A manga (Mangifera indica L.) é cultivada em áreas tropicais e subtropicais, principalmente em países em desenvolvimento. Os maiores produtores são a Índia, China, México, Indonésia, Tailândia, Paquistão e Brasil, mas, por ser uma fruta altamente perecível, suas exportações têm sido limitadas. Durante o amadurecimento, as frutas adquirem características que as tornam adequadas para o consumo como conseqüência de alterações metabólicas dependentes, em larga medida, da expressão de genes específicos. Uma vez que as proteínas são os elementos efetores da expressão gênica, a análise de proteomas pode auxiliar na identificação de pontos de controle do metabolismo determinantes para a qualidade desses alimentos. Assim, o objetivo do trabalho é identificar spots de proteínas diferentemente abundantes durante o amadurecimento a partir dos mapas 2D-DIGE das polpas de mangas (Mangifera indica L.) da cultivar Keitt nos estádios pré-climatérico e climatérico. Após extração das proteínas e separação por 2D-DIGE, as imagens dos géis obtidas foram analizadas com o software PDQuest, utilizando o teste T de Student para a análise estatística. Dentre os spots protéicos bem resolvidos e considerados na análise, os 47 que apresentaram-se diferentemente abundantes entre os estádios estudados foram removidos dos géis, suas proteínas digeridas e, enfim, sequenciadas por espectrometria de massas. Foram obtidas as identidades prováveis de 58 proteínas diferentes a partir da comparação das sequencias obtidas com banco de dados NCBI2010, utilizando o software Mascot. / Mango fruit (Mangifera indica L.) is cultivated in tropical and subtropical areas, mainly in developing countries. India, China, Mexico, Indonesia, Thailand, Pakistan and Brazil are the major producers, but its trade has been limited due the highly perishable nature of the fruit. During ripening, the fruits acquire characteristics that make them appropriate for consumption as a consequence of metabolic changes dependent on the expression of specific genes. As proteins are the effector elements of gene expression, proteome analysis can help the identification of metabolism keypoints that could influence the fruit quality. Thus, the aim of this study was to compare the protein maps of mango pulp (Mangifera indica L. cv. Keitt) in pre-climacteric and climacteric stages, in order to identify protein spots that differ in abundance in these two stages. After protein extraction and separation by 2D-DIGE technique, the gel images obtained were analyzed with PDQuest software, using the Student´s T-test for statistical analysis. We obtained 47 spots differently abundant between the stages studied, that were excised from the gels and its proteins digested with trypsin and sequenced by mass spectrometry. We obtained the identities of 58 distinct proteins from the search of the peptide sequences against NCBI2010 database using the software Mascot.

A manga (Mangifera indica L.) é cultivada em áreas tropicais e subtropicais, principalmente em países em desenvolvimento. Os maiores produtores são a Índia, China, México, Indonésia, Tailândia, Paquistão e Brasil, mas, por ser uma fruta altamente perecível, suas exportações têm sido limitadas. Durante o amadurecimento, as frutas adquirem características que as tornam adequadas para o consumo como conseqüência de alterações metabólicas dependentes, em larga medida, da expressão de genes específicos. Uma vez que as proteínas são os elementos efetores da expressão gênica, a análise de proteomas pode auxiliar na identificação de pontos de controle do metabolismo determinantes para a qualidade desses alimentos. Assim, o objetivo do trabalho é identificar spots de proteínas diferentemente abundantes durante o amadurecimento a partir dos mapas 2D-DIGE das polpas de mangas (Mangifera indica L.) da cultivar Keitt nos estádios pré-climatérico e climatérico. Após extração das proteínas e separação por 2D-DIGE, as imagens dos géis obtidas foram analizadas com o software PDQuest, utilizando o teste T de Student para a análise estatística. Dentre os spots protéicos bem resolvidos e considerados na análise, os 47 que apresentaram-se diferentemente abundantes entre os estádios estudados foram removidos dos géis, suas proteínas digeridas e, enfim, sequenciadas por espectrometria de massas. Foram obtidas as identidades prováveis de 58 proteínas diferentes a partir da comparação das sequencias obtidas com banco de dados NCBI2010, utilizando o software Mascot. / Mango fruit (Mangifera indica L.) is cultivated in tropical and subtropical areas, mainly in developing countries. India, China, Mexico, Indonesia, Thailand, Pakistan and Brazil are the major producers, but its trade has been limited due the highly perishable nature of the fruit. During ripening, the fruits acquire characteristics that make them appropriate for consumption as a consequence of metabolic changes dependent on the expression of specific genes. As proteins are the effector elements of gene expression, proteome analysis can help the identification of metabolism keypoints that could influence the fruit quality. Thus, the aim of this study was to compare the protein maps of mango pulp (Mangifera indica L. cv. Keitt) in pre-climacteric and climacteric stages, in order to identify protein spots that differ in abundance in these two stages. After protein extraction and separation by 2D-DIGE technique, the gel images obtained were analyzed with PDQuest software, using the Student´s T-test for statistical analysis. We obtained 47 spots differently abundant between the stages studied, that were excised from the gels and its proteins digested with trypsin and sequenced by mass spectrometry. We obtained the identities of 58 distinct proteins from the search of the peptide sequences against NCBI2010 database using the software Mascot.

