Biochemistry, Biophysics, and Structural Biology Commons^™

Homogeneous And Functional Group Tolerant Ring-Closing Metathesis For Dna-Encoded Chemical Libraries, Olivier B C Monty, Pranavanand Nyshadham, Kurt M Bohren, Murugesan Palaniappan, Martin M Matzuk, Damian W Young, Nicholas Simmons

Faculty, Staff and Students Publications

Reaction heterogeneity, poor pH control, and catalyst decomposition in the ring-closing metathesis (RCM) of DNA–chemical conjugates lead to poor yields of the cyclized products. Herein we address these issues with a RCM reaction system that includes a novel aqueous solvent combination to enable reaction homogeneity, an acidic buffer system which masks traditionally problematic functional groups, and a decomposition-resistant catalyst which maximizes conversion to the cyclized product. Additionally, we provide a systematic study of the substrate scope of the on-DNA RCM reaction, a demonstration of its applicability to a single-substrate DNA-encoded chemical library that includes sequencing analysis, and the first successful …

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 …

A Broad-Spectrum Antiviral Molecule, Ql47, Selectively Inhibits Eukaryotic Translation, Mélissanne De Wispelaere, Margot Carocci, Dominique J Burri, William J Neidermyer, Calla M Olson, Imme Roggenbach, Yanke Liang, Jinhua Wang, Sean P J Whelan, Nathanael S Gray, Priscilla L Yang

Faculty, Staff and Students Publications

Small-molecule inhibitors of translation are critical tools to study the molecular mechanisms of protein synthesis. In this study, we sought to characterize how QL47, a host-targeted, small-molecule antiviral agent, inhibits steady-state viral protein expression. We demonstrate that this small molecule broadly inhibits both viral and host protein synthesis and targets a translation step specific to eukaryotic cells. We show that QL47 inhibits protein neosynthesis initiated by both canonical cap-driven and noncanonical initiation strategies, most likely by targeting an early step in translation elongation. Our findings thus establish QL47 as a new small-molecule inhibitor that can be utilized to probe the …

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 …

Parallel Quorum-Sensing System In Vibrio Cholerae Prevents Signal Interference Inside The Host., Samit Watve, Kelsey Barrasso, Sarah A Jung, Kristen J Davis, Lisa A Hawver, Atul Khataokar, Ryan G Palaganas, Matthew B Neiditch, Lark Perez, Wai-Leung Ng

College of Science & Mathematics Departmental Research

Many bacteria use quorum sensing (QS) to regulate virulence factor production in response to changes in population density. QS is mediated through the production, secretion, and detection of signaling molecules called autoinducers (AIs) to modulate population-wide behavioral changes. Four histidine kinases, LuxPQ, CqsS, CqsR and VpsS, have been identified in Vibrio cholerae as QS receptors to activate virulence gene expression at low cell density. Detection of AIs by these receptors leads to virulence gene repression at high cell density. The redundancy among these receptors is puzzling since any one of the four receptors is sufficient to support colonization of V. …

Parp1-Targeted Radiotherapies, Stephen Jannetti

Dissertations, Theses, and Capstone Projects

Poly-ADP-ribosylation reactions were first reported by Chambon in 1963 as enzymatic activity that increases incorporation of ATP in the presence of nicotinamide mononucleotide. In the decades since that publication, Poly(ADP-ribose)polymerase 1 (PARP1) and the PARP family enzymes have been widely studied. PARP enzymes are currently known to play various roles in mammals, including anti-aging processes, interactions with Breast Cancer Suppressor Protein-1 (BRCA1), and DNA damage repair. A significant focus of PARP1 research has been elucidating its role in DNA damage repair. PARP1 is recruited to repair single strand DNA (ssDNA) breaks, which can become double stranded DNA (dsDNA) breaks if …

Leveraging Antibodies For Positron Emission Tomography And Near-Infrared Fluorescence Imaging Of Cancer, Kimberly C. Fung

Dissertations, Theses, and Capstone Projects

The high specificity and affinity of antibodies make them attractive for developing drugs to diagnose and treat cancer. The overarching goal of this work is to explore the synthesis and use of antibody-based imaging agents in preclinical models of cancer. This work can be described as two-fold. In the first part, we investigated how the use of a glycans-specific bioconjugation strategy affects Fc gamma RI binding and why it results in improved in vivo performance of immunoconjugates. To do so, we used the clinically relevant positron emission tomography (PET) imaging agent, ⁸⁹Zr-DFO-pertuzumab, in mouse models of human breast cancer. …

