La maladie de Crohn (MC) est une maladie inflammatoire chronique intestinale (MICI). Son incidence et sa prévalence ont augmenté en Europe au cours des dix dernières années (150 pour 100000 habitants) constituant ainsi un problème de santé majeur. L'inflammation chronique dans la MC favorise la mise en place d'une angiogenèse pathophysiologique. Inflammation et angiogenèse sont deux réponses cellulaires suspectées dans la survenue des cancers coliques associés au MICI. Même si les facteurs favorisant la mise en place de la MC restent non élucidés, la contribution des bactéries exogènes est fortement suspectée. Parmi ces bactéries, les E.coli adhérentes et invasives (AIEC), isolées à partir de la muqueuse iléale de patients porteurs de la MC, sont un bon candidat. Les objectifs de mon projet de thèse étaient de caractériser les mécanismes moléculaires induits par les AIEC et impliqués dans la mise en place des réponses pro inflammatoire et pro angiogénique des cellules intestinales épithéliales. Le facteur de transcription hypoxique (HIF-1) est au cœur de l'immunité innée et de l'angiogenèse. J'ai émis l'hypothèse que les AIEC pouvaient moduler le niveau d'expression de HIF-1α et ainsi contrôler les réponses pro inflammatoire et pro angiogénique. Dans mon premier article, j'ai montré que HIF-1α est maximalement exprimé au niveau de l'épithélium iléal des patients porteurs de la MC. Ensuite, j'ai montré sur un modèle murin compétent pour l'infection par les AIEC, les souris CEABAC10, que les bactéries induisent l'augmentation du niveau protéique de HIF-1 α ainsi que l'activation de la voie de signalisation du VEGF, le facteur angiogénique le plus puissant.

Microbial resistance to the current available antibiotics is considered a global health problem, especially for the Multi-Drug Resistant pathogens (MDR) including methicillin resistant Staphylococcus aureus. Recently nanoparticles (NPs) have been involved in variety of antimicrobial applications due to their unique properties of antibacterial effects. However, the molecular mechanisms behind their antibacterial activity are still not fully understood. In this study, we produced silver Ag NPs (average size 27 nm) and silver-Titanium Ag-TiO2 NPs (average size 47 nm) using picosecond laser ablation. Our results showed that both laser NPs had obvious size-dependent antibacterial activity. The laser Ag NPs with a size of 19 nm and Ag-TiO2 NPs with a size 20 nm presented the highest bactericidal effect. The laser generated Ag and Ag-TiO2 NPs with concentrations 20, 30, 40, and 50 Î1⁄4g/ml showed strong antibacterial effect against three bacterial strains: E. coli, P. aeruginosa, and S. aureus, and induced the generation of reactive oxygen species (ROS), lead to cell membrane interruption, lipid peroxidation, DNA damages, glutathione depletion and the eventual cell death. Both types of laser NPs at two concentrations (2.5 and 20 Î1⁄4g/ml) showed low cytotoxicity to the in vitro cultured five types of human cells originated from the lung (A549), kidney (HEK293), Liver (HepG2), skin (HDFc) and blood vessel cells (hCAECs). The antibacterial activity of the laser generated Ag and Ag-TiO2 NPs had lasted for over one year depending on the degree of air exposure and storage conditions. Frequent air exposure increased particle oxidation and reduced the antibacterial durability of the laser generated Ag NPs. The laser generated Ag NPs had lower antibacterial activity when stored in cold compared to that stored at room temperature. The antibacterial activity of laser generated Ag and Ag-TiO2 NPs were also compared with four types of commercial based-silver wound dressings (Acticoat TM, Aquacel® Ag, Contreet ®Foam, and Urgotul® SSD) against E. coli to inform future application in this area. In conclusion, laser generated Ag and Ag-TiO2 NPs have strong bactericidal effect and low toxicity to human cells which could be a type of promising antibacterial agents for future hygiene and medical applications.

Nous nous proposons d'étudier la gestion du bruit stochastique d'expression génique. On s'intéresse plus particulièrement à la dynamique du bruit lors de la réponse cellulaire. Comment évolue le bruit? Quels sont les mécanismes en jeux? Quelle est l'importance du bruit dans le fonctionnement cellulaire? Pour répondre à ces questions, nous nous appuyons sur le réseau de régulation génétique qui gère la réponse au stress nutritionnel chez E. Coli. L'étude du comportement dynamique de ce réseau, au niveau d'une population de bactéries, a été initiée et est portée par la forte collaboration de deux équipes de la région : une de bio-informaticiens (l'équipe de Hidde de Jong de l'INRIA Rhône-Alpes) et la deuxième de biologistes (l'équipe de Hans Geiselmann, Laboratoire d'Adaptation et Pathogénie des Micro-organismes). En profitant donc de l'expérience et de la compréhension acquise par ces équipes, nous étudions les réponses individuelles de chaque bactérie lors de la transition entre état de stress nutritionnel, et état de croissance exponentielle. Le bruit d'expression génique est quantifié dans des nœuds clés du réseau de régulation. Pour ce faire, les bactéries sont suivies individuellement par microscopie de fluorescence sur plusieurs générations. Les données de fluorescence collectées sur cellules uniques permettent d'étudier la variabilité inter-cellulaire. Cette variabilité est quantifiée tout le long de la réponse: à chaque instant, on connaît la distribution des densités de fluorescence cellulaire dans la population de cellules. Et le suivi des lignées individuelles permet de travailler sur une population de cellules saines: les individus malades ou morts qui ne se divisent pas, sont écartés. En réduisant ainsi les phénomènes cellulaires en jeux, on réduit le nombre de paramètres. Les sources de bruit sont moins nombreuses, et il est plus facile de comprendre les mécanismes en jeux. Les informations de lignage cellulaire permettent aussi d'étudier la variabilité introduite par la phase du cycle cellulaire: les événements de division cellulaire peut être artificiellement synchronisés. Le bruit est alors étudié sur une population en phase lors de la division. Cette étude montre que le bruit sondé n'est pas dominé par les différences dans la phase du cycle cellulaire. On peut donc modéliser nos cellules sans tenir compte des différences introduites par le cycle cellulaire. Le modèle testé est simplifié aux étapes de transcription-traduction-maturation. Les paramètres du modèle sont inférés de nos données expérimentales, et le modèle est testé à travers des simulations. / We aim to investigate the management of the stochastic noise in gene expression and more precisely the study of noise in dynamical cellular responses. How the noise varies following a perturbation? What mechanisms are at play? How important is noise in the cellular function? To answer these questions, we are interested in the genetic regulatory network that handles the nutritional stress response in E. Coli. The noise of gene expression is quantified in a key node of the network control. For that bacteria are followed individually by fluorescence and phase contrast microscopy over several generations. This variability between cells is quantified throughout the response to the nutritional perturbation: at every moment, we know the density distribution of cellular fluorescence in the cell population. And monitoring of individual lines allows us to take into account only the population of healthy cells: individuals that do not divide neither grow, are discarded. Thereby reducing other sources of variability (e.g. cellular phenomena) we reduce the number of parameters. Noise sources are less numerous, and it is easier to understand the mechanisms at play. Also the information on cell lineage allow to study the variability introduced by the phase of the cell cycle: the events of cell division can be artificially synchronized. This study shows that the noise sounded is not dominated by differences in the phase of the cell cycle. We can therefore model our cells regardless of the differences introduced by the cell cycle. The tested model is simplified to the steps of transcription-translation-maturation. The model parameters are inferred from our experimental data and the model is tested through simulations.

Hemolytic uremic syndrome (HUS) induced by Shiga toxin-producing E. coli (STEC) is the most common causes of acute kidney injury in children. The therapy of the disease is symptomatic and the main factors leading to the development of severe course of a STEC-HUS are still unknown. In our study, we dealt with factors leading to development of a severe course of STEC-HUS in pediatric patients on both the host and pathogen side. Using retrospective analysis of the courses in children in the Czech Republic, we found that the most common cause of STEC-HUS was serotype O26 and HUS most often affected children under 3 years of age. 63,8 % required dialysis and mortality was 8.62 %. On the host side we focused on the relationship between the activation of the alternative complement pathway and the severity of the course of HUS. We found a significant difference in the level of the C3 part of complement in patients who required dialysis and patients for whom dialysis was not necessary. We also a cut-off value for the C3 part of complement and its reduction below 0.825 g / l was associated with the need for dialysis treatment and a higher incidence of extrarenal complications. Based not only on our results, it can be assumed that the therapeutic effect of complement could affect the severity of the disease....

Membrane protein mechanotransduction is the altered function of an integral membrane protein in response to mechanical force. Such mechanosensors are found in all kingdoms of life, and increasing numbers of membrane proteins have been found to exhibit mechanosensitivity. How they mechanotransduce is an active research area and the topic of this thesis. The methodology employed is classical molecular dynamics (MD) simulations. MD systems are complex, and two programs were developed to reduce this apparent complexity in terms of both visual abstraction and statistical analysis. Bendix detects and visualises helices as cylinders that follow the helix axis, and quantifies helix distortion. The functionality of Bendix is demonstrated on the symporter Mhp1, where a state is identified that had hitherto only been proposed. InterQuant tracks, categorises and orders proximity between parts of an MD system. Results from multiple systems are statistically interrogated for reproducibility and significant differences at the resolution of protein chains, residues or atoms. Using these tools, the interaction between membrane and the Escherichia coli mechanosensitive channel of small conductance, MscS, is investigated. Results are presented for crystal structures captured in different states, one of which features electron density proposed to be lipid. MD results supports this hypothesis, and identify differential lipid interaction between closed and open states. It is concluded that propensity for lipid to leave for membrane bulk drives MscS state stability. In a subsequent study, MscS is opened by membrane surface tension for the first time in an MD setup. The gating mechanism of MscS is explored in terms of both membrane and protein deformation in response to membrane stretch. Using novel tension methodology and the longest MD simulations of MscS performed to date, a molecular basis for the Dashpot gating mechanism is proposed. Lipid emerges as an active structural element with the capacity to augment protein structure in the protein structure-function paradigm.

<p>A neural network model was developed to predict the E. Coli levels and classes in six (6) select Lake Michigan beaches. Water quality observations at the time of sampling and discharge information from two close tributaries were used as input to predict the E. coli. This research was funded by the Indiana Department of Environmental Management (IDEM). A user-friendly Excel Sheet based tool was developed based on the best model for making future predictions of E. coli classes. This tool will facilitate beach managers to take real-time decisions.</p> <p>The nowcast model was developed based on historical tributary flows and water quality measurements (physical, chemical and biological). The model uses experimentally available information such as total dissolved solids, total suspended solids, pH, electrical conductivity, and water temperature to estimate whether the E. Coli counts would exceed the acceptable standard. For setting up this model, field data collection was carried out during 2019 beachgoer’s season.</p> <p>IDEM recommends posting an advisory at the beach indicating swimming and wading are not recommended when E. coli counts exceed advisory standards. Based on the advisory limit, a single water sample shall not exceed an E. Coli count of 235 colony forming units per 100 milliliters (cfu/100ml). Advisories are removed when bacterial levels fall within the acceptable standard. However, the E. coli results were available after a time lag leading to beach closures from previous day results. Nowcast models allow beach managers to make real-time beach advisory decisions instead of waiting a day or more for laboratory results to become available.</p> <p>Using the historical data, an extensive experiment was carried out, to obtain the suitable input variables and optimal neural network architecture. The best feed-forward neural network model was developed using Bayesian Regularization Neural Network (BRNN) training algorithm. Developed ANN model showed an average prediction accuracy of around 87% in predicting the E. coli classes. </p>

Although the etiology and pathogenesis of inflammatory bowel disease (IBD) is not fully understood, it is generally accepted that the inflammation results from aberrant immune responses to antigens of gut microbiota in genetically susceptible individuals (Sartor et al., 2006). Alteration in intestinal microbiota has been found in IBD patients with increased abundance of certain bacteria and decreased abundance of others. Due to the complexity of the disease, multifaceted interactions between genetic factors, host immune response, gut microbiota and environment factors need to be taken into account. In this thesis, the pathogenesis of IBD was first reviewed in respect with the four factors mentioned above. Then we concentrated on the interaction between IBD-associated bacteria and mucosal immune system. We investigated the ability of mucosal-associated bacteria (MAB) from IBD patients to induce spontaneous colitis in germ-free (GF) mice and the impact of those bacteria on the development of dextran sulfate sodium (DSS)-colitis. Together with the analysis of the composition of gut microbiota of MAB colonized mice, we demonstrated the potential deleterious microbes were able to increase the susceptibility to DSS-colitis once they found a suitable niche. We revealed the mechanism of an E.coli strain...