Le remodelage ventriculaire gauche (VG) en post-infarctus du myocarde (IDM) est associé à une augmentation du risque d’insuffisance cardiaque et de décès, mais il demeure difficile à prédire en pratique clinique.L’objectif principal de ma thèse était la recherche de biomarqueurs circulants du remodelage VG par l’approche protéine candidate et par protéomique différentielle dans la population REVE-2.Par l’approche protéine candidate, nous avons confirmé que le peptide natriurétique detype B (BNP) était un puissant facteur prédictif du remodelage VG en post-IDM. La métalloprotéase matricielle-8 (MMP-8), la MMP-9, l’hepatocyte growth factor (HGF), la Créactive protéine (CRP), la troponine I ont également fait la preuve de leur association.Par l’approche protéomique différentielle, en électrophorèse 2D différentielle en fluorescence (2D-DIGE), la clusterine a été identifiée comme biomarqueur potentiel,positivement associée au remodelage VG, nécessitant toutefois des travaux de confirmation.Par SELDI TOF MS, nous avons sélectionné 26 pics définis par leur rapport m/z, commebiomarqueurs potentiels du remodelage VG, dont 12 ont pu être identifiés et devrontdésormais être validés : le pic de m/z 2777 a été identifié comme le peptide N-terminal issu del’albumine après clivage par la pepsine. Les autres pics correspondraient à des fragments protéolytiques de protéines que sont le fibrinogène, le complément C3, C4 et C1q.La découverte de nouveaux biomarqueurs du remodelage VG devrait permettre d’améliorer la stratification du risque en post-IDM afin d’identifier les patients devant bénéficier d’un suivi plus rapproché et peut-être d’une prise en charge thérapeutique plus agressive / Left ventricular (LV) remodelling after myocardial infarction (MI) indicates a high risk of heart failure and death but remains difficult to predict in clinical practice. Biomarkers may help to refine risk stratification. The main purpose was to find circulating biomarkers of LV remodelling after MI, using two strategies : candidate protein approach and differential proteomic approach, working on a population with a clearly defined phenotype, the REVE-2 study, a prospective multicenter study including 246 patients with a first anterior Q-wave MI. Blood samples were obtained at hospital discharge, at 1 month, 3 months and 1 year. An echocardiography was performed at the same time except for the 1st month to assess LVR.By candidate protein approach, we confirmed that B-type natriuretic peptide (BNP) was a powerful predictor of LV remodelling after MI. Additional biomarkers, such as matrix metalloproteinase-8 (MMP-8), MMP-9, hepatocyte growth factor (HGF), C-reactive protein (CRP) and cardiac troponin I were found to be associated with LV remodelling, highlighting several pathways implicated in pathophysiology of LV remodelling. We have also shown that biomarkers in association (BNP and cardiac troponin I, BNP and MMP-8, BNP and MMP-9) could improve risk stratification in post-MI by selecting groups of patients at higher risk.As the ideal biomarker was still not identified, we applied a differential proteomic approach, with no a priori hypothesis, in order to characterize proteomic signature of LV remodelling. The use of a protein enrichment kit, consisting of a library of combinatorial hexapeptide ligands, compressed the protein concentration range of plasma and serum, through the simultaneous onestep dilution of high-abundance and concentration of lowabundance proteins. Protein enrichment kit prior to two-dimensional (2D) electrophoresis or SELDI TOF MS (surface-enhanced laser desorption–ionization time of flight) analysis enabled the detection of proteins that were not detected in native blood sample and the accessibility to proteolytic fragments obtained from major proteins. Clusterin (apolipoprotein J) was identified as a potential biomarker of LV remodelling by 2D-DIfferential Gel Electrophoresis (2D-DIGE). Clusterin was quantified by Western blot and ELISA and was found to be positively associated with LV remodelling. However, this association was not found with all LV remodelling parameters nor at each time during the year following MI, requiring further analysis. Differential proteomic