Thyroid hormones (THs) are vital in the maintenance of homeostasis and in the control of development. One postembryonic developmental process that is principally regulated by THs is amphibian metamorphosis. This process has been intensively studied at the genomic level yet very little information at the proteomic level exists. There is also increasing evidence that changes in the phosphoproteome influence TH action. In addition, the disruption of TH-action by endocrine-disrupting compounds (EDC) is an emerging field and the developmental process of metamorphosis is a target as well as a model system for this research. This work identifies components of the proteome and phosphoproteome in TH-sensitive tadpole tissues that are altered during the initiation stages of TH-induced metamorphosis prior to the overt remodeling of the tissues. Proteomic analyses included two-dimensional (2D) gel electrophoresis for the assessment of differential protein/phosphoprotein expression, combined with mass spectrometry (MS) protein analysis for protein identification. Initial proteomic approaches in Xenopus laevis identified a number of proteins that are differentially expressed in the tadpole tail within 48 h of exposure of premetamorphic tadpoles to 3,5,3’-triiodothyronine (T3). Additionally, a time-course analysis of brain tissue within this 48 h period revealed alterations in phosphoproteins. The importance of phosphoproteome modulation in the process of metamorphosis was further revealed in the TH-induced tail of Rana catesbeiana tadpoles, where the inhibition of cyclin-dependent kinase activity which prevents tail regression, altered the tail phosphoproteome profile. Failure to identify the phosphoproteins involved in these initial studies led me to develop and apply new proteomic approaches. To this end, subcellular and protein fractionation methods were developed and combined with 2D gel electrophoresis and phosphoprotein-specific staining. Altered proteins were identified using MS. Here components of the proteome and phosphoproteome were identified in the tail fin that changed within 48 h of exposure of premetamorphic R. catesbeiana tadpoles to 10 nM T3. This approach allowed the identification of and led to the cloning of a novel Rana larval type I keratin, RLK I, which is a target for caspase-mediated proteolysis upon exposure to T3. In addition, the RLK I transcript level was reduced during T3-induced and natural metamorphosis, consistent with a larval keratin. Furthermore, GILT, a protein involved in the immune system, was changed in phosphorylation state which is linked to its activation. Using a complementary MS technique for the analysis of differentially-expressed proteins, isobaric tags for relative and absolute quantitation (iTRAQ) revealed 15 additional proteins whose levels were altered upon T3 treatment. The success in identifying proteins whose levels changed upon T3 treatment with iTRAQ was enhanced through de novo sequencing of MS data and homology database searching. These proteins are involved in apoptosis, extracellular matrix structure, immune system, metabolism, mechanical function, and oxygen transport. This study demonstrated the ability to derive proteomics-based information from a model species for postembryonic development for which limited genome information is currently available. The early appearance of caspase-cleaved RLK I in the TH-induced process led to its investigation as a contributor to apoptosis. Furthermore, the caspase-cleavage product of RLK I was used as a biomarker in the development of an assay for the detection of disruptors of TH-action based on ex-vivo multi-well culturing of R. catesbeiana tail fin biopsies. This assay was able to detect perturbations in TH-signalling within 48h of exposure demonstrating that it has utility as a novel system for screening of TH disrupting chemicals. The present study identified proteins whose levels and/or phosphorylation states are altered within 48 h of the induction of tadpole metamorphosis prior to overt tissue remodeling and provided important insight into the molecular mechanisms of this postembryonic development. In particular, I have identified a novel keratin that is a target for T3-mediated changes in the tail that can serve as an indicator of early response to this hormone and can be used for the detection of EDCs of TH-action in an ex vivo assay.

