Digital Commons Network^™

Recurrence And Co-Occurrence Of Enhancer-Promoter Interactions Across Human Samples, Satvik Gunjala

Honors Undergraduate Theses

Experimental mapping of enhancer-promoter interactions (EPIs) is resource-intensive, and current computational prediction methods struggle with intrinsic genomic complexity and reliance on limited training data. To address this bottleneck and provide insights for improved computational methods, this study systematically analyzed chromatin contact datasets to investigate the recurrence and co-occurrence of enhancer-promoter interactions across human samples. Putative interactions were evaluated across two HiChIP datasets comprising 218 total samples and one Hi-C dataset comprising 266 samples to assess recurrence across samples and assess sequencing depth related to unique EPIs. Additionally, a preliminary item-based collaborative filtering recommender model was developed to assess co-occurrence patterns …

Magnesium-Based Metal Matrix Nanocomposite Implants And Nanobubble-Based Delivery Systems: Integrated Strategies For Bone Loss Treatment With Cytocompatibility Evaluation, Lucas José Martinho Bizuti

Honors Undergraduate Theses

This thesis intends to investigate the development of different multimodal therapeutic strategies for combating bone loss. Most specifically, this paper will emphasize the utilization of Magnesium-Based Metal Matrix Nanocomposite Implants (MMNC) and Nanobubble-Based Delivery Systems as options for future treatment focus. The effects of biodegradable magnesium implants were evaluated for cytotoxicity and cytocompatibility via Hematoxylin and Eosin, and Masson’s Trichrome staining, as well as radiological images. The Nanobubble-Based Delivery System is being developed and optimized as a delivery system to target osteoclast activity. This paper focused on optimizing experimental parameters, which include Rotational speeds for nanobubble stimulation under microgravity conditions …

Quantifying Amendment Impact On Microbial Respiration Rate, Qwynn Starrwalker

Honors Undergraduate Theses

Wetlands play a critical role in the global carbon cycle by acting as carbon sinks, where the flooded anaerobic conditions cause slow microbial respiration compared to other soils. Comparatively more carbon is stored in the soil as organic matter than is released as carbon dioxide (CO₂). Making wetland pools of soil organic matter less available to microbes for respiration could reduce overall atmospheric CO₂ and slow global warming. This study examined the effect of kaolinite, goethite, and lime on microbial respiration rates in wetland soils under alternating hydrologic conditions. Homogenized soil from a cypress dome was separated …

Exploring Anticholinergic Neurotoxicity: Diphenhydramine's Impact On Neuro-2a Cell Morphology, Expression, And Viability, Jordan B. Mcintyre

Honors Undergraduate Theses

Anticholinergic medications, such as diphenhydramine (commonly known as Benadryl), are increasingly recognized for their association with cognitive impairment and neurodegenerative disease. These medications, which inhibit the action of acetylcholine, a neurotransmitter essential for the formation and utilization of the central and peripheral nervous system, have been implicated in conditions such as dementia and may impact fundamental cellular processes like neurogenesis and cell proliferation. This study investigates the effects of diphenhydramine on neurogenesis when introduced to Neuro-2a cells during differentiation. For all studies cells were plated on coverslips or in 6-well plates with differentiation media containing 0 ng/mL, 50 ng/mL, …

Development Of A Split Deoxyribozyme-Based Assay For Detecting Hepatitis B Virus, Dalila Zovko

Honors Undergraduate Theses

Rapid, accessible nucleic acid-based detection methods are needed for hepatitis B virus (HBV). A split deoxyribozyme assay was developed for sequence-specific fluorescence detection. The assay was evaluated using synthetic target and plasmid-derived material. The assay showed target-dependent fluorescence and low-concentration linear range with a LOD of 1.9 nM. The assay supports detection and semi-quantification of HBV genetic material as shown using plasmid-derived transcript samples from HBV genotypes B, C, and D. The selected target corresponded to nt 363–406 of the HBV genome and was chosen based on sequence alignment showing conservation across most genotypes. Genotype-specific detection remains a future application …

Dna Half-Adder Based Calculator Driven By 4j Molecular Switches, Andrea Gissele Canizalez Covaleda

Honors Undergraduate Theses

DNA nanostructures have computing functions due to the predictable base pairing of nucleic acids (Watson–Crick). This property allows the programming of DNA circuits that integrate DNA logic gates capable of recognizing oligonucleotides. This molecular device offers the advantages of biocompatibility and potential applications in personalized medicine for diagnosis and therapies.

