Life Sciences Commons^™

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 …

The Influence Of Spectral Quality On Primary And Secondary Metabolism Of Hydroponically Grown Basil, Hunter Albright Hammock

Doctoral Dissertations

This dissertation explores the influence of spectral quality from supplemental lighting and seasonal changes on primary and secondary metabolism in hydroponically grown greenhouse basil. It aims to enhance understanding of plant/light interactions and provide practical insights for light emitting diode (LED) manufacturers and commercial growers. The research is premised on the hypothesis that altering spectral quality can significantly impact primary and secondary metabolism, potentially improving flavor and increasing phytonutrients with health benefits. This project involved four phases, each building on the results of the previous ones. In Phase 1, different basil varieties were evaluated to determine aroma volatile profiles and …

Roles Of Soil Pores In Determining Water Retention And Microbial Dynamics, Huihui Sun

Doctoral Dissertations

Soil pore provides an essential habitat for microbial communities to participate in various biogeochemical processes. The complex pore spaces, which are defined by the arrangement of particles of varying sizes, govern the distribution of water for microbial dispersal and movement and microbial interaction with one another, such as bacterial cell-to-cell and bacterium-virus interactions. This research focused on exploring how soil pores influence soil water retention and bacterial interactions and quantify the spatial distribution of bacteria and viruses in fine-scale of soil pores. Using a mathematical model, this study simulated a soil water retention curve based on the relationship between soil …

"You're Not Thriving, You're Just Trying To Survive The Environment That You're In:" Mental Performance Consultants' Narratives Of Emotional Abuse In Sport, Victoria Lynn Bradshaw

Doctoral Dissertations

Emotional abuse is defined as “a pattern of deliberate non-contact behaviors by a person with a critical relationship that has the potential to be harmful” (Stirling & Kerr, 2008, p. 178). Specifically, in the context of sport, emotional abuse is one of the more frequently occurring forms of abuse (Kavanagh, Brown & Jones, 2017; Kirby, Greaves & Hankvisky, 2000; Wilson & Kerr, 2021). Years after the termination of those emotionally abusive experiences, athletes are left to try and cope with and manage the short and long-term impacts that tend to develop as a result of repeated exposure to harmful behaviors …

Retinoic Acid, Insulin, And Cycloheximide Alter Glycogen Homeostasis In Differentiating L6 Myoblasts, Aaron Armstrong

Doctoral Dissertations

Glycogen synthesis in skeletal muscle (SM) is responsible for the majority of post-prandial glucose disposal in healthy individuals. In type 2 diabetes mellitus (T2DM), compromised skeletal muscle glycogen synthesis contributes to hyperglycemia. L6 rat SM cells can develop insulin resistance with prolonged insulin stimulation and provide an in vitro model for mechanistic dysfunction in glycogen homeostasis. SM glycogen is synthesized by glycogen synthase (GS) in response to insulin stimulation. Canonically, insulin signaling increases GS activity through inhibition of its Ser641 regulator glycogen synthase kinase-3β (GSK3β) by protein kinase B (AKT). Proximal insulin signaling activates AKT via Ser473 phosphorylation which proceeds …

Population Abundance And Growth Of Elk (Cervus Canadensis) In Western North Carolina, Jessica Braunstein

Doctoral Dissertations

In an effort to restore extirpated elk to their previous range, 52 elk were reintroduced to Great Smoky Mountains National Park (GRSM) in North Carolina during 2001 and 2002. Since their reintroduction, elk numbers have increased and their range has extended beyond GRSM boundaries. My primary research objectives included estimating population abundance, apparent survival, per capita recruitment, and population growth rate of elk in North Carolina. I used spatially explicit capture-recapture (SECR) models based on fecal DNA to identify individual elk and estimate population abundance and growth in the region. Technicians and I walked a series of transects throughout the …

Phenotyping Regression In A Female Mouse Model For Rett Syndrome Using Computational Neuroethology Tools, Michael J. Mykins

Doctoral Dissertations

Regression is defined as loss of acquired skills over time and is a key feature of many neurodevelopmental disorders such as Rett syndrome (RTT). RTT is caused by mutations in the X-linked gene Methyl CpG-Binding Protein 2 (MECP2) and is characterized by a period of typical development with subsequent regression of previously acquired motor and speech skills in girls. In human and animal models, it is clear syndromic phenotypes are dynamic over time but phenotyping regression over time in animal models has remained elusive. Lack of established timelines to study the molecular, cellular, and behavioral features of regression in female …

Multidimensional Investigation Of Tennessee’S Urban Forest, Jillian L. Gorrell

Doctoral Dissertations

Preserving existing trees in urban areas and properly cultivating urban forest conservation and management opportunities is valuable to the ever-growing urban environment and necessary for creating optimal experiences and educational tools to meet the needs of increasing urban populations. This dissertation contains studies investigating several facets of the urban forest, including environmental effects of deforestation and urbanization, tree equity, and urban forest facility management and accessibility. Community education and outreach at arboreta about the importance of the tree canopy can help promote environmental stewardship. A digital questionnaire was electronically distributed to representatives of arboreta certified through the Tennessee Division of …

Increasing Productivity And Biodiversity Of Tall Fescue Swards By Intercropping Cool And Warm-Season Forage Species, Michael Dereck Corbin

Doctoral Dissertations

Mixed pastures are known to produce greater biomass yields and higher nutritive value than monocultures. Intercropping biologically N fixating legumes, along with the use of intercropping warm-season annual grasses, such as crabgrass [Digitaria ciliaris Retz.], provides the potential to aid tall fescue [Schedonorus arundinaceus (Schreb.) Dumort.] productivity. To determine the benefits of intercropping species into tall fescue forage systems in the Southeastern U.S., two studies were developed. The first study consisted of 9 tall fescue paddocks, in which 3 paddocks contained red clover (Trifolium pratense L. [TRC]) mixed with tall fescue, 3 paddocks contained sunn …

Application Of Machine Learning Approaches To Empower Drug Development, Yue Shen

Doctoral Dissertations

Human health, one of the major topics in Life Science, is facing intensified challenges, including cancer, pandemic outbreaks, and antimicrobial resistance. Thus, new medicines with unique advantages, including peptide-based vaccines and permeable small molecule antimicrobials, are in urgent need. However, the drug development process is long, complex, and risky with no guarantee of success. Also, the improvements in techniques applied in genomics, proteomics, computational biology, and clinical trials significantly increase the data complexity and volume, which imposes higher requirements on the drug development pipeline. In recent years, machine learning (ML) methods were employed to support drug development in various aspects …

Methods To Hasten Zoysiagrass Establishment From Sprigs, Tyler Carr

Doctoral Dissertations

Zoysiagrasses (Zoysia spp. Willd.) are commonly used on golf course fairways and tees in addition to residential and commercial lawns due to lower input requirements relative to bermudagrass (Cynodon spp.). This has led to increased interest in using zoysiagrass for golf course putting greens; however, zoysiagrass establishment from sprigs is prolonged compared to bermudagrass. A series of experiments were conducted in glasshouses in Knoxville, TN in 2022 to evaluate the effects of environmental conditions and management practices on the establishment of Prizm zoysiagrass from sprigs. To determine the optimal soil temperature for Prizm zoysiagrass establishment, sprigs were exposed …

Effects Of A Movement-Based Curriculum On The Motor And Cognitive Development Of Preschool-Aged Children, Aaron Wood

Doctoral Dissertations

Physical activity has been shown to be positively associated with improved motor skill and cognitive development in young children. Intervention designs are often constructed without focus on interrelatedness of the development of motor and cognitive self-regulatory skills. Purpose: To investigate the impact of a movement-based curriculum designed to integrate both motor skill and cognitive development in preschool children. Methods: Preschool-aged children [n=34; intervention group (n=28); control group (n=6)] participated in the study. Locomotor and object control motor skills were assessed via the Test of Gross Motor Development – 3rd Edition. Cognitive self-regulation (attention, working memory, and inhibition) was assessed via …

Induction And Evasion Of Neutrophil Extracellular Traps By Campylobacter Jejuni And Its Implication In Disease, Sean M. Callahan

Doctoral Dissertations

Campylobacteriosis, the foodborne disease caused by Campylobacter spp., infects one out of 10 individuals every year. C. jejuni accounts for 90% of these infections resulting in numerous postinfectious disorders including the development of colorectal cancer, Guillain-Barré syndrome, irritable bowel syndrome, and reactive arthritis. Despite its large impact on human health, the host immune response to the bacterium is largely uncharacterized. Chapter two of this dissertation addresses the development of neutrophil extracellular traps (NETs) within human and ferret campylobacteriosis. We observed NET-associated proteins increase in the feces of C. jejuni-infected patients and that in vitro C. jejuni induces NETs, which …

Investigating Drivers Of Algal Bloom Succession In Lake Erie, Brittany Zepernick

Doctoral Dissertations

Harmful Algal Blooms (HABs) are algae undergoing prolific, unregulated growth. A well-documented HAB taxa is the cyanobacterium Microcystis spp., which induces anthropogenic, ecological, and economic consequences due to the production of toxins and biomass which results in lake hypoxia. Microcystis spp. blooms are globally distributed in freshwater systems, with climate change and the aquatic continuum serving to further exacerbate bloom distribution, duration, and frequency. Thus, there is a need to elucidate the factors driving the ecological success of Microcystis spp., and the ecological “failures” of their competitors, such as diatoms. In Lake Erie, a seasonal pattern of algal bloom succession …

Cell-Free Metabolic Engineering Strategies For Accelerated Biomanufacturing, Jaime Lorenzo N. Dinglasan

Doctoral Dissertations

Biomanufacturing propels the bioeconomy. Accelerating bioeconomic growth thus requires the expedited development of biomanufacturing processes that can expand the current bioproduct portfolio. Lysate-based cell-free systems provide unique advantages for simplified metabolic pathway construction. Their central metabolic pathways and transcriptional-translational (TX-TL) machineries are free from genome regulation and are amenable to direct manipulation, enabling the streamlined construction of biomanufacturing processes. While their utility as prototyping platforms for accelerating cellular metabolic engineering has been demonstrated, the potential to rapidly build commercial “cell-free factories” capable of sophisticated bioconversion has not been fully realized. Lysates with high-yield pathways are projected to enable commercialized cell-free …

Understanding Host-Microbe Interactions In Maize Kernel And Sweetpotato Leaf Metagenomic Profiles., Alison K. Adams

Doctoral Dissertations

Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows …

Computational Analysis Of Microbial Sequence Data Using Statistics And Machine Learning, Zhixiu Lu

Doctoral Dissertations

Since the discovery of the double helix of DNA in 1953, modern molecular biology has opened the door to a better understanding of how genes control chemical processes within cells, including protein synthesis. Although we are still far from claiming a complete understanding, recent advances in sequencing technologies, increased computational capacity, and more sophisticated computational methods have allowed the development of various new applications that provide further insight into DNA sequence data and how the information they encode impacts living organisms and their environment. Sequencing data can now be used to start identifying the relationships between microorganisms, where they live, …

Airborne Transmission Of Pathogens Emerging In The Poultry Industry, Xuan Dung Nguyen

Doctoral Dissertations

Poultry houses might have high levels of airborne pathogens, including Escherichia coli (E. coli) and avian influenza (AI), which may be transmitted through the air and pose risks of infection. The objective of the dissertation is to provide an insightful understanding the of airborne transmission of E. coli and AI which were attached to poultry dust particles.

Chapter I and VI summarized background, gap in knowledge, and discussed the limitations and implications of the study.

Chapter II compared the efficiency of Andersen six-stage impactor, all-glass impinger, and ACD-200 Bobcat, in collecting airborne E. coli carried by dust particles. The results …

Psychological Determinants Of Physical Activity And The Prediction Of Physical Activity Levels In African American Men, Alvin L. Morton Iii

Doctoral Dissertations

African American (AA) men experience disproportionally higher rates of non-communicable, chronic diseases (e.g., cardiovascular, type 2 diabetes, and renal failure) than White men. Physical activity (PA) is known to reduce the progression of CVD, type 2 diabetes, and renal failure. National statistics illustrate that AA men are less likely to get sufficient levels of PA to obtain health benefits. Although many factors (e.g., biomedical, socio-cultural) influence participation in PA, the psychological factors at the individual level are essential to beginning and maintaining activity. Therefore, understanding the psychological determinants of PA in AA men and their associations with meeting national guidelines …

Characterization And Management Of Auxin-Resistant Palmer Amaranth In Tennessee, Delaney C. Foster

Doctoral Dissertations

Palmer amaranth has a long history of evolving resistance to herbicides to the point it has become a significant row crop production obstacle. Cotton and soybean growers were offered new technologies in 2016, expanding in-crop herbicide options to include dicamba or 2,4-D. Within three years of commercialization, dicamba use in these crops increased ten-fold and growers began to report Palmer amaranth escapes in west Tennessee auxin-tolerant production systems. A survey of Palmer amaranth escapes in dicamba and 2,4-D-tolerant cotton and soybean fields in Tennessee was conducted in the fall of 2021 with the objective of determining if poor control was …

Accurate Simulation Of Reads And Improved Strategies For Abundance Estimation Supporting Reduced Representation Sequencing For Metagenomics, Ryan Kuster

Doctoral Dissertations

Next generation sequencing has impacted all areas of biology by providing affordable investigations into some of the most complex processes underpinning life. With its ubiquitous application, there is still benefit in considering the nuances of the technology and its downstream analysis. Sequencing libraries produced by fragmenting DNA with restriction enzyme digests limit the scope of sequencing to a reduced set of genomic loci, allowing for deeper sequencing of those regions at a reduced cost per sample. These sequencing libraries have been used to determine genetic markers within populations of closely related individuals due to their sensitivity and preservation within populations. …

Leveraging Mass Spectrometry-Based Proteomics And Post-Translational Modifications For System-Wide Understanding Of Bioenergy Plants And Their Environment, Him K. Shrestha

Doctoral Dissertations

Bioenergy research focuses on utilizing renewable biomass feedstocks to produce biofuels and bioproducts to address growing concerns about energy security and climate change. To better understand the details of bioenergy crop production and conversion to bioproducts, it is essential to characterize bioenergy plants and their environments at a molecular systems level. Mass spectrometry has emerged as a promising technique for detailed proteomic information, including post-translational modifications (PTMs), of molecular processes and cellular functions of biological systems. In this dissertation, proteomic approaches have been optimized and implemented to deepen our understanding of the interaction of plants and their environment in a …