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Biochemical Characterization Of The Flavivirus-Resistance Mouse Abcf3 Protein And A Review Of The Antibiotic Resistance And Dissemination Mechanisms In Bacteria, Elizabeth A. Peterson

Biology Dissertations

Mammalian ATP-binding cassette subfamily F member 3 (ABCF3) is a class 2 ABC protein that has previously been identified as a partner of the mouse flavivirus resistance protein 2′,5′-oligoadenylate synthetase 1B (OAS1B). The functions and natural substrates of ABCF3 are currently not known. In Chapter 1 of this study, we show that purified ABCF3 is an active ATPase. Binding analyses with a fluorescent ATP analog TNP-ATP suggested unequal contributions by the two nucleotide-binding domains. We further showed that ABCF3 activity is increased by lipids, including sphingosine, sphingomyelin, platelet-activating factor, and lysophosphatidylcholine. However, cholesterol inhibited ABCF3 activity, whereas alkyl ether lipids …

Synthesis Of Gadolinium-Doxorubicin Prodrug Carrying Functional Nanoceria For The Targeted Drug Delivery And Cancer Treatment, Arth Patel

Electronic Theses & Dissertations

The main focus of this research was the development of a polymer-coated nanoceria (PNC) platform to be used as a drug delivery system. Water-dispersible PNC is synthesized using a water-based alkaline precipitation method. Cerium nitrate hexahydrate and poly (acrylic acid) are used for the preparation of PNC. The synthesized PNC was characterized using ZETA, and UV- Vis characterization techniques. Polyacrylic acid (PAA)-coated cerium oxide nanoparticles fabricated for the targeted combination therapy of TNBC (MDA-MB-231) and MCF-7. Using EDC/NHS chemistry, the surface carboxylic acid groups of nanoceria was designed and synthesized with ICAM-1 antibody to target ICAM-1 overexpressing TNBC. Next, doxorubicin …

In Silico Sequence Optimization For The Reproducible Generation Of Dna Structures, Michael D. Tobiason

Boise State University Theses and Dissertations

Biologically, deoxyribonucleic acid (DNA) molecules have been used for information storage for more than 3 billion years. Today, modern synthesis tools have made it possible to use synthetic DNA molecules as a material for engineering nanoscale structures. These self-assembling structures are capable of both resolutions as fine as 4 angstroms and executing programed dynamic behavior. Numerous approaches for creating structures from DNA have been proposed and validated, however it remains commonplace for engineered systems to exhibit unexpected behaviors such as low formation yields, poor performance, or total failure. It is plausible that at least some of these behaviors arise due …

Towards The Synthesis Of An Artificial Fluorescent Siderophore, Ashley Burns

Honors Theses

Siderophores are molecules capable of binding ferric ions with high affinity (Ka = 1052). This thesis outlines our attempts to synthesize an artificial siderophore, which incorporates a signaling group to help monitor the uptake of ferric ions. The artificial siderophore is a tripodal molecular receptor synthesized in a five-step procedure with a proposed final sixth step. Rhodamine 6G azide (95.0% yield) was formed from rhodamine 6G and the synthesis of 2-azidoethanamine was modified from the literature. The tripodal arm portion of the sensor was successfully synthesized by protecting the catechol of 2,3-dihydroxybenzaldehyde to form 3-formyl-1,2-phenylene dimethanesulfonate (98.8% yield). The reduction …

Smart Sensors With Dual Modes Of Signal Transduction For Monitoring Molecules Pertinent To Health And The Environment, Jared T. Wabeke

Dissertations

The dissertation focuses on the design and synthesis of smart materials for the detection of molecules pertinent to environmental protection and healthcare. The use of computational simulations is pivotal toward advancing molecular design for targeted applications. Research was conducted to investigate the use of simulations to develop novel sensors with dual modes of signal transduction. The molecular properties were determined using computational modelling, and then used to elucidate the binding mechanism of the corresponding sensor complexes. Several molecules were produced that respond to important organic analytes, such as glucose and fenthion, an organophosphorus pesticide. Glucose is an exceedingly important biological …

Construction Of G-Quadruplexes Via Self-Assembly: Enhanced Stability And Unique Properties, Ying He

USF Tampa Graduate Theses and Dissertations

This dissertation mainly contains three parts: 1) The construction of well-defined G8-octamers through the monomer conformational design. 2) The construction of cross-layer interactions in the G8-octamer for enhanced stability in H-bond competitive solvents. 3) Design and synthesis of 8-triazole guanosine with photoluminescent properties.

