841 resultados para Cluster Beowulf
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
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Diatraea saccharalis F. is one of the greatest pests of the sugar cane culture. This report aimed to characterize the germanium region of the sugarcane borer by light and transmission electron microscopy, emphasizing the morphological steps of the ovarian cluster formation. In the germanium of this insect, four zones could be morphologically identified during the cluster formation. In the most apical end of each ovariole - Zone I - the germ line stem cells undergo complete mitotic division, originating the cystoblasts. In the Zone II, each cystoblast produces a group of eight cells, the cystocytes, which are interconnected by the ring canals. Clusters containing all the cystocytes in the meiosis, characterizes the Zone III. Germ cells with ultrastructural features of apoptosis are also detected in this Zone. In the Zone IV the cystocytes differentiate, morphologically, into one oocyte and seven nurse cells. Interstitial somatic cells and pre-follicle cells exhibit, in their cytoplasm, heterogeneous vacuoles containing degenerated cellular fragments, characterized as apoptotic bodies. Our results pointed out to the morphological evidences related with important control mechanisms for new clusters/follicles production and for the cellular arrangement into the germanium, resulting from the programmed cell death. We believe that the morphological characterization of ovarian cluster formation in D. saccharalis provided valuable information for the understanding of the initial steps of oogenesis and contributed for the knowledge of the cellular mechanisms related with the oocyte production and with reproduction in insects.
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Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
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The description of the short-range part of the nucleon forces in terms of quark degrees of freedom is tested by supplementing, to the short range quark cluster model, a long range mesonic force well founded theoretically.
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The description of the short-range part of the nucleon-nucleon forces in terms of quark degrees of freedom is tested against experimental observables. We consider, for this purpose, a model where the short-range part of the forces is given by the quark cluster model and the long- and medium-range forces by well established meson exchanges. The investigation is performed using different quark cluster models coming from different sets of quark-quark interactions. The predictions of this model are compared not only with the phase shifts but also directly with the experimental observables. Agreement with the existing pp and np world set of data is poor. This suggests that the current description of the nucleon-nucleon interaction, at short distances, in the framework of the nonrelativistic quark models, is at present only qualitative.
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Strain and vacancy cluster behavior of vanadium and tungsten-doped Ba[Zr(0.10)Ti(0.90)]O(3) ceramics
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Strain and vacancy clusters behavior of polycrystalline vanadium (V) and tungsten (W)-doped Ba[Zr(0.10)Ti(0.90)]O(3), (BZT:2%V) and (BZT:2%W) ceramics obtained by the mixed oxide method was evaluated. Substitution of V and W reduces the distortion of octahedral clusters, decreasing the Raman modes. Electron paramagnetic resonance data indicate that the addition of dopants leads to defects and symmetry changes in the BZT lattice. Remnant polarization and coercive field are affected by V and W substitution due the electron-relaxation mode. The unipolar strain E curves as a function of electric field reach its maximum value for BZT:2%V and BZT:2%W ceramics. (c) 2008 American Institute of Physics.
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A model for describing hybrid spectroscopy similar to the diquark model for baryons is presented. Mass and r.m.s. radii are calculated and compared with experimental results.
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Ten strains of two species in the Drosophila buzzatii cluster (D. serido and D. seriema) were examined as to esterase patterns using polyacrylamide gel electrophoresis. The migration rate of esterases, and their substrate specificity to alpha and beta naphthyl acetates, were analysed. Other esterase features such as inhibition behaviour, presence in males and females and location in the head, thorax or abdomen of flies, were also examined. The present data,together with results obtained by others for eight strains of D. koepferae, D. serido, D. seriema and D. buzzatii, show that 69 bands have been detected in the eighteen strains studied. This total number of bands was used for comparison of strains and species by similarity index, analysis of dependence and cluster analysis. The comparisons confirmed the existence of a high degree of similarity among D. seriema strains and among D. koepferae strains, but indicated differentiation among the D. serido strains. Two strains (D69R2 and D69R5) which differed from the others of the latter species, showed closer affinities with D. buzzatii, which indicates the need for further work on those strains classified as D. serido.
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Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models ford a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools/parmodel. (C) 2004 Elsevier B.V. All rights reserved.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)