Dissertations / Theses on the topic 'Dynamique du génome'
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Ravel, Christophe. "Structure et dynamique du génome de Leishmania (protozoa, kinetoplastida)." Montpellier 1, 1996. http://www.theses.fr/1996MON1T004.
Chelaifa, Houda. "Spéciation allopolyploïde et dynamique fonctionnelle du génome chez les Spartines." Phd thesis, Université Rennes 1, 2010. http://tel.archives-ouvertes.fr/tel-00536586.
Giraud, Delphine. "Dynamique des éléments transposables et évolution du génome des spartines polyploïdes." Thesis, Rennes 1, 2019. http://www.theses.fr/2019REN1B057.
We explored the consequences of divergent speciation or reticulate evolution (resulting from hybridization) during diversification of the Spartina genus in the last 6-10 MY, based on the analysis of repeated sequences, their expression and regulation. Transposable element amounts, genome size, and phylogenetic relationships were found correlated, although differential dynamics of specific transposable element families or satellite sequences were encountered according to lineages, and to divergence times following the speciation events. The abundance of transposable elements appears related to their level of expression and the role of small RNAs in their control. This regulation is rapidly established following interspecific hybridization and explains the "genomic quiescence" (absence of transposable element “burst”) detected in the recent allododecaploid S. anglica. Annotations of transposable elements and small RNAs, new reference transcriptomes generated for different species during this work represent additional resources that will allow a more comprehensive exploration of the Spartina genome history and dynamics for a better understanding of the genomic mechanisms involved in the adaptation and ecology of these “ecosystem engineers” species
Ceschia, Audrey. "Dynamique de la réplication et instabilité du génome chez "S. Cerevisiae"." Montpellier 2, 2005. http://www.theses.fr/2005MON20100.
Poli, Jérôme. "Dynamique de la réplication du génome et réponses cellulaires au stress réplicatif." Thesis, Montpellier 2, 2013. http://www.theses.fr/2013MON20233.
A fluctuating environment is a powerful mean of selection for living organisms, which evolved complex signaling networks to integrate these variations and direct swift and efficient cellular responses. The aim of my work is the identification and characterization of molecular mechanisms involved in the tolerance of replicative stress and DNA damage. First, we show that changes in dNTP pools affect several aspects of replication dynamics in budding yeast. dNTP levels are limiting for normal S-phase progression and determine the temporal program of replication during a replicative stress. Interestingly, we also observed that chromosomal instability (CIN) mutants display expanded dNTP pools due to the constitutive activation of the DNA damage checkpoint. Since increased dNTP levels promote forks progression in the presence of DNA lesions, we propose that CIN mutants adapt to chronic replicative stress by upregulating dNTP pools. Secondly, we bring new lights on the role of Crt10 in vivo, which has been initially identified as a negative regulator of Ribonucleotide Reductase (RNR) genes expression. Deletion of CRT10 neither leads to expanded dNTP pools, nor to a massive deregulation of RNR genes, although crt10Δ cells exhibit faster fork progression. The crt10Δ mutant accumulates at the G1/S transition and exhibits a strong defect of origin firing that could account for its replication phenotype. Moreover, we observed a global decrease in ribosome biogenesis in crt10Δ. The physical interaction of Crt10 with several members of the ribosome biogenesis pathway and its role in the Rtt101-Mms1 complex suggest that Crt10 may regulate ribosome levels in vivo. At last, we identified MRX (Mre11-Rad50-Xrs2) as a bona fide member of the transcription termination of non-coding RNA (ncRNA). ChIP-seq reveals that MRX localized at the same loci than the Nrd1-Nab3-Sen1 complex in vegetative growth. rad50Δ cells exhibit transcriptional read-through and upregulation of unstable cryptic transcripts (CUTs) leading to a misregulation of their associated gene. Finally, MRX seems to be involved in the resolution of branched structures emanating from collision between transcription and replication machineries, as it is the case for Sen1
David, Gabriel. "Structure et dynamique du cytoplasme auto-organisé : exemple par la ségrégation du génome bactérien." Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTS098.
Cellular organisms appear organized. Bacteria use membraneless compartments to confine chemical reactions in space and time. There is a general paradigm of intracellular space self-organization that distinguishes between self-assembly, molecular structures assembled by passive phase transition mechanisms, and dissipative structures, generated for example by reaction-diffusion processes. If self-assemblies correspond to the evolution towards thermodynamic equilibrium, dissipative structures are manifestations of an out-of-equilibrium energy cost. We illustrate this paradigm by studying the segregation of bacterial genome, in this case the F-plasmid segregation of Escherichia coli, based on the ParABS partition system. Segregation is a crucial step in the bacterial cell cycle since it ensures the transmission of genetic information in daughter bacteria before division.The ParABS system consists of a parS centromeric sequence; a ParB protein which is able to bind to DNA, specifically on the parS sequence and not specifically elsewhere; and a ParA ATPase protein than can bind to DNA. Interactions between ParB proteins on DNA and specific adsorption on the parS sequence lead to the formation of a three-dimensional focus called the ParBS complex located around the parS sequence. Interactions between ParA and ParB proteins lead to the positioning of this complex at the center of the cell cytoplasm. After replication, two ParBS complexes exist and are segregated by the action of ParA proteins at positions 1/4 and 3/4 of the intracellular space.We first seek to explain the formation of ParBS complexes by a passive phase separation mechanism between high- and low-density states of ParB proteins in space. We construct two statistical physics models using tools borrowed from the physics of phase transitions. Our second approach rigorously defines all the elements of the biological system consisting of the interacting DNA-polymer and ParB proteins and allows us to formulate a first-order phase transition existence criterion that is verified by the DNA. We can draw the phase diagrams of this transition. These two models allow us to argue that the physiological thermodynamic regime of this biological system is a regime of metastable coexistence in ParB proteins on DNA. The parS sequence plays the role of a defect or nucleation seed. We use a third approach to explain the relationship between the three-dimensional and DNA distributions of ParB proteins around the parS sequence.We try to explain the fluorescence recovery curves from photobleaching experiments on ParBS complexes. We construct an in silico photobleaching method, i.e. we reproduce these recovery curves from a phenomenological equation solved numerically. We then develop a system of equations that describe the evolution of proteins on DNA from the previous statistical physical approach to produce an in silico photobleaching taking into account that ParBS complexes are the result of phase separation. We show that a pure passive system does not allow photobleaching experiments because of the Ostwald maturation undergone by the complexes. We correct this approach by including ParA proteins and their biochemical cycle in our simulations. We show that the interactions between ParA and ParB proteins and the hydrolysis of ATP allows the survival of several ParBS complexes thanks to an inversion mechanism of Ostwald's ripening. This fundamental approach explains the positioning of ParBS complexes during segregation
Theulot, Bertrand. "Étude de la dynamique de réplication du génome de Saccharomyces cerevisiae par séquençage nanopore." Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS565.
