L'un des phénomènes les plus importants survenus pendant la maturation du fruit de tomate est le changement de couleur du vert au rouge. Ce changement a lieu dans les plastes et correspond à la différenciation des plastes photosynthétiques, les chloroplastes, en plastes non-photosynthétiques qui accumulent des caroténoïdes, les chromoplastes. Dans cette thèse, nous présentons d'abord une introduction bibliographique sur le domaine de la transition chloroplaste-chromoplaste, en décrivant les modifications structurales et physiologiques qui se produisent pendant la transition. Puis, dans le premier chapitre, nous présentons des observations microscopiques de plastes isolés à trois stades de mûrissement, puis des enregistrements en temps réel de la fluorescence des pigments sur les tranches de fruits de tomate. Il a été possible de montrer que la transition chloroplaste-chromoplaste était synchrone pour tous les plastes d'une seule cellule et que tous les chromoplastes proviennent de chloroplastes préexistants. Dans le deuxième chapitre, une approche protéomique quantitative de la transition chloroplaste-chromoplaste est présentée, pour identifier les protéines différentiellement exprimées. Le traitement des données a identifié 1932 protéines parmi lesquelles 1529 ont été quantifiées par spectrométrie de masse. Les procédures de quantification ont ensuite été validées par WESTERN blot de certaines protéines. La chromoplastogénèse comprend les changements métaboliques suivants : diminution de l'abondance des protéines de réaction à la lumière et du métabolisme des glucide, et l'augmentation de la biosynthèse des terpénoïdes et des protéines de stress. Ces changements sont couplés à la rupture de la biogenèse des thylakoïdes, des photosystèmes et des composants de production d'énergie, et l'arrêt de la division des plastes. Dans le dernier chapitre nous avons utilisé la lincomycine, un inhibiteur spécifique de la traduction à l'intérieur des plastes, afin d'étudier les effets sur la maturation des fruits et sur l'expression de gènes nucléaires impliqués dans la maturation. Les résultats préliminaires indiquent que l'inhibition de la traduction des protéines dans les plastes affecte la maturation du fruit en réduisant l'accumulation de caroténoides. L'expression de plusieurs gènes nucléaires a été modifiée mais une relation claire avec le phénotype altéré de maturation n'a pas pu être établie. Au total, notre travail donne de nouveaux aperçus sur le processus de différenciation chromoplaste et fournit des données nouvelles ressources sur le protéome plaste / One of the most important phenomenons occurring during tomato fruit ripening is the color change from green to red. This change takes place in the plastids and corresponds to the differentiation of photosynthetic plastids, chloroplasts, into non photosynthetic plastids that accumulate carotenoids, chromoplasts. In this thesis we first present a bibliographic introduction reviewing the state of the art in the field of chloroplast to chromoplast transition and describing the structural and physiological changes occurring during the transition. Then, in the first chapter we present an in situ real-time recording of pigment fluorescence on live tomato fruit slices at three ripening stages. By viewing individual plastids it was possible to show that the chloroplast to chromoplast transition was synchronous for all plastids of a single cell and that all chromoplasts derived from pre-existing chloroplasts. In chapter two, a quantitative proteomic approach of the chloroplast-to-chromoplast transition is presented that identifies differentially expressed proteins. Stringent curation and processing of the data identified 1932 proteins among which 1529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immune-blot evaluation of some proteins. Chromoplastogenesis appears to comprise major metabolic shifts (decrease in abundance of proteins of light reactions and carbohydrate metabolism and increase in terpenoid biosynthesis and stress-related protein) that are coupled to the disruption of the thylakoid and photosystems biogenesis machinery, elevated energy production components and loss of plastid division machinery. In the last chapter, we have used lincomycin, a specific inhibitor of protein translation within the plastids, in order to study the effects on fruit ripening and on the expression of some ripening-related nuclear genes. Preliminary results indicate that inhibiting protein translation in the plastids affects fruit ripening by reducing the accumulation of carotenoids. The expression of several nuclear genes has been affected but a clear relationship with the altered ripening phenotype could not be established. Altogether, our work gives new insights on the chromoplast differentiation process and provides novel resource data on the plastid proteome

