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.

Chronopotentiometric stripping analysis using gold electrodes, an efficient technique for mercury quantification in natural waters

This paper proposes a simple methodology for mercury quantification in natural water by stripping chronopotentiometry at constant current, using gold (film) electrodes constructed from recordable CDs in stationary cell. The proposed method allows the direct measurement of labile mercury in natural waters. To quantify total mercury, a robust and low cost UV irradiation system was developed for the degradation of organic constituents of water. The proposed system presents such advantages as excellent sensitivity, low cost, versatility, and smaller dimensions (portability for on-field applications) when compared with other techniques (ICP, GFAAS, fluorimetry) traditionally utilized for mercury quantification. A large linear region of responses was observed, situated over the range 0.02 - 200 μ g L-1. Various experimental parameters were optimized and the system allowed quantifications in natural samples, with detection limit of 8 ng L-1 and excellent reproducibility (RSD of 1.4% for 48 repetitive measurements using a 10 μ g L-1 mercury solution). Different metal ions were evaluated, including copper, as possible interferences on stripping mercury signals. Applications of the new method were demonstrated for the analysis of certified and groundwater samples spiked with a known amount of mercury and for the quantification of methylmercury in synthetic oceanic water, originally utilized for fishes contamination experiment.

Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus

Crotamine is one of four major components of the venom of the South American rattlesnake Crotalus durissus terrificus. Similar to its counterparts in the family of the myotoxins, it induces myonecrosis of skeletal muscle cells. This paper describes a new NMR structure determination of crotamine in aqueous solution at pH 5.8 and 20 degrees C, using standard homonuclear (1)H NMR spectroscopy at 900 MHz and the automated structure calculation software ATNOS/CANDID/DYANA. The automatic NOESY spectral analysis included the identification of a most likely combination of the six cysteines into three disulfide bonds, i.e. Cys4-Cys36, Cys11-Cys30 and Cys18-Cys37; thereby a generally applicable new computational protocol is introduced to determine unknown disulfide bond connectivities in globular proteins. A previous NMR structure determination was thus confirmed and the structure refined. Crotamine contains an alpha-helix with residues 1-7 and a two-stranded anti-parallel beta-sheet with residues 9-13 and 34-38 as the only regular secondary structures. These are connected with each other and the remainder of the polypeptide chain by the three disulfide bonds, which also form part of a central hydrophobic core. A single conformation was observed, with Pro13 and Pro21 in the trans and Pro20 in the cis-form. The global fold and the cysteine-pairing pattern of crotamine are similar to the beta-defensin fold, although the two proteins have low sequence homology, and display different biological activities. (c) 2005 Elsevier Ltd. All rights reserved.

Periodontal status in smokers and never-smokers: Clinical findings and real-time polymerase chain reaction quantification of putative periodontal pathogens

Background: Smoking is a well-known risk factor for destructive periodontal disease, but its relationship with periodontal status and subgingival microbiota remains unclear. Inherent limitations of microbiological methods previously used may partly explain these mixed results, and real-time polymerase chain reaction (PCR) has been presented as a valid alternative. The aim of the present study was to investigate the clinical condition and microbiological profile of patients with chronic periodontitis as related to the habit of smoking.Methods: Fifty patients (33 to 59 years old), 25 smokers and 25 never-smokers, constituted the sample. The visible plaque index (VPI), gingival bleeding index (GBI), bleeding on probing (BOP), periodontal probing depth (PD), clinical attachment loss (CAL), and gingival crevicular fluid (GCF) volume were recorded. Real-time PCR quantified Porphyromonas gingivalis, Micromonas micros, Dialister pneumosintes, Actinobacillus actinomycetemcomitans and total bacteria in subgingival samples.Results: Smokers and never-smokers showed similar values for VPI, GBI, and BOP. Smokers had deeper PD in buccal/lingual sites and higher CAL independently of the tooth surface. The GCF volume was smaller in smokers, independent of the PD. Similar amounts of total bacteria and P. gingivalis were observed for both groups. Significantly higher numbers of D. pneumosintes and M. micros were present in smokers and associated with moderate and deep pockets. When heavy smokers were considered, higher counts of total bacteria, M. micros, and D. pneumosintes were observed.Conclusions: Smoking seems to have a detrimental impact on the periodontal status and microbiological profile of patients with periodontitis. Compared to never-smokers, smokers had deeper pockets, greater periodontal destruction, and higher counts of some putative periodontal pathogens.