Although its highly infectious nature has led to its classification as a potential bio-terror threat, very little is known about the pathogenesis of Francisella. A complete understanding of the mechanisms employed by Francisella to gain residence and replicate within macrophages will provide valuable insight into the means by which F. tularensis, and other intracellular pathogens such as M. tuberculosis and L. pneumophila, invade host cells, secrete effectors, alter phagosome biogenesis and disrupt vesicle traficking. The overall theme of this dissertation is the analysis of genes encoded within a recently identified Francisella pathogenicity island (FPI). In particular, the chapters will focus on the identification, mutagenesis, and phenotypic analysis of Pathogenicity determinant protein D (pdpD), a ~135 kDa protein encoded within the FPI. Chapter 2 addresses the identification of the Francisella pathogenicity island, and the intramacrophage growth of several mutants found within this loci. One of the greatest strengths in determining the roles of putative virulence genes is the ability of researchers to alter and amplify nucleic acids in a highly developed model platform and subsequently introduce the altered genetic material into a pathogen. Although genetic transformation has been well developed and optimized in E. coli, where it is regularly used in cloning experiments, the introduction of DNA into Francisella has been a major deterrent in the mutagenesis of putative virulence factors. Chapter 3 focuses on engineered genetic elements and methods for transformation, antibiotic selection, deletion mutagenesis, and complementation in Francisella strains. The chromosomes of F. tularensis strains carry two identical copies of the Francisella pathogenicity island, and the FPI of North American-specific biotypes contain two genes, anmK and pdpD, that are not found in biotypes distributed over the entire Northern Hemisphere. Furthermore, unlike other known intracellular pathogens, F. tularensis lacks a functional type III or type IV secretion system, which are necessary for other bacterium to arrest maturation of their respective phagosomes. Chapter 4 focuses on the virulence contribution of anmK and pdpD using F. novicida, which is very closely related to F. tularensis but carries only one copy of the FPI. In addition, the outer membrane localization of PdpD is examined in deletions of FPI genes encoding proteins that are homologues of known components of Type VI secretion systems. Although each chapter is a continuum of research related to the Francisella pathogenicity island, each will be treated as a distinct work consisting of an introduction, materials and methods, results, and a discussion. Chapter 5 of this dissertation will consist of an overall conclusion section which will tie the 3 research chapters together as well as focus on future studies.

Understanding the role of forests in the cycling of methane (CH4) and carbon dioxide (CO2) is of importance to the elucidation of global greenhouse gas budgets. Previous studies have shown aerated forests soils to be net sinks of atmospheric CH4 and sources of carbon dioxide. While much research has focused on the role of forest soils as CO2 sources and CH4 sinks, few studies have utilized 13C-isotope studies to clarify the nature of subsurface CO2 production and CH4 consumption. The present study, carried out in 3 temperate forest environments on Vancouver Island during 2006 and 2007, and a boreal forest in northern Quebec in 2005, is intended to address this paucity of information. The isotope and concentration data corroborates previous studies in suggesting that both temperate and boreal forest environments act as net CH4 sinks and CO2 sources. No clear evidence of methanogenesis is apparent in either Vancouver Island or northern Quebec, where the isotopic composition of subsurface CH4 is influenced by diffusive and biological fractionation. Near-surface photosynthetic uptake may have a strong influence on the isotopic composition of soil CO2 and the resultant fluxes, acting to reduce apparent fluxes due to CO2 consumption. Intra-site variability of CH4 and CO2 fluxes indicates that the use of two static chambers in a single site, while sufficient for the confirmation of gas uptake or emission, may be less adequate in the determination of actual rates of efflux/influx. Future studies should address this by either sampling a larger area, installing a greater number of chambers, or by utilizing entirely different methods, such as the use of eddy covariance techniques.

