Les premiers stades larvaires chez l’huitre creuse, nommée Magallana gigas, constituent une étape clé du bondéroulement du parcours zootechnique et également pour la pérennisation de la production en écloserie. Dans l’objectifde réduire les mortalités observées en écloserie, nous avons recherché de nouveaux peptides antimicrobiens. Larecherche de ces PAM a été réalisée à partir de deux organismes marins, le poisson-lion invasif en mer des caraïbes,Pterois volitans, et la seiche commune présente sur les zones ostréicoles, Sepia officinalis. La recherche de PAM a étéréalisée préférentiellement à partir de transcriptomes de novo obtenus chez ces deux animaux. Chez le poisson lion, àpartir de BLAST, 7 transcrits codant pour des PAM ont été identifiés. Quatre de ces PAM partagent de fortes homologiesde séquences (>90% d’identité) avec des PAM riches en cystéines proches de l’hepcidine, la LEAP-2, la NK-lysine et la bdéfensineidentifiées chez d’autres poissons. Les 3 autres transcrits annotés pteroicidines A, B et C codent pour despeptides apparentés aux piscidines. La présence de la b-défensine et de la pteroicidine a codée par la pteroicidine A a puêtre confirmée dans les extrait de peau du poisson lion par spectrométrie de masse. Une étude approfondie a été menéesur deux formes amidée et non amidée de la ptéroicidine a ainsi que sur plusieurs peptides de différentes tailles issusdes pteroicidines B et C. Les résultats ont permis de mettre en évidence une relation entre la structure, l’amidation et lesactivités antibactériennes et hémolytiques de ces différentes ptéroicidines. Sur le modèle Sepia officinalis, par lesapproches classiques couplant la purification et les tests antibactériens ou par des approches utilisant les BlAST, aucunPAM n’a été mis en évidence. Nous avons donc développé une approche plus originale qui repose sur le « design » depeptides à partir du transcriptome. A partir de 811 petits peptides sans cystéines issus de la base de données APD, nousavons déterminé des critères récurrents concernant la charge, l’hydrophobicité et la composition en acides aminés. Surla base de ces critères et en s’appuyant sur les outils de prédiction de CAMP, douze peptides ont fait l’objet d’une synthèse.Cinq de ces peptides ont révélé un large spectre d’activités antibactériennes. Les peptides antibactériens issus de la seicheayant une activité non hémolytique ont fait l’objet d’un transfert en écloserie. Ce transfert a été optimisé à partir d’uneétude préliminaire sur le peptide de novo K4, particulièrement actif sur les vibrios. Cette étude a mis en évidencel’importance de l’innocuité du peptide antibactérien sur les différents maillons de la chaine trophique, notamment del’huitre, et sur l’importance du stade de développement ciblé. Par ailleurs, nous nous sommes intéressés au devenir despeptides antibactériens de manière à s’assurer de leur biodégradabilité. L’ensemble de ces travaux a permis nonseulement d’identifier de nouveaux PAMs mais également d’apporter les premières données portant sur le potentiel del’utilisation de ces peptides comme alternative aux antibiotiques. / The first larval stages of oyster (Magallana gigas) are key steps in the smooth running of the zootechnical course and inthe sustainability of hatcheries, where mortality levels can be high. That is why we searched for new antimicrobialpeptides (AMPs) on two marine organisms, i.e. lionfish (Pterois volitans), which is invasive in the Caribbean Sea, and thecommon cuttlefish (Sepia officinalis), which is present in French oyster production areas. The search for AMPs wascarried out preferentially from de novo transcriptomes from these two animals. In lionfish, BLAST analyses allowed forthe identification of 7 transcripts encoding AMPs. Four of them shared strong sequence homology (> 90% identity) withAMPs rich in cysteines and close to hepcidin, LEAP-2, NK-lysin and b-defensin identified in other fish. The other 3transcripts, annotated pteroicidins A, B and C, coded for piscidin-related peptides. The presence of b-defensin andpteroicidin a encoded by pteroicidin A was confirmed in lionfish skin extracts by mass spectrometry. An in-depth studywas conducted on two amide and non-amide forms of pteroicidin a, as well as on several peptides of different sizesderived from pteroicidins B and C. The results highlighted a relationship between structure, amidation, and theantibacterial and hemolytic activities of these different pteroicidins. On the other hand, no AMP was highlighted in theSepia officinalis model using conventional approaches coupling purification and antibacterial tests or BLAST approaches.We therefore developed a more original approach that relies on the design of peptides starting from the transcriptome.Starting from 811 small cysteine-free peptides from the APD database, we determined recurring criteria for charge,hydrophobicity, and amino acid composition. Based on these criteria and on CAMP prediction tools, twelve peptides weresynthesized. Five of them revealed a broad spectrum of antibacterial activities. Non-hemolytic antibacterial peptidesderived from cuttlefish were transferred to the hatchery. This transfer was optimized thanks to a preliminary study onthe de novo K4 peptide, which is particularly active on vibrios. The study highlighted the importance of antibacterialpeptide safety on the various links of the trophic chain including oyster, and the importance of the targeted stage ofdevelopment. In addition, we addressed the fate of antibacterial peptides to ensure their biodegradability. Altogether,this work not only helped to identify new AMPs but also to provide the first data on the potential use of these peptidesas an alternative to antibiotics.

