Hypoxia Enhances the Angiogenic Potential of Human Dental Pulp Cells

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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.

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

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Synchronization and Non-Smooth Dynamical Systems

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluating craniofacial asymmetry with digital cephalometric images and cone-beam computed tomography

Introduction: The aim of this study was to evaluate craniofacial asymmetry by using 2-dimensional (2D) poster-oanterior cephalometric images, 3-dimensional cone-beam computed tomography (CBCT), and physical measurements (gold standard). Methods: Ten dry human skulls were assessed, and radiopaque markers were placed on 17 skeletal landmarks. Twenty linear measurements were taken on each side to compare the right and left sides and to compare these measurements with the physical measurements made with a digital caliper. To acquire the 2D posteroanterior radiographs, an Extraoral Phosphor Storage Plate (Air Techniques, Chicago, Ill) was used as the image receptor with a Eureka x-ray-Duocon Machlett unit (Machlett Laboratores, Chicago, Ill). Three-dimensional imaging data were acquired from a CB MercuRay (Hitachi Medical, Tokyo, Japan). Results: on average, the right side was larger than the left for most of the 20 distances evaluated in the digital 2D and the CBCT images, and there was poor agreement between the digital 2D images and the physical measurements (kappa = 0.0609) and almost perfect agreement (kappa = 0.92) between the CBCT and physical measurements when individual measurements were considered. Conclusions: Human skulls, with no apparent asymmetry, had some differences between the right and left sides, with dominance for the right side but with no clinical significance. CBCT can better evaluate craniofacial morphology when compared with digital 2D images. (Am J Orthod Dentofacial Orthop 2011; 139: e523-e531)

The Schrodinger and Pauli-Dirac Oscillators in Noncommutative Phase Space

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Influência do substrato e do tipo de fertilizante na aclimatação de mudas de bananeira 'Prata-Anã'

Objetivando-se avaliar a influência do substrato e tipo de fertilizante na aclimatação de mudas de bananeira 'Prata-Anã', provenientes de micropropagação, foi instalado um experimento em blocos casualizados, no esquema fatorial 5 x 3, com quatro repetições. Os substratos utilizados foram: S1 - Terra de subsolo + casca de arroz carbonizada + substrato comercial Rendimax Floreira®; S2 - Terra de subsolo + casca de arroz carbonizada + composto orgânico Organifol®; S3 - Terra de subsolo + casca de arroz carbonizada + composto orgânico Organifol® 9% SiO; S4 - substrato comercial Technes Vivatto®; S5 - Areia grossa + casca de arroz carbonizada + Rendimax Floreira®, todos na proporção 1:1:1 (v/v/v). Os fertilizantes utilizados foram: SF - sem fertilizante; FLL - fertilizante de liberação lenta, 14-14-14 (5,0 kg m-3) misturado ao substrato; e FLN - fertilizante de liberação normal, 14-14-14 (5,0 kg m-3) aplicado em cobertura, 30 dias após o plantio. As mudas foram plantadas em sacos de polietileno quando apresentavam quatro a cinco folhas, sendo mantidas em viveiro com 50% de sombreamento. Foram feitas medidas de altura, diâmetro do colo e número de folhas, e determinada a massa seca das mudas. As diferenças químicas das misturas utilizadas como substrato, juntamente com o tipo de fertilizante utilizado, proporcionaram crescimento diferenciado das mudas. O substrato S4 pode ser utilizado sem fertilização. Os substratos S2 e S3 devem ser utilizados com fertilizante de liberação normal ou lenta de nutrientes, e S1 e S5, sendo pobres em nutrientes, com fertilizante de liberação lenta.

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 and functional characterization of neuwiedase, a nonhemorrhagic fibrin(ogen)olytic metalloprotease from Bothrops neuwiedi snake venom

