Tesis sobre el tema "Genomics"
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Batzoglou, Serafim. "Computational genomics : mapping, comparison, and annotation of genomes". Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8629.
Texto completoIncludes bibliographical references (leaves 180-191).
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in genomics. In this thesis we address key issues in the different stages of genome research: planning of a genome sequencing project, obtaining and assembling sequence information, and ultimately study, cross-species comparison, and annotation of finished genomic sequence. We present applications of computational techniques to the above areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we present results on the theoretical problem of finding minimum superstrings of hypergraphs, a combinatorial problem motivated by physical mapping. We also present a statistical and simulation study of "walking with clone-end sequences", an important method for sequencing a large genome.
(cont.) (2) Turning to the problem of obtaining the finished genomic sequence, we present ARACHNE, a prototype software system for assembling sequence data that are derived from sequencing a genome with the "shotgun" method. (3) Finally, we turn to the computational analysis of finished genomic sequence. We present GLASS, a software system for obtaining global pairwise alignments of orthologous finished sequences. We finally use GLASS to perform a comparative structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA, the first cross-species comparison-based system for the prediction of protein coding regions in genomic sequences.
by Serafin Batzoglou.
Ph.D.
Roidl, Andreas. "“Functional Genomics”". Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-67491.
Texto completoTiwari, Jitesh. "Assembly and Automated Annotation of the Clostridium scatologenes Genome". TopSCHOLAR®, 2012. http://digitalcommons.wku.edu/theses/1175.
Texto completoSt, Jean Andrew Louis. "Haloarchaeal comparative genomics and the local context model of genomic evolution". Thesis, University of Ottawa (Canada), 1996. http://hdl.handle.net/10393/10308.
Texto completoAl-Nuaimi, Bashar. "Ancestral Reconstruction and Investigations of Genomics Recombination on Chloroplasts Genomes". Thesis, Bourgogne Franche-Comté, 2017. http://www.theses.fr/2017UBFCD042/document.
Texto completoThe theory of evolution is based on modern biology. All new species emerge of an existing species. As a result, different species share common ancestry,as represented in the phylogenetic classification. Common ancestry may explainthe similarities between all living organisms, such as general chemistry, cell structure,DNA as genetic material and genetic code. Individuals of one species share the same genes but (usually) different allele sequences of these genes. An individual inheritsalleles of their ancestry or their parents. The goal of phylogenetic studies is to analyzethe changes that occur in different organisms during evolution by identifying therelationships between genomic sequences and determining the ancestral sequences and theirdescendants. A phylogeny study can also estimate the time of divergence betweengroups of organisms that share a common ancestor. Phylogenetic trees are usefulin the fields of biology, such as bioinformatics, for systematic phylogeneticsand comparative. The evolutionary tree or the phylogenetic tree is a branched exposure the relationsevolutionary between various biological organisms or other existence depending on the differences andsimilarities in their genetic characteristics. Phylogenetic trees are built infrom molecular data such as DNA sequences and protein sequences. Ina phylogenetic tree, the nodes represent genomic sequences and are calledtaxonomic units. Each branch connects two adjacent nodes. Each similar sequencewill be a neighbor on the outer branches, and a common internal branch will link them to acommon ancestor. Internal branches are called hypothetical taxonomic units. Thus,Taxonomic units gathered in the tree involve being descended from a common ancestor. Ourresearch conducted in this dissertation focuses on improving evolutionary prototypesappropriate and robust algorithms to solve phylogenetic inference problems andancestral information about the order of genes and DNA data in the evolution of the complete genome, as well astheir applications
Gaiarsa, S. "EVOLUTION, COMPARATIVE GENOMICS AND GENOMIC EPIDEMIOLOGY OF BACTERIA OF PUBLIC HEALTH IMPORTANCE". Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/525881.
Texto completoThe present thesis is focused on genomic epidemiology of bacterial hospital infections. The hospital environment is unique, as it concentrates a high number of bacterial agents, frequent antibiotic use, and patients with weak immune systems. This combination favours the development and selection of antibiotic resistant strains and the spread of opportunistic infections: in general the thriving of nosocomial pathogens. Genomics and evolutionary approaches have emerged as the cutting edge tools for studying this kind of infections, allowing to study the genomic features of bacterial strains and their evolution. Thanks to the possibility to sequence DNA at a constantly cheaper price, research projects are supported by a growing number of genomes and a considerable amount of genomic data is available in the databases, expanding the amount of possible investigations that can be performed. The first work presented here describes the evolution of the Clonal Complex 258 (CC258) of Klebsiella pneumoniae. Single nucleotide polymorphisms (SNPs) allowed to reconstruct the global phylogeny of the entire species and to collocate the CC258 in its evolutionary context. Furthermore, it was possible to detect the presence of a 1.3 Mb recombination in the genomes of the clade in analysis. A molecular clock approach allowed to date this and other previously discovered recombination events. These findings were used to complete the picture of the evolutionary history of CC258, which is characterized by frequent macro-recombination events. A quick evolutive strategy characterized by exchange of high amount of information is a common feature to other nosocomial pathogens, which develop “superbug” phenotypes. Although common, the macro-recombination evolution model is not shared by all nosocomial infection bacteria. One exception is the SMAL strain of Acinetobacter baumannii, presented in another subproject of this thesis. In this work, the genomes of Sequence Type (ST) 78 of A. baumannii were analyzed. Phylogeny and comparative genomics revealed the presence of two different clades within the ST, presenting different evolutive “lifestyles”. One group (containing the SMAL genomes) was characterized by a lower gene content variability and by the presence of a higher copy number of insertion sequences (ISs). One IS interrupts the comEC/rec2 gene in all the SMAL genomes. This gene codes for a protein involved in the exogenous DNA importation, thus its inactivation limits the gene exchange, suggesting an explanation for the low genomic plasticity. In another work presented in this document, genomic epidemiology was applied to reconstruct the spreading routes of a K. pneumoniae epidemic event in an hospital intensive care unit. At first, a phylogenetic approach was used to separate the isolates that belonged to the outbreak from the sporadic ones. Then the isolation dates and genomic SNPs allowed to build a genomic network, which modelled the chain of infection events in the ward. The reconstruction suggested a star-like diffusion of the pathogen from patient zero to the other infected ones, thus revealing a systematic error in the biosafety procedures of the hospital. This almost-forensic application of genomic epidemiology was also used in two other works presented, both of them concerning the reconstruction of food-borne infections. In one of the works, focused on Salmonella enterica, only synonymous SNPs were used as input to a phylogenetic based investigation, in order to filter out pathoadaptative mutations. In the other article, epidemiological data, molecular typing and SNP-based phylogeny were used to investigate the infection of nine Listeria monocytogenes isolates, which were believed to be part of the same outbreak and in the end proved to be genomically unrelated. Lastly, a review paper on genomic epidemiology is also presented. The article is focused on the latest high impact publications analyzing the genome evolution of bacterial pathogens as well as the propagation dynamics of epidemic outbreaks in very short periods of time. The article also describes the latest historical epidemiological studies, which are possible thanks to modern DNA isolation and sequencing technologies.
Kern, Andrew David. "Drosophila population genomics /". For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.
Texto completoLoman, Nicholas James. "Comparative bacterial genomics". Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/2839/.
Texto completoLin, Ying. "Development and assessment of machine learning attributes for ortholog detection". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 0.31 Mb., 65 p, 2006. http://wwwlib.umi.com/dissertations/fullcit/3220791.
Texto completoMeng, Da. "Bioinformatics tools for evaluating microbial relationships". Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Spring2009/d_meng_042209.pdf.
Texto completoTitle from PDF title page (viewed on June 8, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references.
Shearer, Aiden Eliot. "Deafness in the genomics era". Diss., University of Iowa, 2014. https://ir.uiowa.edu/etd/4750.
Texto completoSeibert, 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.
Texto completoDe, Lazzari Eleonora. "Gene families distributions across bacterial genomes : from models to evolutionary genomics data". Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066406/document.
Texto completoComparative genomics is as a fundamental discipline to unravel evolutionary biology. To overcome a mere descriptive knowledge of it the first challenge is to develop a higher-level description of the content of a genome. Therefore we used the modular representation of genomes to explore quantitative laws that regulate how genomes are built from elementary functional and evolutionary ingredients. The first part sets off from the observation that the number of domains sharing the same function increases as a power law of the genome size. Since functional categories are aggregates of domain families, we asked how the abundance of domains performing a specific function emerges from evolutionary moves at the family level. We found that domain families are also characterized by family-dependent scaling laws. The second chapter provides a theoretical framework for the emergence of shared components from dependency in empirical component systems with non-binary abundances. We defined a positive model that builds a realization from a set of components linked in a dependency network. The ensemble of resulting realizations reproduces both the distribution of shared components and the law for the growth of the number of distinct families with genome size. The last chapter extends the component systems approach to microbial ecosystems. Using our findings about families scaling laws, we analyzed how the abundance of domain families in a metagenome is affected by the constraint of power-law scaling of family abundance in individual genomes. The result is the definition of an observable, whose functional form contains quantitative information on the original composition of the metagenome
Mariotti, Marco. "Computational genomics of selenoproteins". Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/295583.
Texto completoLes selenoproteïnes s’agrupen en una classe heterogènia de proteïnes les quals contenen selenocysteïna, l’aminoàcid 21. La selenocisteïna és insertada durant el procés de traducció, recodificant codons UGA molt específics, mitjançant una maquinàiria dedicada. Els programes estàndard de predicció de gens interpreten el codó UGA només com a senyal d’stop de la traducció, i per aquesta raó els gens de selenoproteïness solen estar mal anotats. En els darrers anys, hem desenvolupat eines computacionals per a predir selenoproteïnes a escala genòmica. Amb aquestes, hem caracteritzat el conjunt de selenoproteïnes en aquells genomes que han estat seqüenciats, inferint la seva història filogenèitca. Hem dedicat especial ateníció a la família selenophosphate synthetase, selenoproteïna necessària per a la síntesi de selenocisteïna, i que per tant pot ser utilitzada com a marcador de codificació de selenocisteïna Mostrem que les selenoproteïnes han patit una evolució molt diversa en diferents llinatges. Tot i que es troben molt conservades en vertebrats, les selenoproteïnes van ser perdudes de manera independent en molts altres organismes. Gràcies a la sequenciació de genomes, vam traçar amb precisió els esdeveniment que van portar a l’extinció de selenoproteïnes a diverses espècies de drosòfila.
Axelsson, Erik. "Comparative Genomics in Birds". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7432.
Texto completoMariotti, Marco 1984. "Computational genomics of selenoproteins". Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/295583.
Texto completoLes selenoproteïnes s’agrupen en una classe heterogènia de proteïnes les quals contenen selenocysteïna, l’aminoàcid 21. La selenocisteïna és insertada durant el procés de traducció, recodificant codons UGA molt específics, mitjançant una maquinàiria dedicada. Els programes estàndard de predicció de gens interpreten el codó UGA només com a senyal d’stop de la traducció, i per aquesta raó els gens de selenoproteïness solen estar mal anotats. En els darrers anys, hem desenvolupat eines computacionals per a predir selenoproteïnes a escala genòmica. Amb aquestes, hem caracteritzat el conjunt de selenoproteïnes en aquells genomes que han estat seqüenciats, inferint la seva història filogenèitca. Hem dedicat especial ateníció a la família selenophosphate synthetase, selenoproteïna necessària per a la síntesi de selenocisteïna, i que per tant pot ser utilitzada com a marcador de codificació de selenocisteïna Mostrem que les selenoproteïnes han patit una evolució molt diversa en diferents llinatges. Tot i que es troben molt conservades en vertebrats, les selenoproteïnes van ser perdudes de manera independent en molts altres organismes. Gràcies a la sequenciació de genomes, vam traçar amb precisió els esdeveniment que van portar a l’extinció de selenoproteïnes a diverses espècies de drosòfila.
Östlund, David. "Genomics in the Cloud". Thesis, Uppsala universitet, Institutionen för informationsteknologi, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-453802.
Texto completovan, Tonder Andries J. "Pneumococcal genomics and evolution". Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:de6ba2cc-a1a6-4c86-ad43-6e4e785be46a.
Texto completoSheikh, Sanea. "Genomics of Sorocarpic Amoebae". Doctoral thesis, Uppsala universitet, Systematisk biologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-320432.
Texto completoPadmanabhan, Babu roshan. "Taxano-genomics, a strategy incorporating genomic data into the taxonomic description of human bacteria". Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5056.
Texto completoMy PhD project was to create a pipeline for taxono-genomics for the comparison of multiple bacterial genomes. Secondly I automated the process of assembly (NGS) and annotation using various open source softwares as well as creating in house scripts for the lab. Finally we incorporated the pipeline in describing several bacterial species from out lab. This thesis is subdivided mainly into Taxono-genomics and Microbiogenomics. The reviews in taxono-genomics section, describes about the technological advances in genomics and metagenomics relevant to the field of medical microbiology and describes the strategy taxono-genomics in detail and how polyphasic strategy along with genomic approaches are reformatting the definition of bacterial taxonomy. The articles describes clinically important bacteria, their whole genome sequencing and the genomic, comparative genomic and taxono-genomic studies of these bacteria
Eriksen, Niklas. "Combinatorial methods in comparative genomics". Doctoral thesis, KTH, Mathematics, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3508.
Texto completoLemay, Matthew Alexander. "Ecological genomics of kokanee salmon". Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/48528.
Texto completoIrving K. Barber School of Arts and Sciences (Okanagan)
Biology, Department of (Okanagan)
Graduate
Schéele, Camilla. "Functional genomics studies of PINK1 /". Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-376-4/.
Texto completoSampson, Joshua Neil. "Clustering genes in genetical genomics /". Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9549.
Texto completoChen, Lin. "Causal modeling in quantitative genomics /". Thesis, Connect to this title online; UW restricted, 2008. http://hdl.handle.net/1773/9577.
Texto completoGreninger, Alexander L. "Genomics and Proteomics of Picornaviruses". Thesis, University of California, San Francisco, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3558423.
Texto completoViruses have long been noted to be composed simply of nucleic acid and protein. This thesis describes this confluence of science of viruses at the interface of genomics and proteomics. Chapter 2 describes the discovery of klassevirus, a new picornavirus in pediatric diarrhea. Chapter 3 shows that klassevirus is likely a human pathogen given the seroconversion of klassevirus-positive individuals against a klassevirus non-structural protein that is not present in the picornavirus virion. Subsequent work failed to obtain a culturable virus from klassevirus-positive stool samples, enabling the transition to culture-independent methods of characterizing picornavirus-host protein interactions. Chapter 4 describes the use of affinity purification mass spectrometry to discovery a novel picornavirus 3A-ACBD3-PI4KB complex that promotes viral replication in the enteroviruses and kobuviruses. Chapter 5 extends upon the methodology to describe a novel host protein interactor of ACBD3 (TBC1D22A/B), whose interaction is altered specifically by the kobuvirus 3A protein. This complex also demonstrates significant interaction with the klassevirus 3A protein, suggesting that the AP-MS work may inform the biology of the uncultured virus. Finally, chapter 6 describes future directions that are opened up by this work.
Wang, Ping 1968 Feb 17. "Structure genomics of zebrafish granulins". Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81452.
Texto completoHershman, Steven Gregory. "Personal Genomics and Mitochondrial Disease". Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10863.
Texto completoRodrigues, Ana Paula da Conceição. "Target selection in structural genomics". Thesis, University of York, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428428.
Texto completoManee, Manee. "Comparative genomics of noncoding DNA". Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html.
Texto completoMikkelsen, Tarjei Sigurd 1978. "Mammalian comparative genomics and epigenomics". Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52808.
Texto completoThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references.
The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes and their functional components, and elucidating how these genes are selectively used to establish and maintain cell types with markedly different behaviors, are key challenges of modern biology. In this thesis we present contributions to our understanding of the structure, function and evolution of the human genome. We rely on two complementary approaches. First, we study signatures of evolutionary processes that have acted on the genome using comparative sequence analysis. We generate high quality draft genome sequences of the chimpanzee, the dog and the opossum. These species share a last common ancestor with humans approximately 6 million, 80 million and 140 million years ago, respectively, and therefore provide distinct perspectives on our evolutionary history. We apply computational methods to explore the functional organization of the genome and to identify genes that contribute to shared and species-specific traits. Second, we study how the genome is bound by proteins and packaged into chromatin in distinct cell types. We develop new methods to map protein-DNA interactions and DNA methylation using single-molecule based sequencing technology. We apply these methods to identify new functional sequence elements based on characteristic chromatin signatures, and to explore the relationship between DNA sequence, chromatin and cellular state.
by Tarjei Sigurd Mikkelsen.
Ph.D.
Ryder, Carol D. "Comparative genomics of Brassica oleracea". Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/51651/.
Texto completoPereira, Anirene Galvão Tavares. "Nellore meat quality and genomics". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11141/tde-01082016-181552/.
