Biochemistry, Biophysics, and Structural Biology Commons^™

Development Of Novel Small Molecule Therapeutics For Myotonic Dystrophy, Xhesika Azis

Biological Sciences

Myotonic Dystrophy type 1 (DM1) results from expanded CUG repeat RNA that sequesters MBNL proteins and disrupts alternative splicing. Small molecules that bind toxic repeat RNA and release MBNL proteins represent a promising therapeutic strategy. This thesis examines newly synthesized modified polycyclic compounds (MPCs) engineered to target CUG RNA with enhanced specificity and efficacy. Through Suzuki–Miyaura coupling and benzoquinone-mediated cyclization, MPC03 was synthesized and characterized by NMR and LC–MS.

The biological activity of these compounds was assessed in DM1 patient-derived myotubes and fibroblasts. MPC03 consistently produced dose-dependent rescue of multiple MBNL-regulated exons, restoring splicing patterns toward those observed in healthy …

Expression, Purification And Characterization Of Full Length Tdp-43, Danya Abouzaid

Honors Theses

TAR DNA-binding protein 43 (TDP-43) is a 43 kDa RNA-binding protein linked to several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. 5-7,28,30,33 Studying full-length TDP-43 has been difficult because of its intrinsic instability and tendency to aggregate.19,25,28,33,36 In this study, we focused on overcoming the difficulties to express full-length TDP-43 in E. coli recombinantly. We focused on expressing full-length TDP-43 as a fusion construct with a maltose-binding protein (MBP) to improve solubility and stability. Our strategy was to purify TDP-43-MBP fusion and make biomolecular condensates with RNA before cleaving the tag with thrombin protease. …

Blood-Based Clinical Markers For Early Dementia Detection: Insights From Ad-Detect-Cohort, Benard Aliwa, Jasmit Shah, Olivera Nesic Taylor,, Samuel Nguku, Juzar Hooker, Dilraj Sokhi, Sylvia Mbugua, Litha Musili, Rachel Maina, Harrison Kaleli, Levi Muyela, Anne Njoki Gitere, Anne Nyambura, Zul Merali, Karen Blackmon, Chinedu Momoh

Brain and Mind Institute

Background: Over 55 million people worldwide live with dementia, with more than60% residing in low- and middle-income countries. Alzheimer’s disease, the mostcommon form of dementia, accounts for 60–70% of cases. Early and accurate diagnosisremains a global challenge, necessitating novel approaches to mitigate the diseaseburden. Biomarkers hold significant promise in improving diagnostic accuracy andpredicting disease progression. Validated biomarkers for the preclinical stages ofdementia are crucial for advancing diagnosis and therapeutic strategies. We aimedto identify potential clinical markers for early dementia detection and assess theirpredictive accuracy in identifying high-risk individuals.

Method: We analyzed blood samples from dementia cases (n = 30) and …

Transcription Factors And Regulatory Proteins In The Control Of Eukaryotic Gene Expression, Maya M. Minkara

Honors Theses

Transcription factors (TFs) function as precision switches that integrate signaling inputs, chromatin state, and protein homeostasis to control gene expression. This thesis unites three interconnected research themes: (1) mechanistic studies of the ubiquitin-proteasome system (UPS) in regulating eukaryotic TFs, focusing on polymerase-associated Factor 1 (Paf1) and TATA-box binding protein-associated factor 2 (Taf2); (2) identification of biomarker genes within odor-related TF networks; and (3) integration of published undergraduate research linking molecular regulation, bioinformatics, and synthetic biology. These themes are purposefully structured so that mechanistic insight into TF control sets up network-level discovery and, in turn, motivates applied and translational directions. In …

Bacillus Subtilis: A Bacterium That Can Potentially Degrade Low-Density Polyethylene (Ldpe) And Polyethylene Terephthalate (Pet), Migdalia Flores

Theses and Dissertations

The widespread application and disposal of plastics, such as low-density polyethylene (LDPE) and polyethylene terephthalate (PET), have raised significant environmental health concerns. Because of each plastic’s stability and durability, these plastics exhibit limited natural degradation in the environment. Recently, the environmentally friendly biodegradation of plastics by living microorganisms has attracted more attention, as they can assist in the natural degradation process. In this study, the bacterial strain Bacillus subtilis ATCC6051 was used to degrade LDPE and PET for 60 days. To measure the degradation of low-density (LDPE) and polyethylene terephthalate (PET), the dry weight was taken, and physical characteristics were …

Investigating The Impacts Of Azole Antifungals On Growth Of Cryptococcus Neoformans, Gnanambika Sindhe

