Chemistry Commons^™

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

Spatial Metabolomics Reveals Glycogen As An Actionable Target For Pulmonary Fibrosis, Lindsey R. Conroy, Harrison A. Clarke, Derek B. Allison, Samuel Santos Valenca, Qi Sun, Tara R. Hawkinson, Lyndsay E. A. Young, Juanita E. Ferreira, Autumn V. Hammonds, Jaclyn B. Dunne, Robert J. Mcdonald, Kimberly J. Absher, Brittany Dong, Ronald C. Bruntz, Kia H. Markussen, Jelena A. Juras, Warren J. Alilain, Jinze Liu, Matthew S. Gentry, Peggi M. Angel, Christopher M. Waters, Ramon C. Sun

Saha Cardiovascular Research Center Faculty Publications

Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high- dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed …

Design And Synthesis Of Peripherally Selective Endocannabinoid Enzyme Inhibitors For Ocular Indications, Kezia Reji Thomas

Senior Honors Theses

Peripherally selective compounds have been found to stimulate endocannabinoid receptor activity, which has been observed to have positive physiological effects such as ocular wound healing and inflammation control. The activation of the cannabinoid 1 receptor via binding of the endogenous ligands, anandamide and 2-arachidonoylglycerol, has been indicated to elicit these effects. Both ligands are controlled by two hydrolase enzymes, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL), which can be targeted for therapeutic inhibition. Sulfonamide derivatives of JZL195 containing carbamate functionalities in the southern region of the inhibitor compounds were produced using novel carbamate exchange reactions. Polar functionalities were …

Computational Design And Molecular Modeling Of Morphine Derivatives For Preferential Binding In Inflamed Tissue, Makena Augenstein, Nayiri Alexander, Matthew Gartner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The opioid epidemic has impacted over 10 million Americans in 2019. Opioids, like morphine, bind non-selectively in both peripheral tissue, leading to effective pain relief, and central tissue, resulting in dangerous side effects and addiction. The inflamed conditions of injured tissues have a lower pH (pH = 6–6.5) environment than healthy tissue (pH = 7.4). We aim to design a morphine derivative that binds selectively within inflamed tissue using molecular extension and dissection techniques. Morphine binds to the μ-opioid receptor (MOR) when the biochemically active amine group is protonated. Fluorination of a β-carbon from the tertiary amine group led to …

Volume 14, Ireland Seagle, Dalton C. Whitby, Cassandra Poole, Rachel Cannon, Heidi Parker-Combes, Devon G. Shifflett, Antonio Harvey

Incite: The Journal of Undergraduate Scholarship

Table of Contents:

• Introduction: Dr. Amorette Barber
• From the Editor: Dr. Larissa "Kat" Tracy
• From the Designers: Rachel English, Rachel Hanson
• Hungry Like the Wolf: The Wolf as Metaphor in Paramount Network’s Yellowstone: Ireland Seagle
• “Floating Cities”: Illustrating the Commercial and Conservation Conflict of Alaskan Cruise Ship Tourism: Dalton C. Whitby
• What Can You Do When Your Genes are the Enemy? Current Applications of Gene Manipulation and the Associated Ethical Considerations: Cassandra Poole
• La doble cara: un tema romántico en las obras de Larra y Hawthorne: Rachel Cannon
• Resolving a Conflict: How to …

Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …

Sharprazor: Automatic Removal Of Hair And Ruler Marks From Dermoscopy Images, Reda Kasmi, Jason Hagerty, Reagan Harris Young, Norsang Lama, Januka Nepal, Jessica Miinch, William V. Stoecker, R. Joe Stanley

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Background: The removal of hair and ruler marks is critical in handcrafted image analysis of dermoscopic skin lesions. No other dermoscopic artifacts cause more problems in segmentation and structure detection. Purpose: The aim of the work is to detect both white and black hair, artifacts and finally inpaint correctly the image. Method: We introduce a new algorithm: SharpRazor, to detect hair and ruler marks and remove them from the image. Our multiple-filter approach detects hairs of varying widths within varying backgrounds, while avoiding detection of vessels and bubbles. The proposed algorithm utilizes grayscale plane modification, hair enhancement, segmentation using tri-directional …

Synthesis And Characterization Of Some Disubstituted Cyclopentadienyl Rhenium Complexes As Potential Candidates In Semiconductive Materials, Chloe Vernon

Senior Honors Theses

Since 2000, when the Nobel Prize in Chemistry as awarded for conductive polymer research few studies have been performed concerning the conductive capabilities of discrete organometallic compounds. For this project, organometallic compounds were formed specifically with a transition metal included in the structure. Through oxidation and reduction reactions, the variation in the electrical conductivity could allow for an analysis of whether this unique structure would allow for tunability. The goal of this research was to begin with aromatic substituted fulvenes and perform various multistep synthesis processes, utilizing thallium salt intermediates, to produce several disubstituted cyclopentadienyl rhenium complexes. In this project, …

