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Price, Meredith Michelle. "DNA and the news media : science journalism and the history of DNA research." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614088.
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Shapiro, Beth Alison. "Inferring evolutionary history and processes using ancient DNA." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288525.
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Daskalaki, Evangelia. "Archaeological Genetics - Approaching Human History through DNA Analysis." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-211156.
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There are a variety of archaeological questions, which are difficult to assess by traditional archaeological methods. Similarly, there are genetic and population genetic questions about human evolution and migration that are difficult to assess by studying modern day genetic variation. Archaeological genetics can directly study the archaeological remains, allowing human history to be explored by means of genetics, and genetics to be expanded into historical and pre-historical times. Examples of archaeological questions that can be resolved by genetics are determining biological sex on archaeological remains and exploring the kinship or groups buried in close proximity. Another example is one of the most important events in human prehistory – the transition from a hunter-gatherer lifestyle to farming - was driven through the diffusion of ideas or with migrating farmers. Molecular genetics has the potential to contribute in answering all these questions as well as others of similar nature. However, it is essential that the pitfalls of ancient DNA, namely fragmentation, damage and contamination are handled during data collection and data analysis. Analyses of ancient DNA presented in this thesis are based on both mitochondrial DNA and nuclear DNA through the study of single nuclear polymorphisms (SNPs). I used pyrosequencing assays in order to identify the biological sex of archaeological remains as well as verifying if fragmented remains were human or from animal sources. I used a clonal assay approach in order to retrieve sequences for the HVRI of a small family-like burial constellation from the Viking age. By the use of low coverage shotgun sequencing I retrieved sequence data from 13 crew members from the 17th century Swedish man-of-war Kronan. This data was used to determine the ancestry of the crew, which in some cases was speculated to be of non-Scandinavian or non-European origin. However, I demonstrate that all individuals were of European ancestry. Finally, I retrieved sequence data from a Neolithic farmer from the Iberian Peninsula, which added one more facet of information in exploring the Neolithization process of Europe. The Neolithic Iberian individual was genetically similar to Scandinavian Neolithic farmers, indicating that the genetic variation of prehistoric Europe correlated with subsistence mode rather than with geography.
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Derksen, Linda Anne. "Agency and structure in the history of DNA profiling : the stabilization and standardization of a new technology /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2003. http://wwwlib.umi.com/cr/ucsd/fullcit?p3083460.
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Duran, Ferrer Martí. "Tracing the developmental history of B-cell tumors by DNA methylation." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/670361.
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The DNA from our cells carries the genetic information to build a human being. This information is interpreted through epigenetic marks that lead to tightly coordinated and cell type-specific gene expression programs. One of these marks is DNA methylation, which has been widely reported to regulate gene expression both in physiological and pathological conditions. Initial studies in cancer identified gene promoter methylation as an alternative to genetic alterations in the silencing of tumor suppressor genes. Nonetheless, genome-wide studies published in the last decade uncovered that the majority of DNA methylation changes in cancer are not directly related to gene regulation, and thus do not have an apparent functional impact. Some of these studies focused on the DNA methylome during B-cell development and malignant transformation to major B-cell neoplasms. These reports unveiled a highly dynamic DNA methylome during B-cell development and provided new insights into the cellular origin, pathogenic mechanisms and clinical behavior of B-cell neoplasms.
Despite these previous studies targeting specific cancers, a holistic perspective of the DNA methylome during the entire normal cell differentiation program and derived neoplasms was missing. This holistic view was neither available for B cells nor for any other human cell lineage, and therefore was the main goal of this thesis. I exploited previously and newly generated data to dissect the sources of DNA methylation variability of major B-cell tumors spanning the whole maturation spectrum in the context of the entire normal B-cell development. These included B-cell acute lymphoblastic leukemia (ALL), mantle cell lymphoma (MCL) (Study 1), chronic lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL) and multiple myeloma (MM). This comprehensive approach using over 2,000 samples showed that the human DNA methylome is more dynamic than previously conceived and uncovered new clinico-biological insights (Study 2). I observed that B-cell tumors display both DNA methylation imprints of normal development and de novo DNA methylation aberrations, which set the basis to build an accurate diagnostic tool for 14 B-cell tumor subtypes with different clinical management. In line with previous knowledge, I identified that most of the DNA methylation changes taking place in individual patients were located in silent chromatin. Remarkably, I could relate this phenomenon to the proliferative history of normal and neoplastic B cells, whereby each cell division seemed to accumulate transcriptionally-inert epigenetic imprints into the genome (Study 3). In general, mitotic activity simultaneously left hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gained or lost DNA methylation. Based on this data, I built the epiCMIT epigenetic mitotic clock considering both hyper- and hypomethylation imprints related to cell division, which significantly improved the performance of previously reported mitotic clocks. Noticeably, the proliferative history traced by the epiCMIT before treatment was highly predictive of future patient outcome, not only in the B-cell tumors studied but also in other human neoplasias. The accumulation of genetic alterations with positive selection increased the epiCMIT, but some specific drivers seemed to confer a particular proliferative advantage to CLL and MCL cells and distinguished patients with a marked adverse outcome (Study 4). Finally, I compared the epiCMIT mitotic clock with another type of epigenetic clock that estimates the chronological age of a person, the so-called Horvath clock. Interestingly, the epiCMIT was strongly associated with an accelerated epigenetic aging in B-cell tumors measured by the Horvath clock, suggesting a crosstalk between mitotic activity and the aging process (Study 3).
In summary, the wealth of data presented in this doctoral thesis uncovers DNA methylation as a holistic tracer of B-cell tumor developmental history and provides new clinico-biological insights for B-cell tumors and cancer in general.L’ADN de les nostres cèl·lules porta la informació genètica necessària per crear un ésser humà. Aquesta informació és interpretada a través de marques epigenètiques que permeten l’ expressió diferencial i altament coordinada dels gens en cada tipus cel·lular. La metilació de l’ADN representa una d’aquestes marques, i ha estat amplament descrita com a reguladora gènica tan en condicions fisiòlogues com en patològiques. Les primeres investigacions en el càncer varen identificar la metilació als promotor dels gens com un mètode alternatiu a les mutacions genètiques per silenciar els gens supressors de tumors. No obstant, estudis del genoma complet durant la darrera dècada han revelat que la majoria de canvis de metilació de l’ADN no estan directament relacionats amb la regulació gènica ,i conseqüentment no tenen aparentment un impacte funcional. Alguns d’aquests estudis s’han centrat en la metilació de l’ADN durant el desenvolupament normal de les cèl·lules B i la seva transformació cap als tipus principals de tumors de cèl·lula B. Aquestes investigacions han descrit un metiloma molt dinàmic durant el desenvolupament de cèl·lules B sanes i han proporcionat nous coneixements sobre la cèl·lula d’origen, els mecanismes patogènics i el comportament clínic de les neoplàsies de cèl·lules B. Malgrat la rellevància d’aquests estudis previs enfocats en cada tumor, faltava una visió holística de la metilació de l’ADN durant un programa sencer de desenvolupament de cèl·lules sanes y les seves neoplàsies derivades. Aquesta visió no estava disponible ni per les cèl·lules B ni per cap altre llinatge humà, i per tant era l’objectiu principal d’aquesta tesis doctoral. Emprant dades prèvies i generades expressament, vaig explorar les fonts de variabilitat en la metilació de l’ADN de les principals neoplàsies de cèl·lula B sorgides al llarg del desenvolupament complet de cèl·lules B sanes. Aquestes neoplàsies varen incloure la leucèmia linfoblàstica aguda de cèl·lules B (LLA), el limfoma de cèl·lules del mantell (LCM) (Estudi 1), la leucèmia limfocítica crònica (LLC), el limfoma difús de cèl·lules B grans (LDCB), i el mieloma múltiple (MM). Aquest enfocament integrador amb més de 2.000 mostres de pacients va desxifrar que el metiloma humà és notablement més dinàmic del que el concebíem, i va revelà nous coneixements biològics i clínics de les neoplasias de cèl·lules B (Estudi 2). Vaig identificar que els tumors de les cèl·lules B presenten empremtes de metilació derivades del desenvolupament normal i canvis adquirits de novo. Ambdós tipus de canvis de metilació de l’ADN varen permetre crear una eina diagnòstica epigenètica molt precisa per 14 subtipus de neoplàsies de cèl·lules B amb diferent abordatge clínic. En consonància amb coneixements previs, vaig identificar que la majoria dels canvis de metilació en l’ADN en el pacients tenien lloc en regions de la cromatina silenciades. Cal destacar que vaig poder relacionar aquest fenomen amb la història proliferativa de les cèl·lules B normals i tumorals, on cada divisió cel·lular semblava que deixava traces epigenètiques en el genoma sense repercussions transcripcionals (Estudi 3). En general, vaig veure que l’activitat mitòtica deixava simultàniament guanys i pèrdues de metilació en l’ADN, però algunes neoplàsies mostraven un biaix cap una direcció o l’altre. Basat en aquestes dades, vaig crear el rellotge mitòtic epigenètic epiCMIT considerant tant guanys com pèrdues de metilació en l’ADN relacionats amb la divisió cel·lular, la qual cosa representa una millora considerable respecte altres rellotges mitòtics proposats prèviament. Cal destacar que la història proliferativa recollida per l’epiCMIT abans del tractament dels pacients va ser altament predictiva del seu futur comportament clínic no només en tumors de cèl·lules B sinó en altres tipus de neoplàsies. Vaig observar que l’acumulació d’alteracions genètiques amb selecció positiva augmentaven l’epiCMIT, però algunes en particular semblaven que conferien una avantatge proliferativa significativa a les cèl·lules de LLC i LCM i distingien pacients amb un comportament clínic molt advers (Estudi 4). Finalment, vaig comparar el rellotge mitòtic epiCMIT amb un altre rellotge epigenètic que identifica de manera molt precisa l’edat cronològica de les persones, l’anomenat rellotge de Horvath. Curiosament, l’epiCMIT estava fortament associat amb una edat accelerada en les neoplàsies de cèl·lula B, suggerint una relació entre l’activitat mitòtica i l’envelliment (Estudi 3). En conclusió, la riquesa de dades presentades en aquesta tesis doctoral revelen la metilació de l’ADN com un traçador holístic del desenvolupament tumoral en les neoplàsies de cèl·lules B, i proporcionen nous coneixements biològics i clínics pels tumors de cèl·lula B i el càncer en general.
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Abernethy, J. K. "Recent human history : inferences from the Y-chromosome and mitochondrial DNA." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1444478/.
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Disciplines such as palaeoanthropology, archaeology, anthropology, and history have been instrumental in formulating hypotheses relating to human history. Genetics has developed into a powerful tool for human population analysis hence it can complement information derived from other disciplines. To date, however, such studies of genetic history have predominantly focussed on prehistoric events. The aim of this thesis was to address several questions formulated from written sources and oral tradition relating to the recent history of populations in the British Isles and Africa. Y-chromosome markers and sequence information from the mitochondrial genome were employed. The male gene pool of the British Isles was investigated using a thorough sampling strategy, with respect to the impact of historical invaders, revealing geographic structuring within the Isles as a result of differential contact with these invaders. With these data for Britain available, the fidelity of (British) surname inheritance was investigated using the Y-chromosome, revealing evidence for the random and non-random adoption of surnames. The scope in Britain was narrowed to the small, but assumed diverse, metropolitan district of Greater London, to assess levels of Y-chromosome and mitochondrial DNA diversity in relation to the rest of Britain and Europe. Finally, the maternal history of the Lemba from Africa was investigated oral tradition and Y-chromosome evidence suggests a Semitic component. The evidence presented here precludes a Jewish maternal heritage, but a Middle Eastern component is possible. This thesis has shown that genetic information can be informative for elucidating the recent history of these populations, therefore confirming the value of including recent events within the scope of genetic history.