Detection and quantification of antibodies to Newcastle disease virus in ostrich and rhea sera using a liquid phase blocking enzyme-linked immunosorbent assay

A liquid phase blocking ELISA (LPB-ELISA) was adapted for the detection and quantification of antibodies to Newcastle disease virus. Sera from vaccinated and unvaccinated commercial flocks of ostriches (Struthio camelus) and rheas (Rhea americana) were tested. The purified and nonpurified virus used as the antigen and the capture and detector antibodies were prepared and standardized for this purpose. The hemagglutination-inhibition (HI) test was regarded as the reference method, the cutoff point for the LPB-ELISA was determined by a two-graph receiver operating characteristic analysis. The LPB-ELISA titers regressed significantly (P < 0.0001) on the HI titers with a high correlation coefficient (r = 0.875). The two tests showed good agreement ( = 0.82; P < 0.0001), relative sensitivity (90.91%) and specificity (91.18%), and accuracy (91.02%), suggesting that they are interchangeable.

Parentage testing in alpacas (Vicugna pacos) using semi-automated fluorescent multiplex PCRs with 10 microsatellite markers

The aim of this study was to assess and apply a microsatellite multiplex system for parentage determination in alpacas. An approach for parentage testing based on 10 microsatellites was evaluated in a population of 329 unrelated alpacas from different geographical zones in Peru. All microsatellite markers, which amplified in two multiplex reactions, were highly polymorphic with a mean of 14.5 alleles per locus (six to 28 alleles per locus) and an average expected heterozygosity (H-E) of 0.8185 (range of 0.698-0.946). The total parentage exclusion probability was 0.999456 for excluding a candidate parent from parentage of an arbitrary offspring, given only the genotype of the offspring, and 0.999991 for excluding a candidate parent from parentage of an arbitrary offspring, given the genotype of the offspring and the other parent. In a case test of parentage assignment, the microsatellite panel assigned 38 (from 45 cases) offspring parentage to 10 sires with LOD scores ranging from 2.19 x 10(+13) to 1.34 x 10(+15) and Delta values ranging from 2.80 x 10(+12) to 1.34 x 10(+15) with an estimated pedigree error rate of 15.5%. The performance of this multiplex panel of markers suggests that it will be useful in parentage testing of alpacas.

Quantification of Peroxide Ion Passage in Dentin, Enamel, and Cementum After Internal Bleaching With Hydrogen Peroxide

The aim of this study was to evaluate the amount of peroxide passage from the pulp chamber to the external enamel surface during the internal bleaching technique. Fifty bovine teeth were sectioned transversally 5 mm below the cemento-enamel junction (CEJ), and the remaining part of the root was sealed with a 2-mm layer of glass ionomer cement. The external surface of the samples was coated with nail varnish, with the exception of standardized circular areas (6-mm diameter) located on the enamel, exposed dentin, or cementum surface of the tooth. The teeth were divided into three experimental groups according to exposed areas close to the CEJ and into two control groups (n=10/group), as follows: GE, enamel exposure area; GC, cementum exposed area; GD, dentin exposed area; Negative control, no presence of internal bleaching agent and uncoated surface; and Positive control, pulp chamber filled with bleaching agent and external surface totally coated with nail varnish. The pulp chamber was filled with 35% hydrogen peroxide (Opalescence Endo, Ultradent). Each sample was placed inside of individual flasks with 1000 mu L of acetate buffer solution, 2 M (pH 4.5). After seven days, the buffer solution was transferred to a glass tube, in which 100 mu L of leuco-crystal violet and 50 mu L of horseradish peroxidase were added, producing a blue solution. The optical density of the blue solution was determined by spectrophotometer and converted into microgram equivalents of hydrogen peroxide. Data were submitted to Kruskal-Wallis and Dunn-Bonferroni tests (alpha=0.05). All experimental groups presented passage of peroxide to the external surface that was statistically different from that observed in the control groups. It was verified that the passage of peroxide was higher in GD than in GE (p<0.01). The GC group presented a significantly lower peroxide passage than did GD and GE (p<0.01). It can be concluded that the hydrogen peroxide placed into the pulp chamber passed through the dental hard tissues, reaching the external surface and the periodontal tissue. The cementum surface was less permeable than were the dentin and enamel surfaces.

