Biochemistry, Biophysics, and Structural Biology Commons^™

Investigations Into The Molecular Mechanisms Of Bacterial Pathogen–Host Interactions: Construction Of A Dual Plasmid System For Incorporation Of Unnatural Amino Acids Into Pseudomonas Syringae Pv. Tomato Dc3000, Scotty D. Raber

Department of Chemistry: Dissertations, Theses, and Student Research

A dual plasmid system for the incorporation of unnatural amino acids into plant pathogen, Pseudomonas syringae pv. tomato DC3000, has been designed. This invention is expected to allow (a) mutations of proteins synthesized by the bacterium, P. syringae pv. tomato DC3000, that can capture molecular targets, especially for such modified proteins secreted by the phytopathogen into the host plant cells of A. thaliana and S. lycopersicum, (b) expression of biological probes in the bacterial species to monitor changes in redox, nutritional, and other small molecule states over pre-, post- and in situ disease stages, and secretion of such biological …

Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia

Boise State University Theses and Dissertations

VPEvolve is a free and open source application that utilizes a Visual Programming Environment (VPE) for the setup of the Genetic Algorithm (GA), for optimization of computational models. Specifically, the User Interface uses connected glyphs to represent the genetic operators of mutation, reproduction, fitness and selection. These glyphs give the user an intuitive way to set the parameters for the GA, and better visualization of the population's flow through these operators.

VPEvolve is currently being developed alongside research being done in Biocomputing to create models of cellular regeneration based on the regenerative properties of Planaria or flatworms. Since these models …

Osteomyelitis Associated With Nocardiopsis Composta In A Dog, Elisa N. Salas, Debra Royal, Lance Kurz, J. Dustin Loy

School of Veterinary and Biomedical Sciences: Faculty Publications

Osteomyelitis can be caused by bacterial or fungal agents or may be idiopathic. Cocci, bacilli, and filamentous bacteria such as members of the Actinomycetes have all been determined to be causes of osteomyelitis. Differential diagnoses for Gram-positive filamentous rods in the family Actinomycetales causing osteomyelitis in the dog, include members of the more frequently encountered genera Nocardia and Actinomyces. Bacteria gain access to the bone via several routes but are most often associated with direct inoculation (such as percutaneous injuries, compound fractures, or secondary to foreign bodies such as surgical or other material including dirt and wood) and fracture …

The Effect Of Activation Induced Cytidine Deaminase Phosphorylation And Herpes Virus Uracil Dna Glycosylase On Antibody Diversification, Marc Macaluso

Dissertations and Theses (Open Access)

Activation-induced cytidine deaminase (AID) is a mutagenic enzyme that is expressed in mammalian B-cells and initiates the antibody diversification processes of somatic hypermuntation (SHM) and isotype class switch recombination (CSR). AID is targeted to the immunoglobulin gene locus where it deaminates cytosines to generate uracil residues in DNA. This generates guanine-uracil (U:G) mismatch lesion which are recognized by uracil DNA glycosylase (UNG), a DNA repair enzyme that removes uracil from DNA and triggers downstream repair of the lesion. While UNG is a ubiquitously expressed DNA repair enzyme, its recognition and removal of AID introduced uracils is essential in both SHM …

In Vitro Studies Of Gold And Gold Silica Nanoparticle Radiosensitization With Kilovoltage X-Rays, Gregory Colarch

UNLV Theses, Dissertations, Professional Papers, and Capstones

Technological advances in the ability to construct and manipulate nanoscale particles have opened up the possibility of using solid metallic nanoparticles and mixed metal nanoshells as a means to increase dose enhancement and treatment efficacy to tumors. In order for nanoparticles to be an effective form of treatment, they must be delivered to tumors in sufficient concentrations so that there is a dose enhancement factor due to ionizing radiation, as well as being essentially non-toxic to healthy cells. Gold nanoparticles and silica-gold nanoshells fit these requirements. Gold has a high atomic number (Z=79), which gives a larger cross section for …

Dna Methylation In Lung Tissues Of Mouse Offspring Exposed In Utero To Polycyclic Aromatic Hydrocarbons, Trevor J. Fish

