Depuis leurs apparitions, les technologies de séquençage à haut débit (NGS) ont permis de révolutionner notre connaissance du transcriptome. Le RNA-Seq ou séquençage à haut-débit des transcrits, permet la numérisation rapide d’un transcriptome sous forme de millions de courtes séquences d’ADN. Contenue dans ces données brutes, l’information des transcrits peut être analysée quantitativement sous forme de profils d’expression. Les séquences obtenues contiennent également une multitude d’informations qualitatives comme les jonctions d’épissage, les variants génomiques ou post-transcriptionnels, ainsi que de nouvelles formes de transcriptions moins conventionnelles comme les ARN circulaires, les gènes de fusions ou les longs ARN non-codants.Peu à peu, le RNA-Seq s’impose comme une technologie de référence dans la recherche en biologie, et, demain dans la médecine génomique.Mes travaux de thèse proposent une vue transversale de la technologie RNA-Seq avec comme point de départ l’optimisation des méthodes d’analyses actuelles dans un contexte donné - via des procédures de benchmarking systématiques s’appuyant sur la simulations de données. Ces optimisations sont ensuite exploitées, dans le cadre d’applications sur la biologie des cancer (Leucémies et Hépatoblastome), afin d’identifier de nouveaux biomarqueurs, ainsi qu’une nouvelle stratification des patients dans le but de proposer des pistes thérapeutiques personnalisées. Enfin, mes derniers travaux portent sur la proposition de deux nouvelles méthodes d’analyse du RNA-Seq par décomposition en k-mers. La première, TranSiPedia, propose un nouveau paradigme, ayant pour objectif d'intégrer les données du transcriptome à très large échelle, via l'indexation systématique de données expérimentales. La seconde méthode, DE-kupl, propose une analyse différentielle - sans apriori - des données RNA-Seq pour l’identification de nouveaux biomarqueurs et la caractérisation de nouveaux mécanismes du transcriptome. / Since their introduction, next generation sequencing technologies (NGS) have shaped our vision of the transcriptome. RNA-seq, or high throughput transcript sequencing, enables the fast digitization of a transcriptome in the form of million of short DNA sequences. The information available in the raw data can be used in a quantitative way to extract expression profiles. The obtained sequences also provides a wide range of qualitative information such as splicing junction, genomic or post-transcriptional variants, as well as new forms of less conventional transcription such as circular RNA, fusion genes or long non coding RNA. Gradually, RNA-Seq is becoming a gold standard in molecular biology and tomorrow in genomic medicine.My thesis work proposes a global vision of the RNA-Seq technology, starting with the optimisation of current analysis methods to a particular context through systematic benchmarking procedures relying on the simulation on synthetic data. These optimizations are later used as a part of a work on the biology of cancer in order to identify new biomarkers in leukemia as well as a new stratification of hepatoblastoma patients to propose personalized treatments. Finally, my last work is focused on the proposal of two new analysis methods for RNA-Seq data, both based on the principle of k-mer decomposition. The first method, TranSiPedia, is a new paradigm to integrate transcriptome data at a very large scale through the systematic indexation of experimental data. The second method, DE-Kupl, is a new strategy to perform differential analysis, without a priori knowledge about the transcriptome. DE-kupl is designed to help the discovery of new biomarkers as well as the characterization of new mechanisms of the transcriptome.

Le développement de la seconde génération de séquenceurs haut débit a généralisé l'accès à l'étude du transcriptome via le protocole RNAseq. Celui-ci permet d'obtenir à la fois la séquence et l'abondance des transcrits d'un échantillon. De nombreuses méthodes bioinformatiques ont été et sont encore développées pour permettre l'analyse des données issues du RNAseq et en tirer le maximum d'information. Ce type d'analyse est notamment possible sans utiliser de génome de référence, et donc pour les espèces modèles ou non-modèles, grâce à des méthodes d'assemblage. Durant ma thèse, j'ai principalement travaillé à partir de données RNA-seq issues d'espèces non modèles. Je me suis intéressée dans un premier temps à l'impacte de l'hybridation inter spécifique sur la stabilité des génomes chez les hybrides issus des croisements réciproques de D. mojavensis et D. arizonae. Nos résultats ne montrent pas une dérégulation globale, mais plutôt quelques gènes et éléments transposables qui sont spécifiquement dérégulés. La pipeline d'analyse mis en place ici sera réutilisée pour l'étude des niveaux d'expression des transcrits chez les mâles ainsi que pour les croisements issus d'autres lignées de D. mojavensis avec D. arizonae, conduisant à une fertilité variable chez les hybrides.Dans un second temps, j'ai participé à la validation du logiciel KisSplice pour la détection de SNP dans des données RNA-seq sans génome de référence. Celui-ci permet de trouver différents types de variants (épissage, indels) directement dans le graphe de de Bruijn construit à partir des lectures séquencées. J'ai également participé au développement d'outils de post-traitement permettant de prédire l'impact des SNP sur les protéines / Next-generation high throughput sequencing technologies provide efficient, rapid, and low cost access to sequencing. Its application to transcriptomes, called RNA-seq, enables the study of both the sequence and the expression of the transcripts. Many bio-informatics methods