Le volume des données ne cesse de croître. À tel point qu'on parle aujourd'hui de "Big Data". La principale raison se trouve dans les progrès des outils informatique qui ont offert une grande flexibilité pour produire, mais aussi pour stocker des quantités toujours plus grandes. Les méthodes d'analyse de données ont toujours été confrontées à des quantités qui mettent en difficulté les capacités de traitement, ou qui les dépassent. Pour franchir les verrous technologiques associés à ces questions d'analyse, la communauté peut se tourner vers les techniques de calcul distribué. En particulier, l'extraction de motifs, qui est un des problèmes les plus abordés en fouille de données, présente encore souvent de grandes difficultés dans le contexte de la distribution massive et du parallélisme. Dans cette thèse, nous abordons deux sujets majeurs liés à l'extraction de motifs : les motifs fréquents, et les motifs informatifs (i.e., de forte entropie). / Le volume des données ne cesse de croître. À tel point qu'on parle aujourd'hui de "Big Data". La principale raison se trouve dans les progrès des outils informatique qui ont offert une grande flexibilité pour produire, mais aussi pour stocker des quantités toujours plus grandes.à l'extraction de motifs : les motifs fréquents, et les motifs informatifs (i.e., de forte entropie).

Magister Artium - MA / The mbopo institution, popularly known as the “fattening room” is a cultural rite of passage for young virgins, who are being prepared for marriage among the Ibibio/Efik people of southern Nigeria. It is a complex cultural institution which marked the change of status from girlhood to nubile womanhood in Ibibio/Efik culture. This study examines the practice of mbopo ritual among the Ibibio/Efik people across the previous century. Through an engaged and detailed visual analysis, the study argues that in the first decade of the 20th century, the mbopo ritual had a degree of vibrancy with an attached sense of secrecy and spiritual mystery. But between 1920 and the present, this vibrancy and spiritual undertone has been subtly but progressively compromised. A buildup of tension on the ritual by modern forces, not only of the outside missionaries, but also indigenous converts set in motion a process that would eventually transform the ritual from a framework of an actual cultural practice into the realms of “cultural reinvention” and re-rendering. Feminist critiques of the 1980s and the 1990s led to the popular awareness of the damaging impact of clitoridectomy, just one core aspect of the ritual. As a direct result, clitoridectomy was outlawed across the country, leaving mbopo to be seen as a morally suspect practice. In recent year, the once vibrant, secret and spiritually grounded rite of seclusion for nubile women has been reimagined and reinvented through the public display in art, painting, cultural dance troupe, music and television shows.

Under most conditions, meiotic recombination is essential for ensuring that organisms adapt to ever changing biotic and abiotic conditions and, as such, it shapes evolutionary change within and between species. The interplay between selection and recombination plays a role shaping levels diversity within populations. Remarkably, recombination is itself an evolving trait that varies at many levels: between distant species of eukaryotes, between closely related species and among populations (and individuals) of the same species. Recombination rates also vary across genomes. Most of the causes and mechanisms of this plasticity in recombination rates and distribution are not clearly understood. Also, our understanding of how this variability in recombination rates influences levels of diversity within populations and across genomes is incomplete. Here, I present a study combining molecular genetics with bioinformatic techniques to characterize recombination landscapes in Drosophila melanogaster. I present a model that accounts for a significant fraction of the variation in crossover rates across the genome of Drosophila melanogaster. Our predictive model suggests that crossover distribution is influenced by both meiosis-specific chromatin dynamics and very local constitutively open chromatin associated with DNA motifs that prevent nucleosome stabilization. I also present a novel method for genomic scans to identify recent events of adaptation in using nucleotide diversity data. In addition, I characterized variability in recombination rates in different populations of D. melanogaster and detected that the highest degree of variability in recombination rates across the genome is associated with intermediate genomic scales, and that this intermediate scale also plays a major role in explaining differences in recombination among populations. Our report is the first linking variation in recombination rates across genomes (genomic) and among populations (evolutionary), possibly suggesting a common mechanistic/genomic cause. Finally, I present preliminary data of the first large-scale project to study the effects of multiple environmental conditions in recombination rates at genome-wide level. In conclusion, these studies provide a new framework to investigate variation in recombination rates and to understand the genomic causes and evolutionary consequences.

The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite promising theoretical studies in recent years, the selective forces which shape signaling network topologies in general remain unclear. Here, we propose prevention of autoactivation as one possible evolutionary design principle. A generic framework for continuous kinetic models is used to derive topological implications of demanding a dynamically stable ground state in signaling systems. To this end graph theoretical methods are applied. The index of the underlying digraph is shown to be a key topological property which determines the so-called kinetic ground state (or off-state) robustness. The kinetic robustness depends solely on the composition of the subdigraph with the strongly connected components, which comprise all positive feedbacks in the network. The component with the highest index in the feedback family is shown to dominate the kinetic robustness of the whole network, whereas relative size and girth of these motifs are emphasized as important determinants of the component index. Moreover, depending on topological features, the maintenance of robustness differs when networks are faced with structural perturbations. This structural off-state robustness, defined as the average kinetic robustness of a network’s neighborhood, turns out to be useful since some structural features are neutral towards kinetic robustness, but show up to be supporting against structural perturbations. Among these are a low connectivity, a high divergence and a low path sum. All results are tested against real signaling networks obtained from databases. The analysis suggests that ground state robustness may serve as a rationale for some structural peculiarities found in intracellular signaling networks.

In 1975, Elongation Factor P (EF-P) protein was first discovered in the bacterium Escherichia coli. EF-P is believed to facilitate the translation of proteins by stimulating peptide bond synthesis for a number of different aminoacyl-tRNA molecules in conjunction with the 70S ribosome peptidyl transferase. Known eukaryotic homologs, eukaryotic translation initiation factor 5A (eIF-5A) of EF-P exist but with very low sequence conservation. Nevertheless, because of the high sequence similarities seen between bacterial EF-Ps and its low sequence similarity with eIF-5A, there is interest in the pharmaceutical industry of developing a novel antibacterial drug that inhibits EF-P. Of 322 completely sequenced bacterial genomes stored in GenBank, only one organism lacked an EF-P protein. Interestingly, sixty-six genomes were discovered to carry a duplicate copy of efp. The EF-P sequences were then used to construct a protein phylogenetic tree, which provided evidence of horizontal and vertical gene transfer as well as gene duplication. To lend support to these findings, EF-P GC content, codon usage, and nucleotide and amino acid sequences were analyzed with positive and negative controls. The adjacent 10 kb upstream and downstream regions of efp were also retrieved to determine if gene order is conserved in distantly related species. While gene order was not preserved in all species, two interesting trends were seen in some of the distantly related species. The EF-P gene was conserved beside Acetyl-CoA carboxylase genes, accB and accC in certain organisms. In addition, some efp sequences were flanked by two insertion sequence elements. Evidence of gene duplication and horizontal transfers of regions were also observed in the upstream and downstream regions of efp. In combination, phylogenetic, sequence analyses, and gene order conservation confirmed evidence of the complex history of the efp genes, which showed incongruencies relative to the universal phylogenetic tree. To determine how efp is regulated, the upstream regions of efp were used to try to predict motifs in silico. While statistically significant motifs were discovered in the upstream regions of the orthologous efp genes, no conclusive similarities to known binding sites such as the sigma factor binding sites or regulatory protein binding sites were observed. This work may facilitate and enhance the understanding of the regulation, conservation, and role of EF-P in protein translation.

In 1975, Elongation Factor P (EF-P) protein was first discovered in the bacterium Escherichia coli. EF-P is believed to facilitate the translation of proteins by stimulating peptide bond synthesis for a number of different aminoacyl-tRNA molecules in conjunction with the 70S ribosome peptidyl transferase. Known eukaryotic homologs, eukaryotic translation initiation factor 5A (eIF-5A) of EF-P exist but with very low sequence conservation. Nevertheless, because of the high sequence similarities seen between bacterial EF-Ps and its low sequence similarity with eIF-5A, there is interest in the pharmaceutical industry of developing a novel antibacterial drug that inhibits EF-P. Of 322 completely sequenced bacterial genomes stored in GenBank, only one organism lacked an EF-P protein. Interestingly, sixty-six genomes were discovered to carry a duplicate copy of efp. The EF-P sequences were then used to construct a protein phylogenetic tree, which provided evidence of horizontal and vertical gene transfer as well as gene duplication. To lend support to these findings, EF-P GC content, codon usage, and nucleotide and amino acid sequences were analyzed with positive and negative controls. The adjacent 10 kb upstream and downstream regions of efp were also retrieved to determine if gene order is conserved in distantly related species. While gene order was not preserved in all species, two interesting trends were seen in some of the distantly related species. The EF-P gene was conserved beside Acetyl-CoA carboxylase genes, accB and accC in certain organisms. In addition, some efp sequences were flanked by two insertion sequence elements. Evidence of gene duplication and horizontal transfers of regions were also observed in the upstream and downstream regions of efp. In combination, phylogenetic, sequence analyses, and gene order conservation confirmed evidence of the complex history of the efp genes, which showed incongruencies relative to the universal phylogenetic tree. To determine how efp is regulated, the upstream regions of efp were used to try to predict motifs in silico. While statistically significant motifs were discovered in the upstream regions of the orthologous efp genes, no conclusive similarities to known binding sites such as the sigma factor binding sites or regulatory protein binding sites were observed. This work may facilitate and enhance the understanding of the regulation, conservation, and role of EF-P in protein translation.

Thèse doctorat : Informatique : Villeurbanne, INSA : 2007. / Titre provenant de l'écran-titre. Bibliogr. p. 121-127. Index.

No description available.

Of the organisms with sequenced genomes, plants appear to possess the most rhomboid protease-encoding genes. However, our knowledge of processes in plants that involve Regulated Intramembrane Proteolysis (RIP) and rhomboid proteases remains low. As expressed recently by other researchers, finding a natural substrate for a rhomboid protease represents the biggest experimental challenge. Using yeast mitochondria-based assays, a potential link between the plastid translocon component Tic40 and organellar rhomboid proteases was recently uncovered. In this particular link, rhomboid proteases appear capable of influencing the pattern of imported Tic40 in yeast mitochondria. Tic40 may thus represent a natural plant target of organellar rhomboid proteases. Here, we obtained further motif-oriented evidence supporting Tic40 as a natural plant rhomboid substrate. A comparative analysis of sequences revealed that Tic40 may also possess similar TMD motifs found in the model substrate, Spitz. Rhomboid proteases often require these motifs to cleave substrates within intramembrane environments. Using site-directed mutagenesis and yeast mitochondria assays, the impact of mutations occurring in the motifs ASISS, GV, QP, and GVGVG of Tic40 was assessed. In terms of cleavage and changing the pattern of imported Tic40, some of the mutations showed decreased activities and a few showed enhancements. More importantly, the overall observed pattern associated with select Tic40 mutations resembled the characteristics reported for the model substrates. In particular, mutations in the Tic40 GV motif produced similar results as that observed with Spitz, by drastically decreasing or increasing cleavage as a function of amino acid sequence. / Thesis (Master, Biology) -- Queen's University, 2010-05-30 10:22:07.72

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