Biochemistry, Biophysics, and Structural Biology Commons^™

Alkylphenol Contamination In Homarus Americanus, Jennifer Renee Urban

Honors Scholar Theses

Alkylphenols are pollutants that are present in marine sediments and fishes. In earlier work it has been discovered that alkylphenols are present in the Homarus americanus, or the American lobster. Research suggests that alkylphenols could behave as endocrine disruptors as they have been found to affect juvenile hormone activity. It has been hypothesized that lobsters may be able to rid themselves of alkylphenol contamination through secreting these compounds into the environment or sequestering them in their tissues. In this study, I address the question of how lobsters may rid themselves of alkylphenols by analyzing hemolymph, muscle, gill, and shell samples …

Glycopeptidome Of A Heavily N-Glycosylated Cell Surface Glycoprotein Of Dictyostelium Implicated In Cell Adhesion, Christa L. Feasley, Jennifer M. Johnson, Christopher M. West, Catherine P. Chia

School of Biological Sciences: Faculty Publications

Genetic analysis has implicated the cell surface glycoprotein gp130 in cell interactions of the social amoeba Dictyostelium, and information about the utilization of the 18 N-glycosylation sequons present in gp130 is needed to identify critical molecular determinants of its activity. Various glycomics strategies, including mass spectrometry of native and derivatized glycans, monosaccharide analysis, exoglycosidase digestion, and antibody binding, were applied to characterize a nonanchored version secreted from Dictyostelium. s-gp130 is modified by a predominant Man8GlcNAc4 species containing bisecting and intersecting GlcNAc residues and additional high-mannose N-glycans substituted with sulfate, methyl-phosphate, and/or core R3-fucose. Site mapping confirmed the occupancy …

The Ubiquitin Ligase Ube4b Is Required For Efficient Epidermal Growth Factor Receptor Degradation, Natalie Sirisaengtaksin

Dissertations and Theses (Open Access)

The length of time that integral membrane proteins reside on the plasma membrane is regulated by endocytosis, a process that can inactivate these proteins by removing them from the membrane and may ultimately result in their degradation. Proteins are internalized and pass through multiple distinct intracellular compartments where targeting decisions determine their fate. Membrane proteins initially enter early endosomes, and subsequently late endosomes/multivesicular bodies (MVBs), before being degraded in the lysosome. The MVB is a subset of late endosomes characterized by the appearance of small vesicles in its luminal compartment. These vesicles contain cargo proteins sorted from the limiting membrane …

Genetic And Biochemical Studies Of Plasmid Pir52-1 In Lactobacillus Helveticus, Cody Alexander Tramp

Undergraduate Honors Capstone Projects

Lactobacillus helveticus is a species of lactic acid bacteria. These bacteria, which produce lactic acid as a major product of carbohydrate metabolism, are used industrially to produce cheese and other fermented dairy products (Ebringer et al., 2008). Many species of lactic acid bacteria also possess probiotic characteristics and when ingested potentially confer increased immune function, regulate gut microbiota, and improve digestion in the host (Reid, 2008). Genetic studies of these probiotic effects and other characteristics of L. helveticus and related species have been hindered by the lack of stably replicating plasmid vectors. Plasmid vectors for several Lactobacillus species have been …

The Rho Family Gtpase: Determining Gef Specificity Through Recombinant Expression, Farrah Steinke

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Comparing Models Of Evolution For Ordered And Disordered Proteins, Celeste J. Brown, Audra K. Johnson, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity ( …

Animal Models Of Alzheimer's Disease, Gemma Casadesus, Gary Arendash, Frank Laferla, Mike Mcdonald

Molecular Biosciences Faculty Publications

No abstract provided.

Phosphorylation Of The Glycine Transporter 1, Javier Vargas Medrano

Open Access Theses & Dissertations

The extracellular levels of the neurotransmitter glycine in the brain are tightly regulated by the high-affinity glycine transporter 1 (GlyT1) and the clearance of glycine depends on its rate of transport and the levels of cell surface GlyT1. Over the past years, it has been shown that PKC activation diminishes the activity and promoted phosphorylation of several neurotransmitter transporters including the dopamine, serotonin and norepinephrine transporters however, its role is unknown for the glycine transporter. To get insights into the role of PKC activation on GlyT1 regulation, we used three N-terminus GlyT1 isoforms stably expressed in porcine aortic endothelial (PAE) …

Regulatory And Functional Aspects Of Foxo3a Transcription Factor And Their Implications In Prostate Cancer, Melissa Elise Dobson

Wayne State University Dissertations

The P13K/Akt pathway is a critical mediator of growth factor signaling involving many cellular functions. The deregulation of this pathway has been shown to be involved in the development of various cancers. One of the main targets of this pathway is FoxO3a, a transcription factor whose target genes are involved in important cellular processes such as apoptosis, cell cycle control, and glucose metabolism. FoxO3a is regulated by various post translational modifications including acetylation, ubiquitination and phosphorylation. The transcription factor is directly phosphorylated by Akt on 3 residues: Threonine 32, Serine 253 and Serine 315. Phosphorylation by Akt generates binding sites …

The Role Of Ledgf/P75 In Transcriptional Regulation, Jeffrey Ryan Kugelman

Open Access Theses & Dissertations

The Lens Epithelial Derived Growth Factor p75 (LEDGF/p75) is a chromatin bound protein whose cellular function is not yet clearly known. A role in transcriptional regulation had been previously proposed based on its interaction with the basal transcriptional machinery and on its effects on the expression of genes involved in the cellular response to environmental stresses. To further elucidate the function of LEDGF/p75, we conducted a global and unbiased evaluation of the role of this protein in gene expression. To that aim, we performed a microarray analysis of cellular gene expression in cells that are severely depleted of LEDGF/p75. To …

Cloning Of "Animal Cryptochrome" Cdna From The Model Organism Chlamydomonas Reinhardtii For Functional Analysis Of Its Protein Product, Shobha Lavanya Silparasetty

Masters Theses & Specialist Projects

reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases …

The Role Of Multiple Ccaat-Binding Factors In Candida Albicans Gene Expression, Lashall Lynn Bates

Graduate Theses and Dissertations

The CCAAT-binding factor is a heterooligomeric transcription factor that is evolutionarily conserved in eukaryotes. In yeast, the DNA-binding component that interacts with the CCAAT consensus sequence in promoters consists of the subunits termed Hap2p, Hap3p and Hap5p. In yeast and fungi, a fourth subunit, Hap4p, is required for regulating gene expression. The goal of this research is to understand the function of the Candida albicans CCAAT-binding factor and how it relates to virulence and pathogenicity. C. albicans is a human opportunistic pathogen responsible for a variety of mucosal and systemic infections that result in significant morbidity and mortality, particularly in …

Characterization And Functional Regulation Of Bioactive Peptides In Avian Macrophages And Heterophils, Lakshmi Kannan

Graduate Theses and Dissertations

Oligopeptides and low molecular weight polypeptides play central roles as effectors and signal transducers acting as hormones, neurotransmitters, growth factors, toxins, and antimicrobial factors that are important for the survival of the organism. Owing to the ubiquitous involvement of peptides in many key regulatory processes, we have been interested to identify native peptides in different cells and tissues and understand their functions. To conduct our studies, we used avian macrophages and heterophils as models of specialized cells which constitute central components of innate immunity. These studies involved (a) qualitative identification and characterization of the peptides associated with high intensity mass …

Integral Membrane Proteins Brr6 And Apq12 Link Assembly Of The Nuclear Pore Complex To Lipid Homeostasis In The Endoplasmic Reticulum, Christine A. Hodge, Vineet Choudhary, Michael J. Wolyniak, John J. Scarcelli, Roger Schneiter, Charles N. Cole

Dartmouth Scholarship

Cells of Saccharomyces cerevisiae lacking Apq12, a nuclear envelope (NE)-endoplasmic reticulum (ER) integral membrane protein, are defective in assembly of nuclear pore complexes (NPCs), possibly because of defects in regulating membrane fluidity. We identified BRR6, which encodes an essential integral membrane protein of the NE-ER, as a dosage suppressor of apq12 Delta. Cells carrying the temperature-sensitive brr6-1 allele have been shown to have defects in nucleoporin localization, mRNA metabolism and nuclear transport. Electron microscopy revealed that brr6-1 cells have gross NE abnormalities and proliferation of the ER. brr6-1 cells were hypersensitive to compounds that affect membrane biophysical properties and to …

Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf

Honors Scholar Theses

Creatine Kinase (CK) is used as a measure of exercise-induced muscle membrane damage. During acute eccentric (muscle lengthening) exercise, muscle sarcolemma, sarcoplasmic reticulum, and Z-lines are damaged, thus causing muscle proteins and enzymes to leak into the interstitial fluid.

Strenuous eccentric exercise produces an elevation of oxygen free radicals, which further increases muscle damage. Muscle soreness and fatigue can be attributed to this membrane damage. Estradiol, however, may preserve membrane stability post-exercise (Brancaccio, Maffulli, & Limongelli, 2007; Carter, Dobridge, & Hackney, 2001; Tiidus, 2001). Because estradiol has a similar structure to Vitamin E, which is known to have antioxidant properties, …

Analysis Of The Phosphorylated Forms Of Protein Kinase R, Christine Quartararo

Honors Scholar Theses

Protein Kinase R (PKR) is induced by interferon and activated by dsRNA. Subsequent autophosphorylation and phosphorylation of eIF2alpha inhibits viral replication. In the latent state PKR exists as an unphosphorylated monomer. Work in the Cole laboratory has shown two additional states, a phosphorylated monomeric state (pPKRm) and a phosphorylated dimeric state (pPKRd). RNA serves as a scaffold bringing two PKRs together allowing dimerization and autophosphorylation to occur. The contribution of each state to the function of PKR remains unclear. Western blots were performed to examine the phosphorylation states of the essential residues,

T446 and T451. Activity assays have shown activation …

Characterizing The Role Of Phaeobacter In The Mortality Of The Squid, Euprymna Scolopes, Brian Shawn Wong Won

Honors Scholar Theses

The subject of our study is the Hawaiian bobtail squid, Euprymna scolopes, which is known for its model symbiotic relationship with the bioluminescent bacterium, Vibrio fischeri. The interactions between E. scolopes and V. fischeri provide an exemplary model of the biochemical and molecular dynamics of symbiosis since both members can be cultivated separately and V. fischeri can be genetically modified 1. However, in a laboratory setting, the mortality of embryonic E. scolopes can be a recurrent problem. In many of these fatalities, the egg cases display a pink-hued biofilm, and rosy pigmentation has also been noted in the deaths of …

Characterization Of A Hypothetical Protein Critical For The Symbiotic Interaction Of Aeromonas Veronii And Hirudo Verbana, Kaitlin Vaughan

Honors Scholar Theses

The digestive tract symbiosis of the medicinal leech, Hirudo verbana, is a model system for studying the genes required for microbial colonization of digestive tracts, as H. verbana has only two species of bacteria that dominate the crop microbiota, Aeromonas veronii and a Rikenella-like bacterium. Signature-tagged mutagenesis (STM) of the A.

veronii strain, HM21R, revealed genes required for the colonization of the digestive tract. One of these mutants, JG573, has an interrupted gene that is predicted to encode a hypothetical protein. The region flanking the transposon insertion of this mutant was sequenced by primer walking.

Comparison of the flanking DNA …

Contribution Of The Novel C-Terminal Domain To The Ribosome Binding Activities Of Virulence Regulator Bipa, Heeren Makanji

Honors Scholar Theses

Bacterial GTPases regulate many cell functions, including the stress response, signal recognition, protein synthesis, and cell differentiation, through a molecular switch that is activated and deactivated depending on their nucleotide bound state (1). A member of the translational family of bacterial GTPases along with LepA and EF-G, BipA is a 67 kD protein that is essential for virulence and the stress response. Crystal structures from the Robinson lab have shown a unique C-terminal domain on BipA that has been implicated in ribosome binding. Using N-terminal deletion constructs, we have shown that the C-terminal domain is necessary, but not sufficient, to …

Knockdown Of Kiaa0319 Reduces Dendritic Spine Density, Daniel Young Kim

Honors Scholar Theses

Developmental Dyslexia is a reading disorder that affects individuals that possess otherwise normal intelligence. Until the four candidate dyslexia susceptibility genes were discovered, the cause of cortical malformations found in post mortem dyslexic brains was unclear. Normal brain development is crucial for the proper wiring of the neural circuitry that allow an individual to perform cognitive tasks like reading. For years, familial and twin studies have suggested that there was a genetic basis to the causation of dyslexia. Kiaa0319 was among the candidate dyslexia susceptibility genes that were ascertained. KIAA0319 is located on Chromosome 6p22.2-22.3 and has been found to …

