Digital Commons Network^™

Soil Health Assessment For The Agroecosystems Of West Tennessee, Surendra Singh

Doctoral Dissertations

Soil health assessment is important for making informed sustainable management decisions in production systems. An established standardized method to quantify soil health is lacking and the validity of the existing methods across agroecoregions and cropping systems is not yet proven. Therefore, this study aims to evaluate the feasibility of widely discussed three soil health tests - Haney’s Soil Health Test (HSHT), Comprehensive Assessment of Soil Health (CASH), and Alabama Soil Health Index (ASHI) to assess soil health in diverse cropping systems of Tennessee. Since these approaches were originally developed for specific agroecoregions, we hypothesized that these tests are not sensitive …

Costs Of Protected Areas In The United States, Diane Le Bouille

Doctoral Dissertations

Protected areas, or land owned in fee by agencies and non-profits to further conservation goals, have traditionally been the go-to choice for conservation interests. The UN Environment World Conservation Monitoring Centre estimates that, currently, close to 15% of all terrestrial and inland water areas are protected. This figure falls short of the Aichi Biodiversity Target of 17% in 2020, that was added to the Convention on Biological Diversity by its 196 signatories in 2010. But as the Convention prepares to set new post-2020 targets, this percentage is expected to keep increasing. Although acquiring a parcel of land is only one …

Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal

Doctoral Dissertations

Computational biophysics methods such as molecular dynamics (MD) simulations are often used in combination with experimental techniques like neutron scattering, NMR, and FTIR to explore protein conformational landscapes. With the improvements in experimental techniques, there is also a need to continually optimize the MD forcefield parameters to make precise predictions that match experimental results. To complement many of these experiments, an accurate model of deuteration is frequently required, but has been elusive. In our work, we developed a novel method to capture isotope effects in classical MD simulations by re-parameterization of the bonded terms of the CHARMM forcefield using quantum …

Efficacy Of A Cycling Intervention With Pedal Reaction Force Augmented Feedback On Reducing Inter-Limb Asymmetries In Patients With Unilateral Total Knee Arthroplasty, Erik T. Hummer

Doctoral Dissertations

Fifteen patients with unilateral total knee arthroplasty (TKA) performed cycling at two workates (80 W and 100 W) and two walking conditions (preferred and fast speeds). Ten of these patients of TKA also participated in a short-term cycling intervention paired with visual augmented feedback of vertical pedal reaction forces for six sessions over two-three weeks. These ten patients of TKA participated in a 2^nd post-training testing session. Study One compared the knee joint biomechanics for all fifteen participants during stationary cycling to ascertain if any biomechanical asymmetries may be present. The replaced limbs displayed significantly lower peak knee extension …

Prevalence Of Rats And Rodent Borne Pathogens Across Post-Katrina New Orleans, Bruno Marco Ghersi

Doctoral Dissertations

Disasters are happening at an increasingly higher rate and intensity a trend that is expected to continue as more humans migrate to coastal urban areas. Disasters, and as importantly, disaster recovery can affect how native and pest populations will recover. My aim was to improve understanding of disease risk by evaluating the socioecological conditions that have shaped commensal rat recovery and distribution, as well as the pathogens they carry, across New Orleans after Hurricane Katrina. I first estimated relative abundance and distribution of commensal rats from rodent trapping conducted between mid-2014 and early-2017 across 96 sites in 10 areas of …

A Review Of Horticultural Therapy And Horticultural Therapy Education In The United States: Addressing Challenges And Opportunities, Derrick R. Stowell

Doctoral Dissertations

The Horticultural Therapy (HT) profession has been formally organized in the United States since 1973. Despite the long history of horticulture being used as therapy, the profession of HT in the United States has not advanced as quickly as other allied healthcare professions. This study will review the current challenges and opportunities for HT and HT education in the United States.

A qualitative study of the status of the profession was conducted to determine what challenges and opportunities the profession of HT currently has and how the profession can meet those challenges and opportunities. The study sample was recruited from …

Probing Structure, Function And Dynamics In Bacterial Primary And Secondary Transporter-Associated Binding Proteins, Shantanu Shukla

Doctoral Dissertations

Substrate binding proteins (SBPs) are ubiquitous in all life forms and have evolved to perform diverse physiological functions, such as in membrane transport, gene regulation, neurotransmission, and quorum sensing. It is quite astounding to observe such functional diversity among the SBPs even when they are restricted by their fold space. Therefore, the SBPs are an excellent set of proteins that can reveal how proteins evolution novel function in a structurally conserved/constrained fold. This study attempts to understand the phenomenon of affinity and specificity evolution in SBPs by combining a set of biochemical, biophysical, and structural studies on the SBPs involved …

Soil Moisture Sensitivity Of Microbial Processing Of Soil Organic Carbon, Shikha Singh

Doctoral Dissertations

Soil organic carbon (SOC) is the largest terrestrial C pool and understanding SOC decomposition in response to environmental factors is critical for accurate predictions of climatic change. Soil moisture is one of the most important, yet less explored, environmental factors controlling soil microbial respiration. The relationship between soil moisture and respiration also varies with soil texture. Currently, it is difficult to predict feedbacks to climatic changes from changes in soil moisture, as most earth system models lack site-specific, experimentally-derived parameters to represent soil moisture-texture-respiration relationships. The overarching goals of this dissertation are to gain a fundamental understanding of the interactive …

Root Stage Distributions And Their Importance In Plant-Soil Feedback Models, Tyler Poppenwimer

Doctoral Dissertations

Roots are fundamental to PSFs, being a key mediator of these feedbacks by interacting with and affecting the soil environment and soil microbial communities. However, most PSF models aggregate roots into a homogeneous component or only implicitly simulate roots via functions. Roots are not homogeneous and root traits (nutrient and water uptake, turnover rate, respiration rate, mycorrhizal colonization, etc.) vary with age, branch order, and diameter. Trait differences among a plant’s roots lead to variation in root function and roots can be disaggregated according to their function. The impact on plant growth and resource cycling of changes in the distribution …

A High Resolution Study Of Long-Term Vertebrate Decomposition In Human And Animal Model Systems, Lois S. Taylor

Doctoral Dissertations

The effects of vertebrate decomposition are wide-ranging across multiple foodwebs, and have been shown to persist in the environment, however there is a lack of systematic assessment of these changes over long periods of time or in sufficiently high resolution as to resolve seasonal flux patterns. The ultimate aim of this body of research was to explore nematode systematics in decomposition environments, culminating in a pair of long-term human decomposition seasonal trials, in high resolution, with the specific intent of integrating the fields of soil chemistry, microbial ecology, and nematology in order to assess the relationships of cross-disciplinary impacts. Of …

Overcoming Dna Restriction-Modification Systems To Enable Transformation And Genetic Engineering In Non-Model Organisms, Lauren Ann Riley

Doctoral Dissertations

Many organisms naturally possess complex physiological traits that are of interest for biotechnology research. These non-model organisms are not routinely used though, due to a lack of foundational knowledge and genetic tools. The development of genetic tools is limited in part by the inability to efficiently transform DNA into these organisms. One of the major barriers to efficient DNA transformation is the native DNA Restriction-Modification systems within bacteria. DNA Restriction-Modification systems act as an immune system to cut heterologous DNA methylated differently than the host. To overcome these systems, DNA needs to be methylated in the same manner as the …

Conservation Of Terrestrial Salamanders Through Hemlock Woolly Adelgid Management In Eastern Hemlock Forests Within Great Smoky Mountains National Park, Jonathan Lawrence Cox

Masters Theses

Hemlock woolly adelgid (Adelges tsugae; HWA), an invasive aphid-like arthropod, was first documented on the east coast of the United States in the 1950s. HWA is an herbivore which primarily feeds at the needle base of hemlock tree species (Pinaceae: Tsuga). With no evolutionary defenses and few biotic controls, the eastern and Carolina hemlock (Tsuga canadensis and Tsuga carolinensis) serve as the primary diet of HWA in eastern North America. The invasive pest began to spread rapidly throughout the hemlock’s range causing defoliation and death of the trees within 4 – 10 years. With the …

