Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity

Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe-SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 angstrom and T. cruzi at 1.9 angstrom resolution, and that from P. falciparum at a higher resolution (2.0 angstrom) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity.

Organizations redesign and building of information systems

Develop software is still a risky business. After 60 years of experience, this community is still not able to consistently build Information Systems (IS) for organizations with predictable quality, within previously agreed budget and time constraints. Although software is changeable we are still unable to cope with the amount and complexity of change that organizations demand for their IS. To improve results, developers followed two alternatives: Frameworks that increase productivity but constrain the flexibility of possible solutions; Agile ways of developing software that keep flexibility with less upfront commitments. With strict frameworks, specific hacks have to be put in place to get around the framework construction options. In time this leads to inconsistent architectures that are harder to maintain due to incomplete documentation and human resources turnover. The main goals of this work is to create a new way to develop flexible IS for organizations, using web technologies, in a faster, better and cheaper way that is more suited to handle organizational change. To do so we propose an adaptive object model that uses a new ontology for data and action with strict normalizing rules. These rules should bound the effects of changes that can be better tested and therefore corrected. Interfaces are built with templates of resources that can be reused and extended in a flexible way. The “state of the world” for each IS is determined by all production and coordination acts that agents performed over time, even those performed by external systems. When bugs are found during maintenance, their past cascading effects can be checked through simulation, re-running the log of transaction acts over time and checking results with previous records. This work implements a prototype with part of the proposed system in order to have a preliminary assessment its feasibility and limitations.

Parasitismo de percevejos-praga do maracujazeiro no Brasil por Hexacladia smithii Ashmead (Hymenoptera: Encyrtidae)

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

Efecto Insecticida del Extracto de Semillas de Neem (Azadirachta indica A. Juss) sobre Collaria scenica Stal (Hemiptera: Miridae)

This work was developed with the objetive to evaluate the insecticidal effect of the Neem (Azadirachta indica A. Juss) seeds against grass bug nymphs Collaria scenica Stal. For that, an extract was prepared from green fruits of Neem by rotaevaporacion. The extract was diluted in three ppm concentrations corresponding to treatments. Using thin-layer chromatography we identified the presence of Azaridactina. DCA essay was carried out with 4 treatments and 5 repetitions that included the three extract concentrations and a control. In each repetition were used 15 nymphs, randomly placed in plastic boxes with food and the corresponding concentration. Every day an extract application was made and recorded mortality percentage, number of exuviae and number of individuals who came to adulthood in each treatment. The results were analyzed using Kruskal-Wallis and Games-Howell for each variable. The three concentrations of Neem seed extract had a negative effect on the development of the bugs. The more concentrated treatment (250 ppm) was the most effective, showing a 97% mortality, fewer exuvias and and fewer adults in the end of the experiment.

Occurrence of Atopozelus opsimus preying on nymphs and adults of Glycaspis brimblecombei

The stink bugs genus Atopozelus (Hemiptera: Reduviidae) is native in the Americas, with five described species of which only three have been recorded in Brazil. In August 2007, Eucalyptus camaldulensis leaves infested by lerp psyllid were collected and taken to the Forest Pest Biological Control Laboratory situated at São Paulo State University. A small green stink bug, identified as Atopozelus opsimus Elkins (Hemiptera: Reduviidae) that fed on nymphs and adult psyllids, was found on the leaves. These stink bugs presented phytophagy, omnivory and ability in opening the lerp (shell) that protect the psyllid. A. opsimus has demonstrated unusual particularities, different from many biological control agents found in nature; this predator thus deserves more attention for its potential to be evaluated.

