L'éthyl tert-butyl éther (ETBE) et le méthyl tert-butyl éther (MTBE) sont des éthers carburants utilisés comme additifs dans les essences sans plomb. Du fait de leur utilisation massive, de nombreux cas de pollutions d'aquifères ont été répertoriés, en particulier pour le MTBE, et ces composés représentent donc un risque sanitaire potentiel. Des travaux récents ont permis de mettre en évidence différents micro-organismes capables de dégrader ces composés malgré leur faible biodégradabilité dans l'environnement. Néanmoins, une meilleure compréhension de l'écologie et de la régulation de ces capacités de dégradation permettrait une meilleure gestion de la bioremédiation de sites contaminés par l'ETBE ou le MTBE.L'objectif de la thèse, réalisée dans le cadre d'un projet ANR Blanc (MiOxyFun), est de mieux comprendre l'écologie des communautés microbiennes impliquées dans la dégradation de ces éthers et leur relation avec la régulation ainsi qu'avec les cinétiques de dégradation de ces composés par des membres spécifiques de ces communautés. Ainsi, à partir de différents échantillons environnementaux venant de sites pollués par l'ETBE ou le MTBE, des enrichissements ont pu être réalisés en laboratoire afin d'étudier leurs microflores. Ces enrichissements ont été étudiés notamment pour leurs cinétiques de dégradation, la composition de leurs communautés bactériennes, et pour l'isolement de souches bactériennes directement impliquées dans la dégradation de ces composés. L'étude des cinétiques de dégradation de l'ETBE ou du MTBE par différents enrichissements obtenus sur ETBE (cinq) et sur MTBE (six) a permis de montrer des profils de dégradation très différents. La dégradation était généralement lente et s'accompagnait d'un faible rendement en biomasse avec parfois accumulation transitoire de tert-butanol (TBA). Les capacités de dégradation d'autres composés des essences (BTEXs et n-alcanes) étaient aussi différentes d'un enrichissement à l'autre, le benzène, entre autres, étant dégradé par 10/11 enrichissements. Des techniques d'empreinte moléculaire (RISA, DGGE) ont permis de constater que les communautés bactériennes présentes dans les cinq enrichissements sur ETBE étaient différentes de celles sur les enrichissements sur MTBE. Les enrichissements sur ETBE ont fait spécifiquement l'objet d'une étude par analyse de banques de clones réalisées à partir des gènes codant l'ARNr 16S de ces enrichissements. Cette étude a montré la prédominance des Proteobacteria dans trois enrichissements, la prédominance des Acidobacteria dans un autre ainsi qu'une composition plus héterogène dans le cinquième. De plus, des Actinobacteria ont été détectées dans les 5 enrichissements.En parallèle, plusieurs souches possédant des capacités de dégradation ont été isolées des enrichissements: Rhodococcus sp. IFP 2040, IFP 2041, IFP 2042, IFP 2043 (dégradant l'ETBE jusqu'au TBA), une Betaproteobacteria IFP 2047 (dégradant l'ETBE), Bradyrhizobium sp. IFP 2049 (dégradant le TBA), Pseudonocardia sp. IFP 2050 (dégradant l'ETBE et le MTBE), Pseudoxanthomonas sp. IFP 2051 et une Proteobacteria IFP 2052 (dégradant le MTBE). Une étude par qPCR sur les gènes codant l'ARNr 16S a montré la prédominance de certaines souches isolées dans les enrichissements ETBE. Enfin, plusieurs gènes connus comme étant impliqués dans la dégradation des éthers carburants ont pu être mis en évidence dans les enrichissements et dans certaines des souches isolées.

