Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that today'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. / Ph. D.

Användningen av biokatalysatorer, särskilt enzymer, inom kemikalie- och läkemedelsindustrin erbjuder betydande fördelar jämfört med de traditionella kemo-katalytiska metoderna som historiskt har dominerat industrin. En viktig klass av enzymer, transaminaser, spelar en central roll i tillverkningen av kirala aminer, som utgör grundläggande byggstenar i dessa industriella sektorer. Denna studie är inriktad på ett specifikt amin transaminas från Silicibacter pomeroyi. Tidigare har detta enzym visat förmåga att katalysera en mängd olika reaktioner för produktion av kirala aminer, men för att realisera dess fulla potential inom industriella tillämpningar krävs förbättrad stabilitet vid högre temperaturer. I motsats till de vanligt förekommande metoderna för proteinteknik, såsom rationell design och riktad evolution, används i denna studie släktsekvensrekonstruktion för att skapa mer temperaturtåliga varianter av detta enzym. Tidigare användning av denna metod har visat sig kunna generera proteiner med högre temperaturtålighet. Genom denna metod, där förfäder till detta enzym återskapas utifrån bevarade sekvenser, förväntas generering av varianter som kan bibehålla sin funktion vid högre temperaturer under en längre tid. Genom att utforska denna alternativa strategi för proteinteknik strävar studien efter att ge mer robusta biokatalysatorer för industriella tillämpningar. Utfallet från denna studie visade att två förfäder hade ökad termostabilitet. Detta visade sig dels genom analys av T5015 som påvisade en 3.9 och 6 C° förbättring för respektive förfader. Vidare påvisade t1/2 mätningar att dessa enzymer kunde utstå 2.06 till 3.72 gånger så lång tid vid 55 C° innan de inaktiverades. De påvisade dock lägre specifik aktivitet vid rumstemperatur, där en bidragande faktor till detta var att enbart en liten fraktion av förfäderna är korrekt veckade. Detta visar att det är nödvändigt med fortsatta förbättringar och fortsatta studier kring substratacceptans och stabilitet i olika lösningsmedel. Sammanfattningsvis påvisar resultaten att släktsekvensrekonstruktion är en proteinteknik som fungerar för att skapa proteiner med ökad termostabilitet och bör ses som ett mer självklart alternativ till riktad evolution och rationell design. / The utilisation of biocatalysts, particularly enzymes, in chemical and pharmaceutical industries presents significant advantages over the traditional chemocatalytic methods that historically dominated the industry. A crucial class of enzymes, transaminases, play a central role in the production of chiral amines, fundamental building blocks in these industrial sectors. This study focuses on a specific amine transaminase from Silicibacter pomeroyi. While this enzyme has previously demonstrated the ability to catalyse a variety of reactions for chiral amine production, realising its full potential in industrial applications requires enhanced stability at higher temperatures. In contrast to commonly employed protein engineering methods such as rational design and directed evolution, this study utilises ancestral sequence reconstruction to generate more temperature-resistant variants of this enzyme. Previous applications of this method have shown promising results in generating proteins with increased thermal stability. Through this approach, wherein ancestors of this enzyme are recreated from extant sequences, it is expected that variants capable of maintaining function at higher temperatures will be produced. By exploring this alternative strategy for protein engineering, the study aims to provide more robust biocatalysts for industrial applications. The outcome of this study is that two ancestors exhibited increased thermostability. This was evidenced by the analysis of T5015, which showed an improvement of 3.9 and 6 °C for each respective ancestor. Furthermore, t1/2 measurements indicated that they remained active for 2.06 to 3.72 fold longer at 55 °C before becoming inactive. However, they exhibited lower specific activity at room temperature, partially due to only a small fraction of the ancestral protein samples being properly folded. This suggests further improvements and continued investigations into substrate acceptance and stability in different solvents are required. In conclusion, this study demonstrates that ancestral sequence reconstruction is a protein engineering technique effective in enhancing protein thermostability and should be considered a more viable alternative to directed evolution and rational design.

No description available.

Cette thèse se concentre sur certains sujets en génétique des populations. Dans la première partie, nous donnons des formules y compris l'espérance et la variance de la hauteur et celles de la longueur du graphe de recombinaison ancestral (ARG) et l'espérance et la variance du nombre de recombinaison et nous montrons que l'espérance de la longueur de l'ARG est une combinaison linéaire de l'espérance de la longueur de la coalescence de Kingman et l'espérance de la hauteur de l'ARG. En outre, nous avons obtenu une relation entre l'espérance la longueur de l'ARG et l'espérance du nombre de recombinaisons. À la fin de cette partie, nous montrons que l'ARG descend de l'infini de telle sorte que X_0 =∞, alors que X_t < ∞ ; pour tout t et on trouve la vitesse à laquelle l'ARG descend de l'infini. Dans la deuxième partie on généralise la formule d'échantillonnage d'Ewens (GESF) en présence de la recombinaison pour les échantillons de taille n = 2 et n = 3. Dans la troisième partie de la thèse, nous étudions l'ARG le long du génome et nous avons trouvé la distribution du nombre de mutations dans le cas avec une seule recombinaison dans la généalogie de l'échantillon. / This thesis is concentrated on some sub jects on population genetics. In the first part we give formulae including the expectation and variance of the height and the length of the ancestral recombination graph (ARG) and the expectation and variance of the number of recombination events and we show that the expectation of the length of the ARG is a linear combination of the expectation of the length of Kingman's coalescent and the expectation of the height of the ARG. Also we show give a relation between the expectation of the ARG and the expectation of the number of recombination events. At the end of this part we show that the ARG comes down from infinity in the sense that we can dfine it with X_0 = ∞, while X_t <∞ ; for all t and we find the speed that the ARG comes down from infinity. In the second part wfind a generalization of the the Ewens sampling formula (GESF) in the presence of recombination for sample of sizes n = 2 and n = 3. In the third part of the thesis we study the ARG along the genome and we we find the distribution of the number of mutations when we have one recombination event in the genealogy of the sample.

[pt] Esta tese de doutorado visa investigar determinados aspectos estéticos e estruturais presentes em produções artísticas que abordam a temática da identidade trans, num atravessamento com questões de raça e classe social. As reflexões teórico-críticas de intelectuais como Paul Preciado e bell hooks fundamentam a discussão acerca dos sistemas de opressão que atuam sobre o convívio dos corpos considerados dissidentes no imaginário de construção, mas também de sua circulação nas cidades. Para isso, esta tese toma um conjunto heterogêneo de figuras monstruosas como a sereia, o anão e o fantasma para questionar as definições de humanidade e a experiência artístico-sensível do exílio através da vivência no processo laboratorial de criação realizado pelo Projeto Genus Radix (numa iniciativa do Museu Nacional Centro de Artes Reina Sofía). No itinerário que atravessou essa pesquisa e esse pesquisador - Argentina, Brasil e Espanha -, atua a metáfora do monstro como um disparador de questões vinculadas à arte e à vida, que instiga a reflexão sobre uma humanidade por vir. As reverberações das histórias dos personagens conceituais e reais elencados nesta pesquisa visam delinear e ressaltar especificidades que corroboram para a construção de uma narrativa estética e/ou performática que suscita a sobrevivência de novas formas de vida num espaço comum. / [es] Esta tesis doctoral tiene como objetivo investigar ciertos aspectos estéticos y estructurales presentes en las producciones artísticas que abordan el tema de la identidad trans, en un cruce con cuestiones de raza y clase social. Las reflexiones teórico-críticas de intelectuales como Paul Preciado y Bell Hooks basan la discusión sobre los sistemas de opresión que actúan ante a la relación de los cuerpos disidentes en el imaginario de las ciudades. Para ello, esta tesis toma un conjunto heterogéneo de “figuras monstruosas” como la sirena, el enano y el fantasma para cuestionar las definiciones de humanidad y la experiencia artístico-sensible del exilio a través del experimentado en el proceso de creación llevado a cabo por el laboratorio del Proyecto Genus Radix (en una iniciativa del Museo Nacional Centro de Artes Reina Sofía). En el itinerario de la investigación y del investigador - Argentina, Brasil y España-, actúa la metáfora del monstruo como detonante de cuestiones relacionadas con el arte y la vida que señalan una humanidad por venir. Las reverberaciones de las historias de los personajes conceptuales y reales enumerados en esta investigación tienen como objetivo delinear y resaltar especificidades que corroboran la construcción de una narrativa estética y / o performance que promueve la supervivencia de nuevas formas de vida en un espacio común.

