Biochemistry, Biophysics, and Structural Biology Commons^™

Analysis Of The Effects Of Astaxanthin On Human Colorectal Cancer Cells, Kara A. Walters

Theses/Capstones/Creative Projects

Astaxanthin (AXT) is an antioxidant carotenoid that is produced by the microalgae Haemococcus pluvialis. This supplement is best known for its potential health benefits including anti-inflammatory, antitumor, immunomodulatory, anticancer and antidiabetic activities. Astaxanthin is marketed as an oral dietary supplement and is widely used in the nutraceutical industry as well as a coloring agent in the food industry. Since Astaxanthin has been increasingly popular as a dietary supplement, cytotoxicity is relevant to consumer exposure. Obtaining the IC50, the concentration that inhibits 50% of cell growth, is important to find how Astaxanthin may interact with cancer, and this can be found …

Acute Effects Of The Psychoactive Pollutant Fluoxetine On The Antipredator Behavior Of The Gulf Killifish (Fundulus Grandis), Semyra Reus

Honors Theses

Pharmaceutical contaminants are increasingly prevalent in aquatic environments, yet their sublethal effects on ecologically relevant behaviors remain poorly understood, particularly in estuarine systems. Selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine, are of particular concern due to the conserved role of serotonin in regulating behavior across vertebrates. Here, we investigated how acute exposure to environmentally relevant concentrations of fluoxetine influences anti-predator behavior in Gulf killifish (Fundulus grandis), a key estuarine fish commonly found in saltmarsh habitats. Killifish were exposed to control (0 ng/L), low (17.8 ng/L), and high (596 ng/L) fluoxetine concentrations and subsequently tested in the presence …

Novel Biomarker Discovery In Multiple Sclerosis, Manisha Gangasani

Honors Theses

Multiple Sclerosis (MS) is a chronic neuroinflammatory disorder affecting the brain, spinal cord, and optic nerve. Patients experience cognitive, motor, autonomic, and emotional symptoms that often overlap with other neurological conditions, making early diagnosis challenging. Current diagnostic criteria require evidence of lesions with dissemination in time and space. Racial disparities in MS outcomes are well documented, with Black individuals often exhibiting greater disease severity, higher relapse rates, and increased disability compared to White individuals. These differences likely reflect a combination of genetic, biological, environmental, and healthcare access factors, underscoring the need to improve early diagnosis and reduce inequities in care. …

Developing A Protocol For Non-Cellular Transplantation Of Donor Mitochondria Into Recipient Cells, Andrew Parton

Honors Theses

Tumor innervation has emerged as a critical feature of cancer progression, with increased nerve density correlating with enhanced aggressiveness, metastatic dissemination, and poor clinical outcome. However, the functional contribution of neurons to tumor biology remains incompletely defined. We recently identified the intercellular transfer of mitochondria from neurons to cancer cells as a mechanism that promotes tumor progression. We therefore hypothesized that disruption of this transfer could attenuate tumor aggressivity. To directly investigate this process, we developed an approach to isolate mitochondria from donor cells and transplant them into recipient cancer cells independently of canonical cell-cell interactions. Transferred mitochondria were tracked …

Understanding Tlr3 Immune Response Activation In Cryptosporidium Parvum And Cryspovirus Pathogenesis, Surayya Hudayberganova

Biochemistry and Molecular Biology

Cryptosporidiosis is a serious gastrointestinal illness caused by a protozoan parasite known as Cryptosporidium. It is particularly dangerous for malnourished children and those with compromised immune systems. My research focuses on the Toll-like receptor 3 (TLR3) response to the Cryptosporidium parvum infection, specifically in the presence of the parasite’s viral mutualist named cryspovirus (CSpV1). Results using research methodologies like ELISA and RT-qPCR have indicated that TLR3 expression increases during the infection process of Cryptosporidium parvum (C. parvum). Furthermore, one intriguing observation concluded during this study suggests that administering the TLR3-specific inhibitor CU-CPT4a to infected cells drastically decreased this activation. This …

