Dissertations / Theses: 'Genomics analyses'

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Seibert, Sara Rose. "Host-parasite interactions: comparative analyses of population genomics, disease-associated genomic regions, and host use." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1590585260282244.

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Steinberg, Julia. "Functional genomics analyses of neuropsychiatric and neurodevelopmental disorders." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:e47d1ac2-de92-47d8-864b-dac0bf6669e8.

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Recent large-scale genome-wide studies for many human disorders have identified associations with numerous genetic variants. The biological interpretation of these variants presents a major challenge. In particular, the identification of biological pathways underlying the association could provide crucial insights into the disease aetiologies. In this thesis, I used functional genomics approaches to increase our understanding of neuropsychiatric and neurodevelopmental disorders. Firstly, in an integrative analysis of autism spectrum disorder (ASD), I looked into the role of genes targeted by Fragile-X Mental Retardation Protein ("FMRP targets"). I found evidence that FMRP targets contribute to ASD via two distinct aetiologies: (1) ultra-rare and highly penetrant single disruptions of embryonically upregulated FMRP targets ("single-hit aetiology") or (2) the combination of multiple less penetrant disruptions of synaptic FMRP targets ("multiple-hit aetiology"). In particular, I developed a pathway-association test sensitive to multiple-hit aetiologies. Secondly, I carried out an integrative analysis of bipolar disorder, following up a previously identified association with long-term potentiation. The association was not consistent across independent SNP and CNV datasets. Thirdly, I addressed the difficulty in identifying functional relationships between genes by integrating different datasets into a gene functional-linkage network tuned to the nervous system ("NsNet"). NsNet identified functional links between the genes disrupted by de novo loss-of-function mutations in ASD and, separately, in schizophrenia probands more sensitively than a general functional-linkage network. Fourthly, I considered the challenge of interpreting the phenotypic impact of gene disruptions, focusing on the identification of haploinsufficient genes. I constructed a gene haploinsufficiency score based on genome-wide datasets. Compared to existing approaches, the new score performed better in identifying less-studied haploinsufficient genes. This work both extends the methodology to detect the contribution of genetic variation to neuropsychiatric disorders and also yields insights into the variant genes and the pathways that underlie them. Firstly, in an integrative analysis of autism spectrum disorder (ASD), I looked into the role of genes targeted by Fragile-X Mental Retardation Protein ("FMRP targets"). I found evidence that FMRP targets contribute to ASD via two distinct aetiologies: (1) ultra-rare and highly penetrant single disruptions of embryonically upregulated FMRP targets ("single-hit aetiology") or (2) the combination of multiple less penetrant disruptions of synaptic FMRP targets ("multiple-hit aetiology"). In particular, I developed a pathway-association test sensitive to multiple-hit aetiologies. Secondly, I carried out an integrative analysis of bipolar disorder, following up a previously identified association with long-term potentiation. The association was not consistent across independent SNP and CNV datasets. Thirdly, I addressed the difficulty in identifying functional relationships between genes by integrating different datasets into a gene functional-linkage network tuned to the nervous system ("NsNet"). NsNet identified functional links between the genes disrupted by de novo loss-of-function mutations in ASD and, separately, in schizophrenia probands more sensitively than a general functional-linkage network. Fourthly, I considered the challenge of interpreting the phenotypic impact of gene disruptions, focusing on the identification of haploinsufficient genes. I constructed a gene haploinsufficiency score based on genome-wide datasets. Compared to existing approaches, the new score performed better in identifying less-studied haploinsufficient genes. This work both extends the methodology to detect the contribution of genetic variation to neuropsychiatric disorders and also yields insights into the variant genes and the pathways that underlie them.

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Beghini, Francesco. "Integrative computational microbial genomics for large-scale metagenomic analyses." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/296396.

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Advancements of DNA sequencing technologies and improvement of analytic methods changed the way we analyze complex microbial communities (metagenomics). In only a few years, these methods have evolved so far as to ease a more precise community profiling and to allow high-level strain resolution. A typical computational metagenomic analysis relies on mapping raw DNA sequencing reads against sets of “reference” microbial genomes usually obtained through single-isolate sequencing. With an almost exponential increase in the number of reference genomes deposited daily in public data sets, current computational methods are incapable of managing and exploiting such a rich reference set, limiting the potential of metagenomic investigations.In my doctoral thesis, I will present my contribution towards fully exploiting the available reference data for metagenomic analysis. I developed ChocoPhlAn, an integrated pipeline for automatic retrieval, organization, and annotation of reference genomes and gene families as the foundation for bioBakery 3, an improved set of computational methods for the analysis of shotgun metagenomics data. Using the latest set of microbial genomic reference data available and processed through ChocoPhlAn, the six bioBakery 3 tools that I updated resulted in more comprehensive and higher resolution taxonomic and functional profiling of microbiomes and allowed strain-level characterization of their constituent strains. After extensive benchmarks with previous versions and competitors, we applied those methods on more than 10,000 real metagenomes and showed how metagenomics can be a more powerful tool for identifying novel links between the gut microbiome and disease conditions such as colorectal cancer and Inflammatory Bowel Disease. Accurate strain-level phylogeny reconstruction and pangenomic analysis of 7,783 metagenomes revealed novel functional, phylogenetic, and geographic diversity of Ruminococcus bromii, a common and highprevalent gut inhabitant. We then focused on the influence of the Eukaryotic fraction of the human microbiome and its potential impact on human gut health, which is a frequently overlooked aspect of microbial communities. To this end, we assessed the presence of the Eukaryotic parasite Blastocystis spp., in more than 2,000 metagenomes from 5 continents for understanding associations with disease statuses and geographic conditions. We showed that Blastocystis is the most common Eukaryotic colonizer of the human gut, and it is particularly prevalent in healthy subjects and non-westernized populations. We further explored intra-subtype diversity by reconstructing and functionally profiling new metagenomic-assembled Blastocystis genomes, showing how metagenomics can be valuable to unravel protists' genomics and providing a genomic resource for additional integration of non-bacterial taxa in metagenomic pipelines.9 By developing and implementing ChocoPhlAn and the new bioBakery tools, we provided the community with improved and efficient microbiome profiling tools and started identifying novel patterns of association between host and niche-associated microbiomes and discovering previously uncharacterized species from human and non-human hosts.

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Shultz, Randall William. "Genomic and Molecular Analyses of the Core DNA Replication Machinery in Plants." NCSU, 2007. http://www.lib.ncsu.edu/theses/available/etd-03132007-124000/.

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Accurate and complete DNA replication is essential for maintaining the integrity of the genome. In eukaryotes, this process requires the coordinated action of numerous molecular machines. Based on yeast and animal model systems, we defined a set of fifty-one ?core DNA replication proteins? that are integral to the initiation, DNA synthesis, and Okazaki fragment maturation functions of DNA replication. We used computational analyses to identify putative homologs in the genomes of two plants, Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice), providing the first comprehensive view of the core DNA replication machinery in plants. Our results indicated that the overall composition of this apparatus is conserved, but plants are unique in that multiple DNA replication genes exist as small gene families. Fourteen of the genes we annotated in this study have not been previously reported in the literature, and we have provided revised gene models for seventeen plant proteins. To better understand how the DNA replication machinery functions in plants, we cloned multiple subunits of the pre-replication complex (pre-RC) from Arabidopsis and generated antibodies against four key components of this complex ? AtORC1, AtORC2, AtMCM5, and AtMCM7. We demonstrated that the pre-RC is developmentally regulated in Arabidopsis and, consistent with a role in DNA replication, is abundant in proliferating tissues. We used immunocytochemical and biochemical methods to characterize MCM7 in plants. We observed two distinct localization patterns for plant MCM7 proteins. In most cells, MCM7 was nuclear and colocalized with DNA. In a small fraction of cells, MCM7 was dispersed throughout the cytoplasmic compartment. Biochemical analysis confirmed that MCM7 binds to chromatin and that it is present in the nucleus at least during the G1, S and G2 cell cycle stages. Together, these analyses support a model where the MCM complex is loaded onto DNA in late M and early G1, released into the nucleoplasm during S phase followed by a brief dispersion into the cytoplasmic compartment concurrent with nuclear envelope breakdown in mitosis.

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Herzog, Rebecca [Verfasser]. "Global change genomics - comparative genomic analyses on environmental associated speciation and adaptation processes in Odonata / Rebecca Herzog." Hannover : Gottfried Wilhelm Leibniz Universität, 2021. http://d-nb.info/1238221785/34.

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Soares, Siomar de Castro. "Pan-genomic analyses of Corynebacterium pseudotuberculosis and characterization of the biovars ovis and equi through comparative genomics." Universidade Federal de Minas Gerais, 2013. http://hdl.handle.net/1843/BUOS-9B8JTZ.

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Corynebacterium pseudotuberculosis is the causative agent of diverse communicable diseases in small ruminants (biovar ovis), horses, camels, buffalo and other animals (biovar equi), which mainly differ in symptoms and site of infection. Additionally, the diseases present a highly important economic problem worldwide and there is still a lack of efficient treatments against C. pseudotuberculosis. In this work, we describe the steps from the first genome sequencing of a strain of C. pseudotuberculosis to the pangenomic analyses of 15 strains isolated from different hosts and countries with diverse symptoms. Briefly, we introduce the genus Corynebacterium and the in silico analyses performed in pathogenic species of this genus to date. Then, we describe the implementation of a software for the prediction of pathogenicity islands (PAIs) in bacteria (PIPS), which outperformed the other available software, and identified 7 PAIs with important virulence factors in C. pseudotuberculosis biovar ovis. Moreover, we extend the analyses of PAIs to strains of C. pseudotuberculosis biovar equi and predict 49 putative vaccine targets, in silico, which are commonly shared by both biovars, ovis and equi. Finally, we present the phylogenomic, pan-genomic, core genomic, singletons and genomic plasticity analyses of the 15 strains of C. pseudotuberculosis, from both biovars. All the analyses performed here point for a clonal-like behavior of C. pseudotuberculosis, which could be the result of the facultative intracellular behavior of the species. Moreover, the biovar equi presents a higher variability in gene content when compared to biovar ovis, specially in PAI regions. Noteworthy, the strains from biovar ovis present a high degree of similarity in pili clusters of genes, whereas the biovar equi strains are very variable. The conservation of pili clusters of genes in biovar ovis could account for the ability of these strains to spread inside host tissues and penetrate live cells to live intracellularly, where they would have less contact to other organisms, thus, possibly explaining the clonal-like behavior of the biovar ovis.

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Itou, Junji. "Functional and comparative genomics analyses of pmp22 in medaka fish." Kyoto University, 2009. http://hdl.handle.net/2433/126464.

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Dumitriu, Alexandra. "Genome-wide expression and genomic data integration analyses in sporadic Parkinson disease." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31542.

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Thesis (Ph.D.)--Boston University
Parkinson disease (PD) is the second most common neurodegenerative disorder, affecting an estimated 2% of the population above 65 years of age. Although familial forms of PD have been linked to specific mutations responsible for the onset of the disease, the majority of PD cases is still of unknown etiology. PD has been traditionally studied using individual genetic methods, such as linkage analysis, genome-wide association (GWAS), or microarray expression studies. Nevertheless, the intrinsic disease genetic variability, and the unilateral analysis approach of available datasets made the detection of robust gene or pathway signals difficult. Studies of PD that combine a range of systems genetics approaches, and integrate complementary disease-relevant genetic datasets, represent a promising approach for accommodating prior inconsistent, as well as diverse results. To investigate the genetics of idiopathic PD, I performed the largest genome-wide expression study in brain tissue to date. The study was carried out on the 1-color Agilent 60-mer Whole Human Genome Microarray, and included 26 neurologically healthy control and 27 PD samples from the frontal cortex Brodmann 9 area (BA9). The selected brain samples were of high quality (high pH and RNA integrity, no significant signs of Alzheimer disease pathology), and had rich documentation of neuropathological and clinical information available. I analyzed the microarray expression results in combination with genotyping data for PD-associated single nucleotide polymorphisms obtained for the microarray brain samples, and detected a pathway of interest for PD involving the FOXO1 (Forkhead box protein O1) gene. This result was verified in additional publically available expression datasets. I then performed a network-based canonical pathway analysis of PD, combining results from available GWAS, microarray expression, and animal model expression studies. The used analysis framework was a human functional-linkage network (FLN), consisting of genes as nodes, and weighted links indicating the confidence of gene-pair involvement in similar biological processes. I demonstrated the relevance of the used FLN for studying PD. Additionally, I ranked genes and pathways based on the available disease datasets. The frontal cortex BA9 study, and an additional non-PD microarray study were used as the positive and negative controls, respectively, for the obtained results.

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Dumitriu, Alexandra. "Genome-wide expression and genomic data integration analyses in sporadic Parkinson Disease." Thesis, Boston University, 2010. https://hdl.handle.net/2144/31542.

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Thesis (Ph.D.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
Parkinson disease (PD) is the second most common neurodegenerative disorder, affecting an estimated 2% of the population above 65 years of age. Although familial forms of PD have been linked to specific mutations responsible for the onset of the disease, the majority of PD cases is still of unknown etiology. PD has been traditionally studied using individual genetic methods, such as linkage analysis, genome-wide association (GWAS), or microarray expression studies. Nevertheless, the intrinsic disease genetic variability, and the unilateral analysis approach of available datasets made the detection of robust gene or pathway signals difficult. Studies of PD that combine a range of systems genetics approaches, and integrate complementary disease-relevant genetic datasets, represent a promising approach for accommodating prior inconsistent, as well as diverse results. To investigate the genetics of idiopathic PD, I performed the largest genome-wide expression study in brain tissue to date. The study was carried out on the 1-color Agilent 60-mer Whole Human Genome Microarray, and included 26 neurologically healthy control and 27 PD samples from the frontal cortex Brodmann 9 area (BA9). The selected brain samples were of high quality (high pH and RNA integrity, no significant signs of Alzheimer disease pathology), and had rich documentation of neuropathological and clinical information available. I analyzed the microarray expression results in combination with genotyping data for PD-associated single nucleotide polymorphisms obtained for the microarray brain samples, and detected a pathway of interest for PD involving the FOXO1 (Forkhead box protein O1) gene. This result was verified in additional publically available expression datasets. I then performed a network-based canonical pathway analysis of PD, combining results from available GWAS, microarray expression, and animal model expression studies. The used analysis framework was a human functional-linkage network (FLN), consisting of genes as nodes, and weighted links indicating the confidence of gene-pair involvement in similar biological processes. I demonstrated the relevance of the used FLN for studying PD. Additionally, I ranked genes and pathways based on the available disease datasets. The frontal cortex BA9 study, and an additional non-PD microarray study were used as the positive and negative controls, respectively, for the obtained results.
2031-01-01

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Dunning, Mark J. "Genome-wide analyses using bead-based microarrays." Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/218542.

