Life Sciences Commons^™

Development Of A Split Deoxyribozyme-Based Assay For Detecting Hepatitis B Virus, Dalila Zovko

Honors Undergraduate Theses

Rapid, accessible nucleic acid-based detection methods are needed for hepatitis B virus (HBV). A split deoxyribozyme assay was developed for sequence-specific fluorescence detection. The assay was evaluated using synthetic target and plasmid-derived material. The assay showed target-dependent fluorescence and low-concentration linear range with a LOD of 1.9 nM. The assay supports detection and semi-quantification of HBV genetic material as shown using plasmid-derived transcript samples from HBV genotypes B, C, and D. The selected target corresponded to nt 363–406 of the HBV genome and was chosen based on sequence alignment showing conservation across most genotypes. Genotype-specific detection remains a future application …

Dna Half-Adder Based Calculator Driven By 4j Molecular Switches, Andrea Gissele Canizalez Covaleda

Honors Undergraduate Theses

DNA nanostructures have computing functions due to the predictable base pairing of nucleic acids (Watson–Crick). This property allows the programming of DNA circuits that integrate DNA logic gates capable of recognizing oligonucleotides. This molecular device offers the advantages of biocompatibility and potential applications in personalized medicine for diagnosis and therapies.

Our lab has developed DNA logic gates formed by the connection of YES strands via DNA four-way junctions (4J), which can function as molecular switches to develop a DNA-based calculator. Our DNA half-adder calculator nanostructure is designed to recognize up to three combinations of DNA inputs using three DNA strands …

Biochemical Investigations Of F420-Dependent Glucose-6-Phosphate Dehydrogenase From Cryptosporangium Arvum, Sarah T. Al-Noubani

2026 Spring Honors Capstones Projects

F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the conversion of glucose-6-phosphate to 6-phosphogluconolactone using the deazaflavin, Cofactor F₄₂₀. FGD from Mycobacterium tuberculosis has been investigated due to its health relevance to prodrug activation. More recently, FGD from Cryptosporangium arvum (Cryar- FGD) has been investigated due to its broader substrate specificity toward multiple sugar phosphates. Kinetic and NMR studies have shown that Cryar-FGD has dual catalytic activity as a dehydrogenase and isomerase. Further investigations are being conducted on Cryar-FGD to characterize key residues involved in catalysis.

To investigate the catalytically active residues of Cryar-FGD, …

Mechanisms Of Glyphosate Toxicity: Uptake, Mitochondrial Function, And Metabolism, Dionysios Patriarcheas

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glyphosate, the most widely used herbicide in the world, is an inhibitor of chorismate biosynthesis, the precursor of aromatic amino acids. The target of glyphosate is absent in animals, but findings reporting toxicity in model organisms without a known mechanism or target are increasing. Saccharomyces cerevisiae is a useful and versatile model for understanding molecular mechanisms of toxicity. In yeast, previous work has shown that the aspartate/glutamate permease Dip5 is the proposed transporter for glyphosate and that mitochondrial metabolism has been implicated in response to glyphosate toxicity. This dissertation aimed to identify the effects of glyphosate on mitochondrial function through …

The Role Of Small Extracellular Vesicles In Modulating Radiation Resistance In H3k27m-Pediatric Diffuse Midline Glioma, Viral Oza

Theses and Dissertations--Molecular and Cellular Biochemistry

Pediatric diffuse midline gliomas with H3K27M alteration (H3K27M-pDMG) are the leading cause of pediatric brain tumor-associated deaths. All H3K27M-pDMG are initially treated with fractionated radiotherapy, the standard of care, and most children succumb to their disease within two years of diagnosis. There are no universally effective chemotherapies and full resection is impossible due to the diffuse nature of the tumor and sensitive location. There has not been a significant clinical advancement in more than 40 years.

Tumors become completely resistant to radiation within the first six months of treatment. The mechanism of radiation resistance is unknown but is thought to …

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Role Of The Osaa Transcription Factor Gene In Development, Secondary Metabolism And Virulence In The Mycotoxigenic Fungus Aspergillus Flavus, Farzana Ehetasum Hossain