approach by SELDI TOF MS selected 26 m/z peaks, as potential biomarkers of LV remodelling. Of them, 12 were identified by mass spectrometry. The 2777 m/z peak was identified directly from the ProteinChip array as being the N-terminal peptide (24–48 aa) generated from albumin by pepsin cleavage. Other peaks were identified after purification using chromatographic columns or liquid-phase isoelectric focusing : most of them were found to be proteolytic fragments of proteins like fibrinogen, C3, C4 and C1q complement. Identifications have now to be validated with specific techniques, usually by immmunoprecipitation and Western blot analysis.Finding new biomarkers of LV remodelling could help refine risk stratification and identify patients in whom more aggressive therapy and/or more frequent follow-up could be needed.

Work related musculoskeletal disorders are the dominating causes of reported ill-health in industrialized countries. These chronic pain conditions are one of the most costly public health problems in Europe and North America. When work related musculoskeletal disorders are considered to be of muscular origin and the trapezius muscle is affected, the common appellation is trapezius myalgia. Since little is known about the genesis or how it is maintained, it is of great importance to better understand the pathophysiology of trapezius myalgia; doing so will better enable recommendations for prevention, treatment and rehabilitation. Several hypotheses have been presented based on biochemical alterations in the muscle, suggesting increased signaling of inflammatory substances and altered metabolism. Previous research has not been able to present the comprehensive picture of the muscle in pain. Thus there is a demand for more comprehensive research regarding the biochemical milleu of the chronic trapezius muscle. Proteomic and metabolomic methods allow non-targeted simultaneous analyses of a large number of proteins and metabolites. The main emphasis in this thesis is on a proteomic method, two-dimensional differential gel electrophoresis (2D-DIGE). The method is validated to human skeletal muscle biopsy research with laboratory specific settings. In the baseline study, there were 14 metabolic, contractile, structural and regulatory proteins that differed significantly in abundance when trapezius and vastus lateralis muscles were compared. Using the validated 2D-DIGE method and the baseline study, a comparison between healthy and myalgic muscles was made. Biopsies from female cleaners with and without myalgia were compared to obtain results from women with the same type of work exposure. In the multivariate model, 28 identified unique proteins separated healthy and myalgic muscle and were grouped according to function: metabolic (n=10), contractile (n=9), regulatory (n=3), structural (n=4), and other (n=2). Finally, a second screening method, metabolomics, was introduced to analyze differences in metabolite content as a complement to and verification of the proteomic results. Gas chromatography-mass spectrometry (GC-MS) was performed on muscle interstitial fluid samples obtained with microdialysis, and differences in the abundance of extracellular metabolites were revealed.  The 2D-DIGE method is a reliable method to analyze human skeletal muscle. The outcomes of the proteomic analyses were dependant on the statistical approach. Systematic differences in protein and metabolite content were detected using a multivariate approach. Univariate analyses were used to analyze individual proteins for their significance. The significant proteins in the baseline study were predominately related to muscle fiber type which correlated with the differences in fiber type content between trapezius and vastus lateralis. The proteomic and metabolomics studies where myalgic and healthy muscles were compared provide us with new clues and new aspects regarding the pathophysiology of the myalgic muscle. Technically advanced methods employed in the thesis enabled an explorative screening of proteins of relevance for the pathophysiology of the myalgic muscle. The results of these analyses may contribute to the formulation of future hypothesis that need to be further evaluated.

