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Bacteria are unicellular organisms that are subject to vigorous environmental changes. In order to survive, they have to respond and adapt quickly to those changes. Therefore, studying their cellular regulation is of great interest and would largely help in understanding the more sophisticated eukaryotic cells. Regulation inside the cell is made of a complex of different levels and entities. At the first level comes the regulation of gene expression, the process by which the genetic code is expressed into proteins. Gene expression is made of two steps: transcription of the DNA into mRNA, and translation of the mRNA into protein. The focus of this thesis is the study of the regulation of the transcriptional process. Transcription is mediated by the interaction of the RNA polymerase, transcription factors and regulatory sequences in the gene. Transcription factors can either activate or repress gene expression. They usually have multiple target genes of related functions, so that the expression of those genes can be orchestrated simultaneously. The target genes can, in turn, regulate the expression of other genes, forming a network of regulatory interactions. Reconstructing this network in bacteria is the goal of this thesis. A great sum of the regulatory interactions have been verified by wet lab experiments. However, laboratory experimentation is tedious and expensive, and the need for computational methods became obvious. Every transcription factor has a semi-conserved sequence to bind to in the gene called motif. Identifying those motifs can be used as a predictive tool to discover unknown regulator-gene interactions. Therefore, in the first part of the thesis we performed in silico motif detection for a set of Salmonella Typhimurium genes, predicted to be targets of the transcriptional regulator of the invasion process, HilA. We were able to identify a motif that overlapped with the previously reported binding site for HilA. The motif was present in previously known targets as well as in some novel ones. We also performed genome-wide motif detection in Bacillus subtilis, using comparative genomics and co-regulation of genes as basis for the search. The motifs predicted in this manner were used as part of the transcriptional regulatory network we constructed in the second part of the thesis. Since transcriptional regulation comes as a cellular response to external and internal stimuli, a regulator-gene interaction does not occur at all times. Instead it is condition-dependent. Thus, gene expression data under different conditions is needed for an accurate representation of the transcriptional network. To this end, all known regulator-gene interactions and predicted ones were put together with gene expression profiles gathered from public data in different experimental conditions. The two types of data were used to infer transcriptional modules in B. subtilis, each module is made of a set of genes that share the same motifs and are co-expressed under the same subset of conditions. Analyzing the inferred network we were able to expand the current known network by predicting novel interactions with high confidence. We were also able to reveal the conditions in which each interaction takes place, giving great insight into the dynamics of the network. Other global and specific features of the network were also revealed.

Academic collection --- 681.3* / / / / / / / / / / / / / / / / / / / / / / / / / / / / --- 579 --- 579 Microbiology --- Microbiology --- Computer science --- Theses

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Ornithose --- Ornithosis --- Chlamydia psittaci --- Pathogénèse --- pathogenesis --- Pathologie --- Pathology --- Réponse immunitaire --- Immune response --- Sciences and engineering --- biological sciences --- biology --- microbiology --- veterinary science --- 579.62 --- 579.882 --- Veterinary microbiology --- Chlamydiales. Chlamydia --- 579.882 Chlamydiales. Chlamydia --- 579.62 Veterinary microbiology --- microbiology. --- veterinary science. --- Biological sciences --- Biology --- Microbiology. --- Veterinary science.

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Produit alimentaire --- foods --- Contamination biologique --- Biological contamination --- Virus --- viruses --- Maladie transmissible par aliment --- foodborne diseases --- diagnosis --- PCR --- Épidémiologie --- Epidemiology --- Résistance à la température --- Temperature resistance --- Détoxification --- Detoxification --- Chlorure de sodium --- Sodium chloride --- Acide acétique --- Acetic acid --- 579.67 --- 57.083.2 --- Food microbiology --- Virological methods and techniques --- 57.083.2 Virological methods and techniques --- 579.67 Food microbiology --- viruses. --- Detoxification.

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Microbiologie --- Microbiology --- Contamination biologique --- Biological contamination --- Pasteurization --- Traitement des aliments --- Food processing --- Technologie haute pression --- High pressure technology --- Technologie alimentaire --- Food technology --- Modèle mathématique --- Mathematical models --- 664.8.035.1 --- 579.67 --- Preservation by gases --- Food microbiology --- Theses --- 579.67 Food microbiology --- 664.8.035.1 Preservation by gases

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Klinische chemie --- Hematologie --- Klinische chemie. --- Hematologie. --- klinische chemie --- klinische hematologie --- hematologie --- laboratoriumonderzoek --- 616.1 --- 579.61 --- Electrochemistry --- General biochemistry --- Clinical chemistry --- Pathological haematology --- Fe (ijzer) --- laboratoriumdiagnostiek --- medische laboratoriumtechnologie --- biochemie --- Ca (calcium) --- elektrochemie --- enzymen