Protein-carbohydrate interactions are pivotal to many biological processes, from plant cell wall degradation to host-pathogen interactions. Many of these processes require the deployment of carbohydrate-active enzymes in order to achieve their intended effects. One such class of enzymes, glycoside hydrolases, break down carbohydrate substrates by hydrolyzing the glycosidic bond within polysaccharides or between carbohydrates and non-carbohydrate moieties. The catalytic efficiency of glycoside hydrolases is often enhanced by carbohydrate-binding modules (CBMs) which are part of the modular structure of these enzymes. Understanding the carbohydrate binding function of these modules is often key to studying the catalytic properties of the enzyme. This thesis investigates the molecular determinants of carbohydrate recognition by CBMs that share similar amino acid sequences and overall three-dimensional structures and thus fall within the same CBM family. Specifically this research focused on two families; plant cell wall binding family 6 CBMs and the alpha-glucan binding family 41 CBMs. Through X-ray crystallography, isothermal titration calorimetry and other biochemical experiments, the structural and biophysical properties of CBMs were analyzed. Studying members of CBM family 6 allowed us to establish the overall picture of how similar CBMs interact with a diverse range of polysaccharide ligands. This was found to be due to changes in the topology of the binding site brought about by changes in amino acid side chains in very distinct regions of the binding pocket such that it adopted a three-dimensional shape that is complementary to the shape of the carbohydrate ligand. Members of CBM family 41 were shown to have nearly identical modes of starch recognition as found in starch-binding CBMs from other families. However family 41 CBMs are distinct as they are found mainly in pullulanases (starch debranching enzymes) and have developed binding pockets which are able to accommodate alpha-1,6-linkages, unlike other starch-binding CBM families. These are the first studies comparing multiple CBMs from within a given CBM family at the molecular level whose results allow us to examine the distinct modes of carbohydrate recognition within a CBM family. Analysis of the family 41 CBMs revealed that these CBMs are mainly found in pullulanases from pathogenic bacteria. Members from Streptococcal species were shown to specifically interact with glycogen stores within mouse lung tissue, leading us to investigate the role of alpha-glucan degradation by the pullulanase SpuA in the pathogenesis of Streptococcus pneumoniae. SpuA targets the alpha-1,6-branches in glycogen granules, forming alpha-1,4-glucan products of varying lengths. The overall three-dimensional structure of SpuA in complex with maltotetraose was determined by X-ray crystallography and showed that its active site architecture is optimal for interacting with branched substrates. Additionally, the N-terminal CBM41 module participates in binding substrate within the active site, a novel feature for CBMs. This is the first study of alpha-glucan degradation by a streptococcal virulence factor and aids in explaining why it is crucial for full virulence of the organism.

WT1 has two main isoforms: WT1(-KTS) and WT1(+KTS). Both are known to bind to a DNA consensus sequence with different affinities, and are thus postulated to play overlapping but distinct functional roles in the cell. WT1 is also known to bind to certain RNA moieties as well as to various protein partners (e.g. Ciao-1). This study focuses on the development of large scale protein purification protocols for WT1 zinc finger (ZF) proteins as well as Ciao-1. By using a combination of his-tag affinity and size exclusion chromatography we were able to purify milligram quantities of these proteins. It was also the intention to obtain crystals of the WT1 ZF protein in complex with any one of its known binding partners, in particular the protein Ciao-1 (a WD40 protein) and the 14 mer consensus sequence of DNA (known as WTE). In conjunction with structural studies it was determined that a previously made SELEX RNA library was not selective for the (+KTS) isoform of WT1 ZF, and therefore no RNA candidate could be identified for future structural studies.

Clostridium perfringens is a gram positive spore forming anaerobe and a causative agent of gas gangrene, necrotic enteritis (pig-bel) and food poisoning in humans and other animals. This organism secretes a battery of exotoxins during the course of infection as well as a variety of virulence factors which may help to potentiate the activities of the toxins. Among these virulence factors is the μ-toxin, a family 84 glycoside hydrolase which acts to degrade hyaluronan, a component of human connective tissue. C. perfringens has 53 open reading frames encoding glycoside hydrolases. About half of these glycoside hydrolases are predicted to be secreted. Among these are CpGH84C, a paralogue of the μ-toxin, and CpGH89. CpGH89 shares sequence similarity to the human α-N-acetylglucosaminidase, NAGLU, in which mutations can cause a devastating genetic disease called mucopolysaccharidosis IIIB. One striking feature of the secreted glycoside hydrolase enzymes of C. perfringens is their modularity, with modules predicted to be dedicated to catalysis, carbohydrate-binding, protein-protein interactions and cell wall attachment. The extent of the modularity is remarkable, with some enzymes containing up to eight ancillary modules. In order to help understand the role of carbohydrate-active enzymes produced by bacterial pathogens, this thesis will focus on the structure and function of the modular extracellular glycoside hydrolase enzymes secreted by the disease causing bacterium, C. perfringens. These structure function studies examine two family 32 CBMs (carbohydrate-binding modules), one from the μ-toxin and the other from CpGH84C. As well we examine the complete structure of CpGH84C in order to help further our understanding of the structure of carbohydrate-active enzymes as a whole. Finally, the catalytic module of CpGH89 is characterized and its relationship to the human NAGLU enzyme is discussed.

WT1 has two main isoforms: WT1(-KTS) and WT1(+KTS). Both are known to bind to a DNA consensus sequence with different affinities, and are thus postulated to play overlapping but distinct functional roles in the cell. WT1 is also known to bind to certain RNA moieties as well as to various protein partners (e.g. Ciao-1). This study focuses on the development of large scale protein purification protocols for WT1 zinc finger (ZF) proteins as well as Ciao-1. By using a combination of his-tag affinity and size exclusion chromatography we were able to purify milligram quantities of these proteins. It was also the intention to obtain crystals of the WT1 ZF protein in complex with any one of its known binding partners, in particular the protein Ciao-1 (a WD40 protein) and the 14 mer consensus sequence of DNA (known as WTE). In conjunction with structural studies it was determined that a previously made SELEX RNA library was not selective for the (+KTS) isoform of WT1 ZF, and therefore no RNA candidate could be identified for future structural studies.

Francisella tularensis is a highly infectious. Gram-negative coccobacillus that is the etiological agent of the acute. febrile. zoonotic disease tularemia. A ca. 35 kb Francisella pathogenicity island (FM) was previously discovered. Two genes. pdpA and pdpD were shown to be required for virulence. The FP1 gene pdpC encodes a protein that has no significant similarities to any motifs, domains, or homologues of known bacterial proteins. This gene of unknown function may encode a novel virulence factor involved in Francisella infection. The role of PdpC in F. novicida intracellular growth was investigated. Results from this study demonstrated that the erythromycin allelic replacement mutant of pdpC was more attenuated in intracellular growth in the murine macrophage-like J774A.1 cells than in bone marrow-derived macrophages from BALB/c mice and that complementation in trans partially complements this mutation. To further investigate the role of pdpC in virulence. partial deletion mutagenesis in the C-terminus of PdpC was performed which resulted in four mutants that showed slight attenuation in J774A.1 intramacrophage growth but behaved like wildtype F, novicida in bone marrow-derived macrophages. Chicken embryos were infected to evaluate the virulence of these pdpC mutants. The virulence of the Em allelic replacement mutant was significantly more attenuated than wildtype F. novicida and complementation partially restored virulence. Partial deletion mutants of pdpC exhibited greater virulence than the EmR mutant in chicken embryos and were able to cause 100% mortality at day 6. Furthermore, eukaryotic expression of triple FLAG-tagged PdpC in chicken embryo fibroblasts resulted in cells that exhibited different morphologies than uninfected fibroblasts which suggests that PdpC may play a role in cytoskeletal rearrangements by altering host cell signaling pathways.

