c-Cbl protein functions as an E3 ligase and scaffolding protein, where three residues, Y700, Y731, and Y774, upon phosphorylation, have been shown to initiate several signaling cascades. In this study, we investigated the role of these phospho-tyrosine residues in the platelet functional responses upon integrin engagement. We observed that c-Cbl Y700, Y731 and Y774 undergo phosphorylation upon platelet adhesion to immobilized fibrinogen, which was inhibited in the presence of PP2, a pan-src family kinase (SFK) inhibitor, suggesting that c-Cbl is phosphorylated downstream of SFKs. However, OXSI-2, a Syk inhibitor, significantly reduced c-Cbl phosphorylation at residues Y774 and Y700, without affecting Y731 phosphorylation. Interestingly, PP2 inhibited both platelet spreading on fibrinogen as well as clot retraction, whereas OXSI-2 blocked only platelet spreading, suggesting a differential role of these tyrosine residues. The physiological role of c-Cbl and Y731 was studied using platelets from c-Cbl KO and c-CblYF/YF knock-in mice. c-Cbl KO and c-Cbl YF/YF platelets had a significantly reduced spreading over immobilized fibrinogen. Furthermore, clot retraction with c-Cbl KO and c-Cbl YF/YF platelets was drastically delayed. These results indicate that c-Cbl and particularly its phosphorylated residue Y731 plays an important role in platelet outside-in signaling contributing to platelet spreading and clot retraction / Physiology

Wnt signaling plays important role in many aspects of embryogenesis such as cell proliferation, cell fate specification, cell polarity and organogenesis(Clevers 2006, van Amerongen and Nusse 2009). Wnt ligands have been shown to activate several intra-cellular signaling cascades, including the canonical or Wnt/-catenin dependent pathway and the non-canonical or -catenin independent pathway. Dishevelled (Dvl) occupies a key position at crossroads of all branches of Wnt signaling cascade. To understand, how Dishevelled (Dvl) may channel signaling into the downstream branches, we sought to identify novel effectors for Dishevelled (Dvl) using a yeast-two hybrid screen. In this study, we used the PDZ domain of Dishevelled (Dvl) as a bait and from this screen, we identified a new binding protein of Dishevelled (Dvl)-termed as Custos. To characterize the functional role of Custos in Wnt signaling pathway, we used mammalian cell culture and zebrafish as a model vertebrate organism. We confirmed the interaction between Custos and Dvl using co-immunoprecipation and GST pull-down. Custos also interacted with -catenin in vivo and this interaction was positively regulated by Wnt stimulation. Immunofluorescence experiments in mammalian cells showed that Custos co-localizes with the nuclear envelope marker, lamin and inhibits translocation of -catenin to the nucleus. In zebrafish embryos, Custos is a maternal gene and expressed throughout development. Spatial in situ hybridization studies showed that Custos was expressed in the dorsal region of the embryo at early stages and in the nervous system in zebrafish at 24hpf. To delineate the biological role of Custos during embryogenesis, we conducted a gain of function and loss of function studies. Overexpression of exogenous Custos and morpholino knockdown of Custos revealed that Custos is critical for embryonic patterning. Knockout of Custos in zebrafish revealed that Custos delays embryonic development and exhibits defects in pigmentation suggesting a plausible role in neural crest development. Taken together, our studies demonstrate that Custos is a novel component of canonical Wnt signaling and required for -catenin translocation into the nucleus and important for embryonic patterning. / Biology

Hepatitis B virus encoded X protein (HBx) contributes centrally to the pathogenesis of hepatocellular carcinoma (HCC). Aberrant activation of the Hedgehog (Hh) pathway has been linked to cancer. Thus, experiments were designed to test the hypothesis that HBx contributes to HCC via activation of Hh signaling. HBx expression correlated with up-regulation of Hh markers in human liver cancer cell lines, in HBx transgenic mice that developed HCC and in liver samples from HBV infected patients with HCC. The findings in human samples provide clinical validation of those in the HBx transgenic mice (HBxTg), and underscore the relevance of these transgenic mice to disease pathogenesis. Further, blockade of Hh signaling inhibited HBx stimulation of cell migration, anchorage independent growth, HCC tumorigenesis in HBx transgenic mice and tumor growth in xenograft model. These results suggest that the ability of HBx to promote cancer is at least partially dependent upon Hh activation and that activation of Hh signaling appears to be important for the development of HBx associated HCC. HBx also activates pathways that stimulate downstream Hh signaling, such as PI3K/AKT and Ras/Raf/MEK, also referred as non-canonical Hh signaling. Upon canonical Hh inhibition, compensatory activation of these pathways was seen in the presence of HBx in liver cancer cell lines and in HBxTg mice. Individual inhibition of these pathways also down-regulated Gli2 expression in HBx positive cell lines. These data suggests that in addition to canonical Hh signaling, activation of PI3K/AKT and ERK pathways by HBx leads to up-regulation of Gli2 expression in HBV-mediated HCC. This work identifies Hh pathway inhibition as a therapeutic strategy to slow tumor development and this work could lead to combination therapies that target Hh, AKT and ERK pathways, which may prevent or delay the appearance/progression of HCC. / Biology

<p> pH6DZ1 is a synthetic deoxyribozyme that is able to couple catalysis with fluorescence signal generation. This deoxyribozyme has the ability to cleave itself at a lone ribonucleotide that is present between a pair of deoxyribothymidines, one modified with a fluorophore (fluorescein) and the other with a quencher (DABCYL). Herein we report on the sequence truncation and secondary structure characterization ofpH6DZ1 as well as the identification of functionally important nucleotides within this deoxyribozyme. Our data indicate that pH6DZ1 has a four-way junction-like secondary structure comprised of four short duplexes, three hairpin loops, and three inter-helical unpaired elements. Ten nucleotides, all located in two separate single-stranded regions, were identified as functionally indispensable nucleotides. Nine nucleotides, most of which are also distributed in three single-stranded DNA elements, were identified as functionally vital nucleotides. Our study has shown that pH6DZ1 has a secondary structure that is more complex than those reported for other RNA-cleaving deoxyribozymes. A trans-acting DNA enzyme was also developed from the minimized version ofpH6DZl, which behaves as a true enzyme with a kcat value of~1 min"1 and generates a large fluorescence signal upon catalysis. This study should facilitate the future exploration of this unique DNAzyme for the development of DNAzyme-based biosensors. </p> / Thesis / Master of Science (MSc)

Iron is among the essential micronutrients for all living organisms and is a cofactor for many cellular redox reactions. Although iron is a highly abundant metal element found in the earth’s crust, it is also a limiting factor in plant development when it is present as insoluble ferric oxides. Plants have evolved two strategies to acquire soluble iron referred to as Strategy I and Strategy II. Our lab has focused on the Arabidopsis thaliana double mutant ysl1ysl3. The mutants display a chlorotic phenotype and are unable to correctly respond to iron deficiency. Grafting is a common method for joining different plant tissues and has been used for studies of long distance signaling. Past studies of iron signaling in Arabidopsis have not been able to provide a mechanism for how plants are able to signal the iron status of the shoot, where iron demand is high, to roots, where iron uptake occurs. The iron signaling experiments included in this thesis follow a seedling-graft approach to understand if grafts are capable of properly sensing iron. A longstanding question of iron homeostasis in plants is the identity of the iron sensors in plants. It was hypothesized that YSL1 and YSL3 have both a transporter function and a receptor function, and therefore function as transceptors. In our predicted model it was proposed that YSL1 and/or YSL3 are directly involved in iron status signaling either in perception and/or transmission of the signal. As evidenced through seedling grafting experiments here, YSLs play a critical part of long distance signaling that plant shoots use to signal their iron status to the roots. In this thesis, YSL1 and YSL3 are shown to be required in the shoots in order for signaling to occur correctly in the roots. To facilitate the analysis of gene expression in the grafts, a FRO3promoter:GUS construct was used in the Col-O WT background. The FRO3 promoter was selected because it is expressed in both leaves and roots under iron deficiency. Experiments showed that the genotype of the shoot used in the grafts is critical for Fe-deficiency induced gene expression in the roots. Thus, grafting has revealed that root iron deficiency responses require YSL1 and YSL3 in leaves for signal transmission. This directly links them to long-distance signaling, and supports the idea that these proteins could be acting as transceptors.

The phosphatidylinositol signaling pathway utilizes inositol-containing second messengers to mediate signaling events. The enzymes that metabolize phosphoinositides can in some cases serve to terminate the signaling actions of phosphoinositides. The inositol polyphosphate 5-phosphatases (5PTases) comprise a large protein family that hydrolyzes 5-phosphates from a variety of inositol phosphate and phosphoinositide substrates. I have examined the substrate specificity of the At5PTase11 protein from the model plant, Arabidopsis thaliana. The At5PTase11 gene (At1g47510) encodes an active 5PTase enzyme that can dephosphorylate the phosphoinositide substrates phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2], phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2], and phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3]. In addition, the At5PTase11 gene is regulated by abscisic acid, jasmonic acid, and auxin, suggesting a role for phosphoinositide action in these signal transduction pathways. To further delineate the function of At5PTase11 in Arabidopsis thaliana, two independent T-DNA insertion mutant lines were isolated (At5ptase11-1 and At5ptase11-2). Analysis of At5ptase11 mutant lines revealed that At5ptase11 mutant seeds germinate slower compared to wild-type seeds. Moreover, At5ptase11 mutant seedlings demonstrated less hypocotyl growth when grown in the dark. These results indicate that At5PTase11 is required for the early stages of seed germination and seedling growth. Since there are 15 predicted 5PTases in Arabidopsis thaliana, a group of 5PTases have been analyzed to identify the 5PTases with similar substrate selectivity. At5PTase1 (At1g34120), At5PTase2 (At4g18010) and At5PTase3 (At1g71710) have been found to hydrolyze all four potential substrates, inositol 1,4,5-trisphosphate [Ins(1,4,5)P3], inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P4], PtdIns(4,5)P2, and PtdIns(3,4,5)P3. At5PTase7 (At2g32010) hydrolyzed PtdIns(4,5)P2, and PtdIns(3,4,5)P3 which is similar to the substrate selectivity of At5PTase11. In addition, At5PTase4 (At3g63240), and At5PTase9 (At2g01900) hydrolyzed only PtdIns(4,5)P2. These results indicate that there are different groups of Arabidopsis thaliana 5PTases based on the substrate selectivity. These results suggest that Arabidopsis thaliana 5PTases with similar substrate selectivity may have overlapping functions. In summary, the findings that At5PTase11 is a phospholipid-specific 5PTase and At5PTase11 functions in the early stages of seed germination and seedling growth indicate that 5PTases play important roles in plant growth and development. / Ph. D.

In the post-genomic era, one of the most important goals for the community of plant biologists is to take full advantage of the knowledge generated by the Arabidopsis thaliana genome project, and to employ state-of-the-art functional genomics techniques to assign function to each gene. This will be achieved through a complete understanding of what all cellular components do, and how they interact with one another to produce a phenotype. Among the proteins encoded by the Arabidopsis genome are 24 related carboxyl methyltransferases that belong to the SABATH family. Several of the SABATH methyltransferases convert plant hormones, like jasmonic acid, indole-3-acetic acid, salicylic acid, gibberellins, and other plant constituents into methyl esters, thereby regulating the biological activity of these molecules and, consequently, myriad important physiological processes. Our research aims to decipher the function of proteins belonging to the SABATH family by applying a combination of genomics tools, including genome-wide expression analysis and gas-chromatography coupled with mass spectrometry-based metabolite profiling. Our results, combined with available biochemical information, provide a better understanding of the physiological role of SABATH methyltransferases, further insights into secondary plant metabolism and deeper knowledge of the consequences of modulating the expression of SABATH methyltransferases, both at the genome-wide expression and metabolite levels. / Ph. D.

The contrasting infection strategy of herpes simplex virus (HSV) consists of an initial primary lytic infection in epithelial cells, followed by establishment of lifelong latency in sensory and autonomic neurons of the peripheral nervous system that innervate the site of infection. Any cellular stress trigger, ranging from external stimuli such as UV radiation or nerve injury to psychological and physiological stress, can reactivate HSV from latency in the neurons, resulting in recurrent disease episodes. Stress hormones and deprivation of neurotrophic factor (NTF) both have a strong correlation with HSV reactivation from neurons. However, neuronal signaling pathways cardinal to HSV latency and reactivation are still not clear. This dissertation provides new understanding of HSV latency and reactivation in response to two orthogonal stress stimuli, viz. stress hormones epinephrine (EPI) and corticosterone (CORT), as well as NTF deprivation that simulates a nerve injury in primary neuronal cultures. In this dissertation, we demonstrate that physiological stress hormones EPI and CORT differentially regulate HSV-1 and HSV-2 reactivation in adult neurons. Both EPI and CORT treatment reactivated only HSV-1 in sympathetic superior cervical ganglia (SCG) neurons, while HSV-2 was reactivated only by CORT in both sensory trigeminal ganglia (TG) neurons and sympathetic superior cervical (SCG) neurons. EPI utilized the combination of α and β adrenergic receptor complex, while CORT signaled through glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) to reactivate HSV in the neurons. NTFs are tissue-target derived growth factors required for neuronal protection and survival. Neurotrophins are also required for maintaining HSV latency, as NTF deprivation reactivates both HSV-1 and HSV-2 in adult sensory TG and sympathetic SCG neurons. In addition, assessing the temporal kinetics of HSV gene expression showed differential expression profiles of viral immediate-early (IE) genes ICP0, ICP4, ICP27 and trans-activator VP16 following treatment with stress hormones and NTF deprivation in HSV-1 and HSV-2 infected neurons. We also show that different molecular mechanisms are involved in HSV latency and reactivation, which are dependent on the stimuli and the type of neurons. Tyrosine kinase receptor-mediated PI3K-Akt-mTORC signaling cascades have been studied for their role in maintaining HSV latency. Activation of β-catenin signalosome expression has also been implicated during HSV latency and following reactivation. GSK3β is a key effector molecule that inter-connects Akt and β-catenin mediated pathways, forming an Akt-GSK3β-β-catenin signaling axis. Analyzing the Akt-GSK3β-β-catenin signaling in response to stress hormone and NTF deprivation revealed significant differences in protein expression levels between HSV-1 and HSV-2 infected sensory and sympathetic neurons. In HSV-1 infected neurons, the Akt-GSK3β-β-catenin maintains the signal transmission in order to keep the neurons alive, but HSV-2 infections obliterated the entire axis in the adult neurons, particularly in sympathetic neurons. In summary, we demonstrate that HSV-1 and HSV-2 do not have a 'one for all' infection mechanism. Establishment of latency and reactivation by HSV is virus specific, stimulus specific and neuron specific. / Doctor of Philosophy / Herpes simplex viruses (HSVs) are common global viral pathogens that are responsible for causing lifelong painful infections and debilitating disease. The two serotypes of HSV include HSV-1, which is associated with oral or ocular disease but can also cause genital disease, and HSV-2, which is predominantly associated with genital herpes. Once infected, both HSV-1 and HSV-2 are present as lifelong reservoirs in our peripheral neurons. Stress stimuli mediated by our stress hormones or external triggers, such as nerve trauma or an axonal injury, can periodically reactivate the latent virus to cause recurrent disease. Clinical manifestation of HSV recurrences range from asymptomatic viral shedding to painful blisters, cold sores, or herpetic keratitis. In some cases, the virus can spread to the central nervous system, causing encephalitis or recurrent meningitis. No vaccines have been approved yet, and the current treatment utilizes nucleoside analogs, such as acyclovir and its prodrug valacyclovir, to ameliorate the symptoms of HSV infection by halting viral replication and if taken as a daily prophylaxis, reduces the chances of clinical recurrence. Given the route and transmission efficiency of HSV, it is practically impossible to prevent herpes infection. To develop strategic therapeutic interventions to lock the virus in its latent phase in the neurons and prevent it from reactivation, a better understanding of neuronal signaling pathways cardinal to HSV latency and reactivation is necessary. However, neuronal signaling pathways cardinal to HSV latency and reactivation are still not clear. In this dissertation, we make contributions to better understand HSV latency and reactivation in response to stress stimuli. We show that different stress stimuli exert preferential reactivation between HSV-1 and HSV-2, and are further dependent upon the neurons where they establish latency. Our study specifically focuses on three neuronal stressors that have been associated with HSV recurrences: two stress hormones, epinephrine (EPI) and corticosterone (CORT), as well as deprivation of neurotrophic factors (NTF) that simulates nerve injury. We also focused on a neuronal signaling cascade involved in the response to all of these stimuli, Akt-GSK3β-β-catenin, and viral gene transcripts that respond to these stimuli during reactivation. Comprehensive understanding of the neuronal processes and viral gene transcripts involved during HSV-1 and HSV-2 reactivation in neurons will help the herpes virology field towards development of targeted therapies and vaccines to prevent reactivation and recurrent disease.

The complex molecular machinery of the cell controls its response to various signals and environmental conditions. A natural approach to study these molecular mechanisms and cellular processes is with protein interaction networks. Due to the complexity of these networks, sophisticated computational techniques are required to extract biological insights from them. In this thesis, I develop and apply network-based algorithms for three different challenges. 1. I develop a novel, highly-scalable algorithm for network-based label prediction methods that enables the integration of functional annotations and interaction networks across many species in order to predict the functions of genes in newly-sequenced bacteria. 2. To overcome the limitations of experimental approaches to find human proteins and processes that are hijacked by SARS-CoV-2, I adapt network propagation approaches for predicting human interactors of the virus. 3. Large-scale experimental techniques to screen chemicals for toxicity have tested their effects on many individual proteins. I integrate human protein-protein interactions with this data to gain insights into the molecular networks those chemicals affect. For each of these research problems, I perform comprehensive evaluations and downstream analyses to demonstrate both the accuracy of our approaches and their utility in obtaining a broader understanding of the molecular systems in question. / Doctor of Philosophy / The functions of all living cells are governed by complex networks of molecular interactions. A major goal of systems biology is to understand the components of this machinery and how they regulate each other to control the cell's response to various conditions and signals. Advances in experimental techniques to understand these systems over the past couple of decades have led to an explosion of data that probe various aspects of a cell such as genome sequencing, which reads the DNA blueprint, gene expression, which measures the amount of each gene's products in the cell, and the interactions between those products (i.e., proteins). To extract biological insights from these datasets, increasingly sophisticated computational methods are required. A powerful approach is to model the datasets as networks where the individual molecules are the nodes and the interactions between them are the edges. In this thesis, I develop and apply network-based algorithms to utilize molecular systems data for three related problems: (i) predicting the functions of genes in bacterial species, (ii) predicting human proteins and processes that are hijacked by the SARS-CoV-2 virus, and (iii) suggesting cellular signaling pathways affected by exposure to a chemical. Developments such as those presented in these three projects are critical to obtaining a broader understanding of the functions of genes in the cell. Therefore, I make the methods and results for each project easily accessible to aid other researchers in their efforts.

Inflammation has been found to play a role in the development of many different tumors. However, a tumor's ability to evade immune cell recognition can be integral to its progression as well. The following works explore this complicated role with a focus on histiocytic sarcoma (HS) and breast cancer. Chapter 1 opens with a broad overview of inflammation in tumorigenesis while Chapter 2 focuses on a review and discussion of current HS literature. Our investigations into the role of inflammation specifically in HS are initiated in Chapter 3 where we explore the role of the regulatory NLR, NLRX1, in the development of HS in mice. NLRX1 is an intracellular patter recognition receptor that functions to regulate pro-inflammatory cell pathways. Our studies reveal that in carcinogen-induced HS in mice, NLRX1 acts as a tumor suppressor. Moreover, when NLRX1 is lost, tumors that develop are associated with increases in expression of genes in NF-κB and AKT pathways. Though uncommon, HS is a clinically relevant tumor in dogs. In Chapter 4, we further investigate the role of the pathways identified in Chapter 3 in canine patients. Not only were these pathways increased, but our results also revealed previously unreported differences in tumors diagnosed as HS versus those diagnosed as hemophagocytic HS. To improve the use of canine HS both as an experimental and translational model, we sought to create a murine xenograft model. In Chapter 5, we discuss the development of our model and the results of pilot studies using targeted drug therapy. The focus of Chapters 3-5 is to further explore the role of inflammation in the development of HS. However, as aforementioned, the role of inflammation in tumorigenesis is quite complicated. In Chapter 6, we aim to address the concept that the lack of inflammation through immune evasion, can also be important in tumors. Breast cancer in humans is traditionally recognized as being highly immunosuppressive. In this final chapter, we investigate the use of an attenuated strain of bacteria to treat these tumors by way of shifting the immunosuppressive tumor microenvironment to a more pro-inflammatory state. / Ph. D.