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Microarrays are now an established tool for biological research and have a wide range of applications. In this thesis I investigate the BeadArray microarray technology developed by Illumina. The design of this technology is unique and gives rise to many computational and statistical challenges. However, I show how knowledge from other microarray technologies can be used to our advantage. I describe the beadarray software package, which is now used by researchers around the world. The development of this software was motivated by the fact that Illumina's software (BeadStudio) gives a summarised view of Illumina data and does not gives users any control over several processing steps that were found to be crucial for other microarray technologies. A main feature of beadarray is the ability to access raw data. The advantages of such data include the ability to perform more detailed quality assessment and greater control over the analysis at all stages. The analysis of a control experiment shows that the processing steps used in BeadStudio can be improved. In particular, utilising variances calculated from the raw data can increase the ability to detect genes which have different expression levels between samples, a common goal for microarray studies. The data from the control experiment are made available for other researchers to use and validate their own analysis methods. One issue discovered during the analysis of the control experiment was that only half of the intended genes could be reliably measured due to problems in the design of the probes targetting particular genes. By considering a large set of publicly available Illumina arrays, I show how such unreliable measurements can affect the analysis of Illumina data. I also show how potential problems can be identified in advance of an experiment and incorporated into an analysis pipeline.

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Anastasi, Elisa. "Comparative genomics and emerging antibiotic resistance in Rhodococcus equi." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25887.

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Rhodococcus equi is a soil-dwelling facultative intracellular pathogen that can infect many mammals, including humans. R. equi is most well known for its ability to cause severe pyogranulomatous disease in foals, primarily involving the lungs although other body systems may also be affected. The disease is endemic on many horse-breeding farms worldwide and poses a severe threat to the horse breeding industry because there is no vaccine available. Current prophylaxis is based on systematic preventative treatments with macrolides combined with rifampicin, which are also used to treat clinical cases of the disease in foals. In this thesis I have used a combination of wet laboratory and bioinformatic approaches to identify the molecular basis of emerging combined resistance to macrolides and rifampicin in R. equi foal isolates from the USA. The genomes of a selection of resistant and susceptible strains from across the USA were sequenced and assembled. Resistance genes were systematically searched by reciprocal best-match BLASTP comparisons to known antibiotic resistance determinants. This led to the discovery of a novel erythromycin ribosomal methylase (erm) gene, erm(46), in all resistant strains. Complementation analysis in a susceptible R. equi strain showed that erm(46) was sufficient to confer resistance to all macrolides, lincosamides, and streptogramin B. The erm(46) gene is carried by an integrative conjugative element (ICE) which is transferable between R. equi strains. The ICE is formed by two distinct parts, a class I integron associated with an IS6100 sequence and the erm(46) determinant carried by a sub-element which contains putative actinobacterial conjugative translocase apparatus and a transposase/integrase. All resistant strains also carry the same non synonymous point mutation in rpoB conferring rifampicin resistance. Thus, these strains are carrying double resistance to the most commonly used antibiotics to treat R. equi worldwide. Phylogenetic analysis based on the core genome demonstrated that all resistant strains are clonal. This indicates that although conjugal acquisition of the erm(46) conjugative element may occur at a high frequency, the need for the concurrent presence of a second rpoB mutation for survival in the macrolide and rifampicin dominated farm environment has effectively selected for the spread of a single clone. In the second section of this work, we sequenced a further 20 R. equi genomes from difference sources (equine, porcine, bovine, human), including representatives of each of the seven major genogroups previously defined in our laboratory based on pulsed field gel electrophoresis. I have used the newly acquired genetic information to study the genome of R. equi and analyse its diversity within and outwith its species group. This enabled us to explore the pan genome and define that R. equi is a genetically well-defined bacterial species. Our results provide definitive evidence that resolves the current dispute over R. equi classification, specifically they do not support the recent proposal (based on classical polyphasic bacterial taxonomical methods) that R. equi should be transferred to a new genus. Our core-genome phylogenomic analyses unambiguously show that the genus Rhodocococcus is monophyletic and that R. equi forms a clade together with the most recently described related environmental species R. defluvii that radiates from within the genus. Together with other shared biological and genetic characteristics, namely the unique niche-adaptive mechanism based on evolutionarily related extrachromosomal replicons, R. equi should be conseidered a bona fide member of the genus Rhodococcus. We also confirm that Rhodococcus spp. and Nocardia spp. are sufficiently distinct to warrant them belonging to different genera. In conclusion, this work used whole genome sequencing to characterize the molecular basis underlying the emergence and clonal spread of multi-resistant R. equi in horse breeding farms in the USA. This work also highlights the limitations of classical taxonomical approaches in bacterial systematics, and illustrates the importance of incorporating modern phylogenomic approaches to understand the evolutionary relationships between bacterial strains and their accurate taxonomic position.

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Kamps-Hughes, Nicholas. "Massively Parallel Sequencing-Based Analyses of Genome and Protein Function." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19234.

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The advent of high-throughput DNA and RNA sequencing has made possible the assay of millions of nucleic acid molecules in parallel. This allows functional genomic elements to be identified from background in single-tube experiments. This dissertation discusses the development of two such functional screens as well as work implementing a third that was previously developed in my thesis laboratory. Restriction-Associated DNA sequencing (RAD-Seq) is a complexity reduction sequencing method that allows the same subset of genomic sequence to be read across multiple samples. Differences in sample collection and data analysis allow manifold applications of RAD-Seq. Here we use RAD-Seq to identify mutant genes responsible for altered phenotypes in Caenorhabditis elegans and to identify hyper-invasive alleles in trout population admixtures. Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. This dissertation describes the development of a technique for simultaneously quantifying the activity of a restriction enzyme across all possible DNA substrates by linking digest of a sequenced genome to Illumina-sequencing in an unbiased fashion. Finally, a powerful approach to analyze transcriptional activation is described. This method quantifies output from millions of potential DNA transcriptional enhancers via RNA amplicon sequencing of covalently-linked randomer tags and is used in conjunction with RNA-Seq to provide a mechanistic view of hypoxic gene regulation in Drosophila. This dissertation includes previously published, co-authored material

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Endo, Yoshinori. "Comparative study of mammalian evolution by genomic analyses and pluripotent stem cell technology." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263514.

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Yang, Bo. "Analyses bioinformatiques et classements consensus pour les données biologiques à haut débit." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112250/document.

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Cette thèse aborde deux problèmes relatifs à l’analyse et au traitement des données biologiques à haut débit: le premier touche l’analyse bioinformatique des génomes à grande échelle, le deuxième est consacré au développement d’algorithmes pour le problème de la recherche d’un classement consensus de plusieurs classements.L’épissage des ARN est un processus cellulaire qui modifie un ARN pré-messager en en supprimant les introns et en raboutant les exons. L’hétérodimère U2AF a été très étudié pour son rôle dans processus d’épissage lorsqu’il se fixe sur des sites d’épissage fonctionnels. Cependant beaucoup de problèmes critiques restent en suspens, notamment l’impact fonctionnel des mutations de ces sites associées à des cancers. Par une analyse des interactions U2AF-ARN à l’échelle génomique, nous avons déterminé qu’U2AF a la capacité de reconnaître environ 88% des sites d’épissage fonctionnels dans le génome humain. Cependant on trouve de très nombreux autres sites de fixation d’U2AF dans le génome. Nos analyses suggèrent que certains de ces sites sont impliqués dans un processus de régulation de l’épissage alternatif. En utilisant une approche d’apprentissage automatique, nous avons développé une méthode de prédiction des sites de fixation d’UA2F, dont les résultats sont en accord avec notre modèle de régulation. Ces résultats permettent de mieux comprendre la fonction d’U2AF et les mécanismes de régulation dans lesquels elle intervient.Le classement des données biologiques est une nécessité cruciale. Nous nous sommes intéressés au problème du calcul d’un classement consensus de plusieurs classements de données, dans lesquels des égalités (ex-aequo) peuvent être présentes. Plus précisément, il s’agit de trouver un classement dont la somme des distances aux classements donnés en entrée est minimale. La mesure de distance utilisée le plus fréquemment pour ce problème est la distance de Kendall-tau généralisée. Or, il a été montré que, pour cette distance, le problème du consensus est NP-difficile dès lors qu’il y a plus de quatre classements en entrée. Nous proposons pour le résoudre une heuristique qui est une nouvelle variante d’algorithme à pivot. Cette heuristique, appelée Consistent-pivot, s’avère à la fois plus précise et plus rapide que les algorithmes à pivot qui avaient été proposés auparavant
It is thought to be more and more important to solve biological questions using Bioinformatics approaches in the post-genomic era. This thesis focuses on two problems related to high troughput data: bioinformatics analysis at a large scale, and development of algorithms of consensus ranking. In molecular biology and genetics, RNA splicing is a modification of the nascent pre-messenger RNA (pre-mRNA) transcript in which introns are removed and exons are joined. The U2AF heterodimer has been well studied for its role in defining functional 3’ splice sites in pre-mRNA splicing, but multiple critical problems are still outstanding, including the functional impact of their cancer-associated mutations. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to define ~88% of functional 3’ splice sites in the human genome. Numerous U2AF binding events also occur in other genomic locations, and metagene and minigene analysis suggests that upstream intronic binding events interfere with the immediate downstream 3’ splice site associated with either the alternative exon to cause exon skipping or competing constitutive exon to induce inclusion of the alternative exon. We further build up a U2AF65 scoring scheme for predicting its target sites based on the high throughput sequencing data using a Maximum Entropy machine learning method, and the scores on the up and down regulated cases are consistent with our regulation model. These findings reveal the genomic function and regulatory mechanism of U2AF, which facilitates us understanding those associated diseases.Ranking biological data is a crucial need. Instead of developing new ranking methods, Cohen-Boulakia and her colleagues proposed to generate a consensus ranking to highlight the common points of a set of rankings while minimizing their disagreements to combat the noise and error for biological data. However, it is a NP-hard questioneven for only four rankings based on the Kendall-tau distance. In this thesis, we propose a new variant of pivot algorithms named as Consistent-Pivot. It uses a new strategy of pivot selection and other elements assignment, which performs better both on computation time and accuracy than previous pivot algorithms

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Rana, Shivani [Verfasser], Michael [Gutachter] Bonkowski, Ludwig [Gutachter] Eichinger, Becker [Gutachter] Burkhard, and Raimund [Gutachter] Wegener. "Genomics analyses in kelp species / Shivani Rana ; Gutachter: Michael Bonkowski, Ludwig Eichinger, Becker Burkhard, Raimund Wegener." Köln : Universitäts- und Stadtbibliothek Köln, 2020. http://d-nb.info/122853442X/34.

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Dhladhla, Busisiwe I. R. "Enumeration of insect viruses using microscopic and molecular analyses: South African isolate of cryotophlebia leucotreta granulovirus as a case study." Thesis, Nelson Mandela Metropolitan University, 2012. http://hdl.handle.net/10948/d1008395.

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Baculoviruses have been used as biocontrol agents to control insect pests in agriculture since the 1970s. Out of the fifteen virus families known to infect insects, baculoviruses offer the greatest potential as insect biopesticides, due to their high host specificity which makes them extremely safe to humans, other vertebrates, plants and non-target microorganisms. They comprise of two genera: nucleopolyhedroviruses (NPVs) and granuloviruses (GVs). The South African isolate of Cryptophlebia leucotreta granulovirus (CrleGV-SA) which is infectious for the false codling moth (FCM), Thaumatotibia leucotreta, (Meyrick) (Lepidoptera: Tortricidae), has been successfully developed into two commercial biopesticides; Cryptogran® and Cryptex®, for the control of FCM in citrus crops. The current method of enumeration used for CrleGV-SA virus particles in routine experiments during the production of the GV as biopesticides, is dark field microscopy. However, due to the small size of GVs (300-500 nm in length), the technique is not easy to perform on these viruses, and no systemic comparison has been made of potential alternative methods. Therefore, the main objective of this study was to develop a quantitative enumeration method for CrleGV-SA occlusion bodies (OBs) which is accurate, reliable, and feasible, and compare the developed methods of enumeration to the current method. Purified and semi-purified CrleGV-SA viral stocks were prepared for enumeration studies using spectrophotometry, dark field microscopy, scanning electron microscopy (SEM) and real time qPCR. Spectrophotometry was found to be an unreliable method for enumeration of GVs in the production, standardisation, and quality control of biopesticides. Dark field microscopy and SEM were found to be accurate, and statistically comparable (p = 0.064) enumeration techniques. qPCR is currently being optimised for the enumeration of GVs. This technique was demonstrated to generate accurate standard curves for absolute quantification of virus particles for pure and semi-pure virus preparations. qPCR offers the greatest potential as an accurate enumeration method because it is not affected by contamination with non-biological contaminating debris, nor by other biological material due to the specificity of PCR primers. Further work is required to fully develop qPCR as an enumeration method for GVs. However, dark field microscopy has been successfully validated as an enumeration method. SEM, which has a high resolution compared to light microscopy, has an added advantage over dark field microscopy, which is to distinguish virus particles in semi-pure viral stock preparations during counting. Therefore, SEM currently provides the most unambiguous and feasible enumeration method for GVs in both purified and semi-purified virus samples.

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Rands, Chris M. D. "Analyses of functional sequence in mammalian and avian genomes." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:27e0ac20-eb27-423c-9493-a8a1c6cc57b8.

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The first draft sequence of the human genome was published over a decade ago, yet interpreting the functional importance of nucleotides in genomes is still an ongoing challenge. I took a comparative genomic approach to identify functional sequence using signatures of natural selection in DNA sequences. Mutations that are purged or propagated by selection mark sequences of significance for biological fitness. I developed and refined methods for estimating the quantity of sequence constrained with respect to insertions and deletions (indels) between two genome sequences, a quantity I termed α_selIndel. This sequence is evolving more slowly than surrounding neutral sequence due to the purging of deleterious indel variants, and thus this sequence is likely to be functional. I estimated α_selIndel between diverse mammalian and avian species pairs, and found a strong negative correlation between α_selIndel and the divergence between the species’ genome sequences. This implies that functional sequence turns over rapidly as it is lost and gained over time. I quantified the variable levels of sequence constraint, and rates of sequence turnover, for different types of human biochemically annotated element. Furthermore, I found that similar rates of functional turnover have occurred across mammalian and avian evolution. Finally, I identified positively selected amino acid residues that may be important for Darwin’s finch beak development, and found evidence of adaptively evolving reproductive proteins in the ancestral songbird lineage. Collectively these results demonstrate the wide-spread nature of lineage-specific functional sequence with implications for understanding species traits and the use of model organisms to inform human biology.

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Anani, Hussein. "La génomique bactérienne : un outil puissant pour la taxonomie et les analyses évolutives." Thesis, Aix-Marseille, 2020. http://theses.univ-amu.fr.lama.univ-amu.fr/200702_ANANI_94nya773wjmhky699k81cng_TH.pdf.

