The bacterium Helicobacter pylori is a human pathogen that infects a large proportion of the world's population and is associated with serious diseases such as gastric ulcers and adenocarcinoma. The motility of this organism, by virtue of sheathed polar flagella is essential to colonisation and persistence in the human host. The sequencing of the H. pylori genome in 1996 identified homologues of the majority of the flagellar genes found in S. enterica serovai typhimurium. These included genes encoding the flagellum ATPase, FliI and FliH a presumptive inhibitor, the primary focus of this study. Sequencing did not originally identify an H. pylori homologue of the flagellar chaperone FliJ, and this is also considered in this study. Bioinformatic analysis and modeling suggests a structural and functional relationship between FliI and homologues such as F1-ATPase α- and β-subunit. In particular, residues 2-91 of FliI resemble the N-terminal domain of the F1-ATPase α- and β-subunits. Biochemical analyses reported in this thesis showed that a truncated FliI-(2- 91) protein was folded, although the N-terminal 18 residues were likely unstructured. Furthermore, deletion mutagenesis showed that this disordered segment of the protein mediates interaction with FliH and very likely forms an amphipathic α-helix upon forming of the FliI-FliH complex. The scanning mutagenesis of this interaction segment of FliI identified a cluster of conserved hydrophobic residues that was critical for the interaction with FliH. Thus, the interaction between FliI and FliH has similarities to the interaction between the N-terminal α-helix of the α-subunit and the globular domain of the δ-subunit of the F1-ATPase. This similarity suggests that FliH, by analogy with the δ-subunit of the F1-ATPase, may function as a molecular stator of the flagellum. The findings presented above have been published (96). The function of a putative H. pylori FliJ homologue, HP0256, was also investigated by knock-out mutagenesis. Disruption of this gene does not abolish flagellar assembly, however further research continued beyond this thesis showed that the knock-out mutant results in impaired motility.

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Yes / Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft whole-genome sequence of a freshwater isolate from Malaysia, A. hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported here. / University of Malaya via High-Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01, no. A-000001- 50001), and aUM-MOHEHIR grant (UM C/625/1/HIR/MOHE/CHAN/ 14/1, no. H-50001-A000027)

Polyomaviruses are small unenvelope DNA viruses, whose replication take place in cell nucleus. Despite its small genome size, these viruses can cause significant changes in the host cell, one of the most significant is cell transformation. Most studies of human pathogens from this family is the focus of clinical research, but do not provide enough information about the individual events of the life cycle of viruses. This thesis mainly aims to determining the exact time when the creation of the individual viral products and generate a timeline of events during natural infection in cells that are targets for BKV in the human body. It was found that the time course of the life cycle of BKV is very similar to those for model polyomaviruses MPyV and SV40 and in permissive cells takes about 40 - 50 hours.

L'objectif de cette thèse est d'appliquer la méthode d'identification bactérienne par spectrométrie de masse MALDI-TOF pour une utilisation en routine dans un laboratoire de microbiologie clinique. Dans un 1er temps et de manière prospective, nous avons évalué la performance et le coût-efficacité de l'identification bactérienne de routine par MALDI-TOF par rapport aux techniques conventionnelles d'identification phénotypique. Durant la période des 16 semaines d'étude, nous avons comparé la performance de la technique par MALDI-TOF aux techniques conventionnelles d'identification phénotypique comprenant la coloration de Gram, la galerie API ANA et le Vitek 2. En cas de résultats discordants entre ces deux techniques, l'identification était réalisée par biologie moléculaire. Nous avons montré que le MALDI-TOF est un moyen efficace et rentable pour l'identification des bactéries de routine. Le MALDI-TOF peut être utilisée en 1ère intention dans l'identification bactérienne avant l'ensemble de techniques phénotypiques. Dans un 2ème temps, nous avons évalué rétrospectivement la performance et le coût-efficacité de l'utilisation exclusive de MALDI-TOF en diagnostic bactériologique de routine en comparaison avec les techniques conventionnelles. En analysant les données des 11 dernières années, nous avons montré que le MALDI-TOF est efficace et tout à fait adaptée pour l'identification d'espèce bactérienne en routine. Nous avons également prouvé que MALDI-TOF est un outil puissant pour identifier les espèces bactériennes rarement impliquées dans les infections humaines. Cette technique pourrait être une alternative aux méthodes moléculaires dans le laboratoire clinique. / The objective of this thesis is to apply the method of bacterial identification by MALDI-TOF MS in daily practice in a routine clinical microbiological laboratory. Firstly, we prospectively evaluated the performance and the cost-effective of bacterial identification by MALDI-TOF in comparison with conventional phenotypic identification methods. During a 16-week study, we compared the performance of MALDI-TOF with conventional techniques of identification including Gram staining, API ANA identification strip and automated identification using the Vitek 2. The unmatched identifications between MALDI-TOF and conventional methods were resolved by molecular identification. In this study, we showed that MALDI-TOF was an effective tool and less expensive for the rapid identification of bacterial species in clinical microbiology laboratory. MALDI-TOF can be used in first intention for identification before Gram staining or other phenotypic identification techniques based on physicochemical properties of bacteria. Secondly, we retrospectively evaluated the performance and the cost-effectiveness of the exclusive use of MALDI-TOF in bacteriological diagnosis in comparison with conventional phenotypic identification. 11-year retrospective analysis of data showed that MALDI-TOF was efficient and completely adapted for the routine identification of bacterial species. We also showed that MALDI-TOF had capacity to identify bacterial species that were rarely involved in human diseases. This technique could be an alternative to molecular methods in the clinical laboratory.