Besides playing its structural function in cellular membranes, ceramide has been recognized as a bioactive signalling molecule playing roles in the regulation of cell growth, differentiation, senescence and programmed cell death. Apoptosis can be induced in cancer cells by elevation of endogenous ceramide levels in response to a variety of apoptotic stimuli such as cytokines (TNF, IL-1), death receptor ligands (Fas ligand), heat stress, oxidative stress, chemotherapeutic agents, and ionizing or ultraviolet radiation. It was shown that use of exogenous cell-permeable short-chain ceramide can also promote apoptotic pathways in cancer cells. Several studies have attempted to further define the specific role of ceramide in cell death. However, the mechanisms by which ceramide mediates antiproliferative pathways or inhibits prosurvival effects are not yet well-defined. So, we investigated the signalling pathways triggered by exogenously-supplied natural long chain ceramide, especially C16-ceramide, to better understand how this messenger induces its biological effects in cancer cells. We first showed that C16-ceramide induced a decrease in viability of adenocarcinoma cells (HCT116), partly due to apoptosis. Using two-dimensional differential in-gel electrophoresis (2D-DIGE) proteomic approach, we identified new proteins involved notably in cell proliferation, apoptosis, protein transport and transcriptional regulation in response to exogenous C16-ceramide. Among them, the death promoting factor Btf (Bcl-2-associated transcription factor) was found to be involved in the ceramide-dependent pro-apoptotic signalling pathway. Indeed, Btf-depleted colon cancer cells were found to be more resistant to death triggered by C16-ceramide. Transfection of GFP-Btf expression plasmid up-regulated p53 and BAX protein levels whereas pBcl-2 and Mdm2 expression were down-regulated. Furthermore, we identified a new signalling pathway specifically induced by C16-ceramide, depending on Btf and leading to down-regulation of the Mdm2 protein expression and MDM2 promoter activity. Thus, we provided new information on molecular mechanisms involved in the ceramide-mediated cell death. Then, we investigated the regulation of Emerin expression and its post-translational modifications induced by ceramide. We found that cAMP-dependent protein kinase A (PKA) could be involved in the C16-ceramide induced-Emerin phosphorylation. However, we did not demonstrate the interaction between Btf and phosphorylated-Emerin upon ceramide treatment. Nevertheless, we showed that one of the pathway induced by ceramide implies Emerin and leads to down-regulation of the MDM2 promoter activity. We also hypothesized that GCL (germ-cell-less) could be an intermediate in the Emerin-Mdm2 pathway triggered by C16-ceramide. Furthermore, we showed that Emerin-depleted cells were not more sensitive to apoptosis induced by C16-ceramide. These results should allow us to further explore the potential functions of Emerin in a ceramide-dependent pathway.

El càncer d'endometri és la malaltia ginecològica més comuna i representa la quarta neoplàsia més freqüent en la dona en els països desenvolupats. Actualment és possible diagnosticar el 80% dels casos de EEC en estadiatge I FIGO, per tant, poder aplicar cirurgia i presentar un bon pronòstic. L'estadiatge I FIGO inclou tres subtipus: afecta l'endometri (IA), infiltra el miometri <50% (IB) i >50% (IC). El nostre grup es va centrar en la identificació de nous gens implicats en el EEC mitjançant l'estudi dels patrons d'expressió gènica diferencial entre teixit endometrial sa, hiperplàsic i tumoral, així com la cerca de nous gens associats al fenotip carcinomatós endometrial amb potencial valor diagnòstic i/o pronòstic. Es va trobar que els dos gens majorment sobreexpressats eren RUNX1/AML1 i ERM/ETV5 i alhora, es troben sobreexpressats en la fase en la qual el EEC esdevé invasiu. Partint d'aquí, vam plantejar la caracterització del mecanisme d'acció del factor de transcripció ERM/ETV5 en el EEC durant els esdeveniments inicials d'invasió i disseminació. La sobreexpressió d'ERM/ETV5 a la línia cel·lular de càncer d'endometri Hec-1A indueix dispersió cel·lular que correlaciona amb un augment de l'activitat gelatinasa de la MMP2. Tant els experiments de ChiP com amb iRNA o l'ús d'un inhibidor específic de MMP2 mostren un nexe funcional entre la sobreexpressió d'ERM/ETV5 i l'activació de MMP2. En el model animal ortotòpic de EEC es demostra que l'augment de l'activitat de MMP2 associat a la sobreexpressió d'ERM/ETV5 confereix major capacitat invasiva als tumors endometrials i aquests mostren un patró més agressiu i infiltrant. Es va confirmar que ERM/ETV5 tenia un paper en els passos inicials de la disseminació endometrial ja que es van localitzar ERM/ETV5 i MMP-2 en el front d'invasió de mostres de EEC humanes amb infiltració miometrial. Per tant podem proposar que en el EEC, ERM/ETV5 actua a través de l'activitat gelatinolítica de MMP-2 per a donar major capacitat invasiva, associat al punt d'inici de la infiltració miometrial. Tot seguit vam plantejar determinar les alteracions moleculars associades a la sobreexpressió del factor de transcripció ERM/ETV5 durant la infiltració miometrial en el EEC, identificant nous marcadors moleculars o dianes terapèutiques que podrien estar sota el control de l'activitat transcripcional d'ERM/ETV5. L'anàlisi comparatiu mitjançant 2D-DIGE i espectrometria de masses dels patrons d'expressió proteica diferencial de la línia cel·lular que sobreexpressa de forma estable GFP-ERM/ETV5 anvers la línia cel·lular sense transfectar i la que presenta el vector GFP buit, determina un llistat de proteïnes diferencialment expressades que es troben implicades en la regulació d'actina i la senyalització per TGF-beta i progesterona. Vam caracteritzar la sobreexpressió específica de la proteïna Hep27 que presenta localització mitocondrial depenent d'ERM/ETV5. Estudis funcionals van demostrar associació amb l'estrès oxidatiu. L'anàlisi dels resultats obtinguts reforcen el paper d'ERM/ETV5 com a factor regulador de la migració i invasió tumoral, i assenyala la seva implicació en la resposta a l'estrès oxidatiu associat a l'inici de la invasió en el carcinoma endometrial. Fins ara, la immunohistoquímica ha estat l'eina utilitzada per a la identificació de proteïnes implicades en la invasió del carcinoma endometrial, sense tenir en compte la percepció global del front d'invasió. En aquest últim treball hem dut a terme una aproximació proteòmica per a caracteritzar components específics del front d'invasió o l'estroma reactiu mitjançant la comparació de l'àrea invasiva d'un carcinoma endometrial anvers l'àrea tumoral superficial no invasiva i el teixit normal provinents de la mateixa pacient. Així hem pogut identificar proteïnes diferencialment expressades en el front d'invasió i que es troben implicades en la morfologia cel·lular, acoblament i moviment, així com els mecanismes moleculars relacionats amb la senyalització i interacció cèl·lula-cèl·lula i la resposta moduladora a l'estrès oxidatiu. / We have recently described the Ets family transcription factor, ERM/ETV5, specifically up-regulated in EEC, and associated with myometrial infiltration. Ets family members have been correlated to tumor progression by up-regulating the expression of matrix-degrading proteases. We investigated the possibility that in EEC, ERM/ETV5 may induce the expression of genes involved in extra-cellular matrix remodeling. The overexpression of ERM/ETV5 induced scattering in the EEC cell line Hec-1A, correlating to increased MMP-2 gelatinase activity. Both ChIP and iRNA experiments and specific MMP-2 inhibitor demonstrated a functional link between ERM/ETV5 overexpression and MMP-2 activation. Orthotopically implanted overexpressing ERM/ETV5 tumors presented a more aggressive and infiltrative pattern of myometrial invasion. The specific localization of ERM/ETV5 and MMP-2 at the invasive front of myometrial infiltrating human EEC reinforced the hypothesis of a role for ERM/ETV5 in the early steps of endometrial dissemination.To understand the role of ETV5 during myometrial infiltration, we analysed by 2D-DIGE technology those proteins whose expression was altered in endometrial cell lines stably over-expressing ERM/ETV5. Pathway analysis pointed to actin regulation and TGF-beta and progesterone signalling as processes regulated by ERM/ETV5. We characterized the specific up-regulation of the nuclear dehydrogenase/reductase Hep27, its ERM/ETV5-dependent mitochondrial localization, and functional studies demonstrated a link with oxidative stress.Overall, the ETV5-related proteomic approach performed in the Hec-1A cell line reinforces a role of this transcription factor in the regulation of the migratory and invasive tumour behaviour, and points to a modulated response to oxidative stress associated with the promotion of invasion in endometrial cancer. To date, the identification of proteins involved in endometrial carcinoma invasion has been essentially conducted by immunohistochemical methods, without a global perception on the invasive front. In this work we attempted a proteomic approach to characterise specific components of the invasive front or reactive stroma by comparing the invasive area of an endometrial carcinoma with the non¬invasive superficial area and normal tissue from the same patients. This led us to identify proteins involved in cellular morphology, assembly and movement, differentially expressed at the invasive front, as well as pathways like cell-to-cell signalling and interaction and a modulated response to oxidative stress as events related to endometrial carcinoma invasion. In conclusion, we describe a novel proteomic approach that specifically deals with endometrial carcinoma invasion front, allowing the identification of new players of myometrial infiltration.

