<p> The molecular mechanisms governing gamma-globin expression in a subset of fetal hemoglobin (alpha₂:gamma₂; HbF) expressing red blood cells (F-cells) and the mechanisms underlying the variability of response to hydroxyurea induced gamma-globin expression in the treatment of sickle cell disease are not completely understood. To explore molecular differences in these conditions, a serum-free <i>in vitro</i> culture system suitable for large scale production of erythroblasts derived from primary human hematopoietic progenitors is optimized. The culture system recapitulates steady-state adult erythropoiesis and can support erythroid differentiation with the addition of cytotoxic hydroxyurea. Using this system, intra-person clonal populations of erythroblasts derived from bone marrow common myeloid progenitors were evaluated for molecular factors associated with gamma-globin expression. Data demonstrate that the level of fetal hemoglobin produced in F-cells negatively correlates with expression of BCL11A, KLF1 and TALL With the addition of hydroxyurea, successful induction of gamma-globin includes a further reduction in BCL11 A, KLF1 and TALI expression along with a decrease in SOX6 expression. These data suggests that expression changes in this transcription factor network modulate gamma-globin expression in F-cells during steady state erythropoiesis and after induction with hydroxyurea.</p>

<p> Meiosis is a highly conserved specialized cell division that occurs in many organisms, including budding yeast and mammals. Meiosis divides the chromosome number of the cell in half to create gametes for sexual reproduction. A single round of chromosome duplication is followed by two rounds of chromosome segregation, Meiosis I (homologs segregate) and Meiosis II (sister chromatids segregate). Proper segregation at Meiosis I requires that homologs are connected by both crossovers and sister chromatid cohesion. Crossovers are formed by the repair of double strand breaks (DSBs) preferentially by the homolog. The choice of repair template is determined at the time of strand invasion, which is mediated by two recombinases, Rad51 and the meiosis-specific Dmc1. Rad51 is necessary for Dmc1 to function properly but its strand exchange activity is inhibited both by Dmc1 and Mek1, a meiosis-specific kinase, which is activated by DSBs. Mek1 suppresses interaction between Rad51 and its accessory factor Rad54 in two ways. First, phosphorylation of Rad54 lowers its affinity for Rad51. Second, phosphorylation stabilizes Hed1, a meiosis-specific protein that binds to Rad51 and excludes Rad54. Although <i>RAD54</i> is not required for wild-type levels of interhomolog recombination, <i> rad54</i>&Delta; diploids exhibit decreased sporulation and spore viability, indicating the presence of unrepaired DSBs. My thesis tested the idea that Mek1 kinase activity is down-regulated after interhomolog recombination to allow Rad51-mediated repair of any remaining DSBs. </p><p> Meiotic recombination occurs in the context of a proteinaecous structure called the synaptonemal complex (SC). The SC is formed when sister chromatids condense along protein cores called axial elements (AEs) comprised of the meiosis-specific proteins, Hop1, Red1 and Rec8. AEs are brought together by interhomolog recombination, which creates stable connections and the gluing together of the AEs by the insertion of the transverse filament protein, Zip1, in a process called synapsis. Pachynema is the stage of meiotic prophase in which chromosomes are fully synapsed and where interhomolog recombination has proceeded to the double Holliday junction (dHJ) stage. </p><p> Meiotic progression requires transcription factor <i>NDT80</i>, a middle meiosis transcription factor required to express >200 genes, including the polo-like kinase, CDC5 (required for Holliday junction resolution and SC disassembly) and <i>CLB1</i> (required for meiotic progression). Diploids deleted for <i>NDT80</i> arrest in pachynema with unresolved dHJs. I used an inducible version of <i>NDT80</i> (<i>NDT80-IN </i>) to separate prophase into two phases: pre-<i>NDT80</i>, when interhomolog recombination occurs and post-<i>NDT80</i>, when it is proposed that inactivation of Mek1 allows intersister recombination to repair residual DSBs. <i>RAD54</i> is sufficient to function after interhomolog recombination, as inducing both <i>RAD54</i> and <i>NDT80</i> simultaneously rescues the spore inviability defects observed in <i>NDT80-IN rad54&Delta;</i> diploids. Using an antibody specific for phosphorylated Hed1 as an indicator of Mek1 kinase activity, I showed that Mek1 is constitutively active in <i>ndt80</i>-arrested cells and that induction of <i>NDT80</i> is