Our lab has developed DNA logic gates formed by the connection of YES strands via DNA four-way junctions (4J), which can function as molecular switches to develop a DNA-based calculator. Our DNA half-adder calculator nanostructure is designed to recognize up to three combinations of DNA inputs using three DNA strands …

Analysis Of Alternative Gene Splicing Of Natural Killer Cell Exhaustion Markers During Siv Infection, Soledad B. Zayas

Honors Undergraduate Theses

Natural killer cells play a critical role in the innate immune response against Human Immunodeficiency Virus and Simian Immunodeficiency Virus infections. During HIV/SIV infection, NK cells undergo functional impairment characterized by an imbalance between activating and inhibitory surface receptors. The upregulation of inhibitory receptors, TIGIT and TIM-3, has proven to contribute to NK cell exhaustion during different retroviral infections. Although alternative splicing regulates immunity related genes, its role in TIGIT and TIM-3 expression during SIV infection remains poorly understood. This study aimed to characterize alternative splicing patterns of TIGIT and TIM-3 and evaluate transcript variant expression during SIV infection in …

Soil Texture Does Not Affect Multi-Mutualist System Benefits In Prairie Legumes, Ambrose O. Cook

Senior Honors Theses and Projects

No abstract provided.

Coral Holobiont Lipidome Response To Global Change, Lauren Zane

Open Access Dissertations

Climate change is fundamentally restructuring macro-scale marine ecosystem structure and function by altering microscale metabolic processes and patterns of energy allocation. Scleractinian corals, as major ecosystem engineers, play outsized roles in ecosystem structure and function. They also occupy diverse habitats that differ in temperature regimes, light environments, hydrodynamics, and other environmental conditions, exposing corals to substantial spatial variation in stress and resource availability. Their fragile nutritional symbiosis with algal endosymbionts helps them navigate these environmental variations, but are also highly sensitive to environmental stress, particularly the timing and magnitude of water temperature changes. As pressure from environmental changes increases, the …

From Needs To Action: Designing Inclusive Writing Workshops For Academics, S. Alison Bolling, Julie Hicks Patrick

2026 Scholarly Teaching Conference: Poster Session Papers

Being productive in academic writing is a critical component of success for graduate students and faculty, yet many scholars report persistent barriers that interfere with successful writing (Kaslow et al., 2025, Sweet et al., 2017). Few faculty and graduate students receive formal training on the art of writing and those who have attended writing programs vary in success (Dankoski et al., 2012). The present study reports results from multiple institutions to inform workshops on writing needs of graduate students, faculty, and postdoctoral scholars.

Data was collected online through a Qualtrics survey distributed by WVU listserv. Participants (N = 26) included …

Interacting With Ideas: How To Engage Stem Students In Active Learning Of Theory Using Technology, Jessica Elizabeth Whitney, Keith Brian Morris

2026 Scholarly Teaching Conference: Concurrent Session Papers

STEM education in the modern age has been subject to much reform – from the integration of technology to an emphasis on student-centered teaching strategies, such as active learning. However, in the wake of virtual and blended-learning environments, student engagement and teacher assessment of student success have been challenged. Tools such as KAHOOT! and iClicker have been promoted to foster an active learning environment while sometimes falling short in regards to student retention of course material. In light of this technological educational revolution, instructors need to be able to determine the most effective tools for their discipline to aid in …

Research In Progress. Why Physiology Feels Hard: Supporting The Transition To Self-Directed Learning In Post-Secondary Physiology, Jaelyn Zoe Rohrbaugh, Mark Paternostro

2026 Scholarly Teaching Conference: Poster Session Papers

Physiology is widely recognized as one of the most challenging courses for STEM students. Contributing factors include the discipline’s inherent complexity, instructional methods, and student preparedness, with both faculty and students identifying the nature of the discipline as the primary challenge. Many undergraduates enter college having experienced predominantly teacher-directed, pedagogical instruction, whereas success in college-level physiology requires self-directed, andragogical learning strategies. We hypothesize that students’ difficulties arise more from a lack of self-directed learning skills than from content complexity alone. To investigate this, we administered an anonymous survey to 340 students spanning freshman to professional levels, achieving a 93% completion …

Bringing Real Research Into Large-Enrollment Biology Labs, Katrina Klugh Stewart, Mathilda Corbett

2026 Scholarly Teaching Conference: Poster Session Papers

Hundreds of WVU students in a large-enrollment introductory biology laboratory course (BIOL 115L) participated in an authentic research experience through the Prevalence of Antibiotic Resistance in the Environment (PARE) Project. This national crowdsourced research initiative engages students in generating environmental DNA data to identify potential antibiotic resistance hotspots. For the Fall 2025 semester, we designed a multi-week lab module to implement a cost-effective, scalable version of the PARE model suitable for a course serving approximately 900 students annually.