Roles Of Select Cytochrome P450 Epoxygenases In Brown Adipogenesis, Katherine Marie Graham

Masters Theses

Brown adipose tissue (BAT) has recently emerged as a novel target for obesity treatment and prevention. Cytochrome P450 (CYP) epoxygenases, primarily CYP2J and CYP2C isoforms, produce epoxy fatty acids (EpFAs), which have been suggested to play important roles in the regulation of white adipogenesis and obesity. However, adipocyte-specific expression of CYP epoxygenases has not been extensively analyzed, and the roles of CYP epoxygenases in brown adipogenesis remain unexplored. In this study, we examined mRNA levels of Cyp2j and Cyp2c isoforms during murine and human brown and white adipocyte differentiation and in various adipose tissue depots of high-fat diet (HFD)-fed and …

Efficacy Of A Mushroom Derived Saltiness Enhancer In Increasing Saltiness And Consumer Acceptance In Low Sodium Applications, Lindsay Jenkinson

Masters Theses

The average American consumes sodium at excessive levels resulting in a multitude of adverse health effects. To reduce these risks, it is imperative to lower consumption rates. When sodium is reduced in a product, the main effect is decreased saltiness and often corresponds with reduced consumer acceptance. In addition to addressing the issue of sodium reduction, attenuating effects such as reduced consumer acceptance is also of importance.

Consuming and perceiving food is a multimodal experience, involving tastes, smells, and trigeminal sensations to produce a singular percept of flavor. This is an example of multisensory integration. When stimuli through different sensory …

Iojap: Morphological And Physiological Phenotype Characterization In Arabidopsis, Thomas Jay Payne

Doctoral Dissertations

IOJAP protein is found in all organisms that contain a ribosome of bacterial origin. The majority of studies suggest that IOJAP plays a role in translation, although this has yet to be thoroughly investigated in plants. Using Arabidopsis thaliana, an extensive phenotype characterization of iojap mutants was performed. Many processes of plant growth were slightly impaired at optimal temperature (22˚C) but became severely hindered at low temperature (12˚C and 4˚C). These cold temperature defects manifested in an overall reduction of plant growth as well as variegation, chlorosis, leaf hyponasty, as well as reduced maximum quantum yield (F_v/F …

Using Second Harmonic Generation To Study Gram-Positive Bacterial Membranes, Lindsey N. Miller

Doctoral Dissertations

Understanding how small-molecules, such as drugs, interact with bacterial membranes can quickly unravel into much more perplexing questions. No two bacterial species are alike, especially when comparing their membrane compositions which can even be altered by incorporating fatty acids from their surrounding environment into their lipid-membrane composition. To further complicate the comparison, discrete alterations in small-molecule structures can result in vastly different membrane-interaction outcomes, giving rise to the need for more "label-free" studies when analyzing drug mechanisms. The work presented in this dissertation highlights the benefits to using nonlinear spectroscopy and microscopy techniques for probing small-molecule interactions in living bacteria. …

Phytophthora Capsici In Tennessee: Fungicide Resistance, Population Genetics And Cultural Control, Timothy Brent Siegenthaler

Masters Theses

Phytophthora capsici, a plant pathogenic oomycete, is the causal agent of the vegetable disease Phytophthora blight of pepper and cucurbits. Since the identification of P. capsici in 1922, a significant amount of research has been conducted to understand its biology and disease management. Despite this, little research had been conducted on this species in the state of Tennessee. Three studies were done from 2018 to 2020, focusing on fungicide resistance, population genetics, and testing management strategies in the field. In 2018 and 2019 a total of 248 isolate of P. capsici were collected from five counties in Tennessee. These isolates …

Summer Foraging Range And Diurnal Roost Selection Of Tri-Colored Bats, Perimyotis Subflavus., Dustin Bradley Thames

Masters Theses

Tri-colored bat populations are declining in eastern North America where the fungal pathogen Pseudogymnoascus destructans has been introduced. The pathogen causes disease and mortality in cave hibernating bats. Once considered a common species in Tennessee, tri-colored bats are now being considered for protection under the Endangered Species Act. There is a paucity of research examining the basic ecology of tri-colored bats. Research to fill these knowledge gaps is needed to inform conservation plans and to define critical habitat. The first objective of my research was to characterize the summer diurnal roosts of tri-colored bats and to examine roost selection at …

Aroma Chemistry Of Daldinia Childiae Fermentation, Andrew Jason Moore

Masters Theses

An investigation to identify odorants responsible for a pleasant woody perfume-like aroma produced in the fermentation broth of the fungus Daldinia childiae (J.D. Rogers & Y.M. Ju) was conducted. Thirty odorants were identified from 30-day old fermentations employing solvent-assisted flavor evaporation (SAFE) and aroma extract dilution analysis (AEDA). Eleven odorants with flavor dilution (FD) factors ≥ 16 were quantitated using stable isotope dilution assays (SIDA), and odor activity values (OAV) determined. Odorants with the highest OAVs included guai-11-en-10-ol (woody, OAV 102689), 1-octen-3-one (mushroom, OAV 9025), sotolon (maple, OAV 458), and (2E)-non-2-enal (fatty, OAV 70). An odor-simulation model formulated …

From Drones To Soil Cores: Comprehensive Ecological Assessments For Enhancing Conservation Management Of Urban Forested Natural Areas, Mia T. Wavrek

Masters Theses

Urban natural areas are vegetated areas within cities that exhibit characteristics of non-urban natural areas in that they have relatively high levels of self-regulation (low or no level of management) of natural ecosystem processes and exhibit high taxonomic, genetic, and structural diversity. When these areas take the form of urban parkland, they are often managed for their social benefits to urban residents, while their ecological potential remains underutilized. Growing interest in enhancing biodiversity conservation in cities has highlighted the importance of improving the ecological planning and management of urban natural areas, particularly forested natural areas. For the variety of agencies …

Forage Species Selection For Transitional Organic Production In The Southeastern United States, Jonathan Kubesch

Masters Theses

Despite the vast production markets for forage and organic products nationally, so far limited work has been done to develop organic forages specifically for Middle Tennessee or the mid-South in general. The present organic research field focuses on vegetable and grain production; however, forage production offers an easier transition for producers moving into certified organic agriculture. The present study seeks to evaluate several forage blends for optimizing forage production under low-input transitional organic conditions. Ideally a forage system could be tailored to the beef cattle operations of Middle Tennessee, the dominant forage consumption market in this region of the mid-South. …

Predicting Voluntary Forage Intake Of Supplemented Beef Cattle, Connor Biehler

Masters Theses

A major priority of beef cattle production is to meet animal nutrient requirements in order to achieve a desired level of productivity. Accurately predicting voluntary forage intake (VFI) is necessary to accurately predict the total nutrient intake of grazing or forage-fed beef cattle that are also supplemented with other sources of nutrients. Therefore, the objectives of this experiment were to utilize data from published literature to 1) identify factors that explain variation in VFI, and 2) develop and validate one or more mathematical models that predict VFI or total nutrient intake of grazing or forage-fed and supplemented beef cattle. A …

More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia

Doctoral Dissertations

This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member …

The Effect Of Nuclear Perturbations On The 3d Organization Of The Genome, Rosela Golloshi

Doctoral Dissertations

Cells in our body experience constant mechanical forces that influence biological functions such as growth and development. The nucleus has been implicated as a key mechanosensor and can directly influence chromatin organization and epigenetic alterations leading to gene expression changes. However, the mechanism by which such mechanical forces lead to genomic alterations and expression of mechanosensitive genes is not fully understood. The work presented in this dissertation investigates the effect of mechanical and epigenetic perturbations on the 3D genome organization. To investigate this 3D genome folding, we use Chromosome Conformation Capture followed by high throughput sequencing (Hi-C) (Chapter-1) which identifies …

3d Genome Architecture Under Stress: A Survey Of Ionizing Radiation, Progeria, And Osmotic Stress, Jacob Tyler Sanders

