Biochemistry, Biophysics, and Structural Biology Commons^™

The Inaugural Mbio Junior Editorial Board—Lessons Learned And The Path Forward Toward Improving The Peer Review Process, Cynthia Ayefoumi Adinortey, Stephen K. Dolan, Sarah Doore, Rebeccah Lijek, Diana Priscila Pires, Wenqi Yu, Elizabeth B. Draganova, Lennart Schada Von Borzyskowski

Molecular Biosciences Faculty Publications

The inaugural Junior Editorial Board (JEB) of mBio consisted of 64 early-career researchers active from 2022 to 2023. The goal of the JEB was to train early-career researchers in the art of peer review under the guidance of experienced editors. JEB members gained hands-on experience in peer review by participating in modules detailing the publishing process through the lenses of the journal, editor, and reviewer. Ultimately, JEB members applied this new knowledge by reviewing mBio manuscripts. Here, we summarize the background, the mission, and the achievements of the first mBio JEB. We also include possible trajectories for the future editions …

Integration Of Algae And Biomass Processes To Synthesize Renewable Bioproducts For The Circular Economy, Jessica Martin

USF Tampa Graduate Theses and Dissertations

Rapid population growth and global industrialization have substantially heightened the demand for fossil-based fuels and products in various sectors of the global economy, including energy production, transportation fuels, and as raw materials for petrochemicals. The intense consumption of fossil fuels has caused immense environmental impacts, especially pertaining to carbon dioxide emissions. Shifting to renewable feedstocks (raw materials) is expected to reduce these emissions by lowering the carbon footprint of fuels and products compared to traditional fossil-derived alternatives. This transition aligns with the goal of creating a sustainable and circular economy, emphasizing efficient resource use, and reducing waste generation through recycling …

Elucidation Of Molecular Mechanisms Underlying Novel Multi-Targeted Therapy Strategies For, Qianqian Hu

USF Tampa Graduate Theses and Dissertations

EML4-ALK fusion non-small cell lung cancer (NSCLC) represents a distinct subset of lung cancers that possesses unique molecular and clinical features, paving the way for targeted therapeutic interventions. Despite the promise of ALK-directed therapies, challenges such as metastasis at the time of diagnosis and treatment resistance persist, necessitating deeper research into the underlying mechanisms and potential solutions. In the context of these challenges, our study embarked on two specific objectives. The first goal, elucidated in Chapter 2, revolved around brain metastasis, an event critically facilitated by cell migration. Here, we assessed the anti-migratory activities of several clinical ALK inhibitors in …

Utilizing Binding-Based Proteomic Profiling And Mass Spectrometry Imaging As Innovative Tools For Lipid Research, Suzeeta Bhandari

USF Tampa Graduate Theses and Dissertations

Mass spectrometry-based omics research involves global identification and quantification of molecules in the biological system, which can form the basis of the multi-omics approach integrating multiple layers of information to provide a comprehensive overview of systems biology. The investigation of fatty acid amides (FAA) is one such research avenue that benefits significantly from the high-throughput, multi-level, and interdisciplinary approach of integrative omics. Currently, FAA research is dominated by lipidomic-based studies that have successfully identified and quantified >100 different FAAs in different model systems. Few studies are credited with exploring the biological function and evolution of FAA-dependent signaling pathways. Previous literature …

Targeting Bet Proteins Downregulates Mir-33a To Promote Synergy With Pim Inhibitors In Cmml, Christopher T. Letson

USF Tampa Graduate Theses and Dissertations

Chronic Myelomonocytic Leukemia (CMML) is a rare myeloid malignancy with a dismal prognosis and no therapeutic options which are capable of altering the natural course of the disease. There remains a significant need for novel therapies that are able to meaningfully improve patient outcomes. In this study we explore the effectiveness of Bromodomain and Extra-Terminal domain protein inhibitor (BETi) combinations in CMML. Preclinical studies in myeloid neoplasms have demonstrated efficacy of BETi. However, BETi demonstrate poor single agent activity in clinical trials. Several studies suggest that combinations with other anti-cancer inhibitors may enhance the efficacy of BETi. To nominate BETi …