O feijão é importante fonte carboidratos, vitaminas, minerais e fibras. No Brasil, a produtividade desta leguminosa é baixa e um dos fatores é a ocorrência de doenças como a antracnose causada pelo Colletothrichum lindemuthianum, que gera perdas de até 100% da produção. Plantas possuem diversos mecanismos de defesa contra patógenos e relatos apontam que o silício é capaz não só de promover mudanças morfológicas nas folhas, mas também de ativar os genes de resistência. O presente trabalho foi dividido em três estudos que tinham como objetivo: (1) entender a resposta de três cultivares de feijoeiro ao silício disponível na solução nutritiva; (2) identificar a contribuição do Si na expressão de genes relacionados à infecção pelo fungo através da construção de duas bibliotecas subtrativas por supressão (SSH), visando selecionar genes diferencialmente representados durante a infecção da planta com a raça 65 de C. lindemuthianum (a) e durante a infeção da planta na presença de uma maior dose silicato de potássio (75 ppm) no substrato (b); (3) identificar a resposta de dez transcritos selecionados no Estudo 2 para tentar entender a resposta dos mesmos em diferentes períodos (0; 6; 42; 72 h) após a inoculação, com ou sem suplemento de Si. Como resultados, foi observado que para as três cultivares avaliadas o Si começa a ser absorvido 14 dias após o transplante. Também foi identificado por de microscopia de varredura (MEV) que não há diferença significativa entre o número de tricomas e cada cultivar, mas que para o número de estômatos a cultivar IAC-Harmonia destacou-se das demais. Além disso, quando as três cultivares foram suplementadas com Si, houve a formação de uma cera epicuticular descrita como mecanismo de defesa da planta contra fungos; e que através de EDX (Energy-dispersive X-ray spectroscopy) foi possível constatar que plantas tratadas com Si apresentam maior teor deste elemento nas folhas. Através de inoculações com a raça 65 do patógeno verificou-se o efeito do mineral na redução da severidade da doença nas cultivares IAC-Harmonia e Pérola. No segundo estudo, duas bibliotecas de hibridização subtrativa por supressão (SSH), foram construídas visando selecionar os genes diferencialmente expressos entre plantas inoculadas e não-inoculadas (A) e entre plantas inoculadas e tratadas ou não com 75 ppm de Si (B). Foram geradas 991 sequências únicas, anotadas através do GeneOntolgy. Quinze genes de cada biblioteca foram selecionados para os experimentos de validação por RT-qPCR. Para a Biblioteca A, 11/15 genes foram positivamente regulados, e em B, 14/15. No terceiro estudo ficou evidenciado que a inoculação com o patógeno alterou positivamente a expressão de sete genes, enquanto que o tratamento com 75 ppm de Si alterou a expressão de oito genes, em pelo menos um dos tempos avaliados / Beans are an important source of carbohydrates, vitamins, minerals and fibers. In Brazil, this legume still has low productivity and one of the factors involved is the occurrence of diseases such as anthracnose, caused by the fungus Colletothrichum lindemuthianum, which causes losses in production of up to 100%. Plants present several defense mechanisms against pathogens and the reports indicate that silicon does not only promote morphological changes in leaves, but also activates resistance genes. This work was divided into three studies aiming: (1) to understand the response of three bean cultivars to a silicon source in a nutrient solution, (2) to identify the contribution of Si in the expression of genes related to the infection by the fungus by constructing two subtractive suppression libraries (SSH), to select genes differentially represented during infection of the plant with race 65 of C. lindemuthianum (a) and during infection of the plant in the presence of higher dose of potassium silicate (75 ppm) in the substrate (b), (3) to identify the response of ten selected transcripts in Study 2 in various periods (0, 6, 42, 72 h) after inoculation, with or without supplemental Si. As a result, it was observed that for all three cultivars Si begins to be absorbed 14 days after transplantation. Was also identified by microscopy (SEM) that there is no significant difference between the number of trichomes among cultivars, but that the number of stomata for the IAC-Harmonia stood out from the rest. Moreover, when the three cultivars were supplemented with Si, thus forming an epicuticular wax described as a defense mechanism against plant fungi, and that by EDX (Energy-dispersive X-ray spectroscopy) it was found that plants treated with Si have higher content of this element in leaves. Through inoculations with race 65 of the pathogen it was verified the effect of the mineral in reducing disease severity in IAC-Pérola and IAC - Harmonia. In the second study, two libraries from suppression subtractive hybridization (SSH) were constructed in order to select the differentially expressed genes between inoculated and non-inoculated (A) and between plants inoculated and treated or not with 75 ppm of Si (B). In total, 991 unique sequences were generated, those recorded by GeneOntolgy. Fifteen genes from each library were selected for the validation experiments by RT-qPCR. For library A, 11/15 genes were positively regulated, and in B, 14/15. In the third study it is showed that inoculation with the pathogen positively altered expression of seven genes, whereas treatment with 75 ppm of Si changed the expression of eight genes, in at least one of the times analyzed

