Life Sciences Commons^™

Commodity Diversification, Technological Innovation, And Market Dynamics: Insights Into Beef Cattle Production And Feeder Cattle Basis In The United States, Nik Berg

All Theses

The beef cattle industry plays an important role in the agricultural economy, contributing to both domestic food supply and global trade. The United States is one of the world's largest producers of beef, with production systems varying widely across regions largely due to differences in available resources and market structures. Market conditions, technological advancements, and policy interventions shape the way producers operate, making research into these factors essential for both industry stakeholders and policymakers.

Producers are continuously adapting to changing economic conditions, environmental challenges, and evolving consumer preferences. By analyzing these factors, researchers can provide insights to support informed decision-making …

Post-Harvest Storage Of Fuzzy Cottonseed: Quality, Airflow Modeling, And Energy Use, Elijah T. Porter

All Theses

Fuzzy cottonseed is a valuable byproduct of the cotton ginning process. When cottonseed exits the cotton gin, it often retains high temperatures and moisture contents. Once in a storage facility, the cottonseed needs to be conditioned for safe storage. The overall objectives of this study were to analyze quality changes in cottonseed according to storage conditions, determine the airflow resistance properties of fuzzy cottonseed, develop a computational fluid dynamics (CFD) model of a representative cottonseed storage facility, and analyze cottonseed aeration fan strategies, runtimes, and costs. Changes in quality dictate the allowable storage time for cottonseed and are impacted by …

Life Cycle Assessment Of The Cultivation Of Lettuce In A Hydroponic System Using The Nutrient Film Technique, Raquel Jordan

All Theses

Hydroponic systems are an emerging method of soilless crop cultivation typically done inside a greenhouse where nutrients are delivered dissolved in water rather than being supplied from the soil. Potential benefits of hydroponic systems include reduced irrigation requirements, higher crop yield per area, and the ability to grow crops year-round in nontraditional areas such as urban settings, cold climates, and sites with contaminated soil. However, hydroponic systems tend to have high energy requirements for lighting and climate control, which can yield significant environmental impacts. To explore the environmental impacts of cultivating lettuce in a nutrient film technique (NFT) hydroponic system, …

The Effects Of Incremental Application Of Chemical Defoliants On Cotton Fiber Quality, Aashish Karki

All Theses

Leaf shedding is a natural process as cotton matures; however, this does not synchronize with harvest timing; therefore, defoliants are used to remove these leaves and improve harvestability of the bolls. A tractor-mounted boom sprayer is typically used to apply defoliants. However, this approach results in low penetration to the bottom canopy, poor defoliation, and, consequently, lower fiber quality. An autonomous robotic spraying system equipped with pulse width modulation technology enables targeted side-spraying of defoliants, overcoming the limitations of conventional over-the-top applications. However, limited information on staggered defoliation timing and its effect on cotton fiber quality is available. Thus, field …

Association Between Gene Family Expansion And The Rapid Diversification Of Pleurocarpous Mosses, Meredith A. Cobb

All Theses

Mosses are the second most species-rich group of land plants. They represent a critical group for understanding the evolution and diversity of land plants. Mosses comprise two major groups, acrocarps and pleurocarps. Despite having a more recent evolutionary origin than acrocarps, pleurocarps are exceptionally diverse. The difference in species richness reflects a rapid species diversification, roughly coincident with the origin and diversification of flowering plants. The speciation events giving rise to pleurocarp diversity happened so rapidly, making it historically difficult to produce strongly supported phylogenies with which to test evolutionary hypotheses. One such hypothesis is whether large-scale changes at the …

Small Stream Restoration In The Piedmont Of South Carolina: Comparison Of Evaluation Tools And Water Quality’S Effects On Salamanders, Camryn Lachica

All Theses

For many years, the United States Army Corps of Engineers (USACE) used the Guidelines for Preparing a Compensatory Mitigation Plan worksheets to guide pre-restoration evaluation and determine post-restoration mitigation credits in South Carolina. Recently, the USACE in South Carolina transitioned to the Stream Quantification Tool (SQT), which provides a more comprehensive assessment framework. Our first objective was to compare these assessment methodologies across different landscape types to determine what the SQT adds to mitigation calculations that were not considered in prior worksheets. We evaluated 16 streams in the Piedmont of South Carolina, with four replicates each of forested, suburban, urban, …

3,5-Dihydroxy-4-Isopropylstilbene (Tapinarof) Is A Partial Aryl Hydrocarbon Receptor Agonist In Fish, Conner A. Dicks

All Theses

The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that is essential in regulating development, immune homeostasis, and drug and xenobiotic metabolism. Activation of the AHR by specific ligands results in its translocation to the nucleus where it induces a myriad of gene products, including cytochrome P450 (CYP) drug metabolizing enzymes (e.g., CYP1A1) and other components of the chemical defensome, as well as inflammatory control. Interestingly, the AHR can bind a wide variety of endogenous and xenobiotic ligands which are able to induce unique downstream effects dependent on cell type, inflammatory context, and ligand stability. The AHR is …

Using Livestreaming Technology To Answer Novel Questions About The Behavior And Physiological Ecology Of The Prairie Rattlesnake (Crotalus Viridis), Max C. Roberts

Master's Theses

Recent advances in remote monitoring technology are opening up new opportunities for developing innovative natural history and biological research methodologies. In particular, the emergence of livestreaming camera technology has made recording remote video of wild and secretive animals much easier and made it possible to collect data at extremely fine temporal resolutions. In 2024, Project RattleCam launched a livestreaming camera at a Prairie Rattlesnake (Crotalus viridis) den in Colorado. The goal of this work was to study Prairie Rattlesnake behavior 24-7 throughout the species’ active season with minimal human disturbance. Additionally, I used this system to study the …

Investigating Rattlesnake Social Networks And Improving Their Public Image Through Unobtrusive Technologies And Community Science, Owen M. Bachhuber

Master's Theses

While technology is often blamed for humans’ increasing disconnect with nature, it can also serve as a tool to facilitate empathy and conservation action for wildlife. Snakes are among the most feared animals on the planet, though their understudied social interactions provide opportunities to make scientific discoveries and change public perceptions. Project RattleCam was founded as a camera trap project in 2021 and launched the first off-grid livestream on a den of wild Prairie Rattlesnakes (Crotalus viridis) in 2024. Both camera types captured hundreds of Prairie Rattlesnakes gathering in the summer as they prepared to give birth to pups before …

Impact Of S-Phase Kinase Protien 2 Blockades On Hematopoetic Stem Cell Metabolism, Nicole Elmaraghy

Electronic Theses, Projects, and Dissertations

Hematopoietic stem and progenitor cells (HSPCs) quiescence is vital for the success of bone marrow transplantation, as it preserves long term self- renewal and prevents premature exhaustion (Takubo et al., 2013; Wilson et al., 2008). However, bone marrow transplant (BMT) failure remains a clinical challenge, often due to lack of long-term engraftment and insufficient stress reliance. Both of these characteristics are tightly linked to disrupted stem cell quiescence and metabolic imbalance (Anso et al., 2017; Vannini et al., 2016). One key player is S-phase kinase protein (SKP2), an E3 ubiquitin ligase that targets cell cycle inhibitors, like p27, for proteosome …

Six Lineages Of Cercospora Are Responsible For Cercospora Leaf Blight And Purple Seed Stain On Soybean In Brazil, Leandro Luiz Borges, Thiago Freitas Ferreira, Marina Garofalo Lana, Isabela Delpupo Caliman, Newton Deniz Piovesan, Burton H. Bluhm, Luiz Orlando De Oliveira

Plant Pathology Faculty Publications and Presentations

The genus Cercospora is widely distributed and causes foliar diseases, including those affecting soybean. Cercosporoid species exhibit high intraspecific variation, and the lack of distinct morphological features has led to host plant association becoming a key criterion for species delimitation. Recently, in addition to C. kikuchii, other species such as C. cf. flagellaris, C. cf. sigesbeckiae, and C. cf. nicotianae have been linked to Cercospora Leaf Blight (CLB) and Purple Seed Stain (PSS) in soybean. In this study, phylogenetic and phylogeographic analyses were used to identify six Cercospora lineages responsible for causing CLB and PSS across Brazil. A total of …

Activation And Suppression Mechanisms Of The Nrg1 Helper Nlrs, Yu-Ru Wang, Ruize Zhang, Daowen Wang, Yong Wang, Zheng Qing Fu

Faculty Publications

No abstract provided.