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La naissance de la génomique a révolutionné la classification des taxons bactériens. Actuellement, grâce au nombre élevé de génomes bactériens disponibles (> 250,000) et d'outils taxonomiques basés sur le génome, il est possible de réaliser des analyses phylogénomiques précises des bactéries pathogènes humaines. Au cours de notre thèse, nous avons d'abord mis en évidence l'intérêt des analyses pangénomiques en microbiologie clinique. De plus, la taxonomie des espèces de Bartonella, les agents de plusieurs maladies infectieuses humaines, étant mal connue, nous avons étudié 148 génomes de toutes les espèces de Bartonella afin de déterminer leur parenté génétique en utilisant plusieurs outils taxonomiques et généré leur premier pangénome. Par conséquent, nous avons défini des seuils spécifiques basés sur le génome pour la classification des isolats au niveau du genre et de l'espèce. De plus, en utilisant la stratégie culturomique, nous avons utilisé l'approche taxono-génomique pour décrire 25 nouveaux taxons bactériens isolés à partir d'un large éventail d'échantillons de différents pays. Nos résultats confirment donc qu'en 2020, la génomique permet de mettre à jour la taxonomie bactérienne traditionnelle et permet de mieux comprendre l'évolution bactérienne
The birth of genomics has revolutionized the classification of bacterial taxa. Currently, thanks to the high number of available bacterial genomes (> 250,000) and genome-based taxonomic tools, inferring accurate phylogenomic analyses of human pathogenic bacteria is achievable. During our thesis, we have first highlighted the usefulness of pangenomic analyses in clinical microbiology. In addition, since the taxonomy of Bartonella species, the agents of several human infectious diseases, is poorly understood, we have studied 148 genomes from all Bartonella species in order to determine their genetic relatedness by using several taxonomic tools and generated their first pangenome. Hence, we have defined specific genome-based thresholds for the classification of isolates at the genus and species levels. Furthermore, using the culturomics strategy, we used the taxono-genomics approach to describe 25 new bacterial taxa isolated from a wide spectrum of samples from different countries. Therefore, our results confirm that, in 2020, genomics enables updating the traditional bacterial taxonomy and help to better understand bacterial evolution

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Hammesfahr, Björn [Verfasser], Martin [Akademischer Betreuer] Kollmar, Burkhard [Akademischer Betreuer] Morgenstern, and Dirk [Akademischer Betreuer] Fasshauer. "Genomics and Phylogeny of Cytoskeletal Proteins: Tools and Analyses / Björn Hammesfahr. Gutachter: Burkhard Morgenstern ; Dirk Fasshauer. Betreuer: Martin Kollmar." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2013. http://d-nb.info/104405185X/34.

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Xu, Ke. "Comparative genomic and epigenomic analyses of human and non-human primate evolution." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52935.

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Primates are one of the best characterized phylogenies with vast amounts of comparative data available, including genomic sequences, gene expression, and epigenetic modifications. Thus, they provide an ideal system to study sequence evolution, regulatory evolution, epigenetic evolution as well as their interplays. Comparative studies of primate genomes can also shed light on molecular basis of human-specific traits. This dissertation is mainly composed of three chapters studying human and non-human primate evolution. The first study investigated evolutionary rate difference between sex chromosome and autosomes across diverse primate species. The second study developed an unbiased approach without the need of prior information to identify genomic segments under accelerated evolution. The third study investigated interplay between genomic and epigenomic evolution of humans and chimpanzees. Research advance 1: evolutionary rates of the X chromosome are predicted to be different from those of autosomes. A theory based on neutral mutation predicts that the X chromosome evolves slower than autosomes (slow-X evolution) because the numbers of cell division differ between spermatogenesis and oogenesis. A theory based on natural selection predicts an opposite direction (fast-X evolution) because newly arising beneficial mutations on the autosomes are usually recessive or partially recessive and not exposed to natural selection. A strong slow-X evolution is also predicted to counteract the effect of fast-X evolution. In our research, we simultaneously studied slow-X evolution, fast-X evolution as well as their interaction in a phylogeny of diverse primates. We showed that slow-X evolution exists in all the examined species, although their degrees differ, possibly due to their different life history traits such as generation times. We showed that fast-X evolution is lineage-specific and provided evidences that fast-X evolution is more evident in species with relatively weak slow-X evolution. We discussed potential contribution of various degrees of slow-X evolution on the conflicting population genetic inferences about human demography. Research advance 2: human-specific traits have long been considered to reside in the genome. There has been a surge of interest to identify genomic regions with accelerated evolution rate in the human genome. However, these studies either rely on a priori knowledge or sliding windows of arbitrary sizes. My research provided an unbiased approach based on previously developed “maximal segment” algorithm to identify genomic segments with accelerated lineage-specific substitution rate. Under this framework, we identified a large number of human genomic segments with clustered human-specific substitutions (named “maximal segments” after the algorithm). Our identified human maximal segments cover a significant amount of previously identified human accelerated regions and overlap with genes enriched in developmental processes. We demonstrated that the underlying evolutionary forces driving the maximal segments included regionally increased mutation rate, biased gene conversion and positive selection. Research advance 3: DNA methylation is one of the most common epigenetic modifications and plays a significant role in gene regulation. How DNA methylation status varies on the evolutionary timescale is not well understood. In this study, we investigated the role of genetic changes in shaping DNA methylation divergence between humans and chimpanzees in their sperm and brain, separately. We find that for orthologous promoter regions, CpG dinucleotide content difference is negatively correlated with DNA methylation level difference in the sperm but not in the brain, which may be explained by the fact that CpG depleting mutations better reflect germline DNA methylation levels. For the aligned sites of orthologous promoter regions, sequence divergence is positively correlated with methylation divergence for both tissues. We showed that the evolution of DNA methylation can be affected by various genetic factors including transposable element insertions, CpG depleting mutations and CpG generating mutations.

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Sidhu, Yaadwinder Singh. "Molecular tools for functional genomic analyses of the stealth pathogenesis of wheat by Zymoseptoria tritici." Thesis, University of Exeter, 2015. http://hdl.handle.net/10871/20219.

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Zymoseptoria tritici is an ascomycete fungus that causes Septoria tritici leaf blotch disease, which is one of the most devastating diseases of wheat. The lack of molecular tools has withheld functional genomics and consequently has left extensive gaps in the knowledge of the biology of infection by Z. tritici. The current research was conducted to develop molecular tools in order to facilitate forward and reserves genetic screens in Z. tritici. These tools include an optimised genetic manipulation protocol, the Z. tritici strains that provide high frequency targeted genome manipulations, a strategy for gene overexpression and protein tagging, and regulatable promoters for controlled gene expression in Z. tritici. The regulatable promoters served to reveal that the Z. tritici β-(1,3)- glucan synthase (BGS1) gene encoded an essential protein, which regulated cell wall stress tolerance and was therefore, a potential drug target. In addition, these molecular tools revealed a virulence-associated role of the glyoxylate cycle in Z. tritici as inactivation of this pathway impeded pre-penetration morphogenesis, which was restored by exogenous glucose application. This result implied that Z. tritici engaged the glyoxylate cycle to produce energy though gluconeogenesis by channelling the by-products of lipolysis. This significance of the glyoxylate cycle during initiation of the bi-phasic infection cycle suggests that Z. tritici is not a hemibiotroph, but a necrotrophic pathogen with an extended asymptomatic phase of infection. Overall, the molecular tools developed in this study will facilitate large-scale functional genomic analyses to interrogate the biology of infection by Z. tritici. The resulting data will inform the development of durable control strategies to combat Z. tritici outbreaks.

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Seshadri, Chitra. "Genome wide epigenetic analyses of Araptus attenuatus, a bark beetle." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4167.

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Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.

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Gustafsson, Susanne. "Population genetic analyses in the orchid genus Gymnadenia : a conservation genetic perspective." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3305.

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Ferrer, Obiol Joan. "The evolutionary history of shearwaters: genomic analyses to resolve a radiation of pelagic seabrids." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/673437.

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How populations differentiate and become new species is a foundational question to the field of evolutionary biology and has important implications for the generation of both local and global patterns of species-level biodiversity. Ernst Mayr emphasised the importance of geographical isolation as a driver of speciation: “populations in separate locations begin a process of differentiation, and once differentiation is sufficient the populations have become two species”. In marine environments, the lack of obvious physical barriers would suggest that panmixia, especially in highly mobile species, or isolation-by-distance, in other cases, will prevail. However, there is some counterintuitive evidence of fine-scale differentiation among populations and species in a number of mobile marine organisms, a phenomenon that has been described as the “marine species paradox”. Seabirds of the order Procellariiformes present some of the most extreme examples of this paradox. On the one hand, Procellariiformes are highly mobile pelagic seabirds with a high dispersal ability and perform some of the longest animal migrations on Earth. On the other hand, they show high philopatry to their breeding grounds, which is expected to limit gene flow and therefore reinforce genetic differentiation. This thesis aims to gain insights into the patterns and processes that contribute to genetic and phenotypic diversification, speciation and dispersal across multiple evolutionary timescales. To this end, I focus on shearwaters (Calonectris, Puffinus and Ardenna), a globally distributed and threatened group of Procellariiformes. Through an integrative approach combining two types of phylogenomic markers, which evolve at different nucleotide substitution rates, and state-of-the-art phylogenetic and introgression analyses, I inferred a robust phylogeny. This approach allowed to discover that the majority of the phylogenetic conflict in shearwaters is generated by high levels of incomplete lineage sorting (ILS) due to rapid speciation events. Divergence time estimation analyses highlighted a severe impact of the Pliocene marine megafauna extinction on shearwaters, probably caused by a sudden reduction in the availability of coastal habitat. Subsequently, the late Pliocene-early Pleistocene was inferred as a period of high and rapid speciation and dispersal, probably promoted by Pleistocene climatic shifts. Biogeographic analyses showed that surface ocean currents promote species dispersal and founder events are a main mode of speciation in shearwaters. Our analysis, combining genomic data with morphological and ecological evidence, did not support any of the current taxonomic classifications for the North Atlantic and Mediterranean Puffinus shearwaters, and so I propose a more accurate taxonomy for the group. Moreover, the detection of fine-scale genetic structure within Puffinus shearwater species, highlights the need for management of evolutionary significant units below the species level. Population genomics analyses identified genetic drift as the major process shaping the genomic landscapes of divergence. In conclusion, the marriage of these various investigations identifies a prevalence of ILS across different timescales, highlights the important role of paleoceanographic events in promoting diversification, and demonstrates the importance of neutral evolution at driving population differentiation in pelagic seabirds. Overall, this thesis showcases the use of multiple genomic approaches, leveraging phylogenetic and population genetic analyses across multiple timescales, to shed light on the evolutionary history of shearwaters.
Una de les preguntes fundacionals del camp de la biologia evolutiva és com es diferencien les poblacions i esdevenen noves espècies, i té importants implicacions en l’establiment dels patrons locals i globals de biodiversitat específica. Ernst Mayr va subratllar la importància de l’aïllament geogràfic com a mecanisme promotor d’especiació: “les poblacions en localitats aïllades comencen un procés de diferenciació i, quan aquesta diferenciació és suficient, les poblacions esdevenen dues espècies”. En l’ambient marí, la manca de barreres físiques evidents suggereix que la panmixi (en espècies amb gran capacitat de moviment) i l’aïllament per distància (en espècies de mobilitat reduïda) són els patrons prevalents. En canvi, s’ha detectat diferenciació a petita escala entre diferents poblacions i diferents espècies en un elevat nombre d’organismes marins mòbils, un fenomen que es coneix com la “paradoxa de les espècies marines”. Els ocells marins de l’ordre dels Procellariiformes representen un dels exemples més extrems d’aquesta paradoxa. Per una banda, els Procellariiformes són ocells marins amb gran capacitat de moviment i alta capacitat dispersiva que duen a terme algunes de les migracions més llargues del planeta. Per altra banda, són espècies molt fidels a les seves zones de cria, fenomen que probablement limiti el flux gènic i reforci la diferenciació genètica. Aquesta tesi té com a objectiu caracteritzar els patrons i processos que contribueixen a la diversificació genètica i fenotípica, a l’especiació i a la dispersió a diferents escales evolutives. Per assolir aquest objectiu, m’he focalitzat en les baldrigues (Calonectris, Puffinus i Ardenna), un grup amenaçat de Procellariiformes distribuït per tot el planeta. Mitjançant una aproximació que combina dos tipus de marcadors filogenòmics que evolucionen amb diferents taxes de substitució nucleotídica, i anàlisis filogenètiques i de detecció d’introgressió infereixo una filogènia ben resolta. Aquesta aproximació ha permès descobrir que la majoria del conflicte filogenètic en les baldrigues és producte dels alts nivells de sorteig incomplet de llinatges (incomplete lineage sorting) degut a esdeveniments ràpids d’especiació. L’anàlisi dels temps de divergència ha demostrat un gran impacte de l’extinció de megafauna marina del Pliocè en les baldrigues, probablement a causa de la sobtada reducció en la disponibilitat d’hàbitats costaners. Posteriorment, el Pliocè tardà i el principi del Pleistocè van ser períodes de molta i ràpida especiació i dispersió, probablement a causa dels canvis climàtics del Pleistocè. Les anàlisis biogeogràfiques han demostrat que els corrents marins promouen la dispersió i que l’efecte fundador és un mecanisme important d’especiació en les baldrigues. Les nostres anàlisis, combinant dades genòmiques amb evidència morfològica i ecològica, no han donat suport a les classificacions taxonòmiques actuals del grup de les baldrigues del gènere Puffinus del nord de l’Atlàntic i del Mediterrani i, per tant, proposo una classificació taxonòmica més adequada pel grup. A més a més, la detecció d’estructura genètica a petita escala en les espècies d’aquest grup de baldrigues destaca la necessitat de gestió d’unitats evolutives significatives per sota del nivell d’espècie. Les anàlisis de genòmica de poblacions han identificat la deriva genètica com a principal promotor de divergència en el genoma. Per concloure, el conjunt de les investigacions d’aquesta tesi identifiquen la prevalença del sorteig incomplet de llinatges al llarg de diferents escales evolutives, destaquen l’important paper dels esdeveniments paleoceanogràfics com a promotors de diversificació i indiquen la importància de l’evolució neutra com a causa de diferenciació poblacional en ocells marins pelàgics. Globalment, aquesta tesi demostra la utilitat de diferents aproximacions genòmiques, mitjançant anàlisis filogenètiques i de genètica de poblacions en diferents escales evolutives per proporcionar nou coneixement sobre la història evolutiva de les baldrigues.

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Gholami, Behjat. "Functional analyses of candidate genes for osteoporosis : RUNX2 and LRP5 interplay during differentiation of the hFOB human osteoblast cell line." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/471516.