Velocidade do fluxo de ar em barra de pulverização no controle químico de Anticarsia gemmatalis, Hübner e percevejos na cultura da soja

A lagarta Anticarsia gemmatalis (Hübner) e os percevejos fitófagos são pragas importantes na cultura da soja no Brasil. Este trabalho objetivou avaliar o controle desses insetos após o tratamento com inseticidas, sob diferentes velocidades do fluxo de ar junto à barra de pulverização nessa cultura. O experimento foi desenvolvido em Botucatu, na cultura da soja [Glycine max (L.) Merrill], var. Conquista (safra 2007/08), no delineamento experimental de blocos ao acaso (quatro velocidades do fluxo de ar: 0, 9, 11 e 29 km h-1), mais testemunha, totalizando cinco tratamentos e quatro repetições. No estádio de desenvolvimento vegetativo (V10) realizou uma aplicação do inseticida deltametrina na dosagem de 6,5 g do i.a. ha-1 para o controle de lagartas e no estádio de desenvolvimento reprodutivo (R6) aplicou o inseticida tiametoxam associado com lambda-cialotrina na dosagem de 25,38 + 19,08 g do i.a. ha-1 para o controle de percevejos. A aplicação foi feita com um pulverizador Advanced Vortex 2000, com pontas de pulverização jato cônico JA2, conferindo um volume de calda de 200 L ha-1. As avaliações antes e após a aplicação foram realizadas pelo método de batidas no pano. Avaliaram-se os danos causados por percevejos, considerando-se a porcentagem de danos às sementes, ao poder germinativo e à produtividade. No geral, o número médio de lagartas e percevejos foram significativamente menores nas parcelas tratadas em relação ao obtido na testemunha. Não houve diferença de produtividade entre os tratamentos. A porcentagem de emergência e sementes picadas por percevejos foram significativamente menores nos tratamentos que receberam o controle em comparação à testemunha.

Desenvolvimento de Holhymenia histrio (Fabr.) (Hemiptera: Coreidae) em frutos de cinco genótipos de maracujazeiro (Passiflora spp.)

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

Estudo de ovos de quatro espécies do gênero Meccus (Hemiptera, Reduviidae, Triatominae), vetores da doença de Chagas

The objective of this work was to analyze the morphological, morphometrical, and histological characteristics of eggs of four triatomine bugs species still not studied, in order to understand phylogenetic aspects and to facilitate parameters used in taxonomy, with the purpose of a specific and generic characterization of these vectors in public health. The eggs of each species had come from the collections of the Laboratory of Triatomine bugs and Culicid mosquitoes of the Faculdade de Saúde Pública - USP (Faculty of Public Health/USP). The morphologic studies were carried out through optic microscopy (OM) and scanning electronic microscopy (SEM). The eggs were measured with the help of the digital paquimeter Starrett® 727. In relation to histological measures, Microtome Leica RM 2145® was used. Similarities were evidenced in the exocorial architecture of the eggs when they were studied by OM and SEM. This similarity among the eggs suggests a recent speciation, probably derived from common ancestry, representing a monophyletic group. Some structures were also detected by the histological cuts. The study has contributed to the magnification and recognition in generic and specific terms of the Triatominae subfamily. These new data will be able to subsidize a better understanding to determine roles for each vector species and to facilitate parameters to be used in taxonomy.

Estimação clássica e Bayesiana em modelos de sobrevida com fração de cura

In Survival Analysis, long duration models allow for the estimation of the healing fraction, which represents a portion of the population immune to the event of interest. Here we address classical and Bayesian estimation based on mixture models and promotion time models, using different distributions (exponential, Weibull and Pareto) to model failure time. The database used to illustrate the implementations is described in Kersey et al. (1987) and it consists of a group of leukemia patients who underwent a certain type of transplant. The specific implementations used were numeric optimization by BFGS as implemented in R (base::optim), Laplace approximation (own implementation) and Gibbs sampling as implemented in Winbugs. We describe the main features of the models used, the estimation methods and the computational aspects. We also discuss how different prior information can affect the Bayesian estimates

Avaliação da contribuição de desenvolvedores para projetos de software usando mineração de repositórios de software e mineração de processos

