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Interactions In The Cpsrp Dependent Targeting Of Light Harvesting Chlorophyll Binding Protein To The Thylakoid Membrane, Rory Henderson

Graduate Theses and Dissertations

Targeting of proteins is a critical component of cellular function. A universally conserved targeting system of the cytosol utilizes a signal recognition particle (SRP) to target many proteins contranslationally to the endoplasmic reticulum in eukaryotes or the inner membrane in prokaryotes. A homologous SRP system exists in the chloroplast that delivers light harvesting chlorophyll binding proteins (LHCP) to they thylakoid membrane. The chloroplast SRP (cpSRP) is a heterodimer composed of a novel 43 kDa subunit and a 54 kDa subunit homologous to a component of the SRP system, SRP54. Many details regarding the interactions between the proteins of the cpSRP …

Engineered Human Acidic Fibroblast Growth Factor (Fgf1) With An Enhanced Thermal And Proteolytic Stability, Duaa Abdullah Almansaf

Graduate Theses and Dissertations

Fibroblast growth factor receptor (FGFR) is made up of three significant domains. The most important domain is the intracellular domain where the dimerization and autophosphorylation occur. Fibroblast growth factor (FGF) interacts with specific FGFR to regulate many cellular processes during the embryonic stage. Furthermore, FGF is significant for adults because FGF plays an important role in regulating cellular differentiation as well as wound healing. The cellular regulating processes are initiated through binding FGF to heparin followed by binding FGF/heparin to FGFR to form FGF/heparin/FGFR complex. Thus, FGFR is dimerized and autophosphorylated. The phosphorylation of FGFR triggers downstream signaling pathways, which …

Fishes As A Template For Reticulate Evolution: A Case Study Involving Catostomus In The Colorado River Basin Of Western North America, Max Russell Bangs

Graduate Theses and Dissertations

Hybridization is neither simplistic nor phylogenetically constrained, and post hoc introgression can have profound evolutionary effects. Most studies have focused on tractable model systems, rather than organisms with complicated phylogenetic histories. Finescale Sucker (genus Catostomus) in western North America is recognized as a paradigm of fish hybridization. Yet, its extent of historic and contemporary introgression is largely unstudied, an aspect that impedes the resolution of its phylogeny as a baseline for conservation. To explore reticulation in this group, I assayed variation of 20 Catostomus species across temporal and geographic scales by analyzing hundreds of samples and employing a combination of …

Effects Of Acute Heat And Oxidative Stress On The Hepatic Expression Of Orexin And Its Related Receptors, Stephanie Khaldi

Graduate Theses and Dissertations

It is widely known that orexin A and B peptides as well as their receptors are expressed in the hypothalamus and distributed throughout the central nervous system, but there have been few studies regarding its presences in other parts of the body. There is now evidence that orexin (ORX) and its receptors (ORXR1/2) are present in the avian liver; however, their regulation under different environmental conditions is still unknown. In the current study, we sought to determine the effects of heat and oxidative stress using hydrogen peroxide (H2O2) and 4-hydroxynonenal (4-HNE) on the hepatic expression of ORX and ORXR1/2 in …

Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead

Graduate Theses and Dissertations

The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks …

Examination Of Pseudomonas Fluorescence As A Recombinant Expression Host: Cloning, Expression, And Chromatography, Ahmed K.Ali Elmasheiti

Graduate Theses and Dissertations

In an effort to expand the pool of bacterium useful for biotechnology applications, Pseudomonas fluorescens, a common gram negative microbe, was examined for its ability to function in a recombinant setting. P. fluorescens is ubiquitous in nature and was initially identified as a soil bacterium found in dirt and is typically associated with plant material. Past literature indicates that it shared characteristics common to Escherichia coli and Bacillus subtilis, including simple growth conditions and potential cloning vectors, providing motivation to look into both the upstream and downstream characteristics of this bacterium. First, it was demonstrated that P. fluorescens could be …

Influence Of Ph And Acidic Side Chain Charges On The Behavior Of Designed Model Peptides In Lipid Bilayer Membranes, Venkatesan Rajagopalan

Graduate Theses and Dissertations

The molecular properties of transmembrane proteins and their interactions with lipids regulate biological function. Of particular interest are interfacial aromatic residues and charged residues in the core helix whose functions range from stabilizing the native structure to regulating ion channels. This dissertation addresses the pH dependence and influence of potentially negatively charged tyrosine, glutamic acid or aspartic acid side chains. We have employed GWALP23 (acetyl-GGALW5LALALALALALALW19LAGA-amide) as favorable host peptide framework. We have substituted W5 with Tyr (Y5GWALP23) and Leu residues with Glu (L12E, L14E or L16E) or Asp (L14D or L16D), and have incorporated specific 2H-labeled alanine residues within the …

Membrane Chromatography For Bioseparations: Ligand Design And Optimization, Zizhao Liu

Graduate Theses and Dissertations

Membrane chromatography, or membrane adsorber, represents an attractive alternative to conventional packed bed chromatography used in downstream processing. Membrane chromatography has many advantages, including high productivity, low buffer consumption and ease to scale up. This doctoral dissertation focuses on developing novel polymeric ligands for protein separations using membrane chromatography. Atom transfer radical polymerization (ATRP), known as a controlled radical polymerization technique, has been used to control the architecture of grafted polymeric ligands. The center theme of this dissertation is to develop new polymeric ligands and investigate how the polymer’s property (e.g. flexibility, hydrophobicity) and architecture (e.g. chain density, chain length) …

Bioorthogonal Reactions: Synthesis And Evaluation Of Different Ligands In Copper Catalyzed Azide-Alkyne1,3-Dipolar Cycloaddition (Cuaac), Zainab Abdullah Almansaf

Graduate Theses and Dissertations

The Copper CatalyzedAzide-Alkyne1,3-Dipolar Cycloaddition (CuAAC) reaction has unique features that qualify it to be one of the best click reactions. Its applications have been shown in different aspects and for multiple purposes. The oxidative degradation of biological systems (labile proteins and live cells) is, however, generally recognized as the major problem when using this reaction in living systems. Reactive oxidation species can be easily produced in the presence of copper(II), ascorbate and air, and this is the main cause of toxicity. However, the uses of ligands have shown a major impact on reducing copper toxicity, protecting Cu(I) from the redox …

Extracellular Matrix Remodeling And The Inflammatory Response During Skeletal Muscle Regeneration In Sarcopenic Obese Mice, Lemuel Arthur Brown

Graduate Theses and Dissertations

AIM: Sarocpenic obesity is a national concern within the United States because this metabolic syndrome is tied with reduced mobility and quality of life. Both obesity and aging are associated with insulin-resistance, chronic low-grade inflammation and muscle weakness. Skeletal muscle regeneration is a process that involves the coordinated effort of myogenic regulatory factors (MRFs), inflammatory signaling, and extracellular matrix (ECM) remodeling for optimal regeneration. It has been demonstrated that obesity and aging have a reduction in muscle regeneration. It has not been examined if sarcopenic obesity will further reduce muscle mass and the regenerative process. The purpose of this study …

Characterization Of Histone Mutants Associated With Mitotic Defects In Saccharomyces Cerevisiae, Md Riajul Hossain

Graduate Theses and Dissertations

Nucleosomes, the basic unit and the building blocks of chromatin have an essential role in the tight packaging of DNA into higher order chromatin. Work from our lab and others have provided information on the contributions of different histone proteins and specific domains within the nucleosome made to create the centromeric chromatin structure required for normal chromosome segregation during mitosis. The DNA entry/exit site is a particular region of the nucleosome where histone H2A, H3 and H4 form critical interactions that appear to be essential for the association of Sgo1, a tension sensing protein that monitors kinetochore-microtubule attachment. In our …

Heparin-Peptide Interactions, Jacqueline Anastasia Morris

Graduate Theses and Dissertations

Heparin is a polydispersed sulfated molecule that is part of the family called glycosaminoglycans found in the extracellular matrix and cell surfaces. This molecule is extremely important for the activation of proteins and protein-receptor interactions that are responsible for downstream cell signaling pathways. Heparin has been isolated from porcine intestine and used as an anticoagulant for the prevention of embolisms, heart thrombosis, and clotting during heart surgeries. This so-called miracle drug was in use until 2008, when isolated batches were found to be contaminated with other glycosaminoglycans similar to heparin. From 2008, there has been a dire need for a …

Applications Of The Gst- Affinity Tag In The Purification And Characterization Of Proteins, Wibke Beatrice Kachel

Graduate Theses and Dissertations

With the latest innovations in biological sciences, large quantities of biologically active polypeptides as well as high throughput screening methods to quickly evaluate if these biomolecules potentially have therapeutic, diagnostic, or industrial purposes are required. The synthesis and purification of peptides and small proteins continue to be demanding as the production of high yields through chemical synthesis can involve large costs. On the other hand, there are only few examples of acquiring those biomolecules through cloning and expression in bacterial systems in form of recombinant fusion proteins. Glutathione S-Transferase (GST) is not only a very commonly used affinity tag to …

Innate Immunity In Chickens: In Vivo Responses To Different Pathogen Associated Molecular Patterns, Kristen Alicia Byrne

Graduate Theses and Dissertations

Pattern recognition receptors (PRRs) on host cells recognize motifs known as pathogen associated molecular patterns (PAMPs) that are common to groups of microbes. Examples include LPS on Gram-negative bacteria, the structural motif PGN common to all bacteria, MDP the smallest immunostimulatory unit of PGN, and poly I:C the dsRNA analog. PAMP recognition by and stimulation of the innate immune system is crucial to an individual’s ability to quickly limit microbial growth and stimulate the adaptive immune system. Characterization of the in vivo immune responses initiated by PAMPs has not been directly addressed. Using growing feathers (GF) as a novel intradermal …

Investigation Of The Interaction Of Dimeric Ruthenium Complexes With Cytochrome B5, Christopher Dain Rupar

Graduate Theses and Dissertations

Photoreactive complexes to study the kinetics of electron transfer of proteins have been in use for a long time. It has always been speculated that complexes bind near the heme or the electron transfer reaction would not occur. But it is unkown exactly how the complex interacts with the protein. The structural, thermodynamic, and kinetic properties of rat liver microsomal cytochrome b5 were investigated when bound to ruthenium dimer complexes. Heteronuclear Single Quantum Coherence studies support a dynamic binding model of a dimer Ru complex bound near the protein’s heme involving residues H39, E44, G42, V61, G62, and H63. The …

Long-Term Supplementation With Leucine Does Not Prevent Development Of Obesity In Rats Fed A High-Fat Diet, Dameon Smith

Graduate Theses and Dissertations

Excess dietary fat consumption has been implicated in the development of obesity and diabetes. Obesity can be characterized by a disproportionate increase in fat mass compared to lean body mass. However, if muscle mass can be increased or maintained in obesity, this may facilitate weight loss by increasing the body’s overall metabolic capacity. Historically, supplementation with the branched-chain amino acid leucine has been shown to increase muscle protein synthesis via the protein kinase mTORC1. Recent studies suggest that supplementation with leucine also has the potential to reduce weight gain and fat deposition in high-fat fed, obese mice. The objective of …

Two-Electron Quenching Of Dinuclear Ruthenium(Ii) Polypyridyl Complexes, Yinling Zhang

Graduate Theses and Dissertations

A bridging ligand 5,5’-Bi- 1,10-phenanthroline, diphen, was prepared using dichlorobis(triphenylphosphine)Ni(II), Ni(PPh3)2Cl2 as catalyst with a yield of 40%. Yellow cubic crystals were able to obtain from the good purity product for single crystal analysis. The torsion angle between the planes of the subunit phenanthrolines is about 66 degrees.

A dinuclear ruthenium (II) polypyridyl complex, (phen)2Ru(diphen)Ru(phen)24+, was synthesized by using polymeric ruthenium carbonyl compound as the entry point, diphen as the bridging ligand and 1,10-phenanthroline, phen, as the terminal legand. Brown needlelike crystals were precipitated from acetonitrile that were not suitable for single crystal diffraction.

The photochemistry of the dimer was …

Mechanism Of Rapid Electron Transfer Reactions Involving Cytochrome Bc1, Cytochrome C And Cytochrome Oxidase, Jeremy Erik Durchman

Graduate Theses and Dissertations

Electron transfer between mitochondrial proteins complexes represents the primary means by which living things acquire the requisite energy for survival. The coupling of electron transfer to proton translocation creates an electrochemical gradient that drives the synthesis of highly energetic compounds such as ATP. The purpose of these studies is to measure rates of electron transfer and elucidate the important governing factors in the redox events involving cytochrome bc1, cytochrome c and cytochrome oxidase. Using rapid initiation of redox events triggered by laser flash excitation of ruthenium compounds, and strategically monitoring unique spectral properties of these proteins in the visible region …

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 …

Proteomic Characterization Of Eggshell Membranes And Their Effect On Poultry Physiology And Immunity, Sarbjeet Kaur Makkar

Graduate Theses and Dissertations

The use of antibiotics in poultry growth and disease control has led to antibiotics resistant problem in human beings, which is a big concern among consumers. With the necessity for judicious use of antibiotics in poultry production, alternative strategies to improve disease resistance in poultry production are necessary. The research is more inclined towards using the natural products available to grow healthier and antibiotic free meat animals. In the context of exploring natural and sustainable resource of alternative to antibiotics, the biochemical milieu of eggshell membranes (ESM) were analyzed by using mass spectrometry techniques including matrix assisted laser desorption ionization …

Oxidative Stress Response In Archaea: Elucidation Of Oxidant Sensing And Tolerance Mechanisms In Methanosarcina Acetivorans, Matthew Edward Jennings

Graduate Theses and Dissertations

Methanogens are archaea possessing a conserved metabolic pathway which produces methane. Many of the enzymes in the methanogenesis pathway are Fe-S proteins, meaning methanogens are sensitive to conditions which disrupt Fe-S clusters. Molecular oxygen is capable of disrupting Fe-S clusters through oxidation of the iron atoms. Furthermore, reduced iron can facilitate the production of reactive oxygen species (ROS), meaning methanogens must possess antioxidant mechanisms. Detection and eradication of ROS is important for all cells, due to the potentially fatal consequences of unchecked oxidation. This dissertation presents two separate projects investigating mechanisms the model methanogen Methanosarcina acetivorans possess for dealing with …

The Ccaat-Binding Factor Dependent Regulation Of The Oxidative Stress Response In Candida Albicans, Ananya Chakravarti

Graduate Theses and Dissertations

The success of Candida albicans as an opportunistic human pathogen has been attributed to several factors, including the ability to survive in limiting iron environments and the ability to evade the respiratory burst of human macrophages and neutrophils. The goal of this research is to elucidate the role of the CCAAT-binding factor in the oxidative stress response of Candida albicans. Prior whole genome microarray studies performed in our lab compared the gene expression of a wild type Candida albicans strain versus a hap5Δ strain under iron-limiting growth conditions. Among the differentially regulated genes, CTA1, encoding catalase, had a four-fold higher …

Genotoxicity Of Graphene In Escherichia Coli, Ananya Sharma

Graduate Theses and Dissertations

Rapid advances in nanotechnology necessitate assessment of the safety of nanomaterials in the resulting products and applications. One key nanomaterial attracting much interest in many areas of science and technology is graphene. Graphene is a one atom thick carbon allotrope arranged in a two-dimensional honeycomb lattice. In addition to being extremely thin, graphene has several extraordinary physical properties such as its exceptional mechanical strength, thermal stability, and high electrical conductivity. Graphene itself is relatively chemically inert and therefore pristine graphene must undergo a process called functionalization, which is combination of chemical and physical treatments that change the properties of graphene, …