Digital Commons Network^™

Characterization Of A Novel Protease In Staphylococcus Aureus, Adam L. Johnson

Theses and Dissertations

A newly discovered cysteine protease, Prp, has been shown to perform an essential, site-specific cleavage of ribosomal protein L27 in Staphylococcus aureus. In Firmicutes and related bacteria, ribosomal protein L27 is encoded with a conserved N-terminal extension that must be removed to expose residues critical for ribosome function. Uncleavable and pre-cleaved variants were unable to complement an L27 deletion in S. aureus, indicating that this N-terminal processing event is essential and likely plays an important regulatory role. The gene encoding the responsible protease (prp) has been shown to be essential, and is found in all organisms …

Hif-Independent Responses In Hypoxia, Divya Padmanabha

Theses and Dissertations

The adaptive response to hypoxia is accompanied by widespread transcriptional changes that allow for prolonged survival in low oxygen. Many of these changes are directly regulated by the conserved hypoxia-inducible factor-1 (HIF-1) complex; however, even in its absence, many oxygen-sensitive transcripts in Caenorhabditis elegans are appropriately regulated in hypoxia. To identify mediators of these non-HIF-dependent responses, I established a hif-1 mutant reporter line that expresses GFP in hypoxia or when worms are treated with the hypoxia mimetic cobalt chloride (cobalt chloride). The reporter is selective and HIF-independent, in that it remains insensitive to a number of cellular stresses, but is …

Elaboration And Design Of Α7 Nachr Negative Allosteric Modulators, Osama I. Alwassil

Theses and Dissertations

α7 Neuronal nicotinic acetylcholine receptors are one of two major classes of receptors responsible for cholinergic neurotransmission in the central nervous system. The existence of α7 neuronal nAChRs in different regions of the nervous system suggests their involvement in certain essential physiological functions as well as in disorders such as Alzheimer’s disease (AD), drug dependence, and depression. This project was aimed toward the discovery and development of small–molecule arylguanidines that modulate α7 nAChR function with improved subtype-selectivity through an allosteric approach. Identifying the required structural features of these small molecules allowed optimization of their negative allosteric modulator (NAM) actions at …

Integrated Nanoscale Imaging And Spatial Recognition Of Biomolecules On Surfaces, Congzhou Wang

Theses and Dissertations

Biomolecules on cell surfaces play critical roles in diverse biological and physiological processes. However, conventional bulk scale techniques are unable to clarify the density and distribution of specific biomolecules in situ on single, living cell surfaces at the micro or nanoscale. In this work, a single cell analysis technique based on Atomic Force Microscopy (AFM) is developed to spatially identify biomolecules and characterize nanomechanical properties on single cell surfaces. The unique advantage of these AFM-based techniques lies in the ability to operate in situ (in a non-destructive fashion) and in real time, under physiological conditions or controlled micro-environments.

First, AFM-based …

Multi-Platform Arabinoxylan Scaffolds As Potential Wound Dressing Materials, Donald C. Aduba Jr

Theses and Dissertations

Biopolymers are becoming more attractive as advanced wound dressings because of their naturally derived origin, abundance, low cost and high compatibility with the wound environment. Arabinoxylan (AX) is a class of polysaccharide polymers derived from cereal grains that are primarily used in food products and cosmetic additives. Its application as a wound dressing material has yet to be realized. In this two-pronged project, arabinoxylan ferulate (AXF) was fabricated into electrospun fibers and gel foams to be evaluated as platforms for wound dressing materials. In the first study, AXF was electrospun with varying amounts of gelatin. In the second study, AXF …

In-Silico Models For Capturing The Static And Dynamic Characteristics Of Robustness Within Complex Networks, Bhanu K. Kamapantula

Theses and Dissertations

Understanding the role of structural patterns within complex networks is essential to establish the governing principles of such networks. Social networks, biological networks, technological networks etc. can be considered as complex networks where information processing and transport plays a central role. Complexity in these net works can be due to abstraction, scale, functionality and structure. Depending on the abstraction each of these can be categorized further. Gene regulatory networks are one such category of biological networks. Gene regulatory networks (GRNs) are assumed to be robust under internal and external perturbations. Network motifs such as feed-forward loop motif and bifan motif …

Emergent Non-Consumptive Predator Effects Alter Habitat Colonization By Dipteran Prey, Ethan G. Staats

Theses and Dissertations

When ovipositing, prey organisms avoid habitat patches containing predator cues because predators consume, and negatively affect the fitness of their prey. Richness of predator species often enhances the strength of consumptive predator effects, but little is known about how multiple predators combined affect prey non-consumptively. We quantified dipteran colonization in aquatic mesocosms in response to varied predator richness. Multiple predator species combined reduced oviposition by Culex mosquitoes, chironomid midges, and the general colonizing dipteran community more than predicted by the effects of the independent predator species. Previous research which quantifies effects of multiple predators on prey as prey abundance, but …

Xlf-Dependent Nonhomologous End Joining Of Complex Dna Double-Strand Breaks With Proximal Thymine Glycol And Screening For Xrcc4-Xlf Interaction Inhibitors, Mohammed Al Mohaini

Theses and Dissertations

DNA double-strand breaks induced by ionizing radiation are often accompanied by ancillary oxidative base damage that may prevent or delay their repair. In order to better define the features that make some DSBs repair-resistant, XLF-dependent nonhomologous end joining of blunt-ended DSB substrates having the oxidatively modified nonplanar base thymine glycol (Tg) at the first (Tg1) , second (Tg2), third (Tg3) or fifth (Tg5) positions from one 3’ terminus was examined in human whole-cell extracts. Tg at the third position had little effect on end-joining even when present on both ends of the break. However, Tg as the terminal or penultimate …

Investigating The Role Of The Nucleosome Remodeling Factor Nurf As A Regulator Of Gene Expression, Aiman S. Alhazmi

Theses and Dissertations

The nucleosome remodeling factor (NURF) is an evolutionary conserved ATP-dependent chromatin remodeling factor. It was first isolated from Drosophila as a complex with enzymatic activity that once recruited to nucleosome, it slides the nucleosome to provide accessibility for transcription factors. Since then, numerous works from animal models and cell lines show the role of NURF as a regulator of gene expression. NURF interacts with H3K4me3 and sequence specific transcription factors that recruit the complex to promoter regions. Whether this is the only mechanism by which NURF regulates gene expression is not known. However, other ATP-dependent chromatin remodeling complexes are known …

A Novel Antimicrobial Drug Discovery Approach For The Periodontal Pathogen Porphyromonas Gingivalis, Victoria N. Stone

Theses and Dissertations

The human body is colonized by more than 100 trillion microbes which make up an essential part of the body and plays a significant role in health. We now know the over use and misuse of broad-spectrum antibiotics can disrupt this microbiome contributing to the onset of disease and runs the risk of promoting antibiotic resistance. With antibiotic research still on the decline, new strategies are greatly needed to combat emerging pathogens while maintaining a healthy microbiome. We therefore set out to present a novel species-selective antimicrobial drug discovery strategy.

Disruption of the homeostasis within the oral cavity can trigger …

Characterization Of Mechanism Of Action Of Hydrogen Sulfide (H2s) In The Regulation Of Smooth Muscle Function, Ancy D. Nalli

Theses and Dissertations

Hydrogen sulfide (H₂S) is receiving increasing interest, as much as nitric oxide (NO) and carbon monoxide have received previously, to understand its physiological functions as it meets all the criteria to define as a third gasotransmitter. Endogenous synthesis from L-cysteine via cystathionine-γ-lyase (CSE) and cystathionine-β-synthase (CBS) and the function of H₂S as an inhibitor of smooth muscle contraction in gastrointestinal tract are known. However, the loci of generation and action of H₂S, and the mechanism of inhibition of contraction are unknown. Hence, my aims in the present study are to: i) identify the expression …

Characterization Of Transfer Of The Mobile Genomic Island Encoding Methicillin Resistance Among Staphylococci, Melissa D. Ray

Theses and Dissertations

The gene encoding methicillin resistance in Staphylococcus aureus (MRSA) is carried in the chromosome on a large genomic island called SCCmec and is always inserted at the att site within orfX. SCCmec has been designated a mobile genetic element but a mechanism by which it moves among different strains and species of staphylococci has never been demonstrated. This work shows that bacteriophage 80α is capable of transducing SCCmec into a recipient cell, after which it can integrate into the bacterial chromosome via homologous recombination. More importantly, this work characterizes a conjugative mechanism of SCCmec transfer. …

Consequences Of Vine Infestation: Linking Abiotic Influences And Biotic Interactions To Successional And Structural Changes In Coastal Communities, Spencer N. Bissett