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Osteoporosis is a general skeletal disorder. It is characterized by a low bone mass and a microarchitectural deterioration of bone tissue, which increase bone fragility and susceptibility to fracture. LRP5 is a widely expressed member of the low-density lipoprotein receptor superfamily, which acts as a co-receptor for Wnt. Wnt/β-catenin signaling plays an important role in the development and maintenance of many organs and tissues, among others bone. In bone, LRP5 is expressed by osteoblasts and not by osteoclasts; however, little is known about its regulation. Genetic studies show that LRP5 has a major influence on BMD. Loss-of-function mutations in the LRP5 gene cause osteoporosis pseudoglioma syndrome (OPPG) and Gain-of-function mutations in the LRP5 gene cause high bone mass phenotype, an autosomal dominant condition of increased BMD. RUNX2 is a member of the Runt family of transcription factors with a major role in the control of osteoblast commitment and differentiation, whose expression is necessary for the regulation of skeletal genes. Mutations in the RUNX2 locus in human cause cleidocranial dysplasia (CCD), which is an autosomal-dominant condition. Skeletons from homozygous Runx2 -/- (knock out) mice showed complete lack of Ossification. The DNA-binding sites of Runx2 in major bone matrix protein genes, including Col1a1; Col1a2; Spp1; Ibsp/BSP; Bglap2; Fn1/fibronectin; Mmp13, and Tnfrsf11b/Opg, have been identified, and Runx2 induced the expression of these genes or activated their promoters in vitro. Until recently, RUNX2 and LRP5 had not been directly connected. Studies have revealed the presence of five RUNX2 binding sites within a 2.9 kb region upstream of LRP5 and documented the binding of RUNX2 to these sites in vitro. To further explore this relationship in vivo, in this thesis, an osteoblast differentiation protocol using the hFOB cell line was employed. Transcriptional levels of RUNX2 and LRP5, together with OCN, SOST and ALP were evaluated along 21 days of differentiation in 5 stages. RUNX2 and LRP5 proteins were evaluated along 21 days of differentiation. RUNX2 occupancy of the 5 binding sites on the LRP5 promoter, chromatin immunoprecipitation assays were performed at 3 time-points during hFOB differentiation. Osteoblast differentiation model based on the hFOB displayed characteristic osteoblastic markers of mineralization and alkaline phosphatase activity. Expression of LRP5, RUNX2 and also ALP, SOST and OCN was observed in hFOB cell line. RUNX2 showed steady increase reaching a maximum of 4-fold at day 14. All the other genes analyzed showed a peak at day 3, more than 5-fold for SOST and above 4-fold for ALP. OCN and SOST showed a clear decrease after day 3, while ALP showed a slow decrease, and LRP5 maintained relatively similar mRNA levels. Both RUNX2 and LRP5 proteins were detected in hFOB at day 0, 3 and 7. Low levels of LRP5 were also observed at day 14. Overall, the protein levels of both RUNX2 and LRP5 decrease during differentiation of hFOB cell lines. Binding of RUNX2 transcription factor to the promoters of the CDKN1A and SERPINE1 genes was observed in day 7. And RUNX2 binding to CDKN1A and SERPINE1 promoters in hFOB cells was described for the first time. Subsequently, binding of RUNX2 to the five RUNX2 elements in the LRP5 promoter was assessed in chromatin from undifferentiated (day 0) and differentiated (days 7 and 21) hFOB cells. Binding at all five sites was observed at day 7 (above 3-fold enrichment in all cases), while it was negligible at days 0 and 21. No acceptable correlation was observed between RUNX2 binding and LRP5 expression, which leaves the functional effect of RUNX2 binding to the LRP5 promoter as an unsolved question.
L'osteoporosi es caracteritza per una baixa massa òssia i un deteriorament de la microarquitectura del teixit ossi. LRP5 és un membre de la superfamília de receptors de lipoproteïnes de baixa densitat, que actua com a co-receptor de la via de Wnt. LRP5 té una gran influència en la densitat mineral òssia. Runx2 és un membre de la família de factors de transcripció Runt amb un paper essencial en el control de la determinació i la diferenciació dels osteoblasts. La seva expressió és necessària per a la regulació dels gens de l'esquelet. Fins fa poc, Runx2 i LRP5 no havien estat connectats directament. Estudis recents han revelat la presència de cinc llocs d'unió de Runx2 en una regió de 2,9 kb upstream de LRP5 i s’ha documentat la unió de Runx2 a aquests llocs in vitro. Per explorar aquesta relació in vivo, en aquesta tesi es va emprar un protocol de diferenciació d’osteoblasts utilitzant la línia cel·lular hFOB. Es van avaluar els nivells de transcripció de RUNX2 i LRP5, juntament amb els de OCN, SOST i ALP al llarg de 21 dies de diferenciació. També es va avaluar les proteïnes Runx2 i LRP5. Per provar la ocupació de Runx2 als 5 llocs d'unió del promotor de LRP5, es van realitzar assaigs d'immunoprecipitació de cromatina durant la diferenciació de les cèl·lules hFOB, (dies 0, 7 i 21). Només es va observar unió en tots els cinc llocs en el dia 7, i no en els dies 0 i 21. La unió de Runx2 al promotor de LRP5 es descriu per primera vegada en aquesta tesi.

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Pickett, Brandon D. "Applications of and Algorithms for Genome Assembly and Genomic Analyses with an Emphasis on Marine Teleosts." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/8997.

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The burgeoning frequency of genome sequencing in recent years is a testament to both the improvements in sequencing technologies and the utility of genomic analyses for biological discovery. The rapid proliferation in technological advancements and availability of complementary data types and techniques has obfuscated the optimal process of genome assembly and raised the barrier to entry to unprecedented levels. In this dissertation, we describe the genome assemblies performed for several marine teleosts and discuss the algorithms and applications required for genome assembly, including some of our specific contributions to the genome assembly and annotation space. In Chapter 1 and Chapter 2, we review the taxonomy, life history, and biogeography of the Roundjaw Bonefish (Albula glossodonta) and describe its genome assembly. The genome assemblies with some analyses are described for the Bluefin (Caranx melampygus) and Giant (Caranx ignobilis) Trevallies in Chapter 3 and Chapter 4, respectively. Chapter 5 and Chapter 6 define and assess algorithms for the annotation of simple sequence repeats in genomic sequences. Publicly available annotations of carbapenem-resistance plasmids were epidemiologically analyzed in Chapter 7. The resiliency of phylogenetic trees to the removal of taxa is explored with a new nodal stability metric and algorithm, TANOS, in Chapter 8. Finally, in Chapter 9, a review of and commentary on vertebrate genome assembly is presented with recommendations for new projects. The aim of this dissertation, and the final chapter in particular, is to explore genome assembly methods and reduce the barrier to entry for new entrants.

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Holzapfel, Marion. "De l’épidémiologie moléculaire aux analyses fonctionnelles de Brucella chez les ruminants, une approche intégrée pour l’identification et l’étude de la diversité phénotypique d’un genre génétiquement homogène." Thesis, Paris Est, 2018. http://www.theses.fr/2018PESC1141.

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La brucellose est une zoonose causée par le genre bactérien Brucella (B.) dont l’incidence mondiale est estimée à 500 000 cas humains par an. Le réservoir est animal, touchant principalement les espèces de rente. Les espèces les plus importantes pour l’Homme sont B. melitensis, B. abortus et B. suis qui partagent plus de 90% d’identité de séquence. Bien qu’elles soient très apparentées sur le plan génétique, elles présentent une diversité de caractéristiques phénotypiques, de préférence d’hôte et de pathogénicité. L’homogénéité génétique de ces espèces peut apparaître comme un atout pour le développement d’outils de diagnostic universels robustes. En revanche, il s’agit d’un challenge pour les distinguer, rendant difficile la caractérisation précise des isolats issus d’un même foyer. Dans le cadre de cette thèse, un outil de diagnostic moléculaire de PCR en temps réel ciblant le genre Brucella a été développé et optimisé. L’outil a été évalué sur des prélèvements de lait de ruminants, ces prélèvements peuvent être une source importante de Brucella et peuvent être utiles au dépistage de la maladie à l’échelle du troupeau. Basée sur la détection de l’élément d’insertion IS711, une séquence présente en plusieurs exemplaires dans le génome, cette méthode affiche des valeurs de sensibilité et de spécificité qui la rendent intéressante pour un schéma global de lutte contre la brucellose. D’autre part, en vue d’améliorer la compréhension de la stabilité génétique de B. melitensis, un panel original de souches isolées dans le cadre d’un foyer et impliquant 4 espèces d’hôtes différentes a été comparé. Ainsi à l’aide de différentes approches complémentaires, leurs séquences génomiques, les caractères phénotypiques ainsi que leurs comportements dans un modèle in vitro ont été comparés. Nos résultats n’ont pas mis en évidence marqueurs qui laisserait à penser que des mutations dans le génome soient indispensables pour s’adapter à un nouvel hôte
Brucellosis is a zoonotic disease caused by the bacterial genus Brucella (B.), whose global incidence is estimated at 500,000 human cases per year. The reservoir is animal, affecting mainly livestock. The most important species for humans are B. melitensis, B. abortus and B. suis, which share more than 90% sequence identity. Although highly genetically related, Brucella spp. exhibit a variety of phenotypic characteristics, host preference and pathogenicity. The genetic homogeneity of these species may appear as an asset for the development of robust universal diagnostic tools. On the other hand, it is a challenge to distinguish them, making it difficult to precisely characterize isolates from the same outbreak. As part of this thesis, a real-time PCR molecular diagnostic tool targeting the genus Brucella was developed and optimized. The method has been evaluated on ruminant milk samples; these samples may be an important source of Brucella and may be useful for herd-scale disease screening. Based on the detection of the IS711 insertion element, a sequence present in several copies within the genome, this method displays sensitivity and specificity values that make it interesting for a global scheme to fight against brucellosis. On the other hand, in order to improve the understanding of the genetic stability of B. melitensis, an original panel of strains isolated in an outbreak and involving four different host species was compared. Thus, using different complementary approaches, their genomic sequences, phenotypic characteristics and their behavior in an in vitro model were compared. Our results did not highlight markers that would suggest that mutations in the genome are essential to adapt to a new host

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Doan, Quoc Khanh. "Genetic and genomic variation of resistance to viral nervous necrosis in wild populations of european seabass (Dicentrachus labrax)." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT094/document.

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Le bar est une espèce économique majeure de l’aquaculture méditerranéenne. La nécrose nerveuse virale (VNN), une maladie qui affecte au moins 70 espèces aquatiques, est devenue la menace la plus grave pour l’aquaculture de cette espèce. Bien que de nombreuses études aient été réalisées afin de contrôler cette maladie, aucune procédure simple et efficace n’est disponible. Dans cette thèse, nous évaluons la variabilité génétique de la résistance à cette pathologie et le potentiel d’amélioration génétique pour lutter contre cette menace.Après une introduction générale (premier chapitre) et une revue de la littérature sur la nodavirose en aquaculture (second chapitre), nous explorons dans le troisième chapitre la variabilité génétique de résistance de populations sauvages de bar, Atlantique Nord (NAT), Méditerranée ouest (WEM), Nord-Est Méditerranée (NEM) et Méditerranée Sud-Est (SEM). Pour ce faire, 2011 descendants d’un croisement factoriel complet, où 9 mères WEM ont été croisées avec 60 pères NAT, WEM, NEM et SEM (15 mâles par population), ont été élevés en "common garden". Après 202 jours, 1472 poissons ont été infectés par injection intrapéritonéale nodavirus à 15.8g de poids moyen. Le reste des poissons a été conservé pour collecter les paramètres de performance. Après la récupération du pedigree, nous révélons une forte variabilité de résistance en fonction de l’origine des pères (de 53 à 90%), les descendants de pères Est-Méditerranéens étant les plus résistants (83 à 90% de survie), les descendants WEM étant intermédiaires (62% de survie) et les descendants de père NAT étant les plus sensibles (53% seulement de la survie). Une héritabilité modérée mais significative pour la résistance (0,26 ± 0,11) a été estimée et des corrélations négatives entre la résistance et les traits de production ont été montrées.Dans le quatrième chapitre une recherche de loci à effets fort (QTL) sur la résistance a été effectuée avec une carte de liaison moyenne-densité. Pour cela, 1717 individus appartenant à 397 familles de plein-frères et leurs parents ont été génotypés pour 2722 marqueurs SNP imprimés sur une puce SNPs. À partir de 1274 loci significatifs, une carte de liaison contenant 24 groupes de liaison, ainsi que des cartes sexe-spécifiques et origine-spécifiques ont été construites. Ces résultats révèlent une hétérochiasmie, avec un taux de recombinaison 1,25 fois plus fort chez les femelles par rapport aux mâles. La recherche de QTL a été effectuée à partir de différentes méthodes, mais bien qu’aucun QTL pour le «temps de survie» ou la survie, n’ait été identifié, nous discutons de l’effet du plan expérimental utilisé.Dans le quatrième chapitre, une étude association génomique a été effectuée en deux étapes: non pondérée (GWAS) puis pondérée (wGWAS) à partir de modèles mixtes linéaires utilisant les mêmes SNP que pour la cartographie de QTL, l’objectif étant de détecter des SNPs liés à la résistance au VNN. Un SNP significatif expliquant 3.11% de la résistance appartenant à LG9 a pu être détecté. Le potentiel de prédiction de la génomique pour la résistance au VNN en utilisant différents modèles génomiques a enfin été évalué, mais aucune différence significative n’a été montrée entre les valeurs génétiques estimées à partir des données génomiques ou à partir du pedigree.En conclusion, cette étude montre forte variation génétique de la résistance au VNN des populations sauvages de bar avec des corrélations génétiques négatives avec les traits de production. Ces derniers résultats sont précieux pour aider à définir des stratégies d’amélioration génétique de la résistance au VNN du bar. Enfin, de premières hypothèses sur l’emplacement de QTL putatifs plaident pour une future cartographie fine pour localiser ces QTLs, une valeur ajoutée dans un schéma de sélection assistée par marqueurs pour améliorer la résistance au VNN du bar
European seabass is one of the most economic species in aquaculture in Mediterranean areas. Viral nervous necrosis (VNN), a disease affecting at least 70 aquatic species, has become the most serious threat to seabass cultured industry. While numerous studies have been performed in order to control this disease, no simple and effective procedures are available. In this thesis, we question genetic variability and the potential of selective breeding as an opportunity to address thwart this threat.After a general introduction (first chapter) and a deep literature review of nodavirus in aquaculture (second chapter), we explore in the third chapter the genetic variability of resistance of different wild populations of European seabass, namely Northern Atlantic (NAT), Western Mediterranean (WEM), Northern-East Mediterranean (NEM) and Southern-East Mediterranean (SEM). To address this question, 2011 fish derived from a full-factorial mating scheme, where 9 WEM dams were crossed with 60 sires originated from NAT, WEM, NEM and SEM (15 sires per population), were reared in “common garden”. At 202 days, 1472 were challenged by nodavirus intraperitoneal injection at a mean body weight of 15.8 g. The rest of fish were kept in a single tank in order to collect performance traits. Strikingly, after pedigree recovery, we reveal a very strong and significant differentiation in VNN resistance among sires’ origin (ranging from 53 to 90%), offspring from East Mediterranean sires being the most resistant (83-90% of survival), offspring from WEM sires being intermediate (62% of survival) and offspring from NAT sires being the most sensitive (53% of survival only). A moderate liability heritability for VNN resistance (0.26±0.11) was estimated and negative correlations between resistance and production traits were shown.In the fourth chapter, a search of Quantitative Trait Loci (QTL) linked to the resistance was performed using a medium linkage map as examined. Therefore, 1717 individuals belonging 397 full-sib families and their parents were genotyped for 2722 SNP markers spotted on a SNPChip. From 1274 significant loci, a 24 linkage groups medium-density linkage map was constructed, as well as sex-specific and Origin-specific linkage maps. From these results, we show a 1.25-fold sex-biased heterochiasmy in favor to female recombination rate. Finally, genome scans for QTLs were performed in different methods, and while no QTLs were identified for both “time to death” or survival, we discuss the effect of the experimental design used.In the fifth chapter, a two-step unweighted then weighted Genome-Wide Association Study (GWAS & wGWAS) was carried out based on linear mixed models using the same SNPs as for QTL mapping. The aim was to determine whether we can detect significant individual SNPs linked to resistance against VNN. After SNPs weight calculation, the wGWAS detected one significant SNP explaining 3.11% of the resistance belonging to LG9. Finally, the potential for genomics prediction for VNN resistance using the different genomic models was performed and extensively presented. However, no significant differences were observed between genomic-based estimated breeding values and pedigree-based estimated breeding values.In conclusion, this study depicts a large genetic variation for VNN resistance in wild seabass populations but with negative genetic correlations with production traits. These latter results are valuable to help to define strategies for genetic improvement of resistance against VNN of European seabass. Moreover, the first assumptions on the location of potential QTLs claim for a fine QTL mapping and an expectable add-value of the use of genomic information in potential marker-assisted selection to VNN resistance in European seabass

