En ville, les systèmes de récupération et d'infiltration des eaux pluviales dans le sous-sol ont pour conséquence d'augmenter la connectivité hydrologique entre la surface et la nappe phréatique. Ces pratiques d'infiltration produisent de nombreuses perturbations physico-chimiques au niveau de la nappe (ex. augmentation des variations thermiques, baisse des concentrations en oxygène dissous, enrichissement de la nappe en matière organique dissoute) mais les conséquences sur le compartiment microbien restent peu connues. L'objectif principal de la thèse est de déterminer les effets de l'infiltration des eaux pluviales sur les communautés microbiennes des nappes phréatiques, aussi bien en termes d'abondance, d'activités que de diversité génétique bactérienne. En se basant sur les changements environnementaux associés à l'infiltration des eaux pluviales et l'analyse des communautés bactériennes, un objectif fondamental est d'évaluer l'importance des phénomènes de dispersion (ex. transferts) et de sélection par des facteurs abiotiques (ex. disponibilité des ressources nutritives) sur les assemblages bactériens au sein des nappes phréatiques. Ces travaux ont été axés sur des expérimentations de terrain utilisant deux approches d'échantillonnage : une méthode active (prélèvements d'eau) et une méthode passive (incubation de substrats artificiels). La description des communautés a été effectuée par une méthode de séquençage de nouvelle génération (i.e. Illumina MiSeq) en se basant sur le gène rrs. Les résultats de ce travail mettent en avant une influence significative des pratiques d'infiltration sur les bactériomes d'un aquifère. En effet, le développement, les activités et la diversité des micro-organismes retrouvés dans la nappe ont été stimulés significativement par l'enrichissement en carbone organique dissous biodégradable engendré par ces pratiques. Néanmoins, cet impact est fortement réduit dans les systèmes étudiés où la zone non saturée est épaisse (> 10 m) et agit comme un filtre physique, chimique et biologique efficace entre le bassin d'infiltration et l'aquifère. Les faibles similarités entre les structures génétiques des bactériomes des eaux d'infiltration et dans la nappe indiquent que la zone non saturée joue un rôle efficace sur la rétention des bactéries dans les systèmes étudiés. En conclusion, cette thèse constitue la première étude d'envergure visant à quantifier la réponse du compartiment microbien des aquifères à des perturbations engendrées par l'infiltration des eaux pluviales en milieu urbain. Elle ouvre aussi de nouvelles perspectives sur les méthodes et outils d'évaluation de la qualité des nappes phréatiques / In urban area, managed aquifer recharge (MAR) systems raises hydrological connectivity between surface and groundwater. These infiltration practices are the cause of many disturbances in groundwaters (e.g. increase of thermal variations, decrease of dissolved oxygen or enrichment in organic matter) but associated consequences on microbial compartment remains unclear. The main aim of the thesis is to determine the effects of stormwater runoff infiltration on microbial communities of groundwater, in terms of abundance, activities and bacterial diversity. Based on environmental changes associated to MAR practices and bacterial community analyses, a fundamental question is to assess the importance of dispersal (e.g. transfers) and selection by abiotic factors (e.g. nutrients availability) on groundwater communities assemblage. This study is based on field experiments with two complementary strategies of sampling: an active one (i.e. groundwater sampling) and a passive one (incubation of artificial substrate). Communities’ description was made by next-generation sequencing (i.e. Illumina MiSeq) of rrs gene. The results showed a significant influence of MAR practices on microbial communities. Growth, activities and diversity of groundwater micro-organisms were mainly stimulated by biodegradable dissolved organic carbon enrichment associated to MAR practices. Nonetheless, this impact was reduced in systems where the vadose zone is thick (> 10 m) and acts as a physical, chemical and biological filter between the infiltration basin and the aquifer. Low similarities between bacterial communities of infiltration waters and bacterial communities of groundwaters reveal that vadose zone is effective on the retention of bacteria in studied systems. To conclude, this thesis constitutes the first major study that aimed to quantify microbial compartment response to disturbances caused by MAR practices in urban area. It also opens new perspectives on assessment tool for groundwater quality

L'identification de gènes ayant permis à des populations de s'adapter à leur environnement local constitue une des problématiques majeures du domaine de la génétique des populations. Les méthodes statistiques actuelles répondant à cette problématique ne sont plus adaptées aux données de séquençage nouvelle génération (NGS). Nous proposons dans cette thèse de nouvelles statistiques adaptées à ces nouveaux volumes de données, destinées à la détection de gènes sous sélection. Nos méthodes reposent exclusivement sur l'Analyse en Composantes Principales, dont nous justifierons l'utilisation en génétique des populations. Nous expliquerons également les raisons pour lesquelles nos approches généralisent les méthodes statistiques existantes et démontrons l'intérêt d'utiliser une approche basée sur l'Analyse en Composantes Principales en comparant nos méthodes à celles de l'état de l'art. Notre travail a notamment abouti au développement de pcadapt, une librairie R permettant l'utilisation de nos statistiques de détection sur des données génétiques variées. / Identifying genes involved in local adaptation is of major interest in population genetics. Current statistical methods for genome scans are no longer suited to the analysis of Next Generation Sequencing (NGS) data. We propose new statistical methods to perform genome scans on massive datasets. Our methods rely exclusively on Principal Component Analysis which use in population genetics will be discussed extensively. We also explain the reasons why our approaches can be seen as extensions of existing methods and demonstrate how our PCA-based statistics compare with state-of-the-art methods. Our work has led to the development of pcadapt, an R package designed for outlier detection for various genetic data.

Magister Scientiae - MSc / Providing carrier grade characteristics for Internet Protocol (IP) communication applications is a significant problem for IP application providers in order to offer integrated services that span IP and telecommunication networks. This thesis addresses the provision of life-cycle management, which is only one carrier grade characteristic, for a SoftBridge application, which is an example of IP communication applications. A SoftBridge provides semi-synchronous multi-modal IP-based communication. The work related to IP-Telecommunication integrated services and the SoftBridge is analyzed with respect to life-cycle management in a literature review. It is suggested to use an Application Server in a Next Generation Network (NGN) to provide life-cyclemanagement functionality for IP-Telecommunication applications. In this thesis, the Application Server is represented by a JAIN Service Logic Execution Environment(JSLEE), in which a SoftBridge application can be deployed, activated, deactivated, uninstalled and upgraded online.Two methodologies are applied in this research: exploratory prototyping, which evolves the development of a SoftBridge application, and empirical comparison, which is concerned with the empirical evaluation of a SoftBridge application in terms of carriergrade capabilities. A SoftBridge application called SIMBA provides a Deaf Telephony service similar to aprevious Deaf Telephony SoftBridge, However, SIMBA’s SoftBridge design and implementation are unique to this thesis. In order to test the life-cycle management ability of SIMBA, an empirical evaluation is carried out including the experiments oflife-cycle management and call-processing performance. The final experimental results of the evaluation show that a JSLEE is able to provide life-cycle management for SIMBA without causing a significant decrease in performance. In conclusion, the life-cycle management can be provided or a SoftBridge application by using an Application Server such as a JSLEE. Futhermore, the results indicate that approach of using Application Server (JSLEE) integration should be sufficiently general to provide life cycle management, and indeed other carrier grade capabilities, for other IP communication applications. This allows IP communication applications to be integrated into an NGN.Providing carrier grade characteristics for Internet Protocol (IP) communication applications is a significant problem for IP application providers in order to offer integrated services that span IP and telecommunication networks. This thesis addresses the provision of life-cycle management, which is only one carrier grade characteristic, for a SoftBridge application, which is an example of IP communication applications. A SoftBridge provides semi-synchronous multi-modal IP-based communication. The work related to IP-Telecommunication integrated services and the SoftBridge is analyzed with respect to life-cycle management in a literature review. It is suggested to use an Application Server in a Next Generation Network (NGN) to provide life-cyclemanagement functionality for IP-Telecommunication applications. In this thesis, the Application Server is represented by a JAIN Service Logic Execution Environment(JSLEE), in which a SoftBridge application can be deployed, activated, deactivated, uninstalled and upgraded online.Two methodologies are applied in this research: exploratory prototyping, which evolves the development of a SoftBridge application, and empirical comparison, which is concerned with the empirical evaluation of a SoftBridge application in terms of carriergrade capabilities. A SoftBridge application called SIMBA provides a Deaf Telephony service similar to aprevious Deaf Telephony SoftBridge, However, SIMBA’s SoftBridge design and implementation are unique to this thesis. In order to test the life-cycle management ability of SIMBA, an empirical evaluation is carried out including the experiments oflife-cycle management and call-processing performance. The final experimental results of the evaluation show that a JSLEE is able to provide life-cycle management for SIMBA without causing a significant decrease in performance. In conclusion, the life-cycle management can be provided or a SoftBridge application by using an Application Server such as a JSLEE. Futhermore, the results indicate that approach of using Application Server (JSLEE) integration should be sufficiently general to provide life cycle management, and indeed other carrier grade capabilities, for other IP communication applications. This allows IP communication applications to be integrated into an NGN. / South Africa

Magister Scientiae - MSc / Telecommunication companies, service providers and large companies are now adapting converged multi-service Next Generation Networks (NGNs). Network management is shifting from managing Network Elements (NE) to managing services. This paradigm shift coincides with the rapid development of Quality of Service (QoS) protocols for IP networks. NEs and services are managed with Policy Based Network Management (PBNM) which is most concerned with managing services that require QoS using the Common Open Policy Service (COPS) Protocol. These services include Voice over IP (VoIP), video conferencing and video streaming. It follows that legacy NEs without support for QoS need to be replaced and/or excluded from the network. However, since most of these services run over IP, and legacy NEs easily supports IP, it may be unnecessary to throw away legacy NEs if it can be made to fit within a PBNM approach. Our approach enables an existing PBNM system to include legacy NEs in its management paradigm. The Proxy-Policy Enforcement Point (P-PEP) and Queuing Policy Enforcement Point (Q-PEP) can enforce some degree of traffic shaping on a gateway to the legacy portion of the network. The P-PEP utilises firewall techniques using the common legacy and contemporary NE management protocol Simple Network Management Protocol (SNMP) while the Q-PEP uses queuing techniques in the form Class Based Queuing (CBQ) and Random Early Discard (RED) for traffic control. / South Africa

Glycopeptides are the so-called last-resort antibiotics in clinical practice used to treat heavier, predominantly nosocomial infections caused by multi-resistant coagulase-negative staphylococci. The origin and genetic basis of resistance to glycopeptide antibiotics has not yet been elucidated within coagulase-negative staphylococci. Research on Staphylococcus aureus has shown, that intermediate resistance to glycopeptide antibiotics is associated with the presence of one or more mutations, rather than being conditioned by the support of a particular genetic element, such as in enterococci. By using various types of in vitro resistant mutant selection, we were able to obtain isogenic pairs of glycopeptide sensitive and resistant strains of Staphylococcus epidermidis and Staphylococcus haemolyticus. By sequencing the genomes of these pairs, one nucleotide polymorphisms were identified and predominantly found in metabolic and cell wall control systems. Phenotypic analysis did not reveal a direct association of glycopeptide resistance with increased biofilm formation. In clinical practice, the cross-resistance of glycopeptides and other antibiotics is problematic. For the non-glycopeptide antibiotics imipenem and rifampicin, the incidence of cross-resistance with glycopeptide antibiotics in S. aureus...

Depuis leur émergence autour de 2006, les technologies de séquençage haut débit ont révolutionné la recherche biologique et médicale. Obtenir instantanément une grande quantité de courtes ou longues lectures de presque tout échantillon biologique permet de détecter des variantes génomiques, révéler la composition en espèces d’un métagénome, déchiffrer la biologie du cancer, décoder l'évolution d’espèces vivantes ou disparues, ou mieux comprendre les schémas de la migration humaine et l'histoire humaine en général. La vitesse à laquelle augmente le débit des technologies de séquençage dépasse la croissance des capacités de calcul et de stockage, ce qui crée de nouveaux défis informatiques dans le traitement de données de séquençage haut débit. Dans cette thèse, nous présentons de nouvelles techniques informatiques pour la localisation (mapping) de lectures dans un génome de référence et pour la classification taxonomique. Avec plus d'une centaine d’outils de localisation publiés, ce problème peut être considéré comme entièrement résolu. Cependant, une grande majorité de programmes suivent le même paradigme et trop peu d'attention a été accordée à des approches non-standards. Ici, nous introduisons la localisation dynamique dont nous montrons qu’elle améliore significativement les alignements obtenus, par comparaison avec les approches traditionnelles. La localisation dynamique est basée sur l'exploitation de l'information fournie par les alignements calculés précédemment, afin d’améliorer les alignements des lectures suivantes. Nous faisons une première étude systématique de cette approche et démontrons ses qualités à l'aide de Dynamic Mapping Simulator, une pipeline pour comparer les différents scénarios de la localisation dynamique avec la localisation statique et le “référencement itératif”. Une composante importante de la localisation dynamique est un calculateur du consensus online, c’est-à-dire un programme qui collecte des statistiques des alignements pour guider, à la volée, les mises à jour de la référence. Nous présentons OCOCO, calculateur du consensus online qui maintient des statistiques des positions génomiques individuelles à l’aide de compteurs de bits compacts. Au-delà de son application à la localisation dynamique, OCOCO peut être utilisé comme un calculateur de SNP online dans divers pipelines d'analyse, ce qui permet de prédire des SNP à partir d'un flux sans avoir à enregistrer les alignements sur disque. Classification métagénomique de lectures d’ADN est un autre problème majeur étudié dans la thèse. Etant donné des milliers de génomes de référence placés sur un arbre taxonomique, le problème consiste à affecter rapidement aux nœuds de l'arbre une énorme quantité de lectures NGS, et éventuellement estimer l'abondance relative des espèces concernées. Dans cette thèse, nous proposons des techniques améliorées pour cette tâche. Dans une série d'expériences, nous montrons que les graines espacées améliorent la précision de la classification. Nous présentons Seed-Kraken, extension sur les graines espacées du logiciel populaire Kraken. En outre, nous introduisons une nouvelle stratégie d'indexation basée sur le transformé de Burrows-Wheeler (BWT), qui donne lieu à un indice beaucoup plus compact et plus informatif par rapport à Kraken. Nous présentons une version modifiée du logiciel BWA qui améliore l’index BWT pour la localisation rapide de k-mers / Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Obtaining instantly an extensive amount of short or long reads from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which still creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for the problems of read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide OCOCO, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, OCOCO can be employed as an online SNP caller in various analysis pipelines, enabling calling SNPs from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major problem studied in the thesis. Having a database of thousands reference genomes placed on a taxonomic tree, the task is to rapidly assign to tree nodes a huge amount of NGS reads, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Os sarcomas uterinos são tumores mesodérmicos raros que compreendem cerca de 3% de todos os cânceres nesse órgão. Apresentam diversidade histológica, comportamento agressivo, disseminação precoce e altas taxas mortalidade. Recentemente, os carcinossarcomas (CS) foram reclassificados histologicamente como carcinomas. Neste trabalho, os CS foram incluídos na casuística tanto para fins de comparação de seu componente mesenquimal, como por ainda fazerem parte da maioria dos estudos sobre sarcomas de corpo uterino e também da última classificação da WHO (Word Health Organization). Devido à sua diversidade e raridade, não há consenso relacionado aos fatores de risco para pior prognóstico e tratamento adequados para esses tumores. Informações sobre seus perfis gênicos e proteicos poderiam contribuir na caracterização de marcadores moleculares que auxiliassem no diagnóstico e prognóstico desses tumores, bem como no entendimento de sua biologia e comportamento clínico. Assim, nos propusemos a avaliar a presença de alterações gênicas nesses tumores, utilizando um painel de 409 genes, oncogenes e supressores de tumor, frequentemente mutados em tumores sólidos. Para isso, foram selecionadas 66 amostras, das quais 14 foram sequenciadas, incluindo, 5 carcinossarcomas (CCS), 4 leiomiossarcomas (LMS), 4 sarcomas de estroma endometrial (SEE) e 1 adenossarcoma (ADS). As reações foram realizadas utilizando a plataforma Ion Proton System (ThermoFisher) de Sequenciamento de Nova Geração. Nas 14 amostras encontramos 27 LoF e 40 mutações missenses, numa média de 39 inserções e 52 deleções por amostra, totalizando 70 mutações. Dessas, 25 encontram-se no banco de dados COSMIC. Os genes mais comumente mutados em nossa amostragem foram: TP53 (50%), KMT2D (36%), ATM (29%), DICER1 (21%), PIK3CA (21%), TRRAP (21%). Nosso objetivo principal era encontrar mutações específicas para cada subtipo histológico, porém apenas os SEEs (PDE4DIP) e os CCS (ERBB4 e PIK3CA) tiveram mutações especificas. Em outra análise, observamos que todos os subtipos histológicos compartilham o gene KMT2D. Embora não tenha sido possível estabelecer um perfil mutacional para cada subtipo histológico avaliado, nossos resultados abrem perspectivas para uma nova linha de pesquisa nos sarcomas de corpo do útero e certamente contribuem para um melhor entendimento dessas neoplasias / Uterine sarcomas are rare mesodermal tumors that comprise about 3% of all cancers in this organ. They present histological diversity, aggressive behavior, early dissemination and high mortality rates. Recently, carcinosarcomas (CCS) were histological reclassified as carcinomas. Here, we have included them in our series for purposes of comparison of the mesenchymal component and also because these tumors still form part of both the majority of studies and the WHO\'s latest classification for uterine sarcomas (Word Health Organization). Because of their diversity and rarity, there is no consensus regarding the risk factors for poor prognosis and appropriate treatment for these tumors. Thus, information about their gene and protein profiles can help in the diagnosis and prognosis of these tumors, as well as in the understanding of their biology and clinical behavior. We performed the New Generation Sequencing of 14 samples of uterine sarcomas (5 CCS, 4 LMS, 4 SEE and 1 ADS, using the Ion Proton System platform (ThermoFisher).) Among the 14 samples, we found 27 LoF (loss of gene function) and 40 missense mutations, with a mean of 39 insertions and 52 deletions per sample, totaling 70 mutations, 25 described in the COSMIC database. The most commonly mutated genes in our sample were TP53 (50%), KMT2D (36%), ATM (29%), DICER1 (21%), PIK3CA (21%), TRRAP (21%).Our main objective was to find specific mutations for each histological subtype, but only SEEs (PDE4DIP) and CCS (ERBB4 and PIK3CA) had specific mutations. In another analysis, we observed that all the histological subtypes share the KMT2D gene, which will be studied in future analyzes. Others analyzes, using a custom panel, are necessary to understand these mutations and its biological implication in uterine carcinosarcoma and sarcomas

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-10-04T12:02:05Z No. of bitstreams: 1 DissVBR.pdf: 1898665 bytes, checksum: 77cd0f5baccb8a694beb9e7f230bab15 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-04T17:30:10Z (GMT) No. of bitstreams: 1 DissVBR.pdf: 1898665 bytes, checksum: 77cd0f5baccb8a694beb9e7f230bab15 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-04T17:30:20Z (GMT) No. of bitstreams: 1 DissVBR.pdf: 1898665 bytes, checksum: 77cd0f5baccb8a694beb9e7f230bab15 (MD5) / Made available in DSpace on 2016-10-04T17:47:42Z (GMT). No. of bitstreams: 1 DissVBR.pdf: 1898665 bytes, checksum: 77cd0f5baccb8a694beb9e7f230bab15 (MD5) Previous issue date: 2014-02-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / We studied patterns of gene expression in two closely related species of fruit flies of the genus Anastrepha (Diptera: Tephritidea), A. fraterculus and A. obliqua, with the goal of finding candidate genes related to the recent differentiation process between these species. In order to do this, we used the Next-generation sequencing (NGS) with RNA-Seq methodology in head tissues of the two species of flies at different stages of the reproductive life for both sexes. After processing and removal of low quality reads we retained over 140 million paired-end reads. These sequences were assembled into individual transcriptomes for each species and a pooled transcriptome, with 154,787 contigs, representing both species. Based on the results of the assemblies, annotation and mapping we prepared two separate manuscripts, one describing the libraries for each species and a combined analysis and a second that investigate the contigs involved with species differences and their patterns of expression. These data reveal 1991 genes with differential expression in at least one comparison among different reproductive stages. It is noteworthy that we observed twice as many genes with differential expression when contrasting males than with females. Several of these genes were associated to odour, such as Odorant Binding proteins and visgum, suggesting that behavioral changes in food sources, mating choice, or breeding and oviposition sites might be involved with species differences.We also identified two large sets of genes that are differentially expressed between the species, one being underexpressed in A. obliqua and overexpressed in A. fraterculus and the other that had a reverse pattern. We used a differentiation index of SNPs per contig () and pairwise tests of positive selection between the sequences, and analysis of the substitution amino acid type caused by SNPs to identify 7 genes there are candidates to be related to the speciation process between A. fraterculus and A. obliqua. / Investigamos os padrões de expressão gênica em tecidos cefálicos de duas espécies de moscas-das- frutas do gênero Anastrepha (Diptera: Tephritidea), A. fraterculus e A. obliqua, proximamente relacionadas, identificando SNPs com alto grau de diferenciação entre as espécies e realizando análises evolutivas com o objetivo de encontrar genes candidatos relacionados ao recente processo de separação dessas espécies. Para isso, utilizamos as novas tecnologias de sequenciamento em larga escala (NGS) com a metodologia de RNA-Seq em tecidos cefálicos das duas espécies de moscas em diferentes fases da vida reprodutiva dos dois sexos. Após processamento e retirada das sequências com baixa qualidade utilizamos mais de 140 milhões de sequências paired-end para montarmos um transcriptoma conjunto das espécies, com mais de 154 mil contigs, e outros dois separados por espécie. Estes resultados estão apresentados em dois manuscritos distintos, um primeiro que descreve as bibliotecas produzidas para as diferentes espécies e um segundo que investiga padrões de expressão e genes envolvidos na diferenciação das espécies. Estes dados revelaram 1991 genes com expressão diferencial em pelo menos uma comparação de fase de vida reprodutiva entre as espécies, sendo que encontramos duas vezes mais genes com diferença na expressão entre as espécies em machos do que em fêmeas. Diversos destes genes foram associados a genes relacionados ao olfato, como a família gênica das Obps (odorant-binding protein) e o gene visgun, o que pode indicar uma mudança comportamental na preferência por alimento, parceiros ou sítios para cópula e oviposição. Encontramos também dois conjuntos de genes que são diferencialmente expressos entre as espécies, sendo um conjunto super-expresso em A. obliqua e sub-expresso em A. fraterculus e outro conjunto com um padrão revertido. Análises de padrão de seleção nestes genes sugerem sete que apresentam indícios de seleção positiva e ao menos um SNP com altos índices de diferenciação entre as espécies.

Submitted by Aelson Maciera (aelsoncm@terra.com.br) on 2017-04-25T19:44:33Z No. of bitstreams: 1 DissVSK.pdf: 2947181 bytes, checksum: 3c3bd8a24247cda4927887b3e6e3218b (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-05-02T13:09:55Z (GMT) No. of bitstreams: 1 DissVSK.pdf: 2947181 bytes, checksum: 3c3bd8a24247cda4927887b3e6e3218b (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-05-02T13:10:02Z (GMT) No. of bitstreams: 1 DissVSK.pdf: 2947181 bytes, checksum: 3c3bd8a24247cda4927887b3e6e3218b (MD5) / Made available in DSpace on 2017-05-02T13:14:36Z (GMT). No. of bitstreams: 1 DissVSK.pdf: 2947181 bytes, checksum: 3c3bd8a24247cda4927887b3e6e3218b (MD5) Previous issue date: 2016-09-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The relationship between latitude and microbial diversity in the ocean is controversial. Niche models predict higher richness at high latitudes in winter, while snapshot field-sampling point towards higher richness at intermediate latitudes, with lower values both towards equatorial and Polar Regions. However, given the dynamic nature of ocean’s ecosystem it is difficult to account for temporal variations in empirical assessments of microbial biodiversity. Here, we compared the components of diversity (richness and evenness) and microbial population stability (coefficient of variation) in two coastal ocean observatories with similar trophic state located in contrasting latitudes, one located in the Equatorial Atlantic Ocean, and one temperate located in the Northwestern Mediterranean Sea, to evaluate which factors drive the dynamics of microbial communities in each site. Our observations support the view that, as animals and plants, microbial communities exhibit higher (or at least similar) richness towards the equator, at least in the coastal ocean. We also found evidence of increasing stability with increasing evenness in tropical microbial communities when compared to the temperate ones. Temperature and silicates drove temperate free-living prokaryotic communities, while tropical ones were driven by stochastic factors such as biotic interactions with eukaryotes. We propose a conceptual framework where microbial community composition would be driven by deterministic factors in higher latitudes and once the factor temperature is removed moving towards the equator, more stochastic factors such as biotic interactions would emerge as the main factors shaping microbial communities. This study highlights the importance of comparative studies on Eulerian time-series distributed at different latitudes to fully understand the diversity patterns of microbial communities in the ocean. / A relação entre a latitude e diversidade microbiana no oceano é controversa. Modelos de nicho preveem maior riqueza em altas latitudes no inverno, enquanto amostragens pontuais indicam uma maior riqueza em latitudes intermediárias, com valores mais baixos para regiões equatoriais e polares. No entanto, dada a natureza dinâmica do ecossistema oceânico, é difícil explicar variações temporais da biodiversidade microbiana nas avaliações empíricas. Nesse trabalho comparamos os componentes da diversidade (riqueza e equitabilidade) e estabilidade das populações microbianas (coeficiente de variação) em dois observatórios oceânicos costeiros com estados tróficos semelhantes, localizados em latitudes contrastantes: um localizado no Oceano Atlântico Equatorial e um em clima temperado localizado no noroeste do Mar Mediterrâneo, a fim de avaliar quais fatores estruturam a dinâmica das comunidades microbianas em cada local. Observamos que tal como animais e plantas, as comunidades microbianas exibem maior (ou pelo menos similar) riqueza no equador pelo menos em águas costeiras. Também encontramos evidências de aumento da estabilidade com o aumento da uniformidade nas comunidades microbianas tropicais, quando comparadas com as de clima temperado. De modo geral, temperatura e silicatos foram as variáveis que condicionaram as comunidades procariotas de vida livre no observatório da região temperada, enquanto que no observatório tropical, fatores estocásticos tais como interações bióticas com eucariotos, foram os fatores que mais influenciaram as comunidades bacterianas. Assim, propomos um quadro conceitual onde a composição da comunidade microbiana seria impulsionada por fatores determinísticos em latitudes mais elevadas, enquanto que em latitudes menores, seriam determinados por fatores mais estocásticos, como interações bióticas. Nosso estudo destaca a importância de estudos comparativos utilizando series temporais Eulerianas em diferentes latitudes para entender os padrões de diversidade das comunidades microbianas no oceano.

A compensação da dosagem gênica entre fêmeas XX e machos XY em mamíferos é adquirida através de um complexo mecanismo epigenético que resulta na inativação de grande parte de um dos cromossomos X nas células femininas. O processo de inativação do cromossomo X (XCI) se inicia cedo durante a embriogênese, concomitantemente à diferenciação celular, e envolve a aquisição de modificações epigenéticas características do cromossomo X inativo (Xi). Uma estabelecido, o padrão de inativação é estavelmente mantido através de todas as mitoses celulares subsequentes e por toda a vida do organismo (exceto para células germinativas que sofrem reativação do Xi). Os mecanismos envolvidos na iniciação e estabelecimento da XCI foram extensivamente estudados, especialmente em camundongos. Embora algumas características epigenéticas associadas à manutenção da XCI tenham sido descritas, a identidade e modo específico de ação de fatores envolvidos durante essa fase da XCI são aspectos ainda não bem compreendidos. Além disso, o processo de XCI apresenta diferenças importantes entre humanos e camundongos e estudos direcionados para a identificação de novos componentes envolvidos na manutenção da XCI em humanos tornam-se de fundamental importância. Triagens funcionais genômicas por bibliotecas de shRNAs constituem uma ferramenta poderosa para a identificação de genes envolvidos em diferentes mecanismos celulares e vias bioquímicas. Sendo assim, utilizamos essa ferramenta para triar genes envolvidos na manutenção da XCI em humanos. Células somáticas femininas primárias HPRT+/-/HPRT- foram transduzidas com uma biblioteca lentiviral de shRNAs e posteriormente tratadas em meio de cultura contendo a droga HAT para seleção de células HPRT+ nas quais esperava-se que o cromossomo Xi presente tivesse sofrido reativação em decorrência do knockdown de genes envolvidos na manutenção da XCI. Essa estratégia nos permitiu identificar 20 novos genes candidatos a estarem envolvidos na manutenção da XCI. Esses candidatos deverão ser avaliados individualmente para confirmar seu papel no processo de controle epigenético do cromossomo X / Transcriptional dosage compensation between mammalian XX females and XY males is acquired through a complex epigenetic mechanism that leads to the inactivation of most part of one of the X chromosomes in the female cells. The X chromosome inactivation (XCI) process takes place early during embryogenesis and involves the acquisition of epigenetic modifications that are characteristic of the inactive X chromosome (Xi). Once silencing is established, the inactivation pattern is maintained in through all the subsequent mitosis and the same X chromosome remains stably silenced in all the descendant cells and throughout the life of the organism (except for the germ line cells that undergo X chromosome reactivation). The initiation of XCI has been studied extensively, especially in mice. Although some epigenetic features associated with the maintenance of XCI have already been described, the identity and specific mode of action of the factors involved in this phase of XCI are largely unknown. Moreover, the XCI process presents important differences between mice and humans, and studies directed to the identification of new players involved in the maintenance of human XCI are fundamentally important. Functional genome-wide screens using multiplex shRNA libraries are a powerful tool for the identification of genes involved in different cellular mechanisms and biochemical pathways. In order to screen for genes involved in the maintenance of XCI in humans, a population of HPRT+/-/HPRT- primary somatic female cells were transduced with a multiplex lentiviral shRNA library and subsequently treated in HAT medium to select for HPRT+ cells in which we expected that the Xi would undergo reactivation as a result of the knockdown of genes involved in the maintenance of XCI. As a result, we identified 20 new candidate genes that could potentially be involved in the maintenance of XCI. These candidates should be individually evaluated in order to confirm their role in the epigenetic control of the X chromosome