BACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.

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Anxiety is a common disorder which affects about 25% of the population and whose pathophysiology is still poorly understood. Animal models of disease have been widely used to investigate the molecular basis of human disorders, including psychiatric illnesses. This thesis is about the study of the genetic basis of a mouse model of anxiety. I have carried out a QTL mapping study of behavioural measures thought to model anxiety. I report results from 1,636 mice, assessed for a large number of phenotypes in five ethological tests. Mice belonged to two F2 intercrosses originated by four lines generated in a replicate selection experiment. By comparing mapping results between the two crosses, I have demonstrated that selection operated on the same relatively small number of loci in the four selected lines. Analysis of genetic effect of QTL across phenotypes has allowed me to identify loci with specific roles on different dimensions of anxious behaviour, therefore enhancing our understanding of the anxiety phenotype in mice. For some of these QTL I have also accomplished fine mapping experiments: a locus on chromosome 15 is now contained in an interval of only 3 centimorgans. This work is the basis for further molecular dissection of the genetic loci that underlie anxiety and provides a starting point for the discovery of genes involved in a common psychiatric condition.

Un xénobiotique subit plusieurs étapes de biotransformations simultanées ou successives dont les principaux sites sont les tissus situés à l’interface entre l’organisme et le milieu extérieur, à savoir : le tube digestif, l’appareil respiratoire, le rein et le foie. Ce dernier étant fonctionnellement le plus important. Les phases réactionnelles principales constituant les étapes de détoxification, phase I, phase II et phase III, ne sont possibles que par l'intervention de systèmes enzymatiques spécifiques. Etant donné la grande diversité des xénobiotiques auxquels l'organisme est exposé, il existe une multitude d'enzymes présentant des spécificités variées. Les réactions de biotransformation des xénobiotiques s'enchaînent rarement de façon linéaire, car deux voies ou plus prennent souvent naissance à partir d'un métabolite donné. On comprend dès lors que l'existence d'un variant enzymatique défectif pour l'une de ces voies réactionnelles pourra orienter le métabolisme d'une substance donnée vers une autre voie. Cette dernière, généralement mineure, prendra donc une grande importance et les polymorphismes qui la concernent pourront orienter le devenir des métabolites ainsi formés. La famille des N-acétyltransférases (NATs) fait partie des enzymes assurant principalement la réaction de conjugaison de la phase II de détoxification des xénobiotiques. Le polymorphisme des NATS représente l'un des exemples de variation pharmacogénétique décrit, et de l'un des plus documentés, depuis sa découverte au début des années 50, en même temps que la découverte de la grande efficacité de l’isoniazide (INH) dans le traitement de la tuberculose.Les travaux de cette thèse avaient pour objectif d’étudier le profil d’acétylation de la NAT2 dans la population sénégalaise afin de les répartir en acétyleurs lents et en acétyleurs rapides, et de déterminer la cinétique de l’isoniazide chez des sujets tuberculeux en corrélation avec les résultats de génotypage. L’étude des mutations du gène NAT2 a été effectuée par PCR-séquençage directe et a permis de mettre en évidence 11 variants alléliques dans la population sénégalaise.l’activité enzymatique de la NAT2 a été déterminée par utilisation du test à la caféine et le rapport des ratios des métabolites majeurs a permis classer les sénégalais en acétyleurs lents et rapides. La cinétique de l’isoniazide a utilisée la chromatographie UPLC-MS/MS. Ce travail présente les premiers résultats de l’étude de la NAT2 dans la population sénégalaise qui pourront être utilisés pour une meilleur optimisation de l’utilisation de l’INH dans la prise en charge de la tuberculose, maladie à forte prévalence en Afrique. / Xenobiotic biotransformation undergoes several stages of simultaneous or successive whose main attractions are the tissues at the interface between the organism and the external environment, namely: digestive, respiratory, kidney and liver. The latter being the most important functionally. The reaction phases constituting the main stages of detoxification, phase I, phase II and phase III, are possible only through the intervention of specific enzyme systems. Given the wide diversity of xenobiotics to which the organism is exposed, there are a multitude of enzymes with various specificities. The biotransformation reactions of xenobiotics are linked linearly rarely, because two or more lanes are often born from a given metabolite. It is therefore understandable that the existence of an enzyme variant defective for one of these reaction pathways can direct the metabolism of a given substance to another track. The latter, usually minor, will therefore important and polymorphisms that concern will guide the fate of metabolites thus formed. The N-acetyltransferases (NATs) is part of enzymes that primarily the conjugation reaction of phase II detoxification of xenobiotics. The polymorphism of NATS is one of the examples of pharmacogenetic variation described, and one of the most documented since its discovery in the early \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'50s, along with the discovery of the high efficacy of isoniazid (INH) in the treatment of tuberculosis. The work of this thesis aimed to study the profile of the NAT2 acetylation in the Senegalese population in order to distribute them in slow acetylators and rapid acetylators, and determine the kinetics of isoniazid in tuberculous subjects correlated with the results of genotyping. The study of mutations of the NAT2 gene was performed by PCR-direct sequencing and allowed to identify 11 allelic variants in the Senegalese population. The enzymatic activity of NAT2 was determined by using caffeine test and the ratios of major metabolites allowed Senegalese classify fast and slow acetylators. The kinetics of isoniazid used UPLC-MS/MS chromatography.