Texto completoO presente trabalho foi desenvolvido com o objetivo de explorar regiões cromossômicas associadas à características de carcaça e carne em bovinos da raça Nelore, explorar suas funções em vias metabólicas e gênicas relacionadas às manifestações dessas características, assim como gerar novos fenótipos para futuros estudos de associação genômica, com vistas a descrever, de forma completa, as características relacionadas à qualidade do produto final. Para isso, 995 animais machos não castrados, genotipados para mais de 770.000 marcadores de polimorfismos de nucleotídeo único (SNP), foram avaliados quanto ao peso corporal ao nascimento, ganho de peso à desmama e ao sobre ano, conformação, precocidade de terminação e musculosidade à desmama e ao sobre ano. Como estas características são correlacionadas, foram aplicadas metodologias de mapeamento genômico com o objetivo de identificar regiões pleiotrópicas. Os resultados destacaram regiões do genoma bovino que contêm genes descritos por influenciarem em características de crescimento e ganho de peso nestes animais, com destaque para o gene PLAG1, pertencente à região do marcador mais significativo associado aos fenótipos, anteriormente associado ao peso, altura e precocidade sexual em animais dessa raça. Para acessar atributos de qualidade de carcaça e carne, 576 machos não castrados foram avaliados quanto ao peso de carcaça quente, área de lombo, espessura de gordura subcutânea, pH após 24 horas do abate, cor (L*, a*, b*) e perdas de peso por exsudação e cozimento e força de cisalhamento em diferentes tempos de maturação (7, 14 e 21 dias). Os animais foram genotipados em duas plataformas, Illumina® BovineHD BeadChip (HD) e GeneSeek® Genomic Profiler Bovine HD™ Illumina Infinium® (GGP), sendo os genótipos deste último imputados para o conjunto de maior densidade. As avaliações de perdas de peso por exsudação e cozimento e força de cisalhamento, utilizada para mensurar maciez, revelam a influencia da estrutura do citoesqueleto e da ação das enzimas proteolíticas, apontando o complexo enzimático serinas/serpinas como candidato na regulação do processo de proteólise e degradação da estrutura da fibra muscular. Foi realizada avaliação dos ácidos graxos no músculo Longissimus thoracis et lumborum de 148 animais com vistas à classificação das amostras quanto aos efeitos esperados no organismo humano (\"benéfico\", \"maléfico\" ou \"neutro\"), assim como prover informação fenotípica para futuros estudos de associação genômica. A identificação de 42 ácidos graxos e 16 índices gerou informação detalhada sobre a gordura presente na carne destes animais, sendo observado, por análise de componentes principais (PCA), que a maior variação entre a composição das amostras avaliadas parece ser em decorrência da diferença de expressão das enzimas elongases e dessaturases. Dessa forma, espera-se que os dados, informações e conhecimento gerados por este trabalho, possam auxiliar os programas de melhoramento genético animal a aprimorar o rebanho brasileiro segundo características de interesse da cadeia produtiva de carne.
Sargsyan, Alex. "Genetics and Genomics in Nursing". Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/etsu-works/8471.
Texto completoBelal, Nahla Ahmed. "Two Problems in Computational Genomics". Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/26318.
Texto completoPh. D.
Pereira, Pagarete Antonio Joaquim. "Functional Genomics of Coccolithophore Viruses". Paris 6, 2010. http://hal.upmc.fr/tel-01111009v1.
Texto completoEmiliania huxleyi Virus (EhV) is a giant nucleo-cytoplasmic double stranded DNA virus that belongs to the Phycodnavirus family. It has the capacity to infect Emiliania huxleyi, the most abundant coccolithophore in today’s oceans. Population dynamics of these eukaryotic microalgae is clearly controlled by the severe lytic action of EhV. After an extended bibliographic review on the current knowledge existing on these viruses, we present a series of bioinformatic and experimental analyses conducted to unveil important functional genomic features of the EhV. Evidence for the transfer of 29 genes between E. Huxleyi’s and the EhV genomes is presented. In particular, we investigate the origin of seven genes involved in the unique viral sphingolipid biosynthesis pathway (SBP) encoded in EhV genome. This is the first clear case of horizontal gene transfer of multiple functionally-linked enzymes in a eukaryotic host-virus system. We then focus on a field E. Huxleyi/EhV system from a mesocosm experiment in Norway. The dynamics of expression for two of the most important homologous, host and virus, genes of this pathway, serine palmitoyl transferase and dihydroceramide desaturase is investigated. Three defined transcriptional stages are reported during the bloom, with the coccolithovirus transcripts taking over and controlling the SBP. Finally, host and virus global transcript abundance occurring along the mesocosm experiment was investigated. The majority of the genes that significantly increased in abundance from pre to post viral takeover corresponded to viral sequences for which there is so far no match in the protein databases. Nonetheless, novel transcription features associated with EhV infection were discovered, namely the utilization of genes potentially related to genetic information processing, posttranslational control, intracellular trafficking mechanisms, and control of programmed cell death. As a conclusion, the entire dataset analysed herein is discussed, followed by the potential implications of these findings and future research perspectives in the field of plankton virology
Bryant, Josephine Maria. "Evolutionary genomics of pathogenic mycobacteria". Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708462.