Cg18562578 Methylquant Assay For The Discrimination Of Monozygotic Twins, Amber P. Chauca

Student Theses

Monozygotic (MZ) twins have identical DNA, making traditional profiling methods insufficient in their discrimination. However, MZ twins can be differentiated by their levels of DNA methylation. Our research group previously developed a methodology to detect cg18562578 DNA methylation levels in MZ twins based on a two- step PCR approach and a cg18562578 MethylQuant Assay. That study generated data for only 64% of the samples it investigated, and showed a discrimination power of 77% to discriminate between MZ twins. Here, we used the same methodology but a different approach to determine DNA methylation in 73 previously unsuccessful twin pairs. We diluted …

Computational Frameworks To Unravel The Immune Landscape, Shan He

Dissertations and Theses (Open Access)

Recent advances in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, face challenges such as resistance and immune-related adverse events, partly due to our limited understanding of the immune signaling pathways. While high- throughput genomic data provide unprecedented resolution into these immune pathways, their full potential is limited by the lack of well-annotated, context-specific immune gene sets. To address this need, I developed a workflow to construct immune gene sets by integrating RNA- seq datasets and performing decomposition. Using this approach, I constructed 28 immune- specific gene sets from 83 bulk RNA-seq datasets and 12 Natural Killer (NK) …

Resolving Intra-Tumoral Heterogeneity Of Breast Cancer Using Single-Cell Multi-Omics, Yun Yan

Dissertations and Theses (Open Access)

Breast cancer is a highly heterogeneous disease characterized by diverse genetic, transcriptional, and epigenetic landscapes. Understanding how intra-tumoral heterogeneity (ITH) influences therapeutic response and drives tumor evolution remains a central challenge in cancer biology. Here, we leverage single-cell multi-omics technologies to dissect the cell states and gene expression programs underlying breast cancer heterogeneity, with a focus on triple-negative breast cancer (TNBC) and estrogen receptor-positive (ER+) breast cancer.

In the first part, we applied single-cell RNA sequencing and spatial transcriptomics to profile over 400,000 cells from 101 treatment-naïve TNBC patients. We identified 4 archetypes at the patient level and 13 metaprograms …

Use Of The Protein Misfolding Cyclic Amplification For Food Safety And Drug Discovery, Maria R. Benavente Garcia-Huidobro

Dissertations and Theses (Open Access)

Prion diseases are fatal neurodegenerative disorders caused by the misfolding of the normal prion protein (PrP^C) into its infectious form (PrP^Sc). While the zoonotic potential of chronic wasting disease (CWD) remains uncertain, the presence of prions in food products raises public health concerns. Additionally, therapeutic strategies for prion diseases remain limited. This thesis presents a methodological exploration of the Protein Misfolding Cyclic Amplification (PMCA) technique to address these challenges in two key areas: (1) detecting CWD prions in processed meats subjected to common cooking procedures, and (2) identifying potential anti-prion compounds through a high-throughput PMCA adaptation. …

Predicting Genetic Interactions Using Functional Interaction Networks, Iulia Veronica Gheorghe

Dissertations and Theses (Open Access)

Mapping genetic interactions is central to understanding cellular systems and identifying therapeutic vulnerabilities, particularly in the context of cancer. Among these interactions, synthetic lethality, where simultaneous loss of two genes is lethal but loss of either alone is tolerated, offers a powerful framework for selectively targeting tumor-specific dependencies. In model organisms like S. cerevisiae, comprehensive double-knockout screens have revealed detailed genetic interaction maps, enabling systems-level insights into pathway structure, gene function, and cellular organization. Replicating this achievement in human cells, however, is complicated by the scale and complexity of the human genome. Recent advances in genome-wide CRISPR knockout screening have …

Structural Functional Investigation Of Hap40, Amanda M. Solbach

Dissertations and Theses (Open Access)

STRUCTURAL FUNCTIONAL INVESTIGATION OF HAP40

Amanda Marie Solbach

Dissertation Advisor: Sheng Zhang, Ph.D.

Huntington’s disease (HD) is a devastating neurodegenerative disorder caused by an expanded CAG trinucleotide repeat in the Huntingtin (HTT) gene, resulting in a mutant huntingtin (mHTT) protein with an elongated polyglutamine tract. While the genetic basis of HD is well established, the mechanisms underlying mHTT toxicity and its impact on cellular function remain incompletely understood. Recent discoveries implicate Huntingtin-associated protein 40 (HAP40) as a critical regulator of HTT stability and intracellular function. However, the physiological and pathological significance of this interaction has not been fully explored.

This …

Investigating The Role Of The Lysine-Specific Demethylase 4c In Pancreatic Ductal Adenocarcinoma, Mennatallah Shaheen

Dissertations and Theses (Open Access)

Deregulation of proteins involved in chromatin regulation is common in pancreatic ductal adenocarcinoma (PDAC). Lysine demethylase 4C (KDM4C) is one of the chromatin modifying proteins frequently overexpressed across multiple solid cancers and is linked to chromatin instability, increased cell proliferation, and enhanced stem cell-like behavior. We observed upregulation of KDM4C protein in a panel of human PDAC cell lines and patient samples compared to non-neoplastic controls. CRISPR/Cas9-mediated deletion of KDM4C in human and murine PDAC cells reduced proliferation, clonogenicity, and increased survival of orthotopically implanted murine PDAC allografts. Transcriptomic and proteomics analyses revealed that loss of KDM4C in both human …

Long-Chain Fatty Acids Promote Candida Albicans Gut Colonization By Restructuring The Fungal Cell Surface, Musfirat Shubaita

Dissertations and Theses (Open Access)

Long-chain fatty acids promote Candida albicans gut colonization by restructuring the fungal cell surface

Musfirat Shubaita, BS

Advisory Professor: J. Christian Perez, Ph.D.

The yeast Candida albicans is a facultative anaerobe residing in the human digestive tract. Although fungal genetic determinants of mammalian host colonization have been identified, little is known about signals and molecules in the intestinal environment that influence C. albicans proliferation. Previously unpublished data from the Perez lab showed that oleic acid, one of the most abundant long-chain fatty acids in nature, promotes C. albicans colonization of the murine intestine. The goal of this research is to …

Studies Of The Mechanisms Of Reverse Signaling By Cd40l, Barbara M. Nassif Rausseo

Dissertations and Theses (Open Access)

CD40 ligand (CD40L) is a transmembrane protein expressed on activated CD4 T cells, traditionally known for its role in forward signaling by engaging CD40 on antigen- presenting cells to promote immune activation. While this pathway is well characterized, there is evidence that CD40L also mediates reverse signaling, acting as a signaling receptor on T cells which enhances T cell function. However, the extent, consequences, and mechanism of CD40L-mediated reverse signaling in CD4 T cells remain poorly defined. This dissertation investigates the mechanisms and effects of CD40L reverse signaling on T cell function using both primary human T cells and the …

Microbial Metabolite Regulation Of Microglial Ahr Signaling In Alzheimer’S Disease, Ghalya E. Alrousan

Dissertations and Theses (Open Access)

Introduction: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by amyloid-β plaque accumulation, neuroinflammation, and cognitive decline. Recent evidence suggests that systemic factors, particularly the gut microbiota and its metabolites, play a significant role in shaping brain immune responses, including microglial activation. However, the mechanisms linking gut dysbiosis to microglial dysfunction in AD are poorly understood. The aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor responsive to tryptophan metabolites, has recently gained attention as a key regulator of neuroinflammation and microglial function. I hypothesize that the loss of beneficial microbial AHR ligands, specifically indole derivatives, during aging and AD …

Ecomorphological Diversification Of Tooth Complexity In The Oral Jaws Of Marine Teleostean Fishes, Keiffer L. Williams

All Dissertations

Teeth are essential biological tools that function as a direct interface between predator and prey, thus providing essential insights into the evolutionary history and ecological diversity of vertebrates. Historically, studies on vertebrate dentitions have been qualitative and focused on mammals. More recently, quantitative methods have been developed that can reliably measure tooth surface complexity. These methods have been applied across both mammals and saurian reptiles to test for correlations with diet, leading to the conclusion that herbivorous species generally possess higher overall tooth complexity than any other dietary group. Surprisingly, the relationship between tooth complexity and diet in the most …

From Cities To Ranches: Assessing Public Support For Jaguar (Panthera Onca) Conservation And Livestock Predation In Colombia, Luz Angelica Solano

All Dissertations

Jaguars are among the most emblematic large carnivores worldwide. Nonetheless, the species has declined by 25% in less than 25 years and their range has been reduced by 55%, approximately, primarily due to habitat loss from increasing agricultural development, retaliatory killings from human-jaguar conflict, and overhunting of their natural prey. Given the anthropogenic nature of these threats, developing effective coexistence strategies and public support for jaguar conservation are increasingly urgent for the continued persistence of this species. I conducted a scoping review to assess trends and gaps in the existing peer-reviewed literature, grey literature, and news articles related to human-jaguar …

Interactions Of Biorational And Synthetic Dmi Fungicides For Control Of Fruit Diseases, Johanna Wesche

All Dissertations

Biological fungicides are increasingly investigated as sustainable alternatives to synthetic fungicides in fruit crop protection. This dissertation examines the interactions between two commercial biological fungicides, Bacillus subtilis AFS032321 (Theia) and metabolites of Pseudomonas chlororaphis AFS009 (Howler EVO); and demethylation inhibitor (DMI) fungicides, with a focus on compatibility, synergistic potential, and resistance implications. In vitro assays revealed that commonly used DMI fungicides difenoconazole, metconazole, tebuconazole, and propiconazole inhibited vegetative growth of B. subtilis at concentrations above 50 µg/ml, whereas mefentrifluconazole promoted colony expansion. Under controlled conditions, lesion development on detached fruit was inhibited synergistically when Theia was combined with the growth-promoting …

