Parametric analyses of anxiety in zebrafish scototaxis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB (R)/SIMULINK (R)

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB (R)/SINIULINK (R) models to structural VHDL-AMS descriptions. The tool developed, named (MSSV)-S-2, reads a SIMULINK (R) model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the SystemVision (TM). To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB (R)/SIMULINK (R). The VHDL-AMS code generated automatically by (MSSV)-S-2, (MATLAB (R)/SIMULINK (R) to SystemVision (TM)), was then simulated in the SystemVision (TM). The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Signaling pathways associated with the expression of inflammatory mediators activated during the course of two models of experimental periodontitis

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

Differential regulation of MMP-13 expression in two models of experimentally induced periodontal disease in rats

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

Susceptibility of Candida albicans to photodynamic therapy in a murine model of oral candidosis

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

Healing, Antioxidant and Cytoprotective Properties of Indigofera truxillensis in Different Models of Gastric Ulcer in Rats

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

Quantitative comparisons and models of time-averaging in bivalve and brachiopod shell accumulations

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

Molecular models of protein targets from Mycobacterium tuberculosis

Structural characterization of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design since some of these proteins may be present in the bacterial genome, but absent in humans. Thus, metabolic pathways became potential targets for drug design. The motivation of this work is the fact that Mycobacterium tuberculosis is the cause of the deaths of millions of people in the world, so that the structural characterization of protein targets to propose new drugs has become essential. DBMODELING is a relational database, created to highlight the importance of methods of molecular modeling applied to the Mycobacterium tuberculosis genome with the aim of proposing protein-ligand docking analysis. There are currently more than 300 models for proteins from Mycobacterium tuberculosis genome in the database. The database contains a detailed description of the reaction catalyzed by each enzyme and their atomic coordinates. Information about structures, a tool for animated gif image, a table with a specification of the metabolic pathway, modeled protein, inputs used in modeling, and analysis methods used in this project are available in the database for download. The search tool can be used for reseachers to find specific pathways or enzymes.

Molecular models of tryptophan synthase from Mycobacterium tuberculosis complexed with inhibitors

The development of new therapies against infectious diseases is vital in developing countries. Among infectious diseases, tuberculosis is considered the leading cause of death. A target for development of new drugs is the tryptophan pathway. The last enzyme of this pathway, tryptophan synthase (TRPS), is responsible for conversion of the indole 3-glycerol phosphate into indol and the condensation of this molecule with serine-producing tryptophan. The present work describes the molecular models of TRPS from Mycobacterium tuberculosis (MtTRPS) complexed with six inhibitors, the indole 3-propanol phosphate and five arylthioalkyl-phosphonated analogs of substrate of the a-subunit. The molecular models of MtTRPS present good stereochemistry, and the binding of the inhibitors is favorable. Thus, the generated models can be used in the design of more specific drugs against tuberculosis and other infectious diseases.

Molecular models of NS3 protease variants of the Hepatitis C virus

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.

Microbiological or Chemical Models of Enamel Secondary Caries Compared by Polarized-Light Microscopy and Energy Dispersive X-ray Spectroscopy

Different secondary caries models may present different results. The purpose of this study was to compare different in vitro secondary caries models, evaluating the obtained results by polarized-light microscopy (PLM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDS). Standardized human enamel specimens (n = 12) restored with different materials (Z250 conventional composite resin-CRZ, Freedom polyacid-modified composite resin-CRF, Vitremer resin-modified glass-ionomer-GIV, and Fuji IX conventional glass-ionomer cement-GIF) were submitted to microbiological (MM) or chemical caries models (CM). The control group was not submitted to any caries model. For MM, specimens were immersed firstly in sucrose broth inoculated with Streptococcus mutans ATCC 35688, incubated at 37 degrees C/5% CO(2) for 14 days and then in remineralizing solution for 14 days. For CM, specimens were submitted to chemical pH-cycling. Specimens were ground, submitted to PLM and then were dehydrated, gold-sputtered and submitted to SEM and EDS. Results were statistically analyzed by Kruskall-Wallis and Student-Newman-Keuls tests (alpha = 0.05). No differences between in vitro caries models were found. Morphological differences in enamel demineralization were found between composite resin and polyacid-modified composite resin (CRZ and CRF) and between the resin-modified glass-ionomer and the glass-ionomer cement (GIF and GIV). GIF showed higher calcium concentration and less demineralization, differing from the other materials. In conclusion, the glass-ionomer cement showed less caries formation under both in vitro caries models evaluated. (C) 2009 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 90B: 635-640, 2009