The study sets to establish trends with regard to the role of the praise singer, the changes with regard to the traditional praise singer's rendition/performance and the material or content of his/her poetry. Thus the study highlights the distinction observed between the praise singer of the past and the present praise singer. The study also shows that the praise singer's performance, in terms of his/her role and content, is in the state of flux. The study also demonstrates that the singer of the past and the present praise singer have the same role and their chants or poetry or songs have the same effect. It also highlights situations where praises are chanted in modern times. These are graduation ceremonies, weddings, political gatherings and traditional ceremonies, for example, the annual rain making ceremonies. These events or occasions are inextricably linked to traditional praises. The study also highlights the fact that traditional praises present the history and heroic deeds of members of the clan to which the beneficiary belongs. They also express the deep feeling of royalty and loyalty. Like in the past they boost morale. / African Languages / M.A. (African Languages)

With the advent of Highly Active Antiretroviral Therapy (HAART), people with the human immune deficiency virus (HIV) infection are increasingly enjoying longer and relatively healthy lives, particularly in developed countries. However, black Africans and African-Caribbean people in the United Kingdom and other developed countries are not yet enjoying the full benefits of HAART, essentially as a result of delayed diagnosis. Delayed diagnosis, in addition to affecting the health of infected individuals, also creates a community reservoir for the spread of the infection; thereby hampering prevention and control strategies by international and NHS guidelines. The delayed diagnosis may be grounded in individual, societal and health service factors that guide help-seeking behaviours of black African and African-Caribbean populations. This study set out to investigate the help-seeking behaviours to diagnose HIV and AIDS among UK based black African and African-Caribbean people, and to investigate the dynamics in those behaviours by place of origin (Africa vs. Caribbean) and by gender. A qualitative methodological approach involving semi-structured interviews was used to explore help-seeking behaviours to diagnose HIV and AIDS among black Africans and African-Caribbean populations in the UK and compared by gender. Thirty (30) purposively selected individuals from patients attending two sexual health clinics in the city of London were interviewed. These included 16 black Africans and 14 African-Caribbean people, and 16 men and 14 women. The symbolic interactionist perspective, and the concepts of broken narratives/silences, biographical disruption and biographical abruption guided the study and interpretation of findings. One main theme ‘Africanness’ and two sub-themes (“African way” and “African thing”) emerged from the findings. The “African way” embodies the risk factors involved in contracting or transmitting HIV and the “African thing” represents the HIV status itself. This is a cultural construction of HIV and AIDS within the acceptable context of participants which helped them to talk about HIV and AIDS without addressing it by the biomedical idiom. The notion of ‘Africanness’ provided a ‘marker’ for African identity. The “African thing” represented a new landscape for naming HIV without necessarily calling it by name and provided a comfortable platform for participants to seek help. The “African way” described the risk behaviours by participants that resulted in the “African thing”. Three sociological concepts; ‘broken narratives or silences, biographical disruption and biographical abruption were key issues in HIV and AIDS diagnosis at a late stage and have formed the basis for the development of a model of help-seeking for diagnosis by participants. Apparently, the main determinants of help-seeking for diagnosis of HIV and AIDS are dependent on cultural factors. Stigma is reinforced by the national health care system practices as well as health professionals themselves. This potentially increases the reluctance among black African and African-Caribbean populations to voluntarily test for HIV. An HIV diagnosis is seemingly a challenging experience because of the impending uncertainties associated with it. Seeking help for diagnosis may even be more difficult because of the anticipated and unpleasant experiences along the path to diagnosis. This may guide the individual to consider other alternatives outside the biomedical pathway, potentially; the biomedical path becomes the least likely choice, especially with black African and African-Caribbean populations. An insufficient cultural understanding is likely to result in inadequate recognition of alternative medical practices, insufficient attention to alternatives to biomedical health systems and potential distortion of the meaning of health messages linking them to practice.

99 leaves printed on single pages, preliminary pages and numberd pages 1-87. Includes bibliography. Digitized at 600 dpi grayscale to pdf format (OCR), using a Bizhub 250 Konica Minolta Scanner. / Thesis (MPhil (Philosophy))--University of Stellenbosch, 2000. / ENGLISH ABSTRACT: Death is a universal phenomenon and each culture develops its own ways of coping with it. The reaction of people to death also involves a complex network of relationships. To appreciate their responses to this phenomenon requires an understanding of the socio-cultural context in which these responses occur because they influence the individual's responses to issues of life and death. In the African context and indeed in the Zulu culture, death is a continuation of life in the world hereafter. The deceased renews his relationship with his ancestral relatives. Various rites and ceremonies are performed to mark his reunion with his ancestral relatives. For the living, the rites and ceremonies mark a passage from one phase of life to another requiring some readjustment. The belief in the existence of life after death also affects the nature of these rites and ceremonies, the social definition of bereavement and the condition of human hope. The belief in the existence of the ancestors forms an integral part African religion and its importance cannot be over-estimated. This belief flows from the strong belief in the continuation of life after death, and the influence the deceased have on the lives of their living relatives. The contact between the living and the living dead is established and maintained by making offerings and sacrifices to the ancestors. The ancestors, therefore, become intermediaries with God at the apex and man at the bottom of the hierarchical structure. However, for the non-African, the relationship seems to indicate the non-existence of God and the worshipping of the ancestors. Women play a pivotal role in issues of life and death, because African people recognize their dependence and the procreative abilities of women to reconstitute and to extend the family affected by the death of one of its members.Social change and Westernisation have affected the way the African people view death. Social changes have been tacked onto tradition. A contemporary trend is to observe the traditional and Christian rites when death has occurred. The deceased is then buried in accordance with Christian, as well as traditional rites. The belief in the survival of some element of human personality is a matter of belief and faith. It lessens the pain and sorrow that is felt upon the death of a loved one by giving the believer hope that one day he will be reunited with his loved one and thereby easing the fear and anxiety of death. Thus, the purpose of this investigation is to critically analyse the African perception of death and its implications with special reference to the Zulu people. The objective is to expose the complexities, diversities and the symbolism of death. The essence is to demystify the African perception of death and to indicate that the perception of death is not necessarily unique to African people in general and to the Zulu people in particular. Other groups like Christians have perceptions of death particularly with regard to the world hereafter. The aim of the investigation of the topic is to reveal some of the underlying cultural beliefs in death, enhance those beliefs that are beneficial to society and discard those that are anachronistic. Since culture is dynamic, not everything about African tradition will be transmitted to the future generation; there is bound to be cultural exchange. / AFRIKAANSE OPSOMMING: Die dood is 'n universele fenomeen en elke kultuur ontwikkel sy eie manier om daarmee om te gaan. Mense se reaksie op die dood geskied binne 'n komplekse netwerk van verhoudinge. Om mense se reaksie op hierdie fenomeen te begryp, is 'n verstaan van die sosio-kulturele konteks nodig waarin hierdie reaksies plaasvind, aangesien dit die individu se reaksie op lewe en dood beinvloed. In die Afrika-konteks en ook in die Zulu-kultuur word die dood beskou as die kontinuasie van lewe in die hiermamaals. Die oorledene hernu sy verhouding met sy voorouers. Verskeie rituele en seremonies vind plaas om hierdie gebeurtenis te identifiseer. Vir die oorlewendes is die rituele en seremonies die oorgang van een lewensfase na 'n ander en vereis dus 'n mate van aanpassing. Die geloof in die lewe na die dood beinvloed die aard van hierdie rituele en seremonies, die sosiale defenisie van rou en die toestand van menslike hoop. Die geloof in die bestaan van die voorvaders vorm 'n integrale deel van Afrika-religie en die belangrikheid daarvan kan nie oorskat word nie. Die geloof vloei voort uit die sterk geloof in die hiermamaals en die geloof aan die invloed wat oorledenes op hulle lewende nasate het. Die kontak tussen die lewendes en die lewende oorledenes word daargestel en onderhou deur offerandes aan die voorvaders. Die voorvaders word dus gesien as intermediere skakel in 'n hierargie met God aan die bokant en die mens aan die onderkant. Maar, vir nie-Afrikane, dui hierdie struktuur op die nie-bestaan van God en die aanbidding van die voorvaders. Vroue speel 'n deurslaggewende rol in kwessies van lewe en dood aangeslen Afrikane hul afhanklikheid besef van vroue se voortplantingsbekwaamhede om die famile wat deur die dood geaffekteer is te herkonstitueer en te vergroot. Sosiale veranderinge en verwestering affekteer Afrikane se houding teenoor die dood. Sosiale veranderinge is bo-oor tradisie geplaas. 'n Hedendaagse neiging is om Christelike sowel as tradisionele rituele na te volg na 'n sterfte. Die oorledene word begrawe in ooreenstemming met sowel tradisionele as Christelike praktyke. Die geloof in die oorlewing van elemente van die menslike persoon is 'n kwessie van geloof. Dit verminder die pyn en lyding na die afsterwe van 'n geliefde deur aan die gelowige oorlewende die hoop van 'n herontmoeting te bied - en verminder dus die vrees en angs wat met die dood gepaard gaan. Dus is die doel van hierdie ondersoek om 'n kritiese analise te maak van die Afrika-siening van die dood en die implikasies daarvan, met spesiale verwysing na die Zulu-nasie. Daar word probeer om die kompleksiteite, verskeidenhede en simbolisme van die dood aan te toon. Die essensie hiervan is om die Afrika-houding teenoor die dood te de-mistifiseer en te wys dat die siening van die dood nie noodwendig uniek van Afrikane in die algemeen en spesifiek van die Zoeloes is nie. Ander groepe soos Christene het beskouinge oor die dood met spesifieke verwysing na die hiernamaals. Die doel van die ondersoek is om sekere onderliggende kulturele oortuiginge aangaande die dood te onthul, om die beskouinge wat voordelig is, te versterk en om die anachronistiese beskouinge aan die kaak te stel en so te diskrediteer. Aangesien kultuur dinamies is, sal nie alles wat betref die Afrika-tradisie oorgedra word aan toekomstige generasies nie; daar sal noodwendig kulturele interaksie wees.

In this thesis we describe subclasses of a class of graphs with three types of edges, called loopless mixed graphs (LMGs). The class of LMGs contains almost all known classes of graphs used in the literature of graphical Markov models. We focus in particular on the subclass of ribbonless graphs (RGs), which as special cases include undirected graphs, bidirected graphs, and directed acyclic graphs, as well as ancestral graphs and summary graphs. We define a unifying interpretation of independence structure for LMGs and pairwise and global Markov properties for RGs, discuss their maximality, and, in particular, prove the equivalence of pairwise and global Markov properties for graphoids defined over the nodes of RGs. Three subclasses of LMGs (MC, summary, and ancestral graphs) capture the modified independence model after marginalisation over unobserved variables and conditioning on selection variables of variables satisfying independence restrictions represented by a directed acyclic graph (DAG). We derive algorithms to generate these graphs from a given DAG or from a graph of a specific subclass, and we study the relationships between these classes of graphs. Finally, a manual and codes are provided that explain methods and functions in R for implementing and generating various graphs studied in this thesis.

Des souris aux baleines en passant par les humains, la diversité écologique des mammifères placentaires est des plus fascinantes. Bien qu'il s'agisse là d'un des groupes les plus étudiés, leur origine fait pourtant l'objet de bien des mystères. Leurs relations de parenté les plus basales restent en effet incertaines, et l'on ignore encore beaucoup du mode de vie qu'avaient nos ancêtres du Crétacé, ces mammifères placentaires qui auraient côtoyé les dinosaures pendant plus de 30 millions d'années.Afin d'aborder ces questions, cette thèse a utilisé l'outil de la génomique comparative. L'une de ses principales originalités est la prise en compte d'un distorteur majeur de notre évolution moléculaire: la conversion génique biaisée. Truquant la loterie génétique, ce mécanisme associé à la recombinaison méiotique avantage les nucléotides G et C au détriment des nucléotides A et T. Façonnés par son influence, nos paysages nucléotidiques présentent ainsi ponctuellement des taux de GC anormalement élevés.Jusque là, ce phénomène n'avait été étudié que chez une poignée d'organismes modèles. Son analyse chez plus d'une trentaine de génomes mammaliens a mis en évidence une série de résultats clés. En particulier, l'évolution du contenu en GC des gènes s'est avéré dépendre de la masse corporelle et la longévité des espèces. E nreliant ainsi évolution moléculaire et traits d'histoire de vie, des reconstructions de séquences ancestrales ont permis d'estimer la durée de vie des premiers mammifères placentaires à plus de 25 ans. Cette longévité va bien au delà de ce que peuvent espérer atteindre les souris ou musaraignes actuelles, des animaux au mode de vie pourtant jusqu'ici supposé comme étant proche de celui de nos ancêtres.Parallèlement à ces résultats, une tendance à produire des phylogénies inexactes a été détectée chez les gènes les plus GC-riches. Moins soumis à la conversion génique biaisée, les gènes AT-riches se sont montrés plus fiables, tout en soutenant que les espèces originaires d'Afrique sont situés à la base de l'arbre des placentaires. Ce résultat suggère ainsi la possible résolution d'un des noeuds les plus controversés de notre histoire évolutive.Du simple nucléotide à la naissance d'une infraclasse de plus de 4000espèces, ce travail révèle comment l'évolution moléculaire peut porter un nouveau regard sur nos origines les plus profondes. / From mice to whales through humans, placental mammals present astunning diversity. Despite being one of the most studied group ever,mysteries persist about their origin. Indeed, their most basalrelationships still remain uncertain, and nothing is really knownabout the lifestyle of our cretaceous ancestors, these placentalmammals which lived side by side with non-avian dinosaurs during 30My.To answer these evolutionnary questions, comparative genomic studiesof placental mammals have been conducted. One of its originalities isto take into account biased gene conversion. Rigging the geneticlottery, this recombination-associated mechanism involves a reparationbias favouring the G and C nucleotides over the A and T ones, whichmark the mammalian genomic landscapes by inducing localized peaks ofGC-content.This phenomenon has been so far studied in few model species. Theexploration of biased gene conversion in more than 30 mammal genomesled to several key results. In particular, GC content evolution hasproved to be correlated to the longevity and the body mass of species.By linking together molecular evolution and life history traits, thereconstruction of ancestral sequences allowed us to estimate alife-span above 25 years for early placental mammals. This value ismarkedly different from that of mice or shrews, although our mammalianancestors have often been represented as such. In addition to these results, GC-rich genes were found to be prone toproduce false phylogenies. Less affected by recombination associatedartifacts, AT-rich genes are shown to be more reliable, and to supportspecies of African origin as the sister group of all other placentalmammals - perhaps resolving one of the most controversial nodes of themammalian tree.From nucleotide to the birth of a 4,000 species infraclass, this workreveals how molecular evolution can shed new light onour deepest origins.