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Beltrán, Margarita Sofía. "The speciation history of Heliconius : inferences from multilocus DNA sequence data." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1446412/.
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Heliconius butterflies, which contain many intermediate stages between local varieties, geographic races, and sympatric species, provide an excellent biological model to study evolution at the species boundary. Heliconius butterflies are warningly coloured and mimetic, and it has been shown that these traits can act as a form of reproductive isolation. I present a species-level phylogeny for this group based on 3834bp of mtDNA (COI, COII, 16S) and nuclear loci (Efla, dpp, ap, wg). Using these data I test the geographic mode of speciation in Heliconius and whether mimicry could drive speciation. Recent sister species display variable degrees of geographic overlap, ranging from almost complete overlap (sympatry) to complete non-overlap (parapatry or allopatry). There are frequent shifts in colour pattern within and between sister species which have a positive and significant correlation with species diversity this suggests that speciation is facilitated by the evolution of novel mimetic patterns. My data is also consistent with the idea that two major innovations in Heliconius , adult pollen feeding and pupal-mating, each evolved only once. By comparing gene genealogies from mtDNA and introns from nuclear Tpi and Mpi genes, I investigate recent speciation in two sister species pairs, H. erato/H. himera and H. melpomene/ H. cydno. There is highly significant discordance between genealogies of the three loci, which suggests recent speciation with ongoing gene flow. Finally, I explore the phylogenetic relationships between races of H. melpomene using an AFLP band tightly linked to the Yb colour pattern locus (which determines the yellow bar in the hindwing). At this locus, races group according to geographical location rather than clades inferred from colour pattern phenotype. This and similar loci can be used to facilitate comparative mapping with other Heliconius species. In summary, the patterns at each phylogenetic level using different gene regions are consistent with a scenario of rapid, adaptively driven divergence and speciation in this group.
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Muller, Romy. "Tuberculosis throughout history : ancient DNA analyses on European skeletal and dental remains." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/tuberculosis-throughout-history-ancient-dna-analyses-on-european-skeletal-and-dental-remains(15084f13-8e8d-4f5f-9806-dc9c99ad2dac).html.
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Tuberculosis (TB) has killed millions of people throughout history and still isone of the leading causes of death. Since the early 1990s, ancient DNA(aDNA) research has made considerable contributions to the study of thisinfectious disease in the past. While early studies used polymerase chainreactions (PCRs) solely to identify the TB-causing organisms, namely theMycobacterium tuberculosis complex (MTBC), later approaches extended thefocus to assign the actual disease-causing species or strains of the MTBCbut were either directed at single or few individuals or only provided few data. This research project has screened a large set of European skeletaland dental samples from individuals of the 1st–19th centuries AD for IS6110,an insertion sequence believed to be specific to the MTBC, and has identifieda number of individuals that may indeed have suffered from TB. Reports ofIS6110-like elements in other mycobacteria, however, challenge thesuitability of IS6110 for detecting MTBC. Two sequences similar but notidentical to IS6110 were revealed from several of the samples analysed,supporting the proposal that IS6110 should not serve as the sole target foridentifying MTBC from archaeological material. It cannot be establishedwhere these sequences derive from, but application of a MycobacteriumspecificPCR and targeting of genomic regions of the MTBC that containsingle nucleotide polymorphism (SNPs) indicate that at least some of thesamples contain a range of unknown, most likely environmental, bacterialand/or mycobacterial species. Yet, screening for IS6110 together with thedetection of large sequence polymorphisms (LSPs) and SNPs in othergenomic regions has identified eight individuals to unambiguously containMycobacterium tuberculosis aDNA. Apart from one individual which wasrecovered from Northern France, these skeletons derived from Britisharchaeological excavation sites. The SNP and LSP results enabled theallocation of infecting MTBC strains into various classification systemsreported in clinical literature and revealed that M. tuberculosis strains variedthroughout different time periods, thereby mainly confirming evolutionarypathways suggested in previous studies. Additionally, it was found thatdistinct strains co-existed temporally, and maybe even spatially, in Britainand that at least one individual harboured two different MTBC strains,suggesting a mixed infection. Application of next generation sequencingenabled one of the 19th century strains from Britain to be characterised ineven more detail, revealing closest similarity to a M. tuberculosis strainisolated at the beginning of the 20th century in North America.
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Shook, Beth Alison Schultz. "Ancient DNA and the biological history and prehistory of northeastern North America /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.
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Fages, Antoine. "The genomic history of horse domestication and management : an ancient DNA perspective." Thesis, Toulouse 3, 2018. http://www.theses.fr/2018TOU30329.
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Parmi tous les animaux domestiques, le cheval est sans aucun doute celui ayant le plus influencé l’histoire des peuplements humains. Le cheval domestique a d’abord fourni à de nombreuses civilisations des ressources primaires essentielles telles que la viande et le lait. Utilisé pour sa force physique et comme moyen de transport, il a eu de profondes conséquences sur les mouvements de personnes et de biens ainsi que sur la diffusion de cultures et d’idées à travers l’Eurasie. Le cheval a ainsi fortement contribué à l’expansion de sociétés et d’empires pendant des millénaires, et ce jusqu’au vingtième siècle. Les différentes étapes de la domestication du cheval restent cependant mal comprises d’un point de vue archéologique et sont complexes à retracer à partir des données génétiques recueillies sur les races chevalines actuelles. L’émergence de la génomique ancienne au début des années 2010 a révolutionné la biologie de l'évolution, en donnant un accès direct à l’histoire des populations anciennes et actuelles. Elle est donc particulièrement adaptée pour étudier la transition historique induite par la domestication du cheval. En s'appuyant sur les dernières avancées en matière d’extraction d'ADN ancien et des technologies de séquençage d’ADN à haut débit, ce travail de doctorat vise à décrypter les modifications génétiques sous-jacentes au processus de domestication du cheval. Pour se faire, nous avons généré le plus grand jeu de données génomiques anciennes jamais rassemblées sur un organisme non humain. Celles-ci ont révélé que les chevaux domestiqués pour la première fois à Botai, dans le nord du Kazakhstan, il y a environ 5 500 ans, ne sont pas les ancêtres des chevaux domestiques ayant vécu pendant ces dernières ~4 100 années. Ce sont les ancêtres des chevaux de Przewalski, que l’on pensait jusqu’alors totalement sauvages. Cette découverte inattendue suggère qu'un remplacement majeur de la population de chevaux domestiques a eu lieu au cours du troisième millénaire avant notre ère, contribuant probablement à faire entrer l'humanité dans l'âge du Bronze. En outre, ces trois années de recherche ont permis d'identifier les signatures génétiques associées à différentes stratégies d’élevage du cheval et ont révélé les dynamiques évolutives en jeu lors des étapes clés de la domestication. En particulier, il ressort des analyses de génomes anciens que les chevaux ibériques n’ont contribué que marginalement à la création du cheval domestique tel qu’on le connaît aujourd'hui. Ce travail de thèse a par ailleurs permis de détecter une influence croissante des chevaux perses dès le début du Moyen AgeAmong all domesticates, the horse can confidently be considered as the animal that most impacted the history of human dynamics. Once they domesticated the horse, human civilizations got hold of essential domestication products including meat and milk, but also invaluable secondary products, such as fast transportation and powerful workforce. The horse thus deeply enhanced the circulation of people, goods, culture and ideas, promoting the spread of vast military and political units across Eurasia up until the 1900s. The various steps underpinning horse domestication are however difficult to track in the archaeological record and still poorly understood based on patterns of DNA variation among modern breeds. In the last decade, the advent of ancient genomics has revolutionized evolutionary biology by providing a direct window into the past history of populations. Ancient genomics therefore provides the necessary time travel machine to investigate the key historical transition in the history of humankind that was induced by the horse domestication. Leveraging the latest advances in ancient DNA recovery and High-Throughput sequencing technologies, this PhD project aimed at deciphering the genetic changes underlying the horse domestication process by generating the largest ancient genome dataset for a non-human organism, spanning the whole temporal and geographic range of horse domestication. This dataset revealed that horses first herded at Botai in Northern Kazakhstan ~5,500 years ago are not the ancestors of modern domestic horses but instead of modern Przewalski’s horses, previously thought to represent last true wild population on Earth. This major discovery also suggests that a swift genomic replacement in the domestic stock took place in the third millennium BCE, probably contributing to precipitating humankind into a new metal era, the Bronze Age. Additionally, this PhD work identified the genetic signatures associated with different management strategies and the evolutionary dynamics at play within distinct domestication stages. In particular, we were able to rule out Iberia as a major contributor to the modern domestic stock and moving towards more recent times, we characterized the growing influence of Persian-like horses starting in the early Middle Ages
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Dudar, J. Christopher. "Reconstructing population history from past peoples using ancient DNA and historic records analysis : the Upper Canadian pioneers and land resources /." *McMaster only, 1998.
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McGlashan, Dugald James, and piscador@hotmail com. "Consequences of Dispersal, Stream Structure and Earth History on Patterns of Allozyme and Mitochondrial DNA Variation of Three Species of Australian Freshwater Fish." Griffith University. Australian School of Environmental Studies, 2000. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030226.152217.
