L’anchois et la sardine appartiennent à la guilde des petits poissons pélagiques, qui tiennent une place considérable à l’échelle des écosystèmes et des pêcheries. Ces deux espèces sont très largement répandues dans les mers et océans du globe et souvent occupent les mêmes écosystèmes. Leurs populations montrent d’importantes fluctuations interannuelles de biomasses, dont les tendances ne suivent pas les mêmes schémas, voire sont parfois déphasées. Une littérature croissante suggère que ces dynamiques sont dues à des sensibilités relatives aux conditions environnementales différentes induites par des traits biologiques distincts. Bien que de prime abord anchois et sardines semblent très similaires, ils montrent notamment des stratégies alimentaires et reproductives quelque peu différentes. Comprendre ces divergences biologiques et de stratégies d’histoire de vie apparait donc essentiel pour appréhender les dynamiques passées et éventuellement anticiper les évolutions futures de ces stocks. L’objectif de cette thèse est de déterminer en quoi se démarquent ces deux espèces en termes de traits biologiques et d’histoire de vie sur une base physiologique. En effet, du fait de la complexité de potentielles interactions entre les traits biologiques et de leurs évolutions ontogéniques, il convient, pour répondre à cette question, de mettre en œuvre une approche intégratrice via la modélisation bioénergétique à l’échelle du cycle de vie. Dans un premier temps l’étude a été dédiée à un indice de condition : la densité énergétique (contenu énergétique par unité de masse). La densité énergétique résulte de nombreux processus physiologiques, intégrant ainsi l’historique des dépenses énergétiques diverses face aux gains acquis via l’alimentation. L’analyse de cet indice a notamment permis d’identifier divers effets sur la condition énergétique du poisson : l’espèce, la taille, la saison et la zone géographique. En lien avec l’énergie observée, un modèle du cycle de vie a été paramétré pour les deux espèces dans le golfe de Gascogne, afin de disposer d’un outil intégrateur, exploratoire et prédictif. Il s’agit d’un modèle bioénergétique basé sur la théorie du « Dynamic Energy Budget » (DEB). Ce cadre vise à prédire le cycle de vie d’un organisme, en fonction de forçages environnementaux, en simulant la résultante des différents flux d’énergies qui s’y produisent. Cette approche a notamment permis de souligner le caractère particulièrement structurant des stratégies reproductives sur le cycle bioénergétique annuel des deux espèces. / Anchovy and sardine belong to the guild of small pelagic fish and are of peculiar importance at the scales of ecosystems and fisheries. Both species are worldwide spread and commonly occur in the same ecosystems. They display large interannual variability in biomass with markedly different trends or even asynchronous. A growing literature suggests that those dynamics are due to respective sensibility to environmental conditions driven by different biological traits. A priori both species are very similar but show slightly distinct feeding behaviours and reproductive strategies. Understanding divergences in both species biology and life history strategies is thus crucial to understand and predict past and future dynamics of these stocks. The aim of this PHD is to assess how both species diverge in terms of biological and life history traits on a physiological basis. Owing to the complexity of biological traits, potential interactions among these traits and ontogenetic evolutions, to answer this question an integrative approach based on a bioenergetics model of the whole life cycle is requested. First the study focus on a condition index: the energy density (energy content per unit of mass). Energy density integrates historic of numerous physiological processes, both gain from food and diverse metabolic expenses. This analysis shows effects on the bioenergetics cycle of the fish, namely species, size, season and geographic area. Linked with bioenergetics data, a full life cycle model has been parametrised for both species in the Bay of Biscay, in order to get an integrative, predictive and exploratory tool. This model is based on the “Dynamic Energy Budget” theory. This theory aims at predicting the life cycle of an organism, using environmental forcing, by simulating energy fluxes inside the organism. This modelling approach underlines the particularly significant feature of reproductive strategies on the bioenergetics annual cycle of both species.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A obesidade, doença resultante do acúmulo excessivo de gordura corporal, é importante fator de risco para diabetes mellitus tipo 2, dislipidemias e doenças cardiovasculares, doenças de alta prevalência em todo o mundo. O processo de transição nutricional decorrente da globalização contribuiu para o crescente número de indivíduos com obesidade, principalmente pela modificação nos hábitos alimentares da população, com ampla inclusão de produtos industrializados ricos em gordura saturada, sal e açúcar, denominada dieta ocidental. Os mecanismos pelos quais a obesidade induzida por dieta leva ao desenvolvimento de doenças cardiovasculares ainda não estão completamente esclarecidos na literatura, porém sabe-se que a obesidade leva ao comprometimento da função cardíaca e do metabolismo energético, aumentando a morbidade e mortalidade. Em grande parte dos estudos relacionados à obesidade, o metabolismo energético celular comprometido associa-se à disfunção mitocondrial. Neste contexto, torna-se importante avaliar a função mitocondrial