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29

Meakin, Nicholas G. "Metagenomic analyses of marine new production under elevated CO2 conditions." Thesis, University of Stirling, 2009. http://hdl.handle.net/1893/1555.

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A mesocosm experiment was carried out in a Norwegian fjord near Bergen in May 2006, with the main objective being the study of the effects of increasing concentrations of atmospheric CO2 (and associated effects such as increased acidification) on blooms of natural marine coastal plankton. Three mesocosms were bubbled with CO2(g) to achieve a high (~700ppm) CO2 concentration (pH ~7.8) to simulate predicted future conditions as a result of rising atmospheric CO2 concentrations. Another three mesocosms were treated as controls and bubbled with ambient air to represent a near pre-industrial scenario (atmospheric CO2 concentration ~300ppm, surface seawater pH ~8.15). Blooms in the mesocosms were stimulated by the addition of nutrients at a near-Redfield ratio ([N:P] ≈ [16:1]), and scientific measurements and analyses were carried out over the course of the blooms for approximately one month. Of particular interest in this study were the autotrophic plankton. The diversity and activities of these microorganisms under the two treatments was therefore investigated. By designing and using new degenerate primers specifically targeting ‘Green-type’ (Form IA and IB), ‘Red-type’ (Form IC and ID) and Form II RuBisCO, analysis of primary producers was carried out using PCR and either gDNA or cDNA (mRNA) templates from key time points spanning the complete duration of the blooms throughout the mesocosm experiment. Over 1250 novel RuBisCO large subunit sequences have been fully annotated and deposited in the NCBI GenBank® database. These sequences revealed distinct changes in the diversity of primary producers both over the courses of the blooms and between treatments. Particularly striking was the effect of acidification on the community structure of the eukaryotic picoplankton, Prasinophytes. A clade of prasinophytes closely related to Micromonas pusilla showed a distinct preference for the high CO2 conditions; a laboratory-based experiment confirmed the high tolerance of Micromonas pusilla to lower pH. Conversely, a clade related to Bathycoccus prasinos was almost entirely excluded from the high CO2 treatments. Clades of form II RuBisCO-containing dinoflagellates were also abundant throughout the experiment in both treatments. The high similarity of some of these clades to the toxin-producing species Heterocapsa triquetra and Gonyaulax polyedra, and apparent high tolerance of some clades to high CO2 conditions, is perhaps cause for concern in a high CO2 world and demands further research. In parallel with the RubisCO work, new primers were designed that target the gene encoding the Fe protein of nitrogenase (NifH). 82 Bergen genomic nifH sequences have been annotated and submitted to GenBank®. These sequences include those from organisms related to Alpha, Beta, and Gammaproteobacteria, and Cluster II and Cluster III sequences that align most closely with anaerobic Bacteria, Gram positive, and/or sulphur-reducing Bacteria. The biggest surprise, however, was the apparent abundance and significance of a Rhodobacter sphaeroides-like microorganism throughout the duration of the experiment in both treatments. Whilst this clade was unsurprisingly absent in the RuBisCO cDNA libraries, all but two of 128 nifH cDNA clones analysed were identical to the gene from Rhodobacter sphaeroides. This shows that this clade was potentially fixing N2 throughout the entire experiment, even in the presence of combined N added to both sets of mesocosms at the start of the experiment. A group of Rhodobacter sphaeroides-like microorganisms present at Bergen may therefore have been an unexpected source of new N during the experiment and contributed to the maintenance of the mesocosm communities as nutrients became depleted. One organism dominated the autotrophic communities after the blooms in both treatments. Synechococcus spp. Form IA rbcL clones most closely related to the coastal strain Synechococcus sp. strain CC9902 were recovered throughout the experiment but were particularly numerous toward the end of the experiment and dominated the “Green-type” libraries at this time. Initially, rbcL clones from these cyanobacteria were mostly derived from the ambient CO2 mesocosms but were equally distributed between treatments by the end of the experiment. This suggests that cyanobacteria related to strain CC9902 may be less tolerant of elevated CO2 (which was greatest at the beginning rather than the end of the experiment). However, despite the mesocosms being Pi-limited at the end of the experiment, several Synechococcus species (including those related to strain CC9902 and another coastal strain, CC9311) thrived. Following on from this observation, Pi uptake and assimilation mechanisms in a Synechococcus species were investigated in the laboratory. This led to the sequencing and characterisation of a pstS gene from the marine cyanobacterium Synechococcus sp. WH 8103. Unlike conventional pstS, it was discovered that the pstS II gene in this organism is constitutively expressed and unresponsive to or only weakly regulated by Pi supply. The use of PstS/pstS as a marker for P-limitation in natural samples, therefore, should be interpreted with caution.

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Batut, Bérénice. "Étude de l'évolution réductive des génomes bactériens par expériences d'évolution in silico et analyses bioinformatiques." Thesis, Lyon, INSA, 2014. http://www.theses.fr/2014ISAL0108/document.

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Selon une vision populaire, l’évolution serait un processus de « progrès » qui s’accompagnerait d’un accroissement de la complexité moléculaire des êtres vivants. Cependant, les programmes de séquençage des génomes ont révélé l’existence d’espèces dont les lignées ont, au contraire, subi une réduction massive de leur génome. Ainsi, chez les cyanobactéries Prochlorococcus et Pelagibacter ubique, certaines lignées ont subi une réduction de 30% de leur génome. Une telle évolution « à rebours », dite évolution réductive, avait déjà été observée pour des bactéries endosymbiotiques, pour lesquelles la sélection naturelle n’est pas assez efficace pour éliminer les mutations délétères comme les pertes de gènes. Cela vient notamment du fait que ces bactéries endosymbiotiques subissent, à chaque reproduction de leur hôte, une réduction drastique de leur taille de population. Cette explication semble peu plausible pour des cyanobactéries marines comme Prochlorococcus et Pelagibacter, qui ont un mode de vie libre et qui font partie des bactéries les plus abondantes des océans. D’autres hypothèses ont ainsi été proposées pour expliquer l’évolution réductive comme l’adaptation à un environnement stable et pauvre en nutriments, des forts taux de mutation, mais aucun de ces hypothèses ne semble capable d’expliquer toutes les caractéristiques génomiques observées. Dans cette thèse, nous nous intéressons au cas de l’évolution réductive chez Prochlorococcus, pour laquelle de nombreuses séquences et données sont disponibles. Deux approches sont utilisées pour cette étude : une analyse phylogénétique des génomes de Prochlorococcus, et une approche théorique de simulation où nous testons différents scénarios évolutifs pouvant conduire à une évolution réductive. La combinaison de ces deux approches permet finalement de proposer un scénario plausible pour expliquer l'évolution réductive chez Prochlorococcus
Given a popular view, evolution is an incremental process based on an increase of molecular complexity of organisms. However, some organisms have undergo massive genome reduction like the endosymbionts. In this case the reduction can be explained by the Muller’s ratchet due to the endosymbiont lifestyle with small population and lack of recombination. However, in some marine bacteria, like Prochlorococcus et Pelagibacter, lineage have undergo up to 30% of genome reduction. Their lifestyle is almost the opposite to the one of the endosymbionts and reductive genome evolution can not be easily explicable by the Muller’s ratchet. Some other hypothesis has been proposed but none can explain all the observed genomic characteristics. In the thesis, I am interested in the reductive evolution of Prochlorococcus. I used two approaches: a theoretical one using simulation where different scenarios are tested and an analysis of Prochlorococcus genomes in a phylogenetic framework to determine the causes and characteristics of genome reduction. The combination of these two approaches allows to propose an hypothetical evolutive history for the reductive genome evolution of Prochlorococcus

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Leconte, Jade. "Analyses de variations génomiques liées à la biogéographie des picoalgues Mamiellales Survey of the green picoalga Bathycoccus genomes in the global ocean Genome Resolved Biogeography of Mamiellales Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans." Thesis, université Paris-Saclay, 2020. https://www.biblio.univ-evry.fr/theses/2020/interne/2020UPASE013.pdf.

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Les Mamiellales sont un ordre d'algues vertes unicellulaires cosmopolites comprenant des espèces d'importance écologique telles que Bathycoccus, Micromonas ou encore Ostreococcus, des contributeurs majeurs à la production primaire. Cette thèse prend pour modèle d'étude ce groupe phytoplanctonique aux génomes de référence connus afin d'analyser au mieux l'impact de l'environnement sur le plancton grâce aux échantillons provenant de l'expédition Tara Oceans.Pour cela, différentes analyses ont été menées afin de définir leur biogéographie et leurs préférences écologiques, d'abord dans les eaux tempérées puis dans les eaux froides et riches en nutriments de l'océan Arctique. Dans les deux cas, il a été montré que la température était le principal facteur distinguant l'environnement dans lequel les différentes espèces ont été trouvées. Nous avons ensuite réalisé une étude plus poussée en particulier sur Bathycoccus prasinos, une espèce abondante dans ces deux milieux distincts afin d'établir la structure de ses populations, qui s'avère séparer clairement trois groupes: les échantillons austral, arctiques et tempérés, montrant encore une fois un impact de la température mais pas uniquement au vu de la distance génomique entre les deux premiers bassins.Finalement, notre étude a pu être étendue avec diverses collaborations, nous permettant d'observer également un groupe de protistes hétérotrophes, les straménopiles, et de réaliser des analyses à l'échelle beaucoup plus large des communautés. L'ensemble de ces résultats concluent encore une fois, entre autre, à un fort impact de la température, menant à un questionnement sur le contexte actuel de changements climatiques et son potentiel impact sur le plancton
Mamiellales are an order of unicellular cosmopolitan green algae with ecologically important species such as Bathycoccus, Micromonas or Ostreococcus, major contributors to the primary production. This thesis uses this phytoplankton group with known reference genomes as a study model in order to better analyze the impact of the environment on plankton using samples from the Tara Oceans expedition.To do this, different analyses were carried out to define their biogeography and ecological preferences, first in temperate waters then in the cold, nutrient-rich waters of the Arctic Ocean. In both cases, temperature was shown to be the main factor distinguishing the environment in which the different genomes were found. We then carried out a more detailed study in particular on Bathycoccus prasinos, a species abundant in these two distinct environments, in order to establish its population structure, which proved to be clearly separated into three groups: southern , arctic and temperate samples, again showing an impact of temperature but not only in view of the genomic distance between the first two basins.Finally, our study was extended with various collaborations, allowing us to observe a group of heterotrophic protists, the stramenopiles, and to perform analyses at the much larger scale of communities. All of these results conclude once again, among other things, on the strong impact of temperature, leading us to contribute to the question about the current context of climate change and its impact on plankton

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Danks, Jacob R. "Algorithm Optimizations in Genomic Analysis Using Entropic Dissection." Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc804921/.

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In recent years, the collection of genomic data has skyrocketed and databases of genomic data are growing at a faster rate than ever before. Although many computational methods have been developed to interpret these data, they tend to struggle to process the ever increasing file sizes that are being produced and fail to take advantage of the advances in multi-core processors by using parallel processing. In some instances, loss of accuracy has been a necessary trade off to allow faster computation of the data. This thesis discusses one such algorithm that has been developed and how changes were made to allow larger input file sizes and reduce the time required to achieve a result without sacrificing accuracy. An information entropy based algorithm was used as a basis to demonstrate these techniques. The algorithm dissects the distinctive patterns underlying genomic data efficiently requiring no a priori knowledge, and thus is applicable in a variety of biological research applications. This research describes how parallel processing and object-oriented programming techniques were used to process larger files in less time and achieve a more accurate result from the algorithm. Through object oriented techniques, the maximum allowable input file size was significantly increased from 200 mb to 2000 mb. Using parallel processing techniques allowed the program to finish processing data in less than half the time of the sequential version. The accuracy of the algorithm was improved by reducing data loss throughout the algorithm. Finally, adding user-friendly options enabled the program to use requests more effectively and further customize the logic used within the algorithm.

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Kittler, Ralf. "Functional genomic analysis of cell cycle progression in human tissue culture cells." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2006. http://nbn-resolving.de/urn:nbn:de:swb:14-1161253856455-48321.