Virtual And In Vitro Screening Of Natural Products Identifies Indole And Benzene Derivatives As Inhibitors Of Sars-Cov-2 Main Protease (MPro), Dony Ang, Riley Kendall, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with …

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 …

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …

Description Of Reaction And Vibrational Energetics Of Co2-Nh3interaction Using Quantum Computing Algorithms, Manh Tien Nguyen, Yueh-Lin Lee, Dominic Alfonso, Qing Shao, Yuhua Duan

Markey Cancer Center Faculty Publications

CO2 capture is critical to solving global warming. Amine-based solvents are extensively used to chemically absorb CO2. Thus, it is crucial to study the chemical absorption of CO2 by amine-based solvents to better understand and optimize CO2 capture processes. Here, we use quantum computing algorithms to quantify molecular vibrational energies and reaction pathways between CO2 and a simplified amine-based solvent model—NH3. Molecular vibrational properties are important to understanding kinetics of reactions. However, the molecule size correlates with the strength of anharmonicity effect on vibrational properties, which can be challenging to address using classical computing. Quantum computing can help enhance molecular …

Development Of An Lcms Method To Detect And Quantify Curcumin In A Novel Oral Formulation Of Turmeric, Brandon Renninger

Annual Research Symposium

No abstract provided.

Inducible Nitric Oxide Synthase Embedded In Alginate/Polyethyleneimine Hydrogel As A New Platform To Explore No-Driven Modulation Of Biological Function, Shaimaa Maher, Lauren A. Smith, Celine A. El-Khoury, Haitham F. Kalil, Khalid Sossey-Alaoui, Mekki Bayachou

Chemistry Faculty Publications

Nitric oxide (NO), a small free radical molecule, turned out to be pervasive in biology and was shown to have a substantial influence on a range of biological activities, including cell growth and apoptosis. This molecule is involved in signaling and affects a number of physiologic functions. In recent decades, several processes related to cancer, such as angiogenesis, programmed cell death, infiltration, cell cycle progression, and metastasis, have been linked with nitric oxide. In addition, other parallel work showed that NO also has the potential to operate as an anti-cancer agent. As a result, it has gained attention in cancer-related …

Clic And Membrane Wound Repair Pathways Enable Pandemic Norovirus Entry And Infection, B. Vijayalakshmi Ayyar, Khalil Ettayebi, Wilhelm Salmen, Umesh C. Karandikar, Frederick H. Neill, Victoria R. Tenge, Sue E. Crawford, Erhard Bieberich, B. V. Venkataram Prasad, Robert L. Atmar, Mary K. Estes

Markey Cancer Center Faculty Publications

Globally, most cases of gastroenteritis are caused by pandemic GII.4 human norovirus (HuNoV) strains with no approved therapies or vaccines available. The cellular pathways that these strains exploit for cell entry and internalization are unknown. Here, using nontransformed human jejunal enteroids (HIEs) that recapitulate the physiology of the gastrointestinal tract, we show that infectious GII.4 virions and virus-like particles are endocytosed using a unique combination of endosomal acidification-dependent clathrin-independent carriers (CLIC), acid sphingomyelinase (ASM)-mediated lysosomal exocytosis, and membrane wound repair pathways. We found that besides the known interaction of the viral capsid Protruding (P) domain with host glycans, the Shell …

Engineered Plga Nanofibers For Drug Delivery, Andrew Mancuso

Dissertations, Theses, and Capstone Projects

Poly-lactic-co-glycolic acid (PLGA) polymers are rapidly gaining momentum as a platform for next-generation drug delivery systems due to their ease and low cost of synthesis, favorable biocompatibility and biodegradability, and lack of toxicity. In particular, the application of drug-loaded PLGA nanofibers directly to a target tissue may represent a promising alternative to traditional routes of drug administration (e.g., oral, injectable) as they offer the potential to greatly improve bioavailability, increase efficacy, and reduce off-target toxicity. Furthermore, the use of such a system may potentially allow for greater flexibility in clinical drug development, by enabling the use of compounds which have …

Synthesis And Biomedical Applications Of Hollow Iron Oxide Nanoparticles, Aloka S. Paragoda Arachchilage

Dissertations, Theses, and Capstone Projects

Nano-scale materials have gained much attention during the past few decades due to the stark differences in their properties compared to bulk material. Thus, they are being studied for a myriad of applications ranging from harnessing solar energy to diagnostics. This thesis focuses on the synthesis of hollow iron oxide nanoparticles using Galvanic replacement reactions and their application in drug delivery. Moreover, the use of a peptide precursor for the enhancement of exosomes is also discussed.

Chapter 1 discusses a simple and economical Galvanic approach used for the synthesis of hollow one-dimensional iron oxide nanotubes. In the initial reaction, the …

Potential Of Biduri Fiber (Calotropis Gigantea) As Material For Oil Spill Absorbent, Anne Sukmawati, Wulan Septiani

Journal of Materials Exploration and Findings

Biduri fiber (Calotropis gigantea) is a natural hollow fiber with hydrophobic and oleophilic properties potentially used as oil spilled sorbent from seawater. This study aims to determine the absorption capacity and efficiency of the Biduri fiber and membrane to fuel oil. Measurement of oil absorption to seawater was carried out at various fiber weights (0.5-1.5 g), fiber composition (50-95%), contact time (10-90 minutes), temperature (30 and 50°C), and compared with commercial products. The results showed that the fiber weight variation of 0.5-1.5 g has an average absorption efficiency of 96.67%, and the highest absorption was obtained in a weight of …

Modification Of Hyaluronic Acid To Enable Click Chemistry Photo-Crosslinking Of Hydrogels With Tailorable Degradation Profiles, Ciara Buckley

Articles

Hyaluronic acid (HA) is a naturally occurring mucopolysaccharide that, due to its inherent bioactivity and extracellular matrix-like structure, has the potential to be utilised extensively in tissue engineering. However, this glycosaminoglycan lacks the properties required for cellular adhesion and photo-crosslinking by UV light, which significantly hinders this polymers applicability. This research presents a method for modifying hyaluronic acid via thiolation and methacrylation to generate a novel photo-crosslinkable polymer with improved physicochemical properties, biocompatibility and the potential to customize biodegradability according to the ratio of monomers used. A decrease in stiffness proportional to increasing thiol concentration was observed when testing the …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …

Split Catalytic Probes For The Detection Of Monkeypox Virus, Jaehyun Ahn

Honors Undergraduate Theses

The COVID-19 outbreak highlighted the important role that diagnostic tests play in the healthcare system. To reduce the impact of infectious disease outbreaks, the development of rapid and cost-effective point-of-care-tests (POCTs) is crucial. With the dissemination of the Monkeypox (Mpox) virus, it became a necessity to produce POCTS that are inexpensive and easy to use. This work explored the construction of two colorimetric assays that aim to detect Mpox genetic signatures. One is based on the split-peroxidase-like deoxyribozyme probes (sPDz), while the other utilizes a cascade system of split RNA-cleaving deoxyribozyme (sDz) and peroxidase-like deoxyribozyme (PDz). Both rely on catalytic …

Development And Praxis Of Ph Drug Delivery System Contra Zika, Julissa Rodriguez

College of Graduate Studies: Theses & Dissertations

As the effects of global warming continue to spread throughout the world, another critical issue is slowly gaining attention in many urban tropical countries. The Emerging Infectious Diseases/ Pathogens list from the National Institutes of Health (NIH) listed the Zika virus as a potential pandemic threat. In 2015, an outbreak of Zika was noted in several South American countries until the spread reached an all-time high of 87 countries in 2017. During the outbreaks, adults affected were noted to have joint and muscle pains, fevers, and rashes. The worst cases reported would ultimately lead to Guillain-Barre symptoms. Still, pregnant women …

Extracting High-Molecular Weight Dna From Cyanobacteria Using Promega's Wizard® Hmw Dna Extraction Kit With A Modified Protocol, Metis, Megan A. Hept, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's Wizard® HMW DNA Extraction Kit to acquire high molecular weight DNA from cyanobacterial species. The protocol used in the kit is the “3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria” protocol. During a key step in the protocol, the lingering remnants of the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification …

Enzymatic Electrochemical Biosensors For Neurotransmitters Detection: Recent Achievements And Trends, Zina Fredj, Baljit Singh Dr., Mohamed Bahri, Peiwu Qin, Mohamad Sawan

Articles

Neurotransmitters (NTs) play a crucial role in regulating the behavioral and physiological functions of the nervous system. Imbalances in the concentrations of NT have been directly linked to various neurological diseases (e.g., Parkinson’s, Huntington’s, and Alzheimer’s disease), in addition to multiple psychotic disorders such as schizophrenia, depression, dementia, and other neurodegenerative disorders. Hence, the rapid and real-time monitoring of the NTs is of utmost importance in comprehending neurological functions and identifying disorders. Among different sensing techniques, electrochemical biosensors have garnered significant interest due to their ability to deliver fast results, compatibility for miniaturization and portability, high sensitivity, and good controllability. …