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and suspected lung carcinogens in humans. PAHs are also known to cause cancer in offspring when provided to a pregnant mouse. Some evidence from cell-based studies points to PAHs as modulators of the epigenome, that is modifications to DNA structure that control the expression of genes. Inappropriate changes to the epigenome and consequently expression of cancer-critical genes are often characteristic of cancer cells. The objective of this thesis research was to determine the impact of transplacental exposure to two model …

Beryllium Is A Potent And Unique Gsk-3Β Inhibitor With Potential To Differentially Regulate Glycogen Synthase And Β-Catenin, Ata Ur Rahman Mohammed Abdul

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glycogen Synthase Kinase-3β (GSK-3β) is an important serine/threonine kinase that phosphorylates/regulates diverse and metabolically important proteins. Some of the important substrates of GSK-3β are glycogen synthase, tau, β-catenin, cyclin D1, axin, c-jun, c-myc, Heat Shock Factor–1, BCL-3, CREB, Histone H1.5, mdm2, p21 (CIP1), pyruvate dehydrogenase and many more. De-regulation of GSK-3β has been implicated in diseases like cancer, Alzheimer’s disease, bipolar disorder and type 2 diabetes mellitus. Currently, GSK-3β is one of the most widely studied proteins and there is a great interest in developing potent and efficient GSK-3β-inhibitors for research as well as therapeutic purposes. We demonstrate that beryllium …

Investigation Of The Role Of The Scaffold Protein Shc In Erk Signaling, Kin Man Suen

Dissertations and Theses (Open Access)

Cells respond to environmental changes by converting extracellular signals into intracellular events. Scaffolding proteins play important roles in generating specificity in intracellular signaling through the combinatorial use of protein domains and posttranslational modifications. Using the scaffold Shc (Src-homology collagen-like) as a model system, we explored novel mechanisms whereby this class of protein shapes signaling output. In the present work, we focused on the role of Shc in the MAP kinase Erk signaling both prior to and post-growth factor stimulation. Prior to growth factor stimulation, we found Erk to be a direct interacting partner of Shc. The two proteins associate through …

Dna Polymerase Θ (Polq) And The Cellular Defense Against Dna Damage, Matthew J. Yousefzadeh

Dissertations and Theses (Open Access)

In mammalian cells, DNA polymerase θ (POLQ) is an unusual specialized DNA polymerase whose in vivo function is under active investigation. The protein is comprised of an N-terminal helicase-like domain, a C-terminal DNA polymerase domain, and a large central domain that spans between the two. This arrangement is also found in the Drosophila Mus308 protein, which helps confer resistance to DNA interstrand crosslinking agents. Homologs of POLQ and Mus308 are found in eukaryotes, including plants, but a comparison of phenotypes suggests that not all of these genes are functional orthologs. Flies with defective Mus308 are sensitive to DNA interstrand crosslinking …

Developmental Origins Of Renal Connecting Tubule And Collecting Duct: Role Of Aqp2+ Progenitor Cells, Lihe Chen

Dissertations and Theses (Open Access)

The connecting tubule interconnects the nephron and collecting duct, which arise from kidney mesenchyme and the ureteric bud, respectively, to generate the functional tubular networks. The collecting duct is comprised of principal cells and intercalated cells, which bear different molecular signatures and regulate sodium/water and acid/base balance, respectively. The progenitor cells of the connecting tubule and the collecting duct remain virtually unknown.

We generated two Aqp2 lineage tracing mouse models. In these models, Aqp2Cre transgene drives Cre expression by the Aqp2 promoter to exclusively either inactivate histone H3 K79 methyltransferase Dot1l (Dot1l^f/f Aqp2Cre) or activate RFP in …

The Structural Mechanism Of Allosteric Modulation Of The Nmda Receptor: A Balance Of Tensions, Rita E. Sirrieh

Dissertations and Theses (Open Access)

N-methyl-D-aspartate (NMDA) receptors are one of the three main types of ionotropic glutamate receptors in the central nervous system. NMDA receptors mediate the rapid excitatory neurotransmission that underlies learning and memory formation. Conversely, NMDA receptors are implicated in a variety of neurological disorders. Studies targeting the mechanism of allosteric modulation, such as this study, hope to contribute to the understanding of how NMDA receptors are modulated to allow for better drug development.

