Thesis (M.Sc.)--Memorial University of Newfoundland, 2005. / Bibliography: leaves 139-147. Also available online.

Thesis (Ph. D.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Flavocytochrome b2 catalyzes the oxidation of lactate to pyruvate. Primary deuterium and solvent kinetic isotope effects have been used to determine the relative timing of cleavage of the lactate OH and CH bonds by the wild type enzyme, a mutant protein lacking the heme domain, and the D282N enzyme. The DVmax and D(V/Klactate) values are both 3.0, 3.6 and 4.5 for the wild type enzyme, flavin domain and D282N enzymes, respectively. The D20Vmax values are 1.38, 1.18, and 0.98 for the wild type enzyme, the flavin domain, and the D282N enzyme; the respective D20(V/Klactate) values are 0.9, 0.44, and 1.0. The Dkred value is 5.4 for the wild type enzyme and 3.5 for the flavin domain, whereas the D2Okred is 1.0 for both enzymes. The V/Klactate value for the flavin domain increases 2-fold at moderate concentrations of glycerol. The data are consistent with the lactate hydroxyl proton not being in flight in the transition state for CH bond cleavage and there being an internal equilibrium prior to CH bond cleavage which is sensitive to solution conditions. Removal of the hydroxyl proton may occur in this pre-equilibrium. Tryptophan 2-monooxygenase catalyzes the oxidative decarboxylation of tryptophan to indoleacetamide, carbon dioxide and water. Sequence alignments identified this enzyme as a member of the L-amino acid oxidase family. The tyrosine and arginine residues in L-amino acid oxidase that bind the carboxylate of o-aminobenzoate are conserved and correspond to Tyr413 and Arg98 in tryptophan 2-monooxygenase. Mutation and characterization of the Y413A, Y413F, R98K and R98A enzymes indicate that these residues are in the active site and interact with the substrate. Deletion of the OH group of Tyr413 increases the Kd for the substrate and makes CH bond cleavage totally rate limiting. The pH V/Ktrp rate profile for the Tyr413 mutant enzymes shows that this residue must be protonated for activity. For both the R98A and R98K enzymes flavin reduction is rate limiting. The Vmax and V/Ktrp pH profiles indicate that the unprotonated form of the substrate is the active form for activity.

This thesis describes the study of the three-dimensional structure and dynamics of the hepatitis B virus (HBV) encapsidation signal, epsilon, by means of nuclear magnetic resonance (NMR) and mutational data. HBV replicates by reverse transcription of an RNA pregenome into the viral DNA genome, which becomes enclosed in viral particles (encapsidation). Epsilon is a stem-loop structure within the RNA pregenome and both the primary sequence and secondary structure of epsilon are strongly conserved, in agreement with its essential function of propagating HBV. Epsilon is therefore a potential target for drug design. Studying the structure of epsilon requires development of new methods in the field of structural biology, as it is such a large RNA. Knowing the structure of epsilon will help to better understand the encapsidation mechanism and priming step of reverse transcription. This will help us in the search for antiviral drugs that block epsilon and prevent the viral reverse transcriptase from binding. NMR spectroscopy is a method that provides detailed structural and dynamical data in solution under natural conditions. However, the size of the molecules that can be studied with NMR is limited. NMR spectra become more and more difficult to interpret as the size of the molecule increases. To circumvent this problem, large RNA molecules can be divided into smaller parts and only the parts essential for NMR studies are selected. The information obtained from these smaller fragments can then be used to determine the structure of the larger molecule. Furthermore, a new method of enzymatically synthesizing nucleoside triphosphates with isotopes suitable for NMR has made it possible to specifically label the RNA molecules. Using this method it is possible to derive highly detailed molecular structures of RNA up to a size of 150 nucleotides. The method of selective isotope labelling was applied to different parts of HBV epsilon. Three RNA fragments of 27 (apical loop), 36 (internal bulge) and 61 (whole epsilon) nucleotides (nt) were synthesized in the unlabelled form. The 27-nt and 36-nt RNAs were also synthesized with (13C, 15N, 1', 3', 4', 5', 5"-2H5)-labelled uridines. The 61-nt sequence was (13C, 15N)-guanidine labelled. This labelling allowed unambiguous assignment of otherwise inaccessible parameters. The unlabelled and labelled RNA sequences provided the necessary data for structure derivation of the whole epsilon. The apical loop of epsilon forms a pseudo-triloop motif. There is only one conformation of the loop that fulfils all the restraints, including experimental chemical shifts. However, the loop adopts several structures that fulfil the experimental distance, torsion angle and residual dipolar coupling restraints. This may reflect true flexibility. Indeed, relaxation studies on the unlabelled and labelled 27-nt sequences show that the residues that show multiple conformations are flexible. This can be an important feature for the recognition and subsequent binding of epsilon to the viral polymerase. The information gained on the HBV encapsidation signal is useful in our understanding of the initiation of replication of the virus. This can in turn contribute to the search for drugs against HBV.

The purpose of this thesis was to experimentally investigate the influence of increasing sulfide concentrations on the 34S isotope enrichment in sulfate during dissimilatory sulfate reduction (DSR). Two independent batch culture experiments with different maximum sulfide concentrations of up to 20 mM in the first and up to 40 mM in the second experiment were conducted using the marine sulfate reducer Desulfobacter latus. A comparison of the results from both experiments revealed a distinct offset towards more positive δ34S(SO42-) values in the 'high-sulfide' experiment, compared to the 'low-sulfide' experiment. While a Rayleigh type fractionation model was able to match the slopes - i.e., enrichment factors - of both experiments, it failed to reproduce the proper y-axis intercept in the 'high-sulfide' experiment. I therefore propose a new fractionation model that allows for a backward flow of ambient H2S into the bacterial cell and a subsequent enzymatically mediated oxidation of H2S to sulfate. The new backward flow increases with elevated H2S concentrations and is described as a first order rate constant. Unlike a Rayleigh type fractionation model, my model explains the slope and y-intercept of both experiments with a single parameter set. The new model with H2S-reflux further suggests that it can be used to determine growth kinetic parameters like the half-saturation constant through δ34S measurements. These findings support the hypothesis of microbially mediated, bi-directional S-fluxes between oxidized and reduced sulfur species. Because the S-transport during DSR appears to be bi-directional, great care must be taken when evaluating culture experiments with a Rayleigh type fractionation model, owing to the fact that an evident S-backward flow violates the prerequisites for applying the Rayleigh model. A variable S-backward flow results in variable enrichment factors which increased from -11 (no H2S) to ≈-17 ‰ (40 mM of H2S) in my experiments. I show for the first time the significance of a bi-directional H2S transport across the cell membrane during DSR and its consequences for the 34S-isotope fractionation in sulfate.

2-(2-mandelyl)thiamin (MTh), the adduct of benzoylformate and thiamin, is an accurate model of 2-(2-mandelyl)thiamin diphosphate, the initial covalent intermediate in the decarboxylation of benzoylformate by benzoylformate decarboxylase (BFDC). The first order rate constant for spontaneous decarboxylation of MTh is about 106 times smaller than the enzymic rate (kcat) for the BFDC reaction. Based on the similarities of MTh and the corresponding enzymic intermediate, as well as the inherent nature of the intermediate, it is not obvious why the enzyme-catalyzed reaction is so much faster. However, earlier studies showed that the decarboxylation of MTh is catalyzed by protonated pyridines and this was proposed to occur through a preassociation mechanism. If this explanation is correct, then the observed 12C/13C kinetic isotope effect (CKIE) will increase in the presence of the catalyst as a more favorable forward commitment is made possible. This provides a specific model for the enzyme-catalyzed process. We developed a technique using headspace analysis and compound specific isotope analysis (CSIA) to determine the CKIE for the decarboxylation of MTh in the presence and absence of pyridinium. We found that the CKIE increases in the presence of the catalyst, as predicted for the preassociation mechanism. In a related study, we investigated the kinetics of decarboxylation of pyrrole-2-carboxylic acid, which was known to be subject to acid catalysis in highly acidic solutions. In the expected mechanism, protonation of the pyrrole ring at C2 destroys the aromaticity of the ring. C-C bond cleavage in the process of decarboxylation will re-establish the aromatic pyrrole. However, the overall reaction rate would not increase as it is counteracted by a larger concentration of the undissociated carboxyl group compared to carboxylate ion necessary for decarboxylation. Since the reaction occurs readily, there must be an alternative pathway for the acid-catalyzed reaction. This can be achieved in an associative mechanism that is initiated by addition of water to the carboxyl group of the carboxyl-protonated reactant. C-C bond cleavage results in formation of pyrrole and protonated carbonic acid, a species that has been recognized as a viable intermediate in related processes. Protonated carbonic acid is spontaneously converted to H3O+ and carbon dioxide. The associative mechanism is consistent with solvent-deuterium kinetic isotope effects and 12C/13C kinetic isotope effects.

An improved ability to assess whether individuals have been added through immigration or natality and lost through emigration or mortality could alleviate several problems in population ecology. Fortunately, advances in stable isotope techniques now allow the movements of individuals to be retraced from tissue values and provide an opportunity to link information about the origins of individuals with demographic rates so that questions about the significance of dispersal can be assessed. I used such an approach by combining feather isotope information with demographic rates derived from capture-mark-recapture of individual mallards (Anas platyrhynchos) breeding in the Canadian aspen parklands, at multiple spatiotemporal scales, to answer questions about population persistence, settling patterns by dispersers, and the fitness of immigrant birds relative to residents.<p> Feather isotope (ä34S, äD, ä15N, and ä13C) values from an independent sample of flightless mallard ducklings sampled from across the mid-continent breeding range was used to validate an existing model used for origin assignments. Spatial resolution analysis within the mid-continent mallard breeding range generally showed a loss in prediction when attempting to assign individuals to more narrowly separated geographic origins among boreal, aspen parkland and prairie regions. For feather äD, spatial resolution may be limited by temporal patterns of local climatic events that produce variability in consumer tissue values. Thus, the use of multiple feather isotope signals would provide more reliable information about the origin of individuals for addressing questions about long-distance dispersal in yearling mallards.<p> Demographic rescue in an apparent population sink near Minnedosa, Manitoba, Canada, was due to elevated survival rates from a highly productive group of nesting female mallards using nest tunnels (i.e., an artificial nesting structure) and recruitment of yearling females having natal origins within the aspen parklands. There was little evidence that immigration by yearling females dispersing long-distances was important to annual population growth rates. Consistently high annual survival rates of adult females using nest tunnels lowered the recruitment rates needed for population stability. While tunnel-origin and within-region recruitment of yearling females were nearly equally important to local population growth rate, fine-scale limitations of isotopic origin assignments prevented further assessment of where recruits originated from within the aspen parkland region.<p> Factors related to breeding area settling patterns of yearling females are not well understood despite implications to local population dynamics. The likelihood that immigrant yearling females would settle in a parkland breeding area was positively correlated with local breeding-pair density and the amount of perennial nest cover, but was negatively correlated with the amount of wetlands. Although these relationships were not well estimated, they are most consistent a hypothesis that females were attracted to breeding sites by conspecific cues rather than avoidance. Immigrants comprised an average of 9% (range: 0 39% over 22 sites) of yearling recruits; most had natal origins in the U.S. prairie pothole region but a non-trivial number originated from the boreal forest, indicating a high degree of connectedness among breeding regions resulting from long-distance natal dispersal.<p> One of the most frequent explanations for strong site fidelity in breeding female ducks is that females benefit from site familiarity. However, evidence for differential reproductive success between immigrant and resident yearling females was weak, On sites with favourable wetland conditions and low breeding-pair densities immigrant females were more likely to breed and nest successfully than were residents whereas under opposite wetland and pair conditions, resident females were favoured. Thus, the costs and benefits of a natal dispersal decision seemed to vary with social context and environmental conditions, and further work is needed to clarify these processes.

The purpose of this thesis was to experimentally investigate the influence of increasing sulfide concentrations on the 34S isotope enrichment in sulfate during dissimilatory sulfate reduction (DSR). Two independent batch culture experiments with different maximum sulfide concentrations of up to 20 mM in the first and up to 40 mM in the second experiment were conducted using the marine sulfate reducer Desulfobacter latus. A comparison of the results from both experiments revealed a distinct offset towards more positive δ34S(SO42-) values in the 'high-sulfide' experiment, compared to the 'low-sulfide' experiment. While a Rayleigh type fractionation model was able to match the slopes - i.e., enrichment factors - of both experiments, it failed to reproduce the proper y-axis intercept in the 'high-sulfide' experiment. I therefore propose a new fractionation model that allows for a backward flow of ambient H2S into the bacterial cell and a subsequent enzymatically mediated oxidation of H2S to sulfate. The new backward flow increases with elevated H2S concentrations and is described as a first order rate constant. Unlike a Rayleigh type fractionation model, my model explains the slope and y-intercept of both experiments with a single parameter set. The new model with H2S-reflux further suggests that it can be used to determine growth kinetic parameters like the half-saturation constant through δ34S measurements. These findings support the hypothesis of microbially mediated, bi-directional S-fluxes between oxidized and reduced sulfur species. Because the S-transport during DSR appears to be bi-directional, great care must be taken when evaluating culture experiments with a Rayleigh type fractionation model, owing to the fact that an evident S-backward flow violates the prerequisites for applying the Rayleigh model. A variable S-backward flow results in variable enrichment factors which increased from -11 (no H2S) to ≈-17 ‰ (40 mM of H2S) in my experiments. I show for the first time the significance of a bi-directional H2S transport across the cell membrane during DSR and its consequences for the 34S-isotope fractionation in sulfate.

2-(2-mandelyl)thiamin (MTh), the adduct of benzoylformate and thiamin, is an accurate model of 2-(2-mandelyl)thiamin diphosphate, the initial covalent intermediate in the decarboxylation of benzoylformate by benzoylformate decarboxylase (BFDC). The first order rate constant for spontaneous decarboxylation of MTh is about 106 times smaller than the enzymic rate (kcat) for the BFDC reaction. Based on the similarities of MTh and the corresponding enzymic intermediate, as well as the inherent nature of the intermediate, it is not obvious why the enzyme-catalyzed reaction is so much faster. However, earlier studies showed that the decarboxylation of MTh is catalyzed by protonated pyridines and this was proposed to occur through a preassociation mechanism. If this explanation is correct, then the observed 12C/13C kinetic isotope effect (CKIE) will increase in the presence of the catalyst as a more favorable forward commitment is made possible. This provides a specific model for the enzyme-catalyzed process. We developed a technique using headspace analysis and compound specific isotope analysis (CSIA) to determine the CKIE for the decarboxylation of MTh in the presence and absence of pyridinium. We found that the CKIE increases in the presence of the catalyst, as predicted for the preassociation mechanism. In a related study, we investigated the kinetics of decarboxylation of pyrrole-2-carboxylic acid, which was known to be subject to acid catalysis in highly acidic solutions. In the expected mechanism, protonation of the pyrrole ring at C2 destroys the aromaticity of the ring. C-C bond cleavage in the process of decarboxylation will re-establish the aromatic pyrrole. However, the overall reaction rate would not increase as it is counteracted by a larger concentration of the undissociated carboxyl group compared to carboxylate ion necessary for decarboxylation. Since the reaction occurs readily, there must be an alternative pathway for the acid-catalyzed reaction. This can be achieved in an associative mechanism that is initiated by addition of water to the carboxyl group of the carboxyl-protonated reactant. C-C bond cleavage results in formation of pyrrole and protonated carbonic acid, a species that has been recognized as a viable intermediate in related processes. Protonated carbonic acid is spontaneously converted to H3O+ and carbon dioxide. The associative mechanism is consistent with solvent-deuterium kinetic isotope effects and 12C/13C kinetic isotope effects.

This thesis investigates the relationships between mercury (Hg) and stable isotope of carbon (δ13C) in marine pelagic zooplankton (Calanus spp., Themisto spp. and Euchaeta spp.) with water mass characteristics in the North Water Polynya (NOW) and in the Mackenzie shelf – Amundsen Gulf area. Two ship based sampling field expeditions were carried out in late summer of 2005 and 2006 in both regions on board the CCGS Amundsen. In the North Water (NOW) polynya, higher levels of water Hg, depleted δ18O, lower salinity and lower nitrate levels were measured at sampling locations near the Prince of Wales glacier (POW) on the eastern coast of Ellesmere Island in the Smith Sound area. These results suggest that the glacier may be a source of Hg to this region which, in turn, is responsible for the correspondingly high concentrations of THg and MMHg measured in Calanus spp. and Euchaeta spp. at the same locations. The Mackenzie shelf – Amundsen Gulf region was characterized by fresher surface water properties (low salinity and depleted δ18O) in the western part and was strongly linked to the influence of the Mackenzie River. Higher THg concentrations in zooplankton were associated with larger fractions of both meteoric water and sea-ice melt. These findings suggest that in the western Arctic, inorganic Hg uptake in zooplankton via-absorption near surface water was highly driven by freshwater inputs into the system. Based on the analysis of three main genus Calanus spp. (mostly adult females Calanus hyperboreus), Euchaeta spp. and Themisto spp. (mostly adult Themisto libellula), THg and MMHg concentrations were the highest in the carnivorous copepod Euchaeta spp. in the North Water polynya followed by the omnivorous hyperiid amphipod Themisto spp. The herbivorous copepod Calanus spp. had both the lowest THg and MMHg concentrations in the Eastern and the Western Arctic. In addition, the Western Arctic is the area in which each zooplankton genus had the most depleted carbon and the most enriched nitrogen. The highest concentrations of THg in Calanus spp., Euchaeta spp. and Themisto spp. were measured in the Western Arctic as well as the highest MMHg in Calanus spp. and Themisto spp. The highest %MMHg was calculated in the Archipelago for Themisto spp., in the Eastern Arctic for Euchaeta spp. and in the Western Arctic for Calanus spp. The relationships observed between THg, MMHg, %MMHg and δ13C in all three major zooplankton taxa and water mass properties were in agreement with what have been previously described in the literature. Our findings suggested that both Hg and δ13C can be used as tracers to help understand zooplankton vertical distribution, feeding ecology and ultimately to predict climate changes impact at lower trophic level in the pelagic food web. The implications for marine mammals foraging in these regions are also discussed. / October 2008