Mathematical models of generalized diffusion

We discuss in this paper equations describing processes involving non-linear and higher-order diffusion. We focus on a particular case (u(t) = 2 lambda (2)(uu(x))(x) + lambda (2)u(xxxx)), which is put into analogy with the KdV equation. A balance of nonlinearity and higher-order diffusion enables the existence of self-similar solutions, describing diffusive shocks. These shocks are continuous solutions with a discontinuous higher-order derivative at the shock front. We argue that they play a role analogous to the soliton solutions in the dispersive case. We also discuss several physical instances where such equations are relevant.

Generalized non-abelian Toda models of dyonic type

The construction of a class of non-abelian Toda models admiting dyonic type soliton solutions is reviewed.

Thermal comfort in reduced models of broilers' houses, under different types of roofing materials

Esta pesquisa foi conduzida com o objetivo de avaliar diferentes tipos de coberturas em instalações para aves, por meio do Índice de Temperatura de Globo Negro e Umidade (ITGU), Carga Térmica de Radiação (CTR) e Entalpia (H). O experimento foi conduzido na Universidade Estadual de Goiás, entre os meses de abril e maio de 2011, sendo composto por cinco tratamentos (coberturas): CA -Telha de cimento-amianto; BA -Telha de bambu; BAP -Telha de bambu pintada de branco; FB -Telha de fibra vegetal e betume; FBP -Telha de fibra vegetal e betume pintada de branco, com 15 repetições, sendo as repetições os dias de medição. Dentre os horários estudados, o considerado menos confortável foi às 14h, sendo que a cobertura de fibra vegetal e betume foi a que apresentou maior valor de ITGU (84,1) quando comparada às demais coberturas, caracterizando uma situação de menor conforto térmico, não sendo observada diferença para CTR e H entre os tratamentos na região estudada.

Immunomodulation and protection induced by DNA-hsp65 vaccination in an animal model of arthritis

We described a prophylactic and therapeutic effect of a DNA vaccine encoding the Mycobacterium leprae 65- kDa heat shock protein (DNA-hsp65) in experimental murine tuberculosis. However, high homology of the vaccine to the corresponding mammalian hsp60, together with the CpG motifs in the plasmidial vector, could trigger or exacerbate an autoimmune disease. In the present study, we evaluate the potential of DNA- hsp65 vaccination to induce or modulate arthritis in mice genetically selected for acute inflammatory reaction (AIR), either maximal (AIRmax) or minimal (AIRmin). Mice immunized with DNA-hsp65 or injected with the corresponding DNA vector (DNAv) developed no arthritis, whereas pristane injection resulted in arthritis in 62% of AIRmax mice and 7.3% of AIRmin mice. Administered after pristane, DNA- hsp65 downregulated arthritis induction in AIRmax animals. Levels of interleukin (IL)- 12 were significantly lower in mice receiving pristane plus DNA- hsp65 or DNAv than in mice receiving pristane alone. However, when mice previously injected with pristane were inoculated with DNA- hsp65 or DNAv, the protective effect was significantly correlated with lower IL-6 and IL-12 levels and higher IL-10 levels. Our results strongly suggest that DNA-hsp65 has no arthritogenic potential and is actually protective against experimentally induced arthritis in mice.