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Cai, Rongman. "New hypotheses about the origin of Pseudomonas syringae crop pathogens." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/37806.
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Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that todayâ s highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants.<br>Ph. D.
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Sealfon, Rachel (Rachel Sima). "Computational investigation of pathogen evolution." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/99858.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 105-118).<br>Pathogen genomes, especially those of viruses, often change rapidly. Changes in pathogen genomes may have important functional implications, for example by altering adaptation to the host or conferring drug resistance. Accumulated genomic changes, many of which are functionally neutral, also serve as markers that can elucidate transmission dynamics or reveal how long a pathogen has been present in a given environment. Moreover, systematically probing portions of the pathogen genome that are changing more or less rapidly than expected can provide important clues about the function of these regions. In this thesis, I (1) examine changes in the Vibrio cholerae genome shortly after the introduction of the pathogen to Hispaniola to gain insight into genomic change and functional evolution during an epidemic. I then (2) use changes in the Lassa genome to estimate the time that the pathogen has been circulating in Nigeria and in Sierra Leone, and to pinpoint sites that have recurrent, independent mutations that may be markers for lineage-specific selection. I (3) develop a method to identify regions of overlapping function in viral genomes, and apply the approach to a wide range of viral genomes. Finally, I (4) use changes in the genome of Ebola virus to elucidate the virus' origin, evolution, and transmission dynamics at the start of the outbreak in Sierra Leone.<br>by Rachel Sealfon.<br>Ph. D.
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Bailes, Elizabeth. "Origins and evolution of primate lentiviruses." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246384.
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Buckee, Caroline O'Flaherty. "The evolution and maintenance of pathogen diversity." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.433383.
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Lipsitch, Marc. "Pathogen transmission and the evolution of virulence." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294342.
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Berg, Femke van den. "The evolution of plant defence against pests : pathogen development and pathogen-induced leaf necrosis." Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421209.
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Shin, Woo Kyung. "The origins and evolution of the bra." Thesis, Northumbria University, 2009. http://nrl.northumbria.ac.uk/3040/.
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This thesis marks the first biography of the evolution of the bra from a designer and patternmaker’s perspective. Although the bra has a very long history, it only became a truly iconic garment in the latter half of the Twentieth Century. To some extent this transformation was driven by rapid social and economic changes, but the evolution of this highly technical garment is also inextricably linked to developments in technology which have led to improvements in materials, design and manufacture. Initially these developments were related to designing a three-dimensional product from a two-dimensional flat patternmaking process, but more recently the advent of the moulded bra has offered opportunities to create a seamless three-dimensional garment without the need to construct a flat pattern, and this has enabled both increased design possibilities and raised the prospect of a better fitting product. Through an investigation of the origins of underwear in general, and the bra in particular, this thesis reviews secondary source historical data to chart major changes in design, patternmaking, and technology from the first recorded uses of underwear to the current challenges facing bra designers and patternmakers in an increasingly globalised industry. This historical review culminates in the identification of two distinctly diverging trends in current bra design and manufacture, both of which face significant challenges in terms of training new designers and producing better sizing and fitting protocols. The two primary source studies which emanate from this historical review contribute new knowledge to each of these diverging directions in bra design. The first study provides an entirely new approach to the teaching, and subsequent current commercial practice of flat patternmaking for what many regard as the ‘traditional’ cut-and-sewn variety of bra. This study culminates in a new way of producing, learning and teaching the art of flat patternmaking, enabling underwear design graduates to leave university with the core skills they need to survive in a fast moving global industry. The second major study investigates the salient challenge of providing an excellent fit for both major types of bra across globally diverse and perhaps ethnically different body types. Consequently, it employs cutting-edge threedimensional body scanning technology to demonstrate how the design, sizing, and 2 fitting of both cut-and-sewn and moulded varieties of garment might be significantly improved in the future. Both primary source data studies therefore stand at the beginning of the future evolution of the most technically complex garment in human history, the not so humble bra.
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Bristow, Ivan Robert. "The origins and evolution of podiatric dermatology." Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/335990/.
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This thesis sets out to demonstrate the significant contribution to the field of podiatric dermatology, through the use of various forms of published documentary evidence, made by the author. In addition to the published papers submitted, a content analysis of British podiatric literature over a period of 21 years has mapped the emergence and development of the specialism of podiatric dermatology within the United Kingdom. This work demonstrates a significant increase in professional interest within this area during this period. This is evidenced through increased reporting of dermatological topics within podiatry journals in terms of related news items, advertisements and editorials. This is accompanied by an increasing number of case studies, peerreviewed papers and continuing professional development articles evident within the literature. The author has presented within this thesis a suite of fifty published articles along with verifiable evidence of professional activities related to the promotion and development of podiatric dermatology. Collectively this evidence represents a significant contribution to the development and evolution of dermatology as a specialist area within podiatry in the United Kingdom over the last fifteen years.
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Ponce, Toledo Rafael Isaac. "Origins and early evolution of photosynthetic eukaryotes." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS047/document.
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Les plastes primaires proviennent d'une cyanobactérie qui a établi une relationendosymbiotique avec un hôte eucaryote. Cet événement a donné naissance au super-groupeArchaeplastida qui inclut les Viridiplantae (algues vertes et plantes terrestres), les Rhodophyta (alguesrouges) et les Glaucophyta. Suite à l'endosymbiose primaire, les algues rouges et vertes ont étendu lacapacité de photosynthèse à d'autres lignées eucaryotes via des endosymbioses secondaires. Bien quedes progrès considérables aient été réalisés dans la compréhension de l'évolution des eucaryotesphotosynthétiques, d'importantes questions sont restées ouvertes, telles que l’identité de la lignéecyanobactérienne la plus proche des plastes primaires ainsi que le nombre et l'identité des partenairesdans les endosymbioses secondaires.Ma thèse a consisté à étudier l'origine et l'évolution précoce des eucaryotes photosynthétiques enutilisant des approches phylogénétiques et phylogénomiques. Je montre par mon travail que les plastesprimaires ont évolué à partir d'un symbiote phylogénétiquement proche de Gloeomargarita lithophora,une cyanobactérie représentant un clade s’étant diversifié précocement et qui a été détectéeuniquement dans les milieux terrestres. Ce résultat fournit des pistes nouvelles sur le contexteécologique dans lequel l'endosymbiose primaire a probablement eu lieu. En ce qui concerne l'évolutiondes lignées eucaryotes avec des plastes secondaires, je montre que les génomes nucléaires deschlorarachniophytes et des euglénophytes, deux lignées photosynthétiques avec des plastes dérivésd'algues vertes, encodent un grand nombre de gènes acquis par transferts depuis des algues rouges.Enfin, je mets en évidence que SELMA, la machinerie de translocation des protéines à travers laseconde membrane externe des plastes rouges secondaires à quatre membranes, a une histoireétonnamment compliquée aux implications évolutives importantes : les cryptophytes ont recruté unensemble de composants de SELMA différent de ceux des haptophytes, straménopiles et alvéolés.Ainsi, ma thèse a permis d’identifier pour la première fois la lignée cyanobactérienne la plus proche desplastes primaires et apporte de nouvelles pistes pour éclaircir les événements complexes qui ontjalonné l’évolution des eucaryotes photosynthétiques secondaires<br>Primary plastids derive from a cyanobacterium that entered into an endosymbioticrelationship with a eukaryotic host. This event gave rise to the supergroup Archaeplastida whichcomprises Viridiplantae (green algae and land plants), Rhodophyta (red algae) and Glaucophyta. Afterprimary endosymbiosis, red and green algae spread the ability to photosynthesize to other eukaryoticlineages via secondary endosymbioses. Although considerable progress has been made in theunderstanding of the evolution of photosynthetic eukaryotes, important questions remained debatedsuch as the present-day closest cyanobacterial lineage to primary plastids as well as the number andidentity of partners in secondary endosymbioses.The main objectives of my PhD were to study the origin and evolution of plastid-bearing eukaryotesusing phylogenetic and phylogenomic approaches to shed some light on how primary and secondaryendosymbioses occurred. In this work, I show that primary plastids evolved from a close relative ofGloeomargarita lithophora, a recently sequenced early-branching cyanobacterium that has been onlydetected in terrestrial environments. This result provide interesting hints on the ecological setting whereprimary endosymbiosis likely took place. Regarding the evolution of eukaryotic lineages with secondaryplastids, I show that the nuclear genomes of chlorarachniophytes and euglenids, two photosyntheticlineages with green alga-derived plastids, encode for a large number of genes acquired by transfersfrom red algae. Finally, I highlight that SELMA, the translocation machinery putatively used to importproteins across the second outermost membrane of secondary red plastids with four membranes, has asurprisingly complex history with strong evolutionary implications: cryptophytes have recruited a set ofSELMA components different from those present in haptophytes, stramenopiles and alveolates.In conclusion, during my PhD I identified for the first time the closest living cyanobacterium to primaryplastids and provided new insights on the complex evolution that have undergone secondary plastid-bearing eukaryotes
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Payne, Joseph D. "Quantum pathogen evolution by integron-mediated effector capture." Thesis, University of the West of England, Bristol, 2017. http://eprints.uwe.ac.uk/32255/.
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Plant pathogenic Pseudomonads are responsible for the loss of millions of pounds in crop revenue each year. They export effector molecules via the type three secretion system into the plants’ cells in order to elicit disease. If the plant has the corresponding resistance genes to detect the type three effector molecule then the plant will mount an immune response called the plant hypersensitive response (HR). Type three effector molecules can also supress the plants’ immune response including pathogen associated molecular pattern triggered immunity and effector triggered immunity. Pseudomonads can evade HR by potentially gaining different effector molecules using mobile DNA elements. Integrons are one such type of element. Integrons are elements that allow bacteria to acquire and store genes from the environment particularly during times of stress. They also allow differential expression of the captured genes dependent on the environmental conditions. Integron-like elements (ILEs) within Pseudomonas syringae pathovars and other Pseudomonads can be identified by using conserved genes such as the xerC integrase and the UV damage repair gene rulB. RulB encodes a DNA polymerase V which appears to be a hotspot for ILE insertion. Using the rulAB operon, the xerC gene and the ILE insertion junction, rulB-xerC, it was possible to identify a number of ILEs. The screening of 164 plant pathogenic Pseudomonas strains revealed new ILEs from 21 strains all containing at least one type three effector molecule. The screening also revealed that the xerC integrase was conserved across multiple ILEs within plant pathogens. Expression studies of the ILE integrase genes, type three effector genes and the disrupted rulB gene showed that the genes on both ILEs present in P. syringae pv. pisi 203 and pv. syringae 3023 are upregulated in times of cellular stress and DNA damage. This led to the conclusion that ILEs may be more active when the bacteria was in need of exogenous genes to overcome the cellular stress. The ILE may also be excised following DNA damage to restore full rulB functionality. It was identified that rulB was a hotspot for ILE insertion but it was not known why the ILEs choose this site or if any other genes were required for ILE insertion. Cloned versions of the rulAB operon from the pWW0 plasmid found in Pseudomonas putida PaW340 showed that only rulAB was required for P. fluorescens ILE insertion but rulAB must be intact. P. syringae ILEs were also tested but did not show any insertion. Due to ILEs inserting into and disrupting rulB their effect on UV tolerance was tested. A range of strains containing an intact rulB gene were tested alongside the ILE containing strains with increasing amounts of UVB irradiation applied. The results showed very minor differences in growth rates between the two groups with only one UVB irradiation amount of 60 seconds causing a significant difference in growth rate at the 95% confidence interval between the two groups of strains. This research has contributed to the understanding of ILEs in phytopathogenic bacteria. It has also increased our understanding of the mechanisms of ILE gene expression, the mechanism surrounding ILE excision and insertion and the effect of ILEs on bacterial growth in high UV environments.
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Turenne, Christine. "The evolution of the pathogen «Mycobacterium avium» subsp «paratuberculosis»." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=32284.
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The genus Mycobacterium is best recognized for its pathogens M. tuberculosis and M. leprae, the etiologic agents of Tuberculosis and Leprosy. Sequencing of their genomes has revealed an evolutionary process of reductive genomics. Another common species, the M. avium complex (MAC), consists of both environmental isolates that can cause opportunistic infection in humans as well as pathogenic isolates that cause disease primarily in birds and livestock. The basis of this variation in disease phenotypes is unknown. Two genome sequences representing a pathogen of cattle, M. avium subsp. paratuberculosis (MAP) and an opportunistic isolate from a human (M. avium subsp. hominissuis) have served as the foundation for the comparative genomics of MAC. This is complicated by a level of genetic variability one log greater than found within the M. tuberculosis complex (MTBC), and by the existence of other MAC subsets beyond the two sequenced strains. In this thesis, I set out to define the phylogenetic relationships of the various members of MAC and explore the evolutionary processes that led to the emergence of the pathogenic species MAP. An identification scheme was developed to unambiguously brand subsets of MAC, a tool lacking in the past thus hampering data interpretation. Expansion to a multilocus sequence analysis (MLSA) system revealed that the MAC consists of a highly variable group with most of the genotypes belonging to what is considered to be the environmental subset. However, both the avian and MAP pathogens manifested as two separate clones that have independently evolved from their larger subset. The distribution and directionality (insertion or deletion) of large se<br>Le genre Mycobacterium est mieux reconnu pour ses espèces pathogènes M. tuberculosis et M. leprae, les agents étiologiques de la tuberculose et de la lèpre. Le séquençage de leur génome a indiqué un processus évolutionnaire de réduction génomique. Des autres espèces communes, le complexe M. avium (MAC) est composé de souches environnementales qui peuvent causer des infections opportunistes chez l'homme aussi bien que de souches pathogènes qui causent la maladie principalement chez les oiseaux et le bétail. La base de cette variation phénotypique est inconnue. Deux séquences génomiques représentant le pathogène de bétail M. avium subsp. paratuberculosis (MAP) et un isolat opportuniste d'humain (M. avium subsp. hominissuis) ont servi de base pour la génomique comparative du MAC. Ceci est compliqué par un niveau de variabilité génétique d'un ordre logarithmique plus grand que celui qui se trouve dans le complexe de M. tuberculosis (MTBC), et par l'existence d'autres sous-ensembles de MAC au-delà des deux souches séquençées. Dans cette thèse, je cherche à définir les rapports phylogénétiques des divers membres du MAC et à explorer les processus évolutionnaires qui ont mené à l'apparition de l'espèce pathogène MAP. Une technique d'identification a été développée pour déterminer clairement les sous-ensembles de MAC, un outil dont l'absence par le passé limitait l'analyse des données. La possibilité d'utiliser un système d'analyse par séquençage multi-locus (MLSA) a révélé que le MAC est composé d'un groupe hautement variable avec la plus grande partie des génotypes appartenant à ce que l'on considère comme étant le$
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Jouet, Agathe. "The adaptive evolution of the plant pathogen Albugo candida." Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/69366/.
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Albugo candida is a plant pathogen that has been reported on many host species. While multiple host-specific races have long been recognized in A. candida, the genetic variation of these races has never been explored in nature and little is known about how the pathogen has adapted to its many hosts. Recently, evidence of genetic exchanges between races suggested that hybridization played an important role in the evolution of A. candida races. The authors also demonstrated that host-specific races of A. candida can co-occur, provided the immune system of the host is compromised by a compatible race. This immunosuppression by A. candida had previously been shown to allow growth of other pathogens. To study both these phenomena (the evolution of and the host immunosuppression imposed by A. candida), a capture array was designed to sequence 187 loci (~660,000 bp) from A. candida and loci from 47 other plant pathogens. In Chapter 3, I explain the rationale and methodology behind this approach. I show that it is cost-effective and that it may be used to identify microorganisms directly from a leaf and make inference about pathogen abundance within samples. In Chapter 4, genetic diversity of A. candida is analysed at a 400 kb contig and 32 diversity-tracking genes. Races are identified based on genetic divergence and recombination is investigated within and between races. In Chapter 5, I investigate genetic diversity at heterozygous sites to study the ploidy level and the reproductive mode of A. candida races as well as to detect mixed A. candida infections and loss-of-heterozygosity events. In this thesis, I demonstrate that A. candida races adapt to their hosts using complex mechanisms and that some may, in the long term, speciate. I also provide a novel method which may be used to interrogate microbial diversity directly from the field.
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Fung, Rowena. "The adaptive evolution of the plant pathogen Albugo candida." Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/69369/.
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Albugo candida is a plant pathogen that has been reported on many host species. While multiple host-specific races have long been recognized in A. candida, the genetic variation of these races has never been explored in nature and little is known about how the pathogen has adapted to its many hosts. Recently, evidence of genetic exchanges between races suggested that hybridization played an important role in the evolution of A. candida races. The authors also demonstrated that host-specific races of A. candida can co-occur, provided the immune system of the host is compromised by a compatible race. This immunosuppression by A. candida had previously been shown to allow growth of other pathogens. To study both these phenomena (the evolution of and the host immunosuppression imposed by A. candida), a capture array was designed to sequence 187 loci (~660,000 bp) from A. candida and loci from 47 other plant pathogens. In Chapter 3, I explain the rationale and methodology behind this approach. I show that it is cost-effective and that it may be used to identify microorganisms directly from a leaf and make inference about pathogen abundance within samples. In Chapter 4, genetic diversity of A. candida is analysed at a 400 kb contig and 32 diversity-tracking genes. Races are identified based on genetic divergence and recombination is investigated within and between races. In Chapter 5, I investigate genetic diversity at heterozygous sites to study the ploidy level and the reproductive mode of A. candida races as well as to detect mixed A. candida infections and loss-of-heterozygosity events. In this thesis, I demonstrate that A. candida races adapt to their hosts using complex mechanisms and that some may, in the long term, speciate. I also provide a novel method which may be used to interrogate microbial diversity directly from the field.
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Young, Ethan A. "The Louisiana Folklife Program| Origins, Evolution and Significance." Thesis, University of Louisiana at Lafayette, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10163273.
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<p> This thesis originally came out of a term paper for Dr. John Troutman’s History 505 class in the spring of 2015, and at first, I was more interested in folklore itself than the organization charged with preserving it. But that soon changed, as did my purposes for writing. These purposes were several. First, to examine the Louisiana Folklife Program—its origins, its evolution, and its achievements—in order to see how it became what it is today. Second, to place the LFP in a national context by examining the factors that gave rise to its birth. Third, to explain why the LFP has endured while similar programs have struggled or faded away. And fourth, to examine the impact that political and academic opposition can and do have upon such programs. My methodology has changed little since I wrote the first page. Most of it entailed archival research coupled with secondary sources gleaned from libraries and Internet searches as well as oral interviews. What I learned in the course of my research has illustrated more than ever the fragility and value of Louisiana’s cultural heritage and the value of preserving it. Some of it was almost wiped out in the early twentieth century, when speaking French was forbidden in schools throughout the state. It is thus incumbent upon both the LFP and the people of Louisiana to each do their part in ensuring that their posterity will be able to enjoy the rich diversity Louisiana has to offer. Stories, recipes, and handicrafts are things that we should not allow to fade away. Once they are gone, there is no restoring them. The LFP has made tremendous advances in this regard, and I sincerely hope they continue to do so, for the sake of all the generations that come after us.</p>
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Brindefalk, Björn. "Mitochondrial and Eukaryotic Origins : A Phylogenetic Perspective." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-100147.
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Mitochondria are eukaryotic cellular organelles responsible for power-generation, believed to have come into existence by an endo-symbiontic event where a bacterial cell was incorporated by an un-specified "proto-eukaryote". Phylogenetic analysis have shown that the mitochondrial ancestor was most related to present-day alpha-proteobacteria, although the exact nature of the mitochondrial progenitor remains disputed. In this work, I have used phylogenetic and other methods to investigate the identity of the organism giving rise to mitochondria, by analysing the evolutionary history of select proteins, the events where they have been transfered to the eukaryotic nucleus, and the time-point of mitochondrial establishment. In addition, a search for mitochondrially related organisms in the ocean metagenome was performed, in the hope that something more related to the mitochondrial progenitor than anything previously identified could be found. Previous analysis have shown that a large fraction of mitochondrial proteins does indeed trace their descent to the alpha-proteobacteria, but I found that the amino-acyl tRNA-synthetases display more general bacterial descent, making it likely that these proteins are of a different origin from the mitochondria themselves. While the synthetases are encoded on the nuclear genome, most mitochondria still posses most of the tRNA on their own genomes. In the cases where the tRNA has been lost from the mitochondrial genome, I found that the probability of loss correspond to the evolutionary history of their synthetase. The ocean metagenome represents an order of magnitude more data than previously available, making it suitable for improving the analyses dealing with mitochondrial placement. This large of amount of data was utilised to improve the phylogenetic analyses, showing that previous works might have suffered from artefacts inflating the support for placement of mitochondria with a specific alpha-proteobacterial group. Eukaryotic/mitochondrial radiation was shown to be as old, or older, than radiation of extant alpha-proteobacteria, casting doubt on previous analysis identifying a specific alpha-proteobacterial group as the mitochondrial ancestor.
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Day, Alexander. "The evolution of virulence in the opportunistic pathogen Pseudomonas aeruginosa." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/47598/.
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Understanding both the mechanistic basis of virulence and the evolutionary processes under which it can arise, is fundamental if we are to increase our knowledge of disease causing bacteria in an era of ever increasing antibiotic resistance. To date, there has been a substantial effort to understand virulence evolution both theoretically and experimentally. However, comparatively little experimental work has focussed on the evolution of virulence in opportunistic pathogens, and how virulence varies across multiple host organisms. In this thesis, the opportunist Pseudomonas aeruginosa was used to study virulence and its evolution in hosts. The virulence levels of different strains of P. aeruginosa, both laboratory and clinical, were tested in the nematode Caenorhabditis elegans. It was found that virulence of P. aeruginosa was lower in clinical strains isolated from chronic infections, and laboratory strains initially isolated from chronic infections, while a strain isolated from an acute infection was substantially more virulent. Using the C. elegans host, a selection experiment was carried out to test the effect of host density on virulence evolution. This resulted in a varied array of P. aeruginosa virulence phenotypes, but the worm evolved bacteria did not exhibit drastically different phenotypes from the worm negative control experiments. However, the degree of evolution observed across all treatment groups, compared with the wild type, highlighted the changes a bacterial population can undergo in vitro, even from a relatively short period of sub culture. Lastly, P. aeruginosa virulence was tested in alternative host organisms, Galleria mellonella (waxmoth larvae) and Vigna radiate (mung bean seedlings). Virulence varied according to the host, with virulence in G. mellonella being universally high, while no virulence was observed in V. radiate. This work highlights that high or low virulence cannot automatically be assumed in different hosts for opportunistic bacteria such as P. aeruginosa. Furthermore, the results highlight the unpredictable nature of virulence evolution, and how dependent the emergence of virulence is on the interaction between the pathogen and the host. A more complete understanding of the principles underlying bacterial evolution and virulence could allow for the construction of more specific and accurate studies, with experimental conditions carefully engineered to best replicate the clinical conditions of interest.
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Keller, Beth A. "The origins of lactase persistence and ongoing convergent evolution." Master's thesis, University of Central Florida, 2011. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4955.
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As a primary factor in human evolution, natural selection is an important component of genetic research. Studies of lactase persistence suggest that positive selection has played a powerful role in the adaptation to a lifelong consumption of fresh milk. Using multiple research studies of lactase persistence and suspected corresponding single nucleotide genetic polymorphisms, this study combines data sources to determine whether evidence exists for natural selection of a specific cytosine-to-thymine genetic mutation located 13,910 base pairs (T-13910) upstream from the lactase gene. This polymorphism has potential to be a causal element for lactase persistence, and data suggest that natural selection has played a role in the rising frequency and distribution of this allele, if only in some regions. European and neighboring regions appear to have the highest frequencies with little or no frequency in Asia, Africa and Indonesia; however the presence of lactase persistence in those areas suggests convergent evolution may be occurring on a phenotypic level. To examine this possibility several other identified polymorphisms in the same region as the T-13910 will be included in this study.<br>ID: 029809385; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (M.A.)--University of Central Florida, 2011.; Includes bibliographical references (p. 69-79).<br>M.A.<br>Masters<br>Anthropology<br>Sciences
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Redmond, Anthony Kieran. "Reconstructing the origins and evolution of immunity with phylogenomics." Thesis, University of Aberdeen, 2018. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=237018.
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The ability to raise an immune response is essential for all life. Despite this, the evolution of immune systems is poorly understood, as immune genes confound many bioinformatic analyses. This is driven by the rapid rates at which immune genes evolve due to the incessant arms race between host and pathogen often causing standard phylogenetic approaches to fail to accurately model the evolutionary history of immune gene families. Many phylogenetic lessons have been learned since the dawn of the phylogenomics era however, and genome sequences of non-model organisms have now been assembled, permitting improved immune gene detection and hence taxon sampling. In this thesis, I have paired sophisticated phylogenomic tools, including outgroup-free rooting methods, and substitution models that account for structural and functional constraints on protein evolution, with new genome and transcriptome sequence data from taxa that allow inference of the ancestral immune state in vertebrates and animals. Using this approach, I have managed to identify the origins of several key immune genes and families. My results support ancestral complexity in the genes that regulate the functioning of vertebrate adaptive immune systems. My findings also support the presence of a complement system, a front-line innate immune defence, in the ancestor of all animals. I show that this system later underwent a period of major remodelling early in vertebrate evolution, generating novel complement systems in at least three major vertebrate taxa. It is clear from my findings that combining sophisticated phylogenetic models with enriched taxon sampling represents a powerful approach with which to gain understanding of the evolutionary history of the immune system, even in the face of gene loss and the inherent complexity of immune gene evolution.
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Littel, John Eamon. "The origins of young stars in the galactic halo." Thesis, Queen's University Belfast, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241382.
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Ishaque, Naveed. "An investigation into the signatures of evolution in pathogen effector genes." Thesis, University of East Anglia, 2012. https://ueaeprints.uea.ac.uk/38817/.
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Mutreja, Ankur. "The origins and evolution of Vibro cholerae O1 E1 Tor." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648490.
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Stahl, Aaron L. "Shedding Light on the Evolutionary Origins of Holometabolous Lens Evolution." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1504779814865935.
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Versteeg, Mila. "Words of liberty : the origins and evolution of constitutional ideas." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.669950.
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It has become almost universal practice for countries to adopt written constitutions that include a bill of rights. Yet we know little about the origins and evolution of the practice of constitution-writing on a global scale. Are bills of rights defining statements of the nation’s character and identity? Or are they more standardized documents that are similar across countries, and vary only at the margins? Are substantive constitutional features rooted in the society for which they are written, or are they borrowed from elsewhere? What are the origins of the world’s “words of liberty”? This thesis presents the first-ever systematic substantive exploration of the world’s written constitutions. It introduces a new database, based on the coding of the constitutions of 188 countries, for the period 1946-2006. With this data, it explores the historical trajectory of the world’s written constitutions and offers explanations for their substantive content. This thesis's most important finding is that constitutions are inherently “transnational” documents. As it turns out, substantive constitutional choices are remarkably unrelated to local needs and values. Constitutions do not express identity or national character. Instead, the most important predictor of whether any particular country adopts any particular constitutional provision is whether other countries previously did the same thing. Constitutions do not tell stories of the nation’s history, but rather tell stories of transnational interactions and international politics. As a result, constitutions have become at least partly standardized documents that vary along a small number of underlying dimensions. But this thesis also shows that not all constitutions are the same, and that there exists no evidence of a global constitutional convergence. Instead, the world’s constitutions divide in a limited number of constitutional families. This thesis is not currently available in ORA.
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Wilson, Daniel John. "Multilocus sequence analysis of the pathogen Neisseria meningitidis." Thesis, University of Oxford, 2005. http://ora.ox.ac.uk/objects/uuid:da523097-d805-45cc-93c6-112c8ee7b101.
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Neisseria meningitidis is the bacterium responsible for meningococcal meningitis and septicaemia in humans. Meningococcal disease is primarily a disease of young children, characterized by rapid deterioration from first symptoms to death, with an 11% fatality rate and a global distribution. Patterns of genetic diversity in meningococcal populations provide an account of their evolutionary history and structure, which can be inferred by population genetics modelling. Understanding these phenomena can inform control and prevention strategies, and provides interesting case studies in evolution. The aim of this thesis is to develop population genetics techniques for inferring the evolutionary history of meningococci. I begin by reviewing the field, and justifying the use of coalescent methods in modelling microparasite populations. Inference on carriage populations of meningococci under the standard neutral model and the neutral microepidemic model is performed using a modification to approximate Bayesian computation. AMOVA and Mantel tests are used to quantify the differentiation between carriage and disease populations, and the extent to which geography and host age structure carriage populations. The results are used to propose revised coalescent models for meningococcal evolution. The role of natural selection in shaping meningococcal diversity is investigated using a novel method that utilises an approximation to the coalescent and reversible-jump Markov chain Monte Carlo to detect sites under selection in the presence of recombination. Having performed a simulation study to assess the statistical properties of the method, I apply it to the porB antigen locus and seven housekeeping loci in N. meningitidis. There is strong evidence for selection imposed by the host immune system in the antigen locus, but not the housekeeping loci which are functionally constrained. Finally I discuss the future direction of population genetic approaches to understanding infectious disease.
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Ball, Colleen. "Understanding pathogen selection pressures at the within- and between-host levels." Thesis, University of British Columbia, 2006. http://hdl.handle.net/2429/57.
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Many infectious pathogens, and in particular viruses, have an
extremely high rate of mutation. This can lead to rapid evolution
driven by selection pressures operating at both the within- and
between-host levels, as strains compete for resources within their
chosen host while also competing to effectively transmit to new
hosts. In the case of chronic viral infections, such as the human
immunodeficiency virus (HIV) or hepatitis C, substantial viral
evolution may take place within a single infected host. The fitness
of a pathogen has been studied at the between-host level and at the
within-host level, but linking the two levels of selection pressure
is a difficult problem that has yet to be studied satisfactorily.
We modify a simple model describing the within host dynamics of HIV
infection by including multiple pathogen strains with different
properties and allowing these strains to mutate. Within the host we
observe different strategies for pathogen success during different
stages of infection, which often leads to different strains
predominating within the host over the course of infection. We then
embed our within-host model into a Monte Carlo simulation that
models the interactions between infected individuals. This approach
allows us to combine selective pressure at the within-host level
with pressures at the between-host level and helps us to predict
which strains are most likely to be present within the population.
We show that under our model assumptions the co-existence of
multiple strains is possible and we explore the factors leading to
the success of a pathogen.
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Davies, Neil. "Origins of diversity : the evolutionary genetics of Caribbean butterflies." Thesis, University College London (University of London), 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309290.
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Gomez-Alpizar, Luis E. "Molecular Evolution of Phytophthora infestans (Mont.)de Bary, the late blight pathogen." NCSU, 2004. http://www.lib.ncsu.edu/theses/available/etd-11302004-224228/.
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Phytophthora infestans (Mont.) de Bary causes late blight of potato and tomato and is one of the world?s most devastating plant diseases. P. infestans left its footprint in human history when, in the 19th century, it was responsible for the Irish Potato Famine. Nuclear and mitochondrial DNA variability was used to examine the population history of P. infestans. DNA sequence data from three nuclear regions (Intron Ras, Ras, and â-tubulin) and two mitochondrial regions (P3 and P4) were obtained from ninety isolates from various locations including Brazil, Bolivia, Ecuador, Peru, Costa Rica, Mexico (Toluca Valley), the USA and Ireland. Population summary statistics show that the Mexican population from the presumed center of origin of P. infestans, harbored less nucleotide and haplotype diversity than South American populations, and was genetically differentiated from other populations, particularly at the mitochondrial loci. Coalescent-based genealogies of mitochondrial (rpl14, rpl5, tRNAs, cox1) and nuclear (Intron Ras+Ras) loci were congruent and demonstrated the existence of two lineages leading to the present day haplotypes of P. infestans associated with potatoes. A third lineage, associated with a group of isolates from Solanum tetrapetalum collected in the Andean Highlands of Ecuador was also found. In the mitochondrial genealogy the two potato lineages corresponded to the mitochrondrial haplotypes Type I and Type II described elsewhere. Mitochondrial haplotypes were associated with different nuclear backgrounds. Haplotypes found in the Toluca Valley population were derived from only one of the two lineages in both mitochondrial and nuclear genealogies, whereas haplotypes found in South American populations (Peru and Ecuador) were derived from both lineages. Haplotypes found in USA and Ireland populations were also derived from both lineages and these populations were not genetically differentiated from the Peruvian populations, suggesting a common ancestry among these populations. Evidence for recombination was found for Mexican and USA populations. Solanum tetrapetalum isolates were highly polymorphic within the regions analyzed and may be a new species. The results support a South American origin of P. infestans and are discussed in relation of previous hypotheses regarding the geographic origin of this plant pathogen.
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Edgell, David R. "Origins and evolution of the archaebacterial and eukaryotic DNA replication apparatus." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq24737.pdf.
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Svenson, Gavin John. "The Origins, Evolution, and Phylogeny of the Praying Mantises (Dictyoptera: Mantodea)." BYU ScholarsArchive, 2007. https://scholarsarchive.byu.edu/etd/1021.
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The relatively small insect order Mantodea (praying mantises) is comprised of approximately 2,366 described species distributed in 436 genera. Members of the group occupy diverse habitats and are distributed across the globe, though their greatest numbers and diversity are concentrated primarily in the tropics. Though continental endemism is common, many groups have a broad global distribution. An immense diversity of morphology is exhibited across the order with adult mantises ranging in size from 2cm to ~25cm, and appearing like a dead leaf, a piece of quartz rock, or a blade of grass. The diversification and specialization of mantises in ecologically diverse and biogeographically dispersed habitats suggest interesting questions about their morphological and behavioral adaptations. Despite their considerable popularity and consistent presence in the history of humanity, praying mantises have received surprising little attention from a phylogenetic or evolutionary standpoint. Though taxonomic studies have been thorough, discrepancies among classifications suggest wide latitude in the interpretation of morphological characters and their relative importance for grouping taxa. To address the lack of evolutionary knowledge surrounding praying mantises, the specific goals of this project were to: a) Reconstruct a comprehensive phylogeny for Mantodea using molecular characters; b) Use the phylogeny to elucidate character system evolution including hunting strategy, auditory evolution, and morphological convergences; and c) Investigate biogeographic patterns and determine the origins of the modern Mantodea. A comprehensive taxonomic and distributional sampling of Mantodea, covering virtually all higher-level groups, was assembled to reconstruct the phylogeny for the order. Sequence data were generated from five mitochondrial and four nuclear loci for 331 mantis species along with ten cockroach and termite species as outgroups. The resulting phylogenetic hypotheses served as the first glimpse of mantis evolutionary relationships and provided a template for further investigation. Only 7 of 15 families, 16 of 48 subfamilies, and 11 of 46 tribes were recovered as monophyletic indicating that phylogeny is largely incongruent with current mantis classification. As is the case in many other orders of insects, 'key characters' that do not reflect phylogeny are largely responsible for delimiting the groups. An investigation of mantis hunting strategy revealed clear transitions from generalist hunting mantises to the more derived strategies of cursorial and ambush hunting. In fact, the ambush hunting strategy appears to have evolved once, which led to a major diversification within the order. Some praying mantises have sensitive ultrasonic hearing arising from a unique 'cyclopean' ear located in the ventral metathorax. This project explored the evolutionary history of the mantis auditory system by integrating large anatomical, neurophysiological, behavioral, and molecular databases. Using an 'auditory phylogeny' based on 13 morphological characters, a primitively earless form of metathoracic anatomy was indentified in several extant taxa. In addition, there are five distinct mantis auditory systems. Three of these can be identified anatomically, and the other two can only be detected neurophysiologically. Mapping these results onto a phylogenetic tree derived from molecular data, shows that the cyclopean mantis ear evolved once 85-90 mya. All the other auditory system types are either varying degrees of secondary loss, or are recent innovations that each occurred independently multiple times. The neurophysiological response to ultrasound is remarkably consistent across all taxa tested, as is the multi-component, in-flight behavior triggered by ultrasound. Thus, mantises have an ancient, highly conserved auditory neural-behavioral system that probably arose for evasion of echolocating predators. Modern bat families diverged ca. 63 mya, but the echolocating ancestors of bats appeared earlier. Alternatively, non-bat predators may have driven the evolution of the unique mantis auditory systems. Mapping biogeographic regions on the phylogeny demonstrated that our results adhere closer to geographic distribution than to the current classification. Specific patterns in distribution suggest that major morphological convergences have confounded taxonomists ability to construct natural groups. It was found that major mantis lineages diverged prior to the isolation of geographic regions and subsequent ecomorphic specializations within these regions led to convergences in morphology. Divergence time estimations place the origins of Mantodea at the beginning of the Jurassic with modern mantises originating on Gondwanaland in the Early Cretaceous. The first major divergence among modern mantises occurred as a result of the splitting of South America from Africa. The subsequent breakup of Gondwanaland continents spurred numerous divergences within the order and led to the contemporary paraphyletic assemblages of taxa within each biogeographic region. In fact, most divergences between Afrotropical and Indomalayan lineages resulted from the slow dissociation between Africa and the Indian subcontinent. Our results also suggest that Antarctica played an important role as a biological conduit during the diversification of some Afrotropical and Indomalayan lineages. Further, Antarctica facilitated the repeated invasions of South America and Australia prior to the separation of these two continents from Antarctica during the Eocene. When India slammed into Asia around 50 million years ago, it released a flood of mantises into Asia and Southeast Asia that diversified and currently comprise the largest component of Indomalayan taxa. The origins, secondary invasions, and regional extinctions have created an order of insects with complex distributional and evolutionary histories.
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Bishop, Wendy. "The origins and evolution of ornamental lakes in English designed landscapes." Thesis, University of East Anglia, 2017. https://ueaeprints.uea.ac.uk/67860/.
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The aim of this thesis is to investigate the origins and evolution of ornamental lakes in England, to establish when they first appeared, how they were constructed and what factors led to their emergence. For the purposes of this study, a lake is defined as a man-made piece of water covering one hectare or more. To aid discussion and analysis, a classification system to describe lakes has been drawn up, the two main categories being geometric and irregular lakes, with sub-divisions. The investigation begins with an appraisal of water in landscapes preceding the eighteenth century, with a focus on fishponds (vivaria), and elements such as moats, millponds and water-gardens. The appearance and development of ornamental lakes in the early eighteenth century is then explored in depth, as is the work of Lancelot Brown. The contribution of other lake-makers such as Richard Woods and William Emes is also examined. Humphry Reptonï¿1⁄2s work, and the impact of the Picturesque on lakes, are evaluated to assess their importance in the evolution of lakes, and the chronological study extends into the late nineteenth century. The construction of lakes is investigated, and related to different lake types. Also, the question of whether lakes were lined to retain water is considered. Geological and topographical factors are also studied in order to see how they might affect the construction and siting of lakes. The reasons for the emergence of ornamental lakes are also explored, and these include the fact that landscapes increased in size around 1700 and became less symmetrical, the effect of the Grand Tour, and the paintings associated with it, and the changing ways in which parks were used.
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Carroll, Sean Michael 1981. "Mechanisms of evolution by gene duplication: The origins of corticosteroid signaling." Thesis, University of Oregon, 2009. http://hdl.handle.net/1794/10444.
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ix, 120 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number.<br>Gene duplication underlies the evolution of many protein functions and is a known stimulus for molecular innovation. Many models exist to explain the maintenance of duplicate genes in the genome and the dynamics that drive the evolution of novel protein functions; few if any of these models, however, incorporate knowledge of how protein structures and functions actually evolve. A growing body of work on the historical mechanisms of molecular evolution and the ways in which proteins evolve in the lab has provided profound insights into the ways in which proteins respond to mutation, selection, and drift. Evolutionary models of duplicate gene evolution could greatly benefit from the knowledge gained from these mechanistic studies of protein evolution.
My dissertation seeks to address this gap in knowledge by reconstructing the process by which novel steroid signaling pathways evolved after gene duplication. I focus specifically on a class of hormones called corticosteroids--critical regulators of the stress response, metabolism, and immunity--and the mineralocorticoid and glucocorticoid receptors that mediate the steroid response. Both the enzymes that synthesize corticosteroids and the hormone receptors are the result of ancient gene duplication events, and I make use of methods in phylogenetics, molecular biology, and structural biology to reconstruct the mechanisms and dynamics by which they evolved.
This dissertation comprises three separate but complementary studies that illuminate the origins of corticosteroid signaling. In the first project, I show how lineage-specific steroid signaling arose in elasmobranchs as a novel hormone exploited the structural promiscuity of preexistent receptors. Next, I describe how degenerative and stabilizing mutations defined the divergence of the glucocorticoid receptor after gene duplication. And finally, I use phylogenetic and functional analyses to reconstruct the origins of corticosteroid synthesis with the duplication of enzymes in the steroid synthesis pathway. Together, I provide a comprehensive reconstruction of the evolution of corticosteroid signaling. This work also highlights specific evolutionary mechanisms--molecular exploitation, structural and functional promiscuity, degenerative mutations, and stabilizing mutations--that could drive the evolution of novel protein functions after gene duplication.
This dissertation includes both previously published and unpublished co-authored materials.<br>Committee in charge: Patrick Phillips, Chairperson, Biology;
Joseph Thornton, Advisor, Biology;
William Cresko, Member, Biology;
John Postlethwait, Member, Biology;
Kenneth Prehoda, Outside Member, Chemistry
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Nurtay, Anel. "Mathematical modelling of pathogen specialisation." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667178.
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L’aparició de nous virus causants de malalties està estretament lligada a l’especialització de subpoblacions virals cap a nous tipus d’amfitrions. La modelització matemàtica proporciona un marc quantitatiu que pot ajudar amb la predicció de processos a llarg termini com pot ser l’especialització. A causa de la naturalesa complexa que presenten les interaccions intra i interespecífiques en els processos evolutius, cal aplicar eines matemàtiques complexes, com ara l’anàlisi de bifurcacions, al estudiar dinàmiques de població. Aquesta tesi desenvolupa una jerarquia de models de població per poder comprendre l’aparició i les dinàmiques d’especialització, i la seva dependència dels paràmetres del sistema. Utilitzant un model per a un virus de tipus salvatge i un virus mutat que competeixen pel mateix amfitrió, es determinen les condicions per a la supervivència únicament de la subpoblació mutant, juntament amb la seva coexistència amb el cep de tipus salvatge. Els diagrames d’estabilitat que representen regions de dinàmiques diferenciades es construeixen en termes de taxa d’infecció, virulència i taxa de mutació; els diagrames s’expliquen en base a les característiques biològiques de les subpoblacions. Per a paràmetres variables, s’observa i es descriu el fenomen d’intersecció i intercanvi d’estabilitat entre diferents solucions sistemàtiques i periòdiques en l’àmbit dels ceps de tipus salvatge i els ceps mutants en competència directa. En el cas de que diversos tipus d’amfitrions estiguin disponibles per a ser disputats per ceps especialitzats i generalistes existeixen regions de biestabilitat, i les probabilitats d’observar cada estat es calculen com funcions de les taxes d’infecció. S’ha trobat un rar atractor caòtic i s’ha analitzat amb l’ús d’exponents de Lyapunov. Això, combinat amb els diagrames d’estabilitat, mostra que la supervivència del cep generalista en un entorn estable és un fet improbable. A més, s’estudia el cas dels diversos ceps N>>1 que competeixen per diferents tipus de cèl·lules amfitriones. En aquest cas s’ha descobert una dependència no monotònica, contraria al que es preveia, del temps d’especialització sobre la mida inicial i la taxa de mutació, com a conseqüència de la realització d’un anàlisi de regressió sobre dades obtingudes numèricament. En general, aquest treball fa contribucions àmplies a la modelització matemàtica i anàlisi de la dinàmica dels patogens i els processos evolutius.<br>La aparición de nuevos virus causantes de enfermedades está estrechamente ligada a la especialización de las subpoblaciones virales hacia nuevos tipos de anfitriones. La modelizaci ón matemática proporciona un marco cuantitativo que puede ayudar a la predicción de procesos a largo plazo como la especialización. Debido a la naturaleza compleja que presentan las interacciones intra e interespecíficas en los procesos evolutivos, aplicar herramientas matemáticas complejas, tales como el análisis de bifurcación, al estudiar dinámicas de población. Esta tesis desarrolla una jerarquía de modelos de población para poder comprender la aparición y las dinámicas de especialización, y su dependencia de los parámetros del sistema. Utilizando un modelo para un virus de tipo salvaje y un virus mutado que compiten por el mismo anfitrión, se determinan las condiciones para la supervivencia únicamente de la subpoblación mutante, junto con su coexistencia con la cepa de tipo salvaje. Los diagramas de estabilidad que representan regiones de dinámicas diferenciadas se construyen en términos de tasa de infección, virulencia y tasa de mutación; los diagramas se explican en base a las características biológicas de las subpoblaciones. Para parámetros variables, se observa y se describe el fenómeno de intersección e intercambio de estabilidad entre diferentes soluciones sistemáticas y periódicas en el ámbito de las cepas de tipo salvaje y las cepas mutantes en competencia directa. En el caso de que varios tipos de anfitriones estén disponibles para ser disputados por cepas especializadas y generalistas existen regiones de biestabilidad, y las probabilidades de observar cada estado se calculan como funciones de las tasas de infección. Se ha encontrado un raro atractor caótico y se ha analizado con el uso de exponentes de Lyapunov. Esto, combinado con los diagramas de estabilidad, muestra que la supervivencia de la cepa generalista en un entorno estable es un hecho improbable. Además, se estudia el caso de los varias cepas N>> 1 que compiten por diferentes tipos de células anfitrionas. En este caso se ha descubierto una dependencia no monotónica, contraria a lo que se preveía, del tiempo de especialización sobre el tamaño inicial y la tasa de mutación, como consecuencia de la realización de un análisis de regresión sobre datos obtenidos numéricamente. En general, este trabajo hace contribuciones amplias a la modelización matemática y el análisis de la dinámica de los patógenos y los procesos evolutivos.<br>The occurrence of new disease-causing viruses is tightly linked to the specialisation of viral sub-populations towards new host types. Mathematical modelling provides a quantitative framework that can aid with the prediction of long-term processes such as specialisation. Due to the complex nature of intra- and interspecific interactions present in evolutionary processes, elaborate mathematical tools such as bifurcation analysis must be employed while studying population dynamics. In this thesis, a hierarchy of population models is developed to understand the onset and dynamics of specialisation and their dependence on the parameters of the system. Using a model for a wild-type and mutant virus that compete for the same host, conditions for the survival of only the mutant subpopulation, along with its coexistence with the wild-type strain, are determined. Stability diagrams that depict regions of distinct dynamics are constructed in terms of infection rates, virulence and the mutation rate; the diagrams are explained in terms of the biological characteristics of the sub-populations. For varying parameters, the phenomenon of intersection and exchange of stability between different periodic solutions of the system is observed and described in the scope of the competing wild-type and mutant strains. In the case of several types of hosts being available for competing specialist and generalist strains, regions of bistability exist, and the probabilities of observing each state are calculated as functions of the infection rates. A strange chaotic attractor is discovered and analysed with the use of Lyapunov exponents. This, combined with the stability diagrams, shows that the survival of the generalist in a stable environment is an unlikely event. Furthermore, the case of N=1 different strains competing for different types of host cells is studied. For this case, a counterintuitive and non-monotonic dependence of the specialisation time on the burst size and mutation rate is discovered as a result of carrying out a regression analysis on numerically obtained data. Overall, this work makes broad contributions to mathematical modelling and analysis of pathogen dynamics and evolutionary processes.
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Archer, Heather. "Evolution of Independent Genetic Pathways for Pathogen Resistance within the Nematode Caenorhabditis remanei." Thesis, University of Oregon, 2013. http://hdl.handle.net/1794/13438.
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Pathogenic host-microbe interactions can result from continuous evolution of a host's ability to resist infection and a pathogen's ability to survive and replicate. Pseudomonas aeruginosa is a versatile and opportunistic pathogen, ubiquitous in soil, and capable of damaging plants, vertebrates, and invertebrates. Previous studies in nematodes suggest that the pathogenic effects of P. aeruginosa can result from multiple distinct pathways: a toxin-based effect that kills within a few hours and a generalized virulence that kills over the course of multiple days. Using experimental evolution in the highly polymorphic nematode Caenorhabditis remanei, I show that nematode resistance to the two modes of pathogenesis in P. aeruginosa evolves through genetically independent pathways. These results demonstrate that multiple virulence factors in a pathogen can result in multiple responses in the host, and the genetic lines established here create resources for further exploration of the genetic basis for resistance to P. aeruginosa.
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Mangione, Michele Ann. "The origins and evolution of somatics: Interviews with five significant contributors to the field /." The Ohio State University, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487848078451933.
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Leak-Garcia, Janet Aree. "Genetic origins and the evolution of invasiveness of Cynara cardunculus in California." Diss., UC access only, 2009. http://proquest.umi.com/pqdweb?index=73&did=1924118031&SrchMode=1&sid=1&Fmt=7&retrieveGroup=0&VType=PQD&VInst=PROD&RQT=309&VName=PQD&TS=1270230178&clientId=48051.
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Cecile, Anna Sarabian. "Exploring the origins of disgust: Evolution of parasite avoidance behaviors in primates." Kyoto University, 2019. http://hdl.handle.net/2433/242653.
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付記する学位プログラム名: 霊長類学・ワイルドライフサイエンス・リーディング大学院<br>Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(理学)<br>甲第21615号<br>理博第4522号<br>新制||理||1649(附属図書館)<br>京都大学大学院理学研究科生物科学専攻<br>(主査)准教授 Andrew MacIntosh, 教授 古市 剛史, 教授 髙井 正成<br>学位規則第4条第1項該当
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Bos, Jorunn Indra Berit. "Function, structure and evolution of the RXLR effector AVR3a of Phytophthora infestans." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1186589341.
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D'Alonzo, Jacopo. "Trần Đức Thảo’s Theory of Language Origins". Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCA096/document.
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Depuis des siècles, plusieurs penseurs et scientifiques ont abordé la relation entre la coopération, le langage et la cognition sociale. Parmi eux, Trần Đức Thảo (1917-1993) mérite une mention spéciale. Le but de la recherche qui suit est de présenter au lecteur la réflexion philosophique de Thảo sur le langage humain et son évolution. Nous essaierons de tracer les grandes lignes de la théorie de Thảo sur les origines du langage dans ses Recherches sur l'origine du langage et de la conscience (1973) dans lesquelles il a essayé de trouver une synthèse entre philosophie, linguistique, psychologie et anthropologie physique. La découverte du marxisme-léninisme a conduit Thảo à proposer une approche matérialiste et dialectique au problème de la relation entre corps esprit. De cette façon, Thảo a proposé une sorte de tournant matérialiste et historique de la philosophie de la conscience de Husserl qui était au cœur de ses premiers intérêts philosophiques. La théorie de Thảo met en relief la nature sociale du langage et de la cognition, de sorte que l’évolution du langage est inextricablement liée aux relations sociales. Une telle conclusion reposait sur l’hypothèse que le travail est une caractéristique exclusivement humaine qui distingue les humains des animaux. Pour lui, la genèse du langage est dans le travail humain et donc le langage se développe parmi nos ancêtres pré-humains ainsi que chez les humains en réponse aux problèmes posés par la vie matérielle. En gardant à l’esprit que le langage découle des exigences sociales et des besoins du monde matériel, selon Thảo le langage se transforme lui-même au fur et à mesure que la société humaine change. Et compte tenu des racines sociales de la pensée et du langage, la conscience évolue continuellement avec le temps. Dans ce cadre, Thảo a voulu déterminer la nature du langage et son rôle dans les sociétés préhistoriques et son évolution à travers les relations sociales<br>Several thinkers and scientists throughout the philosophical and scientific tradition took up the relationship between cooperation, language, and social cognition. Among them, Trần Đức Thảoʼs (1917–1993) deserves a special mention. The purpose of the following research is to introduce the reader to Thảoʼs philosophical reflection on human language and its evolution. We shall attempt to map out the main lines of Thảoʼs theory of language origins set out in his Recherches sur l’origine du langage et de la conscience (1973) that combines philosophy, linguistics, psychology, and anthropology. The discovery of Marxism-Leninism led Thảo to suggest a materialistic and dialectic approach to the mind-body problem. In this way, Thảo tried to suggest a materialist and historical turn of Husserl’s philosophy of consciousness which was at the very heart of his own first philosophical interests. Thảo’s account threw into sharp relief the social nature of both language and cognition, so that language evolution is linked inextricably to social relations. Such a view depended upon the assumption that labour is an exclusively human characteristic which sets humans apart from animals. And the genesis of language is in human labour. In this way of thinking, language develops among both our pre-human ancestors and present humans in response to problems posed by the material life. Bearing in mind that language arises from the social demands and needs of the material world, language is transformed itself as human society changes. And given the social roots of thought and language, consciousness evolves continuously over time. Within this framework, Thảo wanted to determine the nature of language and its role in pre-historical societies and its making through social relations
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Ford, Suzanne. "Coevolutionary interactions between a defensive microbe and a pathogen within a Caenorhabditis elegans model host." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:b78d3a31-a3c0-469c-a45d-42dbfbb934ce.
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Microbes can protect their plant and animal hosts against infection by pathogens, parasites and parasitoids. These âdefensive microbes' can provide a powerful line of defence beyond the host response and are becoming attractive candidates for disease control. In this thesis, I investigated how defensive microbes can interact with pathogens over evolutionary time by measuring the effects of co-passaging a defensive microbe (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within the Caenorhabditis elegans model host. In Chapter 1, I found that co-passaging drove the evolution of reduced pathogen virulence as a by-product of adaptation to microbe-mediated defence. Moreover, I show that the mechanism of pathogen resistance to the defensive microbe can determine the direction of virulence evolution. In chapter two, I discovered that the co-passaged defensive microbe and pathogen populations had undergone coevolutionary interactions within host populations via fluctuating selection dynamics. I then showed that these dynamics resulted in patterns of pathogen local adaptation and increased genetic divergence. Finally, in chapter three, I revealed that these coevolutionary interactions significantly affected the costs and benefits of the defensive microbes to their hosts, but that the relationship between these costs and benefits prevented the transition of defensive microbes across the mutualism-parasitism continuum. Together, this thesis uncovers the potential for defensive microbes to shape the evolution of pathogens and demonstrates that defensive microbes can be an evolutionarily dynamic but stable form of host resistance towards infectious disease. As such, the data presented in this thesis have important implications for how we study host-parasite interactions in nature and question our current understanding of virulence evolution, pathogen local adaptation and the origin of defensive microbes.
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Bank, Gregory Charles. "Testing the Origins of the Blue Ridge Escarpment." Thesis, Virginia Tech, 2001. http://hdl.handle.net/10919/34794.
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Long, linear, high-relief escarpments mark many of the world's passive margins. These Great Escarpments have been interpreted to be the result of isostatic flexure, parallel slope retreat, and divide migration which accompanies rifting. It is unclear whether all these escarpments share this origin. Also uncertain is whether these features are formed via stable, steady-state processes or by climatic shifts or tectonic rejuvenation. The Blue Ridge Escarpment, eastern North America's great escarpment, is no different. A number of hypotheses attempt to explain the Blue Ridge Escarpment. These include lithologic variation between Blue Ridge and Piedmont rocks, the distance to ultimate base level, as well as, escarpment retreat resulting from post/syn-rift warping or faulting. We approach this problem from two directions. The first involves topographic comparisons and geologic observations to recognize and track divide migration. The second approach uses U-Th/He thermochronometry along two scarp-normal transects.
