This work aimed to investigate the evolutionary origin of the involvement of the HIF Prolyl Hydroxylases (PHDs) in oxygen sensing. The &alpha;/&beta;-heterodimer HIF (<u>H</u>ypoxia <u>I</u>nducible <u>F</u>actor) is a master regulator of oxygen homoeostasis in metazoans. In the nucleus, HIF binds to the Hypoxia Responsive Elements and forms a transcriptional complex that activates the transcription of a multitude of downstream genes. Under normoxic conditions, the Fe(II)- and oxygen-dependent PHDs catalyse 4R-prolyl-hydroxylation of the HIF &alpha;-subunit, which subsequently leads to its degradation. It had previously been proposed that the evolution of the HIF-pathway, shared by all metazoans but not found in other organisms, is linked to the rapid diversification of multicellular life during the Cambrian Explosion. This work investigates the structural and biochemical properties of a PHD of the basal metazoan Trichoplax adhaerens (taPHD), and a PHD-like enzyme of the protist Monosiga brevicollis (mbP4H). Two crystal structures of taPHD were obtained (1.2-1.3 Å), one containing a Trichoplax adhaerens HIF&alpha; subunit peptide (taODD). Comparison with crystal structures of human PHD2 showed a high degree of conservation of structural features and enzyme-substrate interactions. The prolyl-residue of taODD, shown to be hydroxylated by taPHD, is occupying the C⁴-endo conformation in the crystal structure, supporting the previously proposed mechanism of HIF&alpha; hydroxylation by PHD2 in humans. A conservation of biochemical properties with human PHD2, such as the formation of a stable enzyme-Fe(II)-2OG complex, was observed and could therefore be key to oxygen sensing by the PHDs. mbP4H was shown to catalyse 4R-prolyl-hydroxylation of taODD. It was proposed that the native substrate of mbP4H is a protein containing a prolyl-hydroxylation site similar to taODD, possibly with a YXXLAP motif. The study of biochemical properties and substrate selectivity of mbP4H suggests that the precursor of PHDs may have had similar properties to mbP4H. Further work on mbP4H could therefore yield clues about the evolutionary origin of HIF-prolyl hydroxylases in oxygen sensing and probe the previously proposed connection between metazoan life and HIF–mediated oxygen sensing.

Thesis (Ph. D.)--University of California, San Diego, 2007. / Title from first page of PDF file (viewed June 13, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 338-387).

Darwin's (1859) theory of evolution by natural selection accounts for the adaptations of organisms, but, as Fisher (1930) famously said, 'natural selection is not evolution.' Evolutionary theory has two major components: i) natural selection, which involves the underlying dynamics of populations; and ii) adaptive evolutionary change, which involves the optimisation of phenotypes for fitness maximisation. Many of the traditional theoretical frameworks in evolutionary theory have focussed on studying optimisation processes that generate biological adaptations. In recent years, however, a number of evolutionary theorists have turned to using frameworks such as the 'replicator dynamics' or 'eco-evolutionary dynamics', to explore the dynamics of natural selection. There has, however, been little attempt to explore how these dynamical systems frameworks relate to more traditional frameworks in evolutionary theory or how they incorporate the principles that embody the process of evolution by natural selection, namely, phenotypic variation, differential reproductive success, and heritability. In this thesis, I use these principles to provide the formal foundations of a general framework - a mathematical synthesis - in which the future state of an evolutionary system can be predicted from its present state; what I will call a 'dynamical systems theory of natural selection.' Given the state of an existing biological system, and a set of assumptions about how individuals within the system interact, the job of the dynamical systems theory of natural selection is no less than to predict the future in its entirety.

Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.