Durante o preparo químico-cirúrgico são utilizados instrumentos e substâncias químicas, que constituem um binômio indivisível e necessário para alcançar a modelagem e a sanificação dos canais radiculares. Assim, propõe-se com este trabalho avaliar in vivo, por meio de método molecular de PCR quantitativo, baseado em DNA (qPCR), a eficiência do preparo químico-cirúrgico empregando como agente de irrigação o Hipoclorito de Sódio (NaOCL) a 2,5% ou o Gel de Endo PTC associado ao Hipoclorito de Sódio a 1,0% na redução bacteriana de canais radiculares de dentes portadores de periodontite apical primária. Foram selecionados 30 pacientes portadores de infecção endodôntica primária, totalizando 30 dentes, com rarefação óssea periapical visível na radiografia, sem tratamento endodôntico prévio. Os pacientes foram divididos de forma randomizada em dois grupos distintos, de acordo com a substância química auxiliar utilizada durante a instrumentação, NaOCL 1% + Endo-PTC leve ou NaOCL 2,5%. Em todos os casos empregou-se instrumentos Reciproc R40 ou R50 e as coletas foram realizadas antes (S1) e após o prepare químico-cirúrgico (S2). A análise de aderência foi realizada por meio do teste de Kolmogorov-Smirnov, as análises intragrupo foram realizadas com teste de Wilcoxon para amostras relacionadas e as comparações entre os dois grupos foram realizadas com o teste de Mann-Whitney, para a análise quantitativa de bactérias. Em ambos os grupos, houve diminuição significativa no número de bactérias entre S1 e S2 (p<0,05). No grupo NaOCL 1% + Endo-PTC leve, houve redução de 3,7x105(S1) para 5,7x104 (S2). No grupo NaOCl 2,5%, redução de 1,3x105 (S1) para 1,1x104(S2). Na comparação entre grupos, o NaOCL a 2,5% (91,62%) promoveu maior redução bacteriana do que o grupo NaOCL 1% + Endo-PTC (84,60%) (p<0,05). / During the chemomechanical preparation, instruments and chemical substances are used, which constitute an indivisible and necessary binomial to achieve modeling and sanification. Knowing the auxiliary chemical substances, understanding their mechanisms of action, being able to use them efficiently, is fundamental, so that the chemical-surgical preparation is well performed by the clinician. Thus, the purpose of this study is to evaluate in vivo, the efficiency of the chemomechanical preparation using as the irrigant agent 2,5% sodium hypochlorite and Endo-PTC gel, associated to 1% sodium hypochlorite, to assess the bacterial reduction of root canals of teeth with primary apical periodontitis, using a molecular quantitative method DNA-based - polymerase chain reaction (qPCR). Were selected 30 patients with primary infection totaling 30 teeth, with visible periapical bone rarefaction on the radiography, without previous endodontic treatment. Patients were randomly divided into two distinct groups according to the auxiliary chemical substances used during the instrumentation, 1% sodium hypochlorite associated with Endo-PTC gel or 2,5% sodium hypochlorite. In all cases, reciproc instruments R40 or R50 were used and the samples were taken before (S1) and after chemical surgical preparation (S2). The adherence analysis was performed using the Kolmogorov-Smirnov test, intragroup analysis were performed with Wilcoxon test for related samples and comparisions between the two groups were performed with the Mann-Whitney test for the quantitative analysis of bacteria. In the both groups, there was a significant decrease in the number of bacteria between S1 and S2 (p<0,05), the inicial sample (S1) of the group Endo-PTC, the median 3,7x105, reduced to 5,7x104. In the other group of NaOCl, the median in S1 was 1,3x105 that reduced to 1,1x104 . In the comparision between groups, the 2,5% NaOCl promoted a greater microbial reduction of 91,62%, than the Endo-PTC associated with 1% NaOCl (p<0,05) 84,60%.

O Brasil é o maior produtor mundial de maracujá azedo (Passiflora edulis f. flavicarpa) sendo esta a espécie de maior expressão comercial dentre as passifloras cultivadas. A bacteriose do maracujazeiro, causada por Xanthomonas axonopodis pv. passiflorae (Xap), é uma das doenças mais severas da cultura, acarretando grandes prejuízos aos produtores. Atualmente, é incipiente o conhecimento sobre a interação maracujá azedo-Xap. Diante disso, a identificação e a caracterização dos genes envolvidos no processo de defesa são passos importantes para dar suporte ao desenvolvimento de variedades resistentes. Assim, o objetivo deste trabalho foi identificar e caracterizar genes de maracujá azedo diferencialmente expressos durante a resposta de defesa à Xap, bem como mensurar a sua expressão. Para isso, foram construídas duas bibliotecas subtrativas de cDNA (forward e reverse) usando o método SSH a partir de transcritos de folhas, que foram inoculadas com o patógeno ou solução salina (controle). Após o sequenciamento dos clones, o processamento e a montagem das sequências, as unisequências foram anotadas através da Plataforma PLAZA e do programa computacional Blast2GO. Genes envolvidos em diversos processos biológicos foram selecionados para a validação das bibliotecas por PCR quantitativo. Usando a Plataforma PLAZA, 78 % (764) das unisequências mostraram similaridade com proteínas de Arabidopsis thaliana, enquanto 87 % (866) delas apresentaram similaridade com proteínas putativas de diversas espécies vegetais, quando se utilizou Blast2GO. Na biblioteca forward, foram identificadas 73 proteínas relacionadas à resposta de defesa, dentre as quais estão proteínas envolvidas na sinalização intracelular, na ativação da transcrição e regulação da expressão de genes de defesa, bem como proteínas de defesa, de resistência e relacionadas à patogênese (PRs). Dentre os 22 transcritos validados, 95 % foram diferencialmente expressos em pelo menos um dos três períodos avaliados; os genes mais expressos em resposta à infecção pelo patógeno são os que codificam as enzimas lipoxigenase, (+)-neomentol desidrogenase e quitinase, as quais participam diretamente nas respostas de defesa vegetal. Dos genes cuja expressão foi mais reprimida, dois codificam proteínas relacionadas à fotossíntese e dois codificam proteínas envolvidas na detoxificação da amônia e do H2O2. Nossos resultados sugerem que a planta utiliza um arsenal de transcritos para responder à infecção; entretanto, este arsenal não é eficiente para impedir a ação do patógeno e, consequentemente, o desenvolvimento