Biochemistry, Biophysics, and Structural Biology Commons^™

Nuclear Import And Interactions Of Potato Yellow Dwarf Virus Nucleocapsid, Matrix, And Phosphoprotein, Gavin Lloyd Franklin Anderson

Theses and Dissertations--Plant Pathology

Potato yellow dwarf virus (PYDV) is the type species of the genus Nucleorhabdovirus and, like all members of this genus, replication and morphogenesis occurs inside the nuclei of infected cells. Protein localization prediction algorithms failed to identify a nuclear localization signal (NLS) in PYDV nucleocapsid (N) protein, although PYDV-N has been shown to localize exclusively to the nucleus when expressed as a green fluorescent protein (GFP):N fusion in plant cells. Deletion analysis and alanine-scanning mutagenesis identified two amino acid motifs, ⁴¹⁹QKR⁴²¹ and ⁴³²KR⁴³³, that were shown to be essential for nuclear import and interaction with …

Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, Juan Pan

Theses and Dissertations--Plant Pathology

Loline alkaloids, found in many grass-Epichloë symbiota, are toxic or feeding deterrent to invertebrates. The loline alkaloids all share a saturated pyrrolizidine ring with a 1-amine group and an ether bridge linking C2 and C7. The steps in biosynthesis of loline alkaloids are catalyzed by enzymes encoded by a gene cluster, designated LOL, in the Epichloë genome. This dissertation addresses the enzymatic, genetic and evolutionary basis for diversification of these alkaloids, focusing on ether bridge formation and the subsequent modifications of the 1-amine to form different loline alkaloids.

Through gene complementation of a natural lolO mutant and comparison …

Characterization Of Ns1 Sumoylation And Its Effect On Influenza A Viral Infection, Katherine Anne Meraz

Open Access Theses & Dissertations

Influenza virus is a contagious respiratory virus responsible for seasonal epidemics and several catastrophic pandemics in the last century. Its genome is comprised of negative sense, single-stranded RNA and, after entering the cell, it is capable of hijacking the host cellular machinery for reproducing its own genetic material. The activation of cellular defenses against influenza viral infection are triggered upon viral entry and help regulate the course of viral infection. This study focused on the interplay between the influenza A virus and the cellular SUMOylation system during viral infection. The first part of this Dissertation deals with the relevance of …

A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender

Legacy Theses & Dissertations (2009 - 2024)

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus belonging to the lentivirus genus of the orthoretrovirinae family. HIV-1 is widely known for causing acquired immunodeficiency syndrome (AIDS) in humans and being responsible for 1.8 million deaths due to AIDS associated illnesses in 201016.

The Sumoylation Of The Non-Structural Protein 1 Of The Influenza A Virus Plays A Dual Role During Viral Infection, Jason Michael Chacon

Open Access Theses & Dissertations

The potential for a highly pathogenic influenza pandemic remains a concern for global health. The ability of the influenza virus to undergo antigenic shift and genetic drift give circulating strains of influenza the high probability of developing resistance to current antiviral therapies. Emerging strains of higher virulence, to which the infected person has not had any previous exposure to viral antigens, pose a greater threat of serious illness and death. Currently, there is no antiviral therapy that is effective against all strains of influenza, emphasizing the need to develop new strategies that target cellular systems required for viral replication to …

The Role Of Intestinal Sweet Taste Receptors (Strs) In The Regulation Of Glucose Absorption: Effects Of Short Term High Sucrose Diet (Hsd), Tania Hussain

HIM 1990-2015

Sweet taste receptors are primarily found in the oral cavity of the mammalian species. However, recent studies have shown that sweet taste receptors can be found in extraoral tissues such as the pancreas, intestines, and adipose tissue. Our lab has previously found that sweet taste receptors are down-regulated on the pancreas in the presence of high plasma glucose levels. In order to assess the possibility that sweet taste receptors respond to high levels of glucose by suppressing its expression, we wanted to see if they reacted similarly on the intestines. We found that intestinal sweet taste receptors are down regulated …