Seleção balanceadora é um processo evolutivo que engloba diversos mecanismos: vantagem do heterozigoto, seleção dependente de frequência, pressões seletivas que variam ao longo do tempo ou do espaço, e alguns casos de pleiotropia. O estudo desses mecanismos em si foi e ainda é um tópico de grande interesse para os biólogos evolutivos, e moldou o estudo da evolução ao longo do último século. Antes de a teoria neutra ter sido proposta, acreditava-se que a seleção balanceadora fosse comum. A descoberta de que muita da diversidade genética observada podia ser explicada por evolução neutra motivou, portanto, uma melhor compreensão da seleção balanceadora como um regime seletivo capaz de manter variantes vantajosas nas populações. O estudo da seleção balanceadora, em seus primórdios, foi restrito a organismos que podiam ser manipulados em laboratório. Com o advento de métodos que permitiam quantificar a variabilidade genética - tais como a eletroforese de proteínas, sequenciamento em pequena escala e re-sequenciamento genômico de milhares de indivíduos -, a variabilidade genética humana passou a ser ativamente estudada e interpretada. Diversos estudos buscaram por assinaturas de seleção natural - i.e., padrões de variação genômica deixadas por tais regimes seletivos - e avaliaram seu significado comparando-as com o que seria esperado sob um cenário estritamente neutro. A maior parte desses esforços foram concentrados no estudo da seleção positiva, tida como o principal mecanismo responsável pela evolução adaptativa. Poucos estudos buscaram assinaturas de seleção balanceadora no genoma humano. Isso se deve em parte à escassez de métodos com alto poder para detectar tais assinaturas. Adicionalmente, estudos prévios não analisaram dados em escala genômica, ou se concentraram principalmente nas regiões codificadoras de proteínas. Aqui, nós descrevemos um método simples e com alto poder para detectar assinaturas de seleção balanceadora. Em humanos, esse método supera outros comumente usados para a detecção de tais assinaturas e, em teoria, poderia ser usado para detectá-las em outras espécies, desde que seu poder seja avaliado caso-a-caso através de simulações neutras. Nosso método (\"Non-Central Deviation\", NCD) é apresentado em duas versões: NCD2, que requer informação acerca dos polimorfismos da espécie analisada e das substituições entre essa espécie e um grupo externo, e NCD1, que requer apenas informação acerca dos polimorfismos da espécie analisada. Embora em humanos NCD2 supere NCD1, este último pode ser utilizado para espécies para as quais não haja informação de um grupo externo. Quando aplicamos NCD2 a dados humanos, usando chimpanzé como grupo ex- terno, encontramos mais de 200 genes codificadores de proteínas com forte assinatura de seleção balanceadora, dos quais apenas 1/3 tinha evidência prévia de seleção balanceadora. Encontramos também um enriquecimento para diversas categorias de ontologia gênica, das quais cerca da metade é relacionada à imunidade. Verificamos que dentre os genes com evidências de seleção balanceadora há um excesso de casos de expressão preferencial em tecidos tais como \"adrenal\" e \"pulmão\", e também um excesso de genes com expressão mono-alélica. No geral, vimos que as regiões selecionadas no genoma humano incluem tanto sítios codificadores quanto regulatórios. Não encontramos um excesso de assinaturas de seleção balanceadora em regiões regulatórias, ao contrário do que reportaram outros estudos. Finalmente, encontramos um excesso de polimorfismos não-sinônimos em relação aos sinônimos nos genes selecionados. Tendo documentado a ocorrência de seleção balanceadora no genoma humano e identificado genes que foram potencialmente alvos deste regime seletivo, nós investi- gamos as consequências evolutivas desse processo. Nós partimos da hipótese que a seleção balanceadora sobre um sítio reduz a eficiência com a qual a seleção purificadora elimina variantes deletérias em sítios vizinhos. Esse processo é uma consequência do quanto a seleção sobre um loco afeta, através de ligação genética, as frequências de sítios não-neutros adjacentes. Testamos essa hipótese examinando se os genes sob seleção balanceadora apresentam um excesso de variantes deletérias em relação a expectativas derivadas a partir do restante do genoma. Usando três diferentes métricas para determinadas se e/ou o quão deletéria é uma dada variante, identificamos um excesso de variantes deletérias dentro dos genes sob seleção balanceadora, e mostramos que tal padrão não pode ser atribuído a efeitos confundidores. Esse achado mostra que, juntamente com os benefícios associados à variação adaptativa, a seleção balanceadora aumenta o fardo de mutações deletérias no genoma humano. De forma geral, nossos achados sugerem que a seleção balanceadora provavelmente mantém variantes genéticas envolvidas em uma miríade de processos biológicos além da imunidade e que ela foi mais comum no genoma humano do que se acreditava anteriormente, afetando entre 1-8% dos genes codificadores de proteínas, bem como diversas regiões não-codificadoras. Adicionalmente, a seleção balanceadora parece ser importante para a evolução humana não apenas por seu efeito sobre a aptidão, mas também por ter sido uma importante força capaz de moldar a diversidade genética observada atualmente em humanos e a susceptibilidade a doenças / Balancing selection is an evolutionary process that encompasses several mechanisms: heterozygote advantage, negative frequency dependent selection, selective pressure that fluctuates in time or in space, and some cases of pleiotropy. The study of these mechanisms .per se has been and still is a topic of great interest for evolutionary biologists, and has shaped the study of evolution throughout the last century. Before the proposition of the neutral theory of molecular evolution, it was believed that balancing selection was pervasive. The realization that much of the observed genetic diversity could be explained by neutral evolution thus motivated a better understanding of balancing selection as a selective regime capable of maintaining adaptive variants in populations. The study of balancing selection, in its early stages, was restricted to organisms that could be manipulated in the laboratory. With the advent of methods that allowed quantification of genetic variation - such as protein electrophoresis, small scale sequencing and genome-wide re-sequencing of thousands of individuals - human variation started to be actively studied and interpreted. Several studies have looked for signatures of natural selection - i.e., patterns of genomic variation that selective regimes leave in the genome - and evaluated their significance by comparing them to what would be expected under a strictly neutral scenario. Most of these efforts focused on the study of positive selection, thought of as the prime mechanism responsible for adaptive evolution. Only a few studies looked for signatures of balancing selection in the human genome. This is partially due to the paucity of powerful methods to detect its signatures. Moreover, previous studies either did not analyze data on genomic scale or focused primarily on protein-coding regions. Here, we describe a powerful and simple method to detect signatures of balancing selection. In humans, it outperforms other methods commonly used to detect such signatures and could in theory be used for other species, provided that its power is evaluated for each species through neutral simulations. Our method (\"Non-Central Deviation\", NCD) has two versions: NCD2, which requires polymorphism information on the ingroup species, as well as divergence information between the ingroup and an outgroup species, and NCD1, which only requires the ingroup information. Although NCD2 is more powerful for humans, NCD1 can be used for species that lack information from an outgroup. When applying NCD2 to human data, using chimpanzee as the outgroup, we found more than 200 protein-coding regions with strong signatures of balancing selection, only 1/3 of which had prior evidence for balancing selection. There was also an enrichment for several gene ontology categories, approximately half of which are related to immunity. We also found that among genes with evidence for balancing selection there was an excess of cases of preferential expression in specific tissues, such as \"adrenal\" and \"lung\", and an excess of genes with mono-allelic expression. Overall, we found that selected regions of the genome include both coding and regulatory sites. We failed to find a marked excess of balancing selection in regulatory regions, as reported in previous studies. Finally, we found an excess of nonsynonymous versus synonymous polymorphisms within the selected genes. Having documented the occurrence of balancing selection in the human genome and identified genes which were potential targets of this selective regime, we next investigated evolutionary consequences of this process. We hypothesized that balancing selection acting on a site reduces the efficiency with which purifying selection purges deleterious variants at nearby sites. This process is a consequence of how the dynamics of selection at one locus, mediated by linkage, can interfere with the frequencies of adjacent non-neutral sites. We tested this hypothesis by examining if the genes under balancing selection show an excess of deleterious variants with respect to expectations derived from the remainder of the genome. Using three different metrics to determine deleteriousness, we identified a significant excess of deleterious variants within balanced genes, and we show that this pattern cannot be attributed to confounding factors. This finding shows that together with the benefits associated with adaptive variation, balancing selection is increasing the burden of deleterious mutations in the human genome. Overall, our findings suggest that balancing selection likely maintains variation in a myriad of biological processes other than immunity and that it has been more common in the human genome than previously thought, affecting between 1-8% of human protein-coding genes, as well as a number of non-protein coding regions. Moreover, balancing selection appears to be important to human evolution not only because of its influence on fitness, but also because it has been an important force shaping current human genetic diversity and susceptibility to disease

Steel has become widespread and now it can be accepted as the candidate of being main material for the structural systems with its excellent properties. Its high quality, durability, stability, low maintenance costs and opportunity of fast construction are the advantages of steel. The correct use of the material is important for steel&rsquo / s bright prospects. The need for weight optimization becomes important at this point. Available sources are used economically through optimization. Optimization brings material savings and at last economy. Optimization can be achieved with different ways. This thesis investigates the effect of the appropriate choice of column orientation on minimum weight design of steel frames. Evolution strategies (ESs) method, which is one of the three mainstreams of evolutionary algorithms, is used as the optimizer in this study to deal with the current problem of interest. A new evolution strategy (ES) algorithm is proposed, where design variables are considered simultaneously as cross-sectional dimensions (size variables) and orientation of column members (orientation variables). The resulting algorithm is computerized in a design optimization software called OFES. This software has many capabilities addressing to issues encountered in practical applications, such as producing designs according to TS-648 and ASD-AISC design provisions. The effect of column orientations is numerically studied using six examples with practical design considerations. In these examples, first steel structures are sized for minimum weight considering the size variables only, where orientations of the column members are initially assigned and kept constant during optimization process. Next, the weight optimum design of structures are implemented using both size and orientation design variables. It is shown that the inclusion of column orientations produces designs which are generally 4 to 8 % lesser in weight than the cases where only size variables are employed.

This study is part of a project which aims to understand evolution of genetic code together with structural and functional analysis of prebiotic proteins. The repertoire of amino acids in the first proteins was probably developing in time and it influenced the development of structure and function of today's proteins. First amino acid alphabet was apparently only half of the size of present alphabet, which contains twenty amino acids. These ten amino acids were probably prebiotically available from endogenous and exogenous sources. This work includes cell-free expression and purification of two randomized protein libraries (containing approximately 1011 variants) with various amino acid composition and following comparison of their propensity to form secondary (using circular dichroism) and tertiary (using proteolytical analysis of sequences) structures. First library contains only ten probably prebiotically available amino acids; second library contains all twenty amino acids in today's genetic code. This project could help us understand benefits of genetic code expansion in terms of developing structure in protein sequences. The whole research could theoretically contribute a few basic questions not only in the fields of protein evolution but also in areas of synthetic biology or protein...

Variation et sélection sont au coeur de l'évolution Darwinienne. Cependant, ces deux mécanismes dépendent de processus eux-mêmes façonnés par l'évolution. Chez les micro-organismes, qui font face à des environnements souvent variables, ces propriétés adaptatives sont particulièrement bien exploitées, comme le démontrent de nombreuses expériences en laboratoire. Chez ses organismes, l'évolution semble donc avoir optimisé sa propre capacité à évoluer, un processus que nous nommons évolution de l'évolution (EvoEvo). La notion d'évolution de l'évolution englobe de nombreux concepts théoriques, tels que la variabilité, l'évolvabilité, la robustesse ou encore la capacité de l'évolution à innover (open-endedness). Ces propriétés évolutives des micro-organismes, et plus généralement de tous les organismes vivants, sont soupçonnées d'agir à tous les niveaux d'organisation biologique, en interaction ou en conflit, avec des conséquences souvent complexes et contre-intuitives. Ainsi, comprendre l'évolution de l'évolution implique l'étude de la trajectoire évolutive de micro-organismes — réels ou virtuels —, et ce à différents niveaux d'organisation (génome, interactome, population, …). L'objectif de ce travail de thèse a été de développer et d'étudier des modèles mathématiques et numériques afin de lever le voile sur certains aspects de l'évolution de l'évolution. Ce travail multidisciplinaire, car impliquant des collaborations avec des biologistes expérimentateur•rice•s, des bio-informaticien•ne•s et des mathématicien•ne•s, s'est divisé en deux parties distinctes, mais complémentaires par leurs approches : (i) l'extension d'un modèle historique en génétique des populations — le modèle géométrique de Fisher — afin d'étudier l'évolution du bruit phénotypique en sélection directionnelle, et (ii) le développement d'un modèle d'évolution in silico multi-échelles permettant une étude plus approfondie de l'évolution de l'évolution. Cette thèse a été financée par le projet européen EvoEvo (FP7-ICT-610427), grâce à la commission européenne. / Variation and selection are the two core processes of Darwinian Evolution. Yet, both are directly regulated by many processes that are themselves products of evolution. Microorganisms efficiently exploit this ability to dynamically adapt to new conditions. Thus, evolution seems to have optimized its own ability to evolve, as a primary means to react to environmental changes. We call this process evolution of evolution (EvoEvo). EvoEvo covers several aspects of evolution, encompassing major concepts such variability, evolvability, robustness, and open-endedness. Those phenomena are known to affect all levels of organization in bacterial populations. Indeed, understanding EvoEvo requires to study organisms experiencing evolution, and to decipher the evolutive interactions between all the components of the biological system of interest (genomes, biochemical networks, populations, ...). The objective of this thesis was to develop and exploit mathematical and numerical models to tackle different aspects of EvoEvo, in order to produce new knowledge on this topic, in collaboration with partners from diverse fields, including experimental biology, bioinformatics, mathematics and also theoretical and applied informatics. To this aim, we followed two complementary approaches: (i) a population genetics approach to study the evolution of phenotypic noise in directional selection, by extending Fisher's geometric model of adaptation, and (ii) a digital genetics approach to study multi-level evolution. This work was funded by the EvoEvo project, under the European Commission (FP7-ICT-610427).

Die vorliegende Arbeit zeigt einen Weg, Kupfer und einphasige Kupferlegierungen mit stark verzwillingten Gefügen durch ein technisch relevantes Umformverfahren herzustellen. Der Drahtzug bildet dabei aufgrund seines Spannungszustands und der entsprechenden Texturentwicklung in kubischflächenzentrierten Metallen ein ideales Umformverfahren, um einen Großteil des Gefüges durch mechanische Zwillingsbildung zu verfeinern. Für die Aktivierung der Zwillingsbildung in reinem Kupfer unter den untersuchten Werkstoffvarianten sind Temperaturen nahe der Temperatur des flüssigen Stickstoffs notwendig. Um den Drahtzug in flüssigem Stickstoff umzusetzen, wurden verschiedene Feststoffschmiermittel auf ihre Eignung hin getestet. Die Textur der mit Stickstoffkühlung hergestellten Halbzeuge ist durch eine dreifache Fasertextur bestehend aus <111>-, <001>- und <115>-Fasertexturkomponente charakterisiert. Anhand der strengen Orientierungsverhältnisse konnte der Volumenanteil von verzwillingtem Material bestehend aus Matrixkörnern und Verformungszwillingen auf 71 vol% durch röntgenografische Globaltexturmessungen abgeschätzt werden, wobei das Volumenverhältnis von Zwillingen zu Matrix bei knapp 0,7:1 liegt. Die Zwillinge zeigen eine breite Zwillingslamellenweitenverteilung von wenigen Nanometern bis einige 100 nm im höchstverformten Stadium. Durch die Absenkung der Umformtemperatur und die daraus resultierende Aktivierung der Zwillingsbildung kann die Zugfestigkeit von reinem Kupfer um 140 MPa im Vergleich zu einem ohne Kühlung hergestellten Draht auf 582 MPa erhöht werden. Dabei reduziert sich die elektrische Leitfähigkeit um 6,5% gegenüber einem grobkorngeglühten Kupfer. Eine Absenkung der Stapelfehlerenergie auf 30 mJ/m² in CuAl2 führt zur Aktivierung der mechanischen Zwillingsbildung beim Drahtzug ohne Kühlung. Durch diese Aktivierung der Zwillingsbildung kann bei fortschreitender Verringerung der Stapelfehlerenergie wie in CuAl7 die Zugfestigkeit des umgeformten Drahtes auf weit über 1 GPa erhöht werden. Das entsprechende Gefüge ist dabei ultrafeinkörnig.