Biochemistry, Biophysics, and Structural Biology Commons^™

Genome Maintenance Roles Of Polycomb Transcriptional Repressors Bmi1 And Rnf2, Anthony Richard Sanchez Iv

USF Tampa Graduate Theses and Dissertations

The coordination of transcription, replication, and DNA damage response (DDR) is vital for maintaining normal cellular homeostasis. All of these processes take place on the chromatin and thus, the temporal and spatial separation of the factors responsible are necessary for each to be correctly completed. Here we detail several novel processes contributing to this network.

BMI1 is a component of the Polycomb Repressive Complex 1 (PRC1) which plays a key role in maintaining epigenetic silencing programs during development. Recently, BMI1 and other members of PRC1 like RNF2 have been implicated gene silencing during the DDR; however, the mechanism through which …

Mechanistic And Translational Studies On Skeletal Malignancies, Jeremy Mcguire

USF Tampa Graduate Theses and Dissertations

New treatment strategies are desperately needed for treating skeletal malignancy. Skeletal malignancies can be either primary cancer that originated in the bone, such as osteosarcoma, or metastatic cancer that spread from another organ to the skeleton, as in the case of breast or prostate cancer. In this thesis, I will detail two projects that focus on the discovery of new treatment strategies for both primary skeletal malignancy and metastatic skeletal malignancy.

The first project focuses on the primary skeletal malignancy, osteosarcoma, a rare cancer that is commonly diagnosed in children and young adults and metastasizes to the lungs. The survival …

Discovery And Characterization Of Small Molecule Inhibitors Of Bromodomains, Md Rezaul Karim

USF Tampa Graduate Theses and Dissertations

The epigenetic “reader” modules bromodomains (BRDs) exert their diverse cellular functions through the recognition of acetylated lysines on histones and other proteins. Small molecule inhibitors of bromodomains have emerged as a promising therapeutic strategy to treat atherosclerotic cardiovascular diseases and cancers. Therefore, a large number of small molecule bromodomain inhibitors have been developed in the last decade, some of which are currently being assessed in the clinic. However, the success of bromodomain inhibitors is currently limited to the bromodomain and extra-terminal domain (BET) subfamily.

To address these, bromodomains outside the BET subfamily (non-BETs) such as TAF1, BRD7/9, TRIM28, and BRD8 …

Surface Runoff Alters Cave Microbial Community Structure And Function, Madison Davis, Maria A. Messina, Giuseppe Nicolosi, Salvatore Petralia, Melvin D. Baker, Christiana K. S. Mayne, Chelsea M. Dinon, Christina J. Moss, Bogdan P. Onac, James R. Garey

Molecular Biosciences Faculty Publications

Caves formed by sulfuric acid dissolution have been identified worldwide. These caves can host diverse microbial communities that are responsible for speleogenesis and speleothem formation. It is not well understood how microbial communities change in response to surface water entering caves. Illumina 16S rRNA sequencing and bioinformatic tools were used to determine the impact of surface water on the microbial community diversity and function within a spring pool found deep in the Monte Conca Cave system in Sicily, Italy. Sulfur oxidizers comprised more than 90% of the microbial community during the dry season and were replaced by potential anthropogenic contaminants …

Study Of The Therapeutic Effects Of Synchronization-Modulation Of The Na/K Pump On Muscle Fatigue, Jason E. Mast

USF Tampa Graduate Theses and Dissertations

It has been shown that by applying a specially designed oscillating external electric field to a cell membrane that the membrane's sodium/potassium pumps can be synchronized to all work at the same rate. Then by slowly increasing the electric field's frequency the pumps' turnover rate can also be increased. By increasing the pumps' turnover rate, the sodium and potassium concentration gradients can be increased, this type of stimulation is called synchronization-modulation. There are three generations of the synchronization-modulation waveform each with different utilities. In particular, the third generation of synchronization-modulation has the ability to use the energy of the external …

Allosteric Control Of Proteins: New Methods And Mechanisms, Nalvi Duro

USF Tampa Graduate Theses and Dissertations

Allostery describes the phenomenon where perturbations in one region of a protein affect protein behavior in another non-overlapping region. Considerable efforts made over decades to understand the molecular basis of allostery, yet an overarching theory that can predict signaling pathways and contributions from chemical components is still lacking. In fact, molecular details in even the most well-studied of model systems, PDZ domains and GPCRs, remain unclear. In this dissertation I use molecular simulation methods to understand the role of allostery in the regulated entry of paramyxovirus into host cells, and also develop a new method to determine time-dependent signaling pathways …

A Novel Intramolecular Interaction In P53, Fan He

USF Tampa Graduate Theses and Dissertations

The p53 tumor suppressor is a sequence-specific DNA binding protein that activates gene transcription to regulate cell survival and proliferation. The activation process involves post-translational modifications that suppress p53 degradation by MDM2 and increase p53 DNA binding affinity. p53 is mutated in ~50% of human tumors, with higher frequency in specific tumor types and after relapse. Mutated p53 loses transcriptional activity and gains new functions that drive tumor progression. Both N-terminus (NT) and C-terminus (CT) of p53 contain intrinsically disordered regions. The p53 CT has well-documented effects in regulating DNA binding. CT truncated p53 mutants showed defective DNA binding and …

To Mid-Cell And Beyond: Characterizing The Roles Of Gpsb And Ypsa In Cell Division Regulation In Gram-Positive Bacteria, Robert S. Brzozowski

USF Tampa Graduate Theses and Dissertations

The bacterial cell division protein FtsZ is a tubulin homolog that forms a ring-like structure at the site of cell division in most bacterial species. There it acts as a scaffold, aiding in the recruitment of other divisome proteins to the site of cell division. Furthermore, studies focusing on the role of FtsZ treadmilling and septal peptidoglycan synthesis implicates that FtsZ plays a direct role in the ultimate closure of the division septum. Thus, many studies in the field of bacterial cell division have focused on FtsZ in terms of its spatial and temporal regulation as well as its ability …

The Role Of Apkcs And Apkc Inhibitors In Cell Proliferation And Invasion In Breast And Ovarian Cancer, Tracess B. Smalley

USF Tampa Graduate Theses and Dissertations

Research has demonstrated that the atypical protein kinase C-zeta (PKC-ζ) is a component of many dysregulated pathways in breast and ovarian cancer, including cellular proliferation, survival, and cell cycle upregulation. Breast and ovarian cancers affect women every day and are second and fifth leading cause of cancer death. Women who seek treatments are commonly met with invasive surgeries or chemotherapy. Protein kinase C (PKC) is a family of serine and threonine phosphorylating kinases that have been shown to modulate and transduce signaling cascades that play roles in the development and survival of cancers. Atypical PKC (aPKC), have been heavily suggested …

Structure Based Inhibitor Discovery Targeting Multiple Β-Lactamases Involved In Antibiotic Resistance, Afroza Akhtar

USF Tampa Graduate Theses and Dissertations

Emergence of antibiotic resistance severely threatens the existing medication and prevention facilities against an over increasing range of infections caused by a wide range of microbes. Specifically, treatment of Gram-negative bacterial infection is getting more problematic due to their resilience against β-lactam antibiotics: the most commonly prescribed antibiotics in clinical settings. Production of β-lactamases is the most prevalent mechanism utilized by various Gram-negative pathogens to become resistant to the β-lactam antibiotics e.g, penicillins, cephalosporins, carbapenems and monobactams. These enzymes mediate their function through hydrolyzing the core β-lactam ring present in all β-lactam antibiotics which causes opening of the ring and …

Development And Application Of Computational Models For Biochemical Systems, Fiona L. Kearns

USF Tampa Graduate Theses and Dissertations

Chemistry is the study of matter and its transformations. Computational chemistry uses computer models to study chemistry in all its intricate complexity. In this thesis I hope to accessibly introduce fundamental concepts central for computational chemistry including quantum mechanics, molecular mechanics, and multiscale modeling. I then present several works which I have conducted throughout my graduate career employing many different computational methods. The investigations described here can be summarized as follows. Chapter 2.1 modeling proteins involved in crustacean molting, and identifying possible inhibitors to this molting. Chapter 2.2 modeling d-fructose bound to synthetic saccharide receptors with hopes of improving saccharide …

Evaluation Of Optimal Technique For Left Breast Irradiation, Amitpal Singh Saini

USF Tampa Graduate Theses and Dissertations

Numerous studies have indicated that radiation therapy reduces the risk of the local recurrence of breast cancer in several cases and that it has increased the overall survival rate. Although radiation therapy is beneficial for the treatment of breast cancer, it is known to increase the risk of both radiation toxicity and secondary breast cancer. In left-sided breast cancer, radiation therapy treatment often leads to the heart and its components—such as the left ventricle and left anterior descending artery—being exposed to high doses of radiation because of the proximity of the heart to the left breast, resulting in cardiac complications …

Bioaccumulation And Biomagnification Of Potential Toxic Elements (Ptes): An Avicennia Germinans–Uca Rapax Trophic Transfer Story From Jobos Bay, Puerto Rico, Michael Martinez-Colon, Henry Alegria, Hatice Kubra-Gul, Ashley Huber, Perihan Kurt-Karakus

USF St. Petersburg Campus Faculty Publications

In southern Puerto Rico along the coastline bordering the Jobos Bay National Estuarine Research Reserve, environmental encroachment has exposed mangrove forest to different sources of pollution. Potentially toxic element concentrations from the F1Tess (exchangeable), F4Tess (oxidizable), mangrove leaf litter (MLL), and fiddler crab whole body soft tissue were analyzed to assess the fate and transport of pollutants from the environment and its transition into flora-fauna via trophic transfer. Geo-accumulation factor values suggest the bay has experienced limited to no pollution when combining the concentrations of potentially toxic elements extracted from the F1Tess and F4Tess sediment fractions. These geochemical sedimentary compartments …

Draft Genome Sequence Of Verrucosispora Sp. Strain Cwr15, Isolated From A Gulf Of Mexico Sponge, Sarah J. Kennedy, Eleonora Cella, Mohammad Jubair, Taj Azarian, Bill J. Baker, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

Here, we present the draft genome sequence of Verrucosispora sp. strain CWR15, a bacterial symbiont of a Gulf of Mexico sponge. The genome consists of 35 contigs encoding 5,840 genes. The genome is the basis for future study and presents an underexplored taxonomy and biosynthetic potential.

Mir146a-Mediated Targeting Of Fancm During Inflammation Compromises Genome Integrity, Devakumar Sundaravinayagam, Hye Rim Kim, Tingting Wu, Hyun Hee Kim, Semo Jun, Jeong-Heon Cha, Younghoon Kee, Ho Jin You, Jung-Hee Lee

Molecular Biosciences Faculty Publications

Inflammation is a potent inducer of tumorigenesis. Increased DNA damage or loss of genome integrity is thought to be one of the mechanisms linking inflammation and cancer development. It has been suggested that NF-κB-induced microRNA-146 (miR146a) may be a mediator of the inflammatory response. Based on our initial observation that miR146a overexpression strongly increases DNA damage, we investigated its potential role as a modulator of DNA repair. Here, we demonstrate that FANCM, a component in the Fanconi Anemia pathway, is a novel target of miR146a. miR146a suppressed FANCM expression by directly binding to the 3’ untranslated region of the gene. …

Cornus Officinalis Promotes Igfbp2 And Autophagy In Human 1.1b4 Pancreatic Cell Line As Revealed By Employing A Global Proteomic Approach Via Mass Spectrometry, Arielle Elizabeth Tawfik, Jennifer Guergues, Stanley M. Stevens Jr, Brant Roger Burkhardt

Molecular Biosciences Faculty Publications

Type 1 diabetes (T1D) results in the loss of pancreatic beta cells and subsequent loss of insulin production. Exogenous insulin is the only effective treatment, but there is still no cure or interventional therapy available to inhibit progression of T1D. Successful T1D interventional therapy must protect pancreatic beta cells from autoimmunity while enhancing beta cell survival and function. Our data suggests Cornus officinalis (CO) may be a candidate for interventional therapy to protect pancreatic beta cells from autoimmune attack and increase their function. CO has been used in traditional Chinese medicine (TCM) for over 2,000 years and has shown characteristics …

Constituent Partitioning Consensus Docking Models And Application In Drug Discovery, Rainer Metcalf

USF Tampa Graduate Theses and Dissertations

This work expounds on some of the current computational tools and programs available and the best practices associated with their use. A high-level introduction, intended for both novices and the semi-experienced, focusing on the more common programs used in scientific literature is the scope of this topic. Both classical and quantum techniques are described. Classical methodologies include Molecular Dynamics, Monte Carlo, energy minimization methods, molecular docking, low-mode, and homology modeling. Quantum chemistry techniques are also discussed encompassing Hartree-Fock, Post-Hartree-Fock theories, and Density Functional Theory along with associated basis sets.

Along with established methodologies, novel theoretical methods are introduced for furthering …

The Role Of Atypical Protein Kinase C In Colorectal Cancer Cells Carcinogenesis, S M Anisul Islam

USF Tampa Graduate Theses and Dissertations

Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer-related death worldwide. CRC is a life-threatening disease due to therapy-resistant cancerous cells. The exact mechanisms of cell growth, survival, metastasis and inter & intracellular signaling pathways involved in CRC are still a significant challenge. Moreover, the treatment of metastatic CRC considered palliative for many years aimed for an improved life, with little hope of a cure, highlighting the need for developing novel targeted therapy for CRC. Hence, investigating new molecular mechanism(s) that lead to colorectal carcinogenesis may give insight into the therapeutic target. …

Amyloid Protein Aggregation And Associated Toxicity, Chamani A. Niyangoda

USF Tampa Graduate Theses and Dissertations

Amyloidosis is a group of diseases in which amyloid fibrils accumulate and deposit into plaques and intracellular inclusions which lead to disruption of the tissue architecture and function. Most of the amyloid diseases are incurable due to a lack of understanding of the amyloid formation, as well as associated toxicity. My research work is focused on three different aspects of amyloid aggregation.

The aim of the first project is to investigate the potential use of deep-blue autofluorescence (dbAF) as an intrinsic optical probe to study amyloid self-assembly. This novel fluorescence signal is excited at the long wavelength edge of the …

The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus, Brittney D. Gimza

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a highly successful pathogen capable of producing a wealth of virulence factors in the human host. Of note, ten extracellular proteases are produced alongside these virulence factors and play a multifaceted role during infection. They not only cleave host proteins to promote bacterial invasion, immune evasion and survival, but also control disease progression by modulating the stability of self-derived pathogenic determinants. The importance of the secreted proteases modulating virulence factor stability is evidenced by our groups previous finding that a protease-null strain has a substantially increased infectious capacity in a murine model of sepsis; resulting from the …

A Novel Cytokine Response Modulatory Function Of Mek Inhibitors Mediates Therapeutic Efficacy, Mengyu Xie

USF Tampa Graduate Theses and Dissertations

Despite the recent success of immune-checkpoint blockade therapy for late-stage non-small cell lung cancer (NSCLC), lung cancer is still the leading cause of cancer deaths worldwide. One of the most important characteristics of lung cancer in therapeutic decision-making are the targetable molecules, including EGFR, ALK, BRAF, and MEK. The excitement of immune-checkpoint blockade therapy has triggered concerted efforts that focus on exploring combinations of immune checkpoint therapy with other approved therapeutic regimens aiming at further augmenting positive outcomes and survival. However, the lack of understanding of underlying mechanisms and evidence-based clinical testing has hindered the progress to a cure. Hence, …

Targeting Bacterial Resistance And Cancer Metastasis: A Structure Based Approach, Kyle Galen Kroeck

USF Tampa Graduate Theses and Dissertations

Current research in pharmaceutical development commonly utilizes a profusion of methods in molecular modeling in order to probe intricate biological problems. Many original and promising compounds have been identified and developed by integrating experimental and computational methods. Structural biology utilizes many different research techniques including x-ray crystallography, NMR, and electron microscopy in order to develop molecular models of macromolecules that are of biological interest. Such techniques can be used in conjunction with molecular docking, which utilizes those molecular models in order to target macromolecules of therapeutic interest by computationally analyzing the conformations adopted by ligands upon interaction with a desired …

An Investigation Into The Heterogeneity Of Insect Arylalkylamine N-Acyltransferases, Brian G. O'Flynn

USF Tampa Graduate Theses and Dissertations

Arylalkylamine N-acyltransferases (AANATs) have in recent years been suggested as potential new insecticide targets. These promiscuous enzymes are involved in the N-acylation of biogenic amines to form N-acylamides. Mammalian AANAT is predominantly associated with circadian rhythm regulation, as it catalyzes the formation of N-acetylserotonin, the precursor of melatonin, from serotonin. In insects, this process is a key step in melanism, as well as hardening of the cuticle, removal of biogenic amines, and in the biosynthesis of fatty acid amides. The unique nature of each insect AANAT (iAANAT) isoform characterized indicates that while catalyzing similar reactions, each insect accommodates …

Modeling Of Interaction Of Ions With Ether- And Ester-Linked Phospholipids, Matthew W. Saunders

USF Tampa Graduate Theses and Dissertations

Phospholipids are present in all parts of cells and are used in many signalling and struc- tural roles. As structural molecules they act as the main component of cellular membranes. Bilayer properties are heavily influenced by the structure of their component polar lipids, and different lipids are found in different organisms. A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. In our work we examine the effects of salt on bilayer structure in the case of both ester- and ether-linked lipid bilayers. We …

Design And Delivery Of Synthetic Mrna By A Peptide Nanoparticle, John H. Lockhart

USF Tampa Graduate Theses and Dissertations

The field of synthetic mRNA therapeutics is a rapidly expanding arm of gene therapies. The use of mRNA provides multiple benefits over viral or DNA vectors. synthetic mRNA vectors are immediately translated into protein after entering the cytoplasm of cells in contrast to DNA vectors that must first be transcribed to mRNA in the nucleus. This allows synthetic mRNA to produce a therapeutic protein in any cell type, including non-dividing cells. In addition, the non-replicative nature of mRNA means that insertional mutagenesis or generation of escape mutants is not a concern. However, the stimulation of innate immune responses by unmodified …

Hybrid Fusion Protein For Inhibition Of Multiple Proteases For Chronic Wound Healing, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Many diseases display a multitude of relevant factors that contribute to the persistence of the disease and difficulty treating it. The multifactorial characteristics of some diseases lead to the requirement of combination of treatments in order to restore health. The latter may necessitate the mixing of treatments, medications, and therapeutics to first halt the disease, then assist the human body in returning itself to a state of normality. For example, chronic wounds exhibit this multifactor characteristic in which there exist many factors that lead to the body’s inability to properly heal in a timely manner. This presents a further threat …

An Insight Into The Biological Functions, The Molecular Mechanism And The Nature Of Interactions Of A Set Of Biologically Important Proteins., Adam A. Aboalroub

USF Tampa Graduate Theses and Dissertations

Characterization of protein structural properties is crucial to determine its role in normal and pathological conditions. In this dissertation, we have employed NMR spectroscopy in a combination of other biochemical and biophysical techniques to investigate the catalytic function, the molecular mechanism, and nature of the interactions of bmAANAT3, Cdc37, and TIMP2, respectively.

In the first project, we have employed an arylalkylamine N-acetyltransferases (AANATs) from Bombyx mori (bmAANAT3) to determine the role of the acetyl-group in coordinating the catalytic cycle in this family of enzymes. We have found that the occupancy of the acetyl-moiety in the catalytic funnel of these enzymes …

Intrinsically Disorder Proteins And Liquid-Liquid Phase Transitions In Neurodegenerative Diseases, April Lynn Darling

USF Tampa Graduate Theses and Dissertations

Neurodegenerative diseases have a negative impact on health and economics, effecting more than 20 million people in the United States and costing around $800 billion in 2018. Additionally, most neurodegenerative diseases such as Alzheimer’s Disease (AD), Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD), and several others are fatal and have no cure or effective treatment. Many of these diseases have a common theme of protein aggregates being present in disease tissue. These aggregates are thought to be toxic to the cell and prevention of pathological aggregation and elimination of these cellular aggregates may serve as a potential therapeutic approach to …

Novel Strategies On Characterizing Biologically Specific Protein-Protein Interaction Networks, Bi Zhao

USF Tampa Graduate Theses and Dissertations

The function, behavior, and environmental response of biological systems are essentially determined by the complex interaction and regulation of biomolecules inside the systems. Therefore, it is critical to characterize the inter-molecular interaction and regulation of biomolecules inside these systems. In this direction, many experimental techniques have been developed and these techniques have been used in many different model systems under various conditions. Consequently, a massive amount of data has been generated. These data cover multiple aspects of molecular interaction and regulation, such as protein-protein interaction, microRNA-RNA interaction, gene expression profiles, etc. While carrying rich information, these data may also contain …

Targeting Pten For Therapy In Cancer And Ptenopathies, Emily Palumbo

USF Tampa Graduate Theses and Dissertations

PTEN, a dual protein and lipid phosphatase, regulates a myriad of cellular functions including PI3K pathway signaling, cell migration, proliferation, invasion and apoptosis. PTEN mutations often lead to multiple malignancies, including prostate, breast, endometrial, skin and brain cancers, associated with hyperactive PI3K signaling. PTEN mutations have also been associated with a variety of other diseases, classified as PTEN Hamartoma Tumor Syndromes (PHTS). In addition, compromised function or reduced expression of PTEN due to non-genomic mechanisms are associated with many types of hyperproliferative diseases, such as restenosis and neoplastic diseases, including melanoma, lung, breast, prostate and colon cancers. Although PI3K pathway …