<p> Bronchopulmonary dysplasia (BPD) is a serious respiratory complication for the preterm newborn characterized clinically by prolonged respiratory distress and histologically by alveolar simplification and decreased pulmonary vasculature. The development of BPD is well linked to oxidative stress suffered by the newborn as a result of a preterm fetal-neonatal transition, supplemental oxygen, infection, increased inflammation, and mechanical ventilation. Damage suffered by oxidative stress may be through direct mechanisms or through alteration of redox&not;sensitive pathways involved in cell death, cell survival, differentiation, and proliferation. Redox&not;sensitive modifications regulating protein function and redox-sensitive pathways have mainly been ascribed to oxidative modification of cysteine thiols. As their modification is critical for protein function, maintenance of the thiol redox status is crucial. Thioredoxin-1 (Trx1) functions in maintenance of thiol redox homeostasis, and its redox activity is intimately linked to antioxidant, cytoprotection, proliferation responses, and cytoprotection. While Trx1 targets of redox regulation have been identified, we hypothesize that additional protein may be redox regulated and that Trx1 target profiles may change during oxidative stress. Therefore a novel immunoprecipitation approach, identified as the substrate trap approach, was developed to identify Trx1 targets. The following demonstrates the use of the substrate trap approach for identification of Trx1 redox targets and further application of the approach to identify alterations in target profiles in response to oxidative stress. Use of nuclear targeted substrate trap was successfully employed to enrich from nuclear Trx1 targets. As a final component the characterization of the Trx1 system in mouse from late embryonic development through the first week of life animals were exposed to room air or hyperoxia (model of BPD). Characterization indicates impairment of the Trx1 system in response to hyperoxic injury. As Trx1 is known to regulate proliferation, cell death, survival, differentiation pathways, impairment of the Trx1 system during early neonatal development may potentiate hyperoxic injury and alterations in lung development. Better understanding of Trx1 interactions occur through the substrate trap in a physiological model of BPD will help elucidate redox-signaling pathways involved in BPD pathogenesis.</p>

Over the past several decades, cell size and its resulting effects on tissue and organ function, as well as on its overall ability of the animal to perform complex tasks, has been studied extensively. Neuronal size (diameter of individual neurons) could have an influence on intelligence, brain capacity, and ability to perform complex behavioral tasks. Furthermore, there appears to be an increase in number of neurons with an increase in brain size in vertebrates. In insects, increased neuron number has also been correlated with more complex behavior. In this thesis, I test the hypothesis that the neuronal number and/or neuronal size correlate with the brain size using an insect model. This may help elucidate the apparent positive correlation between brain size and intelligence. To achieve this goal, I used a species of bumblebee, Bombus impatiens. Bumblebee workers vary extensively in brain and body size and weight, therefore allowing comparison between individuals of the same species. Workers within a colony differ in size and the amount of work a worker does depends on their body size. Larger sized workers have more foraging capability than smaller sized workers and foraging requires a more demanding sensory integration and memory capacity. In my study, it was found that brain volume was positively correlated with bee body size. Three cell body regions of the brain were further analyzed: inside of the mushroom body calyces, a cell body region next to the lobula, and cell bodies associated with the antennal lobe. No significant correlations between neuron number per unit of volume (neuron density) and brain volume were found. Assuming similar neuronal density in large and small brains, increased brain size is thus correlated with an overall increased neuron number.

The liver has a unique capability for regeneration and is particularly resilient to insult. It plays an essential role in drug disposition and metabolism, regulating numerous pathways involved in ADME (absorption, distribution, metabolism, and excretion) processes. In order for a drug to be effective, it must be able to get to its target site in a timely manner and at an appropriate concentration. Chronic liver disease has been of increasing significance and elucidating the driving forces behind disease progression is key to understanding adverse drug reactions and many cases of liver toxicity. Coordinate regulation of liver transporters and drug metabolism enzymes is essential for maintaining homeostasis and effective liver functionality. Nonalcoholic steatohepatitis, a severe inflammatory disease state that progresses from normal steatosis and Nonalcoholic Fatty Liver Disease has shown significant changes in gene expression as pathological disease progression occurs. Transcription factor binding site analysis proves lucrative in elucidating key signaling pathways in disease progression. Several up and down-regulated genes have enriched transcription factor binding sites in the NASH disease state, including members of the HNF, SOX, and LXR families. These transporters and drug metabolizing enzymes are involved in key processes, including inflammatory signaling, liver cell maintenance, bile acid regulation and other processes that are driving factors in liver repair and insult. By identifying key transcription factors in disease progression and looking at the signaling pathways behind the enriched transcription factors, potential driving factors behind disease progression are discovered. As a major contributor to the progression of the disease state, the significance of driving factors for hepatic fibrosis are discussed. The immune system and inflammatory processes are key drivers of fibrosis and cirrhosis, often mediated by cytokines, such as IL-4 and IL-6.

Although a few regulators of memory and addiction have been identified, the biochemical pathways that mediate the development of addiction and memory remain poorly understood. In addition, important questions remain as to how these two phenomena can persist for so long, sometimes for the entire life of an individual.Signaling molecules and transcription factors are activated in response to stimuli that induce long-term neuronal plastic changes. The transcription factor CREB (cAMP-responsive element binding protein) is clearly involved in triggering processes of addiction and memory, but its sustained activation following a course of chronic drug exposure (or learning) returns to baseline within days [1]. Even the enduring increased levels of deltaFosB (a Fos family transcription factor that couples with other proteins in the AP-1 family to form transcriptional activator/repressor complexes) observed in regions of the mammalian brain following chronic drug exposure, persists for only weeks or months. Thus, although CREB and deltaFosB probably initiate the very stable behavioral changes seen with addiction and memory, their alterations cannot mediate those behavioral changes per se [1]. Long-term up- or down-regulation of molecules downstream of these transcription factors, or others, must be responsible for the enduring modifications in synaptic connectivity and structure believed to be required for the maintenance of these durable behavioral states [2].Many believe that more rapid progress will be made toward understanding the molecular basis of addiction if research efforts proceed hand-in-hand with, rather than in isolation from, the overlapping neurobiological study of learning and memory [1, 2]. The importance and utility of using simple model systems such as Drosophila and Aplysia to identify and characterize genes involved in long-term synaptic plasticity, and hence memory formation, is well documented [3-5]. Identification and functional analyses of neuronal genes transcriptionally regulated by AP-1 and CREB in Drosophila would elaborate on molecular mechanisms of long-term plasticity and hence help us understand, and perhaps manipulate, processes that underlie addiction and memory.

Nitric Oxide (NO) regulates cardiovascular homeostasis by binding to soluble guanylate cyclase (sGC), leading to cGMP production, reduced cytosolic calcium concentration ([Ca²⁺]ᵢ) and vasorelaxation. Thrombospondin-1 (TSP-1), a secreted matricellular protein, was recently discovered to inhibit NO signaling and sGC activity. Inhibition of sGC requires binding to cell-surface receptor CD47. Here, I show that a TSP-1 C-terminal fragment (E3CaG1) readily inhibits sGC in Jurkat T cells, and that inhibition requires an increase in [Ca²⁺]ᵢ. Using digital imaging microscopy on live cells, I further show that E3CaG1 binding results in a substantial increase in [Ca²⁺]ᵢ, up to 300 nM. Addition of angiotensin II, a potent vasoconstrictor known to increase [Ca²⁺]ᵢ, also strongly inhibits sGC activity. sGC isolated from calcium-treated cells or from cell-free lysates supplemented with Ca²⁺ remains inhibited, while addition of kinase inhibitors staurosporine, genistein, PP1 or PP2 reverse inhibition, indicating inhibition likely involves a tyrosine kinase, more specifically, a src family kinase. Rat sGC is also inhibited by lysates supplemented with Ca²⁺, suggesting that the site of modification is at an evolutionarily conserved residue. Inhibition is through an increase in K(m) for GTP, which rises to 834 μM for the NO-stimulated protein, a 13-fold increase over the uninhibited protein. Compounds YC-1 and BAY 41-2272, allosteric stimulators of sGC that are of interest for treating hypertension, overcome E3CaG1-mediated inhibition of NO-ligated sGC. Taken together, these data suggest that sGC not only lowers [Ca²⁺]ᵢ in response to NO, inducing vasodilation, but is also inhibited by high [Ca²⁺]ᵢ, providing a fine balance between signals for vasodilation and vasoconstriction.

Adrenomedullin (AM) and pro-adrenomedullin N-terminal 20-peptide (PAMP) are peptides recently identified from a rat pheochromocytoma. Both of these peptides are cleavage products of pre-pro-AM. Specific receptors for AM have been characterised in several species, including rat and human. The aim of this study was to investigate the role of PAMP and AM in the adrenal cortex. Using an intact rat capsule preparation PAMP was shown to cause a dosedependent increase in aldosterone secretion, which was accompanied by a dosedependent increase in cAMP release. The effects of PAMP were inhibited by HA1004, an inhibitor of protein kinase A. These results suggest that PAMP stimulates aldosterone secretion from the zona glomerulosa via cAMP. Ligandbinding studies were then used to demonstrate the presence of specific PAMP receptors. Two classes of receptor were shown in the rat zona glomerulosa (Kdi 1.9 nmol/l, Bmai, 53 fmol/mg protein; Kd2 10 nmol/l, Bmac,2 225 fmol/mg protein). At the latter receptor PAMP was displaced by AM. None of the other competitors tested displaced PAMP. Using the H295R cell line, both PAMP and AM were shown to increase aldosterones ecretion in a dose-dependenmt anner. In both casesa corresponding dose-dependent increase in cAMP was observed. Both PAMP and AM also effected a dose dependent increase in cortisol secretion. mRNA analysis showed that the gene encoding pre-pro-AM was expressed in these cells. Immunocytochemistry confirmed that these cells were producing both PAMP and AM. Immunocytochemistry and mRNA analysis also revealed that both of the candidate receptors for AM, L1 and CRLR, are expressed in this cell line. Taken together these findings demonstrate that both AM and PAMP are produced by adrenocortical cells and likely to have a role in regulating adrenal steroidogenesis. Furthermore, these studies suggest the presence of a specific PAMP receptor in the rat adrenal gland.

The target of rapamycin complex I (TORC1) regulates cell growth and metabolism in all eukaryotes. Previous studies have shown that nitrogen and amino acid signals activate TORC1 via three GTPases; Gtr1, Gtr2, and Rho1, and the SEA-associated Npr2/3 proteins. However, little is known about the way that other nutrient or stress signals are transmitted to TORC1. Here I present two studies identifying how, and at what level, glucose and other environmental stimuli act to tune TORC1 signaling. In the first study I show that the TORC1 pathway populates three additional stress/starvation states. First, in glucose starvation conditions, the AMP-activated protein kinase (AMPK/Snf1) and at least one other factor push the TORC1 pathway into an off state, in which Sch9-branch signaling and PP2A-branch signaling are both inhibited. The TORC1 pathway remains in the glucose starvation state even when cells are simultaneously starved for nitrogen and glucose or treated with rapamycin. Second, in osmotic stress, the MAPK Hog1/p38 drives the TORC1 pathway into a different state, in which Sch9 signaling and PP2A-branch signaling are inhibited, but PP2A-branch signaling can still be activated by nitrogen starvation. Third, in oxidative stress and heat stress, TORC1-Sch9 signaling is blocked while weak PP2A-branch signaling occurs. Together, the data show that the TORC1 pathway acts as an information-processing hub, activating different genes in different conditions to ensure that available energy is allocated to drive growth, amino acid synthesis, or a stress response, depending on the needs of the cell. In the second study I investigate further the observed hierarchy of TORC1 inputs. I show that glucose starvation triggers disassembly of TORC1, and movement of the key TORC1 component Kog1, to a single body near the edge of the vacuole. These events are driven by AMPK/Snf1-dependent phosphorylation of Kog1 at Serine 491/494 and two nearby prion-like motifs. Kog1-bodies then serve to increase the threshold for TORC1 activation in cells that have been starved for a significant period of time. Together, this data shows that Kog1-bodies create hysteresis (memory) in the TORC1 pathway and help ensure that cells remain committed to a quiescent state under suboptimal conditions.

To thrive when conditions are favorable and survive when they are stressful, cells must carefully regulate their growth rate and stress response programs. This requires rapid, coordinated regulation of many genes in response to information about the levels of numerous nutrients and stress conditions. We are beginning to understand how, in eukaryotes, the TORC1 and PKA pathways regulate growth in nutrient rich conditions. However, how cells tune growth and stress responses in suboptimal conditions is largely unknown. To address this, we ran screens to begin reconstructing the growth regulation network in stress conditions. We found many novel regulators, including signaling proteins, components of the vacuolar ATPase, transcription factors, and components of the endomembrane system. In order to place these regulators in the TORC1 pathway, we performed follow up experiments on over 300 of these regulators using the TORC1 inhibitor rapamycin. We were able to place many new components in the TORC1 pathway, including 59 genes that act downstream of TORC1. We were particularly interested in the discovery that Vip1, a conserved inositol pyrophosphate kinase, was necessary for the shutdown of hundreds of growth genes in stress and starvation conditions. In subsequent experiments, we learned that the inositol pyrophosphate second messengers (including 1-PP-IP5, 5-PP-IP4, and 5-PP-IP5) are critical regulators of cell growth and the general stress response, acting in parallel to the TORC1 pathway to control the activity of the class I HDAC Rpd3L. Taken together, this work reveals many new regulators of cell growth and shows how delineation of one such regulator uncovered a global role for a little known family of second messengers.

Thioredoxin-1 is a redox protein upregulated in many cancers. Its functions include inhibition of apoptosis, increasing cellular growth and proliferation. It has been shown that cells displaying increased levels of Trx-1 have increased drug resistance. PX-12 is a Trx-1 inhibitor that shows anti-proloferative and cytotoxic activity in vitro and in vivo. We used surface enhanced laser desorption/ionization time-of-flight mass spectroscopy (SELDI-TOF-MS) to measure plasma Trx-1 levels of patients treated with PX-12 as a side study of a phase-I trial. SELDI-TOF-MS was able to measure a decrease in plasma Trx-1 after PX-12 treatment semi-quantitatively. In addition, SELDI measured 57 other protein peaks in plasma; seven which were found in all plasma samples analyzed. One of these peaks was located at 13.86kDa and identified through LC-MS/MS sequencing to be a variant of Transthyretin. Further studies into these additional peaks are necessary to determine their biological importance in relation to Trx-1 and PX-12.

Proliferating cells have unique metabolic requirements beyond those of quiescent cells. Specifically, blood forming hematopoietic stem cells, during periods of severe blood loss, switch from a quiescent glycolytic state to a state dependent on mitochondrial metabolism during differentiation and proliferation. This dissertation attempts to define some of the signaling details of this switch by using erythropoietin receptor signaling as a model. In cytokine-dependent Ba/F3 cell line expressing the receptor for erythropoietin (EpoR) (Ba/F3-EpoR), chemical inhibition of mitochondrial function by rotenone decreases in erythropoietin(Epo)-stimulated proliferation. This observation led to the examination of whether Epo could stimulate mitochondrial function. To further assess the role of mitochondria in cell proliferation and the metabolic functions of Epo, levels of oxidative phosphorylation markers and signaling molecules important for mitochondrial biogenesis were measured. Western blotting scans showed increased protein levels of cytochrome oxidase subunit IV (CoxIV) and Complex III core protein 2 following 24 hours of Epo treatment. Interestingly, inhibition of Janus Kinase 2 (Jak2), the tyrosine kinase associated with Epo receptor, by AG490 elicited a similar decrease in CoxIV to Epo withdrawal even in the presence of Epo. In addition, Epo increased the levels of the mitochondrial biogenesis regulator AMP-activated protein kinase α (AMPKα) in a Jak2-dependent manner within Ba/F3 cells. Both total and phosphorylated (activated) AMPKα were increased following Epo stimulation. Treatment with the AMPK inhibitor Compound C decreased Epo stimulation of CoxIV, suggesting a linear signaling cascade from Jak2 to mitochondrial biogenesis through AMPKα. Examining potential mechanisms, direct binding of AMPKα to (EpoR) and Jak2 were observed through immunoprecipitations of transfected lysates in a manner exclusive to AMPK regulator subunits β and γ. Furthermore AMPKα was found to be tyrosine phosphorylated in an Epo and Jak2 dependent manner. Taken together, data in this dissertation suggests a role for Epo in regulating mitochondrial biogenesis in cytokine dependent cells through a potential mechanism of forming a signaling complex between EpoR, Jak2, and AMPKα. This signaling complex may provide intersection between Epo's signaling in cell proliferation and metabolism through AMPKα.