Life Sciences Commons^™

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 …

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 …

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 …

Poa Annua: An Annual Species?, Devon E. Carroll

Doctoral Dissertations

Poa annua L. is ranked the most troublesome turfgrass weed but can also be a highly desirable turfgrass species. As the Latin name annua implies, the species is thought to persist via an annual life cycle; yet there are many reports in literature of P. annua persisting perennially. Considering that P. annua senescence patterns do not align with other true annual species such as Triticum spp. and Zea mays L., we hypothesized that P. annua presents itself similarly to other perennial, cool-season, turfgrass species that are subject to a confluence of environmental factors in summer that can cause mortality. …

Nodulin 26 Like Intrinsic Proteins: Structurally Similar Membrane Channels With Diverse Functions In Plant Hypoxia Stress, Metalloid Nutrition & Toxicity, Zachary Beamer

Doctoral Dissertations

Plant nodulin 26 intrinsic proteins are categorized into three groups (NIP I, II, and III) based on pore architecture. NIP II and III participate in metalloid nutrition, whilst the function of a third (NIP I) is less understood. Here we investigate the physiological function of one NIP I protein (Arabidopsis thaliana NIP2;1) as a lactic acid channel, and also explore the structural basis for metalloid and water permeability of NIP I and NIP II proteins in general. In addition, a strategy was developed for the purification and crystallization of soybean nodulin 26 as a step towards structure determination of a …

Plant Community Responses To Interactive Anthropogenic Disturbances Along A Natural-Wildland-Urban Gradient And Undergraduate Students’ Attitudes Toward Disturbances, Mali M. Hubert

Doctoral Dissertations

Anthropogenic disturbances are defined as any change caused by human activity that alters biodiversity. Wildfire and urbanization disturbances are among the most influential on the landscape because of their individual and interactive properties. Areas deemed wildland-urban interfaces (WUI; area where environment intermingles with human-built structures) are increasing near protected lands because of human population growth and movement, which often facilitates fire ignitions by humans. Houses that are adjacent to or overlap with wildland vegetation can complicate protection of urban development and wildlands from fires. The expansion of the WUI due to population growth will exacerbate fire risk, which can ultimately …

Calmodulin Like 38 Is Required For Autophagy Of Hypoxia-Induced Cytoplasmic Rna Granules In Arabidopsis Thaliana, Sterling Field

Doctoral Dissertations

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

Identification And Functional Characterization Of Plant Small Secreted Proteins During Arbuscular Mycorrhizal Symbiosis, Xiaoli Hu

Doctoral Dissertations

Plant small secreted proteins (SSPs) are sequences of 50 – 250 amino acids in size which are transported out of cells to fulfill multiple functions related to plant growth and development and response to various stresses. With the development of more accurate and affordable genome sequencing technology, an increasing number of SSPs have been predicted using diverse computational tools based on machine learning. Although experimentally validated plant SSPs are still limited, some studies have reported that plant SSPs can be induced and involved in mutualistic relationships between plants and microbes. In Chapter I, known SSPs and their functions in various …

Epigenetic Mechanisms Governing Plant Growth, Development, And Responses To Nematode Parasitism, Meredith M. Bennett

Doctoral Dissertations

Epigenetic mechanisms, including histone and DNA methylation and microRNAs, play key roles in mediating transcriptional changes during plant development and stress responses. However, how these interconnected epigenetic components regulate gene expression in a spatiotemporal fashion remains partially known. Here, I generated 15 transgenic Arabidopsis GUS reporter lines for genes involved in DNA methylation and demethylation pathways. The spatiotemporal expression patterns of these genes were profiled in various plant organs during development, exogenous phytohormone response, and plant-parasitic nematode pathogenesis. The analyses revealed unique and overlapping expression patterns in roots, shoots, and reproductive organs, emphasizing the importance of a DNA methylation—demethylation equilibrium. …

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 …

Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, Alessandro Francesco Sarno

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Plasmodesmata (PD) are pores that traverse plant cell walls, providing a route for intercellular trafficking of essential metabolites, nutrients, and signaling molecules between adjacent plant cells, thereby aiding communication. The increased size exclusion limit 2 (ise2) mutant of Arabidopsis thaliana has an increased abundance of branched PD, as well as a greater flux of intercellular trafficking. A search for proteins that interact with ISE2 identified THIOGLUCOSIDE GLUCOHYDROLASE 2 (a myrosinase). A. thaliana also encodes a second, closely-related myrosinase, TGG1. Myrosinases are enzymes that catalyze the hydrolysis of glucosinolates, a type of secondary metabolite that are amino acid derivatives. The breakdown …

Non-Canonical Signaling From The Etr1 And Etr2 Ethylene Receptors In Arabidopsis Thaliana, Arkadipta Bakshi