are still developed for RNA-seq data processing, trying to get the maximum out of it. Assembly methods allow us to study non-model species (no reference genome available) as well as model species. The work presented here is mostly related to RNA-seq data on non-model species.In the first study, to understand the initiation of hybrid incompatibility, we performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses of \emph{D. mojavensis} and \emph{D. arizonae}. We didn't see a global deregerulation of genes or transposable element. Instead, we show that reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. The analytical workflow developed for this project will be used to analyze transcriptomic data from the testis, but also to study the reciprocal crosses from other lines of D. mojavensis with D. arizonae leading to variable levels of sterility in hybrids. A second project tacked here is the identification and quantification of SNPs from RNA-seq data without a reference genome with KisSplice. Kissplice was developed to identified several type of variants (splicing events, indels) directly from the de Bruijn graph, build from the sequenced reads. We also developed other KisSplice-tools, for downstream analyses of the SNPs, including the prediction of their impact on the protein sequence

Les infections intra-mammaires (IMI) responsables de mammites, sont une cause importante de maladie, de mortalité et de pertes de production chez les ruminants laitiers. Le péri-partum est une période où la fréquence des mammites est significativement plus élevée. Parmi les facteurs de risques, le déficit énergétique, fréquent au début de la lactation, est souvent évoqué. Cependant, les bases mécanistiques de l’éventuelle relation entre IMIs et déficit énergétique sont encore peu comprises. L’objectif de ma thèse était ainsi d’évaluer la relation éventuelle entre le déficit énergétique et la prédisposition aux mammites en utilisant la brebis laitière comme modèle. Mes travaux ont montré que les brebis génétiquement prédisposées aux mammites ont également une sensibilité accrue au déficit énergétique et à la cétose. / Intramammary infections and mastitis are a leading cause of diseases, death and production losses in dairy ruminants. Increased susceptibility to mastitis during the peripartal period has been yet widely documented. Negative energy balance is frequent in early lactation and considered as a known risk factor for mastitis. The relationship between energy balance and mastitis susceptibility however remained unclear and poorly described. The aim of my thesis was to examine the relation between a negative energy balance and susceptibility to mastitis in dairy ewes. In particular, my research works showed an enhanced susceptibility to energy restriction in mastitis-susceptible ewes.

Orientadores: Anete Pereira de Souza, Sindélia Freitas Azzoni / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T11:06:28Z (GMT). No. of bitstreams: 1 Crucello_Aline_D.pdf: 3829574 bytes, checksum: b0eb3f1e3e0030f42a0081e3bf8b5ef8 (MD5) Previous issue date: 2014 / Resumo: O Brasil é hoje referência mundial na produção de etanol produzido a partir da cana-de-açúcar, cujo consumo tem aumentado significativamente nos últimos anos. Entretanto, a produção atual de etanol a partir do suco da cana-de-açúcar é insuficiente para atender a demanda do mercado nacional e internacional. Nesse contexto, a produção de etanol celulósico (de segunda geração) emergiu como uma alternativa promissora ao bioetanol de primeira geração. O fungo filamentoso Trichoderma harzianum IOC-3844 é uma linhagem brasileira que se destaca pela alta capacidade de produção de enzimas do complexo das celulases e hemicelulases, característica de grande interesse em biocatálise para conversão de biomassa em monômeros de açúcar fermentáveis. Apesar de seu comprovado potencial, há poucos dados de literatura disponíveis a respeito de sua capacidade celulolítica. Desta forma, este projeto teve como objetivo principal contribuir para o conhecimento básico sobre regiões do genoma de T. harzianum IOC-3844 envolvidas na via de hidrólise de compostos celulósicos, através da construção de uma biblioteca genômica de BAC (bacterial artificial chromosome). A biblioteca de BACs conta com 5760 clones, com insertos de DNA de tamanho médio de 90 kb, o que dá uma cobertura de aproximadamente 12 vezes o genoma de T. harzianum. Através da seleção de clones contendo genes de interesse, foram identificadas regiões com altas concentrações de genes relacionados à hidrólise de biomassa. Além disso, a combinação de dados genômicos, obtidos através da biblioteca de BACs, juntamente com dados de transcriptoma possibilitou a identificação de novos potenciais genes regulatórios. Os resultados trazem grande contribuição para a pesquisa associada a T. harzianum e à genômica de fungos relacionada à produção de etanol de segunda geração / Abstract: Brazil is a world reference in sugarcane ethanol production, whose consumption has increased significantly in recent years. However, the current production of ethanol from sugarcane juice is insufficient to meet the demand of national and international market. In this context, the production of cellulosic ethanol (second generation) has emerged as a promising alternative to first-generation bioethanol. The filamentous fungus Trichoderma harzianum IOC-3844 is a Brazilian strain known for its high ability to produce enzymes of cellulosic and hemicellulosic complex, characteristic of great interest in biocatalysis for conversion of biomass into fermentable sugar monomers. Despite its potential, there are few published data available regarding its cellulolytic ability. Thus, this project aimed to