Software Repository Mining (MSR) is a research area that analyses software repositories in order to derive relevant information for the research and practice of software engineering. The main goal of repository mining is to extract static information from repositories (e.g. code repository or change requisition system) into valuable information providing a way to support the decision making of software projects. On the other hand, another research area called Process Mining (PM) aims to find the characteristics of the underlying process of business organizations, supporting the process improvement and documentation. Recent works have been doing several analyses through MSR and PM techniques: (i) to investigate the evolution of software projects; (ii) to understand the real underlying process of a project; and (iii) create defect prediction models. However, few research works have been focusing on analyzing the contributions of software developers by means of MSR and PM techniques. In this context, this dissertation proposes the development of two empirical studies of assessment of the contribution of software developers to an open-source and a commercial project using those techniques. The contributions of developers are assessed through three different perspectives: (i) buggy commits; (ii) the size of commits; and (iii) the most important bugs. For the opensource project 12.827 commits and 8.410 bugs have been analyzed while 4.663 commits and 1.898 bugs have been analyzed for the commercial project. Our results indicate that, for the open source project, the developers classified as core developers have contributed with more buggy commits (although they have contributed with the majority of commits), more code to the project (commit size) and more important bugs solved while the results could not indicate differences with statistical significance between developer groups for the commercial project

TAXONOMIC POSITION of GUIRATINGIA MENDESI (MEGADESMIDAE) and THE EVOLUTION of PERMIAN ENDEMIC BIVALVE FAUNA of THE PARANA BASIN, BRAZIL

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

Phosphorylation of Histone H3S10 in Animal Chromosomes: Is There a Uniform Pattern?

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Karyotype and spermatogenesis in Triatoma lenti (Hemiptera: Triatominae), a potential Chagas vector

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

Activation of Ca2+-independent membrane-damaging activity in Lys49-phospholipase A(2) promoted by amphiphilic molecules

Association of class-II phospholipase A(2) (PLA(2)) with aggregated phospholipid substrate results in elevated levels of the Ca2+-dependent hydrolytic activity. The Asp49 residue participates in coordination of the Ca2+ ion cofactor, however, in Lys49-PLA(2) homologues (Lys49-PLA(2)S), substitution of the Asp49 by Lys results in loss of Ca2+ binding and lack of detectable phospholipid hydrolysis. Nevertheless, Lys49-PLA2S cause Ca2+-independent damage of liposome membranes. Bothropstoxin-I is a homodimeric Lys49-PLA(2) from the venom of Bothrops jararacussu, and in fluorescent marker release and dynamic light scattering experiments with DPPC liposomes we demonstrate activation of the Ca2+-independent membrane damaging activity by similar to4 molecules of sodium dodecyl sulphate (SDS) per protein monomer. Activation is accomparlied by significant changes in the intrinsic tryptophan fluorescence emission (ITFE) and near UV circular dichroism (UVCD) spectra of the protein. Subsequent binding of 7-10 SDS molecules results in further alterations in the ITFE and far UVCD spectra. Reduction in the rate of N-bromosuccinimide modification of Trp77 at the dimer interface suggests that initial binding of SDS to this region accompanies the activation of the membrane damaging activity. 1-anilinonaphthalene-8-sulphonic acid binding studies indicate that subsequent SDS binding to the active site is concomitant with the second structural transition. These results provide insights in the structural basis of amphiphile/protein coupling in class-II PLA(2)s. (C) 2004 Published by Elsevier B.V.

The interaction between heparin and Lys49 phospholipase A(2) reveals the natural binding of heparin on the enzyme

We have studied at a molecular level the interaction of heparins on bothropstoxin-1 (BthTx-1), a phospholipase A(2) toxin. The protein was monitored using gel filtration chromatography, dynamic light scattering (DLS), circular dichroism (CD), attenuated total reflectance Fourier transform infrared (ATR-FTIR) and intrinsic tryptophan fluorescence emission (ITFE) spectroscopy. The elution profile of the protein presents a displacement of the protein peak to larger complexes when interacting with higher concentration of heparin. The DLS results shows two R-h at a molar ratio of 1, one to the distribution of the protein and the second for the action of heparin on BthTx-I structures, and a large distribution with the increase of protein. The interaction is accompanied by significant changes in the CD spectra, showing two common features: a decrease in signal at 208 nm (3 and 6 kDa heparins) and an isodichroic point near 226 nm (3 kDa heparin). FTIR spectra indicate that only a few amino acid residues are involved in this interaction. Alterations in the ITFE by binding heparins suggest that the initial binding occurs on the ventral face of BthTx-1. Together, these results add an experimental and structural basis on the action mechanism of the heparins over the phospholipases A(2) and provide a molecular model to elucidate the interaction of the enzyme-heparin complex at a molecular level. (c) 2005 Elsevier B.V. All rights reserved.