Digital Commons Network^™

Functionalized Nanodiamonds As Binding Platforms For Single-Stranded Dna, Mallory A. Chapman

Honors Theses

Nanodiamonds (NDs) offer a promising platform for biomolecular applications due to their stability, biocompatibility, and three-dimensional structure. This study focused on developing a nanodiamond–DNA complex in which streptavidin-functionalized NDs would form a protective shell around biotinylated single-stranded DNA (ssDNA), creating a core–shell system like an “M&M” candy with DNA at the center and a protective coating on the outside. DNA has many uses in nanotechnology, including DNA origami, nanomachines, and drug delivery systems, but its degradation limits its practical use, making protective strategies essential.

ND–DNA conjugates were prepared using biotin–streptavidin interactions and analyzed using gel electrophoresis. Initial separation on agarose …

Biochemical Characterization Of Luciferase In Omphalotus Olearius, James H. Martin

Honors Theses

The overall goal of this thesis was to investigate the genetic basis of bioluminescence in Omphalotus olearius, a bioluminescent mushroom. The project initially focused on growing fungal cultures under controlled laboratory conditions and using molecular techniques such as DNA extraction, PCR, and gel electrophoresis to identify the organism and isolate the gene responsible for light production. The main objective was to insert this gene into a bacterial system to confirm its function through observable bioluminescence. However, repeated difficulties in maintaining viable fungal cultures and errors in molecular procedures resulted in inconclusive results, preventing successful gene identification. Due to these …

Ectomycorrhizal Fungal Identity Strongly Influences Soil Properties Relative To Pine Presence And Soil History In A Pine–Eucalyptus System, Braedan Watters

Honors Theses

Invasive Pinus radiata has increasingly spread into native ecosystems in the Southern Hemisphere, including Eucalyptus forests in Australia, where it forms novel hybrid forest systems in which invasive and native tree species coexist. The success of these invasions is closely tied to ectomycorrhizal fungi (EMF) such as Rhizopogon spp., yet the relative roles of pines versus their fungal symbionts in altering soil properties remain poorly understood. This study investigated the independent and interactive effects of soil history (Pinus or Eucalyptus), EMF identity, and pine presence on soil properties using a controlled factorial experiment. Soil from beneath either Pinus …

Community Composition Of Antibiotic-Resistant Bacteria On The Mississippi Gulf Coast, Marisa Martin, Colin Jackson

Honors Theses

The Mississippi Gulf Coast is an important resource for transportation, economic development, and recreation. Given its economic and cultural importance, it is crucial to maintain clean and safe conditions along the coast for public health, but other than routine beach monitoring, few studies have examined microbial contamination of coastal waters in this region. This study aimed to determine the quantity, composition, and distribution of bacteria resistant to six different antibiotics (Vancomycin, Kanamycin, Tetracycline, Ciprofloxacin, Erythromycin, or Amoxicillin) in seawater at seven public beaches along the Mississippi Gulf Coast. No bacteria resistant to Ciprofloxacin were detected, and bacteria resistant to Kanamycin …

Neuroprotective Effects Of Estradiol And Genistein And Interactions With Aromatase Inhibitions Post Cerebellar Lesion In Male Zebra Finches, Grace E. Thompson, Anthony P. Irovic

Honors Theses

Across vertebrates, peripheral and brain-derived estradiol (E₂) promotes neuroplasticity. After injury, E₂ can be derived locally from testosterone via aromatase (AROM), an enzyme that is upregulated in glia at the site of neural injury. E₂disrupts testicular function and elevates cancer and stroke risk, primarily via binding to estrogen receptor alpha (ER α). Genistein (GEN), a phytoestrogen, is similar to E₂ but binds preferentially to estrogen receptor beta (ER β). It may offer neuroprotection without adverse effects of E₂. We used adult male zebra finches (ZF) to model neuroprotective effects of E_{2 …}

Antibiotic Resistance Patterns In Bacterial Isolates From Mississippi Gulf Coastal Environments, Lawler F. Horn

Honors Theses

Coastal environments host diverse microbial communities that play essential ecological roles but may also serve as reservoirs for antibiotic-resistant bacteria. This study investigated patterns of antibiotic resistance in microbial isolates collected from public beaches along the Mississippi Gulf Coast. A total of 143 bacterial isolates exhibited growth and were included in antibiotic susceptibility screening. High levels of antibiotic resistance were observed, with 137 of 143 isolates showing growth on vancomycin, 124 on amoxicillin, and 102 on erythromycin. Resistance to kanamycin (19/143 isolates) and tetracycline (33/143) was less common. Multidrug resistance was widespread, with 101 isolates (70.6%) resistant to three or …