The Membrane Interface Of Chloroplast Signal Recognition Particle-Dependent Protein Targeting, Naomi Jane Marty

Graduate Theses and Dissertations

A novel signal recognition particle (SRP) found in the chloroplast (cpSRP) works in combination with the cpSRP receptor, cpFtsY, to facilitate the post-translational targeting of a family of nuclear-encoded thylakoid proteins to the Alb3 translocase in thylakoid membranes. Work here focused on understanding events at the membrane that take place to ensure targeting of the cpSRP-dependent substrate to Alb3. Specifically, we sought to understand the structural and functional role of membrane binding by cpFtsY, a protein that exhibits the ability to partition between the membrane (thylakoid) and soluble (stroma) phase during protein targeting. We also sought to understand whether a …

Study Of The Dna Damage Complexes Within The Htlv-1 Tax Oncoprotein Interactome, Sidi Mehdi Belgnaoui

Theses and Dissertations in Biomedical Sciences

Human T-cell leukemia virus type 1 (HTLV-1) is a transforming retrovirus that can give rise to adult T-cell leukemia (ATL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Tax is a virally encoded oncoprotein that is involved in HTLV-1 mediated cellular transformation. It has been hypothesized that Tax induces genomic instability via repression of the cellular DNA damage repair response. Our laboratory has previously shown that the interaction between Tax and various proteins involved in the DNA-damage response pathway impairs the ability of these proteins to mount an efficient repair response. As part of these observations, we proposed that Tax induces …

Evolution Of Gene Structure In Multicellular Eukaryotes, Maria Hester

Inquiry: The University of Arkansas Undergraduate Research Journal

We investigated the patterns of intron conservation in eukaryotes for five different genes. The genes examined were ribosomal proteins L8, S14 and S17, along with elongation factor 2B and triose phosphate isomerase. Intron conservation for S14, S17, and triose phosphate isomerase was determined for 32 species representing the major branches of multicellular eukaryotes. For 25 conserved introns 16 were phase 0, five were phase 1, and four were phase 2. Triose phosphate isomerase had five of nine conserved introns shared between plants and animals, where S14 had one of nine and S17 had one of seven. However, there were two …

A Microrna Imparts Robustness Against Environmental Fluctuation During Development, Xin Li, Justin J. Cassidy, Catherine A. Reinke, Stephen Fischboeck, Richard W. Carthew

Faculty Publications

The microRNA miR-7 is perfectly conserved from annelids to humans, and yet some of the genes that it regulates in Drosophila are not regulated in mammals. We have explored the role of lineage restricted targets, using Drosophila , in order to better understand the evolutionary significance of microRNA-target relationships. From studies of two well characterized developmental regulatory networks, we find that miR-7 functions in several interlocking feedback and feedforward loops, and propose that its role in these networks is to buffer them against perturbation. To directly demonstrate this function for miR-7, we subjected the networks to temperature fluctuation and found …

An Rnai Screen Targeting The Protein Tyrosine Kinases Identifies Bruton's Tyrosine Kinase (Btk) As A Breast Cancer Cell Survival Factor, Cheryl Lynne Eifert

Legacy Theses & Dissertations (2009 - 2024)

The receptor protein tyrosine kinases (RPTKs) and the non- receptor protein tyrosine kinases (PTKs) are among the most commonly up-regulated genes found in all types of cancers. Although, a large body of data implicates a majority of tyrosine kinases (TKs) in cancer, few have been extensively evaluated for any potential therapeutic benefit in any of the many subtypes of breast cancer. We have used RNA interference (RNAi) to perform a large-scale loss-of-function analysis to facilitate the identification of individual factors necessary for the survival of an ErbB2 positive breast cancer cell line. We have found that 30% of the TKs …

Hydroxyl Radical Is Produced Via The Fenton Reaction In Submitochondrial Particles Under Oxidative Stress: Implications For Diseases Associated With Iron Accumulation, Carin Thomas, Melissa M. Mackey, Amy A. Diaz, David P. Cox

