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In recent years the United States Navy has concentrated most of its Anti-Submarine Warfare (ASW) research and development efforts toward passive sonar. Its ability to locate enemy targets without being detected gives the passive sonar system a supreme strategic advantage over its active counterpart. One aspect of passive sonar signal processing is the time delay estimation of an underwater acoustic wavefront. From this estimation the location and velocity of the radiating source (target) can then be determined. This report compares two popular methods of estimating time delay utilizing computer simulations of each: the cross correlator and the beamformer.

The extensive relationship between modulation of intracellular Ca2+ content and the control of cell proliferation (Boynton et al. 1974; Whitfield et al. 1979; Berridge and Irvine 1984), differentiation (Bridges et al. 1981; Holliday et al. 1991) and death (Orrenius et al. 2003) has led to much examination into the relationship between Ca2+ signaling pathways and the onset of various pathological conditions, including cancer, cardiac hypertrophy, immunodeficiency, neurodegeneration. Control of Ca2+ signals is achieved via an extensive combination of pumps, channels and exchangers which regulate the concentration of Ca2+ within not only the cytosol but also all intracellular compartments. Accordingly, a great deal of research has focused on the mechanisms which regulate these channels and pumps, and recently the primary mechanism for Ca2+ influx in non-excitable cells has been identified. This process, termed Store-operated calcium entry (SOCe), is a key evolutionarily conserved mechanism whereby decreases in endoplasmic reticulum Ca2+ content (sensed by the ER Ca2+ sensor, STIM1) leads to the influx of Ca2+ across the plasma membrane through the Orai family of Ca2+ channels. However, many questions remain about how this Ca2+ signaling pathway is regulated. In this thesis, I provide evidence regarding the transcriptional and molecular mechanisms regulating SOCe. Initial studies in my thesis work aimed to identify some of the key events leading to dysregulation of Ca2+ homeostasis in the kidney specific pediatric malignancy, Wilms' Tumor. I found that STIM1 expression levels and SOCe signals are significantly reduced in Primary Wilms' Tumor samples. Subsequent analysis of these phenomena led me to the finding that STIM1 expression is under the control of the transcription factors Wilms' Tumor Suppressor 1 (WT1) and Early Growth Response 1 (EGR1). Subsequent investigations were carried out with the purpose to assess how activation of the EGR1 transcription factor alters long term Ca2+ signals. Indeed, I found that receptor-mediated activation of EGR1 leads to induction of STIM1 expression and increases in SOCe. However, unexpectedly through these analyses, I propose a novel role for STIM1 that STIM1 interacts with the Plasma Membrane Ca2+ ATPase (PMCA) through its C-terminal proline-rich domain and reduces PMCA-mediated Ca2+ clearance, effectively creating local, augmented Ca2+ gradients. This coordinated control of Ca2+ entry and exit from the cell has wide-ranging implications for Ca2+ signaling in multiple cell types. / Biochemistry

Cyclic-3',5 '-adenosine monophosphate (cAMP) is an ancient signaling molecule that is found in a variety of species from prokaryotes to eukaryotes and translates extra-cellular stimuli into tightly controlled intra-cellular responses. The two major mammalian cAMP sensors are protein kinase A (PKA), for the phosphorylation of the downstream effectors, and the exchange protein directly activated by cAMP (Epac ), for the guanine nucleotide exchange in the small GTPase Rap proteins. In this study, we investigated the intra-molecular cAMP dependent allosteric network of Epac cyclic nucleotide binding domain (CBD) via solution NMR spectroscopy. Epac proteins have been shown to employ an auto-inhibition strategy in the control of the equilibrium between the active and the inactive states. In the absence of cAMP, the periphery of the Rap recognition site is masked via an ionic interface provided by the N-terminus of the CBD. Binding of cAMP at the distal Phosphate Binding Cassette (PBC), results in weakening of this interface. Here we show that the cAMP binding signal is propagated to the sites important in Epac activation, i.e. the ionic interface, via two key allosteric spots within the CBD. We have also determined the dynamics as a key carrier of cAMP effects to the region forming the ionic interface (ionic latch). Hence entropic enhancements emerged as a key effector in the cAMP mediated ionic latch weakening. We have also provided initial evidence of a negative allosteric contribution from the C-terminal Hinge-Lid region (CHLR) on the cAMP induced Epac activation. In addition to these findings, we also observed critical differences in the mode of cAMP recognition and inter-subdomain communication between the Epac and PKA. A detailed understanding of these two ubiquitous systems, will aid in the development of agonists and antagonists that are relevant in the drug lead development for related diseases, such as Alzheimer's and diabetes. / Thesis / Master of Science (MSc)

The nematode, Caenorhabditis elegans is an ideal animal model to study conserved mechanisms of developmental and postdevelopmental processes. Here, I describe the role of an Axin family member, pry-1, in aging, lipid metabolism, and seam cell development. Our analysis of pry-1 animals showed a catastrophic collapse of adult lifespan, which was accompanied with hallmarks of accelerated aging. Transcriptome profiling of pry-1 mutants revealed altered expression of genes associated with aging and lipid metabolism such as vitellogenins, fatty acid desaturases, lipases, fatty acid transporters and genes involved in cuticle synthesis. Consistent with this, pry-1 animals display significantly reduced levels of somatic lipids. Knockdowns of vitellogenins in the pry-1 background restored lifespan and lipid levels, suggesting that vitellogenins are necessary to mediate pry-1 function in aging and lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomics analysis provided evidence of reduced fatty acid synthesis in pry-1 animals. In agreement with this, an exogenous supply of oleic acid restored depleted lipids in somatic tissues in addition to suppressing the short-lived phenotype of worms. In addition, transcriptome profiling for differentially expressed miRNAs in pry-1(mu38) identified heterochronic miRNAs (lin-4 and let-7 -family members) to act downstream of pry-1 /Axin. In C. elegans, these miRNAs are known to robustly regulate the stem-like, seam cell division. Loss of pry-1 function caused heterochronic defects such that the seam cells divide precociously to produce additional cells. The pry-1-miRNAs are involved in mediating silencing of the heterochronic gene, hbl-1, a C. elegans hunchback homolog, to regulate seam cell division. Furthermore, I report identification of novel miRNAs from C. elegans and C. briggsae. Overall, our findings demonstrate a novel role of the Wnt signaling regulator, pry-1/Axin, in the maintenance of adult lifespan that involves lipid homeostasis and regulation of heterochronic miRNA to control the developmental timing of seam cell division in C. elegans. / Thesis / Doctor of Philosophy (PhD)

