Biochemistry, Biophysics, and Structural Biology Commons^™

Spa47 Is An Oligomerization - Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie Lee Kingsford

Undergraduate Honors Capstone Projects

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa4 7 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 …

Placental ‘€˜Omics’€™ Study To Understand The Pathogenesis Of Preeclampsia, Komal Kedia

Theses and Dissertations

Preeclampsia (PE) is a potentially fatal complication of pregnancy characterized by an increase in blood pressure (>140/90 mmHg) and proteinuria (>300 mg/24 hrs), often accompanied by edema. Symptoms of PE start after 20 weeks of gestation. If PE remains untreated, it can lead to eclampsia, grand-mal seizures responsible for most fatalities. PE is believed to affect 2-10% of pregnancies worldwide, and claims the lives of over 75,000 mothers and 500,000 newborns yearly. No therapeutic agents have been developed to prevent or cure PE. Part of the reason for this is the absence of a complete understanding of the …

Investigation Of Novel Functions For Dna Damage Response And Repair Proteins In Escherichia Coli And Humans, Benjamin A. Hilton

Electronic Theses and Dissertations

Endogenous and exogenous agents that can damage DNA are a constant threat to genome stability in all living cells. In response, cells have evolved an array of mechanisms to repair DNA damage or to eliminate the cells damaged beyond repair. One of these mechanisms is nucleotide excision repair (NER) which is the major repair pathway responsible for removing a wide variety of bulky DNA lesions. Deficiency, or mutation, in one or several of the NER repair proteins is responsible for many diseases, including cancer. Prokaryotic NER involves only three proteins to recognize and incise a damaged site, while eukaryotic NER …

Effects Of Streptozotocin-Induced Diabetes On Gene And Protein Expression In Sinoatrial Node Of Rat Heart, Zannatul Ferdous

Theses

Diabetes mellitus is one of the most common endocrine disorders and its global prevalence is increasing at an alarming rate. Cardiovascular disease is the major cause of morbidity and mortality among diabetic patients. In addition to defects in contraction, the diabetic heart also frequently suffers from disturbances to the electrical conduction system. This study investigates the effects of diabetes on the sinoatrial node (SAN) of the rat heart. Previous in vivo and in vitro experiments have demonstrated reduced heart rate, longer SAN action potential duration, prolonged pacemaker cycle length and Sino-atrial conduction time in streptozotocin (STZ) - induced diabetic rat …

Developing And Using Methyl-Specific Antibodies To Study The Biological Roles Of Arginine Methylation, Vidyasiri Vemulapalli

Dissertations and Theses (Open Access)

Arginine residues can be modified in three different ways to produce asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), and monomethylarginine (MMA). These modifications are catalyzed by a family of nine protein arginine methyltransferases (PRMT1-9), which are of three types (I, II, and III). The majority of Type I enzymes asymmetrically dimethylate Glycine- and Arginine-rich (GAR) motifs, except for PRMT4, which methylates Proline-, Glycine-, and Methionine-rich (PGM) motifs. The same substrates (GAR or PGM motifs) can also be dimethylated by PRMT5 in a symmetric fashion. However, it is not clear whether there are dedicated residues within these motifs for ADMA and SDMA, …

Mechanisms Of Regulation Of Tau Ires Mediated Translation, Niza Nemkul

Dissertations and Theses (Open Access)

The translation of most eukaryotic mRNAs occurs in a cap-dependent manner. However, a subset of mRNAs are capable of initiating translation in a cap-independent manner by utilizing sequences in their 5’ UTR called IRES. It was previously shown that the 5’ UTR of the tau mRNA contains an IRES. In this study I show that IRES dependent translation of tau IRES is regulated at multiple levels in order to regulate the expression of the tau protein.

Tau protein is ubiquitously expressed but is concentrated in the brain. In this study, I utilized neural and non-neural cell lines to show that …

The Roles Of Malt1 In Nf-Κb Activation And Solid Tumor Progression, Deng Pan

Dissertations and Theses (Open Access)

The transcription factor NF-κB plays a central role in many aspects of biological processes and diseases, such as inflammation and cancer. Although it has been suggested thatNF-κB is critical in tumorigenesis and tumor progression, the molecular mechanism by which NF-κB is activated in solid tumor remains largely unknown. In the current work, we focus on growth factor receptor-induced NF-κB activation and tumor progression, including epidermal growth factor receptor (EGFR)-induced NF-κB in lung cancer and heregulin receptor (HER2)-induced NF-κB in breast cancer. We found that Mucosa-associated lymphoma translocation protein 1 (MALT1), also known as paracaspase, is required for EGFR-induced NF-κB activation …

Cll Metabolism Is Regulated By Prognostic Factors, Modulated By Stroma And Abrogated By Pi3k Inhibition, Hima Vangapandu

Dissertations and Theses (Open Access)

Metabolism of chronic lymphocytic leukemia (CLL), a disease characterized by the relentless accumulation of mature B cells has been little explored. Bone marrow stromal cells provide a survival benefit to CLL cells, in part through PI3K/AKT pathway. Compared with proliferative B-cell lines, metabolic fluxes of oxygen and lactate were low in quiescent malignant B lymphocytes from CLL patients. Glycolysis (extracellular acidification rate, ECAR) was consistently low in CLL samples, but oxygen consumption (OCR) varied considerably. Higher OCR was associated with poor prognostic factors such as ZAP 70 positivity, unmutated IgVH, high β2M levels, and higher Rai stage. Co-culture with the …

Preeclampsia: The Roles Of Acute Inflammation And Intrauterine Stress, Nicholas Parchim

Dissertations and Theses (Open Access)

Preeclampsia (PE) is a severe, acute disease of pregnancy affecting approximately 8% of pregnant women after week 20 of gestation. PE is characterized by hypertension and renal damage reflected by proteinuria and has significant morbidity to both mother and fetus. Maternal symptoms range from headaches, nausea, edema, to visual changes, but once maternal symptoms present, damage to the fetus has begun. Mothers who progress untreated through the disease can also experience a condition called eclampsia characterized by seizure, coma, and, ultimately, death. PE-affected newborns experience features similar to prematurity—abnormal lung and renal development, intrauterine growth retardation (IUGR), and, possibly, fetal …

Regulation Of Acute And Chronic Immune Responses By Β-Arrestin2, Hui Yan

Electronic Theses and Dissertations

β-arrestin2, previously recognized as a facilitator for G-protein associated 7 TMR desensitization/ internalization, has now been appreciated as an independent signal transducer that regulates multiple cellular responses including inflammation. Cecal ligation and puncture procedure (CLP) induced septic shock is an acute inflammatory response characterized by uncontrolled systemic inflammation. Myocardial ischemia/reperfusion is a chronic sterilize inflammation that requires the reaction of macrophages, fibroblasts and cardiac stem cells for regeneration and remodeling of the infarcted myocardium. Restrained chronic stress is an immune suppression model in which the inactivation of macrophages may be involved. Here we showed β-arrestin2 overexpression inhibited CLP-induced heart dysfunction …

Gene Expression And Physiological Analysis To Study Differences Between Oryza Sativa Cultivars Susceptible And Resistant To Chalky Grain Formation Subjected To High Nighttime Temperatures., Nicholas Lawson

Graduate Theses and Dissertations

Starch composition and grain quality of rice is greatly influenced by genotype and environmental factors. The detrimental effects of high nighttime temperatures on rice yield and quality has recently become apparent, with some of the warmest average nighttime temperatures being recorded in the past few years. One of the most notable effects of this stress, an increase in grain chalk formation, correlates with a decrease in quality. This effect varies greatly between cultivars as some show less temperature-sensitive quality reduction than others. The goal of this research is to elucidate fundamental changes that occur in developing plants and grains as …

Deciphering The Role Of Glycine134 In The Human Acidic Growth Factor-1’S Binding To Heparin, Adam W. Burroughs

Chemistry & Biochemistry Undergraduate Honors Theses

Human acidic fibroblast growth factor 1 (FGF-1) is a potent modulator of cell survival and exhibits a universal role in various physiological processes. Though potent, FGF-1 unbound to heparin is known to show a poor thermal stability and a relatively short in vivo half-life. Much is known about the structure and relation of FGF-1 with heparin yet there is still unknown information regarding the exact role of heparin in stabilizing FGF-1. Thus, the aim of this study is to mutate glycine at position 134 to glutamic acid in wild type FGF1. G134 is located in the heparin binding pocket, thus …

Synthesis Of Microgel Polymers As Catalysts, Hannah N. Miller

Chemistry & Biochemistry Undergraduate Honors Theses

New developments in organic synthesis show promise in achieving the best catalytic properties for the hydrolysis of glycosidic bonds through microgel polymers and transition metal complexes. A monomer mix of ethylene glycol dimethacrylate, butyl acrylate, and styrene form miniemulsion polymers after sonication and exposure to UV light. Gravimetrical analysis is used to determine the most suitable polymerization conditions by performing experiments at varying pH values, temperatures, monomer amounts, initiator amounts, and lamp heights. The final data show that the best polymerization conditions are a pH of 10.50 at 0°C with a high monomer ratio, 20% initiator amount, and a lamp …

