Life Sciences Commons^™

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, …

Yizhi Sun: Profile Of The Newest Chbc Faculty Member., Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Yizhi Sun, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.

Improving Glycemic Control Mechanisms By Electrical Muscle Stimulation, Jehu Narh Apaflo

Open Access Theses & Dissertations

Introduction: Neuromuscular electrical stimulation (NMES) has emerged as a promising intervention for improving metabolic health in sedentary individuals with overweight or obesity. Its capacity to induce muscle contraction without voluntary movement presents a viable alternative to traditional exercise, especially in mobility-limited populations. NMES may serve as a non-invasive alternative to traditional exercise, especially in high-risk populations who face elevated type 2 diabetes incidence linked to hyperglycemia, obesity, and inactivity. This study investigated the impact of NMES on glycemic control and metabolic health in a sedentary, predominantly Hispanic, overweight or obese population. Methods: This study examined the acute and long-term effects …

Characterization Of Glyt1 Expression And Glycinergic Circuits, Laura Patricia Montes

Open Access Theses & Dissertations

Glycine is one of the main inhibitory neurotransmitters in the central nervous system. Glycine is regulated by the glycine transporters 1 and 2 (GlyT1 and GlyT2, respectively) in the synaptic cleft. Both transporters participate in glycinergic inhibitory neurotransmission. Moreover, GlyT1 also participates in glutamatergic excitatory neurotransmission. GlyT2 is devoted to caudal regions of the brain and is used as a marker for glycinergic neurons. In contrast, GlyT1 is expressed across the brain in the rostrocaudal axis and is highly associated with GlyT1-positive glial cells. Data from our laboratory has identified GlyT1-positive neurons in the rodent brain. Therefore, we hypothesize that …

Temporal Partitioning And Coexistence Among Four Sympatric Felid Species In The Northern Jaguar Reserve, Kylie Marie Rezendes

Open Access Theses & Dissertations

Coexistence among sympatric carnivores is shaped by behavioral strategies that mediate competition and mortality risk in heterogeneous landscapes. Understanding how sympatric carnivores, such as felids, use space and time in relation to one another requires models that account for both spatial and temporal overlap across landscapes. Models incorporating time-to-event probabilities provide a powerful framework for detecting behavioral dynamics across shared landscapes. This study evaluated the spatiotemporal responses of two apex predators â?? the jaguar (Panthera onca) and mountain lion (Puma concolor) - and two mesopredators - bobcat (Lynx rufus) and ocelot (Leopardus pardalis) - across five years of camera trap …

Environmental Drivers Of Vegetation Dynamics In Constructed And Natural Wetlands Of The Chihuahuan Desert, Enrique David Garcia

Open Access Theses & Dissertations

Desert wetlands are critical ecosystems that provide water, food, and habitat for many different species at different trophic levels. Additionally, they have the capacity to recharge aquifers, control floods, and purify water, among others. Unfortunately, they have been facing multiple environmental challenges due to different human activities, sometimes with disastrous consequences. There is an urgent need to better understand the structure and function of wetlands of different types and in different biomes in order to conserve, restore, and even create them so we can continue to obtain all the ecological services they provide. In this dissertation, I investigated how environmental …

Evaluation Of A Forest Restoration Strategy On Small Mammals In Southern Pine Ecosystems, Gage R. Grantham, Jessica L. Glasscock, Christopher M. Schalk, Kathryn R. Kiid, Reuber Antoniazzi

Electronic Theses and Dissertations

Industrial forestry replanted historic native pine forests (e.g., longleaf pine [Pinus palustris] and shortleaf pine [Pinus echinata]) to homogenous, high-density plantations consisting of native off-site species (e.g., loblolly pine [Pinus taeda]) after intensive harvesting for wood products. The contemporary forest structure that remains, consisting of off-site overstory compositions, can potentially serve as an ecological bridge to facilitate a gradual transition to a more desirable canopy species, thereby conserving biodiversity and ecosystem function. Understanding disturbance-sensitive small mammal communities from restoration strategies (retention) can help achieve long-term management goals for ecosystem conservation across larger scales. I …

An Evaluation Of Key Components Of Natural Resource Camps, Undergraduate Persistence And Success In Natural Resources, Brandy Bishop

Electronic Theses and Dissertations

This study explores the key components that connect natural resource camps, undergraduate persistence, and overall success through gainful employment within the natural resource industry. The aim of this study was to assess early interest and attitudes towards natural resource career pathways and how education interventions shape students’ career outcomes thus leading to overall success. A longitudinal mixed method design was used combining Conservation Careers Camp survey data (n = 39) with institutional records for Forestry majors (n =655) in the Arthur Temple College of Forestry and Agriculture on the Stephen F. Austin State University campus. Quantitative data was analyzed through …

Stand Strucuture Of Planted Stands In Storm-Water Retention Basins, Jason Lanza

Electronic Theses and Dissertations

Trees assist in stormwater retention basin functionality as efficient sources of water removal, and determining stand structure and leaf area of forests can be a measure of their effectiveness. The structure of forest stands on these basins managed for runoff mitigation has received little attention. We investigated the structure and species composition/diversity (tree and herbaceous) of planted, managed stands and naturally regenerated stands on stormwater retention basins managed by Harris County Flood Control District in Harris County, Texas. We determined stand structure variables (trees per hectare, basal area per hectare, quadratic mean diameter, relative density, average tree height, and percent …

Effect Of Marination And Storage Time On The Properties And Meat Quality Of Broiler Breast, Mayra Mabel Herrera Rivera

Graduate Theses and Dissertations

Abstract The poultry industry has implemented numerous methods, as marination and aging, to improve meat quality and satisfy consumer demands. Three experiments were developed to assess the effects of vacuum tumble marination and aging on the proteins of chicken breast. These experiments utilized 0.75 % sodium chloride, 0.45 % phosphate, and water in a marinade. In experiment one, 270 fillets were allocated into six treatment groups, each comprising 45 fillets. Six days of storage time were used, marinating and storing the fillets in each group at a temperature of 4°C. Following each day of storage period, the fillets underwent a …

Associations Of Variation In Mtdna With Feed Efficiency In Beef Cattle And The Evaluation Of Transcriptomic Changes In Fetal Kidney Due To Hydrallantois, Lauren Elizabeth Seier

Department of Animal Science: Dissertations, Theses, and Student Research

Project 1 focused on the central role that mitochondria play in ATP production, highlighting that variation within the mtDNA may influence feed efficiency. Variation in the mitochondrial genome was uncovered, and associations with feed efficiency in beef cattle were identified. Growth and feed intake phenotypes, as well as low-pass sequencing, were collected on beef steers across two populations. Protein coding variants were identified and used to classify animals into mitochondrial haplotypes. A linear mixed model was employed, which detected a significant association between mitochondrial haplotype and DMI. A significant haplotype with a variant in Complex I was associated with reduced …

The Effect Of Diet Formulations Containing Different Protein Sources On Energy And Nitrogen Utilization In Lactating Jersey Cows, Kortney Ann Harpestad

Department of Animal Science: Dissertations, Theses, and Student Research

It is well understood that lactating dairy cows require metabolizable protein (MP) for milk yield and milk protein synthesis. Diets with conventional feed sources like corn and soybean meal (SBM) may not sufficiently meet all MP and amino acid (AA) requirements so supplementation with more rumen undegradable protein (RUP) rich feeds or rumen-protected AA can be fed to support animal performance. The growth trajectory of biofuels has resulted in dramatic increases in the production of feeds like heat treated soybean meal (HTSBM). While the chemical composition of this product is understood, there is a need to better understand how HTSBM …

Authentication And Message Integrity Verification For Emerging Wireless Networks, Ebuka Philip Oguchi

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation presents a comprehensive body of research on authentication and message integrity verification for emerging wireless networks, focusing on secret-free and physical layer security techniques across diverse, challenging, and unconventional environments.

It comprises four first-author contributions that span underground wireless systems, over-the-air (OTA) channels, vehicular communications, and nanoscale molecular networks.

The first contribution, Soil-Assisted Trust Establishment for Underground Wireless Networks (STUN), introduces a physical-layer trust bootstrapping protocol that achieves authentication and message integrity without pre-shared secrets. Leveraging underground-to-air propagation laws and trusted relay nodes, STUN resists active signal injection attacks and demonstrates security comparable to the unbalanced oil and …

Impact Of Adoption Of Fall Armyworm And Stemborer Pest Control Practices On Maize Yields In Rwanda: A Multinomial Endogenous Switching Regression Approach, Vincent Gadamba Misango, Jonathan Makau Nzuma, Patrick Irungu, Menale Kassie

All Peer-Reviewed Publications

The use of push-pull technologies (PPT) as an alternative control method for fall armyworms and stemborer pests amongst maize farmers has recently received considerable global attention. However, the impact of adoption of PPT on the maize productivity remains largely unexplored. This study used a multinomial endogenous switching regression (MESR) to evaluate the impact of adoption of PPT on smallholder maize farmer's yields in Rwanda. The MESR model was estimated on a sample of 398 households operating 967 maize plots selected using a stratified random sampling technique. Overall, 25, 20, and 14 percent of the households used traditional methods, PPT and …

Heterogeneous Yield Effects Of Cover Crop Adoption In U.S. Corn And Soybean Systems, Ethan Kendall

Graduate Theses and Dissertations

Identifying the conditions where cover crops will succeed or fail is crucial for advancing conservation agriculture. Cover crops have been widely accepted as a conservation practice that can improve soil health and might improve or stabilize crop yields, though these benefits are not consistent across different regions. This study examines how heterogeneous factors can shape the effectiveness of cover crops on corn and soybean yields across the United States. Using the National Commodity Crop Productivity Index (Index) to measure soil productivity, this study examines how cover crop impacts vary across different levels of soil quality. A county level, 16- year …

Bifunctional Fusion Protein Pdl1sfv/Micae For Cancer Immunothearpy, Junyi Li

All Dissertations

Cancer immunotherapy has highlighted the importance of immune checkpoint blockade and innate immune cell engagement in battling tumor-mediated immune suppression in the past few decades. However, with cancer development, advanced tumors are often found to develop resistance towards single-target immunotherapy due to the complexity of the immunosuppressive mechanisms within the tumor microenvironment (TME). To address this, we developed a novel bifunctional fusion protein, PDL1sFv/MICAe, which combines the tumor-targeting capability of an anti-PDL1 single-chain variable fragment (sFv) with the NK cells immunostimulatory properties of the MICA extracellular domain.

In vitro functional assays revealed that PDL1sFv/MICAe significantly enhanced cytotoxicity towards natural killer …

Evolutionary Biomechanics In Cetartiodactyla: Impacts Of Ecological Shifts On Bone Material Properties And Control Surface Morphology, Danielle S. Adams

All Dissertations

Extreme ecological transitions expose organisms to novel selective pressures that can reshape morphology and performance. This dissertation investigates how the transition from land to water has influenced form and material properties in cetaceans (whales, dolphins, and porpoises), a clade that has undergone dramatic morphological and physiological adaptations to a fully aquatic lifestyle. I integrate comparative morphology, material property testing, and phylogenetic analyses, to explore how ecological demands, particularly related to foraging mode and prey detection, have shaped multiple aspects of cetacean morphology and function. Using nanoindentation and microCT, I measured elastic modulus and bone density of the skull and mandible …