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Freshwater systems offer important opportunities to investigate the consequences of intrinsic biological and extrinsic environmental factors on the distribution of genetic variation, and hence population genetic structure. Drainages serve to isolate populations and so preserve historical imprints of population processes. Nevertheless, dispersal between and within drainages is important if the biology of the species confers a good dispersal capability. Knowledge of the population genetic structure or phylogeographic patterns of Australia's freshwater fish fauna is generally depauperate, and the present study aimed to increase this knowledge by investigating patterns of genetic diversity in three Australian species of freshwater fish. I was interested in the relative importance of dispersal capability, the hierarchical nature of stream structure and the consequences of earth history events on patterns of genetic diversity among populations. I examined three species from three families of Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), Craterocephalus stercusmuscarum (Atherinidae) and Hypseleotris compressa (Gobiidae). These species are abundant, have wide overlapping distributions and qualitatively different dispersal capabilities. I was interested in attempting to unravel how the biological, environmental and historical factors had served to influence the patterns and extent of genetic diversity within each species, thereby inferring some of the important evolutionary processes which have affected Australia's freshwater fauna. I used allozyme and 500-650bp sequences from the ATPase6 mitochondrial DNA (mtDNA) gene to quantify the patterns of genetic variation at several hierarchical levels: within populations, among populations within drainages and among drainages. I collected fish at several spatial scales, from species wide to multiple samples within drainages; samples were collected from the Northern Territory, Queensland and New South Wales. The species with the highest potential for dispersal, H. compressa, exhibited the lowest levels of genetic differentiation as measured at several allozyme loci (H. compressa: FST=0.014; P. signifer FST=0.58; C. stercusmuscarum FST=0.74). Populations of H. compressa also had low levels of mtDNA differentiation, with many recently derived haplotypes which were widespread along the coast of Queensland. This suggested either considerable gene flow occurs or recent demographic change in the populations sampled. As there was no relationship between geographic distance and genetic differentiation, the populations appeared to be out of genetic drift - gene flow equilibrium, assuming the two-dimensional stepping stone model of gene flow. Estimating contemporary gene flow was thus difficult. It was apparent that there has been a recent population expansion and / or contraction of H. compressa populations. It was concluded that there has been considerably more connectivity among populations of H. compressa in the recent past than either of the other study species. Populations of P. signifer showed considerable genetic subdivision at different hierarchical levels throughout the sampled range, indicating gene flow was restricted, especially between separate drainages. Two widely divergent regional groups which had high ATPase6 sequence divergence and approximately concordant patterns at allozyme loci were identified. Interestingly, the groups mirrored previous taxonomic designations. There was also significant subdivision among drainages within regional groups. For example, the adjacent Mulgrave-Russell and Johnstone drainages had individuals with haplotypes that were reciprocally monophyletic and had large allozyme frequency differences. This allowed me to examine the patterns of genetic differentiation among populations within drainages of two essentially independent, but geographically close systems. There was as much allozyme differentiation among populations within subcatchments as there was between subcatchments within drainages, and significant isolation by distance among all populations sampled within a drainage. This suggested that the estuarine confluence between subcatchments was not a barrier to P. signifer, but that distance was an important component in the determination of the distribution of genetic diversity within drainages in P. signifer. There were three main areas of investigation for C. stercusmuscarum: comparing upland and lowland streams of the drainages in north Queensland, investigating the consequences of eustasy on coastal margin populations and examining the intriguing distribution of the two putative sub species, C. s. stercusmuscarum and C. s. fulvus in south east Queensland. First, as populations in upland areas of east coast flowing rivers are above large discontinuities in the river profile, their occurrence is presumably the result of gene flow to and / or from lowland areas, or the result of invasions via the diversion of western flowing rivers. Concordant patterns at both genetic markers revealed that the latter possibility was the most likely, with fixed allozyme differences between upland and lowland populations, and large mtDNA sequence divergence. Indeed, it appeared that there may have been two independent invasions into the upland areas of rivers in North Queensland. Second, lowland east coast populations also had large, although not as pronounced, levels of population subdivision. Lack of isolation by distance, but with a concomitant high level of genetic differentiation among many comparisons, was consistent with a scenario of many small, isolated subpopulations over the range. Interestingly, widespread populations in central Queensland coastal populations (drainages which receive the lowest rainfall) were relatively genetically similar. This was consistent with the widest part of the continental shelf which at periods of lower sea level apparently formed a large interconnected drainage, illustrating the effect of eustatic changes on populations inhabiting a continental margin. Third, putative C. s. fulvus in lowland coastal Queensland drainages were genetically more similar to a population of C. s. fulvus collected from a tributary of the Murray-Darling (western flowing) than they were to adjacent putative C. s. stercusmuscarum. This implied that populations in south east Queensland, north to approximately the Burnett River, appeared to be derived from western flowing streams, and not via dispersal from other lowland east coast populations. Determining the relative importance of intrinsic and extrinsic factors to the development of population genetic structure is a difficult task. The present study demonstrated that the species with the highest dispersal potential had the lowest levels of genetic differentiation, waterfalls can limit gene flow, eustasy acts to join and separate populations leading to complex genetic patterns and that drainage rearrangements are important in determining the distribution of genetic diversity of populations now inhabiting isolated drainages. A difficulty with generalising about population genetic structure in obligate freshwater animals is the unique history of not only each drainage, but also the streams within that drainage and the idiosyncratic biological dynamics of the populations inhabiting those drainages.
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Dudar, John Christopher. "Reconstructing population history from past peoples using ancient DNA and historic records analysis, the Upper Canadian pioneers and land resources." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp03/NQ50990.pdf.
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Haynes, Susan. "The history of wild and domesticated vertebrates deduced from modern and ancient DNA sequences." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325669.
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Ashworth, David. "The application of DNA fingerprinting to the conservation of threatened species." Thesis, University of Nottingham, 1992. http://eprints.nottingham.ac.uk/29183/.
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The human polycore minisatellite probes 33.6 and 33.15 developed by Prof. Alec Jeffreys and colleagues have been shown to detect hypervariable minisatellites in many taxonomically dispersed species. The mRNA derivatives of these two probes, pSPT19.6 and pSPT18.15, have here been used to probe the genomes of four species currently maintained in captivity. The wild populations of these species, Rothschild's mynah, the Rodrigues fruit bat, the British Merlin and the New Zealand falcon, are threatened with extinction to varying degrees. By using the technique of DNA fingerprinting, it has been possible to assess the levels of minisatellite variation remaining in these stocks, to confirm or refute the parent/offspring allocations made within, and in the case of Rothschild's mynah, to demonstrate that at least two of the founders of the stock were closely related. In addition, it has been possible to show that there is a significant positive relationship between the similarity coefficient calculated between two adults and the inbreeding coefficient calculated for their offspring.
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Jeffery, Brett. "The role of PPARa in Cytochrome P450 gene expression and DNA synthesis." Thesis, University of Nottingham, 2001. http://eprints.nottingham.ac.uk/10402/.
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Cytochrome family P450 4A encode a major group of enzymes which are involved in the mechanism of peroxisome proliferation in rodents. Induction of CYP4A expression by peroxisome proliferators is due to transcriptional activation, mediated via the peroxisome proliferator activated receptor alpha. Cyp4a enzymes catalyse the w-hydroxylation of fatty acids and eicosanoids, and it has been suggested they thereby play a pivotal role in blood pressure regulation. Murine Cyp4a10, Cyp4a14 and Cyp4a12 genes have been reported by Bell et al (1993) and Heng, et al (1997). There is contradictory evidence in the literature concerning the expression of lauric acid hydroxylase (LAH) and Cyp4a-related protein in mouse liver and kidney. We have previously shown that Cyp4a12 is expressed at high level in a male-specific fashion in liver and kidney of mouse (Bell et al 1993). However, various workers have reported the presence, or absence, of Cyp4a proteins, or LAH, in male mouse liver. Work by Hiratsuka et al (1996) demonstrate that ddY mice show a male specific expression of LAH and Cyp4a-related protein in the liver, while other strains Balb/c and C57BL/6 exhibit no sex difference in neither enzyme or protein. In the kidney, ddY, Balb/c and C57BL/6 all show sexual dimorphism in the expression of both LAH and Cyp4a related protein. The aim of this project was to characterise the expression of mouse Cyp4a12 and resolve the conflicting results in the literature. Findings demonstrate that there is a male specific expression of Cyp4a12 in male liver and kidney. The data differs from Hiratsuka et al in that their findings present no sex difference in Balb/c and C57BL/6 expression of Cyp4a proteins. Hiratsuka et al also determined that in the kidney of ddY, Balb/c and C57BL/6 there is no sex difference in expression of neither enzyme or protein. Data here agrees with these findings and suggests that the sexual dimorphism exhibited by the LAH and Cyp4a related protein in the kidney is due to constitutive expression of Cyp4a12. Thus it appears that there is till a discrepancy between the Cyp4a12 hepatic expression pattern presented here and that of the enzyme and protein determined by Hiratsuka et al. An explanation may infer that the LAH and Cyp4a-related protein measured by Hiratsuka et al is not only Cyp4a12 but also another member of the Cyp4a family. Further work is required to establish what Cyp4a is expressed predominately in the female. Work by Henderson et al (1994) supports the case that this Cyp4a candidate may be Cyp4a10. Continuing studies will clarify the expression pattern of the Cyp4a and also investigate the mechanism of regulation of the Cyp4a family genes and the expression of male specific genes.
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Hoddell, Richard James. "A mtDNA study of aspects of the recent evolutionary history and phylogeographic structure of selected teleosts in coastal environments of south-western Australia." Hoddell, Richard James (2003) A mtDNA study of aspects of the recent evolutionary history and phylogeographic structure of selected teleosts in coastal environments of south-western Australia. PhD thesis, Murdoch University, 2003. http://researchrepository.murdoch.edu.au/99/.
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At present, there is a general lack of information regarding the spatial genetic architecture and genetic diversity of estuarine and coastal freshwater fish in Australia or about the interacting intrinsic, extrinsic and historical influences responsible for sculpting these patterns. This thesis represented the first investigation of the phylogeographic structure and recent evolutionary histories of teleost fishes from the coastal and estuarine environments of south-western Australia, using the resolution afforded by mtDNA sequence data. Available evidence indicated that, to different degrees, these species have limited potential for dispersal amongst local assemblages from different water bodies. As this theoretically reduces the confounding effects of recent gene flow on extant genetic structure, these fishes were well suited to studying the influences of historical factors. Historical influences were expected to be particularly profound, given that these coastal environments underwent massive modifications during Late Quaternary eustatic fluctuations.
The thesis consists of four major components, which explored different aspects of interspecific and intraspecific phylogeny and p hylogeograp hy of three teleost species, based on mtDNA control region and cytochrome b fragments. First, the relationship between the endemic, 'strictly estuarine' Leptatherina wallacei (Atherinidae) and the more widespread, 'estuarine and marine' 6. presbyteroides was examined, with a view to establishing whether 6. wallacei represents a monophyletic or polyphyletic lineage and whether this species was derived recently (i.e. in Holocene estuaries). Second, the phylogeographic structure and genetic diversity of L. wallacei were investigated and compared with data from L. presbyteroides, with a view to using this information to interpret the recent evolutionary histories of each congener. Third, the divergence between assemblages of L. wallacei inhabiting two isolated coastal lakes was used to estimate a maximal substitution rate for the control region, which was then used to infer general time frames for the divergence between the two Leptatherina species and between the major phylogeographic partitions within each species. Fourth, investigations were initiated into phylogeographic patterns and levels of genetic diversity within and among assemblages of Pseudogobius olorum (Gobiidae) from several coastal lakes and an estuary.
Phylogenetic analyses indicated that the two Leptatherina species were characterised by exclusive and reciprocally-monophyletic lineages of aplotypes from both mtDNA regions, supporting the monophyletic origins of L. wallacei. Both 6. wallacei and 6. presbyteroides exhibited high levels of genetic diversity and extensive overall subdivision (e.g. Qsr = 0.691 and 0.644 respectively for control region data). There was a profound phylogeographic break in both species between all conspecific assemblages from the lower west coast (LWC phylogroup) and all those from the south coast (SC phylogroup), which suggested the influences of shared extrinsic and/or historical factors. There was limited genetic structuring within the two major phylogroups of either Leptatherina species, apparently reflecting recent connectivity amongst local assemblages, with subsequent fragmentation and insufficient time for lineage sorting. However, two major phylogeographic breaks distinguished monophyletic control region phylogroups of L. wallacei from the isolated coastal Lake Clifton and Lake Walyungup, consistent with their independent evolution following lacustrine entrapment during the Holocene.