Bien que le rejet humoral en transplantation rénale soit de mieux en mieux caractérisé, des difficultés diagnostiques persistent et son pronostic reste sombre. Objectifs : dans un tel contexte, nous avons privilégié 2 objectifs : (1) préciser les mécanismes physiopathologiques en cause lorsque des signes d’inflammation microvasculaire tels qu’une glomérulite sont observés isolément sur biopsie systématique ; (2) évaluer le rôle de l’autoimmunité au cours de la transplantation dans le but d’identifier d’éventuels marqueurs prédictifs d’une évolution particulière au cours de la greffe. Méthodes : dans un premier temps, nous avons effectué une analyse clinico-pathologique d’une cohorte de 20 patients avec glomérulite isolée sur biopsie systématique à 3 mois de la greffe, couplée à un phénotypage par analyse transcriptomique. Après cette première étape, les distorsions du répertoire B induites par la greffe ont été évaluées de manière séquentielle par technique d’immuno-empreinte chez 43 patients transplantés rénaux dans l’optique de la caractérisation éventuelle de nouveaux biomarqueurs à valeur diagnostique et pronostique. Résultats et conclusion : il n’y avait pas de différence significative à 3 ans de la transplantation entre le groupe de patients avec glomérulite isolée et le groupe témoin.Cependant, la cohorte de patients étudiée est hétérogène puisqu’une évolution péjorative a été observée chez une minorité de patients, pour lesquels des anticorps anti-HLA (non spécifiques du donneur) étaient plus souvent présents et le grade lésionnel plus élevé. L’étude du répertoire B illustre l’importante hétérogénéité interindividuelle des profils de réactivitévis à vis du tissu rénal. Après transplantation, l’apparition de bandes de réactivité additionnelles était notée chez 19/43 patients, et ce dans toutes les catégories anatomocliniques représentées. L’identification des cibles antigéniques est un complément indispensable de cette approche. / X

OBJECTIVE: This study attempts to characterize CIII malocclusion phenotypes in order to identify distinct subgroups for which genetic susceptibility could be identified. METHODS: Sixty-three lateral cephalometric variables were measured from pre-treatment records of 292 CIII Caucasian adults. Principal component analysis (PCA) and cluster analysis (CA) were used to identify the most homogeneous groups of individuals representing distinct CIII phenotypes and thus reducing genetic heterogeneity. RESULTS: PCA resulted in 6 principal components that accounted for 81.17% of the variation. The first three components represented variation on mandibular and maxillary horizontal and vertical position and lower incisor angulation, respectively. The cluster model identified 5 distinct subphenotypes of CIII malocclusion. CONCLUSIONS: A spectrum of phenotypic definitions was obtained which may enhance the identification of human susceptibility genes underlying CIII malocclusion.

Objectives: About 2% of the US population suffers from severe malocclusion discrepancies that are beyond the limits of orthodontics alone. This study explores correlations between 3D malocclusion phenotypes and craniofacial development genes. Methods: CBCTs (124) or digital casts (161) of 285 subjects with skeletal Class I (n=60), II (n=143) and III (n=82) malocclusion were digitized with 48 dental landmarks. 3D coordinates were superimposed prior to Principal Component (PC) analyses to identify symmetric (sym) and asymmetric (asym) aspects of shape variation related to malocclusion. PCs explaining 51%-67% of total shape variation were regressed on 200 variants genotyped within 75 genes adjusting for race, gender, age and data source. Results: Significant correlations (p<0.01) were found for sym variation with BMP3, PITX2, MAFB, SNAl3, FGF8, ABCA4-ARHGAP29, FOXL2 and asym variation PAX7, TBX1, LEFTY1, SATB2, SOX2, TP63 and the 400Kb region containing D1S435. Conclusion: Results suggest genetic pathways associated with malocclusion.