The cyclopentadienone-fused dihydropyrenes 46 and 47 were synthesized. The internal methyl resonances, the coupling constants, NICS calculations and X-ray results confirmed that the cyclopentadienone displays antiaromatic character resulting in bond localization in the annulene ring consistent with a 4n-pi fused system. The ring current of the dihydropyrene fragment is reduced by fusion of the antiaromatic system by about 80% of that caused by benzene. The syntheses of the methylfulvene fused dihydropyrene 56 and the phenylfulvene fused dihydropyrene 58 have been accomplished. The calculated and experimental NMR data and NICS calculations all demonstrated that the fulvenes had weak diatropic ring currents and caused bond localizations in the DHP rings, in which phenyl fulvene has a larger effect than that of methyl fulvene. A number of bis-dihydropyrene systems, bis-dihydropyrene ketone 117, bis-benzo[e]dihydropyrene ketone 119, benzo[e]dihydropyrene dihydropyrene ketone 122, bis-benzo[e]dihydropyrene methylene 124 and the benzo[e]dihydropyrene- dihydropyrene acetylene 130, have been synthesized, in which 117, 119 and 124 are homo-systems and 122 and 130 are hetero-systems. The multiple photoswitching properties study found that all of these systems except 130 showed multi-states during the photo opening and photo closing processes, which means that each end of the DHP units photo opens or closes separately rather than synchronously. In the homo switches 117, 119 and 124, the two DHP units act independently, but the relative differentiation is not very significant. On the other hand, the hetero-switch 122 showed fully differentiated photo opening process and almost a pure open-closed intermediate 122’ could be achieved. This is the first example which clearly showed four states in the UV closing process. The relative photo opening and closing rates compared to benzoDHP 36 have also been studied. It was found that while the carbonyl linker largely increased the relative photo opening rate (117, 119 and 122), the methylene linker only increased it slightly (124). The photo closing processes were always fast as usual. The studies of the thermal return reactions of these systems showed that while the carbonyl linker substantially slowed down the thermal return reactions of the DHP units (117, 119 and 122), the methylene linker speeded it up slightly (124). The mono-iron tricarbonyl benzo[e]dihydropyrene complex 152, the bis-iron tricarbonyl benzo[e]dihydropyrene complex 153 and the iron tetracarbonyl dihydropyrene complex 151 were synthesized. The structures of 152 and 153 were determined by X-ray crystallography. The coordinations of iron tricarbonyl moieties to the DHP rings caused a distortion of ca. 30 degree away from the central DHP plane. Coordination also increased bond alternation and reduced ring currents in the DHP rings. 1H-NMR and X-ray studies showed that 152 showed a weak paratropic ring current in the DHP ring. Iron coordination of the DHP completely stopped the photochromic properties of the dihydropyrenes.

The synthesis of benzo[e]dimethyldihydropyrene (BDHP) photoswitches with ter-27, quarter-36, and quinque-28 thiophene oligomers attached on the same side of the switch was achieved using Stille coupling reactions. BDHP photoswitches with bi-75, ter-76 and quinque-77 thiophene oligomers attached directly to the switch on one side, and via a carbonyl spacer on the opposite side of the switch were also synthesized. Dimethyldihydropyrene (DHP) photoswitches with a naphthoyl functional group in the 2 position were synthesized using a Friedel Crafts reaction, and ter-96, quinque-97 and septi-98 thiophene oligomers were attached on opposite sides of the switch using Stille coupling reactions. All compounds were characterized by NMR, IR UV-vis spectroscopy and mass spectrometry. The relative rates of the photo-opening reactions under excess light conditions and the UV closing reactions versus BDHP were measured. Improvements in the photo-opening properties of the oligothiophene functionalized switches compared to BDHP were observed. The most dramatic photo-opening improvement was found for the quinquethienyl substituted DHP switch 97 which photo-opened when irradiated with visible light over 100 times faster than BDHP. UV closing rates were virtually the same as that of BDHP. However the addition of oligothiophenes led to an increase in the thermal closing reaction rates. Compounds with the naphthoyl functional group in the 2 position of DHP were found to have dramatically increased thermal closing rates. The electrochemical properties of oligothiophene functionalized BDHP and naphthoyl functionalized DHP switches in the closed form were studied by cyclic voltammetry and spectroelectrochemistry. During the oxidation cycle, a closing reaction from the cyclophanediene (CPD) form to the DHP form of the switches occurred which prevented the study of the electrochemical properties of the switches in the open form. Conductivity testing was performed on the quinquethienyl substituted DHP switch 97 using a gold interdigitated micro electrode array. The conductivity of undoped 97 was greater in the closed DHP isomer than in the open CPD isomer. Irradiation with red or blue light allowed for repetitive switching between the more highly conducting closed form and the less conducting open form. When electrochemically doped, 97 showed improved conductivity over the undoped form but only the conductivity of the closed doped form could be measured due to electrochemically induced closing.