Duikers are a species rich subfamily of threatened African antelope whose recent origin poses a challenge to the molecular identification of taxa and estimation of their phylogeny. I test the ability of DNA barcodes to identify all taxa within this group. I then use mitochondrial and nuclear genes to estimate a multi-locus species tree and to date divergence times. DNA barcodes are unable to distinguish many sister taxa, calling into question the utility of barcodes for the regulation of duiker trade or in identification of field-collected feces. The multi-locus phylogeny provides support for the relationships among major duiker lineages and placement of two problematic taxa, but challenges the validity of the savanna genus and identifies hybridization between taxa. This study reveals that most duikers diverged during the Pleistocene, meriting further inquiry into the role that Pleistocene glacial cycling played in the diversification and population structuring of duikers.

Oxidative phosphorylation apparatus (OXPHOS) is responsible for production of majority of ATP in mammalian organisms. This process, occurring in the inner mitochondrial membrane, is partly regulated by nuclear-encoded subunits of cytochrome c oxidase (COX), the terminal enzyme of electron transport chain. Cox4 subunit, participating in OXPHOS regulation, is an early-assembly state subunit, which is necessary for incorporation of Cox2 catalytic subunit, thus for assembly of catalytically functional COX enzyme. Moreover, regulated expression of two isoforms (Cox4i1, Cox4i2) of Cox4 subunit is hypothesized to optimize respiratory chain function according to tissue oxygen supply. However, the functional impact of the isoform switch for mammalian tissues and cells is still only partly understood. In the present thesis, unique HEK293 cell line-based model with complete absence of subunit Cox4 (knock-out, KO) was prepared employing novel CRISPR CAS9-10A paired nickase technology and further characterized. Knock-out of both isoforms Cox4i1 and Cox4i2 (COX4i1/4i2 KO clones) showed general decrease of majority of Cox subunits resulting in total absence of fully assembled COX. Moreover, detected Complex I subunits as well as the content of assembled Complex I were decreased in COX4i1/4i2 KO clones. On the...

Este trabalho consiste em estudar o comportamento eletroquímico de biomoléculas imobilizadas sobre o eletrodo de carbono vítreo, utilizando materiais biocompatíveis como meios imobilizadores para detecções em meios aquosos. Foram utilizados inicialmente compósitos de hidrogéis capazes de auxiliar a permanência da enzima sobre a superfície do eletrodo e beneficiar a transferência de carga entre a enzima e o eletrodo de trabalho. Para melhorar a resposta eletroquímica do biossensor, também foram estudados métodos que utilizam líquidos iônicos no processo de imobilização da enzima. Deste modo a eletroatividade da enzima foi inicialmente estudada por voltametria cíclica, a fim de evidenciar tal eletroatividade no meio totalmente iônico, como também avaliar o melhor método de imobilização, para futuras aplicações em detecções de analitos. Os líquidos iônicos utilizados são compostos por cátions alquil-imidazol com ânions de natureza orgânica ou inorgânica. Como se sabe os íons que compõem o líquido iônico podem distinguir sua funcionalidade, pois é o tamanho desses íons que influencia na maioria das suas propriedades físico-químicas, tais como hidrofobicidade e viscosidade. / The aim of this work is to study the electrochemical behavior of biomolecules immobilized on a glassy carbon electrode, using biocompatible materials as a way for immobilizing detection in aqueous media. Initially, hydrogels composite were used because they are able to assist the permanence of the enzyme on the electrode surface and they are benefit to the charge transfer between enzyme and electrode surface. To improve the electrochemical response of the biosensor, methods using ionic liquids in the process of immobilization of the enzyme were also studied. Thus the electroactivity of the enzyme was initially analyzed by cyclic voltammetry in order to show that the electroactivity remains in an entirely ionic media, as well as evaluating the best method of immobilization, for future applications in biosensors. The ionic liquids used are composed of imidazole-alkyl cations with anions of organic or inorganic nature. As it is well known, the ions in the ionic liquid can distinguish its functionality, due to the fact that it is the size of these ions that influences most on their physicochemical properties such as hydrophobicity and viscosity.

Este trabalho consiste em estudar o comportamento eletroquímico de biomoléculas imobilizadas sobre o eletrodo de carbono vítreo, utilizando materiais biocompatíveis como meios imobilizadores para detecções em meios aquosos. Foram utilizados inicialmente compósitos de hidrogéis capazes de auxiliar a permanência da enzima sobre a superfície do eletrodo e beneficiar a transferência de carga entre a enzima e o eletrodo de trabalho. Para melhorar a resposta eletroquímica do biossensor, também foram estudados métodos que utilizam líquidos iônicos no processo de imobilização da enzima. Deste modo a eletroatividade da enzima foi inicialmente estudada por voltametria cíclica, a fim de evidenciar tal eletroatividade no meio totalmente iônico, como também avaliar o melhor método de imobilização, para futuras aplicações em detecções de analitos. Os líquidos iônicos utilizados são compostos por cátions alquil-imidazol com ânions de natureza orgânica ou inorgânica. Como se sabe os íons que compõem o líquido iônico podem distinguir sua funcionalidade, pois é o tamanho desses íons que influencia na maioria das suas propriedades físico-químicas, tais como hidrofobicidade e viscosidade. / The aim of this work is to study the electrochemical behavior of biomolecules immobilized on a glassy carbon electrode, using biocompatible materials as a way for immobilizing detection in aqueous media. Initially, hydrogels composite were used because they are able to assist the permanence of the enzyme on the electrode surface and they are benefit to the charge transfer between enzyme and electrode surface. To improve the electrochemical response of the biosensor, methods using ionic liquids in the process of immobilization of the enzyme were also studied. Thus the electroactivity of the enzyme was initially analyzed by cyclic voltammetry in order to show that the electroactivity remains in an entirely ionic media, as well as evaluating the best method of immobilization, for future applications in biosensors. The ionic liquids used are composed of imidazole-alkyl cations with anions of organic or inorganic nature. As it is well known, the ions in the ionic liquid can distinguish its functionality, due to the fact that it is the size of these ions that influences most on their physicochemical properties such as hydrophobicity and viscosity.

Electrospray ionization is a technique widely used in mass spectrometry. Almost every material, specifically large molecules like proteins or polymers can be ionized directly out of solution. During the ionization process molecules are not fragmented. In this work a prototype apparatus for creating three-dimensional patterns in a ultra high vacuum environment using an electrospray ion source was optimized for higher ion currents hence deposition rate by improving the core component of the apparatus, an electrodynamic ion funnel. The major improvements are a redesigned heated vacuum inlet, modified gas flow inside the ion funnel because of sealing the ion funnel against perpendicular gas flow and a better measurement setup for the transmitted current. The transmission of the ion funnel was improved from 25% to 82% resulting in ion currents of up to 7nA (500pA before advancements) focused through the ion funnel. At this rate an area of 1 cm² can be coated with a molecular monolayer of Cytochrome C in 64 minutes.

The influence of genotype variation on phenotype has been a longstanding question in biology but it is now one of the greatest challenges of the post-genomics era. Discovering the link between common gene variants that affect phenotypes within and between populations is likely to provide insight into the molecular physiology of phenotypic traits and the mechanisms by which they evolve. The overall goal of this thesis is to link naturally occurring genotypic variation with the organism??s phenotype. The specific goal of this thesis is to connect natural variation in the mitochondrial genotype with the organismal phenotype using the model organism Drosophila simulans. Mitochondria are intracellular organelles found in most eukaryotes and produce over 90% of the energy needed by cells. Determining the connection of mitochondrial genotype to whole organism phenotype is of particular interest because of the broad use of mitochondrial (mt) DNA as a molecular marker in evolutionary biology and population genetics, the organelle??s central role in cellular energy production, the potential for the mitochondria to influence organismal distribution particularly in the face of climate change and in human degenerative disease. I use the model organism D. simulans because it has high genetic variability, can be easily sampled from the wild and manipulated in the lab, and the energy producing reactions that take place in its mitochondria are highly conserved among metazoa. I studied naturally occurring mutations to understand the influence of these changes in natural populations. The four studies in this thesis have employed a Genotype-Biochemistry-Phenotype (GBP) model to link naturally occurring variation in the mitochondrial genotype with organism phenotype in D. simulans mitochondria. Three major conclusions can be drawn from the thesis that follow the genotype to biochemistry to phenotype model. Firstly, a subset of the mutations in genes that comprise the mitochondrial genotype is functionally significant. Secondly, the biochemical efficiency of OXPHOS is regulated by mitochondrial homeostasis. Thirdly, key organismal life history traits influenced by the mitochondrial genotype and this is mediated through the biochemistry of OXPHOS.

Le but principal de mon projet de thèse était de développer un instrument de mélange en vol de microgouttes pour jets d'encre synchronisés. Les microgouttes balistiques passent voir l'air peut être pensé comme des navires de réaction avec des volumes en bas à la pl-gamme. Les réactifs restent limités dans les microgouttes pendant leur trajectoire. Les effets de tondage induits de la présence murale ne jouent pas de rôle; bien que la compression mécanique de la solution pendant le processus d'éjection puisse influencer l'intégrité structurelle de protéines fragiles. J'ai exploré dans ma thèse pour la première fois la combinaison de microgouttes balistiques avec des techniques de microdiffusion stroboscopique. L'effort instrumental principal était donc de développer une installation stable avec deux jets d'encre pour étudier mélange de microgouttes en vol à ligne de lumière ID13, ESRF utilisant expériences de diffusion centrale et de diffraction de rayons X stroboscopique. J'ai utilisé ces techniques pour étudier la paraffine liquide en vol et des microgouttes de cytochrome C et la coalescence de microgouttes de cytochrome C avec des microgouttes de tampon de Na-acetate. J'ai également exécuté des expériences exploratoires de diffraction de rayons X à la ligne de lumière ID13 sur des microgouttes de paraffine solide déposés sur des surfaces et la diffraction dépendante de la température sur le solide de paraffine pour calibrer les données stroboscopiques. Des expériences statiques de diffusion centrale ont été exécutées à la ligne de lumière ID02 pour obtenir des courbes de la référence pour les états de conformation de solutions du cytochrome C .

Nous avons montré la faisabilité d 'une approche de capteur où les fonctions de détection et de signalisation sont séparées. Nous avons choisi comme supports lumineux des nanosphères fluorescentes. Elles servent de transducteurs. Nous avons exploré la modularité du capteur en essayant plusieurs molécules sondes adsorbées à la surface des billes. Nous avons montré que l'information entre la détection (sonde) et la signalisation (bille) est relayée par transfert d'énergie.

Galig, gène interne au gène de la galectine-3, code deux protéines la mitogaligine et la cytogaligine. Ce travail de thèse a montré que l'expression de galig conduit à une mort cellulaire présentant des marqueurs caractéristiques de l'apoptose. Ainsi, la co-expression de Bcl-XL, protéine anti-apoptotique, réduit significativement la libération de cytochromec et la mort cellulaire. Cependant, certains caractères apoptotiques ne sont pas mis en évidence suggérant une nouvelle forme de mort cellulaire programmée. Des études de relation structure-fonction ont permis de délimiter le signal d'adressage mitochondrial en position interne dans la mitogaligine. Des anticorps anti-cytogaligine polyclonaux ont été produits puis utilisés en immunofluorescence et en western-blot. Un test de PCR quantitative a également été mis au point. Ces outils devraient permettre de quantifier l'expression du gène galig et la production des protéines in vivo dans différents échantillons de tissus humains.

L'étude dynamique des hémoprotéines, indispensable à la compréhension du fonctionnement de leur site actif, a considérablement progressé grâce aux expériences de spectroscopie. Nous avons étudié dans ce cadre le transfert du ligand CO au sein du site actif bimétallique de la cytochrome c oxydase, du Fer de l'hème à l'atome de Cuivre, par spectroscopie femtoseconde infrarouge. Les expériences dans l'infrarouge permettent d'analyser les caractéristiques vibrationnelles des molécules et de suivre ainsi directement le transfert du ligand par l'intermédiaire de sa signature vibrationnelle. Afin de résoudre le transfert étudié, qui se produit sur une échelle subpicoseconde, l'expérience doit avoir une résolution femtoseconde. Deux expériences pompe-sonde femtoseconde dans le domaine infrarouge, une expérience intégrée spectralement et une expérience résolue spectralement, ont été mises en place. Ces deux expériences ont apporté des informations complémentaires sur le transfert du ligand CO au sein du site actif de la cytochrome c oxydase. Dans le cas de l'expérience intégrée spectralement, un signal supplémentaire dû à l'absorption des molécules d'hème a été identifié et soustrait aux cinétiques afin d'isoler le signal induit par le transfert du CO. Le temps caractéristique de ce transfert a ainsi pu être évalué à 400 fs. Lors de l'expérience résolue spectralement, l'évolution des raies d'absorption du CO présente un décalage de 200 fs qui suggère une composante balistique dans le transfert. L'expérience résolue spectralement a été réalisée à l'aide d'une nouvelle technique de mesure du spectre infrarouge par conversion vers le visible, développée au laboratoire. Cette technique, qui offre un meilleur rapport signal sur bruit et une meilleure résolution que les approches concurrentes, a permis d'acquérir un ensemble de spectres différentiels suffisant pour valider expérimentalement une nouvelle technique de filtrage des oscillations de cohérence. Nous avons réalisé des simulations de dynamique moléculaire qui modélisent le transfert du ligand CO dans la cytochrome c oxydase, du Fer de l'hème vers l'atome de Cuivre. Ces simulations sont en bon accord avec les résultats expérimentaux et ont montré que le trajet emprunté par le CO lors de son transfert est reproductible, ce qui corrobore un transfert balistique.