Influence Of Cholesterol On Single Arginine-Containing Transmembrane Helical Peptides, Jordana K. Thibado

Chemistry & Biochemistry Undergraduate Honors Theses

An essential component of animal cells, cholesterol exerts significant influence on the physical properties of the cell membrane and in turn, its constituents. One such category of constituents, the membrane proteins, are responsible for diverse and essential biological functions and often contain polar amino acids. Although sparse within the hydrophobic interior of lipid-bilayer membranes, polar amino acid residues are highly conserved and may play pivotal roles in determining specific structural and functional properties of key proteins. To gain greater understanding of the lipid membrane environment, and more broadly, cellular function, a model peptide framework termed “GWALP23” (acetyl-GGALWLALALAL¹²AL^{14 …}

Genetic Variation In Long-Term And Short-Term Physiological Changes In Daphnia Magna During Acclimation To High Temperature, Bret L. Coggins

Undergraduate Honors Theses

The aquatic zooplankton crustacean Daphnia magna must be able to tolerate thermal stress in order to survive their native shallow ponds that are susceptible to drastic seasonal and diurnal temperature fluctuations as well as to globally increasing temperatures. Survival in such variable environments requires plastic responses that must include fundamental aspects of Daphnia biochemistry and physiology. Adaptive response to selection favoring such plastic phenotypes requires the presence of genetic variation for plastic response in natural populations. Adverse effects of elevated temperature on aquatic organisms are diverse and so are their plastic responses; among the most severe challenges aquatic organisms face …

In Vitro Investigation Of The Effect Of Exogenous Ubiquitin On Processes Associated With Atherosclerosis, Chase W. Mussard

Undergraduate Honors Theses

Atherosclerosis, characterized by the build-up of cholesterol, immune cells and cellular debris within arterial walls, is accelerated following myocardial infarction by poorly understood mechanisms. Ubiquitin, a small, well-studied intracellular protein involved in protein turnover via the proteasome pathway, has recently been shown to exert extracellular effects on cardiac myocytes, in vitro, and in mice undergoing myocardial remodeling. This study investigates the potential role of extracellular ubiquitin in atherosclerosis by determining its effects on two critical atherosclerotic processes: the migration of vascular smooth muscles cells and the uptake of modified LDL by monocyte/macrophages in foam cell formation. In the presence …

Identification Of N-Acylethanolamine Hydrolyzing Enzyme In Solanum Lycopersicum, Derek A. Stuffle

Undergraduate Honors Theses

N-acylethanolamines (NAEs) are fatty acid derivatives that occur naturally in plant and animal systems. In mammals, they regulate physiological functions, including neurotransmission, immune responses, vasodilation, embryo development and implantation, feeding behavior, and cell proliferation. NAEs are metabolized by fatty acid amide hydrolase (FAAH), which belongs to the amidase signature family. It is hypothesized that putative FAAH functions as the catalyst in the metabolism of N-acylethanolamine in tomato plants. To test the hypothesis, FAAH protein homologs were identified in tomato via in silico analysis. Among the six homologs identified, FAAH1 and FAAH2 were selected for further validation. This study …

Evaluation Of The Effects Of Radiation On The Positioning Of Histones And Other Proteins, Ashley Elizabeth Foster

School of Biological Sciences: Dissertations, Theses, and Student Research

Nucleosomes and the secondary structure of DNA play an important role in many cellular processes that are contingent on DNA accessibility, such as replication, transcriptional regulation, and DNA repair. Recently, there is also growing evidence that the association of histones and DNA to form a nucleosome offers protection from DNA degradation. Specifically, that the inherent structural properties of DNA organization can help protect DNA from exogenous damage such as radiation. In this study, we sought to evaluate the effects of radiation on the positioning of histones and other proteins.

In this experiment, we optimized established protein protocols in Saccharomyces cerevisiae. …

The Role Of Cellulose Synthase-Like D Genes In Tip Growth Of Physcomitrella Patens, Erin E. Killeavy, Arielle Chaves, Alison Roberts

Senior Honors Projects

Physcomitrella patens is a non-vascular plant with a relatively small genome and is amongst the few eukaryotic organisms that have a high rate of homologous recombination. This is valuable in biological research because it allows for targeted genetic modification of the organism. In vascular plants like Arabidopsis thaliana, a model organism, Cellulose Synthase-like D (CSLD) genes have been discovered to be important in tip growth. This type of growth is observed in the pollen tubes and root hairs of these plant types. The CSLD genes in Arabidopsis were found to play a crucial role in the growth of …

Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …