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.

Fast chromatographic determination of polycyclic aromatic hydrocarbons in aerosol samples from sugar cane burning

Sugar cane burning in Brazil causes remarkable amounts of organic compounds to be emitted amongst which the polycyclic aromatic hydrocarbons (PAHs) represent serious health hazards. Therefore, 24-h aerosol samples (< 10 mum aerodynamic diameter) were collected in Araraquara city (São Paulo state) during the harvest season using a Hi-Vol sampler. PAHs were recovered using an Accelerated Solvent Extractor and analyzed by low-pressure gas chromatography-ion trap mass spectrometry (LP-GC-IT-MS). The fully automated extraction process was performed in less than 25 min with a solvent consumption of approximately 20 ml. The use of a deactivated 0.6 m x 0. 10 mm i.d. restrictor coupled to a 10 m wide-bore analytical column allowed most of the 16 PAHs in EPA's priority list to be identified and quantified in only 13 min. Concentrations of PAHs in Nraraquara aerosols ranged between 0.5 and 8.6 ng m(-3). (C) 2003 Elsevier B.V. All rights reserved.

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.

Action of auxins, boron and harvest season on the rooting of kiwi fruit stem cuttings (Actinidia chinensis Pl cv Monty)

Action of auxins on the rooting of stem cuttings of kiwi (Actinidia chinensis P. cv Monty). This work studies the effects of some synthetic auxins and B in the rooting of kiwi (Actinidia chinensis Planch cv Monty) stem cuttings. The treatments used were as follows: T1 (H2O); T2 (NAA 300 ppm); T3 (IBA 300 ppm); T4 (NAA 300 ppm + B); T5 (IBA 300 ppm + B); T6 (NAA 0,5%-talc) and T7 (IBA 0,5%-talc), applied to the bases of the cuttings. These were then placed in rooting dishes with pure vermiculite in a misty nebulization chamber until collection day (120 days). The evaluation of auxin and boric acid effects on kiwi stem cuttings were made based on the following observations: 1. The percentage of rooted stem cuttings; 2. reducing sugars and total sugar analyses (in g/100 g of dry matter); and 3. tryptophan analyses (in mu g/100 mg of dry matter). The results show that summer is the best season for rooting Actinidia chinensis Planch cv Monty stem cuttings. The use of IBA talc 0,5% on the bases of the cuttings shamed positive results too.

Greenhouse gas balance due to the conversion of sugarcane areas from burned to green harvest in Brazil

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

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.

Greenhouse gas balance due to the conversion of sugarcane areas from burned to green harvest, considering other conservationist management practices

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Use of Natural Products for Post-Harvest Preservation of 'Vega' Cut Roses

Use of natural products as floral preservatives has helped to reduce the indiscriminate use of chemical products in flower preservation. In this study, we tested the ability of certain natural products to maintain the quality and to increase the commercial durability of 'Vega' cut roses. We employed a randomized factorial design with six post-harvest treatments and four evaluation dates. The following treatments were tested: 1) distilled water; 2) methyl jasmonate (350 mu M) applied in a four-hour pulse; 3) methyl jasmonate (500 mu M) spraying; 4) mint oil (100 ppm); 5) ginger oil (100 ppm); and 6) propolis (0.05%) as a maintenance solution. Flowers were kept at 20+/-2 degrees C and 67+/-3% RH. Physiological and qualitative evaluations were conducted. Natural products had a beneficial effect on the shelf life of the flowers. However, for all evaluated parameters, the methyl jasmonate spray was the most efficient treatment to maintain floral quality, resulting in less fresh-mass loss and a lower flower respiratory rate. Methyl jasmonate spray also improved the maintenance of coloration, relative water content and concentration of reducing sugars, thus extending the shelf life of roses.

Total and harvest-date yield of processing tomato cultivars

The productivity of 28 tomato cultivars was evaluated over three stages of harvest. The study was carried out during from June to December of 1999 in an open field at the experimental area of the Section of Olericulture and Aromatic Medicinal Plants, Department of Crop Production at FCAV-UNESP, Jaboticabal, SP, Brazil. The cultivars studied were H 7155, Hypeel, Andino, U 573, H 9036, IPA 6, H 9494, AG 33, Yuba, RPT 1294, AG 72, Pelmeech, Curico, Hypeel 45, RPT 1478, H 9492, H 9498, H 2710, Hitech 45, Halley, Botu 13, H 9553, U 646, NK 1570, AG 45, RPT 1095, RPT 1570, and PSX 37511. The experimental design was a randomized block design with four repetitions, with five plants per plot. Productivity was evaluated at three stages of harvest at 119, 149 and 179 days after seeding. There were no significant differences among the cultivars at the first harvest (119 days). The majority of the cultivars produced their highest yield at the second harvest; the most productive cultivars were Curicó and AG 72, which yielded 4.69 and 4.67 kg/plant, respectively, although they did not differ statistically from the cultivars Hypeel 45 (4.35 kg/plant) and H 9498 (4.16 kg/plant). Yields of the cultivars Andino and H 9494 were evenly distributed between the second and third harvests. At the third harvest, cultivar IPA 6 had the highest yield (2.9 kg/plant) and was statistically different from all other cultivars except H 9036 (2.34 kg). These two cultivars had the most delayed and concentrated maturity, making them suitable for mechanical harvesting, although at a later time. Cultivar AG 72 had the greatest total yield (5.76 kg/plant), but it was not statistically different from cultivars Hypeel 45 (5.43 kg), Curico (4.17 kg), H 9498 (4.83 kg), H 7155 (4.58 kg) and Halley (4.55 kg). All of the cultivars, with the exception of cultivars H 9036, IPA 6, Andino and H 9494 showed in the second harvest concentrated maturity, making it suitable for mechanical harvesting.

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.

Cone-beam computed tomography analysis of the apical third of curved roots after mechanical preparation with different automated systems

The present study evaluated by cone-beam computed tomography (CBCT) the apical canal transportation and centralizing ability of different automated systems after root canal preparation. The mesiobuccal canals of maxillary first molars (n=10 per group) were prepared with: GI - reciprocating system with K-Flexofile; GII - reciprocating system with NiTiFlex files; GIII - rotary system with K3 instruments; GIV - rotary system with RaCe instruments. CBCT scans were taken before and after biomechanical preparation up to a #40.02 diameter. Canal transportation was determined by measuring the smallest distance between the inner canal walls and the mesial and distal sides of the root. The centralization ability corresponded to the difference between the measurements from transportation evaluation, using the linear voxel to voxel method of analysis. The mean transportation was 0.06 ± 0.14 mm, with a tendency to deviate to the mesial side of the root (n=22), with no statistically significant difference among the groups (p=0.4153). The mean centralization index was 0.15 ± 0.65 also without statistically significant difference among the groups (p=0.0881). It may be concluded that apical canal transportation and centralization ability were not influenced by the type of mechanical movement and instruments used.

Fault section estimation in automated distribution substations

In this paper, a methodology based on Unconstrained Binary Programming (UBP) model and Genetic Algorithms (GAs) is proposed for estimating fault sections in automated distribution substations. The UBP model, established by using the parsimonious set covering theory, looks for the match between the relays' protective alarms informed by the SCADA system and their expected states. The GA is developed to minimize the UBP model and estimate the fault sections in a swift and reliable manner. The proposed methodology is tested by utilizing a real-life automated distribution substation. Control parameters of the GA are tuned to achieve maximum computational efficiency and reduction of processing time. Results show the potential and efficiency of the methodology for estimating fault section in real-time at Distribution Control Centers. ©2009 IEEE.

Optimal energy generation with biomass of sugarcane harvest

The aim of this work is the application of the Interior Point and Branch and Bound methods in multiobjective optimization models related to sugarcane harvest residual biomass. These methods showed their viability to help on choosing the sugarcane planting varieties, searching to optimize cost and energy balance of harvest residual biomass, which have conflitant objectives. These methods provide satisfactory results, with fair computing performance and reliable and consistent solutions to the analyzed models. © 2011 IEEE.

Pre-harvest sugarcane burning: Determination of emission factors through laboratory measurements

Sugarcane is an important crop for the Brazilian economy and roughly 50% of its production is used to produce ethanol. However, the common practice of pre-harvest burning of sugarcane straw emits particulate material, greenhouse gases, and tropospheric ozone precursors to the atmosphere. Even with policies to eliminate the practice of pre-harvest sugarcane burning in the near future, there is still significant environmental damage. Thus, the generation of reliable inventories of emissions due to this activity is crucial in order to assess their environmental impact. Nevertheless, the official Brazilian emissions inventory does not presently include the contribution from pre-harvest sugarcane burning. In this context, this work aims to determine sugarcane straw burning emission factors for some trace gases and particulate material smaller than 2.5μm in the laboratory. Excess mixing ratios for CO2, CO, NOX, UHC (unburned hydrocarbons), and PM2.5 were measured, allowing the estimation of their respective emission factors. Average estimated values for emission factors (g kg-1 of burned dry biomass) were 1,303 ± 218 for CO2, 65 ± 14 for CO, 1.5 ± 0.4 for NOX, 16 ± 6 for UHC, and 2.6 ± 1.6 for PM2.5. These emission factors can be used to generate more realistic emission inventories and therefore improve the results of air quality models. © 2012 by the authors; licensee MDPI, Basel, Switzerland.