The three-week sequence integrates core scientific practices, including hypothesis generation, field sampling, DNA extraction, PCR amplification of antibiotic resistance genes, gel electrophoresis, …

Illusions Of The Brain, Vaso Manakou

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The Role Of Small Extracellular Vesicles In Modulating Radiation Resistance In H3k27m-Pediatric Diffuse Midline Glioma, Viral Oza

Theses and Dissertations--Molecular and Cellular Biochemistry

Pediatric diffuse midline gliomas with H3K27M alteration (H3K27M-pDMG) are the leading cause of pediatric brain tumor-associated deaths. All H3K27M-pDMG are initially treated with fractionated radiotherapy, the standard of care, and most children succumb to their disease within two years of diagnosis. There are no universally effective chemotherapies and full resection is impossible due to the diffuse nature of the tumor and sensitive location. There has not been a significant clinical advancement in more than 40 years.

Tumors become completely resistant to radiation within the first six months of treatment. The mechanism of radiation resistance is unknown but is thought to …

Scientific Kenyon: Neuroscience Edition (Full Issue)

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Letter From The Founder And Professor

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Get The Fruc(Tose) Out Of My Food, Johanna Huelsman

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

My Brain Didn't Get The Memo That It Was Virtual, Samantha Ofori

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Epigenetic Hangovers: Your Brain On Alcohol, Cindy Chen

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Ctrl + Alt + Neuron, Stuart Hilton

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Losing Yourself To Find Yourself: The Neuroscience Ego Dissolution, Mike D'Eletto

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

What The Body Feels, The Mind Reveals: How Inflammation Shapes Emotions, Jamie Murphy

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Smile! Your Brain Is On Camera, Natalie Stone

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

When Empathy Goes Quiet, Miko Warshaw

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The 400 Millisecond Mind, Adrian Mangine

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

The Effect Of Cover Crop Management Strategies On Nutrient Availability In No-Till Corn, Emily C. Marsh

Theses and Dissertations--Plant and Soil Sciences

Cover crops are reported to have long-term soil health improvements, one of which is reducing erosion. However, popular cereal cover crops, such as rye (Secale cereale L.), have the potential to cause a yield penalty in the following corn (Zea mays L.) crop due to a reduction in available nitrogen. Legumes, such as Austrian winter pea (Pisum sativum L. var. arvense), are thought to reduce this yield penalty due to their capacity to fix nitrogen. Sulfur is another nutrient of interest, especially as rates of atmospheric deposition of sulfur have declined, leading to more deficiencies being …

Mineral-Associated Organic Nitrogen Pool Size, Composition, And Accessibility Mediated By Agricultural Management And Soil Geochemical Characteristics, Gabriella M. Griffen, Andrew H. Whitaker, Emma L. Bergh, Marian Carrell, Erik Knatvold, Aniko Konya, A. Stuart Grandy, Andrea Jilling Ph.D., Marco Keiluweit, Rachel Hestrin

Faculty Publications

Mineral-associated organic matter (MAOM) contains a substantial portion of soil nitrogen (N). MAOM-N could serve as an important N source for crops, but its availability and response to agricultural management across different soil types remains largely unknown. We characterized MAOM-N isolated from nine paired soils spanning a range of geochemical characteristics and maintained under two land uses—more intensively managed annual cropping systems or less intensively managed grasslands. On average, we found that MAOM contained approximately two-thirds of total soil N. Across all soil types, more intensive agricultural management resulted in a 50% decline in MAOM-N stocks, as well as a …

Hydroponics In The Classroom: Cultivating Plants, Captivating Young People, Stacy A. Adams, Christian Stephenson, Theresa James, Kim Todd

Department of Agronomy and Horticulture: Faculty Publications

Few students take the initiative to pursue coursework beyond that required for progression to graduation. Limited are opportunities that connect educational content to industry application, potentially inspiring young people towards impactful careers. The United States government has emphasized the importance of STEM education to ensure national security and to maintain economic competitiveness globally. STEM education is not a defined discipline but an approach for building knowledge through application and engagement. Developing and managing a hydroponics prototype provides numerous opportunities for embedding STEM content into a fun and interactive project. This poster provides inspiration for constructing a simple deep water culture …