In eukaryotes, DNA replication initiates from multiple origins activated throughout S-phase. Each origin forms two diverging replication forks that synthesize DNA. Although genome duplication depends on a proper fork progression, the governing factors are poorly understood, and little is known about replication fork velocity variations along eukaryotic genomes. My thesis project aimed at generating in the budding yeast S. cerevisiae the first ever genome-wide map of fork progression based on individual fork rates. Our laboratory has recently introduced a high-throughput, high-resolution, single molecule-based replication mapping technique relying on the detection by nanopore sequencing of 5-bromo-2’-deoxyuridine (BrdU), a thymidine analogue incorporated in replicating DNA. In collaboration with bioinformaticians, I have developed NanoForkSpeed (NFS), a method capable of positioning, orienting and extracting the velocity of replication forks from BrdU tracks synthesized during a brief pulse-labelling of asynchronously growing cells. In addition, I have engineered the BT1 yeast strain which exhibits highly efficient BrdU incorporation and wild-type growth, allowing the measurement of fork progression in physiologically relevant conditions. NFS retrieves previous S. cerevisiae mean fork speed estimates (≈2 kb/min) and precisely quantifies speed changes in cells with altered replisome progression or exposed to hydroxyurea. The positioning of >125,000 fork velocities provides a genome-wide map of fork progression based on individual fork rates, showing a uniform fork speed across yeast chromosomes except for a marked slowdown at known pausing sites, namely centromeres, telomeres, the ribosomal DNA and some tRNA genes. During my PhD, I have also created Nanotiming, a novel method to study the replication timing (RT) of S. cerevisiae's genome. Nanotiming relies on the quantification of BrdU rates in nanopore reads: since thymidine concentration increases during S-phase in yeast, BrdU incorporation will be lower in late replicating than in early replicating regions. In contrast to reference techniques based on DNA copy number analysis, which are either low-resolution or difficult to implement as they require cell synchronization or sorting, Nanotiming only demands the labeling of asynchronously growing yeast cells with BrdU during one doubling. RT profiles obtained both in wild-type cells and in a mutant strain where Rif1, a key RT regulator, has been inactivated are remarkably similar to those established by high-resolution methods, validating my approach. In addition to its simplicity, Nanotiming also paves the way for high-throughput analysis of single molecule RT and in-depth study of inter-individual RT variability
Le, Rouzic Arnaud. "Modélisation de la dynamique évolutive des éléments transposables : naissance, vie et mort d'un parasite génomique." Paris 11, 2005. http://www.theses.fr/2005PA112201.
Transposable elements are one of the main components of the genomes, and they can be found in almost every living organism. However, except in a few "molecular domestication" events, they seem to maintain themselves in the genomes thanks to their own multiplication ability, and they are thus generally considered as "parasitic" DNA sequences. In the present work, we have investigated, through a simulation software, a population genetics model of a transposable element family. The different stages of the "life cycle" of the element have been studied, from the very first generations following its arrival in a new species, to its long-term co-evolution with the other elements and genes in the genome. The results presented here highlight the complexity of the evolution of these genomic parasites, and several realistic evolutionary scenarios can be proposed. In the most cases, a stable equilibrium state appears to be unlikely, and the invasion of a transposable elements family seems to be a dynamic process, depending not only on the features of the element, but also on the interactions existing between the host genome and its parasitic DNA sequences
Wirth, Bénédicte. "Dynamique et évolution d'ORFs dupliquées chez les levures hémiascomycètes : Etude de la famille multigénique DUP." Université Louis Pasteur (Strasbourg) (1971-2008), 2006. http://www.theses.fr/2006STR13070.
Tempel, Sébastien. "Dynamique des hélitrons dans le génome d'arabidopsis thaliana : développement de nouvelles stratégies d'analyse des éléments transposables." Rennes 1, 2007. https://tel.archives-ouvertes.fr/tel-00185256.
Helitrons are the main transposable element in Arabidopsis. We are developped a new syntactical model for detect them in genome. We have shown the relationship between autonomous and nonautonomous helitrons and discovered new families. Analysis of their internal sequence shows a strong variability. We have also created a new tool nammed DomainOrganizer which can visualize the modularity of nonautonomous transposable elements. This study have permit to understand the evolution of helitron family. Last, we have begin to understand the regulatory effect of helitrons
Roulin, Anne. "Dynamique des rétrotransposons à LTR chez les Poaceae : vers un nouveau modèle d'évolution des éléments transposables." Perpignan, 2009. http://www.theses.fr/2009PERP0928.
In plants transposable elements and more particularly LTR-retrotransposons constitute a main component in genome size evolution. They are now kown to be involved in gene regulation and their dynamic of evolution is now well understood. LTR-retrotransposons become rapidely inactive because of epigenetic mutations. They are also deleted from the genome through recombination and it is therefore difficult to explain how transposable elements are maintained in all eukaryotic lineages despite their rapid elimination from the genome. Our work demonstrates that even if they are reproductively isolated, some species can exchange genetic information, including LTR-retrotransposons, through a process referred to as horizontal transfer. This process could explain why transposable element are ubiquitous in Eukaryotes. We have therefore proposed a new model of transposable element evolution in which horizontal transfer allows the introduction of a new set of functional copies which are still able to transpose and can thus colonize and be maintained in new genomes
El, Baidouri Moaine. "Les éléments transposables chez les plantes : impact sur la dynamique et l'évolution des génomes." Perpignan, 2012. http://www.theses.fr/2012PERP1109.
Aci, Samia. "Etude par simulation de dynamique moléculaire de la variabilité conformationnelle du dimère de la séquence SL1 du génome de VIH-1." Orléans, 2004. https://tel.archives-ouvertes.fr/tel-00008151v3.
Kaltenbach, Sophie. "Rôle des facteurs de la réparation de l’ADN dans la dynamique du génome au sein du système immunitaire." Thesis, Sorbonne Paris Cité, 2015. http://www.theses.fr/2015PA05T038/document.
The immune system is particularly dependent on DNA damage response (DDR) pathways. The development of the adaptive immune system requires certain DDR mechanisms, in particular during the V(D)J recombination and during class switch recombination (CSR), furthermore, the hematopoietic system is very sensitive to spontaneous DNA lesions. Therefore, there are many immune deficiencies in human directly related to a DDR deficiency. The identification of the responsible gene is important for appropriate genetic counseling. Today, we have access to powerful genetic screening tools, in particular next generation sequencing (NGS) and the list of genes responsible for immune deficiency is growing rapidly. The first part of this work focuses on the development of a new screening tool for DDR defects, in particular in the case of immune deficiency, and evaluation of clinical interest. This test is based on the observation of a bias of the TCRα repertoire in circulating T lymphocytes when thymocytes lifespan is diminished and we know that DDR defect causes decreased thymocyte survival. We have developed two techniques, by molecular biology and by flow cytometry, to detect a potential bias of the TCRα repetoire and assess the suitability of this test in some immunodeficiencies linked to a DDR defect. A significant bias was detected in the case of ATM and NHEJ factor deficiency. Furthermore, we have established a cohort of patients suffering from common variable immunodeficiency (CVID) with a clinical presentation highly suggestive of DDR defect, in collaboration with the Clinical Immunology Service of Hôpital Saint-Louis (Paris). Functional test for DDR defect and genetic analysis (CGHarray, whole exome sequencing) were performed in these patients to identify new genes involved in CVID. Among the 18 patients analyzed until now, five cases of cellular sensitivity to genotoxic agents have been detected and a candidate gene was identified in 15 of them. These results are still preliminary and our team will pursue genetic and functional characterization of the identified mutations. Finally, we undertook genetic and functional exploration of two mutations identified in a young patient with combined immunodeficiency (CID) associated with a lymphoproliferative disease and autoimmunity, and in whom a cellular hypersensitivity to mitomycin C, a DNA crosslinking agent, was detected. The first mutation was identified in the ELKS gene, which codes for a factor involved in DNA repair. Functional complementation of this gene demonstrates the involvement of this mutation in the hypersensitivity of patient’s cells to MMC. We have developed a conditional knockout mouse model of this gene in hematopoietic cells that did not show any defect in development of the immune system. The second mutation was identified in BACH2 gene encoding a transcriptional repressor involved in the development of the immune system. Knockout mice for this gene have a similar phenotype to the immune deficiency described in this patient. Investigations on this mutation are ongoing in the patient and among family members that also carry the mutation
Boutin, Thibaud S. "Les effets de la sexualité sur la dynamique des éléments transposables." Paris 11, 2010. http://www.theses.fr/2010PA112190.
Within species the gene flow between individuals depends of the mating system, it plays a key role in the evolution of species as well as into the genome architecture by impacting the dynamics of the different genomic components, as the transposable elements for example. Transposable elements are "selfish" DNA sequence able to invade and multiply within a genome independently of their impact on this one. They spread all among the tree of life and they are present in nearly all organisms. Sequenced genomes revealed that transposable elements could be an (very) important portion of the genome. Nowadays, it is essential to decipher their dynamics to have a better understanding of the architecture and the evolution of the genome. The research presented here focus on the effect of the mating system of the host species to the dynamics of transposable element. Theoretical models and computational methods were used to simulate the dynamics of transposable elements within different host populations reproducing with different mating systems (e. G. , asexuality and self-fertilization) including switch from a system to an other (e. G; outcrossing to selfing). The simulations can be performed from the first step of invasion to the long-term transposable elements/genome coevolution within the host population. These simulations generated numerous data sets and their analysis highlighted a number of interesting trends resulting from the interaction between evolutionary forces (e. G. , natural selection, genetic drift and mating system) and transposable element dynamics on genome architecture
Hadjadj, Djihad. "Régulations de la réplication du génome au cours de l'oncogenèse." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC332.
DNA replication is a highly regulated molecular process that maintains the stability of the human genome over the generations of cells. Before each division, the cells must duplicate their genetic material as accurately as possible in order to transmit a single, complete and faithful copy to the daughter cells. This process corresponds to the phase S of the cell cycle that is composed of three stages : initiation, elongation with the synthesis of two new DNA strands, and termination. The replication process must adapt to different genetic contexts (coding sequences, repeated sequences, centromeres, etc.) but also to variable epigenetic environments (opened or closed chromatin). During my thesis, I have been interested in different processes regulating DNA replication in physiological and pathological conditions of the whole human genome. Thus, I chose three complementary approaches : the first deals with the regulation of the replication timing in 6 human cell lines. The second deals with the dynamics of replication forks along the human genome. Finally, the third part focuses on the transcriptional regulation of DNA replication genes in adrenocortical carcinomas
Nabholz, Benoît. "Dynamique évolutive de l'ADN mitochondrial des oiseaux et des mammifères : Mutation, Sélection et Taille des populations." Montpellier 2, 2008. http://www.theses.fr/2008MON20115.
The origin and evolution of mitochondrial genome is fascinating. Currently, it makes up less than 1% of the whole organism genome, but contains some of the most important genes. A particularly intriguing feature of the animal mitochondrial genome is its hypermutability. The first goal of this work is to progress in our understanding of the determinism of mitochondrial DNA (mtDNA) substitution rate variations by distinguishing between two classical hypotheses of evolutionary biology –the generation time hypothesis and the metabolic rate hypothesis– and an other hypothesis that comes from biomedecine, namely the longevity hypothesis. Using a phylogenetic approach, we obtained lineage-specific mitochondrial mutation rates across more than one thousand bird and mammalian species. This analysis reveals an unexpectedly high level of mitochondrial mutation rate variation between lineages. The bird/mammal comparison and a within-class analysis suggest that this variation could be linked to species longevity through a (direct or indirect) selective pressure reducing the mitochondrial mutation rate in long-lived species. In the second part of this work, we address the impact of natural selection and genetic drift on mtDNA. Recent evidence of positive selection acting on mtDNA (mostly in invertebrates) was used as a starting point. We showed that, contrary to invertebrates species, bird and mammal mtDNA evolution is mainly under purifying selection. Surprisingly, even in the absence of positive selection, population size variations have no effect on mtDNA genetic diversity, but influence the rate of non-synonymous substitutions. This result could be explained by strong stochasticity of population sizes. All these results contribute to increase our understanding of an unusually evolving genome, and also have implications for the numerous users of mtDNA as a tool to reconstruct population and species history
Lengronne, Armelle. "Dynamique de la réplication et instabilité du génome chez la levure S. Cerevisiae en l'abscence de l'inhibiteur de CDKs, Sic1p." Paris 11, 2002. http://www.theses.fr/2002PA112087.
Sic1p belongs to the CKI family (Cyclin-Dependent-Kinase Inhibitor), like p21 or p27 in mammalian cells, and is expressed from the end of mitosis to the end of G1 phase of the cell cycle in the budding yeast S. Cerevisiae. One of the main goals of my thesis was to gain a better understanding of the molecular basis of the genomic instability observed in cells lacking the SIC1 gene. These strains show a decrease in viability, an increase of chromosome loss and are delayed in mitosis. Previous work in the laboratory had suggested, based on genetic evidences, that sic1 mutants suffer from a reduction in the number of competent replication origins. In the first part of my thesis, to better characterize potential replication defects of sic1 strains, I have developed a set of molecular, electrophoretic and microscopic techniques that allow precise monitoring of S phase progression in yeast cells using BrdU incorporation. In the second part of my thesis, using these techniques, I showed that cells lacking Sic1 initiate DNA replication from fewer origins, have an extended S phase and inefficiently separate sister chromatids during anaphase. To our surprise, sic1d cells were not retarted at metaphase as expected if the S/M checkpoint were triggered to allow completion of replication before mitosis. Sic1d mutants show a 600-fold increase in the frequency of gross chromosomal rearrangements, probably as a consequence of inappropriate entry into anaphase. We propose that precocious CDK activation causes genomic instability by altering the dynamics of S phase which then hinders normal chromosome segregation
Lesecque, Yann. "La conversion génique biaisée : origine, dynamique et intensité de la quatrième force d’évolution des génomes eucaryotes." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10122/document.
Usually, three main forces are considered when studying sequences evolution in comparative genomics : mutation, selection and genetic drift. Recently, a fourth process has been identified during the study of base composition landscapes in genomes : biased gene conversion (BGC). This phenomenon introduces an overrepresentation of certain alleles in meiosis products (gametes or spores) leading to an increase of the frequency of those variants in the population. Thus, it is able to mimic and interfere with natural selection. Hence, it is important to describe this phenomenon in order to be able to trustfully distinguish BGC and selection in the study of adaptation at the molecular scale. So, the main goal of this work is to analyze the molecular origin, the intensity and the dynamics of BGC. To do so, we use two model species. First, we use the yeast Saccharomyces cerevisiae because, for this specie, a high-resolution recombination map is available which allows a fine study of the conversion process. Analyzing this map led us to shed the light on the molecular mechanisms of BGC. Secondly, recent discoveries on the role of the PRDM9 protein in the determination of recombination landscapes in mammals allowed us to quantify the dynamics and intensity of BGC in the recent human history. Thanks to those two studies, we first confirmed that BGC is the fourth force of molecular evolution and we also provided hypotheses about the evolutionary origin of this process
Brambilla, Elisa. "Investigation of E. coli genome complexity by means of fluorescent reporters of gene expression." Electronic Thesis or Diss., Paris 6, 2014. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2014PA066607.pdf.
Escherichia coli is able to survive in many different environments. The information necessary for this adaptation is encoded in the chromosome. This circular molecule is condensed in a compact DNA-protein structure, called the nucleoid. The chromosome is not uniform, and shows uneven distributions of nucleoid-associated proteins (NAPs) binding sites, AT-rich sequences and general protein occupancy domains. It has been demonstrated that the position of important genes is highly conserved in ?-Proteobacteria. These differences along the chromosome and the conserved position of important genes suggest that the position of the gene can influence gene expression. To test this hypothesis, I studied the expression of a fluorescent reporter gene inserted in different positions around the chromosome. The expression of the reporter is driven by differently regulated promoters, one repressed by the important NAP H-NS, one non regulated and one subject to supercoiling and stringent control. We studied the dynamical expression of these promoters in different growth conditions, growth phases, upon nutritional upshift and under stress. We showed that the expression of the H-NS dependent promoter depends on the location on the chromosome, because H-NS repression is enhanced in presence of AT-rich sequences. We also studied the influence of a divergent gene on the reporter expression as a function of chromosomal position, and showed that this influence depends on the location of the gene. With our study we have been therefore able to show the impact of chromosomal position on gene expression and to give a new perspective on genome complexity
Cleynen, Alice. "Approches statistiques en segmentation : application à la ré-annotation de génome." Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00913851.
Brambilla, Elisa. "Investigation of E. coli genome complexity by means of fluorescent reporters of gene expression." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066607/document.
