Thesis (Ph.D.)--Baylor University, 2005. / Includes bibliographical references (p. 259-273).

Evolutionarily conserved Pumilio (Pum) RNA-binding proteins act as translational repressors during embryo development and cell fate specification. Previous work in the lab has shown that over-expression of Pum2 (Pum2-EML) supports maintenance and suppresses mutilineage differentiation of murine multipotent HSC/MPP-like cell line EML. The subsequent analysis of HSC markers and functional analysis has revealed that wt EML cells share the LKS CD34 positive phenotype, whereas the majority Pum2-EML cells are similar to LKS CD34 negative. The CD34 positive wt EML cells can be divided into CD34low, CD34med and CD34high subpopulations, whereas Pum2-EML CD34 positive cells correspond to CD34low subpopulation. Colony forming assays have revealed that the overall multilineage differentiation of wt EML and Pum2-EML cells strongly correlates with the CD34 expression levels. Multiple experiments have revealed that purified CD34 negative and CD34 positive wt EML cells can generate each other and among CD34 positive wt EML cells the CD34low cells have the highest capacity to give rise to CD34 negative EML cells. We have proposed a model in which CD34 negative EML cells are more primitive cells in an "inactive" (differentiation inhibited) state, that give rise to CD3low "active" (differentiation ready) EML cells. The CD34low EML cells can revert back to the CD34 negative state or give rise to CD34med/high cells that can readily differentiate into multiple lineages. Based on that model, the over-expression of Pum2 leads to increased maintenance of cells in inactive CD34 negative state, and blocks development of CD34 positive cells past the CD34low stage. Cumulatively, these results support the notions that Pum2 could be involved in maintaining the balance between inactive and active state of multipotent hematopoietic cells. The c-kit receptor plays a vital role in self-renewal and differentiation of hematopoietic stem cells (HSC) and multipotent progenitors (MPPs). We have discovered that besides c-kit, the murine multipotent HSC/MPP-like cell line EML expresses the transcript and protein for a truncated form of c-kit, called tr-kit. Notably, the tr-kit transcript and protein levels were down-regulated during cytokine induced differentiation of HSC/MPP-like cell line EML into myelo-erythroid lineages. RT-PCR results show tr-kit is transcribed solely in cell populations enriched for LTR-HSC, STR-HSC and MPPs. The observation that tr-kit is co-expressed with c-kit only in more primitive, HSC and MPP-enriched cell populations raises an exciting possibility that tr-kit functions either as a new component of SCF/c-kit pathway, or is involved in a novel signaling pathway, present exclusively in HSC and MPPs. These findings necessitate functional characterization of tr-kit, and analysis of its potential role in the self-renewal, proliferation and/or differentiation of HSC and multipotent progenitors.

Carbohydrates are known to play a large number of significant roles in various biological and pathological processes such as cancer metastasis and cellular communication. This is because of their ability to bind a wide range of hosts within the human body such as proteins and viruses. Due to these important interactions, carbohydrate sensing has long been a main focus of research. These research strategies have included the use of aptamers, non-covalent interactions, and boronic acid-based receptors. Boronic acid-based sensors are of particular interest due to their selectivity for 1,2- or 1,3-diols. Within these boronic acid-based studies, a large variety of techniques were employed for detection including different fluorescent, electrochemical, polymeric, and colorimetric studies, as well as various surface bound sensors. One type of technique that has rarely been applied is Surface Enhanced Raman Spectroscopy or SERS. This strategy would be beneficial as it provides information about functional groups, which would aid in the identification of the bound sugar. In this thesis, we present work based on the development of a boronic acid-based carbohydrate receptor that will be used to study carbohydrate binding through SERS. The receptor design includes an aryl boronic acid for carbohydrate recognition, a nitrogen atom in close proximity to the boron center to enhance binding, and a terminal thiol for attachment to a metal surface for SERS. This sensor will be used to study the binding of different saccharides for sensing applications.

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2006. / Includes bibliographical references (leaves 60-71).

A major obstacle for developing new antidepressants has been limited knowledge of the structure and function of a central target, the serotonin transporter (SERT). Established SERT inhibitors (SSRIs) were docked to an in silico SERT model to identify likely binding pocket amino acid residues. When mutated singly, no one of five implicated residues was critical for high affinity in vitro binding of SSRIs or cocaine. The in silico SERT model was used in ligand virtual screening (VS) of a small molecule structural library. Selected VS "hit" compounds were procured and tested in vitro; encouragingly, two compounds with novel structural scaffolds bound SERT with modest affinity. The combination of computational modeling, site-directed mutagenesis and pharmacologic characterization can accelerate binding site elucidation and the search for novel lead compounds. Such compounds may be tailored for improved serotonin receptor selectivity and reduced affinity for extraneous targets, providing superior antidepressants with fewer adverse effects. / Mylan School of Pharmacy and the Graduate School of Pharmaceutical Sciences; / Pharmacology / MS; / Thesis;