Theses and Dissertations

Located at the interfaces of terrestrial and marine environments, coastal habitats are inherently vulnerable to the effects of global change. Barrier island systems in particular serve not only as protective buffers against storm events, but also as sentinel ecosystems for observation of the impacts of sea level rise, and of increasing storm frequency and intensity. In the mid-Atlantic region, shrub thickets of Morella species compose the dominant forest community. The often monospecific nature of these plant community assemblages is advantageous to ecological studies and cross-scale applications; the relatively low diversity facilitates transitions between scales. My objective was to investigate the …

The Effect Of Statins On Il-33 Mediated Mast Cell Function, Marcela Taruselli

Theses and Dissertations

This study demonstrates original findings of statin effects on IL-33 stimulated mast cells. Statins are a class of drugs used to lower cholesterol production by targeting HMG CoA reductase. These commonly prescribed drugs have been shown to be immunomodulatory. In this study, we have found that pretreatment with statins has a variety of effects on IL-33 stimulated mast cells. Atorvastatin suppresses TNF and IL-6 production, while fluvastatin significantly enhances release of these proinflammatory cytokines in BMMCs. Although they have differing effects on cytokine production, both statins lowered ST2 expression on the cell surface, decreased cell viability, and enhanced expression of …

Mysteries Of The Trypanosomatid Maxicircles: Characterization Of The Maxicircle Genomes And The Evolution Of Rna Editing In The Order Kinetoplastida, Preethi Ranganathan Iyengar

Theses and Dissertations

The trypanosomatid protists belonging to Order Kinetoplastida are some of the most successful parasites ever known to mankind. Their extreme physiological diversity and adaptability to different environmental conditions and host systems make them some of the most widespread parasites, causing deadly diseases in humans and other vertebrates.

This project focuses on their unique mitochondrion, called the kinetoplast, and more specifically involves the characterization of a part of their mitochondrial DNA (also called kinetoplast DNA or kDNA), the maxicircles, which are functional homologs of eukaryotic mitochondrial DNA in the kinetoplastid protists. We have sequenced and characterized the maxicircle genomes of 20 …

The Effect Of Dexamethasone On Il-33-Mediated Mast Cell Activation, Oksana I. Chernushevich

Theses and Dissertations

Dexamethasone has been shown to inhibit IgE-mediated mast cell activation, and the present research investigated its role in suppressing IL-33-mediated mast cell activation. We have found that micromolar concentrations of Dexamethasone are capable of suppressing IL-33-mediated mast cell cytokine production, on several genetic backgrounds, and in not only bone marrow derived mast cells, but also peritoneal mast cells. Intracellular staining demonstrated that Dexamethasone significantly reduces expression of the IL-33 receptor, T1/ST2, in mast cells; however, the cytokine suppression is independent of T1/ST2 downregulation. At the same time, Dexamethasone pretreatment significantly reduced ERK phosphorylation, but our data suggests that inhibition occurs …

Speed And Resolution In The Age Of Technological Reproducibility, Shawn Taylor

Theses and Dissertations

The rate of acceleration of the biologic and synthetic world has for a while now, been in the process of exponentially speeding up, maxing out servers and landfills, merging with each other, destroying each other. The last prehistoric relics on Earth are absorbing the same oxygen, carbon dioxide and electronic waves in our biosphere as us. A degraded .jpeg enlarged to full screen on a Samsung 4K UHD HU8550 Series Smart TV - 85” Class (84.5” diag.). Within this composite ecology, the ancient limestone of the grand canyon competes with the iMax movie of itself, the production of Mac pros, …

Development Of Clinically Relevant In Vitro Performance Tests For Powder Inhalers, Xiangyin Wei

Theses and Dissertations

While realistic in vitro testing of dry powder inhalers (DPIs) can be used to establish in vitro–in vivo correlations (IVIVCs) and predict in vivo lung doses, the aerodynamic particle size distributions (APSDs) of those doses and their regional lung deposition remains unclear. Four studies were designed to improve testing centered on the behavior of Novolizer®. Different oropharyngeal geometries were assessed by testing different mouth-throat (MT) models across a realistic range of inhalation profiles (IPs) with Salbulin® Novolizer®. Small and large Virginia Commonwealth University (VCU) and Oropharyngeal Consortium (OPC) models produced similar ranges for total lung dose in vitro (TLD …

Clinical And Genomic Characterization Of Two Vaginal Megasphaera Species, Abigail L. Glascock

Theses and Dissertations

Two vaginal phylotypes of the genus Megasphaera (phylotype 1 and phylotype 2) were recently associated with bacterial vaginosis (BV), an infection characterized by vaginal dysbiosis. Through an analysis of 16S rRNA profiles of 3,986 women enrolled in the Vaginal Human Microbiome Project, we confirmed that while both phylotypes were associated with BV, Megaspheara phylotype 1 had higher specificity for the condition. Megasphaera phylotype 2 was strongly associated with trichomoniasis. Previous studies have reported that BV-associated organisms are excluded in pregnancy. We observed that Megasphaera phylotype 1, which has been associated with adverse pregnancy outcomes, exhibited a trend of increased prevalence …

Heterosandwich Assay Of Nicotinic Acetylcholine Receptors, Augustine J. Pagan Iv

Theses and Dissertations

Using the technology afforded by Winschel et al., cyclen-1, a high affinity, strong complexation agent for 8-hydroxypyrene-1,3,6 trisulfonate and derivatives, a new assay has been developed for fluorescently labeling proteins of interest (POIs). Ligation of the endogenous ligand for nicotinic acetylcholine receptors (nAChRs), acetylcholine, using click chemistry afforded the triazole derivative of an alkynyl-acylcholine (compound 1) with 8-azidopyrene-1,3,6 trisulfonate (compound 2). Liposomes encapsulated with Rhodamine B were used to strengthen the initial fluorophore response of compound 2, using an anchored form of cyclen-1 complex. Using a palmitoyl tail as the lipophilic moiety for liposomal amplification, the …

A Structure/Function Analysis Of Nhsl1b In Facial Branchiomotor Neurons, John Ojumu

Theses and Dissertations

The goal of this study was to identify critical regions of a novel gene, Nance-Horan syndrome-like 1b (nhsl1b). It was previously discovered that C-terminal truncation of the Nhsl1b protein in nhsl1b mutants resulted in a loss of migration in the facial motor neurons of the hindbrain (Walsh et al. 2011). As nhsl1b expresses many isoforms, multiple targets were investigated in order to determine which transcript bears the largest impact on the motor neurons. Using confocal microscopy to observe immunostained embryos, we examined a mutation in an nhsl1b transcript that encodes a WHD, a domain that is known to …

Phenotypic Characterization Of Pnpase Knockdown In C. Elegans, Laura A. Lambert

Theses and Dissertations

The multifunctional exoribonuclease protein PNPase is implicated as a potential target for cancer therapy as well as causing mitochondrial disorders in humans, but there has yet to be a whole animal knockdown model created. In this study, C. elegans was used to investigate the effect of knocking down pnpt-1, the gene that encodes PNPase. It was discovered that pnpt-1 knockdown significantly extends lifespan via an increase in superoxide production similar to other known mitochondrial lifespan extension pathways. Additionally, mitochondrial networks, size and respiration are affected indication of other mitochondrial dysfunction..

PNPase is also known to transport small RNAs into the …

Behavioral Responses Of Male Parasitic Wasps To Plant Cues: A Comparison Of Two Host-Plant Complex Sources Of Cotesia Congregata (Say), Megan Ayers

Theses and Dissertations

Prior exposure to plants cues can enhance assortative mating in insects. We hypothesized that, as previously reported for females, males of Cotesia congregata would display inherent responses to plant cues that could be modified by postemergence experience and further, that males originating from two different host-plant complexes (HPCs) would display different behavioral responses to these HPCs. In no-choice contact assays with a non-host plant, searching responses of males and females increased sharply at Day 2 and remained stable through Day 4. In no-choice assays with potential host plants, males searched longer on catalpa than tobacco; responses were not modified by …

Responses Of The Catalpa Sphinx, Ceratomia Catalpae, And Its Primary Parasitoid, Cotesia Congregata, To Varying Levels Of Iridoid Glycosides In Catalpa, Jessica L. Bray

Theses and Dissertations

The catalpa sphinx, Ceratomia catalpae, is a specialist on Catalpa trees, which produce iridoid glycosides (IGs). Whereas some trees are defoliated every year, others escape herbivory. Caterpillar populations are either heavily parasitized by the braconid wasp, Cotesia congregata, or remain unparasitized. We hypothesized that these patterns could be explained by variable IG concentrations among trees and insect responses to these chemicals. IG concentrations varied among trees. Percent defoliation was positively related to IG concentration. In comparisons of insect responses to relatively high or low IG concentrations, moths preferred to oviposit on trees with high IG concentrations. Caterpillars did …

Coarse Woody Debris And The Carbon Balance Of A Moderately Disturbed Forest, Amy V. Schmid

