm and local optimal solutions. Fuzzy set theory is employed to extract the best compromises of the Pareto set. Results for the IEEE-30, RTS-96 and IEEE-354 test systems are presents to validate the efficiency of proposed model and solution technique.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTEs were assembled into 81,429 contigs. of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTEs sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTEs coincided with DNA regions predicted as encoding exons by GENSCAN.

Plasmodium falciparum: sequence diversity and antibody recognition of the Merozoite surface protein-2 (MSP-2) in Brazilian Amazonia

The merozoite surface protein-2 (MSP-2) of Plasmodium falciparum comprises repeats flanked by dimorphic domains defining the allelic families FC27 and IC1. Here, we examined sequence diversity at the msp-2 locus in Brazil and its impact on MSP-2 antibody recognition by local patients. Only 25 unique partial sequences of msp-2 were found in 61 isolates examined. The finding of identical msp-2 sequences in unrelated parasites, collected 6-13 years apart, suggests that no major directional selection is exerted by variant-specific immunity in this malaria-endemic area. To examine antibody cross-reactivity, recombinant polypeptides derived from locally prevalent and foreign MSP-2 variants were used in ELISA. Foreign IC1-type variants, such as 3D7 (currently tested for human vaccination), were less frequently recognized than FC27-type and local IC1-type variants. Antibodies discriminated between local and foreign IC1-type variants, but cross-recognized structurally different local IC1-type variants. The use of evolutionary models of MSP-2 is suggested to design vaccines that minimize differences between local parasites and vaccine antigens. (C) 2004 Elsevier B.V. All rights reserved.

The water factor in the protein-folding problem

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

A influência da deficiência estrogênica no processo de remodelação e reparação óssea

INTRODUÇÃO: Nestes últimos anos, descobriu-se a complexidade dos mecanismos que influenciam a atividade óssea, e grande parte das pesquisas direcionou-se para o estudo de fatores capazes de modular as funções ósseas. Essa expansão da pesquisa deve-se, em parte, ao reconhecimento da osteoporose como importante problema na velhice. A osteoporose constitui uma das osteopatias mais comuns, caracterizando-se pela redução da massa óssea, determinada, por sua vez, pelo desequilíbrio entre reabsorção e neoformação. OBJETIVO: Apresentar uma revisão da literatura sobre os principais aspectos da remodelação e da reparação associados à deficiência estrogênica. Remodelação óssea: O osso apresenta processo contínuo de remodelação, entretanto anormalidades nesse processo ocorrem em algumas doenças, entre elas a osteoporose, sendo que a deficiência estrogênica parece ter o papel principal na sua gênese. Reparação óssea: Tal processo envolve uma cascata complexa de respostas biológicase, assim como a remodelação, é afetado por fatores locais e externos e regulado pela interação de diferentes mecanismos. Portanto, o aumento ou o decréscimo da capacidade de reparação óssea têm sido relacionados a alterações ocorridas na remodelação. Deficiência estrogênica e metabolismo ósseo: A maioria dos autores sugere uma redução na capacidade de remodelação e de reparação do tecido. DISCUSSÃO: Ainda não está determinado qual estágio da reparação é mais alterado, se a fase inicial de formação do calo ósseo, se a de mineralização ou se a fase tardia da reparação, a remodelação óssea. CONCLUSÃO: Como os mecanismos fisiológicos e a patogênese das alterações ósseas causadas pela deficiência estrogênica não estão completamente estabelecidos, novas pesquisas ainda são necessárias.