Life Sciences Commons^™

Structure Of Ergosteryl-Aspartate Synthase Reveals How An Entrapped Trna Is Used Like A Prosthetic Swinging Arm In The Synthesis Of Aminoacylated Sterols, Hanako Murayama, Nathaniel Yakobov, Nassira Mahmoudi, Sasha Legrosdidier, Nicolas Fournier, Solène Zuttion, Kanata Matsumoto, Michihiro Nishimura, Jingwei Ji, Bruno Senger, Laurence Huck, Howard Gamper, Yoshiaki Kise, Ralph Kleiner, Mathieu Frechin, Ya-Ming Hou, Hubert Becker, Yuzuru Itoh, Frédéric Fischer, Osamu Nureki

Department of Biochemistry and Molecular Biology Faculty Papers

Ergosteryl-3β-O-L-aspartate synthase (ErdS) catalyzes tRNA-dependent aspartylation of ergosterol, a lipid essential for fungal cell membrane integrity. However, the functional significance of ergosteryl-aspartate and the molecular mechanisms underlying its synthesis remain unclear. Here, we show that ErdS localization is highly dynamic and that Erg-Asp is required for proper hyphal growth, sporulation, and spore germination, and likely influences stress tolerance. The cryo-electron microscopy structure of ErdS revealed an unprecedented sterol-binding pocket. In addition, the structures in complex with a non-hydrolyzable Asp-N-tRNAAsp show a tRNA-guided intramolecular aminoacyl transfer mechanism between two functional domains of the enzyme. The CCA end of tRNAAsp undergoes a …

High-Throughput Robotic Ethanol Inhibition Assays For Engineered Thermophilic Biofuel Strains, Kevin He, Daniel Olson, Marybeth Maloney, Anthony Lanahan

Wetterhahn Science Symposium Posters

Ethanol stress assays are commonly used to evaluate microbial tolerance, metabolic adaptation, and fermentation performance. However, manual liquid handling introduces variability across replicate wells and small-volume pipetting steps, limiting reproducibility and throughput. This study developed an automated OT-2 robotic workflow to generate replicated ethanol concentration gradients for high-throughput inhibition assays in engineered thermophilic biofuel strains. Kinetic plate-reader measurements were used to quantify ethanol-dependent growth responses under anaerobic fermentation conditions. The reasearch question is: How do engineered thermophilic biofuel strains differ in ethanol-dependent growth inhibition under anaerobic fermentation conditions, and can automated robotic assays improve the reproducibility of these measurements? Can …

Somatic Prosthetics For Planetary Resonance, Disha Dharesh Kumar R

Masters Theses

This thesis investigates how industrial design can transcend extractive technological paradigms in favor of relational interfaces that foster planetary attunement. Framing the climate crisis as a 'crisis of imagination', the research challenges the Western bifurcation of nature and culture by drawing on Indic cosmologies- which recognize stones, plants, and ecosystems as conscious at different levels and participants in a shared cosmic field. By synthesizing research in Biosemiotics, Quantum Information Pansycishm, and Neuroscience, the project redefines intelligence as a distributed, more-than-human phenomenon.

The research materializes as a speculative design artifact: a device that functions as a somatic prosthetic for planetary resonance. …

Crystal Structure Of Mouse Dxo In Complex With The Udp-N-Acetylglucosamine Cap And Molecular Mechanism For The Decapping Reactions, Najeeb Ullah, Selom K. Doamekpor, Liang Tong

Department of Biochemistry and Molecular Biology Faculty Papers

Noncanonical metabolite 5' caps have recently been identified on RNAs, and the DXO/Rai1 family of enzymes can remove these caps in eukaryotes. While the binding modes of NAD, FAD and dephospho-CoA (dpCoA) caps in the active site of mouse DXO have been determined, how DXO recognizes the UDP-glucose (UDP-Glc) and UDP-N-acetylglucosamine (UDP-GlcNAc) caps is not known. In addition, the molecular mechanism by which DXO catalyzes the decapping reactions is still poorly understood, especially the location of the water/hydroxide that attacks the scissile phosphate to initiate the decapping. Here we report the crystal structure of mouse DXO in complex with UDP-GlcNAc …

Combating Β-Lactamase Resistance: From Inhibitor Design To Substrate Evolution, Lian M.C. Jacobs

USF Tampa Graduate Theses and Dissertations

β-lactamase production by bacteria is a major mechanism of antibiotic resistance. These enzymes hydrolyze β-lactam antibiotics, preventing them from binding to and inhibiting PBPs. Although new β-lactam scaffolds and inhibitors are continually introduced into the clinic, resistance often emerges within a few years. Therefore, the development of cross-class inhibitors with novel scaffolds is critical to mitigate this resistance. In parallel, a deeper understanding of the structural and mechanistic basis of β-lactamase resistance is essential. Together, these approaches provide an effective strategy for combating antibiotic resistance.

The first project addressed the need of effective cross-class β-lactamase inhibitors capable of targeting SBL …

The Heterogeneous Response Of Astrocytes In Different Brain Regions Under Metabolic Stress, Pawan Kumar Thapaliya

USF Tampa Graduate Theses and Dissertations

Astrocytes play a central role in maintaining ionic homeostasis, neurotransmitter clearance, and brain en-ergy metabolism. Their excitability, reflected in activity-evoked intracellular sodium (Na+, [Na+]i) and calcium (Ca2+,[Ca+]i) dynamics, is increasingly recognized as a critical determinant of neuronal function and vulnerability, particularly under metabolic stress. Despite their importance, the mechanisms underlying astrocytic ionic signaling and its regional heterogeneity remain incompletely understood. In this thesis, I developed detailed computational and biophysical models to investigate astrocytic Na+ and Ca2+ dynamics, their bioenergetic consequences, and the roles of key ion transporters under physiological and metabolically stressed conditions, validating the models against experi- mental data. …

In Vitro Reversal Of Abc Transporter Mediated Multidrug Resistance In Human Ovarian And Non-Small Cell Lung Cancer Models, Alison K. Kellom, Pia D. Vogel

Biological Sciences Theses and Dissertations

One of the major causes of treatment failure in aggressive cancers is multidrug resistance (MDR), which is linked to the overexpression of membrane efflux proteins that export chemotherapeutics from cancer cells. This mechanism prevents chemotherapeutic drugs from reaching cytotoxic concentrations intracellularly, allowing the cancer to survive. Two primary mediators of this mechanism are P-glycoprotein (P-gp) and Breast Cancer Resistance Protein (BCRP). P-gp and BCRP are transmembrane ATP-binding cassette (ABC) transporters that are frequently overexpressed in MDR cancers. They utilize the binding and hydrolysis of ATP to transport a diverse range of amphipathic molecules of varying size (Schinkel and Jonker, 2003), …

Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos

Student Theses and Dissertations

Microtubules, composed of a/b-tubulin heterodimers, play a central role in breast cancer tumor growth by polymerizing, leading to metastasis and depolymerizing, contributing to proliferation. Human enzymes protein kinase Ca (PKC-a) and cyclin-dependent kinase 1 (Cdk-1) mediate phosphorylation at sites a:Ser165 and b:Ser172, respectively, influencing the growth of microtubules. It is possible that alternating phosphorylation at these sites contribute to an a/b-tubulin “toggle switch” that mediates microtubule instability and tumor growth.

The project investigates the influence of the toggle switch model on microtubule stability by determining the impact of mutants (a:S165D, a:S165N, a:S165S_P, b:S172S_P and a:S165S_P/b:S172S …

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …

Virus-Like Particle Peptoid Conjugate As A Triple-Negative Breast Cancer Targeting Delivery System, Ricky Zhu

Chemistry Theses

Triple-negative breast cancer (TNBC), an aggressive form of breast cancer, characterized by its lack of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER2) poses a therapeutic challenge as common treatment options are rendered ineffective. Here is a strategy to develop a drug delivery system utilizing poly-glycinated LC129 8, a TNBC targeting peptoid, covalently attached to HK97 virus-like particles (VLP) containing a C-terminal LPETG sequence via a sortase mediated reaction. Using the properties of the cage-like structure of VLPs and the TNBC specificity of the LC129-8, high doses of chemotherapy can be efficiently loaded into the …

Skin Of Frog And Scale Of Dragon: Nutritional Cues, Life Cycle Kinetics, And Secretome Dynamics In Batrachochytrium Dendrobatidis, Naomi C. Okada

UNLV Theses, Dissertations, Professional Papers, and Capstones

Nearly 50% of amphibian species are at risk of extinction, making them the most threatened group of vertebrates on the planet. A major driver of these declines is the pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the fatal skin disease chytridiomycosis. Since its discovery in the late 1990s, Bd has been directly implicated in the extinction of 90 species of amphibians and the declines of hundreds more. Despite this devastating ecological impact, relatively little is known about its basic cellular biology.

Bd has a multi-stage asexual life cycle consisting of a motile and infectious zoospore, which encysts (into a …

The Effects Of Cinnamaldehyde On Tetrahymena Thermophila, Sydney Kurland

Publications and Research

In addition to their common use as spices in cooking and baking, cinnamon plants, Cinnamomum zeylanicum and Cinnamomum cassia for example, have long been used in herbal remedies worldwide. Cinnamon contains many vital oils and active compounds including cinnamaldehyde (CMD). Numerous studies looking at potential therapeutic effects of cinnamon have demonstrated its antioxidant, anti-inflammatory, and antimicrobial properties (1, 2, 3).   Therefore, it is important to continue studying the efficacy, benefits, and mechanisms of action of cinnamon and CMD to have a complete understanding of its full potential. Tetrahymena thermophila is a ciliated protozoan commonly used as a model organism to …

Developing Antibodies Against Galectin-3 And Galectin-9 To Target Endometriosis, Ashleigh Burger, Noah Farnsworth, Jared J. Reisnouer, Cheyenne Vue

2026 Symposium

Endometriosis is a disease characterized by pelvic pain and the formation of endometrial-like tissue on the outside of the uterine lining. This condition affects nearly 10% of women across the globe and confirming whether someone has endometriosis requires visualization in surgery. While the specific causes of this disease remain unclear, the over-expression of the Galectins 3 and 9 in ectopic endometrial tissues suggests a role in the development and maintenance of the condition. Monoclonal antibodies (mAbs) are highly specific proteins with potential as diagnostic or treatment tools. The goal of this study is to generate antibodies against Gal3 and Gal9. …

The Influence Of Prosthetic Obturators On Quality Of Life In Individuals With Maxillectomy Defects, Minseok Kim

Oral Health

Abstract

Introduction: In recent years, there has been a growing focus on understanding the impact of oral cancer on patients' quality of life. Prosthetic rehabilitation techniques, such as maxillary obturators, often in conjunction with reconstructive surgery, have emerged as interventions to address the challenges posed by post-maxillectomy abnormalities.

Objective: This study aims to systematically review and evaluate the effectiveness of maxillofacial prosthetic rehabilitation using obturators in enhancing the quality of life of patients following maxillectomy.

Methodology: Systematic review of identified literature spanning the timeframe from 2000 to 2020 was used. The comprehensive search encompassed widely recognized databases including PubMed, …

Windows Of Developmental Susceptibility To Tetrahydrocannabivarin (Thcv) Reveal Stage-Dependent Morphological And Biological Effects, Mirielle Clayton

Honors Theses

Tetrahydrocannabivarin (THCV), a minor cannabinoid found in Cannabis sativa, is gaining attention for its potential therapeutic applications, yet its effects on early development remain poorly understood. This study investigated how the timing of THCV exposure influences morphological, behavioral, and bioaccumulation outcomes in zebrafish (Danio rerio) embryos. Embryos were exposed to 2 μM THCV during discrete developmental windows (6–30, 30–54, 54–78, 78–102) and continuous 6–102 hours post-fertilization (hpf), designed to model early stages of human gestation. Behavioral analysis using a larval photomotor response assay revealed significant reductions in locomotor activity during dark phases, with the strongest hypoactivity observed …

Bax Activation Through The N-Terminal Bh3-Like Domains Of Vdac1 And Vdac2, Autumn A. Peters

Honors Theses

Voltage-dependent anion channels (VDACs) are central to mitochondrial function by mediating metabolite diffusion across the mitochondrial outer membrane (MOM). Two isoforms­­­­­­­­­­­,­­­­­­­­­­­­­­­­­­­­­­­­­­­­ VDACs 1 and 2, are also implicated in apoptosis based on interactions with Bcl-2 family proteins that control this process, including Bax and Bcl-xL. Activation of the pro-apoptotic protein Bax by interaction with ‘BH3-only’ proteins, such as Bim or Bid, induces MOM permeabilization to signal apoptosis, yet accumulating evidence indicates VDACs 1 and 2 may also affect Bax. We discovered that the VDAC N-terminal domains contain high sequence similarity to the conserved BH3 domains within Bcl-2 family members that …

Functionalized Nanodiamonds As Binding Platforms For Single-Stranded Dna, Mallory A. Chapman

Honors Theses

Nanodiamonds (NDs) offer a promising platform for biomolecular applications due to their stability, biocompatibility, and three-dimensional structure. This study focused on developing a nanodiamond–DNA complex in which streptavidin-functionalized NDs would form a protective shell around biotinylated single-stranded DNA (ssDNA), creating a core–shell system like an “M&M” candy with DNA at the center and a protective coating on the outside. DNA has many uses in nanotechnology, including DNA origami, nanomachines, and drug delivery systems, but its degradation limits its practical use, making protective strategies essential.

ND–DNA conjugates were prepared using biotin–streptavidin interactions and analyzed using gel electrophoresis. Initial separation on agarose …

Unc-45b As A Potential Chaperone For The Transcription Factor, Gata-4, Kaylah Owings

Electronic Theses and Dissertations

The cardiac myosin–specific chaperone UNC-45B has been shown to physically interact with the cardiac myosin transcription factor GATA-4. Specifically, this interaction occurs within the chaperoning region of UNC-45B, known as the UCS domain. However, the precise nature of this interaction has not yet been fully elucidated. The present study was conducted to confirm earlier findings and to evaluate whether UNC-45B functions as a chaperone for GATA-4 using bioinformatic approaches. Analysis of the interaction using AlphaFold 3 modeling verified not only that binding occurs at the UCS (chaperoning) domain of UNC-45B, but also that the interaction is associated with an increase …

Biochemical Characterization Of Luciferase In Omphalotus Olearius, James H. Martin

Honors Theses

The overall goal of this thesis was to investigate the genetic basis of bioluminescence in Omphalotus olearius, a bioluminescent mushroom. The project initially focused on growing fungal cultures under controlled laboratory conditions and using molecular techniques such as DNA extraction, PCR, and gel electrophoresis to identify the organism and isolate the gene responsible for light production. The main objective was to insert this gene into a bacterial system to confirm its function through observable bioluminescence. However, repeated difficulties in maintaining viable fungal cultures and errors in molecular procedures resulted in inconclusive results, preventing successful gene identification. Due to these …

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …

Bioinformatic Resolution Of Candidate Stress-Response Homologs In Cryptosporidium Parvum: P53-Family Vs Sestrin Identity, Freeman Tobechukwu Ezeala Mr.

Biochemistry and Molecular Biology

Cryptosporidium parvum is an apicomplexan protozoan of major public-health importance, but accurate genome annotation in this organism remains difficult because of its compact genome, deep protein divergence, and the presence of compositionally biased or low-complexity regions that can mislead similarity-based analysis.

In this thesis, I examined one such annotation problem involving a conserved Cryptosporidium stress-response candidate protein, CPATCC_0028580_t1 (833 aa). The central question was whether this protein is better interpreted as a member of the p53 family, based on similarity to p53-like DNA-binding domains (PF00870), or as a member of the Sestrin family associated with the PA26 domain.

I explored …

Optimizing Expression Conditions For The Overexpression Of Iron Regulatory Protein Bol2 From C. Glabrata, Jade Ikahihifo-Bender, Dr. Caryn Outten, Mrs. Evan Talib

Caravel Undergraduate Research Journal

Due to its unique ability to serve as both an electron donor and acceptor, iron is utilized as a co-factor for many biological processes, including electron transfer, oxygen binding, and vitamin synthesis. Iron is also a key factor during fungal infections as the human host and invading pathogens battle over limited iron pools. The primary iron-responsive transcription factor Aft1 in the opportunistic pathogenic yeast Candida glabrata responds to iron deficiency by activating expression of iron acquisition genes. However, the mechanisms for sensing intracellular iron levels and regulating Aft1 activity in response to iron are unknown. The C. glabrata iron regulation …

The Universe Under A Microscope, Claire Chabot

Caravel Undergraduate Research Journal

No abstract provided.

Discovering The Southern Appalachian Grassy Balds, Nicholas Lenze

Caravel Undergraduate Research Journal

Grassy balds are unique Appalachian wonders, open meadows in the mountains where, ecologically, there should be trees. It has been hypothesized that some of the balds originated more than ten thousand years ago and were kept open by the grazing of large herbivores such as the mastodon and the wooly mammoth. Over the course of earth’s history, environmental and anthropogenic factors have shaped, modified and maintained the balds. Up to one hundred grassy balds were once recognized to exist in the southern Appalachians, but fewer exist today due to forest succession (Gersmehl, 1970). Collectively, the grassy balds share a common …

Ai×Life 2026: Advances In Computational Biology Across Scales For Life & Health Sciences, Suma Mohan S., Devika N. T., Pranavathiyani G.

Conference Proceedings

Book of Abstracts of the International Conference, AIxLife 2026: Advances in Computational Biology Across Scales for Life & Health Sciences, held on 17–18 April 2026, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, INDIA 

About the Conference

Conventional computational biology laid the foundation for biological data analysis through statistical models, algorithms, and curated databases, enabling insights into genes, proteins, and pathways. Today, the integration of artificial intelligence, spanning machine learning, deep learning, and large language models (LLMs) is driving a transformative shift across biological scales, from atomic and molecular interactions to pathways, cellular systems, organisms, and populations.

AI-powered approaches …

Cyanine Dyes As Next-Generation Fluorophores: Applications In Cell Sorting And Fingerprinting Technologies, Super-Multiplexed Spectroscopy, Biomedical Imaging, And Beyond, Lucas Allen Davis

Undergraduate Honors Thesis Collection

As biochemical, pharmaceutical, and medical sciences advance, the demand for technologies capable of probing multiple cellular targets simultaneously continues to increase. Super-multiplexed spectroscopic techniques offer a pathway toward comprehensive cellular fingerprinting by overcoming the spectral limitations of conventional fluorescence labeling. By circumventing the traditional “color barrier,” cyanine-based Raman tags enable the simultaneous discrimination of numerous cellular morphologies, allowing spectroscopy and imaging to be integrated for high-dimensional cellular analysis. Technologies developed in Goda Lab—including high-throughput flow cytometry, virtual freezing fluorescence imaging (VIFFI), Fourier-transform coherent anti-Stokes Raman spectroscopy (FT-CARS), and MERdot nanoparticles—address longstanding trade-offs between throughput, resolution, sensitivity, and multiplexing capacity. Central …

Shark Immunology And Its Biomedical Potential: Evolution, Innovation, And The Imperative Of Conservation, Reesha Bhagat

Undergraduate Honors Thesis Collection

This review aims to shed light on a significant ecological deficit and its implications for the future of science and medicine. Sharks possess a uniquely adaptive, cancer-resistant, and evolutionarily refined immune system with transformative biomedical potential, making their conservation a scientific and medical imperative. We are losing something medically irreplaceable, and we don’t even fully understand it yet. Shark conservation is a pressing scientific imperative because sharks are ecologically essential and represent an irreplaceable biomedical resource.

Sequence Determinants Of Rna G-Quadruplex Unfolding By Arg-Rich Regions, Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui-Ting Lee, Jun Zhang

Faculty Publications

RNA sequences with the potential to form G-quadruplexes (rGQs) are widespread but largely unfolded in cells by unknown mechanisms. rGQ folding status is a critical regulator of RNA splicing and translation. We show that rGQs can be unfolded by SR proteins, SR-related proteins, and other Arg-rich proteins, including SRSF1, SRSF3, SRSF9, U1-70K, and U2AF1. The length and composition of Arg-rich regions are key determinants of this activity: Arg residues are the primary drivers, while acidic residues attenuate the unfolding activity. To unfold ARPC2 rGQ, at least 13 Arg residues are required. Our findings identify Arg-rich proteins as previously unrecognized, helicase-independent …

Evaluation Of Flt3 Inhibition With Quizartinib During Busulfan Conditioning For Hematopoietic Stem Cell Transplantation, Catherine Jankovic

Biochemistry and Molecular Biology

Hematopoietic stem cell transplantation (HSCT) is one of the only curative therapy options for many hematologic malignancies. HSCT relies on effective conditioning regimens to deplete host hematopoietic cells and enable donor engraftment. The alkylating agent Busulfan is widely used in myeloablative conditioning strategies due to its potent cytotoxic effects on hematopoietic cells and ability to clear the bone marrow. However, optimization of conditioning strategies remains an important area of investigation to improve transplant outcomes and reduce toxicity. Preliminary studies have shown that the FLT3 inhibitor Quizartinib synergizes with some chemotherapeutic agents, suggesting that targeted inhibitors may enhance conventional conditioning regimens. …

Genome-Wide Phenotypic Characterization Of Mycobacteriophage Mercurio, Tyler Downs

Departmental Honors & Graduate Capstone Projects

Bacteriophages, or phages, are being piloted as a supplemental or alternative therapeutic to antibiotics against drug-resistant Mycobacterium pathogens, such as M. tuberculosis, which pose a global public health crisis.  Characterizing bacteriophage genomes can provide insights into efficacy in phage therapy before implementation or elucidate new targets to manipulate bacterial growth.  Overexpression of individual phage genes is useful to study a gene product’s function independent of others.  Here, the results of phage Mercurio plasmid library overexpression in plate-based assays are described.  Mercurio infects nonpathogenic Mycobacterium smegmatis and is genetically related to bacteriophages infecting pathogenic Mycobacterium species.  Eleven gene products of …