contribute to the basic knowledge about regions of the genome of T. harzianum IOC-3844 involved in the hydrolysis of cellulosic compounds pathway, through the construction of a genomic BAC (bacterial artificial chromosome) library. The BAC library comprises 5,760 clones with an average DNA insert size of 90 kb, which represents about 12-fold coverage of the T. harzianum genome. Through the selection of clones containing genes of interest, regions containing high concentrations of genes related to biomass hydrolysis were identified. Furthermore, the combination of genomic data obtained from BAC library together with transcriptome data allowed the identification of novel potential regulatory genes. The results bring great contribution to studies related to T. harzianum and to fungal genomics regarding second generation bioethanol production / Doutorado / Genetica de Microorganismos / Doutora em Genética e Biologia Molecular

A proteobactéria Pseudomonas aeruginosa é um patógeno oportunista em humanos, sendo associado a queimaduras e infecções pulmonares crônicas em pacientes com fibrose cística. Essas infecções são difíceis de erradicar devido à resistência intrínseca de P. aeruginosa a antibióticos e à formação de biofilmes. Essa bactéria é altamente capaz de adaptar ao ambiente, tem um metabolismo versátil e pode direcionar a expressão de genes por vários fatores sigma alternativos. Estes são subunidades para transcrição de conjuntos específicos de genes em bactérias e interagem com o cerne da RNA polimerase, levando ao reconhecimento do promotor e início da transcrição. Os fatores sigma alternativos permitem que bactérias redirecionem a sua expressão genética. Um grupo de fatores sigma alternativos é o grupo dos fatores sigma de função extracitoplasmática (ECF) que são envolvidos principalmente em funções do envelope celular. Esse trabalho teve como objetivo caracterizar dois fatores sigma ECF de função desconhecida, PA14_21550 e PA14_46810. A linhagem mutante Δ21550 foi analisada quanto a sua sobrevivência a diferentes estresses, observando-se que é mais resistente ao choque de 45°C que a linhagem selvagem. Esse fator sigma não é essencial para crescimento da bactéria em meio LB e meio mínimo M63 acrescido de glicose ou succinato. Além disso, observou-se que a superexpressão desse fator sigma aumenta a expressão da proteína hipotética PA14_30100, usando-se uma abordagem proteômica. O mutante de transposon para o fator sigma PA14_46810 apresenta melhor crescimento que a bactéria selvagem em meio M63 acrescido de glicose. Essa linhagem mostrou mesmo fenótipo para biofilme e formação de exopolissacarídeo que a bactéria selvagem. Ademais, foi realizada análise de transcritoma por RNA-Seq com a superexpressão do fator sigma PA14_46810 na linhagem selvagem. Na linhagem de superexpressão Observou-se que ocorre indução de genes envolvidos com a desnitrificação, transporte de moléculas e metabolismo de uma maneira geral, em relação à linhagem controle. Por outro lado, o excesso de PA14_46810 reprime principalmente genes envolvidos com a tradução de proteínas e síntese de espermidina. Este trabalho, portanto, trouxe novas informações sobre as funções de diferentes fatores sigma ECF de P. aeruginosa, contribuindo assim para um maior entendimento da fisiologia desta bactéria e sua adaptação a diferentes condições. / The proteobacterium Pseudomonas aeruginosa is an opportunistic pathogen in humans, and it is associated to chronic pulmonary infections in patients with cystic fibrosis and burn wounds. These infections are difficult to eradicate due to P. aeruginosa intrinsic resistance to antibiotics and formation of biofilms, which allow the bacteria to adhere to biotic and abiotic surfaces. This bacterium is highly adaptaptable to the environment has a versatile metabolism and can direct the expression of genes by several alternative sigma factors. The sigma factors bind to the RNA polymerase core, providing recognition to promoter and transcription initiation. Therefore, the alternative sigma factors can redirect bacterial genetic expression by recognizing specific promoters. One subfamily of alternative sigma factors is the extracytoplasmic function (ECF) sigma factors, involved mostly in cell envelope functions. The aim of this work was characterize two ECF sigma factors with unknown function in P. aeruginosa, PA14_21550 and PA14_46810. The strain Δ21550 was analyzed for its survival in different stress conditions and it is more resistant in heat shock conditions at 45°C than the wild type strain. It was also observed that PA14_21550 sigma factor is not essential for bacterial growth in LB and M63 minimal medium added with glucose or succinate as the carbon source. Furthermore, overexpression of this sigma factor increases the expression of hypothetical protein PA14_30100, as verified by a proteomic approach. A strain insertionally inactivated in the PA14_46810 gene has better growth than the wild type strain in M63 added with glucose and the same phenotype regarding to biofilm formation and exopolysaccharide production as the wild type strain. Moreover, transcriptome analysis was carried out by RNA-Seq with overexpression of the PA14_46810 sigma factor in the wild type strain. Induction of genes involved in denitrification, transport of molecules and energetic metabolism in relation to the control strain was observed. On the other hand, excess of PA14_46810 represses genes involved in protein translation and spermidine synthesis. This work, therefore, brought new information about the functions of two ECF sigma of P. aeruginosa, thus contributing to a greater understanding of the physiology of this bacterium and its adaptation to different conditions.