na obesidade, visto que as mitocôndrias são organelas com funções-chave no metabolismo energético. No presente estudo, avaliamos inicialmente o efeito obesogênico da dieta ocidental em camundongos Swiss por 16 semanas a partir do desmame. Para tal, analisamos a ingestão alimentar, evolução da massa corporal, Índice de Lee, peso das gorduras epididimal e retroperitoneal, peso e morfologia do fígado, relação entre o peso do fígado/massa corporal, peso do ventrículo esquerdo (VE)/massa corporal, glicemia de jejum e teste intraperitoneal de tolerância à glicose. Avaliamos também o consumo de oxigênio das fibras cardíacas através da respirometria de alta resolução. Além disso, o conteúdo das proteínas envolvidas no metabolismo energético: Carnitina Palmitoil Transferase 1 (CPT1), proteína desacopladora 2 (UCP2), Transportadores de glicose 1 e 4 (GLUT1 e GLUT4), proteína quinase ativada por AMP (AMPK), proteína quinase ativada por AMP fosforilada (pAMPK), receptor de insulina &#946; (IR&#946;) e substrato do receptor de insulina 1 (IRS-1) foi determinado por western blotting. Nossos resultados confirmaram o caráter obesogênico da dieta ocidental, visto que os camundongos submetidos a esta dieta (GO), apresentaram-se hiperfágicos (P<0,001) e obesos (72,031,82, P<0,001), com aumento progressivo no ganho de massa corporal. Além do aumento significativo dos parâmetros: Índice de Lee (362,902,44, P<0,001), gorduras epididimal e retroperitonial (3,310,15 e 1,610,11, P<0,001), relação entre o peso do fígado/massa corporal (0,060,003, P<0,001) e peso de ventrículo esquerdo (VE)/massa corporal (0,080,002, P<0,01), hiperglicemia de jejum (192,1014,75, P<0,01), intolerância à glicose (P<0,05, P<0,01) e deposição ectópica de gordura no fígado. A respirometria de alta resolução evidenciou disfunção mitocondrial cardíaca no grupo GO, com reduzida capacidade de oxidação de carboidratos e ácidos graxos (P<0,001) e aumento do desacoplamento entre a fosforilação oxidativa e a síntese de ATP (P<0,001). Os resultados de western blotting evidenciaram aumento nos conteúdos de CPT1 (1,160,08, P<0,05) e UCP2 (1,080,06, P<0,05) e redução no conteúdo de IRS-1 (0,600,08, P<0,05). Não houve diferença significativa nos conteúdos de GLUT1, GLUT4, AMPK, pAMPK, pAMPK/AMPK e IR&#946;. Em conclusão, o consumo da dieta ocidental resultou no desenvolvimento de obesidade com disfunção mitocondrial associada a alterações no metabolismo energético. / Obesity, a disease resulting from excessive accumulation of body fat is a risk factor for type 2 diabetes, dyslipidemia and cardiovascular diseases, which are of high prevalence worldwide. Nutritional transition, a process associated with globalization, has contributed to growing obesity, mainly by changing eating habits of the population, with broad inclusion of industrial products high in saturated fat, salt and sugar, the called Western diet. The mechanisms by which diet-induced obesity leads to cardiovascular disease are not completely understood, but it is known that obesity leads to impairment of cardiac function and energy metabolism, increasing morbidity and mortality. In most obesity studies, the related cellular energy metabolism is compromised associated with mitochondrial dysfunction. In this context, it becomes important to asses mitochondrial function in obesity, since mitochondria are organelles with key roles in energy metabolism. In the present study, we evaluated the effect of the Western diet in Swiss mice for 16 weeks from weaning. We analyzed the food intake, changes in body weight, Lee index, weight of epididymal and retroperitoneal fat, weight and morphology of the liver, the ratio of liver weight /body weight, weight of the left ventricle (LV)/body weight , fasting plasma glucose and intraperitoneal glucose tolerance test. We also evaluated the oxygen consumption of cardiac fibers by high-resolution respirometry. Furthermore, proteins content involved in energy metabolism: carnitine palmitoyl transferase 1 (CPT1), uncoupling protein 2 (UCP2), glucose transporters 1 and 4 (GLUT1 and GLUT4), AMP-activated protein kinase (AMPK), AMP-activated protein kinase phosphorylated (pAMPK), insulin receptor &#946; (IR&#946;) and insulin receptor substrate 1 (IRS-1) was determined by western blotting. Our results confirmed the obesogenic role of the Western diet. Thus, mice subjected to Western diet (WG), presented hyperphagia (P<0.001) and obesity (72.031.82, P<0.001), with a progressive increase in body mass gain. Also, the WG group compared to control had statistically significant increase of the all parameters studied: Lee index (362.902.44, P<0.001), epididymal and retroperitoneal fat (3.310.15 and 1.610.11, P<0.001), ratio of liver weight/body weight (0.060.003, P<0.001) and weight of the left ventricle (LV)/body weight (0.080.002, P<0.01), fasting hyperglycemia (192.1014.75, P<0.01), glucose intolerance (P<0.05, P<0.01) and ectopic fat deposition in liver. High-resolution respirometry showed cardiac mitochondrial dysfunction in the WG group, with reduced capacity of oxidation of carbohydrates and fatty acids and increased uncoupling between oxidative phosphorylation and ATP synthesis. Western blotting results revealed an increase in CPT1 (1.160.08, P<0.05) and UCP2 (1.080.06, P<0.05) content and reduction in IRS-1 content (0.600.08, P<0.05). There was no statistically significant difference in the GLUT1, GLUT4, AMPK, pAMPK, pAMPK/AMPK and IR&#946; content. In conclusion, the Western diet consumption resulted in the development of obesity with mitochondrial dysfunction associated to alterations in energy metabolism.