Advanced Computational Methodologies To Study Binding Free Energies Of Biomolecular Complexes, Rajat Kumar Pal

Dissertations, Theses, and Capstone Projects

Molecular recognition is the basis of biological mechanisms and is a key element to consider while formulating effective and safe drugs. Pharmaceutical drugs are designed so as to bind a target protein even at very low concentrations to alter the diseased conditions without interfering with normal biological processes. In a rational drug design process, this is achieved by acquiring information about the chemical structure and the physical and chemical properties of the target protein receptor to gain insights on how changing the chemical composition of the substrate drug could affect the protein-drug interaction and binding affinities. Computational models are used …

Hur Ubiquitination By Brca1/Bard1 And Its Role In Controlling Gene Expression During Dna Damage Response, Gamage M. Aruggoda

Dissertations, Theses, and Capstone Projects

Despite our understanding of the biochemistry of the BRCA1/BARD1 E3 ligase, we know very little of the mechanism by which its cellular substrates, how they are chosen, how its E3 Ub ligase activity is regulated, which are the cofactors involved in this regulation, and how the substrates are modified during DDR. In this dissertation, I further evaluate BRCA1/BARD1-mediated E3 ligase activity and how CstF-50 and p97 regulate this reaction working as cofactors. My data show that BRCA1/BARD1 is an E3 ligase that ubiquitinates the RNA binding protein Human antigen R(HuR).

HuR is abundant in the nucleus and is transported to …

Mutational Analysis And Domain Characterization Of The Apolipoprotein L-1 Ion Channel, Charles M. Schaub

Dissertations, Theses, and Capstone Projects

The human innate immunity factor Apolipoprotein L-1 (APOL1) protects against Trypanosoma brucei brucei infection. Recent studies have shown recombinant APOL1 (rAPOL1) inserts into planar lipid bilayers at an acidic pH 5.6 and forms a cation-selective channel, which opens upon subsequent neutralization, pH 7.2. This corresponds with the pH changes APOL1 would encounter during endosome recycling, suggesting that APOL1 forms a pH-gated ion channel in the plasma membrane of the parasite, leading to uncontrolled ion flux and osmotic imbalance. However, structural and domain characteristics of the APOL1 channel are poorly understood, despite potential similarities to diphtheria and colicin toxins. Utilizing E. …

Through The Back Door: Proteins Escape Cells Without Conventional Permission, Michael J. Cohen

Dissertations, Theses, and Capstone Projects

Proteins secreted to the extracellular environment play a fundamental role as signals, in metabolism, and a variety of other processes. The process of secretion through the endoplasmic reticulum and Golgi to the plasma membrane is well documented, and all cargo in this pathway contains a signal peptide. However, a variety of proteins secreted from eukaryotes lack a signal peptide and are called unconventionally secreted proteins. Here we discuss known mechanisms of unconventional protein secretion, as well as model proteins which follow characterized pathways. Additionally, we summarize the roles various unconventionally secreted proteins play outside of cells and suggest criteria for …

Trait Differentiation And Modular Toxin Expression In Palm-Pitvipers, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson

Publications

Background

Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis …

Differentiation Of Mannheimia Haemolytica Genotype 1 And 2 Strains By Visible Phenotypic Characteristics On Solid Media, Emily L. Wynn, Gennie Schuller, John D. Loy, Aspen M. Workman, T. G. Mcdaneld, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

Genotype 2 Mannheimia haemolytica associate with the lungs of cattle with bovine respiratory disease more frequently than genotype 1 strains. Different colony colors and morphologies were identified between genotype 1 and 2 solid media cultures. Genotype of strains, and frequency differences between them in mixed cultures are discernable by visual inspection.

Supplements attached

Hydrolysis Of Palm Oil Mill Effluent Using Enzymes From Spent Mushroom Substrate Of Pleurotus Pulmonarius (Fr.) Quel, Mat Yunan Nurul Anisa

Student Works (2020-2029)

Mushroom cultivation and palm oil industry in Malaysia have contributed to the large volumes of lignocellulosic residues. Lignocellulolytic enzymes profiles (lignin peroxidase, laccase, xylanase, endoglucanase, and β-glucosidase) of Pleurotus pulmonarius (parents strains UMP001 and UMP 002, and the hybrid UMH004) during growth in sawdust substrate bags were investigated. The enzymes extracted from the spent mushroom substrate (SMS) of the strain with the highest enzymes productivity was used to hydrolyse palm oil mill effluent (POME). Optimization of parameters for POME hydrolysis to release reducing sugar was conducted using central composite design (CCD) of response surface methodology (RSM). The potential of hydrolysed …

A Retrospective Matched-Cohort Study Of 3994 Lower Extremity Wounds Of Multiple Etiologies Across 644 Institutions Comparing A Bioactive Human Skin Allograft, Theraskin, Plus Standard Of Care, To Standard Of Care Alone, Geoff C Gurtner, Aimee D Garcia, Katie Bakewell, Jason B Alarcon

Faculty, Staff and Students Publications

Most chronic wounds are related to comorbidities, for which no clinical trials are performed. This retrospective propensity matched-cohort study examined data from 2 074 000 lower extremity wounds across 644 institutions to determine the effectiveness of TheraSkin plus standard of care (SOC; n = 1997) versus SOC alone (n = 1997). Multivariate modelling comparing outcomes such as healing rates, percent area reductions (PARs), amputations, recidivism, treatment completion, and medical transfers were evaluated. A higher proportion of wounds in the treatment group compared with the controls were more likely to close (68.3% versus 60.3%), particularly wounds with exposed structures (64% versus …

Losartan Rescues Inflammation-Related Mucociliary Dysfunction In Relevant Models Of Cystic Fibrosis, Michael D Kim, Nathalie Baumlin, Makoto Yoshida, Deepika Polineni, Sebastian F Salathe, Joseph K David, Charles A Peloquin, Adam Wanner, John S Dennis, Juliette Sailland, Philip Whitney, Frank T Horrigan, Juan R Sabater, William M Abraham, Matthias Salathe

Faculty, Staff and Students Publications

Rationale: Despite therapeutic progress in treating cystic fibrosis (CF) airway disease, airway inflammation with associated mucociliary dysfunction remains largely unaddressed. Inflammation reduces the activity of apically expressed large-conductance Ca²⁺-activated and voltage-dependent K⁺ (BK) channels, critical for mucociliary function in the absence of CFTR (CF transmembrane conductance regulator).

Objectives: To test losartan as an antiinflammatory therapy in CF using CF human bronchial epithelial cells and an ovine model of CF-like airway disease.

Methods: Losartan’s antiinflammatory effectiveness to rescue BK activity and thus mucociliary function was tested in vitro using primary, fully redifferentiated human airway epithelial cells homozygous for …

Investigation On The Potential Of Dried Blood Stain For The Detection Of Amphetamine Type Stimulants By Enhanced Methods Of Liquid Chromatography Tandem-Mass Spectrometry, Ahmad Zubaidi Fathiah

Student Works (2020-2029)

The investigation on the potential of dried blood stain for Amphetamine Type Stimulants (ATS) has been divided into four major parts, from which independent conclusions are drawn. The first part is the development and validation of a novel method for the simultaneous determination of the drugs using liquid chromatography with electrospray ionization tandem mass spectrometer (LC-ESI-MS/MS). The method is enhanced from normal Multi-Reaction Mode (MRM) to Multi-Reaction Mode-Enhanced Product Ion Mode- Multi-Reaction Mode 3 (MRM-EPI-MRM3) and tested in whole blood specimens (WBS), dried blood stain (DBS) and urine specimens as well as applied to real forensic cases in Malaysia. The …

Potential Use Of Biotherapeutic Bacteria To Target Colorectal Cancer-Associated Taxa, Gareth Lawrence, Maire Begley, Paul D. Cotter, Caitríona M. Guinane

Department of Biological Sciences Publications

The role of the gut microbiome in human health and disease is the focus of much attention. It has been widely agreed upon that our gut bacteria play a role in host immunity, nutrient absorption, digestion, metabolism, and other key drivers of health. Furthermore, certain microbial signatures and specific taxa have also been associated with the development of diseases, such as obesity; inflammatory bowel disease; and, indeed, colorectal cancer (CRC), which is the focus of this review. By extension, such taxa represent potential therapeutic targets. In particular, the emerging human pathogen Fusobacterium nucleatum represents an important agent in CRC development …

Protein Tyrosine Phosphatase 4a3 (Ptp4a3/Prl-3) Drives Migration And Progression Of T-Cell Acute Lymphoblastic Leukemia In Vitro And In Vivo, Min Wei, Meghan G. Haney, Dylan R. Rivas, Jessica S. Blackburn

Molecular and Cellular Biochemistry Faculty Publications

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive blood cancer. There are no immunotherapies and few molecularly targeted therapeutics available for treatment of this malignancy. The identification and characterization of genes and pathways that drive T-ALL progression are critical for the development of new therapies for T-ALL. Here, we determined that the protein tyrosine phosphatase 4A3 (PTP4A3 or PRL-3) plays a critical role in T-ALL initiation and progression by promoting leukemia cell migration. PRL-3 is highly expressed in patient T-ALL samples at both the mRNA and protein levels compared to normal lymphocytes. Knock-down of PRL-3 expression using short-hairpin RNA (shRNA) …

Identification Of Uncommon Antibiotic-Producing Illinois Soil Isolates, Lesly Muniz, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from the soil. We researched tester strains B. subtilis and E. coli from the soil isolates obtained. We further verified if the isolates were common antibiotic bacteria. Unfortunately, this project heavily relied on biochemical tests, colony morphology, and Gram stains to reject or fail to reject our hypothesis. Our goal was to discover new antibiotic-producing bacteria that could be beneficial in combating ESKAPE strains. A proper PCR and DNA extraction would be required …

Putative Antibiotic Producer: A Pseudomonas Genus With Antibiotic Properties, John Tworek, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

There is a series antibiotic crisis in the world with catastrophic consequences if action is not take. Many diseases caused by bacteria are becoming untreatable because of the amount of pathogens resistant to the effect of antibiotics. The most prolific bacteria are the ESKAPE bacteria. They are nonsocomial pathogens that exhibit multi-drug resistance and virulence. My project will be working alongside the Tiny Earth Project (TEPI) to educate the public about the antibiotic crisis as well as obtaining a soil sample to possible discover new antibiotics. The DNA sequencing data retrieved from soil isolates against the two ESKAPE tester strains …

Screening For Antibiotic-Producers In Soil From A Garden, Long Tran, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

Multidrug-resistant pathogens are the leading cause of nosocomial infection, which killed more than 30,000 people in the United States every year. Among these, ESKAPE strains bugs, which comprise six highly drug-resistant bacteria, pose the greatest challenge to the healthcare system. In order to fight the antibiotic-resistant crises, novel antibiotic-producers must be discovered. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from the soil. Pseudomonas was revealed to produce a zone of inhibition against Bacillus subtilis on LB media. The next step …

Molecular Composition And Photochemical Lifetimes Of Brown Carbon Chromophores In Biomass Burning Organic Aerosol, Lauren T. Fleming, Peng Lin, James M. Roberts, Vanessa Selimovic, Robert Yokelson, Julia Laskin, Alexander Laskin, Sergey A. Nizkorodov

Chemistry and Biochemistry Faculty Publications

To better understand the effects of wildfires on air quality and climate, it is important to assess the occurrence of chromophoric compounds in smoke and characterize their optical properties. This study explores the molecular composition of light-absorbing organic aerosol, or brown carbon (BrC), sampled at the Missoula Fire Sciences laboratory as a part of the FIREX Fall 2016 lab intensive. A total of 12 biomass fuels from different plant types were tested, including gymnosperm (coniferous) and angiosperm (flowering) plants and different ecosystem components such as duff, litter, and canopy. Emitted biomass burning organic aerosol (BBOA) particles were collected onto Teflon …

10th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The Annual Postdoctoral Science Symposium (APSS) was initiated on August 4, 2011, by the MD Anderson Postdoctoral Association to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience.

APSS is a scientific symposium organized by postdoctoral fellows from The University of Texas MD Anderson Cancer Center that welcomes submissions and presentations from postdoctoral fellows from all Texas Medical Center affiliated institutions and other Houston area institutions. The APSS provides a professional venue for postdoctoral scientists to develop, clarify and refine their research as result of formal reviews and critiques …

Trka Undergoes A Tetramer-To-Dimer Conversion To Open Trkh Which Enables Changes In Membrane Potential, Hanzhi Zhang, Yaping Pan, Liya Hu, M Ashley Hudson, Katrina S Hofstetter, Zhichun Xu, Mingqiang Rong, Zhao Wang, B V Venkataram Prasad, Steve W Lockless, Wah Chiu, Ming Zhou

Faculty, Staff and Students Publications

TrkH is a bacterial ion channel implicated in K+ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting …

Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

The recent emergence of antibiotic resistance bacterial strains presents a significant challenge and threat to human healthcare. While new methods of treatment such as bacteriophage therapy and combinations of existing antibiotics are being researched, the human population is in dire need of new antibiotics to replace those that are ineffective. This research addresses this need by identifying antibiotic producing bacteria in a soil sample from Davenport, IA. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from soil. Microbiology lab techniques and 16S …

Synthesis And Preliminary Ex Vivo Testing Of Sirna Targeting Tcrb: A Proposed Therapy For The Treatment Of Autoimmunity, Nicholas J. Magazine

LSU Doctoral Dissertations

Abstract

Background:

As of 2018, the United States National Institutes of Health estimate that over half a billion people worldwide are affected by autoimmune disorders. Though these conditions are prevalent, treatment options remain relatively poor, relying primarily on various forms of immunosuppression which carry potentially severe side effects and often lose effectiveness overtime. Given this, new forms of therapy are needed. We propose small-interfering RNA (siRNA) for hypervariable regions of the T-cell receptor β-chain gene (TCRb) as a highly targeted, novel means of therapy for the treatment of autoimmune disorders.

Objectives:

To develop methods to produce siRNA targeting …

The Mitochondrial Hsp90 Paralog Trap1 Forms An Oxphos-Regulated Tetramer And Is Involved In Mitochondrial Metabolic Homeostasis, Abhinav Joshi, Li Dai, Yanxin Liu, Jungsoon Lee, Nastaran Mohammadi Ghahhari, Gregory Segala, Kristin Beebe, Lisa M Jenkins, Gaelyn C Lyons, Lilia Bernasconi, Francis T F Tsai, David A Agard, Len Neckers, Didier Picard

Faculty, Staff and Students Publications

BACKGROUND: The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there is no consensus on the relevant TRAP1 interactors. This calls for a more comprehensive analysis of the TRAP1 interactome and of how TRAP1 and mitochondrial metabolism mutually affect each other.

RESULTS: We show that the disruption of the gene for TRAP1 in …

A Transcriptional Regulatory System Of The S. Cerevisiae Ole1 Gene Responds To Fatty Acid Species And Intracellular Amount, And Not Simply Membrane Status, Marshall Willey, Matthew Ochs, Clara Schriemer, Virginia Mcdonough

Faculty Publications

We examined the effects of unsaturated fatty acid (UFA) species and their concentration on the expression of OLE1, which encodes the stearoyl CoA desaturase, in Saccharomyces cerevisiae. We controlled the amount of UFA taken up by the cell by varying the concentration of tergitol in the medium. When cultured with 1 mM fatty acid in 0.1% tergitol, cells took up much more fatty acid than when cultured with the same concentration of fatty acid at 1% tergitol, although the amount incorporated was dependent on UFA species. For each fatty acid tested, we found that the higher uptake (0.1% tergitol condition) …

Dominant Negative Effects By Inactive Spa47 Mutants Inhibit T3ss Function And Shigella Virulence, Jamie L. Burgess, Heather B. Case, R. Alan Burgess, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Type three secretion systems (T3SS) are complex nano-machines that evolved to inject bacterial effector proteins directly into the cytoplasm of eukaryotic cells. Many high-priority human pathogens rely on one or more T3SSs to cause disease and evade host immune responses, underscoring the need to better understand the mechanisms through which T3SSs function and their role(s) in supporting pathogen virulence. We recently identified the Shigella protein Spa47 as an oligomerization-activated T3SS ATPase that fuels the T3SS and supports overall Shigella virulence. Here, we provide both in vitro and in vivo characterization of Spa47 oligomerization and activation in the presence and absence …