Using linear algebra for protein structural comparison and classification.

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Genesis and classification of soils from subtropical mountain regions of Southern Brazil.

Soils formed in high mountainous regions in southern Brazil are characterized by great accumulation of organic matter (OM) in the surface horizons and variation in the degree of development. We hypothesized that soil properties and genesis are influenced by the interaction of parent materials and climate factors, which differ depending on the location along the altitudinal gradient. The goal of this study was to characterize and classify the soil, evaluate soil distribution, and determine the interactive effects of soil-forming factors in the subtropical mountain regions in Santa Catarina state. Soil samples were collected in areas known for wine production, for a total of 38 modal profiles. Based on morphological, physical, and chemical properties, soils were evaluated for pedogenesis and classified according to the Brazilian System of Soil Classification, with equivalent classes in the World Reference Basis (WRB). The results indicated that pedogenesis was strongly influenced by the parent material, weather, and relief. In the areas where basic effusive rocks (basalt) were observed, there was formation of extensive areas of clayey soils with reddish color and higher iron oxide contents. There was a predominance of Nitossolos Vermelhos and Háplicos (Nitisols), Latossolos Vermelhos (Ferralsols), and Cambissolos Háplicos (Cambisols), highlighting the pedogenetic processes of eluviation, illuviation of clay, and latosolization in conditions of year-long, large-volume, well-distributed rainfall and stability of land forms. In areas with acid effusive rocks (rhyodacites), medial or clayey soils were observed with lower iron oxide content, invariably acidic, and with low base content. For these soils, relief promoted substantial removal of material, resulting in intense rejuvenation, with a predominance of Cambissolos Háplicos (Cambisols) and lesser occurrence of Nitossolos Brunos (Nitisols) and Neossolos Litólicos (Leptosols). Soils formed from sedimentary rocks also tended to be more acidic, but with higher sand content, and the soils identified were Cambissolos Háplicos and Húmicos (Cambisols). Cluster analysis separated the soil profiles into three groups: the first and largest was formed by profiles originating from sedimentary rocks and rhyodacites; the second, smaller group was formed by four profiles in the Água Doce region (acidic rocks); and the third was formed by profiles derived from basalt. Discriminant analysis was effective in grouping soil classes. Thus, the study highlighted the importance of geology in the formation of soils in this landscape associated with climate and relief.

Numeric model to estimate pesticide deposition and losses from aerial spraying.

Pesticides applications have been described by many researches as a very inefficient process. In some cases, there are reports that only 0.02% of the applied products are used for the effective control of the problem. The main factor that influences pesticides applications is the droplet size formed on spraying nozzles. Many parameters affects the dynamic of the droplets, like wind, temperature, relative humidity, and others. Small droplets are biologically more active, but they are affected by evaporation and drift. On the other hand, the great droplets do not promote a good distribution of the product on the target. In this sense, associated with the risk of non target areas contamination and with the high costs involved in applications, the knowledge of the droplet size is of fundamental importance in the application technology. When sophisticated technology for droplets analysis is unavailable, is common the use of artificial targets like water-sensitive paper to sample droplets. On field sampling, water-sensitive papers are placed on the trials where product will be applied. When droplets impinging on it, the yellow surface of this paper will be stained dark blue, making easy their recognition. Collected droplets on this papers have different kinds of sizes. In this sense, the determination of the droplet size distribution gives a mass distribution of the material and so, the efficience of the application of the product. The stains produced by droplets shows a spread factor proportional to their respectives initial sizes. One of methodologies to analyse the droplets is a counting and measure of the droplets made in microscope. The Porton N-G12 graticule, that shows equaly spaces class intervals on geometric progression of square 2, are coulpled to the lens of the microscope. The droplet size parameters frequently used are the Volumetric Median Diameter (VMD) and the Numeric Median Diameter. On VMD value, a representative droplets sample is divided in two equal parts of volume, in such away one part contains droplets of sizes smaller than VMD and the other part contains droplets of sizes greater that VMD. The same process is done to obtaining the NMD, which divide the sample in two equal parts in relation to the droplets size. The ratio between VMD and NMD allows the droplets uniformity evaluation. After that, the graphics of accumulated probability of the volume and size droplets are plotted on log scale paper (accumulated probability versus median diameter of each size class). The graphics provides the NMD on the x-axes point corresponding to the value of 50% founded on the y-axes. All this process is very slow and subjected to operator error. So, in order to decrease the difficulty envolved with droplets measuring it was developed a numeric model, implemented on easy and accessfull computational language, which allows approximate VMD and NMD values, with good precision. The inputs to this model are the frequences of the droplets sizes colected on the water-sensitive paper, observed on the Porton N-G12 graticule fitted on microscope. With these data, the accumulated distribution of the droplet medium volumes and sizes are evaluated. The graphics obtained by plotting this distributions allow to obtain the VMD and NMD using linear interpolation, seen that on the middle of the distributions the shape of the curves are linear. These values are essential to evaluate the uniformity of droplets and to estimate the volume deposited on the observed paper by the density (droplets/cm2). This methodology to estimate the droplets volume was developed by 11.0.94.224 Project of the CNPMA/EMBRAPA. Observed data of herbicides aerial spraying samples, realized by Project on Pelotas/RS county, were used to compare values obtained manual graphic method and with those obtained by model has shown, with great precision, the values of VMD and NMD on each sampled collector, allowing to estimate a quantities of deposited product and, by consequence, the quantities losses by drifty. The graphics of variability of VMD and NMD showed that the quantity of droplets that reachs the collectors had a short dispersion, while the deposited volume shows a great interval of variation, probably because the strong action of air turbulence on the droplets distribution, enfasizing the necessity of a deeper study to verify this influences on drift.