Life Sciences Commons^™

The Role Of Autophagy And Senescence In The Responses Of Non-Small Cell Lung Cancer Cells To Chemotherapy And Radiation, Nipa H. Patel

Theses and Dissertations

Cancer-associated deaths account for the second-highest mortality rates in the United States. Primary modalities of treatment often include surgery, radiation, and chemotherapy, and may also incorporate targeted therapy and immunotherapy. However, resistance to these treatments remains high, resulting in disease reoccurrence and poor survival rates. While apoptosis or cell death of tumor cells is the ideal outcome for anti-cancer therapy, this is often not the case, and in fact cancer cells may upregulate several pathways, such as autophagy and senescence, as a means to undergo alternative cell fate and evade apoptotic cell death. An essential tumor suppressor gene, TP53, …

Influence Of Metal Sleeves In The Accuracy Of Dental Implant Placement Using Guided Implant Surgery, Coleman Adams

Theses and Dissertations

The fabrication of implant surgical guides through stereolithographic 3D printing has become a staple in dental implant guided surgery over the last couple decades. These surgical guides have typically utilized metal sleeves to assist in guidance of the drills during osteotome preparation. The metal sleeves can be costly and potentially cause deviations if improperly placed during post-processing of the guide. This research explored a novel method for the utilization of sleeve-free surgical guides by comparing the dimensional and angulational deviations between the implant guides with and without a metal sleeve. To achieve this goal, two separate aims were pursued. Our …

Searching For Gold: Using A Novel Land Cover Classification To Identify Multiscale Drivers Of Site Occupancy By A Flagship Species For Early-Successional Habitat Conservation, Baron Lin

Theses and Dissertations

Understanding habitat selection at multiple scales is an important step in guiding conservation programs and reversing species declines. This, however, is difficult for species that occupy early-successional habitats (ESH) due to a lack of accurate representation of shrub cover in publicly available land cover data. The Golden-winged Warbler (Vermivora chrysoptera; GWWA) is a threatened species of conservation concern and a flagship for ESH conservation. We used a novel, LIDAR-derived land cover classification that accurately identifies shrubs at a fine resolution (1m) to investigate how habitat composition and configuration influence GWWA site occupancy. We aggregated this same land cover …

Plant Communities In Dynamic Systems: How Disturbance Influences Coastal Plant Community Structure And Function, Joseph K. Brown

Theses and Dissertations

As the climate continues to change it is difficult to predict how barrier island function will respond to global change drivers accompanying predicted climate change. Disturbance frequency and nutrient enrichment in coastal regions are drivers of plant community change that increase with climate change. Plant communities on barrier islands are not only tightly connected to barrier island function but are also some of the first communities affected by environmental change, making them a critical piece in understanding how current drivers of global change will impact the future of barrier islands. The objective of my dissertation was to observe and manipulate …

Conformational Modulation Of Α-Helical N-Acetylated Α-Synuclein, Ricardo Fernandez

Theses and Dissertations

Human N-acetylated α-synuclein (^NAcαSyn) has long been accepted as an intrinsically disordered protein (IDP) predominantly found in terminal nerve regions in healthy subjects. ^NAcαSyn structural fluidity enables the formation of transient or dynamic assemblies. Some of these assemblies may serve functional, yet undefined purposes. ^NAcαSyn is highly susceptible to the surrounding environment, leading to misfolding under high cytosolic oxidative stress conditions, which in turn assemble in the form of toxic oligomers or amyloid fibrils. These ^NAcαSyn inclusions along with their accretion and migration within neurons, are pathological hallmarks of Parkinson’s disease (PD), dementia, and multiple …

A Mechanism Behind The Mechanotransduction Of Surface Characteristics In Osteoblasts, Otto J. Juhl Iv

Theses and Dissertations

Biomaterials for use in bone regeneration and healing range from metal and metal alloy implants to hydrogel-based solutions. These materials can be optimized to increase bone healing and integration by improving the mechanical and biological properties. Regardless of the material itself, the cell-substrate interaction is key to the success of the biomaterial once implanted. Substrate surface characteristics such as roughness, wettability, and particle density are well-known contributors to a substrate’s overall osteogenic potential, and therefore the substrate's overall success. Unfortunately, it is still unknown how these substrate surface characteristics are transduced into intracellular signals by cells, preventing specific tailoring of …

Computational Analysis And Prediction Of Intrinsic Disorder And Intrinsic Disorder Functions In Proteins, Akila I. Katuwawala

Theses and Dissertations

COMPUTATIONAL ANALYSIS AND PREDICTION OF INTRINSIC DISORDER AND INTRINSIC DISORDER FUNCTIONS IN PROTEINS

By Akila Imesha Katuwawala

A dissertation submitted in partial fulfillment of the requirements for the degree of Engineering, Doctor of Philosophy with a concentration in Computer Science at Virginia Commonwealth University.

Virginia Commonwealth University, 2021

Director: Lukasz Kurgan, Professor, Department of Computer Science

Proteins, as a fundamental class of biomolecules, have been studied from various perspectives over the past two centuries. The traditional notion is that proteins require fixed and stable three-dimensional structures to carry out biological functions. However, there is mounting evidence regarding a “special” class …

Nature-Inspired Material Strategies Towards Functional Devices, Sayantan Pradhan

Theses and Dissertations

Naturally sourced, renewable biomaterials possess outstanding advantages for a multitude of biomedical applications owing to their biodegradability, biocompatibility, and excellent mechanical properties. Of interest in this dissertation are silk (protein) and chitin (polysaccharide) biopolymers for the fabrication of functional biodevices. One of the major challenges restricting these materials beyond their traditional usage as passive substrate materials is the ability to combine them with high-resolution fabrication techniques. Initial research work is directed towards the fabrication of micropatterned, flexible 2D substrates of silk fibroin and chitin using bench-top photolithographic techniques. Research is focused on imparting electrochemical properties to silk proteins using conducting …

Movement, Home Ranges, And Population Estimates Of Spotted Turtles (Clemmys Guttata) During A Rainy Breeding Season In Virginia, Lauren J. Jurczak

Theses and Dissertations

Spotted turtles (Clemmys guttata) use a complex of wetland and terrestrial habitats for survival and reproduction. Precipitation expands and creates larger and more numerous ephemeral pools available to spotted turtles on the landscape. In this study, I investigated the effects of precipitation on movement patterns and ephemeral pool usage by spotted turtles in southeastern Virginia. I conducted a 4-month capture-mark-recapture study alongside a telemetry study to estimate population size and to quantify movement of spotted turtles across the landscape during the breading season. A change point analysis was used to detect discrete changes in turtle behavior and whether …

Validating The Methods And Assays Necessary For Establishing An Effective In Vitro Lung Cancer Transformation Model, Crystal Turner

Theses and Dissertations

In my research, I developed tools and performed assays to study the in vitro transformation of immortalized lung epithelial cells by oncogenic KRAS^G12V. I delivered the KRAS by transfection and lentiviral transduction, and after confirming the cells expressed KRAS, I evaluated transformation using several experimental approaches including monitoring of EMT markers and various types of growth assays. I also conducted preliminary experiments that quantified sphingolipid alterations in the cells that had markers indicative of having gone through EMT. The goal of these experiments was to assess whether sphingolipids are altered in cells that are transformed in vitro by …

Mechanistic Insights Of Mitochondrial Reactive Oxygen Species In Alzheimer's Disease Models, Jakob C. Green

Theses and Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disease that results in impaired cognition, disorientation, confusion, poor judgement, and behavioral changes. The mitochondrial cascade hypothesis (MCH), which postulates that accumulating oxidative stress and mitochondrial dysfunction plays an integral role in the development of the disease, potentially upstream, in conjunction with or independent of Aβ and tau. The literature supports the critical role of mitochondrial dysfunction in the progression and development of AD, but is inconclusive about what precise role, as initiator or delegate, it performs. Regardless, the impact that oxidative stress and mitochondrial dysfunction have on AD deserves further study and investigation. …

Evolution And Clinical Relevance Of Vaginal Bifidobacterium Breve In The Vaginal Environment, Nicole R. Jimenez

Theses and Dissertations

The vaginal microbiome is important in reproductive health and disease and is often dominated by lactobacilli. However, there are many other community state types dominated by single species that are still not well characterized. Bifidobacterium species such as Bifidobacterium breve and Bifidobacterium longum have been observed to dominate vaginal profiles. Bifidobacteria are important in infant gut development, but little is known about their role in vaginal health. Thus, we sought to use a multisystem approach to better characterize Bifidobacterium species present in the vaginal microbiome with an emphasis on B. breve. Eight strains of B. breve were isolated from vaginal …

A Novel Immunostimulatory Platform For Amplifying The Abscopal Response Rates Of Radiation Therapy, Patrick A. Paez

