No description available.

Hundreds of wetland bird species use ricelands annually in the Gulf Coast Prairie region of Louisiana and Texas. Much of the original ecosystem was transformed for rice and other crops, cattle ranching, flood control, and other human uses. Flooded production and idled ricelands provide critical foraging habitat for breeding, migrating, and wintering wetland birds. Ricelands in coastal Louisiana and Texas provide approximately 42% of the estimated habitat carrying capacity for wintering waterfowl in this region. In 2010, the Deepwater Horizon oil spill in the Gulf of Mexico prompted enactment of the Migratory Bird Habitat Initiative (MBHI) by USDA Natural Resources Conservation Service. The MBHI provided avian habitat, including flooded ricelands, inland from oil impacted areas. My objectives were to: 1) estimate and model variation in biomass of waste rice and natural seeds as potential waterfowl forage in Gulf Coast Prairie ricelands, 2) estimate and model variation in wetland bird use of ricelands, and 3) conduct sensitivity analyses of bioenergetics models by varying foraging thresholds and true metabolizable energy (TME) values. A growing season of ~270 days allows Gulf Coast rice producers to grow two rice crops (i.e., the second termed ratoon). Waste rice was greatest in production fields with harvested and standing ratoon crops, and natural seed biomass was greatest in idled fields with standing vegetation. Wetland bird species richness and waterbird abundance were greatest in shallowly flooded (1–15 cm) ricelands with sparse vertical vegetation (1–20 cm), and duck abundance was greatest in shallow–intermediately (1–30 cm) flooded ricelands with short vegetation (1–15 cm). Shallowly flooded rice fields containing harvested or standing ratoon crops, and shallowly flooded idled fields with standing vegetation provided abundant potential foods for waterfowl and waterbirds. Bioenergetics models indicated that planners in the Gulf Coast Prairie region may be underestimating riceland habitat requirements for waterfowl by 10,000 ha. Models were most sensitive to changes in seed biomass estimates, and less sensitive to changes in foraging thresholds and TME values. Collectively, these results will facilitate conservation partners to refine models for conserving habitats for waterfowl and other waterbirds in the Gulf Coast Prairie.

Background: Adipose-derived stem/stromal cells (ASCs) isolated from the stromal vascular fraction are a source of mesenchymal stem cells that have been shown to be beneficial in many regenerative medicine applications. ASCs are an attractive source of stem cells in particular, due to their lack of immunogenicity. This study examines differences between mitochondrial bioenergetic profiles of ASCs isolated from adipose tissue of five peri-organ regions: pericardial, thymic, knee, shoulder, and abdomen. Results: Flow cytometry showed that the majority of each ASC population isolated from the adipose tissue of 12 donors, with an n = 3 for each tissue type, were positive for MSC markers CD90, CD73, and CD105, and negative for hematopoietic markers CD34, CD11B, CD19, and CD45. Bioenergetic profiles were obtained for ASCs with an n = 4 for each tissue type and graphed together for comparison. Mitochondrial stress tests provided the following measurements: basal respiration rate (measured as oxygen consumption rate [pmol O-2/min], ATP production, proton leak, maximal respiration, respiratory control ratio, coupling efficiency, and non-mitochondrial respiration. Glycolytic stress tests provided the following measurements: basal glycolysis rate (measured as extracellular acidification rate [mpH/min]), glycolytic capacity, glycolytic reserve, and non-glycolytic acidification. Conclusions: The main goal of this manuscript was to provide baseline reference values for future experiments and to compare bioenergetic potentials of ASCs isolated from adipose tissue harvested from different anatomical locations. Through an investigation of mitochondrial respiration and glycolysis, it was demonstrated that bioenergetic profiles do not significantly differ by region due to depot-dependent and donor-dependent variability. Thus, although the physiological function, microenvironment and anatomical harvest site may directly affect the characteristics of ASCs isolated from different organ regions, the ultimate utility of ASCs remains independent of the anatomical harvest site.

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.

Mon objectif a consisté à élucider à l'échelle moléculaire le fonctionnement des systèmes enzymatiques complexes impliqués dans des processus de conversion d'énergie chez les êtres vivants. Je m'intéresse en particulier à la compréhension de deux étapes clés du fonctionnement commun à un grand nombre de ces systèmes, à savoir (i) les étapes d'interaction de ces complexes avec les quinones membranaires et (ii) les mécanismes catalytiques au niveau des sites actifs à molybdène. Le système modèle que j'étudie est la nitrate réductase A issue de la bactérie E. coli, en collaboration avec l'équipe du Dr. Axel Magalon (LCB, Marseille). Il permet la respiration anaérobie en catalysant la réduction du nitrate en nitrite et joue un rôle important dans le cycle biogéochimique de l'azote. Ma recherche vise en particulier à identifier les facteurs moléculaires qui permettent d'ajuster la réactivité de ces systèmes. Cela nécessite l'obtention d'informations structurales à l'échelle atomique sur ces complexes macromoléculaires. La stratégie utilisée a consisté dans un premier temps à générer des intermédiaires paramagnétiques clefs du fonctionnement de ces systèmes (radicaux semiquinones ou ion MoV). Puis j'ai caractérisé leurs propriétés rédox par potentiométrie suivie par spectroscopie RPE. Enfin, j'ai utilisé les techniques de spectroscopie RPE impulsionnelle à haute résolution, notamment la spectroscopie de corrélation des sous niveaux hyperfins (HYSCORE) pour sonder l'environnement magnétique local de ces intermédiaires à travers la détection des interactions nucléaires hyperfines et quadripolaires qui sont trop faibles pour être visibles par spectroscopie RPE classique. / The aim of my work is to elucidate at the molecular level the structure and the function of enzymes involved in energy conversion processes in living organisms. In particular, it is focused on the understanding of two important steps found in many of these systems, namely (i) their interaction with membrane quinones acting as electron/proton shuttles and (ii) the catalytic mechanism at the molybdenum active site. The nitrate reductase A (NarGHI) from the bacterium Escherichia coli is used as a model for these studies. This membrane-bound complex reduces nitrate into nitrite during anaerobic respiration and plays therefore an important role in the global nitrogen cycle. The goal of my research is mainly devoted to the identification of the molecular factors tuning the reactivity of this system at the two active sites. For this purpose, I mainly relied on the structural characterization of key paramagnetic intermediates e.g. semiquinone radicals or Mo(V) ion using electron paramagnetic resonance (EPR) spectroscopy in combination with rédox potentiometry. High resolution pulse EPR methods, especially Hyperfine Sublevel Correlation (HYSCORE) spectroscopy, were used to probe their local environment through the detection of hyperfine (and eventually quadrupole interactions) to nearby magnetic nuclei that are otherwise too weak to be measurable in conventional continuous wave EPR spectroscopy.

No description available.

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. [...]

The field of bioenergetics deals with the flow and transformation of energy within and between living organisms and their environment. The work presented in this thesis report focuses on cellular respiration and more specifically on the first enzyme of the respiratory chain, NADH:ubiquinone oxidoreductase (Complex I). This was done to clarify details about its function and its implication in disease. First, the creation of a sensor involving the biomimetically immobilized enzyme is presented and probed through a combination of surface enhanced infrared absorption spectroscopy (SEIRAS) and electrochemistry. This sensor is then tested against different substrates and inhibitors. In a second part, the interaction of Complex I with lipids, inhibitors (Zn2+ and NADH-OH) and the role of a Tyrosine residue situated in the NADH binding pocket are investigated through electrochemically induced UV-Vis and FTIR difference spectroscopies. The results gathered through these experiments are then explored under a structural perspective and a coupling mechanism between quinone reduction and proton translocation by Complex I is proposed.

The Kittlitz's murrelet (Brachyramphus brevirostris) is a species of conservation concern over the entirety of its known range, which spans coastal Alaska and northeastern Russia. Concerns about the status of the species have been raised due to evidence of population declines in key breeding areas, low reproductive output, and perceived threats to adult survival. A general lack of information related to vital rates and natural history for this species has hampered efforts to address potential threats and drivers of population decline. This thesis addresses the hypothesis that foraging conditions and nutritional stress may be related to the observed low reproductive output and apparent population declines. I used stable isotope analysis of Kittlitz's murrelet feathers and blood to assess foraging habits during four separate periods across the annual cycle. I also used stable isotope signatures (δ¹⁵N and δ¹³C) in feathers from museum specimens collected in southeastern Alaska during 1907–1984 to investigate potential long-term trends in food habits and foraging ecology. I found that δ¹⁵N progressively increased by 5‰ between the vernal pre-alternate molt and the autumnal pre-basic molt, equivalent to an increase of 1.5 trophic levels for assimilated prey, whereas seasonal patterns in δ¹³C suggest shifts in foraging habitat between breeding and non-breeding periods. These results indicate that the pre-breeding diet was comprised primarily of low trophic level prey from offshore habitats, such as macrozooplankton and/or larval fish. During the summer breeding season, Kittlitz's murrelets gradually switched to consuming higher proportions of planktivorous fish from nearshore habitats. By the post-breeding period, during the pre-basic molt, the diet was comprised almost exclusively of higher trophic level prey, presumably forage fish, from offshore habitats. Based on stable isotope signatures of murrelet feathers from museum specimens, these seasonal patterns were evident during the past century (1907-2009). δ¹³C in feathers grown during pre- and post-breeding (pre-alternate and pre-basic molts, respectively) became significantly more depleted over the last century, however, suggesting either a gradual change in diet and/or foraging habitat or a long-term shift in the isotopic composition of prey. I investigated potential energy constraints on reproduction in Kittlitz's murrelets by constructing a bioenergetics model to estimate energy budgets for breeding adult Kittlitz's murrelets under different scenarios of prey energy content and commuting distance between foraging areas and nest sites. Estimated field metabolic rate (FMR) of breeding Kittlitz's murrelets during the chick-rearing period exceeded the hypothetical maximum sustainable working capacity (MSWC; 4 times basal metabolic rate [BMR]) under empirically derived scenarios of prey energy content and commuting distance. This suggests that, under conditions of low energy content in available prey and/or long commuting distances to inland nest sites, Kittlitz's murrelets would be required to expend energy at a rate that, if maintained over an extended period, could be detrimental to subsequent adult survival and overall fitness. In addition, energy expenditure rates at the high end of the estimated range may exceed the rate at which food energy can be assimilated by adult murrelets. Metabolism of fat reserves, as indicated by mass loss during the breeding season, may be a partial, although limited, solution to periods of high energy demand for breeding adults. This thesis research is the first to indicate that Kittlitz's murrelets rely on distinctly different prey resources during different periods of the annual cycle. The previously unappreciated seasonal complexity of Kittlitz's murrelet foraging ecology offers a new perspective on potential factors limiting survival and reproduction in this species of conservation concern. In addition, my research suggests an adaptive explanation for the low breeding frequency and low reproductive output of Kittlitz's murrelets that is related to the exceptionally high energy expenditure rates required to raise young at nest sites as much as 70 km inland from the coast and up to 2,500 m above sea level. Because of their high level of reproductive effort, Kittlitz's murrelets may be more dependent on the high availability of high-lipid marine prey than other seabirds. / Graduation date: 2012

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.