A fibrino(geno)lytic nonhemorrhagic metalloprotease (neuwiedase) was purified from Bothrops neuwiedi snake venom by a single chromatographic step procedure on a CM-Sepharose column, Neuwiedase represented 4.5% (w/w) of the crude desiccated venom, with an approximate Mr of 20,000 and pI 5.9, As regards the amino acid composition, neuwiedase showed similarities with other metalloproteases, with high proportions of Asx, Glx, Leu, and Ser, Atomic absorption spectroscopy showed that one mole of Zn2+ and one mole of Ca2+ were present per mole olf protein. The cDNA encoding neuwiedase was isolated by RT-PCR from venom gland RNA, using oligonucleotides based on the partially determined amino-acid sequences of this metalloprotease. The fall sequence contained approximately 594 bp, which codified the 198 amino acid residues with an estimated molecular weight of 22,375. Comparison of the nucleotide and amino acid sequences of neuwiedase with those of other snake venom metalloproteases showed a high level of sequential similarity, Neuwiedase has two highly conserved characteristics sequences H(142)E(143)XXH(146)XXG(140)XXH(152) and C164I165M166. The three-dimensional structure of neuwiedase was modeled based on the crystal structure of Crotalus adamanteus Adamalysin II. This model revealed that the zinc binding site region showed a I high structural similarity with other metalloproteases,, the proteolyitc specificity, using the B beta-chain of oxidized insulin as substrate, was shown to be directed to the Ala(14)-Leu(15) and Tyr(16)-Leu(17) peptide bonds which were preferentially hydrolyzed. Neuwiedase is a A alpha,B beta fibrinogenase, Its activity upon the A alpha chain of fibrinogen was detected within 15 min of incubation. The optimal temperature and pH for the degradation of both A alpha and B beta chains were 37 degrees C and 7.4-8.0, respectively. This activity was inhibited by EDTA and 1,10-phenantroline, Neuwiedase also showed proteolytic activity upon fibrin and some components of the extracellular matrix. However, it did not show TAME esterase activity and was not able to inhibit platelet aggregation. (C) 2000 Academic Press.

Light and scanning electron microscopic study of the palatine mucosa of nine-banded armadillo (Dasypus novemcinctus)

The three-dimensional structure of the lamina propria of the hard and soft palatine mucosa of the nine-banded armadillo was observed by scanning electron microscopy. Sodium hydroxide cell maceration method was applied to demonstrate the architecture of the connective tissue papillae. The palatine mucosa of the armadillo had a triangular shape and measured appr. 6.5 cm length. The hard palate showed 9 transverse palatine plicae while the soft palate was smooth. In the 10% NaOH treated specimens, the lamina propria of the hard palatine mucosa showed numerous connective tissue papillae with a general finger-like shape. These structures were composed by a meshwork of collagen fibers arranged in several directions. on the other hand, the connective tissue papillae of the soft palate mucosa were scattered and small. Numerous openings of glandular ducts with circular or elliptical shape were located in the interplicae area and in the soft palate.

Bulk photochromism in a tungstate-phosphate glass: A new optical memory material?

In this work, we present a new photochromic tungstate based glass which have both absorption coefficient and refractive index modified under laser exposure. The photosensitive effect is superficial under ultraviolet (UV) irradiation but occurs in the entire volume of the glass under visible irradiation. The effect can be obtained in any specific point inside the volume using an infrared femtosecond laser. In addition, the photosensitive phenomenon can be erased by specific heat treatment. This glass can be useful to substitute actual data storage supports and is a promising material for 3-dimensional (3D) and holographic optical storage.

Comparison of accuracy between compression- and injection-molded complete dentures

Statement of problem. A clinically significant incisal pin opening may occur after processing complete dentures if a compression molding technique is used. To recover the proper vertical dimension of occlusion, a time-consuming occlusal adjustment is necessary that often destroys the anatomy of the artificial teeth. A new injection molding process claims to produce dentures that require few, if any, occlusal adjustments in the laboratory after processing.Purpose. This laboratory study compared incisal pin opening, dimensional accuracy, and laboratory working time for dentures fabricated by this new injection system with dentures constructed by the conventional compression molding technique.Material and methods. Two groups of 6 maxillary and 6 mandibular dentures were evaluated as follows: group 1 (control), Lucitone 199, compression molded with a long cure cycle; and group 2, Lucitone 199, injection molded with a long cure. Incisal pin opening was measured with a micrometer immediately after deflasking. A computerized coordinate measuring machine was used to measure dimensional accuracy of 3-dimensional variations in selected positions of artificial teeth in 4 stages of denture fabrication. Analysis of variance (ANOVA) and t tests were performed to compare the groups.Results. A significant difference was found in pin opening between groups (t test). Horizontal dimensional changes evaluated with repeated measures ANOVA revealed no significant differences between groups. However, analysis of vertical dimensional changes disclosed significant differences between the groups. There was no appreciable difference in laboratory working time for flasking and molding denture bases between the injection and compression molding techniques when polymethyl methacrylate resin was used.Conclusion. The injection molding method produced a significantly smaller incisal pin opening over the standard compression molding technique. The injection molding technique, using polymethyl methacrylate, was a more accurate method for processing dentures. There were no appreciable differences in laboratory working time between the injection and compression molding techniques.

Molecular model for the binary complex of uropepsin and pepstatin

The three-dimensional structure of human uropepsin complexed with pepstatin has been modelled using human pepsin as a template. Uropepsin is an aspartic proteinase from the urine, produced in the form of pepsinogen A in the gastric mucosa. The structure is bilobal, consisting of two predominantly beta -sheet lobes which, as observed in other aspartic proteinases, are related by a pseudo twofold axis. A structural comparison between binary complexes of pepsin:pepstatin and uropepsin:pepstatin is discussed. (C) 2001 Academic Press.

Structural and functional characterization of myotoxin I, a Lys49 phospholipase A(2) homologue from Bothrops moojeni (Caissaca) snake venom

Myotoxin-I (MjTX-I) was purified to homogeneity from the venom of Bothrops moojeni by ion-exchange chromatography on CM-Sepharose. Its molecular weight, estimated by SDS-PAGE, was 13,400 (reduced) or 26,000 (unreduced). The extinction coefficient (E-1.0 cm(1.0 mg/ml)) of MjTX-I was 1.145 at lambda = 278 nm, pH 7.0, and its isoelectric point was 8.2 at ionic strength mu = 0.1. When lyophilized and stored at 4 degrees C, dimeric, trimeric, and pentameric forms of the protein were identified by SDS-PAGE. This heterogeneous sample could be separated into three fractions by gel filtration on Sephadex 6-50. The fractions were analyzed by isoelectric focusing, immunoelectrophoresis, and amino acid composition, which indicated that heterogeneity was the result of different levels of self-association. Protein sequencing indicated that MjTX-I is a Lys49 myotoxin and consists of 121 amino acids (M-r = 13,669), containing a high proportion of basic and hydrophobic residues. It shares a high degree of sequence identity with other Lys49 PLA(2)-like myotoxins, but shows a significantly lower identity with catalytically active Asp49 PLA(2)s. The three-dimensional structure of MjTX-I was modeled based on the crystal structures of three highly homologous Lys49 PLA(2)-like myotoxins. This model showed that the amino acid substitutions are conservative, and mainly the beta-wing region, and the C-terminal extended random coil. MjTX-I displays local myotoxic and edema-inducing activities in mice, and is lethal by intraperitoneal injection, with an LD50 value of 8.5 +/- 0.8 mg/kg, In addition, it is cytotoxic to myoblasts/ myotubes in culture, and disrupts negatively charged liposomes. In comparison with the freshly prepared dimeric sample, the more aggregated forms showed significantly reduced myotoxic activity. However, the edema-inducing activity of MjTX-I was independent of molecular association. Phospholipase A(2) activity on egg yolk, as well as anticoagulant activity, were undetectable both in the native and in the more associated forms. His, Tyr, and Trp residues of the toxin were chemically modified by specific reagents. Although the myotoxic and lethal activities of the modified toxins were reduced by these treatments, neither its edema-inducing or Liposome-disrupting activities were significantly altered. Rabbit antibodies to native MjTX-I cross-reacted with the chemically modified forms, and both the native and modified MjTX-I preparations were recognized by antibodies against the C-terminal region 115-129 of myotoxin II from B. asper, a highly Lys49 PLA(2)-homologue with high sequencial similarity. (C) 2000 Academic Press.

Methods to estimate the number of surface nucleation sites on glass particles

Based on the Johnson-Mehl-Avrami-Kolmogorov (JMAK) theory, we propose two new models to describe the crystallisation kinetics of glass particles and use them to determine the density of nucleation sites, N(s), on glass powders. We tested these models with sintered compacts of diopside glass particles using sinter-crystallisation treatments at 825 degrees C (T(g)similar to 727 degrees C), that covered from null to almost 100% crystallised volume time fraction. We measured and compared the evolution of the crystallised volume fractions by optical microscopy and x-ray diffraction. Then we fit our expressions to experimental data using Ns and R (the average particle radius) as adjustable parameters. For comparison, we also fit to our data existing expressions that describe the crystallised volume fraction in glass powders. We demonstrate that all the methods allow one to estimate N(s) with reasonable accuracy. For our ground and water washed diopside glass powder, N(s) is between 10(10)-10(11) sites.m(-2). The reasonable agreement between experimental and adjusted R confirms the consistency of all five models tested. However, one of our equations does not require taking into account the change of crystallisation mode from 3-dimensional to 1-dimensional, and this is advantageous.