Biochemistry, Biophysics, and Structural Biology Commons^™

Out Of This World: An Exoplanetary Workshop, Monica Storss, Bart Kuipers

ELO (un)supervised 2026

The workshop investigates how scientific constraints can productively defamiliarize human experience and create new frameworks for creativity and expression. Participants will produce original work while considering broader questions about environment, perception, and cultural formation in speculative contexts, and how the arts, sciences, and technology inform each other in relational multiplicities. This generative workshop explores how astronomical data from confirmed exoplanets can generate new poetic forms and linguistic constraints. Participants will examine how exoplanetary conditions can shape language, metaphor, and narrative structure. We'll develop from writing exercises that respond to non-terrestrial physical parameters: alternative light spectra, gravitational variations, and atmospheric compositions. …

Multicomponent Deoxyribozyme Probes For Targeted Detection Of Cancer Associated Gene Insertions, Samuel R. Veleke

Honors Undergraduate Theses

Insertions and deletions (indels) in DNA sequences of genes are linked with cancers such as glioblastoma (GB). Thus, indels may be used as potential cancer biomarkers. In the NANOG gene, its pseudogene NANOGP8 has a 22 base pair insertion sequence for GB patients. In this work, the NANOG gene and the insertion sequence were detected in one sample using a dual-fluorescent assay containing two multicomponent split deoxyribozyme (Dz) probe complexes. One complex used TXR fluorescence to detect the gene regardless of the insertion’s presence. The other complex used fluorescein (FAM) fluorophore to detect the insertion. The probes were able to …

Interaction Of The Dap-10 Fluorescent Light-Up Aptamer With An Environment-Sensitive Dye, Crystal Violet, Marina Tsukanova

Honors Undergraduate Theses

Crystal violet (CV) is an environment-sensitive dye whose fluorescence is strongly influenced by microenvironment polarity and viscosity, increasing markedly when rotational and vibrational motions are restricted. While the fluorescence enhancement of CV by fluorescent light-up aptamers (FLAPs) has been noted in literature, the specific binding interactions between CV and aptamers in the DAP-10 family have remained under-investigated.  The objective of this work is to elucidate the binding site interactions between CV and the DAP-10-42 FLAP. It is hypothesized that positions 34 and 35 of the aptamer’s sequence reside in a proposed quadruplex-duplex junction that form the dye-binding pocket of DAP-10 …

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 …

Exploring Anticholinergic Neurotoxicity: Diphenhydramine's Impact On Neuro-2a Cell Morphology, Expression, And Viability, Jordan B. Mcintyre

Honors Undergraduate Theses

Anticholinergic medications, such as diphenhydramine (commonly known as Benadryl), are increasingly recognized for their association with cognitive impairment and neurodegenerative disease. These medications, which inhibit the action of acetylcholine, a neurotransmitter essential for the formation and utilization of the central and peripheral nervous system, have been implicated in conditions such as dementia and may impact fundamental cellular processes like neurogenesis and cell proliferation. This study investigates the effects of diphenhydramine on neurogenesis when introduced to Neuro-2a cells during differentiation. For all studies cells were plated on coverslips or in 6-well plates with differentiation media containing 0 ng/mL, 50 ng/mL, …

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 …

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 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 …

Optimization Of L-Citrulline Production In Corynebacterium Glutamicum, And The Effect Of The Human Small Intestine Environment, Simran S. Ghulldu

Honors Undergraduate Theses

L-citrulline is a crucial amino acid involved in nitric oxide production, which supports cardiovascular health, physical performance, and intestinal well-being. Nitric oxide deficiency is linked to conditions like hypertension, highlighting the need for efficient L-citrulline production. This study attempts to enhance L-citrulline synthesis in Corynebacterium glutamicum, a bacterium widely used in industrial amino acid production, as well as test a The hypothesis is that overexpressing carAB, which encodes carbamoyl phosphate synthetase, will increase carbamoyl phosphate levels and boost L-citrulline production. Two C. glutamicum strains were used: a wild type and the CRBG strain, which has mutations that promote …

Climate Change And Coastal Development Impacts On Oyster Abundances In Mosquito Lagoon, Fl, Emily Suchonic

Graduate Thesis and Dissertation 2023-2024

Live eastern oyster (Crassostrea virginica) reefs have declined by 62.6% in Mosquito Lagoon (ML) along the eastern Florida coast since 1943. While this species creates reefs by successive generations of oysters recruiting to conspecific shells, C. virginica can also attach to non-reef substrates including mangrove roots and armoring (e.g., seawalls), which may help counteract reef habitat loss. In recent decades, warmer winters have enabled red (Rhizophora mangle) and black (Avicennia germinans) mangrove expansion in subtropical salt marshes and temperate estuaries where oyster reefs occur. Additionally, 11.8% of ML's shorelines have been armored as of …

Rhizophora Mangle (Red Mangrove) Seedling Success In Different Habitats In Mosquito Lagoon, Florida, Usa, Mekail N. Negash

Graduate Thesis and Dissertation 2023-2024

Mangroves provide many ecosystem services in coastal environments around the world. These include water quality improvement, creating habitats for terrestrial and aquatic species, and stabilizing shorelines. In central Florida, the red mangrove Rhizophora mangle is a common species in coastal wetlands, and recently the number of individuals successfully recruiting to intertidal oyster reefs has greatly increased, possibly because biogeochemical hot spots are present on oyster reefs due to nutrient-rich biodeposits from the live oysters. To understand how well R. mangle responds in terms of survival and growth to the suite of variables associated within these two unique habitats, I tracked …

Hybridization Kinetics Of Four-Way Junctions Localized On A Dna Scaffold, Katherine N. Taylor

Honors Undergraduate Theses

DNA computing is an ever-growing field with scientists trying to design structures that optimize logic gate communication to develop fast, biologically compatible, computational structures. We hypothesize that by using the principles of DNA computing, it is possible to design a DNA tile capable of studying localized DNA hybridization that can differentiate between oligonucleotides of different structural conformations. This includes synthetically manipulating DNA into a nanostructure that can perform Boolean logic functions to calculate the different rates of hybridization. To test our hypothesis, we designed a DNA Tile that incorporated a 4WJ using YES logic. Linear and hairpin single-stranded (ss) DNA …

Effect Of Molecular Crowders On The Activation Of Cholera Toxin By Protein Disulfide Isomerase, Niral Shah

Honors Undergraduate Theses

Cholera toxin (CT) is a classic A-B type protein toxin that has an A subunit (A1 + A2) and a pentameric B subunit. The catalytic A1 domain is linked to the A2 domain via a disulfide linkage. CTA1 must be dissociated from the rest of the toxin to cause a cytopathic effect. Protein disulfide isomerase (PDI) can reduce the CTA1/CTA2 disulfide bond, but disassembly of the reduced toxin requires the partial unfolding of PDI that occurs when it binds to CTA1. This unfolding event allows PDI to push CTA1 away from the rest of the toxin.

My research question is …

Following Faculty Engaging In Collaborative Action Research To Approach Curricular Change In Undergraduate Biochemistry, Christopher Nix

Electronic Theses and Dissertations, 2020-2023

This study engaged in a curricular redesign of an undergraduate biochemistry course undertaken by a collaborative action research group. The initial portion of this study investigated student conceptual understanding of foundational concepts via a rigorously tested concept inventory. the impact of the redesign on the student foundational conceptual understanding was determined by comparison with a baseline data set. Findings suggest that students enter and exit the biochemistry course with little understanding of key foundational concepts. Examination of student performance after the incorporation of creative exercises showed a significant impact of the curricular changes on two of the concepts of interest. …

Investigation Of Catalysis Of Nitration By Cytochrome P450s, Lannika Johnson

Honors Undergraduate Theses

TxtE is a protein related to cytochrome P450 enzymes, which catalyze a number of reactions that typically involve oxygen and not nitrogen. It has been discovered that TxtE can nitrate tryptophan through an unusual reaction in which it uses nitric oxide (NO) as a nitrogen donor to install the nitro group despite NO typically being considered toxic to bacteria. This project will determine if all cytochromes P450 can catalyze nitration as long as they are given NO. This will have an impact on understanding drug delivery and metabolism for which nitration is important.

