Estrutura de um trecho de floresta Amazônica na bacia do alto rio Xingu

Este estudo apresenta a estrutura de florestas em Gaúcha do Norte-MT (13° 10'S e 53° 15' O), na borda sul-amazônica. Para o levantamento fitossociológico, três áreas amostrais de 1ha foram subdivididas em 50 parcelas de 10x20m, nas quais foram amostrados todos os indivíduos com perímetro à altura do peito (PAP) >15 cm. Para verificar a similaridade estrutural entre as áreas utilizou-se a Análise de Correspondência. As espécies indicadoras dos ambientes de interflúvio e das áreas sujeitas à inundação foram obtidas através do TWINSPAN e de um sistema de pesos. Concluiu-se que as florestas presentes na bacia do rio Pacuneiro pertencem à mesma unidade fitogeográfica, mas com subtipos florísticos e estruturais de acordo com a posição no relevo, a proximidade dos cursos d'água e o estrato analisado, apresentando predominância de algumas espécies, ou até mesmo possíveis endemismos, em determinados trechos ou estratos. A formação apresentou baixa diversidade alfa (2,91 a 3,50) e beta (3,62 a 3,86), o que não é comum em florestas amazônicas. Várias hipóteses podem explicar essa baixa diversidade, entre elas a baixa precipitação e a alta sazonalidade, o ambiente físico regional aparentemente homogêneo e favorável às espécies competidoras, ou os eventos históricos, relacionados à possível exploração por tribos indígenas ou à recente expansão dessas florestas sobre as áreas savânicas.

Agelaia MP-I: A peptide isolated from the venom of the social wasp, Agelaia pallipes pallipes, enhances insulin secretion in mice pancreatic islets

Peptides isolated from animal venoms have shown the ability to regulate pancreatic beta cell function. Characterization of wasp venoms is important, since some components of these venoms present large molecular variability, and potential interactions with different signal transduction pathways. For example, the well studied mastoparan peptides interact with a diversity of cell types and cellular components and stimulate insulin secretion via the inhibition of ATP dependent K + (K ATP) channels, increasing intracellular Ca 2+ concentration. In this study, the insulin secretion of isolated pancreatic islets from adult Swiss mice was evaluated in the presence of synthetic Agelaia MP-I (AMP-I) peptide, and some mechanisms of action of this peptide on endocrine pancreatic function were characterized. AMP-I was manually synthesized using the Fmoc strategy, purified by RP-HPLC and analyzed using ESI-IT-TOF mass spectrometry. Isolated islets were incubated at increasing glucose concentrations (2.8, 11.1 and 22.2 mM) without (Control group: CTL) or with 10 μM AMP-I (AMP-I group). AMP-I increased insulin release at all tested glucose concentrations, when compared with CTL (P < 0.05). Since molecular analysis showed a potential role of the peptide interaction with ionic channels, insulin secretion was also analyzed in the presence of 250 μM diazoxide, a K ATP channel opener and 10 μM nifedipine, a Ca 2+ channel blocker. These drugs abolished insulin secretion in the CTL group in the presence of 2.8 and 11.1 mM glucose, whereas AMP-I also enhanced insulin secretory capacity, under these glucose conditions, when incubated with diazoxide and nifedipine. In conclusion, AMP-I increased beta cell secretion without interfering in K ATP and L-type Ca 2+ channel function, suggesting a different mechanism for this peptide, possibly by G protein interaction, due to the structural similarity of this peptide with Mastoparan-X, as obtained by modeling. © 2012 Elsevier Ltd.

Estudo da relação estrutura/atividade para as ações neurotóxica/neuroprotetora das acilpoliaminotoxinas NSTX-3 e JSTX-3 em sistema nervoso central de ratos

Pós-graduação em Ciências Biológicas (Biologia Celular e Molecular) - IBRC

Análise da hidrofobicidade na evolução de proteínas

Pós-graduação em Biofísica Molecular - IBILCE

Persistência comportamental e topografia de controle de estímulos coerente em treino de discriminação simples e escolha condicional por identidade ao modelo com quatro escolhas em macacos-prego (Cebus apella)

