Abstract Mitochondria contain a maternally inherited 16,568bp genome (mtDNA) that encodes for 13 out of more than 70 subunits of complexes of the respiratory chain that produce ATP by oxidative phosphorylation (OXPHOS). As a byproduct of OXPHOS, reactive oxygen species (ROS) are formed, which may play a role in ageing. MtDNA has accumulated numerous polymorphisms during evolution, leading to haplogroups characterized by ancient polymorphisms and defined by letters. MtDNA polymorphisms are thought to be neutral, but some may be slightly deleterious or even advantageous and may influence phenotypes of complex traits. Interestingly, several complex traits such as longevity and maximal aerobic power show maternal inheritance. Associations between mtDNA polymorphisms and longevity have been reported, but no systematic study has been made of the role of mtDNA in longevity. In addition, there are no previous reports on mtDNA haplogroups in elite athletic performance. Associations are demonstrated here between mtDNA haplogroups J, K and U and longevity in Finns. Interestingly, subhaplogroup J2 and haplogroup K, which were found in increased frequency among the 225 very old subjects studied, were not found among the 52 endurance athletes but were present in 11% of the 89 sprint athletes Uncoupling of OXPHOS reduces ATP and ROS production. Thus, a mitochondrial genome with a higher level of uncoupling may promote longevity but may not be favourable in situations that require a high level of ATP production, such as elite endurance performance. A more detailed analysis also showed an association between a combination of three common mtDNA polymorphisms and longevity in both the Finns and the Japanese, providing the first epidemiological support for the assumption that the nature of a mutation is determined by interactions with other mutations in mtDNA. In addition, a systematic approach was applied to study the role of mtDNA in longevity. Association analyses of mtDNA allele combinations in longevity revealed that the mtDNA control region, the tRNA and rRNA genes and the nucleotide repeats in mtDNA may play a role in longevity, since the alleles and allele combinations that showed the strongest associations with longevity, either negative or positive, were among these genes. Differences in overall variation in mtDNA between the very old and their controls were also studied, revealing more differences at synonymous (silent) sites than at non-synonymous (amino acid altering) sites. The findings support previous data suggesting that certain mtDNA haplogroups are associated with longevity. In addition, those haplogroups that increased in frequency among the very old Finns were not found among Finnish endurance athletes. Also, a novel systematic approach was applied to study mtDNA alleles, allele combinations and overall sequence variation in longevity, suggesting that there are interactions between various mtDNA positions and that the tRNA and rRNA genes and short tandem repeats in mtDNA may play a role in longevity.

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Agriculture, with different Neolithic cultures, starts in the Near East more than 10,000 years ago. This new way of life has very different archaeological manifestations that previous Mesolithic. After its Near Eastern emergence, the farming practices rapidly penetrated into southeastern Europe and the first signs of Neolithic in Central Europe are already 7,000 years old. It is being considered that the cultural innovations influenced demographic growth of the populations that have taken part in the Neolithic spread. In such situation, new mutations would have to fix and could form new specific haplogroups for Europe with ancestral ties to the Near East. Phylogeographic studies such as founder analysis of European and Near Eastern mtDNA sequences found that the European Neolithic component was enriched mainly by haplogroups J and T1, and that the genetic contribution of farming economy in European gene pool is about 10 - 20%. However, studies like these have not been yet realized in particular parts of Europe. The aim of this thesis is to disentangle the internal variability of Central European haplogroups J and T1 thought to be involved in the Neolithic demic diffusion. We classified these haplogroups from the HVS-I mtDNA sequences of 281 samples of the recent population of the Czech Republic. We...