Through the structural conformational design, we have developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (2’,3’-isopropylidene). This unique design has led to the formation of the first discrete G8-octamer with structure characterized by NMR, MS and single crystal X-ray diffraction. The selectivity between monovalent (K+) and divalent cat-ions (Ba2+ and Sr2+) …

Synthesis, Optical, And Thermal Properties Of 2,4,6-Tris(4-Substituted Phenyl)Pyrylium Tosylates And Triflimides, Pradip Kumar Bhowmik, Christina Inbok Lee, Jung Jae Koh, Haesook Han, Ahamed Jubair, Vladimir Kartazaev, Swapan Kumar Gayen

Chemistry and Biochemistry Faculty Research

A group of five 2,4,6-tris(4-substituted phenyl)pyrylium tosylates were synthesized in one-pot reaction from para-substituted benzaldehyde and para-substituted acetophenones using tosic acid as a condensing agent. The tosylate salts were converted to the corresponding triflimide salts by metathesis reactions. Chemical structures, as well as optical spectroscopic and thermal properties of these salts were studied using pertinent experimental techniques. Trimethyl- and trihalo-substituted pyrylium salts emitted strong blue light with peaks in the 456 nm–479 nm range and trimethoxy-pyrylium salts emitted intense green light with maxima around 526 nm in acetonitrile solution. Quantum yields of the solutions were rather low, but the salts …

Use Of Spectrofluorometry To Detect Petroleum Hydrocarbons In The Marine Environment, Mary Iris Abercrombie

USF Tampa Graduate Theses and Dissertations

The genesis of this research was the Deepwater Horizon oil spill, which discharged petroleum and gas into the Gulf of Mexico for 87 days in 2010. High-resolution fluorescence spectroscopy was employed for the detection of petroleum in seawater samples following the oil spill. Fluorescence arises from the chemical structure of π-bonding in C=C bonds, especially those in aromatic structures. Spectrofluorometry was also used to observe and track the formation of petroleum plumes in seawater undergoing controlled physical dispersion in a wave tank, both with and without the addition of chemical dispersant. Further, the changing fluorescence characteristics of a broad range …

Optical Meets Mechanical: Use Of Luminescence Spectroscopy To Assess Ageing In Biodegradable Films, Louis Colaruotolo

Masters Theses

With the growing concern of the accumulation of plastic-based food packaging waste, the search for bio-based biodegradable packages is on the rise. These materials differ from their petro-based counterparts in their degradation rates, which are much higher in the former. Not only do bio-based biodegradable materials degrade faster during post-usage processes but also they age faster during usage and storage, which affects their performance and functionality. The application of noninvasive testing methods with the capability to report on the matrix’s state could assist in the development of a more ubiquitous way to assess ageing in food packaging, particularly in biodegradable …

Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach

Adam R Urbach

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …

A Graphene Oxide-Based Fluorescence Assay For Sensitive Detection Of Dna Exonuclease Enzymatic Activity, Xiao Liu, Yingfen Wu, Xu Wu, Julia Zhao

Chemistry Faculty Publications

The 3′–5′ exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π–π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3′-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an …

A Microspectra Analysis Of Synthetic Wig Fibers, Jaclyn R. Beshlian

Student Theses

The goal of this study was to determine whether differentiation between 20 visually similar light brown synthetic wig fibers was possible with the use of a microspectrophotometer (MSP). Visually similar fibers were chosen to display the power of the instrument over the human eye. An MSP is an instrument that has the ability to aid in the analysis of certain microscopical samples. With this particular instrument one is able to collect the absorption and fluorescence spectra of microscopical colored samples without destroying the piece of evidence itself. Prior to any analysis with the MSP, the material of the fibers was …

Spectroscopic And Mechanistic Investigation Of Two Flavin-Dependent Enzymes: Nitronate Monooxygenase And Choline Oxidase, Dan Su

Chemistry Dissertations

Propionate 3-nitronate (P3N) is a natural toxin that irreversibly inhibits mitochondrial succinate dehydrogenase. P3N poisoning leads to a variety of neurological disorders and even death. Nitronate monooxygenase (NMO) from Cyberlindnera saturnus (CsNMO) and Pseudomonas aeruginosa PAO1 (PaNMO) serve as paradigms for Class I NMO, which catalyze the oxidation of P3N involving single electron transfer. In this dissertation, the crystallographic structure of CsNMO was solved and demonstrated a highly conserved three-dimensional structure and active site with respect to NMO from PaNMO. The role of conserved residues in the active site of Class I NMO, e.g. …

Footprint Of Calcium On Regulation Of Extracellular Calcium-Sensing Receptor And Connexin26, Rakshya Gorkhali

Chemistry Dissertations

Calcium (Ca²⁺) functions as a primary and secondary messenger regulating crucial cellular processes. We study two central membrane proteins, extracellular calcium-sensing receptor (CaSR) and connexin26 (Cx26) gap junction (GJ) channel, that are regulated by Ca²⁺ and play critical roles in regulating Ca²⁺ homeostasis and communication between the intra- and extra- cellular milieu. Mutations in CaSR are associated with abnormal Ca²⁺ homeostasis, hypoparathyroidism, myocardial infarction and cancers. Similarly, mutations in Cx26 are implicated in many hereditary deafness and dermatological disorders. The role of Ca²⁺ in CaSR biosynthesis, CaSR mediated intracellular Ca²⁺ signaling, Cx26 regulation …

Investigating Ions’ Effects On The Fluorescent Protein Dendra2, Benjamin Waterman

Honors College

While superresolution microscopy has opened the doors to insights into biological phenomena we couldn’t have dreamed of in the last century, its methodology is naturally limited. We aim to push the envelope of its capabilities by testing the effect that Ca2+ and H+ ions have on the fluorescent protein Dendra2. Utilizing a newly designed perfusion chamber, we flow separate solutions containing Ca2+ and H+ ions into a cellular environment, in which the cells in question have been tagged with Dendra2. Utilizing the superresolution technique known as Spectral Fluorescence Photoactivation Localization Microscopy, we are able to obtain information about the emission …

Effects Of Ionic Liquid Alkyl Chain Length On Denaturation Of Myoglobin By Anionic, Cationic, And Zwitterionic Detergents, Joshua Y. Lee, Katherine M. Selfridge, Eric M. Kohn, Timothy Vaden, Gregory A. Caputo

Faculty Scholarship for the College of Science & Mathematics

The unique electrochemical properties of ionic liquids (ILs) have motivated their use as solvents for organic synthesis and green energy applications. More recently, their potential in pharmaceutical chemistry has prompted investigation into their effects on biomolecules. There is evidence that some ILs can destabilize proteins via a detergent-like manner; however, the mechanism still remains unknown. Our hypothesis is that if ILs are denaturing proteins via a detergent-like mechanism, detergent-mediated protein unfolding should be enhanced in the presence of ILs. The properties of myoglobin was examined in the presence of a zwitterionic (N,N-dimethyl-N-dodecylglycine betaine (Empigen BB®, EBB)), cationic (tetradecyltrimethylammonium bromide (TTAB)), …

Fluorogenic Atom Transfer Radical Polymerization In Aqueous Media As A Strategy For Detection, Zachary T. Allen, Jemima R. Sackey-Addo, Madeline P. Hopps, Danyal Tahseen, Joseph T. Anderson, Tyler A. Graf, Christina B. Cooley

Christina B Cooley

The development of novel approaches to signal amplification in aqueous media could enable new diagnostic platforms for the detection of water-soluble analytes, including biomolecules. This paper describes a fluorogenic polymerization approach to amplify initiator signal by the detection of visible fluorescence upon polymerization in real-time. Fluorogenic monomers were synthesized and co-polymerized by atom transfer radical polymerization (ATRP) in water to reveal increasing polymer fluorescence as a function of both reaction time and initiator concentration. Optimization of the fluorogenic ATRP reaction conditions allowed for the quantitative detection of a small-molecule initiator as a model analyte over a broad linear concentration range …

Autofluorescence To Study The Effects Of Acid Concentration On Cellular Metabolism In Vitro, Robin L. Raley

Chemistry & Biochemistry Undergraduate Honors Theses

Ultraviolet (UV) radiation-induced sunburns and their accompanying afflictions are a growing public health concern in the United States. There is a need for techniques that can accurately and non-invasively characterize the physiology of sunburned skin tissue directly after UV-damage and applying a topical skin treatment to relieve pain and promote healing. Two-photon excited fluorescence (TPEF) microscopy and fluorescence lifetime imaging (FLIM) can be used to investigate metabolic processes in live cells through endogenous fluorescence of the cofactors, NADH and FAD. These methods employ the optical redox ratio of FAD/(NADH+FAD), mean NADH lifetime, and the separation of the free and bound …

Low Molecular Weight Fluorescent Probes (Lmfps) To Detect The Group 12 Metal Triad, Ashley D. Johnson, Rose M. Curtis, Karl J. Wallace

Faculty Publications

Fluorescence sensing, of d-block elements such as Cu²⁺, Fe³⁺, Fe²⁺, Cd²⁺, Hg²⁺, and Zn²⁺ has significantly increased since the beginning of the 21st century. These particular metal ions play essential roles in biological, industrial, and environmental applications, therefore, there has been a drive to measure, detect, and remediate these metal ions. We have chosen to highlight the low molecular weight fluorescent probes (LMFPs) that undergo an optical response upon coordination with the group 12 triad (Zn²⁺, Cd²⁺, and Hg²⁺), as these metals have …

Quantifying Anthropogenic Indicators And Changes In Dissolved Organic Matter In Coastal Urban Aquatic Ecosystems Exposed To High Tidal Flooding, Gonzalo E. Eyzaguirre

Department of Biological Sciences

Sea-level rise is causing an increase in tidal flooding in coastal urban areas. Extreme high tides, also known as king tides, are peak tide moments in which tidal amplitude is increased and shallow groundwater flows from the underlying water table are introduced. During tidal flooding in urban areas, accumulated anthropogenic indicators of different water sources are released from groundwater to surface waters, but how these tidal events affect the contributions of different water sources to urban flood waters is uncertain. We quantified tracers of anthropogenic origin including fluoride, fecal coliform bacteria, as well as dissolved organic carbon (DOC) concentrations and …

Effects Of Electrical Stimulation On Glioma Cells In Vitro With Implications For Treating Chronic Pain: Development Of A Model System, David C. Platt

Theses and Dissertations

Glial cells comprise over 70% of the central nervous system cells and exhibit diverse functions including regulation of synaptic transmission, neuron protection/repair, maintenance of neuronal metabolism, and are implicated in the development of persistent neuropathic pain. In addition, a perturbation in the concentration of intracellular reactive oxygen species (ROS) and reactive nitrogen species (RNS) has likewise been associated with the development of a chronic pain state. This perturbation in ROS/RNS creates an environment of oxidative stress. However, the mechanism by which the pain signal transmission is modulated, and the roles ROS play in the perpetuation of the pain state are …

Virus Adsorption To Colloids In Water: Interactions Between Bacteriophage Ms2, Kaolinite, And Fiberglass, Ashlee N. Ellis

Theses and Dissertations

Virus adsorption to colloidal particles is an important issue in the water quality community, and it is a particularly important issue for conventional wastewater treatment plants that accept biohazardous waste. Colloids impact the transport of viruses in engineered treatment systems, and they also provide protection against oxidants and other destructive mechanisms. This study evaluated the adsorption of bacteriophage MS2 to colloidal suspensions of kaolinite (KAO) and fiberglass (FG). A series of laboratory batch tests were carried out over a range of experimental conditions to determine kinetic rate constants and characterize bond strength, and computational experiments were done to assess both …

L-Tryptophan Adsorption Differentially Changes The Optical Behaviour Of Pseudo-Enantiomeric Cysteine-Functionalized Quantum Dots: Towards Chiral Fluorescent Biosensors, Faezeh Askari, Abbas Rahdar, John F. Trant

Chemistry and Biochemistry Publications

Water-soluble chiral graphene quantum dots (GQDs) with a strong blue emission were synthesized by covalently immobilizing l-cysteine or d-cysteine onto the GQDs. Either the amine or the thiol group of cysteine was used to make the bond through amide coupling or thiol-ene click chemistry respectively. The functionalized chiral GQDs were the characterized by FT-IR and UV–vis. The enantiomeric pairs exhibit equal but opposite bands in circular dichroism spectra suggesting that there is no difference in the efficacy of conjugation. The fluorescent response of these chiral GQDs when exposed to l-tryptophan was then studied. The fluorescence of the amide-conjugated GQDs was …

N-Methyl Mesoporphyrin Ix As A Highly Selective Light-Up Probe For G-Quadruplex Dna, Ariana Yett , '21, Linda Yingqi Lin , '20, Dana Beseiso , '21, Joanne Miao , '22, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss …

Fluorogenic Atom Transfer Radical Polymerization In Aqueous Media As A Strategy For Detection, Zachary T. Allen, Jemima R. Sackey-Addo, Madeline P. Hopps, Danyal Tahseen, Joseph T. Anderson, Tyler A. Graf, Christina B. Cooley

Chemistry Faculty Research

The development of novel approaches to signal amplification in aqueous media could enable new diagnostic platforms for the detection of water-soluble analytes, including biomolecules. This paper describes a fluorogenic polymerization approach to amplify initiator signal by the detection of visible fluorescence upon polymerization in real-time. Fluorogenic monomers were synthesized and co-polymerized by atom transfer radical polymerization (ATRP) in water to reveal increasing polymer fluorescence as a function of both reaction time and initiator concentration. Optimization of the fluorogenic ATRP reaction conditions allowed for the quantitative detection of a small-molecule initiator as a model analyte over a broad linear concentration range …

Cpef Is The Bilin Lyase That Ligates The Doubly Linked Phycoerythrobilin On Phycoerythrin In The Cyanobacterium Fremyella Diplosiphon, Wendy M. Schluchter, R. B. Cole, D. M. Kehoe, M. N. Boutaghou, J. A. Karty, A. Gutu, L. S. Hernandez, J. P. Frick, C. V. Hernandez, C. M. Kronfel

Biological Sciences Faculty Publications

Phycoerythrin (PE) is a green light-absorbing protein present in the light-harvesting complex of cyanobacteria and red algae. The spectral characteristics of PE are due to its prosthetic groups, or phycoerythrobilins (PEBs), that are covalently attached to the protein chain by specific bilin lyases. Only two PE lyases have been identified and characterized so far, and the other bilin lyases are unknown. Here, using in silico analyses, markerless deletion, biochemical assays with purified and recombinant proteins, and site-directed mutagenesis, we examined the role of a putative lyase-encoding gene, cpeF, in the cyanobacterium Fremyella diplosiphon. Analyzing the phenotype of the cpeF deletion, …

Influence Of Sporulation And Germination Behavior Of Bacillus Licheniformis On Microbial Quality Of Skim Milk Powder, Nancy Awasti

Electronic Theses and Dissertations

This dissertation includes modeling of sporulation and germination behavior of Bacillus licheniformis strains during raw milk holding, tracking the survival of sporeformers and spores of high sporulating Bacillus strain during skim milk powder manufacturing. In addition, preliminary studies were done to standardize a rapid spore detection technique by using ratiometric fluorescence. To understand the role of strain variability during raw milk holding conditions, population dynamics of two strains of Bacillus licheniformis, ATCC 6634 and 14580, were modeled as a function of temperature (4.0 -12.0˚ C) and duration (0 - 72 h), using regression analysis. Based on initial spiking of vegetative …

Significance Of Rna 2'-5' Linkage And Metal-Ion Mediated Base Pairs, Fusheng Shen

Legacy Theses & Dissertations (2009 - 2024)

It has been known that the template-directed RNA chemical replication reaction produces mixture of backbones containing both 3’-5’ and 2’-5’ linkages. This backbone heterogeneity has been a significant problem in studying the emergence of RNA World from the prebiotic chemistry. However, very recently, it is reported that FMN binding aptamer and a hammerhead ribozyme are still able to retain considerable functions in the presence of certain 2’-5’ linkages, indicating that RNA backbones may be quite flexible and this backbone heterogeneity problem may not be as severe as originally thought. This finding also brings two related important questions: First, how does …

Synthesis, Design, And Evaluation Of The Fluorescent Detection Of Polychlorinated Biphenyls(Pcbs) In Aqueous System, Irfan Ahmad

Theses and Dissertations--Chemical and Materials Engineering

The exposure to halogenated persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), has been linked to numerous inflammatory diseases, including diabetes, cancer and lowered immune response. PCBs have low solubility in water, and they interact with other contaminants, making their detection quite challenging. While, there have been several attempts at improving the ease of detection and sensing of PCBs, gas chromatography-mass spectrometry (GC-MS) remains the gold standard. However, despite its ubiquitous use, GC-MS is a challenging technique that requires high skill and careful sample preparation, which are time-consuming and costly. As such, there is still a need to develop …

Delta-Aminolevulinic Acid-Mediated Photodiagnoses In Surgical Oncology: A Historical Review Of Clinical Trials., Joseph F Georges, Amber Valeri, Huan Wang, Aaron Brooking, Michael Kakareka, Steve S Cho, Zein Al-Atrache, Michael Bamimore, Hany Osman, Joseph Ifrach, Si Yu, Carrie Li, Denah Appelt, John Y K Lee, Peter Nakaji, Kristin Brill, Steven S. Yocom

PCOM Scholarly Papers

Fluorescence imaging is an emerging clinical technique for real-time intraoperative visualization of tumors and their boundaries. Though multiple fluorescent contrast agents are available in the basic sciences, few fluorescence agents are available for clinical use. Of the clinical fluorophores, delta aminolevulinic acid (5ALA) is unique for generating visible wavelength tumor-specific fluorescence. In 2017, 5ALA was FDA-approved for glioma surgery in the United States. Additionally, clinical studies suggest this agent may have utility in surgical subspecialties outside of neurosurgery. Data from dermatology, OB/GYN, urology, cardiothoracic surgery, and gastrointestinal surgery show 5ALA is helpful for intraoperative visualization of malignant tissues in multiple …