Digital Commons Network^™

Self-Assembling Rna Nanostructures Are Highly Sensitive To Environmental Conditions, Jordan Aposhian, Surya Pratap S. Deopa, Scott Horowitz, Joseph D. Yesselman

Chemistry and Biochemistry: Faculty Scholarship

Recent developments in RNA nanotechnology have led to an increase in the design of specific, higher-order RNA structures, which will ultimately be used in drug delivery and immunomodulation applications. As researchers create RNA nanostructures with the intention of making them a standard tool in molecular biologists' toolkits, further investigation is required into the robustness of RNA designs. Primarily, in what different molecular contexts are the designed and intended nanostructures stable? In this work, we show that RNA nanostructure self-assembly is highly sensitive to environmental conditions by using second-order right-angle light scattering. While a test RNA hexagonal grid nanostructure forms correctly …

A Genetic Interaction Between Ded1 And Hat1 In Saccharomyces Cerevisiae Reveals A Role For Hat1p In Cytoplasmic Rna Granule Accumulation, Audrey J. Panko, Aidan Winters, Nicholas R. Rothbard, Angela K. Hilliker

Biology Faculty Publications

Ded1p is an essential translation initiation factor that interacts with and is modulated by eIF4F. Ded1p also promotes the assembly and disassembly of stress granules, which contain nontranslating mRNAs and translation initiation factors. As Ded1p affects both mRNA storage and translation initiation, regulation of Ded1p's function may affect whether mRNAs are translated or localized to cytoplasmic RNA granules. To identify regulators of Ded1p in Saccharomyces cerevisiae, we screened for overexpression suppressors of the severe growth defect conferred by high levels of Ded1p. We found that overexpression of HAT1, a lysine acetyltransferase, can suppress the growth defect conferred by …

Macroinvertebrate Community Dynamics In A Recovering, Hypersaline Estuary, Catherine M. Eckert, Claudia A. Tamez, Erin E. Easton, David Hicks

School of Earth, Environmental, & Marine Sciences Faculty Publications

The Bahia Grande is a 6,500—acre tidal basin located at the southernmost tip of Texas. Tidal flow into this coastal estuary was cut off in the 1930s, causing the basin to dry up for ~70 y. A pilot channel connecting the Bahia Grande to tidal waters was constructed in 2005, allowing flooding of the basin to occur. Throughout the period reported herein (2005–2019), the system remained characterized by persistent spatial and temporal episodes of extreme hypersalinity (>70)—a critical factor influencing estuarine community composition and driving key ecological processes. With additional rehabilitation actions forthcoming, characterization of the estuary is essential …

Regulation Of Chromatin Remodeling By The Post-Hsa Domain Of Brg1, A Subunit The Baf Atp-Dependent Chromatin Remodeling Complex, Min Sze Ewe

Theses & Dissertations

The ATP-dependent chromatin remodeler BAF complex regulates nucleosome positioning, chromatin accessibility, and tissue specific gene expression. Its catalytic subunit, BRG1, contains several regulatory domains including the post-HSA region, proposed to modulate ATPase activity. Multiple cancer-associated mutations map to these regulatory regions underscoring their importance, yet the precise role of the post-HSA region in chromatin remodeling remains poorly understood.

To investigate the function of the post-HSA domain, we ectopically expressed FLAG-tagged BRG1 with post-HSA deletion (Δpost-HSA BRG1) in mouse embryonic stem cells. Western blot analysis confirmed expression of the mutant protein. To determine the effects of mutant protein expression on chromatin …

Exposures, Protections, And Barriers: Advancing Understanding Of Agricultural Worker Health, Alexandra A. Farfalla

Theses & Dissertations

Farming is a hazardous occupation. Exposures are multifactorial, variable, and shaped by overlapping tasks, environments, and social contexts. This dissertation aimed to illustrate the complexity of agricultural exposures and the barriers to protective practices through three complementary studies.