Orientadores: Anete Pereira de Souza, Renato Vicentini dos Santos / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T17:18:13Z (GMT). No. of bitstreams: 1 Cardoso-Silva_ClaudioBenicio_D.pdf: 32808891 bytes, checksum: 4081a73930869562c59e7e44894da977 (MD5) Previous issue date: 2015 / Resumo: A cana-de-açúcar é uma das espécies de maior importância econômica no mundo devido ao seu potencial bioenergético. No entanto, o seu alto nível de complexidade genética é um desafio para a aplicação de ferramentas moleculares no melhoramento. Os recentes avanços das tecnologias de sequenciamento e genotipagem indicam o potencial de aumentar o nosso entendimento sobre a genética e a biologia molecular desta espécie. As sequências genômicas e de transcriptomas são valiosa fonte de informação para o desenvolvimento de ferramentas moleculares que permitam a identificação de regiões no genoma que estejam relacionadas com características de interesse para o melhoramento. O uso das novas tecnologias de sequenciamento de alto desempenho tem grande potencial de impacto nestas pesquisas. A presente tese objetivou analisar o transcriptoma de seis variedades comerciais e dados genômico da variedade R570, com a finalidade de identificar genes potencialmente úteis para o desenvolvimento de marcadores moleculares. A partir do método RNA-Seq, foram geradas mais de 400 milhões de sequências, as quais permitiram obter um total de 72.269 transcritos representados por uma única isoforma montados com auxílio do programa Trinity. Estes transcritos foram alinhados com sequências de Viridiplantae, gramíneas, e exclusivamente contra proteínas de sorgo, arroz, milho e transcriptoma de cana-de-açúcar, depositados em banco de dados público. Esta análise permitiu identificar o conjunto de genes de cana-de-açúcar compartilhados com outras gramíneas, bem como levou à identificação de novos transcritos que não haviam sido catalogados para cana-de-açúcar, além de longos RNAs não codificantes. Os transcritos foram anotados no Cluster of Orthologous Groups (COG) e no Gene Ontology (GO), com posterior análise de enriquecimento dos termos GO, a partir da qual foram anotados os transcritos, possivelmente relacionados a genes que conferem características de importância agronômica. No transcriptoma foram identificados mais de 700 mil SNPs e aproximadamente cinco mil regiões microssatélites. Analisando um total de 32 Mbp de sequências genômicas da variedade R570 foram identificados 4.342 microssatélites, com frequência média de sete SSR/Kb. As sequências geradas e exploradas neste trabalho são valiosa fonte de informações para entender a arquitetura genética da cana-de-açúcar, principalmente para o desenvolvimento de marcadores moleculares, os quais podem ser utilizados no mapeamento genético / Abstract: The sugarcane is one of the most economically important species in the world, due to their energy potential. However, high level of genetic complexity has been a major challenge for the use of molecular tools applied to improvement of this crop. Recent advances in sequencing and genotyping technologies indicate the potential to increase our understanding of the genetics and molecular biology of this specie. The genomic and transcriptomic are valuable sources of information for the molecular tools development that allow identification of regions in the genome that are related to characteristics of interest for the improvement. The high-throughput sequencing technologies have great impact of this research. This thesis aimed to analyze the transcriptome of six commercial varieties and genomic sequencing from R570 variety, in order to identify genes potentially useful for the molecular markers development. From RNA-Seq method were generated over 400 million sequences, which allowed obtain a total of 72,268 transcripts representing a single isoform assembled by Trinity. These transcripts were aligned against Viridiplantae, grasses, and exclusively against sorghum, rice and maize proteins, and sugarcane transcriptome available in the public database. This analysis allowed identifying a set of shared genes with other grasses, new transcripts that had not yet been cataloged for sugarcane and long non-coding RNAs. The transcripts were also annotated using the COG (Cluster of Orthologous Groups) and GO (Gene Ontology) database, followed by enrichment analysis for GO terms, from which it was possible to identify genes that play roles, possibly related to traits of agronomic importance. In the transcriptome were identified over 700 thousands SNPs and five thousands microsatellites regions. In the genomic sequences from R570 variety, in a total of 32 Mbp were identified 4,342 microsatellites, with an average frequency of seven SSR / Kb. The sequences generated and explored in this work is a valuable source to understand the genetic architecture of the sugarcane, mainly for molecular markers development, which can be used in genetic mapping / Doutorado / Genetica Vegetal e Melhoramento / Doutor em Genetica e Biologia Molecular

A glândula de veneno da serpente Bothrops jararaca é uma glândula exócrina relacionada a glândula salivar dos mamíferos. Diferentemente de outras glândulas exócrinas, esta possui um lúmen central no qual o veneno produzido fica estocado. Os mecanismos envolvidos na regulação da síntese e secreção de toxinas pela glândula de veneno são pouco conhecidos. Sabe-se que a inervação noradrenérgica possui um papel essencial no ciclo de produção de veneno, pois serpentes Bothrops jararaca tratadas com reserpina, um potente bloqueador da atividade simpática, não acumulam veneno no lúmen. Porém a ativação direta dos adrenoceptores α e β, através da ação de agonistas, tem a capacidade de reverter a ação da reserpina. No presente trabalho utilizamos métodos combinados de análise de expressão gênica em larga escala a fim de identificar os processos celulares sob controle do sistema simpático durante o ciclo de produção de veneno da glândula de veneno de Bothrops jararaca. Foi construído um array de cDNA em membrana da náilon contendo 4608 clones provenientes da biblioteca de cDNA construída a partir das glândulas de veneno de um macho e uma fêmea, adultos, de Bothrops jararaca. Para a análise temporal da expressão gênica foram utilizados machos adultos de B. jararaca. As glândulas de veneno foram extraídas em diferentes dias do ciclo de produção de veneno (0, 1, 2, 4 e 15 dias). Através da análise do perfil de expressão gênica identificamos que os transcritos de toxinas e de não toxinas (celulares) possuem perfil semelhante de expressão ao longo do ciclo, sendo que no 2° dia do ciclo ocorre o pico de expressão desses transcritos. Para identificar os processos celulares sob controle da inervação noradrenérgica machos adultos de B. jararaca foram submetidos a tratamento farmacológico com reserpina (glândula 4dR) e com reserpina e agonistas dos adrenoceptores α e β (glândula 4dA). Na análise da expressão gênica utilizando macroarranjos, entre os clones com expressão aumentada na glândula 4dR, aproximadamente 51% eram de toxinas, indicando que a inibição da atividade simpática não interfere na transcrição das toxinas. A análise dos transcritos celulares confirmou que os processos de transcrição e tradução não são afetados pelo tratamento com reserpina. A análise da expressão por PCR quantitativo em tempo real, confirmou que as toxinas são expressas normalmente na glândula 4dR. Além disso, a análise da expressão de genes envolvidos nos processos de enovelamento protéico e secreção revelou que genes responsivos a estresse de retículo endoplasmático apresentam aumento na expressão na glândula 4dR. Também realizamos a análise transcriptômica por sequenciamento em larga escala (RNA-seq) da glândula 4d e da glândula 4dR. Entre os contigs identificados como toxinas não houve diferenças quantitativas nem qualitativas significativas entre as glândulas 4d e 4dR, confirmando que o processo de transcrição de toxinas ocorre independentemente da ativação dos adrenoceptores α e β. A análise de enriquecimento de termos do gene ontology revelou predominância de processos biológicos relacionados a resposta a estresse de retículo endoplasmático entre os transcritos mais expressos na glândula 4dR e de processos envolvendo a formação de vesículas de transporte entre os transcritos menos expressos na glândula 4dR. Na análise dos transcritos exclusivos da glândula 4d e exclusivos da glândula 4dR identificamos diversas isoformas de small GTPases da família Ras (Rab) que possuem papel fundamental na regulação da formação de vesículas. Assim, nesse trabalho mostramos que o processo de transcrição de toxinas ocorre independentemente da ativação dos adrenoceptores α e β e que a ativação dos adrenoceptores parece ser necessária para que ocorra a formação de vesículas secretoras. Já a inibição do processo pela ação da reserpina possivelmente provoca a ativação da resposta UPR (unfolded protein response), o que pode estar associado com o acúmulo de proteínas no lúmen do retículo endoplasmático. / The venom gland of the Brazilian venomous snake Bothrops jararaca (Crotalinae, Viperidae) is an exocrine tissue related to the salivary gland. The venom gland has a central lumen where the venom is stored. When the venom is released, the production of new venom is triggered by the activation of noradrenaline on both α1- and β-adrenoceptors. But the genes involved and the regulation of venom production cycle are poorly known. When the Bothrops jararaca is treated with reserpine, a depletor of catecholamine, the venom production is inhibited. At present work we used combined methods of high throughput analysis of gene expression to identify cellular process controlled by the sympathetic system during the cycle of venom production in the venom glands of Bothrops jararaca. Was constructed a cDNA array with 4608 clones from a cDNA library of the venom glands of one male and one female of B.jararaca. In order to get a time series analysis adult males of B.jararaca were used. The venom gland was extracted at different time points of the venom production cycle (0, 1, 2, 4 and 15 days). The resulting profile of the gene expression of toxins and non-toxins during the cycle was shown to be similar, and the higher level of gene expression was found at the 2nd day of the venom production cycle. A differential gene expression analysis was performed also with venom glands of B.jararaca treated with reserpine. Although previous results reported that venom glands under effect of reserpine are not able to produce venom, we found that 51% of upregulated clones of the venom gland treated with reserpine (4dR) are toxins. Moreover, most of the non-toxins clones were involved with transcription and translation processes, showing that these processes are not affected by the inhibition of the sympathetic system. The analysis of gene expression by quantitative real-time PCR confirmed that in the venom gland treated with reserpine (4dR) the toxins are normally produced, and the genes responsive for unfolded protein response (UPR) are upregulated. We also performed the next generation sequencing to produce a transcriptomic profile (RNA-seq) of normal venom gland (4d) and venom gland treated with reserpine (4dR). The comparison between the transcripts of toxins found at 4d and 4dR transcriptomes revealed no qualitative or quantitative differences, confirming that the toxins transcription are independent of the activation of α1- and β-adrenoceptors. The enrichment analysis of Gene Ontology terms revealed that the unfolded protein response are activated at 4dR venom gland and the membrane trafficking are possibly inhibited. We also identify many isoforms of Ras family small GTPases (Rab proteins) that has a key role ate regulation of membrane trafficking. At present work we showed that the transcriptional control of the toxins in the venom gland are independent of the activation by α1- and β-adrenoceptors, however, the adrenoceptors seems to be necessary to activate the secretory pathway. The inhibition of the activation of α1- and β-adrenoceptor by reserpine seems to be recruiting an unfolded protein response, probably due to the accumulation of proteins at the lumen of the endoplasmic reticulum.

Haemophilus influenzae (Hi) é uma bactéria Gram-negativa comensal da nasofaringe e um patógeno oportunista cujo único hospedeiro natural conhecido é o ser humano. As cepas de Hi que possuem cápsula de polissacarídeo estão associadas a doenças invasivas mais graves, sendo as de sorotipo b (Hib) as principais causadoras da meningite bacteriana em populações não vacinadas. Para produzir a vacina contra Hib, o polissacarídeo purificado desta bactéria é conjugado quimicamente ao toxóide tetânico. Industrialmente, a produção do polissacarídeo é realizada cultivando esse micro-organismo em biorreatores, entretanto o rendimento em polissacarídeo é baixo, mesmo com fornecimento de nutrientes, controle de pH e outros ajustes das condições no decorrer do cultivo. O estudo dos diferentes perfis fisiológicos da população bacteriana de Hib no decorrer do cultivo através da transcritômica traz a possibilidade de aprofundar o conhecimento sobre o metabolismo desse micro- organismo. As taxas de transcrição dos genes expressos em diferentes momentos considerados como pontos metabolicamente significativos do cultivo de Hib linhagem GB 3291 em batelada alimentada conduzido em Biorreator de 10 L, com aeração submersa e controles de pH (7,0) e temperatura (30° C) foram obtidas através de sequenciamento de RNA paralelo massivo (RNA-seq). A análise de co-expressão dos genes foi realizada com WGCNA, em que oito módulos de genes co-expressos foram identificados, quatro dos quais apresentaram correlação alta com dados fenotípicos dos cultivos, inclusive produtividade de acetato e de polissacarídeo. Análise de enriquecimento funcional identificou vias metabólicas associadas a ribossomo, síntese de parede celular, transportadores e consumo de carbono. A análise de expressão diferencial permitiu observar o comportamento desta bactéria durante o cultivo. Através da análise das taxas de transcrição dos genes foi possível identificar as principais vias de síntese de acetato e de polissacarídeo capsular, sendo esta última feita principalmente através da via de pentose fosfato, em detrimento da via de interconversão pentose-glucuronato. Nossos dados mostram que as diferentes etapas do cultivo de Hib leva à ação conjunta de vários grupos de genes, com destaque àqueles ligados às funções celulares básicas, como a síntese de proteínas e de parede celular, o transporte e a síntese de aminoácidos. Esses resultados contribuem para o entendimento dos processos bioquímicos e celulares que ocorrem durante o processo de cultivo de Hib, possibilitando que sejam feitas sugestões de modificações genéticas em Hib e alteração no processo de cultivo com propósito de diminuir produção de acetato e aumentar produção do polissacarídeo. / Haemophilus influenzae (Hi) is a nasopharynx commensal Gram-negative bacterium and an opportunistic pathogen whose only known natural host is human being. Hi strains with polysaccharide capsule are related to more severe invasive diseases, wherein type b capsule (Hib) strains are the main cause of bacterial meningitis in unvaccinated population. To produce Hib vaccine, purified polysaccharide of this bacterium is chemically conjugated to tetanus toxoid protein. Industrially, polysaccharide production is performed by cultivating this micro-organism in bioreactors; however, the yield of polysaccharide is low, even with supply of nutrients, pH control and further adjustments of the fermentation conditions during cultivation. The study of different physiological profiles of Hib bacterial population during cultivation by transcriptomics brings the possibility to deepen the knowledge about the metabolism of this micro-organism. Transcription of genes expressed at different times considered metabolically significant points of Hib strain GB 3291 grown in fed-batch conducted in a 10 L bioreactor with submerged aeration and pH (7.0) and temperature (30 ° C) control rates were obtained through massive parallel RNA sequencing (RNA-seq). Gene co-expression analysis was performed with WGCNA, in which eight modules of co-expressed genes were identified, four of which showed high correlation with cultivation data traits, including acetate and polysaccharide productivity. Enrichment analysis identified pathways related to ribosome, cell wall synthesis, transports and carbon consumption. Differential expression analysis allowed to observe this bacteria behaviour during cultivation. Through transcription rate analysis, it was possible to identify the main pathways for acetate and polysaccharide synthesis, which is through pentose phosphate pathway instead of glucoronate-pentose pathway. Our data show that different stages in Hib cultivation leads to joint action of several gene groups, highlighting genes related to basic cellular roles, like protein and cell wall synthesis, transport and aminoacid synthesis. These results contribute to the understanding of biochemical and cellular processes that ocurr during Hib cultivation process, allowing suggestions to be made to modify Hib gene circuitry and to change cultivation process in order to decrease acetate production and to decrease acetate production and increase polysaccharide production.

L’infertilité masculine est actuellement considérée comme un problème majeur qui pose une situation alarmante sur la santé publique. L’oligozoospermie, l’asthénozoospermie et la tératozoospermie sont les trois anomalies les plus connues des spermatozoïdes. Elles affectent, respectivement, la densité, la motilité et la morphologie des spermatozoïdes. Un spermatozoïde anormal est très souvent corrélé à des altérations génétiques et épigénétiques qui peuvent affecter considérablement le transcriptome. Dans ce sens, le séquençage aléatoire du transcriptome entier des spermatozoïdes ou RNA-seq constitue un outil puissant pour caractériser ces maladies. Jusqu’à présent, il n’existe aucune étude exploitant des données RNA-seq chez des hommes présentant de telles anomalies spermatiques. L’objectif principal de notre étude fût d’identifier des profils distincts des modifications du transcriptome de chaque phénotype d’infertilité pour ainsi révéler des gènes-signatures qui tamponnent une spermatogenèse pathologiquePour ce faire, les transcriptomes des spermatozoïdes de 60 sujets infertiles atteints soit d’oligozoospermie, d’asthénozoospermie ou de tératozoospermie ont été comparés à ceux de 20 patients fertiles. Ces analyses supervisées nous ont conduit à identifier: (i) les gènes clés spécifiques aux différentes anomalies des spermatozoïdes (ii) les voies de signalisation associées, (ii) les différents longs ARNs non codants dérégulés dans ces anomalies. Au niveau de l’oligozoospermie, les transcrits de spermatozoïdes dérégulés étaient associées à divers stades de la spermatogenèse, y compris le cycle cellulaire méiotique, l’assemblage du complexe synaptonémal, la cohésion des chromatides sœurs, les processus métaboliques de piRNA, le processus catabolique protéique dépendant de la voie de l’ubiquitine, à la réponse aux dommages de l'ADN et particulièrement le processus de fécondation. Quant à l’asthenozoospermia, la spermatogenèse, l’assemblage du cil, des voies métaboliques reliées à la spermatogenèse, la chimiotaxie et la physiologie des cellules immunitaires ont été significativement dérégulés. De plus, ce qui nous a intéressé au plus était l’analyse des transcrits sous-exprimés qui a permis l’identification de nombreux transcrits associées aux modifications des histones. Nous avons aussi mis en évidence une sous expression des gènes différentiellement exprimés qui définit la tératozoospermie. Cette sous expression est associée au système ubiquitine-protéasome, à l’organisation du cytosquelette, au cycle cellulaire, à la SUMOylation en réponse aux dommages de l'ADN et aux protéines de réparation ainsi qu’à de nombreux modulateurs épigénétiques. Les gènes signature de l'oligozoospermie ont été liés au processus de fécondation et les composants de la matrice extracellulaire, tandis que ceux de la tératozoospermie sont liés à la spermatogenèse et la morphogenèse cellulaire, alors que les gènes signature de l'asthénozoospermie sont impliqués dans l'assemblage du ribosome et du flagelle. En complément de cette étude, nous avons réalisé une étude très globale du paysage épigénétique du sperme des hommes infertiles. Nous avons, ainsi comparé les niveaux des espèces réactives de l’oxygène (ERO), de méthylation de l’ADN, ainsi que l’intégrité de la chromatine dans les spermatozoïdes de 30 individus infertiles avec ceux de 33 individus fertiles. Nos analyses montrent des niveaux élevés d’ERO chez les individus infertiles. Ces niveaux sont d’une part négativement corrélés avec les niveaux de méthylation globale de l’ADN et d’autre part négativement corrélés avec ceux de la 5-hydroxyméthylcytosine et de la 5-formylcytosine (intermédiaire dans le processus de déméthylation active). Ces derniers suggèrent qu’une infertilité associée au stress oxydatif conditionne l’épigénome du sperme. En conclusion, l’ensemble de notre travail apporte des ressources précieuses et originales dans la compréhension des pathologies de sperme. / Male infertility is actually considered as a public alarming health problem. The sperm pathologies spectrum ranges between different phenotypes including oligozoospermia, asthenozoospermia and teratozoospermia depending on the sperm conventional parameters abnormalities. Abnormal sperm is characterized by genetic alterations and epigenetic alterations which can affect the transcriptome extensively. These alterations in RNA profiles are retrospectively indicative of aberrant spermatogenic events. RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome. To date, RNA-seq analysis of sperm from infertile men has not been reported. Our objectives are: (i) recognize key clusters, key pathways and specific gene transcripts for different sperm abnormalities; (ii) catalog the spermatozoal lncRNAs in different sperm pathologies; (iii) identify signature genes which are mechanistically important in the cascade of events driving a pathological spermatogenesis; (iii) portray the global epigenetic landscape in sperm from infertile men. Expression data from 60 sperm samples from 3 groups of infertile men (oligozoospermia, asthenozoospermia, and teratozoospermia) were generated on Illumina HiSeq platform, compared to 20 fertiles, and the resulting gene expression patterns were analyzed for functional enrichment. Our supervised analyses identified numerous differentially expressed genes between fertile and infertile men. In oligozoospermia, the deregulated spermatozoal transcripts were associated with various stages of spermatogenesis including meiotic cell cycle, synaptonemal complex assembly, sister chromatid cohesion, piRNA metabolic process, ubiquitin-dependent protein catabolic process, cellular response to DNA damage stimulus and interestingly fertilization. As for asthenozoospermia, spermatogenesis, cilium assembly, metabolic-related pathways, chemotaxis and immune cell physiology were most significantly differentially expressed. Interestingly, numerous transcripts associated with histone modifications were highly down-regulated. With regards to teratozoospermia, we evidenced sperm-specific differentially expressed genes which are involved in the ubiquitin-proteasome, cytoskeleton organization, the cell cycle pathway, SUMOylation of DNA damage response and repair proteins, as well as many putative epigenetic modulators of gene expression.. We also attempted to identify distinct patterns of gene expression changes that were definite to the different abnormal sperm phenotypes in infertile men relative to controls. Signature genes of oligozoospermia were over-enriched by genes involved in fertilization and extracellular matrix components, while signature genes of teratozoospermia were enriched by genes involved in spermatogenesis and cellular components involved in morphogenesis, whilst signature genes of asthenozoospermia were enriched by genes implicated in ribosome and cilium assembly.We complemented this work by a parallel epigenetic analysis of the global epigenetic landscape in infertile men. We compared the levels of reactive oxygen species (ROS), DNA integrity and global epigenetic parameters in sperm from 33 infertile subjects with abnormal semen parameters compared to fertile individuals. We pointed out that infertile men are characterized by strikingly high levels of reactive oxygen species (ROS) which were in part negatively correlated with the global DNA methylation, and positively correlated with the levels of 5-hydroxymethylcytosine and 5-formylcytosine (active demethylation intermediates). These findings suggest that male infertility associated with oxidative stress shapes the sperm epigenetic landscape. In summary, this original work yielded a transcriptional portrait of sperm abnormalities and provided valuable resources that would further elucidate sperm pathologies.