College Of Natural Sciences Spring Newsletter, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

[Page 1] Dean's Message
[Page] 2 Awards & Recognitions // Student Spotlights
[Page] 3 Zhang Named to Landsat Science Team // The Power of Teaching
[Page] 4 “Science as Art” Competition Welcomes High School Artists
[Page] 5 Testing for “Forever Chemicals” in Surface Water // New Faculty Spotlight
[Page] 6 Ambassador Initiated Outreach
[Page] 7 57th Annual Geography Convention
[Page] 8 Twice the Impact on On Call with the Prairie Doc
[Page] 9 Making Staple Foods Healthier // Halaweish & Cole-Dai Retire
[Page] 10 Drone Day 2026
[Page] 11 Student Research, Scholarship, and Creative Activity Day (SRSCAD)
[Page] 12 Ceremony …

Sensing Rna’S Conformation With A Solid-State Nanopore Device At Various Ph And Temperature, Haopeng Li

Graduate Theses and Dissertations

This study uses solid-state nanopore technology to investigate the stability and dynamics of RNA molecules under thermal stress and pH fluctuations. Two distinct mRNA samples were analyzed: (1) heat shock protein (HSP)-encoding mRNA extracted from Sulfolobus solfataricus P2, a thermophilic archaeon inhabiting extreme environments such as geothermal sulfuric hot springs (pH < 4, temperature range: 65–90°C), and (2) total RNA extracted from White Leghorn chickens, which thrive under standard physiological conditions. ΦX174 virion single-stranded DNA (ssDNA) were included as a comparative reference. Nanopores, fabricated in silicon nitride membranes, were used to electrically characterize the structural properties of individual RNA molecules in solution, close to their native environments. The nanopore membrane separates two chambers containing salt buffer solution, where ionic current is the primary measurement parameter. When a voltage bias is applied across the membrane, ion flow and an ionic current can be measured. Charged RNA molecules driven translocation through the nanopore induces pore resistance changes, resulting in detectable current blockade events. Variations in these events provide insights into RNA secondary structure and conformational dynamics. By systematically altering pH and temperature, this study elucidates the effects of environmental stressors on RNA stability and structural integrity. The findings reveal distinct responses between thermophilic HSP-encoding mRNA and mesophilic RNA, underscoring the adaptive mechanisms of thermophilic RNA under extreme conditions. These results contribute to a better understanding of RNA behavior under stress and establish a foundation for future applications in RNA-based diagnostics and biotechnology development.

Unveiling The Biochemical Pathway Responsible For Ankyloglossia (Tongue-Tie) By Tracking Enzymatic Activity Of Apoptosis Pathways, Becca Ringstad

Celebrating Scholarship and Creativity Day (2018-)

Ankyloglossia (Tongue-tie) is a condition that is caused by failed cellular degeneration leading to a short lingual frenulum. This short lingual frenulum tethers the tongue to the bottom palate of the mouth and leads to problems, including breastfeeding for infants, depriving them of important proteins that build the gut microbiome, strengthen the immune system, and fight off antigens. If left untreated, it leads to problems with speech articulation, airway development, and obstructive sleep apnea. Treatment involves a frenectomy, which is the release of the short lingual frenulum using surgical scissors or a laser. Ankyloglossia can occur with conditions such as …

Phenotypic Contribution And Regulation Of Vibrio Parahaemolyticus Cold-Shock Protein Homologue Vp1889, Oleg Borisovich Ermolinsky

Theses and Dissertations

Vibrio parahaemolyticus is the primary causative agent of a form of gastroenteritis called vibriosis commonly acquired from ingestion of raw and undercooked seafood. The primary mitigation of seafood-borne illnesses is immediate storage on ice following catch, which inhibits bacterial metabolism and replication. Mesophilic bacteria such as V. parahaemolyticus induce expression of cold-shock proteins in a process named the cold shock response, which facilitates survival at low temperatures. V. parahaemolyticus bears 3 homologues of the major Escherichia coli cold-shock protein CspA, an RNA chaperone. Induction of E. coli CspA at low temperatures depends on autogenous modulation by its mRNA structure, which …

Ethanol State-Dependent Learning In The Honey Bee (Apis Mellifera), Ethan Neil Govea

Theses and Dissertations

Ethanol disrupts neural circuits involved in addiction and withdrawal, yet the molecular mechanisms underlying these effects remain poorly understood. One possibility is that ethanol alters an animal’s perceptual or internal state, causing a stimulus learned while intoxicated to be processed differently when the animal is sober. This study examined how ethanol exposure affects odor learning, recall, and discrimination in honey bees, a useful model because of their robust olfactory learning and experimentally accessible neural systems. Bees were differentially conditioned with appetitive reward (sucrose) during hexanol exposure and aversive stimulus (quinine) during decanol exposure. To assess olfactory processing and state dependency, …

Identification Of Peptides For A Muc13 Cancer Vaccine, Abigail Olivia Gomez

Theses and Dissertations

Mucin 13 (MUC13) is a transmembrane glycoprotein that is frequently overexpressed in epithelial cancers. Its extracellular domains and cytoplasmic signaling potential contribute to disrupted cell adhesion, increased invasion, and cancer-promoting pathways, making MUC13 a promising target for immunotherapy. This project used an in-silico approach to identify MUC13-derived peptides predicted to bind HLA class I molecules and support CD8+ T cell-mediated immune responses. Bioinformatics tools were used to screen candidate epitopes for HLA binding affinity, antigenicity, toxicity, IFN-γ-inducing potential, and population coverage, allowing rational prioritization of peptide candidates for experimentation. Selected peptides were evaluated in THP-1-derived macrophages using RT-PCR, Western blotting, …

Comparative Biomechanics: Blattodea Antennal Morphology And Physiology, Lucas W. Marsh

All Theses

Equipped with muscle-free antennae, many insects can twist and bend their antennae on demand. We hypothesized that hemolymph circulating through the antennae provides pressure that facilitates twisting and bending and provides a feedback control channel for tactile sensing in insects. To test this hypothesis, we conducted a thorough morphological and physiological analysis of antennae in three Clades of Blattodea. We studied morphology by evaluating the distinguishable features of the body and antenna, as well as the internal structure of the antennal lumen. Then, in a series of experiments on live cockroaches, we measured blood pressure along the antenna. This was …

Membrane Organization Of Rheb And Rhoa: Roles In Function And Allosteric Druggability, Chase M. Hutchins

Dissertations and Theses (Open Access)

Small GTPases of the Ras superfamily are membrane-bound molecular switches that regulate nearly all major cellular processes, and their dysregulation drives cancers, neurological disorders, and metabolic diseases. While anchored to cellular membranes, the catalytic domains of small GTPases undergo orientation dynamics, adopting distinct configurations that can occlude or expose effector-binding surfaces and modulate signaling output. These dynamics have been characterized in the Ras oncoproteins, but whether they extend across the superfamily and influence allosteric druggability has remained unknown.

In this dissertation, I address these questions through Rheb and RhoA, two small GTPases with complementary differences in subfamily lineage, membrane localization, …

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 …

A Novel Method Of Protein Purification Using Hedgehog Proteins As An Inducible, Self-Cleaving Tag, Antonia Kladias

Undergraduate Honors Theses

Because removing extraneous purification tag sequences from native proteins can be challenging and costly, there is demand for simple all-in-one techniques that directly furnish a tagless, functional protein-of-interest (POI). Current tagless purification systems are based on intein biochemistry; however, intein-based purification requires expensive, specialized resins and the POI often must be fused to the intein’s C-terminus. In this thesis, I present a novel approach for tagless POI purification in which the Drosophila melanogaster hedgehog protein catalytic domain (HhC) is repurposed as a small-molecule inducible, self-cleaving element dubbed Gtag. With Gtag, the POI is fused to the N-terminus of HhC/Gtag with …

Isolation, Purification, And Characterization Of Α-Galactosidase From Watermelon (Citrullus Lanatus), Christopher Henley Jr.

Chemistry & Biochemistry Undergraduate Honors Theses

The enzyme α-galactosidase is a type of glycosidase that removes galactose sugar units from larger molecules in cells. Compounds that inhibit glycosidases have been useful for understanding the structure and function of the enzymes they inhibit, and some have been used to treat certain diseases. Using inhibitors of α-galactosidase to study its characteristics and mechanisms may provide insights into its role in disease and its general utility. Advances in fields such as agriculture, sustainable fuels, and biomedicine may be facilitated by inhibition studies of α-galactosidase, but the current library of known inhibitors is relatively lacking. Obtaining α-galactosidase enzymes from chemical …

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 …

Assessing The Use Of Exon-Skipping Morpholino Antisense Oligonucleotides Targeting The Different Sumo Paralogs As Enhancers Of The Antitumor Activity Of Chemotherapeutic Agents, Andrea Teresa Garcia-Morin

Open Access Theses & Dissertations

Post-translational modifications (PTMs) are critical regulators of protein function, stability, and localization, with SUMOylation emerging as a key modulator of cellular stress response and survival in cancer. Non-small cell lung cancer (NSCLC) is characterized by heightened dependence on SUMOylation to sustain pro-survival signaling, DNA repair, and resistance to chemotherapy. This dissertation investigates a novel chemosensitization strategy based on the splice-switching of SUMO transcripts in NSCLC cells using exon-skipping morpholinos (ESMs), which redirect splicing toward non-conjugatable SUMO alpha isoforms, thereby reducing global SUMOylation. We hypothesized that decreasing global SUMOylation through forced alternative splicing of SUMO transcripts would impair the stress-protective functions …

Design And Optimization Of Peptide Inhibitors Targeting Kinesin: Molecular Modeling Studies And Virtual Screening For Therapeutic Candidate Development, Maraf Mbah Bake

Open Access Theses & Dissertations

Kinesins are ATP-driven molecular motors essential for intracellular transport and mitotic spindle assembly, and their mechanochemical behavior has been extensively characterized through computational tools. The first project reviews decades of advances in molecular dynamic simulations, including all-atom and coarse-grained molecular dynamics, Markov state models, Brownian dynamics, and free-energy approaches, which have collectively deepened our understanding of conformational transitions, microtubule-binding interfaces, and ligand interactions, especially for the mitotic motor Eg5. The second review examines the rapid emergence of quantum computing as a transformative technology for drug discovery, highlighting key historical milestones, recent progress in hybrid quantum-classical algorithms, quantum-enhanced docking, and quantum …

Novel Roles Of G-Beta-Gamma Signaling In Microtubule Dynamics And Neurodegeneration, Diana I. Olivas

Open Access Theses & Dissertations

Neurodegenerative disorders (NDDs), including Alzheimer's disease (AD), are characterized by progressive neuronal dysfunction, cytoskeletal disruption, and cognitive decline. Although Tau hyperphosphorylation and neurofibrillary tangle (NFT) formation are classical hallmarks of AD, emerging evidence suggests that microtubule (MT) dysfunction may precede and occur independently of Tau pathology. Understanding upstream regulators of MT dynamics is therefore critical for elucidating early mechanisms of neurodegeneration. Previous work from our laboratory demonstrated that G protein βγ (Gβγ) subunits directly interact with tubulin and promote MT assembly. However, the mechanism of Gβγ signaling in neuronal cytoskeletal stability and neurodegeneration remained poorly understood. The present study investigated …