Biochemistry, Biophysics, and Structural Biology Commons^™

Using Lateral Flow Assay To Assess The Prevalence Of Trachemys Hybridization, Lillian Groves

Honors Program Theses

The current study focuses on Trachemys species, which is a group of freshwater turtles found throughout the Greater Antilles. The role of studying an isolated island, such as the Dominican Republic, is significant because it serves as a way to better understand how the combined effects of species migration, mass tourism, and climate change can greatly impact isolated species. Of particular significance is how these forces interact in complex ways to reshape habitats and threaten biodiversity. Additionally, the introduction of a highly invasive species, Trachemys scripta elegans (T. scripta), in this environment pressures native species by acting as a source …

Target Cell-Associated Cd47 Suppresses Nadph Oxidase Activity In Macrophages During Antibody Dependent Cellular Phagocytosis, Seuly Akter

Electronic Theses and Dissertations

CD47-SIRPα signaling is a well-known immune checkpoint that suppresses macrophage-mediated antibody-dependent cellular phagocytosis (ADCP). In this study, we explored how CD47 influences reactive oxygen species (ROS) production driven by Fcγ receptor (FcγR) signaling. Our results show that macrophages produce significantly more ROS when encountering IgG coated target cells lacking CD47.Polarization with IFNγ further amplified this effect. ThusCD47-SIRPα interactions limit phagocytosis and suppress oxidative ROS production by macrophages. We found that CD47 blockade and IFNγ stimulation enhanced ADCP through distinct mechanisms. CD47 blockade removed the inhibitory "don't eat me" signal supporting ADCP and ADROS. Similarly, IFNγ enhances ADCP by upregulating FcγRI …

Bridging The Gap Between Structural And Cellular Biology: Insight Into The Organization Of Glycolytic Enzymes In Cells, Heather Hansen

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glycolytic enzymes are spatially organized in the cytoplasm, and are shown to localize with cellular structures such as the plasma membrane, F-actin, mitochondria, or associate independently within the cytosol. The assembly of these enzymes is hypothesized to regulate pathway flux to meet the energetic needs of the cell. However, it is unclear whether all of these assemblies have the same mechanism of formation or function in the cell. We investigated the role of glycolytic enzyme assemblies in cells, using the glycolytic “gatekeeper” enzyme phosphofructokinase-1 (PFK1). PFK1 is extensively regulated by multiple mechanisms, including over 20 allosteric ligands, post translational modifications, …

Probing The 10-23 Dnazyme Catalytic Core: Insights From Structural And Mechanistic Studies, Evan Rhyse Cramer

Graduate Theses, Dissertations, and Problem Reports (ETD)

The 10-23 DNAzyme is a catalytically active DNA oligonucleotide capable of cleaving RNA at purine-pyrimidine junctions in the presence of divalent metal ions, most notably magnesium. Despite its promise as a programmable RNA knockdown tool, its clinical and biotechnical utility has been hampered by limited structural characterization, low catalytic efficiency under physiological conditions, and poor understanding of its in-cell activity. This dissertation presents a comprehensive framework for the structural and functional analysis of DNAzymes using the 10-23 DNAzyme as a model system. In the absence of high-resolution structures, we first employed detailed in vitro biochemical assays to map essential residues …

Characterization Of P38alpha And Nitric Oxide Synthase 3 Binding, Gillyan M. Jewett

Master's Theses

P38alpha is a member of the mitogen activated protein kinase (MAPK) family. This family is important for mediating signal transduction pathways through phosphorylation of downstream substrates. Previous work has described the ability of p38alpha to bind and phosphorylate nitric oxide synthase 3 (NOS3) at two sites, the autoinhibitory loop (AI) at S600 and the N-terminal MAPK binding site (NtMAP) at S114. P38alpha has two substrate binding domains, the common docking groove (CD-groove) and a hydrophobic pocket (DEF) that are important in binding and phosphorylating various substrates specific to each pocket. Utilizing biolayer interferometry, this work describes the importance of both …

Green Chelation Strategy For Deashing Of Algal Biomass, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

This study investigated a green chelation strategy for deashing algal biomass using nitrilotriacetic acid (NTA) and deionized water (DI) to enhance its suitability for biofuel and bioproduct applications. Solid-state algal turf scrubber (SS ATS), green algal turf scrubber (ATS), and Scenedesmus were analyzed, with Scenedesmus selected for detailed evaluation due to its high ash removal efficiency. The objective was to optimize a purification process that minimizes ash and heavy metal content while preserving biochemical integrity. Algal biomass underwent sequential washing with DI, NTA, and NTA+DI under varying temperatures (90-130 °C). Analytical techniques including Fourier Transform Infrared (FTIR) spectroscopy, Inductively Coupled …

Environmentally Friendly Chelation For Enhanced Algal Biomass Deashing, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

High ash content in algal biomass limits its suitability for biofuel production by reducing combustion efficiency and increasing fouling. This study presents a green deashing strategy using nitrilotriacetic acid (NTA) and deionized (DI) water to purify Scenedesmus algae, which was selected for its high ash removal potential. The optimized sequential treatment (DI, NTA chelation, and DI+NTA treatment at 90–130 °C) achieved up to 83.07% ash removal, reducing ash content from 15.2% to 3.8%. Elevated temperatures enhanced the removal of calcium, magnesium, and potassium, while heavy metals like lead and copper were reduced below detection limits. CHN analysis confirmed minimal …

Rwanda's Natural Remedies: A Fresh Look At The Fight Against Malaria, Leandre Nsabimana Ndisanze

Pomona Senior Theses

Malaria remains one of the most devastating parasitic diseases globally, disproportionately affecting sub-Saharan Africa, where Rwanda continues to face high transmission rates and rising resistance to conventional interventions. Despite decades of control efforts, the emergence of drug-resistant Plasmodium falciparum and insecticide-resistant Anopheles mosquitoes threatens to reverse recent gains. This research responds to the urgent need for sustainable and culturally relevant alternatives by exploring the therapeutic potential of Rwandan traditional medicinal plants. These indigenous remedies, long used by local healers, offer an underexplored reservoir of bioactive compounds that may provide the basis for novel antimalarial drugs.

The central hypothesis of this …

Extended Inter-Laboratory Characterization Of The New Coastal Seawater Dissolved Organic Matter Reference Material Trm-0522, Alexander J. Craig, Lydia Babcock-Adams, Maxime C. Bridoux, Charlotte Brun, Juliana D'Andrilli, Aleksandar I. Goranov, Patrick G. Hatcher, Oliver Lechtenfeld, Hang Li, Rebecca Matos, Garrett Mckay, Amy M. Mckenna, Madelyn Miller, Sasha Wagner, Margot E. White, Alexander Zherebker, Jeffrey A. Hawkes

Chemistry & Biochemistry Faculty Publications

Dissolved organic matter (DOM) reference materials are critical to ensuring reliable comparability of measurements across experiments and between labs. TRM-0522, isolated in 2022 from 45 m deep seawater off of Sweden’s west coast, fills the niche of a previously unavailable coastal marine DOM reference material. After its isolation, we detailed a limited number of metrics for TRM-0522, initially disclosing Orbitrap high-resolution mass spectrometry, nuclear magnetic resonance, carbon proportion, absorbance, and fluorescence data. With TRM-0522 becoming more widely used, a variety of labs have generated different metrics that help to characterize and define the chemical properties of this coastal reference material. …

From Biophysics To Cellular Function: Neural Telcs-Membrane-Anions Capacitor Transmembrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Based on the transmembrane-electrostatically localized protons/cations charges (TELCs) theory, neural transmembrane potential including both resting and action potential is now well elucidated as the voltage contributed by the TELCs-membrane-anions capacitor biophysics in a neuron. Accordingly, neural transmembrane potential has an inverse relationship with TELCs surface density, which may represent a substantial progress in bettering the fundamental understanding of neuroscience. In this article, I will present a review on the latest development of the TELCs neural transmembrane potential theory and address Silverstein’s interesting arguments regarding the TELCs model that may constitute a complementary development to both the Hodgkin-Huxley classic cable theory …

Experimental Demonstration And Study Of Transmembrane-Electrostatically Localized Protons Prevail, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In this review in relation to some interesting arguments from Silverstein, it is now reaffirmed that the experimental demonstration of transmembrane-electrostatically localized protons (TELPs) was successfully accomplished through 1) using an aluminum film as a TELPs sensor in a biomimetic anode water-membrane-water cathode system, 2) analyzing the water-electrolysis current curve, and 3) measuring bulk liquid phase pH. Formation of induced TELPs was subsequently discovered in an anode water-membrane-water-membrane-water cathode system. The discovery of induced TELPs enabled clean experimental tests on the cation-TELPs exchange process by using sodium bicarbonate or potassium bicarbonate solution in the central liquid chamber. The sodium/TELPs exchange …

Validating A Novel Capability Of Assessing Pathways Of Animal Water Gain And Loss, Zachary T. Steele, Karen Caceres, Zachary A. David, Lisa M. Shollenberger, Alexander R. Gerson, Seth D. Newsome, John P. Whiteman

Biological Sciences Faculty Publications

Understanding variations in the routes by which wild animals gain and lose water is challenging, and common methods require longitudinal sampling, which can be prohibitive. However, a new approach uses Δ′¹⁷O_BW (Δ′¹⁷O of animal body water), calculated from measurements of δ′¹⁷O and δ′¹⁸O in a single sample, as a natural tracer of water flux. Δ′¹⁷O_BW is promising, but its relationship to organismal variables such as metabolic rate and water intake have not been validated. Here, we continuously measured oxygen influxes and effluxes of captive deer mice (Peromyscus maniculatus), and manipulated their water intake and metabolic rate. We used …

Caspases Protect Against Hyperglycemia Induced Necroptosis-Like Cell Death In Brain Endothelial Cells, Aleena S. Mathew

Theses and Dissertations

Acute diabetes characterized by high spikes in blood glucose levels in association with severe hyperglycemia can lead to an increased risk of ischemic stroke in the brain. To better understand high blood glucose levels, hyperglycemia, in the brain we explored its effects on endothelial cells. Endothelial cells line the inner walls of blood vessels and are directly impacted in hyperglycemia. Brain endothelial cells are a major component of the blood brain barrier (BBB) which tightly regulates the brain’s microenvironment. The type of cell death such as apoptosis, caspase dependent, or necroptosis, caspase independent, can exacerbate diabetes associated complications. There is …

Characterization Of Dietary And Hormonal Influences On Renal Sodium Transporters And Channels In Rodent Models, Evelyn Chan

Scripps Senior Theses

Within kidneys, a diverse array of renal epithelial cells works to maintain electrolyte and water balance to regulate blood pressure and pH. These cells contain varying types of sodium transporters that adjust sodium reabsorption according to the body’s needs. Previous studies have observed sex-specific differences in renal sodium transporter regulation, which are thought to optimize reproduction in females. In this study, we performed high resolution microscopy and detailed characterization of cell type-specific expression and localization of major sodium transporters and channels in rodents in response to dietary and hormonal influences. Specifically, we examined the impact of dietary salt intake and …

Exploring The Effects Of Road Salt On Earthworm Species, Alea Mry Koston

Williams Honors College, Honors Research Projects

This study examines the effects of two road salts, sodium chloride (NaCl) and calcium magnesium acetate (CMA), on the health of two earthworm species: Eisenia fetida and Lumbricus terrestris. Over a 4-week period, approximately 168 earthworms were exposed to varying concentrations of either NaCl, CMA, or mixed ratios of both, with a control group included for comparison. The experiment involved monitoring the changes in earthworm weight and measuring their contraction rates to determine physiological responses. Statistical analysis revealed no significant differences in weight or activity between NaCl and CMA treatments for either species. However, higher concentrations of NaCl resulted in …

Expression And Purification Of Cytochrome P450 46a1 For Resonance Raman Spectroscopy, Lauren Jirles

Williams Honors College, Honors Research Projects

Researchers are targeting cytochrome P450 46A1 (CYP46A1), an enzyme critical for brain cholesterol homeostasis, as a potential therapeutic approach for neurological diseases. CYP46A1 plays a key role in cholesterol turnover in the brain by catalyzing the conversion of cholesterol to 24S-hydroxycholesterol (24HC) and is linked to Alzheimer’s disease pathophysiology. Given its critical role in brain health, CYP46A1 represents a promising target for therapeutic intervention in neurological disorders. The goal of this project was to express the CYP46A1 protein in GC5 E. coli cells and purify the protein using chromatographic techniques including affinity and ion exchange chromatography. Ultraviolet-Visible (UV-Vis) spectroscopy was …

Elongate Locomotors Show Consistent Torque Patterns Across Substrates, Spencer Bradford, Henry Astley

Williams Honors College, Honors Research Projects

The four main movements found in snakes are understood mainly due to external study; however, muscular forces and resulting torques are poorly known. The main research objective is to study the torque production on different substrates using a snakebot. The study will give a rudimentary model for torque production on different substrates. It can then be compared against biological systems to understand snake movement at a muscular level. This study used a snakebot, allowing direct assessment of the current being run through each of its motors (proportional to torque). Data was then examined using a Principal Component Analysis test for …

Impact Of Tetrahydrocannabinol (Thc) On Daphnia Magna Heart Rate, Ashley Cosgrave

Williams Honors College, Honors Research Projects

Marijuana (Cannabis) is currently federally illegal within the United States and classified as a Schedule I drug. This leaves a large research gap on the impacts of Tetrahydrocannabinol (THC) use. Daphnia magna are frequently used as a model organism for the human heart and toxicology screenings due to their myogenic heart, similarities in physiological pathways, and sensitivity to toxins. As such, in order to bridge the research gap and uncover potential use of Daphnia magna as a model organism for humans in regard to impact on heart rate, we hypothesized that if Daphnia magna possess CB1 receptors or an equivalent …

Targeting Als: A Multi-Cellular Study On The Potential Therapeutic Role Of Azole-Based Compounds, Alisha R. Kennedy

Theses and Dissertations

Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig’s disease, is a progressive neurodegenerative disorder that leads to the degeneration of motor neurons, which control voluntary muscle movements such as eating, speaking, and breathing. As these neurons are damaged, voluntary movement ceases, leading to a fatal outcome. The survival time of ALS patients varies, ranging from a few months to up to 10 years. Chapter 1 of this thesis provides an overview of ALS, highlighting the role of transactive response DNA-binding protein 43 (TDP-43), a key feature in ALS and other neurodegenerative diseases. The aggregation of TDP-43, particularly due to …

Estrogen Receptor-Mediated Effects Of Resveratrol On Muscle Function, David Ayi-Bonte

Open Access Master's Theses

Artemis missions are set to send the next man and the first woman back to the moon and enable long-term missions on the lunar surface. However, exposure to lunar gravity has significant physiological effects characterized by loss of muscle mass, weakness and decreased bone density. Nutraceutical countermeasures such as Resveratrol (RSV), a naturally occurring polyphenol, have been identified as promising strategies to preserve musculoskeletal health; however, its pleiotropic effect hinders our ability to identify the primary cellular pathways through which it delivers its benefits. Furthermore, its efficacy in simulated lunar gravity is unknown. Based on the benefits observed with RSV …