Reproductive diseases, mainly those resulting in the infertility affect the chances of human being to reproduce. On the contrary, the heart disease, cancer and degenerative diseases currently account for majority of deaths in the world. Usually, these lifestyle diseases need longer lifespan to become the cause of death. The proteins secreted by cells carry important information about the cell's well-being, as well as about the condition of the tissues formed by these cells. Once secreted, these proteins may also be transferred throughout the body by means of body fluids, many of which are easily accessible for further 'in-depth' studies. Cellular and secreted proteins are often a focus of studies using proteomic means and the revelation of protein alterations can lead us to new ideas about the molecular mechanisms of diseases as well as possible identification of proteins that may be used as new targets for pharmaceutical intervention or molecules that could be used for diagnostic or prognostic purposes. Taking into consideration the above aspects, this research was undertaken to find proteins that could: (a) characterise the human follicular fluid as microenvironment of the maturing oocyte, to increase understanding of reproductive processes to improve the techniques of assisted repro- duction;...

Les propriétés du bois de pin maritime varient aux niveaux chimique, anatomique et mécanique. Six types de bois peuvent être trouvés au sein d’un même arbre : bois précoce, bois tardif, bois de couronne, bois de base, bois de compression et bois opposé. Au cours de cette thèse, nous avons testé l’hypothèse selon laquelle la variabilité phénotypique des propriétés de bois, serait liée à l’expression différentielle des protéines lors de la xylogénèse. Par une approche protéomique basée sur l’électrophorèse bidimensionnelle et la spectrométrie de masse en tandem (LC ESI MS/MS), nous avons identifié 165 protéines différentiellement exprimées le long d’un gradient d’âge cambial (bois juvénile vs. bois mature) ainsi que 93 protéines différentiellement exprimées au cours de la saison de végétation (bois de printemps vs. bois d’été) chez le pin maritime. Une analyse chimique complémentaire des échantillons a été réalisée par pyrolyse analytique. Nos résultats montrent que le xylème secondaire formé en début de saison ainsi que celui qui est initié par un cambium jeune présentent une sur-expression de protéines participant à la division cellulaire. Dans le xylème issu d’un cambium âgé ou formé à la fin de l’été nous avons mis en évidence des protéines impliquées dans la défense cellulaire (dont le rôle serait de retarder la mort cellulaire programmée), ainsi que des protéines impliqués dans la biosynthèse des éléments constitutifs de la paroi. Cette étude contribue à renforcer nos connaissances sur les acteurs moléculaires intervenant lors de la xylogénèse. Elle ouvre par ailleurs des pistes de recherche sur la détection de gènes impliqués dans le contrôle génétique des propriétés du bois dans un objectif de sélection assisté par marqueurs. / Wood properties in maritime pine are highly variable at chemical, anatomical and mechanical levels. Six types of wood can be found in a single tree, early wood, late wood, crown wood, base wood, compression wood and opposite wood. In this thesis report, we tested the hypothesis that the observed variability at the phenotypic level, can be bound to the differential expression of proteins during the process of wood formation. We use the tools of proteomics, Bidimensional electrophoresis and LC ESI MS/MS for the discovery of 165 proteins differentially expressed in a cambial age gradient, (from base wood to crown wood), an 93 overexpressed proteins in a seasonal gradient (from early wood collected at the beginning of the growing season, to late wood, collected at summer) Complementary, chemical characterization of the samples was performed using analitycal pyrolisis. Our results showed that the secondary xylem formed at the beginning of the growing season, and the xylem formed by a young cambium, present a overexpression of proteins participating in the intense cell division, characteristical of those tissues, e.g. Biogenesis of cytoskeleton and hemicelluloses, RNA transcription, synthesis, folding and modification of proteins. In the xylem formed at the base of the trunk and at the end of the growing season we have found an over-expression of proteins from cell defense (they role will be to delay programmed cell death) and cell wall formation related proteins e.g. lignin biosynthesis. This study contributes to reinforce our knowledge over the molecular actors involved in the xylogenesis process. It opens, in another hand , research guides for the detection of genes involved in the genetic control of wood properties towards an objecive of marker assisted selection.