Staphylococcus aureus is a remarkably successful pathogen, accounting for an estimated 95,000 invasive infections annually in the U.S. alone. The burden of MRSA infections on public healthcare continues to rise, particularly with the continued spread of antibiotic resistant strains and the hyper-virulent CA-MRSA strains. The pathogenic nature of S. aureus can be attributed to the cache of virulence factors encoded within the genome of this organism. Typically, these are secreted toxins which directly interact with the host during infection, and facilitate pathogenesis. A previous screen in our laboratory investigating proteases in S. aureus identified a mutant in aminopeptidase Z as being attenuated in disease causation. Classically aminopeptidases function in the bioactivation/inactivation of proteins; and/or the utilization of imported peptides for cellular nutrition. We therefore hypothesize that cells deficient in one of these two processes would have decreased fitness levels, resulting in reduced virulence. We therefore sought to explore the role of PepZ in S. aureus; either in the processing of exogenous oligopeptides for nutrition, or in protein bioactivation/inactivation, and protein stability. We determined that S. aureus strains deficient in PepZ are less viable when cultured under conditions of starvation or while in competition for nutrients with the parent strain, and does not appear to be peptide driven. Using protein analysis approaches we have identified PepZ externalization, suggesting a potential for the aminopeptidase beyond the confines of the cell membrane. Additionally, we have also identified a potential role for PepZ in protein stability in this organism. Lastly, we present the essential role for PepZ in S. aureus virulence.

Physical activity can prevent cardiovascular disease, obesity, type II diabetes and some types of cancer. With only 3.5% of adults meeting the recommended physical activity guidelines, research has focused on the regulatory factors that influence physical activity level. Genetic influence accounts for the majority of physical activity regulation. However, there is limited information on the mechanisms that affect physical activity, in part, because of a lack of reliable methods to silence genes in vivo. The purpose of this dissertation was to identify mechanisms in skeletal muscle that influence physical activity. The methods used to accomplish the purpose of this dissertation were the evaluation of Vivo-morpholinos as a gene silencing tool in skeletal muscle and brain, identification of proteins in skeletal muscle associated with increased physical activity level, and the use Vivo-morpholinos to transiently knockdown the identified skeletal muscle proteins as a means to elucidate mechanisms for the peripheral regulation of physical activity. Overall, this study showed that Vivo-morpholinos effectively silenced genes in skeletal muscle yet required the use of a pharmacological aid to achieve gene silencing in the brain. Additionally proteins associated with calcium regulation (Annexin A6 and Calsequestrin 1) and the Kreb’s (TCA) cycle were found to be over expressed in the high active animals. The knockdown of Annexin A6 and Calsequestrin 1 resulted in a significant decrease in physical activity, thus showing that calcium regulation could influence the physical activity response. While these results provide a potential mechanism for the peripheral regulation of physical activity, a side effect observed was that Vivo-morpholinos can hybridize resulting in increased mortality rates of the treatment animals. Therefore, we developed methods to alleviate the toxic effects of Vivo-morpholinos. Thus, this dissertation refined a technique for determining a gene’s effect in an in vivo model and identified two candidate proteins (Annexin A6 and Calsequestrin 1) that play a role in regulating daily physical activity.

