Molecular Biology Commons^™

Sirna Knockdown Of Rptor Alters Gene Expression In Ewing Sarcoma Cells, Sergio Cipriano, David Leavitt, Michael Oliva, Liam Valdez

Posters - 2026

Ewing sarcoma is a highly aggressive cancer that primarily affects children and young adults. Although treatment options exist, many patients do not respond effectively, showing the need for improved targeted therapies¹. RPTOR is a key in mTORC1 complex which regulates cell growth, proliferation, and survival². LY2874455 is a selective pan-FGFR inhibitor that targets growth factor signaling pathways involved in tumor progression³, and FGFR signaling interacts with pathways such as mTOR, making it a potential target for combination therapies. We hypothesized that silencing RPTOR in Ewing sarcoma cells would disrupt mTOR signaling and alter expression of genes linked to cell survival …

Discovering Drug-Like Compounds By Targeting Protein-Protein Interactions Using A Yeast-3-Hybrid System, Chesley C. Blake

Senior Theses

Protein-protein interactions are important targets in cancer biology as they can make historically “undruggable” proteins viable drug targets. However, the current approach to targeting protein-protein interactions relies on the use of small molecule drugs, which have low efficiencies as they must cover a large surface area of the interaction. Further, traditional drug therapies often lead to off-target toxicity, limiting therapeutic specificity. The objective of this project is to develop a selection system in yeast to identify short peptide sequences that can disrupt protein-protein interactions specific to cancer cells. Following proof of principle and development of the AH109 yeast strain having …

Exploring Base Excision Repair Using Gene Knockout, Gregory Guantos, Cailyn Brock, Kamily Visser, Dylan Vargas

Posters - 2026

•             Base Excision Repair (BER) fixes damaged 3DNA bases throughout the cell cycle by removing damaged bases and replacing either one nucleotide in short-patch BER or a short stretch of nucleotides in long-patch BER. (Hindi, 2021, Cellular and Molecular Life Sciences:CMLS)

•             4G-quadruplexes (G4s) are 4 stranded secondary DNA structures formed in guanine rich areas of DNA and RNA. (Rhodes, 2015, Nucleic Acids Research)

The URA3 plasmid was used as a PCR template to make a gene deletion construct, then yeast were transformed so APN1 was replaced by URA3. 2APN1 encodes a major DNA repair enzyme in yeast, and strains …

Sox18 Unleashed Exploring The Transcriptomic Landscape - Differential Gene Expression Analysis Via Rna Seq In Overexpressed Sox18, Van Nguyen, Kahlie Hernandez, Monabelle Elbayeh

Posters - 2026

Cancer remains a leading cause of death worldwide, and childhood sarcomas such as Rhabdomyosarcoma (RMS) and Ewing Sarcoma (ES) are particularly aggressive with limited targeted treatment options. Despite advancements in cancer therapies, metastatic sarcomas still have a survival rate below 30%, emphasizing the need for new therapeutic targets. SOX18, a transcription factor has played a role in vascular development and endothelial differentiation, functioning as a key driver of angiogenesis. In cancer, increased SOX18 expression has been linked to dysregulated cell migration, invasion, and therapy resistance mechanisms. However, the extent to which SOX18 influences RMS and ES at the transcriptional level …

The Role Of Emerin In Myogenic Differentiation, Nicholas Marano

Theses and Dissertations

The nucleus harbors genetic material encapsulated by the nuclear envelope which is composed of an inner and outer nuclear membrane. The establishment and organization of chromatin at the INM is essential for cell fate during the differentiation program. Integral INM proteins are responsible for chromatin organization at the nuclear envelope. Emerin is a highly conserved type II integral INM protein with roles in chromatin organization, cell signaling, and nuclear structure. Mutations in the emerin gene cause Emery Dreifuss Muscular Dystrophy 1 (EDMD1). Emerin is ubiquitously expressed, but loss of emerin function affects specifically skeletal muscle and cardiac tissue. The precise …

Effect Of Novel Antimicrobial Compounds On Fungal And Bacterial Pathogens, Megan Wilderman

Honors Program: Senior Projects (Public)