Made available in DSpace on 2015-05-07T15:09:24Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 831896 bytes, checksum: 75be69cfb5ffa4cc817ad82169c44356 (MD5) Previous issue date: 2014-05-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The aim of this study was to analyze the postural grounding, conceived as the psycho-corporal experience contact with the own body, the ground and reality, in activities during physical education classes with male and female students aged between 10 and 13 years, establishing a connection between such activities and the bioenergetics&#8223; principles. According to the theoretical model of Bioenergetics' Analysis, the grounding corresponds to be self-sustaining process with balance and ability of self-expression, a process in which the individual develops contact with himself, with the space, with his internal and external reality, in the physical, symbolic and emotional levels. Such process promotes cohesion between the movement, the feeling and the expression and coherence between the psychological and corporal functioning. From this theoretical model, it was asked: In which activities of Physical Education the postural grounding is required? To collect data, a protocol of observation was developed specifically for the study, besides the semi-structured interview. Analyzing the results through the categorical content analysis of Bardin, it was concluded that therapeutic postures systematized in the Bioenergetics Analysis are experienced in Physical Education classes through activities that require erect posture, not rigid, equilibrated spine, knee joints slightly flexed, body weight on the rounded part of the feet, forward, centering on the abdomen and the ground movements that tend to move up and down with balance, to receive , release , trap, dribble, pass or kick a ball, or even to advance in space in games like basketball and soccer and in the activities of jump rope, wheelbarrow and catch the dragon&#8223;s tail, for example, developing the grounding. In this process, to have a higher level of consciousness and more assertive response, teachers need intentional interventions in educational planning, which are suggested in this work. / O objetivo deste estudo foi de analisar o grounding postural, entendendo-o como experiência psicocorporal de contato com o próprio corpo (propriocepção), com o solo e com a realidade, em atividades nas aulas de Educação Física Escolar com discentes de faixa etária entre 10 e 13 anos, de ambos os sexos, estabelecendo uma aproximação entre tais atividades e os princípios bioenergéticos. Pelo modelo teórico da Análise Bioenergética, o grounding corresponde ao processo de autossustentar-se com equilíbrio e capacidade de autoexpressão, processo em que o indivíduo desenvolve o contato consigo próprio, com o espaço, com sua realidade interna e externa, em nível físico, simbólico e afetivo. Tal processo promove uma coesão entre o movimento, o sentimento e a expressão e uma coerência entre o funcionamento psíquico e o corporal. A partir desse modelo teórico, questionou-se: Em quais atividades na Educação Física Escolar o grounding postural é solicitado? Para a coleta dos dados, utilizou-se um protocolo de observação elaborado especificamente para o estudo, além da entrevista semiestruturada. Analisando os resultados através da análise de conteúdo categorial de Bardin, foi possível concluir que posturas terapêuticas sistematizadas na Análise Bioenergética são vividas nas aulas de Educação Física através de atividades que requerem postura ereta, não rígida, coluna equilibrada, articulação dos joelhos ligeiramente fletidas, peso do corpo na parte arredondada dos pés, à frente, centramento no abdômen e de movimentos que tendem ao chão para subir e descer com equilíbrio, para receber, lançar, interceptar, quicar, passar ou chutar uma bola, ou, ainda, para avançar no espaço em jogos como o basquete e o futebol e nas atividades de pular corda, de carrinho de mão e de pega rabo, por exemplo, desenvolvendo o grounding. Nesse processo, para haver um nível de conscientização mais elevado e respostas mais assertivas, os docentes precisam de intervenções intencionais no planejamento didático as quais são sugeridas neste trabalho

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / A obesidade, doença resultante do acúmulo excessivo de gordura corporal, é importante fator de risco para diabetes mellitus tipo 2, dislipidemias e doenças cardiovasculares, doenças de alta prevalência em todo o mundo. O processo de transição nutricional decorrente da globalização contribuiu para o crescente número de indivíduos com obesidade, principalmente pela modificação nos hábitos alimentares da população, com ampla inclusão de produtos industrializados ricos em gordura saturada, sal e açúcar, denominada dieta ocidental. Os mecanismos pelos quais a obesidade induzida por dieta leva ao desenvolvimento de doenças cardiovasculares ainda não estão completamente esclarecidos na literatura, porém sabe-se que a obesidade leva ao comprometimento da função cardíaca e do metabolismo energético, aumentando a morbidade e mortalidade. Em grande parte dos estudos relacionados à obesidade, o metabolismo energético celular comprometido associa-se à disfunção mitocondrial. Neste contexto, torna-se importante avaliar a função mitocondrial na obesidade, visto que as mitocôndrias são organelas com funções-chave no metabolismo energético. No presente estudo, avaliamos inicialmente o efeito obesogênico da dieta ocidental em camundongos Swiss por 16 semanas a partir do desmame. Para tal, analisamos a ingestão alimentar, evolução da massa corporal, Índice de Lee, peso das gorduras epididimal e retroperitoneal, peso e morfologia do fígado, relação entre o peso do fígado/massa corporal, peso do ventrículo esquerdo (VE)/massa corporal, glicemia de jejum e teste intraperitoneal de tolerância à glicose. Avaliamos também o consumo de oxigênio das fibras cardíacas através da respirometria de alta resolução. Além disso, o conteúdo das proteínas envolvidas no metabolismo energético: Carnitina Palmitoil Transferase 1 (CPT1), proteína desacopladora 2 (UCP2), Transportadores de glicose 1 e 4 (GLUT1 e GLUT4), proteína quinase ativada por AMP (AMPK), proteína quinase ativada por AMP fosforilada (pAMPK), receptor de insulina &#946; (IR&#946;) e substrato do receptor de insulina 1 (IRS-1) foi determinado por western blotting. Nossos resultados confirmaram o caráter obesogênico da dieta ocidental, visto que os camundongos submetidos a esta dieta (GO), apresentaram-se hiperfágicos (P<0,001) e obesos (72,031,82, P<0,001), com aumento progressivo no ganho de massa corporal. Além do aumento significativo dos parâmetros: Índice de Lee (362,902,44, P<0,001), gorduras epididimal e retroperitonial (3,310,15 e 1,610,11, P<0,001), relação entre o peso do fígado/massa corporal (0,060,003, P<0,001) e peso de ventrículo esquerdo (VE)/massa corporal (0,080,002, P<0,01), hiperglicemia de jejum (192,1014,75, P<0,01), intolerância à glicose (P<0,05, P<0,01) e deposição ectópica de gordura no fígado. A respirometria de alta resolução