Texto completoDong, Xin. "Comparative genomics of rickettsia species". Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.
Texto completoThe Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways
Sentausa, Erwin. "Intraspecies comparative genomics of Rickettsia". Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5082/document.
Texto completoThe Rickettsia genus is composed of Gram-negative, obligate intracellular bacteria that cause a range of human diseases around the world. New techniques have led to progress in the identification and classification of Rickettsia, including the introduction of molecular methods like sequence comparison (16S rRNA, ompA, ompB, gltA, sca4 …) and the creation of the subspecies status. Genomics and next-generation sequencing have opened a new way to learn more about the pathogenesis and evolution of Rickettsia. The first part of this thesis is a review on the advantages and limitations of genomics in prokaryotic taxonomy, while the second part consists of the genomic analyses of five Rickettsia subspecies and a new Rickettsia species. Using high-throughput sequencing methods, we obtained the draft genomes of R. sibirica sibirica, R. sibirica mongolitimonae, R. conorii indica, R. conorii caspia, R. conorii israelensis, and R. gravesii. This work can be a basis of further studies to increase the understanding on the disease-causing mechanisms, evolutionary relationships, and taxonomy of rickettsiae
Tsai, Isheng Jason. "Population genomics of Saccharomyces yeasts". Thesis, Imperial College London, 2009. http://hdl.handle.net/10044/1/4361.
Texto completoBeatson, Scott. "Pseudomonas aeruginosa genomics and pathogenesis /". [St. Lucia, Qld.], 2002. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16848.pdf.
Texto completoBenevides, Leandro. "Comparative Genomics of Faecalibacterium spp". Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.
Texto completoWithin 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
CALABRIA, ANDREA. "Data integration for clinical genomics". Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19219.
Texto completoRousset, Francois. "CRISPRi screens in bacterial genomics". Electronic Thesis or Diss., Sorbonne université, 2020. http://www.theses.fr/2020SORUS373.
Texto completoAdvances in sequencing technologies over the past decade have significantly expanded the field of bacterial genomics. In this context, new experimental methods are still required to better understand gene function. The discovery of CRISPR-Cas systems in bacterial adaptive immunity led to the development of a variety of biotechnological tools to target DNA in a sequence-specific manner. In particular, the dCas9 protein can be guided towards a target DNA sequence by short RNAs called sgRNAs to inhibit gene expression in a mechanism called CRISPRi. The present thesis describes the development of a high-throughput screening method based on the pooled synthesis and cloning of sgRNAs libraries. We first showed that CRISPRi screens can confidently predict essential genes in E. coli. We also exploited this method during infection by different bacteriophages to determine which host genes are required for a successful infection. While most genomics studies rely on model strains which fail to represent the genetic diversity of the species, we next developed a CRISPRi platform that is compatible with most isolates from E. coli and closely-related species. A sgRNA library targeting ~3,300 persistent genes from the E. coli species was designed and implemented in a collection of natural isolates to determine the impact of genetic diversity on the essentiality of core genes. We demonstrated how horizontally-transferred genes can modulate core gene essentiality. Altogether, this work shows the potential of high-throughput CRISPRi screens in bacterial genomics
Woo, Yong. "Characterizing the Dynamics of Genome Evolution in Tumorigenesis". Fogler Library, University of Maine, 2009. http://www.library.umaine.edu/theses/pdf/WooY2009.pdf.
Texto completovan, Rensburg Melissa Jansen. "The genomic epidemiology of Campylobacter from the Republic of South Africa". Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:983f9d81-94ea-4149-adae-d5ec397504a8.
Texto completoNelson, Thomas. "The Origins and Maintenance of Genomic Variation in the Threespine Stickleback (Gasterosteus aculeatus)". Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22660.
Texto completoBertoldi, Loris. "Bioinformatics for personal genomics: development and application of bioinformatic procedures for the analysis of genomic data". Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421950.
Texto completoNell’ultimo decennio, l’enorme diminuzione del costo del sequenziamento dovuto allo sviluppo di tecnologie ad alto rendimento ha completamente rivoluzionato il modo di approcciare i problemi genetici. In particolare, il sequenziamento dell’intero esoma e dell’intero genoma stanno contribuendo ad un progresso straordinario nello studio delle varianti genetiche umane, aprendo nuove prospettive nella medicina personalizzata. Essendo un campo relativamente nuovo e in rapido sviluppo, strumenti appropriati e conoscenze specializzate sono richieste per un’efficiente produzione e analisi dei dati. Per rimanere al passo con i tempi, nel 2014, l’Università degli Studi di Padova ha finanziato il progetto strategico BioInfoGen con l’obiettivo di sviluppare tecnologie e competenze nella bioinformatica e nella biologia molecolare applicate alla genomica personalizzata. Lo scopo del mio dottorato è stato quello di contribuire a questa sfida, implementando una serie di strumenti innovativi, al fine di applicarli per investigare e possibilmente risolvere i casi studio inclusi all’interno del progetto. Inizialmente ho sviluppato una pipeline per analizzare i dati Illumina, capace di eseguire in sequenza tutti i processi necessari per passare dai dati grezzi alla scoperta delle varianti sia germinali che somatiche. Le prestazioni del sistema sono state testate mediante controlli interni e tramite la sua applicazione su un gruppo di pazienti affetti da tumore gastrico, ottenendo risultati interessanti. Dopo essere state chiamate, le varianti devono essere annotate al fine di definire alcune loro proprietà come la posizione a livello del trascritto e della proteina, l’impatto sulla sequenza proteica, la patogenicità, ecc. Poiché la maggior parte degli annotatori disponibili presentavano errori sistematici che causavano una bassa coerenza nell’annotazione finale, ho implementato VarPred, un nuovo strumento per l’annotazione delle varianti, che garantisce la migliore accuratezza (>99%) comparato con lo stato dell’arte, mostrando allo stesso tempo buoni tempi di esecuzione. Per facilitare l’utilizzo di VarPred, ho sviluppato un’interfaccia web molto intuitiva, che permette non solo la visualizzazione grafica dei risultati, ma anche una semplice strategia di filtraggio. Inoltre, per un’efficace prioritizzazione mediata dall’utente delle varianti umane, ho sviluppato QueryOR, una piattaforma web adatta alla ricerca all’interno dei geni causativi, ma utile anche per trovare nuove associazioni gene-malattia. QueryOR combina svariate caratteristiche innovative che lo rendono comprensivo, flessibile e facile da usare. La prioritizzazione è raggiunta tramite un processo di selezione positiva che fa emergere le varianti maggiormente significative, piuttosto che filtrare quelle che non soddisfano i criteri imposti. QueryOR è stato usato per analizzare i due casi studio inclusi all’interno del progetto BioInfoGen. In particolare, ha permesso di scoprire le varianti causative dei pazienti affetti da malattie da accumulo lisosomiale, evidenziando inoltre l’efficacia del pannello di sequenziamento sviluppato. Dall’altro lato invece QueryOR ha semplificato l’individuazione del gene LRP2 come possibile candidato per spiegare i soggetti con un fenotipo simile alla malattia di Dent, ma senza alcuna mutazione nei due geni precedentemente descritti come causativi, CLCN5 e OCRL. Come corollario finale, è stata effettuata un’analisi estensiva su varianti esomiche ricorrenti, mostrando come la loro origine possa essere principalmente spiegata da imprecisioni nel genoma di riferimento, tra cui regioni mal assemblate e basi non corrette, piuttosto che da errori piattaforma-specifici.
Schwartz, Marín Ernesto. "Genomic sovereignty and "the Mexican genome"". Thesis, University of Exeter, 2011. http://hdl.handle.net/10036/3500.
Texto completoMigeon, Pierre. "Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17". Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35377.
Texto completoGenetics Interdepartmental Program
Sanzhen Liu
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.