Philosophiae Doctor - PhD / Drought is the most complex phenomenon that remained to be a potential and historic challenge to human welfare. It affects plant productivity by eliciting perturbations related to a pathway that controls a normal, functionally intact biological process of the plant. Sorghum (Sorghum bicolor (L.) Moench), a drought adapted model cereal grass is a potential target in the modem agricultural research towards understanding the molecular and cellular basis of drought tolerance. This study reports on the genomic and proteomic findings of drought tolerance in sorghum combining the results from in silica and experimental analysis. Pipeline that includes mapping expression data from 92 normalized cDNAs to genomic loci were used to identify drought tolerant genes. Integrative analysis was carried out using sequence similarity search, metabolic pathway, gene expression profiling and orthology relation to investigate genes of interest. Gene structure prediction was conducted using combination of ab initio and extrinsic evidence-driven information employing multi-criteria sources to improve accuracy. Gene ontology was used to cross-validate and to functionally assign and enrich genes. An integrated approach that subtly combines functional ontology based semantic data with expression profiling and biological networks was employed to analyse gene association with plant phenotypes and to identify and genetically dissect complex drought tolerance in sorghum. The gramene database was used to identify genes with direct or indirect association to drought related ontology terms in sorghum. Where direct association for sorghum genes were not available, genes were captured using Ensemble Biomart by transitive association based on the putative functions of sorghum orthologs in closely related species. Ontology mapping represented a direct or transitive association of genes to multiple drought related ontology terms based on sorghum specific genes or orthologs in related species. Correlation of genes to enriched gene ontology (GO)-terms (p-value < 0.05) related to the whole-plant structure was used to determine the extent of gene-phynotype association across-species and environmental stresses.

The eukaryotic cell cycle orchestrates the precise duplication and distribution of the genetic material, cytoplasm and membranes to daughter cells. In multicellular eukaryotes, cell cycle regulation also governs various organisatorial processes ranging from gametogenesis over multicellular development to tissue formation and repair. Consequently, defects in cell cycle regulation provoke a variety of human cancers. A global view of genes and pathways governing the human cell cycle would advance many research areas and may also deliver novel cancer targets. Therefore this work aimed on the genome-wide identification and systematic characterisation of genes required for cell cycle progression in human cells. I developed a highly specific and efficient RNA interference (RNAi) technology to realize the potential of RNAi for genome-wide screening of the genes essential for cell cycle progression in human tissue culture cells. This approach is based on the large-scale enzymatic digestion of long dsRNAs for the rapid and cost-efficient generation of libraries of highly complex pools of endoribonuclease-prepared siRNAs (esiRNAs). The analysis of the silencing efficiency and specificity of esiRNAs and siRNAs revealed that esiRNAs are as efficient for mRNA degradation as chemically synthesized siRNA designed with state-of-the-art design algorithms, while exhibiting a markedly reduced number of off-target effects. After demonstrating the effectiveness of this approach in a proof-of-concept study, I screened a genome-wide esiRNA library and used three assays to generate a quantitative and reproducible multi-parameter profile for the 1389 identified genes. The resulting phenotypic signatures were used to assign novel cell cycle functions to genes by combining hierarchical clustering, bioinformatics and proteomic data mining. This global perspective on gene functions in the human cell cycle presents a framework for the systematic documentation necessary for the understanding of cell cycle progression and its misregulation in diseases. The identification of novel genes with a role in human cell cycle progression is a starting point for an in-depth analysis of their specific functions, which requires the validation of the observed RNAi phenotype by genetic rescue, the study of the subcellular localisation and the identification of interaction partners of the expressed protein. One strategy to achieve these experimental goals is the expression of RNAi resistant and/or tagged transgenes. A major obstacle for transgenesis in mammalian tissue culture cells is the lack of efficient homologous recombination limiting the use of cultured mammalian cells as a real genetic system like yeast. I developed a technology circumventing this problem by expressing an orthologous gene from a closely related species including its regulatory sequences carried on a bacterial artificial chromosome (BAC). This technology allows physiological expression of the transgene, which cannot be achieved with conventional cDNA expression constructs. The use of the orthologous gene from a closely related species confers RNAi resistance to the transgene allowing the depletion of the endogenous gene by RNAi. Thus, this technology mimics homologous recombination by replacing an endogenous gene with a transgene while maintaining normal gene expression. In combination with recombineering strategies this technology is useful for RNAi rescue experiments, protein localisation and the identification of protein interaction partners in mammalian tissue culture cells. In summary, this thesis presents a major technical advance for large-scale functional genomic studies in mammalian tissue culture cells and provides novel insights into various aspects of cell cycle progression. (Die Druckexemplare enthalten jeweils eine CD-ROM als Anlagenteil: 217 MB: Movies, Rohdaten - Nutzung: Referat Informationsvermittlung der SLUB)

La fusariose des épis est l’une de maladies les plus dommageables des céréales tempérées et est principalement causée par le champignon toxinogène Fusarium graminearum (Fg). Ces dix dernières années, de nombreuses études ont rapporté l’induction transcriptionnelle de gènes de la plante codant pour des cytochromes P450 (P450) en réponse l’infection par Fg. Les P450s constituent une famille enzymatique impliquée dans de nombreuses voies métaboliques, certaines avec des intérêts potentiels dans la résistance face aux maladies. Nous avons utilisé la petite graminée modèle Brachypodium distachyon (Bd) pour caractériser fonctionnellement le premier gène codant pour un P450 induit chez la plante au cours de la fusariose des épis par l’utilisation de lignées altérées dans la séquence ou l’expression du gène Bradi1g75310 codant le P450 BdCYP711A29. Nous avons montré qu’en plus d’être un facteur de sensibilité à la maladie, le gène Bradi1g75310 est impliqué dans une voie de biosynthèse hormonale chez Bd, celle des strigolactones (SLs). En effet, en plus de complémenter génétiquement les phénotypes aériens de la lignée mutante max1-1 d’Arabidopsis thaliana altérée dans le gène homologue MAX1 (AtCYP711A1), une lignée de Bd surexprimant Bradi1g75310 (lignée OE) exsude davantage d’orobanchol, une SL spécifique, que la lignée sauvage ou mutante. Une analyse préliminaire de l’impact direct de l’orobanchol sur la croissance de Fg semble indiquer une activation des étapes précoces du développement du champignon (germination) qui pourrait être à l’origine de l’induction plus rapide de gènes de défenses observée chez une lignée OE de Bradi1g75310. Nous avons également montré que les 4 paralogues de Bradi1g75310 chez Bd, qui codent également pour des CYP711A, sont tous capable de complémenter la lignée max1-1 et avons généré du matériel végétal fondamental pour la poursuite de l’étude de la diversification des SLs chez la plante monocotylédone modèle Bd. Au global, ce projet constitue une première étape dans la caractérisation de l’implication des P450 dans la réponse de la plante face à l’infection par Fg en plus de donner de nouveaux indices concernant le rôle des SLs dans les interactions plante-pathogène. Les résultats obtenus au cours de ce travail de thèse pourront permettre l’amélioration de caractères tant développementaux que de résistance à la fusariose chez les céréales cultivées. / Fusarium Head Blight (FHB) is one of the most important diseases of temperate cereals and is mostly caused by the toxin producing-fungus Fusarium graminearum (Fg). This last decade, several studies reported the transcriptional activation of cereal cytochrome P450-encoding genes (P450s) in response to Fg infection. P450s constitute an enzymatic family participating in very diverse metabolic pathways with potential interest for disease resistance. We used the model temperate cereal Brachypodium distachyon (Bd) to functionally characterize the first FHB-induced P450- encoding gene using Bd lines altered in the locus or gene expression of the Bradi1g75310 gene encoding the BdCYP711A29 P450. We showed that in addition to be a plant susceptibility factor towards the disease, the Bradi1g75310 gene is involved in the hormonal biosynthetic pathway of strigolactones (SLs) in Bd. Indeed, in addition to genetically complement the shoot phenotypes of the Arabidopsis thaliana mutant line for the homologous gene MAX1 (AtCYP711A1, max1-1 line), a Bd linewhich overexpresses the Bradi1g75310 gene (OE) exudes more orobanchol, a specific SL, compared to wild-type or mutant lines. Preliminary analysis of the direct impact of orobanchol on Fg growth suggests an activation of early fungal development (germination) likely to induce faster induction of defense-related genes during FHB, observed in Bradi1g75310 OE line. We showed that the four paralogs of Bradi1g75310 encoding BdCYP711A P450s are all able to genetically complement max1-1 line and provide important plant material for studying SLs diversification in the model monocot B. distachyon. Overall, this project constitutes a first step in the characterization of P450s involvement in plant response towards Fg infection in addition to give new evidences about the role of SLs in plant-pathogen interactions. Results obtained during this Ph.D. project will allow the improvement of both developmental and FHB-related traits in cereal crops.

Indiana University-Purdue University Indianapolis (IUPUI) / Alcohol related problems and abuse continue to be serious problems in the U.S. today affecting nearly 17.6 million Americans. Understanding of the specific genes and related behaviors associated with alcohol use may provide substantial preventative measures for those who are at an increased risk. Genetically selected lines such as the high-alcohol preferring (HAP) and low-alcohol preferring (LAP) mice have been created to examine which endophenotypes co-segregate with alcohol preference. One behavioral trait that has been commonly associated with alcohol related problems is impulsivity. Impulsivity is the inability to withhold a response (motor impulsivity) or to act without forethought (cognitive impulsivity). The latter comprises much of the research and literature today using delay discounting models to tease out differences in subject’s wiliness to discount larger reinforcers for smaller immediate reinforcers. This study utilized relatively two newer paradigms associated with motor impulsivity in attempt to test differences in response disinhibition between two independent replicate HAP and LAP lines. It is hypothesized that the genes responsible for alcohol preference would be genetically correlated with motor impulsivity as HAP mice would display a greater degree of response disinhibition. Two independent replicates consisting of 48 mice (24 HAP II and 24 LAP II, representing the 37th generation; 24 HAP III and 24 LAP III, representing the 13th generation) were tested in two separate identical experiments. Each experiment was comprised of three phases. Phase I utilized a fixed interval (FI) 120s procedure for 30 days. After the 30 days of FI exposure mice were immediately moved to phase II for 10 days which implored a differential reinforcement of low rate procedure (DRL) at a time interval of 20s. Phase III used the same procedures as Phase II except the DRL was increased to 32s. As hypothesized, there was a moderate genetic correlation between alcohol preference and impulsivity as the HAP II mice displayed greater response disinhibition throughout all three phases compared to the LAP II mice. No differences were observed amongst the replicate III mice in any of the three phases. The findings from this study provide additional support that a genetic correlation between alcohol preference and impulsivity exists as seen in the delay discounting literature. Though this was observed in only one of the two replicates, interpretations must be taken at caution as the replicate III mice are still in the early stages of selection. It is possible at this stage in the selection process that increases in alcohol over successive generations are associated with selecting for taste until a threshold is met where selection shifts to pharmacologic drinking relevance. Until later generations of replicate III mice are studied where pharmacologic drinking occurs, conclusions from this study provide a moderate genetic correlation between alcohol preference and impulsivity.

Sepsis is the systemic inflammatory response to an infection. Severe sepsis with multi organ failure is one of the commonest causes of admission to intensive care units, and is associated with poor early and late outcomes. The pathophysiology of sepsis is complex, and poorly understood. This is reflected in the limited and contentious treatment options for sepsis. Genetic factors have been shown to be associated with the risk of and subsequent outcomes from infection. However, clear associations with bacterial sepsis are rare, and even when associations are present their functional effects are often unknown. Gene expression signatures in sepsis are investigated in this project using serial samples obtained from patients admitted to intensive care units with community-acquired pneumonia or faecal peritonitis. The evolving gene expression signatures that define the response to sepsis were identified with large changes seen in genes coding for ribosomal proteins RPS4Y1 and RPS26P54. The differences in the sepsis response between the two diagnostic classes were examined. The gene expression predictors of mortality in sepsis were determined and include genes from the class II MHC HLA-DRB4, HLA-DRB5 and the T cell differentiation protein MAL. The effects of important covariates on gene expression were investigated and their impact on survival related expression determined. The findings were confirmed in a validation cohort. A novel clustering of samples representing distinct inflammatory patterns in a clinically homogeneous population of sepsis patients was identified and related to differences in clinical behaviour. The biological relevance of the differentially expressed genes was ascertained by identifying enriched gene sets. The gene expression changes in sepsis were examined in the context of related clinically relevant immune phenomena: the sterile systemic inflammatory response in patients undergoing elective cardiac surgery and the phenomenon of endotoxin tolerance in PBMCs derived from healthy volunteers. The results highlight the complexities of clinical sepsis and identify hypotheses for future investigations.