Graduate Research Theses & Dissertations

Aspergillus flavus colonizes oil-seed crops, contaminating them with aflatoxins; highly carcinogenic mycotoxins that cause severe health and economic losses. Genetic studies may reveal new targets for effective control strategies. Here, we characterized a putative WOPR transcription factor gene, osaA, in A. flavus. Our results revealed that osaA regulates conidiation and sclerotial formation. Importantly, deletion of osaA reduces aflatoxin B1 production, while, unexpectedly, transcriptome analysis indicated upregulation of aflatoxin biosynthetic genes, suggesting post-transcriptional or cofactor-mediated regulation. Cyclopiazonic acid production also decreased in the absence of osaA. In addition, the osaA mutant exhibited upregulation of genes in the imizoquin and aspirochlorine clusters. …

Patterns Of Ovarian And Gonadotropin Hormones In Emerging Adult Oral Contraceptive Users, Summer Mcormond

UROP Posters

Oral contraceptives (OCs) are often initiated during adolescence and emerging adulthood, a period of continued maturation of the hypothalamic–pituitary–gonadal (HPG) axis. Because hormonal exposure during this window may shape emotional, biological, and reproductive outcomes, it is important to understand the specific formulations young women take and the hormonal profiles these formulations produce. This study characterizes OC formulation features and measured hormone levels in young adult OC users (n = 30).

Ethinyl estradiol (EE) doses ranged from 0.01–0.035 mg (mean = 0.022 mg), with 70% using ≤0.02 mg. Pill regimens included 21/7 packs (83%), 24/4 packs (10%), and 84/7 regimens (3%). …

Mxene-Enabled Wearable Biosensors: A Design Framework For Autonomous Biosensing, Jegan Rajendran, Gymama Slaughter

Center for Bioelectronics Publications

MXenes, a rapidly expanding family of two-dimensional transition metal carbides and nitrides, have emerged as leading materials for wearable bioelectronics due to their metallic conductivity, termination-rich surfaces, mechanical compliance, and tunable interlayer structures. However, wearable biosensor performance does not arise from conductivity alone, but from coupled interactions among surface termination chemistry, heterointerface engineering, hierarchical architecture, and device integration under dynamic physiological conditions. This review establishes a predictive structure-interface-device framework linking MXene chemistry to system-level performance across electrochemical, mechanical, gas, optical, and energy-storage modalities. We analyze how termination-controlled adsorption governs charge transfer and selectivity, how heterojunction formation modulates carrier density and …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

N-Allylation Of Secondary Amides With Unsymmetrical Propionates, Remi Graff

Honors Theses

The combination of trimethylsilyl trifluoromethanesulfonate (TMSOTf) and Et3N promotes the N-allylation of 4-methoxyacetanilide 2 with unsymmetrical propionates 1 (eq 1). The amide substrate is believed to undergo conversion to a nucleophilic silyl imidate in the presence of TMSOTf and the amine base, which concurrently promotes carbocation formation in the same flask through the loss of trimethylsilyl propionate, leading to N-allylation of the amide. A range of unsymmetrical propionates, accessed by varying the R and R’ substituents, react efficiently in this one-pot process with yields ranging from 44% to 99%, affording regioselective ratios of up to >20:1 through formation of regioisomers …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

The Importance Of The Proline Residue In The Ldiapa Motif Of Cholera Toxin, Akash Bharathan

Honors Undergraduate Theses

Cholera is currently on its seventh global pandemic, disproportionately affecting developing countries. Vibrio cholerae, the bacterial etiologic agent, is able to cause infection by adhering to intestinal epithelial cells and secreting cholera toxin (CT), an AB-type exotoxin that dysregulates signaling pathways. Previous research by the Teter lab has shown that Hsp90, a host cytosolic chaperone, is required for CT to enter the cytosol where it produces toxic effects. Hsp90 binds to CT at two specific motifs, RPPDEI and LDIAPA. The prolines in the RPPDEI motif are essential for binding, but the proline in the LDIAPA has yet to be …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk, Yasir A. Alshehry, Matthew S. Halquist Phd, Sandro R.P. Da Rocha Phd

Graduate Research Posters

Background

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Channel-Opening Kinetics Of Complex Kainate Receptors, Noah S. Saunders

Electronic Theses & Dissertations (2024 - present)

Ionotropic glutamate receptors (iGluRs) are found both pre- and postsynaptically in neuronal membranes, and mediate the majority of fast excitatory synaptic transmission in response to the binding of glutamate, a major excitatory neurotransmitter in the central nervous system (CNS). Ionotropic glutamate receptors are divided into three distinct subtypes: kainate, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and N-methyl-D-aspartic acid (NMDA) receptors. Auxiliary proteins specific to each receptor subtype also play a role in tuning both receptor expression and gating properties, such as neuropilin and tolloid-like (NETO) proteins that modulate kainate receptors, and transmembrane AMPA receptor regulatory proteins (TARPs) that regulate AMPA receptors. Like …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Generating Concentrated Ring Polymers Through Supercoiled And Open Circle Pdna Isoform Separation, Kelsey E. Hodsdon

Honors Theses and Capstones

DNA can serve as a model polymer due to its high uniformity compared to synthetic polymers. Plasmid DNA (pDNA) in particular offers a well-defined, low-dispersity model for studying topologically uniform systems of a cyclic nature. pDNA has unique isoforms known as open circle (OC) and supercoiled (SC). Using fast protein liquid chromatography (FPLC), specifically anion exchange chromatography (AEX), these OC and SC isoforms can be separated in order to access their unique material properties. Our lab was able to yield the pure SC isoform. However, OC isoform separation has been more challenging. Various difficulties arose during this process, including imaging …

Fgf Signaling Is Necessary For Newt Lens Regeneration, Leo Alexander Napoleon

Honors Theses and Capstones

The Iberian ribbed newt Pleurodeles waltl can regenerate the lens by transdifferentiating iris pigmented epithelial (IPE) cells into lens epithelial cells (LECs), but the mechanism by which this occurs remains largely uncharacterized. We aim to mechanistically show an early and critical role for FGF signaling by using small molecules to inhibit FGF receptors and observe the histological and intracellular effects. Two inhibitors were found to completely stall lens regeneration. Cell cycle analysis revealed decreased DNA synthesis and uniformly low but unchanged entry to mitosis under signaling inhibition by staining for EdU incorporation and phospho-histone H3 (pH3), respectively. Western blot revealed …

Generating A Gfp Reporter Via Crispr To Visualize Ssa4 Export, Aara Khairollahi, Rebecca Adams

SPARK Symposium Presentations

In eukaryotic cells, the transport of mRNA from the nucleus to the cytoplasm is a very regulated process controlled by nuclear pore complexes (NPCs). During stress conditions, such as heat shock, most mRNA export is inhibited in Saccharomyces cerevisiae, yet the transcript for SSA4, a gene responsible for refolding denatured essential proteins, is exported. The mechanism behind this selective export remains unknown. To investigate this, we used CRISPR-Cas9 to generate a reporter strain in which the SSA4 open reading frame was replaced or inserted with green fluorescent protein (GFP). This reporter is designed to produce GFP only under conditions that …

Soil Nutrient Sufficiency Versus Plant Nutrient Status In Compost-Amended Soils: Plant Tissue Analysis As A Diagnostic Tool, Chandralekha Joga Miss

Murray State Theses and Dissertations

This study evaluated whether Mehlich III soil nutrient sufficiency ratings reliably predict plant nutrient status and chlorophyll response across contrasting compost application histories. A greenhouse pot experiment was conducted with Chijimisai (Brassica rapa) planted in three treatment soils that had no compost (T1), moderate compost history (T2), and long-term hog manure compost application (T3). Plant performance was assessed through weekly shoot length and chlorophyll content (SPAD) measurements, leaf number at maturity, and leaf tissue nutrient analysis conducted at harvest. Soil test results indicated adequate to high nutrient levels across all three treatments. Leaf tissue analysis, however, revealed substantial …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

The Synergy Between A Silver-Ruthenium Antimicrobial And Aminoglycosides Is Based On Severe Macromolecular Damage, Emmanuel Parkay Oladokun

Theses and Dissertations

The rise of multidrug-resistant (MDR) bacterial pathogens, including uropathogenic Escherichia coli (UPEC), highlights the urgent need for alternative treatment strategies to restore antibiotic efficacy. The silver-ruthenium antimicrobial AGXX exerts potent bactericidal effects through the production of reactive oxygen species (ROS); however, its potential synergy with antibiotics has not been thoroughly investigated. Here, we show that sublethal concentrations of AGXX strongly enhance aminoglycoside-mediated killing across a diverse panel of Gram-negative and Gram-positive MDR clinical isolates, including highly aminoglycoside-resistant strains. Combinational treatments significantly reduced the effective concentrations of gentamicin, tobramycin, kanamycin, and amikacin required to kill bacteria. Mechanistic analyses revealed that AGXX/aminoglycoside …

Interaction Of The Gram-Positive Human Pathogen Staphylococcus Aureus With Host Lipids, Sharanya Paul

