Digital Commons Network^™

Synthetic Studies Of Potential New Ketogenic Molecules, Mohammad Nazmus Sakib

USF Tampa Graduate Theses and Dissertations

The ketogenic diet has gained popularity in the past few decades among people and physicians due to its various health benefits. A significant amount of research has been done for the modification of the original ketogenic diet and investigation of its potential health benefits. However, synthesis of novel ketogenic compounds as a dietary supplement has not received the same level of attention. That is the primary objective of this research project. The first chapter of this manuscript describes the synthesis of various short and medium chain esters of different polyols that have been done so far, and areas of their …

First Optimization Of Novel, Potent, Selective Pde11a4 Inhibitors For Age-Related Cognitive Decline, Shams Ul Mahmood, Mariana Lozano Gonzalez, Sreedhar Tummalapalli, Jeremy Eberhard, Judy Ly, Charles S. Hoffman, Michy P. Kelly, John Gordon, Dennis Colussi, Wayne Childers, David P. Rotella

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Phosphodiesterase 11A4 (PDE11A4) is a dual-acting cyclic nucleotide hydrolase expressed in neurons in the CA1, subiculum, amygdalostriatal transition area and amygdalohippocampal area of the extended hippocampal formation. PDE11A4 is the only PDE enzyme to emanate solely from hippocampal formation, a key brain region for the formation of long-term memory. PDE11A4 expression increases in the hippocampal formation of both humans and rodents as they age. Interestingly, PDE11A knockout mice do not show age-related deficits in associative memory and show no gross histopathology. This suggests that inhibition of PDE11A4 might serve as a therapeutic option for age-related cognitive decline. A novel, yeast-based …

Introductory Chemistry, Mona Muzammil

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Introductory Chemistry, this edition is designed for a one-semester, introductory or preparatory chemistry course. Students taking this course need to develop problem-solving skills-but they also must see why these skills are important to them and to their world. Introductory Chemistry extends chemistry from the laboratory to the student's world. It motivates students to learn chemistry by demonstrating how it plays out in their daily lives.

This book draws students into the course through engagement and building their foundational knowledge – while introducing new content and resources to help students build critical thinking and problem-solving skills. allowing students flexibility and ensuring …

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

USF Tampa Graduate Theses and Dissertations

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

Dynamic Regulation Of Store-Operated Calcium Entry By Protein S-Acylation, Goutham Kodakandla

Theses and Dissertations

Calcium plays a pivotal role in many physiological functions in cells. Cytosolic calcium levels are finely tuned by calcium ion channels, pumps, and intracellular organelles. Store-operated calcium entry (SOCE) is when depletion of endoplasmic reticulum (ER) calcium stores activates a calcium sensor known as stromal interaction molecule 1 (STIM1). Activation of STIM1 leads to a conformational change from a compact state to an extended state. This extended state of STIM1 allows it to bind to a calcium channel in the plasma membrane (PM) known as Orai1. The binding of Orai1 and STIM1 leads to opening of Orai1 channels and calcium …

Low-Cost, 3d Printed Irradiation System For In Vitro Photodynamic Therapy Experiments, Chris Acquah, Zachary Pabis, Sourav Kanti Seth, Liraz Levi, Carlos E. Crespo-Hernández

Faculty Scholarship

The development of a suitable irradiation setup is essential for in vitro experiments in photodynamic therapy (PDT). While various irradiation systems have been developed for PDT, only a few offer practical and high-quality setups for precise and reproducible results in cell culture experiments. This report introduces a cost-effective illumination setup designed for in vitro photodynamic treatments. The setup consists of a commercially available light-emitting diode (LED) lamp, a cooling unit, and a specially designed 3D-printed enclosure to accommodate a multiwell plate insert. The LED lamp is versatile, supporting various irradiation wavelengths and adjustable illumination fields, ensuring consistent and reliable performance. …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Analysis Of Cd74 Occurrence In Oncogenic Fusion Proteins, Jasmine Vargas, Georgios Pantouris

Pacific Faculty Work

CD74 is a type II cell surface receptor found to be highly expressed in several hematological and solid cancers, due to its ability to activate pathways associated with tumor cell survival and proliferation. Over the past 16 years, CD74 has emerged as a commonly detected fusion partner in multiple oncogenic fusion proteins. Studies have found CD74 fusion proteins in a range of cancers, including lung adenocarcinoma, inflammatory breast cancer, and pediatric acute lymphoblastic leukemia. To date, there are five known CD74 fusion proteins, CD74-ROS1, CD74-NTRK1, CD74-NRG1, CD74-NRG2α, and CD74-PDGFRB, with a total of 16 different variants, each with unique genetic …

