Life Sciences Commons^™

Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie

Doctoral Dissertations

Prescribed fires in Southern Appalachian forests are vital in ecosystem management and wildfire risk mitigation. However, understanding the intricate dynamics between these fires, soil microbial communities, and overall ecosystem health remains challenging. This dissertation addresses this knowledge gap by exploring selected aspects of this complex relationship across three interconnected chapters.

The first chapter investigates the immediate effects of prescribed fires on soil microbial communities. It reveals subtle shifts in porewater chemistry and significant increases in microbial species richness. These findings offer valuable insights into the interplay between soil properties and microbial responses during the early stages following a prescribed fire. …

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 …

Novel Microbial Guilds Implicated In N2o Reduction, Guang He

Doctoral Dissertations

N₂O is a long-recognized greenhouse gas (GHG) with potential in global warming and ozone depletion. Terrestrial ecosystems are a major source of N₂O due to imbalanced N₂O production and consumption. Soil pH is a chief modulating factor controlling net N₂O emissions, and N₂O consumption has been considered negligible under acidic conditions (pH <6). In this dissertation, we obtained solids-free cultures reducing N₂O at pH 4.5. Furthermore, a co-culture (designated culture EV) comprising two interacting bacterial population was acquired via consecutive transfer in mineral salt medium. Integrated phenotypic, metagenomic and metabolomic analysis dictated that the Serratia population excreted certain …

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

Doctoral Dissertations

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

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 …

Investigating The Role Of Spatial Compartmentalization And Genomic Translocations In Metastatic Cancer: A Multi-Omic Analysis, Joshua Harris Garretson

Chancellor’s Honors Program Projects

No abstract provided.

Variability And Genetic Structure Of The Montezuma Quail Cyrtonyx Montezumae In The Northern Limit Of Its Distribution, Eduardo Sánchez Murrieta, Alberto Macías-Duarte, Reyna A. Castillo-Gámez, Angel B. Montoya, Alejandro Varela-Romero, Nohelia G. Pacheco Hoyos

National Quail Symposium Proceedings

A species’ geographic distribution of genetic variability is influenced by different factors including size of geographic distribution, dispersal capability, mating system, and migration. For instance, a low migration rate among populations may cause a decrease in genetic variation. Such is the case of the Montezuma quail (Cyrtonyx montezumae), a popular game bird with a limited flight capacity that prevents long-distance dispersal. In the northern limit of the species’ distribution in Arizona, New Mexico, and Texas in the United States, the species inhabits oak forests that are separated from one another by deserts. Consequently, Montezuma quail populations are distributed …

What I Talk About When I Talk About Integration Of Single-Cell Data, Yang Xu

Doctoral Dissertations

Over the past decade, single-cell technologies evolved from profiling hundreds of cells to millions of cells, and emerged from a single modality of data to cover multiple views at single-cell resolution, including genome, epigenome, transcriptome, and so on. With advance of these single-cell technologies, the booming of multimodal single-cell data creates a valuable resource for us to understand cellular heterogeneity and molecular mechanism at a comprehensive level. However, the large-scale multimodal single-cell data also presents a huge computational challenge for insightful integrative analysis. Here, I will lay out problems in data integration that single-cell research community is interested in and …

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 …

Computational Analysis Of Transcriptional And Post-Transcriptional Feedback Loops In Development And Cell Differentiation, Benjamin Rigel Nordick

Masters Theses

Regulation of gene expression is critical to organism development and health. Positive and negative feedback in networks of gene regulatory interactions are associated with the maintenance of distinct cell states/types or oscillations, respectively. Recent computational studies identified two structures of positive feedback relevant to establishment of cell type: interconnected transcriptional “high-feedback” loops and a purely post-transcriptional feedback loop arising from multiple microRNA molecules cooperatively regulating one mRNA. The goals of this work were to develop methods for analyzing often-unintuitive high-feedback loops in large networks, generalize the two new regulatory structures to consider oscillation, and further explore the ability of post-transcriptional …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …

Crispr-Cas In The Field Of Dentistry: A Comprehensive Collection Of The Potential Uses Of Crispr-Cas9 In Dental Health Care, Lexi Elaine Bales

Chancellor’s Honors Program Projects

No abstract provided.

Mutations In The N-Terminus Of The Mod(Mdg4) Btb Domain Reveal An Unexpected Role Of Mod(Mdg4) In Chromosome Segregation In Female Meiosis, Gwyneth D E Walker, Bruce D. Mckee

Chancellor’s Honors Program Projects

No abstract provided.

Conservation Status Assessment Of The Egg-Mimic Darter (Percidae: Etheostoma Pseudovulatum) Using A Multi-Faceted Approach, Zachary L. Wolf, John W. Johansen, Rebecca E. Blanton

Southeastern Fishes Council Proceedings

The imperiled Egg-mimic Darter (Etheostoma pseudovulatum) is a headwater-adapted fish restricted to an area less than 1000 km² in Tennessee. It is found in only six tributaries of the Duck River and the large, mainstem of this system may act as a barrier to dispersal, restricting population connectivity. The only status assessment of this species was over two decades ago; genetic diversity and the degree of population connectivity have never been evaluated. We conducted a conservation status assessment using a multi-faceted approach to better inform conservation management plans, including examining its current distribution, assessing habitat quality, estimating …

A Systematic And Biogeographic Study Of Trillium (Melanthiaceae), Jayne A. Lampley

Doctoral Dissertations

Trillium (Melanthiaceae, Parideae) has a disjunct distribution occurring in eastern and western North America, and eastern Asia. Past studies have examined the phylogeny and historical biogeography of Melanthiaceae and Parideae, however these studies either did not fully examine these aspects within Trillium or did not employ sufficiently broad taxonomic or character sampling to clarify relationships among taxa. The first phylogenetic analysis presented in this study provides a resolved phylogeny for Trillium s.l. and Paris s.l. by using a dataset of 70 plastid coding genes and by sampling broadly from Trillium s.s., Pseudotrillium, Trillidium, Paris s.s., Daiswa, and Kinugasa. The results …

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 …

Molecular Markers Within And Beyond Viburnum: A Single Set Of Ssrs For An Immense Genus, Trinity Paige Hamm

Masters Theses

Comprised of more than 160 species, Viburnum is the largest genus in the Viburnaceae (formerly Adoxaceae) alongside Adoxa and Sambucus. The native range of Viburnum species spans much of the Northern Hemisphere and extends into the mountains of South America and Southeastern Asia. Their wide geographic range has made Viburnum particularly interesting to phylogeographers and phylogeneticists. This diverse genus is also horticulturally valuable with varying traits such as fragrance, fruit color, and bud and inflorescence form. There is sufficient morphological diversity in the genus for there to be more than 70 species and intraspecific hybrids in cultivation, and in …

Understanding The Novel Role Of Checkpoint Protein Rough Deal In Homolog Orientation And Centromeric Cohesion In Drosophila Male Meiosis, Qiutao He

Doctoral Dissertations

Meiosis is a central mechanism in sexual reproduction, through which the diploid precursor cells in the germline produce haploid gametes. After fertilization, a new set of diploid genome forms in the offspring with the characteristics of mother and father. The faithful transmission of genetic material to next generation relies on the fidelity of chromosome segregation during meiosis. A variety of mechanisms regulate the chromosome segregations in meiosis, including homolog interaction, chromosome cohesion, and sister-chromatid orientation. In most eukaryotic organisms, homolog interactions are built by the formation of chiasmata resulted from crossovers, but it is absent in male Drosophila in which …

Evaluating The Winter Diet Of A Reintroduced Herd Of Elk In The Cumberland Mountains, Tennessee, Using Next-Generation Sequencing Techniques, Dailee L. Metts

Masters Theses

A distinct subspecies of elk (Cervus canadensis), the North American elk (C. canadensis canadensis), once inhabited portions of the southeastern United States, including Tennessee, until their extirpation in the mid 1800s. From 2000 to 2008, 201 Manitoban elk were reintroduced on the North Cumberland Wildlife Management Area (NCWMA). A year-long food habits study using histological analysis of plant material from feces was completed for the NCWMA elk from 2003 to 2004 and has since aided managers in their landscape planning. Since then, more elk have been released onto the area, food plots have been established throughout …

A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Gene expression encompasses the flow of genetic information from DNA to mRNA (transcription) and from mRNA to protein (translation) along with the regulatory mechanisms underlying these processes. Omics technologies offer a powerful toolset with which to study gene expression at each of these stages. A recently published dataset integrating transcriptomic, proteomic and phospho-proteomic measurements from 30 Arabidopsis thaliana tissues provides a unique resource to explore gene expression.¹ The translational machinery (the ribosome, and its initiation, elongation, and termination factors) are a core component in gene expression. Defects in translation can be lethal or lead to major developmental defects and …

Applications Of Comparative Genomics And Data Science To Agricultural And Clinical Research, Katrina A. Schlum

Doctoral Dissertations

The advent of inexpensive, high-throughput whole genome sequencing (WGS) technologies has led to the generation of thousands of related genomes, even from a single study. Large-scale genome analysis has resulted in hypothesis-generating approaches in the fields of clinical, human and agriculture genomics. Additionally, population-level genomic sampling has resulted in a decrease in false positives in genotype-phenotype associations and an increase in understanding of the basis of disease, antibiotic and pesticide resistance. Deeper understanding of migration, genetic divergence and evolution has also been made possible due to WGS. This research applies comparative genomics, population genomics and data science approaches to whole …

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. …

Using Multi-Omics Approaches To Study Flowering Time And Fruit Development In Perennial Fruit Species, Jiali Yu

Doctoral Dissertations

Perennial fruiting plants coordinate their reproductive activities with seasonal changes in the temperate climates, with a pattern of bud set, dormancy establishment, fulfillment of chilling, flowering, fruit set, and fruit ripening. These processes have been optimized for the production of orchard plants that reliably produce quality fruit for human consumption. The understanding of molecular controls of dormancy in fruit trees has grown rapidly in the past decade, however, the complex mechanisms remain largely unknown. This dissertation presents my findings on genetic and epigenetic changes in Prunus species from dormancy to flowering using transcriptomics and epigenomics approaches. First, I compared the …

Diagnosis And Distribution Of Florida Sand Darter, Ammocrypta Bifascia (Teleostei; Percidae), In The Flint River, Georgia, Camm C. Swift, Gregory R. Moyer, Christine E. Fallon, Brett Albanese

Southeastern Fishes Council Proceedings

Abstract: In 2013, we observed the presence of an undocumented Ammocrypta species in the lower Flint River, Georgia. The occurrence represents the first record of the genus in Georgia. Subsequent surveys at 24 sites, using seining or snorkeling, documented additional specimens from mainstem sites (n = 3) between Albany and Bainbridge and from Ichawaynochaway Creek (n = 5 sites), a large tributary to the Flint River. We used morphological and genetic data to identify specimens to species. Morphological examination included 23 morphometric and 8 meristic characters from fifteen specimens that were compared to specimens from Williams (1975). For genetic analyses, …

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 …

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. …