NMDA receptors are obligate heterotetramers, typically composed of glycine-binding GluN1 subunits and glutamate-binding GluN2 subunits. The GluN2 subunits can be one of four subtypes (A-D). Each subunit is …

Selection Methods For Genetically-Modified T Cells: In Support Of Translational Therapy, David Rushworth

Dissertations and Theses (Open Access)

T cells are blood cells which organize the immune system of the host. These cells are necessary for the host to respond appropriately to threats from foreign organisms and cancerous growth. However, in the case of certain infections and cancer, T cells are unable to respond appropriately to a threat and establish immunity. This leads to disease when the infection or cancer is not sufficiently eliminated. On the other hand, T cells can lack tolerance for healthy tissue and perceive healthy tissue as infected. The ensuing over-reactive immune response also leads to disease. A delicate balance must exist between immunity …

Investigating The Roles Of P63 And P73 Isoforms To Therapeutically Treat P53-Altered Cancers, Avinashnarayan Venkatanarayan

Dissertations and Theses (Open Access)

Investigating the roles of p63 & p73 isoforms to therapeutically treat

p53-altered cancers

Avinashnarayan Venkatanarayan, M.S.

Supervisory Professor: Elsa R. Flores, Ph.D.

The TP53 tumor suppressor is mutated in approximately 50% of human cancers rendering cancer therapies ineffective. p53 reactivation suppresses tumor formation in mice. However, this strategy has proven difficult to implement therapeutically. An alternate approach to overcome p53 loss is to manipulate the p53-family members, p63 and p73, which interact and share structural similarities to p53. p63 and p73, unlike p53 are less frequently mutated and have two major isoforms with distinct functions …

Measuring Single Cell Responses To Lapatinib In A Heterogeneous Population, Preety Priya

Dissertations and Theses (Open Access)

Cancer is notonedisease butasaga of diseases and is the outcome of disturbed homeostasis in the normal cells due to the deregulation of its genetic makeup. With advent of technologies thatallowdetailed molecular characterizationoftumors, targeted therapies have emerged as a more promising and specific mode of treatment. However, a major challenge with targeted therapy is the acquired resistance in the cancer cells to these therapies, quite often very rapidly in the course of a few months. One of the major targets in cancer has been the EGFR/ErbB2 network in breast and other cancer types. Prior work from our lab and others have …

Regulation Of Cell Adhesion By The Ferm Proteins, Ptpn14 And Merlin, Patty Dimarco Hewitt

Dissertations and Theses (Open Access)

Cell-cell adhesion is critical for the control of tissue organization and homeostasis. A family of proteins that regulate cell-cell adhesions is the FERM (4.1 protein, Ezrin, Radixin, Moesin) domain-containing proteins.One FERM domain protein, the non-receptor tyrosine phosphatase PTPN14, is mutated or deleted in several human cancers suggesting that it may be involved in tumor development and/or progression. Additionally, the loss of the FERM domain protein Merlin is associated with tumor development and metastasis.Both PTPN14 and Merlin have been shown to localize and possibly regulate adherens junction (AJ) functions. This work sought to determine if …

Development, Validation, And Application Of Analytical Methods For Characterizing Adsorbed Protein Orientation, Conformation, And Bioactivity, Aby Thyparambil

All Dissertations

The structure and bioactivity of adsorbed proteins are tightly interrelated and play a key role in their interaction with the surrounding environment. These factors are of critical importance in many biotechnological applications. However, because the bioactive state of an adsorbed protein is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary …

Phosphotransacetylase And Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase: Two Eukaryotic Partners Of Acetate Kinase, Tonya Taylor

All Dissertations

Although acetate is a predominant metabolite produced by many eukaryotic microbes, far less attention has been given to acetate metabolism in eukaryotes than in bacteria and archaea. Acetate kinase (Ack), which catalyzes the reversible phosphorylation of acetate from ATP, is a key enzyme in bacterial acetate metabolism. Ack primarily partners with phosphotransacetylase (Pta), which catalyzes the generation of acetyl phosphate from acetyl-CoA, but can also partner with xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp), which produces acetyl phosphate from either xylulose 5-phosphate or fructose 6-phosphate. The Ack-Pta pathway, found primarily in bacteria, is also present in lower eukaryotes such as the green …

Phenotypic And Functional Genomics Analyses Of Salmonella For Food Safety Applications, Turki Dawoud