Objetiva ensinar a três macacos-prego adultos jovens, um macho e duas fêmeas, experimentalmente ingênuos, relações condicionais de identidade (IDMTS) com quatro comparações, identificando e produzindo topografias de controle de estímulo supostamente facilitadoras da formação de relações de equivalência. Analisada a persistência comportamental, apoiando-se nas teorias da coerência de topografia de controle de estímulos e do momento comportamental, e nos estudos já realizados na Escola Experimental de Primatas. Os participantes foram treinados a tocar estímulos projetados na tela sensível de um computador acoplado a uma câmara experimental e passaram por: 1) Treino de discriminações simples simultâneas e mudanças de discriminações, no qual alternaram-se tentativas com uma e quatro escolhas, imitando o display de sessões de IDMTS; 2) Treino de IDMTS com quatro modelos e duas ou três comparações, alternando os estímulos com função de S-; 3) Treino de IDMTS com quatro comparações. O responder persistente do M21 nas mudanças de discriminações simples foi resolvido com a retirada do S+ anterior quando um novo estímulo passava a funcionar como S+. A semelhança estrutural entre as sessões de discriminação simples e IDMTS não foi suficiente para o estabelecimento de um responder sob controle do modelo. M18 e M21 chegaram ao desempenho de IDMTS, enquanto M20 passou por treino com exigência de razão randômica ao modelo e vem apresentando melhora gradual de desempenho.

Arcabouço para aprovisionamento de QoS e QoE em redes sem fio heterogêneas WiMAX/Wi-Fi com garantia de equidade entre vazões

Recentemente a sociedade está vivendo em meio a um aglomerado de dispositivos móveis com múltiplas interfaces sem fio que permitem que clientes móveis domésticos e corporativos solucionem problemas rotineiros no menor espaço de tempo e em diversas localizações. Por outro lado, a disponibilidade de diversas tecnologias de acesso sem fio como: Wi-Fi (Wireless Fidelity), WiMAX (Worldwide Interoperability for Microwave Access) e LTE (Long Term Evolution), proporcionam um cenário heterogêneo com diversas oportunidades de conectividade para o usuário de dispositivos com múltiplas interfaces. Alguns dos desafios atuais no contexto da concepção da então denominada NGN (Next Generation Networks) são o desenvolvimento de arcabouços e mecanismos que viabilizem tanto o suporte adequado à Qualidade de Serviço (QoS – Quality of Service) e à Qualidade de Experiência (QoE – Quality of Experience) para aplicações multimídia, quanto a garantia de equidade entre vazões de diferentes aplicações em ambiente heterogêneo. Esta dissertação propõe um arcabouço para o aprovisionamento de QoS e QoE em redes sem fio heterogêneas formada por redes WiMAX e Wi-Fi. Especificamente, nossa solução provê mapeamento estático de QoS entre as classes de serviços WiMAX e categorias de acesso Wi-Fi. Além disso, nossa proposta também combina funcionalidades de equidade entre vazões com a solução de mapeamento, a fim de alcançar um bom compromisso tanto para o operador da rede, quanto para o usuário, através de uma nova metodologia de coleta e calculo de vazão agregada e algoritmo de decisão de handover vertical. A avaliação quantitativa da proposta foi realizada através de modelos de simulação no ns-2 (Network Simulator). Os resultados de desempenho demonstram a eficiência da arquitetura em termos de métricas de QoS (vazão, vazão média e atraso) e QoE (PSRN - Peak Signal to Noise Ratio, SSIM - Structural Similarity Index e VQM - Video Quality Metric).

Uma abordagem híbrida e semiautomática para estimativa de regiões cobertas por nuvens e sombras em imagens de satélite: análise e avaliação

Os principais objetivos deste trabalho são propor um algoritmo eficiente e o mais automático possível para estimar o que está coberto por regiões de nuvens e sombras em imagens de satélite; e um índice de confiabilidade, que seja aplicado previamente à imagem, visando medir a viabilidade da estimação das regiões cobertas pelos componentes atmosféricos usando tal algoritmo. A motivação vem dos problemas causados por esses elementos, entre eles: dificultam a identificação de objetos de imagem, prejudicam o monitoramento urbano e ambiental, e desfavorecem etapas cruciais do processamento digital de imagens para extrair informações ao usuário, como segmentação e classificação. Através de uma abordagem híbrida, é proposto um método para decompor regiões usando um filtro passa-baixas não-linear de mediana, a fim de mapear as regiões de estrutura (homogêneas), como vegetação, e de textura (heterogêneas), como áreas urbanas, na imagem. Nessas áreas, foram aplicados os métodos de restauração Inpainting por suavização baseado em Transformada Cosseno Discreta (DCT), e Síntese de Textura baseada em modelos, respectivamente. É importante salientar que as técnicas foram modificadas para serem capazes de trabalhar com imagens de características peculiares que são obtidas por meio de sensores de satélite, como por exemplo, as grandes dimensões e a alta variação espectral. Já o índice de confiabilidade, tem como objetivo analisar a imagem que contém as interferências atmosféricas e daí estimar o quão confiável será a redefinição com base no percentual de cobertura de nuvens sobre as regiões de textura e estrutura. Tal índice é composto pela combinação do resultado de algoritmos supervisionados e não-supervisionados envolvendo 3 métricas: Exatidão Global Média (EGM), Medida De Similaridade Estrutural (SSIM) e Confiança Média Dos Pixels (CM). Finalmente, verificou-se a eficácia destas metodologias através de uma avaliação quantitativa (proporcionada pelo índice) e qualitativa (pelas imagens resultantes do processamento), mostrando ser possível a aplicação das técnicas para solucionar os problemas que motivaram a realização deste trabalho.

Definição de framework para a padronização de processos em um periódico científico com base em revisão da literatura e nos objetivos de desempenho

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Applying enhancement filters in the pre-processing of images of lymphoma

Lymphoma is a type of cancer that affects the immune system, and is classified as Hodgkin or non-Hodgkin. It is one of the ten types of cancer that are the most common on earth. Among all malignant neoplasms diagnosed in the world, lymphoma ranges from three to four percent of them. Our work presents a study of some filters devoted to enhancing images of lymphoma at the pre-processing step. Here the enhancement is useful for removing noise from the digital images. We have analysed the noise caused by different sources like room vibration, scraps and defocusing, and in the following classes of lymphoma: follicular, mantle cell and B-cell chronic lymphocytic leukemia. The filters Gaussian, Median and Mean-Shift were applied to different colour models (RGB, Lab and HSV). Afterwards, we performed a quantitative analysis of the images by means of the Structural Similarity Index. This was done in order to evaluate the similarity between the images. In all cases we have obtained a certainty of at least 75%, which rises to 99% if one considers only HSV. Namely, we have concluded that HSV is an important choice of colour model at pre-processing histological images of lymphoma, because in this case the resulting image will get the best enhancement.

Interaction of giant extracellular Glossoscolex paulistus hemoglobin (HbGp) with ionic surfactants: A MALDI-TOF-MS study

The giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) is constituted by approximately 144 subunits containing heme groups with molecular masses in the range of 16-19 kDa forming a monomer (d) and a trimer (abc), and around 36 non-heme structures, named linkers (L). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS) analysis was performed recently, to obtain directly information on the molecular masses of the different subunits from HbGp in the oxy-form. This technique demonstrated structural similarity between HbGp and the widely studied hemoglobin of Lumbricus terrestris (HbLt). Indeed, two major isoforms (d(1) and d(2)) of identical proportions with masses of 16,355+/-25 and 16,428+/-24 Da, respectively, and two minor isoforms (d(3) and d(4)) with masses around 16.6 kDa were detected for monomer d of HbGp. In the present work, the effects of anionic sodium dodecyl sulfate (SDS) and cationic cethyltrimethyl ammonium chloride (CTAC) on the oligomeric structure of HbGp have been studied by MALDI-TOF-MS in order to evaluate the interaction between ionic surfactants and HbGp. The data obtained with this technique show an effective interaction of cationic surfactant CTAC with the two isoforms of monomer d, d(1) and d(2), both in the whole protein as well as in the pure isolated monomer. The results show that up to 10 molecules of CTAC are bound to each isoform of the monomer. Differently, the mass spectra obtained for SDS-HbGp system showed that the addition of the anionic surfactant SDS does not originate any mass increment of the monomeric subunits, indicating that SDS-HbGp interaction is, probably, significantly less effective as compared to CTAC-HbGp one. The acid pI of the protein around 5.5 is, probably, responsible for this behavior. The results of this work suggest also some interaction of both surfactants with linker chains as well as with trimers, as judged from observed mass increments. Our data are consistent with a recent spectroscopic study showing a strong interaction between CTAC and HbGp at physiological pH [P.S.Santiago, et al, Biochim. Biophys. Acta. 1770 (2007) 506-517.]. (C) 2007 Elsevier B.V. All rights reserved.

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

EDGE-PRESERVING SPECKLE TEXTURE REMOVAL BY INTERFERENCE-BASED SPECKLE FILTERING FOLLOWED BY ANISOTROPIC DIFFUSION

Ultrasonography has an inherent noise pattern, called speckle, which is known to hamper object recognition for both humans and computers. Speckle noise is produced by the mutual interference of a set of scattered wavefronts. Depending on the phase of the wavefronts, the interference may be constructive or destructive, which results in brighter or darker pixels, respectively. We propose a filter that minimizes noise fluctuation while simultaneously preserving local gray level information. It is based on steps to attenuate the destructive and constructive interference present in ultrasound images. This filter, called interference-based speckle filter followed by anisotropic diffusion (ISFAD), was developed to remove speckle texture from B-mode ultrasound images, while preserving the edges and the gray level of the region. The ISFAD performance was compared with 10 other filters. The evaluation was based on their application to images simulated by Field II (developed by Jensen et al.) and the proposed filter presented the greatest structural similarity, 0.95. Functional improvement of the segmentation task was also measured, comparing rates of true positive, false positive and accuracy. Using three different segmentation techniques, ISFAD also presented the best accuracy rate (greater than 90% for structures with well-defined borders). (E-mail: fernando.okara@gmail.com) (C) 2012 World Federation for Ultrasound in Medicine & Biology.

Batroxase, a new metalloproteinase from B. atrox snake venom with strong fibrinolytic activity

The structures and functional activities of metalloproteinases from snake venoms have been widely studied because of the importance of these molecules in envenomation. Batroxase, which is a metalloproteinase isolated from Bothrops atrox (Para) snake venom, was obtained by gel filtration and anion exchange chromatography. The enzyme is a single protein chain composed of 202 amino acid residues with a molecular mass of 22.9 kDa, as determined by mass spectrometry analysis, showing an isoelectric point of 7.5. The primary sequence analysis indicates that the proteinase contains a zinc ligand motif (HELGHNLGISH) and a sequence C164I165M166 motif that is associated with a "Met-turn" structure. The protein lacks N-glycosylation sites and contains seven half cystine residues, six of which are conserved as pairs to form disulfide bridges. The three-dimensional structure of Batroxase was modeled based on the crystal structure of BmooMP alpha-I from Bothrops moojeni. The model revealed that the zinc binding site has a high structural similarity to the binding site of other metalloproteinases. Batroxase presented weak hemorrhagic activity, with a MHD of 10 mu g, and was able to hydrolyze extracellular matrix components, such as type IV collagen and fibronectin. The toxin cleaves both a and beta-chains of the fibrinogen molecule, and it can be inhibited by EDTA. EGTA and beta-mercaptoethanol. Batroxase was able to dissolve fibrin clots independently of plasminogen activation. These results demonstrate that Batroxase is a zinc-dependent hemorrhagic metalloproteinase with fibrin(ogen)olytic and thrombolytic activity. Published by Elsevier Ltd.

Crystal structure of dihydroorotate dehydrogenase from Leishmania major

Dihydroorotate dehydrogenase (DHODH) is the fourth enzyme in the de novo pyrimidine biosynthetic pathway and has been exploited as the target for therapy against proliferative and parasitic diseases. In this study, we report the crystal structures of DHODH from Leishmania major, the species of Leishmania associated with zoonotic cutaneous leishmaniasis, in its apo form and in complex with orotate and fumarate molecules. Both orotate and fumarate were found to bind to the same active site and exploit similar interactions, consistent with a ping-pong mechanism described for class 1A DHODHs. Analysis of LmDHODH structures reveals that rearrangements in the conformation of the catalytic loop have direct influence on the dimeric interface. This is the first structural evidence of a relationship between the dimeric form and the catalytic mechanism. According to our analysis, the high sequence and structural similarity observed among trypanosomatid DHODH suggest that a single strategy of structure-based inhibitor design can be used to validate DHODH as a druggable target against multiple neglected tropical diseases such as Leishmaniasis, Sleeping sickness and Chagas' diseases. (C) 2012 Elsevier Masson SAS. All rights reserved.

Molekulare Untersuchung des Wolf-Hirschhorn-Syndroms

Das Wolf-Hirschhorn-Syndrom (WHS) ist ein komplexes und variables Fehlbildungs- Retardierungssyndrom, das durch Deletion in der distalen Chromosomenregion 4p16.3 hervorgerufen wird und dessen Ätiologie und Pathogenese bisher weitgehend unverstanden sind. Die Zielsetzung in der vorliegenden Arbeit bestand in der Identifizierung und vorläufigen Charakterisierung neuer Gene, die an der Entstehung des Syndroms beteiligt sein könnten. Die Wolf-Hirschhorn-Syndrom-kritische Region (WHSCR) konnte zu Beginn der vorliegenden Arbeit auf einen ca. 2 Mb großen Bereich zwischen den Markern D4S43 und D4S142 eingegrenzt werden. Für die Identifizierung neuer Gene wurden zunächst drei größere genomische Cosmid-/PAC-Contigs (I-III) im Bereich der Marker D4S114 bis D4S142 erstellt und mittels Exonamplifikation auf transkribierte Bereiche (Exons) untersucht. Es konnten insgesamt 67 putative 'Exons' isoliert werden, von denen einige bereits bekannten Genen (ZNF141, PDEB, MYL5, GAK, DAGK4 und FGFR3) entsprechen. Zwei dieser Gene konnten im Rahmen dieser Arbeit erstmals (DAGK4) bzw. genauer (GAK) in die distale Region 4p16.3 kartiert werden. Die restlichen Exons können aufgrund von Homologievergleichen und/oder EST-cDNA-Homologien vermutlich neuen Genen oder auch Pseudogenen (z. B. YWEE1hu) zugeordnet werden. Durch die im Verlaufe der vorliegenden Arbeit publizierte weitere Eingrenzung der WHSCR auf einen 165 Kb-großen Bereich proximal des FGFR3-Gens konzentrierten sich weitere Untersuchungen auf die detaillierte Analyse der WHSCR zwischen dem Marker D4S43 und FGFR3. Mit Hilfe von Exonamplifikation bzw. computergestützter Auswertung vorliegender Sequenzdaten aus diesem Bereich ('GRAIL', 'GENSCAN' und Homologievergleiche in den EST-Datenbanken des NCBI) konnten mehrere neue Gene identifiziert werden. In distaler-proximaler Reihenfolge handelt es sich dabei um die Gene LETM1, 51, 43, 45, 57 und POL4P. LETM1 kodiert für ein putatives Transmembran-Protein mit einem Leucin-Zipper- und zwei EF-Hand-Motiven und könnte aufgrund seiner möglichen Beteiligung an der Ca2+-Homeostase und/oder der Signal-transduktion zu Merkmalen des WHS (Krampfanfällen, mentale Retardierung und muskuläre Hypotonie) beitragen. Das Gen 51 entspricht einem in etwa zeitgleich durch Stec et al. (1998) und Chesi et al. (1998) als WHSC1 bzw. MMSET bezeichnetem Gen und wurde daher nicht weiter charakterisiert. Es wird genauso wie das Gen 43, das zeitgleich von Wright et al. (1999b) als WHSC2 beschrieben werden konnte und eine mögliche Rolle bei der Transkriptionselongation spielt, ubiquitär exprimiert. Das in der vorliegenden Arbeit identifizierte Gen 45 zeigt demgegenüber ein ausgesprochen spezifisches Expressionsmuster (in Nervenzellen des Gehirns sowie in Spermatiden). Dies stellt zusammen mit der strukturellen Ähnlichkeit des putativen Genprodukts zu Signalmolekülen einen interessanten Zusammenhang zu Merkmalen des WHS (beispielsweise Kryptorchismus, Uterusfehlbildungen oder auch neurologische Defekte) her. Demgegenüber handelt es sich bei dem Gen 57 möglicherweise um ein trunkiertes Pseudogen des eRFS-Gens auf Chromosom 6q24 (Wallrapp et al., 1998). Das POL4P-Gen schließlich stellt allein aufgrund seiner genomischen Lokalisation sowie seiner möglichen Funktion (als DNA-Polymerase-ähnliches Gen) kein gutes Kandidatengen für spezifische Merkmale des Syndroms dar und wurde daher nicht im Detail charakterisiert. Um die Beteiligung der Gene an der Ätiologie und Pathogenese des Syndroms zu verstehen, ist die Entwicklung eines Mausmodells (über das Einfügen gezielter Deletionen in das Mausgenom) geplant. Um dies zu ermöglichen, wurde in der vorliegenden Arbeit die Charakterisierung der orthologen Region bei der Maus vorgenommen. Zunächst wurden die orthologen Gene der Maus (Letm1, Whsc1, Gen 43 (Whsc2h), Gen 45 und Pol4p) identifiziert. Durch die Erstellung sowie die genaue Kartierung eines murinen genomischen P1/PAC-Klon-Contigs konnte gezeigt werden, daß die murinen Gene Fgfr3, Letm1, Whsc1, Gen 43 (Whsc2h), Gen 45 und Pol4p sowie einige weitere der überprüften EST-cDNA-Klone der Maus in einem durchgehenden Syntänieblock zwischen Mensch (POL4P bis FGFR3) und Maus (Mmu 5.20) enthalten sind, der in seiner genomischen Ausdehnung in etwa den Verhältnissen beim Menschen (zwischen POL4P und FGFR3) entspricht.