The divergence between these two isolated lacustrine assemblages of Leptatherina wallaceiformed the basis for an estimate of the maximal substitution rate of the control region. While these data were unable to provide a precise estimate of the actual rate of molecular evolution, all the evidence suggested that it was proceeding very rapidly. The maximal rate estimate of 172.3% lineage-' MY-' was among the fastest ever reported. Based on this rate, the two Leptatherina species diverged at least 1 SKya, thus rejecting a Holocene origin for L. wallacei. The divergence between the LWC and SC phylogroups of L. wallacei has been ongoing for at least GKya, while the equivalent divergence in L. presbyteroides has been ongoing for at least 11 Kya. As the time frames of these divergences were consistent with periods of massive environmental modifications associated with the end-Pleistocene fall in sea level and the HMT, it was likely that these factors have played important roles in sculpting the species' divergence and intra-specific genetic structure. Although useful in temporally scaling genetic divergences within and between the two Leptatherina species, wider application of this rate estimate to questions regarding other taxa was limited. For example, evident rate heterogeneity between the genera precluded its use with even the relatively closely-related atherinid Atherinosoma elongafa.
Phylogeographic analyses identified high levels of genetic diversity and extensive genetic subdivision (e.g. st = 0.652 for control region) amongst an estuarine and several lacustrine assemblages of Pseudogobius olorum, although phylogeographic structure was shallower than in either Leptatherina species. There was increased divergence between three assemblages from the lower west coast and two from the south coast, consistent with the profound break evident in the Leptatherina. One lacustrine assemblage appeared to represent a distinct lineage and a preliminary maximal rate estimate (~61.4% lineage-1 MY-1) was calculated based on the minimum divergence of this assemblage from its nearest conspecifics. Although slower than the rate calculated for L. wallacei, this was still high for teleost fishes.
Overall, this study indicated that historical environmental factors, especially those related to Quaternary eustatic changes, have played important roles in sculpting the phylogeography and evolution of three teleost species from south-western Australia. Moreover, as these species have differential dependencies on estuarine environments (is. 'strictly estuarine' vs 'estuarine and marine') and represented two different taxonomic groups (i.e. Atherinoidei and Gobioidei), historical environmental factors may have exerted similar influences on other coastal species in the region.
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Candemir, Guray Fehmi. "Trouble In The Sky." Master's thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12605440/index.pdf.
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DNA supercoiling is an important determinant of variety
of molecular processes because of its influence on substrate
properties of DNA. Many proteins that bind DNA interact in
a negatively supercoil dependent manner. The higher free
energy associated with negative supercoiling is utilized for
binding and subsequent transactions. Protein components of
DNA replication, segregation, transcription and
recombination machinery interact with DNA in topology
dependent manner. Topoisomerases, thus play essential role
in DNA transaction processes. Owing to their influence on
diverse cellular functions, the enzymes are considered as
global regulators. Movement of macromolecular assemblies
along the DNA helix generates internal torsional strain
during replication and transcription. This strain manifests
itself as local domains of supercoils ahead and behind the
helix tracking machinery. If left unchecked, accumulation of
these supercoils could severely affect the survival of the
cells. Cellular systems thus employ more than one
topoisomerase, which act in concert to regulate DNA
topology and maintain a steady-state level of supercoiling
necessary for integrity and functionality of DNA molecules.
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Doura, Menahem Baguio. "Phylogenetic Inference and Neanderthal Mitochondrial DNA: Comparison of Parsimony and Distance Models." Oberlin College Honors Theses / OhioLINK, 2000. http://rave.ohiolink.edu/etdc/view?acc_num=oberlin1544694857120158.
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Heintzman, Peter David. "The preservation and postglacial history of ice age Holartic beetles, as inferred from museum and ancient DNA." Thesis, University of London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.589607.
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Degraded DNA can be recovered from specimens that are preserved in museums and the natural environment. Data generated from such DNA have provided valuable evidence for the assessment of a suite of biologically important questions. However, research of this nature is limited for invertebrate taxa, despite their diversity and ecological necessity. Using DNA data from dry-stored museum and permafrost- preserved ancient specimens, this thesis greatly extends the study of degraded DNA from invertebrates. The thesis focuses on two arctic ground beetle species (Amara alpina, Pterostichus brevicornisi, which are abundant in museum collections and permafrost deposits. A lack of data that characterises the preservation and potential of degraded beetle DNA, and thereby assessment of future possibilities for this emerging field, provided the impetus for the first three results chapters. Using two different sequencing approaches, the preservation of DNA in museum and ancient specimens was investigated. In addition, the taxonomic utility of DNA extracted from these specimens was assessed. These chapters demonstrate that DNA could be routinely recovered from museum specimens. DNA from ancient specimens could be recovered . from A. alpina but not P. brevicornis. In most cases therefore, degraded DNA from these beetles could be used to address further questions. The final two results chapters focus on the response of ~he two study species to a past period of climatically driven change, using DNA data from museum and ancient specimens. In these chapters, the mode of postglacial colonisation of Canada at the end of the last ice age was investigated. It was found that existing models of this process were broadly, but not wholly, correct. This may have implications for models of how beetles will respond to future climatic change. Although some challenges lie ahead, this thesis demonstrates the potential for museum and ancient permafrost-preserved beetle specimens in future, DNA-based, large-scale investigations.
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Kvist, L. (Laura). "Phylogeny and phylogeography of European Parids." Doctoral thesis, University of Oulu, 2000. http://urn.fi/urn:isbn:9514255364.
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Abstract
Mitochondrial DNA sequences were used to study the phylogeny, population structure and colonisation history of Parus species.
The phylogenetic relationships of seven European and three American species were examined by sequencing a part of the cytochrome b gene. Phylogenetically the closest species were the great tit (Parus major) and the blue tit (P. caeruleus). Subgenus Poecile was divided into two clades, one consisting of the Siberian tit (P. cinctus), the Carolina chickadee (P. carolinensis) and the Black-capped chickadee (P. atricapillus) and the other consisting of the marsh tit (P. palustris) and the willow tit (P. montanus). The coal tit (P. ater) and the crested tit (P. cristatus) did not group with any of the species studied.
The population structure and the colonisation history of the willow tit, the great tit and the blue tit were examined by using control region sequences. The results suggest that the historical effective population size in the willow tit has been large and not contracted by the last ice age. Current gene flow must also be extensive as no population structuring was detected.
No population structuring was evident either in the great tit and the populations showed distinctive signs of a recent population expansion. The patterns of genetic variation probably reflect a population bottleneck during the ice age, and a recolonisation of the European continent thereafter, presumably from a refugium situated in the Balkans.
Two maternal lineages were found in the blue tit. The southern lineage was restricted to the Iberian peninsula whereas the northern lineage was detected from all the populations. The colonisation history has been similar to the one suggested for the great tit. The southern lineage, however, may have survived the ice age in a different refugium in the Iberian peninsula and was not as successful as the northern lineage in colonising available regions when the ice retreated. Both, the blue tit and the great tit have continued to expand their distribution northwards during this century and gene flow plays an important role in homogenising the populations.
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Blount, Susan. "Damage to DNA by reactive oxygen species : relevance to the pathogenesis of systemic lupus erythematosus." Thesis, University of Birmingham, 1991. http://etheses.bham.ac.uk//id/eprint/8827/.
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The purpose of this work was to study the effects of reactive oxygen species (ROS) on DNA and to investigate the relevance of ROS-induced DNA damage in systemic lupus erythematosus (SLE). Using model systems of ROS generation, it was found that DNA was damaged by ROS at all levels of its structure, causing strand breaks, base modifications and conformational changes. Hydrogen peroxide, a ROS generated during inflammation in vivo, produced a characteristic type of site-specific damage dependent on the DNA-bound metal ion catalysis of its degradation. 8-hydroxydeoxyguanosine (8OHDG), a modified DNA base, was used as a marker of oxidative damage to investigate the role of DNA damage in the aetiopathogenesis of SLE. Excretion of this adduct was detected in normal urine and is believed to arise from normal oxidative metabolic processes. In patients with active rheumatoid arthritis, this level of 8OHDG excretion was significantly elevated. In contrast, in SLE patients with inflammatory activity, 8OHDG was undetectable in the urine. Investigation of the mechanism responsible for this showed that SLE cells had aberrant removal of 8OHDG from DNA following oxidative stress in vitro compared to normal cells, and that ROS-denatured DNA accumulated in circulating immune complexes associated with the disease. SLE is also characterised by circulating anti-DNA antibodies. These antibodies were found to bind better to ROS-DNA than to native double-stranded DNA. Furthermore, ROS-DNA was able to stimulate lymphocytes to produce anti-DNA antibodies. The pattern of DNA damage seen in SLE patients was typical of that induced by hydrogen peroxide in vitro. This suggests that inflammation generates ROS which cause DNA damage. As a result of defective repair within cells, ROS-DNA is released into the circulation following cell death which can form complexes with anti-DNA antibodies. In addition, the ROS-DNA can stimulate further anti-DNA antibody production by acting directly on cells thus perpetuating the disease process and contributing to immune complex deposition, a deleterious manifestation of the disease process.
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Fehren-Schmitz, Lars, Bastien Llamas, Elsa Tomasto, and Wolfgang Haak. "Ancient DNA and the Early Population History of Western South America: What Have We Learned So Far and Where Do We Go From Here." Pontificia Universidad Católica del Perú, 2014. http://repositorio.pucp.edu.pe/index/handle/123456789/113534.
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Even though the analysis of DNA from archaeological bone comes with some major limitations, it constitutes the most directmeans of investigating prehistoric population dynamics. The interdisciplinary contextualization of genetic data with the archaeological and palaeoecological record helps to reconstruct past population histories and the demography of ancient populations. For South America, palaeogenetic studies have become increasingly important. Here we review the existing ancient DNA data from pre-Columbian individuals to assess their potential to contribute to our understanding of early South American population history. The spatial and temporal distribution of ancient South American populations analysed to date is very uneven and the data resolution of the analysed genetic markers is low. Nevertheless, the data suggest that there were population dynamic processes accompanying cultural development in Western South America. With the new methodologies and better sampling strategies employed in current paleogenetic projects and more effective interdisciplinary cooperations it will be soon possible to achieve a better understanding of the peopling of the continent and the succeeding population history.Aún cuando el análisis de ADN de huesos arqueológicos tiene algunas grandes limitaciones, constituye la manera más directa de investigar eventos prehistóricos de dinámica poblacional. La contextualización interdisciplinaria de los datos genéticos con los registros arqueológico y paleoecológico permite reconstruir las historias poblacionales pasadas y la demografía de sociedades antiguas. Por otro lado, el número de estudios paleogenéticos en Sudamérica se está incrementando. En este artículo revisamos los datos de ADN antiguo de individuos prehispánicos que existen en la actualidad con la finalidad de evaluar su potencial para contribuir a nuestro entendimiento de la historia temprana del poblamiento de Sudamérica. La distribución espacial y temporal de las poblaciones sudamericanas antiguas muestreadas a la fecha es muy irregular y la resolución de los marcadores genéticos analizados esbaja. Sin embargo, los datos sugieren que existieron procesos de dinámica poblacional que acompañaron el desarrollo cultural de la parte oeste de Sudamérica. Con las nuevas metodologías y mejores estrategias de muestreo que se emplean hoy en día en los proyectos de paleogenética, y con una cooperación interdisciplinaria más efectiva, pronto será posible lograr un mejor entendimiento del poblamiento del continente, así como de los hechos sucesivos de su historia poblacional.
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Cranford, Aaron B. "Limits of Life History in Taxonomic Classification of Lampreys with Implications for Conservation." Ohio University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1367849044.
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Garcia-Sancho, Miguel. "Sequencing as a way of work : a history of its emergence and mechanisation : from proteins to DNA, 1945-2000." Thesis, Imperial College London, 2007. http://hdl.handle.net/10044/1/7966.