Graduate Theses and Dissertations

Non-typhoidal Salmonella species have been major foodborne zoonotic pathogens causing serious problems in public health and food industry for several decades. Numerous Salmonella species have frequently been associated with different food commodities mainly poultry meat, eggs, and their products. This dissertation begins with a literature reviews discussing many aspects of Salmonella generally; and subsequently focused on two serotypes, Salmonella Enteritidis and S. Typhimurium as they are at the top of all other serovars responsible for most illness cases and outbreaks. In addition, some Salmonella strains have exhibited their ability to tolerate and survive many food processing treatments. We can divide …

Functional Significance Of Gill Claudin Proteins In Rainbow Trout (Oncorhynchus Mykiss) Osmoregulation, Joanna Katarzyna Bujak

Graduate Theses and Dissertations

Claudin proteins, a key element of tight junction complexes, are known to control paracellular permeability. In euryhaline fish, changes in claudin abundance and localization are critical during salinity acclimation. In seawater, a leaky paracellular pathway that facilitates sodium extrusion is hypothesized to be controlled by claudin proteins. The aim of this study was to evaluate the role of Claudin-10c, -10d -10e and Claudin-30 in gill function in freshwater (FW) and seawater (SW) rainbow trout (Oncorhynchus mykiss). I examined mRNA and protein abundance along with cellular localization. A tissue distribution survey showed that all of the claudins studied were predominantly expressed …

Impacts Of Micrornas On Skeletal Muscle Protein Synthesis And Mitochondrial Quality, David Lee

Graduate Theses and Dissertations

microRNA (miRNA) post-transcriptional modification is becoming a well-established mechanism for controlling mRNA translation. microRNAs -1, -133, and -206 are under the control of skeletal muscle promoters and affect muscle plasticity and metabolic health. A detailed review on the generation and processing of miRNAs with a view to skeletal muscle brings up intriguing connections in the transcriptional connections between multiple miRNAs. Additionally, exciting new research has defined a role of miRNAs in skeletal muscle mitochondria showing an additional, direct link to metabolic function. Multiple investigations in models of exercise, aging, hypertrophy, and injury have shown how these interventions can affect miRNA …

The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio

Senior Honors Projects

The field of genomics originated in the 1970’s starting with the sequencing of small organisms’ genomes such as the bacterium, Haemophilus influenzae, and the yeast, Saccharomyces cerevisiae. A genome is the complete ordered sequence of DNA bases (A, C, G, and T) comprising all of the protein- and RNA-coding genes, as well as all of the regulatory sequences necessary for the construction of an organism. Over time, scientists sequenced the genomes of larger and more complex organisms, eventually leading to the sequencing of the human genome. The Human Genome Project (HGP) was initiated in 1990 and took over ten …

Synthesis And Characterization Of Carbonized Poly (Divinylbenzene) Microspheres For Carbon/Nanodiamond/Polymer-Based Core-Shell Materials And Applications Of This Mixed-Mode Phase To High-Performance Liquid Chromatography, Chuan-Hsi Hung

Theses and Dissertations

This work focuses on improving the quality of carbon-based core-shell materials for high performance liquid chromatography (HPLC) via the characterization of the core materials, and also the development of chromatographic methods (separations) for them. In the early part of this work, I applied organic synthesis to make uniform, spherical poly(divinylbenzene) (PDVB) microspheres, and then carbonized them to prepare carbon core materials for core-shell particle synthesis. Here, I studied in detail the surface and material properties of these particles with multiple instruments, which allowed me to describe the physical and chemical changes that took place during each treatment. The uniform, spherical …

Recyclable Organocatalysis Of One-Pot Michael/Mannich/Lactamization Sequence For Asymmetric Synthesis Of Fluorinated Poly-Substituted 2-Piperidinones, Anthony P. Tran

Honors College Theses

2-piperidinone (δ-lactam), a bio-interesting nitrogen-containing six-membered ring compound, has attracted much interest from researchers both in synthetic and medicinal chemistry. Polysubstituted piperidine derivatives, such as the δ-lactam, serve as a synthon for numerous biologically relevant structures and pharmaceutical agents. A novel one-pot asymmetric Michael/Mannich/Lactamization sequence promoted by recyclable fluorous bifunctional cinchona alkaloid–thiourea organocatalysts is introduced for the synthesis of polysubstituted 2-piperidinones bearing four contiguous stereocenters, one of which is a fluorinated quaternary chiral center with excellent stereoselectivities (ee up to >99%, dr up to >20:1).

