Digital Commons Network^™

Structure Of The Spoiie Protein In Clostridioides Difficile, Robert B. Bauer

Biological Sciences Undergraduate Honors Theses

Clostridioides difficile is an opportunistic pathogen responsible for severe gastrointestinal infection. C. difficile-related infection is extremely prevalent in healthcare facilities, causing roughly 30,000 deaths annually in the United States alone. Its main mechanism of virulence is sporulation, which is directed by the SpoIIE protein. This makes SpoIIE an attractive target for the remedy and prevention of infections. The objective of this study was to analyze its structure using both lab techniques and artificial intelligence modeling. A truncated version of this protein, SpoII∆TM, was expressed and analyzed using optimal conditions previously determined in the lab. SDS-PAGE results and analyses confirmed …

Efficacy Of Tick Sampling Methods In Urban Parks., Emma Staples

College of Arts & Sciences Senior Theses

Amblyomma americanum (Lone star ticks) are parasites and vectors of diseases, including Ehrlichiosis. Questions remain about how an urban environment affects the host-seeking behavior of A. americanum across different life stages and thus the efficacy of different sampling methods. We sought to compare the efficacy of different sampling methods on A. americanum ticks in urban parks during the fall season and explore how the urban heat island (UHI) effect may impact each method’s efficacy. We hypothesized that, where the UHI effect is weaker near the city’s periphery, the CO₂ trapping method would collect more A. americanum adults and nymphs …

Ai×Life 2026: Advances In Computational Biology Across Scales For Life & Health Sciences, Suma Mohan S., Devika N. T., Pranavathiyani G.

Conference Proceedings

Book of Abstracts of the International Conference, AIxLife 2026: Advances in Computational Biology Across Scales for Life & Health Sciences, held on 17–18 April 2026, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, INDIA 

About the Conference

Conventional computational biology laid the foundation for biological data analysis through statistical models, algorithms, and curated databases, enabling insights into genes, proteins, and pathways. Today, the integration of artificial intelligence, spanning machine learning, deep learning, and large language models (LLMs) is driving a transformative shift across biological scales, from atomic and molecular interactions to pathways, cellular systems, organisms, and populations.

AI-powered approaches …

Group B Streptococcus In Pregnant Women: Universal Guidelines And Protocols, Dania Presteguin

Undergraduate Honors Thesis Collection

Background: Group B Streptococcus (GBS) is a leading cause of maternal sepsis and neonatal mortality globally. Variability in screening and treatment guidelines influences global disease burden.

Objective: This study uses a cross-national analysis to compare screening and treatment guidelines and their impact on prevalence, screening, intrapartum antibiotic prophylaxis (IAP), and maternal-neonatal clinical manifestations Methodology: A systematic review of secondary literature was conducted using PubMed, Scopus, and CINAHL (2010-2025). Inclusion criteria include maternal GBS colonization and one or more measures of interventions and neonatal infection rates. No geographic or demographic restrictions were applied. A total of 67 studies were screened, and …

Shark Immunology And Its Biomedical Potential: Evolution, Innovation, And The Imperative Of Conservation, Reesha Bhagat

Undergraduate Honors Thesis Collection

This review aims to shed light on a significant ecological deficit and its implications for the future of science and medicine. Sharks possess a uniquely adaptive, cancer-resistant, and evolutionarily refined immune system with transformative biomedical potential, making their conservation a scientific and medical imperative. We are losing something medically irreplaceable, and we don’t even fully understand it yet. Shark conservation is a pressing scientific imperative because sharks are ecologically essential and represent an irreplaceable biomedical resource.

The Effects Of Heat Stress On White Blood Cell Profiles And Antibody Concentrations In Broilers Genetically Selected For Low Water Conversion Ratio Compared To The Modern Random Bred Broiler, Luke B. Janski

Poultry Science Undergraduate Honors Theses

Heat stress (HS) is one of the most significant environmental stressors impacting poultry production worldwide, reducing growth, feed efficiency, welfare, and immune competence. With global temperatures rising, understanding physiological and immunological adaptations to HS is essential for sustainable production. Broiler chickens selectively bred for low water conversion ratio (LWCR) have shown potential for reduced water consumption under environmental challenges; however, their immune resilience under HS conditions compared with modern random-bred (MRB) broilers remains unclear. This study investigated the effects of cyclic HS on red- (RBC) and white- (WBC) blood cells and humoral immunity in LWCR and MRB broilers. Birds were …

Exploring Google Trends In Assessing Personal Finance Needs For Cooperative Extension Service Programming, Megan Wells

Graduate Theses and Dissertations

The Cooperative Extension Service (CES) relies on systematic needs assessments to guide program development; yet, traditional approaches often depend heavily on stakeholder input and professional judgment, offering limited insight into consumer level needs. This mixed methods study explored Google Trends as a complementary, consumer driven data source for assessing Family Resource Management (FRM) needs within the Arkansas CES. Grounded in Witkin and Altschuld’s three level needs assessment framework and Uses and Gratifications Theory, the study integrated three data sources representing stakeholders, service providers, and consumers: (1) Family and Consumer Sciences (FCS) advisory committee reports, (2) survey of Family Consumer Science …

Clinical And Demographic Characteristics Of Hospitalized Patients With Xylazine-Related Wounds, Elizabeth Novick, Nikhil Seval, Dagan Coppock, Mollie Tucker, Daniel Taupin, John Zurlo, Carolyn Kramer

Department of Medicine Faculty Papers

OBJECTIVES: Little is known about the demographic and clinical features of patients with xylazine-related wounds. We sought to characterize hospitalized patients with substance use disorder (SUD) and xylazine-related wounds seen for infectious diseases consultation.

METHODS: We retrospectively reviewed the medical records of 193 patients diagnosed with SUD at 3 Philadelphia hospitals between October 2023 and January 2024. Patients were identified as either being diagnosed with (n=73) or without (n=120) xylazine-related wounds. We compared the demographic and clinical features between the 2 groups.

RESULTS: Patients diagnosed with wounds were younger ( P < 0.001), more likely to be White or Hispanic and less likely to be Black/AA ( P < 0.001), more likely to have tested positive for fentanyl ( P < 0.001), amphetamines ( P < 0.001), and cocaine ( P 0.001), more likely to acknowledge injection ( P < 0.001), and more likely to leave the hospital by patient-directed discharge (PDD) ( P < 0.001). Most patients had multiple wounds (75%), and more than half (53%) had at least one wound greater than 10 cm at its widest dimension. Although most patients diagnosed with wounds received antibiotics, many did not have symptoms or signs of infection.

CONCLUSIONS: Xylazine-related wounds are highly associated with illicitly manufactured …

Genome-Wide Phenotypic Characterization Of Mycobacteriophage Mercurio, Tyler Downs

Departmental Honors & Graduate Capstone Projects

Bacteriophages, or phages, are being piloted as a supplemental or alternative therapeutic to antibiotics against drug-resistant Mycobacterium pathogens, such as M. tuberculosis, which pose a global public health crisis.  Characterizing bacteriophage genomes can provide insights into efficacy in phage therapy before implementation or elucidate new targets to manipulate bacterial growth.  Overexpression of individual phage genes is useful to study a gene product’s function independent of others.  Here, the results of phage Mercurio plasmid library overexpression in plate-based assays are described.  Mercurio infects nonpathogenic Mycobacterium smegmatis and is genetically related to bacteriophages infecting pathogenic Mycobacterium species.  Eleven gene products of …

Antimicrobial Activity Of Sulbactam-Durlobactam Against Acinetobacter Baumannii-Calcoaceticus Complex Strains Causing Non-Respiratory And Non-Bloodstream Infections From The United States (2023–2025), Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Acinetobacter baumannii most often causes pneumonia in critically ill patients. However, A. baumannii is also an important cause of a broader range of infections, including skin/wound and urinary tract infections. This study aims to evaluate the in vitro activity of sulbactam-durlobactam and comparator antibiotics, including meropenem and cefiderocol against A. baumannii-calcoaceticus complex isolates from non-respiratory and non-bloodstream sources. Samples included 285 A. baumannii-calcoaceticus complex isolates enriched for carbapenem resistance collected across 17 states in the United States (January 2023–May 2025). Antimicrobial susceptibility tests were conducted by manual broth microdilution and interpreted according to Clinical and Laboratory Standards Institute (CLSI) and …

Integrating Growth Performance And Pathogen Detection To Investigate Disease Resilience In Commercial Swine, Emmalise Hope Marie Meyer

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

Disease resilience is an important trait in commercial swine production, influencing both animal health and growth performance under natural disease challenge. The primary objective of this study was to integrate growth performance data with longitudinal pathogen detection to better understand factors contributing to disease resilience in commercial pigs. A population of 1,014 pigs across four batches was monitored from weaning through the grow-finish phase, with body weights collected to calculate average daily gain (ADG). Genome-wide association analyses were conducted using BayesC and BayesIM approaches to identify genomic regions associated with growth performance. Longitudinal pathogen surveillance was performed using pen-level oral …

The Hitchhiker's Guide To The Host: Fleas And The History Of Pikas In North America, Josh Pletcher

All NMU Master's Theses

Parasite phylogenetics can offer windows into the cryptic evolutionary history of hosts, often highlighting events that are not recorded by the phylogenetics of the host. Pikas (small lagomorphs) host a diverse parasite community comprising endoparasites (e.g., coccidians, nematodes, and cestodes) and ectoparasites (e.g., fleas and mites). Phylogenetic analysis of pika endoparasites has revealed pikas evolved in Asia and colonized North America in two waves, and that contact between these two pika lineages allowed parasites to be transferred from one lineage to another and to survive the extinction of their original host. To uncover these cryptic histories, understanding the biogeography of …

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

The Impact Of Nutrition On Insecticide Resistance And Gene Expression In Aedes Aegypti, Esmeralda Guadalupe Rosas

Theses and Dissertations

The development of insecticide resistance in Aedes aegypti, a major vector of dengue and Zika viruses, threatens vector control efforts, particularly in endemic regions such as South Texas. Insecticides remain widely used; however, their overuse has accelerated metabolic resistance mediated by cytochrome P450 enzymes. Environmental factors such as larval nutrition may influence mosquito physiology and resistance-associated gene expression, yet this relationship remains poorly understood. This study examines how larval nutritional conditions affect the expression of cytochrome P450 genes linked to pyrethroid resistance in Aedes aegypti. Larvae were reared under five dietary treatments differing in lipid and protein ratios, and adults …

A Tractable Nematode Model For The Emerging Fungal Pathogen, Candida Auris, Melissa Martinez

Dissertations and Theses (Open Access)

Candida auris is an emerging multidrug-resistant opportunistic fungal pathogen. It

poses a significant threat to immunocompromised patients and those with prolonged stays in

healthcare facilities. C. auris spreads rapidly in health care facilities through enhanced

colonization of skin and abiotic surfaces. The genetic factors contributing to this ability and to

the virulence, drug resistance, and stress-tolerant nature of C. auris are largely unknown.

Current animal models of C. auris infections are not well standardized and report conflicting

results. Additional animal models of virulence are needed, especially those amenable to high-

throughput analysis. The nematode Caenorhabditis elegans has been validated as …

Characterization Of Staphylococcus Aureus Clinical Isolates From Deep Musculoskeletal Infections For An In Vitro Biofilm Model For Phage Therapy, Raquel C. Luna

Dissertations and Theses (Open Access)

The rise of multidrug-resistant (MDR) infections is a growing concern in the treatment of deep musculoskeletal infections (MSKIs) and orthopaedic device-related infections (ODRIs). Staphylococcus aureus is responsible for about one third of these infections due to its strong biofilm forming capacity, presence on human skin, and the large number of antibiotic-resistant variants. Bacteriophage (phage) therapy is now being considered as a treatment for MDR MSKIs/ODRIs. We are investigating the use of phage encapsulated into or adsorbed onto biodegradable microspheres for local delivery to the site of these MDR infections. We determined that the anti-staphylococcal phage K effectively lyses the S. …

From Antigen Presentation To Tumor Control: Mechanisms Of Type I Conventional Dendritic Cell-Based Cancer Vaccines, Josue E. Pineda

Dissertations and Theses (Open Access)

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma.

As expected, MHC-I- or MHC-II-deficiency had minimal impact on …

Understanding Epigenomic Landscapes In Cancer Progression And Immunotherapy Response, Jonathan Schulz

Dissertations and Theses (Open Access)

Nonmutational epigenomic reprogramming has emerged as a key hallmark of cancer that plays crucial roles in tumor evolution during its progression and response to therapy. However, the extent and nature of epigenomic reprogramming remains poorly understood. This dissertation examines how epigenetic regulation shapes cancer progression and response to immunotherapy. Working at the intersection of cancer biology and computational genomics, it develops analytical frameworks for characterizing chromatin structure and DNA methylation across diverse tumor contexts and uses these frameworks to address two complementary biological questions: how promoter-associated chromatin organization varies across cancer types, and how epigenetic perturbation modulates tumor immunogenicity in …

Abnormal Trafficking And Processing Of Multiple Matrix Metalloproteinases Drive Cartilage Defects In Congenital Disorders Of Glycosylation, Chia-Lun Wu

All Dissertations

Congenital Disorders of Glycosylation (CDG) are rare metabolic diseases caused by defects in glycosylation. Despite identification of over 200 CDG types, the mechanisms linking glycosylation defects to diverse clinical phenotypes remain unclear. This dissertation uses zebrafish models of PMM2-CDG and STT3-CDG to redefine CDG pathogenesis, shifting from a simple glycan deficiency model to one involving disrupted cellular spatial organization.

We identify a protease-dependent pathway underlying craniofacial cartilage defects. Specifically, defective proteolytic processing of N-cadherin, a key adhesion molecule in chondrogenesis, is a central driver of pathology. We further uncover an unconventional trafficking mechanism in which ER stress and altered secretory …

Understanding The Role Of Toxs As A Bile Sensing Component Of The Toxrs Virulence Regulatory System In Vibrio Spp., Minje Kim

Dartmouth College Ph.D Dissertations

Pathogenic Vibrio bacteria, such as V. cholerae and V. parahaemolyticus, colonize in the human small intestine to cause severe gastrointestinal disease. During the infection, these bacteria encounter bile salts, antimicrobial cholesterol metabolites secreted into the intestine. Pathogenic Vibrio species have evolved to utilize bile salts as signals to regulate virulence. The signaling depends in part on ToxRS, a conserved co-component transmembrane transcription regulator. ToxRS consists of the transcription factor ToxR and its membrane-tethered binding partner ToxS. ToxS is required for ToxR stability and full transcriptional activity. Although bile salts are known to influence ToxRS-dependent virulence gene expression, the molecular …

Drug Repurposing Against Giardia Targeting Lipid Rafts, Extracellular Vesicles, And Sphingolipid Synthesis, Breanna Chantal Pence

Open Access Theses & Dissertations

Giardia lamblia is a protozoan parasite responsible for the intestinal disease giardiasis worldwide. Giardia is one of the major intestinal parasites in the world, with over 500,000 new cases annually. Symptoms of giardiasis include diarrhea, abdominal pain, and nausea. Children are particularly vulnerable to giardiasis, with cases of malnutrition, stunted growth, and cognitive impairment in countries where the disease is endemic. Giardia consists of two morphologic forms: an infective cyst which transmits the disease and a motile trophozoite which attaches to the epithelium of the small intestine during infection. Metronidazole is a common treatment for giardiasis, but cases of toxicity …

Determining Zap-70 Signaling Pathways Mediated By Ccr7 In Tcr T Cell Activation, Vivian Torres

Open Access Theses & Dissertations

Activation of T lymphocytes is the main event that occurs in the adaptive immune response after engagement of the T cell receptor (TCR) with the peptide of the major histocompatibility complex (pMHC) molecules that are demonstrated by antigen presenting cells [1]. A key step in this process is the recruitment and activation of the zeta chain associated protein of 70 kDa (ZAP-70). ZAP-70 couples TCR engagement to downstream intracellular signaling pathways through phosphorylation of tyrosine residues within intracellular tyrosine activation motifs (ITAMs) [2]. Although there have been extensive studies on the signaling response through TCR activation, the regulatory influence of …

Exploring The Correlation Between Malnutrition And Food And Nutrition Insecurity In Inflammatory Bowel Disease, Heather Burr

All Graduate Theses and Dissertations, Fall 2023 to Present

Inflammatory Bowel Disease (IBD) may increase the risk of malnutrition because of nausea, vomiting, diarrhea and restrictive eating. In addition, patients with IBD may experience food and nutrition insecurity. Therefore, we conducted an online survey to assess risk of malnutrition and food and nutrition insecurity among adult patients with IBD in outpatient and community settings. Patients were recruited between July and December 2025, aiming to reach adults in the Rocky Mountain Region diagnosed with IBD. Data collected included demographics, health-related factors, risk of nutrition insecurity, risk of food insecurity, and barriers and facilitators to dietary management of IBD.

Fifty-seven patients …

Characterization Of The Antiviral Activity Of Mouse Schlafen Proteins, Wendy Paola Alvarez Leal

Open Access Theses & Dissertations

The goal of this work was to characterize the anti-viral role of mouse Schlafen8 and Schlafen9. Expression of these proteins is induced by type I interferon in response to viral infections. Importantly, their human functional orthologs exhibit anti-viral functions, and the structural element required for these activities are conserved in Schlafen8 and Schlafen9. Therefore, it is expected that these proteins will also impair viral replication. An important limitation in this field is that the anti-viral function of human SLFNs has been evidenced only in in vitro cellular models. No informative mutations have been described in human populations so far. Thus, …

Exploring A 'Fishy' Solution: Uncovering Human Norovirus Using A Zebrafish Model, Sahaana Chandran

Graduate Theses and Dissertations

Human norovirus (HuNoV) is the leading cause of acute gastroenteritis worldwide; however, the lack of robust laboratory culture systems and reliable animal models has limited progress in understanding viral replication and developing effective intervention strategies. While alternative models such as the zebrafish system have been explored, gaps remain in evaluating their ability to support replication across diverse HuNoV strains and in identifying factors that influence infectivity. This dissertation provides a comprehensive investigation into the use of the zebrafish model for studying viral replication, host interactions, and potential inhibition strategies. Initial studies focused on optimizing viral delivery methods using Tulane virus …

Bats And Bacteria: Infection Dynamics At The Human-Wildlife Interface, Isabella Katherine Deanglis

Graduate Theses and Dissertations

As the second most diverse mammalian order, bats host an array of pathogens, some of which are known to infect humans. Synanthropic bats share spaces with humans, resulting in bat-borne pathogen exposure. While most bat-borne disease research has focused on viral pathogens, bats host numerous bacterial pathogens with zoonotic potential. By integrating a global meta-analysis with field studies in Sub-Saharan Africa, I characterize the structural attributes that facilitate shared interfaces, the bacterial pathogens present in synanthropic bats of rural Kenya, and the physiological and environmental dynamics influencing odds of infection in these synanthropic bats. Finally, I evaluate the clinical relevance …

Optimized Ultrasound Imaging Of Phase-Change Nanodroplets, Charles R Dyall, Dmitry Nevozhay, Andy Liu, Trevor M Mitcham, George J Lu, Konstantin V Sokolov, Richard R Bouchard

Faculty, Staff and Student Publications

Phase-change nanodroplets (PCNDs) continue to generate significant research interest due to their potential to extravasate into tissue, to be targeted for molecular imaging and drug delivery, and to undergo an induced phase-change to "activated" microbubbles (MBs) for ultrasound (US) imaging. To accurately quantify molecular markers, however, one assumes a consistent proportion of PCNDs in a region of interest (ROI) are stably activated and imaged. Herein we present a framework for developing a diagnostic sequence that is optimized for PCND activation uniformity, contrast, and acquisition time. To develop this framework, activation was examined at three scales of increasing complexity: single, adjacent, …

Potential Impact Of Parasites In The Transmission Of Chronic Wasting Disease, Paulina Soto, Rodrigo Morales

Faculty, Staff and Student Publications

No abstract provided.

Exploring The Biocultural Profile Of The Undocumented Populations Of The Sonoran Corridor: A Skeletal Assessment Of The Prevention Through Deterrence Strategy, Mary A. Vaughn

Department of Anthropology: Theses and Student Research

Over the last thirty years the mortality rate of the undocumented population at the US-Mexico border has risen, requiring methods distinguishing US-born individuals from immigrants to improve the likelihood of identification and repatriation through foreign consulates. Forensic anthropologists with the Pima County Office of the Medical Examiner (PCOME) have advocated for the use of the biocultural profile, combining the biological profile with factors including oral health, osteological stress, and personal effects. The biocultural profile serves two purposes, functioning both as a tool for identification and with which to document structural inequality within communities of origin.

This study examines changes in …

Comparing Microbial Communities Of Diseased And Healthy Isopora Palifera Corals And Adjacent Waters At The Cocos (Keeling) Islands, Sophie Preston, Jacquelyn Jones, Megan J. Huggett, Arne A.S. Adam, Nicole E. White, Kar Chun Tan, Zoe Richards

Research outputs 2022 to 2026

Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no …