• Refine Query
  • Source
  • Publication year
  • to
  • Language
  • 29
  • 8
  • 5
  • 2
  • 2
  • 1
  • 1
  • 1
  • 1
  • Tagged with
  • 59
  • 59
  • 14
  • 13
  • 9
  • 9
  • 9
  • 8
  • 7
  • 7
  • 7
  • 5
  • 5
  • 5
  • 5
  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Tuberculosis throughout history : ancient DNA analyses on European skeletal and dental remains

Muller, Romy January 2013 (has links)
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.
2

Population genetics of Western Mediterranean islands : Malta, a case study

Caruana, Josef January 2013 (has links)
In order to gain a greater understanding of the genetic makeup of the Maltese population, mitochondrial DNA HVR1 and HVR2, and Y-chromosomal and autosomal STRs were amplified in a representative sample of the Maltese population. The results showed that the Maltese have close genetic ties with Sicily and mainland Italy both from a matrilineal and a patrilineal perspective, whilst no conclusive evidence was found for a Phoenician link between the Maltese and the Lebanese population. In order to try and gain an insight into the Maltese population throughout time, a study was conducted on three Maltese archaeological burial places dating from the Neolithic to the Roman period. The study extracted and amplified ancient DNA sequences from these three sites and compared the resulting mtDNA sequences with the modern Maltese population. The results showed that aDNA survives in the Maltese archaeological record, and that some haplotypes found during the Roman period in Malta are also found in the modern day population, whilst other haplotypes present in the archaeological samples are not visible in the modern Maltese population.
3

The origins and spread of the Neolithic in the Old World using ancient genomes

Gallego Llorente, Marcos January 2018 (has links)
One of the biggest innovations in human prehistory was the advent of food production, consisting of the ability to grow crops and domesticate animals for consumption. This wide-scale transition from hunting and gathering to food production led to more permanent settlements, and set in motion major societal changes. In western Eurasia, this revolution spread from the Near East into Europe, Africa and diverse regions of Asia. Agriculture was brought into Europe by the descendants of early Anatolian farmers starting approximately 8,000 years ago. But little was known of the people who developed agriculture in the Fertile Crescent: where they all closely related to the early Anatolian farmers, or were there multiple ethnic groups who developed agriculture in parallel? In the first data chapter, I use the first genome from a Neolithic woman from Ganj Dareh, in the Zagros Mountains (Iran), a site with evidence of early goat domestication 10,000 years ago. I showed that Western Iran wan inhabited by populations mostly similar to Hunter- gatherer populations from the Caucasus, but remarkably, very distinct from the Anatolian farmers who spread the Neolithic package into Europe. While a degree of cultural diffusion between Anatolia, Mesopotamia and the Zagros highlands likely happened, genetic dissimilarity supports a model in which Neolithic societies of that area were distinct. The second chapter deals with how Africa was affected by population movements, originating in the Near East, during the Neolithic times. Characterising genetic diversity in Africa is a crucial step for analyses reconstructing human evolution. Using Mota, an ancient genome from a male from the Ethiopian highlands, I showed a backflow into Africa by populations closely related to the Anatolian Neolithic farmers. The third chapter deals with some common problems and themes in the analysis of ancient DNA, such as merging capture datasets with diverse number of ascertained SNPs, combining capture and shotgun data in the same analysis, and the effect of UDG treatment in ancient samples. I describe the most common problems and their effect in summary statistics, and propose a guide on how to work with ancient DNA to avoid data compatibility problems.
4

Ancient DNA evidence of population replacement following the Aztec conquest of Xaltocan, Mexico

Mata-Míguez, Jaime 16 April 2013 (has links)
The Aztec empire emerged in AD 1428 as a result of the triple alliance among the city-states of Tenochtitlan, Texcoco, and Tlacopan. Although it is well documented that the Aztecs conquered numerous polities in the Basin of Mexico over the next 100 years, the demographic consequences of this expansion remain unclear. At the influential Otomi city-state of Xaltocan, for example, colonial documents suggest that the Aztec conquest led to a replacement of the original Otomi population, whereas archaeological finds suggest that a significant portion of the original population may have remained at the city under Aztec rule. To help resolve questions about Xaltocan’s population history during this period, I extracted ancient DNA from 21 individuals that can be divided into two temporal subpopulations (roughly predating and postdating the hypothesized replacement event). I determined mitochondrial DNA haplogroups through RFLP analyses and constructed haplotypes based on 372 bp of HVR1 sequence. Statistical analyses show significant differences between the mitochondrial composition of the two subpopulations. Altogether, the results of this study support the hypothesis that matrilines at Xaltocan underwent a significant replacement event following the Aztec conquest, and they suggest that the Aztec expansion may have had a substantial genetic impact on certain Mesoamerican populations. / text
5

An Ancient DNA Study of Four Sympatric Species of Moa (Aves: Dinornithiformes) from Holocene Deposits in North Canterbury, South Island, New Zealand

Allentoft, Morten Erik January 2010 (has links)
Ancient DNA (aDNA) was isolated from the bones of 290 individuals and four species of extinct New Zealand moa. All sampled bones had been recovered from a small geographic area (~10 km radius) near Waikari in North Canterbury. A total of 217 specimens were 14C-AMS dated, providing a temporal framework for the genetic analyses and an unprecedented opportunity to study extinct megafauna at the population level. Taxon and sex were determined for each individual, using aDNA technology. This revealed a large excess of females (overall ♂:♀ = 1:5.1), and significant compositional differences for the moa assemblages between fossil sites. Balanced sex ratios were observed among juvenile moa, suggesting that a gender-bias developed as the birds matured, probably as a result of higher male mortality. Female territoriality and ecological niche-separation are discussed in this context. Mitochondrial DNA (mtDNA), amplified using a quantitative PCR procedure, provided a measure of DNA preservation in each radiocarbon-dated fossil. This assessment showed that DNA degrades over thousands of years according to an exponential decay model, and the average molecular half-life for the here targeted DNA fragment was estimated to be 521 years. By using high-throughput sequencing, six polymorphic moa microsatellite markers were identified and characterised. These are the first microsatellite primers developed exclusively for extinct taxa. A high-resolution genetic study of the four sympatric moa populations was carried out, combining information from mtDNA, microsatellites, sex-identification, and radiocarbon age. Genetic diversity, past demography, kinship, and other aspects of moa biology were analysed. The populations showed a remarkable extent of genetic stability throughout the 3000-4000 years preceding their extinction, suggesting that they were large and viable before suddenly disappearing. The results represent significant advances in aDNA research and thanks to the high resolution in microsatellite markers, moa have here been studied, almost as if they were still alive.
6

The geographic distributions of Saccharomyces cerevisiae and Saccharomyces paradoxus, and the potential to detect past yeast populations with ancient DNA

Robinson, Heather Anne January 2016 (has links)
It is acknowledged that some microbes have interrupted distributions, yet these distributions have rarely been correlated with environmental variables. The wild biogeography of the fermenting yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus are explored in this study, considering multiple environmental variables as potential effectors of each species' geographical distributions. I demonstrate that summer temperatures predict maximum species distribution limits for both S. paradoxus and S. cerevisiae on oak bark, and that S. paradoxus is more likely to be isolated from larger, older trees. Modelling these data predicts a generally denser southern European population of S. paradoxus, with S. cerevisiae being scarce on oak bark throughout Europe. It was not possible to recover ancient Saccharomyces DNA sequences from samples of sub-fossilized oaks, from Greco-Roman and North African amphora residues, or from North African 6th-14th Century pottery residues, which may be a consequence of the low concentration of these species in comparable modern environmental samples. Even from air dried breads and recent wines, Saccharomyces aDNA was not recovered as part of this study, although ancient DNA sequences from plants and other yeasts were identified in other samples via the same methods. Any future recovery of ancient Saccharomyces sequences may therefore be challenging. Novel plant sequences possibly belonging to the Musaceae family and Pinus genus were identified from 6th-14th century AD North African pottery; as well as a Vicia-like DNA sequence from a 13th-12th century BC North African amphora.
7