All Faculty Scholarship for the College of the Sciences

Mitochondrial dysfunction and reactive oxygen species (ROS) are often implicated in diseases involving oxidative stress and elevated iron. As mitochondria produce ATP by oxidative phosphorylation, ROS by-products are generated from the electron transport chain. Although superoxide and hydrogen peroxide have been thoroughly investigated, little evidence documents hydroxyl radical (HO•) production in mitochondria. In order to determine whether HO• is generated under oxidative stress conditions by a Fenton-type mechanism, bovine heart submitochondrial particles were examined for HO• in the presence and absence of iron ligands, antioxidant enzymes and HO• scavengers. HO• was measured as 2,3- and 2,5-dihydroxybenzoic acid (DHBA), using HPLC …

Protection Of Macrophages J774a.1 By Purine Nucleoside Analogues From Bacillus Anthracis Mediated Necrosis, Zadkiel R. Alvarez

UNLV Theses, Dissertations, Professional Papers, and Capstones

Eight years after the lamentable anthrax attacks, major scientific effort continues to be done, in order to stop imminent acts of bioterrorism. Innovative ways of therapy against the anthrax disease are being investigated. B. anthracis, the etiological agent of the infection, has a dormant stage in its life cycle known as the endospore. When conditions become favorable spores germinate, transforming into vegetative bacteria. In inhalational anthrax, the most fatal manifestation of the disease, spores enter the organism through the respiratory track, and are phagocytosized by alveolar macrophages of the lungs. Spores are able to sense nutrient availability, activating their germination …

An Inositolphosphorylceramide Synthase Is Involved In Regulation Of Plant Programmed Cell Death Associated With Defense In Arabidopsis, Wenming Wang, Xiaohua Yang, Samantha Tangchiaburana, Roland Ndeh, Jennifer E. Markham, Yoseph Tsegaye, Teresa M. Dunn, Guo-Liang Wang, Maria Bellizzi, James F. Parsons, Danielle Morrissey, Janis E. Bravo, Daniel V. Lynch, Shunyuan Xiao

Department of Biochemistry: Faculty Publications

The Arabidopsis thaliana resistance gene RPW8 triggers the hypersensitive response (HR) to restrict powdery mildew infection via the salicylic acid–dependent signaling pathway. To further understand how RPW8 signaling is regulated, we have conducted a genetic screen to identify mutations enhancing RPW8-mediated HR-like cell death (designated erh). Here, we report the isolation and characterization of the Arabidopsis erh1 mutant, in which the At2g37940 locus is knocked out by a T-DNA insertion. Loss of function of ERH1 results in salicylic acid accumulation, enhanced transcription of RPW8 and RPW8-dependent spontaneous HR-like cell death in leaf tissues, and reduction in plant stature. …

Nanosecond Pulsed Electric Fields Induce A Mitochondria-Independent Apoptosis In B16f10 Melanoma Cells In Vitro, Wentia Elissa Ford

Theses and Dissertations in Biomedical Sciences

Nanosecond pulsed electric fields (nsPEFs) are ultra-short pulses that induce direct electric field and biological effects that initiate apoptosis. Here the application of ten 300ns pulses ranging in electric fields from 12kV/cm-60kV/cm was administered to determine the effects on B16F10 melanoma cells evaluated by in vitro studies. Initial application of nsPEFs demonstrated apoptosis induction in an electric field- and pulse number-dependent manner measured by caspase activation that correlated with decrease in cell viability 24hr post pulse. In addition caspase activity was shown to be independent of calcium mobilization though ions may play a part in other aspects of apoptosis. The …

Expression Analysis Of Plant Defense Responses During The Establishment Of Biotrophy And Role Of Abiotic Stress In The Infection Of Dyer’S Woad (Isatis Tinctoria) By Puccinia Thlaspeos, Elizabeth Thomas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The kinetics and amplitude of the salicylic acid-responsive pathogenesis-related (PR) genes and the cytochrome P450 gene ItCYP79B2 in the compatible interaction between Puccinia thlaspeos and dyer’s woad (Isatis tinctoria) during the first 72 hours of inoculation were examined. Immediately following penetration of the host by the rust pathogen, there was a modest up-regulation of PR genes but a significant down-regulation of ItCYP79B2 expression. During haustoria formation, a significant pathogen-mediated suppression of PR genes was observed with a corresponding up-regulation of ItCYP79B2. This potentially facilitates haustoria formation by P. thlaspeos. After haustoria formation, a more …