Beyond The Bug: How The Covid-19 Pandemic Exposed Longstanding Systemic Failures In The United States Workforce And Economy, Abbey M. Markley

Honors Theses

The purpose of this thesis is to investigate and discuss how longstanding systemic failures in the United States exacerbated the effects the COVID-19 pandemic had on the American economy, essential healthcare workers, and overall public trust in institutions. A review of the existing literature surrounding this topic and the subsequent results of various studies were used to compose this thesis. The United States has a painful lack of worker protections and tends to view members of its workforce as expendable, even in times such as pandemic when they are deemed essential. Healthcare workers in particular faced increasing threats to their …

Life History, Stock Status, And Movement Ecology Of Narrow-Barred Spanish Mackerel, Scomberomorus Commerson (Lacépède, 1800) In The Southern Arabian Gulf, Mohamed Abdulla Almusallami

Thesis/ Dissertation Defenses

The narrow-barred Spanish mackerel, Scomberomorus commerson, is the most commercially valuable pelagic fish species in the Arabian Gulf. This thesis integrated three studies to comprehensively assess the life history, stock status, and movement ecology of this species in Abu Dhabi waters. Life history traits were characterized from data collected during a 15-month monitoring program (January 2019–May 2020). Fork length ranged from 30.5 to 132 cm. Growth parameters were k = 0.14–0.15 year⁻¹ and L∞ = 128.9–135.4 cm for males and females, respectively. Size-at-maturity (Lm₅₀) was 78.7 cm FL for females and 69.7 cm FL for males. The spawning season occurred …

Invasive Macrofungi In The United States: A Mushrooming Crisis, Emily Torres

Student Theses 2015-Present

Globalization has accelerated the spread of invasive species, making them one of the largest contributors to biodiversity loss worldwide. While invasive macrofungi remain largely absent from scientific discourse on invasive species, they represent a growing ecological concern throughout the United States. Invasive macrofungi disrupt forest ecosystems, alter soil communities, and displace native fungi. Beyond these ecological impacts, their presence and establishment profoundly affect human-nature relationships, most notably mushroom foraging and cultivation practices. This paper adopts a multidisciplinary approach to examine the ecological, economic, and anthropogenic impacts of invasive macrofungi in the United States. Chapter 1 provides a quantitative overview of …

Membrane Progestin Receptors Α And Β (Paqr7 And 8) Are Necessary For Oogenesis In Zebrafish, Md. Almamun Farid, Md. Razain Tanvir, Takumi Mouri, Eisei Tsutsumi, Md. Sohanur Rahman Sohan, Md. Ekramul Hasan, Md Saydur Rahman, Chihiro Yamamoto, Akiteru Maeno, Toshinobu Tokumoto

School of Integrative Biological & Chemical Sciences Faculty Publications

Paqr7 and paqr8 are genes encoding membrane progestin receptor αand β (mPRα and mPRβ, respectively), which are currently classified as members of the progestin and adipoQ receptor (PAQR) family. For mPRα, the first identified mPR gene, there are two paralogs in zebrafish, paqr7a and paqr7b. In order to elucidate the physiological functions of the mPR subtypes, we created gene knockout (KO) fish by editing seven paqr genes in zebrafish and analyzing their phenotypes. The null-mutant strains of paqr7a, paqr7b, and paqr8 presented no significant abnormalities in reproductive functions. Thus, we generated a triple-gene knockout (TKO) strain of …

Isolation And Quantification Of Rna From Extracellular Vesicles Derived From A549 Human Non-Small Cell Lung Cancer Cells Using Ultracentrifugation, Yousef Dimian, Vanessa Pizutelli, Dimitri Pestov

Rowan-Virtua Research Day

Extracellular vesicles (EVs) have gained attention as potential diagnostic tools due to their presence in body fluids and their ability to carry nucleic acids, including RNA. EV-derived RNA, particularly ribosomal RNA (rRNA), may reflect cellular stress and disease states, making it a promising biomarker1, 2. This project focuses on optimizing methods to isolate EVs and quantify their RNA content using human cell culture models. Differential ultracentrifugation was used to separate vesicle populations based on size, followed by RNA extraction and quantification using a high-sensitivity assay. Initial experiments using media from three 150 mm culture dishes yielded no detectable RNA, whereas …

Invisible Shipwrecks And Neurological Endangerment: The Trade-Off In Seeking Asylum - Reframing The Neurobiological Cost Of Forced Migration, Eisha Giran

CISLA Senior Integrative Projects

Forced migration along the Spain–Morocco route represents one of the most visible humanitarian crises of the twenty-first century, yet its neurological dimensions remain insufficiently examined. This paper investigates how prolonged displacement and trauma reshape neural systems involved in stress regulation, memory, and emotional processing. It introduces the concept of neurological endangerment, defined as a condition of prolonged and inescapable threat exposure during forced migration in which stress-response systems remain chronically activated, opportunities for recovery are structurally constrained, and cumulative neurobiological risk persists beyond the period of immediate danger.