Neuroendocrine Regulation Of Chemokine Receptor-Mediated Leukocyte Migration Via Heteromeric G Protein-Coupled Receptor Complexes, Garrett Enten

USF Tampa Graduate Theses and Dissertations

Neuroendocrine regulation of the innate immune system is a well-documentedphenomenon. The underlying mechanisms, however, are not well understood. Here we show that at least 20 members of the human chemokine receptor (CR) family heteromerize with one or more members of the α1-adrenergic receptor (AR) family and that all CRs, apart from CXCR1, heteromerize with arginine vasopressin receptor 1A (AVPR1A) in recombinant systems. These heteromeric complexes are detectable in human monocytes and the monocytic leukemia cell line THP-1. Though currently technical limitations prevent the direct visualization of endogenously expressed higher-order hetero-oligomeric receptor complexes, we provide evidence through functional analysis and proximity-based …

Thermodynamic Frustration Of Tad2 And Prr Contribute To Autoinhibition Of P53, Emily Gregory

USF Tampa Graduate Theses and Dissertations

The intrinsically disordered transcription factor and tumor suppressor p53 binds to promoter response element DNA upon cellular stress and activates genes associated with cell cycle arrest, senescence, and apoptosis. Disruption of sequence specific binding to target gene promoters is heavily implicated in human health, where a majority of cancers contain mutations localized to the DNA binding domain (DBD) of p53. p53 DNA binding is regulated by posttranslational modifications, associations with cellular factors, and by an autoinhibitory intramolecular interaction. The autoinhibitory intramolecular interaction occurs when the disordered N-terminal transactivation domain (TAD) interacts with the ordered DBD. Previous work in the Daughdrill …

Development Of Bioactive Peptidomimetics, Lei Wang

USF Tampa Graduate Theses and Dissertations

In the past two decades, a lot of different peptidomimetics, such as β-peptides, oligoureas, azapeptides, peptoids, aromatic oligoamides, and others, have been developed. These peptidomimetics with distinctive scaffolds have shown potential in protein surface recognition and mimicry, PPI regulation, catalysis, etc. Moreover, these bioactive peptidomimetics demonstrate much better bioavailability and biostability than the bioactive peptides. To expand the application of peptidomimetics, our group have developed a new sequence-specific peptidomimetics- γ-AApeptide, which is derived from chiral γ-PNA. It shows excellent advantages including highly resistant to various proteolytical degradations and has the potential to increase chemodiversity. γ-AApeptide also exhibits remarkable biomedical applications, …

Development Of Antiviral Peptidomimetics, Songyi Xue

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions (PPIs) are essential for biological processes and are associated with a number of diseases, including cancer, infectious diseases, and neurodegenerative diseases. As a result, modulation of PPIs has been recognized as one of the most promising strategies to develop the novel drugs. Peptide modulators always exhibit higher specificity and affinities with targets than small compounds or monoclonal antibodies, but their broad medicinal effectiveness is constrained by their poor bioavailability and biostability. Peptidomimetics, which have been developed to mimic the structure as well as function of bioactive peptides and proteins, have shown excellent potential in protein surface mimicry and …

Role Of Short Interspersed Nuclear Elements (Sines) Of Maternally Imprinted Microrna Clusters In Hemochorial Placental Antiviral Immunity, Ishani Wickramage

USF Tampa Graduate Theses and Dissertations

The evolution of hemochorial placentas in which the fetal trophoblast is bathed in maternal blood has vastly improved fetal development and survival in primates and rodents, due to the enhanced efficiency of nutrient, gas and waste exchange between the mother and the fetus. However, the extensive contact between the fetal tissues and maternal blood in these placentas also poses an increased risk of vertical transmission of pathogens such as viruses from the mother to the fetus. In response to this selection pressure, hemochorial placentas have evolved robust defense mechanisms to protect the immunologically naive fetus. Unlike somatic cells that require …

Defining A Factor-Induced Signaling Signature For Endothelial Tubulogenesis, Sprouting, And Pericyte Recruitment, Prisca Kuanting Lin

USF Tampa Graduate Theses and Dissertations

Endothelial cells (ECs) form the inner lining of blood capillary walls. Our laboratory has developed a serum-free, defined Factor system that allows for human ECs to sprout, form lumens and tube networks, recruit pericytes, and induce capillary basement membrane deposition in 3D extracellular matrices. We have shown that the Factor system drives morphogenesis through the activation of multiple signaling pathways; however, we do not know if all factors in the Factor system are needed to induce maximal EC morphogenesis. If so, we have yet to identify why the Factors are critical to the model other than that they induce activation …

Novel Roles Of The Blm Syndrome Dna Helicase In Genome Maintenance And Mitochondrial Regulation, Brian B. Rodemoyer

USF Tampa Graduate Theses and Dissertations

Bloom syndrome (BS) is an extremely rare autosomal recessive genetic disorder caused by defects in the BLM gene. Patients with BS display a broad phenotypic spectrum including abnormally short stature, microcephaly, sun sensitivity, insulin resistance, perpetual oxidative stress, and a ~300-fold greater propensity for developing cancer than the general population. As such, BS patients typically do not live past their 20’s. The BLM gene encodes the BLM helicase, a member of the highly conserved RecQ family of 3’ to 5’ DNA helicases. Most of our cellular understanding of BLM is through its role in DNA damage repair through the homologous …

Withaferin A And Immune Checkpoint Blocker Therapy For The Treatment Of Non-Small Cell Lung Cancer, Roukiah Khalil

USF Tampa Graduate Theses and Dissertations

Lung cancer is the first cause of cancer-related deaths in both men and women with an overall five-year survival rate of 28%. Although immune checkpoint blockers (ICBs) are currently FDA-approved for the treatment of non-small cell lung cancer (NSCLC), only 17-20% of patients achieve durable responses by the induction of immunologic memory. The lack of response in most patients can be attributed to the tumor-intrinsic or tumor-extrinsic immune resistance mechanisms. A biomarker of importance is the Programmed Death Ligand-1 (PD-L1), as higher PD-L1 expression is usually associated with a better response to ICBs. Although studies have attempted to combine ICBs …

Exploring Strain Variation And Bacteriophage Predation In The Gut Microbiome Of Ciona Robusta, Celine Grace F. Atkinson

USF Tampa Graduate Theses and Dissertations

Current microbiome studies have shown that the maintenance of homeostasis betweenmicrobial populations (e.g. bacteria, viruses) and the host immune system (e.g. innate immune molecules) is necessary for balancing health and disease outcomes within the host. These studies most often utilize vertebrate models; however, research in this field can benefit from diverse model systems that facilitate our ability to conduct experiments to identify phylogenically conserved rules influencing homeostasis in the gut of animals. The Dishaw has developed the use of a filter-feeding marine invertebrate chordate, Ciona robusta, to model such fundamental interactions[1]–[6]. While most biological diversity and functional contribution within microbiomes …

Effect Of Dual Inhibition Of Atypical Pkc Signaling And Pi3k/Akt Signaling On Cell Viability And Apoptosis In Clear Cell Renal Cell Carcinoma (Ccrcc)., Khandker M. Khalid

USF Tampa Graduate Theses and Dissertations

Renal Cell Carcinoma (RCC) is the most common type of kidney cancer (85%); 75% of the cases involve conventional clear cell RCC (ccRCC). The choice of treatments recommended for clear cell carcinoma and non-clear cell carcinoma include partial nephrectomy (Stage I), radical nephrectomy (Stages II and III), and chemotherapy (stage IV). Phosphatidylinositol-3-kinase (PI3K) inhibitors can be a viable candidate in the chemotherapy of ccRCC because the PI3K/Akt pathway is frequently activated in RCC. Hence, PI3K inhibitors like Alpelisib (BYL719) can be chosen as a treatment. In addition, aPKCs (PKC-ί and PKC ζ) are overexpressed in most cancer cells, and they …

Institutional And Individual Approaches To Change In Undergraduate Stem Education: Two Framework Analyses, Stephanie B. Feola

USF Tampa Graduate Theses and Dissertations

The overarching goal of this dissertation is to examine institutional change initiatives in STEM and to understand the impact of engaging with a specific change strategy on a biochemistry educator’s instructional practice. Institutional change initiatives involve executing an intentional strategy to influence teaching practices within a specific institution. This research investigates NSF-funded change initiatives at three public research universities that were focused on encouraging the adoption of evidenced-based instructional practices (EBIPs) by STEM faculty. As part of an effort to understand how the three institutions approached this task, framework analysis was performed using the initiative’s annual reports to NSF. Further …

Protein Folding Kinetics Analysis Using Fluorescence Spectroscopy, Dhanya Dhananjayan

USF Tampa Graduate Theses and Dissertations

The conformational changes that occur during the folding of a protein is an intensely researched area because of the impact that it has on human health and cellular functions. Protein stability is crucial in the context of protein misfolding and aggregation due to its implications on misfolding diseases such as amyloid fibril degenerative diseases (Alzheimer’s, Parkinson’s). By examining the kinetics of protein folding, we can gain valuable information about the folding mechanism and help us identify potential targets for many of the protein misfolding diseases.

In this study, we present the folding and unfolding kinetics of TEM-1 β-lactamase from Escherichia …

A Novel Role For Enos In Regulating Lymphatic Valve Development During Embryogenesis, Drishya Iyer

USF Tampa Graduate Theses and Dissertations

Lymphedema is a disease that occurs when lymph flow is impaired, resulting in tissue swelling, fibrosis, chronic inflammation and recurrent secondary infections. Lymphatic valves play a critical role in maintaining unidirectional lymph flow and evidence for valve defects have been reported in lymphedema patients. The lack of drugs that can correct lymphatic valve defects warrants a better understanding of the molecular regulators of lymphatic valve development and maintenance. Lymphatic valves first develop during embryogenesis in response to mechanotransduction signaling pathways triggered by oscillatory lymph flow. Since eNOS (gene name: Nos3) is a well characterized mechanotransduction signaling molecule in blood vessels, …

A Forward Genetic Screen Identifies Genes Involved In Gametocyte Development Of The Human Malaria Parasite Plasmodium Falciparum., Jyotsna Chawla

USF Tampa Graduate Theses and Dissertations

Transmission of the deadly malaria parasite Plasmodium falciparum from human to mosquito is achieved by specialized intraerythrocytic sexual forms called gametocytes. Circulating in the vertebrate host, relatively few intraerythrocytic gametocytes are picked up during a bloodmeal to continue sexual development in the mosquito vector. Human-to-vector transmission thus represents an infection bottleneck in the parasite's life cycle for therapeutic interventions to prevent malaria. Though the crucial regulatory mechanisms leading to gametocyte commitment have recently come to light, networks of genes that control sexual development remain to be elucidated. Here, we report a forward genetic approach to identify genes associated with gametocyte …

Apkcs Role In Neuroblastoma Cell Signaling Cascades And Implications Of Apkcs Inhibitors As Potential Therapeutics, Sloan Breedy

USF Tampa Graduate Theses and Dissertations

Neuroblastoma (NB) is a cancer that develops in the neuroblasts. It is the most common cancer in children under the age of 1 year, accounting for approximately 6% of all cancers. The prognosis of NB is linked to both age and degree of cell differentiation. This results in a range of survival rates for patients, with outcomes ranging from recurrence and mortality to high survival rates and tumor regression. Our previous work indicated that PKC-ι promotes cell proliferation in NB cells through the PKC-ι/Cdk7/Cdk2 cascade. We report on two atypical protein kinase inhibitors as potential therapeutic candidates against BE(2)-C and …

Dcaf14 Regulates Cdt2 To Promote Set8-Dependent Replication Fork Protection, Neysha Tirado-Class, Caitlin Hathaway, Anthony Nelligan, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

DDB1- and CUL4-associated factors (DCAFs) CDT2 and DCAF14 are substrate receptors for Cullin4–RING E3 ubiquitin ligase (CRL4) complexes. CDT2 is responsible for PCNA-coupled proteolysis of substrates CDT1, p21, and SET8 during S-phase of cell cycle. DCAF14 functions at stalled replication forks to promote genome stability, but the mechanism is unknown. We find that DCAF14 mediates replication fork protection by regulating CRL4CDT2 activity. Absence of DCAF14 causes increased proteasomal degradation of CDT2 substrates. When forks are challenged with replication stress, increased CDT2 function causes stalled fork collapse and impairs fork recovery in DCAF14-deficient conditions. We further show that stalled fork protection …

Otud5 Limits Replication Fork Instability By Organizing Chromatin Remodelers, Angelo De Vivo, Hongseon Song, Yujin Lee, Neysha Tirado-Class, Anthony Sanchez, Sandy D. Westerheide, Huzefa Dungrawala, Younghoon Kee

Molecular Biosciences Faculty Publications

Proper regulation of replication fork progression is important for genomic maintenance. Subverting the transcription-induced conflicts is crucial in preserving the integrity of replication forks. Various chromatin remodelers, such as histone chaperone and histone deacetylases are known to modulate replication stress, but how these factors are organized or collaborate are not well understood. Here we found a new role of the OTUD5 deubiquitinase in limiting replication stress. We found that OTUD5 is recruited to replication forks, and its depletion causes replication fork stress. Through its C-terminal disordered tail, OTUD5 assembles a complex containing FACT, HDAC1 and HDAC2 at replication forks. A …

The Identification Of Two M20b Family Peptidases Required For Full Virulence In Staphylococcus Aureus, Nathanial James Torres, Devon Rizzo, Maria A. Reinberg, Mary-Elizabeth Jobson, Brendan C. Totzke, Jessica K. Jackson, Wenqi Yu, Lindsey Neil Shaw

Molecular Biosciences Faculty Publications

We have previously demonstrated that deletion of an intracellular leucine aminopeptidase results in attenuated virulence of S. aureus. Herein we explore the role of 10 other aminopeptidases in S. aureus pathogenesis. Using a human blood survival assay we identified mutations in two enzymes from the M20B family (PepT1 and PepT2) as having markedly decreased survival compared to the parent. We further reveal that pepT1, pepT2 and pepT1/2 mutant strains are impaired in their ability to resist phagocytosis by, and engender survival within, human macrophages. Using a co-infection model of murine sepsis, we demonstrate impairment of dissemination and survival …

Structural And Biochemical Characterization Of Epigenetic And Fusion Tyrosine Kinase Cancer Targets For Drug Development, Melissa Bikowitz

USF Tampa Graduate Theses and Dissertations

Cancer is a significant global health burden, as ~40% of the human population is diagnosed with cancer over a lifetime, half of which succumb to the disease. To develop novel compounds as potential cancer therapeutics, an in-depth structural and biochemical understanding of proteins involved in oncogenesis is key. This dissertation centers around the comprehensive structural and biochemical characterization of two classes of proteins critical for cancer cell survival: bromodomain-containing proteins (BRDs) and fusion tyrosine kinases (FTKs).In 2010, small molecule inhibitors targeting bromodomains (epigenetic reader proteins) became heavily popularized due to the druggability and potent anticancer effects of BET inhibitors. …

To Be Or Not To Be: A Tale Of Staphylococcal Gpsb, Lauren R. Hammond

USF Tampa Graduate Theses and Dissertations

There are two big drivers motivating studies into bacterial cell division. The first is a desire to understand life around us. One of the defining characteristics of life is the ability for a cell to grow and divide, and without in-depth knowledge of this process, we cannot truly understand the complexities that allow for life on this planet. The second motivator is to identify new drug targets in the ongoing fight against antimicrobial resistance. Many infectious organisms have become resistant to commonly used antibiotics, and the bacterial cell division machinery is a largely untapped essential process with many potential therapeutic …

Lord Of The Z-Rings: Uncovering The Role Of Mraz And Ftsl In Bacillus Subtilis Cell Division, Maria Louise White

USF Tampa Graduate Theses and Dissertations

Cell division is a complex and highly orchestrated process that requires careful coordination. The process of cell division in prokaryotes primarily occurs via binary fission, where one mother cell becomes two genetically identically and equally sized daughter cells. In most bacteria a key protein, FtsZ, forms a FtsZ ring (Z-ring) to mark the division site and recruit proteins involved in cytokinesis. Whilst much has been learned about the contents and assembly of the divisome in model organisms such as Escherichia coli and Bacillus subtilis factors governing the regulation of divisome are much more poorly understood. …

X-Linked Ubiquitin-Specific Peptidase 11 Increases Tauopathy Vulnerability In Women, Yan Yan

USF Tampa Graduate Theses and Dissertations

Women experience significantly higher tau burden and increased risk for Alzheimer’s disease (AD) than men, yet the underlying mechanism for this vulnerability has not been explained. Here, we demonstrate through in vitro and in vivo models, as well as human AD brain tissue, that X-linked ubiquitin specific peptidase 11 (USP11) augments pathological tau aggregation via tau deubiquitination initiated at lysine-281. Removal of ubiquitin provides access for enzymatic tau acetylation at lysines 281 and 274. USP11 escapes complete X-inactivation, and female mice and people both exhibit higher USP11 levels than males. Genetic elimination of usp11 in a tauopathy mouse model preferentially …

Identification Of Secondary Structural Elements Contained Within The Intrinsically Disordered N-Terminal Tail Of The Bloom’S Syndrome Helicase., Vivek Somasundaram

USF Tampa Graduate Theses and Dissertations

The Bloom’s Syndrome Helicase (BLM) is one of five human RecQ helicases and is necessary for maintenance of genome stability. Whilst a crystal structure exists for the C-terminal domain of BLM, very limited structural knowledge is known about the intrinsically disordered N-terminal tail. This lack of insight exists, despite the fact that the N-terminus of BLM is essential for the overall biological activity of BLM. Here we provide an Nuclear Magnetic Resonance spectroscopy based approach that we used to identify two distinct ⍺-helices contained within the first 100 residues of BLM. In addition, we propose a mutagenesis-based approach involving rationally …

The Role Of Protein Palmitoylation In Two Disorders; X-Linked Intellectual Disability And Covid-19, Ahmed A. Ramadan

USF Tampa Graduate Theses and Dissertations

The spike proteins of enveloped viruses are transmembrane glycoproteins that typically undergo post-translational attachment of palmitate on cysteine residues on the cytoplasmic facing tail of the protein. The role of spike protein palmitoylation in virus biogenesis and infectivity is being actively studied as a potential target of novel antivirals. Here, we report that palmitoylation of the first five cysteine residues of the C-terminal cysteine-rich domain of the SARS-CoV-2 S protein are indispensable for infection, and palmitoylation-deficient spike mutants are defective in membrane fusion. The DHHC9 palmitoyltransferase interacts with and palmitoylates the spike protein in the ER and Golgi, and knockdown …

Regulation Of The Heat Shock Response Via Lysine Acetyltransferase Cbp-1 And In Neurodegenerative Disease In Caenorhabditis Elegans, Lindsey N. Barrett

USF Tampa Graduate Theses and Dissertations

The decline of proteostasis is a hallmark of aging that is, in part, affected by the dysregulation of the heat shock response (HSR), a highly conserved cellular response to proteotoxic stress in the cell. The heat shock transcription factor HSF-1 is well-studied as a key regulator of proteostasis, but mechanisms that could be used to modulate HSF-1 function to enhance proteostasis during aging are largely unknown. In this study, we examined lysine acetyltransferase regulation of the HSR and HSF-1 in C. elegans. We performed an RNA interference screen of lysine acetyltransferases and examined mRNA expression of the heat-shock inducible gene …