Master of Science / Biochemistry / John Tomich / One of the important keys to characterize the biological function of a protein is the study of post-translational modification (PTM). Formation of disulfide bond linkages between cysteine residues within a protein is a common PTM which not only contributes to folding and stabilizing the protein structure, but also to accomplishing its native function. Therefore, the study and discovery of structural-functional relationships of expressed proteins using an isolated proteomics approach has been one of the biggest advances within the field of structural biology in recent years. In this study, rapid disulfide bond mapping of freshly obtained equine serum albumin (ESA) was performed using matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Highly sensitive MALDI-TOF MS is commonly used for the investigation of disulfide bond linkages in the proteomics field. However, it has also been known that the presence of disulfide bond linkages absorbs the energy which is created by the cysteine-cysteine kinetic vibration, resulting in a decrease of the instrumental sensitivity. To overcome this problem, the disulfide bond mapping method was optimized by applying a combination of chemical labeling, proteolytic enzymes, and matrices. With the optimized method, we were also able to achieve high protein sequence coverage. Obtaining higher sequence coverage of a protein provides more information about a protein which helps to identify the protein by peptide mass fingerprint (PMF) technique. These analyses eventually contribute to the estimation of the possible PTM sites.

Cell surface proteins play an important role in understanding cell-cell communication, cell signaling pathways, cell division and molecular pathogenesis in various diseases. Commonly used biotinylation regents for cell surface mapping have shown some potential drawbacks such as crossing the cell membrane, difficult recovery of biotinylated proteins from streptavidin/avidin beads, interference from endogenous biotin and nonspecific nature of streptavidin. With aim to solve these problems, we introduced sulfo-N-hydroxysuccinimidyl (NHS) ester functionalized magnetic nanoparticles containing cleavable groups to label solvent exposed primary amine groups of proteins. Silica coated iron oxide magnetic nanoparticles (Fe3O4@SiO2 MNPs) were linked to NHS ester groups via a cleavable disulfide bond. Additionally, the superparamagnetic properties of Fe3O4@SiO2 MNPs facilitate efficient separation of the labeled peptides and removal of the detergent without any extra step of purification. In the last step, the disulfide bond between the labeled peptides and MNPs was cleaved to release the labeled peptides. The disulfide linked NHS ester modified Fe3O4@SiO2 MNPs were tested using a small peptide, and a model protein (bovine serum albumin) followed by liquid chromatography-tandem mass spectrometry analysis (LC-MS/MS) of labeled peptides. In the next step, disulfide linked, NHS ester modified Fe3O4@SiO2 MNPs (150 nm) successfully labeled the solvent exposed cell surface peptides of Saccharomyces cerevisae. Electron microscopic analysis confirmed the cell surface binding of NHS ester modified Fe3O4@SiO2 MNPs. Mass spectrometric analysis revealed the presence of 30 unique proteins containing 56 peptides. Another MNPs based labeling reagent was developed to target solvent exposed carboxyl acid residues of peptides and proteins. The surface of Fe3O4@SiO2 MNPs was modified with free amine groups via a disulfide bond. Solvent exposed carboxyl groups of ACTH 4-11 and BSA were labeled by using1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) chemistry. Upon cleaving the disulfide bond, labeled peptides were analyzed by LC-MS/MS. The MNPs containing labeling reagents offers specific labeling under physiological conditions and rapid magnetic separation of labeled peptides prior to mass spectrometric analysis. The ability of large Fe3O4@SiO2 MNPs to specifically attach to cell surface makes them a potential candidate to study the surface of variety of different cell types and complex proteins surrounded by lipid bilayer.

No description available.

La maladie du sommeil ou Trypanosomose Humaine Africaine (THA) est une parasitose vectorielle due à un protozoaire flagellé sanguicole du genre Trypanosoma et d'espèce brucei. Deux sous-espèces de ce parasite sont pathogènes pour l'Homme : T. b. gambiense et T. b. rhodesiense ; transmis par les mouches Tsé-Tsé présentes en Afrique subsaharienne. Cette maladie évolue classiquement en deux stades : le stade hémolyphatique qui est marqué par la présence du parasite dans le sang et la lymphe et le stade nerveux caractérisé par la présence du trypanosome dans le Système Nerveux Centrale. En l’absence de traitement cette maladie est mortelle. Actuellement les traitements accessibles à la population sont stades-dépendants. Pour contrôler un jour cette pathologie, la recherche et l’amélioration des outils de diagnostic de la maladie et le diagnostic de stade sont essentielles. C’est dans ce but que nous avons exploité une biobanque d’échantillons composée de patients infectés par T. b. gambiense et d’individus non-infectés pour : 1) Évaluer l’efficacité de biomarqueurs de stade déjà existants -Néoptérine et CXCL-13- et nous avons évalué leur potentiel sur les échantillons recueillis lors du suivi des patients post-traitements. 2) Rechercher de nouveaux biomarqueurs protéiques par spectrométrie de masse LCMS/MS. Notre étude a permis d’identifier, grâce à l’établissement d’un nouveau catalogue protéomique un grand nombre de biomarqueurs potentiels dans le liquide céphalo-rachidien, l’urine et la salive de patients. Certaines de ces protéines pourraient améliorer la prise en charge et le suivi des patients à l’avenir. / Sleeping sickness, or Human African Trypanosomiasis (HAT), is a parasitic disease caused by a flagellar protozoan of the genus Trypanosoma and brucei species. Two subspecies of this parasite are pathogenic for humans: T. b. gambiense and T. b. rhodesiense; transmitted by Tsé-Tse flies present in sub-Saharan Africa. This disease classically evolves in two stages: the hemolymphatic stage which is define by the presence of the parasite in the blood and lymph and the nervous stage characterized by the presence of trypanosome in the central nervous system. Without treatment, this disease is lethal. Currently the available treatments for patients are stage-dependent. In order to control this pathology one day, research and improvement of tools for the diagnosis of the disease and the staging is fundamental. In this context, we have exploited a samples biobank composed of T. b. gambiense-infected patients and uninfected controles to: 1) evaluate the efficacy of existing stage biomarkers -Neopterin and CXCL-13- and we assessed their potential on the samples collected during post-treatment followup of patients. 2) determine new protein biomarkers using LC-MS/MS mass spectrometry. Our study identified a large number of potential biomarkers in cerebrospinal fluid, urine and saliva through the establishment of a new proteomic catalogue. Taking into account some of these proteins may improve patient management and follow-up in the future.

>Magister Scientiae - MSc / Drought is a major abiotic stress which causes not only differences between the mean yield and the potential yield but also yield variation from year to year. Although selection for genotypes with improved productivity under drought environments has been a central goal of numerous plant breeding programs, the molecular basis for plant tolerance towards drought stress is still poorly understood. Exposure of plants to this abiotic stress is known to trigger excessive formation of reactive oxygen species (ROS), which induce cell death and reduce growth. Part of the mechanism of plant responses to drought involves alterations in the expression of antioxidant enzymes and biosynthesis of different compatible solutes such as proline. Sorghum is regarded as generally more drought tolerant than maize, and it is a potential key model system for investigating the physiological and molecular mechanisms conferring drought tolerance. Comparative studies in crop plants to decipher differences in drought tolerance are essential for crop improvement to sustain a higher level of production, which in turn will improve food security, under severe drought conditions resulting from climate change. On this basis, the aim of this study is to determine molecular differences between Zea mays and Sorghum bicolor in response to drought stress in an attempt to identify novel biomarkers for drought tolerance. The physiological and molecular responses of maize and sorghum were studied for changes in growth, chlorophyll content, relative water content, ROS content, lipid peroxidation level, proline content, and antioxidant enzyme activity. Spectral Count Label-free Quantitation analysis was conducted to reveal the changes in protein profiles under drought in attempt to identify drought-responsive molecular mechanisms in the leaves of the two plant species. In this study, water deficit triggered mechanisms that resulted in overproduction of ROS in both Zea mays and Sorghum bicolor. However, Sorghum bicolor showed less oxidative damage under water stress compared to Zea mays. Drought-induced proline accumulation in the roots of Sorghum bicolor was associated with enhanced water retention. Significant changes were identified in the antioxidant enzyme activity between the two plant species in response to drought conditions. Proteomics results showed differing patterns for drought-responsive proteins in the two species. Together with the physiological, biochemical and proteomic profiling results between Zea mays and Sorghum bicolor, potential proteins and/or metabolic pathways underlying drought tolerance were identified. The findings obtained through this study provide insight towards understanding the molecular basis of crop drought tolerance.