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Melé, Messeguer Marta. "Incorporating recombination into the study of recent human evolutionary history." Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/22684.
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En aquest treball es pretén utilitzar la informació que deixa la recombinació al nostres genomes per fer inferències sobre la història evolutiva recent de les poblacions humanes. Per fer-ho, s’ha desenvolupat un mètode novedós, anomenat IRiS, que permet la detecció de recombinacions antigues específiques en un conjunt de seqüències. Hem validat extensivament IRiS i l'hem sotmès a diferents escenaris per tal d’avaluar-ne l’ eficàcia. Un cop els events de recombinació són detectats, es poden utilitzar com a marcadors genètics per estudiar els patrons de diversitat de les poblacions humanes. Finalment, hem aplicat aquesta innovadora aproximació a un conjunt de poblacions humanes del Vell Món, que varen ser genotipades específicament amb aquesta finalitat, aportant nous coneixements en la història evolutiva recent dels humansThe aim of this work is to use the information left by recombination in our genomes to make inferences on the recent evolutionary history of human populations. For that, a novel method called IRiS has been developed that allows detecting specific past recombination events in a set of extant sequences. IRiS is extensively validated and studied in whole set of different scenarios in order to assess its performance. Once recombination events are detected, they can be used as genetic markers to study the recombinational diversity patterns of human populations. We apply this innovative approach to a whole set of different human populations within the Old World that were specifically genotyped for this end and we provide new insights in the recent human evolutionary history of our species.
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Do, Kimberly Fearn. "A Determination of Phylogeny and Hybridization History Within Clematis L. (Ranunculaceae) Using Actin and Nitrate Reductase Intron Sequences." Scholar Commons, 2006. http://scholarcommons.usf.edu/etd/3753.
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The phylogeny of Clematis, section Viorna, was characterized in this study using molecular data. Two nuclear introns were sequenced for a variety of taxa: actin and nitrate reductase. Actin intron sequence data yielded very little phylogenetic information. Some basal clades were resolved, but there were very few well supported relationships between species of the Viorna section in both the neighbor joining and maximum parsimony analyses. Nitrate reductase intron sequence data was slightly more variable. The number of well supported relationships in both the neighbor joining and maximum parsimony analyses for nitrate reductase was greater, but still not sufficient to yield an informative tree. Two possible explanations for the lack of variation are that these species have not evolved many differences in these intron sequences or that common alleles are flowing between the species. Hybrid analysis using the actin intron was inconclusive because the experimentally generated hybrid possessed an allele that neither parents tested had. More sampling from multiple individuals from both parent and multiple hybrid individuals is necessary to answer this question. The hybrid specimen tested was homozygous for the nitrate reductase intron marker, and both parents also possessed the allele. This did not directly support or refute the use of these markers for tracking the hybridization history within Clematis.
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Palmé, Anna. "Evolutionary history and chloroplast DNA variation in three plant genera: Betula, Corylus and Salix. : The impact of post-glacial colonisation and hybridisation." Doctoral thesis, Uppsala University, Department of Conservation Biology and Genetics, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3281.
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The great difference in the level of chloroplast variation and its geographic structure among the three main species studied here demonstrates that forest species do not form a homogeneous group. Hazel shows a genetic structure similar to many other thermophilous species and this structure, in combination with fossil evidence, indicates that the post-glacial colonisation of most of Europe originated in a refugium in western France while the Balkan and Italy were colonised from a south-eastern refugium.
In sallow and silver birch the chloroplast DNA variation and its structure does not fit with a scenario of glacial restriction to southern refugia and survival at intermediate latitudes is suggested for both species. The chloroplast DNA variation in silver birch suggests the presence of one western and one eastern European post-glacial colonisation route and limited contribution of southern populations in the colonisation of the rest of Europe. Unique haplotypes by the Ural Mountains indicates the possibility of a separate glacial origin of these populations.
The study of chloroplast DNA in species closely related to sallow and silver birch indicate that extensive hybridisation and cytoplasmic gene flow occurs within both the Salix and Betula genera in Europe. The nuclear and chloroplast phylogenies of 14 Betula species were not in complete agreement with each other or with the classical division of the Betula genus into subgenera or sections. The phylogenetic structure implies that hybridisation has played a role in the evolution of the Betula genus.
This thesis focuses on the chloroplast DNA variation in three forest tree genera: Corylus, Betula and Salix. Chloroplast PCR-RFLP is used to evaluate the post-glacial history of hazel, Corylus avellana, silver birch, Betula pendula and sallow, Salix caprea and to explore the possibility of introgression in the Salix and Betula genera. In addition, the chloroplast matK gene, its flanking regions and the nuclear ADH gene were used to study the phylogenetic relationships within the Betula genus.
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Richner, Sharon M. "The measurement of genetic diversity in mycobacterium tuberculosis using random amplified polymorphic DNA profiling." Thesis, Rhodes University, 2000. http://hdl.handle.net/10962/d1004068.
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Mycobacterium tuberculosis has caused a resurgence in pulmonary disease in both developed and developing countries in recent times, particularly amongst people infected with the human immunodeficiency virus. The disease has assumed epidemic proportions in South Africa and in the Eastern Cape Province in particular. Of further concern is the isolation of increasing numbers of multiply drug resistant strains. Knowledge of the genetic capability of this organism is essential for the successful development of novel antibiotics and vaccines in an attempt to bring the global pandemic under control. Measurement of the genetic diversity of the organism may significantly contribute to such knowledge, and is of vital importance in monitoring epidemics and in improving treatment and control of the disease. This will entail answering a number of questions related to the degree of genetic diversity amongst strains, to the difference between urban and rural strains, and between drug resistant and drug sensitive strains, and to the geographical distribution of strains. In order to establish such baseline information, RAPD profiling of a large population of isolates from the western and central regions of the Eastern Cape Province was undertaken. A smaller number of drug resistant strains from a small area of KwaZulu-Natal were also analysed, with a view to establishing the genetic difference between strains from the two provinces. Cluster analysis, analysis of molecular variance and Geographical Information Systems technology were used to analyse the RAPD profiles generated. An unexpectedly high degree of genetic diversity was detected in strains from both provinces. While no correlation was seen between genetic diversity and either urban-rural situation or geographical location, a small degree of population structure could be correlated with drug resistance in the Eastern Cape. Furthermore, a significant degree of population structure was detected between strains from the two provinces, although this was still within the parameters for conspecific populations. Future work is necessary to further characterise strains from rural areas of both provinces, as well as from the eastern region of the Eastern Cape in an attempt to pinpoint the cause of the separation of the provincial populations.
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Dalén, Love. "Distribution and abundance of genetic variation in the arctic fox." Doctoral thesis, Stockholms universitet, Zoologiska institutionen, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-726.
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This thesis investigates how changes in population size and spatial movements of individuals have shaped the distribution and abundance of neutral genetic variation in the arctic fox. This is done through mitochondrial and microsatellite DNA analyses on samples covering most of the species’ distribution, but with special emphasis on Scandinavia. On the species level, nucleotide diversity was relatively low, which indicated a historical expansion in population size in connection with the onset of the last Ice Age. It is thus possible that the glacial cycles have affected the arctic fox, and other cold-adapted species, in a way opposite to their effect on temperate species. Gene flow seemed to be high among arctic fox populations on a circumpolar scale, especially between populations where lemmings are the main food source, which could be explained by the spatial synchrony in lemming fluctuations. In Scandinavia, the arctic fox went through a severe demographic bottleneck in the beginning of the 20th century. Although some genetic variation was lost during this bottleneck, the loss was much smaller than expected, probably due to post-bottleneck gene flow from Russia. The arctic fox in Scandinavia is divided into four relatively isolated populations. Within each population, dispersal seemed to be high despite the high availability of empty territories close to natal dens, which supported the hypothesis that lemming fluctuations influence arctic fox dispersal. Genetic analyses on samples collected between 1989 and 2004 indicated an ongoing genetic drift and inbreeding within the Scandinavian populations. Furthermore, individual genetic variation was negatively associated with fitness, which could be attributed to an ongoing inbreeding depression. Analyses on faecal samples suggested that arctic foxes move higher up in the mountains and farther from the tree-line during summer compared to winter. This seasonal shift in distribution is probably caused by interspecific competition from the red fox, which is likely to be higher during summer due to red fox predation on arctic fox cubs. The results presented in this thesis have several implications for the conservation of the Scandinavian arctic fox. The finding of four isolated populations within Scandinavia and an ongoing inbreeding depression suggests that the risk of extinction is higher than previously thought. Conservation actions need to be taken in all populations to be effective, and could include genetic restoration through translocation.
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Popp, Magnus. "Disentangling the Reticulate History of Polyploids in Silene (Caryophyllaceae)." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3918.
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Pachon, Adriana Marcela Robles. "Filogeografia a partir de DNA de cloroplasto da orquídea neotropical Epidendrum orchidiflorum (Orchidaceae: Laeliinae) no Brasil." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-05012017-150613/.
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A filogeografia é o campo de estudo que pode revelar a história evolutiva das espécies, sua diversidade e a estrutura genética atual das populações. Neste estudo, foi avaliada a diversidade genética de 13 populações de Epidendrum orchidiflorum (Orchidaceae) utilizando uma abordagem filogeográfica, na tentativa de reconstruir a história evolutiva desta espécie ao longo da Chapada Diamantina e suas serras próximas, do litoral de Bahia e litoral do Rio de Janeiro.Foram usados como marcadores moleculares regiões de DNA de cloroplasto - cpDNA, as quais por serem de herança materna, natureza não recombinante e se encontrarem abundantemente nas plantas, são ideais para este tipo de estudos. Com os dados obtidos do seqüenciamento de duas regiões de cpDNA (rps16-trnK e rpl32-trnL), foram calculados os índices de diversidade para as 13 localidades amostradas, sendo que o número total de haplótipos foi 12. A diversidade haplotípica (Hd) variou de 0 para a população do Litoral da Bahia, Restinga (RE) a 0,889 para a população de Seabra (SE), próxima da Chapada Diamantina. O haplótipo mais freqüente foi o H2 apresentando-se em nove populações. A população RE só apresentou um haplótipo (H2), enquanto que a população de maior diversidade (SE) apresentou seis haplótipos. Além disso, em três populações (SE, Morro do Chapéu e Arraial do Cabo) foram encontrados haplótipos únicos. A análise de variância molecular (AMOVA) indicou que a diferenciação genética encontrada entre populações (FST = 47,5%) é elevada, mostrando que existem diferenças entre populações para esta espécie. No entanto, a proporção de variabilidade de haplótipos encontrados dentro das populações (52,5%, P<0,001) foi maior do que entre as populações.As análises geradas para diferentes agrupamentos testados nas AMOVAS e no programa Migrate-n, sugerem que o melhor modelo que explicaria a conectividade entre as populações seria o modelo de uma grande população panmítica que reúne as populações das serras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI e SE) com migração para as populações do litoral da Bahia (RE) e a população do Rio de Janeiro (AC). Estas análises são suportadas pelas análises geradas da Modelagem de Nicho Ecológico (EEM), indicando que as populações próximas a Chapada Diamantina se encontram conectadas desde a interglaciação e a última glaciação, porém a população do Rio de Janeiro foi separada durante a ultima glaciação, permanecendo isolada, divergindo ao longo do tempo devido à deriva genética e à mutação.Phylogeography is the field of study that may reveal the evolutionary history of the species, their diversity and the current genetic structure of populations. In this study, we evaluated the genetic diversity of 13 populations of Epidendrum orchidiflorum (Orchidaceae ) using a phylogeographic approach in an attempt to reconstruct the evolutionary history of this species along the Chapada Diamantina and its nearby sierras, the Bahia coastline and the Rio de Janeiro coastline. We used as molecular markers chloroplast DNA regions - cpDNA, which are maternally inherited, non-recombinant and found abundantly in plants, and for these reasons are ideal for this type of studies. With the data obtained from the sequencing of two regions of cpDNA(rps16-trnK and rpl32-trnL), the diversity index for the 13 sampled locations were calculated, and the total number of haplotypes was 12.The haplotype diversity (Hd) ranged from 0.0 for the Coastal population of Bahia, Restinga (RE) to 0.889 for the population of Seabra (SE), near the Chapada Diamantina. The most common haplotype was the H2 found in nine populations. The RE population showed only one haplotype (H2), while the population of greater diversity (SE) showed six haplotypes. Moreover, in three populations (SE, Morro do Chapéu and Arraial do Cabo) unique haplotypes were found. The analysis of molecular variance (AMOVA) showed that the genetic difference found between populations (FST = 47.5%) is high, showing that there are differences between populations for this species. However, the proportion of haplotypes variability found within populations (52.5%, P <0.001) was higher than among populations. The analyses generated for different groups tested in AMOVAS and in the Migrate-n program suggest that the best model to explain the connectivity between populations would be the model of a large panmitic population that brings together the populations of the Sierras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI and SE) with migration towards the populations of the coast of Bahia (RE) and the population of Rio de Janeiro (AC). These analyses are supported by the analyses generated by the Ecological Niche Modeling (EEM), indicating that the populations near the Chapada Diamantina are connected since the interglacial and the last glaciation, but the population of Rio de Janeiro was separated during the last glaciation, remaining isolated and diverged over time due to genetic drift and mutations.