Improved Rumen Microbiome Interpretation Via Empirical Filtration Derived From Known Mock Microbiomes, Wesley A. Tom

School of Biological Sciences: Dissertations, Theses, and Student Research

The rumen microbiome plays a critical role in ruminant health and performance. As a consequence, many studies investigate microbial community composition using 16S rDNA based sequencing. As such, data quality and data filtering are critical to accurately identify microbial community composition. In this study we use mock communities to empirically select data filtering parameters to reduce artifact populations and compared the effect of filtering using different bioinformatic pipelines using rumen bacterial community data. The filtering parameters identified provides consistent estimates of rumen microbial diversity, regardless of bioinformatic pipeline utilized and provides a more accurate view of microbiome structure and composition. …

Comparison Of Sodium Deoxycholate And Sodium Dodecyl Sulphate In Milk Fat Globular Membrane Protein Recovery, Manujaya W. Jayamanna Mohottige, Angela Juhasz, Mitchell G. Nye-Wood, Katherine A. Farquharson, Utpal Bose, Michelle L. Colgrave

Research outputs 2022 to 2026

This study aims to investigate detergent sodium deoxycholate (SDC) and sodium dodecyl sulphate (SDS) treatments, with a focus on each detergent's ability to enhance the extraction of immune-related proteins from camel milk fat globular membrane. Milk was separated into cream and skimmed milk. The cream was then treated using 0.4 % SDS, 2 % SDC, 6 % SDC or 10 % SDC. Extracted proteins were trypsin digested and analysed using liquid chromatography-tandem mass spectrometry. Higher SDC concentrations (6 % and 10 %) resulted in marginal improvements in protein identification (44 unique protein groups). Protein abundance distributions showed minimal differences across …

Generation Of Ph-Responsive Starch And Alginate-Pectin Hydrogels Using Coaxial 3d Food Printing: The Release Of Methylene Blue, Que-Anh Truong-Le, Matthias D.R. Lenie, Ali Ubeyitogullari

Food Science Faculty Publications and Presentations

This article presents the development of a 3D food printing (3DFOODP) system incorporating a core-shell structure to encapsulate a model compound, methylene blue (MB). A coaxial nozzle configuration was employed to fabricate 3D-printed samples, featuring a starch core and a pH-responsive alginate-pectin (Al-P) shell. The optimal 3D printing conditions were determined as 11 wt% starch as the core along with 2 wt% Al-P with 0.02 M CaCl2 as the shell at printing temperatures of 95 degrees C and ambient temperature (23 degrees C), respectively. The overall 3D printability at this condition was 98 %, closely matching the digital 3D design. …

The Role Of Androgen Receptor And B2/Alu Sine Rna Interaction In Hippocampal Dendritic Development, Troy A. Richter

Graduate Doctoral Dissertations

Once dismissed as “junk”, transposable elements have recently gained recognition for their regulatory roles, especially in the brain. During development, circulating androgens promote proper morphological development of hippocampal neurons. We and others have shown that murine B2 SINE RNA is a regulator in the rodent hippocampus. It is unknown, however, if B2 is necessary for the proper development of hippocampal neurons. This dissertation investigates the role of murine B2 in the development of primary hippocampal neurons in combination with androgen treatment. We first examined the role of ALU SINE and androgen receptor in a prostate cancer cell model and found …

Molecular And Clinical Insights Into Role Of Gper In Hepatocellular Carcinoma (Hcc), Hossain Ahmed

Theses and Dissertations

Metabolic dysfunction–associated steatotic liver disease (MASLD), encompassing stages from steatosis (MASLD) to steatohepatitis (MASH), cirrhosis, and hepatocellular carcinoma (HCC), is the most prevalent chronic liver disease worldwide, yet molecular markers of progression remain limited. The G protein–coupled estrogen receptor (GPER), a non-genomic estrogen receptor with metabolic and anti-inflammatory roles, emerges as a candidate regulator in hepatic pathophysiology. In this Dissertation thesis, we have delineated for the first time clinicopathological assessment of liver biopsies across MASLD stages revealing a robust inverse correlation between GPER expression and disease severity. Higher GPER levels in early MASLD associated with favorable metabolic and biochemical profiles, …