Complex Dna Mixture Deconvolution By Single Cell Genomics: Direct Physical Cell Subsampling And High Sensitivity Dna Typing, Kaitlin Huffman

Electronic Theses and Dissertations, 2020-2023

Biological evidence is often found at crime scenes and can comprise of DNA from the victim(s) and perpetrator(s) to a crime as well as from individuals with no direct relationship to the incident. This can complicate analysis as DNA mixtures are one of the more difficult sources of biological evidence to interpret. Probabilistic genotyping (PG) has greatly aided in mixture analysis. However, even with PG, standard bulk mixture approaches do not always result in probative results as allele overlap, artifacts, or low-level minor contributors inevitably cause genotype information loss. Therefore, deconvolution of forensic DNA mixtures into their individual component DNA …

G-Quadruplex Reporters: Structural Studies And Application For Visual And Fluorescent Detection Of Point Mutations In Nucleic Acid Sequences, Ryan Connelly

Electronic Theses and Dissertations, 2020-2023

DNA-based diagnostics traditionally utilize hybridization probes: strands of DNA complimentary to a target sequence that, upon binding, generate a signal to indicate the presence of the target. The classic hybridization probes are the molecular beacon (MB) and TaqMan probes, both single DNA strands with a fluorophore and quencher at opposing ends. Despite their widespread use in applications such as qPCR due to their ability to multiplex with a variety of bound fluorophores, these probes have several shortcomings: temperature limitations for selective target recognition and differentiating single-nucleotide polymorphisms, intrinsic design limitations to interrogate some target sequences, and a high relative cost …

Harnessing The Power Of The Nitro Group In Natural Product Synthesis, Katelyn Bobek

Electronic Theses and Dissertations, 2020-2023

The high reactivity and electron-withdrawing ability of the nitro group makes it a powerful tool in synthesizing a diverse range of bioactive natural products. The potential of the nitro group was employed via two main methodologies: iron (III)-mediated oxidative dearomatization and oxime carbonate butyrolactone formation to reach three important heterocyclic scaffolds; spiro, tropone and γ-butyrolactone. Nitro precursors were enantioselective synthesized by key nitro-aldol (Henry) and nitro-Michael reactions. A library of polysubstituted butyrolactone oxime carbonates were formed under mild DMAP and Boc2O conditions from readily available δ-nitroalcohols in good to high yields with broad functional group tolerability. Six lignan γ-butyrolactone natural …

Characterization Of A Malachite Green Dna Aptamer And Development Of Malachite Green Dna Aptamer Sensor, Martin O'Steen

Electronic Theses and Dissertations, 2020-2023

Hydrogels have been extensively studied for use in applications such as tissue engineering, drug delivery systems, wound dressing, actuators, valves, and sensors in Micromechanical Systems (MEMS), among others. Thermo-responsive hydrogels in particular pose various advantages such as their capability to respond to an external stimulus and reverse the response when the stimulus is removed and the ability to imbibe a significant amount of solvent and increase their volume by over 1000%. Extensive research has been conducted to tune and improve hydrogel's rate and degree of swelling and mechanical properties. Previous work showed that when synthetic clay (Laponite) is cross-linked with …

A Look Into Alzheimer’S Disease—Interventions At The Molecular Level, Priscila Feliciano Nieves

Honors Undergraduate Theses

There are puzzle pieces to the cure for Alzheimer’s Disease (AD), and such can emerge by inspecting the biomolecular interactions and their effects on neuronal cells. The upcoming presented literature review will cover the molecular changes caused by AD pathological progression, explore the relationship between non-AD molecules and AD molecules in the body, and analyze potential contributing factors in AD. In addition, the information to be provided will highlight medicinal alternatives respective to a particular stage in AD.

Investigation Of Dna Hybridization In Localized Systems In Close Proximity, Ashley M. Sewsankar

Honors Undergraduate Theses

Hybridization of two or more DNA or RNA strands is well documented for the process taking place with all strands free in solution or when one strand is immobilized on a substrate. This study contributes to the investigation of the hybridization process when two single DNA strands (ssDNA) are in close proximity. We took advantage of an X sensor in which hybridization of four DNA strands enables the formation of a DNA four-way junction (crossover or X) structure. We immobilized multiple layers of crossover structures to study its hybridization being triggered by short ssDNA coming from solution and further investigate …

Characterization Of A Label-Free Fluorescent Assay For Point Mutation Discrimination Based On Split Aptamer Probes, Shannon A. Beaton

Honors Undergraduate Theses

Due to the misuse of antibiotics, multi-drug resistant (MDR) bacteria have become more rampant in our society; these MDR have given rise to diseases that are not readily curable. One such agent is the Mycobacterium tuberculosis complex, which is a causative agent of tuberculosis (TB). Timely diagnostics of the bacterial infection and detection of bacterial drug-susceptibility profiles helps to initiate the necessary treatment in a timely fashion and to limit transmission of the disease. For more affordable detection of bacterial diseases, such as TN, tag-free split aptamer probes are advantageous. This proposal aims at designing split aptamer probes for detection …

Development Of A Computer Algorithm For Generation Of Primers For Nucleic Acid Sequence Based Amplification (Nasba), Rohit Karnati

Honors Undergraduate Theses

Nucleic acid sequence based amplification (NASBA) is a primer based isothermal method of RNA/DNA amplification. Currently, primer design for NASBA has been restricted to hand creating sequences of oligonucleotides that must follow a set of rules to be compatible for the amplification process. This process of hand-creating primers is prone to error and time intensive. The detection of mutants, post amplification, also offers a benefit in point of care scenarios and the design of hybridization probes for sequences in the region of amplification is also an erroneous and time intensive process. By creating a program to design primers and hybridization …

Probing The Secondary Structure Of Intrinsically Disordered Squid Reflectin Protein Through Ssnmr, Harriet Austin

Digital Repository: Showcase of Undergraduate Research Excellence

No abstract provided.

Optimization Of Dapoxyl Aptamer For Label-Free Bioanalysis, Jack E. Mordeson, Ryan P. Connelly, Pedro F. Madalozzo, Yulia Gerasimova

Digital Repository: Showcase of Undergraduate Research Excellence

No abstract provided.

All Nuts And No Bolts: The Evolution Of Undergraduate Research At A Small State School, James Hawker

Florida Statewide Symposium: Best Practices in Undergraduate Research

In fall of 2017, students first started doing research with their biology instructor, and just a few terms later, two students have earned Portz Interdisciplinary Fellowships. In some ways, the program is going well with students participating in high numbers, but organizers still have questions about the “nuts and bolts” of establishing the program within the institution. Enthusiasm is high! However, key metrics are not being tracked and the workload needs to be distributed more evenly. The organizers will be talking with the audience about different ways to integrate UGR into the institution.

Application And Comparison Of Active Learning Implementation Methods In Biochemistry Education, Dylan Thibaut

Honors Undergraduate Theses

Biochemistry has continued to be one of the most complex and important subjects in science education. The purpose of this research is to investigate active learning implementation methods in a Biochemistry I context to determine the most effective means of preparing current science undergraduates. Two Biochemistry I classes over two semesters were analyzed in this study, with class A using a variable active learning schedule and class B using a consistent active learning schedule. Four aspects were analyzed to determine active learning validity: perception of different active learning properties, standardized final exam grades, class grade, and teaching implementation. The consistent …

Split Probe Detection Of The Influenza A Virus For Improved Diagnostics In A Point Of Care System, Tamar Yishay

Honors Undergraduate Theses

A group of Influenza viruses, RNA containing viruses of the Orthomyxoviridae family, consists of Influenza virus types A-D and has been known to cause the Flu, a respiratory illness associated with numerous detrimental symptoms that can lead to death. Influenza A virus (IAV) is constantly changing and is capable of causing pandemics. Currently used diagnostic methods include virus culturing, immunoassays including rapid influenza detection tests (RIDTs), and molecular assays including those based on RT-PCR. Most of the methods can be only performed in the certified diagnostic laboratories equipped with sophisticated instrumentation and/or special biosafety facilities. The results using these methods …

Urinalysis Screening Of Drugs In Adulterated Samples Via Direct Analysis In Real Time -- High Resolution/ Mass Spectrometry (Dart-Hr/Ms), Bianca E. Olivieri

Honors Undergraduate Theses

Current screening methods for drug analysis with urine samples includes examination of the sample with an immunoassay. These methods are used to determine the concentration of drug metabolites contained within the sample prior to further confirmatory testing. Drug testing plays a crucial role in maintaining safe workplace environments and safety of individuals. However, a positive result can lead to heavy consequences for the employee including suspension or removal from the workplace. Therefore, a majority of individuals add commonly known products into the sample to evade detection by developing a false negative result. Although specimen integrity examinations are performed to identify …