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The eukaryotic cell cycle orchestrates the precise duplication and distribution of the genetic material, cytoplasm and membranes to daughter cells. In multicellular eukaryotes, cell cycle regulation also governs various organisatorial processes ranging from gametogenesis over multicellular development to tissue formation and repair. Consequently, defects in cell cycle regulation provoke a variety of human cancers. A global view of genes and pathways governing the human cell cycle would advance many research areas and may also deliver novel cancer targets. Therefore this work aimed on the genome-wide identification and systematic characterisation of genes required for cell cycle progression in human cells. I developed a highly specific and efficient RNA interference (RNAi) technology to realize the potential of RNAi for genome-wide screening of the genes essential for cell cycle progression in human tissue culture cells. This approach is based on the large-scale enzymatic digestion of long dsRNAs for the rapid and cost-efficient generation of libraries of highly complex pools of endoribonuclease-prepared siRNAs (esiRNAs). The analysis of the silencing efficiency and specificity of esiRNAs and siRNAs revealed that esiRNAs are as efficient for mRNA degradation as chemically synthesized siRNA designed with state-of-the-art design algorithms, while exhibiting a markedly reduced number of off-target effects. After demonstrating the effectiveness of this approach in a proof-of-concept study, I screened a genome-wide esiRNA library and used three assays to generate a quantitative and reproducible multi-parameter profile for the 1389 identified genes. The resulting phenotypic signatures were used to assign novel cell cycle functions to genes by combining hierarchical clustering, bioinformatics and proteomic data mining. This global perspective on gene functions in the human cell cycle presents a framework for the systematic documentation necessary for the understanding of cell cycle progression and its misregulation in diseases. The identification of novel genes with a role in human cell cycle progression is a starting point for an in-depth analysis of their specific functions, which requires the validation of the observed RNAi phenotype by genetic rescue, the study of the subcellular localisation and the identification of interaction partners of the expressed protein. One strategy to achieve these experimental goals is the expression of RNAi resistant and/or tagged transgenes. A major obstacle for transgenesis in mammalian tissue culture cells is the lack of efficient homologous recombination limiting the use of cultured mammalian cells as a real genetic system like yeast. I developed a technology circumventing this problem by expressing an orthologous gene from a closely related species including its regulatory sequences carried on a bacterial artificial chromosome (BAC). This technology allows physiological expression of the transgene, which cannot be achieved with conventional cDNA expression constructs. The use of the orthologous gene from a closely related species confers RNAi resistance to the transgene allowing the depletion of the endogenous gene by RNAi. Thus, this technology mimics homologous recombination by replacing an endogenous gene with a transgene while maintaining normal gene expression. In combination with recombineering strategies this technology is useful for RNAi rescue experiments, protein localisation and the identification of protein interaction partners in mammalian tissue culture cells. In summary, this thesis presents a major technical advance for large-scale functional genomic studies in mammalian tissue culture cells and provides novel insights into various aspects of cell cycle progression. (Die Druckexemplare enthalten jeweils eine CD-ROM als Anlagenteil: 217 MB: Movies, Rohdaten - Nutzung: Referat Informationsvermittlung der SLUB)

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Mungall, Christopher. "Next-generation information systems for genomics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5020.

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The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the translational potential of this technology we will need advanced information systems to integrate and interpret this deluge of data. These systems must be capable of extracting the location and function of genes and biological features from genomic data, requiring the coordinated parallel execution of multiple bioinformatics analyses and intelligent synthesis of the results. The resulting databases must be structured to allow complex biological knowledge to be recorded in a computable way, which requires the development of logic-based knowledge structures called ontologies. To visualise and manipulate the results, new graphical interfaces and knowledge acquisition tools are required. Finally, to help understand complex disease processes, these information systems must be equipped with the capability to integrate and make inferences over multiple data sets derived from numerous sources. RESULTS: Here I describe research, design and implementation of some of the components of such a next-generation information system. I first describe the automated pipeline system used for the annotation of the Drosophila genome, and the application of this system in genomic research. This was succeeded by the development of a flexible graphoriented database system called Chado, which relies on the use of ontologies for structuring data and knowledge. I also describe research to develop, restructure and enhance a number of biological ontologies, adding a layer of logical semantics that increases the computability of these key knowledge sources. The resulting database and ontology collection can be accessed through a suite of tools. Finally I describe how the combination of genome analysis, ontology-based database representation and powerful tools can be combined in order to make inferences about genotype-phenotype relationships within and across species. CONCLUSION: The large volumes of complex data generated by high-throughput genomic and systems biology technology threatens to overwhelm us, unless we can devise better computing tools to assist us with its analysis. Ontologies are key technologies, but many existing ontologies are not interoperable or lack features that make them computable. Here I have shown how concerted ontology, tool and database development can be applied to make inferences of value to translational research.

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Rubanova, Natalia. "MasterPATH : network analysis of functional genomics screening data." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC109/document.

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Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour ce phénotype en utilisant la « hit-liste » des expériences « omics » qui travaille dans le réseau intégré (le réseau comprend des interactions protéine-protéine, de transcription, l’acide ribonucléique micro-l’acide ribonucléique messager et celles métaboliques). La méthode tire des sous-réseaux qui sont construit des voies de quatre types les plus courtes (qui ne se composent des interactions protéine-protéine, ayant au minimum une interaction de transcription, ayant au minimum une interaction l’acide ribonucléique micro-l’acide ribonucléique messager, ayant au minimum une interaction métabolique) entre des hit –gènes et des soi-disant « exécuteurs terminaux » - les composants biologiques qui participent à la réalisation du phénotype finale (s’ils sont connus) ou entre les hit-gènes (si « des exécuteurs terminaux » sont inconnus). La méthode calcule la valeur de la centralité de chaque point culminant et de chaque voie dans le sous-réseau comme la quantité des voies les plus courtes trouvées sur la route précédente et passant à travers le point culminant et la voie. L'importance statistique des valeurs de la centralité est estimée en comparaison avec des valeurs de la centralité dans les sous-réseaux construit des voies les plus courtes pour les hit-listes choisi occasionnellement. Il est supposé que les points culminant et les voies avec les valeurs de la centralité statistiquement signifiantes peuvent être examinés comme les membres possibles des voies moléculaires menant à ce phénotype. S’il y a des valeurs expérimentales et la P-valeur pour un grand nombre des points culminant dans le réseau, la méthode fait possible de calculer les valeurs expérimentales pour les voies (comme le moyen des valeurs expérimentales des points culminant sur la route) et les P-valeurs expérimentales (en utilisant la méthode de Fischer et des transpositions multiples).A l'aide de la méthode masterPATH on a analysé les données de la perte de fonction criblage de l’acide ribonucléique micro et l'analyse de transcription de la différenciation terminal musculaire et les données de la perte de fonction criblage du procès de la réparation de l'ADN. On peut trouver le code initial de la méthode si l’on suit le lien https://github.com/daggoo/masterPATH
In this work we developed a new exploratory network analysis method, that works on an integrated network (the network consists of protein-protein, transcriptional, miRNA-mRNA, metabolic interactions) and aims at uncovering potential members of molecular pathways important for a given phenotype using hit list dataset from “omics” experiments. The method extracts subnetwork built from the shortest paths of 4 different types (with only protein-protein interactions, with at least one transcription interaction, with at least one miRNA-mRNA interaction, with at least one metabolic interaction) between hit genes and so called “final implementers” – biological components that are involved in molecular events responsible for final phenotypical realization (if known) or between hit genes (if “final implementers” are not known). The method calculates centrality score for each node and each path in the subnetwork as a number of the shortest paths found in the previous step that pass through the node and the path. Then, the statistical significance of each centrality score is assessed by comparing it with centrality scores in subnetworks built from the shortest paths for randomly sampled hit lists. It is hypothesized that the nodes and the paths with statistically significant centrality score can be considered as putative members of molecular pathways leading to the studied phenotype. In case experimental scores and p-values are available for a large number of nodes in the network, the method can also calculate paths’ experiment-based scores (as an average of the experimental scores of the nodes in the path) and experiment-based p-values (by aggregating p-values of the nodes in the path using Fisher’s combined probability test and permutation approach). The method is illustrated by analyzing the results of miRNA loss-of-function screening and transcriptomic profiling of terminal muscle differentiation and of ‘druggable’ loss-of-function screening of the DNA repair process. The Java source code is available on GitHub page https://github.com/daggoo/masterPATH

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Liu, Yuan. "Mixed anova model analysis of microarray experiments with locally polled error /." Electronic version (PDF), 2004. http://dl.uncw.edu/etd/2004/liuy/yuanliu.pdf.

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Tchitchek, Nicolas. "Novel statistical and geometrical methods for integrative genomics." Paris 7, 2011. http://www.theses.fr/2011PA077207.

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Durant les trois années de mon projet de doctorat, j'ai développé plusieurs méthodes complémentaires pour l'analyse de données de type -omique, dont: (i) un modèle pour la génomique intégrative dans lequel toutes les sortes d'informations qui peuvent être obtenues sur un génome sont modélisées d'une manière probabiliste unifiée, permettant ainsi d'analyser les corrélations entre des données hétérogènes à l'échelle du génome, (ii) un test statistique ayant pour critère l'amplification de l'expression pour l'identification de gènes différentiellement et similairement exprimés entre deux conditions biologiques, et permettant la détermination d'intervalles de confiance concernant l'amplification, (iii) de nouvelles méthodes de réduction de dimensionnalité qui surpassent les autres méthodes existantes et produisant des représentations géométriques plus facilement interprétables dans le contexte de grands ensembles de données. Ces méthodes ont été appliquées à plusieurs nalyses et études biologiques dans le cadre de collaborations scientifiques: (i) afin d'identifier des domaines fonctionnels dans les régions promotrices de gènes candidats impliqués dans le pseudohypoaldostéronisme. (ii) pour découvrir les réponses transcriptionnelles qui sous-tendent les différences entre les virus pulmonaires faiblement et fortement pathogènes basé sur un ensemble de réponses transcriptomiques. (iii) afin d'étudier la progression du virus de l'hépatite C chez des patients infectés ayant subi une transplantation hépatique (iv) afin d'analyser une banque de marqueur de séquences exprimées obtenues à partir de cellules de sang périphérique de singes verts africains infectés ou non par le SIV
During the three years of my Ph. D. Project, I developed several complementary methods and frameworks for the analysis of -omics data, such as: (i) a framework for integrative genomics in which every kind of information that can be obtained about the genomic processes and features are modeled in a common probabilistic manner, allowing then to analyze the correlations among the heterogeneous genome-wide information, (ii) a fold-change based statistical test for the identification of differentially and similarly expressed genes between two biological conditions, allowing also the determination of confidence intervals of specific confidence levels for the fold-change. (iii) novel dimensionality reduction methods that outperform other related existing methods and provide more interpretable geometrical representations in the context of large dataset of-omics data. These methods have been applied to several biological analyses and studies as part of different scientific collaborations: (i) to identify functional Glucocorticoid Response Elements in the promoter regions of specific candidate genes involved in Type 1 Pseudohypoaldosteronism. (ii) to uncover the host transcriptional responses underlying differences between low- and high- pathogenic pulmonary viruses based on a compendium of host transcription responses of infected cells from mouse lungs. (iii) to study the progression of the hepatitis C virus in infected patients who underwent orthotopic liver transplantation, based on a cohort of transcriptome profiles for liver biopsy specimens, (iv) to analyze an Expression Sequence Tag library obtained from PBMC of African green monkeys infected or not by the SIV

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38

Prakash, Amol. "Algorithms for comparative sequence analysis and comparative proteomics /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6904.

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39

Benevides, Leandro. "Comparative Genomics of Faecalibacterium spp." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.

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Dans le côlon humain, le genre Faecalibacterium est le membre principal du groupe Clostridium leptum et comprend le deuxième genre représentatif le plus commun dans les échantillons fécaux, après Clostridium coccoides. Il a été reconnu comme une bactérie importante favorisant la santé intestinale et est aujourd'hui considéré comme un probiotique de prochaine génération. Jusqu'à récemment, on croyait qu'il n'y avait qu'une seule espèce dans ce genre, mais depuis 2012, certaines études ont commencé à suggérer l'existence de deux phylogroupes dans le genre. Cette nouvelle proposition de reclassification dans ce genre augmente l'importance de nouvelles études, toutes souches confondues, pour mieux comprendre la diversité, les interactions avec l'hôte et les aspects sécuritaires dans son utilisation comme probiotique. Brièvement, dans ce travail, nous introduisons les analyses de génomique comparative au genre Faecalibacterium en effectuant une étude phylogénétique profonde et en évaluant les aspects de sécurité pour son utilisation comme probiotique. Les analyses phylogénétiques comprenaient non seulement l'utilisation classique du gène de l'ARNr 16S, mais aussi l'utilisation de 17 génomes et techniques complets comme le typage de séquence multi-locus (wgMLST), l'identité nucléotidique moyenne (ANI), le synténie génique et le pangénome. C'est aussi le premier travail à combiner une analyse du développement du pangénome avec l'analyse ANI afin de corroborer l'attribution de souches à de nouvelles espèces. Les analyses phylogénétiques ont confirmé l'existence de plus d'une espèce dans le genre Faecalibacterium. De plus, l'évaluation de la sécurité impliquait (1) la prédiction des régions acquises horizontalement (îlots de résistance aux antibiotiques, îlots métaboliques et régions phagiques), (2) la prédiction des voies métaboliques, (3) la recherche de gènes liés à la résistance aux antibiotiques et des bactériocines. Ces analyses ont identifié des îlots génomiques dans tous les génomes, mais aucun d'entre eux n'est exclusif à une souche ou à une génospécie. En outre, ont été identifiés 8 gènes liés aux mécanismes de résistance aux antibiotiques répartis entre les génomes. 126 voies métaboliques ont été prédites et parmi certaines ont été mises en évidence: la dégradation du bisphénol A, le métabolisme du butanoate et la biosynthèse de la streptomycine. En outre, nous avons étudié le contexte génomique d'une protéine (molécule anti-inflammatoire microbienne - MAM) décrite pour la première fois par notre groupe. Cette recherche montre que la MAM apparaît proche des gènes liés au processus de sporulation et, dans certaines souches, proche d'un transporteur ABC
Within the human colon, the genus Faecalibacterium is the main member of the Clostridium leptum cluster and comprises the second-most common representative genus in fecal samples, after Clostridium coccoides. It has been recognized as an important bacterium promoting the intestinal health and today is considered as a potential next generation probiotic. Until recently, it was believed that there was only one species in this genus, but since 2012, some studies have begun to suggest the existence of two phylogroups into the genus. This new proposition of reclassification into this genus increases the importance of new studies, with all strains, to better understand the diversity, the interactions with the host and the safety aspects in its use as probiotic. Briefly, in this work we introduce the comparative genomics analyzes to the genus Faecalibacterium performing a deep phylogenetic study and evaluating the safety aspects for its use as a probiotic. The phylogenetic analyzes included not only the classical use of 16S rRNA gene, but also the utilization of 17 complete genomes and techniques like whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome. Also, this is the first work to combine an analysis of pangenome development with ANI analysis in order to corroborate the assignment of strains to new species. The phylogenetic analyzes confirmed the existence of more than one species into the genus Faecalibacterium. Moreover, the safety assessment involved the (1) prediction of horizontally acquired regions (Antibiotic resistance islands, Metabolic islands and phage regions), (2) prediction of metabolic pathways, (3) search of genes related to antibiotic resistance and (4) search of bacteriocins. These analyzes identified genomic islands in all genomes, but none of than are exclusive to one strain or genospecies. Also, were identified 8 genes related to antibiotic resistance mechanisms distributed among the genomes. 126 metabolic pathways were predicted and among than some were highlighted: Bisphenol A degradation, Butanoate metabolism and Streptomycin biosynthesis. In addition, we studied the genomic context of one protein (Microbial Anti-inflammatory Molecule - MAM) first described by our group. This investigation shows that MAM appears close to genes related to sporulation process and, in some strains, close to an ABC-transporter

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Pethick, Florence Elizabeth. "Comparative genomic analyses of Corynebacterium pseudotuberculosis." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4287/.

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This study set out to sequence the genome of Corynebacterium pseudotuberculosis (Cp) 3/99-5, an ovine strain isolated from a naturally-occurring case of caseous lymphadenitis (CLA) in Scotland. The isolate was sequenced and assembled by 454 Life Sciences, and then gap closure performed by ‘PCR bridging’. The resulting sequence consisted of three contigs with a length of 2,319,079 bp and a G+C content of 52.18%. The genome was then annotated and predicted to contain 2,153 coding sequences. Analysis of the coding sequences revealed the presence of several putative virulence factors, including four sortases with multiple sortase target proteins containing LPXTG motifs. A further two Cp strains, an Australian ovine and a North American equine isolate, as well as C. ulcerans NCTC 12077 were sequenced for comparison. Comparative genomics, both intra- and inter-species showed all the genomes to be highly homologous. However, the C. ulcerans genome is larger than the Cp genomes and is more distinct; it was found to be more similar to the equine Cp 1/06-A isolate which is the most diverged of the Cp isolates. Phylogenetic analyses of the Corynebacterium genus were performed using house-keeping loci but also secreted protein loci from Cp 3/99-5. Bayesian analysis of house-keeping loci distinguished the bacteria to a species level. Inclusion of secreted protein loci did not distinguish the isolates any further. The main objective of this work was to utilise the Cp genome sequence to identify potential diagnostic targets which could be used to augment the available ELITEST CLA or replace it. The ELITEST CLA is the only diagnostic test for CLA that exists on the commercial market in the UK. However, due to low specificity and sensitivity, it is only operated on a flock/group basis. Analyses of the Cp 3/99-5 genome identified several potential diagnostic candidates and seven protein targets were investigated further. Attempts were made to express these candidates as recombinant proteins, however, only two recombinants were successfully expressed and purified, Cp3995_0570 and CP40. The seroreactivity of these were then assessed by IgG ELISA using a panel of ten positive and ten negative CLA ovine sera. The sera were previously defined as positive or negative by PLD and whole cell ELISAs; both of which showed a significant difference between sera types. However, neither Cp3995_0570 nor CP40 distinguished between sera originating from Cp-infected and Cp-naïve animals.

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Wilson, Ian. "Comparative genomic analyses of Entamoeba species." Thesis, University of Liverpool, 2014. http://livrepository.liverpool.ac.uk/2007270/.

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Amoebiasis is the third-most common cause of mortality worldwide from a disease borne of a parasitic infection. It affects up to 50 million people annually, of which 40,000 to 100,000 cases are fatal. Entamoeba histolytica is an obligate protozoon parasite of humans and is the aetiological agent of the disease. Recent suggestions that other members of the Entamoeba genus are human-infective, and potentially pathogenic, have been investigated here. A draft assembly and annotation of the 25 Mb genome of E. moshkovskii strain Laredo is presented, to which multiple E. moshkovskii strains were mapped. The E. moshkovskii genome was found to be approximately 200 times more variable than that of E. histolytica. Performance of the four-haplotype test revealed that genetic recombination does not seem to occur in E. moshkovskii. As such, it is suggested that it be referred to as a ‘species complex’, rather than an individual species. A comparative genomic analysis of E. histolytica HM-1:IMSS, E. moshkovskii Laredo, E. invadens IP-1 and the avirulent E. dispar SAW760 was performed. Subsequent comparative analyses against members of genera representative of the diversity in the Unikonts clade enabled the identification of orthologous gene families unique to the Entamoeba genus. Analysis of virulence factors within this set revealed that gene families involved in adhesion of amoebic trophozoites to host cells play a key role in the development of invasive amoebiasis. The Gal/GalNAc lectins and members of the BspA family are of particular interest, being present in all analysed species, except for E. dispar. The presence of these key families, plus cysteine proteases, in the E. moshkovskii genome suggests that some sequence types within this species complex may be pathogenic. E. invadens was found to possess larger numbers of more variable genes within many virulence factor families, including the BspA family and the Gal/GalNAc lectins. This suggests that sequence diversity facilitates E. invadens’ polyxenous lifestyle. Finally, a novel species recently isolated from a human faecal sample - E. bangladeshi, strain 8237 – was sequenced. Its genome was assembled using multiple de novo genome assemblers and coding sequences were assembled individually. A combination of all methods tested was found to be beneficial in maximising the number of gene sequences assembled, which is advised as good practice in future similar assemblies. The phylogeny of E. bangladeshi, achieved using the combined assemblies’ outputs suggested that the novel species is human-infective. The work presented here utilised modern comparative genomic techniques to improve understanding of Entamoeba species, their capacity for causing disease and their potential impact upon the epidemiology of amoebiasis.

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Selman, Mohammed. "Genomic Analysis of Encephalitozoon Species." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30314.

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Microsporidia are obligate intracellular pathogens of medical and ecological importance whose genomes have been studied extensively over the last decade. Their parasitic lifestyle has lead them to lose a great number of genes and, thus, biochemical pathways capacities, but these reductive processes have been often offset by the acquisition of several genes by means of horizontal gene transfer (HGT). First, in this thesis, we will describe the complete genomes of Encephalitozoon hellem and Encephalitozoon romaleae. Both species also were found to harbor a number of protein-coding genes absent in other microsporidia, which products assembled complete metabolic pathways. All these genes are functionally related to DNA and folate metabolism, and all appear to have been acquired from HGT events from different eukaryotic and prokaryotic donors. Interestingly in E. romaleae genes involved in de novo synthesis of folate are all pseudogenes, highlighting the transient nature of transferred genes. Secondly, we took a closer look at the ploidy and sexual status of Encephalitozoon cuniculi, a vertebrate pathogen, by mapping Illumina sequence reads against the genomes of four strains of this species. We identified the presence of low level of heterozygosity in all strains investigated; a feature that revealed the diploid nuclear state of the species. This reductive intra-individual genetic diversity could result from the long-term propagation of these strains under laboratory conditions, but we propose that it could also reflect an intrinsic capacity of these vertebrate pathogens to self-reproduce. Overall, the work presented in this thesis resulted in a much greater understanding of the genome evolution of a medically and economically important group of parasites.

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Tam, Mandy Chi-Mun. "Genomic analysis of mouse tumorigenesis." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37454.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2006.
Includes bibliographical references.
The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be valuable in two major ways: in validating mouse models and in identifying genes that are common to mouse and human tumorigenesis. Many analytic tools have emerged in recent years for human genome mining. Some of these tools have been translated to the murine versions. The work in this thesis described the application of two new whole-genome analytic techniques to study mouse tumorigensis: Representational Oligonucleotide Microarray Analysis (ROMA) for tumor DNA copy number asessment and single nucleotide polymorphism (SNP) genotyping using the SNaPshotM system (Applied Biosystems) to detect loss of heterozygosity (LOH) in mouse tumors. The murine version of ROMA was tested on DNA from early-stage KrasGJ2D-derived lung cancers and metastatic retinoblastoma in mice with retinal-specific Rb and p130 deletions. We were interested in identifying the additional genetic lesions that got positively selected during tumorigenesis of these mice.
(cont.) Several recurrent chromosomal copy number gains and losses were observed in the DNA of KrasGJ2D-derived lung tumors. In addition, a focal amplification of the murine N-Myc locus was detected in the metastatic retinoblastomas, demonstrating the capability of ROMA to detect copy number changes at a single-gene resolution. For genome-wide allelotyping, a panel of 147 mouse SNPs were individually validated in 129S4/SvJae vs. C57BL/6J strains and were chosen as markers in the genotyping panel. We worked out a multiplex protocol to genotype the SNPs in an efficient manner. Through this protocol, we generated low-density global LOH maps of lung tumors from mice expressing KrasG12D. LOH that spanned entire chromosomes was seen in a subset of the tumors. A loss of the wild-type p53 allele was also observed in some cases.
by Mandy Chi-Mun Tam.
Ph.D.

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Collinet, Claudio. "System Survey of Endocytosis by Functional Genomics and Quantitative Multi-Parametric Image Analysis." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-38278.

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Endocytosis is an essential cellular process consisting of the internalization of extracellular cargo and its transport towards different intracellular destinations. Multiple endocytic routes are tailored for the internalization and trafficking of different types of cargo and multiple endocytic organelles provide specialized biochemical environments where different molecular events take place. Membrane receptors and cargo molecules are internalized by both Clathrin-dependent and –independent endocytosis into early endosomes. From here two main endocytic routes are followed: 1) the recycling route, mainly followed by membrane receptor and other molecules like Transferrin, brings the cargo back to the plasma membrane and 2) the degradative route, followed by molecules like Epidermal Growth Factor (EGF) and Lipoprotein particles (LDL), leads the cargo to degradation into late endosomes/lysosomes. In addition to the basic function of intracellular cargo transport, the endocytic system fulfils many other cellular and developmental functions such as transmission of proliferative and survival signals and defence against pathogens. In order for cells to properly perform their various and numerous functions in organs and tissues, the activity of the endocytic system needs to be coordinated between cells and, within individual cells, integrated with other cellular functions. Even though molecules orchestrating the endocytic sorting and transport of different types of cargo have long been investigated, our understanding of the molecular machinery underlying endocytosis and its coordination into the cellular systems remains fragmentary. The work presented in this thesis aimed at understanding how this high-order regulation and integration is achieved. This requires not only a comprehensive analysis of molecular constituents of the endocytic system but also an understanding of the general design principles underlying its function. To this end, in collaboration with several members of the Zerial group and with the HT-Technology Development Studio (TDS) at MPI-CBG, I developed a new strategy to accurately profile the activity of human genes with respect to Transferrin (Tfn) and Epidermal Growth Factor (EGF) endocytosis by combining genome-wide RNAi with several siRNA/esiRNA per gene, automated high-resolution confocal microscopy, quantitative multi-parametric image analysis and high-performance computing. This provided a rich and complex genomic dataset that was subsequently subjected to analysis with a combination of tools such as a multi-parametric correlation of oligo profiles, phenotypic clustering and pathways analysis, and a Bayesian network reconstruction of key endocytic features. Altogether, the genomic endeavour and the subsequent analyses provided a number of important results: first, they revealed a much higher extent of off-target effects from RNAi and provided novel tools to infer the specific effects of genes loss of function; second, they identified a large number of novel molecules exerting a regulatory role on the endocytic system, including uncharacterized genes and genes implicated in human diseases; third, they uncovered the regulatory activity of signalling pathways such as Wnt, Integrin, TGF-β, and Notch, and found new genes regulating the sorting of cargo to a specialized subset of early endosomes that function as intracellular signalling platforms; and fourth, a systems analysis by Bayesian networks revealed that the cell specifically regulates the number, size, concentration of cargo and intracellular position of endosomes, thus uncovering novel properties of the endocytic system. In conclusion, the work presented here not only provided a dataset extremely rich of information whose potential has just begun to be uncovered but also shows how genomic datasets can be used to reveal design principles governing the functioning of biological processes.

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Lorentzen, Marc. "Diversity and genomic characteristics of Oenococcus oeni." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0428.

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Oenococcus oeni est une espèce de bactérie lactique adaptée à l'environnement hostile de la fermentation du vin. Elle montre un degré de spécialisation remarquable face au stress provoqué par le faible pH et la forte teneur en éthanol, ce qui lui permet de proliférer là où la plupart des bactéries ne survivent pas. Cette bactérie est très importante dans la production de vin, car elle réalise la fermentation malolactique, qui se produit après la fermentation alcoolique, et au cours de laquelle l'acide malique est métabolisé en acide lactique et où le vin est désacidifié. L'espèce accumule des mutations plus vite que les autres espèces de bactéries lactiques, ce qui a probablement accéléré le processus de domestication. Son degré de spécialisation a été démontré par la présence de populations spécifiques adaptées aux vins rouges ou aux vins blancs dans la même région. Dans cette étude, nous avons utilisé des approches de séquençage haut débit et de génomique pour élucider la diversité des souches d’O. oeni, identifier leurs caractéristiques génomiques et mesurer leur dispersion dans différents environnements ainsi que leur dynamique au cours des fermentations. En raison de son importance pour la vinification, plusieurs centaines de souches ont été isolées et séquencées. Dans ce travail, nous avons augmenté la collection de génomes en séquençant des souches de cidre et de kombucha et en effectuant des analyses phylogénétiques afin de clarifier la structure de la population de l'espèce. En calculant un pangénome à l'échelle de l'espèce, nous avons effectué une analyse génomique comparative afin d'explorer des gènes spécifiques à une ou plusieurs sous-populations. Avec le séquençage de nouvelle génération, nous avons produit des génomes entièrement circularisés à partir des principales sous-populations et analysé leurs arrangements génomiques. Ces nouveaux génomes ont été annotés avec de nouveaux pipelines automatiques et une curation manuelle pour la première fois depuis la publication du génome de référence PSU-1. L’évolution des communautés bactériennes au cours de la fermentation, du moût de raisin au vin fini, a été examinée par le séquençage de fragments 16S dans quatre exploitations du bordelais. À l’aide d’amorces universelles et spécifiques, nous avons comparé la biodiversité des espèces dans des vins issus d’agriculture biologique ou conventionnelle. De plus, en se basant sur les groupes phylogénétiques de souches d’O. oeni nouvellement définis, nous avons développé une méthode de qPCR pour analyser la dispersion des groupes de souches d’O. oeni et leur dynamique au cours des fermentations. Cette nouvelle méthode a également été utilisée pour analyser la diversité des souches d’O. oeni dans les vins de base de Cognac et au cours de la production de cidre, deux produits qui se distinguent des productions de vins traditionnels par la non-utilisation de sulfites. Les deux autres espèces du genre Oenococcus, O. kitaharae et O. alcoholitolerans, se retrouvent également dans les environnements de boissons fermentées. O. kitaharae ne possède pas de gène malolactique fonctionnel, mais O. alcoholitolerans, découvert plus récemment, serait capable de réaliser la réaction malolactique. Nous l’avons caractérisée, ainsi que sa tolérance aux facteurs de stress de l'environnement vin. Constatant qu'elle était incapable de survivre dans le vin, nous avons produit un génome entièrement circularisé d'O. alcoholitolerans et effectué une analyse de génomique comparative afin d'identifier les gènes d'O. oeni lui permettant de tolérer le pH et l'éthanol, ce qui manque à O. alcoholitolerans et à O. kitaharae. En conclusion, nous avons utilisé les nouvelles technologies de séquençage de nouvelle génération pour produire des génomes de haute qualité et effectuer des analyses comparatives approfondies à l’échelle de l’espèce qui nous ont permis d’identifier des gènes susceptibles d’expliquer l’adaptation d’O. oeni à l’environnement
Oenococcus oeni is a lactic acid bacteria species adapted to the inhospitable environment of fermenting wine, where it shows a remarkable degree of specialization to the stress of low pH and high ethanol that allows it to proliferate where most bacteria fail to survive. The bacteria is supremely important in wine production, because it carries out malolactic fermentation, a process that occurs after alcoholic fermentation, where malic acid is metabolised into lactic acid and the pH of the wine is raised. The species has only a small genome and accumulates mutations several orders of magnitude faster than other lactic acid bacteria due to a loss of DNA mismatch repair genes. This has likely sped up the process of domestication to wine. The degree of specialization has been demonstrated by finding specific populations adapted to red or white wines in the same region. In this study, we used high throughput sequencing and genomics approaches to elucidate the diversity of O. oeni strains, to identify their genomic characteristics and measure their dispersion in different environments as well as their dynamics during fermentation. Because of its importance to wine-making, several hundred strains have been isolated and sequenced. In this work, we have expanded upon the collection of genomes by sequencing strains from cider and kombucha and performing phylogenetic analyses to clarify the population structure of the species. By calculating a species-wide pangenome, we performed comparative genomics to explore gene clusters that were specific to one or more sub-populations. With next generation sequencing, we produced fully circularized genomes from the major sub-populations and analysed their genomic arrangements. These new genomes were annotated with new, automatic pipelines and manual curation for the first time since the publication of the reference genome PSU-1. The evolution of bacterial communities over the course of fermentation, from grape must to finished wine, was examined with 16S amplicon sequencing in four Bordeaux wineries. Using a universal and a specific primer-set, we compared the biodiversity in wines resulting from organic or conventional farming practices. In addition, with the newly defined phylogenetic groups, we developed a qPCR experiment to detail the composition of O. oeni in the fermentations and cemented the dispersal of even rarely isolated strain sub-populations in grape must. This new method was also used to analyse the diversity of O. oeni strains in the base wines of Cognac and during the production of cider, two products that are distinguished from traditional wine production by not using sulfite. The two other species in the Oenococcus genus, kitaharae and alcoholitolerans, are also found in the environments of fermenting beverages. O. kitaharae does not have a functional malolactic gene, but the more recently discovered O. alcoholitolerans was thought capable of performing the malolactic reaction. We characterized this, as well as the species tolerance for the stressors of the wine environment. Finding it unable to survive in wine, we produced a fully circularized genome of O. alcoholitolerans and performed a comparative genomics analysis to identify the O. oeni genes that enable it to tolerate the pH and ethanol, which O. alcoholitolerans and O. kitaharae lacks. In conclusion, we have used the new technologies of next generation sequencing to produce high-quality genomes and performed extensive, species-wide comparative analyses that allowed us to identify patterns in gene presence that provide likely explanations for environmental adaptation

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46

Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.

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47

Schroeder, Michael Philipp 1986. "Analysis and visualization of multidimensional cancer genomics data." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/301436.

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Cancer is a complex disease caused by somatic alterations of the genome and epigenome in tumor cells. Increased investments and cheaper access to various technologies have built momentum for the generation of cancer genomics data. The availability of such large datasets offers many new possibilities to gain insight into cancer molecular properties. Within this scope I present two methods that exploit the broad availability of cancer genomic data: OncodriveROLE, an approach to classify mutational cancer driver genes into activating and loss of function mode of actions and MutEx, a statistical measure to assess the trend of the somatic alterations in a set of genes to be mutually exclusive across tumor samples. Nevertheless, the unprecedented dimension of the available data raises new complications for its accessibility and exploration which we try to solve with new visualization solutions: i) Gitools interactive heatmaps with prepared large scale cancer genomics datasets ready to be explored, ii) jHeatmap, an interactive heatmap browser for the web capable of displaying multidimensional cancer genomics data and designed for its inclusion into web portals, and iii) SVGMap, a web server to project data onto customized SVG figures useful for mapping experimental measurements onto the model.
El cancer és una malaltia complexa causada per alteracions somàtiques del genoma i epigenoma de les cèl•lules tumorals. Un augment d’inversions i l'accés a tecnologies de baix cost ha provocat un increment important en la generació de dades genòmiques de càncer. La disponibilitat d’aquestes dades ofereix noves possibilitats per entendre millor les propietats moleculars del càncer. En aquest àmbit, presento dos mètodes que aprofiten aquesta gran disponibilitat de dades genòmiques de càncer: OncodriveROLE, un procediment per a classificar gens “drivers” del càncer segons si el seu mode d’acció ésl'activació o la pèrdua de funció del producte gènic; i MutEx, un estadístic per a mesurar la tendència de les mutacions somàtiques a l’exclusió mútua. Tanmateix, la manca de precedents d’aquesta gran dimensió de dades fa sorgir nous problemes en quant a la seva accessibilitat i exploració, els quals intentem solventar amb noves eines de visualització: i) Heatmaps interactius de Gitools amb dades genòmiques de càncer a gran escala, a punt per ser explorades, ii) jHeatmap, un heatmap interactiu per la web capaç de mostrar dades genòmiques de cancer multidimensionals i dissenyat per la seva inclusió a portals web; i iii) SVGMap, un servidor web per traslladar dades en figures SVG customitzades, útil per a la transl•lació de mesures experimentals en un model visual.

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Landfors, Mattias. "Normalization and analysis of high-dimensional genomics data." Doctoral thesis, Umeå universitet, Institutionen för matematik och matematisk statistik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-53486.

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In the middle of the 1990’s the microarray technology was introduced. The technology allowed for genome wide analysis of gene expression in one experiment. Since its introduction similar high through-put methods have been developed in other fields of molecular biology. These high through-put methods provide measurements for hundred up to millions of variables in a single experiment and a rigorous data analysis is necessary in order to answer the underlying biological questions. Further complications arise in data analysis as technological variation is introduced in the data, due to the complexity of the experimental procedures in these experiments. This technological variation needs to be removed in order to draw relevant biological conclusions from the data. The process of removing the technical variation is referred to as normalization or pre-processing. During the last decade a large number of normalization and data analysis methods have been proposed. In this thesis, data from two types of high through-put methods are used to evaluate the effect pre-processing methods have on further analyzes. In areas where problems in current methods are identified, novel normalization methods are proposed. The evaluations of known and novel methods are performed on simulated data, real data and data from an in-house produced spike-in experiment.

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49

Revilla, Sánchez Manuel. "Genomic and functional genomic analysis of fatty acid composition in swine." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/405710.

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El cerdo es una de las principales fuentes de carne consumida por el hombre y las preferencias de los consumidores hacia productos de alta calidad han aumentado durante los últimos años. Por lo tanto, conocer los mecanismos moleculares que afectan a la producción y a la calidad de esta carne ayudaría a la selección de estos caracteres. La calidad de la carne está determinada en gran medida por la composición de los ácidos grasos (AG) y la comprensión de los procesos moleculares subyacentes a éstos son el objetivo general de esta tesis. En este trabajo, se han identificado QTLs en el cromosoma 8 porcino (SSC8) para la composición de AG en grasa dorsal (GD) y se han identificado dos regiones cromosómicas con SNPs asociados, localizadas a 93 y 119 Mb. Las señales estadísticamente más significativas para ambas regiones se observaron para el ácido palmitoleico y los índices C18:0/C16:0 y C18:1(n-7)/C16:1(n-7). Los genes MAML3 y SETD7 fueron estudiados como genes candidatos posicionales para la región localizada a 93 Mb. Los dos nuevos microsatélites analizados en el gen MAML3 y el SNP del gen SETD7 (SETD7:c.700G>T) no mostraron las asociaciones más significativas en esta región, descartando estos polimorfismos como las mutaciones causales. Además, en la región localizada a 119 Mb, el SNP ELOVL6:c.-533C>T mostró la asociación más significativa con el porcentaje de los ácidos palmítico y palmitoleico y los índices de elongación en GD. Los resultados obtenidos para el gen ELOVL6, gen candidato posicional del QTL localizado a 119 Mb refuerzan la hipótesis de su efecto pleiotrópico sobre la composición de AG en GD y en músculo, y su papel en la determinación del QTL del SSC8 para el perfil de AG. Por otra parte, se utilizaron datos del genoma completo de cerdos ibéricos y landrace para identificar 1.279 variaciones en el número de copias (CNV), las cuales se fusionaron en 540 regiones de CNVs (CNVRs). El impacto de cuatro de ellas fue estudiado para caracteres de crecimiento y composición de AG. Se encontró asociación con la longitud de la canal y la composición de AG en grasa intramuscular y GD para el CNVR112. Este CNVR contiene el gen GPAT2 que cataliza la biosíntesis de triglicéridos y glicerofosfolípidos. Los resultados obtenidos subrayan la importancia de los CNVRs en la determinación de caracteres económicamente importantes en el cerdo. Finalmente, se analizó la expresión de 44 genes candidatos relacionados con el metabolismo lipídico en 115 animales. El estudio de asociación genómico con los datos de expresión (eGWAS) identificó 193 eSNPs localizados en 19 eQTLs. Tres de los eQTLs correspondientes a los genes ACSM5, FABP4 y FADS2 se clasificaron como cis-eQTLs; mientras que los 16 eQTLs restantes mostraron efectos reguladores en trans. Estos hallazgos, junto con los polimorfismos evaluados para alguno de estos genes, mejoran nuestro conocimiento sobre los mecanismos funcionales implicados en la variación de los caracteres relacionados con la calidad de la carne porcina.
Pork is one of the main sources of human-consumed meat and consumer’s preference towards high quality meat is increasing. Hence, understanding the molecular mechanisms affecting meat production and quality would help in the selection of these traits. Meat quality is determined largely by its fatty acid (FA) composition and understanding the underlying molecular processes of FA composition is the general objective of this thesis. We analyzed quantitative trait loci (QTL) on porcine chromosome 8 (SCC8) for FA composition in backfat, identifying two trait-associated SNP regions at 93 Mb and 119 Mb. The strongest statistical signals for both regions were observed for palmitoleic acid and, C18:0/C16:0 and C18:1(n-7)/C16:1(n-7) elongation ratios. MAML3 and SETD7 genes were analyzed as positional candidate genes in the 93 Mb region. The two novel microsatellites analyzed in the MAML3 gene, and the SETD7:c.700G>T SNP in the SETD7 gene did not show the strongest signal in this region, discarding these polymorphisms as the causal mutations. Furthermore, in the 119 Mb region, the ELOVL6:c.-533C>T SNP showed a strong association with the percentage of palmitic and palmitoleic acids and elongation ratios in backfat. These results for ELOVL6 gene, support the hypothesis that it has a pleiotropic effect in backfat and muscle for the 119 Mb QTL, and reinforce this gene as a strong candidate for the SSC8 QTL for FA composition. Moreover, whole genome sequence (WGS) data from Iberian and Landrace pigs were used to identify 1,279 copy number variations (CNVs), merging into 540 swine CNV regions (CNVRs). The impact of four of them in growth and FA composition in intramuscular fat and backfat was studied. Association with carcass length and FA composition in backfat and intramuscular fat was showed for the CNVR112, containing the GPAT2 gene which catalyse the biosynthesis of triglycerides and glycerophospholipids. These results underline the importance of CNVRs affecting economically important traits in pigs. Finally, the adipose tissue mRNA expression of 44 candidate genes related with lipid metabolism was analyzed in 115 animals. The expression genome-wide association (eGWAS) identified 193 eSNPs located in 19 expression QTLs (eQTLs). Three out of 19 eQTLs corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs had trans-regulatory effects. These findings and the polymorphisms evaluated for some of these genes provide new data to further understand the functional mechanisms implicated in the variation of meat quality traits in pigs.

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Ming, Jingsi. "Statistical methods for integrative analysis of genomic data." HKBU Institutional Repository, 2018. https://repository.hkbu.edu.hk/etd_oa/545.

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Thousands of risk variants underlying complex phenotypes (quantitative traits and diseases) have been identified in genome-wide association studies (GWAS). However, there are still several challenges towards deepening our understanding of the genetic architectures of complex phenotypes. First, the majority of GWAS hits are in non-coding region and their biological interpretation is still unclear. Second, most complex traits are suggested to be highly polygenic, i.e., they are affected by a vast number of risk variants with individually small or moderate effects, whereas a large proportion of risk variants with small effects remain unknown. Third, accumulating evidence from GWAS suggests the pervasiveness of pleiotropy, a phenomenon that some genetic variants can be associated with multiple traits, but there is a lack of unified framework which is scalable to reveal relationship among a large number of traits and prioritize genetic variants simultaneously with functional annotations integrated. In this thesis, we propose two statistical methods to address these challenges using integrative analysis of summary statistics from GWASs and functional annotations. In the first part, we propose a latent sparse mixed model (LSMM) to integrate functional annotations with GWAS data. Not only does it increase the statistical power of identifying risk variants, but also offers more biological insights by detecting relevant functional annotations. To allow LSMM scalable to millions of variants and hundreds of functional annotations, we developed an efficient variational expectation-maximization (EM) algorithm for model parameter estimation and statistical inference. We first conducted comprehensive simulation studies to evaluate the performance of LSMM. Then we applied it to analyze 30 GWASs of complex phenotypes integrated with nine genic category annotations and 127 cell-type specific functional annotations from the Roadmap project. The results demonstrate that our method possesses more statistical power than conventional methods, and can help researchers achieve deeper understanding of genetic architecture of these complex phenotypes. In the second part, we propose a latent probit model (LPM) which combines summary statistics from multiple GWASs and functional annotations, to characterize relationship and increase statistical power to identify risk variants. LPM can also perform hypothesis testing for pleiotropy and annotations enrichment. To enable the scalability of LPM as the number of GWASs increases, we developed an efficient parameter-expanded EM (PX-EM) algorithm which can execute parallelly. We first validated the performance of LPM through comprehensive simulations, then applied it to analyze 44 GWASs with nine genic category annotations. The results demonstrate the benefits of LPM and can offer new insights of disease etiology.

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Dissertations / Theses on the topic 'Genomics analyses'

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