Traditional water monitoring encounter limitations due to the large number of contaminants present in our waters possible giving raise to mixture effects. This thesis aimed to investigate how the emerging omics approaches (transcriptomics, proteomics and metabolomics) can be used as an effect-based monitoring approach to assess and predict adverse effects in the freshwater environment. Moreover, this thesis analysed challenges and barrier with omics. A systematic literature search was conducted using Scopus and Web of Science to find case-studies using omics in field studies and reviews regarding challenges and barriers. The results in this thesis suggest that the use of fish species (either collected in the wild or in situ set-ups), transcriptomics and investigations of WWTP recipient was the most common way to apply omics. In order to interpret omics-data multiple studies conducted chemical monitoring in conjunction, investigated additional traditional biomarkers and/or used omics to identify altered biological or functional pathways that possible could lead to adverse effects at higher levels. According to the challenges and barriers identified in this thesis, the future of omics in environmental monitoring rely on the possibility to characterise and quantify natural variability, define appropriate critical effect sizes (i.e. thresholds of critical effects) and define baseline data. Moreover, it is necessary to develop frameworks and standardisations for omics-approaches (e.g. study-designs) to promote the interpretation of the results. Future research is also needed to develop and increase the understanding of how the proteomics and metabolomics can be applied. By improving the use of omics a more holistic water monitoring can be achieved including screenings for biological responses and the ability to detect early warnings which will enhance the prioritisation and site management of polluted water bodies, including those with limited prior knowledge regarding potential contaminants.

A saliva humana é um fluído, que exerce diversas funções na saúde oral e geral. A análise do proteoma das glândulas salivares em especial da glândula parótida, são importantes para a compreensão das proteínas individuais presentes na saliva humana e do seu comportamento na saúde, para desta forma entender a patogênese de certas doenças. Esse trabalho é um catálogo de todas as proteínas expressas na saliva da glândula parótida de indivíduos saudáveis em fluxo contínuo de alta intensidade (1ml/min), de baixa intensidade (0,25ml/min) e na situação de estresse. Também foram realizadas as análises quantitativas e qualitativas da saliva avaliada em pool salivar ou individualmente. As proteínas foram identificadas através de técnicas em espectrometria de massas. Os resultados mostraram uma grande variação individual e as proteínas identificadas estão envolvidas em numerosos processos celulares, desde função estrutural até atividades catalíticas/enzimáticas. Esse estudo tenta, pela primeira vez, criar um padrão ouro para a coleta salivar, possibilitando a comparação entre pesquisas para melhor compreensão da composição salivar. / Human saliva is a fluid that performs various functions in oral and general health. The analysis of the proteome of the salivary glands, especially the parotid gland, are important to understanding the individual proteins present in human saliva and their behavior in health. This work is a catalog of all the proteins expressed in saliva of the parotid gland of healthy individuals in continuous flow of high intensity (1ml / min), low intensity (0.25ml / min) and in the stress situation. Quantitative and qualitative analyzes of saliva evaluated in a salivary pool or individually were also performed. Proteins were identified by mass spectrometric techniques. The results showed a large individual variation and the proteins identified are involved in numerous cellular processes, from structural function to catalytic / enzymatic activities. This study attempts, for the first time, to create a gold standard for salivary collection, making it possible to compare researches for a better understanding of salivary composition.