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.

Bacillus stearothermophilus phosphofructokinase (BsPFK) is a homotetramer that is allosterically inhibited by phosphoenolpyruvate (PEP), which binds along one dimer-dimer interface. The substrate, fructose-6-phosphate (F6P), binds along the other dimer-dimer interface. The different functional forms BsPFK can take when in the presence of F6P and PEP can be described by the following diproportionation equilibrium: XE + EA <--> XEA + E where XE is the enzyme bound to PEP, EA is the enzyme bound to F6P, E represents the apo enzyme, and XEA is the ternary complex formed when both substrate and inhibitor are bound. Currently in the Protein Data Bank (PDB) there are two relevant forms of wild-type BsPFK, the EA form and the X'E form, which represents the enzyme bound to the PEP analog, phosphoglycolate (PGA). When comparing the EA and the X'E structures, a 7° rotation about the substrate-binding interface is observed and is termed the quaternary shift. The current study uses methyl TROSY NMR to examine the different liganded states of BsPFK, and for the first time structural data for the XEA species is shown. In addition, crystallography was used to obtain the first apo structure of BsPFK. To distinguish between changes associated with the quaternary shift and those associated with the intra-subunit tertiary changes, the variant D12A BsPFK was studied using kinetics, crystallography, and NMR. Crystal structures of apo and PEP bound forms of D12A BsPFK both indicate a shifted structure similar to the X'E form of wild-type. Kinetic studies of D12A BsPFK, when compared to wild-type, show a 50-fold diminished F6P binding affinity, 100-fold enhanced binding affinity, and a similar coupling constant. A conserved hydrogen bond between D12 and T156 takes place across the substrate binding interface in the EA form of BsPFK. The variant T156A BsPFK shows similar binding, coupling, and structural characteristics to D12A BsPFK. PEP still inhibits these variants of BsPFK despite the fact that the enzymes are in the quaternary shifted position prior to PEP binding. Therefore the quaternary shift of BsPFK primarily perturbs ligand binding but does not directly contribute to heterotropic allosteric inhibition.

The sources and sinks of energy for transient waves in the Martian atmosphere are investigated, applying diagnostic techniques developed for the analysis of terrestrial baroclinic waves to output from a Mars General Circulation Model. These diagnostic techniques include the vertically averaged eddy kinetic energy and regression analysis. The results suggest that the primary source of the kinetic energy of the waves is baroclinic energy conversion in localized regions. It is also shown that there exist preferred regions of baroclinic energy conversion. In addition, it is shown that downstream baroclinic development plays an important role in the evolution of the waves and in the baroclinic energy conversion process. This is the first time that evidence for downstream baroclinic development has been found for an atmosphere other than the terrestrial one.

The study was aimed to establish the aerobic capacity of women aerobics athletes of different age and different mastership, physiological changes and energetics during competitive activities. The main conlusions are as follows: 1. The aerobic capacity of representatives of aerobic gymnastics is by 25% higher the norm values of girls of similar age but it is considerably (about 35 %)) smaller than the respective indices of athletes developing endurance. The absolute VO2max during continuous incremental treadmill test is 2.5 l/min (95% CI [2.2 – 2.8]; the relative one – 45 ml/kg/min, CI [41.6 – 48.0],the maximum pulmonary ventilation reaches 87 l/min, CI [78.0 – 95.1], and the maximum HR – 190 beats/min, CI [183.6 – 197.0]. The first ventilation threshold VE manifests itself O2 consumption having reached 74% of the maximum wren HR is – 171 beats/min or 90% of the maximum.The maximum and submaximum respiratory gas exchange and HR values during the continuous incremental treadmill test were similar (p>0.05) in groups of aerobic gymnastics with different level of training. 2. The telemetric registration and analysis of respiratory gas and HR has shown that changes in the form of the exponent are typical for all the indices mentioned when after a fast increase at the onset of the exercise they become nearly stabilized. The rate of changes in separate indices is not the same. Thus, the fastest change occur in HR.VO2 changes slower and VE – the slowest with time constant being 17.2... [to full text]