Bayesian and multivariate methods applied to favorability quantification in recôncavo Basin and Ribeira Belt, Brazil

A methodology to define favorable areas in petroleum and mineral exploration is applied, which consists in weighting the exploratory variables, in order to characterize their importance as exploration guides. The exploration data are spatially integrated in the selected area to establish the association between variables and deposits, and the relationships among distribution, topology, and indicator pattern of all variables. Two methods of statistical analysis were compared. The first one is the Weights of Evidence Modeling, a conditional probability approach (Agterberg, 1989a), and the second one is the Principal Components Analysis (Pan, 1993). In the conditional method, the favorability estimation is based on the probability of deposit and variable joint occurrence, with the weights being defined as natural logarithms of likelihood ratios. In the multivariate analysis, the cells which contain deposits are selected as control cells and the weights are determined by eigendecomposition, being represented by the coefficients of the eigenvector related to the system's largest eigenvalue. The two techniques of weighting and complementary procedures were tested on two case studies: 1. Recôncavo Basin, Northeast Brazil (for Petroleum) and 2. Itaiacoca Formation of Ribeira Belt, Southeast Brazil (for Pb-Zn Mississippi Valley Type deposits). The applied methodology proved to be easy to use and of great assistance to predict the favorability in large areas, particularly in the initial phase of exploration programs. © 1998 International Association for Mathematical Geology.

Quantification of sex pheromone from Anocentor nitens by gas chromatography-mass spectrometry-selected ion monitoring

Two highly sensitive and selective methods based on gas chromatography coupled to mass spectrometry (GC-MS) in the selected ion monitoring (SIM) mode have been developed for the quantification of 2,6-dichlorophenol (2,6-DCP), a sex pheromone of the tick females of Anocentor nitens. Standard addition method and calibration curve techniques using 5-bromine-4-hydroxy-3- methoxybenzaldehyde (5-BrV) as internal standard (IS) afforded detection limit of 0.1ngml-1. The calibration curve was linear over the concentration range from 0.5 to 500ngml-1 for 2,6-DCP. Results show that the concentration range of sex pheromone in the extracts samples was 1.08-10.35ngml-1. The methods developed provided reliable procedures to determine amounts of 2,6-DCP present in ticks. © 2003 Elsevier B.V. All rights reserved.

GPS performance in the quantification of integrated water vapor in Amazonian regions

The Amazonian regions are characterized by large space-time variability in the humidity fields due to the intense convective process in those areas associated with the great humidity potential generated by high temperatures. An experiment denominated RACCI/DRY-TO-WET (RAdiation, Cloud, and Climate Interactions in the Amazonia during the DRY-TO-WET Transition Season) was carried out in the Brazilian Amazonian Region in 2002. The IWV values from GPS and other techniques, such as radiosondes, radiometer and humidity sounding satellites were used in this experiment to supply subsidies to evaluate the aerosols influence in the associated processes modifications to seasonality of atmospheric water vapor. Those regions are one of the most humid of the planet, where IWV (Integrated Water Vapor) average values are in the order of 50 kg/m2. As according the literature the IWV quantification using GPS has not been explored in those circumstances, the objective this paper is to present the preliminary results obtained in the evaluation of the GPS performance in Amazonian Regions when comparing with other techniques. The tendency measurement values indicated that the IWV values from GPS tend to be larger than those from radiosondes and smaller than those from radiometer. On the other hand, IWV values from GPS are very close of the average values supplied by radiosondes and radiometer. Due to the great amount of atmospheric water vapor existent in this region, the results obtained in the experiment in percentile terms are quite better than those found in the literature, which are around of 10%.

Automated extraction of road network from medium-and high-resolution images

This paper presents an automatic methodology for road network extraction from medium-and high-resolution aerial images. It is based on two steps. In the first step, the road seeds (i.e., road segments) are extracted using a set of four road objects and another set of connection rules among road objects. Each road object is a local representation of an approximately straight road fragment and its construction is based on a combination of polygons describing all relevant image edges, according to some rules embodying road knowledge. Each road seed is composed by a sequence of connected road objects in which each sequence of this type can be geometrically structured as a chain of contiguous quadrilaterals. In the second step, two strategies for road completion are applied in order to generate the complete road network. The first strategy is based on two basic perceptual grouping rules, i.e., proximity and collinearity rules, which allow the sequential reconstruction of gaps between every pair of disconnected road segments. This strategy does not allow the reconstruction of road crossings, but it allows the extraction of road centerlines from the contiguous quadrilaterals representing connected road segments. The second strategy for road completion aims at reconstructing road crossings. Firstly, the road centerlines are used to find reference points for road crossings, which are their approximate positions. Then these points are used to extract polygons representing the contours of road crossings. This paper presents the proposed methodology and experimental results. © Pleiades Publishing, Inc. 2006.