Theses and Dissertations

Radiation therapy (RT) is one of the primary treatment modalities for head and neck squamous cell carcinoma (HNSCC). At the time of diagnosis two-thirds of HNSCC patients have local-advanced disease and 50-60% of these patients will experience a local-regional or metastatic relapse within three years. Improving the immunogenic response of RT may help address this clinical problem. However, current RT regimens have failed to reliably generate robust antitumor immunity as evidenced by the rarity of clinical abscopal responses. Recently we engineered a chimeric fusion molecule called Flagrp170, a novel immunostimulatory agent highly capable of promoting antigen presentation and T-cell activation. …

Effects Of Abiotic And Biotic Factors On Hornworm Distributions, Emelia O. Kusi

Theses and Dissertations

Determining the drivers of species occurrences is a central topic in ecology. Both abiotic and biotic factors are important predictors of species distributions, yet most species distribution models consider abiotic variables only. In this study, the influence of abiotic and biotic factors on current distributions of herbivores, Manduca sexta, and Manduca quinquemaculata, their major cultivated and wild host plants, and a parasitoid, Cotesia congregata, was quantified using an ensemble of three models (generalized linear model, maximum entropy, and random forest). The predictive ability of abiotic-only, biotic-only, and abiotic-biotic models was evaluated. Winter temperatures and precipitation (i.e., precipitation of …

Identifying Genes Downstream Of Mef2 That Influence Ethanol Sedation In Drosophila Melanogaster, Ananya Talikoti

Theses and Dissertations

Alcohol use disorder is a global public health issue that affects millions across the world. It can result in negative physical and mental health outcomes, and currently treatment options are limited and rates of relapse are high. Identifying genes that affect aspects of ethanol behaviors in model organisms, such as Drosophila melanogaster, can serve to eventually develop more robust therapeutic interventions for those experiencing alcohol dependence. Previous studies have identified a relationship between a person's initial sensitivity to alcohol and their abuse potential for the drug in later life. Therefore, we can study sedation behaviors in Drosophila melanogaster to …

Cryogenic Electron-Microscopy (Cryo-Em) Analysis Of Mscs, Ynai, Connexin 26 And Bioinformatic Analysis Of Cysteine And Serine In Experimental Protein Structures, Claudio Catalano

Theses and Dissertations

Functional insights into macromolecules lie in the arrangement of their molecular structures. Investigating the atomic framework of a biomolecule could unwind its biochemical mechanism, providing aid to many relevant biological questions, thus facilitating drug discovery processes. Two approaches have been used to gain knowledge at the atomic level of a protein function: experimental and computational methodologies.

From an experimental perspective, membrane proteins (MPs) were investigated. Such proteins represent ~20% of the human proteome, and ~60% of them are drug targets since they are exposed to the surface of cells and are responsible for a wide range of fundamental functions like …

Examining The Impact Of High Sodium Intake On Blood Flow Regulation, Exercise Tolerance, And Oxidative Stress In Salt Resistant Individuals, Kevin P. Decker

Theses and Dissertations

Excessive dietary sodium consumption increases the risk for high blood pressure (BP), and therefore recommended for dietary sodium intake to be ≤ 2,300 mg/day. Recommendations are based on salt-sensitive individuals who report elevated BP with high sodium (HS) intake, but many individuals are salt-resistant (SR) who experience little to no change in BP with HS intake. Currently, less is known about the adverse cardiovascular effects of HS intake independent of BP. A potential source of impaired blood vessel function (micro- and macro-) from HS intake is oxidative stress, or the imbalance between antioxidant defense and oxidants, in favor of oxidants. …

Glycosaminoglycan Modulation Of Key Proteins In Alzheimer's Disease, Tamim Chiba

Theses and Dissertations

Glycosaminoglycans (GAGs) are linear polysaccharides whose disaccharide building blocks consist of an amino sugar (D-glucosamine) and either uronic acid (D-glucuronic acid or L-iduronic acid) or galactose. Nearly all GAGs (with the exception of hyaluronic acid) are covalently attached to proteins, forming proteoglycans, and are ubiquitous in nature. The monomeric units, chain length, degree and pattern of sulfation, and epimerization are important properties that determine the influence of these molecules. Through Coulombic forces, hydrogen bonds and hydrophobic interactions, they regulate many physiological and pathophysiological processes such as blood coagulation, cell growth and differentiation, inflammatory processes, host defense and viral infection mechanisms. …

Investigating Cannabinoid Type-1 Receptor (Cb1r) Positive Allosteric Modulators (Pams) In Mouse Models Of Overt Cannabimimetic Activity, Subjective Drug Effects, And Neuropathic Pain, Jayden Elmer

Theses and Dissertations

Chronic pain affects between 20 and 30 percent of the adult population in western countries and represents a wide array of specific etiologies (Berge, 2011). Neuropathic pain secondary to traumatic nerve injury, chemotherapeutic toxicity, or diseases (e.g., diabetes mellitus) is often refractory to conventional analgesics, with patients receiving less than 50% pain relief compared to placebo (Finnerup et al. 2010). The endocannabinoid system has shown potential as a therapeutic target for neuropathic pain wherein CB1 agonism via administration of exogenous agonists or pharmacological blockade of endocannabinoid catabolic enzymes exhibits efficacy in reversing allodynia in the chronic constriction injury (CCI) model …

Characterization Of Cytochrome P450 3a4 Structure And Ligand Binding Mechanism In Anionic Nanodiscs, David T. Sweeney

Theses and Dissertations

The Cytochromes P450 superfamily are ubiquitous throughout life and are present in some viruses. Humans encode for 57 of these enzymes that are involved in the metabolism of ~90% of all chemicals. These membrane-bound monooxygenase enzymes utilize a heme protoporphyrin at their active site to activate molecular oxygen and oxidize their substrates through an intermediate deemed nature's most powerful oxidizer. They are a powerful system at our disposal yet understanding of their structure and ligand binding mechanisms in the presence of a lipid bilayer remains poorly understood. The focus of this work is on Cytochrome P450 3A4 (CYP3A4). We set …

Pharmacophoric Evaluation Of 5-Ht2a And 5-Ht2b Serotonin Recpeptors, Prithvi Hemanth

Theses and Dissertations

Serotonin (5-HT) receptors represent a class of receptors involved in a variety of physiological processes including regulation of mood, perception, cognition, appetite, and heart function, and thus serve as drug targets of several drugs such as antipsychotic agents, hallucinogenic drugs, and appetite suppressant drugs. Due to the structural similarity of certain 5-HT receptor subtypes, particularly 5-HT₂ receptors (5-HT_2A, 5-HT_2B receptors) determination and refinement of pharmacophore models of these receptor subtypes can greatly improve the therapeutic efficacy of drugs that target them.

The goals of this study were to define and/or refine existing pharmacophore models for 5-HT …

Impact Of Targeting Glycosylated Ceramides On Tumorigenic Properties, And Characterization Of Sphingolipids In Head And Neck Tumors, Katherine E. Hylton

Theses and Dissertations

Sphingolipids play a crucial role in signaling, membrane structure, and migration, making them important molecules in cancer development, metastasis, and drug resistance. While some sphingolipids have been associated with pro-apoptotic or pro-survival behaviors, the role of many sphingolipids in cancer remains poorly defined. Chapter 1 of this study investigated the impact of three enzymes that compose most of the ceramide to Lc3 ceramide pathway – UGCG, GBA, and B3GNT5 – and how their alteration impacts chemoresistance and basal membrane invasion in vitro. It was found that the CΒE-induced inhibition of GBA, which converts glucosylceramide to ceramide, has no effects on …

Interclass Gpcr Heteromerization Affects Localization And Trafficking, Rudy Toneatti

Theses and Dissertations

Class A serotonin (5-hydroxytryptamine) 2A (5-HT_2AR) and class C metabotropic glutamate 2 receptors (mGluR2) are seven transmembrane receptors (7TMRs or G protein-coupled receptors – GPCRs) involved in multiple neuropsychiatric disorders including schizophrenia. Previous findings from our laboratory reported that 5-HT_2AR and mGluR2 are dysregulated in the prefrontal cortex of patients suffering from this psychiatric condition, although 5-HT_2AR’s expression was recovered in antipsychotic-medicated patients. Genome-wide association studies on schizophrenia reported that endosomal trafficking that regulates cell surface abundance of another 7TMR implicated in this disease (dopamine D2 receptor) can be altered. Ligand-activated receptors, including the …

Evaluating Neuromuscular Function Of The Biceps Brachii After Spinal Cord Injury: Assessment Of Voluntary Activation And Motor Evoked Potential Input-Output Curves Using Transcranial Magnetic Stimulation, Thibault Roumengous

Theses and Dissertations

Activation of upper limb muscles is important for independent living after cervical spinal cord injury (SCI) that results in tetraplegia. An emerging, non-invasive approach to address post-SCI muscle weakness is modulation of the nervous system. A long-term goal is to develop neuromodulation techniques to reinnervate (i.e. resupply nerve to) muscle fiber and thereby increase muscle function in individuals with tetraplegia. Towards this goal, developing monitoring techniques to quantify neuromuscular function is needed to better direct neurorehabilitation. Assessment of voluntary activation (VA) is a promising approach because the location of the stimulus can be applied cortically using transcranial magnetic stimulation (TMS) …

The Cb1 Receptor Positive Allosteric Modulator, Zcz011, Attenuates Naloxone-Precipitated Withdrawal Signs In Oxycodone-Dependent Mice And Inhibits Small Intestinal Transit In Mice, Julien Dodu

Theses and Dissertations

The endogenous cannabinoid system tightly regulates a myriad of physiological and pathophysiological functions. Effects of cannabinoids in ameliorating opioid withdrawal signs has been known for decades. Naloxone precipitates several withdrawal signs (e.g., diarrhea, weight loss, jumps, paw flutters, and head shakes) in opioid dependent rodents. ∆⁹-tetrahydrocannabinol (THC) has been shown to ameliorate opioid withdrawal in mice through the activation of cannabinoid type-1 (CB₁) receptors. Inhibition of the endocannabinoid degradative enzymes also attenuates these withdrawal signs (i.e., diarrhea, weight loss, jumps, paw flutters, and head shakes) in opioid-dependent mice. Specifically, inhibition of fatty acid amide hydrolase (FAAH), …

Nebulizer-Based Systems To Improve Pharmaceutical Aerosol Delivery To The Lungs, Benjamin M. Spence

Theses and Dissertations

Combining vibrating mesh nebulizers with additional new technologies leads to substantial improvements in pharmaceutical aerosol delivery to the lungs across therapeutic administration methods. In this dissertation, streamlined components, aerosol administration synchronization, and/or Excipient Enhanced Growth (EEG) technologies were utilized to develop and test several novel devices and aerosol delivery systems. The first focus of this work was to improve the poor delivery efficiency, e.g., 3.6% of nominal dose (Dugernier et al. 2017), of aerosolized medication administration to adult human subjects concurrent with high flow nasal cannula (HFNC) therapy, a form of continuous-flow non-invasive ventilation (NIV). The developed Low-Volume Mixer-Heater (LVMH) …

Development And Evaluation Of A Combinatorial Rt-Qpcr Multiplex For Forensic Body Fluid Identification, Carolyn A. Lewis

Theses and Dissertations

Body fluid identification is essential in the forensic biology workflow that assists DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the sensitivity and specificity molecular techniques can achieve; therefore, molecular methods, such as microRNA and microbial signatures, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance. A disadvantage of RNA analysis in forensic …

Comparing The Sensitivity And Specificity Of Cbct And Mri In Detecting Osteoarthritis Of The Tmj: A Systematic Review, Gabriel R. Saavedra

Theses and Dissertations

The aim of this systematic review was to compare the sensitivity and specificity of cone-beam computed tomography (CBCT) and magnetic resonance imaging (MRI) in detecting osteoarthritis (OA) of the temporomandibular joint (TMJ). This was done by using computed tomography (CT) and the research diagnostic criteria for temporomandibular disorders (RDC/TMD) as reference methods and using CBCT and MRI as index methods. A specific search strategy was developed and applied to these electronic databases: PubMed, Embase, DOSS, and Cochrane. The search results returned 802 articles, which were then narrowed down using the inclusion/exclusion criteria, to four final articles that were included in …

The Rho1 Gtpase-Activating Protein Sac7 Is A Negative Regulator Of Clathrin-Independent Endocytosis In Yeast, La'tila Abbott

Theses and Dissertations

Endocytosis, or internalization of material from the plasma membrane, is an important process for many aspects of eukaryotic cell function. Although clathrin-mediated endocytosis (CME), which requires the coat protein clathrin to facilitate endocytic vesicle formation, is the predominant mechanism for internalization, numerous clathrin-independent (CIE) pathways exist that remain poorly characterized. While the budding yeast Saccharomyces cerevisiae has been a powerful model organism for studying CME, it was long thought to lack any CIE pathways. Recently, a mutant yeast strain defective in CME was used to discover the first known yeast CIE pathway, which requires the small GTPase Rho1. Rho1 regulates …

Il-36g Cytokine Induction In Oral Epithelial Cells Triggered By Treponema Denticola And Their Role In Chronic Periodontitis, Christopher Blake

Theses and Dissertations

Periodontal disease is a polymicrobial disease affecting 10-15% of the population. Periodontal disease affects the quality of life by reducing mastication and potentially causing tooth loss. Periodontal disease is also linked to more severe, systemic diseases such as cardiovascular disease and rheumatoid arthritis. Development of the diseased state occurs when the plaque biofilm shifts from healthy to dysbiotic. The shift to a dysbiotic biome brings with it a shift in bacterial presence, specifically an increase in gram-negative bacteria, such as T. denticola. T. denticola is a gram-negative, anaerobic spirochete whose relationship with oral epithelial cells is poorly understood. Preliminary data …