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.

Do brazilian states engage in the fiscal war of ports? An empiric study of tax competition and an analysis of a natural experiment: the brazilian senate resolution 13/2012

O fim do ano de 2014 marcou o segundo aniversário da Resolução 13/2012 (R13) do Senado brasileiro. Grosso modo, R13 constituiu-se de um normativo do Senado cujo objetivo era o de por um fim na Guerra Fiscal dos Portos (FWP), uma competição fiscal entre os estados que se dá através da concessão de benefícios fiscais sobre operações interestaduais com mercadorias importadas de modo a atrair empresas importadoras para o território do estado concedente. R13 diminuiu o nível da tributação sobre tais operações, esperando com isso diminuir os lucros auferidos e a propensão das firmas de aceitarem tais regimes especiais de incentivação fiscal. Nada obstante, R13 gerou uma grande discussão sobre se os benefícios da atração de investimentos para um estado em particular superariam ou não os custos que esse estado incorreria em renunciar receitas tributárias em razão concessão desses benefícios fiscais. O objetivo do presente trabalho é o de dar uma contribuição a essa discussão, testando se um comportamento de interação estratégica entre estados, tal como aquele que supostamente ocorre no contexto da FWP, de fato emerge dos dados de importação coletados de janeiro de 2010 a maio de 2015, e, também, testando se a R13 de fato afetou tal comportamento de interação estratégica. Utiliza-se aqui um modelo de econometria espacial, no qual se especifica uma matriz de pesos que agrega o nível de importação das jurisdições concorrentes, organizando os dados em um painel de efeitos fixos. Os resultados sugerem que existe um comportamento de interação estratégica entre os estados e que a R13 de fato impactou tal comportamento.

Potassium Leaching as Affected by Soil Texture and Residual Fertilization in Tropical Soils

Potassium (K) leaching is affected by soil texture and available K, among other factors. In this experiment, effects of soil texture and K availability on K distribution were studied in the presence of roots, with no excess water. Soils from two 6-year field experiments on a sandy clay loam and a clay soil fertilized yearly with 0, 60, 120, and 180 kg ha-1 of K2O were accommodated in pots that received 90 kg ha-1 of K2O. Soybean was grown up to its full bloom (R2). Under field conditions, K leaching below the arable layer increased with K rates, but the effect was less noticeable in the clay soil. Potassium leaching in a sandy clay loam soil was related to soil K contents from prior fertilizations. With no excess water, in the presence of soybean roots, K distribution in the profile was significant in the lighter textured soil but was not apparent on the heavier textured soil.

Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis

Eukaryotic translation initiation factor 5A (eIF5A) is a protein that is highly conserved and essential for cell viability. This factor is the only protein known to contain the unique and essential amino acid residue hypusine. This work focused on the structural and functional characterization of Saccharomyces cerevisiae eIF5A. The tertiary structure of yeast eIF5A was modeled based on the structure of its Leishmania mexicana homologue and this model was used to predict the structural localization of new site-directed and randomly generated mutations. Most of the 40 new mutants exhibited phenotypes that resulted from eIF-5A protein-folding defects. Our data provided evidence that the C-terminal alpha-helix present in yeast eIF5A is an essential structural element, whereas the eIF5A N-terminal 10 amino acid extension not present in archaeal eIF5A homologs, is not. Moreover, the mutants containing substitutions at or in the vicinity of the hypusine modification site displayed nonviable or temperature-sensitive phenotypes and were defective in hypusine modification. Interestingly, two of the temperature-sensitive strains produced stable mutant eIF5A proteins - eIF5A(K56A) and eIF5A(Q22H,L93F)- and showed defects in protein synthesis at the restrictive temperature. Our data revealed important structural features of eIF5A that are required for its vital role in cell viability and underscored an essential function of eIF5A in the translation step of gene expression.