O gênero Bothrops apresenta ampla distribuição pelo território brasileiro, sendo a espécie B. jararaca seu representante de maior importância médica na região sudeste. Análises genéticas e filogeográficas descrevem a existência de um grupo monofilético, denominado grupo Jararaca, que inclui, além da espécie B. jararaca, as espécies insulares B. alcatraz e B. insularis. A proximidade evolutiva entre estas espécies, cujo desenvolvimento se iniciou no Pleistoceno, e suas diferenças quanto à dieta, levantam subsídios para o entendimento de seus venenos e suas atividades biológicas. O objetivo deste estudo foi a caracterização dos componentes do veneno de B. alcatraz por diferentes metodologias analíticas com a finalidade de aprofundar o conhecimento sobre os venenos do gênero Bothrops e sobre a evolução dos venenos das espécies do grupo Jararaca. As abordagens analíticas utilizadas foram a avaliação do proteoma dos venenos do grupo Jararaca por eletroforese e identificação de proteínas por digestão com tripsina e análise por cromatografia líquida acoplada à espectrometria de massas (LC-MS/MS), análise do N-terminoma e do peptidoma do veneno de B. alcatraz por LC-MS/MS e análise da glicosilação dos venenos do grupo Jararaca pelo tratamento com glicosidases, cromatografia de afinidade à lectinas (concanavalin A, ConA; wheat germ agglutinin, WGA; peanut agglutininin, PNA) e caracterização do N-glicoma por MSn. Os perfis eletroforéticos unidimensionais, obtidos com e sem redução das proteínas, mostraram que o veneno de B. alcatraz difere dos venenos de B. jararaca (adultos e filhotes) e do veneno de B. insularis (adultos). O perfil eletroforético bidimensional do veneno de B. alcatraz corroborou estas diferenças e revelou que a coleta do veneno na presença ou ausência de inibidores de proteinases tem influência no número de spots visualizados. Os resultados da análise dos proteomas dos venenos do grupo Jararaca mostraram que não há diferenças qualitativas significantes entre eles, e que os três apresentam um padrão similar de distribuição das classes de toxinas. A análise quantitativa label free dos proteomas revelou algumas diferenças, indicando que o veneno de B. alcatraz apresenta maior conteúdo de metaloproteinses e fosfolipases A2, que os venenos de B. jararaca e B. insularis. A identificação do peptidoma do veneno de B. alcatraz mostrou diversas formas de peptídeos potenciadores de bradicinina, além de produtos de degradação de diferentes classes de toxinas. A avaliação da glicosilação das proteínas dos três venenos revelou que após a remoção das cadeias de N-glicanos e O-glicanos os perfis eletroforéticos se mostram mais parecidos. A identificação das proteínas do veneno de B. alcatraz que mostraram afinidade pelas lectinas revelou que a ConA interagiu com um número maior de componentes, seguida por WGA e PNA. As análises qualitativa e quantitativa do N-glicoma dos venenos do grupo Jararaca mostrou que os três venenos compartilham as mesmas estruturas de N-glicanos e em abundância relativa similar. Em conjunto, os resultados deste estudo indicaram que no grupo Jararaca, os proteomas dos venenos das espécies B. jararaca e B. insularis apresentam similaridade entre si, e se diferem do veneno de B. alcatraz, principalmente com relação ao grau de glicosilação de suas proteínas. / The Brothrops genus is largely distributed on the Brazilian territory, and B. jararaca is the species of most medical importance in the Southeastern region. Genetic and phylogeographic analyses describe the existence of a monophyletic group, named Jararaca group, which is composed of B. jararaca and of the insular species B. alcatraz and B. insularis. The close evolutionary relationship between these species, which started in the Pleistocene era, and their diet-related differences, are important aspects for the understanding of their venoms and biological activities. The aim of this study was to characterize the venom of B. alcatraz by different analytical methodologies, in order to advance the knowledge on the venoms of Bothrops genus and on the evolution of the venoms of species of the Jararaca group. The analytical approaches used in this study included the charactrization of the proteomes of the venoms of the Jararaca group by electrophoresis and protein identification by trypsin digestion and analysis by liquid chromatography coupled to mass spectrometry (LC-MS/MS), N-terminomic and peptidomic analyses of the venom of B. alcatraz by LC-MS/MS and glycosylation analyses of the venoms of the Jararaca group by treatment with glycosidases, affinity chromatography to lectins (concanavalin A, Con A; wheat germ agglutinin, WGA; peanut agglutininin, PNA) and characterization of the N-glicomes by MSn. The one-dimensional electrophoretic profiles were evaluated under reducing and non-reducing conditions and showed that the venom of B. alcatraz differs from B. jararaca (newborn and adult) and B. insularis (adult) venoms. The two-dimensional electrophoretic profile of B. alcatraz venom corroborated these differences and revealed that the milking of the venom in the presence or in the absence of proteinase inhibitors influences the number of spots visualized on the gel. The results of the analysis of venom proteomes of the Jararaca group showed no significant qualitative differences between them; moreover, the three venoms showed a similar pattern of distribution of toxins classes. However, the label free quantitative analysis of these proteomes revealed some differences, and indicated that the venom of B. alcatraz has a higher content metaloproteinses and phospholipase A2 than B. jararaca and B. insularis venoms. The identification of B. alcatraz venom peptidome showed various forms of bradykinin-potentiating peptides, as well as products of the degradation of different toxins classes. The assessment of the glycosylation level of proteins of the three venoms showed that after removal of N-glycan and O-glycan chains their electrophoretic profiles become more similar. The identification of B. alcatraz venom proteins that showed affinity for lectins indicated that ConA interacted with a larger number of components, followed by WGA and PNA. The qualitative and quantitative analysis of the N-glicome of the venoms of the Jararaca group showed that they share the same N-glycan structures, which were also found in similar relative abundance. Taken together, the results of this study indicate that in the Jararaca group, the venom proteomes of B. jararaca and B. insularis show similarity to each other and differ from the venom of B. alcatraz, especially with respect to the degree of protein glycosylation.

Le cervelet est une structure cérébrale impliquée dans de multiples fonctions motrices mais aussi cognitives et dont le développement postnatal est sous le contrôle de divers types de facteurs dont les neuropeptides. Les peptides capables d’agir sur le développement du cortex cérébelleux présentent généralement un profil d’expression particulier, avec chez le rongeur un pic d’expression au cours des 2 premières semaines postnatales. L’objectif de cette étude était d’identifier d’autres peptides présentant ce même type d’expression et de caractériser leurs potentiels effets au cours du développement du cortex cérébelleux, et plus particulièrement dans la mise en place des neurones en grain qui sont les plus abondants de cette structure. Pour cela, des cervelets de rats âgés de 8 à 90 jours ont été analysés par spectrométrie de masse. Parmi les 33 peptides identifiés, 4 présentent le profil recherché et nous avons choisi d’étudier l’un d’entre eux, la nociceptine. La mesure de l’expression du gène de la nociceptine et de son récepteur montre un profil d’expression similaire à celui observé en peptidomique. De plus, ces 2 gènes sont retrouvés principalement exprimés dans la couche granulaire interne du cortex cérébelleux par microdissection et qPcr. La recherche de la fonction de la nociceptine montre qu’elle exerce un effet neurotrophique en augmentant la survie et la différenciation des neurones en grain, sans affecter la motilité de ces cellules. Des tests préliminaires réalisés in vivo indiquent que la nociceptine est aussi capable de bloquer la toxicité induite par l’alcool. La dernière partie de l’étude avait pour but d’identifier de nouveaux neuropeptides exprimés dans le cervelet en utilisant une approche par séquençage de novo. L’application de filtres comme la récurrence des séquences peptidiques ou leur régulation au cours du développement a permis de ne retenir que 6 séquences pour la suite de l’analyse. Des études génomiques permettront de restreindre encore ce nombre afin de focaliser les tests d’activité