Doctoral Dissertations

The gaseous phytohormone ethylene regulates several physiological and developmental processes in higher plants. There are five ethylene receptor isoforms that mediate the responses to ethylene in the model plant Arabidopsis thaliana. Prior research has shown that these five ethylene receptor isoforms in Arabidopsis have both overlapping and non-overlapping roles in regulating diverse responses such as growth in air, growth recovery after removal of ethylene, and ethylene stimulated nutational bending. Functional divergence of ETR1 has been determined in controlling some of these traits and in some of these cases, ETR1 subfunctionalization requires the receiver domain. Using homology modeling and sequence …

Effects Of Mycorrhizal Fungi On Vigna Radiata Growth In Soil Differing In Fertilizer Concentration, Ming Sum Jessica Cheng

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Mycorrhizal fungi form mutualistic relationships with the roots of some plants, allowing the plant access to nutrients and minerals while the fungi obtain food from the plant. Given that this relationship is beneficial to the plant, this paper investigates the nature of the impact of presence of mycorrhizal fungi on the growth of Vigna radiata (mung beans) in soil of differing chemical environments. Through comparing the stem lengths of plants seven days after germination, it is found that in soil with 0.0% fertilizer, the presence of locally collected, unclassified mycorrhizal fungi impacts the growth of Vigna radiata negatively; in intermediate …

Myosin Xi-I Works In Tandem With A Microtubule-Associated Mechanism To Position The Nucleus In Arabidopsis Root Hairs, Ian Andrew Windham

Chancellor’s Honors Program Projects

No abstract provided.

Evaluation Of Off-Type Grasses In Interspecific Hybrid Bermudagrass [Cynodon Dactylon (L.) Pers. X C. Transvaalensis Burtt-Davy] Putting Greens, Eric Hall Reasor

Doctoral Dissertations

The economic impact of the golf industry in the United States (U.S.) in 2011 was estimated to be $176.8 billion. Interspecific hybrid bermudagrasses [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] are some of the most widely utilized grasses on golf courses throughout tropical, subtropical, and temperate climates. In 2007, bermudagrass was grown on 80% of putting green acreage in the southern U.S. ‘Tifgreen’ and ‘Tifdwarf’ were two of the first widely established cultivars on putting greens, but their genetic instability led to the occurrence of phenotypically different off-type (OT) grasses. Several OT grasses were selected and released as …

Evaluation Of Hall’S Panicgrass (Panicum Hallii Vasey) As A Model System For Genetic Modification Of Recalcitrance In Switchgrass (Panicum Virgatum (L.)), Joshua Nathaniel Grant

Masters Theses

While switchgrass (Panicum virgatum (L.)) has long been recognized as a viable bioenergy feedstock, it and other plants have cell walls with recalcitrance to processing. Recalcitrance is recognized as a major barrier to broad adoption of switchgrass and other feedstocks for cellulosic bioenergy. In an effort to reduce recalcitrance, transgenic plants have been generated with altered cell wall phenotypes such as reduced lignin. Unfortunately, stable transformation of switchgrass and other C4 grasses is time intensive, costly, and genetic analysis is further complicated by polyploid genomic structures. Unlike switchgrass, which can be tetraploid to octoploid, a closely related species, Hall’s …

Protein, Methionine, And Cysteine Upregulation In Phaseolus Vulgaris ‘Black Turtle Bean’ Seeds Through Sulfur Fertilization At V2 And R2 Stages Of Growth, Hannah Paige Barry

Masters Theses

The purpose of this research was to increase protein, methionine, and cysteine content in Phaseolus vulgaris L., common bean in relation to the inhibitory compound tannin. Previous research has shown that sulfur fertilization increases total protein, methionine and cysteine content in various crops, but always in tandem with inhibitory compound increases. If successful, the resulting bean seed will have a better nutrient profile for malnourished populations around the world.

Granular gypsum was applied at 0 kg S ha^-1 [kilograms of sulfur per hectare], 10 kg S ha^-1, 20 kg S ha^-1, 40 kg S ha …

Comparison Of Mesophyll Protoplast Isolation And Transformation Between Panicum Virgatum And Panicum Hallii, Andrea Grace Collins

Masters Theses

Protoplasts are appropriate targets for genome editing, DNA functional screens and transgenesis. This project focuses on the comparison of inexpensive mesophyll protoplast isolation via the use of food-grade enzymes and transformation between diploid Panicum hallii Vasey (PAH) and polyploid cellulosic feedstock Panicum virgatum L (switchgrass), a relative of PAH. PAH has great potential as a C4 model species for crop and bioenergy research. Here an inexpensive switchgrass and PAH mesophyll protoplast isolation and transformation system was developed; the first protoplast system for PAH. Using low-cost commercial food-grade enzymes, a cost reduction of ~1000-fold was achieved compared to traditional protoplast isolating …

Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest

Doctoral Dissertations

Translation of mRNA into protein is a critical step in gene expression, but the principles guiding its regulation at the genome level are not completely understood. Translation can be quantified at a genome scale by measuring the ribosome loading of mRNA—the extent to which mRNA is associated with ribosomes. In this dissertation, I present investigations into how genome-wide ribosome loading is controlled in Arabidopsis thaliana. In chapter 1, I give an overview of regulation of ribosome loading and translation. In chapter 2, I present research demonstrating for the first time that genome-wide ribosome loading in plants is partially controlled by …

Modification Of Carbohydrate Active Enzymes In Switchgrass (Panicum Virgatum L.) To Improve Saccharification And Biomass Yields For Biofuels, Jonathan Duran Willis

Doctoral Dissertations

The natural recalcitrance of plant cell walls is a major commercial hurdle for plant biomass to be converted into a viable energy source as alternative to fossil fuels. To circumvent this hurdle manipulation of carbohydrate enzymes active in the cellulose and hemicellulose portions of the plant cell wall can be utilized to improve feedstocks. Production of cellulolytic enzymes by plants have been evaluated for reducing the cost associated with lignocellulosic biofuels. Plants have successfully served as bioreactors producing bacterial and fungal glycosyl hydrolases, which have altered plant growth to improve saccharification. A bioprospecting opportunity lies with the utilization of insect …

Decoding The Cellular Zipcode: Functional Analysis Of Transit Peptide Motifs And Mechanistic Implications In Plastid Targeting And Import, Kristen N. Holbrook

Doctoral Dissertations

Eukaryotic organisms are defined by their compartmentalization and various organelles. The membranes that define these organelles require complex nanomachines (known as translocons) to selectively mediate the import of proteins from the cytosol where they are synthesized into the organelle. The plastid, (specifically the chloroplast) which is characteristic of plant cells, possibly represents the most complex system of protein sorting, requiring many different translocons located in the three membranes found in this organelle. Despite having a small genome, the vast majority of plastid-localized proteins are nuclear-encoded and must be post-translationally imported from the cytosol. These proteins are encoded as a larger …

Testing The Temporal Stability Of The Climate Response Of Tree Species At Norris Dam State Park, Tennessee, U.S.A., Allison Elizabeth Ingram

Masters Theses

Temporal stability of the climate-tree growth relationship means that over time, tree species were responding to a specific climate variable and continue to respond to that variable into the present. The stability of this response is important to test prior to attempting to reconstruct past climate. In this study, I sampled oaks (white oak = Quercus alba L. and chestnut oak = Quercus montana Willd.) and pines (Virginia pine = Pinus virginiana Mill. and shortleaf pine = Pinus echinata Mill.) growing in Norris Dam State Park in eastern Tennessee and tested the temporal stability of these species and their potential …

Computational Identification Of Terpene Synthase Genes And Their Evolutionary Analysis, Qidong Jia

Doctoral Dissertations

Terpenoids, the largest and most structurally and functionally diverse class of natural compounds on earth, are mostly synthesized by plants to be involved in various plant environment interactions. Some terpenoids are classified as primary metabolites essential for plant growth and development. Terpene synthases (TPSs), the key enzymes for terpenoid biosynthesis, are the major determinant of the tremendous diversity of terpenoid carbon skeletons. The TPS genes represent a mid-size family of about 30-100 functional genes in almost all major sequenced plant genomes. TPSs are also found in fungi and bacteria, but microbial TPS genes share low levels of sequence similarity and …

Rooting Characteristics And Antioxidant Pigment Responses Of Three Hybrid Bermudagrass [Cynodon Dactylon (L.) Pers. × Cynodon Transvaalensis Burtt- Davy] Cultivars Exposed To Drought, Cory Alan Yurisic

Masters Theses

With recent changes in global climate, water use and its conservation have become important topics of discussion. Turfgrasses for lawns, parks, and other recreational areas are often perceived negatively due to the need for irrigation. The identification of turfgrasses possessing an improved ability to withstand water deficit is an important goal in science to curb irrigation requirements in the landscape. Newly released cultivars of hybrid bermudagrass (C. dactylon L. x. C. transvaalensis Burtt-Davy) have demonstrated improved tolerance to stresses such as cold, traffic, and water deficit; however, drought resistance mechanisms of these new cultivars have been largely uninvestigated. Drought …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Developing Expressed Sequence Tag Libraries And The Discovery Of Simple Sequence Repeat Markers For Two Species Of Raspberry (Rubus L.), Jill M. Bushakra, Kim S. Lewers, Margaret E. Staton, Tetyana Zhebentyayeva, Christopher A. Saski

Entomology & Plant Pathology Publications and Other Works

Background

Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders.

Methods

Leaf and meristem tissue from ‘Heritage’ red raspberry (Rubus idaeus) and ‘Bristol’ black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA …