Recursive hierarchic segmentation analysis of bone mineral density changes on digital panoramic images

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structural studies of shikimate 5-dehydrogenase from Mycobacterium tuberculosis

Tuberculosis (TB) remains the leading cause of mortality due to a single bacterial pathogen, Mycobacterium tuberculosis. The reemergence of TB as a potential public health threat, the high susceptibility of human immunodeficiency virus-infected persons to the disease, the proliferation of multi-drug-resistant strains (MDR-TB) and, more recently, of extensively drug resistant isolates (XDR-TB) have created a need for the development of new antimycobacterial agents. Amongst the several proteins and/or enzymes to be studied as potential targets to develop novel drugs against M. tuberculosis, the enzymes of the shikimate pathway are attractive targets because they are essential in algae, higher plants, bacteria, and fungi, but absent from mammals. The mycobacterial shikimate pathway leads to the biosynthesis of chorismate, which is a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Here we report the structural studies by homology modeling and circular dichroism spectroscopy of the shikimate dehydrogenase from M. tuberculosis (MtSDH), which catalyses the fourth step of the shikimate pathway. Our structural models show that the MtSDH has similar structure to other shikimate dehydrogenase structures previously reported either in presence or absence of NADP, despite the low amino acid sequence identity. The circular dichroism spectra corroborate the secondary structure content observed in the MtSDH models developed. The enzyme was stable up to 50 degrees C presenting a cooperative unfolding profile with the midpoint of the unfolding temperature value of similar to 63-64 degrees C, as observed in the unfolding experiment followed by circular dichroism. Our MtSDH structural models and circular dichroism data showed small conformational changes induced by NADP binding. We hope that the data presented here will assist the rational design of antitubercular agents.

Purification, sequencing and structural characterization of the phospholipase A(1) from the venom of the social wasp Polybia paulista (Hymenoptera, Vespidae)

The biochemical and functional characterization of wasp venom toxins is an important prerequisite for the development of new tools both for the therapy of the toxic reactions due to envenomation caused by multiple stinging accidents and also for the diagnosis and therapy of allergic reactions caused by this type of venom. PLA(1) was purified from the venom of the neotropical social wasp Polybia paulista by using molecular exclusion and cation exchange chromatographies; its amino acid sequence was determined by using automated Edman degradation and compared to the sequences of other vespid venom PLA(1)'s. The enzyme exists as a 33,961.40 da protein, which was identified as a lipase of the GX class, liprotein lipase superfamily, pancreatic lipases (ab20.3) homologous family and RP2 sub-group of phospholipase. P. paulista PLA(1) is 53-82% identical to the phospholipases from wasp species from Northern Hemisphere. The use restrained-based modeling permitted to describe the 3-D structure of the enzyme, revealing that its molecule presents 23% alpha-helix, 28% beta-sheet and 49% coil. The protein structure has the alpha/beta fold common to many lipases; the core consists of a tightly packed beta-sheet constituted of six-stranded parallel and one anti-parallel beta-strand, surrounded by four alpha-helices. P. paulista PLA(1) exhibits direct hemolytic action against washed red blood cells with activity similar to the Cobra cardiotoxin from Naja naja atra. In addition to this, PLA(1) was immunoreactive to specific IgE from the sera of P. paulista-sensitive patients. (c) 2007 Elsevier Ltd. All rights reserved.

Structural biology of membrane-acting peptides: Conformational plasticity of anticoccidial peptide PW2 probed by solution NMR

The bottleneck for the complete understanding of the structure-function relationship of flexible membrane-acting peptides is its dynamics. At the same time, not only the structure but also the dynamics are the key points for their mechanism of action. Our model is PW2, a TRP-rich, cationic peptide selected from phage display libraries that shows anticoccidial activity against Eimeria acervulina. In this manuscript we used a combination of several NMR techniques to tackle these difficulties. The structural features of the membrane-acting peptide PW2 was studied in several membrane mimetic environments: we compared the structural features of PW2 in SDS and DPC micelles, that were reported earlier, with the structure properties in different lipid vesicles and the peptide free in water. We were able to unify the structural information obtained in each of these systems. The structural constraints of the peptide free in water were fundamental for the understanding of plasticity necessary for the membrane interaction. Our data suggested that the WWR sequence is the region responsible for anchoring the peptide to the interfaces, and that this same region displays some degree of conformational order in solution. For PW2, we found that affinity is related to the aromatic region, by anchoring the peptide to the membrane, and specificity is related to the N- and C-termini, which are able to accommodate in the membrane due to its plasticity. (C) 2007 Elsevier B.V. All rights reserved.

Parmodel: a web server for automated comparative modeling of proteins

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.

Structural studies of NaPO3-MoO3 glasses by solid-state nuclear magnetic resonance and raman spectroscopy

Vitreous samples were prepared in the (100 - x)% NaPO3-x% MoO3 (0 <= x <= 70) glass-forming system by a modified melt method that allowed good optical quality samples to be obtained. The structural evolution of the vitreous network was monitored as a function of composition by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), Raman scattering, and solid-state nuclear magnetic resonance (NMR) for P-31, Na-23, and Mo-95 nuclei. Addition of MoO3 to the NaPO3 glass melt leads to a pronounced increase in the glass transition temperatures up to x = 45, suggesting a significant increase in network connectivity. For this same composition range, vibrational spectra suggest that the Mo6+ ions are bonded to some nonbridging oxygen atoms (Mo-O- or Mo=O bonded species). Mo-O-Mo bond formation occurs only at MoO3 contents exceeding x = 45. P-31 magic-angle spinning (MAS) NMR spectra, supported by two-dimensional J-resolved spectroscopy, allow a clear distinction between species having two, one, and zero P-O-P linkages. These sites are denoted as Q(2Mo)((2)), Q(1Mo)((2)), and Q(0Mo)((2)), respectively. For x < 0.45, the populations of these sites can be described along the lines of a binary model, according to which each unit of MoO3 converts two Q(nMo)((2)) sites into two Q((n+1)Mo)((2)) sites (n = 0, 1). This structural model is consistent with the presence of tetrahedral Mo(=O)(2)(O-1/2)(2) environments. Indeed, Mo-95 NMR data suggest that the majority of the molybdenum species are four-coordinated. However, the presence of additional six-coordinate molybdenum in the MAS NMR spectra indicates that the structure of these glasses may be more complicated and may additionally involve sharing of network modifier oxide between the network formers phosphorus and molybdenum. This latter hypothesis is further supported by Na-23{P-31} rotational echo double resonance (REDOR) data, which clearly reveal that the magnetic dipole-dipole interactions between P-31 and Na-23 are increasingly diminished with increasing molybdenum content. The partial transfer of modifier from the phosphate to the molybdate network former implies a partial repolymerization of the phosphate species, resulting in the formation of Q(nMo)((3)) species and accounting for the observed increase in the glass transition temperature with increasing MoO3 content that is observed in the composition range 0 <= x <= 45. Glasses with MoO3 contents beyond x = 45 show decreased thermal and crystallization stability. Their structure is characterized by isolated phosphate species [most likely of the P(OMo)(4) type] and molybdenum oxide clusters with a large extent of Mo-O-Mo connectivity.

Functional and structural analysis of two fibrinogen-activating enzymes isolated from the venoms of Crotalus durissus terrificus and Crotalus durissus collilineatus

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

Modeling of pre-regulator boost ZCS interleaved operating in critical conduction mode and with high power factor

This paper presents a new pre-regulator boost operating in the boundary area between the continuous and discontinuous conduction modes of the boost inductor current, where the switches and boost diode performing zero-current commutations during its turn-off, eliminating the disadvantages related to the reverse recovery losses and electromagnetic interference problems of the boost diode when operating in the continuous conduction mode. Additionally, the interleaving technique is applied in the power cell, providing a significant input current ripple reduction. It should be noticed that the main objective of this paper is to present a complete modeling for the converter operating in the critical conduction mode, allowing an improved design procedure for interleaved techniques with high input power factor, a complete dynamic analysis of the structure, and the possibility of implementing digital control techniques in closed loop.

Small-angle x-ray scattering study of the structural evolution of the drying of sonogels with the liquid phase exchanged by acetone

The structural evolution on the drying of wet sonogels of silica with the liquid phase exchanged by acetone, obtained from tetraethoxisilane sonohydrolysis, was studied in situ by small-angle x-ray scattering (SAXS). The periods associated to the structural evolution as determined by SAXS are in agreement with those classical ones established on basis of the features of the evaporation rate of the liquid phase in the obtaining of xerogels. The wet gel can be described as formed by primary particles (microclusters), with characteristic length a ∼ 0.67 nm and surface which is fractal, linking together to form mass fractal structures with mass fractal dimension D=2.24 in a length scale ξ∼6.7 nm. As the network collapses while the liquid/vapor meniscus is kept out of the gel volume, the mass fractal structure becomes more compacted by increasing D and decreasing ξ, with smoothing of the fractal surface of the microclusters. The time evolution of the density of the wet gels was evaluated exclusively from the SAXS parameters ξ, D, and a. The final dried acetone-exchanged gel presents Porod's inhomogeneity length of about 2.8 nm and apparently exhibits an interesting singularity D →3, as determined by the mass fractal modeling used to fit the SAXS intensity data for the obtaining of the parameters ξ and D.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB®/SIMULINK®

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®/SIMULINK® models to structural VHDL-AMS descriptions. The tool developed, named MS 2SV, reads a SIMULINK® 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 System Vision™. To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB®/ SIMULINK®. The VHDL-AMS code generated automatically by MS 2SV, (MATLAB®/SIMULINK® to System Vision™), was then simulated in the System Vision™. 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.

Biophysical and Structural Characterization of the Recombinant Human eIF3L

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

Modeling of piezoelectric energy harvesting considering the dependence of the rectifier circuit

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Artificial Immune Systems Applied to the Analysis of Structural Integrity of a Building

This paper presents the application of artificial immune systems for analysis of the structural integrity of a building. Inspired by a biological process, it uses the negative selection algorithm to perform the identification and characterization of structural failure. This paper presents the application of artificial immune systems for analysis of the structural integrity of a building. Inspired by a biological process, it uses the negative selection algorithm to perform the identification and characterization of structural failure. This methodology can assist professionals in the inspection of mechanical and civil structures, to identify and characterize flaws, in order to perform preventative maintenance to ensure the integrity of the structure and decision-making. In order to evaluate the methodology was made modeling a two-story building and several situations were simulated (base-line condition and improper conditions), yielding a database of signs, which were used as input data for the negative selection algorithm. The results obtained by the present method efficiency, robustness and accuracy.

Structural properties of beds packed with agro-industrial solid by-products applicable for solid-state fermentation: Experimental data and effects on process performance

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)