Topographic analysis used data extracted from DEMs to compare three zones - the Upland, the Piedmont and the scarp zone itself. Parameters such as relief, drainage density, hypsometry, and slope are often used as proxies for relative erosion rates and the degree of maturity of a landscape. Results from these analyses indicate that the Upland and Piedmont zones are distinct landscapes, sharing very few topographic similarities, yet neither appears significantly more erodible than the other. Examination of parameters in the proximity of the escarpment point toward more rapid erosion here. Field evidence of this rapid scarp erosion (and thus divide migration) lies in the presence of beheaded stream channels, cobble roundness, and clast provenance.
U-Th/He thermochronometry is a low temperature technique that allows us to calculate when rock cooled below 60-70C. Temperature is used as a proxy for depth, from which we can extract an exhumation rate. This method allows us to further test scarp genesis hypotheses. Preliminary results show older ages (~160) from the Upland surface than on the Piedmont lowland (~100 Ma). This confirms that the Piedmont surface is distinct from the Upland and demonstrates that it has experienced greater erosion. There is also some indication that ages "jump" across the Bowens Creek/Brevard fault system. Lastly, the ages appear to become younger approaching the escarpment which is indicative of scarp migration. As these results are preliminary, more data is required to prove or disprove these conclusions.<br>Master of Science
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Melnyk, Anita. "The Evolution of Antibiotic Resistance in Experimental Populations of Bacteria." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/34556.
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Antibiotic resistance is a major threat to public health. Understanding how it evolves,
and the genes that underlie resistance, is the main goal of my Ph.D. research. After a resistance mutation arises, it’s fate within a pathogen population will be etermined in part by its fitness: mutations that suffer little or no fitness cost are more likely to persist in the absence of antibiotic treatment. My research centers on understanding this process better by gaining knowledge about the spectrum of fitness effects associated with antibiotic resistance mutations.
Using a meta-analysis framework I find that, across a range of antibiotics and pathogens, on average single resistance mutations exhibit fitness costs in the absence of drug, however, there are instances of cost-free mutations. To evaluate the conditions leading to the persistence of resistance in the absence of antibiotic, I use experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa and the antibiotic ciprofloxacin to investigate the phenotypic and genetic differences associated with constant and fluctuating drug treatment. I find that fluctuating drug treatment leads to the evolution of cost-free resistance. At the genetic level, cost-free resistance is the result of second-site mutations that compensate for the fitness cost associated with ciprofloxacin-resistance mutations. Further examination of the resistance mutations shows a lack of epistatic interactions between co-occurring mutations that confer resistance within a single isolate. To investigate the repeatability of the genetic causes of resistance, I execute a second evolution experiment using multiple clinical strains of P. aeruginosa adapting to a constant ciprofloxacin selective pressure. I find a remarkable lack of parallel evolution at the genomic level both within and between different P. aeruginosa strains.
I have shown that antibiotic resistance is costly, and that these costs can be ameliorated by second-site mutations that readily arise over short time scales. Additionally, different strains of the same bacteria can gain resistance through a diverse set of genetic mutations. On an applied level these results are not positive; combating resistance evolution will be difficult because pathogens can easily compensate fitness costs of resistance, and resistance itself can be gained via a large number of genetic targets.
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Ashton, Paul Allan. "Multiple origins of Senecio cambrensis Rosser, and related evolutionary studies in British Senecio." Thesis, University of St Andrews, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242898.
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Nelson, Adam Michael. "Genomic analysis of pathogen evolution virulence gene acquisition and genetic erosion in Escherichia coli /." Diss., Connect to online resource - MSU authorized users, 2008.
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Paul, Sinu. "Host-pathogen interactions and evolution of epitopes in HIV-1: understanding selection and escape." Kent State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=kent1334509644.
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Ervin, Jeremy Alan. "Effects of student ontological position on cognition of human origins." Columbus, Ohio : Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1061402311.
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Thesis (Ph. D.)--Ohio State University, 2003.<br>Title from first page of PDF file. Document formatted into pages; contains xiv, 131 p.; also includes graphics. Includes abstract and vita. Advisor: David L. Haury, College of Education. Includes bibliographical references (p. 97-104).
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Shamai, Patricia Daisy. "The stigmatisation of certain contemporary weapons of war: Its origins, evolution and development." Thesis, University of Southampton, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.539011.
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Yang, Grant. "WIMP and Beyond: The Origins, Evolution, and Awaited Future of User Interface Design." Scholarship @ Claremont, 2015. http://scholarship.claremont.edu/cmc_theses/1126.
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The field of computer user interface design is rapidly changing and diversifying as new devices are developed every day. Technology has risen to become an integral part of life for people of all ages around the world. Modern life as we know it depends on computers, and understanding the interfaces through which we communicate with them is critically important in an increasingly digital age. The first part of this paper examines the technological origins and historical background driving the development of graphical user interfaces from its earliest incarnations to today. Hardware advancements and key turning points are presented and discussed. In the second part of this paper, skeuomorphism and flat design, two of the most common design trends today, are analyzed and explained. Finally, the future course of user interface is predicted based off of emergent technologies such as the Apple Watch, Google Glass, Microsoft HoloLens, and Microsoft PixelSense. Through understanding the roots and current state of computer user interface design, engineers, designers, and scientists can help us get the most out of our ever-changing world of advanced technology as it becomes further intertwined with our existence.
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Tonkes, Bradley. "On the origins of linguistic structure : computational models of the evolution of language /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16529.pdf.
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Delgado, Jorge Eduardo. "Counter-insurgency in Colombia : the origins and evolution of a military strategic tradition." Thesis, King's College London (University of London), 2016. https://kclpure.kcl.ac.uk/portal/en/theses/counterinsurgency-in-colombia(b411b659-7e82-4f30-a7c3-31ff159a866a).html.
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This research proposes to examine the composition and evolution of the Colombian military’s approach to counter-insurgency since the origins of the internal armed conflict that affects the country. Following the lineaments of strategic theory, it will endeavour to understand how the military came to view the utilisation of armed force, amongst other means, since the beginning of the armed conflict. To construct the Colombian military strategic tradition, it will attempt to identify its value–system, that is, the ideological precepts, motivational patterns and assumptions that throughout the years have influenced the military’s use of the main instruments at its disposal. It will explore how these diverse factors have shaped different understandings of the character of the conflict, views of its political conduct, and of the role and limits of armed force, amongst other issues. This analysis will allow to establish lines of continuity and change in Colombian military thinking. In this respect, the research argues that the formative years of the Colombian strategic tradition during the 1960s, and in particular the influence of counter-insurgency thinking, has been fundamental in shaping the military’s different, and at times conflicting, judgements about the conflict, the nature of their enemies and the limits of armed force during the past 20 years of escalation of violence in Colombia. Overall, the research shows that the inherent tensions visible in Colombian military thinking have undermined the formulation of strategy, that is, the translation of means into political ends.
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Ross-Gillespie, Adin. "Model socialite, problem pathogen : the evolution and ecology of cooperation in the bacterium Pseudomonas aeruginosa." Thesis, University of Edinburgh, 2008. http://hdl.handle.net/1842/3134.
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In recent decades we have learned that cooperation is an important and pervasive feature of microbial life. This revelation raises exciting possibilities. On the one hand, we can now augment our understanding of how social phenomena evolve by using microbial model systems to test our theories. On the other hand, we can use concepts from social evolution to gain insight into the biology of the microbes we hope to control or kill. In this thesis I explore both possibilities. First, I consider the theoretical problem of how and when microbial cooperation might be subject to frequency- and densitydependence. Formerly, vague theory and a scant, sometimes contradictory empirical literature made it unclear when such patterns could be expected. Here, I develop theory tailored to a microbial context, and in each case, I test key predictions from the theory in laboratory experiments, using as my model trait the production of siderophores by the bacterium Pseudomonas aeruginosa. Secondly, I consider the ecological consequences of cooperator-cheat dynamics in the context of an infection. Specifically, I use experimental infections of diverse host models to investigate the role of two cooperative traits, siderophore production and quorum sensing, in the pathogenesis of P. aeruginosa. When a successful infection requires cooperation among pathogens, theory predicts that conflict among coinfecting strains can undermine cooperation and hence decrease virulence; whereas, in the absence of cooperation, conflict could lead to heightened exploitation and hence increased virulence. This exciting idea has received little empirical attention to date but here I address this using multiple pathogen strains, multiple social traits, and multiple model hosts.