Life Sciences Commons^™

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 …

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 …

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 …

Root Phosphomonoesterase As A Vital Component Of Increasing Phosphorus Availability In Tropical Forests, Kristine Grace Manno Cabugao

Doctoral Dissertations

Tropical forests, relative to other terrestrial ecosystems, exchange the largest amount of carbon with the atmosphere and also constitute a significant carbon sink. However, nutrient limitation, particularly of phosphorus (P), could limit growth of tropical forests and their function with the global carbon cycle. Thus, understanding root mechanisms to acquire P is necessary to representing the P cycle and corresponding interactions with plant growth. A large portion of total soil P in tropical forests occurs in organic forms, only accessible through root and microbial production of phosphatase enzymes. These phosphatase enzymes mineralize organic P into orthophosphate, the form of P …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Genetic And Epigenetic Control Of Soybean Agronomic Traits, Daniel Niyikiza

Doctoral Dissertations

Greater soybean productivity depends on the genetic improvement of yield components, epigenetic effects and the interactions with surrounding environment. We explored the possibility of soybean improvement by conventional biparental crossing of soybean lines, differing by seed quality, yield, and resistance to a range of pathogens, including soybean cyst nematode (SCN). We investigated the role of Resistance to Heterodera glycines (Rhg) 1 and 4 loci in soybean resistance to SCN, race 2 and 3. Further, we evaluated the adaptability of temperate-origin soybean lines in tropical environments of Rwanda. Lastly, we examined gene expression, RNA splicing, DNA methylation and their interactions in …

Investigating Transmembrane-Lipid Interactions Of Epha2 And Ph Responsive Peptides, Katherine M. Stefanski

Doctoral Dissertations

Single-pass membrane receptor signaling plays vital roles in human development and maintaining homeostasis. These membrane receptors can also have causative functions in several diseases including cancer. Much is known about the structure and signaling outcomes of these receptors but the mechanistic details of how they pass an extracellular signal across the membrane and into cytoplasm via the transmembrane (TM) domain is unclear. It is further unknown how or if interactions with membrane lipids facilitate and/or regulate these events. Here we use the TYPE7 peptide to target the TM region of a receptor tyrosine kinase, EphA2. EphA2 engages in both tumorigenic …

Costs Of Protected Areas In The United States, Diane Lebouille

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 …

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. …

Theoretical And Quantitative Methods Connecting Characterizing Micoribal Metabolism Diversity: Implciations From Phylogenetics, Community Diversity, And Organic Geochemistry, Taylor Royalty

Doctoral Dissertations

Biogeochemistry is controlled by microorganisms obtaining nutrients and energy. Thus, microbial metabolisms directly link microbial ecology and geochemistry. The extent that microbial ecology and geochemistry microbial ecology and geochemistry affects the other requires constraint on the spatiotemporal distribution and abundance of microbial metabolisms with respect to geochemistry, or the microbial niches. Elucidating microbial metabolisms was challenging prior to the advent of ‘omics sequencing technologies, as most microbial lineages lack cultured representatives. Although revolutionizing microbial ecology, challenges still exist in fully leveraging information derived from ‘omics technologies. This dissertation attempts to address a small subset of these challenges that include quantifying …

Enteric Biopolymer Composite Coatings To Enhance The Viability Of Powdered Probiotics During Preparation, Storage, And Simulated Digestions, Anyi Wang

Doctoral Dissertations

Due to suppressed metabolisms, powdered probiotics are generally more stable and more convenient for applications than the liquid form, but much work is needed to improve viability of powdered probiotics during processing, storage, and digestions. The goal of this dissertation was to fabricate delivery systems with an enteric biopolymer coating and a core of powdered probiotic ingredients. The principle of preparing powdered probiotics was to directly mix a concentrated cell suspension with hygroscopic food ingredient powders. Amorphous spray-dried lactose (SDL) was first studied to prepared powdered Lactobacillus salivarius NRRL B-30514 in chapter 2. A smaller amount of cell suspension resulted …

Lower Extremity Muscle Contributions To Acl Loading In Healthy And Acl-Reconstructed Females, Shelby Peel

Doctoral Dissertations

Females are 16 times greater to sustain a second ACL injury compared to their healthy female counterparts. Many of these females return to play their respective sport after an ACL-reconstruction (ACLR). However, little is known about the influence fatigue in sport has on lower extremity mechanics of ACLR females. The purpose of this study was to investigate the influence muscular fatigue may have on lower extremity mechanics in healthy and ACLR females. It was hypothesized that 1) healthy control and ACLR females would demonstrate different hip, knee, and ankle mechanics, regardless of fatigue, 2) fatigue would influence hip, knee, and …

Formulation And Evaluation Of Gemcitabine Plus Romidepsin + Cisplatin Combination For Controlling Tumors, Pawat Pattarawat

Doctoral Dissertations

Cancer is a deadly malignant disease that is costly to treat and still impossible to cure. Cancer treatments often come with side effects that impact the overall health of patients. Breast cancer is the most common type of cancer in the United State and bladder cancer mortality and recurrence rates are still high among cancer patients. Thus, safe and effective regimens are needed to combat these diseases.

In this study, the safe and efficacious combination of gemcitabine, cisplatin, and romidepsin (Gem plus Rom+Cis) to treat two types of cancer: bladder and breast cancer, was formulated. In vitro data from this …

Examining The Physical Activity Levels Of Youth With Intellectual And Developmental Disabilities During Physical Education And Recess, Vincenzo Nocera

Doctoral Dissertations

Introduction: It is currently believed that children with intellectual and/or developmental disabilities (IDD) are less physically active than their peers. The school setting may offer a promising solution to allow children with and without IDD to engage in physical activity (PA). However, the current school-based PA levels of this population remain unclear. Therefore, the purpose of this investigation was to compare the PA levels and related context of youth with and without IDD during the total school day, physical education, and recess. Methods: A total of 13 children (n = 3 with IDD) enrolled in first- and second grade participated …

Exploring The Effects Of Traditional And Expert-Derived Attentional Focus Cue Structures On Complex Skill Learning, Kaylee Woodard

Doctoral Dissertations

Instructions that direct attention externally have been shown to enhance motor performance. However, research on learning effects has produced mixed findings, particularly in skilled populations, and particularly when realistic instructional protocols have been used. Most studies have presented an overly simplistic view of attention, such that all-internal focus protocols are contrasted with all-external focus protocols. Expert performers, however, have reported adopting combined approaches, revealing the need for research to test more realistic instructions. The current project was a two-part study designed to investigate the effects of realistic focus instructions on performance and learning. Study 1 was an exploratory study of …

Microemulsions Of Cinnamon And Orange Oils As An Antimicrobial Delivery System For Salmonella Biofilms On Stainless Steel, Jennifer Vuia-Riser

Doctoral Dissertations

Essential oils (EOs) are natural antimicrobials that can be used to develop intervention strategies to inhibit pathogens, but EOs are lipophilic. Colloidal systems, such as microemulsions, are needed for food industry applications. This dissertation focused on the development and characterization of a microemulsion composed of cinnamon oil (CO, Cinnamomum zeylanicum) and orange oil (OO, Citrus sinensis) to be used against Salmonella Enteritidis H4267 biofilms formed on stainless steel disc surfaces.

First, the antimicrobial activity of CO and OO against S. Enteritidis H4267, either used in combination or in a microemulsion system, was determined. CO had a greater antimicrobial …

Social-Ecological Systems Considerations For Wildlife Reintroduction And Conservation, Cristina Elisa Watkins

Doctoral Dissertations

Wildlife management, especially projects requiring reintroduction, are complex undertakings requiring interdisciplinary approaches. This dissertation combines social science, ecology, economics, and policy to advance wildlife reintroduction science and improve conservation outcomes. The central focus of this dissertation involves wildlife reintroduction management, with a specific emphasis on the reintroduction of elk into East Tennessee. The dissertation is divided by three studies, each taking a unique interdisciplinary approach to wildlife reintroduction. The first study uses structural equation modeling to examine the social psychology constructs of risk perception and trust to examine their influence on attitudes towards reintroduced elk in Tennessee and support for …

Needles In A Haystack Of Protein Diversity: Interrogation Of Complex Biological Samples Through Specialized Strategies In Bottom-Up Proteomics Uncover Peptides Of Interest For Diverse Applications, Manuel I. Villalobos Solis

Doctoral Dissertations

Peptide identification is at the core of bottom-up proteomics measurements. However, even with state-of the-art mass spectrometric instrumentation, peptide level information is still lost or missing in these types of experiments. Reasons behind missing peptide identifications in bottom-up proteomics include variable peptide ionization efficiencies, ion suppression effects, as well as the occurrence of chimeric spectra that can lower the efficacy of database search strategies. Peptides derived from naturally abundant proteins in a biological system also have better chances of being identified in comparison to the ones produced from less abundant proteins, at least in regular discovery-based proteomics experiments. This dissertation …