da bacteriose nas condições estudadas. Nosso estudo é inédito e gerou informações sobre a reprogramação transcricional durante a interação maracujá azedo-Xap, o que constitui um importante passo para o melhor entendimento sobre este patossistema. / Brazil is the main producer of yellow passion fruit (Passiflora edulis f. flavicarpa) worldwide, which is the most widely commercialized crop among the cultivated passifloras. The bacterial leaf spot induced by Xanthomonas axonopodis pv. passiflorae (Xap) is one of the most severe diseases of the crop, causing great losses to producers. Currently, we understand very little about the yellow passion fruit-Xap interaction. Therefore, the identification and characterization of genes involved in the defense process are important steps to support the development of resistant varieties. Thus, the objective of this study was identify and characterize differentially expressed genes during the defense response to Xap, as well as to measure their expression. For that, we constructed two subtractive cDNA libraries (the forward and the reverse) by performing the SSH method from leaf transcripts, which were inoculated with the pathogen or saline solution (control). After sequencing the clones and sequence data processing, sequences were assembled into unique sequences, which were annotated using the PLAZA Platform and the computational program Blast2GO. Genes involved in several biological processes were selected to validate the libraries by quantitative PCR. When PLAZA was used for sequence similarity searches, 78 % (764) of the yellow passion fruit unique sequences showed similarity to proteins of Arabidopsis thaliana; when Blast2GO was used, 87 % (866) of the unique sequences showed similarities to putative proteins of several plant species. For the forward library, 73 proteins related to defense response were identified, such as those involved in intracellular signaling, transcription activation and regulation of defense gene expression, as well as defense and resistance proteins, and pathogenesis-related proteins (PRs). Of the 22 validated transcripts, 95 % were differentially expressed during at least one of the three periods evaluated; the genes up-regulated in response to the pathogen infection were those that code for the enzymes lipoxygenase, (+)-neomenthol dehydrogenase and chitinase, which participate directly in plant-defense responses. Out of down-regulated genes, two code for photosynthesis-related proteins, and two for ammonia and H2O2 detoxification. Our results suggest the plant uses an arsenal of transcripts to respond to infection; however, this arsenal is not effective to prevent pathogen action and consequently the occurrence of bacterial leaf spot under the evaluated conditions. The present study is the first to produce information on the transcriptional reprogramming during the passion fruit-Xap interaction, which represents an important step for a better understanding of this pathosystem.

A digestão anaeróbia tem se apresentado como um processo de grande interesse sob a ótica da potencial produção de energia renovável (H2 e CH4), considerando-se a ampla variedade de compostos orgânicos que podem ser utilizados. Neste estudo desejou-se avançar na compreensão do sistema de reatores anaeróbios de duas fases (acidogênico seguido de metanogênico) operados em condições termofílicas (55&#176;C), alimentados com melaço da cana-de-açúcar, subproduto da indústria sucroalcooleira. Os experimentos foram conduzidos em reatores anaeróbios de leito fixo estruturado com fluxo ascendente e o melaço foi diluído com água de abastecimento, para adequação da concentração aos processos de tratamento de águas residuárias. Na 1ª Etapa dois reatores acidogênicos foram operados em paralelo para avaliar diferentes formas de inoculação e meios suportes, a fim de manter a produção continua e estável de hidrogênio. Para isso foram aplicadas diferentes cargas orgânicas (2,5, 5 e 10 gDQO.L-1) que resultam em COV de 30, 60 e 120 g.DQO.Lreator1.dia-1, com TDH fixo de 2 horas. A expressão do gene hidrogenase foi detectado em ambos os reatores, mas em maior proporção no reator inoculado com lodo de reator UASB e usando como material suporte a espuma de poliuretano. Sequencialmente a este reator, foi acoplado um reator metanogênico, alimentado com efluente do reator acidogênico, estabilizado nas condições apresentadas, e operado com COV crescentes de 1, 2, 5, 7, 14, 17 e 26,5 gDQO.Lreator-1.dia-1 e consequente diminuição do TDH de 240, 96, 48, 32, 24, 16 e 12 horas. O reator acidogênico na 2ª etapa foi operado por 417 dias consecutivos e COV de 120 g.DQO.Lreator1.dia-1, produzindo hidrogênio continuamente, alcançado valores de produção bruta de H2 de 7,60 LH2.dia-1. O reator metanogênico foi operado por 251 dias consecutivos, produzindo metano e alcançado valores de produção bruta de CH4 de 5,90 LCH4.dia-1. A eficiência de remoção de DQO do sistema de reatores foi de aproximadamente 90&#37;, com contribuição aproximadamente de 10&#37; para o reator acidogênico e contribuição aproximadamente de 80&#37; para o reator metanogênico. O reator acidogênico alcançou rendimento de produção de hidrogênio por kg de melaço aplicado de 392 LH2.kgmelaço-1 e o reator metanogênico de 387 LCH4.kgmelaço-1. Para finalidade de comparações e aplicabilidade, o ganho energético global do sistema de reatores de duas fases foi de aproximadamente 5,7 kWh.kgmelaço-1 (1,4 kWh.kgmelaço-1 para o reator acidogênico e 4,3 kWh.kgmelaço-1 para o reator metanogênico). A produção continua de H2 obtida neste estudo está relacionada à associação das vias dos ácidos produtores de hidrogênio já consolidados pela literatura pertinente (acético e butírico) e pela produção de hidrogênio pela rota do ácido lático, devido a associação entre as comunidades de microrganismos estabelecidas no reator. O sequenciamento massivo MiSeq mostrou a seleção de diversos gêneros de microrganismos com redundância funcional e pertencentes principalmente aos Filos Firmicutes, Proteobacteria e Thermotogae, tais como Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium e Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella e Petrobacter (Proteobacteria) e Fervidobacterium (Thermotogae). Microrganismos produtores de ácido lático também foram selecionados tais como: Lactobacillus, Leuconostoc, Sporolactobacillus e Trichococcus. Dos pontos de vista científico e tecnológico este estudo deu mais um passo para a compreensão dos bioprocessos envolvidos nos sistemas anaeróbios em dois estágios produzindo H2 e CH4 continuamente por longo período de tempo. / Anaerobic digestion has shown as an interesting process for renewable energy production (H2 and CH4), for a wide variety of organic compounds (carbon source). This study aimed to advance the understanding of a two-stage process anaerobic system (acidogenic bioreactor followed by methanogenic bioreactor) under thermophilic condition (55&#176;C) fed with molasses, a sugarcane industry by-product. The experiments were conducted at up-flow structured bed reactors and sugarcane molasses was diluted with tap water, to adjust the concentration to the wastewater treatment. At first stage two acidogenic reactors were operated in parallel to evaluate different source of inocula and support bed, to obtain continuous and stable hydrogen production. It was applied 2.5, 5 and 10 gCOD.L-1 resulting in OLR of 30, 60 and 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours of hydrogenase gene was detected in both reactors but with higher number of copies of the gene in the reactor that showed higher hydrogen production: the reactor sed with sludge of UASB reactor and using polyurethane foam as support material. To this reactor was coupled a methanogenic reactor fed with effluent from acidogenic reactor and operated with increasing OLR (1, 2, 5, 7, 14, 17 e 26,5 gCOD.Lreactor-1.day-1) decreasing the HRT (240, 96, 48, 32, 24, 16 and 12 hours). The acidogenic reactor was operated during 471 days with OLR of 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours, with continuous hydrogen production with a gross production of 7.60 LH2.day-1. The methanogenic reactor was operated for 251 days, with continuous methane production of up to 5.90LCH4.day-1. The COD removal efficiency using the two-stage system was approximately 90&#37; , with 10&#37; contribution by the acidogenic reactor and 80&#37; contribution by the methanogenic reactor. The acidogenic reactor achieved hydrogen yield per kg of applied molasses equal to 392 LH2.kgmolases-1. The methanogenic reactor achieved methane yield per kg of applied molasses equal to 387 LCH4.kgmolasses-1. For comparison and applicability purposes, the overall energy yield using the two stage reactor system was approximately 5.7 kWh.kgmolasses-1 (Acidogenic reactor 1.4 kWh.kgmolasses-1 and Methanogenic reactor 4.3 kWh.kgmolasses-1). The continuous production of H2 obtained in this study is related to the association of the hydrogen producer acids pathway established by the relevant literature (acetic and butyric) and the hydrogen production by the lactic acid pathway due to the microorganisms association established in the reactor. Metagenomic analysis by MiSeq Plataform revealed that hydrogen production was due the selection of microorganisms with functional redundancy mainly of Phyla Firmicutes, Proteobacteria and Thermotogae, such as Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium, Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella and Petrobacter (Proteobacteria) and Fervidobacterium (Thermotogae). Genera of acid latic producers, such as Lactobacillus, Leuconostoc, Sporolactobacillus and Trichococcus, were also selected. From the scientific and technological point of view this study has taken another step towards the understanding of bioprocesses involving two stage anaerobic systems for a long term continuous production of H2 and CH4.

Nous avons développé un nouveau test de prédiction de l’efficacité de thérapies anti-cancéreuses. Ce concept se base sur la détermination d’une signature moléculaire tumorale par RT-qPCR. Cette signature est issue d’un algorithme de normalisation innovant de comparaison des données d’expression relative des cibles de la tumeur avec celles de tissus de référence. Cette normalisation offre à chaque cible de la signature un rang et un score spécifique permettant de hiérarchiser les voies pro-tumorales afin de trouver la ou les cibles dominantes responsables du développement de la tumeur. La signature comprend des cibles donnant des informations générales sur le statut et l’hétérogénéité de la tumeur, sur l’angiogenèse et la lymphangiogenèse, sur le microenvironnement tumoral et enfin sur l’activité migratoire. Une validation préclinique dans les modèles du cancer colorectal, de la prostate et du glioblastome, a montré que le test est prédictif de l’efficacité thérapeutique. / We developed a new tool for prediction of cancer treatment efficacy. Our process is based on the determination of the molecular signature which is intended to provide a clinician’s decision tool helping to select which tumor signaling pathway(s) has/have to be targeted for best therapeutic effect. This signature representing a scoring obtained by RT-qPCR through a sequential normalization process of the expression level of target genes in the tumor compared to cancer type-specific references. These genes were selected because of a good knowledge of related biological functions, a correlation between expression level and aggressiveness of the tumor, the existence of a therapeutic arsenal already in clinical use. This signature is validated in a preclinical model of colorectal cancer and prostate cancer and glioblastoma. The results obtained show that the test we developed allows to identify the most important signaling pathway implicated in the disease and to choose the best drug.

L’esca est une maladie du bois de la vigne complexe et mal connue, contre laquelle aucun moyen de lutte efficace n’existe à ce jour. Ce travail s’est concentré sur les interactions précoces entre Vitis vinifera L. et les champignons associés au « young esca » P. chlamydospora et P. aleophilum dans deux types de tissus lignifiés : l’entre-nœud et le nœud (modèle plaie de taille). La colonisation 6 et 12 semaines après traitement des souches transformées P. aleophilum::gfp7 et P. chlamydospora::gfp1 a été observée. Les deux espèces coloniseraient différents tissus dans les premières semaines suivant l’infection. Les fibres du xylème constitueraient un tissu essentiel lors de l’interaction précoce entre P. aleophilum et la vigne, tandis que P. chlamydospora::gfp1 a seulement colonisé les vaisseaux du xylème après 12 semaines. Le bois de la vigne présenterait des réponses spécifiques à la présence de P. aleophilum 6 semaines après traitement, puis générales à la blessure 12 semaines après traitement, en microscopie. L’hypothèse de la spécificité de la réponse induite dans le bois de la vigne par ces deux espèces a été confirmée en étudiant l’expression de 11 gènes associés à la défense 10 h, 24 h, 48 h et 120 hpi. La réponse précoce du bois de la vigne serait spécifique suivant l’identité des pathogènes. Les tissus de l’entre-nœud ont été induits différemment par la blessure par rapport aux tissus dans la région nodale. Un modèle pour le criblage d’agents de biocontrôle ou d’éliciteurs contre l’esca en quelques mois en conditions de laboratoire a permis le développement d’un moyen de lutte durable et novateur, l’eau ozonée. L’eau ozonée présente des propriétés sporicides remarquables contre P. aleophilum in vitro. In planta l’application d’eau ozonée sur une blessure infectée en modèle plaie de taille a réduit de moitié la quantité de mycélium capable de se développer dans le bois 9 semaines après inoculation. / Esca is a complex pathosystem, poorly understood, affecting grapevine’s trunk. Currently there is not efficient tools to control esca disease. This study investigated early events between grapevine and fungi associated to young esca P. aleophilum and P. chlamydospora in two different woody tissues: at the internode and at the nodal (pruning wound model) levels. The colonization of transformed strains P. aleophilum::gfp7 and P. chlamydospora::gfp1 was observed 6 and 12 weeks post inoculation. Fungal species colonized different tissues during the first weeks of infection. Xylem fibres could be the key site of P. aleophilum-grapevine early interactions, whereas P. chlamydospora::gfp1 only colonized xylem vessels 12 weeks post inoculation. Grapevine wood may respond specifically to P. aleophilum after 6 weeks. This response seemed to be related to healing in microscopy, and thus aspecific 12 weeks post inoculation. The specificity of induced response in the wood of Vitis vinifera L. was confirmed by studying gene expressions of 11 defense-related genes 10 h, 24 h, 48 h and 120 hpi. The early response of woody tissues could be specific to pathogens identity in grapevine. Wounding damages induced defense-related genes differently according the tissues (internode vs node). A model for screening biological control agents or elicitors in laboratory conditions, within months, has been used to develop a sustainable and original control tool: ozonated water. Ozonated water presented remarkable sporicidal properties on P. aleophilum in vitro. Infected pruning wound treated with ozonated water reduced the P. aleophilum inoculum able to develop in the injured wood by a factor two 9 weeks post inoculation.

Talaromyces versatilis est un champignon filamenteux d’intérêt industriel grâce à sa capacité deproduction d’enzymes hydrolytiques. La Société Adisseo commercialise un cocktail enzymatiqueproduit par fermentation à partir de T. versatilis, sous le nom de Rovabio™. Ce cocktail est utilisé entant qu'additif alimentaire en nutrition animale, car la grande variété d'enzymes hydrolytiques qu’ilcontient peut dégrader les polysaccharides présents dans l’enveloppe des céréales, améliorant ainsila digestibilité la valeur nutritionnelle des matières premières agricoles. Malgré les efforts consentispour mieux connaître la biologie de T. versatilis, très peu est connu sur ce champignon.L’étudeprésentée ici vise à décrire les réseaux de régulation qui contrôlent l’expression des gènes codantpour ces enzymes hydrolytiques, en utilisant des approches génomiques et transcriptomiques.Avoir accès à une annotation correcte de la séquence génomique et posséder les outilsnécessaires pour l'ingénierie génétique sont essentiels pour réaliser des études de génomiquefonctionnelle. Donc, le premier volet de cette thèse a été l’analyse de la séquence génomique et lacuration manuelle de l'annotation, ce qui nous a conduits à évaluer le vaste potentiel génétique de T.versatilis pour la production et la sécrétion d'enzymes hydrolytiques impliquées dans la dégradationde la lignocellulose. Deuxièmement, un système de délétion des gènes initialement conçu pourAspergillus niger a été adapté à T. versatilis. Cette méthode permet le recyclage du marqueur desélection et est efficace dans des souches dont le système NHEJ est actif (Delmas, et al., 2014, AEM).Au cours de ce travail, deux mutants de délétion de T. versatilis ont été obtenus: ΔxlnR et ΔclrA.La première approche mise en place pour avoir une meilleure compréhension des réseaux derégulation via une vue globale du transcriptome, fut l’utilisation de la technique de RNAseq sur troiséchantillons issus de la souche sauvage de T. versatilis exposée au glucose, à la paille de blé et auglucose et paille de blé simultanément comme sources de carbone, respectivement. Les données ontmontré une augmentation massive des niveaux d’expression de nombreux gènes, en particulier ceuxcodant pour des enzymes hydrolytiques, lorsque le mycélium est exposé à la lignocellulose. Enfin, la dernière partie du projet s’est appuyée sur la la RT-qPCR, technique appropriée pourétudier un nombre limité de gènes dans une grande variété de conditions. Toutefois la normalisationdes données est une étape essentielle du flux de travail qui peut conduire à une interprétationbiologique incorrecte de la régulation des gènes. Le travail effectué sur les données de RNAseq nousa amené à reconsidérer la nature des gènes de référence classiquement utilisés, puisque la plupartd'entre eux présentaient des changements d'expression considérables en présence de lignocellulose.En conséquence, un nouvel ensemble de gènes de référence putatifs a été identifié et la stabilité deleur expression validée par RT-qPCR chez T. versatilis cultivé dans plus de 30 conditions différentes.Des jeux de données de RNAseq de 18 champignons filamenteux phylogénétiquement éloignés ontpar ailleurs été collectés, afin de démontrer que la sélection des gènes candidats pour lanormalisation des données de RT-qPCR chez T. versatilis peut être étendue à d'autres champignons(Llanos et al., 2014, BMC Genomics). Ces aspects méthodologiques validés, nous avons enfin réaliséune étude plus détaillée de la transcription d'un groupe de gènes d'intérêt par RT-qPCR, dans unegrande variété de conditions et 2 souches différentes, la souche sauvage et la mutante ΔxlnR.L'analyse de ces données a permis d'identifier des gènes aux profils d'expression similaires, quirépondent de la même façon aux substrats inducteurs et qui partagent probablement les mêmesmécanismes de régulation. / Talaromyces versatilis is an industrially important enzymes producing filamentous fungus.Adisseo Company commercializes the enzymatic cocktail, produced from T. versatilis fermentation,with the name of Rovabio™. This cocktail is applied as an animal feed additive as it contains a widevariety of hydrolytic enzymes that can degrade the polysaccharides present in the seed-coat and thusimproves the digestibility and increases the nutritional value of the agricultural raw materials.Although efforts have been done to study different aspects of the biology of T. versatilis, very little isknown about this fungus. This study aimed to describe the regulatory networks of genes encodingplant cell wall-degrading enzymes from this biotechnologically important fungus using genomic andtranscriptomic approaches.Having a correct annotation of the genomic sequence together with efficient tools for genomeengineering are essential for downstream functional genomics works and characterization of theregulatory networks. Therefore, the first task carried out an analysis of the genomic sequence and amanual curation of the annotation, which led us to assess the vast genetic potential of T. versatilis forthe production and secretion of hydrolytic enzymes involved in the degradation of lignocellulosicmaterials. Secondly, I adapted a gene deletion system initially designed for Aspergillus niger. Thismethod allows recycling of the selection marker and is efficient in a non-homologous end-joining(NHEJ)-proficient strain (Delmas, Llanos et al., 2014, AEM). During this work, two deletion mutants ofT. versatilis were obtained: ΔxlnR and ΔclrA.Towards better understanding of the regulatory network, I first contributed to an RNAseq-basedtranscriptomic study that was performed on the wild type strain of T. versatilis exposed to glucoseand wheat straw as carbon sources. The data showed a massive increase in transcript levels ofnumerous genes, in particular those encoding hydrolytic enzymes, when the mycelium wasincubated with lignocellulose.If RT-qPCR is indeed a suitable technique to study a limited number of genes in a large variety ofconditions, data normalisation is a critical step of the workflow that can lead to incorrect biologicalinterpretation of gene regulation. The work done on the RNA-seq data led me to reconsider the useof the classical reference genes, since most of them exhibited expression changes in the presence oflignocellulosic substrate. I therefore identified a new set of putative reference genes and validatedtheir expression stability by RT-qPCR in T. versatilis cultivated under more than 30 differentconditions. Then, I collected about a hundred RNA-seq datasets from 18 phylogenetically distantfilamentous fungi, to demonstrate that the use of the suitable candidates for RT-qPCR datanormalisation in T. versatilis can be extended to other fungi (Llanos et al., 2014 BMC genomics (minorrevisions)). Thereafter, I performed a more detailed RT-qPCR based transcriptional study of a groupof genes of interest, in a wide variety of conditions and in 2 strains, the wild-type and the ΔxlnRmutant. The analysis of expression data of the genes of interest allowed to identify genes with similarexpression patterns, which probably share the same regulatory mechanisms and also the substratesthat act as inducers for their expression

Des recherches en sciences judiciaires ont montré récemment une possible corrélation entre le temps d’entreposage d’échantillons de fluides corporels et la dégradation de l’ARN dans ceux-ci. Le moment où une tache a été déposée sur une scène de crime peut être important pour déterminer la pertinence d’un échantillon dans une enquête. Dans ce mémoire, nous rapportons les profils de dégradation de quatre ARN différents mesurés par RT-qPCR, soit l’ARN ribosomique 18S et les ARNm de la β-actine, de la glyceraldehyde-3-phosphate déhydrogénase et de la cyclophiline A, obtenus de taches de sang, de salive et de sperme, entreposés à la température de la pièce ou au congélateur à -80°C sur une période de 6 mois. Nos résultats montrent une faible variation interindividuelle pour le sang et le sperme, mais une différence importante entre les donneurs pour la salive. De plus, le profil de dégradation est semblable pour tous les transcrits, mais diffère entre les fluides. La congélation des échantillons stabilise les ARN avant leur analyse. Finalement, la quantité d’ARN détecté est en relation avec le temps d’entreposage et pourrait être utilisée afin d’estimer l’âge des échantillons lorsque l’impact des conditions d’entreposage sur la dégradation de l’ARN sera mieux connu. / Recent studies in forensic science have shown a possible correlation between the degradation rate of some RNA transcripts and the age of bloodstains. The time of deposition of a stain can be of major importance to determine the relevance of a sample in a forensic investigation. In this thesis, we describe the degradation profiles of the 18S ribosomal RNA and the β-actin, glyceraldehyde-3-phosphate dehydrogenase and cyclophilin A mRNAs, measured by RT-qPCR and obtained from dried blood, semen and saliva stains stored at room temperature or frozen at -80°C up to 6 months. Our results showed low inter-individual variation for blood and semen stains, but a high variation was observed between donors for saliva. Moreover, degradation profile of each transcripts was similar, but differed between fluids. Freezing samples prevented RNA degradation over time. Finally, RNA quantity was in relation with the time of storage and could be used to estimate the time since deposition of a stain when the effects of various storage conditions on RNA degradation profiles will be better documented.

Norovirus som orsakar vinterkräksjukan är en av de vanligaste vintersjukdomarna i Sverige. Sjukdomstiden varar generellt i en till tre dagar med symptomen kräkning och/eller diarré. Till den totala sjukdomsbilden världen över gällande akut gastroenterit, bidrar norovirus med 18 %. Trots att sjukdomen är mycket vanlig är kunskapen om norovirusets förfarande till stor del okänd.Syftet med studien var att göra en tidsserieanalys, även så kallad One-Step Growth analys, av koncentrationen minus-RNA i celler som infekterats med olika koncentrationer av murint norovirus (MNV). För att detektera minus-RNA användes RT-qPCR med SYBR Green. Målet var att se om startkoncentrationerna av virus vid någon tidpunkt korrelerar med mängden minus-RNA i cellerna. Efter 4 och 8 timmar fanns ett exponentiellt samband mellan den initiala viruskoncentrationen och minus-RNA-uttrycket i cellerna. Koncentrationen minus-RNA i de infekterade cellerna ökade mellan de undersökta tiderna 4, 8 och 24 timmar. Vidare visade resultaten att det krävs 4 timmar för att minus-RNA skulle vara kvantifierbar vid en högre infektionskoncentration av viruspartiklar, medan det krävs 24 timmar för den lägre infektionskoncentrationen av viruspartiklar. / Norovirus causes winter vomiting disease and is one of the commonest cause of winter illness in Sweden. The disease period generally lasts one to three days with symptoms like vomiting and/or diarrhea. To the disease burden of acute gastroenteritis worldwide, norovirus contributes with 18 %. Even though the illness is very common, the knowledge about norovirus is poor and largely unknown.The purpose of the study was to do a time series analysis, a so-called One-Step Growth analysis, of the minus-RNA concentration in cells infected with different concentrations of murine norovirus (MNV). For the detection of minus-RNA RT-qPCR was used with SYBR Green. The goal was to correlate start concentration of virus at any time with the amount of minus-RNA in the cells. At 4 and 8 hours there was an exponential connection by the initial virus concentration and minus-RNA development in the cells. The concentration of minus-RNA in the infected cells increased between 4, 8 and 24 hours. Further, the results can be interpreted as requiring 4 hours for the higher concentrations to become quantifiable, while requiring 24 hours for the lower concentrations to become quantifiable.