Inducing And Characterizing M2c Macrophages At A Non-Degradable Implant In Vivo, Geoffrey David Keeler

Graduate Theses and Dissertations

The implantation of biomaterials in the body leads to a reaction known as the foreign body response (FBR) which leads to the eventual encapsulation of the biomaterial. This encapsulation proves to be detrimental to certain biomaterials, such as implanted glucose sensors, which rely on interacting with the extracellular space for proper function. Altering the FBR has become of interest in an effort to increase the longevity and integration of biomaterials. One strategy for altering the FBR is by targeting the macrophage, shown to play an important role in the FBR. In this work, the microdialysis sampling technique was used to …

Local Modulation And Measurement Of Macrophage-Derived Bioactive Proteins From Implanted Biomaterials In Rat, Geetika Bajpai

Graduate Theses and Dissertations

Fibrosis around the implanted medical devices is a severe problem that can plague long-term device reliability. Activation of macrophage phenotype (macrophage polarization) has emerged as a new and possible means for reducing fibrosis in the fields of biomaterials and regenerative medicine. Macrophages are phagocytic cells that respond to microenvironmental cues that direct their phenotype. Macrophage activation has been widely studied in mouse and human in the context of tumor biology, yet little information is available regarding how macrophage activation could be used in a biomaterials context. Further, rats rather than mice are the common subjects in biomaterials experiments. A significant …

Binding Interactions Of (R)- And (S)-Hydroxypropyl-Com Dehydrogenases And The Zinc Knuckle Proteins Air1 And Air2, Jeremy W. Bakelar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A thorough understanding of protein function requires knowledge of how proteins interact with their substrates and with other proteins. The work entailed in this dissertation describes the binding interactions of proteins from two different model systems: (1) the dehydrogenase enzymes R- and S-HPCDH and (2) the zinc knuckle proteins Air1 and Air2.

R- and S-HPCDH are highly similar enzymes (42% identical) that function in a unique metabolic pathway found in the soil bacterium Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate the transformation of two different forms of the organic …

Development Of Genetic Goat And Hamster Models Of Atrial Fibrillation And Long Qt Syndrome; And Genetic Hamster Models Of Middle East Respiratory Syndrome, Dane A. Rasmussen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Atrial fibrillation (AF) and long QT syndrome (LQTS) are potentially lethal heart rhythm disorders that can be caused by mutations in the potassium channel gene KCNQ1. Middle East Respiratory Syndrome (MERS) is a viral infection with the potential to replicate the devastating effects of the SARS outbreak in 2003. All three of these diseases are in need of genetic animal models.

To address these needs, my thesis project focused on the development of genetic goat and hamster models of AF and LQTS, and genetic hamster models of MERS. Because of the goat’s similar organ size/physiology and the hamster’s similar lipid …

Microbial-Derived Oils And Value-Added Products: Biosynthesis And Applications For Biofuel Production, Alex T. Mccurdy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Efforts are being made to replace petroleum-derived fuels with biofuels in a cost competitive manner. It is apparent that the continued use of petroleum is futile as population and technological growth put increasing pressure on the demand for cheap energy and chemicals. Diminishing resources, civil unrest in the Middle East, and the impact of using petrochemicals on the environment are critical driving forces for research in generating renewable petroleum replacements that can be produced with a limited carbon-footprint. Today, biofuels are derived mostly from land-based plants, but their potential for displacing petroleum is limited due to the competition with available …

Heterogeneous Dynamics In Dna Site Discrimination By The Structurally Homologous Dna-Binding Domains Of Ets-Family Transcription Factors, Gaofei He, Ana Tolic, James Bashkin, Gregory Poon

Chemistry & Biochemistry Faculty Works

The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only …

Whole Genome Comparison Of A Large Collection Of Mycobacteriophages Reveals A Continuum Of Phage Genetic Diversity, Welkin H. Pope, Charles A. Bowman, Daniel A. Russell, Deborah Jacobs-Sera, David J. Asai, Steven G. Cresawn, William R. Jacobs Jr, Roger W. Hendrix, Jeffrey G. Lawrence, Graham F. Hatfull, Dr. Kathleen Cornely

Chemistry & Biochemistry Faculty Publications

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows …