Life Sciences Commons^™

Exploring The Dark Matter Of Proteomics, Armin G. Geiger

Doctoral Dissertations

Proteomics, particularly mass spectrometry (MS)-based proteomics, has become an essential tool in understanding biological complexity and function at the molecular level. However, a significant fraction of spectral data generated in these studies, often referred to as the "Dark Matter of Proteomics'', remains unexplored and unidentified, concealing potentially vital biological insights. This dissertation addresses the challenge of uncovering this dark matter through the innovative use of computational techniques to enhance peptide identification and quantification in Kalanchoë fedtschenkoi, a model organism for Crassulacean Acid Metabolism (CAM).

The research employs a quantification-centered approach to MS data analysis, leveraging both MS1 and MS2 …

Assessment Of Genetic Diversity Of The Invasive Callery Pear, Pyrus Calleryana Decne. Using Mitochondrial Microsatellites And Its Molecular Detection Using Lamp, Alina Pokhrel

Masters Theses

Pyrus calleryana Decne. (Callery pear; [PC]) is a popular ornamental tree in the urbanized areas of the United States of America (US), owing to its aesthetical value, with showy white blossoms in early spring and vibrant fall foliage. The tree native to Asia is now becoming one of the most problematic invasive tree species in the eastern US. From its introduction in the early 20^th century, PC has been commercially used as rootstocks for propagating fruiting pears, alongside other closely related pear species. Several states are restricting the sale of rootstocks to limit the ongoing spread of PC. As …

Bee Friendly Beef: Integrating Pollinator-Friendly Native Forbs Into Native Grass Pastures, Jessica Prigge

Doctoral Dissertations

Native pastures present an opportunity to diversify that can support an array of animals, including pollinators and livestock. A variety of insect pollinators, important for both crop production and wild fauna persistence, are in population decline and benefit from native floral resources to sustain across the landscape. The goals of our work were to document blooming and forage characteristics of a variety of native forbs and to determine their establishment, persistence, and forage characteristics under different grazing rest regimens. We also sought to measure animal productivity between grass and diversified pastures under continuous stocking. Forbs established and persisted differently based …

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 …

Identification, Creation, And Characterization Of Bio-Based Antifreeze Agents, Joshua Samuel Saad

Masters Theses

Ice recrystallization is a key problem leading to quality deterioration of frozen foods and biomedical materials. Molecules possessing ice recrystallization inhibition (IRI) activity can control ice crystal size after freezing, reducing the degree of freezing-induced damage. While these IRI active molecules have shown promise in maintaining the quality of frozen foods, their slow discovery, limited creation strategies, and lack of mechanistic understanding limit their hypothesis-driven design. In this work, we address these above-stated needs required for the streamlined implementation of these materials into frozen systems by the creation of a machine-learning-based IRI screening method, the development of a new IRI …

Enhanced Efficiency Nitrogen Fertilizer As Tool To Control Nitrogen Loss In Row Crop Production, Samuel Kudzo Okai

Masters Theses

The efficiency of urea-based fertilizers is substantially reduced through nitrogen (N) losses via ammonia volatilization. Soil pH, clay content, soil organic matter (SOM), and field capacity can affect ammonia loss. Incubation experiments were conducted on eight soils using a controlled environment system to study the effects of soil properties on ammonia volatilization from urea and urea ammonium nitrate (UAN) applied at 134.5 kg N/ha. Each experiment was set up as a randomized complete block design with four replicates. Ammonia loss was measured on 1, 2, 3, 4, 5, 6, 7, 9, 11, 13, and 16 DAF (days after N application). …

Pollen-Specific Expression Of Ecori Restriction Endonuclease For Bioconfinement In Panicum Virgatum L., Jessica Nicole Stockdale

Masters Theses

The dispersal of pollen from genetically engineered (GE) crops can lead to unintended transgene flow, especially in wind-pollinated and obligate-outcrossing species such as switchgrass (Panicum virgatum L.). Various bioconfinement approaches have been studied for their potential to eliminate transgene flow from GE crops including selective male sterility, which aims to inhibit the germination of transgenic pollen grains. In this study, pollen-specific promoters controlling the expression of the EcoRI endonuclease, interrupted by a catalase intron, was evaluated for its efficacy to produce sterile pollen. The TaPSG719, PvPS1, Osg6B, OsRTS, and Zm13 promoters were assessed for pollen-specific expression patterns, none …

Agrobacterium-Mediated Transformation Of Hemp (Cannabis Sativa L.)., Carthel Tyler Newton

Masters Theses

Agrobacterium­-mediated transformation has long been utilized as a method of producing stable, transgenic plants. This project describes an attempt to develop a system of producing stably transformed hemp (C. sativa (L.)) plants. Because of its recalcitrance to in vitro tissue culture and regeneration, transformation studies of hemp have been severely limited. In this study, I combined media components that have been shown to improve tissue culture health and regeneration. Additionally, I used hemp cultivars and explant sources that have been reported to function well in in vitro systems. The results showed that the improved media components did not …

Aquatic Transitions And Interspecific Relationships In Fissidens Mosses, Julia R. Butler

Masters Theses

Embryophytes have undergone numerous re-invasions to aquatic habitats, impacting their morphological evolution. Despite the prominence of these transitions, their phylogenetic implications and morphological adaptations are just beginning to be investigated, especially as molecular methodologies become more accessible. We investigate these phenomena using the genus Fissidens, a diverse group of mosses encompassing both terrestrial and aquatic species. Our study integrates phylogenetic methods with morphological analyses to elucidate the evolutionary patterns within Fissidens and explore correlations between habitat transitions and morphological traits. Through extensive taxon sampling from herbarium specimens, DNA extraction, and sequencing, we construct robust phylogenetic trees using concatenated and …

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. …

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 …

Establishing And Optimization Of Tissue Culture Work With Erigeron Canadensis, Robert Petursson

Masters Theses

Glyphosate resistance among weed species has been an increasing problem in crop production over the past two decades. Glyphosate resistant Erigeron canadensis (horseweed) has been found on multiple continents and 20 U.S. states. It appears that the resistance is of non-target type, with mechanisms of action that have yet to be elucidated at the gene level. For the first portion of the study, I focused on reproducing the original indirect organogenesis protocol but discovered biotype variability can influence regeneration success. An improved indirect organogenesis method was then developed using the previously published methods that could be used across biotypes. A …

A Robust Agroinfiltration Method, Bryce N. Trull

Masters Theses

Stable transformation of soybean (Glycine max) is a markedly slow and laborious process. Thus, a tool that enables rapid evaluation of genetic elements in planta is critical to advance complex research and genetic engineering in soybean. To that end, a substantially robust agroinfiltration method was innovated in this work. Agroinfiltration is a technique that leverages Agrobacterium-mediated transient transformation to deliver genetic elements to the cells of whole plant tissues, usually leaves. Several factors were found to be relevant to successful soybean leaf agroinfiltration, including genotype, surfactant, developmental stage, and Agrobacterium culture medium. The research represents not only …

Bioregenerative Dietary Supplementation: Optimizing Brassica Production For Space Travel Through Light Intensity, Photoperiod, And Harvest Methodology, Ethan W. Darby

Masters Theses

Bioregenerative dietary supplementation, a component of bioregenerative life support, will be necessary for the success of future exploration-length space endeavors. Plants, as autotrophic producers of calories, nutrients, and oxygen, will be indispensable in the development of these systems. Previous work has identified leafy greens from the genus Brassica as promising candidates for in-flight production of necessary human nutrients such as vitamins C, B₁, and K₁, in addition to β-carotene, the primary vitamin A precursor in the human diet. These plants also produce lutein and zeaxanthin, two compounds important in protecting the eye from radiation-induced damage, as …

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 …

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 …

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 …

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 …

A Field Guide To Foodways And Foraging In Southern Appalachia, Aeryn Lorraine Longuevan

Chancellor’s Honors Program Projects

No abstract provided.

Agronomic And Economic Comparison Of Potential Winter Oilseed Species And Varieties For Tennessee, Stefanie B. Keadle

Masters Theses

Winter oilseed crops are annual cool season Brassica crops which fit well within typical corn and soybean rotations. They are currently being adopted in Midwestern conventional agriculture systems. The ability to produce sustainable aviation fuel (SAF) from oil pressed from the seeds is the driving force of recent interest in the crops. The three main crops of interest in this study are canola (Brassica napus), pennycress (Thlaspi arvense L.), and camelina (Camelina sativa). To determine if production of winter oilseeds is feasible in Tennessee, three experiments were conducted. First, a field study variety trial was …

Fungicide Sensitivity, Race Structure, And Host Pathogenicity Of Phytophthora Nicotianae In Tennessee And North Carolina, Taylor Giovanna Miller