Xanthomonas oryzae pv. oryzae (Xoo) est une bactérie phytopathogène responsable de la bactériose vasculaire du riz, maladie pouvant engendrer de fortes pertes de rendement à travers le monde. La course à l'armement entre la bactérie et sa plante hôte correspond d'une part à la mise en place de la virulence par le microorganisme et d'autre part en la résistance du végétal face à l'agression. Comprendre les mécanismes par lesquels Xoo accompli son cycle infectieux est d'une importance cruciale pour le développement futur de nouvelle méthode de luttes. Plusieurs approches complémentaires ont été mises en uvre afin de caractériser des éléments associés au pouvoir pathogène de Xoo.Dans un premier temps nous avons effectué une analyse protéomique comparative. Cette approche a permis l'identification chez une souche Africaine de Xoo d'un jeu de protéines induites par HrpX et susceptibles de jouer un rôle dans la virulence. Dans un second temps, l'implication de deux peptides dans la virulence Xoo a été étudiée. Le premier de ces peptides, supposé être le facteur d'avirulenceAvrXa21, a fait l'objet d'une caractérisation fonctionnelle et phylogénique. Le second peptide est synthétisé par un cluster NRPS, similaire à l'un de ceux présent chez Xanthomonas albilineans. Afin d'élucider l'importance de la molécule synthétisée par cette voie pour Xoo, une étude préliminaire impliquant la mutation d'un élément régulateur des NRPS a été effectuée. En dernier lieu, des informations nouvelles ont été apportées sur la topologie de la protéine membranaire HrcR qui est une composante essentielle du système de sécrétion de type III chez la plupart des bactéries appartenant au genre Xanthomonas. / Xanthomonas oryzae pv. oryzae (Xoo) is the agent of bacterial leaf blight BLB in rice, a disease which causes considerable yield losses throughout the world. In the arms race underlying the interactions between the microorganism and the host, the presence of virulence factors in the former parallels that of resistance factors in the latter. Understanding the mechanisms of Xoo's infectious cycle is of paramount importance for the elaboration of new fighting strategies to combat BLB. To achieve this, several complementary approaches to characterize components of Xoo's pathogenicity have been employed.First, we performed comparative proteomics that allowed us to identify novel HrpX-induced candidate pathogenicity factors of an African Xoo strain. Second, the involvement of two peptides in Xoo's pathogenicity has been investigated. One was speculated to be the avirulence factor AvrXa21 and has been characterized both functionally and phylogenetically. The other one was found to be synthesized by a Non-Ribosomal Peptide Synthetase (NRPS), reminescent to NRPS genes found in Xanthomonas albilineans. In order to determine the role of NRPS-mediated synthesis in Xoo virulence, we studied a strain carrying a mutated regulatory gene of the NRPS pathway. Finally, we provide new information on the topology of the HrcR membrane protein which is a conserved component of the type III secretion system of most Xanthomonas.

<p>Developmental toxicology is an important part of preclinical drug toxicology as well as environmental toxicology. Assessing reproductive and developmental toxicity is especially expensive and time demanding, since at least two generations of animals are needed in the tests. In light of this there is a great need for alternative test methods in many areas of developmental toxicity testing.</p><p>The complete set of RNA transcripts in any given organism is called the transcriptome. Proteomics refers to the study of the proteins in a given organism or cell population. The work of this thesis has focused on the use of high throughput screening methods in transcriptomics and proteomics to search for molecular markers of developmental toxicity.</p><p>We have studied the global gene expression effects of the developmentally toxic substance valproic acid (VPA) using microarray technology. Several genes were found that display the same gene expression pattern <i>in vivo</i> using mouse embryos as the pattern seen <i>in vitro</i> using the embryocarcinoma cell line P19. Based on these observations, the gene Gja1 was suggested as one potential molecular marker of VPA induced developmental toxicity and potential marker of histone deacetylase (HDAC) inhibition <i>in vitro</i>. </p><p>Using 2D-DIGE technology, which measures relative protein abundances, the effect of neonatal exposure to the flame retardant PBDE-99 was studied in mouse brain (cortex, hippocampus and striatum) 24 hr after exposure. Differentially expressed proteins in the cortex and the striatum indicate that PBDE-99 may alter neurite outgrowth.</p><p>Finally, we have suggested several improvements in the use of the 2D-DIGE technology. Novel methods for normalizing data were presented, with several advantages compared to existing methods. We have presented a method named DEPPS that makes use of all identified proteins in a dataset to make comprehensive remarks about biological processes affected.</p>