Using Wastewater-Based Epidemiology To Study Chlamydia Occurrence On A College Campus, Jessie E. Chin Quee

Honors Undergraduate Theses

Chlamydia is a sexually transmitted disease caused by Chlamydia trachomatis, commonly affecting sexually active college-aged adults. Presently, opportunistic testing, self-testing, and information campaigns are methods to screen vulnerable populations and raise awareness about chlamydia. Chlamydia remains underdiagnosed and undertested due to a lack of participation by individuals who may have been exposed to it. Wastewater-based epidemiology is a rising biomonitoring tool that detects the presence of disease- and drug-specific biomarkers in a community's wastewater. In this study, wastewater-based epidemiology was used to detect the presence of C. trachomatis on the University of Central Florida campus. Wastewater samples were collected …

Investigating Visinin-Like Protein 1 And Ubiquitinated Visinin-Like Protein 1 As Mild Traumatic Brain Injury Biomarkers, Yueming Wu

Theses and Dissertations--Chemistry

Traumatic brain injury (TBI) continues to be a significant cause of morbidity and mortality worldwide. Despite significant progress in understanding the complex pathophysiology of TBI, the underlying mechanisms remain poorly understood. The primary brain damage is acute and irreversible. However, secondary brain injuries often develop gradually over months to years, creating an opportunity for critical therapeutic interventions. In the past decade, research on TBI biomarkers has seen significant progress. This progress has been driven by the diverse nature of TBI pathologies and the challenges they present for evaluation, management, and prognosis. TBI biomarker proteins resulting from axonal, neuronal, or glial …

Deposited Cigarette Smoke As A Driver Of Oxidation And Partitioning Processes On Indoor Surfaces, April Hurlock

Honors Theses

Despite the large amount of time that individuals spend indoors during their lives, very little attention was paid to the chemistry that occurs on indoor surfaces until recently. Although not visible to the naked eye, physical and chemical processes, such as partitioning and oxidation, are occurring on virtually every indoor surface in a typical household. Indoor pollutants, ranging from skin oils to environmental cigarette smoke, drive a lot of these processes. The transformation of indoor surfaces by indoor pollutants can increase chemical exposure risks as new irritants or carcinogens can be introduced to the surfaces. In this thesis, I describe …

Sound The (Smaller) Alarm: The Triphosphate Magic Spot Nucleotide Pgpp, Areej Malik, Megan A. Hept, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

It has recently become evident that the bacterial stringent response is regulated by a triphosphate alarmone (pGpp) as well as the canonical tetra- and pentaphosphate alarmones ppGpp and pppGpp [together, (p)ppGpp]. Often dismissed in the past as an artifact or degradation product, pGpp has been confirmed as a deliberate endpoint of multiple synthetic pathways utilizing GMP, (p)ppGpp, or GDP/GTP as precursors. Some early studies concluded that pGpp functionally mimics (p)ppGpp and that its biological role is to make alarmone metabolism less dependent on the guanine energy charge of the cell by allowing GMP-dependent synthesis to continue when GDP/GTP has been …

Halogen Bonding Interactions Of Haloaromatic Endocrine Disruptors And The Potential For Inhibition Of Iodothyronine Deiodinases, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Halogen bonding (XB) is a potential mechanism for the inhibition of the thyroid-activating/deactivating iodothyronine deiodinase family of selenoproteins through interactions with halogenated endocrine disrupting compounds (EDCs). Trends in XB interactions were examined using density functional theory for a series of polyhalogenated dibenzo-1,4-dioxins, biphenyls, and other EDCs with methylselenolate, a simple model of the Dio active site selenocysteine. The strengths of the interactions depend upon the halogen (Br>Cl), the degree of substitution, and the position of the acceptor. In terms of donor-acceptor energies, interactions at the meta position are often the strongest, suggesting a link to the topology of THs, …

Para-Methoxybenzylidene Acetal-Protected D-Glucosamine Derivatives As Ph-Responsive Gelators And Their Applications For Drug Delivery, Jonathan Bietsch, Logan Baker, Anna Duffney, Alice Mao, Mary Foutz, Cheandri Ackermann, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low molecular weight gelators (LMWGs) are compounds with the capability to self-assemble into complex molecular networks within a solvent, leading to solvent immobilization. This process of gel formation depends on noncovalent interactions, including Van der Waals, hydrogen bonding, and π–π stacking. Due to their potential applications in environmental remediation, drug delivery, and tissue engineering, these molecules have emerged as an important area of research. In particular, various 4,6-O-benzylidene acetal-protected D-glucosamine derivatives have shown promising gelation abilities. In this study, a series of C-2-carbamate derivatives containing a para-methoxy benzylidene acetal functional group were synthesized and characterized. These compounds exhibited good …