Paleophysiology of oxygen delivery in the extinct Steller’s sea cow, Hydrodamalis gigas

Signore, Anthony 07 February 2017 (has links)
The order Sirenia is one of only two mammalian groups to have completely forgone terrestrial life. While extant sirenians are confined to the tropical waters, the recently extinct Steller’s sea cow (Hydrodamalis gigas) evolved to exploit the frigid waters of the North Pacific Ocean. As limits on O2 availability during submergence and decreased tissue temperature impose severe constraints on oxygen delivery, the oxygen binding (globin) proteins of sirenians are expected to have evolved under strong selection pressures. My comparative molecular analyses indicate that selection pressures on two globin genes (HBA and HBZ-T1) increased in transitional sirenians. As these genes encode the α-chains of all Hb isoforms throughout sirenian development, the resulting functional consequences to adult sirenian Hbs were tested using recombinant Hbs of Steller’s sea cow, the dugong (Dugong dugon), their last common ancestor, and the Florida manatee (Trichechis manatus latirostris). These tests reveal that high affinity Hbs—exceeding those of other mammals examined to date—arose early in sirenian evolution, presumably to maximize O2 extraction from the lungs and limit premature O2 offloading during submergence. Moreover, I demonstrate that the Hb–O2 affinity of the extinct sub-Arctic Steller’s sea cow is less affected by temperature than other sirenians, safeguarding O2 delivery to cool peripheral tissues. However, while this phenotype has primarily been attributed to the binding of additional allosteric effectors to the Hb moiety, Steller’s sea cow Hb binds relatively few of these ligands. Instead, my results suggest the thermodynamic properties of discrete allosteric effector sites are altered by epistatic interactions, a phenomenon that appears to be a critical component to cold adaptation in mammalian Hbs. As the HBA and HBZ-T1 loci also encode sirenian prenatal Hbs, the functional properties these proteins were tested to reveal their O2 affinity increased in parallel to maternal Hb. Notably, Steller’s sea cow HbF has the highest reported O2 affinity of any mammalian Hb tested to date. As the HBA gene encodes the -subunit of both the prenatally expressed HbF and adult expressed HbA proteins, the molecular remodeling of this locus may have concurrently increased the affinity of each protein. / February 2017
8

Past human health and migration : the analysis of microbial DNA associated with human remains recovered from a glacier in Canada

