>Magister Scientiae - MSc / The burden of non-communicable diseases (NCDs) in South Africa is predicted to increase substantially in the next decades if the necessary preventative measures are not taken. The two most common NCDs associated with rapid mortality increase are diabetes mellitus (DM) and hypertension (HTN). Both of these diseases, i.e DM and HTN, can be a result of a combination of modifiable risk factors (behavioral) and non-modifiable risk factors (genetic, physiological, and environmental). New strategies implemented to manage these diseases should include addressing both modifiable and non-modifiable risk factors for patients with NCDs. The aim of this study was to contribute to the reduction of incidence of uncontrolled T2DM among patients taking metformin as a first-line anti-diabetic drug, through the development of individualized therapy for this drug. When implemented, this could be one of the healthcare strategies to address non-modifiable risk factors for patients with T2DM as an important NCD. The first objective of the study was to explore the prevalence and risk factors of DM and HTN in South Africa, especially within the economically disadvantaged population.

NADPH-P450 oxidoreductase (POR) is a membrane bound flavoprotein that donates electrons to a wide spectrum of heme-containing proteins, among which are several steroidogenic and many xenobiotics-metabolizing enzymes. Given the important role of POR protein in drug metabolism and pharmacogenomics, there is a particular need to understand the contributions of POR genetic variants to these processes. Mutations in POR gene cause a disorder called POR deficiency, which manifests with a wide phenotypic spectrum ranging from disordered steroidogenesis to skeletal malformation, namely, Antley-Bixler syndrome (ABS). The aim of the present work was to investigate the POR gene in patients suspected to have POR deficiency syndrome from Czech Republic and to perform genotyping in Czech and Jewish control populations. We analyzed 644 alleles in unrelated individuals from the general Czech population and 1128 alleles in Jewish population, where 330 alleles were of Askhenazi and 798 of Sephardic Jews. We have also studied the impact of selected new genetic variants on POR activity and identified fourteen amino acid variations, two of which we have studied in detail to establish their influence on POR activity. Using the available human POR three-dimensional structure, we then modelled the newly identified variants...

L'un des objectifs centraux de la biologie est de comprendre comment l'ADN, la séquence primaire, donne lieu à des traits observables. À cette fin, nous examinons ici des méthodes pour identifier les composants génétiques qui influencent les traits microbiens. Par « identifier », nous entendons l'élucidation à la fois l'état allélique et de la position physique de chaque variante causale d'un phénotype d'intérêt à la résolution des nucléotides de paires de bases. Nous nous sommes concentrés sur les études d'association génomique (genome-wide association studies; GWAS) en tant qu'approche générale d’étudier l'architecture génétique des traits. L'objectif global de cette thèse était d'examiner de manière critique les méthodologies GWAS et de les considérer en pratique dans des populations microbiennes fortement clonales et non- clonales (i.e. avec recombinaison fréquent). Le domaine de la GWAS microbienne est relativement nouveau par rapport aux quinze dernières années de la GWAS humaine, et en tant que tel, nous avons commencé par un examen de l'état de la GWAS microbienne. Nous avons posé deux questions principales : 1) Les méthodes GWAS humaines fonctionnent-elles facilement et sans modification pour les populations microbiennes ? 2) Et sinon, quels sont les problèmes méthodologiques centraux et les modifications nécessaires pour la GWAS microbienne? À partir de ces résultats, nous avons ensuite détaillé le déséquilibre de liaison (linkage disequilibrium; LD) comme principal obstacle dans la GWAS microbien, et nous avons présenté une nouvelle méthode, POUTINE, pour relever ce défi en exploitant les mutations homoplasiques pour briser implicitement la structure LD. Le reste de la thèse présente à la fois les méthodes traditionnelles GWAS (comptage des allèles) et POUTINE (comptage d’homoplasies) appliquées à une population hautement recombinogène de génomes de vibrions marins. Malgré une taille d'échantillon modeste, nous donnons un premier aperçu de l'architecture