sufficient to abolish Mek1 activity. Furthermore, inactivation of Mek1 by Ndt80 can occur in the absence of interhomolog strand invasion and synapsis. Mek1 inactivation correlates with the appearance of <i>CDC5</i> and the degradation of Red1. My work demonstrates that the sole target of <i>NDT80</i> responsible for inactivating Mek1 is <i>CDC5</i>. </p><p> Unrepaired DSBs trigger the meiotic recombination checkpoint resulting in prophase arrest, which requires Mek1 and works by sequestering Ndt80 in the cytoplasm. Mek1 also delays meiotic progression in wild-type cells, likely through inactivation of Ndt80. My work shows that Ndt80 in turn negatively regulates Mek1. Based on my observations, as well as published work showing that synapsis results in the removal of Mek1 from chromosomes, I propose that recombination and meiotic progression are coordinated by regulation of Mek1. </p>

<p> Ovarian cancer (OC) takes the lives of nearly 14,000 US women every year. Although platinum is one of the most effective drugs in treating ovarian cancer, the development of platinum resistance is one of the biggest challenges facing patients. I have shown that the long non-coding RNA HOTAIR contributes to platinum-resistant OC and determined the regulators and targets of HOTAIR during the platinum-induced DNA damage response. My published data supports the role of HOTAIR in contributing to DNA damage induced cellular senescence and secretion of pro-inflammatory cytokines leading to cisplatin resistance. My unpublished work (under review) analyzed the interaction of HOTAIR with the PRC2, its known interacting partner. In this study, I developed a novel strategy blocking HOTAIR-PRC2 interaction and resensitized ovarian tumors to platinum in mouse studies. The results offer a pre-clinical proof of concept for targeting long non-coding RNAs as a therapeutic approach and may represent a strategy to overcome chemotherapy resistance in tumors exhibiting high expression of HOTAIR, a frequent observation in high grade serous OC.</p>

<p>When a plant emerges from the soil, it faces a critical developmental transition from utilizing stored energy to grow rapidly toward the light, to developing chloroplasts and beginning photosynthesis. While it is known that this process involves massive transcriptional reprogramming of the nuclear and plastidial genomes, the connections between chloroplast development and nuclear light signaling events are not well understood. One very promising target for investigating these connections is HEMERA (HMR), a dual-localized regulatory protein that is found in both nuclei and chloroplasts. HMR was previously identified as pTAC12, an essential component of the plastid-encoded RNA polymerase complex responsible for transcription of chloroplast photosynthetic genes. In the nucleus, HMR acts within the phytochrome signaling pathway as a transcriptional co-activator of a subset of growth-relevant genes in response to light, to regulate the elongation of the embryonic stem, or hypocotyl. HMR’s combination of roles in the nucleus and chloroplasts are dramatically demonstrated by the phenotypes of the hmr mutant, with a long hypocotyl and albino leaves when grown in the light. </p><p>While the functions of HMR in each compartment have been studied separately, the mechanisms by which the HMR protein is targeted to each compartment have not yet been determined. To address this, I characterized the localization signals of HMR with a combination of in vitro approaches and characterization of transgenic Arabidopsis lines. These experiments revealed that HMR has a cleavable N-terminal chloroplast transit peptide within its first 50 amino acids, while two predicted nuclear localization signals proved not to be highly functional. Surprisingly, HMR in the chloroplasts and nucleus appeared to both be the same cleaved form of the protein. We thus identified the mature form of HMR by mass spectrometry, finding that it begins from lysine as the result of transit peptide cleavage and possibly additional N-terminal processing. Through GST pull-down assays, we determined that this mature form of HMR was fully capable of interacting light signaling components. However, analysis of transgenic lines showed that expression of mature HMR alone could not complement the long-hypocotyl phenotype of the hmr mutant. Analysis of the transcription of HMR nuclear target genes confirmed that mature HMR lacked nuclear functionality. </p><p>Further investigation revealed that mature HMR does not accumulate within the nucleus, most likely as a result of its nonfunctional nuclear localization signals. However, addition of the transit peptide from the small subunit of Rubisco fully restored nuclear accumulation and function of mature HMR in Arabidopsis. Additional experiments testing the localization of a simple model of dual-targeted proteins with two types of localization signal showed that transit peptides might take priority over nuclear localization signals. These results together suggest an unexpected model of localization where HMR is first targeted to the chloroplasts, and then it is subsequently re-localized to the nucleus, thus connecting its nuclear and plastidial functions. Further investigation of this proposed retrograde plastid-to-nucleus translocation pathway promises to shed additional light on the link between nuclear light signaling events and chloroplast development.