Masters Theses

Phytophthora nicotianae, a hemibiotrophic oomycete, is the causal agent of disease of over 300 hosts, notably tobacco, tomato, citrus, strawberry, and ornamentals. Black shank of tobacco is a devastating disease that can result in up to 100% yield loss if left untreated, and buckeye rot of tomato compromises the marketability and yield of fruit impacted by P. nicotianae. Black shank and buckeye rot have been reported throughout the state of Tennessee, and the goal of this work was to analyze fungicide sensitivity of P. nicotianae isolated from tobacco and tomato, characterize the race structure of P. nicotianae, …

Impact Of Cover Crop Species Diversity On Soil Nutrient Availability And Crop Productivity, Amanda Kramer

Masters Theses

Cover crops provide multiple environmental benefits that improve both soil and water quality; however, farmers only utilize them on approximately 5% of harvested U.S. cropland. Low adoption rates are attributed to yield impact concerns, seed and planting costs, and lack of advocacy. This study, which began in October 2019, assessed the effects of nitrogen rate and cover crop diversity on weed biomass, soil coverage, in-situ residue decomposition, soil nitrogen and phosphorus availability, and cash crop yield to better understand the costs and benefits of cover crop adoption at two locations in Tennessee (Milan and Spring Hill). Treatments were replicated 4 …

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 …

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 …

Functional Analysis Of Soybean Proteinase Inhibitor Genes And Cyst Nematode-Inducible Synthetic Promoters For Insects And Nematode-Resistance In Plants, Mst Shamira Sultana

Doctoral Dissertations

Proteinase inhibitors (PIs) from legumes have the potential for use as protectants in response to pests and pathogens. Soybean (Glycine max) contains two trypsin inhibitors (TIs): Kunitz trypsin inhibitor (KTI) and Bowman-Birk inhibitor (BBI). In this study, the possible role of soybean TIs in plant defense against insects and nematodes was investigated. In addition to the three known TIs (KTI1, KTI2 and KTI3), novel inhibitors KTI5, KTI7, and BBI5 were identified in soybean. Their functional role was further examined by overexpression in soybean and Arabidopsis. In vitro enzyme inhibitory assays showed significant increase in trypsin and chymotrypsin inhibitory …

Winter Wheat Cover Crop Increased Subsoil Organic Carbon In A Long-Term Cotton Cropping System In Tennessee, Rounak Patra, Debasish Saha, Sindhu Jagdamma

Biosystems Engineering and Soil Science Publications and Other Works

Long-term cover-cropping and no-tillage practices can facilitate soil organic carbon (SOC) accumulation in agroecosystems for soil health and climate mitigation benefits. However, the contribution of these conservation management practices to SOC gain from the subsoil layers is not been extensively studied. To understand this knowledge gap, it is essential to determine the distribution of total SOC and SOC fractions in response to management practices across the soil profile. Therefore, this study was conducted by leveraging a 40-year replicated field experiment in a continuous cotton (Gossypium hirsutum) system. The management treatments examined included three cover crop treatments: 1) hairy vetch, HV …

Corn (Zea Mays L.) Production In Living Mulch Systems, Grazing Potential, And Economic Viability, Marcia Peireira Quinby

Doctoral Dissertations

Living mulch (LM) is a practice in which forages are grown simultaneously with the main crop, serving as a living cover throughout the growing season. The LM systems were developed to alleviate concerns of soil depletion and finding ways to reduce tillage negative effects on soil productivity. In addition, when legumes are use can decrease the reliance on N fertilizer. The use of corn in LM have been previously studied due to the crop being a large commodity in the U.S.; In addition, the ability to graze the LM after corn production can increase the land use efficiency. To determine …

Better Understanding Genomic Architecture With The Use Of Applied Statistics And Explainable Artificial Intelligence, Jonathon C. Romero

Doctoral Dissertations

With the continuous improvements in biological data collection, new techniques are needed to better understand the complex relationships in genomic and other biological data sets. Explainable Artificial Intelligence (X-AI) techniques like Iterative Random Forest (iRF) excel at finding interactions within data, such as genomic epistasis. Here, the introduction of new methods to mine for these complex interactions is shown in a variety of scenarios. The application of iRF as a method for Genomic Wide Epistasis Studies shows that the method is robust in finding interacting sets of features in synthetic data, without requiring the exponentially increasing computation time of many …

Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates

Doctoral Dissertations

Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.

Populus and Salix are …