Virus Purification, Detection And Removal, Khrupa Saagar Vijayaragavan

Dissertations, Master's Theses and Master's Reports - Open

The biopharmaceutical industry has a growing demand and an increasing need to improve the current virus purification technologies, especially as more and more vaccines are produced from cell-culture derived virus particles. Downstream purification strategies can be expensive and account for 70% of the overall manufacturing costs. The economic pressure and purification processes can be particularly challenging when the virus to be purified is small, as in our model virus, porcine parvovirus (PPV). Our efforts are focused on designing an easy, economical, scalable and efficient system for virus purification, and we focused on aqueous two-phase systems. Industry acceptable standards for virus …

Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, Jeanette Cecilia Gonzalez

Open Access Theses & Dissertations

It is of huge concern the possibility that at some point in the future we may face a new pandemic involving a highly pathogenic virus due to our current preventive and treatment options to fight this viral disease. The main reason for such limitations is the ability of the virus to go over constant antigenic shifts and drifts on its viral surface proteins HA and NA. The constant mutations that affect this virus cause the need of developing new vaccines for each influenza season. Periodically, the World Health Organization (WHO) reports that around 10% of the world population gets infected …

The Role Of Surface Chemistry In The Toxicity Of Manufactured Cerium Dioxide Nanomaterials To Caenorhabditis Elegans, Emily Kay Oostveen

Theses and Dissertations--Plant and Soil Sciences

Manufactured CeO₂ nanomaterials (CeO₂-MNMs) are used for a wide variety of applications including diesel fuel additives and chemical/mechanical planarization media. To test the effects of CeO₂-MNM surface coating charge on to model organism Caenorhabditis elegans, we synthesized 4 nm CeO₂ with cationic (DEAE-), anionic (CM-), and neutral (DEX) coatings. In L3 nematodes exposed for 24 hours, DEAE-CeO₂ induced lethality at lower concentrations than CM- or DEX-CeO₂. Feeding slightly decreased CeO₂ toxicity, regardless of coating. In L2 nematodes exposed for 48 hours with feeding, DEAE-CeO₂ caused lethality at the …

The Burden Of Avian Influenza Viruses In Community Ponds In California, Zin Htway

Walden Dissertations and Doctoral Studies

Emerging influenza viruses continue to challenge public health. The problem is public health science professionals have been battling emerging human influenza diseases with tactile and reactionary methods because there is a lack of knowledge and data at the human-animal interface. This research was a baseline study of the proportion of influenza A virus (IAV) in urban and rural communities in California. The population was artificial recirculating water ponds in the geographic locations of rural and urban Californian communities. Surface water samples [N = 182] were collected from artificial recirculating ponds in California. Positivity for IAV was verified by real time …

A Summary Of Three Antibiotic Resistant Bacteria Studies Of Plaster Creek, Yeaeun Lee, David P. Warners

Faculty and Professional Research

No abstract provided.

Nine Year Assessment Of Soil Treatment On Aguacatillo (Nectandontisii And Ocotea Austinii, Lauraceae) Seedling Success In The Restoration Of A Costa Rican Cloud Forestra Cufo, Sheila Devries, David Warners

Faculty and Professional Research

We tracked seedling growth of two species of aguacatillo (Nectandra cufodontisii (O. C. Schmidt) C. K. Allen and Ocotea austinii C. K. Allen) that were planted into an early successional cloud forest hillside in San Gerardo de Dota, Costa Rica over nine years. Seedlings were collected from underneath nearby mother trees and transplanted into one of three soil treatments: indigenous soil; a 50:50 mixture of horse manure and indigenous soil; and a 50:50 mixture of kitchen compost and indigenous soil. After seedlings were transplanted they were measured and each specific location was evaluated for light exposure. Two months later seedlings …

Characterizing Dsrna Production In Virus-Infected Fish Cells, Amal Brek Aloufi

Theses and Dissertations (Comprehensive)

Viral dsRNA is produced by almost all viruses sometime during their replicative cycle. These viral nucleic acids are potent inducers of both innate and adaptive immune responses, and are therefore considered important immuno-modulators. Previous studies have shown that viruses produce dsRNA when replicating in mammalian cells; however, to date no one has demonstrated viral dsRNA production in virus infected fish cells. Therefore, the goal of this study is to investigate dsRNA production by fish viruses in fish cells, verifying production and performing initial characterization of the dsRNA molecules being produced. Three different rainbow trout cell lines were used in this …

The Glycine And Proline Reductase Systems: An Evolutionary Perspective And Presence In Enterobacteriaceae, Joshua Witt

HIM 1990-2015

The Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia [1-5]. These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the cell [5, 8]. Though evolutionary studies have been conducted on ammonia producing bacteria [9] none has been done to directly characterize these …

Study Of Coronavirus Protease Using Cfp-Yfp Fluorescent Assay, Caitlin E. Specht, Andrew Mesecar Ph.D., Katrina Molland Ph.D.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Middle Eastern Respiratory Syndrome (MERS) is an emerging viral disease originating in the Arabian Peninsula with a current mortality rate of nearly fifty percent throughout Europe and Asia according to the World Health Organization. Characterization of this disease is being done to understand the basis of viral replication. One target for viral inhibition are replication proteases. Replication proteases are enzymes that cleave proteins specific to cell growth and reproduction that form the viral replicase complex making them an ideal target for viral replication inhibition. First, replication proteases were characterized using a fluorescence resonance energy transfer (FRET) construct by measuring the …

Bacterial Transcription Factors Grea, Greb And Dksa: Characterization Of Their Interaction With Rna Polymerase And Molecular Mechanism Of Action, Andrey Parshin

Graduate School of Biomedical Sciences Theses and Dissertations

The activity of RNA polymerase (RNAP), the key enzyme of transcription process, is regulated by a large number of transcription factors acting at each step of the transcription cycle. Our research project is focused on studying the structure and function of bacterial transcript cleavage factors GreA, GreB and the stringent response regulator DksA. Gre factors bind in the secondary channel of RNAP in backtracked (inactive) ternary elongation complexes and stimulate the enzyme's intrinsic RNase activity, which is required for suppression of transcription pause and arrest, enhancement of transcription fidelity, and efficient promoter escape. DksA also acts through the RNAP secondary …

Structural Studies On The Rubella Virus Capsid Protein And Its Organization In The Virion, Vidya Mangala Prasad

Open Access Dissertations

Rubella virus is a leading cause of birth defects due to infectious agents. When contracted during pregnancy, rubella infection leads to severe damage in fetuses. Despite its medical importance, very little is known about the structure of the pleomorphic rubella virus as compared to its alphavirus relatives. The rubella capsid protein is a critical structural component of virions as well as a key factor in virus-host interactions. Three crystal structures of the structural domain of the rubella capsid protein have been described here. The polypeptide fold of the capsid protomer has not been observed previously. The capsid protein structure, along …

Mscs-Like Mechanosensitive Channels In Plants And Microbes, Margaret E. Wilson, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. …

A Supramolecular Strategy To Assemble Multifunctional Viral Nanoparticles, Limin Chen, Xia Zhao, Yuan Lin, Yubin Huang, Qian Wang

Faculty Publications

Using a one-pot approach driven by the supramolecular interaction between β-cyclodextrin and adamantyl moieties, multifunctional viral nanoparticles can be facilely formulated for biomedical applications.

Evidence For Sigma Factor Competition In The Regulation Of Alginate Production By Pseudomonas Aeruginosa, Yeshi Yin, T. Ryan Withers, Xin Wang, Hongwei D. Yu

Biochemistry and Microbiology

Alginate overproduction, or mucoidy, plays an important role in the pathogenesis of P. aeruginosa lung infection in cystic fibrosis (CF). Mucoid strains with mucA mutations predominantly populate in chronically-infected patients. However, the mucoid strains can revert to nonmucoidy in vitro through suppressor mutations. We screened a mariner transposon library using CF149, a non-mucoid clinical isolate with a misssense mutation in algU(AlgU^A61V). The wild type AlgU is a stress-related sigma factor that activates transcription of alginate biosynthesis. Three mucoid mutants were identified with transposon insertions that caused 1) an overexpression of AlgU^A61V, 2) an overexpression of …

The Effects Of Growth Hormone And Thyroxine Treatment On The Insulin Signaling Of Female Ames Dwarf Mouse Skeletal Muscle Tissue, Andrew Do

HIM 1990-2015

Ames dwarf (df/df) mice are deficient in anterior pituitary hormones: growth hormone (GH), thyroid stimulating hormone (TSH), and prolactin (PRL) due to a spontaneous, homozygous mutation of prop1[superscript df] gene. These dwarf mice exhibit characteristics such as delayed growth and development coupled with delayed aging, increased lifespan, overall increased insulin sensitivity, as well as resistance to certain diseases and cancers. The mutant mice possess low blood glucose, low serum insulin, and lower body temperature. Their enhanced longevity (about 40-60% longer lifespan than normal mice) is associated with their GH deficiency and disruption in the somatotropic axis (GH/IGF-1 hormonal pathway) as …

Divergent Mechanisms Of Interaction Of Helicobacter Pylori And Campylobacter Jejuni With Mucus And Mucins, Julie Ann Naughton, Karina Mariño, Brendan Dolan, Colm Reid, Ronan Gough, Mary Gallagher, Michelle Kilcoyne, Jared Gerlachscience,, Lokesh Joshi, Pauline Rudd, Stephen Carrington, Billy Bourke, Marguerite Clyne

Articles

Helicobacter pylori and Campylobacter jejuni colonize the stomach and intestinal mucus, respectively. Using a combination of mucus-secreting cells, purified mucins, and a novel mucin microarray platform, we examined the interactions of these two organisms with mucus and mucins. H. pylori and C. jejuni bound to distinctly different mucins. C. jejuni displayed a striking tropism for chicken gastrointestinal mucins compared to mucins from other animals and preferentially bound mucins from specific avian intestinal sites (in order of descending preference: the large intestine, proximal small intestine, and cecum). H. pylori bound to a number of animal mucins, including porcine stomach mucin, but …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

Manipulating Aktivated Metabolism Via Mtorc1, Ivan Von Hack Prestinary

HIM 1990-2015

Although poorly understood, normal cells and cancerous cells of the same type exhibit different patterns of nutrient consumption, processing and utility of metabolic substrates. Differences in substrate uptake, preference, and alternately emphasized metabolic pathways offer opportunities for selective targeting of cancer versus stroma. This may be accomplished by using a sequential approach of nutrient deprivation and pharmaceutical perturbation of metabolic pathways to inhibit cellular proliferation. The purpose of this study was to investigate the effects of restricting glucose and glutamine concentrations, in vitro, to levels that resemble a potential human fasting state. The mammalian target of rapamycin (mTOR), a mediator …

Interaction Of Bacillus Anthracis Exosporium Protein Bcla With Complement Factor H And Spore Persistence In The Lung, Sarah A. Jenkins

Dissertations and Theses (Open Access)

Anthrax outbreaks in the United States and Europe and its potential use as a bioweapon have made Bacillus anthracis an interest of study. Anthrax infections are caused by the entry of B. anthracis spores into the host via the respiratory system, the gastrointestinal tract, cuts or wounds in the skin, and injection. Among these four forms, inhalational anthrax has the highest lethality rate and persistence of spores in the lungs of animals following pulmonary exposure has been noted for decades. However, details or mechanisms of spore persistence were not known. In this study, we investigated spore persistence in a mouse …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. A. Khan, Madeline M. Lopez-Munoz, Charles W. Kaspar, Kai F. Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. Khan, Madeline Lopez-Munoz, Charles Kaspar, Kai Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Characterization Of Myxococcus Xanthus Mazf And Implications For A New Point Of Regulation, Tye O. Boynton, Jonathan L. Mcmurry, Lawrence J. Shimkets

Faculty Articles

During development, Myxococcus xanthus cells undergo programmed cell death (PCD) whereby 80% of vegetative cells die. Previously, the MazF RNA interferase has been implicated in this role. Recently, it was shown that deletion of the mazF gene does not eliminate PCD in wild-type strain DK1622 as originally seen in DZF1. To clarify the role of MazF, recombinant enzyme was characterized using a highly sensitive assay in the presence and absence of the proposed antitoxin MrpC. In contrast to previous reports that MrpC inhibits MazF activity, the hydrolysis rate was enhanced in a concentration-dependent manner with MrpC or MrpC2, an N-terminally …