Global ETD Search

1	Evolution, connectivity, and resilience in deep-sea chemosynthetic-based ecosystems Perez, Maeva 05 1900 (has links) La machinerie pour l’exploitation des ressources minérales qui se trouvent au fond des océans est déjà opérationnelle et la délivrance de permis miniers est imminente malgré d’inquiétantes lacunes de connaissances sur ces écosystèmes. En effet, dans une optique de sauvegarde, il est particulièrement important de mieux connaître les processus clés de l’écologie des profondeurs. Quelles sont les conséquences évolutives de la symbiose si répandue dans les écosystèmes profonds? Comment les sources hydrothermales sont-elles connectées? Quelles adaptations permettent la résilience des espèces endémiques de ces milieux? Dans le Pacifique est, la faune hydrothermale est caractérisée par de denses populations de palourdes de la famille Vesicomyidae et de vers polychètes tubicoles qui servent de niche à une multitude d'autres espèces. Ces deux groupes d'invertébrés dépendent pour leur nutrition de bactéries symbiotiques chimiolithotrophes. Celles-ci sont directement transmises de génération en génération chez les palourdes, et acquises de novo à partir de sources environnementales chez les vers. De plus, les vers possèdent une grande plasticité phénotypique associée aux conditions environnementales très variées (en terme de température, d’oxygène et de concentration de minéraux) dans lesquelles ils se retrouvent. Du fait du contraste dans leurs mode de transmission des symbiotes, de leur distribution étendue, et de leur rôle écologique important, ces deux groupes taxonomiques sont un excellent modèle pour étudier l’évolution, la connectivité et la résilience dans les écosystèmes marins profonds basés sur la chimiosynthèse. Ainsi, les objectifs de ma thèse sont de 1) déterminer les conséquences du mode de transmission des symbiotes sur leur évolution, 2) comparer la connectivité inter-sources entre les populations d’hôtes et de symbiotes, et 3) caractériser la méthylation de l'ADN chez les polychètes des sources hydrothermales et déterminer si ce mécanisme épigénétique joue un rôle adaptatif important. Ces objectifs sont abordés dans trois études indépendantes qui révèlent que 1) des processus à la fois neutres et sélectifs façonnent les génomes des symbiotes bactériens, 2) les populations de symbiotes bactériens dans les cheminées hydrothermales ne sont pas panmictiques mais sont influencées par des modèles locaux de connectivité, et 3) la méthylation de l'ADN est un mécanisme important d'adaptation dans les grands fonds marins. Ultimement, ces études permettent d'établir des lignes directrices en matière de conservation pour les opérations minières, et aident à l’établissement d’aires marines protégées. / The mining industry is ready to exploit the mineral resources lying on the seafloor and the issuing of mining permits is imminent despite concerning knowledge gaps about the key evolutionary and ecological processes at play in these ecosystems. What are the evolutionary consequences of symbioses which are ubiquitous in deep-sea benthic ecosystems? How are chemosynthetic-based ecosystems connected? What kind of adaptations enable the resilience of vent endemic species to their extreme environment? In the eastern Pacific, chemosynthetic-based communities are characterized by dense aggregations of vesicomyid clams (in hydrocarbon seeps) or tubeworms (in hydrothermal vents) both of which offer habitat for many other species. Both invertebrates rely on chemolithotrophic bacteria for their nutrition. In the clams these symbionts are transmitted directly to the next generation through the eggs whereas in the tubeworms the symbionts are acquired de novo from the environment. The tubeworms also display striking phenotypic plasticity according to the physico-chemical conditions of their habitat. Because of their contrasting symbiont transmission mode, extended distribution, and ecological significance, these two taxonomic groups constitute an excellent model to study evolution, connectivity, and resilience in deep-sea chemosynthetic-based ecosystems. Thus, the objective of my thesis are to 1) identify the consequences of symbiont transmission mode on their evolution, 2) compare host and symbiont populations connectivity, and 3) characterize DNA methylation in deep-sea polychaetes and assess whether this epigenetic mechanism could explain their resilience. These objectives were addressed in three independent studies which revealed that 1) both neutral and selective processes participate in shaping the genomes of bacterial symbionts, 2) the populations of bacterial symbionts in hydrothermal vents are not panmictic but are influenced by local patterns of connectivity, and 3) DNA methylation is an important mechanism of adaptation in the deep-sea. Ultimately, these studies provide conservation guidelines for mining operations and help with the establishment of marine protected areas. Génomique Épigénomique Microbiologie Symbiose Évolution Genomic Epigenomic Microbiology Symbiosis Evolution Biology / Biologie (UMI : 0306)
2	Microfluidics for low input epigenomic analysis and application to oncology and brain neuroscience Liu, Zhengzhi 07 September 2023 (has links) Microfluidics is a versatile tool with many applications in biology. Its ability to manipulate small volumes of liquid precisely has led to the development of many microfluidic assay platforms. They could handle small amounts of samples and carry out analysis with high sensitivity and throughput. Microfluidic assays have provided new insights into scarce biological samples at higher resolution. In this thesis, we developed microfluidic tools to conduct low input ChIP-seq and ChIRP-seq. We applied them to a variety of samples profiling different targets. The native MOWChIP-seq platform was developed to map RNA polymerase II, transcription factors and histone deacetylase binding in 1,000-50,000 cells. We examined mouse prefrontal cortex and cerebellum using this technology. We found extensive differences that correlated with distinct neurological functions of the brain regions. The same platform and workflow were used to profile five key histone modifications in human lung tumor and normal tissue samples. Integrative analysis with gene expression data revealed extensive chromatin remodeling in lung tumor. Spatial histone modification mapping was conducted in mouse neocortex in a similar fashion. We generated an epigenomic tomography that demonstrated the molecular state of the brain in 3D. Lastly, we developed a microfluidic version of the ChIRP-seq process which successfully conducted the assay using only 500K cells. This improvement makes ChIRP-seq in tissue samples feasible. / Doctor of Philosophy / Microfluidics is a type of technology that can control small volumes of liquid in a miniature system. It can carry out reactions on very small scales with higher precision and sensitivity than conventional methods. Microfluidics has found many uses in the field of biology, especially dealing with samples available in limited quantities. These low input microfluidic platforms have helped researchers gain new knowledge on many complex questions. In this thesis, we developed microfluidic tools to carry out low input ChIP-seq and ChIRP-seq. These are two established techniques used to map where certain targets are located on the genome of an organism. These targets include specific chemical modifications to the wrapper protein of DNA (histone modification), proteins that take part in transcription and expression of genes (RNA polymerase II, transcription factors) and other molecules. Our nMOWChIP-seq system removed the need for fixation by chemicals. It was able to examine RNA polymerase II, transcription factors and other enzymes using 1,000-50,000 cells. Traditional ChIP-seq requires more than 10 million cells and time-consuming chemical treatment steps. Our technology greatly improved sensitivity and ease of use. We also used this platform to test five important histone modifications in human lung tumors and healthy tissues. We constructed a spatial map of histone modification in mouse brain by analyzing slices of the cortex. Finally, we developed a microfluidic version of ChIRP-seq process to map locations of long non-coding RNAs in cultured human cells. The cells needed for a successful test were reduced to 500K from 20 million of the original workflow. microfluidics epigenome chromatin immunoprecipitation next generation sequencing histone modification RNA polymerase II transcription factor chromatin isolation by RNA purification epigenomic tomography non-small cell lung cancer
3	Etude des variations épigénétiques liées aux séquences répétées comme source de changements phénotypiques héritables chez Arabidopsis thaliana / Study of epigenetic changes associated with repeated sequences as a source of heritable phenotypic changes in Arabidopsis thaliana Cortijo, Sandra 10 September 2012 (has links) Des changements de méthylation de l’ADN peuvent affecter l’expression des gènes et pour certains être transmis au travers des générations. De telles « épimutations » qui concernent des groupes de cytosines à proximité ou dans les gènes sont donc une source potentielle de variation phénotypique héritable en absence de changements de la séquence de l’ADN. Chez les plantes la méthylation de l’ADN est cependant principalement observée au niveau des séquences répétées. Il reste à déterminer dans quelle mesure les changements de méthylation au niveau de ce type de séquences peuvent être héritées et affecter les phénotypes. Afin de répondre à ces questions, plus de 500 épiRIL (epigenetic Recombinant Inbred Lines) quasi-isogéniques a été générée chez Arabidopsis thaliana. Cette population a été obtenue par le croisement d’un parent sauvage et d’un parent mutant pour le gène DDM1 présentant une très forte réduction du taux de méthylation de l’ADN. Après un rétrocroisement de la F1 avec une plante sauvage, les individus sauvages pour le gène DDM1 ont été sélectionnés et propagées sur 6 générations par autofécondation. Nous avons montré par l’analyse du méthylome de plus de 100 épiRIL que l’hypométhylation induite par ddm1 présente selon les séquences affectées différents degrés de transmission au travers des générations. La réversion de l’hypométhylation concerne des régions associées à une abondance élevée en sRNA de 24 nt. Nous avons utilisé l’hypométhylation stablement transmise dans les épiRIL induite par ddm1 afin de détecter des QTL (Quantitative Trait Loci) affectant le temps de floraison et la longueur de la racine primaire, deux caractères pour lesquels les variations observées dans les épiRIL présentent une héritabilité importante. En dernier lieu, nous avons recherché par différentes approches les variations causales de ces QTL. / Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations, which concern clusters of cytosines located near or within genes, are thus a source of heritable phenotypic variation in the absence of DNA sequence change. In plants however, DNA methylation targets repeat elements predominantly and it remains unclear to which extent DNA methylation changes over repeat sequences can be inherited and affect phenotypes. To address these issues, a population of near-isogenic, epigenetic Recombinant Inbred Lines (epiRILs) was generated in Arabidopsis thaliana. These were derived from a cross between a wild type and an isogenic ddm1 mutant line, in which DNA methylation is compromised specifically over repeat elements. After backcrossing of the F1 and selection of the progeny homozygous for wild-type DDM1, the epiRILs were propagated through six rounds of selfing. Analysis of the methylomes of more than 100 epiRILs and of the parents, indicates that ddm1-induced hypomethylation exhibit different patterns of inheritance through generations. Reversion of ddm1-induced hypomethylation is observed for regions associated with high level of 24 nt siRNA. Based on these findings, stable ddm1-induced hypomethylated regions were used to map quantitative trait loci (QTL) for flowering time and primary root length, two complex traits for which substantial heritable variation is observed in the epiRIL population. We finally analysed these QTL by different approaches to find their causal variations. Epigénétique Méthylation de l’ADN Epigénomique Quantitative trait locus Génétique quantitative Racine Arabidopsis thaliana Epigenetic DNA methylation Epigenomic Quantitative trait locus Quantitative genetic Root Arabidopsis thaliana
4	A Novel Approach to Identify Candidate Imprinted Genes in Humans Shapiro, Jonathan 21 March 2012 (has links) Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood. Allele Allele-specific DNA Methylation Allele-specific Gene Expression Allele-specific Expression Allele-specific Methylation AnCHM Androgenetic Androgenetic Mole Mole Complete Mole Hydatidiform Mole Complete Hydatidiform Mole Androgenetic Hydatidiform Mole Androgenetic Complete Hydatidiform Mole Biparental Tissue Bisulfite Bisulphite Blood Blood DNA Computational Biology DNA Methylation DNA Methylation Profiling Epigenetic Epi-genetic Epigenomic Epi-genomic Expression Expression Regulation Gene Expression Gene Expression Regulation Genetic Genetic Imprint Genetic Imprinting Genomic Genomic DNA Genomic Imprint Genomic Imprinting Human Imprint Imprinting Teratoma Ovarian Teratoma Cystic Teratoma Mature Teratoma Mature Cystic Teratoma Mature Ovarian Teratoma Cystic Ovarian Teratoma Mature Cystic Ovarian Teratoma MCT Methylation Cytosine Methylation Microarray Neoplasm Ovarian Neoplasm Placenta Profiling Promoter Promoter Region Sodium Bisulfite Sodium Bisulphite Uniparental Tissue WB WBC Imprinted Gene Polymorphic Imprinting Parent-of-origin Parent-of-origin-specific Methylation Parent-of-origin-specific Expression 0369 0307
5	A Novel Approach to Identify Candidate Imprinted Genes in Humans Shapiro, Jonathan 21 March 2012 (has links) Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood. Allele Allele-specific DNA Methylation Allele-specific Gene Expression Allele-specific Expression Allele-specific Methylation AnCHM Androgenetic Androgenetic Mole Mole Complete Mole Hydatidiform Mole Complete Hydatidiform Mole Androgenetic Hydatidiform Mole Androgenetic Complete Hydatidiform Mole Biparental Tissue Bisulfite Bisulphite Blood Blood DNA Computational Biology DNA Methylation DNA Methylation Profiling Epigenetic Epi-genetic Epigenomic Epi-genomic Expression Expression Regulation Gene Expression Gene Expression Regulation Genetic Genetic Imprint Genetic Imprinting Genomic Genomic DNA Genomic Imprint Genomic Imprinting Human Imprint Imprinting Teratoma Ovarian Teratoma Cystic Teratoma Mature Teratoma Mature Cystic Teratoma Mature Ovarian Teratoma Cystic Ovarian Teratoma Mature Cystic Ovarian Teratoma MCT Methylation Cytosine Methylation Microarray Neoplasm Ovarian Neoplasm Placenta Profiling Promoter Promoter Region Sodium Bisulfite Sodium Bisulphite Uniparental Tissue WB WBC Imprinted Gene Polymorphic Imprinting Parent-of-origin Parent-of-origin-specific Methylation Parent-of-origin-specific Expression 0369 0307

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