</p> / Dissertation

<p> Here we present the results of two distinct projects in the field of cellular mechanics. In the first project, we describe a non-monotonicity in the scaling of force production in actomyosin stress fibers. We develop a continuum mechanical model to explain that non-monotonicity and, using both analytical and numerical techniques, conclude that the scaling is due to an interaction between different physical lengthscales inherent in the actomyosin force-production system. Using singular perturbation methods, we study the model further to make predictions about the physical conditions under which a cell can break symmetry. In the second project, we explore how lipid flow in the plane of the plasma membrane contributes to membrane translocation during cell migration. By numerically solving the Stokes equations, we quantify the magnitude of the force necessary to generate this flow, and analyze how the presence of transmembrane protein obstacles influences the resulting front-to-rear membrane tension gradient. We make several analytic estimates of the mechanical importance of this membrane tension for cell motility.</p>

<p> Chronic alcohol induced liver disease (ALD) comprises of a spectrum of disease stages progressing from fatty liver, steatohepatitis, fibrosis, to cirrhosis that may eventually lead to death. Although, the early stages of ALD are reversible, 40% of the patients develop advanced stage liver disease characterized by significant hepatic fibrosis and cirrhosis, for which, currently, liver transplantation is the only curative approach. However, the number patients waiting for liver transplantation far exceeds the meager number of available donors resulting in premature mortality of such patients. Hence, there is an urgent need for therapies for not only prevention and early intervention to stop the disease progression, but also to effectively regenerate the remaining healthy liver so that the patient can be reasonably functional before they can fully recover with a liver transplantation. Thus, any biologically natural modulator that can effectively prevent the progression of ALD until the donor liver is available for transplantation would be desirable even if it cannot completely cure the disease. </p><p> Thymosin &beta;4 (T&beta;4) is an immune modulating natural peptide secreted by thymus gland that is known to prevent inflammation and fibrosis, and promote wound healing and regeneration in the eye, skin and heart. Previous work from our laboratory has also shown that T&beta;4 protects against carbon tetrachloride induced acute liver injury in rat. However, not much is known of the role of T&beta;4 in alcoholic liver injury. Therefore, in this dissertation research, the role of T&beta;4 was investigated in acute on chronic ethanol and lipopolysaccharide (LPS) induced hepatic oxidative stress, inflammation, and fibrosis in an in vivo mouse model, as well as its regenerative potential was studied in chronic ethanol fed mice after partial hepatectomy. Furthermore, the underlying molecular mechanism by which T&beta;4 exerts its action, particularly on fibrosis was examined using human hepatic stellate cells (HSC), the main fibrogenic cells of the liver. </p><p> Based on the well accepted two-hit model for ALD, in the hepatocytes, ethanol acts as the first hit and is oxidized to acetaldehyde, the highly toxic first metabolite of ethanol oxidation by alcohol dehydrogenase (ADH) and ethanol-inducible cytochrome P450 2E1 (CYP2E1) leading to the generation of reactive oxygen species (ROS), resulting in oxidative stress. On the other hand, ethanol-induced leaky gut results in the release of endotoxin (LPS) that acts as the second hit and activates nuclear factor Kappa B (NF?B) in the Kupffer cells and the subsequent production of the pro-inflammatory cytokines that propagates liver inflammation. ROS and the pro-inflammatory cytokines act as fibrogenic stimuli for the activation of HSC and their trans-differentiation from quiescent lipid storing phenotype to activated myofibroblasts that express fibrogenic genes and proliferate and migrate to the site of injury and form a fibrous scar, resulting in fibrosis. This is essentially due to the fact that the quiescent HSC exhibit up-regulated adipogenic gene, peroxisome proliferator-activated receptor gamma (PPAR&gamma;), and down-regulated fibrogenic gene, methyl CpG binding protein (MeCP2), whereas the reverse is true upon their activation to myofibroblasts. </p><p> The experimental results showed that T&beta;4 reduced the ethanol and LPS induced levels of ROS by increasing the levels of the antioxidants, glutathione and superoxide dismutase. It also inhibited the nuclear translocation of NF&kappa;B by blocking the phosphorylation of the inhibitory protein I&kappa;B and thereby prevented the up regulation of pro-inflammatory genes, TNF-&alpha;, IL-1&beta;, and IL-6. T&beta;4 also prevented the activation of HSC by up-regulating miRNA 132, thus suppressing MeCP2, that coordinately reversed the down-regulated adipogenic gene, PPAR&gamma;, and the up-regulated fibrogenic genes (&alpha;-smooth muscle actin, PDGF-&beta; receptor, collagen 1, and fibronectin), and fibrosis. Moreover, T&beta;4 also promoted liver regeneration after partial hepatectomy in chronic ethanol fed mice by increasing hepatocyte growth factor and its receptor, c-Met; &alpha;-fetoprotein; proliferation markers, proliferating cell nuclear antigen and Ki-67 as well as the liver progenitor cell marker, cytokeratin 19.</p><p> Furthermore, it was discovered that in human HSC cultures, T&beta;4 prevented PDGF-BB induced fibrogenesis and also abolished PDGF-BB induced HSC proliferation and migration by blocking the phosphorylation of Akt by preventing the binding of Akt to actin. Moreover, experiments with two bioactive peptides of T&beta;4, the amino terminal peptide (1-15 aa) and the actin binding peptide (17-23 aa) revealed that T&beta;4 exerts most of its anti-fibrotic actions <i> via</i> its actin binding domain.</p><p> In conclusion, these data suggest that T&beta;4 has antioxidant, anti-inflammatory, anti-fibrotic and hepatic regenerative potential against alcoholic liver injury. </p>

<p> The aim of this thesis is to evaluate the impact of somatostatin receptor subtype-4 (SSTR4) actions on microglia cell viability, towards the understanding and advance of pharmacological treatments for Alzheimer&rsquo;s disease (AD). As of March 2016, there were 5 million people living in the United States with AD. Current drugs for AD have highly variable effects from patient to patient and are palliative at best. This thesis project focuses on the study of the BV2 cell line and the compound NNC 26-9100 (NNC). BV2 cells are immortalized microglial cells that maintain most of their morphology. The data collected suggests that BV2 cells can phagocytize amyloid-? peptides (A?), respond to lipopolysaccharide (LPS), and have the somatostatin receptor subtype-4 (SSTR4). NNC is a selective agonist of the SSTR4 and we have found that it causes BV2 cells to increase in number. The effects of NNC were able to be reduced with a somatostatin receptor pan-antagonist, cyclosomatostatin, and the adenyl cyclase activator forskolin. NNC can alter BV2 numbers by binding to the SSTR4, creating an intracellular cascade that results in the inhibition of adenyl cyclase and an increase in cell count. Collectively, a potential therapeutic mechanism for AD is increasing the number of microglial cells to increase both amyloid beta (A?) phagocytosis and degradation of A? by neprilysin.</p>

<p>Light is a critical environmental signal that regulates every phase of the plant life cycle, from germination to floral initiation. Of the many light receptors in the model plant <italic>Arabidopsis thaliana</italic>, the red- and far-red light-sensing phytochromes (phys) are arguably the best studied, but the earliest events in the phy signaling pathway remain poorly understood. One of the earliest phy signaling events is the translocation of photoactivated phys from the cytoplasm to the nucleus, where they localize to subnuclear foci termed photobodies; in continuous light, photobody localization correlates closely with the light-dependent inhibition of embryonic stem growth. Despite a growing body of evidence supporting the biological significance of photobodies in light signaling, photobodies have also been shown to be dispensable for seedling growth inhibition in continuous light, so their physiological importance remains controversial; additionally, the molecular components that are required for phy localization to photobodies are largely unknown. The overall goal of my dissertation research was to gain insight into the early steps