Life Sciences Commons^™

Next-Generation Sequencing Shows Increasing Temperatures Affect Stream Fungal Communities, Regan Hodgson

Electronic Theses and Dissertations

Under climate change predictions, surface air temperature is expected to continue to rise and will likely affect functioning of stream ecosystems and microbial communities. Aquatic hyphomycetes are key fungal decomposers of plant litter in headwater streams controlling carbon, energy, and nutrient flows to higher trophic levels. This project addressed the effects of temperature on stream fungal communities in two recently conducted experiments (microcosm and streamside channel studies) using Illumina sequencing. The objectives were to determine (1) if temperature affects community structure of stream fungi based on relative abundances of ITS2 rDNA sequences, (2) if the effects of temperature on aquatic …

Sequencing And Functional Characterization Of A Latrodectus Geometricus Defensin, Lg-Defensin, Jacklyn Victoria Thompson

Electronic Theses and Dissertations

Defensins are small, cysteine-rich, immune related proteins described to be the most widespread family of invertebrate antimicrobial peptides. Presently, there is limited information regarding spider defensins. In this study, a new defensin peptide was described in Latrodectus geometricus, Lg-defensin. The full open reading frame was resolved using RACE and de novo assembly, followed by a bioinformatical analysis and phylogenetic alignment to determine conserved sequence patterns and structural similarities to other defensins. Next, the functionality of Lg-defensin was determined using in vitro RNA interference to assess what impact silencing had on the spider’s ability to control a gram-positive and gram-negative bacterial …

Re-Engineering Cardio-Oncology Testing Using Biomimetic Heart Slice Cultures., Jessica Miller

Electronic Theses and Dissertations

28% of drug withdrawal from the market are due to unforeseen disruptions in cardiomyocyte contractility and electrophysiology. The most commonly used platforms for drug testing are in vivo animal models and in vitro cell culture models. While both have been of paramount importance for the discovery and detection of many cardiotoxicities and mechanisms of action, they lack the ability to model an intact human myocardium. This work aims to establish cardiac tissue slices, which are 300-micron thin tissue sections taken from the left ventricular myocardium, as an alternative platform for cardio-oncology studies, specifically cardiotoxicity testing. Additionally, this work aims to …

Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler

Electronic Theses and Dissertations

Microbial communities contain densely packed cells where competition for space and resources are fierce. These communities are generally referred to as biofilms and provide advantages to individual cells against immunological and antimicrobial intervention, dehydration, and predation. High intracellular pools of cyclic diguanylate monophosphate (c-di-GMP) cause cells to aggregate during biofilm formation through the production of diverse extracellular polymers. Genes that encode c-di-GMP catalytic enzymes are commonly mutated during chronic infections where opportunists display enhanced resistance to phagocytosis and antibiotics. Our lab uses an emergent multicellular trait in the model organism Pseudomonas fluorescens Pf0-1 to study the emergence of c-di-GMP mutations …

Determination Of The Functional Role Of Rab-Ggt In Physcomitrium Patens., Hyun Jin Jung

Electronic Theses and Dissertations

Protein prenylation, a common lipid post-translational modification, is required for growth and development in eukaryotes. Rab geranylgeranylation involves the addition of one or two 20-carbon geranylgeranyl moieties to Rab-GTPase target proteins, which regulate intracellular vesicle trafficking. The reaction is carried out by heterodimeric Rab geranylgeranyltransferase (Rab-GGT), which is composed of two associated α- and β-subunits, with the assistance of an additional protein called Rab escort protein (REP). Loss of function of the Rab-GGT α subunit RGTA1 has not been reported in any plant. While knockout of either of the two β subunits RGTB1 or RGTB2 results in …

Applications Of Nuclear Magnetic Resonance Spectroscopy: From Drug Discovery To Protein Structure And Dynamics., Mark Vincent C. Dela Cerna

Electronic Theses and Dissertations

The versatility of nuclear magnetic resonance (NMR) spectroscopy is apparent when presented with diverse applications to which it can contribute. Here, NMR is used i) as a screening/ validation tool for a drug discovery program targeting the Phosphatase of Regenerating Liver 3 (PRL3), ii) to characterize the conformational heterogeneity of p53 regulator, Murine Double Minute X (MDMX), and iii) to characterize the solution dynamics of guanosine monophosphate kinase (GMPK). Mounting evidence suggesting roles for PRL3 in oncogenesis and metastasis has catapulted it into prominence as a cancer drug target. Yet, despite significant efforts, there are no PRL3 small molecule inhibitors …

A Computational Model Of The Line-1 Retrotransposon Life Cycle And Visualization Of Metabolic Networks In 3-Dimensions., Michael D. Martin

Electronic Theses and Dissertations

Computational modeling of metabolic reactions and cellular systems is evolving as a tool for quantitative prediction of metabolic parameters and reaction pathway analysis. In this work, the basics of computational cell biology are presented as well as a summary of physical processes within the cell, and the algorithmic methods used to find time dependent solutions. Protein-protein and enzyme-substrate interactions are mathematically represented via mass action kinetics to construct sets of linear differential equations that describe reaction rates and formation of protein complexes. Using mass action methods, examples of reaction networks and their solutions are presented within the Virtual Cell simulation …

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

The Role Of Foxd1 In Clear Cell Renal Cell Carcinoma, Kyle H. Bond

Electronic Theses and Dissertations

Renal cell carcinoma (RCC) is the 8^th most common cancer in the United States, with the clear cell variant (ccRCC) being the most prevalent. Over 14,000 people die every year to RCC, with rates continuing to increase with an aging general population. Patients suffering from metastatic RCC (mRCC) have extremely poor prognoses, with a 5-year survival of only 11.2%. Current treatment options include resection of primary lesions, tyrosine kinase inhibition (Sunitinib, Pazopanib), mTOR inhibition (Temsirolimus, Everolimus), and immune checkpoint inhibition (Nivolumab, Atezolizumab). Recent attention has been drawn to inhibition of transcription factors like HIF2α (Belzutifan). There is a need …

Cannabinoids And Retinal Fibrotic Disorders., Lucy June Sloan

Electronic Theses and Dissertations

Retinal fibrosis is detrimental to vision. Retinal pigment epithelial (RPE) cells contribute to several retinal fibrotic diseases. Upon exposure to TGF-β, a key fibrotic cytokine, RPE cells trans-differentiate to myofibroblasts marked by the integration of α-SMA fibers into F-actin stress fibers, which confer strong contractility. Myofibroblasts produce and contract the collagen-rich fibrotic scar and disrupt retinal architecture. In this study, we investigated the in vitro effects of the putative endocannabinoid compound N-oleoyl dopamine (OLDA) on TGF-β2 induced porcine RPE cell contraction and α-SMA expression. Using an in vitro collagen matrix contraction assay, we found that OLDA inhibited TGF-β2 induced contraction …

The Pathophysiological Mechanisms Of Alzheimer's Disease; Investigating Therapeutic Interventions For Disease Onset, Alexandra A. Sandberg

Electronic Theses and Dissertations

Alzheimer’s Disease is a multifarious disease that progressively affects more people as both the proportion of older adults in the population and life expectancy increase in both the United States and worldwide. This devastating disease is a result of rampant neuronal loss in the memory centers of the brain that robs the independence of those who are diagnosed and places a heavy burden on those who care for them. Traditionally speaking, research has focused on the hallmark pathology of amyloid plaques, targeting them to try and prevent disease onset. However, countless failures in clinical trials aimed at this said pathology …

Organellar Zn2+ Homeostasis And The Role Of Trpml Channels In Neuronal Lysosome Physiology And Axonal Transport, Taylor Franklin Minckley

Electronic Theses and Dissertations

Zinc (Zn²⁺) is crucial for proper cellular function, and as such it is important to measure and track Zn²⁺ dynamics in living cells. Fluorescent sensors have been used to estimate Zn²⁺ content of subcellular compartments, but little is known about endolysosomal Zn2+ homeostasis. Similarly, although numerous sensors have been reported, it is unclear whether and how Zn²⁺ can be released from intracellular compartments into the cytosol due to a lack of probes that can detect physiological dynamics of cytosolic Zn²⁺. My dissertation started with comparing and characterizing different Zn²⁺ sensors including the …

Antioxidant Biomarkers And Nutraceutical Therapeutics In Neurodegeneration And Neurotrauma, Lilia A. Koza

Electronic Theses and Dissertations

Mild traumatic brain injury (mTBI), yielding a Glascow Coma Scale of 13-15, is the most commonly occurring severity of TBI. Pathology from mTBI consists of blood brain barrier disruption, neuroinflammation, oxidative stress, excitotoxicity, mitochondrial dysfunction, protein aggregation, axonal degeneration, and resulting neuronal death. These processes deplete the body’s endogenous antioxidant system. We report a retrospective analysis of antioxidant blood biomarkers in patients with a history of mTBI from a local sports medicine clinic, Resilience Code. We found persistent sex-specific antioxidant depletions in mTBI patients associated with worsened symptomology.

Certain populations, such as athletes, are at high risk for repetitive mTBI …

Leveraging Queueing Theory To Develop Advanced Synthetic Biological Circuits, Prajakta K. Jadhav

Electronic Theses and Dissertations

The complexity and redundancy in the network topology of the cell hinder our understanding of the natural system, making it challenging to engineer living organisms with the desired functionality. The long-term goal of synthetic biology and bioengineering is to engineer cells to perform specific functions with increased robustness. The robust engineered systems can be easily applied to different species with the same outcome. An effective approach is a bottom-up approach where we tease apart the biological pathways and study them independently. Understanding the underlying mechanisms of biological pathways can be further applied to construct complex biological circuits that function similarly …

Rnp Granules In Toxoplasma Gondii: Function And Formation, Scott Roscoe

Electronic Theses and Dissertations

Toxoplasma gondii is an obligate intracellular parasite capable of infecting mammals, birds, reptiles, and fish. T. gondii only undergoes sexual reproduction in a feline host. In all other organisms the parasite reproduces asexually, either as fast growing tachyzoites or slow growing bradyzoites. Bradyzoites form latent cysts inside the host cell that can lay dormant for years and convert back to tachyzoites when the host’s immune system becomes weakened. Tachyzoites rapidly replicate in the host cell, eventually causing it to lyse. While extracellular, tachyzoites repress their own translation by phosphorylating the eukaryotic initiation factor eIF2α and form microscopically visible aggregates of …

Epigenetic Buffering In Introduced House Sparrows, M. Ellesse Lauer

Electronic Theses and Dissertations

Epigenetic buffering, as an environmentally induced increase in variance of epigenetic states that increases phenotypic variation to buffer populations against decreased fitness, may be a factor that resolves the genetic paradox of introduced species. DNA methylation is a molecular mechanism that could facilitate epigenetic buffering by changing in response to environmental stress. Therefore, epigenetic buffering can be detected through increased variance in DNA methylation in novel or heterogeneous environments. Introduced house sparrows (Passer domesticus) have well-documented phenotypic changes with low genetic diversity, high epigenetic diversity, and high variance in DNA methylation that provide a characteristic signature of epigenetic buffering. …