evidenciou disfunção mitocondrial cardíaca no grupo GO, com reduzida capacidade de oxidação de carboidratos e ácidos graxos (P<0,001) e aumento do desacoplamento entre a fosforilação oxidativa e a síntese de ATP (P<0,001). Os resultados de western blotting evidenciaram aumento nos conteúdos de CPT1 (1,160,08, P<0,05) e UCP2 (1,080,06, P<0,05) e redução no conteúdo de IRS-1 (0,600,08, P<0,05). Não houve diferença significativa nos conteúdos de GLUT1, GLUT4, AMPK, pAMPK, pAMPK/AMPK e IR&#946;. Em conclusão, o consumo da dieta ocidental resultou no desenvolvimento de obesidade com disfunção mitocondrial associada a alterações no metabolismo energético. / Obesity, a disease resulting from excessive accumulation of body fat is a risk factor for type 2 diabetes, dyslipidemia and cardiovascular diseases, which are of high prevalence worldwide. Nutritional transition, a process associated with globalization, has contributed to growing obesity, mainly by changing eating habits of the population, with broad inclusion of industrial products high in saturated fat, salt and sugar, the called Western diet. The mechanisms by which diet-induced obesity leads to cardiovascular disease are not completely understood, but it is known that obesity leads to impairment of cardiac function and energy metabolism, increasing morbidity and mortality. In most obesity studies, the related cellular energy metabolism is compromised associated with mitochondrial dysfunction. In this context, it becomes important to asses mitochondrial function in obesity, since mitochondria are organelles with key roles in energy metabolism. In the present study, we evaluated the effect of the Western diet in Swiss mice for 16 weeks from weaning. We analyzed the food intake, changes in body weight, Lee index, weight of epididymal and retroperitoneal fat, weight and morphology of the liver, the ratio of liver weight /body weight, weight of the left ventricle (LV)/body weight , fasting plasma glucose and intraperitoneal glucose tolerance test. We also evaluated the oxygen consumption of cardiac fibers by high-resolution respirometry. Furthermore, proteins content involved in energy metabolism: carnitine palmitoyl transferase 1 (CPT1), uncoupling protein 2 (UCP2), glucose transporters 1 and 4 (GLUT1 and GLUT4), AMP-activated protein kinase (AMPK), AMP-activated protein kinase phosphorylated (pAMPK), insulin receptor &#946; (IR&#946;) and insulin receptor substrate 1 (IRS-1) was determined by western blotting. Our results confirmed the obesogenic role of the Western diet. Thus, mice subjected to Western diet (WG), presented hyperphagia (P<0.001) and obesity (72.031.82, P<0.001), with a progressive increase in body mass gain. Also, the WG group compared to control had statistically significant increase of the all parameters studied: Lee index (362.902.44, P<0.001), epididymal and retroperitoneal fat (3.310.15 and 1.610.11, P<0.001), ratio of liver weight/body weight (0.060.003, P<0.001) and weight of the left ventricle (LV)/body weight (0.080.002, P<0.01), fasting hyperglycemia (192.1014.75, P<0.01), glucose intolerance (P<0.05, P<0.01) and ectopic fat deposition in liver. High-resolution respirometry showed cardiac mitochondrial dysfunction in the WG group, with reduced capacity of oxidation of carbohydrates and fatty acids and increased uncoupling between oxidative phosphorylation and ATP synthesis. Western blotting results revealed an increase in CPT1 (1.160.08, P<0.05) and UCP2 (1.080.06, P<0.05) content and reduction in IRS-1 content (0.600.08, P<0.05). There was no statistically significant difference in the GLUT1, GLUT4, AMPK, pAMPK, pAMPK/AMPK and IR&#946; content. In conclusion, the Western diet consumption resulted in the development of obesity with mitochondrial dysfunction associated to alterations in energy metabolism.

Le mécanisme de régulation des enzymes à travers les changements conformationnels est un processus clé dans le contrôle du fonctionnement cellulaire. Cette thèse est focalisée sur l’étude de trois complexes protéiques qui reflètent comment l’activité de protéines peut être est régulée par différents effecteurs. Pour cela, différentes spectroscopies ont étaient utilisées pour suivre les changements conformationnels des structures secondaire et tertiaire d’une protéine. La première protéine d’intérêt est PDZ1 de MAGI-1, impliquées dans la signalisation cellulaire. Ce domaine d’échafaudage est connu d’interagir avec la protéine E6 de HPV16. Il était démontré que les différents états conformationnels et leurs affinités vis-à-vis le C-terminal de la protéine virale sont régulées par la dynamique des liaisons hydrogène formées par un réseau qui connecte des acides aminés localisés dans les trois domaines de la protéine. Ces résultats suggère que les différences d’affinités sont directement corrélées aux liaisons hydrogène, ce qui mène à conclure que la pathogénicité et la prévalence d’un virus particulier comme le HPV16 sont liées à son habilitée à former un réseau de liaison hydrogène très solide comparé au substrat naturel. La deuxième protéine d’intérêt est une protéine modèle qui représente un petit prototype du changement conformationnel observé dans des protéines plus complexes. Il s’agit d’un peptide court capable de coordonner le cuivre. Ce n’est autre que le peptide β-amyloïde, connu d’être impliqué dans la maladie d’Alzheimer. L’objectif ici est de décrire l’effet des ligands histidine lors de la réduction du cuivre, qui est une réaction électrochimique critique pour le développement d’Alzheimer. La spectroscopie IRTF différentielle a montré deux sphères de coordination pour le Cu(I) et le Cu(II). Les majeurs changements spectraux sont dominés par les vibrations de l’imidazole des différentes histidines (His6, His13 et His14) ainsi que la contribution des résidus Asp1 et Tyr10. Les modifications de la géométrie de coordination peuvent être la cause de la dépendance-pH de l’agrégation du peptide observée en présence du Cu(I). Pour cela, il est possible de suggérer que la formation des fibrilles observées chez les patients d’Alzheimer n’est pas seulement stimulée par la présence du cuivre même mais elle est fortement affectée par ses réactions rédox.La dernière protéine d’intérêt est une métalloprotéine, la NADH:ubiquinone oxidoréductase (complexe I), qui joue un rôle majeur dans la bioénergétique cellulaire. Cette protéine contient plusieurs centres Fe-S et une flavine et son activité est régulée par l’énergie produite par la liaison avec un substrat ainsi que le transfert d’électrons de ces cofacteurs. Les vibrations métal-ligands de ces cofacteurs à l’état oxydé et à l’état réduit sont décrites ici. En utilisant l’électrochimie couplée aux spectroscopies IRTF, Raman de résonance et de fluorescence, les investigations sur le complexe I ont conduit à conclure que les propriétés des centres métalliques sont largement influencées par l’environnement proche. De plus, les changements conformationnels de la protéine ont un effet considérable sur les propriétés rédox et par la même, sur le bon fonctionnement de la protéine. Par ailleurs, la mutagenèse dirigée était utilisée pour étudier les propriétés des centres N1a et N2. A part des cofacteurs métalliques, cette étude a montré l’existence d’un nouveau cofacteur, une quinone localisée proche du domaine membranaire.[...] / The mechanism of enzyme regulation through conformational changes is a key pattern in governing cell behavior. In this thesis the focus is on three protein complexes that reflect how protein activity can be regulated by different effectors. Different spectroscopic techniques, like IR and Raman spectroscopy, were used is order to follow the secondary and tertiary conformational changes in protein structure to identify their roles. The first protein of interest was PDZ1 from MAGI-1, involved in cellular signaling. This scaffold domain is known to interact with the E6 protein from HPV16. It was demonstrated that the different conformational states and their affinities to the C-terminus of the viral protein is regulated by the dynamics of the hydrogen bonding network formed by the connection of specific amino acids in three regions of the protein. Study of mutations around the C-terminal area of the protein and the βC strand were performed; demonstrating that both regions are crucial for assembly of the hydrogen bonding network to stabilize the substrate binding. These results leads to conclude that the pathogenicity and prevalence of a particular virus like HPV16 is in its ability to build a stronger hydrogen bonding network in comparison to the natural binder. The allosteric model and the “shift population” model agree that, upon binding, conformational changes distant from a carboxylate binding group might be the key to understanding the binding dynamics between the PDZ domains and the viral proteins.The second protein of interest was a model that constitutes a small scale prototype of the conformational changes observed in more complex proteins; it is a short Copper-binding peptide, the amyloid-beta peptide, known to beinvolved in Alzheimer’s disease. The objective with this model was to describe the effect of histidine ligands in the metal centers upon Copper (Cu) reduction, a key electrochemical reaction in the development of Alzheimer’s. FTIR difference spectroscopy showed two different spheres of coordination for Cu(II) and Cu(I). The major changes in the structure are dominated by the contribution of the imidazole ring of His residues (His6, His13 and His14), in addition to Asp1 and Tyr10 residues. Changes in the coordination geometry could be key to the pH-dependency of the aggregation observed in the presence of Cu(I). Accordingly, it can be suggested that the formation of the fibrils observed in Alzheimer’s patients is not only triggered by the presence of Cu but it is strongly affected by its redox state. The last system of interest was a metalloprotein, the NADH:ubiquinone oxidoreductase (complex I), which plays a key role in the cellular bioenergetics. This protein bears several Fe-S clusters and one flavin and its activity is regulated by the energy produced by a bound substrate and the electron transfer of its cofactors. The metal ligand-vibrations of the cofactors are described in their oxidized and reduced states. Using electrochemistry coupled to FTIR, Resonance Raman and Fluorescence spectroscopies, the investigation of complex I led to the conclusion that the properties of the metal centers are dictated, to a large extent, by their surrounding environment. [...]

[pt] O mercúrio usado no garimpo do ouro na região amazônica é liberado para a atmosfera, solo e rios. Uma vez na atmosfera, o metal é oxidado e imediatamente se deposita. Na água, ocorre a transformação para o metilmercúrio principalmente pela ação de microrganismos. A formação do metilmercúrio aumenta a dispersão e biodisponibilidade do elemento no ambiente aquático. O metilmercúrio pode ser incorporado pelo plancton entrando, assim, na cadeia alimentar. A concentração do metal aumenta a medida que se ascende nos níveis tróficos da cadeia, atingindo os valores mais elevados em peixes carnívoros como o tucunaré. Dessa forma, as emissões de mercúrio provocam a contaminação dos recursos naturais e aumentam os riscos para a saúde dos consumidores habituais de pescado. O objetivo deste trabalho é testar um modelo de bioacumulação de mercúrio em peixes para estimar concentrações em predadores de topo da cadeia alimentar. O modelo pode ser usado como ferramenta para a gestão ambiental de ecossistemas aquáticos potencialmente contaminados com mercúrio. Este objetivo foi atingido através da combinação dos modelos de balanço de massa de Trudel e bioenergético de Wisconsin, aplicados em espécies tropicais do gênero Cichla (tucunaré) da bacia do rio Tapajós. O modelo bioenergético de Wisconsin foi usado para determinar as taxas de consumo de alimento a partir de dados de crescimento estimados. Os parâmetros usados nos modelos foram obtidos na literatura. A habilidade da modelagem na predição dos teores de mercúrio em tucunarés foi avaliada através da comparação com dados de campo obtidos nos anos 1992 e 2001, no rio Tapajós e no sistema de lagos Maicá. Os melhores resultados foram alcançados para os espécimes coletados no ano 1992, o que parece estar relacionado com uma melhor estimativa da concentração de mercúrio no alimento neste ano. / [en] The mercury used in the artisanal mining (garimpo) of gold in the Amazon region is emitted to the atmosphere, soil and rivers. Once in the atmosphere, the metal is oxidized and immediately deposited. In the water, the transformation to methylmercury takes place mostly due to the action of microorganisms. The formation of methylmercury increases the dispersion and bioavailability of the element in the aquatic environment. The methylmercury can be assimilated by the plankton and enters the food chain. The concentration of the metal increases further up in the trophic levels of the chain and reaches the highest values in carnivorous fishes like tucunaré. Thus, the mercury emissions cause the contamination of natural resources and enhance the risks to the health of regular fish consumers. The objective of this work is to test a model for bioaccumulation of mercury in fishes. The model calculates concentrations in top predators of the food chain and can be used as a tool for the management of aquatic ecosystems potentially contaminated with mercury. This objective was accomplished through the combination of the Trudel mass balance and Wisconsin bioenergetics models, applied to tropical species of the Cichla (tucunaré) genre of the Tapajós river basin. The Wisconsin bioenergetics model was utilized to determine the rates of food consumption from estimated fish growth data. The parameters used in the models were found in the literature. The ability of the models to predict mercury contents in tucunarés was evaluated by comparison with the field data, obtained in 1992 and 2001, in the Tapajós River and in the Maicá lakes. The best results were attain ed for specimens collected in 1992 what seems to be related to a better estimate of mercury concentration in the food in this year.

Au cours de ces deux dernières décennies, la culture du pétoncle (Argopecten purpuratus) s’est développée dans les baies côtières péruviennes. La disponibilité trophique liée au système d’upwelling est favorable à la production du pétoncle. Cependant, les côtes péruviennes sont également connues pour présenter une forte variabilité environnementale surtout en domaine océanique. Bien que les élevages du pétoncle soient vulnérables aux aléas de production (mortalité, croissance faible), la variabilité environnementale dans les baies côtières du Pérou et ses effets sur la croissance, la reproduction et survie de cette ressource socialement sensible ont été peu étudiées. La baie de Paracas au Pisco-Pérou est une zone traditionnelle de culture du pétoncle où des hauts et des bas productifs liés aux conditions environnementales ont été enregistrés au long de son histoire. Dans le but d’approfondir nos connaissances sur cette problématique, cette étude se pose sous trois approches : (1) l’observation in situ, (2) l’expérimentation en physiologie et (3) la modélisation du bilan énergétique de A. Purpuratus. Un suivi environnemental mené dans la baie de Paracas montre que la variabilité océanographique peut être importante, en particulier pendant l’été. Des variations de température de 8°C et des conditions oxiques allant de la sursaturation à l’anoxie (absence d’oxygène) dans le cours d’une journée ont été observées. L’enregistrement haute fréquence a permis de révéler une exposition chronique, sévère et prolongée de la baie de Paracas aux conditions hypoxiques. Les pétoncles cultivés sur le fond, où l’exposition à l’hypoxie était importante (47% du temps observé) ont montré une croissance et les conditions de reproduction plus faibles. Cependant, au cours de l’été, les événements hypoxiques prolongés et sévères ont touché les deux profondeurs de culture- les pétoncles cultivés en suspension comme sur le fond-, causant des pertes de poids de tissu somatique ainsi que l’arrêt de la reproduction. Durant les expériences en laboratoire, les pétoncles ont montré une importante capacité à réguler leur respiration face à la diminution de la saturation en oxygène jusqu’à 24%. De manière surprenante, nous avons trouvé que cette espèce est capable de maintenir une filtration, quoique diminuée, même à des saturations en oxygène basses (5%). Sur la base des réponses physiologiques du pétoncle face à l’hypoxie et le rendement énergétique moindre du métabolisme anaérobie par rapport au métabolisme aérobie, nous faisons l’hypothèse d’une diminution de l’ensemble du métabolisme à des saturations en oxygène en dessous de la capacité de régulation de l’espèce. Des simulations d’un modèle incluant cette restriction énergétique (sur les flux d’assimilation et de mobilisation de la réserve) en conditions d’hypoxie parviennent à reproduire avec succès les observations de terrain effectuées dans la baie de Paracas : une plus grande exposition à l’hypoxie a pour conséquence une croissance réduite et un arrêt de la reproduction. Alors que le pétoncle possède des adaptations physiologique /métaboliques pour faire face à des conditions limitantes en oxygène, la croissance et la reproduction peuvent être compromises, affectant ainsi la productivité des cultures de cette espèce (cela en fonction de la fréquence, durée et intensité de l’hypoxie). Les résultats des observations, des expériences et des simulations réalisées lors de cette étude fournissent des informations utiles pour mieux gérer la culture de pétoncle péruvien. Sur la base de ces travaux, des estimations de capacité de charge des baies, et des évaluations de zones et profondeurs favorables pour la culture de ces pétoncles pourront être réalisées. / During the past two decades, the scallop (Argopecten Purpuratus) culture developed in the Peruvian coastal bays. The trophic availability linked to the upwelling system supports the production scallop. However, the Peruvian coasts are also known to have a high environmental variability especially in oceanic domain. Although scallop farms are vulnerable to production hazards (mortality, low growth), environmental variability in coastal bays of Peru and its effects on growth, reproduction and survival of this socially sensitive resource have been poorly studied. Paracas Bay in Pisco Peru is a traditional farming area where scallop highs and lows in productivity related to environmental conditions were recorded throughout its history. In order increase our knowledge on this issue, this study arises from three approaches : (1) observation in situ, (2) experimental physiology and (3) modelling of the energy budget of A. Purpuratus. An environmental monitoring conducted in the Paracas Bay shows that the oceanographic variability can be important, especially during the summer. Temperature variations of 8°C and oxic conditions ranging from supersaturation to anoxia (absence of oxygen) in the course of a day were observed. The high frequency monitoring has revealed a chronic, severe and prolonged hypoxic condition in Paracas Bay. Scallops grown on the bottom, where exposure to hypoxia was important (47% of the observed time) showed lower growth and reproductions conditions. However, during the summer, prolonged and severe hypoxic events affected both deep culture – scallops grown in suspension and on bottom- causing weight somatic tissue losses and cessation of reproduction. During the laboratory experiments, scallops showed significant ability to regulate their oxygen uptake face to decreased oxygen saturation up to 24%. Surprisingly, we found that this species is able to maintain filtration, although diminished, even at low oxygen saturations (5%). Based on the physiological responses of the Peruvian scallops face to hypoxia and the energy performance aerobic end anaerobic metabolism ; it is hypothesized that there exist a restriction in the energy flow available for metabolism at oxygen saturations below the regulation capacity of the organism. Model simulations including this energy restriction (on assimilation and reserves mobilization fluxes) against hypoxia can reproduce successfully field observations of Paracas Bay : greater exposure to hypoxia results in a reduced growth and reproductive conditions. Although the scallop has physiological adaptations/metabolism to deal with limited oxygen conditions, growth and reproduction can be compromised, affecting culture productivity of this species (according to the frequency, duration and intensity hypoxia). The results of observations, experiments and simulations obtained during this study provide useful information to better manage of Peruvian scallop cultures (ex. Load capacity estimates in the bays, evaluations of adequate areas/depths for culture, etc.).

Cancer cells have been known for some time to have very different metabolismas compared to that of normal non proliferating cells. As metabolism is involvedin almost every aspect of cell function, there has been a recent resurgence ofinterest in inhibiting cancer metabolism as a therapeutic strategy. Inhibitors thatspecifically target altered metabolic components in cancer cells are being developedas antiproliferative agents. However, many such inhibitors have not progressedinto the clinic due to limited efficacy either in vitro or in vivo. In this study weexplore the hypothesis that this is often due to the robustness of the metabolicnetwork and the differences between individual cancer cell lines in their metaboliccharacteristics. We take a systems biology approach. We investigate the cellular bioenergetic profiles of a panel of five non-small celllung cancer cell lines before and after treatment with a novel inhibitor of theglutaminase-1 (GLS1) enzyme. Additionally, we explore the effects of this inhibitoron intracellular metabolism of these cell lines as well as on the uptake and secretionof glucose, lactate and amino acids. To be able to do the latter robustly, wehad to modify the experimental assay considerably from procedures that seemto be standard in the literature; using these earlier procedures the metabolicenvironment of the cells was highly variable, leading to misleading results onthe metabolic effects of the inhibitor. We reduced cell density, altered mediumvolume and changed the time-window of the assay. This led to the cells growingexponentially, appearing indifferent to the few remaining changes. In this newassay, the metabolic effects of the glutaminase inhibitor became robust. One of the most significant results of this study is the metabolic heterogeneitydisplayed across the cell line panel under basal conditions. Differences in themetabolic functioning of the cell lines were observed in terms of both theirbioenergetic and metabolic profile. The amount of respiration attributed tooxidative phosphorylation differed between cell lines and respiratory capacity wasattenuated in most cells. However, the rate of glycolysis was similar betweencell lines in this assay. These results suggest that the Warburg effect arisesthrough a greater diversity of mechanisms than traditionally assumed, involvingvarious combinations of changes in the expression of glycolytic and mitochondrialmetabolic enzymes. The effects of GLS1 inhibition on cellular bioenergetics and metabolism alsodiffered between cell lines, even between resistant cell lines, indicating that theremay also be a diversity of resistance mechanisms. The metabolomic response ofcell lines to treatment suggests potential resistance mechanisms through metabolicadaptation or through the prior differences in the metabolic function of resistantcell lines. Part of the metabolome response to GLS1 inhibition was quite specificfor sensitive cells, with high concentrations of IMP as the strongest marker. Our results suggest that the metabolome is a significant player in what determinesthe response of cells to metabolic inhibitors, that its responses differ between cancercells, that responses are not beyond systems understanding, and that thereforethe metabolome should be taken into account in the design of and therapy withanti-cancer drugs.

A indústria biotecnológica vem ganhando destaque em função das negativas atreladas ao uso de recursos fósseis. Nesse cenário, o Brasil se destaca por seu programa de produção de bioetanol bem estabelecido e pelo uso de cana-de-açúcar como matéria prima barata. O presente trabalho construiu Saccharomyces cerevisiae transgênicas para aprodução de compostos de interesse econômico cuja biossíntese consome energia livre (ATP). Para tanto, a expressão de proteínas heterólogas e engenharia evolutiva foram realizadas em levedura de modo que a produção de determinados compostos se torne energicamente viável. / The biotechs industry is a growing field since fossil resources are being attached to ecological and geopolitical constraints. In this scenario, Brazil has a major role due to its large experience in the bioethanol industry and sugarcane use as a cheap feedstock. The aim of this work is to optimize Saccharomyces cerevisiae allowing them to occupy a new niche: the production of economically valuable chemicals that require cellular free energy (ATP) on their biosynthesis. In this context, heterologous protein expression and evolutionary engineering were done. Therefore, this work will potentially contribute to make certain energy demanding chemicals production economically viable.

