Biochemistry, Biophysics, and Structural Biology Commons^™

Genetic Factors Of Campylobacter Jejuni Required For Its Interactions With Free-Living Amoeba, Deepti Pranay Samarth, Asim Z. Abbasi, Young Min Kwon

Poultry Science Faculty Publications and Presentations

Acanthamoeba, a free-living amoeba ubiquitous in environmental water, has been considered as the environmental reservoir of certain bacterial pathogens, including Campylobacter jejuni, an intracellular human pathogen causing self-limiting gastroenteritis. Acanthamoeba-C. jejuni interaction mechanisms may help clarify how the otherwise fastidious bacterium C. jejuni survives in environmental waters. In this study, we constructed single deletion mutants of C. jejuni strain 81-176 for the 10 selected genes (motAB, ciaB, kpsE, virB11, cheY, flaAB, cstII, docB, sodB, and cadF) previously shown to be important for the interaction (invasion and intracellular survival) of C. jejuni with mammalian hosts. We used a modified gentamicin protection …

Structural And Functional Lessons Learned About Regulation Of Enterotoxigenic E. Coli Virulence Regulatory Factor, Rns, Jessica Dianne Tolbert

Dartmouth College Ph.D Dissertations

Antibiotic resistance has exacerbated the global health crisis of diarrheal diseases caused by enteric bacterial pathogens. Investigating pathogens, such as Enterotoxigenic Escherichia coli (ETEC) and Vibrio cholerae (cholera), helps to uncover mechanisms for the inhibition of virulence gene expression. A notable member of the AraC transcription factor family in ETEC, Rns, regulates virulence factors including pili and fimbriae, which are essential for adherence and colonization of the intestinal epithelial layer. This microbe–host interaction initiates the release of toxins, leading to the water and ion loss in clinically diagnosed as diarrhea.

In the canonical N-terminal domain of Rns, mutagenesis of the …

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

Ion-Dna Interactions As A Key Determinant Of Uracil Dna Glycosylase Activity., Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Because of their ubiquitous presence, ions interact with numerous macromolecules in the cell and affect critical biological processes. Here, we discuss how cations including Mg²⁺ alter the enzymatic activity of a DNA glycosylase by tuning its affinity for DNA. The response of uracil DNA glycosylase (UNG2) to Mg²⁺ ions in solution is biphasic and paradoxical, where low concentrations of the ion stimulate the enzyme, but high concentrations inhibit the enzyme. We analyzed this phenomenon by modeling experimental data with a statistical framework that we empirically derived to understand molecular systems that display biphasic behaviors. Parameters from our statistical …

Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs

Undergraduate Honors Theses

Suppressor of IKK epsilon (SIKE) is a protein that is implicated in immune response signaling pathways. SIKE interaction networks suggest roles in cell motility and macromolecular complexes mediating kinase/phosphatase activity. In this project, we aim to better understand the function of SIKE by analyzing amino acid sequences across different species. In human SIKE, viral infection leads to phosphorylation of SIKE at defined serine residues. Comparing SIKE sequences, and specifically these phosphorylation sites, allows us to discover its ancestral connections to innate immune function. This has particular applications in bridging the evolutionary gap between fungi and metazoa SIKE sequences. Multiple sequence …

Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel

Electronic Theses & Dissertations

The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …

The Effects Of Ataxin-1 Overexpression In The Central Nervous System On Specific Behavioral And Physiological Characteristics Of Drosophila Melanogaster, Sydney Davis

Theses and Dissertations

Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited neurodegenerative disease caused by a CAG repeat expansion in the ataxin-1 gene, which results in an abnormally long polyglutamine tract. Similarly, overexpression of wildtype Ataxin-1 (wt-Atx-1) in Drosophila melanogaster leads to neurodegeneration, reduced lifespan, and impaired negative geotaxis. Observations include disruptions in sleep-wake cycles, increased oxidative stress biomarkers (like protein carbonyls), and dysregulation of developmental genes such as armadillo (arm) and nemo kinase (nmo). Additionally, elevated expression of SUMOylation-related genes (Aos-1, Uba2, and dSmt3 or dSumo) and increased SUMO protein levels indicate enhanced SUMOylation in the brain. Quantitative analysis of neuronal …

Exploring Sexual Dimorphism In A Drosophila Melanogaster Model Of Spinocerebellar Ataxia Type 1, Madelyn Hunter

Theses and Dissertations

Neurodegenerative diseases affect over 36 million people and are characterized by loss of motor control, neuronal degradation, and behavioral changes. The most common of these diseases exhibit sexually dimorphic effects. In this study, Spinocerebellar ataxia type 1 (SCA1) was modeled in the Drosophila central nervous system using the yeast hybrid UAS/GAL4 system. Locomotor activity and clock gene expression was monitored for male and female SCA1 and control flies. Clock genes such as per, tim, Clk, and cyc were monitored over a 24-hour period using qRT-PCR, and distinct sexual dimorphism was detected in locomotor activity and in gene expression for SCA1 …

Generation Of A Transgenic Vector For The Purpose Of Transforming Charcoal Rot Resistance Into Soybeans (Glycine Max), John M. Bear Jr

Electronic Theses & Dissertations

Charcoal rot, caused by Macrophomina phaseolina, is among the most devastating fungal pathogens affecting G. max, particularly in drought-susceptible regions such as the midwestern United States. Traditional agricultural practices have included crop rotation and irrigation, which have proved ineffective or economically unfeasible. Charcoal rot infects over 500 other species of plants and can overwinter as dormant sclerotia which can germinate once soybeans are re-planted and infect young plants. As a result, transgenic solutions have offered a promising alternative for the development of disease-resistant soybeans. This thesis documents the construction of a transgenic vector to express BOZO, a …

Assessing The Effects Of Streptozotocin-Induced Hyperglycemia On Amyloid Beta Accumulation And Cognitive Behavior In A Mouse Model Of Alzheimer’S Disease-Related Pathology, Andrew Adonay Ortiz

UNLV Theses, Dissertations, Professional Papers, and Capstones

Alzheimer’s disease (AD) is an irreversible and devastating neurodegenerative disease characterized by progressive synaptic, dendritic, glial, and neuronal loss, collectively leading to impairments in learning, memory, and deterioration of cognitive and behavioral functions. AD is the most common form of dementia accounting for 60-80% of all cases. AD affects approximately 7 million Americans and is the 6th leading cause of death in the US. Furthermore, by 2050, the US is projected to spend over $1.1 trillion on AD-related treatments. Pathological hallmarks of AD include beta-amyloid (Aβ) plaques, intracellular neurofibrillary tangles (NFTs), and chronic neuroinflammation, which can promote and exacerbate both …

Detection And Quantification Of Total Airborne Fungi And Coccidioides Species In Environmental Samples, Theresa T. Roehr

UNLV Theses, Dissertations, Professional Papers, and Capstones

Fungal exposure can cause acute and chronic illnesses or exacerbate existing illnesses. Some fungi are opportunistic pathogens and can lead to serious systemic fungal infections. In 2020, more than 150 million cases of severe fungal infections were reported globally resulting in an estimated 1.7 million deaths. Coccidioidomycosis, or Valley fever, is classified as a serious fungal infection caused by the fungi Coccidioides immitis and C. posadasii. These particular fungi are prevalent in the soil of the Southwestern United States, including Las Vegas, Nevada. In 2024, there were a total of 269 cases of Valley fever reported in Nevada, and …

Chronic Inflammation: The Link Between A High Added Sugar Diet And Disease, Anna Collins

Senior Honors Theses

The modern diet includes many processed foods that contain added sugars, resulting in a significant increase in daily glucose and fructose consumption. Considering this, there is an increased effort to uncover the effects of excess sugar intake on the body’s health and metabolism. Strong evidence supports the connection between a high added sugar diet and the presence of chronic, low-grade inflammation due to cellular distress and metabolic dysfunction. Prolonged inflammatory responses are linked to tissue damage and the development of various metabolic diseases that are prevalent in modern society, such as obesity, fatty liver disease, cardiovascular disease, and type 2 …

Phosphomimetic Substitution Of Serine Residue Ser260 With Aspartate Suggests Regulation Of Activity Of Human Cytosolic Malate Dehydrogenase By Phosphorylation, Charles Pelagalli '25, Luke Tischio, Kathleen Cornely

Chemistry & Biochemistry Faculty Publications

Human cytosolic malate dehydrogenase (MDH1) is a key enzyme involved in the malate-aspartate shuttle of eukaryotic cells, and which catalyzes the reaction of oxaloacetate to malate. As MDH1 is responsible for maintaining redox homeostasis by regeneration of NAD+ for glycolysis, its regulation is of particular interest in pharmaceutical applications, specifically in treating cancer cells that proliferate quickly and hence rely greatly on glycolysis. While the regulation of MDH1 by the phosphorylation of key residues has been previously documented, work still remains in identifying the specific residues involved in regulation of the enzyme by phosphorylation. In this study, we used …

Mannose: The Hands Of Fate – Overexpressing A Pinus Taeda Hemicellulose Biosynthesis Gene In Populus Tremula × Alba Leads To Increased Height And A Modified Cell Wall Sugar Profile, Joseph Baxter Colbert

Dissertations - ALL

Lignocellulosic biomass as an input for biofuel generation has gained popularity in recent decades due to attainable feedstock ubiquity and an anatomical propensity to fix and sequester carbon. A major challenge facing the integration of such feedstocks is the presence of recalcitrant polymers that are extant in their cell walls, namely lignin and various hemicellulose species. Many studies have illustrated methods in which cell wall modification through genetic means has produced phenotypic improvements with regard to biomaterial generation, though to this point, none have overexpressed exogenous hemicellulose genes to shift the composition of the Populus tremula × alba cell walls. …

Cholesterol Mass Fingerprinting To Probe Cholesterol-Protein Interactions, Warren Lowther

Electronic Theses and Dissertations

Cryomicroscopy, crystallography and NMR have been considered the “gold standard” of structural biophysics for some time. Recent successes in using these techniques has provided us with a plethora of insight into the architecture of different macromolecules like channels, transporters, and other molecular machines. However, information is often limited to a single allosteric state with the macromolecule in a non-native environment. Additionally, these traditional methods tend to be expensive and labor-intensive, requiring samples that are concentrated and highly purified. Chemical crosslinking coupled with mass spectrometry (CX-MS) has emerged as the ideal accessory for the aforementioned structural tools. In order to address …

Cholestasis And Fluid Flow Are Biomechanic Regulators Of Cholangiocarcinoma Progression, Andrew Oleksijew

Theses & Dissertations

Cholestasis, altered or absent bile flow, is associated with poor survival in patients with cholangiocarcinoma, an aggressive cancer of the biliary epithelium. Changes in bile flow often result in stricture or obstruction. Experimental cholestasis promoted tumor growth and progression. However, studies are needed that directly assess the mechanical interaction between bile flow, or bile shear stress, and cholangiocarcinoma signaling. We hypothesized that cholestasis and absent bile shear stress activated cancer signaling and increased aggressive cellular behaviors such as proliferation and migration. Fluid shear stress approximating bile flow was applied by orbital culture plate method and compared to identical static culture …

Drivers And Mechanisms Of Golgi Fragmentation As A Modulator Of Disease, Amanda Macke

Theses & Dissertations

The Golgi apparatus plays a pivotal role in post-translational modification, trafficking, and secretion of proteins, ensuring proper cellular function. As a result, its fragmentation has been implicated in multiple pathological conditions, including alcohol-induced liver injury and prostate cancer (PCa). Despite its known impact on cellular homeostasis, the molecular mechanisms governing Golgi fragmentation remain to be clarified. Additionally, we have only just begun to understand the vast consequences of Golgi disorganization on disease progression.

This dissertation investigates the drivers and mechanisms of Golgi fragmentation, with a focus on its role as a modulator of disease. Using both in vitro and in …

Apolipoprotein E4, Tauopathy, And Brain Injury: Molecular Insights Into Alzheimer's Disease Pathology, Nashanthea J. Roland

Theses & Dissertations

Alzheimer’s disease (AD) is the world’s leading cause of dementia, characterized by progressive atrophy of the hippocampal and cortical brain regions, synapse damage and loss, and a buildup of senile plaques and neurofibrillary tangles composed of β-amyloid peptides and hyperphosphorylated tau, respectively. While age is the most significant risk factor for developing AD, apolipoprotein E4 (APOE4) is the strongest genetic risk factor for AD. Although it is known that APOE4 influences tau pathology, the molecular mechanisms by which APOE4 drives AD pathogenesis and progression remain unclear. In addition to intrinsic contributions to AD, there are many extrinsic factors that can …

Developing Novel Radical Protein Footprinting Methods For Application In Living Systems, Lyle Tobin

Honors Theses

Radical protein footprinting (RPF) is a family of structural biology techniques that generate radicals in situ to label solvent-accessible amino acid residues. Coupled with liquid chromatography/mass spectrometry, RPF enables the characterization of protein higher order structure and sites of protein-protein and protein-ligand interactions. While traditionally performed in vitro, recent advancements have extended RPF to ex vivo and in vivo applications, including intact cells, nematodes, and 3D cell cultures. RPF in living systems allows the structural analysis of proteins and protein complexes in their native environment, preserving physiological interactions, dynamic conformational changes, and structural contexts that might otherwise be lost …

Monitoring Cellular Glycolysis Pathway Kinetics In The Extracellular Medium Using Label-Free, Raman Spectroscopy, Nitin Patil, Zohreh Mirveis, Hugh J. Byrne

Articles

This study explored the potential of Raman spectroscopy to holistically monitor the glycolysis pathway kinetics as a function of time through the extracellular medium. Initially, the collinearity of individual metabolites of interest- glucose and lactic acid as a function of their concentration was tested followed by the sensitivity analysis of the approach by elucidating the limits of detection (0.85 mM and 2.8 mM) and quantification (2.5 mM and 9.5 mM) for glucose and lactic acid respectively in the biological range. In the process several datamining approaches were also explored. Finally, the A549 cell culture was used for kinetic spectral acquisition …

Performative Biomechanics : Evolving Buildings Into Inhabitable Organisms, Josh Lopez

Bachelor of Architecture Theses - 5th Year

There has always been a connection between biology and architecture. Michael Pawlyn, in Biomimicry in Architecture, coined “biomechanical designs” to describe structural techniques derived from creatures. This study investigates chitin-based creatures. Crustaceans, insects, and microscopic organisms all have exoskeletons in nature. With a focus on crabs, other crustaceans and bugs, this study examines and evaluates the formal characteristics of chitin-based organisms. The architectural creations of OXMAN, NOX, which was founded by Lars Spuybroek; and Lebbeus Woods are among those that are analyzed and studied due to their inspiration from living things. They follow functional effectiveness in nature, which is why …

Joe Rogan And The Manosphere In The Age Of Modern Misogyny, Alexandra Klocker

CSB and SJU Distinguished Thesis

Much scholarly research analyzes extreme misogynistic language in “manosphere” forums, due to their connections to radicalization and violence. However, less attention has been given to the prevalence of such content in mainstream media, such as podcasts. The Joe Rogan Experience (JRE) podcast, a prominent and influential platform, has been praised for its wide-ranging discussions but critiqued for fostering and amplifying harmful ideologies, including misogyny. Despite its controversy, limited research has explored how pre-existing misogynistic rhetoric in online communities might shape or influence the content of JRE episodes. This study examines how misogynistic language and themes proliferate in JRE episodes through …

Prevalence Rates Of Tetb, Teta, And Tetm Tetracycline Resistance Genes In Environmental Escherichia Coli Isolates From Local Waterways, Caris Cianelli

Honors Projects

The purpose of this study was to determine the prevalence rates of the tetracycline resistance genes tetA, tetB, and tetM in environmental Escherichia coli isolates. Samples were from both an urban and an agricultural waterway were filtered and incubated with Coliscan™ medium to differentiate for fecal coliforms. The resulting colonies were streaked onto EMB and then TSA plates to ensure isolation and presence of E. coli. All media used were supplemented with 10 µg/mL tetracycline in order to maintain selective pressure on the isolates. DNA from the isolates was then extracted and PCR was run using tetA, tetB, and tetM …

A Comparative Analysis Of Small Nuclear Rna Sequences In Spinacia Oleracea, Arabidopsis Thaliana, And Homo Sapiens, Nhi T. Nguyen

2025 Spring Honors Capstone Projects - Archive

In eukaryotes, the structure and function of the Sm core and its associated small nuclear ribonucleoproteins (snRNPs) play a significant role in pre-mRNA splicing. These snRNPs exhibit a high degree of conservation. While plants also utilize alternative splicing, the conservation of plant snRNAs and other non-coding RNA such as snoRNA and scaRNA, which assemble the Sm core, remains largely unexplored. In this study, plant sequences were compared with human sequences using the multiple sequence alignment program Jalview to determine the conservation of snRNPs in other non-coding RNA. Sequences analysis showed that the Sm site in Spinacia oleracea and Arabidopsis thaliana …

Novel Chloroviruses With Unique Glycans On Their Major Capsid Proteins, Cayden J. Homolka

Honors Program: Senior Projects (Public)

Chloroviruses, of the family Phycodnaviridae, are large, dsDNA viruses with a genome of 290 to 410 kb. These virus genomes are so large that they are classified as “giant viruses”. Within this genome, up to 16 tRNAs and 330 to 450 proteins are encoded. Among the massive amounts of genes and proteins are unique carbohydrate synthesis/metabolism genes, which are responsible for the glycosylation of chloroviruses major capsid proteins. In most viruses, these proteins are glycosylated by the host enzymes located in the endoplasmic reticulum. Instead, Chloroviruses encode their own glycosylation machinery; essentially decorating themselves. Furthermore, these chlorovirus glycans are unlike …

Navigating The Challenges Of Coccidioides Surveillance: Insights From The Environment Of El Paso County, Texas, Tanzir Hossain

Open Access Theses & Dissertations

Coccidioidomycosis, or Valley fever, is a fungal infection resulting from the inhalation of spores from the Coccidioides species (C. immitis and C. posadasii), native to arid areas of the Western Hemisphere. Coccidioidomycosis presents considerable health hazards and can be fatal. It affects between 206,000 and 360,000 individuals annually, leading to 700 to 1,100 fatalities in the United States alone. In response to these issues, extensive research has concentrated on therapeutic goals for this infectious disease. Nonetheless, more limited research has focused on the environmental detection of its causative fungi, which is crucial for forecasting treatment needs and formulating preventive strategies. …

Investigation Into Mycorrhizae Associated With Native Venus' Flytrap Root Tissue, Anna Carnaggio

Electronic Theses and Dissertations

Dionaea muscipula, a plant commonly known as the Venus' flytrap, is found native to the southeast corner of North Carolina and the northeast corner of South Carolina. Several populations of native Venus' flytraps are known to exist in the nutrient-poor peat bog conditions in and around Lewis Ocean Bay Heritage Preserve (LOBHP) in Northeastern South Carolina. Anthropogenic pressures in Horry County, specifically surrounding LOBHP, have resulted in a loss of habitat for several native and endangered species. As a result, conservation efforts are focused on relocating native Venus' flytraps into adjacent habitats to ensure survival. This is only a temporary …

Synthesis And Characterization Of 3,5 Trifluoromethyl Tpm With A Metal Carbonyl Complex, Emily P. Berkman

Undergraduate Honors Thesis Collection

Tris(pyrazolyl)methane (Tpm) ligands have a central carbon with 3 pyrazole rings attached. These were discovered in 1970 and have since been synthesized with many substituents on the rings. Based on the parent structure, my goal was to synthesize a fluorinated Tpm derivative. By adapting existing procedures, I have synthesized a Tpm derivative with trifluorinated methyl groups in the 3 and 5 positions of the pyrazole ring. The fluorinated ligand is expected to be electron withdrawing and exhibit interesting chemistry when bound to a metal center. Future directions of the project will be discussed.

Disulfide-Cleavable Linkers In Antibody-Drug Conjugates For Targeted Cancer Therapy, Emily Hwang

Undergraduate Honors Thesis Collection

This project aims to discover a way to improve the safety of and reduce adverse side effects of disulfide-linked antibody-drug conjugates. Disulfide-cleavable linkers for antibody-drug conjugates function by exploiting the differential concentrations of dominant thiol species in the blood plasma and in the cytosol of malignant cells. This project aimed to identify a relationship between the stability of disulfide cleavable linkers in the blood plasma and disulfide linker structure, to prevent premature release of the cytotoxic drug. Three disulfide linker analogs with varying carbon chain lengths were synthesized through reaction with 2,2’-dipyridyl disulfide. Each analog was conjugated to a fluorescent …

Cultural Health Benefits And Challenges Of Food Preparation And Consumption: A Comparative Study Of The United States, Italy, And Norway, Natalie G. Link

Undergraduate Honors Thesis Collection

This study aims to investigate the cultural health benefits and challenges associated with food preparation and consumption in the United States, Italy, and Norway, with a particular focus on citizens in lower socioeconomic levels. By examining the dietary habits, social structures, and health outcomes in these three countries, this research aims to uncover broader insights into the health status and well-being of their respective populations. The study will employ secondary data analysis approach examining existing research on cultural practices and social support systems. The findings of this research will contribute to a deeper understanding of the complex interplay between food …