DOCTOR OF PHILOSOPHY (2019) McMaster University, Hamilton, Ontario (Medical Sciences) TITLE: Serotonergic antagonists affect the activity of breast tumor initiating cells in human and mouse models of breast cancer. AUTHOR: William D. Gwynne, BSc SUPERVISOR: Dr. John A. Hassell NUMBER OF PAGES: XXI; 255 / Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer-related death amongst women worldwide. The relatively unchanging breast cancer-associated mortality rate is in part due to the existence of rare tumor cells (breast tumor initiating cells; BTIC) that possess stem-like properties permitting them to survive therapy and initiate disease recurrence. Hence, identifying agents capable of eradicating these cells would be a favourable therapeutic strategy to improve the durability of breast cancer remissions. To achieve the latter objective our lab screened over 35,000 small molecules for their capacity to inhibit the viability of BTIC-enriched mouse tumor cells. Unexpectedly, several antagonists of the serotonin (5-hydroxytryptamine; 5-HT) transporter and select receptors were among the hit compounds identified in the screen. This thesis aims to establish a connection between serotonergic activity and BTIC. We accomplished the latter by assessing whether components of the 5-HT signaling system are expressed in mouse and human breast tumor cells and whether inhibition of their activity affects BTIC frequency using multiple orthogonal assays. Our data suggest that breast tumor cells of both mouse and human origin express the components necessary for 5-HT synthesis, activity and metabolism and that inhibition of these proteins with selective antagonists reduces the capacity of these cells to form tumorspheres. We demonstrate that highly selective antagonists of SERT and HTR5A target BTIC as established ex vivo cell transplantation assays. We also discovered that these agents synergize with chemotherapy in vivo to affect the growth of mouse breast tumor allografts and human breast tumor xenografts. To validate the molecular targets of these agents, we attempted to phenocopy their effects in functional assays by knocking out their respective genes using CRISPR-Cas9 technology. Collectively, this thesis contributes to an understanding of how 5-HT signaling affects BTIC and identifies serotonergic antagonists as novel anticancer agents. / Dissertation / Doctor of Philosophy (PhD) / Despite improvements in screening technologies and the development of targeted therapies breast cancer remains the second leading cause of cancer-related death among Canadian women. Whereas the current standard of care is effective at treating the majority of patients diagnosed with breast cancer, there remains a substantial proportion of patients that experience relapse after undergoing therapy. Recurrence is due in part to the existence of rare, stem-like tumor cells, termed breast tumor-initiating cells (BTIC) that are insensitive to existing anticancer agents. Hence, identifying drugs capable of targeting these cells is a desirable goal. To pursue the latter, our lab screened approximately 35,000 compounds for their capacity to affect the growth of BTIC-enriched tumor cell populations. Among the hit compounds were antagonists of the serotonin transporter and serotonin receptors, including FDA-approved psychiatric medications. Here, we explore a connection between serotonin-related proteins and BTIC activity with the aim of identifying novel therapeutic agents.

Staphylococcus aureus causes nosocomial- and community- acquired infections. This versatile pathogen expresses virulence factors (VF) that enhance establishment of infection and immune evasion. Our research focused on defining the roles of S. aureus VF on host immune responses during intracellular or extracellular infections. Accessory gene regulator (agr) controls VF expression and intracellular survival. Our goal was to determine mammary epithelial cells (MEC) responses to intracellular infection and subsequent polymorphonuclear leukocyte (PMN) responses. Intracellular S. aureus increased thrombomodulin expression by MEC and activated protein C (APC) production. APC inhibited PMN chemotaxis. Findings depicted an indirect role for VF on PMN responses, so next we determined signaling pathways and cytokine responses of PMN to S. aureus toxins. Live S. aureus infections increased activation of stress signaling pathways and highlighted a role for agr-regulated genes in MAPK p38 phosphorylation and α-hemolysin in ERK phosphorylation and IL-8 expression in PMN. Continuing our studies of VF, chemotaxis inhibitory protein of S. aureus (CHIPS) inhibits monocyte chemotaxis. We hypothesized that CHIPS inhibited C5a receptor (C5aR) signaling. Monocytes pretreated with CHIPS did not inhibit C5aR signaling. Nevertheless, signaling pathways can reduce PMN function in models such as glucocorticoid treatment. Immunosuppressive effects of glucocorticoids on PMN are restored with OmniGen-AF® supplementation. Glucocorticoid receptor and Toll-like receptor signaling potentially crosstalk to restore PMN function. OmniGen-AF® supplementation restored dexamethasone-induced immunosuppression in a MyD88-dependent manner. Overall, this research focused on characterizing immune responses to S. aureus infections and PMN signaling pathways and how it is key to understanding pathogenesis. / Ph. D.