Determination of the numerical parameters of a continuous damage model for the structural analysis of clay brick masonry

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

Biomechanical and histologic analysis in aortic endoprosthesis using fibrin glue

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

Molecular characterization and phylogenetic analysis of JussuMP-I: A RGD-P-III class hemorrhagic metalloprotease from Bothrops jararacussu snake venom

Snake venom metalloproteases (SVMPs) embody zinc-dependent multidomain enzymes responsible for a relevant pathophysiology in envenomation. including local and systemic hemorrhage. The molecular features responsible for hemorrhagic potency of SVMPs have been associated with their multidomains structures which can target these proteins them to several receptors of different tissues and cellular types. BjussuMP-I. a SVMP isolated from the Bothrops jararacussu venom, has been characterized as a P-III hemorrhagic metalloprotease. The complete cDNA sequence of BjussuMP-I with 1641bp encodes open reading frames of 547 amino acid residues, which conserve the common domains of P-III high molecular weight hemorrhagic metalloproteases: (i) pre-pro-peptide, (ii) metalloprotease, (iii) disintegrin-like and (iv) rich cysteine domain. BjussuMP-I induced lyses in fibrin clots and inhibited collagen- and ADP-induced platelet aggregation. We are reporting, for the first time, the primary structure of an RGD-P-III class snake venom metalloprotease. A phylogenetic analysis of the BjussuMP-1 metalloprotease/catalytic domain was performed to get new insights into the molecular evolution of the metalloproteases. A theoretical molecular model of this domain was built through folding recognition (threading) techniques and refined by molecular dynamics simulation. Then, the final BjussuMP-I catalytic domain model was compared to other SVMPs and Reprolysin family proteins in order to identify eventual structural differences, which could help to understand the biochemical activities of these enzymes. The presence of large hydrophobic areas and some conserved surface charge-positive residues were identified as important features of the SVMPs and other metalloproteases. (C) 2006 Elsevier B.V. All rights reserved.

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

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

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

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

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

Joint Experimental and Theoretical Analysis of Order Disorder Effects in Cubic BaZrO3 Assembled Nanoparticles under Decaoctahedral Shape

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

Simulation and economic analysis of bovine sex selection

A simulation model implemented in the programming software Delphi XE® was applied to evaluate sex selection in bovine. The hypothesis under investigation was that a dynamic model with stochastic and deterministic elements could detect the sexed semen technique to minimize pregnancy cost and to determine the adequate number of recipients required for in vivo (ET) and in vitro embryo production (IVP) in the proposed scenarios. Sex selection was compared through semen sexed using flow cytometry (C1) and density gradient centrifugation techniques (C2) in ET and IVP. Sensibility analyses were used to identify the adequate number of recipients for each scenario. This number was reinserted into the model to determine the biological and financial values that maximized ET and IVP using sexed semen (C1M and C2M). New scenarios showed that the density gradient technique minimized pregnancy cost based on the proposed scenarios. In addition, the adequate number of recipients (ET - C1M - 115 and C2M - 105)/(IVP - C1M - 145 and C2M - 140) per donor used was determined to minimize the pregnancy cost in all scenarios.

Quantitative analysis of mineral content in enamel using laboratory microtomography and microhardness analysis. - art. no. 631823

This study evaluates laboratory microtomography and microhardness analysis for quantifying the mineral content of bovine enamel. Fifty enamel blocks were submitted individually for 5 days to a pH-cycling model at 37 degrees C and remained in the remineralizing solution for 2 days. The blocks were treated twice daily for 1 min with NaF dentifrices (Placebo, 275, 550, 1,100 mu g F/g and Crest (R)) diluted in deionized water. Surface microhardness changes (%SMH) and mineral loss (Delta Z) were then calculated. Laboratory microtomography was also used to measure total mineral lost (LMM). Pearson's correlation (p < 0.05) was used to determine the relationship between different methods of analysis and dose-response between treatments. Dentifrice fluoride concentration and %SMH and Delta Z were correlated (p < 0.05). There was a positive relationship (p < 0.05) when comparing LMM vs. Delta Z; a negative relationship (p < 0.05) was found for %SMH vs. LMM and %SMH vs. Delta Z. Therefore, both mineral quantification techniques provide adequate precision for studying the bovine enamel-pH-cycling demineralization/remineralization model.

Application of the modified Cam-Clay model to a residual soil

The modified Cam - Clay model was used to model experimental results of a saturated residual sandy soil from Sao Carlos - SP. Triaxial compression tests were performed using Bishop - Wesley cell with internal transducers to measure axial and radial strains. It was observed that the model fairly fitted experimental results, specially the principal stress difference at critical state. In general it was observed a good qualitative agreement between experimental and predicted strain values, considering compression or expansion of the samples. However, in all the stress path used, but 100 degrees and 140 degrees, the model yielded strains larger than that measured in the tests.