The RNA-binding protein (RBP) and Hu/ELAV family member HuD regulates mRNA metabolism of genes that encode proteins involved in neuronal differentiation, learning and memory, and certain neurological diseases. Given the important functions of HuD in a variety of processes, we set out to characterize the 5’ genomic region of the mammalian HuD gene and determine the mechanisms that regulate its mRNA expression in neurons using P19 cells and mouse brain as models. Bioinformatic and 5’RACE (rapid amplification of cDNA ends) analyses of the HuD 5’ genomic flanking region identified eight conserved leader exons (E1s), two of which are novel. Expression of all E1 variants was established in differentiating P19 cells, mouse embryonic (E14.5) and adult brains. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in differentiating neurons. Sequential deletion of the 5’ regulatory region upstream of the predominantly expressed E1c variant revealed a well-conserved 400 bp DNA region that contains five E-boxes and is capable of directing expression of HuD specifically in neurons. Using electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitations (ChIPs), and E1c 5’ regulatory region (RR) deletion and mutation analysis, we found that two of these E-boxes are targeted by neurogenin 2 (NGN2/NEUROG2) and that this mechanism is important for induction of HuD mRNA in neurons. Additional deletion and mutation of the E1c 5’ RR revealed that putative cis-acting elements for Kruppel-like factors (KLFs) and nuclear DEAF-1-related (NuDR) transcription factors also positively regulate transcription of HuD. Together, our findings reveal that the intricate transcriptional regulation of mammalian HuD involves eight leader exons and potentially alternate promoters. We further demonstrate that transcription of HuD requires neuron-specific control by NGN2 and possibly KLF and NuDR transcription factors. To our knowledge, this is the first study to identify transcriptional events that positively regulate expression of HuD.

The RNA-binding protein (RBP) and Hu/ELAV family member HuD regulates mRNA metabolism of genes that encode proteins involved in neuronal differentiation, learning and memory, and certain neurological diseases. Given the important functions of HuD in a variety of processes, we set out to characterize the 5’ genomic region of the mammalian HuD gene and determine the mechanisms that regulate its mRNA expression in neurons using P19 cells and mouse brain as models. Bioinformatic and 5’RACE (rapid amplification of cDNA ends) analyses of the HuD 5’ genomic flanking region identified eight conserved leader exons (E1s), two of which are novel. Expression of all E1 variants was established in differentiating P19 cells, mouse embryonic (E14.5) and adult brains. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in differentiating neurons. Sequential deletion of the 5’ regulatory region upstream of the predominantly expressed E1c variant revealed a well-conserved 400 bp DNA region that contains five E-boxes and is capable of directing expression of HuD specifically in neurons. Using electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitations (ChIPs), and E1c 5’ regulatory region (RR) deletion and mutation analysis, we found that two of these E-boxes are targeted by neurogenin 2 (NGN2/NEUROG2) and that this mechanism is important for induction of HuD mRNA in neurons. Additional deletion and mutation of the E1c 5’ RR revealed that putative cis-acting elements for Kruppel-like factors (KLFs) and nuclear DEAF-1-related (NuDR) transcription factors also positively regulate transcription of HuD. Together, our findings reveal that the intricate transcriptional regulation of mammalian HuD involves eight leader exons and potentially alternate promoters. We further demonstrate that transcription of HuD requires neuron-specific control by NGN2 and possibly KLF and NuDR transcription factors. To our knowledge, this is the first study to identify transcriptional events that positively regulate expression of HuD.

Graduation date: 1991

Growth hormone binding protein (GHBP) may be an important factor in the regulation of growth as well as an indirect, less invasive way of predicting the status of growth hormone receptors. Several factors (age, nutritional status, sex, and glucocorticoid administration) have been reported to influence circulating growth hormone (GH) levels, growth hormone receptor (GHR) activity and/or GHBP in mammalian species. Therefore, the studies conducted in this research were designed to determine if these factors have any affect on serum GHBP in the young broiler chicken. Serum GHBP activity was expressed as a percent specifically bound ¹²⁵IhGH (%SB), as measured by a dextran-coated charcoal assay. Serum GHBP activity was highest (mean %SB= 14.6 ± 1.2) at hatch aniedecreased linearly (r= -.9516) to 4 wk of age (mean %SB= 4.1 ± 0.6). Sex had no significant affect on serum GHBP activity from hatch to 4 wk of age. Short term nutrient deprivation (24 h fast) of 4 wk old birds had no significant affect on serum GHBP activity, nor did refeeding. Feeding birds nutrient poor diets (low energy, low protein or low energy and low protein) did not significantly affect serum GHBP activity when compared to birds fed a commercial broiler diet. Pulsatile delivery of cortisone acetate (1, 5 and 10 mg/d/b) had no affect on serum GHBP activity at any dose. These results suggest that serum GHBP activity in the chicken is not affected by many factors which do influence GHBP in mammalian species. The lack of response to nutrient deprivation and cortisone acetate may be a factor related to the age of the birds used in these studies. / Graduation date: 1993

Streptococcus pyogenes (Group A Streptococcus) is a Gram-positive bacterial pathogen that causes significant superficial and invasive diseases. Iron acquisition is an important component of GAS pathogenesis in the human host. The 10 gene sia operon of GAS is involved in the acquisition of iron via heme or heme-binding proteins and encodes an ABC transporter as well as the large multifunctional receptor Shr. Domain analysis of Shr shows that it contains two copies of the DUF1533 (domain of unknown function) in its N-terminal part and two NEAT (NEAr Transporter) domains. NEAT domains are found in variable copy number in surface proteins of Gram-positive pathogens and are implicated in binding to various ligands. A new recombinant Shr protein was cloned and a purification protocol was developed, improving the yield of the full-length protein. A solid phase binding assay was developed and used to demonstrate Shr binding to hemoglobin. Several truncated Shr proteins were expressed and purified: the N-terminal Domain (NTD) up to but not including the first NEAT domain of Shr, the NTD plus the first NEAT domain (NTD-NEAT1) and the second NEAT domain alone (NEAT2). It was determined that Shr’s NTD mediates hemoglobin binding, demonstrating that a new protein pattern in Shr is involved in hemoglobin binding, and implicating the DUF1533 in this process. It was also determined that NTD-N1 and NEAT2 bind heme while NTD does not. Therefore, both NEAT domains may participate in the capture of heme from the host hemoglobin by Shr.