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Ferguson, Chad D. "Conservation genetics of a near threatened freshwater mussel species (Lampsilis cardium) and improved prospects for recovery: how nuclear and mitochondrial DNA analyses inform natural history and conservation." Wright State University / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=wright1244144062.
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Costa, Carolina Lemes Nascimento 1989. "Dinâmica populacional ancestral de Poecilia vivipara (Teleostei: Poeciliidae) : a influência das mudanças paleoclimáticas." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/315891.
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Orientadores: Sérgio Furtado dos Reis, Sergio Ivan PerezDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Mudanças climáticas são fenômenos responsáveis por influenciar dinâmicas de populações ao longo da história evolutiva das espécies. Quando mudanças no clima ocorrem de maneira abrupta suas consequências podem ser refletidas na distribuição, no tamanho e na persistência das populações sob o efeito destas mudanças. O Quaternário foi uma época caracterizada por mudanças climáticas rápidas e intensas. Estimar a demografia histórica de populações nesta escala de tempo é uma forma de avaliar como flutuações no clima influenciaram populações ancestrais. Dados genéticos nos permitem recuperar informação sobre o tamanho populacional em escalas de tempo amplas e buscar associações entre flutuações no tamanho das populações e variações no clima. A demografia histórica de populações do peixe de água doce Poecilia vivipara habitantes da planície Quaternária do norte do Rio de Janeiro foi estimada com o objetivo de avaliar se fenômenos em escalas de tempo ancestrais deixaram uma assinatura no genoma dos indivíduos de populações contemporâneas. Subsequentemente, foi avaliado se as assinaturas genéticas são reflexo de respostas populacionais às variações climáticas intensas ocorridas no Quaternário. Para estimar a demografia histórica de P. vivipara, utilizou-se o método Skyline-Plot Bayesiano (BSP), sendo o gene mitocondrial citocromo b o marcador molecular analisado. A dinâmica populacional ancestral de P. vivipara revelou uma mudança de regime nos últimos 75 mil anos, que pode estar associada direta ou indiretamente às variações climáticas do Quaternário. Flutuações no nível do mar, geradas pelas mudanças climáticas do Quaternário, podem estar relacionadas com as flutuações no tamanho populacional de P. vivipara. Estudos incluindo outras regiões do genoma e com maior detalhamento sobre variações climáticas locais podem contribuir para gerar estimações mais confiáveis da história populacional de P. vivipara e sua potencial relação com eventos climáticos
Abstract: Paleoclimatic changes are responsible to influence population dynamics through the evolutionary history of species. When climatic changes occur suddenly its consequences can be reflected in the distribution, size and persistence of populations. The Quaternary was a time of massive climatic changes. The estimation of the demographic history of populations at such timescales allows the assessment of how climatic fluctuations have influenced ancestral populations. Genetic data are available and allow recovering information about population sizes in wide timescales and searching for associations between population size fluctuations and climatic change. The historical demography of freshwater fish Poecilia vivipara populations inhabiting the Rio de Janeiro Northern Quaternary Plain was estimated aiming to evaluate if phenomena in ancestral timescales leaves a signature in the genomes of its modern representatives. Subsequently, we evaluate if the genetic signatures are the result of population responses to massive climatic changes occurred in Quaternary. The Bayesian Skyline-Plot (BSP) was utilized to estimate the demographic history of P. vivipara, with the mitochondrial gene cytochrome b as molecular marker. The ancestral population dynamics of P. vivipara revealed a regime change in the last 75,000 years, which can be direct or indirectly associated to Late Quaternary climatic variations. Sea level fluctuations, generated by Quaternary climatic changes, could be related to population size fluctuations of P. vivipara. Studies including other genome regions and with more details about local climatic variations can create more reliable estimations of the P. vivipara population history and its potential relationship with climatic events
Mestrado
Biodiversidade Animal
Mestra em Biologia Animal
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Mantellatto, Aline Meira Bonfim [UNESP]. "Padrões de distribuição histórica, relações filogenéticas e filogeográficas de veado-mateiro-pequeno, Mazama bororo DUARTE, 1996 (Mammalia: Cervidae)." Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/144487.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Considerada a espécie de cervídeo brasileira mais ameaçada de extinção, Mazama bororo, foi recentemente descrita em 1996. Devido a isso, aspectos básicos de sua biologia ainda são desconhecidos. Dessa maneira, o presente trabalho teve como objetivo utilizar DNA extraído de espécimes recentes e de museus para descrever a sua distribuição histórica, investigar a existência de padrões filogeográficos, avaliar a taxonomia da espécie e os erros de identificação no material analisado pertencente aos acervos científicos de museus. Para tanto, foi realizada a extração de DNA de 200 amostras de ossos turbinais obtidos em museus de história natural e 78 destes espécimes foram identificados a partir de iniciadores do gene citocromo b (224bp). O total de 22 espécimes identificados como pertencentes à espécie Mazama bororo permitiu conhecer áreas inéditas da distribuição histórica e, possivelmente atuais, da espécie, como os estados de Rio Grande do Sul, Minas Gerais, Goiás, Espírito Santo e Bahia. Além disso, a comparação entre o DNA dos holótipos de Mazama bororo e de Mazama americana jucunda indica que a espécie M. bororo corresponde à subespécie M. americana jucunda, descrita em 1913, demonstrando a necessidade de elevar essa subespécie à categoria de espécie. Análises filogeográficas da espécie demonstram que M. bororo não apresenta uma estruturação populacional histórica e que diversidade genética é baixa quando comparada a outras espécies, um indicativo de que políticas de manutenção e conservação dessa espécie são essenciais a sua permanência. Comparando-se as identificações morfológicas presentes nos museus com as identificações obtidas a partir do marcador molecular utilizado observa-se que a taxa de erro decorrente da classificação baseada em caracteres morfológicos foi de 26%. Entretanto, espera-se que, com o auxílio do DNA de coleções científicas, a seleção de caracteres morfológicos não convergentes para este grupo seja possível, permitindo assim a realização de identificações morfológicas corretamente.
Mazama bororo was recently described in 1996 and is considered the most threatened species of Brazilian deer. Due to this, basic aspects of its biology are still unknown. Thus, this research project aims to use DNA extracted from recent specimens and from natural history collections to review the taxonomy, to describe historical distribution and to investigate the existence of phylogeographic patterns on M. bororo. For this purpose, we extracted DNA from 200 samples of turbinate bones obtained from natural history collections and 78 of these were identified from cytochrome b initiator (224bp). We obtained a total of 22 specimens identified as M. bororo. This result allowed identify unpublished areas on historical and perhaps current distribution of M. bororo in states such as Rio Grande do Sul, Minas Gerais, Goiás, Espírito Santo and Bahia. Moreover, the comparison among the DNA from holotype of M. bororo and Mazama americana jucunda indicates that M. bororo corresponds to the subspecies M. americana jucunda, described in 1913, highlighting the need to raise this subspecies to full species status. Our results also demonstrates that M. bororo did not show a genetic structuration of their populations and that their genetic diversity is lower than other species, highlighting the need to increase conservation and environment policy efforts to maintenance of this species. Finally, when we compare the morphological identification available on natural history collections with the identification obtained from molecular markers we found that the error rate resulting from the classification based on morphological characters was 26%. Nevertheless, we expect with the help of DNA from natural history collections will be possible to select non-convergent morphological characters for this group, allowing thus correct morphological identifications.
FAPESP: 2013/05944-7
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Sandoval, Mendoza Karla. "Ethnicity, linguistics, and genetic diversity in native Mexicans : reconstructing the population history of Mesoamerica." Doctoral thesis, Universitat Pompeu Fabra, 2010. http://hdl.handle.net/10803/7236.
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Mesoamerica is one of the main centers of New World civilization. It represents today a large geographical area exhibiting one of the highest genetic, cultural, and archeological diversity in the Americas. Moreover, its geographic position has been a key factor for acting as a natural corridor between North and Central-South America, thus becoming a direct witness not only of the initial and subsequent human migration waves but also of the many civilizations that flourished later on. Therefore, Mesoamerica deserves special attention in the study of American history. Following a molecular anthropological approach, this thesis evaluates the genetic diversity of a representative sample of the extant Native American gene pool within Mexico, and by constructing continental datasets, it also intends to contribute to the reconstruction of Mesoamerican history and the peopling of the Americas. For that purpose, this work focuses on the study of uniparental markers located in the human mitochondrial DNA and Y-chromosome, which constitutes the main part of the analyses. Additionally, autosomal STR variation, linguistic diversity, and ethnographic data were also investigated. Our results, based on both mtDNA and Y-chromosome, show a clear differentiation of the Native Mexican groups that belong to Mesoamerica, suggesting that population dynamcs occurring within this cultural area were unique during the America's colonization process and thus uniquely shaped the native Mexican genome.Mesoamerica merece especial atención dentro del estudio de la historia del Nuevo Mundo debido a que es una de las principales áreas geográficas con mayor diversidad genética, cultural y arqueológica en América. Un factor clave es su posición geográfica, ya que ha actuado como un corredor natural de unión entre Norte y Centro-Suramérica, convirtiéndose en testigo directo no solo de las primeras y subsecuentes oleadas migratorias, sino también del posterior florecimiento de grandes civilizaciones mesoamericanas. Siguiendo un enfoque antropomolecular, la presente tesis doctoral evalúa la diversidad genética de una muestra representativa del pool genético actual de las poblaciones nativas de México. Asi mismo, por medio de la construcción de bases de datos a nivel continental, pretende contribuir a la reconstrucción de la historia Mesoamericana y del Poblamiento de América. Con este objetivo, se analizaron marcadores uniparentales localizados en el ADN mitocondrial y el cromosoma Y, lo cual constituye el principal componente del trabajo. Complementarianente, también se analizó la variabilidad observada a nivel de STRs autosómicos, clasificacion lingüística y caracterisitcas etnográficas, lo cual aporta un enfoque multidisciplinario a la investigación. Nuestros resultados, basados tanto en ADNmt como en cromosoma Y, muestran una clara diferenciacion de los grupos nativos pertenecientes a Mesoamerica en comparacion con el resto, sugieriendo la presencia de una dinámica poblacional única y enfatizando la relevancia de esta área cultural en el proceso de colonización de América.