Doctoral Dissertations

The human nucleus contains 2 meters of DNA which is intricately folded into a three-dimensional (3D) structure. It has become increasingly clear that this 3D structure plays an important role in the expression of genes. Proper gene expression is necessary for cellular homeostasis, cell state, and response to environmental/physical perturbations. Faithful repair of damage DNA damage is necessary to prevent genomic aberrations, such as translocations, which may lead to misregulation of gene expression. Hi-C, a sequencing technique that labels proximal chromatin interactions, provides a clearer picture of how the genome is spatially organized within the nucleus. Here, we discuss the …

Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz

Doctoral Dissertations

A diverse community of bacteria populates the mammalian gastrointestinal tract. These populations exist in a balance with the host assisting with key functions, particularly metabolism of intractable fibers and immune modulation. Disruption of this balance can lead to diseases such as infection, inflammatory bowel syndrome, and obesity. Common symptoms include chronic pain, chronic inflammation, and altered metabolism. Several taxonomic classifications of bacteria have been associated with these diseases, but Recent studies have indicated that these finding are not always statistically valid. An explanation for this is that microbial communities between individuals and even across time can vary substantially even when …

Genome-Wide Associations Detect Allele Dose-Dependent Metabolism And Transport Genes As Basis For Variation In Sweetpotato Storage Root Culinary Profiles, Tara Elizabeth Rickman

Masters Theses

Previously considered a poor man’s crop, sweetpotato production is increasing globally due to its complex carbohydrates and other health benefits. Developing superior cultivars for various emerging market niches is imperative to sustaining and growing the production of sweetpotatoes. Culinary profiles such as sugar composition, organic acids and storage root color are vital for selecting sweetpotatoes targeted for various value-added products. To determine the genetic architecture and candidate genes underlying these culinary profiles, a genome wide association study on 23 traits was performed in over 700 sweetpotato accessions representing global genetic diversity. A new NGS-based quantitative reduced representation sequencing approach (omeSeq/qRRS), …

Improvements To Solanum Tuberosum Cv. ‘Desireé’ Cell Suspension Culture And Nicotiana Tabacum Cv. ‘Petit Havana’ Shoot Induction., Jessica Slade Layton

Masters Theses

Since the 1980s, progress in biotechnology has harnessed the incredible potential of plant biology. Plants have been engineered to be pest and herbicide resistant, enhance stress tolerance, and produce pharmaceutical proteins. Despite these feats of genetic engineering, plant tissue culture remains a limiting factor for future research. Unfortunately, the pressure to quickly innovate and produce novel products has pushed aside research to optimize tissue culture and exploring underlying molecular mechanisms for improved culture conditions. Efficient tissue culture methods are limited to a few plant taxa and are sometimes described in an oversimplified manner under the assumption they are facile to …

Defining Bee Pollinator Community Composition In Tennessee Soybean, Andrew L. Lawson

Masters Theses

Two planting dates of various soybean varieties were planted in Jackson and Knoxville, TN during 2018 and 2019 with the overall intent of surveying the diversity bee (Hymenoptera) genera in these agroecosystems and also to assess the potential for using late maturing soybean as a food resource for bees during the dearth of floral resources that often occurs during the fall. We also investigated how manipulating planting dates and soybean variety selection affected the occurrence of insect pests that occurred in the soybean.

Both active (netting) and passive (bee bowls and blue-vane traps) sampling were used to collect the bees, …

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

Subaerial biofilms (SABs) grow at the interface between the atmosphere and rock surfaces in terrestrial and subterranean environments around the world. Multi-colored SABs colonizing relatively dry and nutrient-limited cave surfaces are known to contain microbes putatively involved in chemolithoautotrophic processes using inorganic carbon like carbon dioxide (CO₂) or methane (CH₄). However, the importance of CO₂ and CH₄ to SAB biomass production has not been quantified, the environmental conditions influencing biomass production and diversity have not been thoroughly evaluated, and stable carbon and nitrogen isotope compositions have yet to be determined from epigenic cave SABs. …