Les ribozymes sont des ARN naturels ou artificiels possédant une activité catalytique. Les ribozymes artificiels ont été identifiés in vitro par la méthode SELEX, et plusieurs d'entre eux ont été caractérisés par des études cinétiques. Ces molécules sont impliquées dans des réactions de clivage, de ligation, de modification d'extrémités d'ARN, de polymérisation, de phosphorylation et d'activation de groupements acyl. Parce qu'elle est nécessaire à la traduction, l'aminoacylation des ARN joue un rôle évolutif important dans la transition du monde de l'ARN vers le monde moderne de l'ADN et des protéines, et elle est centrale à l'établissement du code génétique. Plusieurs ribozymes catalysant le transfert d'acides aminés à partir de cofacteurs activants ont pu être isolés et caractérisés depuis une vingtaine d'années, ce qui a documenté la possibilité d'aminoacylation d'ARNt en l'absence des aminoacyl ARNt synthétases. En développant un nouveau protocole SELEX basé sur l'oxydation au périodate, le but de notre travail est de découvrir de nouveau ribozymes d'une taille de l'ordre d'une vingtaine de nucléotides pouvant combiner la catalyse de l'activation des acides aminé et la transestérification. Bien que des molécules catalysant l'une ou l'autre des deux réactions ont été identifiées, aucun ribozyme n'existe à ce jour qui puisse utiliser des acides aminés libres et un cofacteur activant pour réaliser l'aminoacylation en 3' dans un même milieu réactionnel. La sélection de molécules actives dans une approche SELEX exige la présence de régions constantes sur les deux extrémités des séquences pools aléatoires initiaux. Ces régions sont nécessaires pour l'amplification par PCR, mais elles imposent des contraintes importantes pour l'identification de ribozymes car elles peuvent complètement inhiber leur activité par interférence structurelle. Nous présentons un protocole optimisé qui minimise la taille de ces régions constantes. D'autre part, notre nouveau design est très spécifique pour la sélection d'ARN aminoacylés sur l'extrémité 3'. Ce protocole a été utilisé pour réaliser 6 à 7 cycles de sélection avec différents pools, et un enrichissement en séquences spécifiques a pu être mis en évidence. Bien que certains tests avec les pools sélectionnés a révélé une activité possible, des essais avec des séquences spécifiques de ces pools n'ont pour l'instant pas pu confirmer l'activité catalytique recherchée. Un protocole basé sur le même principe de sélection a été utilisé dans une étude parallèle pour identifier les ARN aminoacylés présents dans l'ARN total d'Escherichia coli. Dans ce deuxième travail, note but est d'identifier tous les d'ARN aminoacylés par séquençage massif, avec à la clé la découverte possible de molécules autres que les ARNt et ARNtm. En utilisant les ARNt comme modèle, nous nous sommes aperçus qu'un protocole RNAseq standard n'était pas adapté à cause des bases modifiées présentes sur ces molécules. Nous avons développé et mis au point un nouveau protocole pour l'identification de n'importe quelle séquence aminoacylée en 3'. La nouvelle approche présentée devrait permette l'étude exhaustive de l'aminoacylation de toutes les séquences présentes dans l'ARN total. / Ribozymes are natural or in vitro selected RNA molecules possessing a catalytic activity. Artificial ribozymes have been extensively investigated by in vitro SELEX experiments, and characterized by kinetic assays. Ribozymes are involved in RNA cleavage, ligation, capping, polymerization, phosphorylation and acyl activation. Because it is required for translation, RNA aminoacylation plays an important role in the evolution from the late RNA world to the modern DNA and protein world, and is central to the genetic code. Several ribozymes catalyzing amino acid transfer from various activating groups have already been selected and characterized in the past two decades, documenting the possibility of tRNA aminoacylation in the absence of aminoacyl tRNA synthetase. With a newly designed SELEX protocol based on periodate oxydation, the aim of our investigation is to uncover small ribozymes of the order of 20 nucleotides that could catalyze both amino acid activation and transesterification. Although molecules catalyzing either reaction have been identified, no existing ribozyme could use free amino acids and activating cofactor(s) as substrates for 3' esterification in a single reactional context. The selection of active molecules in a SELEX procedure requires the presence of constant tracks on both ends of the sequences constituting the initial random pools. These tracks are required for PCR amplification, but they impose significant burden to the identification of ribozymes because they can prevent any activity through structural inhibition. We present an optimized protocol that significantly minimizes the size of these constant tracks. At the same time, our newly design protocol is very specific for the selection of 3'-end aminoacylated RNA. Working with this protocol, we performed 6 to 7 cycles of selection with different pools, and observed an enrichement with specific sequences. Although some experiments performed with entire pools did reveal a possible activity, no activity could be so far confirmed with specific sequences. A similar protocol was also applied in a parallel study to identify aminoacylated RNA from total RNA in Escherichia coli. In this other approach, our goal is to possibly identify new classes of aminoacylated RNA while using the deep sequencing technology. Using tRNA to validate our protocol, we realized that a standard RNAseq procedure could not work due to the presence of modified bases. We established a new method for bank preparation to identify any sequence aminoacylated at the 3' end. Ultimately, this new approach will allow us to study the level of aminoacylation of any sequence present in total RNA.