Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpa (hER alpha) and beta (hER beta). Because the levels and relative proportion of hER alpha and hER beta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hER alpha and hER beta. Significant statistical coefficients were obtained (hER alpha, q(2) = 0.76; hER beta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hER alpha and hER beta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design or novel hER modulators with improved selectivity.

Inhibition of Mycobacterium tuberculosis tyrosine phosphatase PtpA by synthetic chalcones: Kinetics, molecular modeling, toxicity and effect on growth

Tuberculosis (TB) is a major cause of morbidity and mortality throughout the world, and it is estimated that one-third of the world`s population is infected with Mycobacterium tuberculosis. Among a series of tested compounds, we have recently identified five synthetic chalcones which inhibit the activity of M. tuberculosis protein tyrosine phosphatase A (PtpA), an enzyme associated with M. tuberculosis infectivity. Kinetic studies demonstrated that these compounds are reversible competitive inhibitors. In this work we also carried out the analysis of the molecular recognition of these inhibitors on their macromolecular target, PtpA, through molecular modeling. We observed that the predominant determinants responsible for the inhibitory activity of the chalcones are the positions of the two methoxyl groups at the A-ring, that establish hydrogen bonds with the amino acid residues Arg17, His49, and Thr12 in the active site of PtpA, and the substitution of the phenyl ring for a 2-naphthyl group as B-ring, that undergoes p stacking hydrophobic interaction with the Trp48 residue from PtpA. Interestingly, reduction of mycobacterial survival in human macrophages upon inhibitor treatment suggests their potential use as novel therapeutics. The biological activity, synthetic versatility, and low cost are clear advantages of this new class of potential tuberculostatic agents. (C) 2010 Elsevier Ltd. All rights reserved.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

DIAGNOSTIC TECHNIQUES OF LOCAL INFLUENCE IN SPATIAL ANALYSIS OF SOYBEAN YIELD

Modeling of spatial dependence structure, concerning geoestatistics approach, is an indispensable tool for fixing parameters that define this structure, applied on interpolation of values in places that are not sampled, by kriging techniques. However, the estimation of parameters can be greatly affected by the presence of atypical observations on sampled data. Thus, this trial aimed at using diagnostics techniques of local influence in spatial linear Gaussians models, applied at geoestatistics in order to evaluate sensitivity of maximum likelihood estimators and restrict maximum likelihood to small perturbations in these data. So, studies with simulated and experimental data were performed. Those results, obtained from the study of real data, allowed us to conclude that the presence of atypical values among the sampled data can have a strong influence on thematic maps, changing, therefore, the spatial dependence. The application of diagnostics techniques of local influence should be part of any geoestatistic analysis, ensuring that the information from thematic maps has better quality and can be used with greater security by farmers.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

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

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

Analysis of Structure and Tendencies of Qualified Immigrant Workforce on the Swedish Labor Market

The purpose of this paper is to make quantitative and qualitative analysis of foreign citizens who may participate on the Swedish labor market (in text refers to as ‘immigrants’). This research covers the period 1973-2005 and gives prediction figures of immigrant population, age and gender structure, and education attainment in 2010. To cope with data regarding immigrants from different countries, the population was divided into six groups. The main chapter is divided into two parts. The first part specifies division of immigrants into groups by country of origin according to geographical, ethnical, economical and historical criteria. Brief characteristics and geographic position, dynamic and structure description were given for each group; historical review explain rapid changes in immigrant population. Statistical models for description and estimation future population were given. The second part specifies education and qualification level of the immigrants according to international and Swedish standards. Models for estimating age and gender structure, level of education and professional orientation of immigrants in different groups are given. Inferences were made regarding ethnic, gender and education structure of immigrants; the distribution of immigrants among Swedish counties is given. Discussion part presents the results of the research, gives perspectives for the future brief evaluation of the role of immigrants on the Swedish labor market.

The Secret Aria on Shame : An Analysis of Narrative Structure and Theme in Coetzee's "Diary of a Bad Year"

Coetzee’s last novel Diary of a Bad Year (2007) has an intriguing triple-voiced narrative structure and deals with the grey area of shame. The narrative is divided between a writer, his written contribution to a book called “Strong Opinions”, and his secretary’s thoughts about both the opinions in the manuscript and her employer’s circumstances. This essay explores the relation between form and theme in Diary of a Bad Year; to see in what way these two fundamental elements of the novel intervene and support each other. By doing so the narrative structure is read through Freud’s structural model of personality, whereby each narrator’s voice is related to the notions of the super-ego, the ego and the id. In other words, this essay argues that the specific threefold narrative structure in Diary of a Bad Year, by reflecting the interrelated parts of human identity, helps in creating and developing the theme of shame, which only exists connected to the human psyche. This connection in turn gives special meaning to the entire narratology of the novel.

A Study On The Flow Characteristics Influenced By Hydraulic Structure At A Channel Junction

Natural riversare consisting of various networks as junction andstreams. And sediment and erosion are occurred by specific stream condition. When flood season,large discharge flew in the river and river bed changed by high flow velocity. Especially junction area’s flow characteristics are very complex. The purpose of this study is to analyze the flow characteristics in channel junction, which are most influenced by large discharge like flooding and input water from tributary. We investigate the flow characteristics by using hydrodynamics and transport module in MIKE 3 FM. MIKE 3 FM model was helpful tool to analysis 3D hydrodynamics, erosion and sediment effect from channel bed. We analyze flow characteristics at channel junction. Also we consider hydraulic structures like a bridge pier which is influencing flow characteristics like a flow velocity, water level, erosion and scour depth in channel bed. In the model, we controlled discharge condition according to Froude Number and reflect various grain diameter size and flow ratio change in main stream and tributary. In the result, flow velocity, water level, erosion and sediment depth are analyzed. Additionally, we suggest a these result relationship with equations. This study will help the understand flow characteristics and influence of hydraulic structure in channel junction. Acknowledgments This research was supported by a grant (12-TI-C01) from Advanced Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.

RWater – A Cyber Enabled Tool For Hydrologic Modeling And Analysis

Existing distributed hydrologic models are complex and computationally demanding for using as a rapid-forecasting policy-decision tool, or even as a class-room educational tool. In addition, platform dependence, specific input/output data structures and non-dynamic data-interaction with pluggable software components inside the existing proprietary frameworks make these models restrictive only to the specialized user groups. RWater is a web-based hydrologic analysis and modeling framework that utilizes the commonly used R software within the HUBzero cyber infrastructure of Purdue University. RWater is designed as an integrated framework for distributed hydrologic simulation, along with subsequent parameter optimization and visualization schemes. RWater provides platform independent web-based interface, flexible data integration capacity, grid-based simulations, and user-extensibility. RWater uses RStudio to simulate hydrologic processes on raster based data obtained through conventional GIS pre-processing. The program integrates Shuffled Complex Evolution (SCE) algorithm for parameter optimization. Moreover, RWater enables users to produce different descriptive statistics and visualization of the outputs at different temporal resolutions. The applicability of RWater will be demonstrated by application on two watersheds in Indiana for multiple rainfall events.

Country factors and the dynamic modeling of capital structure : an empirical study of latin american firms

Desenvolvemos modelos de ajuste parcial e de duration para testar a relevância de fatores específicos de países na determinação da estrutura de capital de empresas listadas nas bolsas de valores brasileira, chilena e mexicana. Utilizamos dados em painel, em um período que se estende do quarto trimestre de 1996 ao segundo trimestre de 2010, abrangendo 4403 observações relacionadas a 139 empresas diferentes. Os resultados obtidos sugerem que a dinâmica da estrutura de capital varia por país e que idiossincrasias locais são determinantes-chave dos níveis de alavancagem das empresas. Não detectamos comportamento explicado pela Teoria de Trade Off entre as empresas brasileiras, chilenas e mexicanas, o que indica que teorias alternativas possam comandar os processos de decisão de financiamento dos gestores latino americanos.

Analysis an development of a prototype based on media wiki and semantic media wiki integrated with a design modeling that allows modeling of organizations based on demo

In a world where organizations are ever more complex the need for the knowledge of the organizational self is a growing necessity. The DEMO methodology sets a goal in achieving the specification of the organizational self capturing the essence of the organization in way independent of its implementation and also coherent, consistent, complete, modular and objective. But having such organization self notion is of little meaning if this notion is not shared by the organization actors. To achieve this goal in a society that has grown attached to technology and where time is of utmost importance, using a tool such as a semantic Wikipedia may be the perfect way of making the information accessible. However, to establish DEMO methodology in such platform there is a need to create bridges between its modeling components and semantic Wikipedia. It’s in that aspect that our thesis focuses, trying to establish and implement, using a study case, the principles of a way of transforming the DEMO methodology diagrams in comprehensive pages on semantic Wikipedia but keeping them as abstract as possible to allow expansibility and generalization to all diagrams without losing any valuable information so that, if that is the wish, those diagrams may be recreated from the semantic pages and make this process a full cycle.

Criteria for analysis of the structure of electronic scientific journals

This paper is the result of the Masters dissertation studying the role and history of scientific communication, especially the changes that have occurred after the appearance of electronic communication and computer networks. This study showed that hypertext systems are increasingly being used in the scientific and academic world in the production of electronic journals; this makes it possible for the user to rapidly access information in their area. However, these systems need to be improved to help the user during search and access to information. Both printed journals migrating to electronic media, and the exclusively electronic journals should present the current quality indicators. The attempt was made to discover whether characteristics related to printed journals are being maintained in their electronic counterparts. For this, a prototype model was developed to analyze the structure of electronic scientific journals; it composes 14 criteria expressing aspects of quality for these journals. It includes elements of Website Information Architecture and those already in place in printed scientific journals in order to ensure that basic functions - archiving and dissemination - are maintained in electronic publishing. Each criterion consists of variables, which measure the maintenance of these functions both in the migrating printed journals and the exclusively electronic ones. This prototype model was used to analyze Ciência da Informação On-line and DataGramaZero - Revista de Ciência da Informação. Results indicate that this model is able to find out if the basic functions of archiving and dissemination are being maintained in electronic journals. Therefore, its implementation is justified in electronic journals. The model can help librarians, authors, and users of electronic journals to identify quality journals, and assist editors in developing their projects. The material from the study may be included in the preservice and inservice education of Information Science professionals and to support editors of scientific journals.

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.

Modeling and analysis of artificial neural networks applied in operations research

Artificial neural networks are dynamic systems consisting of highly interconnected and parallel nonlinear processing elements. Systems based on artificial neural networks have high computational rates due to the use of a massive number of these computational elements. Neural networks with feedback connections provide a computing model capable of solving a rich class of optimization problems. In this paper, a modified Hopfield network is developed for solving problems related to operations research. The internal parameters of the network are obtained using the valid-subspace technique. Simulated examples are presented as an illustration of the proposed approach. Copyright (C) 2000 IFAC.