All Theses

Cryptococcus neoformans, an opportunistic fungal pathogen is responsible for cryptococcosis, leading to approximately 181,000 deaths annually, predominantly in regions such as Sub-Saharan Africa. Fluconazole, a widely used fungistatic azole, is often administered due to its relative affordability and lower toxicity. However, resistance to fluconazole in C. neoformans can arise through aneuploidy, complicating treatment efforts. This study aims to deepen our understanding of resistance mechanisms to azole drugs by comparing fluconazole with other azoles, including both clinical and agricultural azole antifungals. Disk diffusion assays were performed to evaluate the ability of C. neoformans to develop resistance to these compounds, focusing …

Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk

Dissertations and Theses (Open Access)

Over two decades ago, Dicer was discovered as the primary enzyme responsible for the generation of small RNAs known as the microRNAs (miRNAs) and short interfering RNAs (siRNAs). Spatiotemporal regulation of Dicer-dependent small-RNA biogenesis affects many aspects of biology, including aging, disease progression, fertility, and cancer. Interestingly, a distinct population of Dicer-dependent small RNAs, known as the endogenous siRNAs (endo-siRNAs), are uniquely abundant in the germ cells and gametes, and are critical for normal fertility. Despite their function regulating new life, the mechanisms controlling their biogenesis and subsequent germ cell functions remain poorly defined. Work to parse these mechanisms in …

Exploring Glycosomes As Therapeutic Targets For Trypanosoma Brucei, Sabrina Sutton Pizarro

All Dissertations

Trypanosoma brucei is a protozoan parasite which causes human African trypanosomiasis and the livestock wasting disease, nagana. These parasites have highly specialized peroxisomes, called glycosomes, which house a variety of essential metabolic pathways, including glycolysis. Glycolysis is the sole means of energy production in the infective life stage of T. brucei making glycosomes and the glycolytic pathway promising targets for therapeutic strategies. In this work, we have studied the glycosome as a therapeutic target from multiple perspectives. The first portion of this work addresses drug trafficking. The efficacy of small-molecule inhibitors of glycosomal enzymes is restricted by the rate of …

A Molecular Mechanism Of Epithelial To Mesenchymal Transition (Emt): An Evidence Based Lesson Applying Molecular Biology Through The Lens Of Cancer, Sophie Hasson, Melissa Rowland-Goldsmith

Open Educational Resources

This lesson aims to strengthen students’ critical thinking and molecular biology data analysis skills as well as their understanding of concepts related to the hallmark of cancer: tissue invasion and metastasis. Students begin by learning about the invasion of cancer cells, Epithelial-Mesenchymal Transition (EMT), and an important protein involved in EMT: E-cadherin. They then apply molecular biology knowledge to analyze data from multiple papers to infer the relationship between Snail and E-cadherin in different types of cancers. Next, they continue to interpret data from many papers to determine that a repressor transcription factor is present during EMT in cancer cells …

Engineered An Ultrasmall Curcumin Oral Nanoformulation Restores Intestinal Integrity And Gut Microbiota Dysbiosis, Vivek Sharma, Prateeksha Prateeksha, Balwant Paliya, Sateesh Gupta, Sarvendra Singh, Anand Anunay, Sushil Agrahari, Shailendra Singh, Chandana Rao, Saroj Barik, Brahma Singh

Department of Biochemistry and Molecular Biology Faculty Papers

Antibiotic therapy for bacterial infections often disrupts gut microbiota (GM) and intestinal integrity, inducing chronic inflammation and inflammatory bowel diseases. An effective therapeutic intervention is urgently needed to alleviate the aforementioned adverse effects of antibiotics. Curcumin (CUR) reveals great potential to restore intestinal integrity and GM dysbiosis due to its strong antiinflammatory and prebiotic effects. However, the weak solubility and stability of CUR result in limited bioavailability and a short half-life, which restricts its clinical uses. An ultra-small CUR oral nanoformulation was created using a carboxylated galactomannan (cGM), facilitated by hydrogen bonding between the phenolic hydroxyl groups of CUR and …

Mitochondria-Mediated Epigenetic Transfer Between Chondrosarcoma And Wild-Type Cells, Caleb C. J. Wyckoff

Biomedical Sciences Theses & Dissertations

Glioblastoma (GB), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), cholangiocarcinoma, and chondrosarcoma (CS) cancers all contain mutations in the gene isocitrate dehydrogenase 2 (IDH2). The mutant IDH2 enzyme exhibits transformation of alpha-ketoglutarate (αKG) into the oncometabolite D-2-hydroxyglutarate (D2HG) in the mitochondria of these cancers. Mitochondrial-mediated transfer between cancer cells and recipient cells is a significant event that impacts the physiology of the receiving cell, specifically the epigenetic landscape. Previous experiments indicating increased DNA methylation in mesenchymal stem cells exposed to IDH1 or IDH2 conditioned medium underscore the potential role of D2HG to alter methylation states. Additionally, the presence of …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Dna Extrusion Size Determines Pathway Choice During Cag Repeat Expansion, Mayuri Bhatia, Ashutosh S. Phadte, Anna Lakhina, Anthony R. Monte Carloi Iii, Sarah Barndt, Anna Pluciennik

Department of Biochemistry and Molecular Biology Faculty Papers

DNA triplet repeat expansion causes several primarly neurological disorders like Huntington's disease, myotonic dystrophy type 1, and fragile-X related disorders. There is general consensus that recognition of extrahelical extrusions or hairpin-loop structures (formed by strand slippage) by the DNA mismatch repair protein MutSβ leads to repeat expansion by a mutagenic process. By contrast, the FAN1 nuclease attenuates triplet repeat expansion, the molecular basis of which was explained by our recent finding that FAN1 nuclease cleaves and initiates removal of extrahelical extrusions. Here we show that extrusions containing two or more triplet repeats are subject to recognition and processing by either …

Synthesis Of Disulfide Triazole Phosphorus Fire Retardant Via Photochemical Conditions, Jason Liu

Undergraduate Research Symposium Lightning Talks

The development of fire retardants is critical to enhancing fire safety and advancing fire science. The novel synthesis of a disulfide triazole phosphorus thiolacid fire retardant under photochemical conditions, along with relevant testing on plume generation performance, aims to answer our research goals.The proposed specific synthesis and conditions provide for a more efficient and environmentally greener route compared to conventional methods, utilizing photochemical click reactions. Furthermore, the addition of sulfur element to conventionally sole phosphorus-based FR reduces the chance of leaching by increasing the molecular weight of the compound and overcoming the obstacle of low molecular weight problems while also …

Liver-Directed Base Editing Of Abcc6 Prevents Ectopic Calcification In A Variant-Humanized Mouse Model Of Pseudoxanthoma Elasticum, Lauren C. Testa, Dora Obiri-Yeboah, Hooda Said, Ping Qu, Michael A. Levine, Mohamad-Gabriel Alameh, Kiran Musunuru, Qiaoli Li, Xiao Wang

Department of Biochemistry and Molecular Biology Faculty Papers

Pseudoxanthoma elasticum (PXE) is an autosomal recessive connective tissue disorder characterized by ectopic calcification of elastic fibers throughout the skin, retina, and arteries. It is caused by pathogenic variants in ABCC6 , which encodes a transmembrane transporter that primarily localizes to hepatocytes. Loss of ABCC6 function in hepatocytes leads to systemic deficiency of inorganic pyrophosphate (PPi), a potent inhibitor of calcification; such depletion of PPi from the circulation is responsible for multisystemic ectopic calcification seen in PXE. Therefore, liver-targeted variant correction by genome editing and subsequent restoration of systemic PPi may offer a one-and-done therapeutic approach for PXE. The ABCC6 …

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Data-Driven Modeling Of Dynamics And Adaptation In Mapk Pathway, Elisha Erzoah, Maria Emelianenko, Mariaelena Pierobon

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

[Kadel] A Multilevel Extension Of Boolean Networks Captures Topologically-Stable Hybrid Attractors, Kishore Hari

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Parameterizing Ion–Lipid Interactions From Local Clusters To Reproduce Experimental Bulk Properties Of Lipid Bilayers, W. Matthew Saunders

USF Tampa Graduate Theses and Dissertations

Phospholipids are the main component of cell membranes, providing a delimiting boundary for cells from their environments or from their organelles from the cytosol. Thiscompartmentalization allows cells to maintain quite different solutions within their cells and organelles, including different mixtures dissolved ions. Consequently, these membranes are constantly flanked by complex mixtures of salts at varied concentrations. To study membrane structure, one cannot neglect the contribution of the salts in the local solution. Ions perturb bilayer structure via specific interaction with the phospholipids, primarily with the headgroups. Experimental studies of these systems are somewhat at odds — scattering experiments with different …

Improving Coral Restoration Outcomes Through Novel Molecular Applications, Matthew H. Gamache

USF Tampa Graduate Theses and Dissertations

Coral reef ecosystems are declining globally from numerous stressors, including localized pollution, disease, and marine heatwaves induced by climate change. To preserve these ecosystems, it is critical to identify corals that can withstand stressors—primarily future marine heatwaves—and prioritize them for coral restoration efforts until these stressors are mitigated. Coral responses to thermal stress can be influenced by several partners, including mutualistic microalgae and a vast prokaryotic community. Here, I use advanced molecular techniques to examine which partners (coral host, algal symbiont, and microbial communities) are associated with coral health, how they contribute to holobiont physiology, and their potential to increase …