A Região do Betara, objeto desta pesquisa, localiza-se a nordeste da Cidade de Curitiba, entre os Municípios de Rio Branco do Sul e Campo Largo. Inclui Rochas granito-gnáissicas proto a miloníticas (Núcleo Betara) e seqüências metavulcanossedimentares de baixo a médio grau metamórfico (Formação Betara). Esses terrenos ocorrem na porção sul da Faixa Ribeira, em meio a seqüências metavulcanossedimentares da Formação Votuverava. Este trabalho teve como objetivo principal realizar estudos geológico-geocronológicos (UPb zircão) de rochas metabásicas associadas à seqüências metavulcanossedimentares (Formação Betara), bem como dos terrenos granito-gnáissicos proto a miloníticos (Núcleo Betara). Na região centro-sul do Betara, foram reconhecidas rochas granodioríticas proto a miloníticas formadas durante o paleoproterozóico (~2200 Ma) com heranças (núcleos de zircões) arqueanas (~2800 Ma). Valores arqueanos (~3200 Ma) foram obtidos através do método Sm-Nd (TDM) indicativos da época de derivação do manto dos protolitos crustais dessas rochas. Estes terrenos são limitados a sul pela Zona de Cisalhamento Lancinha, que baliza o domínio da Faixa Apiaí (à norte) daquele pertencente ao Complexo Atuba (a sul). Neste contexto tectônico, os terrenos granodioríticos proto à miloníticos representam lascas de embasamento, possivelmente relacionadas ao cráton do Paranapanema. Tal correlação, no entanto, não é tarefa fácil, uma vez que as características geológicas acopladas ao padrão geocronológico são bastante similares às observadas para o Núcleo Setuva (Siga Júnior et al., 2006 no prelo) e para o Complexo Atuba ( Siga Júnior et al., 1995 e Sato et al., 2003). Em contato tectônico com os terrenos granodioríticos ocorrem rochas sienograníticas proto a miloníticas, intimamente associadas a rochas metabásicas (mistura de magmas ? mixing, mingling). Os valores U-Pb (zircão) obtidos para os litotipos sienograníticos referem-se ao paleoproterozóico superior (1780 ? 1750 Ma; Kaulfuss, 2001 e Cury et al., 2003), similar às idades aqui obtidas para as rochas metabásicas (U-PB, zircão de 1789+-22 Ma). A ocorrência de rochas sienograníticas associadas a rochas metabásicas, com características anorogências, sugestivas de regimes extencionais representa um importante marco na região, relacionado à Tafrogênese Estateriana. Acrescente-se ainda a possibilidade de haver sedimentação associada a esse magmatismo de natureza anorogênica, relacionado a bacias do tipo rift desenvolvidas nesse período. Idades desse intervalo (1800 ? 1600 Ma) ocorrem no âmbito da Faixa Apiaí, em rochas sienograníticas proto à miloníticas do Núcleo do Tigre, a sul do corpo granítico Passa Três e no setor NE do batólito granítico Três Córregos (Kaulfuss, 2001; Cury et al., 2003 e Prazeres Filho, 2005). No continente Sul-Americano são reconhecidos ao longo de grande parte de sua porção centro-oriental (Província Borborema, Sistema Espinhaço, Grupo São João Del Rei, Província Tocantins e Faixa Ribeira), conforme discutido em Brito Neves et al. (1995). Esses registros tafrogenéticos, embora relativamente sincrônicos, variam em magnitude e extensão e são na maioria das vezes, caracterizados como rifts crustais com magmatismo de natureza alcalina ou sub-alcalina e sedimentação siliciclástica associada. Devem representar importantes cicatrizes associadas à rupturas de grandes massas continentais aglutinadas durante o Paleoproterozóico (Supercontinente Atlântica ? Rogers, 1996), ou mesmo durante o Paleo-Mesoproterozóico (Supercontinente Columbia; Rogers e Santos, 2002; Zhao et al., 2004). Os estudos geológicos relativos as seqüências metavulcanossedimentares (Formação Betara), em contato tectônico com os terrenos sienograníticos e granodioríticos (Núcleo Betara), permitiram reconhecer três unidades maiores: Sequência metapsamítica (basal) representada principalmente por quartzitos, uma Sequência de mármores, calciossilicáticas e metamargas (intermediária) e uma Sequência metapelítica (superior) onde predominam filitos com metabásicas associadas. Os dados geocronológicos obtidos através do método U-Pb (zircão) referem-se a corpos de rochas metabásicas (possíveis sills ou diques), que ocorrem intercalados concordantemente com a Sequência pelítica superior. O estudo petrográficos e geoquímicos desses corpos, embora bastante preliminar indica a natureza orto derivada dessas rochas e um quimismo de basaltos subalcalinos sugestivos de ambientes tectônicos distensivos. As idades obtidas do intervalo de 1500-1450 Ma são aqui interpretadas como mínimas de deposição da Formação Betara, possivelmente próxima desta. Valores de intervalo (1500-1450 Ma.) foram recentemente obtidos para as seqüências metavulcanossedimentares das Formações Votuverava, Perau e Água Clara. O Mesoproterozóico representa portanto, um importante marco relacionado a deposição de grande parte das seqüências metavulcanossedimentares do sul da Faixa Ribeira. O padrão geológico-geocronológico aliado ao padrão estrutural observado para a região do Betara, sugere que a colocação desses terrenos a níveis crustais superiores