The first study examined co-exposures to solvents and noise as risk factors for hearing loss (HL) among 7,495 farmers and ranchers in a 7-state region. Results indicated nearly 60% of co-exposed participants reported hearing loss, with an adjusted odds ratio nearly six-fold (OR=6.03, [4.67-7.78]) for moderate/severe HL. This work highlights the importance of recognizing chemical exposures as a modality in HL in …

Single-Nucleus Multiomics Reveals The Disrupted Regulatory Programs In Three Brain Regions Of Sporadic Early-Onset Alzheimer’S Disease, Andi Liu, Citu Citu, Nitesh Enduru, Xian Chen, Chia-Hao Tung, Tirthankar Sinha, Sofia E Sepulveda, Astrid M Manuel, Damian Gorski, Brisa S Fernandes, Meifang Yu, Paul E Schulz, Lukas M Simon, Claudio Soto, Zhongming Zhao

Faculty, Staff and Student Publications

Sporadic early-onset Alzheimer’s disease (sEOAD) represents a substantial but less-studied subtype of Alzheimer’s disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of nine individuals with or without sEOAD. Comprehensive analyses were conducted to delineate cell type–specific transcriptomic changes and linked candidate cis-regulatory elements (cCREs) across brain regions. We prioritized eight conservative transcription factors in glial cells in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in regulating sEOAD-associated genes. Moreover, we identified the top 25 altered intercellular signaling between glial cells …

Enhancing Public Health Strategies: Addressing The Rsv Burden In Alabama Through Clinical Treatment, Community Prevention, And Surveillance Approaches, Martha K. Findley Roper, Jennifer S. Dawson

Journal of Public Health in the Deep South

Introduction: Respiratory Syncytial Virus (RSV) is a highly contagious pathogen driving morbidity, hospitalizations, and economic burden. This review uses the epidemiological triad and National Wastewater Surveillance System data to assess transmission, viral load spikes in Alabama, and strategies for treatment and prevention.

Methods: A review of literature on supportive care, vaccination, monoclonal antibodies, and emerging nanomedicine was reviewed to evaluate strategies for reducing viral burden and complications.

Results: Trends from December 2024–January 2025 were assessed with National Wastewater Surveillance System data. Primary prevention includes immunization, hygiene, air quality maintenance, and early diagnostics. Tertiary care addresses complications such as secondary …

Elucidating The Role Of Hd5 In Colonic Wound Healing, Lavin Radiro

Student Scholar Symposium

Crohn’s colitis (CC), a subtype of inflammatory bowel disease (IBD), causes chronic inflammation in the large intestine, leading to malnutrition, diarrhea, and severe pain. Early and accurate diagnosis of CC is crucial, as misdiagnosis with ulcerative colitis (UC) can result in inappropriate treatment and worsened outcomes. The innate immune peptide human alpha-defensin 5 (HD5) is upregulated in CC but not in UC, suggesting a potential role in disease pathogenesis. Preliminary data from our lab indicates that HD5 impairs wound healing in colonic epithelial cells, but the molecular mechanisms remain unclear.

Hypothesis We hypothesize that HD5 increases RNA and protein levels …

Investigating The Potential Ability Of The Tlr4-Nf-Κb Axis To Reduce Aryl Hydrocarbon Receptor Expression In Intestinal Epithelial Cells, Gabriella Longoria

Student Scholar Symposium

Necrotizing enterocolitis (NEC) primarily affects premature infants and is characterized by intestinal necrosis, inflammation, and high mortality. Toll-like receptor 4 (TLR4)-induced apoptosis of intestinal epithelial cells is thought to drive NEC development. Upon binding bacterial lipopolysaccharide (LPS), TLR4 signaling activates NF-κB, leading to inflammatory gene expression. Indole-3-carbinol (I3C), a pro-ligand of the aryl hydrocarbon receptor (AhR), prevents NEC in a mouse model by downregulating TLR4, despite reduced AhR expression in NEC-affected intestines. However, the molecular mechanism behind the reduced expression of AhR in NEC is unclear. To model NEC in vitro, we treated IEC-6 enterocytes with LPS, which reduces AhR …

Investigating The Role And Mechanism Of Faecalibacterium Prausnitzii In Fatty Acid Metabolism And Obesity Using The Drosophila Melanogaster Model, Jackson Head, Whitley Whitehead

Student Scholar Symposium

The obesity epidemic has increased to enormous numbers with 890 million adults being classified as obese (BMI≥30). Obesity is of extreme concern as it is a comorbidity to coronary heart disease, type-2 diabetes, and cancer. Although obesity has classically been attributed to genetics and lifestyle, there is a growing interest in other factors, including the gut microbiome. Germ-free mice are resistant to weight gain even when placed on a high-calorie diet, establishing that metabolites produced by gut microbiota can dramatically inhibit metabolism. Here, we use Faecalibacterium prausnitzii, which has been previously shown to be reduced in obese individuals; however, …

Indole Improves Outcomes Of Cronobacter Sakazakii Infection In C. Elegans Through Ahr-1, Cayden Durrough

Student Scholar Symposium

Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease primarily affecting premature infants. Toll-like receptor 4 (TLR4)-mediated epithelial damage allows microbial translocation, triggering inflammation that can lead to sepsis and death. The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor, and AhR ligands have been shown to prevent NEC in a mouse model. Indole, an AhR ligand, has been reported to extend the healthspan of C. elegans, and we have shown previously it mitigates poor outcomes in wild-type worms infected with Cronobacter sakazakii (Cs), a bacterial pathogen linked to NEC. We hypothesized that C. elegans must express ahr-1, the ortholog …

Indole Treatment Of C. Elegans Rescues Cronobacter Sakazakii Induced Illness, Joshua Asselin

Student Scholar Symposium

Necrotizing enterocolitis (NEC) is a severe and often life-threatening inflammatory condition of the intestine primarily affecting premature infants. The opportunistic pathogen Cronobacter sakazakii (Cs) has been implicated in NEC. While activation of the ligand-dependent transcription factor aryl hydrocarbon receptor (AhR) has been shown to prevent NEC in a mouse model, its potential as a therapeutic target for established NEC remains unclear. We hypothesize here that the AhR ligand indole can reverse Cs-mediated illness in the model organism Caenorhabditis elegans. Our results demonstrate that exposure to live Cs, but not heat-killed Cs, significantly impaired worm motility, demonstrating Cs is an effective …

Exploring The Functional Role Of Neprilysin In Pi3k/Akt1 Signaling In Triple-Negative Breast Cancer, Ariadna Daniela Menjivar

Student Scholar Symposium

Our lab is investigating the protein Neprilysin (NEP) and its role in Triple-Negative Breast Cancer (TNBC). Previous bioinformatics data from Dr. Conway’s research indicated that in TNBC cells high in Neprilysin expression (HCC38), the PI3K pathway was the most active signaling pathway. This information suggests that Neprilysin is positively upregulating the PI3K pathway in this cell line. This is interesting given the fact that in the context of TNBC, Neprilysin has been shown to negatively regulate the PI3K/AKT signaling pathway. The PI3K/AKT pathway is the most commonly mutated pathway in breast cancer. AKT is the central mediator protein in this …

Levels Of Beta Catenin With Treatment Of Hd5 In Iec-6 Rat Cells, Audrey Birdwell, Josiah Stafford, Obaid Ashari, Emily Powell, Maryam Gerges, Maryam Mina

Student Scholar Symposium

Human Defensin 5 (HD5) is an antimicrobial peptide present in the small intestine that plays a role in gut homeostasis. We have been investigating the role of HD5 in colon cells, but research shows that HD5 levels in the small and large intestine vary significantly in Crohn's. Previous data from our lab suggests that HD5 leads to a decrease in wound healing and an increase in apoptosis in colon cells, we want to see if the same is true in the small intestine. So, we are investigating the effect of HD5 on expression of β-catenin, a key protein in the …

6ppd-Quinone In Middle Tennessee Waters: Assessing Ecological Impact, Andrew Davis Todd, Raphael Marquise Chandler, Kerolos Gerges Basalos, Denise Lori Loewinger

Student Scholar Symposium

This poster presents the dangers of a toxic chemical used on car tires that is entering aquatic ecosystems and harming fish populations.

Function Of Drosophila Melanogaster Domesticated Transposable Element Protein Dplg3 In Oogenesis And Total Fitness, Aron Herrera

2025 Fall Honors Capstones Projects - Archive

Transposable elements (TEs) are selfish DNA segments capable of self-replication and reinsertion within genomes, often harming hosts. Rarely, host genomes can adopt TEs and use their proteins for new cellular functions through molecular domestication. One example primarily expressed in Drosophila melanogaster ovaries is DPLG3. Previous Betrán Lab students generated DPLG3 loss-of-function flies and found that their ovaries misregulated one primordial and 14 testis-specific genes, leading to variable ovarian malformations. However, it is unclear when during oogenesis these misexpressions occur. We will extract RNA from non-rudimentary ovaries at early and late stages to generate cDNA for qRT-PCR analysis of three …

Impact Of Gas Supersaturation On The Development Of Gas Bubble Trauma In Paedomorphic Eurycea Salamanders, Trent Furr

Biology Theses

There are eleven species of paedomorphic lungless salamanders endemic to Texas. Of these, eight are considered threatened by the International Union for Conservation of Nature (IUCN). One of these, the Barton Springs Salamander (Eurycea sosorum), is found only in springs and aquifers in and around Austin, Texas. A large population of this species is found in Barton Springs, located in Austin, TX–where dissolved gas saturation has been measured as high as 134%. Morbidity and mortality events in Barton Springs Salamanders have been documented coinciding with periods of dissolved gas supersaturation. This study seeks to understand what environmental conditions lead to …

Understanding Pancreatic Islet Stress Responses And Developing Strategies To Improve Transplantation Grafts, Marlie Maria Maestas

Arts & Sciences Graduate Student Theses and Dissertations

Diabetes mellitus is a chronic metabolic disorder affecting millions worldwide, characterized by hyperglycemia resulting from defects in insulin secretion or action. While current treatments range from pharmacotherapy to experimental cell-based therapies, progress remains hampered by donor scarcity and an incomplete understanding of islet stress responses. This dissertation investigates cellular stress responses in pancreatic islets and strategies to improve stem cell-derived islet (SC-islet) transplantation. The first chapter provides an overview of diabetes pathophysiology, modeling approaches, and treatment options. In the second chapter, we use single-cell RNA sequencing to investigate cell-type-specific responses to diabetes-associated stress in primary human islets exposed to endoplasmic …

Rapid Detection Of Chicken Residues On Poultry Plant Surfaces Using Color And Fluorescence Spectrometry, Clark Griscom, Dongyi Wang, Corliss A. O'Bryan, Rimmo Room, Philip G. Crandall

Food Science Faculty Publications and Presentations

Color and fluorescence spectrometry were evaluated as rapid, objective tools for verifying the cleanliness of poultry-processing food-contacting surfaces contaminated with a model chicken solution across six common materials. Both techniques detected chicken residues at dilutions several orders of magnitude below human visual and olfactory thresholds, with stainless steel and blue plastic yielding the largest color differences between clean and contaminated states and fluorescence measurements remaining highly sensitive on all tested surfaces. Representative limits of detection were on the order of 1:50-1:100 dilution of chicken residue for color measurements on most surfaces and approximately 1:50 for fluorescence measurements, compared with human …

Transposable Element-Derived Mir-28-5p And Mir-708-5p: Exploring Potential Roles In Lung Cancer, Sergiu Chira, Cornelia Braicu, Stefan Strilciuc, George A Calin, Ioana Berindan-Neagoe

Faculty, Staff and Student Publications

Background: Transposable elements are normally silenced by epigenetic mechanisms; however, during malignant transformation, epigenetic alterations enable transposons to produce functional molecules like miRNAs. Among these, LINE-2 (L2) elements can generate miRNAs capable of regulating key genes, including tumor suppressors. Two L2-derived miRNAs, miR-28 and miR-708, have been linked to lung cancer, yet the mechanisms underlying their dysregulation remain poorly understood. Our study reveals how genomic context contributes to aberrant gene expression through comprehensive bioinformatic analyses.

Methods: Using bioinformatics analysis, we evaluated the expression of miR-28 and miR-708 in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) datasets from TCGA. …

Integration Of Algae In Buildings: Challenges And Opportunities, Marwa Said Saad, Mostafa Refaat, Ashraf Nessim

Mansoura Engineering Journal

Buildings produce 40% of energy-associated CO2 emissions and 35% of worldwide energy use which makes it one of the main factors of global warming. The use of bioactive materials on building façades is a creative way to address the aforementioned problems. The biotechnical potential of microalgae architecture to achieve net-zero energy architecture while simultaneously advancing ecological sustainability and occupant well-being has drawn attention. This paper aims to analyzing and investigating techniques of integration of algae in architecture showing the challenges and opportunities of this implementation. Analytical and Comparative analytical method were used in this paper, Initially, a thorough literature review …

Understanding The Role Of Hd5 In Colonic Epithelial Cell Death, Maryam M. Gerges, Amanda D. Williams

Student Scholar Symposium

Inflammatory bowel disease (IBD) is an autoimmune disorder where the immune system attacks healthy tissue. IBD can occur in both adults and children, describing Ulcerative Colitis (UC) and Crohn’s Colitis (CC). Our lab studies human alpha defensin 5 (HD5), an antimicrobial peptide that normally maintains small intestinal sterility. However, in CC patients, HD5 is overexpressed in the colon. Preliminary data suggests that HD5 increases colonic cell death. This project aims to determine if HD5 induces apoptosis and its mechanisms. To this end, we will test if the suppression of caspase enzymes with a pan-caspase inhibitor reduces cell death triggered by …

Impact Of Zar1l Expression On Drug Response In Breast Cancer Cells, Maryam M. Gerges, Smita Misra

Student Scholar Symposium

Breast cancer (BC) is the most common cancer in women worldwide and the second leading cause of cancer-related deaths among females. BC arises from the uncontrolled proliferation of breast epithelial cells. A crucial gene associated with BC is the Breast Cancer Susceptibility Gene 2 (BRCA2), a tumor suppressor that aids in DNA repair. Proper BRCA2 function helps prevent BC. Our lab studied the cell cycle-dependent expression of BRCA2 revealing that its promoter exhibits bi-directional activity. During cell division, forward activity transcribes BRCA2, while in the resting phase, reverse activity transcribes ZAR2 (Zygote Arrest 1 Like). ZAR2, an RNA-binding protein with …

The Role Of Human Alpha Defensin 5 (Hd5) In Disrupted Wound Healing Processes In Crohn’S Colitis, Jafer Aljorani, Amanda Williams

Student Scholar Symposium

Wound healing is a complex biological process requiring the coordinated function of multiple proteins. In chronic inflammatory bowel disease (IBD), particularly Crohn’s Colitis (CC), this process is dysregulated, leading to delayed tissue repair and increased disease burden. Prior studies indicate that Human Alpha Defensin 5 (HD5) is over-expressed in the colonic epithelium of CC patients, yet its impact on wound healing remains poorly understood. Our laboratory has identified that HD5 may impair wound healing by modulating key structural and regulatory proteins. Preliminary findings suggest that HD5 reduces the expression and function of desmoplakin, a critical desmosomal protein essential for maintaining …

Pediatric Glioblastoma Molecular Mechanisms, Ariana Trabachino, Joshua Owens

Student Scholar Symposium

Powerpoint presentation

Functionality Of The Ryanodine Receptor Type 1 (Ryr1) In The Development Of Malignant Hyperthermia (Mh), Cesar Medina, Joshua Owens

Student Scholar Symposium

Malignant Hyperthermia (MH) is a rare but potentially lethal pharmacogenetic disorder, affecting roughly 1 in 30,000 children and 1 in 100,000 adults undergoing surgery. MH can be triggered by agents used for general anesthesia. These may include volatile anesthetics such as sevoflurane, isoflurane, desflurane, halothane or depolarizing neuromuscular blockers such as succinylcholine. Upon administration of a trigger, an MH susceptible (MHS) patient can develop a hypermetabolic state during the intraoperative or postoperative periods. If not treated quickly, an MH episode could result in organ dysfunction or death. The primary mechanisms involved in the development of an MH crisis include the …

Effects Of Valerobetaine In Fatty-Acid Induced Breast Cancer Cell Proliferation, Carolyn Tran, Maryam Mina, Diyar Fadhil

Student Scholar Symposium

Breast cancer is the second leading cause of cancer deaths among women with 287,500 new cases of invasive breast cancer and 43,250 deaths reported in 2022. In fact, 75% of these deaths aren’t from the initial tumor but due to the spread of breast cancer tumors to other sites, also known as metastases. Breast cancer occurs when breast tissue cells mutate and proliferate uncontrollably, resulting in a lump or mass. In breast cancer, the origin of proliferation, or the primary site, for cancer cells is mostly within the milk ducts. Then, tumor cells can start migrating away from its primary …

Elucidating The Effects Of Hd5 On Actc1 Expression In Crohn's Disease, Carolyn Tran, Sohir Abdelnour, Joyce Lawson, Ellis Puscas

Student Scholar Symposium

Approximately 1.6 million Americans currently have Crohn’s Disease (CD), a condition that affects the gastrointestinal (GI) tract, particularly the small intestine, leading to chronic inflammation, abdominal pain, severe diarrhea, and fatigue. Although treatments exist, misdiagnosis remains a challenge due to symptom overlap with other inflammatory bowel diseases (IBD). Previous studies have shown an increase in Human Alpha Defensin (HD5) in Crohn’s Colitis, resulting in slower wound healing closure, increased apoptosis, and potential effects regarding alpha-actin expression. However, its effects in the small intestine remain unclear. Alpha-actin is a cytoskeletal protein that maintains cellular structure through cell migration, tissue remodeling, and …

Utilizing Hot Water Treatment Methods On Shallow Rooted Herbaceous Invasive Species In Temperate Deciduous Forests, Ana Manning

Student Scholar Symposium

Abstract

People have been searching for new and innovative ways to control

invasive plant species for centuries. These methods have been categorized into three sections: mechanical,

biological, and chemical. The changing landscape of invasive plant management requires industry professionals to consider innovative technologies when developing their integrated pest management plans. The hypothesis of this research is that utilizing hot water treatment methods on shallow-rooted herbaceous invasive species in temperate deciduous forests will produce equal or better results than traditional integrated pest management methodologies. Six research plots in two locations were developed to test the Heatweed® hot water treatment tool on …

Have You Had Your Vitamins Today? Development Of An Lc-Ms/Ms Method With A 100% Aqueous Gradient To Simultaneously Measure B Vitamins In Plasma From Study Participants In A “Greens” Nutritional Supplement Clinical Trial, Kennedy Brothers, Abigail Davis, Anna Losher, Yusra Ahmed, Sora Ghanem, Matthew J. Vergne

Student Scholar Symposium

This study assessed the absorption of key micronutrients from the multi-ingredient supplement using a novel developed LC-MS/MS method capable of analyzing B vitamins in a single run.

The study a randomized, double-blind, placebo-controlled crossover trial with 16 healthy participants (8 males, 8 females) to measure plasma nutrient appearance over 8 hours after supplement consumption. Serial blood samples were collected pre-consumption and at specified intervals post-ingestion. The novel LC-MS/MS method simultaneously quantified biotin, nicotinamide, pyridoxine, riboflavin, and thiamin in blood samples.

Results:The LC-MS/MS method had a range of 0.1 ng/mL to 1000 ng/mL and it proved to be robust and …