Dans le contexte actuel des changements globaux, les êtres vivants sont soumis à de nouvelles pressions sélectives dans des environnements modifiés par les activités anthropiques, et nous assistons à l’émergence de pièges évolutifs. Se déplacer peut être appréhendé comme une conséquence de ces changements, mais aussi comme l’opportunité pour un individu, une population ou une espèce, de s’adapter, à diverses échelles spatio-temporelles, en changeant de site d’alimentation, de domaine vital ou d’aire de répartition. Dans mon travail de thèse, je me suis intéressée aux comportements de prospection alimentaire du vautour fauve (Gyps fulvus), appartenant à la guilde fonctionnelle des nécrophages stricts, qui est la plus menacée parmi les oiseaux à l’échelle mondiale. Des plans de conservation ont été mis en place pour enrayer leur déclin, dont certaines mesures de gestion comme le soutien alimentaire (SA) peuvent néanmoins constituer de véritables pièges évolutifs (des sites attractifs sous-optimaux) pour les vautours. A partir de l’analyse des déplacements journaliers à fine échelle d’individus équipés de balises GPS, et par l’étude des domaines vitaux, j’ai mis en évidence des différences intra- et inter-populationnelles en termes de stratégies d’occupation de l’espace et de recherche alimentaire chez les vautours fauves présents dans deux régions françaises où le SA est élevé (Causses) ou faible (Pyrénées). Grâce à de nouvelles méthodes pour quantifier les routines comportementales, j’ai démontré que les visites des vautours aux sites de SA sont peu stéréotypées et routinières dans les Causses, tant au niveau spatial que temporel. Malgré une utilisation de l’espace à large échelle très différente entre les Causses et les Pyrénées, ainsi qu’un budget temps différent (plus longue durée de vol dans les Causses), le budget énergétique diffère peu entre les deux populations. Au-delà du niveau de prévisibilité des ressources – inhérent au SA - j’ai identifié d’autres facteurs influençant vraisemblablement les prises de décision comportementales des individus : l’état motivationnel de l’individu lié à son statut de reproduction, et les conditions aérologiques locales. Inscrit à l’interface entre écologie comportementale et biologie de la conservation, mon travail de doctorat participe à une meilleure compréhension des patrons d’utilisation de l’espace et des processus en jeu à différentes échelles spatio-temporelles chez une espèce nécrophage stricte. Les acteurs de la conservation pourront s’appuyer sur mes résultats et propositions de gestion pour maintenir les comportements naturels des vautours, et à termes, la viabilité des populations. / In the current context of global change, organism are exposed to new selective pressures in their environments modified by human activities, and we observe the emergence of evolutionary traps. Moving can be interpreted as a consequence of these global changes, but also as the opportunity for an individual, a population or a species to adapt, at different spatio-temporal scales, by modifying their feeding sites, home range or distribution area. During my PhD, I was interested in studying the foraging of Griffon vultures (Gyps fulvus) belonging to the functional guild of obligate scavengers, which are the most threatened birds worldwide. Conservation plans have been carried out to limit their decline, proposing management practices such as supplementary feeding (SF) that may constitute an ecological trap (attractive but suboptimal sites) for vultures. Analysing of fine-scale daily movements and home ranges of individuals equipped with GPS devices, I found significant differences of foraging strategies and space use patterns in vultures from two French regions with low vs high SF (Pyrenees vs Causses). Using recent methods to quantify behavioral routines, I demonstrated that vultures visited SF stations in the Causses with low level of routine, both spatially and temporally. In spite of the distinct large-scale movement patterns between the individuals in the Causses and the Pyrenees, as well as different time-budgets (birds spending more time in flight in the Causses), energy expenditure estimated at the population level are quite similar. Beyond the level of resource predictability - inherent to SF - I highlighted other factors likely to influence individuals’ behavioral decision-making: the individual’s motivational state related to its breeding status, and local aerological conditions. At the interface between behavioral ecology and conservation biology, my work should contribute to a better understanding of the space use patterns in an obligate scavenger and the processes involved at different spatio-temporal scales. Conservationist will be able to use my results and management recommendations to maintain the natural behavior of vultures and, finally, populations’ viability.