Theses and Dissertations

Landscapes are comprised of multiple ecosystems shaped by disturbances varying in severity and source. Moderate disturbance from weather, pathogens, insects, and age-related senescence, in contrast to severe disturbances that fell trees, may increase standing woody debris and alter the contribution of coarse woody debris (CWD) to total ecosystem respiration (R_E). However, woody debris dynamics are rarely examined following moderate disturbances that substantially increase standing dead wood stocks. We used an experimental manipulation of moderate disturbance in an upper Great Lakes forest to: 1) examine decadal changes in CWD stocks through a moderate disturbance; 2) quantify in situ CWD …

The Genetic Architecture Of Water-Use Efficiency Within And Between Two Natural Populations Of Foxtail Pine, Douglas E. Harwood

Theses and Dissertations

The goal of this project was to determine the genetic architecture of water-use efficiency (WUE) for foxtail pine, which included genomic loci, and effect sizes of this trait. Foxtail pine is a subalpine endemic conifer that inhabits two distinct regional populations separated by 500 km in the mountains of California. In order to achieve this goal, a robust linkage map containing thousands of genetic markers was created using four megagametophyte arrays ranging in size from approximately 70 to 95 megagametophytes. Quantitative trait loci (QTL) discovered for WUE were mapped along the linkage map using linear mixed models and five half-sibling …

Regulation Of Tie2 Extracellular Complex Formation In Angiogenesis, Annamarie Dalton

Theses and Dissertations

Pathological angiogenesis is an essential component of tumor growth, development, and metastasis for which few effective therapeutic options exist. Though many cancer therapies target the function of cell surface receptors, mechanisms regulating membrane receptor crosstalk remain unclear. Two important families of receptors in angiogenesis, the Ties and Integrins, respond to the extracellular environment via outside-in and, in the case of Integrins, also inside- out signaling. Recent reports showed that the endothelial specific tyrosine kinase receptor, Tie2, forms complexes with two of the endothelial Integrin heterodimers, α₅β₁ and α_Vβ₃, providing a convenient mechanism for …

Development Of Non-Traditional Platinum Anticancer Agents: Trans-Platinum Planar Amine Compounds And Polynuclear Platinum Compounds, Daniel E. Lee

Theses and Dissertations

Development of Non-Traditional Platinum Anticancer Agents: trans-Platinum Planar Amine Compounds and Polynuclear Platinum Compounds

By Daniel E. Lee, Ph.D.

A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University.

Virginia Commonwealth University, 2015

Major Director: Nicholas P Farrell, Ph.D., Professor, Department of Chemistry

Platinum anticancer compounds with cis geometry, similar to cisplatin, have been explored to circumvent the cisplatin resistance; however, they were not considered broadly active in cisplatin cells due to exhibiting similar or same cell death mechanism as cisplatin. Platinum compounds with trans geometry were less studied …

The Role Of Adam10, Adam17, And Spag6 In Humoral Immunity And Secondary Lymphoid Tissue Architecture, Lauren Folgosa Cooley

Theses and Dissertations

ADAM10, ADAM17, and SPAG6 contribute significantly to humoral immunity and secondary lymphoid tissue architecture. ADAM10 and ADAM17 are two closely related zinc-metalloproteinases. Through cleavage of their ligands CD23 and TNF, respectively, they greatly influence IgE production and secondary lymphoid tissue architecture maintenance. Th1 prone WT strains initially exhibit increased ADAM17 and TNF yet reduced ADAM10 relative to Th2 prone WT strains. In the absence of B cell ADAM10, a compensatory increase in ADAM17 and TNF cleavage is noted only in Th1 prone C57Bl/6, not Th2 prone Balb/c. B cell TNF homeostasis is important for maintaining secondary lymphoid tissue architecture. We …

Prediction Of Protein-Protein Interactions In Escherichia Coli From Experimental Data In Treponema Pallidum, Marco A. Abreu

Theses and Dissertations

Protein – Protein interactions (PPIs) are thought to be conserved between species, although this has not been systematically investigated. This problem was explored in Escherichia coli from experimental data in Treponema pallidum by predicting PPIs, focusing on protein domains of little or unknown function. The comparison of T. pallidum to a model organism such as E. coli can not only reveal additional data about T. pallidum but also reveals how E. coli is similar to this distantly related, obligate parasite. A set of novel T. pallidum interactions, enriched for proteins of unknown function, were the basis of over 23,000 predicted …