Life Sciences Commons^™

Tgif1 Physiological Levels Limit Β-Cell Distress And Neonatal Diabetes, Creighton J. Friend

Theses and Dissertations

TGIF1 belongs to the superfamily of homeodomain proteins, which regulate a wide variety of biological functions, including cell stemness and specification of cell fate during early development. Perhaps surprisingly, we found that enforced expression in pancreatic progenitor cells during embryogenesis resulted in severe diabetes, hinting at the possibility that TGIF1 might regulate pancreas development. Subsequent genetic experiments targeting β-cells showed that TGIF1 affected β-cell function and homeostasis. Transcriptomic analysis revealed that TGIF1 expression inhibits the expression of essential components of UPR signaling, underscoring a potential mechanism in which TGIF1 disrupts protein folding and secretion. Congruently, TGIF1 expression led to a …

Evaluating How Acidic Solutions Affect The Microhardness Of Bioceramic Sealers, Colton Fischer

Theses and Dissertations

Introduction: With growing use of bioceramic sealers (BCS) in root canal therapy, there have been challenges when retreating BCS cases. Weak acids may be effective in removing BCS and their efficacy as a solvent can be measured by their influence on the microhardness of BCS. Microhardness can be used as an indirect measurement of material hardness. The purpose of this study was to investigate the microhardness of BCS when placed in contact with various acidic solutions to assess their potential use as a solvent for retreatment procedures.

Methods: EndoSequence BC Sealer (Brasseler USA) was injected into four 10 × 3mm …

Incorporating A Developmental Perspective Into Gene Identification Models For Alcohol Use Behaviors, Nathaniel S. Thomas

Theses and Dissertations

Frequent alcohol use can lead to alcohol use disorder, which accounts for three million deaths and over 133 million life years lost to disability and death worldwide per year. Alcohol use behaviors unfold across development, beginning with initiation of drinking and progressing through various escalating stages of use. Alcohol use behaviors are also under genetic influence. Genome-wide association represents the state-of-the-science statistical methodology for identifying genes associated with alcohol use outcomes. However, contemporary genome-wide association study (GWAS) methods typically do not account for variability in genetic effects throughout development. In this project, I applied novel multivariate genomic methods to combine …

Effects Of Hiv-1 Tat And Opiates On Gene Regulation Of Oligodendrocyte Lineage Cells: Identification Of Myrf As A Novel Target, Kelly M. Flounlacker

Theses and Dissertations

HIV-associated neurocognitive disorders remain pervasive even with increased efficacy/use of antiretroviral therapies. Opioid use/abuse among HIV+ individuals is documented to exacerbate deficits. White matter (WM) alterations (myelin pallor, volume/structural) detected by diffusion tensor imaging, are common observations in HIV+ individuals. Using transgenic mice expressing HIV-1 Tat, we examined effects of 2-6 weeks of Tat/morphine exposure on WM using genomic/biochemical methods. RNA sequencing of striatal tissue after 2-weeks revealed robust changes in mRNAs associated with oligodendrocyte populations/myelin integrity, including Transferrin, Ndrg1, and myelin regulatory factor (Myrf/Mrf), an oligodendrocyte-specific transcription factor involved in differentiation/maturation. Immunoblots conducted after 6-weeks exposure in …

Patterns, Mechanisms, And Characterization Of Carbon Cycling Stability Following Partial Forest Disturbance, Kayla C. Mathes

Theses and Dissertations

Among the most essential questions in the era of climate change is how the forest carbon (C) cycle will respond to an increase in the extent of biotic disturbances from insects and pathogens. While research has focused on stand-replacing disturbance regimes, less is known about C cycling stability following partial disturbances that produce gradients of disturbance severity. Belowground C cycling responses to disturbance are especially poorly understood, even though temperate forest soils contain up to 50% of total ecosystem C and soil respiration (R_s) accounts for more than half of temperate forest C loss. Interpreting trends and mechanisms …

Quantifying Insect Emergence In Tidal Freshwaters And The Importance Of Aquatic Prey In Wetland-Dependent Songbird Diet, Samantha L. Rogers

Theses and Dissertations

Insectivorous birds and their arthropod prey are experiencing widespread population declines, driven largely by anthropogenic disturbance and climate change. For wetland-dependent insectivores that consume a mixture of terrestrial and aquatic insects, understanding the availability, consumption, and nutritional qualities of aquatic diet subsidies is important for conservation. I use prothonotary warblers (Protonotaria citrea) as a model species throughout this work, because their breeding season aligns with aquatic insect emergence and they include aquatic insects when provisioning nestlings. In the first chapter, I estimate aquatic insect emergence from tidal freshwaters, which are understudied compared to nontidal systems. Using continuous field …

Modulation Of Opioid-Induced Respiratory Depression By Stimulants And Their Associated Monoaminergic Receptor Mechanisms In Mice Using Whole Body Plethysmography, Harrison J. Elder

Theses and Dissertations

Opioid overdose and associated deaths involving opioid-induced respiratory depression (OIRD) began to accelerate beginning in 2015 with the emergence of illicitly manufactured fentanyl and its analogs and currently represents one of the most significant public health challenges in the United States. The increases in overdose deaths have occurred despite the increased availability of the opioid overdose reversal agent, naloxone, to first responders and the public. This new phase of the opioid epidemic has been paralleled by substantial growth in the co-use of opioids with stimulants, particularly methamphetamine. The objective of this dissertation is to ascertain whether fentanyl is particularly resistant …

Interactions Between Hiv And Opioids On Antiretroviral Accumulation, The Blood Brain Barrier, And The Inflammatory Response In The Brain., Kara Rademeyer

Theses and Dissertations

The complex mechanisms related to HIV infection, neurodegeneration, and chronic neuroinflammation collectively describe neuroHIV (Hauser et al. 2007; Chang et al. 2014; Smith et al. 2014). Specifically, opioid abuse, poor penetration of antiretroviral (ARV) drugs, chronic inflammation and neuronal injury/degeneration are all implicated in neuroHIV (Fantuzzi et al. 2003; Letendre et al. 2004; Verani et al. 2005; Duncan and Sattentau 2011; Hong and Banks 2015; Simoes and Justino 2015; Olivier et al. 2018; Murphy et al. 2019; Osborne et al. 2020). For the first time, we demonstrate that morphine, fentanyl, and methadone in vivo alter the brain accumulation of ARVs, …

Plant Trait Effects On Tidal Wetland Methane Emission, Adam M. Dunn

Theses and Dissertations

High rates of carbon (C) sequestration exhibited by coastal wetlands is an important natural climate solution to global environmental change. At the same time, however, wetlands are the largest natural source of methane (CH₄) to Earth’s atmosphere, a potent greenhouse gas that influences the global climate. Wetland CH₄ emissions display high degrees of uncertainty in accounting for spatial and temporal variations in emissions due to the complex interactions between biotic and abiotic factors that influence methane production and transport, in addition to simultaneous influences from climate-driven effects on wetlands such as rapid sea level rise and increased …

The Hepatic Immunological Pattern Shaped By Dominant-Subdominant Cellular Interactions Creates A Collective Function Beyond The Function Of Each Cellular Constituent To Orchestrate Progression Of Hepatocellular Carcinoma, Nicholas J. Koelsch

Theses and Dissertations

Abundance of data on the role of inflammatory immune responses in the progression or inhibition of hepatocellular carcinoma (HCC) has failed to offer a curative immunotherapy for HCC. This is largely because of taking reductionist approaches and missing the collective function of the hepatic immune system by focusing on specific immune cell types. To this end, we propose that focusing on the dominant-subdominant patterns of the immune cells would allow understanding of the mechanism by which a collective immune function emerges. To identify the collective immune function through a systems immunology perspective, we performed high-throughput analysis of snRNAseq data collected …

Epithelial Membrane Protein 3 (Emp3b) Is A Novel Regulator Of Sympathetic Nervous System Development In Zebrafish., Jessica M. White

Theses and Dissertations

Notable progress has been made in understanding the development of the neural crest (NC). Neural crest cells (NCCs) can be divided into 4-5 subpopulations. A major lineage among trunk NC derivatives are sympathoadrenal (SA) cells, which give rise to the sympathetic nervous system (SNS). Trunk NCCs follow a ventromedial migration pathway where signals derived from the dorsal aorta instruct migrating NCCs to a SA cell fate. Defects in NC development can result in syndromes known as neurocristopathies. Neuroblastoma is one of the most common forms of pediatric cancer affecting nearly 800 infants each year in the United States (Takita et …

Exploring The Relationship Between The Epigenome And Metabolism In Mycn-Amplified Neuroblastoma, Krista M. Dalton

Theses and Dissertations

High risk neuroblastoma (NB) is responsible for nearly 15% of all cancer related deaths in the pediatric population. The transcription factor MYCN is the most studied oncogene in NB, automatically conferring high-risk and has been found to be difficult to target. One way that MYCN amplification in NB functions to support tumorigenicity is through altered metabolism, satisfying the demand for rapid proliferation by increasing the nutrient flux through biosynthetic pathways. We performed an unbiased screen on select metabolic targeted therapy combinations and correlated sensitivity with over 20 subsets of cancer. We found that MYCN-amplified NB is hypersensitive to the …

Association Of Interpersonal Trauma And Polygenic Risk Scores With Depressive Symptoms In College Students, Rowan K. O'Hara

Theses and Dissertations

Major depression is considered a complex trait influenced by both polygenic risk factors and environmental exposures, such as childhood trauma. This study applied statistical genetic methods to calculate aggregate genetic risk for major depression to predict depressive symptoms scores in a college student sample. Data were from the Spit for Science (S4S) study in which college students from a large urban university self-reported interpersonal trauma (IPT) exposure prior to college and depressive symptoms from the past month (N = 7502; ancestry group: 20% African [AFR], 12% Admixed Americas [AMR], 10% East Asian [EAS], 49% European [EUR], 8% South Asian [SAS]). …

A Standardized Pipeline For Isolation And Assembly Of Genomes From Symbiotic Bacteria In Whole Louse Genomic Sequence Data., Mohammad Mikail I. Bala

Theses and Dissertations

Many insects are known to harbour intracellular and heritable bacteria (endosymbionts), which provide their hosts with adaptive traits. Whole insect gDNA shotgun sequencing projects often sequence the genome of endosymbiont, in addition to the insect’s genome. There are approximately 600 whole genome shotgun libraries from insects available on the public repository (NCBI), which can be mined to obtain endosymbiont genomes. The assembly and annotation of endosymbiont genomes can contribute towards the exploration of their role as obligate symbiotic partners. However, de novo assembly of an endosymbiont genome, continues to be challenging, when the host and/or enteric bacterial gDNA is present …

Unraveling The Consequence Of Adult Onset Sulfatide Depletion: Its Implications In Myelin And Axonal Heath In The Context Of Neurodegenerative Disease, Elizabeth Dustin

Theses and Dissertations

Multiple Sclerosis is an immune mediated disease of the CNS. MS is diagnosed through detection of demyelinated regions. However, recent studies demonstrate that Normal Appearing White Matter (NAWM) contains substantial pathology. One such pathology observed in the NAWM is the reduction of sulfatide. The proper stoichiometry of lipids in myelin acts to maintain rapid conduction velocity, provide trophic support to the neuron, and protect the axon from degeneration. We previously characterized a mouse lacking sulfatide’s synthesizing enzyme, CST through constitutive gene disruption and demonstrate that sulfide is required for proper stability of the myelin sheath. However, since MS is typically …

Mechanistic Insight Into Traumatic Brain Injury Induced Neuronal Membrane Disruption: Cathepsin B Relocalization And A Neun Negative Cortical Neuron Subpopulation, Martina L. Hernandez

Theses and Dissertations

Traumatic brain injury (TBI) is a mechanical insult to the head that leads to brain damage and, in turn, causes long-term sensory, motor, cognitive, and affective dysfunction. Diffuse pathologies seen following such injury are associated with these life-altering outcomes that impact the daily lives of TBI survivors. The diffuse pathology that this body of work focuses on is neuronal membrane disruption; it is characterized by increased permeability of the neuron’s plasma membrane. Moreover, our lab had previously found that membrane disruption is exacerbated with intracranial pressure (ICP) elevation. We set out to measure the duration of membrane disruption following injury …

Probing The Porphyromonas Gingivalis Nitrosative Stress Response Network, Alexandra Galina

Theses and Dissertations

Objective: To persist in the oral cavity, the perio-pathogen Porphyromonas gingivalis must have an efficient nitrosative stress response mechanism. To better understand how P. gingivalis responds to nitrite (NO₂^-) we must determine what genes are involved in the nitrosative stress response network.

Methods: Through genomic screening, a list of genes was generated that were hypothesized to be part of the nitrosative stress response network and believed to be involved in nitrate/nitrite metabolism or redox state of the cells. Protein coding regions were replaced with the ermF sequence by allelic exchange mutagenesis. 15 mutants were created …

Treponema Denticola Synthesizes C-Di-Amp And Encodes The Cdaa-Type Diadenylate Cyclase Cdaa, Claire R. O'Brien

Theses and Dissertations

Periodontitis is a form of oral disease characterized by dysbiosis of the oral microbiome, leading to inflammation, bone resorption, and in severe cases, entire tooth loss, affecting 42% of adults in the US. One of the bacteria most associated with periodontal disease progression is Treponema denticola (Td), an oral spirochete which inhabits the mouth in small quantities during health but which can dominate the biofilms that form during periodontal disease. The ability of Td to survive in a disease environment and contribute to the progression of disease requires the use of robust signaling networks. Analysis of Td cultures …

Stage-Structured Predator-Prey Interactions In A Warming World: A Case Study In Riverine Rock Pools, Andrew T. Davidson

Theses and Dissertations

Warming can impact predator-prey interactions through a variety of mechanisms. For example, warming can both alter the rate at which predators consume prey and the rate prey develop through vulnerable life stages. Thus, the overall effect of warming on consumer-resource interactions will depend upon the strength and asymmetry of warming effects on predator and prey performance. Here, we describe the consequences of these asymmetrical responses to temperature by first developing a simple stage-structured modeling framework, then applying that framework to predation of American rock pool mosquito larvae, Aedes atropalpus, by several common predators in riverine rock pools. We then …

Protacs – A Novel And Rapidly Developing Field Of Targeted Protein Degradation, Hannah R. Gatley

Theses and Dissertations

There is a continued need for new technology and strategies for tackling cancer and other diseases, and within the current century a novel therapeutic strategy has emerged in the realm of targeted protein degradation called Proteolysis-Targeting Chimeras (PROTACs). This technology specifically targets and degrades disease-causing proteins via the ubiquitin-proteasome system, and has seen an explosion of research and intrigue in both academia and industry over the past two decades. The diversity of PROTAC classes based on the E3 ligase recruiting ligand and the target protein allows for a universal molecular structure that can be customized for a specific target and …

Population Demography Of A Neotropical Migratory Songbird In The Face Of A Changing Climate, Adele Balmer

Theses and Dissertations

This dissertation investigates the population dynamics and demographic trends of the Prothonotary Warbler (Protonotaria citrea), a migratory songbird that breeds in North America during the spring and summer and overwinters in Central and northern South America. The primary objective of this dissertation is to examine the combined implications of variation in weather and individual traits on demographic traits and to project the effects of climate change on population trajectories of the Prothonotary Warbler.

The analyses conducted in this dissertation centered around female Prothonotary Warblers; however, visual identification of a nestling’s sex is impossible in most altricial bird species, …

Dune Building Dynamics Impact Cross-Island Connectivity And Barrier Island Characteristics, Alexander Sabo

Theses and Dissertations

Located at the land-sea interface, barrier islands are important protective features that reduce wave energy and erosion from mainland areas. Further, barrier islands provide habitat for many different organisms and serve as popular areas for recreation and tourism. As sandy landforms, barrier islands are easily disturbed, but often recover after disturbance as a result of island plant communities, specifically dune building grasses. Disturbance on barrier islands is driven by storms, tides, and overwash events. After disturbance has occurred, dune grasses colonize the dunes allowing for dune building and habitat restoration. On the Virginia barrier islands, there are three dominant dune …

Evaluation Of Spliceai For Improved Genetic Variant Classification In Inherited Ophthalmic Disease Genes, Melissa Reeves

Theses and Dissertations

ABSTRACT

EVALUATION OF SPLICEAI FOR IMPROVED GENETIC VARIANT CLASSIFICATION IN INHERITED OPHTHALMIC DISEASE GENES

By Melissa Jean Reeves, 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, 2023

Major Director: Melissa Jamerson, PhD, MLS(ASCP)

Associate Professor, Department of Medical Laboratory Sciences

Inherited ophthalmic diseases impact individuals around the globe. Inherited retinal diseases (IRDs) are the leading cause of blindness in individuals aged 15 to 45. The personal, social, and economic impact of vision loss is profound. Due to individual differences, symptoms can be variable, and …

The Type Iv Pilus Secretin Bfpb: Structural Analysis And Binding Interactions, Janay I. Little

Theses and Dissertations

Enteropathogenic Escherichia coli (EPEC) causes severe diarrhea in young children. The type IV pilus (T4P) of EPEC, known as the bundle-forming pilus (BFP), plays an important role in EPEC pathogenesis. T4Ps are a family of surface appendages that are important for adhesion, colonization, biofilm formation, virulence, twitching motility and many other functions. One essential component of the BFP system is the secretin, BfpB. Secretins are a large family of integral outer membrane proteins found in T4Ps as well as type II and type III secretion systems, and filamentous phages. Details of the secretin structure have been limited to the overall …

Integrative Post-Gwas Analyses Of Psychiatric Disorders: Identifying Putative Risk Genes And Gene Sets Using Transcriptome, Proteome And Methylome Information, Huseyin Gedik

Theses and Dissertations

Genome-wide association studies (GWAS) of psychiatric disorders (PD) yield numerous loci with significant signals, but often they do not implicate specific protein coding genes. Because GWAS risk loci are enriched in expression/protein/methylation quantitative loci (e/p/mQTL, hereafter xQTL), transcriptome/proteome/methylome-wide association studies (T/P/MWAS, hereafter XWAS), which integrate information from GWAS and x-level (mRNA, protein or DNA methylation levels) coming from largest xQTL studies, can link GWAS signals to effects on specific genes. For gene level analyses, researchers use mendelian randomization (MR) methods to fine-map the association between x-levels and trait. However, none of the previous studies ever jointly analyzed XWAS of multiple …

Characterizing The Effects Of Antiandrogens And Senolytics To Enhance The Therapeutic Response To Castration-Resistant Prostate Cancer, Justin M. Silverman

Theses and Dissertations

Prostate cancer is the most frequently diagnosed cancer in males and the second most common cause of cancer deaths. Androgen deprivation therapy, whether through surgical or chemical castration, is the mainstay for treatment of advanced prostate cancer; however, despite an initial response, most patients eventually develop a progressive PSA rise, and castration- sensitive prostate cancer gives rise to castration-resistant prostate cancer. The standard of care therapy includes the antiandrogens such as enzalutamide and abiraterone acetate as well as the microtubule poison, docetaxel, and various immunotherapies; however, while prostate cancer research is progressing, there continues to be a compelling need for …

Novel Strategies In Head And Neck Tumor Therapy; Contribution Of Senescence In Therapy Response, And Resistance Development After Cisplatin Treatment, Fereshteh Ahmadinejad

Theses and Dissertations

Therapeutic outcomes achieved in head and neck squamous cell carcinoma (HNSCC) patients by concurrent cisplatin-based chemoradiotherapy initially reflect both tumor regression and tumor stasis. However, local, and distant metastasis and disease relapse as well as cisplatin-induced resistance are common in HNSCC patients. In the current work, we demonstrate that cisplatin treatment induces senescence in both p53 wild- type HN30 and p53 mutant HN12 head and neck cancer models. We also show that tumor cells can escape from senescence both in vitro and in vivo. We further established a cisplatin-resistant cell line from HN30 parental cell line that underwent brief senescence …

Pre-Clinical Trials With Precision-Medicine Based Therapeutics In Basal-Like Patient-Derived Xenografts, David C. Boyd

Theses and Dissertations

Breast cancer treatments have improved over time, but the diseases seeing the most benefit from these improvements have the estrogen receptor, progesterone receptor, or are positive for HER2. Basal-like breast cancer tends to not have these biomarkers, which necessitates their treatment to be traditional, untargeted therapeutics which are less effective and tend to have harsh adverse effect profiles – this is an important unmet need. These studies utilize a variety of techniques, including tissue culture, viability assays, high-throughput screening, in vivo drug treatments and imaging, pathway analyses, molecular techniques such as Western blot, antibody arrays, RNA sequencing, sc RNA sequencing, …

Intrinsic Efficacy As A Determinant Of Opioid Effectiveness In Treatment Of Pain-Depressed Behavior, Edna Santos

Theses and Dissertations

Pain is a major public health concern that is commonly associated with behavioral depression, and a major goal in pain treatment is alleviation of pain-related behavioral depression. High-efficacy mu opioid receptor (MOR) agonists (e.g. fentanyl, morphine, oxycodone) are effective to treat pain, but their use is limited by side effects that not only endanger the patient but may also obscure analgesic rescue of pain-depressed behavior. The ongoing epidemic of opioid abuse and overdose deaths has stimulated research to discover non-opioid alternative analgesics; however, this search neglects the clinical potential of safer intermediate-efficacy MOR agonists (e.g. buprenorphine). The objective of the …

Salinization Impacts On Heterotrophic Respiration, Ecosystem Respiration, And Plant Productivity In Tidal Freshwater Marshes, Kelsie J. Moses

Theses and Dissertations

Tidal freshwater marshes have preserved substantial stocks of soil carbon, which represents carbon dioxide that is no longer in the atmosphere. There is conflicting evidence in the literature about how disturbances such as sea level rise and associated wetland salinization impact the accumulation and long-term stability of this stored carbon. The goal of this experiment was to quantify how salinization impacts total ecosystem respiration and its component parts, autotrophic and heterotrophic respiration. This was a microcosm experiment using a C4 plant (Spartina cynosuroides) grown in soil derived from C3 plant matter and exposed to different salinities (0 to …