Direct hydrocarbon fuel cells are fuel cells than use hydrocarbons directly as fuel instead of the most commonly used fuel in a fuel cell, hydrogen. Studies are being done on direct hydrocarbon fuel cells because they have the potential to be energetically more efficient than hydrogen fuel cells. There are many different hydrocarbons that are available to use as a feed stock and each one reacts at different reaction rates. As the current density of a fuel cell is linked to the reaction rate, it is important to know the energetics of an oxidation reaction that is occurring. Density Functional Theory (DFT) is a technique that can be used to predict the energy states of intermediate reaction steps in a given mechanism. The focus of this study is the using DFT to explore the energetics of the oxidation of ethane to ethylene in a nickel-anode catalyst fuel cell. DFT was used in adsorption runs to optimize the geometries beginning (adsorbed ethane) and end (adsorbed ethylene) of the oxidation reaction. DFT was then used to calculate the energy of transition states by varying bond lengths. It was determined the removal of the second hydrogen from the ethyl radical is the most energy intensive step and, thus, the rate limiting step. Hydrogen, ethane, and ethylene were all explored in this study. The heats of adsorption varied from largest to smallest in the order of ethylene, hydrogen, and ethane. It was determined that the heat of adsorption of hydrogen is sufficient to meet the energy requirements for the dissociation reaction. This may help explain why hydrogen reacts so readily in fuel cells. Conversely, the heats of adsorption for the hydrocarbons did not meet the energy requirements for the dissociation reactions. This may help explain why ethane and ethylene react more slowly in a fuel cell as compared to hydrogen. Also, the oxidation of ethane to ethylene requires two large activation energies. These two additional activation energies may help explain why ethylene reacts more readily than ethane in a fuel cell.

In order to protect natural resources and ecosystems at Eglin Air Force Base (EAFB), a strategy must be developed for the containment and/or treatment of explosive contaminants on testing and training ranges under continuous use. Phytoremediation is the direct use of living plants for in situ (in place) remediation of contaminated soil, sludges, sediments, and groundwater through contaminant removal, degradation, or containment. Due to its ability to continuously treat large areas at low cost with low impact to the site, phytoremediation was implemented through a field study at EAFB in order to increase range sustainability.

In keeping with the goals of our laboratory, efforts in this thesis are directed towards improving our understanding, and therefore our ability to calculate, the energetics of protein-ligand interactions. Electrostatic contributions to protein-ligand binding events are poorly understood, and underrepresented in data sets used to parameterize the energetics of protein unfolding and binding. Therefore, the focus in this thesis is placed on ion-protein interactions as model systems that can give insight into the contribution of charge-charge interactions to the enthalpy, entropy, and heat capacity changes associated with binding. In order to measure the energetics of charge-charge interactions, both differential scanning calorimetry and isothermal titration calorimetry are employed. The use of linked equilibria to determine binding energetics for both extremely tight, and extremely weak binding events is described in the context of ligand binding linked to protein unfolding. The implications for drug screening methods based on protein unfolding are discussed. The theoretical development is then used to measure ion binding to proteins in two different systems that exhibit very different ion binding sites and system features. The first system involves anion binding to a protein-protein complex, in which the binding site is formed when the protein-protein complex is formed. Binding of phosphate and sulfate occur with the same energetics, indicating that net charge is not dominating the observed energetics. Further, no salt-dependence to the binding of anions is observed. In the second system ions bind to the active site of a ribonuclease. Again, phosphate and sulfate bind to the ribonuclease with the same energetics, however comparing the energetics of binding for these anions between systems reveals differences in the energetic profiles. Further, in the ribonuclease case, there is a strong salt-dependence observed for the binding of a nucleotide inhibitor. The apparent discrepancies in the observed energetics and salt-dependencies in these systems can be resolved by considering the role of desolvation upon binding as well as the binding site geometries. This analysis leads to important considerations for interpreting an observed salt-dependence to a binding event. Furthermore, it is indicated that the current structure-based energetics calculations underestimate the contributions arising from charge-charge interactions.

Perovskite-type oxides show irrefutable potential for feasible thermochemical solar-driven CO2 conversion. These materials exhibit the exact characteristics required by the low temperature reverse water-gas shift chemical looping process. These properties include structural endurance and high oxygen redox capacity, which results in the formation of numerous oxygen vacancies, or active sites for CO2 conversion. A major drawback is the decrease in oxygen self-diffusion with increasing perovskite particle size. In this study, the La0.75Sr0.25FeO3 (LSF) perovskite oxide was combined with various supports including popular redox materials CeO2 and ZrO2 along with more abundant alternatives such as Al2O3, SiO2, and TiO2, in view of its potential application at industrial scale. Supporting LSF on SiO2 by 25% mass resulted in the largest increase of 150% in CO yields after reduction at 600 °C. This result was a repercussion of significantly reduced perovskite particle size confirmed by SEM/TEM imaging and Scherrer analyses of XRD patterns. Minor secondary phases were observed during the solid-state reactions at the interface of SiO2 and TiO2. Density functional theory-based calculations, coupled with experiments, revealed oxygen vacancy formation only on the perovskite phase at these low temperatures of 600 °C. The role of each metal oxide support towards suppressing or enhancing the CO2 conversion has been elucidated. Through utilization of SiO2, the reverse water-gas shift chemical looping process using perovskite-based composites was significantly improved.

Fish populations are regulated by both external environmental factors, e.g., water quality parameters and habitat, and internal reproductive biology and physiology processes. For many species and populations there is often ample external information, while critical internal, i.e., life-history trait (LHT), information is not available. For this study, I determined LHTs and energy allocation patterns for Epinephelus guttatus (red hind), E. striatus (Nassau grouper), and Mycteroperca venenosa (yellowfin grouper) harvested from The Bahamas. I determined age ranges, and how growth patterns and rates differed among the study species. The maximum ages were: 17, E. guttatus; 22, E. striatus; and 13, M. venenosa. Epinephelus striatus was estimated to have the slowest, while M. venenosa had the fastest growth rate. A gonad histological classification system and the ageing data were used to determine the spawning seasons, sex ratios, size and age of sexual maturation and sex change and gonadosomatic indices (GSIs) for the study species. The peak spawning months were January-February for E. guttatus, December-January for E. striatus and March-April for M. venenosa. The fifty-percent sexual maturity estimates were 235 total length mm (Tlmm) (2.05 year old, yo), 435 Tlmm (4.00 yo), and 561 Tlmm (4.66 yo) for E. guttatus, E. striatus and M. venenosa, respectively. The size and age range of sex change for E. guttatus was between 257-401 Tlmm, ~4-5 years old and between 716-871 Tlmm, ~8-9 yo for M. venenosa. I determined protein and lipid concentrations in muscle and gonad tissues to ascertain energy allocation patterns. For all species and sexes except for female E. guttatus, the proportion of energy delegated to somatic growth declines as a fish grows longer, while reproduction energy allocation increases. The results of each study were compared to previous studies conducted throughout the tropical western Atlantic Ocean, and were related to species-specific ecological and spawning behaviors. The findings of each study highlight that the LHTs of the study species greatly differ and these differences will impact population dynamics and need to be considered for management initiatives. In the final chapter, the effects of fishing on LHTs are reviewed and fishery management options are discussed.

SHAPE-DEPENDENT MOLECULAR RECOGNITION OF SPECIFIC SEQUENCES OF DNA BY HETEROCYCLIC CATIONS by YI MIAO Under the Direction of Dr. W. David Wilson ABSTRACT DB921 and DB911 are biphenyl-benzimidazole-diamidine isomers with a central para- and meta-substituted phenyl group, respectively. Unexpectedly, linear DB921 has much stronger binding affinity with DNA than its curved isomer, DB911. This is quite surprising and intriguing since DB911 has the classical curved shape generally required for strong minor groove binding while DB921 clearly does not match the groove shape. Several biophysical techniques including thermal melting (Tm), circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) have been utilized to investigate the interactions between these compounds and DNA. The structure of the DB921-DNA complex reveals that DB921 binds to DNA with a reduced twist of the biphenyl for better fit of DB921 into the minor groove. A bound water molecule complements the curvature of DB921 and contributes for tight binding by forming H-bonds with both DNA and DB921. Structure-affinity relationship studies of a series of DB921 analogs show that the benzimidazole group is one of the key groups of DB921 for its strong binding to the minor groove. Thermodynamic studies show that the stronger binding of DB921 is due to a more favorable binding enthalpy compared to DB911 even though the complex formation with DNA for these compounds are all predominantly entropically driven. DB921 also has more negative heat capacity change than DB911. The initial studies of inhibition of the interaction between an AT hook peptide of HMGA proteins and its target DNA by a set of diamidine AT-minor groove binders using biosensor-SPR technique show that the inhibitory ranking order is consistent with that of binding affinity and linear-shaped DB921 still has excellent inhibitory effects. These heterocyclic cations rapidly inhibit the binding of DBD2 peptide to the DNA and may only block the specific AT binding of the peptide without hindering the non-specific binding interaction. The results of this project have shown that DB921 represents a new novel effective minor groove binder that does not fit the traditional model and is a potential inhibitor for DNA/protein complexes. INDEX WORDS: Molecular recognition, DNA binding, Minor groove binding, Linear shape, Compound curvature, Binding affinity, Binding kinetics, Thermodynamics, Surface plasmon resonance, Isothermal titration calorimetry, Inhibition

Habitat selection theory presumes that organisms are not distributed randomly in their environments because of habitat-specific differences in reproductive success and survival; unfortunately, many previous studies were either unable or failed to look for evidence of processes shaping nest site selection patterns. Furthermore, little is known about adaptive nest site selection in northern environments where habitats often have little vegetation and time and climatic constraints may be pronounced. Therefore, I investigated patterns of nest site selection by common eider ducks (<i>Somateria mollissima</i>) at an island colony in Canadas Eastern Arctic, and looked for evidence of selective processes underlying these patterns by employing experimental and observational techniques.<p>I characterized physical features of (a) non-nest sites (b) active nest sites and (c) unoccupied nest sites that had been used in previous years. Habitat features that distinguished non-nest sites from unoccupied nest sites were also important in distinguishing between active and unoccupied nest sites during the breeding season. Active nest sites were closer to herring gull (<i>Larus argentatus</i>) nests, farther from the ocean and had organic substrates. In general, habitat features associated with nest use were not strongly associated with success after the onset of incubation. Nests near fresh water ponds were more successful in one study year, but in the other two study years successful nests were initiated earlier and more synchronously than were unsuccessful nests. Common eiders settled to nest first near the geographic centre of the colony, whereas sites near the largest fresh water pond were occupied later; distance to ocean had no observable effect on timing of nesting. Nest density was greater farther from the ocean, but timing of nest establishment did not differ between high and low density plots. <p>I tested whether moss or duck down placed in nest bowls could increase nest establishment, or advance laying date. I placed this extraneous material in bowls before nesting and found no difference in likelihood of nest establishment; however, bowls containing duck down were initiated earlier (or had higher survival) than those containing no nesting material. To investigate the role of nest shelter and microclimate in nest site choices and female body condition, I placed plywood nest shelters over established nests. Temperature probes indicated that artificially-sheltered females experienced more moderate thermal environments and maintained higher body weight during late incubation than did unsheltered females. However, few eiders nested at naturally-sheltered sites, possibly because nest concealment increases susceptibility to mammalian predators. My results suggest that eider nest choices likely reflect trade-offs among selective pressures that involve the local predator community, egg concealment, nest microclimate and energy use.

Structures within very large displacement, mature fault zones, such as the North Branch San Gabriel Fault (NBSGF), are the product of a complex combination of processes. Off-fault damage within a damage zone and first-order geometric asperities, such as bends and steps, are thought to affect earthquake rupture propagation and energy radiation, but the effects are not completely understood. We hypothesize that the rate of accumulation of new damage decreases as fault maturity increases, and damage magnitude saturates in very large displacement faults. Nonetheless, geometric irregularities in the fault surface may modify damage zone characteristics. Accordingly, we seek to investigate the orientation, kinematics, and density of features at a range of scales within the damage zone adjacent to an abrupt 13 degree bend over 425 m in the NBSGF in order to constrain the relative role of the initiation of new damage versus the reactivation of preexisting damage adjacent to a bend. Field investigation and microstructural study focused on structural domains before, within, and after the fault bend on both sides of the fault. Subsidiary fault fabrics are similar in all domains outside the bend, which suggests a steady state fracture density and orientation distribution is established on the straight segments before and after the bend. The density of fractures within and outside the bend is similar; however, subsidiary fault orientations and kinematics are different within the bend relative to the straight segments. These observations are best explained by relatively low rates of damage generation relative to rates of fault reactivation during the later stages of faulting on the NBSGF, and that damage zone kinematics is reset as the host rock moves into the bend and again upon exiting the bend. Consequently, significant energy released during earthquake unloading can be dissipated by reactivation and slip on existing fractures in the damage zone, particularly adjacent to mesoscale faults. Thus, areas of heightened reactivation of damage, such as adjacent to geometric irregularities in the fault surface, could affect earthquake rupture dynamics.

Habitat selection theory presumes that organisms are not distributed randomly in their environments because of habitat-specific differences in reproductive success and survival; unfortunately, many previous studies were either unable or failed to look for evidence of processes shaping nest site selection patterns. Furthermore, little is known about adaptive nest site selection in northern environments where habitats often have little vegetation and time and climatic constraints may be pronounced. Therefore, I investigated patterns of nest site selection by common eider ducks (<i>Somateria mollissima</i>) at an island colony in Canadas Eastern Arctic, and looked for evidence of selective processes underlying these patterns by employing experimental and observational techniques.<p>I characterized physical features of (a) non-nest sites (b) active nest sites and (c) unoccupied nest sites that had been used in previous years. Habitat features that distinguished non-nest sites from unoccupied nest sites were also important in distinguishing between active and unoccupied nest sites during the breeding season. Active nest sites were closer to herring gull (<i>Larus argentatus</i>) nests, farther from the ocean and had organic substrates. In general, habitat features associated with nest use were not strongly associated with success after the onset of incubation. Nests near fresh water ponds were more successful in one study year, but in the other two study years successful nests were initiated earlier and more synchronously than were unsuccessful nests. Common eiders settled to nest first near the geographic centre of the colony, whereas sites near the largest fresh water pond were occupied later; distance to ocean had no observable effect on timing of nesting. Nest density was greater farther from the ocean, but timing of nest establishment did not differ between high and low density plots. <p>I tested whether moss or duck down placed in nest bowls could increase nest establishment, or advance laying date. I placed this extraneous material in bowls before nesting and found no difference in likelihood of nest establishment; however, bowls containing duck down were initiated earlier (or had higher survival) than those containing no nesting material. To investigate the role of nest shelter and microclimate in nest site choices and female body condition, I placed plywood nest shelters over established nests. Temperature probes indicated that artificially-sheltered females experienced more moderate thermal environments and maintained higher body weight during late incubation than did unsheltered females. However, few eiders nested at naturally-sheltered sites, possibly because nest concealment increases susceptibility to mammalian predators. My results suggest that eider nest choices likely reflect trade-offs among selective pressures that involve the local predator community, egg concealment, nest microclimate and energy use.