tenha ocorrido durante o Neoproterozóico, função de uma tectônica controlada em grande parte por cisalhamentos. / The Betara region was located at nothwest of the Curitiba City between the Campo Largo and Rio Branco do Sul municipal districts. This region includes granite-gnaissic rocks, proto to milonitics (Betara Nucleous) and metavolcanossedimentary sequences with low to intermediate metamorphic grade (Betara Formation). These terrains occur at the southern portion of the Ribeira Belt, surrounded by metavolcanossedimentary sequences of the Votuverava Formation. The main objective of this work was realize geologic-geochronologic studies (U-Pb zircon) of metabasic rocks associated with the metavolcanossedimentary sequences (Betara Formation), as well the metabasic rocks associated with the proto milonitic to milonitic granite-gnaissic terrains (Betara Nucleous). At the center-southern portion of the Betara Region, was recognized granodioritic rocks, proto to milonitic formed during the Paleoproterozoic (~2200 Ma) with archean inheritances (zircon nucleous ~2800 Ma). Archean values (~3200Ma) where obtained with Sm-Nd (TDM) method. This values where indicative for the mantle carries away ages for the crustal protolites of these rocks. These terrains are limited at the south by the Lancinha Shear Zone, who separates the Apiaí Domain (north) from the Atuba Complex (south). In this tectonic context, the proto to milonitc ganodioritic terrains represents peaces from the basement and possibly can be related to the Paranapanema Cratonic Region. This correlations are not a simple work and the geologic propers with the geologic patterns was to close to that observed for the Setuva Nucleous (Siga Júnior et al., 2006 no prelo) and for the Atuba Complex ( Siga Júnior et al., 1995 e Sato et al., 2003). In tectonic contact with the granodioritic terrains occurs some sienogranitic rocks proto to milonitics associated with metabasic rocks (magma mixing and/or magma mingling). The U-Pb zircon values obtained to the sienogranitic rocks was related to the Upper Paleoproterozoic (1780-1750 Ma; Kaulfuss, 2001 e Cury et al., 2003), very close to the ages obtained for the metabasic rocks (U-Pb zircon at 1789+-22 Ma). The occurrence of the sienogranitic rocks associated with metabasic rocks; with anorogenic characteristics may imply extensional systems and represents an important frame on this region, related to the Estatherian Tafrogenetic Event. Increases the possibilities to occur some sedimentation associated to this anorogenic magmatism, related to rift type basins developed during this period. Ages from this interval (1800 - 1600 Ma) occurs at the Apiaí Belt for the sienogranites proto to milonitics from the Tigre Nucleous at the south of the Passa Tres granitic body and at the nothwesthern portion of the granitic bathollite Três Córregos (Kaulfuss, 2001; Cury et al., 2003 e Prazeres Filho, 2005). In the South American Continent was recognized at a great part of this center west portion (Borborema Province, Espinhaço System, São João Del Rei Group, Tocantins Province and Ribeira Belt) according with Brito Neves et al. (1995). This tafrogenetic record was relatively synchronic, but variate in magnitude and extension and at most part of the time was related to crustal rifts with alkaline to sub alkaline magmatism associated with siliciclastic sedimentation. Might represent important scars associated with the breakage of some large continental masses agglutinated during the Paleoproterozoic (Atlantica Suercontinent, Rogers, 1996) or as same during the Paleo-Mesoproterozoic (Columbia Supercontinet; Rogers and Santos, 2002; Zhao et al., 2004). The geologic studies of the metavolcanossedimentary sequences (Betara Formation) in tectonic contact with sienogranitic-granodioritic terrains (Betara Nucleous) admit to recognize three major units: Metapsamitic sequence (lower), recognized mainly by quartzites, a marble, calciossilicatic and marly sequence (intermediary) and a metapelitic sequence (upper) where predominate phyllites associated with metabasic rocks. The geochronological data obtained from the U-Pb (zircon) method refers to metabasic rock bodies (dikes or sills) who occurs in conformity and intercalated with the upper pelitic sequence. The geochemical studies of this bodies indicates this ortho derived nature and a subalkaline chemical characteristics who suggests a distensive ambient. The ages obtained in a range between 1500-1450 Ma can be interpreted like minimal ages to deposition for the Betara Formation. Values at this same range (1450-1500 Ma) were obtained recently to the Votuverava, Perau and Água Clara Formations. The Mesoproterozoic represents an important frame related to deposition of the great part of the metavolcanossedimentary sequences of the southern Ribeira Belt. The geologic-geochronologic patterns, with the structural patterns observed to the Betara Region suggests whom the placement of this terraines at the upper crustal levels occurs at the Neoproterozoic, function of a shear-controlled tectonics.

No description available.

De nos jours, l’augmentation du volume des données de séquençage est bien plus forte que celle de notre capacité à analyser ces données. En lien avec ce déluge de données et le besoin urgent de nouveaux outils bioinformatiques pour les analyser, notre travail consiste à développer de nouveaux algorithmes pour mieux comprendre les relations entre séquence, structure, et fonction des protéines. Les protéines contiennent de larges portions de séquences périodiques, qui forment des motifs d’acides aminés répétés les uns à la suite des autres que l’on appelle des répétitions en tandem. Elles se retrouvent dans 14% des protéines. De nombreuses études ont montré leur importance fonctionnelle ainsi que leur implication dans de nombreuses maladies humaines, notamment le cancer. Ici, nous montrons l’importance d’adopter une approche incluant plusieurs outils de détection de répétition en tandem afin de s’assurer d’obtenir le jeu de données le plus complet. Nous avons ainsi réalisé un pipeline approprié, et développé deux outils spécifiques : un filtre, pour gagner en rapidité, et un score, pour sélectionner les répétitions les plus pertinentes dans les régions structurées des protéines. Enfin, nous avons utilisé ce pipeline sur une sélection de 94 protéomes. Cette analyse a permis de mettre à jour le précédent recensement des répétitions, montrant que 64% des protéines contenaient des répétitions en tandem. Elle a également permis de mieux comprendre les répétions en tandem dans leurs caractéristiques, leurs compositions et leurs implications dans les maladies humaines. / Today, the growth of protein sequencing data significantly exceeds the growth of capacities to analyze these data. In line with this data deluge and urgent needs in new bioinformatics tools our work deals with the development of new algorithms to better understand the sequence-structure-function relationship. Proteins contain a large portion of periodic sequences representing arrays of repeats that are directly adjacent to each other, so called tandem repeats (TRs). TRs occur at least in 14% of all proteins. Highly divergent, they range from a single amino acid repetition to domains of 100 or more repeated residues. Numerous studies demonstrated the fundamental functional importance of such TRs and their involvement in human diseases, especially cancers. Here we show the importance of integrating several TR detectors to get the most complete set of TRs in proteomes. We designed an appropriate pipeline and developed a filter to speed the process as well as a new scoring module to select relevant structured TRs. In addition, we undertook a large scale analysis of TRs in 94 proteomes. This large scale analysis allowed us to update previous census of TR showing that TRs occurs in 64% of all proteins and leads to a better understanding of TR in terms of their characteristics, composition and implication in human disease.

No description available.

In order to identify Leishmania proteins which may be immunologically relevant or may play a role in interactions between Leishmania and its mammalian host, a Leishmania major genomic DNA library was constructed in the vector λgt11 and screened with antibodies raised to Leishmania major promastigote membranes. Two recombinant DNA clones were identified which encoded repetitive sequences (Clone 20 and Clone 39). Clone 20 encoded a repetitive peptide of 14 amino acids and clone 39 encoded an unrelated repetitive peptide of 10 amino acids. Analysis of one of these clones, Clone 20, indicated that there were two RNA transcripts of 9500 and 5200 nucleotides expressed which corresponded to this clone in Leishmania major and Leishmania donovani and this expression was not stage-specific. The results of genomic DNA analysis and isolation of additional clones encoding Clone 20 sequences indicated that there were two genes which corresponded to Clone 20 in both Leishmania major and Leishmania donovani and that these genes differed from one another with respect to the number of repeats which they contained. Antibodies against the fusion protein produced by Clone 20 recognized a series of Leishmania major proteins of apparent mol wt 250,000. Analysis of Clone 39 indicated that there was a single transcript of 7500 nucleotides expressed which corresponded to this clone in both Leishmania major and Leishmania donovani and that there was a single gene (or two identical genes) which encoded this transcript. The genomes of many protozoan parasites exhibit a high degree of plasticity with respect to chromosome size and number. The presence of highly repetitive regions within their DNA may be involved in maintaining this plasticity, allowing the parasite to evolve rapidly under selective pressure. Repetitive regions have been identified within many Plasmodia antigens and have been implicated in the ability of this parasite to evade the host immune system. The presence of Leishmania genes encoding proteins containing tandemly repeating peptides may indicate that these proteins play a similar role in evading the host immune system during the course of Leishmania infections. The possible evolution and functions of repetitive proteins in protozoan parasites is discussed. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

A evolução in vitro é um método laboratorial criado para a evolução de moléculas, principalmente de proteínas. Por meio de mutações, o método busca novas propriedades de moléculas, objetivando criar novas proteínas e, com isso, intensificar o estudo e a cura de doenças, pelo desenvolvimento de novos fármacos. O grande desafio na evolução in vitro é criar o maior número possível de moléculas de proteínas que atinjam propriedades desejadas, uma vez que apenas uma fração infinitesimal das diversidades geradas utilizando-se seqüências de DNA é aproveitada. Para se obter moléculas com funcionalidade adequada por meio dessa técnica, é requerido muito tempo e aporte financeiro. Com o objetivo de avaliar computacionalmente a funcionalidade de proteínas variantes a partir das seqüências de aminoácidos buscando reduzir o custo e o tempo desprendido em laboratório, este trabalho propõe o uso de técnicas de computação inteligentes (evolução in silicio), baseadas em aprendizado de máquina e computação evolutiva. Para o emprego de técnicas de AM, bancos de dados com elevado número de informações são fundamentais. Neste sentido, escolheu-se investigar as moléculas mutantes de hemoglobina, uma vez que a quantidade de informações disponíveis sobre a mesma é bastante extensa na literatura. Os resultados obtidos mostram que é possível desenvolver algoritmos eficientes para determinar a funcionalidade de variantes de hemoglobina. Com esses resultados, busca-se contribuir no desenvolvimento de técnicas de evolução dirigida com suporte computacional / In vitro evolution is a laboratorial method developed to molecule evolution mainly proteins. By producing mutations, this method looks for new molecule properties, aiming achieve new proteins for the development of drugs for diseases. The great challenge of in vitro evolution is the development of the highest possible number of molecules that reaches desired properties. This objective is a great challenge to be transposed, since only one infinitesimal fraction of generated proteins using DNA sequencies is usefull to obtain molecules with the desired function. Besides high financial support and time are required to apply this technique. With the objective of evaluating computacionaly and functionality of proteins mutants starting from aminoacids sequences looking for to reduce the cost and the time loosened at laboratory, this work proposes the use of intelligent computation techniques based on learning of it conspires and evolutionary computation. On the other hand, when machine learning techniques are used, it is fundamental to access data mining with high number of information. In order to reduce these difficulties, this work proposes a machine learning (ML) based on approach to evaluate computationaly hemoglobin variants. ML techniques require, in general, large data base. In order to supply this requirement, hemoglobin variants were used because there is a large number of hemoglobin variants available in the literature. The obtained results shown that is possible to develop efficient algorithms to determine hemoglobin variant function. These results can contribute for development of molecule evolution techniques

Digital encoders are electro-mechanical sensors that measure linear or angular position using special binary patterns. The properties of these patterns influence the traits of the resulting encoders, such as their maximum speed, resolution, tolerance to error, or cost to manufacture. We describe a novel set of patterns that can be used in encoders that are simple and compact, but require some initial movement to register their position. Previous designs for such encoders, called absolute incremental encoders, tend to incorporate separate patterns for the functions of tracking incremental movement and determining the absolute position. The encoders in this work, however, use a single pattern that performs both functions, which maximizes information density and yields better resolution. Compared to existing absolute encoders, these absolute incremental encoders are much simpler with fewer pattern tracks and read heads, potentially allowing for lower-cost assembly of high resolution encoders. Furthermore, as the manufacturing requirements are less stringent, we expect such encoders may be suitable for use in D.I.Y. %27maker%27 projects, such as those undertaken recently by our lab.

The neotropical genus Exostema comprises 25 species of trees and shrubs, ranging in distribution from Bolivia to Mexico and throughout the West Indies, with most species endemic to the Greater Antilles. Infrageneric relationships and species-level patterns of evolution were investigated in phylogenetic analyses using morphological, molecular, and combined data sets. All data sets resolved three main species groups which correspond to the three sections recognized by McDOWELL (1996). However, the analyses of ITS sequence data placed the two South American species basal to the three main clades. Otherwise, the morphological and molecular data are highly compatible, and produce a more robust yet consistent phylogeny in the combined data analysis. Morphological evolution in Exostema involves many specializations for xeric habitats, reflecting repeated ecological shifts from moist forest to exposed, seasonally dry environments during the diversification of the genus. Both moth and bee pollination syndromes are found in Exostema, and shifts in pollination ecology appear pivotal to the differentiation of the three sections. Biogeographically, Exostema likely originated in South America and migrated via Central America to the Greater Antilles, where the morphological diversification and speciation are most extensive.

In this paper, we study the properties of k-omnisequences of length n, defined to be strings of length n that contain all strings of smaller length k embedded as (not necessarily contiguous) subsequences. We start by proving an elementary result that relates our problem to the classical coupon collector problem. After a short survey of relevant results in coupon collection, we focus our attention on the number M of strings (or words) of length k that are not found as subsequences of an n string, showing that there is a gap between the probability threshold for the emergence of an omnisequence and the zero-infinity threshold for E(M).

In this paper, we study the properties of k-omnisequences of length n, defined to be strings of length n that contain all strings of smaller length k embedded as (not necessarily contiguous) subsequences. We start by proving an elementary result that relates our problem to the classical coupon collector problem. After a short survey of relevant results in coupon collection, we focus our attention on the number M of strings (or words) of length k that are not found as subsequences of an n string, showing that there is a gap between the probability threshold for the emergence of an omnisequence and the zero-infinity threshold for E(M).