biologique sur la ou les cibles qui ont la plus grande probabilité de correspondre à des peptides biologiquement actifs. / The cerebellum is a structure involved in many motor and cognitive functions whose development occurs after birth under the control of various factors, including neuropeptides. Peptides acting on cerebellar cortex development often exhibit a specific pattern of expression with in rodents a high expression over the 2 first postnatal weeks which then decreases at adulthood. The aim of this study was to identify additional peptides with such expression profile and to characterize their putative functions in the development of the cerebellar cortex and more particularly, in the establishment of cerebellar granule neurons which are the most abundant cells of the cerebellum. To address this, cerebella of rats aged from 8 to 90 days-old were analyzed by mass spectrometry. Among the 33 peptides identified in the cerebellum, 4 had the particular expression profile we were looking for. We choose to study further one of them, i.e. the nociceptin, and confirmed peptidomic results by measuring the expression of its gene precursor and of its receptor. Combining laser microdissection and qPCR approaches revealed that both nociceptin and its receptor genes were expressed in the internal granular layer of the cerebellar cortex. Functional studies showed that nociceptin exerts a neurotrophic effect on granule neurons by increasing their survival and differentiation, but had no effect on their motility. Preliminary in vivo experiments indicate that nociceptin can also counteract ethanol-induced toxicity. The last part of the present study aimed to identify new neuropeptides expressed in the rat cerebellum by using de novo sequencing. The large amount of peptide sequences initially found was then reduced to only 6 candidates for further analysis, by using filters such as recurrence of the sequences and their differential expression in between the four developmental stages considered. Additional genomic studies will help to decrease even further this number, in order to focus the biological tests on the targets which are most likely to code for biological active peptides.

L'aquaculture est en pleine expansion et fournit aujourd'hui la moitié des produits aquatiques destinés à la consommationhumaine. Elle constitue ainsi un secteur clé pour le maintien et l'amélioration de la sécurité alimentaire dans lemonde. Le développement de l'aquaculture est étroitement lié à celui des formules alimentaires. Ces dernières années,la part des farines de poisson dans la formulation des aliments a particulièrement diminué au profit des farines d'originevégétale pour répondre aux nombreuses contraintes économiques et environnementales. Néanmoins, ces matièrespremières sont moins adaptées aux besoins nutritionnels des poissons carnivores et leur utilisation peut entraîner unebaisse des performances de croissance et d'efficacité alimentaire. L'ajout d'additifs et d'ingrédients fonctionnels devientalors indispensable. Les hydrolysats protéiques issus des co-produits de la pêche et de l'aquaculture sont des ingrédientsà fort potentiel appétence, nutritionnel et bioactif. Ces ingrédients sont des mélanges complexes riches en peptides hydrolytiqueset en acides aminés libres, mais dont la composition varie en fonction de l'origine de la matière première etdes paramètres d'hydrolyse appliqués lors de leur fabrication. Au cours de ces travaux de thèse, nous avons développéet mis en pratique des outils permettant d'approfondir la caractérisation structurale et les propriétés fonctionnellesdes hydrolysats de protéines. Dans un premier temps, nous avons développé une méthode analytique basée sur unenormalisation des échantillons suivie d'une détermination de l'abondance et de la richesse en peptides par chromatographied'exclusion stérique et chromatographie liquide couplée à la spectrométrie de masse de type électro-spray,respectivement. Les résultats présentés sous forme d'un diagramme 2D permettant de classer et comparer facilementles hydrolysats de protéines de forme galénique, d'origine et de process différents. Nous avons également développé unoutil in vitro sur l'intestin de bar européen, Dicentrarchus labrax, permettant de déterminer les activités myotropesdes hydrolysats. Nous avons pu notamment démontrer que l'hydrolysat de crevettes possède une plus forte activitémyotrope que les hydrolysats de poissons et que cette activité est portée par un pentapeptide KNPEQ clivé à partirde l'hémocyanine lors du process d'hydrolyse appliqué sur les co-produits de crevette. Enfin, dans un second temps,un conditionnement alimentaire de 65 jours a été conduit chez le bar européen nourri avec un aliment pauvre en farinede poisson supplémenté en hydrolysat de différentes origines et couplé à une analyse d'expression génique (approcheen RNA-Seq Illumina). Cette étude a permis de montrer que les hydrolysats de protéines appliqués sur un alimentfaible en farine de poisson (5%) sont capables de restaurer des performances de croissance équivalentes à celles d'unrégime contenant 20% de farine de poisson mais qu'ils portent par ailleurs des propriétés fonctionnelles spécifiques.Il a également été montré que le mélange des deux hydrolysats permet de moduler les transcriptomes intestinal ethépatique de façon plus profonde que lorsque que les hydrolysats sont utilisés séparément. Ces résultats confirmentl'intérêt des hydrolysats de protéines pour la formulation d'aliment à faible teneur en farines de poisson et apportentde nouveaux outils de caractérisation de ces ingrédients complexes, qui seront utiles pour leur optimisation et leurstandardisation ainsi que pour la compréhension de leurs mécanismes d'action chez les poissons. / Aquaculture is a key sector for supporting and improving the food security worldwide. The global production of farmedfish and shrimp has grown dramatically over the past decades and now contributes to half of the aquatic productsintended for human consumption. Aquaculture will require feeds to support its growth but availability of some raw materialssuch as fish meal are limited. The use of fish meal in aquafeed has particularly declined in favor of plant proteinsources to fit with economic and environmental constraints. But plant proteins do not meet perfectly the nutritionalrequirements of carnivorous fish and their utilization often results in lower growth and feed performances. Proteinhydrolysates manufactured from fishing and aquaculture co-products are ingredients with a high palatable, nutritionaland bioactive potential. They are rich in hydrolytic peptides and free amino acids, but they are complex mixtureswhose composition could vary according to raw material origin and hydrolysis parameters. During this PhD study, wedeveloped and implemented tools to further characterize the structure and functional properties hydrolysates. On afirst step, we developed a fast methodological tool based on sample standardization, followed by the determination ofthe abundance and richness of peptides using size exclusion chromatography and liquid chromatography coupled toelectro-spray mass spectrometry, respectively. We merged the results into a 2D diagram that made it easy to classifyand compare hydrolysates having different galenic, origin and process. We also developed a tool on isolated intestinefrom European seabass (Dicentrarchus labrax ) to rank protein hydrolysates according to their myotropic property.We demonstrated that shrimp hydrolysate showed a higher myotropic activity than fish hydrolysates and that thisactivity was carried by a unique pentapeptide KNPEQ produced by the enzymatic clivage of haemocyanin during thehydrolysis process applied on shrimp co-products. On a second step, a 65-day feeding trial was conducted in Europeanseabass fed a low fish meal diet supplemented with protein hydrolysates of different origin, and coupled to a studyof the intestine and liver transcriptomic response (Illumina RNA sequencing). It has been shown that protein hydrolysatesincluded in a low fish meal diet (5%) restored growth performances to the same level than a diet containing20% of fishmeal, and that they exhibited very specific functional properties. These results showed that a mixture oftwo hydrolysates impacted more deeply the intestine and liver transcriptomes than hydrolysate tested alone. ThisphD study confirmed that protein hydrolysates are very interesting candidates for formulating low fish meal feed andoffer new tools for characterizing such complex ingredients, which will be useful to optimize and standardize proteinhydrolysate while understanding their mechanisms of action in fish.

Preeclampsia (PE) is a potentially fatal complication of pregnancy characterized by an increase in blood pressure (>140/90 mmHg) and proteinuria (>300 mg/24 hrs), often accompanied by edema. Symptoms of PE start after 20 weeks of gestation. If PE remains untreated, it can lead to eclampsia, grand-mal seizures responsible for most fatalities. PE is believed to affect 2-10% of pregnancies worldwide, and claims the lives of over 75,000 mothers and 500,000 newborns yearly. No therapeutic agents have been developed to prevent or cure PE. Part of the reason for this is the absence of a complete understanding of the pathogenesis of this disease. PE has long been regarded as a “disease of theories”, and the pathophysiology of PE continues to be the subject of debate. Nonetheless, several abnormalities have been observed to precede established, clinical PE and have in turn been proposed to be involved in the causation of this disease, all with involvement of the mother's placenta as a central feature. Removal of placenta is the only cure for PE and results in a rapid resolution of the symptoms. Thus, the placenta remains an organ of substantial interest and many research groups have attempted to identify abnormal placental features occurring in PE. None of these studies have focused on less abundant, low molecular weight (LMW) biomolecules, which play important roles in the pathophysiology of many diseases. There are a number of alterations that are believed to affect the placenta and contribute to the pathogenesis of PE. The most widely accepted ones include hypoxia, oxidative stress, and an increase of pro-inflammatory mediators in the mother's placenta. The goal of my initial study was to identify which of these hypothesized causative pathways has a significance in the etiology of this syndrome as well as to investigate which less abundant, low molecular weight biomolecules change in response to these abnormalities. For this purpose, we first adapted and optimized a previously developed methodology that studied LMW biomolecules in tissue specimens to study placental biomolecules. This approach involved a tissue homogenization step followed by protein depletion using acetonitrile. We compared two regions of human placenta: the chorionic plate and the basal plate to find differences in the LMW fraction. We discovered 16 species with statistically significant differences between the two sides, and identified 12 of them using tandem mass spectrometry. In the second study we collected normal human term placentas from elective C-section deliveries and exposed explants to each of the above-mentioned provocative agents or stress conditions for 48 hrs. Other explants without any stressors were cultured in parallel for the same amount of time. The processing of explants was divided into five steps: 1) explant culture; 2) tissue homogenization; 3) acetonitrile precipitation to remove high abundance, high molecular weight proteins; 4) injection of the protein-depleted specimen into a capillary liquid chromatography–mass spectrometer; 5) analysis of MS data to identify quantitative differences between cases (stressed explants) and controls (normal explants). In total, we observed 146 molecules changed in abundance between the treated explants and the controls with 75 of these molecules changed in response to hypoxic treatment, 23 changed due to hypoxia-reoxygenation, a process generating reactive oxygen species, and 48 changed due to tumor necrosis factor–alpha (TNFα), a pro-inflammatory cytokine. We were successful in identifying 45% of all these molecules by tandem MS. Statistical modeling that applied LASSO analysis allowed for the development of a model that used 16 of the 146 differentially expressed biomolecules to accurately classify and differentiate each of the 4 stressed conditions. In my third study, I then submitted actual preeclamptic and non-diseased placental tissue to our established homogenization and acetonitrile precipitation protocol to see if any of the differences in LMW biomolecules produced under stress conditions in normal placenta were recapitulated in actual diseased placenta. In a preliminary statistical analysis, 8 of the original 146 differentially expressed species, displayed significant or near significant changes in the actual disease placenta. After applying two stringent statistical tests that eliminated any potential influence of gestational age, four out of the 146 biomarkers previously studied, continued to be differentially expressed in both stringent analyses. Of the four, 1 biomarker (m/z 649.49 (+1)) showed an increased abundance in hypoxic placental explants as well as in PE placenta; 2 (461.06 (+1), 476.24 (+1)) were increased in response to TNFα-exposed placental explants and in these PE placentas and 1 (426.35 (+1)) increased in response to hypoxia-reoxygenation-treated placental explants was also increased in PE placenta. We have chemically characterized 2 of the 4 biomarkers. One was a phospholipid (m/z 476.24) while the other was an acyl-carnitine (m/z 426.35). This suggests that features of PE appear to arise from the predicted early abnormalities that affect the placenta. In conclusion, I was successful in developing an ‘omics’ approach to study less abundant, low molecular weight biomolecules in human placenta as well as investigate which biomarkers show differential expression in human placenta when exposed to proposed abnormalities of PE and have data to suggest that these same responses are present in PE placenta.

La réaction de cycloaddition entre un azoture et un alcyne catalysée par le cuivre (I) (CuAAC) pour former un 1,2,3-triazole 1,4-disubstitué est très utilisée dans de nombreux domaines de la chimie. Cette réaction a très vite été utilisée en synthèse peptidique notamment du fait du caractère isostère du noyau triazole et de la liaison amide. Toutefois l'impact de l'insertion d'un triazole sur la structure secondaire de peptides n'a été que faiblement exploré. Ainsi, pour étudier l'effet d'un tel remplacement nous avons choisi deux peptides modèles structurés le premier modèle est un peptide linéaire de la famille des peptaibols et le second est un peptide cyclique la tamandarine B. Dans un premier temps, nous avons optimisé une voie de synthèse de peptaibols que nous avons appliqué à l'alaméthicine F50/5 et à un analogue de la bergofungine D. Pour cela, nous avons utilisé une synthèse peptidique en phase solide sous irradiation micro-ondes en profitant d'un cocktail de réactifs efficaces contenant du diisopropylcarbodiimide comme agent de couplage et de l'oxyma. Cette méthode de synthèse a été étendue à l'obtention d'analogues silylés de l'alamethicine en substituant dans différentes positions l'acide aminobutyrique par un résidu hydrophobe et encombré : la bis-triethylsilyl-dipropylglycine (TES-Dpg). Dans la deuxième partie nous avons développé la synthèse de dipeptides à motif triazole. Puis nous avons défini les conditions réactionnelles nécessaires pour leur utilisation en SPPS et synthétisé des peptides contenant plusieurs motifs triazoles. Ces dipeptides ont ensuite été utilisés pour réaliser un scan triazole sur les deux peptaibols modèles. Les études structurales par dichroïsme circulaire, RMN et les tests biologiques de différents analogues nous permettent de conclure que le triazole affecte la structure secondaire des peptaibols et par conséquence induit une perte d'activité. Ainsi il apparaît que le concept de triazole comme isostère de la liaison peptidique doit être employé avec prudence. Dans l'optique de comprendre l'impact de triazole sur l'activité et la structure secondaire de peptides cycliques, nous avons généré des analogues simplifiés de la tamandarine B un depsipeptide cyclique d'origine marine. Nous rapportons les résultats préliminaires de cette étude. / The cycloaddition reaction between an azide and an alkyne catalyzed by copper (I) (CuAAC) to form a 1,2,3-triazole 1,4-disubstituted is widely used in many areas of chemistry. This reaction was rapidily used in peptide synthesis because of the isosteric nature between the triazole ring and the amide bond. However, impact of the insertion of a triazole on the secondary structure of peptides was only scarcely explored. Thus, to study the effect of such a replacement we chose two models of structured peptides. The first models are linear peptides of the peptaibols family and the second is the cyclic peptide tamandarin B.First, we have optimized a peptaibols synthesis that was applied to alamethicin F50 / 5 and to an analog of bergofungin D. For this we used a solid phase peptide synthesis under microwave irradiation taking advantage of the efficient cocktail consisting of diisopropylcarbodiimide as a coupling agent and Oxyma. This synthesis has been extended to silylated analogues of alamethicin by substituting in different positions the aminobutyric acid by the hydrophobic and crowded residue: bis-triethylsilyl-dipropylglycine (Dpg-TES).In the second part we have developed the synthesis of dipeptides containing a triazole motif. Then we defined the reaction conditions necessary for their use in SPPS and synthesized peptides containing several triazoles rings. These dipeptides were then used to perform a triazole scan on the two peptaibols models. The structural studies by circular dichroism, NMR and biological tests of various analogs allow us to conclude that the triazole affect the secondary structure of peptaibols and consequently induces a loss of activity. Thus it appears that the concept of triazole as isosteric of the peptide bond should be used with caution.In order to understand the triazole impact on the activity and the secondary structure of cyclic peptides, we generated simplified cyclic analogues of tamandarin B a depsipeptide of marine origin. We report the preliminary results of this study.

Preeclampsia (PE) is a multisystem disorder that contributes to maternal and fetal mortality and morbidity worldwide. It is characterized by de-novo hypertension and proteinuria or other maternal organ damage after 20 weeks of gestation. Evidence suggested that endogenous digitalis-like factor (EDLF) contributes to the pathogenesis of PE, and that the potential source of EDLF is the placenta. EDLF can inhibit the sodium pump (SP) specifically and may lead to hypertension, it has also been associated with hypoxia, oxidative stress and other abnormalitites present in PE.We studied whether normal human placenta responded to SP inhibition casued by EDLF with a change in abundance of lipids in the placental cytosol, and whether there was a characteristic set of lipid changes that could serve as a signature for EDLF exposure if there were such changes. Placenta tissues from 20 normal pregnancies were incubated for 48 hr in the presence and absence of ouabain, a widely studied EDLF, followed by tissue homogenization, lipid extraction, and the study of lipids using a mass spectrometery (MS) based lipidomics approach. 1207 lipidomic markers were surveyed by paired Student t-test, among which 26 markers had significantly different abundances between cases and control at the FDR=0.05 level. A set of 8 lipidomic markers were selected by a statistical model built with a sparse partial least squares discriminant analysis method (sPLS-DA) and a bootstrap procedure. All eight markers were then chemically characterized and partially identified using tandem MS. These markers might be used to identify placentas that have been previously exposed to EDLF in return.Endogenous peptides and small proteins might contribute to the pathophysiology of various diseases. Therefore, we investigated the potential peptidomic profile of placenta tissues in response to EDLF exposure as well. Placenta tissues from 20 normal pregnancies were incubated for 25 hr with and without the addition of ouabain, followed by homogenization, protein depletion, and the study of the peptides by a LC-MS based peptidomics approach. 275 peptidomic markers were evaluated by Student t-test. A set of 8 markers was chosen using a logistic regression model build with the Akaike information criterion (AIC). However, no peptidomics markers or set of markers showed specific, statististically significantly different changes in abundances between cases and controls after applying a false discovery rate (FDR) correction or using more conservative methods to overcome over-fitting. Using an optimal sPLS- DA, cross-validation studies and logistic regression models, we also found that the addition of any peptidomic marker to the previously selected lipidomic profile was unlikely to help identify placentas that had been exposed to EDLF.Alzheimer's disease (AD) is the most common form of dementia and the number of AD cases worldwide is currently estimated to be 36 million. The exact pathogenesis of AD remainsiielusive and available therapeutic strategies can only delay its progession temporarily. Several hypotheses have been proposed regarding the pathophysiology of AD and the beta-amyloid (Aβ) hypothesis is considered the core mechanism. However, the majority of studies concerning AD, or AD biomarkers specifically, have ignored a potentially important variable that is gender, despite reported gender differences in the risk of developing AD, the risk factors, clinical symptoms and CSF biomarkers of the disease, among many other aspects.We analyzed data obtained from a previous study of diagnostic serum lipid biomarkers for AD with the consideration of potential gender difference. Firstly, we studied the interaction between gender and disease stage using analysis of variance (ANOVA) and analysis of covariance (ANCOVA). Lipid markers that showed statistically significant interaction were selected after applying a FDR correction. Secondly, using a lasso logistic regression model with binary classification (control vs. all AD stages), we identified gender-specific markers and found different coefficient estimates for different genders as well. Lastly, we build a new ordinal model with the addition of a gender-specific marker using a Bayesian lasso probit ordinal regression model. The predictive performance of the new model was found to be statistically significantly better than the previous model which was built without the consideration of gender.In conclusion, we successfully discovered, chemically characterized lipidomic markers indicative of EDLF exposure in placenta and detected gender-specific lipid markers for AD.

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from αS- and β-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of β-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from αS-caseins. The numbers of lactosylated peptides increased with harsher processing.

Bypass or resection of the stomach and oesophagus, has long been recognised to result in profound changes in the handling of ingested nutrients. This results in significant morbidity after radical surgery for oesophago-gastric cancer, in particular post-prandial hypoglycaemia, altered appetite, early satiety and noxious post-prandial symptoms. By profiling and challenging the gut hormone axis in healthy volunteers and patients who had undergone total or subtotal gastrectomy, or oesophagectomy, this thesis explores the possible causative mechanisms for the challenges faced by this patient population. In the surgical groups, an oral glucose tolerance test (OGTT) resulted in enhanced secretion of satiety and incretin gut hormones (GLP-1, GIP, PYY) and insulin, followed by hypoglycaemia in a cohort of patients. Continuous glucose monitoring of gastrectomy participants over two weeks of normal lifestyle identified an increased incidence of day and night time hypoglycaemia. RNAseq and mass spectrometry based peptidomics of human and murine enteroendocrine cells in the pre- and post-operative populations revealed no significant change in the underlying cellular pathways for nutrient sensing and gut hormone secretion, indicating that the altered hormone secretion is primarily driven by accelerated nutrient transit, rather than adaptive changes in the gut. Finally, specific blockade of the GLP-1 receptor in post-gastrectomy patients using Exendin 9-39 normalised insulin secretion and prevented reactive hypoglycaemia after an OGTT. In conclusion, profound changes in gut hormone secretion as a result of enhanced nutrient transit after foregut surgery likely underlie the early and late post-prandial symptoms seen in this group, and therapies specifically targeting the gut hormone axis, and GLP-1 in particular, could be the first targeted treatments for post-gastrectomy syndromes.