Thesis (PhD (Chemical Engineering))--Cape Peninsula University of Technology, 2019 / The agro-processing industry is currently facing losses due to microbial spoilage of agricultural produce and associated value-added products such as beverages. Decay and undesired fermentation of fruit and beverages by fungal, yeast and bacterial spoilage organisms are among the major contributors of product losses in the food industry. When looking at the different level of food spoilage, it is common to find different spoilage organisms occurring in the same food item; which usually requires food producers to utilise a mixture of synthetic preservatives for spoilage organism control. Some of the synthetic chemical compounds with growth inhibition properties that have been used in food preservation are sulphur dioxide, benzoic, lactic, sorbic and acetic acid. These compounds act against a variety of spoilage microorganisms. In post-harvest control of fungi, triazoles, hydroanilide fenhexamid, dicarboximides and succinate dehydrogenase are also being used. Some spoilage organisms have been found to be resistant to the use of synthetic chemical preservatives which usually favour the use of higher dosage of preservatives in food. The use of synthetic chemicals as preservative and as postharvest control agents has been found to present serious health risks such as cardiovascular diseases, muscles and stomach pains, eyesight and skin damages and impairment of brain functions. The problem posed by the current use of synthetic chemicals in food put pressure on food producers and exporters to seek alternatives that will allow for the eradication of the use of synthetic chemicals as preservative in beverages and as postharvest control agents on fruits. Yeasts have been found to have the ability to grow at a faster rate on cheap media and to colonise dried surfaces rapidly. It has also been found that yeasts produce extracellular compounds of proteinaceous and volatile organic nature with growth inhibition properties against spoilage organisms. The current findings lack some engineering concept that could assist in the design of a production system for high scale production of biopreservation compounds from yeasts. The availability of a cost effective production media, the growth and production kinetics data using a cheaply available nutrient sources as well as the biological thermodynamic data are some of the gaps in biopreservation bioprospecting. Although several yeasts have already been studied to have great inhibition properties against fruit fungal pathogens, it was still unclear what was the minimum inoculum dose to be able to have a fungistatic and fungicidal effect on the growth of fruit spoilage organisms. The concept of combination of biopreservatives and the interaction effect of their biopreservation activity against consortia of spoilage organisms has also been lacking. As an attempt to seek alternatives to the use of synthetic chemicals as preservatives or postharvest control agents, Candida pyralidae Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 strains were assessed for antimicrobial activity against spoilage yeasts (Dekkera bruxellensis, Dekkera anomala, Zygosaccharomyces bailii) and spoilage fungi (Botrytis cinerea, Colletotrichum acutatum and Rhizopus stolonifer). As alternative to refined media, a cost effective approach was explored whereby the use of agro-waste, i.e. grape pomace extracts (GPE), as production medium for biopreservation compounds, was studied. Production kinetics using modified existing models, subsequent to optimization using response surface methodology (RSM) for biopreservation compounds production was studied for the three biocontrol yeasts using GPE broth as the fermentation medium. The evaluation of the interaction study between mixtures of crude biopreservatives against consortia of common spoilage organisms present in beverages was also conducted by producing the crude biopreservation compounds separately from yeasts and then formulating growth inhibition combinations (GICs); GIC 1 (Candida pyralidae Y1117 and Pichia kluyveri Y1125); GIC 2 (C. pyralidae Y1117 and P. kluyveri Y1164), GIC 3 (P. kluyveri Y1125 and Pichia kluyveri Y1164); GIC 4 (C. pyralidae, P. kluyveri Y1125 and P. kluyveri Y1164). The spoilage organism consortia combinations, i.e. SC1, D. anomala and D. bruxellensis; SC2 (D. anomala and Z. bailii); SC3 (D. bruxellensis and Z. bailii) and SC4 (D. anomala, D. bruxellensis and Z. bailii) were also prepared. This study also investigated the effect of varying inoculum dose (ID) of Candida pyralidae strain Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 on the biocontrol of Botrytis cinerea by contaminating the headspace of the growth medium with a fungal plug subsequent to biotreatment with different initial inoculum dose of the respective biocontrol yeasts. Finally, grape pomace extracts was used as fermentation medium to study the biological thermodynamics of biopreservation compound production from the three biocontrol yeasts. The results obtained demonstrated some interesting results. The antagonistic properties of C. pyralidae and P. kluyveri were observed on cheap solidified medium (grape pomace extracts) as well as on fruits (grapes and apples). These yeasts produced extracellular volatile organic compounds (VOCs) that could be responsible for yeast and fungal growth inhibition. Twenty-five VOCs in the category of alcohols, organic acids and esters were identified by GC-MS. The results of the kinetic study showed that the highest volumetric zone of inhibition (VZI) was 1.24 L contaminated solidified media (CSM) per mL biopreservation compounds used (BCU) when Candida pyralidae Y1117 was inoculated in a pH 3-diluted GPE broth (150 g L−1) incubated at 25 °C for 24 h. Similar conditions were applied for Pichia kluyveri Y1125 and P. kluyveri Y1164, albeit under slightly elongated fermentation periods (up to 28 h), prior to the attainment of a maximum VZI of only 0.72 and 0.76 L CSM mL−1 ACU, respectively. The potential biopreservation compounds produced were identified to be isoamyl acetate, isoamyl alcohol, 2-phenyl ethylacetate and 2-phenyl ethanol. The growth inhibition interaction study showed a variation in growth inhibition proficiency depending on the spoilage organisms or the consortia of spoilage organisms being deactivated. It was then suggested that, a food environment contaminated with a consortium of spoilage organisms can be controlled by employing either the crude biopreservation compounds from individual yeast or those of the following yeast combinations, GIC1-4, which showed a better growth inhibition proficiency against SC1-3. The fungistatic and fungicidal effects on the fungal pathogen were dose dependent. The fungistatic characteristics against Botrytis cinerea were displayed after 7 days when 102-105 cells mL-1 of Candida pyralidae Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 were independently used in-vitro and in-vivo. However, 106-108 cells mL-1 inoculum doses displayed fungicidal characteristics. Additionally, the fungicidal property of yeasts studied was also confirmed on table grape (in vivo studies) using closed jar method. The biological thermodynamic study showed that, dried biomass molecular weight of 28.9 g/C-mol, 29.163 g/C-mol, and 27.176 g/C-mol were obtained for Candida pyralidae strain Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 respectively. The results obtained successfully established useful biological thermodynamic data applicable to the design of adequate biopreservatives production system from yeasts using cheaply available nutrients source.