Theses and Dissertations

Staphylococcus aureus is a prominent pathogen that is known to incorporate straight-chain unsaturated fatty acids (SCUFAs) into its lipids in addition to the normally biosynthesized branched-chain fatty acids (BCFAs) and straight-chain fatty acids (SCFAs). Furthermore, it has recently been shown that the incorporation of oleic acid into S. aureus lipids significantly enhanced the growth of the organism at low temperatures due to the greater fluidity imparted to the membrane. Together with others in the Wilkinson and Dahl laboratory, I have shown that low-temperature growth is enhanced by various SCUFAs, including the human antimicrobial fatty acids sapienic acid, linoleic acid, and …

Shedding Light On Cellular Glycolysis Pathway Kinetics: Combining Kinetic, Mechanistic Modelling Approaches With Label Free Microspectroscopic Imaging. (Spectralomics), Nitin Patil

Doctoral

Cellular metabolism and its intricate biochemical mechanisms which allow the conversion of nutrients into energy to sustain life are well understood, leading to numerous breakthroughs in science and technology, human health and wellbeing. From an industrial perspective the pathway kinetics are significant for monitoring cellular bioprocesses, screening desired metabolite phenotypes in drug discovery processes, etc.

An initial review of glycolysis pathway kinetics highlighted the lack of sophisticated approaches to monitor the metabolic pathway kinetics as a function of time in a non-destructive, non-invasive, label-free manner. Fluxomics, a metabolomics based approach providing high-throughput insights, can be considered a gold standard approach, …

Evaluating Novel Targeted Combination Therapies For Gastrointestinal Cancers, Joseph A. Goode

Graduate Studies Theses and Dissertations 2026

Gastrointestinal (GI) cancers remain among the leading causes of cancer-related mortality worldwide, with therapeutic resistance continuing to limit the effectiveness of current treatments. Three complementary studies were conducted to identify therapeutic vulnerabilities and evaluate novel combination strategies in pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC).  First, dual inhibition of fibroblast growth factor receptor 4 (FGFR4) and phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling was investigated in PDAC models. A combination of targeted drug treatments reduced viability, clonogenic survival, migration, and suppressed signaling pathways involved in translational control. This supported a functional interaction between FGFR4 and PI3K-mTOR co-activation in …

The Biosynthesis Of The Natural Product N-Nitroglycine, Gabriel Padilla

Graduate Studies Theses and Dissertations 2026

N-Nitroglycine (NNG) is a nitramine [R(R′)N–NO2; R′=H or alkyl] natural product (NP) produced by certain actinomycetes, such as Streptomyces noursei. At the beginning of this project, the biosynthesis of this NP was unknown. The goal was to determine how NNG and its nitramine moiety are enzymatically formed. This could lead to the discovery of novel nitramine NPs with diverse applications as well as alternative/green synthesis of nitramine explosives. This work begins by examining diverse biochemical N–N bond formation strategies. Nitrogen cycle enzymes, nitration of NPs, kutzneride biosynthesis, the aspartate/nitrosuccinate superfamily, hydrazinoacetic acid (HAA) biosynthesis, and streptozocin biosynthesis are among the …

Cell Type-Specific Fatty Acid Signalling And Its Sex Dependence, Emeline Masterson

Graduate Studies Theses and Dissertations 2026

Dietary fat is a highly palatable, energy-dense nutrient whose oral detection powerfully shapes ingestion patterns and metabolic outcomes. Despite clear behavioral and physiological evidence that fat can evoke distinct taste signals, the cellular and molecular mechanisms underlying its transduction remain poorly understood. A critical gap exists in our understanding of the cell-type-specific molecular pathways and how these signals are modulated by hormonal status. This dissertation delineates estrogen-dependent plasticity in FA transduction within the peripheral taste system, revealing coordinated, sex and cell-type-specific modulation of these pathways. To understand the missing mechanisms, FA-evoked responses were compared in Type II cells from wild-type …

Physicochemical Characterization Of Small Extracellular Vesicles: Effects Of Immobilization, Isolation, And Disease State, Bianca M. Mercado Velez

Dissertations, Master's Theses and Master's Reports

Cancer treatments and survival outcomes have improved significantly in the last couple of decades, with survival rates increasing in the U.S. Despite improvements in treatment outcomes, early detection and treatment are crucial for improving cancer prognosis and survival rates. The standard cancer diagnostic procedure of tissue biopsy is highly invasive, leading to the further spread of cancer in some cases. Alternatively, the extraction of biofluids from cancer patients, also called a liquid biopsy, is increasingly popular because it is less invasive and more representative of the tumor microenvironment, which contains cancer cells, tumor genetic material, and extracellular vesicles, including small …