Life Sciences Commons^™

Understanding The Conformational Dynamics Of The A2a Adenosine Receptor By Single-Molecule Fluorescence, Shushu Wei

Doctoral Dissertations

G protein-coupled receptors (GPCRs) are one of the largest transmembrane receptor families. The wide expression and diverse signal transduction functions make them an ideal target for characteristic drug design. The A_2A adenosine receptor (A_2AAR), a representative of class A GPCRs, has been extensively used to reveal the structural information of class A GPCRs. As a purinergic receptor, A_2AAR is activated by adenosine in the human body, triggering cyclic adenosine monophosphate (cAMP) and immunosuppression pathways. A_2AARs are highly expressed in the brain and are crucial in regulating glutamate and dopamine release. As a result, …

Investigating And Developing Strategies For The Expression Of Biosynthetic Genes In Vitro And In Vivo, Tien Thuy Tran

Doctoral Dissertations

Natural products have historically served as a rich source for a wide range of useful applications such aspesticides, veterinary agents, therapeutics, and bioproducts. To discover new natural products, manipulate them for analog generation, and harness the potential of these bioactive compounds for synthetic biology, it is necessary to develop robust methods for the expression of biosynthetic genes. A broad range of clinically useful natural products originate fromactinomycetes, especially those from the genus Streptomyces, which have been recognized as one of the predominant sources of microbial bioactive natural products. Actinobacteria are known for their large genomes, Guanine-Cytosine rich, and complex …

Investigating Habitat, Ties To Aquatic Food Webs, And Ecotoxicological Threats To Common And Declining Bat Species, Ashleigh B. Cable

Doctoral Dissertations

Bats face many threats globally including habitat loss, emerging wildlife diseases and pollution. In North America (NA), insectivorous bat species are in decline due to white-nose syndrome (WNS). Herein, we investigate current and emerging threats to NA bats. First, we fill knowledge gaps in habitat requirements of the tricolored bat (Perimyotis subflavus), a once common but now declining bat species. We found that females forage in open areas (i.e., edges and grasslands), riparian zones and around the fingers of lakes, and over open water of rivers and lakes. Second, it investigates the role of ecotoxicological threats to insectivorous …

Phenology, Olfactory Response, And Tritrophic Interactions Of Helicoverpa Zea And Chloridea Virescens On Hemp, Cannabis Sativa, Julian B. Cosner

Doctoral Dissertations

Industrial hemp, Cannabis sativa L., production has been revived in the United States following its legalization through the Agricultural Improvement Act of 2018 (a.k.a. 2018 Farm Bill). The corn earworm, Helicoverpa zea (Boddie), has been considered one of the most harmful insect pests in outdoor hemp production as larvae feed on the marketable grain and inflorescences where cannabinoid concentrations are highest. However, in Tennessee, a Heliothine complex, including corn earworm and the tobacco budworm, Chloridea virescens (F.), occurs on hemp. To investigate the seasonal incidence of these hemp pests, larvae were collected from hemp grown in different regions of Tennessee …

Physical Activity On Multiuse Trails And In A Novel Bike Park Within An Urban Wilderness, Douglas Gregory

Doctoral Dissertations

Research has shown that the presence of, access to, and use of parks and trails is associated with increased levels of PA. However, little research exists on nature-based, recreational multiuse trails and bike-specific amenities within parks and their impact on PA. Therefore, to explore the effect trails and bike parks have on PA, this dissertation conducted three investigations to: 1) determine the impact of trail/greenway interventions on PA, 2) investigate how seasonality and weather influence nature-based recreational trail use, and 3) develop a demographic and PA profile of bike park users.

Investigation 1 (Chapter 4) systematically reviewed the literature specific …

Computational Study Of Confined Cytoskeletal Assemblies: Simple Rules, Complex Behavior, Oghosa Honor Akenuwa

Doctoral Dissertations

The actin cytoskeleton is crucial for cellular processes and proper organization in cells. Physical regulators like actin crosslinking proteins, molecular motors, and physical confinement significantly impact the organization of the actin cytoskeleton. Despite advances, much remains unknown about how these physical regulators affect actin organization. In this thesis, we employ coarse-grained computer simulations to investigate the effect of physical regulators on the dynamics and organization of semiflexible actin filaments. First, we explore the role of crosslinker properties and confinement shape on actin organization by varying the system shape, the number and type of crosslinking proteins, and the length of filaments. …

Of Hosts And Habitats: The Ecological And Evolutionary Patterns Of The Amphibian Skin Microbiome, Benjamin Houston Holt

Doctoral Dissertations

The skin microbiome of amphibian hosts can inhibit growth of pathogenic fungi, contribute to anti-predator compounds in newts, and is linked with sex-specific scents in frogs. However, despite growing evidence of symbiont importance to amphibians, how symbionts are acquired and maintained on hosts remains poorly resolved. Microbiomes exist on a dynamic spectrum from casual assemblages to intricate systems, and community members vary in fidelity and association to hosts. The establishment of these communities involves complex interactions between symbionts, host traits, and source communities. I seek to enhance our understanding by assessing the spatial-temporal patterns of the salamander skin microbiome relative …

Impacts Of Climate Change On Mammalian Species Of Concern Within The Appalachian Ecoregion, Lauren M. Lyon

Doctoral Dissertations

Climate change and growth anthropogenic presence is a phenomenon impacting all species globally. Fortunately, with protection of key areas of suitable habitat and climate, we can alleviate the worst of biodiversity loss utilizing climate change refugia. This is apparent in the eastern United States, where the Appalachian Ecoregion naturally form a refugium compared to the surrounding landscape for many taxa and rare ecosystems. Particularly of interest are the at-risk relict boreal ecosystems found at elevation, which are otherwise restricted to the northern US and Canada, and numerous endemic taxa found only in this biodiverse region.

Recent studies have focused either …

Xyway Lfr@Fmc Fungicide: Improving Corn (Zea Mays L.) Water Use Efficiency And Productivity Under Water-Deficit Stress And Dryland Conditions, Isha Poudel

Doctoral Dissertations

Triazole fungicide has the ability to protect crops from varying water stresses. Xyway LFR^@FMC is a triazole, at-plant fungicide and has been observed to improve plant performance under limited water conditions. A greenhouse study was conducted to assess the potential of Xyway LFR^@FMC in altering the ability of corn plants to control transpiration rates under water deficit-stress (DS) conditions. Greenhouse grown plants were treated with Xyway LFR^@FMC at 0.56, 0.77, 1.11,1.26 L ha^-1. Plants treated with 1.11 L ha^-1 reduced the amount of water loss in response to DS and had the highest fraction …

Applying A One Health Approach To Expand Disease Surveillance In Eastern Wildlife, Eliza L. Baker

Doctoral Dissertations

Urban wildlife carry numerous diseases of veterinary and human health importance. Many of these diseases are emerging into new geographic areas, including the southeastern United States, due to a combination of climate change, urbanization, and migration. Urban wildlife can act as excellent sentinels for these diseases, providing doctors and veterinarians with a better understanding of the risks to their patients. We sought to better understand a variety of diseases of human and animal concern via urban wildlife surveillance. We found a high prevalence of numerous zoonotic and companion animal diseases in wildlife, both with and without significant health impacts on …

Bridging Biological Systems With Social Behavior, Conservation, Decision Making, And Well-Being Through Hybrid Mathematical Modeling, Maggie Renee Sullens

Doctoral Dissertations

Mathematical modeling can achieve otherwise inaccessible insights into bio-logical questions. We use ODE (ordinary differential equations) and Game Theory models to demonstrate the breadth and power of these models by studying three very different biological questions, involving socio-behavioral and socio-economic systems, conservation biology, policy and decision making, and organismal homeostasis.

We adapt techniques from Susceptible-Infected-Recovered (SIR) epidemiological models to examine the mental well-being of a community facing the collapse of the industry on which it’s economically dependent. We consider the case study of a fishing community facing the extinction of its primary harvest species. Using an ODE framework with a …

Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are functional proteins that lack stable tertiary structures in the unbound state. They frequently remain dynamic even within specific complexes and assemblies. IDPs are major components of cellular regulatory networks and have been associated with cancers, diabetes, neurodegenerative diseases, and other human diseases. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for mechanistic understanding of IDPs in biology, diseases, and therapeutics. However, accurate simulation of the heterogeneous ensembles and dynamic interactions of IDPs is extremely challenging because of both the prohibitive computational cost and demanding force field …

The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson

Doctoral Dissertations

This research focuses on a specific example of replicated evolution: the grass awn. Awns are typically extensions of the lemma, but may also appear on glumes or paleas. The lemma is a leaf-like organ on the exterior of the grass flower, the glumes are a pair of bracts subtending the basic unit of grass inflorescences, the spikelet, and the palea is the floral organ opposite the lemma. Awns are often described as "hair-" or "bristle-" like, but appear in many different shapes. Many awns are “twisted & geniculate", in which the awn has two sections, a lower twisted column, and …

Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro

Doctoral Dissertations

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …

Associations Between Early Childhood Sleep, Memory Function, And Brain Development Across The Nap Transition, Sanna Lokhandwala

Doctoral Dissertations

Preschool-age children often distribute their sleep across a midday nap and overnight sleep. Skipping the nap is suggested to increase the duration and depth of deep sleep (i.e., slow wave activity; SWA). Moreover, missing the midday nap has been shown to impair learning processes. This may be because children’s brains at this point in development are immature, necessitating the intervening nap period to strengthen memories before they are forgotten. Nonetheless, at some point during the preschool years, many children begin transitioning naturally out of napping. It is unclear whether the memory benefits of overnight SWA after a skipped nap depend …

Analysis Of Micro(Nano)Plastics In Food Using Raman Microscopy, Xin Guo

Doctoral Dissertations

Microplastic pollution has emerged as a global concern in both aquatic and terrestrial environments. The presence of microplastics in the food chain poses a potential threat to human health. To accurately assess the risks associated with microplastics, it is crucial to have a reliable analytical technique capable of detecting, quantifying, and identifying microplastics of varying materials, sizes, and shapes in environmental, agricultural, and food samples. Spectroscopic techniques, specifically vibrational spectroscopy (Raman and Infrared), are extensively utilized in microplastic analysis. These techniques enable rapid and high-throughput identification, while also providing size and shape information. However, there are certain gaps in the …

High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre

Doctoral Dissertations

Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …

A Ground-Based L-Band Radar System For Monitoring Forest Temporal Dynamics, Xingjian Chen

Doctoral Dissertations

L-band FMCW radar is implemented for monitoring forest dynamics. It took short-term and long-term measurements with an internal calibration system that guarantees stability and precision. The radar data is compared to in-situ measurement, which infers causal relationships between radar backscatter signal and forest physiology index such as tree dielectric. This paper explains the relationship between radar signals and environmental components such as precipitation based on the measurement. The radar demonstrates some interesting observations, for example, trees' daily activity and freeze-thaw process.

The Impacts Of Environment And Host Evolutionary Relationships On Lemur Microbiota, Rachel B. Burten

Doctoral Dissertations

Recent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity …

The Wild Tomato Clade Offers Insights Into Fleshy Fruit Trait Evolution At The Phenotypic And Molecular Levels, Jacob R. Barnett

Doctoral Dissertations

Biologists have long been fascinated by the diversity of fleshy fruits, yet questions remain as to how this variety has evolved. According to the dispersal syndrome hypothesis, flowering plants improved their reproductive success by producing fleshy fruits with appealing combinations of traits that attract animal dispersers. However, animal preferences may not be the only selective pressure driving fruit trait diversity—conflicting forces include damage-inflicting seed predators and pathogens, abiotic habitat conditions, or constraints stemming from non-adaptive mechanical, developmental, or phylogenetic limitations. Few studies have examined the early stages of fleshy fruit evolution across an entire clade of recently diverged plant species. …

Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun

Doctoral Dissertations

Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all genetic processes. Any protein or drug that binds DNA must either cooperate or compete with nucleosomes. Given that a nucleosome contains 147 base pairs of DNA, there are approximately 4^147 or 10^88 possible sequences for a single nucleosome. Exhaustive studies are not possible. However, genome wide association studies can identify individual nucleosomes of interest to a specific mechanism, and today's supercomputers enable comparative simulation studies of 10s to 100s of nucleosomes. The goal of this thesis is to develop and present and end-to-end workflow that serves …

Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie

Doctoral Dissertations

Prescribed fires in Southern Appalachian forests are vital in ecosystem management and wildfire risk mitigation. However, understanding the intricate dynamics between these fires, soil microbial communities, and overall ecosystem health remains challenging. This dissertation addresses this knowledge gap by exploring selected aspects of this complex relationship across three interconnected chapters.

The first chapter investigates the immediate effects of prescribed fires on soil microbial communities. It reveals subtle shifts in porewater chemistry and significant increases in microbial species richness. These findings offer valuable insights into the interplay between soil properties and microbial responses during the early stages following a prescribed fire. …

The Identification Of Small Molecule Inhibitors To Candida Albicans Phosphatidylserine Synthase, Yue Zhou

Doctoral Dissertations

Candida albicans phosphatidylserine (PS) synthase, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis due to its importance in virulence, absence in the host and conservation among fungal pathogens. This dissertation is focused on the identification of inhibitors for this membrane enzyme. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif present within Cho1, and here we revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1. For serine, we have predicted a …

Characterization Of Radiotolerance In Potato And Development Of A Gamma Radiation Phytosensor., Robert Graham Sears

Doctoral Dissertations

As humans pursue space travel and nuclear energy, the risk of harm from ionizing radiation increases. On Earth or in space, plants are essential to our personal and environmental health. Plants serve as sentinels, bioremediators and food sources in areas of high ionizing radiation, therefore it is essential to understand how ionizing radiation affects plant biology. This work aimed to understand plant responses to ionizing radiation in the potato chassis and apply that knowledge to generate novel phenotypes for nuclear energy and space applications. The first gamma radiation phytosensor was developed for monitoring at standoff distances greater than three meters. …

Impact Of Cadmium Stress On Soil Virus Reproduction And The Persistence Of Viruses Under Abiotic Conditions, Zhibo Cheng

Doctoral Dissertations

Soil viruses are ubiquitous and greatly impact the structure and function of soil microbial communities, with their effects modulated by various environmental factors. This study investigates the inactivation of naturally occurring soil viruses in sterilized soil, as well as the effects of cadmium (Cd) exposure and carbon (C) and nitrogen (N) nutrient availability on the population dynamics of virus-host communities in agricultural soil.

Lab-scale slurry and unsaturated experiments were performed to examine virus inactivation in the absence of host bacteria in sterilized soil. In slurry experiments, virus abundance declined by over 90% after 10 days of incubation. The addition of …

Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn

Doctoral Dissertations

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated …

Characterization Of Lignin Structural Variability And The Associated Application In Genome Wide Association Studies, Nathan D. Bryant

Doctoral Dissertations

Poplar (Populus sp.) is a promising biofuel feedstock due to advantageous features such as fast growth, the ability to grow on marginal land, and relatively low lignin content. However, there is tremendous variability associated with the composition of biomass. Understanding this variability, especially in lignin, is crucial to developing and implementing financially viable, integrated biorefineries. Although lignin is typically described as being comprised of three primary monolignols (syringyl, guaiacyl, p-hydroxyphenyl), it is a highly irregular biopolymer that can incorporate non-canonical monolignols. It is also connected by a variety of interunit linkages, adding to its complexity. Secondary cell wall …

Regulation Of Protein Synthesis In Arabidopsis Thaliana Through A Bioinformatic And Mathematical Lens, Ricardo Andres Urquidi Camacho

Doctoral Dissertations

Organisms exist under constantly varying environmental and internal conditions, which necessitate the differential regulation of gene expression. To synthesize proteins, the ribosome translates the information encoded in the nucleotide sequence of an mRNA into the final, functional amino acid sequence. Knockouts of ribosomal proteins lead to lethality. One such protein is the ribosomal protein 6 of the small subunit (eS6/RPS6). We confirmed that the knockout of either one of two eS6 paralogs in Arabidopsis leads to stunted growth and chlorosis. Here, these phenotypes have been further characterized in seedlings by precisely quantifying the ribosome loading of mRNAs as well as …

Exploring The Regulation Of A Bacillus Pumilus Bioplastic Degrading Protein, Elise Keara Phillips

Doctoral Dissertations

Biodegradable plastics are being adopted to reduce the environmental impacts associated with petroleum-based plastics, including long residence times, and reliance on fossil fuels as a feedstock. Microbial degradation of bioplastics is still poorly understood, which leads to inconsistent degradation outcomes and challenges for implementation. Bacillus pumilus B12 degrades the biodegradable bioplastic polylactic acid (PLA) via the protease AprE, but the regulatory mechanisms controlling aprE expression in B. pumilus B12 are largely unknown. To explore this question, we established developed a conjugation- based method to introduce DNA into B. pumilus B12 and diverse Bacillus species that is applicable to environmental and …

Novel Microbial Guilds Implicated In N2o Reduction, Guang He

Doctoral Dissertations

N₂O is a long-recognized greenhouse gas (GHG) with potential in global warming and ozone depletion. Terrestrial ecosystems are a major source of N₂O due to imbalanced N₂O production and consumption. Soil pH is a chief modulating factor controlling net N₂O emissions, and N₂O consumption has been considered negligible under acidic conditions (pH <6). In this dissertation, we obtained solids-free cultures reducing N₂O at pH 4.5. Furthermore, a co-culture (designated culture EV) comprising two interacting bacterial population was acquired via consecutive transfer in mineral salt medium. Integrated phenotypic, metagenomic and metabolomic analysis dictated that the Serratia population excreted certain …