Doctor of Philosophy / Cystic fibrosis (CF) is the most common inherited lethal disorder among Caucasian populations. Chronic pulmonary infections, particularly from Pseudomonas aeruginosa, are the major determinant of the morbidity and mortality of people with CF. It is generally accepted that people with CF acquire this pathogen independently from their surrounding environment, and that individual CF patients carry unique strains different from others. The spread of this pathogen from patient to patient is thought to be rare and occurs particularly among closely contacted cases such as CF siblings. However, over the past decade, there have been several reports of an emergence of clonal P. aeruginosa strains commonly found infecting a number of CF patients. One such report is from the CF paediatric clinic at the Royal Children’s Hospital in Melbourne in which more than half of the patients were infected with a single strain or clone, subsequently called Australian epidemic strain 1 or AES-1. A preliminary survey showed that AES-1 had spread extensively along the Australian eastern seaboard among CF patients attending other CF centres in Melbourne, Sydney and Brisbane, including adult patients at the Royal Prince Alfred Hospital (RPAH), Sydney. Another clonal strain, subsequently called AES-2, was identified in both CF adults and children at the Prince Charles Hospital and the Royal Children’s Hospital, in Brisbane. The total extent of prevalence of the AES-1 and AES-2 strains at the RPAH as well as the clinical status of patients who carried these strains was unknown. Moreover, the pathogenicity of these two clonal strains had not been investigated. The studies presented in this thesis investigated the prevalence of these clonal strains among CF patients attending the adult CF clinic at RPAH, Sydney by using pulsed-field gel electrophoresis. Overall, 50% of 112 patients with P. aeruginosa were found to be infected with clonal strains. The AES-1 and AES-2 strains were identified in 38% and 5% of the patients respectively. Two new clonal strains, called Sydney-1 and Sydney-2, were also identified. Patients with clonal strains had a significant increase in their number of exacerbations and hospitalisation days, and tended to have lower pulmonary functions when compared to patients infected with non-clonal strains. By using a variety of bioassays to examine the pathogenicity of the clonal and non-clonal strains, it was found that both AES-1 and AES-2 produced more virulence factors and were more resistant to antibiotics when compared to the non-clonal strains. AES-1 and AES-2 were associated with increased production of proteases, including elastase, alkaline protease and protease IV. Overall the results presented in this thesis suggest that there may be a link between virulence and transmissibility of this pathogen. The studies presented in this thesis also compared the biofilm forming capacities of the AES-1 and non-clonal isolates. AES-1 was shown to have greater biofilm-forming capacity than the non-clonal strains, when they were grown on a glass surface, suggesting a possible association between clonality and biofilm formation. A model for the study of bacteria grown in conditions similar to CF sputum was also developed. P. aeruginosa grown in this model was found to develop into clumps which may be comparable to the biofilm structure in the CF lung. This model was shown to be beneficial for transcriptomic and proteomic studies which are underway within the research group. AES-1 was also found to have phenotypic variations between isolates. By applying the amplified fragment length polymorphism technique, more subtypes of this clone were revealed. However, these detected subtypes did not correlate with the different phenotypes, suggesting minor mutations such as single point polymorphisms may be responsible for the phenotypic diversity within the clone. The final part of this thesis was devoted to examining the safety of a novel CF treatment: hypertonic saline (HS) inhalation. HS was shown to increase airway mucociliary clearance, while increased osmolarity associated with the use of HS was also shown to have an inhibitory effect on the formation of biofilms. Findings in this study proved that there was no evidence of strain selection in patients who received the long-term treatment with HS. The study also demonstrated that AES-1 was significantly more persistent in the CF lung than the non-clonal strains. The present thesis not only defines the clonal strains of P. aeruginosa and their implications for infected patients, but also provides a general understanding into the pathogenesis of both clonal and non-clonal strains infecting CF lungs.