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Raia, Pierre. "Détermination de la structure de l’ADN polymérase D par cristallographie aux rayons X et cryo-microscopie électronique." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS338.
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Dans toutes les formes de vie, les ADN polymérases jouent un rôle central dans la réplication du génome, sa maintenance et sa réparation. Toutes les ADN polymérases ont été classées en sept familles distinctes en se basant sur leur homologie de séquence : PolA, PolB, PolC, PolD, PolX, PolY et les reverse transcriptases. La dernière famille d’ADN polymérase pour laquelle la structure et le mécanisme moléculaire demeurent inconnus est la PolD. La PolD est l’une des ADN polymérases réplicatives des Archées. C’est une polymérase hétérodimérique composée d’une sous-unité DP1, qui catalyse l’activité de relecture exonucléase 3’-5’, et d’une sous-unité DP2, qui catalyse l’activité de polymérisation 5’-3’. Afin de résoudre l’incertitude concernant les origines évolutives de la PolD, j’ai déterminé la structure cristallographique des domaines catalytiques des sous-unités DP1 et DP2 de Pyrococcus abyssi et la structure du complexe DP1-DP2 lié à l’ADN, par cryo-microscopie électronique (cryo-EM). Ces structures révèlent que la PolD est une ADN polymérase atypique qui diffère de celle des autres ADN polymérases caractérisées à ce jour. De plus, DP2 partage une homologie structurale inattendue avec les ARN polymérases à ‘deux-tonneaux-β’. Ces travaux clarifient les relations évolutives entre toutes les ADN polymérases et mettent en lumière le mécanisme d'acquisition et d'échange de domaines qui s'est produit au cours de l'évolution du réplisome eucaryoteIn all forms of life, DNA polymerases play central roles in genome replication, maintenance and repair. All DNA polymerases have been grouped in different families, using sequence alignments: PolA, PolB, PolC, PolD, PolX, PolY and reverse transcriptases. The only class of DNA polymerases left whose structure and molecular mechanism are unknown is PolD. PolD is an archaeal replicative DNA polymerase made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). To help resolve the uncertainty concerning the evolutionary origins of PolD, I determined the crystal structures of two large fragments of both DP1 and DP2 subunits of the Pyrococcus abyssi PolD. Crystal structures of both DP1 and DP2 subunits revealed that PolD is an atypical DNA polymerase. We also determined the cryo-electron microscopy (cryo-EM) structure of the DP1-DP2 complex bound with DNA. Structures of both polymerase and proofreading active sites differ from other structurally characterized DNA polymerases. In addition, PolD shares an unexpected structural homology with the ‘two-barrel’ family of RNA polymerases. By many aspects, this work provides new insights on the evolutionary history of DNA and RNA polymerases
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Batisteti, Caroline Belotto [UNESP]. "Os estudos de Avery, Macleod e Mccarty e a idéia do DNA como responsável pela hereditariedade: interpretações historiográficas e apontamentos para o ensino de biologia." Universidade Estadual Paulista (UNESP), 2010. http://hdl.handle.net/11449/90888.
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Um dos momentos históricos interessantes no estabelecimento da Biologia Molecular diz respeito às pesquisas realizadas por Avery, MacLeod e McCarty, que indicaram que a natureza química do princípio transformante bacteriano era o DNA. A nosso ver, esse episódio pode ser explorado do ponto de vista histórico, e assim fornecer elementos relevantes para o Ensino de Ciências. Em relação à perspectiva histórica, embora os estudos de Avery e colaboradores sejam atualmente considerados referência no estabelecimento de relações entre DNA e hereditariedade, há na literatura apontamentos sobre a provável não aceitação imediata desses pela comunidade científica da época (1944). Assim, o objetivo da presente pesquisa foi investigar, por meio da análise de fontes primárias, como artigos, documentos e correspondências que envolvem Avery e colaboradores, os motivos para a resistência inicial aos resultados de seus trabalhos. Dentre as razões levantadas, podemos mencionar dúvidas de cunho técnico, que indicavam a presença de proteínas nos preparados utilizados por Avery e colaboradores, a suposta timidez de Avery e a idéia de sua proposta ter sido cientificamente prematura. Outra razão, que aparentemente, abrange um maior número de aspectos envolvidos no processo de construção do conhecimento em questão, refere-se à hipótese de que a idéia do DNA como responsável pela hereditariedade encontrou dificuldades em ser aceita, pois, foi produzida e apresentada inicialmente fora da área de domínio da temática de interesse, no caso, a Genética. Acerca da utilização do episódio histórico em questão no Ensino, essa se justifica, pois possibilita a observação de diversos elementos que caracterizam e estão envolvidos na produção científica, como por exemplo: implicações metodológicas, subjetividade dos indivíduos, coletividade...
One of the interesting historical moment on the establishment of Molecular Biology is related to Avery, MacLeod and McCarty’s research, which indicated that the chemical nature of the transforming principle in bacteria was DNA. In our view, this episode can be explored from a historical perspective, and thus provide relevant information to the Teaching of Science. Regarding the historical perspective, although Avery and his colleague’s studies are now considered landmark in the establishment of relations between DNA and heredity, in literature there are notes on the probable immediate rejection of this by the scientific community of that time (1944). The objective of this research was to investigate, through analysis of primary sources such as articles, documents and correspondence involving Avery and his colleagues, the reasons for the initial resistance to the results of their work. Among the reasons raised, we can mention technical-doubt, which indicated the presence of protein in the preparations used by Avery and his colleagues, the alleged Avery’s timidity and the idea of his proposal was scientifically premature. Another reason, which apparently includes a greater number of issues involved in building the knowledge in discussion, refers to the hypothesis that the idea of DNA as responsible for heredity found difficulties to be accepted, because it was produced and presented initially outside of Genetics field. As far as use of the referred historical episode in Education or in Teaching of Biology, this is justified because it enables the observation of several elements that characterize and are involved in scientific research, such as: methodological implications, the subjectivity of individuals, collective production of knowledge, social influences (hostility), the impact of the journal in which they release a specific publication, ... (Complete abstract, click electronic access below)
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Batisteti, Caroline Belotto. "Os estudos de Avery, Macleod e Mccarty e a idéia do DNA como responsável pela hereditariedade : interpretações historiográficas e apontamentos para o ensino de biologia /." Bauru : [s.n.], 2010. http://hdl.handle.net/11449/90888.
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Resumo: Um dos momentos históricos interessantes no estabelecimento da Biologia Molecular diz respeito às pesquisas realizadas por Avery, MacLeod e McCarty, que indicaram que a natureza química do princípio transformante bacteriano era o DNA. A nosso ver, esse episódio pode ser explorado do ponto de vista histórico, e assim fornecer elementos relevantes para o Ensino de Ciências. Em relação à perspectiva histórica, embora os estudos de Avery e colaboradores sejam atualmente considerados referência no estabelecimento de relações entre DNA e hereditariedade, há na literatura apontamentos sobre a provável não aceitação imediata desses pela comunidade científica da época (1944). Assim, o objetivo da presente pesquisa foi investigar, por meio da análise de fontes primárias, como artigos, documentos e correspondências que envolvem Avery e colaboradores, os motivos para a resistência inicial aos resultados de seus trabalhos. Dentre as razões levantadas, podemos mencionar dúvidas de cunho técnico, que indicavam a presença de proteínas nos preparados utilizados por Avery e colaboradores, a suposta timidez de Avery e a idéia de sua proposta ter sido cientificamente prematura. Outra razão, que aparentemente, abrange um maior número de aspectos envolvidos no processo de construção do conhecimento em questão, refere-se à hipótese de que a idéia do DNA como responsável pela hereditariedade encontrou dificuldades em ser aceita, pois, foi produzida e apresentada inicialmente fora da área de domínio da temática de interesse, no caso, a Genética. Acerca da utilização do episódio histórico em questão no Ensino, essa se justifica, pois possibilita a observação de diversos elementos que caracterizam e estão envolvidos na produção científica, como por exemplo: implicações metodológicas, subjetividade dos indivíduos, coletividade... (Resumo completo, clicar acesso eletrônico abaixo)Abstract: One of the interesting historical moment on the establishment of Molecular Biology is related to Avery, MacLeod and McCarty's research, which indicated that the chemical nature of the transforming principle in bacteria was DNA. In our view, this episode can be explored from a historical perspective, and thus provide relevant information to the Teaching of Science. Regarding the historical perspective, although Avery and his colleague's studies are now considered landmark in the establishment of relations between DNA and heredity, in literature there are notes on the probable immediate rejection of this by the scientific community of that time (1944). The objective of this research was to investigate, through analysis of primary sources such as articles, documents and correspondence involving Avery and his colleagues, the reasons for the initial resistance to the results of their work. Among the reasons raised, we can mention technical-doubt, which indicated the presence of protein in the preparations used by Avery and his colleagues, the alleged Avery's timidity and the idea of his proposal was scientifically premature. Another reason, which apparently includes a greater number of issues involved in building the knowledge in discussion, refers to the hypothesis that the idea of DNA as responsible for heredity found difficulties to be accepted, because it was produced and presented initially outside of Genetics field. As far as use of the referred historical episode in Education or in Teaching of Biology, this is justified because it enables the observation of several elements that characterize and are involved in scientific research, such as: methodological implications, the subjectivity of individuals, collective production of knowledge, social influences (hostility), the impact of the journal in which they release a specific publication, ... (Complete abstract, click electronic access below)
Orientador: João José Caluzi
Coorientador: Elaine Sandra Nicolini Nabuco de Araujo
Banca: Maria Elice Brzezinski Prestes
Banca: Ana Maria de Andrade Caldeira
Mestre
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Zhao, Wanying. "Genetic, Age, and Spatial Structure to Improve Management of Common Privet (Ligustrum vulgare)." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1325115045.
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Ross, Jeremy D. "The Evolutionary History, Demographic Independence and Conservation Status of Two North American Prairie Bird Species: The Greater Prairie Chicken and the Lark Sparrow." Bowling Green State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1303855437.
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Cervoni, Nadia. "DNA demethylation and histone acetylation." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38166.
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Unlike in somatic cells, cancer cells adopt an aberrant pattern of methylation as well as histone acetylation, and therefore distort the chromatin structure. Chapters 2--4 of this thesis look at mechanisms carried out by the recently cloned DNA demethylase, how its demethylation activity is closely linked with the semblance of acetylation of chromatin, and how this relationship can be skewed in cancer. The three intriguing mechanisms described provide attractive models by which to explain general genome wide demethylation, site specific demethylation of genes upon their activation, and the relationship between aberrant methylation and histone acetylation in cancer. The thesis begins by characterizing the mechanism of demethylation carried out by the bona fida DNA demethylase---an enzyme identified and cloned in our laboratory found to demethylate both hemi and double-stranded DNA in vitro. This enzyme manifests the removal of methyl groups from DNA without damaging the DNA and is therefore a candidate protein responsible for hypomethylation seen during development as well as in transformed cells. One essential property of an enzyme that removes methylation from wide regions of the genome could be processivity. Southern blot analysis and sodium bisulfite mapping experiments determine that purified demethylase demethylates DNA in a processive manner in vitro. Experiments in Chapter 3 demonstrate how an active demethylase enzyme is involved in shaping patterns of methylation relative to the state of histone acetylation. We present evidence suggesting demethylase activity is directed by the state of histone acetylation, therefore contrasting the accepted dogma, and suggesting that the local histone acetylation state determines the resulting methylation pattern. Aberrant DNA methylation and histone deacetylation are frequently associated with silencing of tumor suppressor genes in cancer and yet cannot simply be explained by the level of methyltransferase(s) enzyme(s)
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Boisse, Bernard Chazan Mireille. "La tenture de choeur de la Cathédrale d'Auxerre Lectures et interprétations /." [S.l.] : [s.n.], 2005. ftp://ftp.scd.univ-metz.fr/pub/DEA/Histoire/Boisse.Bernard.DEAH13_2005.pdf.
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Ferreira, Marilane de Jesus. "A história da ciência como subsídio para a construção do conhecimento do conceito da dupla hélice." Universidade Tecnológica Federal do Paraná, 2015. http://repositorio.utfpr.edu.br/jspui/handle/1/1646.
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Acompanha: Dupla-hélice: a construção de um conhecimentoA presente análise abordou a relevância da História da Ciência para a prática da Educação em Ciência, de modo mais específico para a aprendizagem no Ensino Médio na disciplina de Biologia, considerando significativa a ideia de que a aprendizagem em ciência, isto é, sobre as dimensões históricas, filosóficas e culturais da ciência (MONK; OSBORNE, 1997) são emergentes para a educação científica. Em vista da escassez de materiais contendo episódios históricos filosóficos que permitem realizar uma transposição didática, faz-se necessário a construção de textos contendo a História da Ciência que desempenha um papel fundamental na elaboração do conceito do DNA no Ensino Médio. A elaboração do texto “Dupla hélice: A construção de um conhecimento” contendo a evolução histórica do modelo da dupla hélice na versão e-book como produto educacional, pode auxiliar na concepção do conceito do DNA no Ensino Médio. Neste contexto, buscou-se fundamentos à discussão das necessidades formativas do professor do referido ensino e nível de escolaridade. Analisou-se aspectos sobre a visão e concepções de ciências e a inserção da história e filosofia da ciência na prática pedagógica dos professores de Biologia. Apresentou-se o percurso metodológico da pesquisa, partindo do delineamento básico da pesquisa (problema, questões norteadoras, objetivos, objeto e sujeitos da pesquisa e produto educacional) para depois situar a perspectiva teórico-metodológica adotada, para a apreensão da pesquisa. Elegeu-se o estudo qualitativo para nortear a pesquisa, os questionários e a entrevista como técnica para coleta de dados. Concluímos, conforme a análise dos dados fornecidos pelos sujeitos da pesquisa, que o e-book contendo episódio histórico filosófico é um dispositivo didático útil para tornar o ensino médio mais interessante, possibilitando a aprendizagem de conceitos complexos da biologia, como o DNA. Outro ponto a ressaltar é que episódios históricos contribuem no processo da construção do conhecimento de maneira gradativa e lenta, promovendo uma visão concreta real da Natureza da Ciência com seus métodos, técnicas, modelos, acertos e erros, promovendo a formação de um cidadão crítico mediante o conhecimento científico. Para tanto, a necessidade de capacitação de professores para a utilização do material foi percebida por meio das análises.
This analysis addressed the relevance of the History of Science for the practice of science education, more specifically for learning in high school in biology discipline, considering significant the idea that learning in science, that is, about the dimensions historical, philosophical and cultural science (MONK; OSBORNE, 1997) are emerging for science education. In view of the shortage of materials containing philosophical historical episodes that allow you to perform a didactic transposition, the construction of texts it is necessary containing the history of science which plays a key role in preparing the DNA of the concept in high school. The drafting of the text "Double Helix: The construction of knowledge" containing the historical evolution of the model of the double helix in the e-book version as an educational product, can assist in the design DNA of the concept in high school. In this context, it sought to foundations to discuss the training needs teacher of that school and education level. Analyzed aspects of the vision and ideas of science and the inclusion of the history and philosophy of science in the teaching practice of teacher Biology. He presented the methodology of the survey route, starting from basic research design (problem, guiding questions, goals , object and subject of research and educational product) and then place the theoretical and methodological perspective adopted for the seizure of the research. The qualitative study was elected to guide the research, questionnaires and interview as a technique for data collection. We conclude, as the analysis of data provided by the research subjects, the e-book containing philosophical historical episode is a didactic device useful for making high school more interesting, enabling learning complex concepts of biology, such as DNA. Another point to emphasize is that historical episodes contribute in the process of construction of knowledge gradually and slowly, promoting a real concrete vision of Nature of Science with their methods, techniques, models, hits and misses, promoting the formation of a critical citizen by scientific knowledge. Therefore, the need for teacher training for the use of the material was perceived through the analysis.
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Pichler, Garwin. "Crosstalk between DNA methylation and histone modifications." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-143799.
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Linger, Jeffrey G. "The role of histone chaperones in double-strand DNA repair and replication-independent histone exchange /." Connect to full text via ProQuest. IP filtered, 2006.
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Thesis (Ph.D. in Biochemistry) -- University of Colorado, 2006.Typescript. Includes bibliographical references (leaves 153-171). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Eklöf, Jenny. "Gene technology at stake : Swedish governmental commissions on the border of science and politics." Doctoral thesis, Umeå University, Historical Studies, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1424.
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This thesis examines the Swedish political response to the challenges posed by gene technology, seen through the prism of governmental commissions. It discerns and analyses continuities and changes in the Swedish political conception of gene technology, over the course of two decades, 1980–2000. This is done by thematically following ideas of “risks” and “ethics” as they are represented in the inner workings and reception of three governmental commissions. The Gene-Ethics Commission (1981–1984), the Gene Technology Commission (1990–1992) and the Biotechnology Commission (1997–2000) form the empirical focal points of this analysis. The first two provided preparatory policy proposals that preceded the implementation of the Swedish gene technology laws of 1991 and 1994. The last one aimed at presenting a comprehensive Swedish biotechnology policy for the new millennium.
The study takes into account the role of governmental commissions as arenas where science and politics intersect in Swedish political life, and illuminates how this type of “boundary organisation”, placed on the border of science and politics, impinges on the understanding of the gene technology issue. The commissions have looked into the limits, dangers, possibilities and future applications of gene technology. They have been appointed to deal with the problematic task of distinguishing between what is routine and untested practices, realistic prediction and “science fiction”, what are unique problems and what are problems substantially similar to older ones, what constitutes a responsible approach as opposed to misconduct and what it means to let things “get out of hand” in contrast to being “in control”. Throughout a period of twenty years, media reports have continued to frame the challenges posed by gene technology as a task of balancing risks and benefits, walking the fine line between “frankenfoods” and “miracle drugs”.
One salient problem for the commissions to solve was that science and industry seemed to promote a technology the public opposed and resisted, at least in parts. For both politics and science to gain, or regain, public trust it needed to demonstrate that risks – be it environmental, ethical or health related ones – were under control. Under the surface, it was much more complicated than “science helping politics” to make informed and rational decisions on how to formulate a regulatory policy. Could experts be trusted to participate in policy-making in a neutral way and was it not important, in accordance with democratic norms, to involve the public?
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Dobosy, Joseph R. "Involvement of histone deacetylases in DNA methylation in Neurospora crassa, and characterization of four other histone acetylation associated genes /." view abstract or download file of text, 2003. http://wwwlib.umi.com/cr/uoregon/fullcit?p3102161.
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Thesis (Ph. D.)--University of Oregon, 2003.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 91-96). Also available for download via the World Wide Web; free to University of Oregon users.
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Clayton, Alison Louise. "Core histone acetylation of active genes." Thesis, University of Portsmouth, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240358.
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Ou, Jing Ni. "Epigenetic crosstalk between DNA demethylation and histone acetylation." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=32413.
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Abnormal methylation patterns such as regional hypermethylation and genomic hypomethylation often result in transcriptional changes of critical genes that are central to the progression of human cancers. It is therefore important to identify the mechanisms that are responsible for the alterations in order to identify proper pharmacological targets. This thesis examines whether specific cellular factors are involved in establishing the state of DNA hypomethylation in cancer cells and whether changes in chromatin structure could affect DNA methylation. MBD2 is a protein that has been previously characterized to possess distinct transcription activities; it can either function as a methylation-dependent transcription repressor, a methylation-independent transcription activator, as well as an inducer of DNA demethylation. Chapters 3 and 4 demonstrate that MBD2 induces gene-specific DNA demethylation in pancreatic and bladder cancer cells by recruiting transcriptional activator AP-2, Sp1 and the histone acetyltransferase CBP to the associated promoters. These results substantiate the idea that demethylation induced by MBD2 might facilitate the recruitment of transcription factors to the gene to activate its expression. Histone deacetylase (HDAC) inhibitors are drugs designed to target chromatin modification. In chapter 5, we showed that increasing histone acetylation by HDAC inhibitor TSA was associated with a significant decrease in global methylation. TSA also induces histone acetylation, DNA demethylation and expression of specific methylated tumor suppressor genes, such as E-CADHERIN and RARβ2 in different human cancer cell lines. Our findings provide evidence for aUn patron de méthylation anormal, tel que l'hyperméthylation régionale ou l'hypométhylation génomique, modifie la transcription de gènes critiques jouant ainsi un rôle central dans la progression de nombreux cancers chez l'humain. Il est donc devenu essentiel d'identifier les mécanismes responsables de ces altérations afin de développer des traitements pharmacologiques ciblés. Le but principal de cette thèse est d'examiner si certains facteurs cellulaires sont impliqués dans l'établissement de l'ADN hypométhylé des cellules cancéreuses, ainsi que l'effet des changements dans la structure de la chromatine sur la méthylation de l'ADN. Il a été préalablement démontré que la protéine MBD2 possède plusieurs rôles distincts lors de la transcription, elle peut agir à la fois comme un répresseur de la transcription dépendant de la méthylation, comme un inducteur de la déméthylation ainsi qu'un activateur de la transcription indépendant de la méthylation. Les chapitres 3 et 4 présentés dans cet ouvrage démontrent que MBD2 induit la déméthylation de gènes spécifiques dans les cellules cancéreuses pancréatiques et urinaires grâce au recrutement des activateurs transcriptionnels AP-2, Sp1 ainsi que de l'histone acétyltransférase CBP au promoteur impliqué. Ces résultats supportent l'hypothèse selon laquelle la déméthylation induite par MBD2 faciliterait le recrutement de facteurs de transcription au sein du gène afin d'activer son expression. Les inhibiteurs de l'Histone déacétylase (HDAC) sont des drogues pharmaceutiques développées afin de cibler les modifications de la chromatine. Nous sommes parvenus à démontrer, dans le