To address the gap between biological measurement and lived experience, this paper …

A Conserved Role For Cyclin C In Regulated Cell Death Across Yeast And Humans, Samar Emami, David Stieg, Daniel Smethurst, Justin Bauer, Randy Strich

Rowan-Virtua Research Day

Background: Programmed cell death (PCD) is a tightly regulated process that maintains tissue homeostasis and eliminates damaged, infected, or malignant cells. A key regulator of this process is Cyclin C (CCNC), which functions as a component of the mediator complex to regulate gene transcription. During cellular stress, CCNC translocates from the nucleus to the mitochondria, where it associates with Dnm1 to promote mitochondrial fragmentation and  apoptosis.

Objective: This study aimed to unravel conservation of CCNC’s function between yeast and humans by investigating whether human CCNC can induce apoptosis in yeast and whether it does so through interaction with …

Identification Of Genes Regulating The Gli Protein Tra-1 In ​Caenorhabditis Briggsae Through A Genetic Suppressor Screen​, Alexander Glenn Cabrera, Sanese Brown-White, Ronald Ellis

Rowan-Virtua Research Day

BACKGROUND:
Gli proteins are conserved transcription factors that regulate cell fate, proliferation, and patterning. In Caenorhabditis briggsae, the Gli protein TRA-1 functions as the terminal regulator of the sex-determination pathway to control sexual development. These nematodes lack Hedgehog signaling, so TRA-1 is regulated by other factors. The missense mutation tra-1(v48) disrupts TRA-1 activator function, resulting in complete feminization of XX animals, which would otherwise be hermaphrodites.

HYPOTHESIS:
Suppressor screens using tra-1(v48) mutants will identify novel cofactors required for TRA-1–mediated Gli activation and spermatogenesis.

METHODS:
Ethyl methanesulfonate (EMS) mutagenesis was performed on tra-1(v48) strains to induce random mutations. Dominant suppressors were …

The Longevity Of Dna From Bloodstains And Its Forensic Implications, Nadia Walter

Senior Honors Theses

Human DNA is valuable forensic evidence, helping to solve a wide range of cases. It is often sourced from biological fluids found at a scene such as blood, saliva, semen, and urine. Many different factors can influence the longevity of DNA sourced from bloodstains, including the type of substrate, storage conditions, and weather. The quality of a DNA sample from a bloodstain found at a crime scene may influence its admissibility in court.

Original research was done on a surgical table from the last major battle of the American Civil War, extracting DNA from latent bloodstains. Some full profiles were …

Acquisition Behavior Response: Investigating The Ability Of Leptoglossus Phyllopus To Choose Between A “Good” Versus “Sub-Optimal” Strain Of Caballeronia, Irene L. Pham

2026 Spring Honors Capstones Projects

Leptoglossus phyllopus is a polyphagous pest that primarily feasts on citrus, tomatoes, and legumes. They must form a mutualistic symbiosis with Caballeronia every generation by ingesting the bacterium from their environment. However, not all species of Caballeronia confer the same fitness on the L. phyllopus host, raising the question of whether L. phyllopus possesses a partner choice mechanism that would allow it to distinguish between a good (GAOX1) and a suboptimal (Lep1P3) symbiosis partner. This was examined by conducting a choice experiment in which the two symbionts (GAOX1 vs. Lep1P3) were placed in a plastic box, and the bug’s roaming …

Quantifying Genetic Diversity In Nematode Feeding Rate, Jacob King

Honors Theses

Understanding how populations persist under changing environmental conditions is a central question in ecology and evolutionary biology. Variation in traits related to resource acquisition may play a key role in determining population survival when resources are limited or fluctuate over time. In this study, I investigated how variation in feeding-related traits influences population persistence using a combination of computational modeling and laboratory experiments. I developed a stochastic, individual-based consumer–resource model to simulate population dynamics across varying levels of trait variance and resource regimes. Across 60,000 simulated populations, increased trait variation consistently reduced extinction risk and extended persistence time, although the …

Optimization Of Refolding, Purification, And Analytical Characterization Of Proinsulin(F25d) Soluble Antigen Array Immunotherapy, Abigail Richardson

McKelvey School of Engineering Graduate Student Theses & Dissertations

Type 1 Diabetes (T1D) is characterized by autoreactive immune responses to insulin and its precursor, proinsulin. Soluble antigen arrays (SAgAs) displaying the metabolically inactive proinsulin variant, proinsulin(F25D), represent a promising antigen‑specific immunotherapy candidate for T1D. However, the production of these platforms is hindered by substantial practical challenges, including protein aggregation, inefficient refolding, and the lack of sensitive analytical tools to verify quality and dosage. This work establishes an integrated, scalable pipeline for the purification, conjugation, and quantification of a proinsulin(F25D) SAgA. First, we optimized the refolding of recombinant methionine-proinsulin(F25D) (M-PI(F25D)) from inclusion bodies using controlled buffer systems and created a …

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …

Faith, Science, And Choice: Vaccine Attitudes Among Religious University Students, Jamie Jensen

ScholarsArchive Data

These data comprise a Q-methodology study conducted at Brigham Young University among undergraduate students to determine vaccine attitudes in relation to religious and political ideologies. It includes raw sort data, templates for running Q-methodology, and interview transcripts.

Proteomics And Alkaloid Signature Of Narrow Leaf Lupin Leaves Reveal Key Enzymes In Quinolizidine Alkaloid Biosynthesis And Transportation, Tawfeek Khedr, Ling Ling Gao, Lars G. Kamphuis, Utpal Bose, Mitchell G. Nye-Wood, Angéla Juhász, Michelle L. Colgrave

Research outputs 2022 to 2026

Quinolizidine alkaloids (QAs) are toxic secondary metabolites in narrow-leafed lupin that defend against herbivores but constrain food and feed use. We developed a single-sample multiomics workflow for simultaneous extraction and quantitative analysis of QAs and proteins from individual leaves using urea/thiourea/CHAPS extraction with acetone precipitation, validated for QA quantification by LC–MS/MS. Data-independent acquisition proteomics of eight lupin accessions (four bitter, four sweet) identified 4437 proteins, with 183 differing significantly between bitter and sweet groups. Bitter accessions were enriched in lysine biosynthesis and stress-response pathways, whereas sweet accessions showed enrichment in phenylpropanoid and other defense-related processes. Coexpression network analysis linked protein …

The Meaning Of Physical Activity In The Context Of Health Sciences: A Concept Analysis, Martín G. Farinola

International Journal of Physical Activity and Health

Physical activity has been defined in numerous ways. Thus, this study aimed to conduct a concept analysis of the existing physical activity definitions in the health sciences literature to evaluate its conceptual precision and assess the need for a revised or novel concept better suited for this domain. The concept analysis was accomplished using tools derived from philosophical semantics. The analysis identified six definitions that explicitly state what physical activity is with sufficient clarity to allow for conceptual examination. The findings indicated that these definitions frequently merge the concept of physical activity with its contextual attributes. To address these semantic …

Herbularyo (Folk Healer): An Herbal Medicine Card Game, Maryjane T. Magsino, Inah Marie Q. Rivera, Armando M. Guidote, Genejane M. Adarlo

Chemistry Faculty Publications

Herbularyo, a card game teaching about herbal plants (HPs), was created and evaluated as a viable educational card game based on Tuomisto and Aksela’s criteria. A quasi-experiment was performed on 81 Grade 8 students from a private high school and 50 Grade 11 from a public high school. Independent t-test revealed that the control group (CG) and experimental group (EG) (p=0.386), and EG1 (played ≤5) and EG2 (played >5) (p=0.681) are not comparable with each other. Paired t-test showed EG performed better (p=0.001) than CG (p=0.901) whereas ANCOVA showed that playing Herbularyo improved students’ information retention (p=0.006). EG1 and EG2 …

Bioinformatic Resolution Of Candidate Stress-Response Homologs In Cryptosporidium Parvum: P53-Family Vs Sestrin Identity, Freeman Tobechukwu Ezeala Mr.

Biochemistry and Molecular Biology

Cryptosporidium parvum is an apicomplexan protozoan of major public-health importance, but accurate genome annotation in this organism remains difficult because of its compact genome, deep protein divergence, and the presence of compositionally biased or low-complexity regions that can mislead similarity-based analysis.

In this thesis, I examined one such annotation problem involving a conserved Cryptosporidium stress-response candidate protein, CPATCC_0028580_t1 (833 aa). The central question was whether this protein is better interpreted as a member of the p53 family, based on similarity to p53-like DNA-binding domains (PF00870), or as a member of the Sestrin family associated with the PA26 domain.

I explored …

Pest Risk Modelling For Climate-Smart Vegetable Production In East Africa, Marc Marin Agbodjan, Komi Mensah Agboka, John Odindi, Elfatih Abdel-Rahman, Onisimo Mutanga, Frank Chidawanyika, Chrysantus Tanga, Daniel Munyao Mutyambai, Sevgan Subramanian, Bonoukpoè Mawuko Sokame

All Peer-Reviewed Publications

Agricultural productivity in East Africa is increasingly threatened by climate-sensitive insect pests. This study investigates the occurrence of key vegetable pests: Brevicoryne brassicae, Plutella xylostella, Maruca vitrata, and Liriomyza mik. A comparative species distribution modelling evaluated pest risk projections under climate change. Four variable selection strategies were tested: case 1 (correlation and variance inflation factor [VIF] filtering across all predictors), case 2 (correlation and VIF filtering of bioclimatic variables merged with other predictors), case 3 (filtering based on environmental values at species occurrence point to approximate realized niches), and case 4 (dimensionality reduction using principal component analysis). These strategies were …

Attentional Mechanisms Of Language In Infants With Down Syndrome, Fragile X Syndrome And Siblings Of Children With Autism, Isabelle Robinson

Caravel Undergraduate Research Journal

Children with Down syndrome (DS), fragile X syndrome (FXS), or younger siblings of a child with autism spectrum disorder (ASIB) often exhibit atypical object exploration and social engagement, which can affect important learning opportunities. The purpose of this study was to examine group differences in social attention shifting and attentional disengagement between infants with DS, FXS, and ASIBs. This study utilized data from a longitudinal study collected from 12-month-old infants with DS (n = 13), FXS (n = 14), and ASIBs (n = 24). No group differences were seen for social attention shifting. However, infants with DS …

Examining Biobehavioral Indicators Of Adhd In Children With Fxs, Hannah Pressler, Kayla Smith, Ramsey Coyle, Elizabeth Will, Jane E. Roberts

Caravel Undergraduate Research Journal

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterized by inattention and hyperactivity/impulsivity behaviors that are inconsistent with developmental age. Children with fragile X syndrome (FXS), a genetic neurodevelopmental disorder, are often diagnosed with comorbid ADHD (53–59% of males with FXS). Despite the prevalence of ADHD in FXS, little is known about the early manifestation of ADHD. The current project aims to explore group differences in play behaviors between children with FXS and typically developing (TD) children as well as the relationship between infant play behavior and heart activity to future ADHD attention outcomes. Participants included male children with FXS and …

Optimizing Expression Conditions For The Overexpression Of Iron Regulatory Protein Bol2 From C. Glabrata, Jade Ikahihifo-Bender, Dr. Caryn Outten, Mrs. Evan Talib

Caravel Undergraduate Research Journal

Due to its unique ability to serve as both an electron donor and acceptor, iron is utilized as a co-factor for many biological processes, including electron transfer, oxygen binding, and vitamin synthesis. Iron is also a key factor during fungal infections as the human host and invading pathogens battle over limited iron pools. The primary iron-responsive transcription factor Aft1 in the opportunistic pathogenic yeast Candida glabrata responds to iron deficiency by activating expression of iron acquisition genes. However, the mechanisms for sensing intracellular iron levels and regulating Aft1 activity in response to iron are unknown. The C. glabrata iron regulation …

The Universe Under A Microscope, Claire Chabot

Caravel Undergraduate Research Journal

No abstract provided.

Early Behavioral And Physiological Predictors Of Autism In 12-Month-Old Siblings Of Children With Autism, Nicolas Poupore, Kayla Smith, Abigail L. Hogan, Jane E. Roberts Ph.D.

Caravel Undergraduate Research Journal

Autism spectrum disorder (ASD) is a neurodevelopmental disorder defined by social-communicative deficits and repetitive behaviors. Complementing behavioral (i.e., The Autism Observation Scale for Infants (AOSI) scores) and physiological markers (i.e., respiratory sinus arrhythmia (RSA), heart rate (HR)) may improve early identification of ASD and provide insights into the neurobiological mechanisms contributing to early ASD symptoms. Younger siblings of a child with ASD (ASIBs) had significantly higher AOSI Total Scores and AOSI Marker Scores in comparison to Low Risk Controls (LRCs). RSA significantly decreased from a Baseline to AOSI for both groups, but only for the ASIB group was a negative …