Antimicrobial resistance is a growing concern in medicine¹ leading to a need for the development of novel compounds. Two compounds were tested in this study, 2-hydroxyethylhydrazine (HEH) and para-nitrophenyl-isocyanide (NPIC). HEH targets phosphatidylcholine (PC) production², and NPIC targets mitochondrial function³. Choline (Cho) is a compound that bypasses the inhibition of HEH through the Kennedy pathway.² Two-fold serial dilutions were conducted in 96-well plates to test the sensitivity of different bacteria to HEH and fungi to HEH and NPIC in different media types. A choline condition was also included in the HEH dilutions to test …

The Molecular Determinants Of Deglycation And Substrate Specificity In Fructosamine Kinases, Jenet Matlack

USF Tampa Graduate Theses and Dissertations

Protein glycation is a universal, non-enzymatic modification that occurs when a sugar covalently attaches to a primary amine. These spontaneous modifications may have deleterious or regulatory effects on protein function, and their removal is mediated by the conserved metabolic kinase fructosamine-3-kinase (FN3K). Despite its crucial role in protein repair, we currently have a poor understanding of how FN3K engages or phosphorylates its substrates. Additionally, the molecular basis for the distinct yet overlapping substrate specificities of FN3K and its paralog, ketosamine-3 kinase (KT3K), remains unresolved. By integrating structural biology, biochemistry, and ancestral protein reconstruction (APR), this thesis elucidates the catalytic mechanism …

Recombinant Hagfish Intermediate Filament Proteins Enable Neural Culture Substrates That Promote Neurite Extension And Reduce Oxidative Stress, Justin Jones, Kristin Durrant

Browse all Datasets

This dataset supports the production, characterization, and biological validation of a novel recombinant hagfish intermediate filament (rHIF) protein functionalized with spider silk motifs (rHIF-alpha-GRGGL). The data demonstrates a scalable bioprocess resulting in a 7.76 g/L yield, high structural alpha-helicity (77.2%), and significant support for N2a cells.

Tlr3 Mediated Type I Interferon Response In Mammalian Cell Defense Against Cryptosporidium Parvum Infection., Anjelica Matias

Biochemistry and Molecular Biology

Cryptosporidium parvum is a major cause of a diarrheal disease which affects many children in the USA as well as the rest of the world, yet the contribution of its double stranded RNA (dsRNA) viral symbiont, Cryspovirus (CSpV1) to host innate immunity remains unclear. This study investigated whether CSpV1 activates Toll Like Receptor 3 (TLR3) signaling pathways and downstream Interferon type I (IFN I) responses in mammalian intestinal epithelial cells. Confluent Human Ileocecal Colorectal Adenocarcinoma cells (HCT8) were exposed to CSpV1, and the expression levels of Tumor Necrosis Factor Receptor-Associated Factor 3 (TRAF3), Nuclear Factor-𝜅-light chain enhancer of activated B-cells …

Disrupted Nuclear Function And Nucleocytoplasmic Transport In Parkinson’S Disease, Ichiro M. Matoba

The Cardinal Edge

No abstract provided.

The Role Of Fkbp51 In The Regulation Of Reproductive Aging And Prenatal Stress-Impaired Ovarian Function And Development, Monica C. Moore

USF Tampa Graduate Theses and Dissertations

FK506-binding protein 51 (FKBP51) is an immunophilin that acts as a co-chaperone with heat shock protein 90 that negatively regulates transcriptional activity of glucocorticoid receptor (GR) and progesterone receptor (PR), and FKBP51 levels are increased by stress conditions. Our previous studies demonstrate that Fkbp5 gene depletion was protective against maternal re-strained stress-induced preterm birth (PTB), fetal growth restriction (FGR), and maternal stress-induced age-related decline in live births. We hypothesize that FKBP51 contributes to impaired ovarian development and folliculogenesis induced by prenatal stress (PNS). Timed-pregnant Fkbp5+/+ (wild-type) and Fkbp5−/− (knockout) mice were randomly assigned to either the undis-turbed (nonstress) or PNS …

Characterization And Advancement Of Molluscan Venom Gland Cell Model Systems, James V. Parziale

Dissertations, Theses, and Capstone Projects

Venomous mollusks, including cone snails and coleoid cephalopods, produce rich repertoires of bioactive peptides with profound effects on cellular physiology, yet there are few tractable experimental systems that exist to study their development, maintenance, and venom secretion. Although therapeutics such as the cone snail peptide Ziconotide demonstrate the biomedical potential of molluscan venoms, progress in understanding how venom glands form, function, and evolve has been hindered by the lack of reliable husbandry and the complete absence of in vitro cell models. Modern comparative genomics has revealed widespread convergent evolution across venomous lineages, but molluscan datasets remain underrepresented, limiting insights into …

Dna Stability In Aqueous Solutions: A Case Study On Poly A - Poly T Duplex Using Molecular Dynamics Simulations, Haripriya Chennuru

Biochemistry and Molecular Biology

This thesis relies on molecular dynamics (MD) simulations, which apply the AMBER software package to analyze the structural stability, energetics, and dynamics of Poly A - Poly T DNA duplexes. This work is mainly concerned with testing configurations of non-bonded interaction cutoffs (12 Å and 15 Å) on the Generalized Born solvation models (IGB1 and IGB2) to determine the most appropriate conditions regarding computation time and physical reliability in DNA molecular dynamics. The solvation models enable effective simulation of solvent effects, facilitating the calculation of simulation parameters to evaluate structural stability within different environmental conditions. Overall, the performance indicates that …

4e-Bp1 Differentially Regulates Translation Of A Subset Of Human Mrnas, Mehreen Mahbub

Dissertations, Theses, and Capstone Projects

Elevated levels of eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) influence cap-independent translation by forming a complex with eukaryotic initiation factor 4E (eIF4E) (eIF4E•4E-BP1). Certain mRNAs—including those encoding hypoxia-inducible factor-1α (HIF-1α), fibroblast growth factor-9 (FGF-9), and two isoforms of tumor suppressors, p53 (p53_A, and p53_B)—contain structured 5’untranslated regions (UTRs) that enable translation either via cap-independent translation enhancer (CITE)-like or internal ribosomal entry site (IRES)-like mechanisms. However, how 4E-BP1 modulates these mechanisms remains unclear. Using fluorescence-based anisotropy assays, we showed that the eIF4E•4E-BP1 binds more tightly to the 5’ m⁷G-cap of these mRNAs than eIF4E …

Computational And Functional Characterization Of Terebrid Venom Peptides, Favour T. Achimba

Dissertations, Theses, and Capstone Projects

Venom peptides represent a natural repertoire of bioactive compounds that are potent modulators of ion channels. Teretoxins, venom peptides from terebrid snails, remain underexplored despite their structural and functional diversity. This thesis is the first to comprehensively explore the structure and function of teretoxins using a comparative computational sequence and structure model followed by experimental assays. The majority of the functional focus has been on identifying the ion channel molecular targets of uncharacterized teretoxins. Teretoxins, like other venom peptides, are hypothesized to manipulate the cellular function of a diversity of ion channels. Dysregulation of ion channels leads to several …

An Antioxidant Cocktail Of Tert-Butylhydroquinone And A Manganese Porphyrin Induces Toxic Levels Of Oxidative Stress In Cancer Cells, Sandra Tamarin, Hannah Jung, Joseph Lamorte, Laura Biesterveld, Gabriel Piñero, Grace Turchetta, Molly Myers, Rebecca Oberley-Deegan, Aimee Eggler

Student Papers, Posters & Projects

Despite significant advancement in cancer treatments, therapies with minimal toxicity to healthy cells are still limited. One targetable weakness of cancer cells is their sensitivity to oxidative stress. We find that the combination of two antioxidants—the common food additive tert-butylhydroquinone (tBHQ) and a manganese porphyrin in clinical trials, MnTnBuOE-2-PyP5+ (MnBuOE)—increases oxidative stress and causes apoptotic death in several cancer cell lines, but not in mouse primary fibroblasts. Investigating the mechanism of cell death, MnBuOE is observed to catalyze the oxidation of tBHQ, producing the electrophilic quinone tert-butylquinone (tBQ). A critical role for tBQ and its electrophilic character was revealed with …

Dapagliflozin Attenuates Cisplatin-Induced Nephrotoxicity In Rats Through Modulation Of Ros/Nf-Κb, Bcl2/Bax And Pink1/Parkin Signaling Pathways, Esraa K. Khallaf, Eman A. Ramadan, Mohey M. Elmazar, Marwa M. Safar

Pharmacy

Dapagliflozin (DPG), an anti-diabetic drug, has gained attention for its renal protective effects through multiple molecular pathways, yet its impact on mitophagy in cisplatin (CIS) nephrotoxicity remains unclear. This study aimed to examine the impact of DPG against CIS-induced nephrotoxicity in rats, targeting mainly PINK1/Parkin-mediated mitophagy and inflammatory/apoptotic pathways. Male Sprague Dawley rats received DPG (10 mg/kg; p.o) daily for 14 consecutive days and AKI was induced by a single injection of CIS (7 mg/kg; i.p) on day 10. Blood glucose, serum levels of creatinine and urea nitrogen, oxidative stress, inflammatory, apoptotic, mitophagy markers, and histological changes were assessed. DPG …

Defining Rna Oligonucleotides That Reverse Deleterious Phase Transitions Of Rna-Binding Proteins With Prion-Like Domains., Lin Guo, Jacob Mann, Jocelyn Mauna, Katie Copley, Hejia Wang, Jack Rubien, Cristian Bergmann, Jenny Carey, Jessica Merjane, Marilyn Ngo, Jiazhen Xu, Hana Odeh, Jiabei Lin, Bo Lim Lee, Laura Ganser, Emma Robinson, Kevin Kim, Anastasia Murthy, Tapas Paul, Bede Portz, Amanda Gleixner, Zamia Diaz, Ashleigh Smirnov, George Padilla, Ellen Lavorando, Carolann Espy, Yulei Shang, Eric Huang, Alessandra Chesi, Nicolas Fawzi, Sua Myong, Christopher Donnelly, James Shorter

Department of Biochemistry and Molecular Biology Faculty Papers

RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs that prevent FUS fibrillization by promoting liquid phases and distinct short RNAs that prevent and reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. We define a short RNA that dissolves cytoplasmic FUS aggregates, restores nuclear FUS, and mitigates FUS toxicity in optogenetic models and ALS …

Antiestrogens As Bone Protective Therapeutics For Estrogen Receptor-Positive Breast Cancer In The Presence Of Osteoporosis, Faith E. Parker, Emily K. Zboril, David C. Boyd, Rachel Myrick, J. Chuck Harrell

UROP Posters

Breast cancer (BC) is one of the most significant causes of mortality among women and the second leading cause of cancer death in women. The estrogen receptor (ER) is a key oncogenic driver in the majority of breast cancer. ER+ BC is the most common molecular subtype of BC. Management of ER+ breast cancer varies depending on menopausal status. For premenopausal women, the goal is to suppress estradiol production from the ovaries with surgical oophorectomy and/or aromatase inhibitors. In postmenopausal women, endocrine therapy (ET) serves to suppress estradiol production from sources other than the ovaries. During the menopausal transition, estradiol …

Fluorescent Protein Imaging Approaches Uncover Dynamic Subcellular Distribution Of Core Clock Proteins In Neurospora Crassa, Ziyan Wang

Dartmouth College Ph.D Dissertations

Circadian clocks are endogenous self-sustained timekeeping systems that allow organisms to anticipate and adapt to daily environmental cycles. Found in diverse forms of life, these molecular clocks regulate the expression of ~ 40% of the genome in animals, fungi, and plants. In animals and fungi, circadian oscillators are built on transcription-translation feedback loops (TTFLs), in which positive regulators drive the expression of negative regulators which, once synthesized and imported into the nucleus, inhibit their own activators. This precisely regulated negative feedback incorporates multiple steps of delays that are essential for generating ~24-hour rhythms. Through these mechanisms, circadian clocks temporally coordinate …