An Insight Into The Physicochemical, Drug-Likeness, Pharmacokinetics And Toxicity Profile Of Kigelia Africana (Lam) Bioactive Compounds, Sulyman Olalekan Ibrahim, Halimat Yusuf Lukman, Marili Funmilayo Zubair, Oluwagbemiga Tayo Amusan, Fatimah Ronke Abdulkadri, Bashir Lawal, Lateefat Bello Abdulfatah, Olubunmi Atolani

Al-Bahir

Kigelia africana plant is multipurpose plant whose therapeutic potential has been thoroughly investigated. The physicochemical, solubilities, ADMET, pharmacological, and drug-like properties of this plant have not been reported in details. This study makes use of the information that is currently known on the chemical make-up of the plant to forecast its overall toxicity as well as the potential for the phytochemicals it contains to be employed in medication discovery. The study also employed free web servers for the lipophilicity, water solubility, drug-likness, bioavailability score, medicinal chemistry and toxicological profiling of the compounds of K. africana. Artemether, a known antimalaria …

Coupling Chemical And Genomic Data Of Marine Sediment-Associated Bacteria For Metabolite Profiling, Stephanie P. Suarez

USF Tampa Graduate Theses and Dissertations

Marine sediment-associated bacteria house many new and exciting novel secondary metabolites. These metabolites can be tested for bioactivity against various types of cancer and fungal, bacterial, and viral infections. In this thesis, we investigated the combination of biosynthetic gene cluster information with mass spectra to perform a chemical profiling of sediment- associated bacteria. Furthermore, we utilized a scoring technique to provide an identification and confidence score to each annotated compound. The sediment was collected from east Arthur Harbor, Palmer Station, Antarctica, at depths of 20 ft and 60 ft. After plating on agar, 52 unique bacterial strains were isolated, with …

Green Synthesized Silver Nanoparticles-Based Sensing For Monitoring Water Pollution: An Updated Review, Muhamad Allan Serunting, Muhammad Ali Zulfikar, Henry Setiyanto, Dian Ayu Setyorini, Vienna Saraswaty

Karbala International Journal of Modern Science

Water is a basic human need and has been heavily contaminated. Therefore, it becomes a concern to remove the pollutant and monitor its quality. The removal methods include precipitation, filtration, adsorption, and photodegradation. Meanwhile, the monitoring can be done by measuring and analyzing the contaminant using spectrophotometry and chromatography. Nevertheless, those methods usually need a complicated preparation, and are expensive. Thus, a simple method is necessary to overcome these drawbacks by developing a sensor. In recent years, the sensor performance has been enhanced by using nanomaterials, such as silver nanoparticles (AgNPs). AgNPs can be synthesized using plant extracts through a …

Synthesis And Characterization Of Zirconium Oxide Nanoparticles Using Z. Officinale And S. Aromaticum Plant Extracts For Antibacterial Application, M. J. Tuama, M. F. A. Alias

Karbala International Journal of Modern Science

Abstract The dramatic rise in bacterial infections and increased resistance to conventional antibiotics has led to the exploration of biologically derived nanomaterials to counteract bacterial activity. Nanotechnology, which deals with materials at the atomic or molecular level, is a promising way to achieve this goal. Zirconium oxide nanoparticles (ZrO2NPs) have shown strong antibacterial effects due to the increased surface-to-volume ratio at the nanoscale. This study focused on the production of ZrO2NPs in an environmentally friendly manner, which included extracts from Zingiber officinale (ginger), where G-ZrO2NPs were produced, and Syzygium aromaticum (clove), which produced S-ZrO2NPs. Various techniques were used, such as …

Soft Microreactors For The Deposition Of Microstructures And The Related Surface Chemistries Of Polymeric Materials, Jessica Wagner

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The precise control over small volumes of liquids is of great interest to various fields such as biotechnology, drug development, and diagnostics. Working at small scales reduces cost, time, and waste, which is why microfluidic lab-on-chip technologies have become popular in a wide range of industries and applications. Additionally, there are differences in properties such as mass transport and heat dissipation at the micron scale compared to in bulk. Microfluidic devices contain several interfaces to consider when preparing to fabricate devices. The substrate/device, substrate/solution, and solution/device interfaces are all of importance and must carefully be tuned depending on the desired …

Development Of Poly(Acrylamide)-Based Hydrogel Composites With Powdered Activated Carbon For Controlled Sorption Of Pfoa And Pfos In Aqueous Systems, Maria Victoria X. Klaus, Angela M. Gutierrez, J. Zach Hilt

UK CARES Faculty Publications

Per- and polyfluoroalkyl substances (PFAS) are anthropogenic compounds developed for various applications; some are connected to adverse health impacts including immunosuppression and higher susceptibility to some cancers. Current PFAS remediation treatments from aqueous sources include granular activated carbon (GAC) adsorption, membrane separation, and anion- exchange resin (AER) removal. Each has specific disadvantages, hence the need for a new and efficient technology. Herein, acrylamide-based hydrogel composites were synthesized with powdered activated carbon (PAC) and characterized to determine their affinity for PFAS. Physicochemical characterization included Fourier-Transform infrared spectroscopy (FTIR) to identify chemical composition, thermogravimetric analysis (TGA) to confirm PAC loading percentage, and …

Modification Of Cellulose Fibers By Acyl Grafting For Oil Spill Remediation, Fatima Saif Alhumaidi

Theses

Oil spills represent a significant source of aquatic pollution with substantial repercussions on the environment as well as the economic and societal well-being of coastal communities. This research project is focused on the utilization of chemically modified cellulose-based fibers to remediate oil-contaminated water. The hydroxyl groups present in cellulose were acetylated under optimized conditions, thereby rendering the fibers hydrophobic and enhancing their affinity for crude oil. The modified cellulosic material was characterized by several physical and chemical techniques (IR, TGA, contact angle measurement, SEM, and back titration) to determine the extent of acylation and assess their morphological properties. The derivatized …

Oxidative Stress In Health And Disease, V. Prakash Reddy

Chemistry Faculty Research & Creative Works

Oxidative stress, resulting from the excessive intracellular accumulation of reactive oxygen species (ROS), reactive nitrogen species (RNS), and other free radical species, contributes to the onset and progression of various diseases, including diabetes, obesity, diabetic nephropathy, diabetic neuropathy, and neurological diseases, such as Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD). Oxidative stress is also implicated in cardiovascular disease and cancer. Exacerbated oxidative stress leads to the accelerated formation of advanced glycation end products (AGEs), a complex mixture of crosslinked proteins and protein modifications. Relatively high levels of AGEs are generated in diabetes, obesity, AD, and other …

The Trifluoromethyltetrafluoro-Λ6-Sulfanyl Group In Organic And Polymer Chemistry, Muqian Deng

Legacy Theses & Dissertations (2009 - 2024)

Fluorine atom was widely applied in the organic chemistry and medicinal chemistry due to its strong electronegativity and lipophilicity. Fluorine atom, trifluoromethyl (CF3) moiety, trifluoromethyl sulfenyl (CF3S) moiety, pentafluoromethylsulfenyl (SF5) moiety have already been applied in the medicinal chemistry. These fluorinated groups brought the good chemical stability, oral stability, low toxicity, and longer half-life compared with the analogs. Fluorine containing compounds can be synthesized via radical reaction, electrophilic fluorinated source as well as nucleophilic sources. Additionally, the fluorinated compounds can also be synthesized via chlorofluoro-oxidation and SN2 reactions. In our lab, we introduced the super fluorine rich moiety (trans-CF3SF4 group) …

Openasap: An Affordable 3d Printed Atmospheric Solids Analysis Probe (Asap) Mass Spectrometry System For Direct Analysis Of Solid And Liquid Samples, Robert Samples, Rico Mukoyama, Jacob Shaffer, Jill Mikucki, Lesley Ann Giddings

Chemistry: Faculty Publications

Atmospheric Solids Analysis Probe (ASAP) mass spectrometry is a versatile technique allowing direct sampling of solid and liquid samples, but its adoption is limited due to the high cost of commercial ASAP systems. To address this, we present OpenASAP, an open-source ASAP system for mass spectrometers that can be fabricated for $20 or less using 3D-printing. Our design is readily adaptable to instruments from different manufacturers and can be produced with a variety of additive manufacturing techniques on consumer-grade 3D-printers. The probe allows for rapid sampling of solid and liquid samples without sample preparation, making it useful for high throughput …

Calorimetric Analysis Using Dna Thermal Stability To Determine Protein Concentration, Matthew W. Eskew, Patrick Reardon, Albert S. Benight

Chemistry Faculty Publications and Presentations

It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm’s. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and C …

Hydroxyapatite-Based Coatings On Silicon Wafers And Printed Zirconia, Antoine Chauvin

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Dental surgery needs a naturally attract implant design that can ensure both osseointegration and soft tissue integration. Hydroxyapatite (HAp), the main mineral constituent of dentine and tooth enamel, is commonly used as a coating component, notably for overlaying titanium– or ceramics–based implants. This thesis aims to investigate the behavior of a HAp-based coating, specifically designed to be compatible with a porous substrate. Coating layers are made by sol–gel dip coating by immersion of porous substrates made by additive manufacturing into solutions of HAp, having been mixed with polyethyleneimine (PEI), to improve the adhesion of HAp on the substrate. First, the …

University Of Arkansas, Chemistry And Biochemistry Department Graduate Student Publications, 2018- November 2023. 39p., Jeremy Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a compilation of the research publications by the Chemistry and Biochemistry (CHBC) Graduate students for the period: 2018-November 2023. It includes publications by the CHBC graduates and those where a CHBC faculty was the main advisor. It includes a summary of the research. The listing is organized according to type of publications within specific years.

University Of Arkansas, Chemistry And Biochemistry Department Research Publications, 2014- November 2023. 107p., Jeremy Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a compilation of the research publications by the Chemistry and Biochemistry faculty for the period: 2014 - November 2023. The information was gathered from major databases in science and technology including Web of Science, SciFinder, Reaxys, PubMed, IEEE Explore and Engineering Index. At least one author in each of the publications has the CHBC department as its affiliation. It includes a table summarizing the research. The listing is organized according to type of publications within specific years.

Controlling Guest Binding To Transition Metal Hosts Via Redox Stimuli, Jasmine S. Sanford

LSU Doctoral Dissertations

Several metal complexes were investigated as potential hosts to execute controllable host- guest interactions using a redox stimulus. Previously, our group has synthesized new Cu^II m-xylylenebis(pyridyltriazole) (m-xpt) hosts and their redox properties were analyzed. In Chapter 2, we take advantage of the Cu^II host’s ability to perform redox to investigate its interaction with chloride guest ions. This study was executed with two main Cu-xpt hosts: [Cu₂(m- xpt)₂(NO₃)₂](PF₆)₂ and [Cu₂(m-xpt)₂Cl₂]Cl₂. The host-guest interaction was analyzed with additions …

Phthalocyanines Prepared From 4,5-Dihexylthiophthalonitrile, A Popular Building Block, Derya Topkaya Taşkiran, Zeynel Şahi̇n, Ümi̇t İşci̇, Fabi̇enne Dumouli̇n

Turkish Journal of Chemistry

Phthalocyanines are tetrapyrrolic artificial porphyrinoids that play major roles in advanced biological and technological applications. Research on this family of dyes is particularly active in Türkiye, with many derivatives being prepared from 4,5-dihexyl-thiophthalonitrile DiSHexPN, which is one of the most popular noncommercially available building blocks for phthalocyanines. This review summarizes the phthalocyanines and their versatile properties and applications that have been published since 1994, when the synthesis of DiSHexPN was first described, to emphasize the importance of this building block in plentiful applications, all with bio-medical or technological impact.

Homoprotocatechuate Dioxygenase Active Site: Imitating The Secondary Sphere Base Via Computational Design, Muhammed Buyuktemiz, Yavuz Dede

Turkish Journal of Chemistry

Oxidative ring cleavage reactions have attracted great interest and various studies on the catechol ring-cleaving enzyme homoprotocatechuate dioxygenase (HPCD) have been reported in the literature. The available data on how the proton transfer takes place led us to design a potential HPCD model structure. A secondary sphere effect of utmost importance, the assistance of His200, which is critical for the catechol proton to migrate to dioxygen, was cautiously included on the first coordination shell. This was done mainly by modifying the axial ligands in the first coordination shell of HPCD such that the dual basic/acidic role in the proton transfer …

Combination Of Smartphone Digital Image Colorimetry And Uv-Vis Spectrophotometry As Detection Systems With Solidified Floating Organic Drop Microextraction As Preconcentration Method For The Quantification Of Methyl Red In Wastewater Samples, Mi̇ray Bombom, Ayça Gi̇rgi̇n, Buse Tuğba Zaman, Fatma Turak, Sezgi̇n Bakirdere

Turkish Journal of Chemistry

In this study, a portable smartphone-based digital image colorimetric system (SDIC) was designed and integrated with a solidified floating organic drop microextraction method (SFODME) for the quantification of methyl red in textile wastewater samples. The RGB (red, green, and blue) data were evaluated for each captured image, and the green channel was selected for quantification due to its linear response for the analyte. Under optimal conditions, an acceptable linear range was recorded for the analyte. The proposed method recorded a limit of detection (LOD) value of 0.046 mg/L. The developed microextraction method was also combined with UVVis spectrophotometry, which recorded …

Cibacron Blue F3ga Ligand Dye-Based Magnetic Silica Particles For The Albumin Purification, Nurhak Tatar, Semra Akgönüllü, Handan Yavuz Alagöz, Adi̇l Deni̇zli̇

Turkish Journal of Chemistry

Dye-ligand affinity chromatography is among the increasingly popular affinity chromatography based on molecular recognition for the purification of albumin. This study focuses on the binding of Cibacron Blue F3GA ligand dye with magnetic silica particles and purification by separation. Mono-disperse silica particles with bimodal pore size distribution were employed as a high-performance adsorbent for human serum albumin (HSA) protein purification under equilibrium conditions. The synthesized ligand-dye affinity based magnetic silica particles were characterized by electron spin resonance, Fourier-transform infrared spectroscopy, scanning electron microscopy, vibrating sample magnetometer, elemental analysis, and dispersive X-ray analysis. The HSA purification performance of the proposed material …

The Chemical And Electrochemical Stimuli Viologen Substituted Phthalocyanine With Tunable Optical Features1, Özge Di̇lara Ateş, Gülenay Tunç, Ahmet Şenocak, Burcu Dedeoğlu, Mehmet Menaf Ayhan, Ayşe Gül Gürek

Turkish Journal of Chemistry

In this study, viologen-tetrasubstituted Zn(II) phthalocyanines (PcV1 and PcV2) were designed and synthesized to achieve the tunable optical features via redox-active viologen groups. Several parameters relevant to the evaluation of the tunable optical features have been investigated: UV-Vis, cyclic voltammetry (CV), EPR, square wave voltammetry (SWV), and theoretical analyses. The results showed that upon reductions and oxidations of viologen groups either chemically or electrochemically, the optical features of PcV1 and PcV2 change drastically with switchable processes. These outcomes indicate that achieving control over optical features of large organic chromophores such as Pc with our rational design can be used for …

Electrochemical Dna Biosensors Developed For The Monitoring Of Biointeractions With Drugs: A Review, Kadri̇ye Arzum Erdem Gürsan, Muhammed Hüseyi̇n Şentürk, Esma Yildiz Göz, Meltem Maral, Ayla Yildirim, Ayşen Bozoğlu, Burak Kivrak, Nesli̇han Ceren Ay

Turkish Journal of Chemistry

The interaction of drugs with DNA is important for the discovery of novel drug molecules and for understanding the therapeutic effects of drugs as well as the monitoring of side effects. For this reason, many studies have been carried out to investigate the interactions of drugs with nucleic acids. In recent years, a large number of studies have been performed to electrochemically detect drug-DNA interactions. The fast, sensitive, and accurate results of electrochemical techniques have resulted in a leading role for their implementation in this field. By means of electrochemical techniques, it is possible not only to demonstrate drug-DNA interactions …

Sonophotochemical And Photochemical Efficiency Of Thiazole-Containing Metal Phthalocyanines And Their Gold Nanoconjugates, Nazli Farajzadeh, Hacer Yasemi̇n Yeni̇lmez, Göknur Yaşa Atmaca, Ali̇ Erdoğmuş, Zehra Bayir

Turkish Journal of Chemistry

This study presents the synthesis of some metal {M = Zn(II), Lu(III), Si(IV)} phthalocyanines bearing chlorine and 2-(4-methylthiazol-5-yl) ethoxy groups at peripheral or axial positions. The newly synthesized metal phthalocyanines were characterized by applying FT-IR, 1 H NMR, mass, and UV-Vis spectroscopic approaches. Additionally, the surface of gold nanoparticles was modified with zinc(II) and silicon(IV) phthalocyanines. The resultant nanoconjugates were characterized using TEM images. Moreover, the effect of metal ions and position of substituent, and gold nanoparticles on the photochemical and sonophotochemical properties of the studied phthalocyanines was investigated. The highest singlet oxygen quantum yield was obtained for the lutetium …