Swanston, Treena Marie 26 March 2010
In paleopathology, the assessment of disease occurs through macroscopic observation, which is dependent on the preservation of the sample and the experience of the observer. Many disease events do not leave any visible signatures and therefore go undetected. The relatively new field of paleomicrobiology incorporates molecular techniques where microbial DNA, if present, is amplified from an archaeological sample. The identification of genetic material from micro-organisms, including bacteria and viruses, can confirm a diagnosis that was originally based on visible osteological or mummified tissue changes. Even more promising is the capability of molecular technology to detect microbial DNA evidence of disease processes that were not visibly evident.<p> Based on phylogenetic analyses of modern isolates, scientists have concluded that micro-organisms such as <i>Mycobacterium tuberculosis</i> and <i>Helicobacter pylori</i> have been associated with humans for thousands of years. <i>M. tuberculosis</i> is the causative agent of the disease tuberculosis, and <i>H. pylori</i> is known for its role in gastritis and peptic ulcers. Both are pathogenic bacteria that still impact the health of modern populations. Through the analysis of microbial DNA from these two bacteria in skeletal and mummified tissue, data can be accumulated regarding the spatial and temporal impact of these infections. Interestingly, due to the lengthy association between these bacteria and humans, phylogenetic studies on modern strains have shown that strain characterizations of both <i>M. tuberculosis</i> and <i>H. pylori</i> bacteria reveal connections with past human migrations.<p> In 1999, human remains were discovered eroding out of a glacier in northern British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations. The Aboriginal elders named the site Kwäday Dän Tsìnchi, which means long ago person found. Radiocarbon testing of bone collagen and artifacts from the site suggested a time-frame of approximately AD 1670 to 1850, which is either pre-European contact or early post-contact for that area. I analyzed the tissues of the ancient individual specifically for genetic evidence of <i>M. tuberculosis</i> and <i>H. pylori</i> to identify partial health status and determine if a connection could be made to strains associated with European populations to clarify whether the site was pre or post-European contact.<p> Through polymerase chain reaction (PCR) testing of the individuals tissues with primers specific for the IS<i>6100</i> insertion sequence, <i>TbD1</i>, and <i>Rv3479</i>, <i>katG</i> and <i>gyrB</i> genes, I identified evidence of a possible latent tuberculosis infection. Genetic characterization of the <i>katG</i> gene associated with the ancient <i>M. tuberculosis</i> strain revealed a potential connection with European strains. Amplification and sequencing of the <i>gyrB</i> gene fragment indicated the presence of two alleles that may have been the result of a selective pressure.<p> PCR testing of the individuals stomach tissue with specific primers for regions with the <i>vacA</i> gene resulted in a positive identification of <i>H. pylori</i> DNA. Genetic characterization of this virulence-associated gene indicated that the strain contained a <i>vacA</i> signal (s) region s2 allele. This allele is more commonly identified in Western strains that do not cause disease, which suggests that the individual had no gastric symptoms and that European strains were present in northwestern Canada at that time. The vacA middle (m) region contained a hybrid m2a/m1d sequence. Modern hybrids are rare but they have been identified in Asian strains. Studies have shown that the m2a allele is more common in Western strains. A phylogenetic analysis identified that the m1d region clusters with previously published novel strains associated with Aboriginal individuals that are closely related to Asian strains. This indicates a past connection between the ancient individual and his ancestors who arrived in the New World from Asia thousands of years ago.
9

Past human health and migration : the analysis of microbial DNA associated with human remains recovered from a glacier in Canada

Swanston, Treena Marie 26 March 2010 (has links)
In paleopathology, the assessment of disease occurs through macroscopic observation, which is dependent on the preservation of the sample and the experience of the observer. Many disease events do not leave any visible signatures and therefore go undetected. The relatively new field of paleomicrobiology incorporates molecular techniques where microbial DNA, if present, is amplified from an archaeological sample. The identification of genetic material from micro-organisms, including bacteria and viruses, can confirm a diagnosis that was originally based on visible osteological or mummified tissue changes. Even more promising is the capability of molecular technology to detect microbial DNA evidence of disease processes that were not visibly evident.<p> Based on phylogenetic analyses of modern isolates, scientists have concluded that micro-organisms such as <i>Mycobacterium tuberculosis</i> and <i>Helicobacter pylori</i> have been associated with humans for thousands of years. <i>M. tuberculosis</i> is the causative agent of the disease tuberculosis, and <i>H. pylori</i> is known for its role in gastritis and peptic ulcers. Both are pathogenic bacteria that still impact the health of modern populations. Through the analysis of microbial DNA from these two bacteria in skeletal and mummified tissue, data can be accumulated regarding the spatial and temporal impact of these infections. Interestingly, due to the lengthy association between these bacteria and humans, phylogenetic studies on modern strains have shown that strain characterizations of both <i>M. tuberculosis</i> and <i>H. pylori</i> bacteria reveal connections with past human migrations.<p> In 1999, human remains were discovered eroding out of a glacier in northern British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations. The Aboriginal elders named the site Kwäday Dän Tsìnchi, which means long ago person found. Radiocarbon testing of bone collagen and artifacts from the site suggested a time-frame of approximately AD 1670 to 1850, which is either pre-European contact or early post-contact for that area. I analyzed the tissues of the ancient individual specifically for genetic evidence of <i>M. tuberculosis</i> and <i>H. pylori</i> to identify partial health status and determine if a connection could be made to strains associated with European populations to clarify whether the site was pre or post-European contact.<p> Through polymerase chain reaction (PCR) testing of the individuals tissues with primers specific for the IS<i>6100</i> insertion sequence, <i>TbD1</i>, and <i>Rv3479</i>, <i>katG</i> and <i>gyrB</i> genes, I identified evidence of a possible latent tuberculosis infection. Genetic characterization of the <i>katG</i> gene associated with the ancient <i>M. tuberculosis</i> strain revealed a potential connection with European strains. Amplification and sequencing of the <i>gyrB</i> gene fragment indicated the presence of two alleles that may have been the result of a selective pressure.<p> PCR testing of the individuals stomach tissue with specific primers for regions with the <i>vacA</i> gene resulted in a positive identification of <i>H. pylori</i> DNA. Genetic characterization of this virulence-associated gene indicated that the strain contained a <i>vacA</i> signal (s) region s2 allele. This allele is more commonly identified in Western strains that do not cause disease, which suggests that the individual had no gastric symptoms and that European strains were present in northwestern Canada at that time. The vacA middle (m) region contained a hybrid m2a/m1d sequence. Modern hybrids are rare but they have been identified in Asian strains. Studies have shown that the m2a allele is more common in Western strains. A phylogenetic analysis identified that the m1d region clusters with previously published novel strains associated with Aboriginal individuals that are closely related to Asian strains. This indicates a past connection between the ancient individual and his ancestors who arrived in the New World from Asia thousands of years ago.
10