Un des rôles de la mitochondrie, qui possède son propre ADN (ADNmt), est la production de l'énergie nécessaire à la cellule, qu'elle synthétise sous forme d'ATP grâce aux oxydations phosphorylantes (OXPHOS). Ainsi, une altération du métabolisme énergétique mitochondrial peut provoquer l'apparition de pathologies mitochondriales dont, généralement, la sévérité est inversement proportionnelle à l'âge de début. De nombreuses études s'intéressent aux mécanismes d'apparition et de développement de ces maladies afin de mieux les comprendre et de pouvoir proposer des thérapies. Cependant, à ce jour, il est encore difficile de transformer l'ADNmt de façon ciblée (remaniement ou mutation). De plus, il existe encore peu de modèles animaux de pathologies mitochondriales qui permettraient de réaliser des études intégratives et d'essayer d'éventuelles molécules thérapeutiques. Dans le cadre de cette thèse, nous avons étudié deux types de modèles impliquant la modification du métabolisme mitochondrial. Dans un premier temps, nous nous sommes intéressés à la réalisation d'un modèle murin exprimant un grand nombre de caractéristiques du syndrome de Leigh, une maladie neurologique progressive. Pour cela nous avons utilisé une neurotoxine (MPTP) qui est connue pour sa toxicité envers les neurones dopaminergiques et aussi comme inhibiteur de la chaine respiratoire. Nous avons analysé l'activité de chaque complexe OXPHOS de différents tissus cérébraux et de tissus périphériques (cœur, foie, muscle et rein), prélevés sur des souris traitées et non-traitées. Nous avons retrouvé une inhibition des complexes III et/ou IV de la chaîne respiratoire dans le foie, le cortex, le striatum et le cervelet. Ces résultats, ajoutés à une neuro- dégénérescence accrue retrouvée dans une étude précédente, sont tous caractéristiques du syndrome de Leigh. Ces souris traitées par le MPTP semblent donc être un bon modèle pour l'étude de cette pathologie mitochondriale. Dans un second projet, nous nous sommes intéressés à l'effet des haplogroupes de l'ADNmt sur le métabolisme mitochondrial. En effet, bien qu'ils soient définis par des mutations neutres de l'ADNmt (polymorphismes), plusieurs études ont démontré des associations entre les haplogroupes et les pathologies, suggérant que les haplogroupes sont capables d'avoir un effet protecteur ou aggravant dans l'apparition d'une pathologie. Récemment, notre laboratoire a montré que certains haplogroupes avaient la capacité d'influencer le fonctionnement du métabolisme énergétique mitochondrial. Mon projet de recherche a donc consisté à mettre en place un modèle afin d'étudier les mécanismes cellulaires et moléculaires impliqués dans ce phénomène. Pour cela, nous avons recherché des haplogroupes d'intérêt dans la population française afin d'élaborer une collection de " cybrides " où chaque lignée de cellules possède un haplogroupe particulier mais un fonds génétique nucléaire commun à toutes les lignées. Nous avons caractérisé ces cybrides de manière biochimique (analyse de l'activité et des paramètres cinétiques de chaque complexe) et phénotypique (courbes de croissance). L'ensemble de ces résultats a été intégré dans un modèle informatique spécifiquement développé dans notre laboratoire pour modéliser la physiologie de la mitochondrie. Ce projet nous a permis de mettre en évidence l'influence des haplogroupes de l'ADNmt sur le métabolisme mitochondrial et de proposer une vision modulée des pathologies mitochondriales tant pour leur étude que pour leur diagnostic, en faisant ressortir la notion de médecine personnalisée. A l'avenir, il sera nécessaire de tenir compte du contexte génétique de l'ADNmt pour trouver de nouvelles stratégies ou de nouvelles cibles pour les thérapies des maladies mitochondriales. / The mitochondrion is an intracellular organelle responsible for the cellular energy production, by synthesizing ATP through the oxidative phosphorylation (OXPHOS). One of the characteristics of this organelle is that it has its own DNA (mtDNA) encoding for subunits of OXPHOS complexes. Any alterations of mitochondrial energy metabolism cause mitochondrial pathologies whose severity is generally inversely proportional to the age of onset. Some scientific studies are looking at the mechanisms of occurrence and development of these diseases in order to better understand them and to be able to offer therapies. However, there is no tool that can transform mtDNA in a targeted way by mutation or DNA rearrangement. Moreover, there are still few animal models of mitochondrial pathology that would allow integrative studies on the one hand, and on the other hand, to try out possible therapeutic molecules. In this thesis, we studied two types of models involving the modification of mitochondrial metabolism either by chemical treatment or by the use of mutations found in individuals. In a first part, we were interested in the realization of mouse model with a large number of characteristics of the Leigh syndrome, a progressive neurological disease characterized by neuropathological lesions associating a damage of the brain stem and the basal ganglia. For this study, we have used the 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP) neurotoxin, known for its toxicity to dopamine neurons and also as an inhibitor of mitochondrial respiratory chain. We analyzed the activity of the OXPHOS complexes I to IV on brain tissues (cerebelum, cortex, striatum and substancia nigra) and peripheral tissues (heart, liver, muscle and kidney) from treated and untreated mice. Inhibition of complexes III and/or IV in the liver, cortex, striatum and cerebellum was found. These results, combined with an increased neurodegeneration found in a previous study, are all characteristics of Leigh Syndrome. Mice treated with MPTP seem to be a good model for this mitochondrial pathology. In the second project, we looked at the effect of mtDNA haplogroups (haplotypes grouping) on mitochondrial metabolism. Although, haplogroups are defined by neutral mutations of mtDNA (polymorphism), several studies have shown associations between haplogroups and some pathologies suggesting that haplogroups are able to have a protective effect or being a risk factor in the pathology development. Recently, our laboratory has confirmed that some haplogroups may not be neutral and have the ability to influence the mitochondrial energy metabolism functioning. Therefore, my research project consisted of setting up a model to study these cellular and molecular mechanisms. We looked for haplogroups of interest in the population in order to elaborate a cellular collection where each cell line has a particular haplogroup but with a common nuclear genetic background in all the cell lines. This collection was obtained by cybride constructions. We characterized these cybrides biochemically by analyzing the activity of each complex, determining kinetic parameters (KM and Vmax) and titration specific respiratory chain inhibitors. Concomitantly, we defined cell parameters via growth curves. All these results were integrated into a computer model specifically developed in our laboratory to model mitochondrial processes. This project gives us some evidence of the mtDNA haplogroups' influence on mitochondrial metabolism and to propose a modulated vision of mitochondrial pathologies for their study and their diagnosis, highlighting the notion of personalized medicine. As each haplogroup modulates in the different way the mitochondrial metabolism, each individual could have a personal response to the same mutation or pathology. In future, the mtDNA genetics background should be taken into account to find new strategies or new targets for the therapies of mitochondrial diseases.

<p>Initially, a pilot study was carried out in order to reconstruct the major paternal and maternal lineages of the Muslim population living in the Cape metropolitan area. The Study has shown the ability of molecular genetic tools to give insight into the origins and history of local communities. The study was also used as a point of reference for the Strand Muslim Community project. Genetic variations of the Y-chromosome and mitochondrial DNA for the pilot study were analyzed using the RFLP technique. The SNaPshot mini-sequencing technique was used to genotype single nucleotide polymorphisms (SNP) on the Y-chromosome and mitochondrial DNA in 115 males from the Strand Muslim community.</p>

<p>Initially, a pilot study was carried out in order to reconstruct the major paternal and maternal lineages of the Muslim population living in the Cape metropolitan area. The Study has shown the ability of molecular genetic tools to give insight into the origins and history of local communities. The study was also used as a point of reference for the Strand Muslim Community project. Genetic variations of the Y-chromosome and mitochondrial DNA for the pilot study were analyzed using the RFLP technique. The SNaPshot mini-sequencing technique was used to genotype single nucleotide polymorphisms (SNP) on the Y-chromosome and mitochondrial DNA in 115 males from the Strand Muslim community.</p>

Mitochondrial diseases encompass a broad range of devastating disorders that typically affect tissues with high-energy requirements. These disorders have been difficult to diagnose and research because of the complexity of mitochondrial genetics, and the large variability seen among patient populations. We have devised and carried out a mechanistic study to generate a cell based model for Leigh’s disease caused by mitochondrial DNA mutation 8993 T>G. Leigh’s disease is a multi-organ system disorder that depends heavily on the mutation burden seen within various tissues. Using new reprogramming and sequencing technologies, we were able to show that Leigh’s disease patient fibroblasts reprogrammed to induced pluripotent stem cells maintain the same level of mutation burden seen in the original patient cell line. Mutation burden was maintained through several passages and spontaneous differentiation. This cell based model could be useful for future pathogenesis studies, or therapeutic drug screenings in a patient and tissue specific manner.

The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...

Magister Scientiae - MSc / Initially, a pilot study was carried out in order to reconstruct the major paternal and maternal lineages of the Muslim population living in the Cape metropolitan area. The Study has shown the ability of molecular genetic tools to give insight into the origins and history of local communities. The study was also used as a point of reference for the Strand Muslim Community project. Genetic variations of the Y-chromosome and mitochondrial DNA for the pilot study were analyzed using the RFLP technique. The SNaPshot mini-sequencing technique was used to genotype single nucleotide polymorphisms (SNP) on the Y-chromosome and mitochondrial DNA in 115 males from the Strand Muslim community. / South Africa

Abstract Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are the two most common neurodegenerative diseases leading to early onset dementia (&lt; 65 years). Mutations in the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) genes cause a proportion of familial early-onset AD (eoAD), while the microtubule-associated protein tau (MAPT) and progranulin (PGRN) mutations have been identified in FTLD patients. Only a few PSEN1 and APP mutations have previously been found in Finnish AD patients, and one MAPT mutation in a FTLD family, while the role of PGRN in Finnish FTLD patients is unknown. Increasing evidence suggests that mitochondrial dysfunction and oxidative stress also play an important role in neurodegenerative diseases. The aim here was to investigate the genetics of eoAD and FTLD in the population of the province of Northern Ostrobothnia, Finland. Sequencing analysis of the APP, PSEN1 and PSEN2 genes was performed to determine whether mutations in these genes could be detected. The MAPT and PGRN genes were analysed in the FTLD patients by sequencing and MAPT haplotypes were determined. The contributions of mtDNA and its maintenance enzymes to eoAD and FTLD were studied by comparing the frequencies of mtDNA haplogroups and their clusters between the patient groups and controls and by screening for the five common POLG1 mutations (T251I, A467T, P587L, W748S, Y955C), two common mtDNA mutations (m.3243A>G, m.8344A>G) and mutations in the PEO1 and ANT1 genes. This is the first report of a significant association between the mtDNA haplogroup cluster IWX and FTLD. The H2 MAPT haplotype was also associated with FTLD in our cohort. No significant differences in the frequencies of the mtDNA haplogroups were observed between the eoAD patients and controls, nor were there any pathogenic mutations detected in the genes analysed. The findings suggest that possession of the mtDNA haplogroup cluster IWX and the H2 MAPT haplotype may be possible risk factors for FTLD in our cohort. The absence of any pathogenic mutations in the MAPT, PGRN, APP or PSEN genes in our series, together with the previous reports of only a few mutations found in this region, supports a minor role for these genes in the aetiology of eoAD and FTLD in Northern Ostrobothnia and indicates that this population may have its own genetic features. There may be other, still unknown genetic factors to be discovered, that explain familial diseases in the region.