génétique de la résistance aux bactériophages dans une population naturelle, tout en montrant que les récepteurs des bactériophages jouent un rôle primordial. Ce résultat est en pleine cohérence avec des expériences en laboratoire de coévolution phage-bactérie. Il est important de noter que cette architecture met en évidence à quel point la sélection positive peut sculpter certains traits microbiens différemment de nombreux traits complexes humains, qui sont généralement soumis à une faible sélection purificatrice. Plus précisément, nous avons identifié des mutations à effet important à haute fréquence qui sont rarement observées dans les phénotypes complexes humains où de nombreuses mutations à faible effet contribuent à l'héritabilité. La thèse se termine par des perspectives sur les voies à suivre pour la GWAS microbienne. / One of the central goals of biology is to understand how DNA, the primary sequence, gives rise to observable traits. To this aim, we herein examine methods to identify the genetic components that influence microbial traits. By "identify" we mean the elucidation of both the allelic state and physical position of each causal variant of a phenotype of interest down to the base-pair nucleotide resolution. Our focus has been on genome-wide association studies (GWAS) as a general approach to dissecting the genetic architecture of traits. The overarching aim of this thesis was to critically examine GWAS methodologies and to consider them in practice in both strongly clonal and highly recombining microbial populations. The field of microbial GWAS is relatively new compared to the over fifteen years of human GWAS, and as such, we began this work with an examination of the state of microbial GWAS. We asked and attempted to answer two main questions: 1) Do human GWAS methods readily work without modification for microbial populations? 2) And if not, what are the central methodological problems and changes that are required for a successful microbial GWAS? Building from these findings, we then detailed linkage disequilibrium (LD) as the primary obstacle in microbial GWAS, and we presented a new method, POUTINE, to address this challenge by harnessing homoplasic mutations to implicitly break LD structure. The remainder of the thesis showcases both traditional GWAS methods (allele counting) and POUTINE applied to a highly recombining population of marine vibrio genomes. Despite a small sample size, we provide a first glimpse into the genetic architecture of bacteriophage resistance in a natural population and show that bacteriophage receptors play a primary role consistent with experimental populations of phage-bacteria coevolution. Importantly, this architecture highlights how strong positive selection can sculpt some microbial traits differently than many human complex traits, which are generally under weak purifying selection. Specifically, we identified common frequency, large-effect mutations that are rarely observed in human complex phenotypes where many low-effect mutations are thought to contribute to the bulk of heritability. The thesis concludes with perspectives on ways forward for microbial GWAS.

Huntington diseases(HD) is a fatal autosomal neurodegenerative genetic disorder, caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene, resulting in a toxic gain-of-function in the mutant huntingtin protein(mHTT). To date, there is no approved treatment to either cure or halt the course of HD. It has been established that wild-type(wt) HTT protein is essential for development and has a critical role for maintaining neuronal health, thus, a preferable approach for treatment is an mHTT specific lowering maintaining the wild type HTT expression. The achievement of an allele specific therapies depends on targetable allele variation, hence in this project, was the allele frequency in the Swedish population investigated and compared with both the total population and the European population selective. The data demonstrated that there is significant differences between populations. Additionally, the gene expression in five human fibroblast from HD patients with CAG repeats varying from 40 up to180, was analyzed as well as the gene variation across tissue , where the human HD brain and two animal brains; a nonhuman primate and a transgenic minipig, was compared. The result demonstrated that there is similarity in the gene expression between the two models and the human brain, where the highest expression was seen in the prefrontal cortex. The results from the gene expression analyze in the cell lines of fibroblast demonstrated that there is difference in expression between CAG repeats. Furthermore could it be seen that there were only two cell lines, HD180 and HD70, that was heterozygous for dACTT, rs362307, and for the SNP, rs7223906, in exon 67. There are various therapeutic approaches in the pipeline for HD as shown in this thesis, and hopefully a treatment for the disease in the not too distant future. / Huntingtons sjukdom är en dödlig autosomal neurodegenerativ genetisk avvikelse, orsakad av en specifik DNA-sekvens, CAG, upprepning i arvsanlaget som kodar för proteinet huntingtin (HTT). Det muterade HTT skadar nervcellerna i hjärnan och leder till att cellerna bryts ner. Idag finns ännu inga godkända terapier för att bota eller stoppa förloppet av Huntingtons sjukdom. Det har konstaterats att det friska HTT protein är betydelsefullt för utvecklingen och att den har en kritisk roll för att upprätthålla hjärnans nervceller. Därför skulle det vara fördelaktigt att som behandling sänka nivåerna av det muterade HTT och samtidigt behålla nivåerna av det friska HTT i en så kallad allel-specifik strategi. Utförandet av en allel-specifik behandling är beroende allel variationen mellan den friska genen och den muterade. Därför undersöktes allel-frekvensen i den svenska populationen och jämfördes mellan den europiska populationens frekvens. Resultatet från denna undersökning påvisade att det finns tydliga skillnader mellan förekomst av allel-variationer mellan olika populationer. Utöver detta undersöktes även genuttrycket i fem mänskliga friboblaster från patienter med Huntingtons med varierande CAG längd, från 40 repetitioner upp till 180 repetitioner, samt genvariationen mellan vävnader i hjärnan. För den sistnämnda användes data från en mänsklig hjärnan med Huntingtons sjukdom och två djurhjärnor; en ifrån en icke-mänsklig primat och ifrån en transgen minigris. Resultatet påvisade likheter mellan genuttrycket mellan den mänskliga hjärnan och djurhjärnorna, och det högsta uttrycket återfanns i prefrontala cortex. Resultat från fibroblastproverna visade att det finns skillnader i genuttryck mellan patienter som innehar olika längd på CAG-sekvensen. D, dessutom var det endast två cellinjerna, HD180 och HD70, som var heterozygoter för dACTT, rs 362307, var det enda somoch variationen i exon 67, rs7223906. Det finns varierande en multitud av tillvägagångssätt som anges i denna uppsats för att behandla utvecklandet av Huntingtons sjukdom i utveckling, , som anges i denna uppsats, och förhoppningsvis är finns ett botemedel inte i en inte alltför avlägsen framtid.

Die räumliche Organisation des Chromatins im Zellkern ist für die Regulierung der Genexpression von großer Bedeutung. Genomische Varianten können die räumliche Organisation jedoch stören und Fehlbildungen und Krankheiten verursachen. In diploiden Genomen sind die meisten genomischen Varianten heterozygot und beeinflussen hauptsächlich das homologe Chromosom, auf dem sie sich befinden. Daher ist eine allelspezifische Analyse wichtig, erweist sich aber mit aktuellen Methoden zur Erfassung der Chromatinkonformation als äußerst schwierig. Erstens ist der Haplotyp, der die Verteilung unterschiedlicher Allele über die homologen Chromosomen beschreibt, oft unbekannt. Zweitens ist, insbesondere in Genomen mit geringer Variantendichte, wie dem menschlichen Genom, eine eindeutige Zuordnung der sequenzierten Genomabschnitte (Reads) zu ihrem Ursprungschromosom häufig nicht möglich, was die Erstellung haplotypspezifischer Chromatinkontaktmatrizen von guter Qualität verhindert. Genome Architecture Mapping (GAM) ist eine vielversprechende neue Methode mit dem Potential zur haplotypspezifischen Analyse der Chromatinkonformation. In dieser Dissertation zeige ich zunächst, dass GAM-Daten wertvolle Haplotypinformationen enthalten. Dann stelle ich GAMIBHEAR vor, einen graphenbasierten Ansatz, der die von GAM-Daten abgeleiteten Phaseninformationen nutzt, um genaue und vollständige Haplotypen zu rekonstruieren. Schließlich stelle ich Co-Phasing vor, eine neue Read-Phasing-Strategie, die erstmalig die eindeutige Zuordnung von variantenfreien Reads zu ihrem homologen Ursprungschromosom ermöglicht und somit auch die Erstellung detaillierter haplotypspezifischer Chromatinkontaktmatrizen in Maus und Mensch. Im Gegensatz zu früheren Erkenntnissen belegen meine Ergebnisse große Unterschiede in der räumlichen Organisation homologer Chromosomenkopien und ermöglichen erstmals einen sehr detaillierten Einblick in die haplotypspezifische Chromatinkonformation des menschlichen Genoms. / The spatial organization of chromatin in the nucleus plays an essential role in precise gene expression. Genomic variants can disrupt this spatial organization, potentially causing malformations and diseases. In diploid genomes, most genomic variants are heterozygous and mainly influence the homologous chromosome they reside on. Studying the effects of these variants in an allele-specific manner is crucial but has proven challenging using current state-of-the-art techniques. First, the haplotype describing the distribution of variant alleles over the homologous chromosomes is often unknown. Second, especially in genomes with a low variant density, such as the human genome, most sequencing reads map to genomic regions that are identical between homologous chromosomes, making it difficult to determine their origin. Thus, the read-phasing efficiency is insufficient to generate haplotype-specific chromatin contact matrices of good quality. Genome Architecture Mapping (GAM) is a promising new method for haplotype-specific analysis of chromatin conformation. In this thesis, I first demonstrate the ability of GAM data to provide valuable haplotype information. Then, I introduce GAMIBHEAR, a graph-based approach that leverages the GAM-derived phase information to infer accurate and complete haplotypes. Finally, building on GAMIBHEAR, I present Co-Phasing, a novel read-phasing strategy that allows for the unique assignment of variant-free reads to their homologous chromosome of origin and thus enables the creation of detailed haplotype-specific chromatin contact matrices in mouse and human. In contrast to previous findings, my results show significant differences in the spatial organization of homologous chromosomes and provide the first detailed view of haplotype-specific chromatin conformation in the human genome.

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Viruses constitute the vast majority of all biological entities in the biosphere and represent one of the biggest reservoirs of undetected genetic diversity on Earth. Of all the viral particles inhabiting the ocean, phages are the most abundant and can affect the overall microbial composition of marine ecosystems and the dynamics of global biogeochemical cycles. The interaction between prokaryotic cells and their phages is among the oldest and most intertwined host-parasite relationships on the planet. It has been extensively studied by culture, molecular biology, and experimental evolution. However, due to the difficulties of culture with environmental samples, only a few studies have analyzed the mechanisms of phage-host interaction in the marine environment. Here, we have studied the genes involved in viral host recognition and their evolutionary dynamics by focusing on two species of the marine copiotrophic bacterium Alteromonas and several phages infecting them. We described the genomic and morphological characterization of the first Alteromonas phage belonging to the Myoviridae family (Alteromonas myovirus V22) that was isolated in coastal waters of the Mediterranean Sea, and we identified its receptor-binding protein (RBP) used for host recognition by combining fluorescence microscopy and spectrometry. In addition, using size-exclusion chromatography, we showed how this protein required co-expression with a downstream protein to be functional, which later was identified as a new type of intermolecular chaperone crucial for RBP maturation. We also identified a conserved host recognition module in V22 and other unrelated alterophages belonging to different viral families and with completely different morphologies, suggesting horizontal gene transfer between the ancestors of these phages. Furthermore, we described the first coevolution study of a host-parasite system performed with Alteromonas using a metagenomics-like approach. Finally, we analyzed the micro- and macrodiversity of an alterophage population that was able to survive over a long period of time and showed remarkable genomic stability, indicating stable interactions over time between phage-host recognition structures. Overall, this study has contributed to extend the knowledge of known phage-host recognition mechanisms present in the marine ecosystem and has provided a first glimpse of the evolutionary dynamics in phages infecting Alteromonas.

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