Diachonic DNA analyses of animal breeds and populations

Campana, Michael Gray January 2011 (has links)
Humans are dependent on the animals they raise and breed for food and secondary products. Archaeological and genetic investigations can provide critical insights into the history and development of these breeds and help understand human activities in the past. Furthermore, many well-adapted breeds are endangered and archaeological and genetic data can help inform future breed conservation choices. Utilising ancient DNA data could potentially permit detailed diachronic analyses of the development of animal breeds. Ancient DNA analyses have typically focussed on large-scale biogeographic patterns in time and space, such as the spread of domesticates or the movements of peoples. Few studies have attempted fine-scale diachronic analysis within single animal populations or breeds. This is largely due to restricted sample availability and the limited phylogenetic resolution provided by the mitochondrial genome, the most commonly used ancient DNA marker. In this thesis, I demonstrate that fine-scale diachronic analyses within single animal populations and breeds over short time scales are feasible. First, in order to address the limitations of sample size, I assessed three sample screening methods’ abilities (maximum mitochondrial DNA amplicon length, NanoDrop® spectrometry and collagen preservation) to select samples in which DNA was preserved and analysed the utility of parchment as a novel source of ancient and historic DNA. None of the screening methods accurately predicted DNA preservation, but collagen preservation was able to weed out extremely poorly preserved samples from further analysis. All but one of the tested parchments produced multiple sequences matching several different species. Parchment therefore was not appropriate for fine-scale diachronic analyses. Next, I assessed whether analysing the nuclear genome could permit fine-resolution diachronic genetic studies. Since single nucleotide polymorphisms are ideal candidate nuclear markers for diachronic DNA analyses, I assessed the accuracy of the nuclear SNP-typing methodology, SNaPshot™, by genotyping three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. The SNaPshot™ protocol was found to provide accurate genotypic information in all cases. Finally, as a proof of method, I compared the diachronic information provided by the mitochondrial and nuclear genomes in Icelandic and Thoroughbred horses. Specifically, in the Icelandic horse, I analysed the mitochondrial D-loop and three coat colour genes in modern and historic populations. In the Icelandic horse, I found statistically significant evidence for genetic change in the mitochondrial genome over the last 150 years. I found no evidence for change in coat colour allele frequencies. Conversely, in the biased and small historic Thoroughbred dataset, the mitochondrial genome was insufficient to provide population-level information, but I was able to show that allele frequencies in the nuclear MSTN gene, a gene previously shown to influence racing performance, have changed significantly in the past century.

Page generated in 0.1117 seconds