of phy signaling by further defining the role of photobodies in this process and identifying additional intragenic and extragenic requirements for phy localization to photobodies. </p><p>Even though the domain structure of phys has been extensively studied, not all of the intramolecular requirements for phy localization to photobodies are known. Previous studies have shown that the entire C-terminus of phys is both necessary and sufficient for their localization to photobodies. However, the importance of the individual subdomains of the C-terminus is still unclear. For example a truncation lacking part of the most C-terminal domain, the histidine kinase-related domain (HKRD), can still localize to small photobodies in the light and behaves like a weak allele. However, a point mutation within the HKRD renders the entire molecule completely inactive. To resolve this discrepancy, I explored the hypothesis that this point mutation might impair the dimerization of the HKRD; dimerization has been shown to occur via the C-terminus of phy and is required for more efficient signaling. I show that this point mutation impairs nuclear localization of phy as well as its subnuclear localization to photobodies. Additionally, yeast-two-hybrid analysis shows that the wild-type HKRD can homodimerize but that the HKRD containing the point mutation fails to dimerize with both itself and with wild-type HKRD. These results demonstrate that dimerization of the HKRD is required for both nuclear and photobody localization of phy.</p><p>Studies of seedlings grown in diurnal conditions show that photoactivated phy can persist into darkness to repress seedling growth; a seedling's growth rate is therefore fastest at the end of the night. To test the idea that photobodies could be involved in regulating seedling growth in the dark, I compared the growth of two transgenic Arabidopsis lines, one in which phy can localize to photobodies (<italic>PBG</italic>), and one in which it cannot (<italic>NGB</italic>). Despite these differences in photobody morphology, both lines are capable of transducing light signals and inhibiting seedling growth in continuous light. After the transition from red light to darkness, the PBG line was able to repress seedling growth, as well as the accumulation of the growth-promoting, light-labile transcription factor PHYTOCHROME INTERACTING FACTOR 3 (PIF3), for eighteen hours, and this correlated perfectly with the presence of photobodies. Reducing the amount of active phy by either reducing the light intensity or adding a phy-inactivating far-red pulse prior to darkness led to faster accumulation of PIF3 and earlier seedling growth. In contrast, the <italic>NGB</italic> line accumulated PIF3 even in the light, and seedling growth was only repressed for six hours; this behavior was similar in <italic>NGB</italic> regardless of the light treatment. These results suggest that photobodies are required for the degradation of PIF3 and for the prolonged stabilization of active phy in darkness. They also support the hypothesis that photobody localization of phys could serve as an instructive cue during the light-to-dark transition, thereby fine-tuning light-dependent responses in darkness.</p><p>In addition to determining an intragenic requirement for photobody localization and further exploring the significance of photobodies in phy signaling, I wanted to identify extragenic regulators of photobody localization. A recent study identified one such factor, HEMERA (HMR); <italic>hmr</italic> mutants do not form large photobodies, and they are tall and albino in the light. To identify other components in the HMR-mediated branch of the phy signaling pathway, I performed a forward genetic screen for suppressors of a weak <italic>hmr</italic> allele. Surprisingly, the first three mutants isolated from the screen were alleles of the same novel gene, <italic>SON OF HEMERA</italic> (<italic>SOH</italic>). The <italic>soh</italic> mutations rescue all of the phenotypes associated with the weak <italic>hmr</italic> allele, and they do so in an allele-specific manner, suggesting a direct interaction between SOH and HMR. Null <italic>soh</italic> alleles, which were isolated in an independent, tall, albino screen, are defective in photobody localization, demonstrating that SOH is an extragenic regulator of phy localization to photobodies that works in the same genetic pathway as HMR.</p><p>In this work, I show that dimerization of the HKRD is required for both the nuclear and photobody localization of phy. I also demonstrate a tight correlation between photobody localization and PIF3 degradation, further establishing the significance of photobodies in phy signaling. Finally, I identify a novel gene, <italic>SON OF HEMERA</italic>, whose product is necessary for phy localization to photobodies in the light, thereby isolating a new extragenic determinant of photobody localization. These results are among the first to focus exclusively on one of the earliest cellular responses to light - photobody localization of phys - and they promise to open up new avenues into the study of a poorly understood facet of the phy signaling pathway.</p> / Dissertation

<p> Throughout development, canonical Wnt signaling contributes to the formation and maintenance of a wide array of cells, tissues, and organs. Dys-regulated Wnt signaling during embryonic development is implicated in developmental defects known as neurochristopathies, including craniofacial and heart defects, as well as defects in neural development. Due to its roles in stem cell maintenance and self-renewal, tissue homeostasis, and regeneration, aberrant Wnt signaling in adult tissues can result in various forms of cancer, including colorectal cancer, breast cancer, lung cancer, and gastro-intestinal cancer, among others. Dys-regulated Wnt signaling is also implicated in other pathologies including bone disease, and metabolic diseases, such as Type II diabetes. Our lab has previously identified a novel crosstalk between canonical Wnt signaling and ephrin signaling. Ephrin signaling occurs through the interaction of ephrin ligands and Eph receptor tyrosine kinases, and is bidirectional. Due to the roles of ephrin signaling in tissue development and maintenance, aberrant ephrin signaling is implicated in many diseases including bone remodeling diseases, diabetes, and cancer. The molecular mechanism of the crosstalk between canonical Wnt signaling and ephrin-B signaling remains unknown. &beta;-catenin is a key intracellular effector of canonical Wnt signaling that transduces the signal to the nucleus, where &beta;-catenin interacts with the TCF/LEF transcription factors and activates transcription of target genes. Due to its central role in transducing the canonical Wnt signal to the nucleus, we predict that ephrin-B signaling antagonizes canonical Wnt signaling by affecting the stability and/or sub-cellular localization of &beta;-catenin, or the interaction between &beta;-catenin and TCF/LEF transcription factors. By employing mouse ephrin-B constructs in human cell lines, we show that the canonical Wnt - ephrin-B crosstalk is conserved between frogs and mammals. We also found that ephrin-B antagonism of canonical Wnt signaling is likely independent of ubiquitin proteasome system (UPS)-mediated degradation of &beta;-catenin. Furthermore, confocal immunofluorescence microscopy revealed that overexpression of ephrin-B in HEK293T cells treated with lithium chloride (LiCl) seems to promote membrane localization of &beta;-catenin, particularly at the apical Z sections. These results suggests that re-localization of &beta;-catenin to the cell membrane may contribute to the ephrin-B antagonism of canonical Wnt signaling.</p>

<p>The basement membrane (BM) is a highly conserved form of extracellular matrix that underlies or surrounds and supports most animal tissues. BMs are crossed by cells during various remodeling events in development, immune surveillance, or during cancer metastasis. Because BMs are dense and not easily penetrable, most of these cells must open a gap in order to facilitate their migration. The mechanisms by which cells execute these changes are poorly understood. A developmental event that requires the opening of a BM gap is C. elegans uterine-vulval connection. The anchor cell (AC), a specialized uterine cell, creates a de novo BM gap. Subsequent widening of the BM gap involves the underlying vulval precursor cells (VPCs) and the π cells, uterine neighbors of the AC through non-proteolytic BM sliding. Using forward and reverse genetic screening, transcriptome profiling, and live-cell imaging, I investigated how the cells in these tissues accomplish BM gap formation. In Chapter 2, I identify two potentially novel regulators of BM breaching, isolated through a large-scale forward genetic screen and characterize the invasion defect in these mutants. In Chapter 3, I describe single-cell transcriptome sequencing of the invasive AC. In Chapter 4, I describe the role of the π cells in opening the nascent BM gap. A complete developmental pathway for this process has been elucidated: the AC induces the π fate through Notch signaling, after which the π cells upregulate the Sec14 family protein CTG-1, which in turn restricts the trafficking of DGN-1 (dystroglycan), a laminin receptor, allowing the BM to slide. Chapter 5 outlines the implications of these discoveries.</p> / Dissertation