Escherichia coli is able to survive in many different environments. The information necessary for this adaptation is encoded in the chromosome. This circular molecule is condensed in a compact DNA-protein structure, called the nucleoid. The chromosome is not uniform, and shows uneven distributions of nucleoid-associated proteins (NAPs) binding sites, AT-rich sequences and general protein occupancy domains. It has been demonstrated that the position of important genes is highly conserved in ?-Proteobacteria. These differences along the chromosome and the conserved position of important genes suggest that the position of the gene can influence gene expression. To test this hypothesis, I studied the expression of a fluorescent reporter gene inserted in different positions around the chromosome. The expression of the reporter is driven by differently regulated promoters, one repressed by the important NAP H-NS, one non regulated and one subject to supercoiling and stringent control. We studied the dynamical expression of these promoters in different growth conditions, growth phases, upon nutritional upshift and under stress. We showed that the expression of the H-NS dependent promoter depends on the location on the chromosome, because H-NS repression is enhanced in presence of AT-rich sequences. We also studied the influence of a divergent gene on the reporter expression as a function of chromosomal position, and showed that this influence depends on the location of the gene. With our study we have been therefore able to show the impact of chromosomal position on gene expression and to give a new perspective on genome complexity
Lesecque, Yann. "La conversion génique biaisée : origine, dynamique et intensité de la quatrième force d'évolution des génomes eucaryotes." Phd thesis, Université Claude Bernard - Lyon I, 2014. http://tel.archives-ouvertes.fr/tel-01064609.
Calderon, Virginie. "Méthodes bioinformatiques d'analyses de données génomiques, transcriptomiques et cliniques pour l'étude des mécanismes de résistances aux drogues et leurs relations avec la formation de biofilms." Toulouse 3, 2013. http://www.theses.fr/2013TOU30200.
Genes from the Chaperon-Usher patway, allowing the assembly of fimbriae at the surface of bacteria involved in adhesion and biofilm formation, are mainly found in genomes from Gram negative bacteria. The developpement of a new stratgy of annotation and classification, the evolutive analysis and the ancestral state reconstruction allowed to determine the dynamics of these systems implying multiple gains and losses, and homologous recombination events within complete genomes, of a genus or a species. To understand the relationship between biofilm formation and antibiotic resistance in P. Aeruginosa, analysis of transcriptomic data from clinical and laboratory strains allows i) to establish specific expression signatures in clinical strains according to the stage of infection in the patient and ii) to determine the regulon of the response regulator PprB from the two-component system PprA/B
Imbert, Claret Jean Loup. "A plusieurs, on est meilleur : du rôle des duplications dans l’adaptation aux insecticides chez les moustiques." Electronic Thesis or Diss., Université de Montpellier (2022-....), 2023. http://www.theses.fr/2023UMONG029.
Duplications are structural variants at the origin of an important genetic diversity upon which natural selection can act. A contemporary example of adaptive duplications is studied in mosquitoes. Following the massive use of insecticides, a point mutation in the ace-1 gene (R allele) quickly spread in several mosquito species, where it appeared independently. This allele (R) allows resistance to these insecticides, but is highly deleterious in their absence compared to the susceptible one (S). Duplicated alleles associated with a wide range of phenotypes representing different fitness trade-offs were discovered: homogeneous duplications associating several R copies, or heterogeneous duplications linking R and S copies, or D alleles. We studied the parallel evolution of these alleles in two species complexes that diverged ~145 Ma, Culex pipiens s.l. and Anopheles gambiae s.l. Using an unprecedented dataset, we characterised numerous genomic structures on a global scale in Cx. pipiens s.l., and evidenced in wild populations of An. gambiae s.l. a high polymorphism of D alleles, all sharing the same genomic structure. These results highlight the convergent response in both species complexes to face the same insecticide selection pressure, where the same types of duplications generate similar phenotypes. This work, some of which remains in progress, has allowed us to better understand the origin of diversity and the adaptive role of these duplications, and has paved the road for understanding the impact of their selection on genomic diversity at different scales
Garcia-Meunier, Pascale. "Dynamique des éléments transposables de type rétroposon chez les muridés : cas des familles multigéniques GAPDH et LINEL." Montpellier 2, 1994. http://www.theses.fr/1994MON20231.
Lorenzi, Jean-Noël. "Dynamique des génomes du genre Streptomyces." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS097.
Streptomyces possess a large linear chromosome (8-12 Mb) consisting of a conserved central region flanked by variable arms covering several megabases. In order to study the evolution of the chromosome across evolutionary times, a representative panel of Streptomyces strain and species (110) whose chromosome are completely sequenced was identified. The pangenome of the genus was modelized and shown to be open with a core-genome reaching 803 genes. The evolution of the Streptomyces chromosome was analyzed by carrying out pairwise comparisons, and by monitoring indexes measuring the conservation of gene order and the rate of orthology. This method, applied at the global level, was also applied at the local level, making it possible to measure recombination intensity along the chromosome. Using the phylogenetic depth offered by the chosen panel, it was possible to infer that the chromosomal arms evolved faster than the central region under the combined effect of rearrangements and the addition of new information from the horizontal transfer
Dupeyron, Mathilde. "Dynamique et évolution de deux lignées remarquables de rétrotransposons à LTR dans le genre Coffea (famille des Rubiacées)." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT128/document.
Transposable elements (TEs) are DNA fragments that are able to move and to increase their copy numbers. Two transposition mechanisms corresponding to the two main TE classes are found in almost all organisms. LTR retrotransposons (Long Terminal Repeats, LTR-RTs), belonging to Class 1, are the main components of plant genomes. Genome organisation, size variation, evolution and gene activity can be strongly impacted by their proliferation.Worldwide consumed and produced by South countries, coffee is obtained from two African cultivated species: Coffea arabica and C. canephora. The Coffea genus includes 139 species occurring in diverse habitats in Africa, Madagascar, Mascarene Islands, Comoros, India, Southeast and Tropical Asia and North Australia. All the species are diploids, except the noteworthy allotetraploid C. arabica, originated from a recent inter-specific hybridisation between two diploids: C. canephora and C. eugenioides. However, genome size of diploid species can vary for up to two folds. Today, the numerous genomic data available for Coffea allows the study of LTR- RTs, constituting at least 42% of C. canephora genome, the sequenced species available in public databases.In this work, two notable LTR-RT lineages, Bianca and SIRE, have been studied by bioinformatics approaches. Bianca s.s., is present only in Monocots and it is represented in Dicots by the Divo family, poorly studied nowadays. The recent activation of Divo, without leading to its own structuring, is closely associated to the genetic differentiation of C. canephora. However, this activation seems sporadic as being present in all the coffee-trees species studied here. On the opposite, SIRE elements, which are the only Copia LTR-RTs carrying an envelope-like gene as retroviruses, show an important structuring variation between accessions among C. arabica progenitors, and in parallel to the genus evolution.Our work shows that understanding the LTR-RTs dynamics in a genus allows a better perception of its evolutionary history, with the possibility of different evolutionary timing given by different LTR-RTs families. Our results also indicate that both the biogeographic clades (coffee molecular phylogeny) and also some diploid accessions have peculiar histories, probably related to the colonisation of new ecological niches and to the LTR- RTs dynamics
Achaz, Guillaume. "Étude de la dynamique des génomes : les répétitions intrachromosomiques." Paris 6, 2002. http://www.theses.fr/2002PA066382.
Mitsiouk, Anton. "Contribution à l'optimisation des systèmes dynamiques : application au génie des procédés." Phd thesis, Toulouse, INPT, 2007. http://oatao.univ-toulouse.fr/7650/1/mitsiouk.pdf.
Flores, Ferrer Alheli. "Modélisation mathématique des dynamiques hôtes-parasites ; de l’écologie parasitaire à l’écologie du génome." Thesis, Perpignan, 2019. http://www.theses.fr/2019PERP0010/document.
This document is dedicated to the dynamic modeling of host-parasite interactions. It is about two distant biological models, who are studied using standard epidemiological models built from dynamic compartmental models. The first contribution is the implementation of a 'micro-parasites' model to study the transmission of the protozoan parasite Trypanosoma cruzi, the etiological agent of American trypanosomiasis (or 'Chagas' disease), within a host community of synanthropic and domestic animals. The analysis of the mathematical model shows for the first time in this biological system a dilution effect associated with avian hosts, as well as the possibility of reducing the transmission to humans by modifying the composition of the domestic host communities. The second contribution deals with the dynamics of the "genomic parasites" that are the transposable elements. Using the analogies between genomics and ecology concepts proposed by the "Genome Ecology" approach, it was possible to adapt models developed for 'macro-parasites' to the dynamics of transposable elements of class 1, retro-transposons. The analysis of these models makes it possible toformulate hypotheses on the relative importance of the host demography, the distribution of the number of copies between individuals and the molecular mechanisms of silencing of these elements, on their persistence within the population of hosts reproducing asexually
Arshakuni, Konstantin. "La génèse et la dynamique des nouvelles entreprises." Phd thesis, Université Panthéon-Sorbonne - Paris I, 2006. http://tel.archives-ouvertes.fr/tel-00140388.
Labaille, Jennifer. "Conception d'un vaccin recombinant contre la maladie de Marek d'après l'étude de la dynamique des populations de variants du vaccin CV1988/RISPENS." Thesis, Tours, 2013. http://www.theses.fr/2013TOUR4014.
Gallid herpesvirus 2 (GaHV-2), responsible for T-cell lymphomas chicken, is controlled by the vaccine CVI988/Rispens. My work has shown that the vaccine contains, unlike virulent strain, a viral variants population mostly deleted from the promoter region and a variable portion of the 5' end of the gene LAT encoding microRNA and associated with viral latency. In a vaccine approach, a recombinant virus corresponding to a majority variant of the CVI988/Rispens vaccine was generated from a hypervirulent strain GaHV-2, cloned as bacmid. We showed that recombinant, with an almost total loss of pathogenicity, was able to significantly protect chickens against challenge with virulent strains GaHV-2. This work lays the basis for the development of new vaccines from emerging virulent strains
Bignaud, Amaury. "Organisation et dynamique des génomes bactériens et viraux dans les populations microbiennes." Electronic Thesis or Diss., Sorbonne université, 2023. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2023SORUS637.pdf.
Although invisible to the human eye, microbial communities are ubiquitous on earth, and different populations of microbes have been detected in all ecosystems. Their role is fundamental to the regulation of biogeochemical cycles, the recycling of organic matter and human health. These populations, made up of a variety of micro-organisms including bacteria, archaea and eukaryotes, also include numerous "parasitic" elements such as viruses and plasmids. Among these elements, viruses play a central role in the dynamics and evolution of microbial genomes. Not only do they act as predators, directly regulating populations and exerting strong selection pressure ; they also participate in horizontal gene transfers, helping bacteria to adapt to their environment. These transfers include antibiotic resistance genes and defense mechanisms against other mobile genetic elements. This thesis is devoted to understanding the mechanisms underlying genetic dynamics within these microbial communities, focusing on phage-bacteria interactions at different scales. Using in vitro and in vivo experimental models, we have developed analytical methods for studying these interactions in populations of increasing complexity. In particular, these tools have enabled us to reconstruct numerous viral genomes and characterize their interactions with bacteria s in diverse environmental samples. This research extends our understanding of virus-bacteria interactions, offering unprecedented insight into the evolution of microbial genomes and the mechanisms of coevolution within microbial populations. It could lead to important implications for human health, particularly with regard to the dynamics and spread of antibiotic resistance genes. The study also provides new insights into microbial ecosystems and new tools for studying them
Hellequin, Anne Peggy. "Génèse et dynamique des centres historiques en Méditerranée américaine." Université Paris-Est Créteil Val de Marne (UPEC), 1998. http://www.theses.fr/1998PA120004.
The city have to be seen in its unity and its diversity. Three historic centers, old havana, old san juan, and the french quarter in new orleans can show this division. This three historic centers are only in front of the city and they are different each other. History can explain unity and diversity. We have thought that urban growth and evolution of the urban core were causes of unity. Historic preservation from state and private entities were responsible of diversity. Havana, san juan and new orleans were very interesting because very different for their urban policy. The historical study display that even historic preservation was different, evolution of historic centers is comparable. Old havana, old san juan and the french quarter of new orleans have to be seen like a tourist-historic city with variations of size. So, we can conclude that another dimension, perhaps globalization, can explain diversity of three historic centers. Economoic problems in cuba for example stop all programs of historic preservation
Michely, Stéphanie. "Dynamique des génomes et évolution du métabolisme lipidique chez les levures du clade Yarrowia." Thesis, Paris, AgroParisTech, 2014. http://www.theses.fr/2014AGPT0021/document.
Yarrowia lipolytica belongs to a group of yeasts that have diverged very early from most other hemiascomycetous yeasts. This yeast is able to use various hydrophobic substrates as unique carbon source and to synthesize new free fatty acid from non hydrophobic compounds. These characteristics make Y. lipolytica a known oleaginous model for the lipid metabolism survey of yeasts. Its oleaginous capacity is facilitated by protein family expansions that occurred across evolution after the divergence of the Yarrowia clade. Indeed, among 190 genes involved in the lipid metabolism in Y. lipolytica, more than 67% are grouped into 30 multigenic families with up to 16 members in the lipase family. The recent sequencing of 5 genomes within the Yarrowia clade enabled to compare their gene content. The study of gene families of the lipid metabolism allowed to highlight the evolutionary mechanisms involved in this clade. All the functions necessary to lipid metabolism are present in all species studied with at least one gene per family even for species that have 500 to 1,000 fewer genes than Y. lipolytica. These species are also found to be all oleaginous through physiological studies. The observed gene families derive from multiple gene duplications of which each copy evolves independently by different processes of sub- or neofunctionalisation, fixation, pseudogenization or loss. Contractions and expansions of protein families, gene expression, synteny and relative localisation of genes in the genome were investigated. More particularly, the selection pressure acting on these gene families was compared with those acting on the rest of the genome. The combination of these approaches, physiology, genomics and transcriptomics, has improved the comprehension of the lipid metabolism, its evolution and gene regulation within a clade of oleaginous yeasts
Ricard, Rémi. "Compensation dynamique de mécanismes parallèles." Thesis, Université Laval, 2006. http://www.theses.ulaval.ca/2006/23770/23770.pdf.
Teyssier, Corinne. "Les bactéries du genre Ochrobactrum : des bactéries pathogènes opportunistes à génomes complexes et dynamiques." Aix-Marseille 2, 2003. http://www.theses.fr/2003AIX22078.
Cerveau, Nicolas. "Dynamique évolutive des éléments transposables de type séquence d'insertion dans les génomes des bactéries endosymbiotiques Wolbachia." Phd thesis, Université de Poitiers, 2011. http://tel.archives-ouvertes.fr/tel-00966872.
Cerveau, Nicolas. "Dynamique évolutive des éléments transposables de type séquence d’insertion dans les génomes des bactéries endosymbiotiques Wolbachia." Poitiers, 2011. https://tel.archives-ouvertes.fr/tel-00966872.
Transposable elements (TE) are one of the major driving forces of genome evolution. Eukaryotic TE evolution can easily be reconstructed thanks to many degraded copies. By contrast, in prokaryotes, TE are considered to be recently acquired, which complicates the study of their dynamics. Insertion sequences (IS) are the most abundant TE in prokaryotes. Models predict a high turn-over that starts by TE acquisition by horizontal transfers, followed by copy number increase and subsequent elimination. In addition, models predict that genomes of intracellular bacteria should have few or no IS. Genome sequencing of obligate intracellular bacteria, as Wolbachia, have questioned models, because some have a considerable abundance of IS. Our work was based on the study of five sequenced Wolbachia genomes. We have realized a detailed IS annotation for each genome. In addition, experimental analyses were performed to test the hypothesis based on in silico analyses. We confirmed that Wolbachia genomes contained a considerable abundance of IS. Surprisingly, the majority of IS copies were degraded, which allowed us to study their evolutionary dynamics. Past IS activity in Wolbachia genomes was not constant during time. We identified phases of high activity alternating with phases of relative quiescence. High activity phases needed to be preceded by horizontal transfers of IS that we experimentally detected in abundance in Wolbachia genomes. Finally, expression analyses suggested that IS activity is not exclusively controlled by IS themselves, but it also depends on the genomic environment of the IS copies
Fiston-Lavier, Anna-Sophie. "Etude de la dynamique des répétitions dans les génomes eucaryotes : de leur formation à leur élimination." Paris 6, 2008. https://tel.archives-ouvertes.fr/tel-00283414.
Nouvel, Laurent-Xavier. "Etude de la diversité génétique de Mycoplasma agalactiae : plasticité des génomes, mobilome et dynamique de surface." Thesis, Toulouse, INPT, 2009. http://www.theses.fr/2009INPT013A/document.
Mycoplasma agalactiae is responsible of contagious agalactia, a disease of small ruminants that is still difficult to control and is listed by the OIE. In order to evaluate the genetic diversity of this pathogen, 101 isolates were compared using three techniques (VNTR, RFLP, vpma repertoire). Results revealed a high genetic homogeneity with the PG2 type strain as representative. Some isolates however diverged such as the 5632 which was sequenced and analysed here. Whole comparative genomic and proteomic analyses of the 5632 and PG2 strains indicate that their genomic plasticity resides in important genes flux and in the presence of several mobile genetic elements (10% of the genome). These analyses also revealed that specific loci encoding repertoire of surface proteins are highly dynamic. For these minimal bacteria that lack a cell-wall, these events have most likely played a major role in their survival and adaptation to complex hosts
Coorevits, Patrice. "Maillage adaptatif anisotrope : application aux problèmes de dynamique." Cachan, Ecole normale supérieure, 1993. http://www.theses.fr/1993DENS0002.
Faucher, Marion. "Le transfert horizontal de gènes chez les mycoplasmes : de l'acquisition de l'antibiorésistance à la dynamique des génomes." Thesis, Toulouse, INPT, 2018. http://www.theses.fr/2018INPT0117/document.
Mycoplasmas are wall-less bacteria often portrayed as minimal cells because of their reduced genomes. Several species are pathogenic and have a significant economic impact on livestock production, especially for ruminants. Mycoplasmas are also concerned with the worldwide increase in antibiotic resistance. In contrast to the majority of bacteria, these simple bacteria are deprived of conjugative plasmids that are frequently implicated in the horizontal dissemination of resistance genes: in mycoplasmas antibiotic resistance mainly relies on chromosomal mutations in target genes. In Mycoplasmas, the horizontal gene transfer (HGT) has long been underestimated. Recently, two conjugative mechanisms of HGT were described in Mycoplasma agalactiae: the transfer of an integrative and conjugative element (ICE), and the unconventional transfer of chromosomal DNA further designed by “MCT” for Mycoplasma Chromosomal Transfer. Our current study focused on exploring MCT mechanisms and on estimating its impact on antibiotic resistance dissemination. Comparative genomic analyses were performed from the sequencing (i) of spontaneous resistant mutants and (ii) of transconjugants selected by mating experiments and selected based on their resistance. Data revealed that MCT generated the simultaneous transfer of multiple, unrelated donor-fragments following a distributive process. In one conjugative step involving two strains, MCT generated a variety of highly mosaic genomes. This phenomenon was also shown to accelerate the dissemination of antibiotic resistance, by allowing in one step the acquisition of multiple and dispersed mutations associated with resistance. Due to the limitless ability of this phenomenon in reshuffling genomes, MCT may offer a valuable contribution in other adaptive processes such as virulence or host specificity. Finally, the distributive nature and the extent of MCT explain the origin of genes transfers detected in silico in several mycoplasma species. MCT is certainly a major player in the evolution of these minimal bacteria and a key factor of their persistence and virulence
Schmidt, Franziska. "Systèmes dynamiques et incertitudes." Lyon, INSA, 2009. http://theses.insa-lyon.fr/publication/2009ISAL0024/these.pdf.
[Civil Engineering structures often undergo uncertainties, which can come from different sources and which can be of different natures. Ln this PhD thesis, we deal with sorne shapes of these uncertainties. First. We study the consequence of uncertain initial conditions and uncertain parameters in the motions of non smooth dynamical systems. This is done by means of an indicator of tangent variation. This study is applied to sorne special examples, among others the fa of a rock on a slope of constant angle and a linear oscillator with impacts. Then, the impact of an unknown forcing, modelled by a white noise, is studied by means of the Fokker-Planck equation. This one is solved numerically with the finite differences method to obtain the probability density function of the states of the system. Particularly, this is done for the linear oscillator, the oscillator of Duffing, with friction and a dynamical system leading to energy pumping. A third part deals with the study of Lyapunov exponents. Ln a first chapter, they are calculated infinite ti me. Ln thal case, they depend on lime, on initial conditions, on spa ce, on initial divergence. . . And they can be different from their value in infinite ti me. Then, we test an innovative method for calculating these exponents using the evolution matrix of the system. Lt is applied to different dynamical systems, which makes il possible to assess ils efficiency. Finally, uncertainty on behavior of structures is studied in the case of a system leading to energy transfer. Different behaviors are studied, among which elastic, pure elastoplastic, elastoplastic with damage and robustness of the phenomenon of energy transfer is assessed. ]
Marceau-Fortier, Guillaume. "Culture "dynamique" : impact sur la reconstruction de tissus conjonctifs par génie tissulaire." Thesis, Université Laval, 2010. http://www.theses.ulaval.ca/2010/27891/27891.pdf.
Rouland, Serge. "Acquisition, capitalisation et réutilisation dynamique de connaissances dans le secteur génie civil." Chambéry, 2001. http://www.theses.fr/2001CHAMS025.
Genatios, Carlos. "Contribution à l'évaluation des procédés experimentaux pour la détermination des propriétés dynamique des structures : application à deux cas de structures de Génie civil." Toulouse, INSA, 1991. http://www.theses.fr/1991ISAT0018.
Marion, Romain. "Contribution à la modélisation du magnétisme statique et dynamique pour le génie électrique." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00839041.
El, Achouri-Ait Lamine Ghizlane. "Rôle des isoformes de la dynamine mitochondriale OPA1 : identification d'une nouvelle fonction dans le maintien de l'intégrité du génome mitochondrial." Montpellier 1, 2009. http://www.theses.fr/2009MON1T031.
Mitochondria is an intracellular organelle from bacterial origin with its own genome, which plays key roles in energy metabolism and apoptosis. The mitochondrial dynamics resu1ting from fusion and fission of the membranes, leading to a change in the morphology of mitochondrial network. The mitochondrial dynamin OP Al plays a key role in structuring the inner membrane required for fusion of the mitochondrial network, energy metabolism, and control of apoptosis. OP A1 is also responsible for the Dominant Optic Atrophy, and it exist's in the fonn of 8 isofonns generated by alternative splicing of 3 exons: 4, 4b and Sb. The objective of my thesis was to study the functions associated with different isofonns of OP A1. I have shown that variants containing exon 4 are involved in mitochondrial fusion, whereas variants containing exon Sb, are invojved in apoptosis, by structuring the cristae junctions responsible for mitochondnal cytochrome c trapping in the intra-cristae volume Furthemore, I demonstrated for the first tune m mammals a link between OPA1-4b and the maintenance of mitochondrial genome Indeed, I show that the peptide resulting from cleavage of OP AI-4b, allows anchoring the nucleoid to the inner membrane, a process essential for the initiation of replication and distribution of nucleoids. These observations corroborate the work produced in yeast with MGMI/Mspl, the orthologs of OPA1, and help define a new concept correlating the dynamics of inner mitochondrie membrane to maintain the integrity of the mitochondrial genome