Plusieurs souches cliniques de Candida albicans résistantes aux médicaments antifongiques azolés surexpriment des gènes encodant des effecteurs de la résistance appartenant à deux classes fonctionnelles : i) des transporteurs expulsant les azoles, CDR1, CDR2 et MDR1 et ii) la cible des azoles 14-lanostérol déméthylase encodée par ERG11. La surexpression de ces gènes est due à la sélection de mutations activatrices dans des facteurs de transcription à doigts de zinc de la famille zinc cluster (Zn2Cys6) qui contrôlent leur expression : Tac1p (Transcriptional activator of CDR genes 1) contrôlant l’expression de CDR1 et CDR2, Mrr1p (Multidrug resistance regulator 1), régulant celle de MDR1 et Upc2p (Uptake control 2), contrôlant celle d’ERG11. Un autre effecteur de la résistance clinique aux azoles est PDR16, encodant une transférase de phospholipides, dont la surexpression accompagne souvent celle de CDR1 et CDR2, suggérant que les trois gènes appartiennent au même régulon, potentiellement celui de Tac1p. De plus, la régulation transcriptionnelle du gène MDR1 ne dépend pas seulement de Mrr1p, mais aussi du facteur de transcription de la famille basic-leucine zipper Cap1p (Candida activator protein 1), un régulateur majeur de la réponse au stress oxydatif chez C. albicans qui, lorsque muté, induit une surexpression constitutive de MDR1 conférant la résistance aux azoles. Ces observations suggèrent qu’un réseau de régulation transcriptionnelle complexe contrôle le processus de résistance aux antifongiques azolés chez C. albicans. L’objectif de mon projet au doctorat était d’identifier les cibles transcriptionnelles directes des facteurs de transcription Tac1p, Upc2p et Cap1p, en me servant d’approches génétiques et de génomique fonctionnelle, afin de i) caractériser leur réseau transcriptionnel et les modules transcriptionnels qui sont sous leur contrôle direct, et ii) d’inférer leurs fonctions biologiques et ainsi mieux comprendre leur rôle dans la résistance aux azoles. Dans un premier volet, j’ai démontré, par des expériences de génétique, que Tac1p contrôle non seulement la surexpression de CDR1 et CDR2 mais aussi celle de PDR16. Mes résultats ont identifié une nouvelle mutation activatrice de Tac1p (N972D) et ont révélé la participation d’un autre régulateur dans le contrôle transcriptionnel de CDR1 et PDR16 dont l’identité est encore inconnue. Une combinaison d’expériences de transcriptomique et d’immunoprécipitation de la chromatine couplée à l’hybridation sur des biopuces à ADN (ChIP-chip) m’a permis d’identifier plusieurs gènes dont l’expression est contrôlée in vivo et directement par Tac1p (PDR16, CDR1, CDR2, ERG2, autres), Upc2p (ERG11, ERG2, MDR1, CDR1, autres) et Cap1p (MDR1, GCY1, GLR1, autres). Ces expériences ont révélé qu’Upc2p ne contrôle pas seulement l’expression d’ERG11, mais aussi celle de MDR1 et CDR1. Plusieurs nouvelles propriétés fonctionnelles de ces régulateurs ont été caractérisées, notamment la liaison in vivo de Tac1p aux promoteurs de ses cibles de façon constitutive et indépendamment de son état d’activation, et la liaison de Cap1p non seulement à la région du promoteur de ses cibles, mais aussi celle couvrant le cadre de lecture ouvert et le terminateur transcriptionnel putatif, suggérant une interaction physique avec la machinerie de la transcription. La caractérisation du réseau transcriptionnel a révélé une interaction fonctionnnelle entre ces différents facteurs, notamment Cap1p et Mrr1p, et a permis d’inférer des fonctions biologiques potentielles pour Tac1p (trafic et la mobilisation des lipides, réponse au stress oxydatif et osmotique) et confirmer ou proposer d’autres fonctions pour Upc2p (métabolisme des stérols) et Cap1p (réponse au stress oxydatif, métabolisme des sources d’azote, transport des phospholipides). Mes études suggèrent que la résistance aux antifongiques azolés chez C. albicans est intimement liée au métabolisme des lipides membranaires et à la réponse au stress oxydatif. / Many azole resistant Candida albicans clinical isolates overexpress genes encoding azole resistance effectors that belong to two functional categories: i) CDR1, CDR2 and MDR1, encoding azole-efflux transporters and ii) ERG11, encoding the target of azoles 14-lanosterol demethylase. The constitutive overexpression of these genes is due to activating mutations in transcription factors of the zinc cluster family (Zn2Cys6) which control their expression. Tac1p (Transcriptional activator of CDR genes 1), controlling the expression of CDR1 and CDR2, Mrr1p (Multidrug resistance regulator 1), regulating MDR1 expression and Upc2p (Uptake control 2), controlling the expression of ERG11. Another determinant of clinical azole resistance is PDR16, encoding a phospholipid transferase, whose overexpression often accompanies that of CDR1 and CDR2 in clinical isolates, suggesting that the three genes belong to the same regulon, potentially that of Tac1p. Further, MDR1 expression is not only regulated by Mrr1p, but also by the basic-leucine zipper transcription factor Cap1p (Candida activator protein 1), which controls the oxidative stress response in C. albicans and whose mutation confers azole resistance via MDR1 overexpression. These observations suggest that a complex transcriptional regulatory network controls azole resistance in C. albicans. My Ph.D. studies are aimed at identifying the direct transcriptional targets of Tac1p, Upc2p and Cap1p using genetics and functional genomics approches in order to i) characterize their regulatory network and the transcriptional modules under their direct control and ii) infer their biological functions and better understand their roles in azole resistance. In the first part of my studies, I showed that Tac1p does not only control the expression of CDR1 and CDR2, but also that of PDR16. My results also identified a new activating mutation in Tac1p (N972D) and revealed that the expression of CDR1 and PDR16 is under the control of another yet unknown regulator. The combination of transcriptomics and genome-wide location (ChIP-chip) approaches allowed me to identify the in vivo direct targets of Tac1p (PDR16, CDR1, CDR2, ERG2, others), Upc2p (ERG11, ERG2, MDR1, CDR1, others) and Cap1p (MDR1, GCY1, GLR1, others). These results also revealed that Upc2p does not only control the expression of ERG11 but also that of MDR1 and CDR1. Many new functional features of these transcription factors were found, including the constitutive binding of Tac1p to its targets under both activating and non-activating conditions, and the binding of Cap1p which extends beyond the promoter region of its target genes, to cover the open reading frame and the putative transcription termination regions, suggesting a physical interaction with the transcriptional machinery. The characterization of the transcriptional regulatory network revealed a functional interaction between these factors, notably between Cap1p and Mrr1p, and inferred potential biological functions for Tac1p (lipid mobilization and traffic, response to oxidative and osmotic stress) and confirmed or suggested other functions for Upc2p (sterol metabolism) and Cap1p (oxidative stress response, regulation of nitrogen utilization and phospholipids transport). Taken together, my results suggest that azole resistance in C. albicans is tightly linked to membrane lipid metabolism and oxidative stress response.

Sugarcane smut is a worldwide distributed disease important to agribusiness, since it can affect sugarcane yield drastically. The disease is caused by the Basidiomycete Sporisorium scitamineum, a biotrophic fungus that colonizes mainly sugarcane. Sugarcane-smut interaction has been extensively studied by this research group for the past few years in their various aspects, considering both the pathogen attack and plant defenses. This work aimed to functionally address fungal candidate effector proteins associated with this pathosystem. Effectors are essential to modulate host metabolism to allow pathogen colonization. The identification of such proteins may assist in recognition of resistance genes relevant to genetic breeding programs. Based on the complete genome sequence of S. scitamineum and the dual transcriptomic data candidate genes were selected in silico. Selection strategies were based on the predicted secretome and differential expression levels of the genes in planta. Candidate effectors were analyzed regarding their expression pattern, subcellular location and influence over basal plant defenses and plant immunity. The results showed that the S. scitamineum candidate effector genes are expressed under the influence of the host genotype. It was observed various expression patterns in the set of selected genes and differential subcellular localization patterns. These results will enable future researches considering virulence level of different isolates and also help decision making in plant breeding programs. / O carvão da cana-de-açúcar é uma doença cosmopolita de grande importância para o agronegócio, uma vez que pode afetar a produtividade da cultura. A doença é causada pelo basidiomiceto Sporisorium scitamineum, fungo biotrófico que coloniza exclusivamente a cana-de-açúcar. A interação cana-carvão vem sendo extensivamente estudada por este grupo de pesquisa nos últimos anos em seus vários aspectos, considerando as atividades de ataque e defesa do patógeno e da planta, respectivamente. Este trabalho teve como finalidade o estudo funcional de proteínas candidatas a efetores neste patossistema. Efetores são moléculas essenciais na manipulação do metabolismo e fisiologia do hospedeiro de forma a permitir sua colonização. A identificação de tais proteínas auxilia no reconhecimento de genes de resistência podendo gerar informações relevantes a programas de melhoramento genético na produção de variedades resistentes. A estratégia de seleção utilizada se baseia em características do secretoma predito e da expressão diferencial de genes do patógeno in planta. Os candidatos foram analisados quanto ao padrão de expressão gênica, à localização sub celular e sua influência sobre a defesa basal e imunidade em plantas. Os resultados demonstraram que a expressão dos genes que codificam para as proteínas efetoras de S. scitamineum e é influenciada pelo genótipo das plantas infectadas. Foram observadas variações no padrão de expressão entre o conjunto de efetores selecionados, bem como padrões diferenciais de localização sub celular e influência sobre a imunidade em plantas. Os resultados gerados por este trabalho servirão de subsídio para estudos futuros sobre os níveis de virulência dos diferentes isolados do patógeno bem como para auxiliar a tomada de decisão em programas de melhoramento genético de variedades resistentes ao carvão da cana.

O Cancro Cítrico, um dos mais graves problemas fitossanitários da citricultura atual, é uma doença causada pelo fitopatógeno Xanthomonas axonopodis pv. citri (Xac). Um estudo funcional do genoma de Xac foi iniciado com o intuito de identificar interações proteína-proteína envolvidas em processos de patogenicidade de Xac. Através da utilização do sistema duplo-híbrido de levedura, baseado nos domínios de ligação ao DNA e ativação da transcrição do GAL4, nós analisamos os principais componentes dos mecanismos de patogenicidade de Xac, incluindo o Sistema de Secreção do Tipo III (TTSS), Sistema de Secreção do Tipo IV (TFSS) e Sistema de \"Quorum Sensing\" composto pelas proteínas Rpf. Componentes desses sistemas foram utilizados como iscas na triagem de uma biblioteca genômica de Xac. O TTSS é codificado pelos genes denominados hrp (\"hypersensitive response and pathogenicity\"), hrc (\"hrp conserved\") e hpa (\"hrp associated\") localizados no locus hrp do cromossomo de Xac. Esse sistema de secreção é capaz de translocar proteínas efetoras do citoplasma bacteriano para o interior da célula hospedeira. Nossos resultados mostraram novas interações proteínaproteína entre componentes do próprio TTSS além de associações específicas com uma proteína hipotética: 1) HrpG, um regulador de resposta de um sistema de dois componentes responsável pela expressão dos genes hrp, e XAC0095, uma proteína hipotética encontrada apenas em Xanthomonas spp; 2) HpaA, uma proteína secretada pelo TTSS, HpaB e o domínio C-terminal da HrcV; 3) HrpB1, HrpD6 e HrpW, 4) HrpB2 e HrcU e 5) interações homotrópicas envolvendo a ATPase HrcN. Em Xac, foram encontrados dois loci vir que codificam proteínas que possuem similaridade com componentes do TFSS envolvido em processos de conjugação/secreção bacteriana: TFSS-plasmídeo localizado no plasmídeo pXAC64 e TFSS-cromossomo localizado no cromossomo de Xac. O TFSS-plasmídeo, o qual possui maior similaridade com sistemas de conjugação, mostrou interações envolvendo proteínas cujos genes estão localizados na mesma região do plasmídeo pXAC64: 1) interação homotrópica da TrwA; 2) XACb0032 e XACb0033; 3) interações homotrópicas da proteína XACb0035; 4) VirB1 e VirB9; 5) XACb0042 e VirB6; 6) XACb0043 e XACb0021b. O TFSS-cromossomo apresentou interações envolvendo as proteínas: 1) VirD4 e um grupo de 12 proteínas que contém similaridade entre si, incluindo XAC2609 cujo gene encontra-se no locus vir, 2) XAC2609 e XAC2610; 3) Interações homotrópicas da VirB11; 4) XAC2622 e VirB9. A análise do sistema de \"Quorum-Sensing\" composto pelas proteínas Rpf mostrou interações envolvendo componentes do próprio sistema: 1) RpfC e RpfF; 2) RpfC e RpfG; 3) interações homotrópicas da RpfF; 4) RpfC e CmfA, uma proteína similar a Cmf de Dictyostelium discoideum que, neste organismo, é fundamental para processos de \"quorum-sensing\". As interações proteína-proteína encontradas permitiram-nos entender melhor a composição, organização e regulação dos fatores envolvidos na patogenicidade de Xac. / Citrus Canker, caused by the bacterial plant pathogen Xanthomonas axonopodis pv. citri (Xac) presents one of the most serious problems to Brazilian citriculture. We have initiated a project to identify protein-protein interactions involved in pathogenicity of Xac. Using a yeast two-hybrid system based on GAL4 DNA-binding and activation domains, we have focused on identifying interactions involving subunits, regulators and substrates of: Type Three Secretion System (TTSS), Type Four Secretion System (TFSS) and Quorum Sensing/Rpf System. Components of these systems were used as baits to screening a random Xac genomic library. The TTSS is coded by the hrp (hypersensitive response and pathogenicity), hrc (hrp conserved) and hpa (hrp associated) genes in the chromosomal hrp locus. This secretion system can translocate efector proteins from the bacterial cytoplasm into the host cells. We have identified several previously uncharacterized interactions involving: 1) HrpG, a two-component system response regulator responsible for the expression of Xac hrp operons, and XAC0095, a previously uncharacterized protein encountered only in Xanthomonas spp; 2) HpaA, a protein secreted by the TTSS, HpaB and the C-terminal domain HrcV; 3) HrpB1, HrpD6 and HrpW; 4) HrpB2 and HrcU; 5) Homotropic interactions were also identified for the ATPase HrcN. Xac contains two virB gene clusters, one on the chromosome and one on the pXAC64 plasmid, each of which codes for a unique and previously uncharacterized TFSS. Components of the TFSS of pXAC64, which is most similar to conjugation systems, showed interactions involving proteins coded by the same locus: 1) Homotropic interactions of TrwA; 2) XACb0032 and XACb0033; 3) XAC0035 homotropic interactions; 4) VirB1 and VirB9; 5) XACb0042 and VirB6; 6) XACb0043 and XACb0021 b. Components of the chromosomal TFSS exhibited interactions involving: 1) VirD4 and a group of 12 uncharacterized proteins with a common C-terminal domain motif, include XAC2609 whose gene resides within the vir locus; 2) XAC2609 and XAC261 O; 3) Homotropic interactions of VirB11; 4) XAC2622 and VirB9. Analysis of Quorum Sensing/Rpf System components revealed interactions between the principal Rpf proteins which control Xanthomonas quorum sensing: 1) RpfC and RpfF; 2) RpfC and RpfG; 3) RpfF homotropic interactions; 4) RpfC and CmfA, a protein that presents similarity with Cmf (conditioned medium factor) of Dictyostelium discoideum, which contrais quorum sensing in this organism. The protein-protein interactions that we have detected reveal insights into the composition, organization and regulation of these important mechanisms involved in Xanthomonas pathogenicity.

Dans le contexte actuel de changement global et particulièrement de réchauffement climatique et de pollution chimique chronique, se pose la question de la vulnérabilité des écosystèmes côtiers et notamment des populations d’invertébrés filtreurs jouant un rôle structurant dans la plupart de ces écosystèmes. Dans ces travaux de thèse, une approche couplée d’écophysiologie et de génomique fonctionnelle a été mise à profit afin de mieux comprendre les processus moléculaire, cellulaire et physiologique de réponse à une contamination chimique chronique modérée et d’évaluer la capacité à faire face à une augmentation de température chez des populations naturelles de moules bleues (Mytilus spp.) de la Rade de Brest. Les résultats obtenus révèlent qu’une contamination chronique modérée induit des réponses adaptatives au niveau subcellulaire chez les moules exposées, prévenant ainsi l’apparition de souffrances physiologiques et permettant aux populations de se maintenir dans un environnement variable. Ces réponses impliquent en particulier, une activation des mécanismes de défense cellulaire (métabolisme énergétique et défenses antioxydantes) et d’élimination des xénobiotiques. Par ailleurs, l’exposition à une augmentation de température en conditions expérimentales ne met pas en évidence de sensibilité particulière au stress thermique chez les moules provenant d’un site exposé à une contamination chronique modérée. En revanche, les résultats indiquent que ces dernières pourraient avoir une plus grande capacité à compenser grâce à des réponses adaptatives, les effets délétères générés par une augmentation de température. Cependant, le fort coût énergétique généré par la contamination chimique ainsi que les effets importants du stress thermique mis en évidence dans ces travaux indiquent que la combinaison de ces deux sources de stress pourrait provoquer des dysfonctionnements métaboliques et représenter à l’avenir, une menace pour les populations naturelles de moules bleues. Ces travaux de thèse ont également contribué au développement de nouvelles méthodologies permettant respectivement, de quantifier des contaminants environnementaux dans des tissus biologiques marins, d’étudier des réponses génomiques précoces de stress et de mesurer des paramètres physico-chimiques in situ. Ces méthodologies pourront contribuer à améliorer les performances du diagnostic de l’état de santé des populations naturelles de moules et au delà, d’espèces-sentinelles de mollusques bivalves dans un contexte de contamination chimique mais également de changements climatiques. / In the current context of chronic chemical pollution and on-going climate change, coastal ecosystems, and in particular keystone filter-feeding bivalve populations inhabiting them, appear vulnerable. In this thesis, an approach coupling ecophysiology and functional genomics was used to study the molecular, cellular and physiological responses of wild blue mussel populations of the Bay of Brest to a moderate chronic chemical contamination, and to assess the ability of these populations to face a heat stress. Results indicate a moderate chronic chemical contamination induces adaptive responses in wild mussel populations from the Brest harbour area, which prevents severe physiological disturbances and sustain long-term population survival. These responses include an activation of cellular stress response [energetic metabolism and antioxidant defences) and xenobiotic elimination mechanisms. Furthermore, experimental heat stress exposure does not highlight a higher sensitivity to a temperature increase in mussels sampled in a moderately contaminated area but suggests that these mussels could have a better ability to offset the adverse effects of heat stress thanks to adaptive responses. However, the high energetic cost of chemical contamination and the strong effects of heat stress presented in this work, suggest combined chemical and heat stress could be a future threat for wild blue mussel populations. This work also contributes to the development of new methodologies to, respectively, quantify environmental contaminants in marine biota, study early warning genomic stress responses and to survey physicochemical parameters in situ. These methodologies contribute to improving the health diagnostics of natural mussel populations and thus, appear as useful tools to assess health of bivalve sentinel species populations in biomonitoring studies, in a context of chemical contamination and climate change.

<p>Prostate cancer is one leading cause of cancer-related death among men in Western countries. The standard therapies for localized prostate cancer include radical prostatectomy and radiation therapy. Such measures are relatively effective in the short term, but many patients ultimately relapse. These patients may benefit from a combination of standard therapy and oncolytic virus therapy. My work aimed to develop viruses for this purpose.</p><p>TARP is a protein that in males is specifically expressed in prostate epithelial and cancer cells. In my thesis, I characterized the TARP promoter and showed that TARP expression is regulated at the transcriptional level by testosterone through binding of the androgen receptor in the proximal TARP promoter. I further developed TARP promoter-based regulatory sequences for prostate-specific gene expression. A sequence comprising a PSA enhancer, a PSMA enhancer and the TARP promoter was constructed and designated PPT. An adenoviral vector containing the PPT sequence shielded from transcriptional interference by an H19 insulator showed high prostate-specific transcriptional activity in human cells both in the presence and absence of testosterone. However, in experimental murine prostate cancer the PPT sequence is not active. Therefore, a two-step transcriptional amplification (TSTA) system was used together with the PPT sequence to develop an adenovirus that confers prostate-specific transgene expression also in murine cells.</p><p>I constructed a conditionally replicating adenovirus where the E1A gene expression is controlled by an H19 insulator-shielded PPT regulatory sequence, Ad[I/PPT-E1A]. This virus exhibited absolute prostate specificity in terms of E1A expression, viral replication and cytolysis <i>in vitro</i> and <i>in vivo</i>. Importantly, our virus is active both in the presence and absence of testosterone, which may prove beneficial for patients treated by hormonal withdrawal. </p><p>Hopefully, my work will improve existing gene therapy strategies for prostate cancer and in the long term improve the prognosis for patients with prostate cancer.</p>