Digital Commons Network^™

Fret Study Of Ligand Binding And Exchange Kinetics On The Surface Of Cdse/Zns Quantum Dots, Randee Jean Mcbride

Graduate Theses and Dissertations

Quantum dots are a valuable tool in many research applications and commercial development. Their applications are far reaching and as such have become a topic of great interest. One of their greatest assets is the ability to utilize them as water soluble fluorescent labels. Rendering the nanocrystals water soluble can be accomplished in several ways, but one very popular method is by capping them with water-soluble multi-functional organic ligands. However, these ligands, when attached to the quantum dot surface, are labile and can be exchanged which can be problematic when using the quantum dots in research applications. This projects investigates …

Development And Application Of Mass Spectrometry-Based Biophysical Approaches, Ying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher …

The Synthesis And Study Of The Biological And Colloidal Properties Of Bolaamphiphiles, Louis M. Damiano

Senior Honors Projects, 2010-2019

Over the past decade, antibiotic resistant bacteria have caused infections in patients throughout the world.^[1] The rise in antibiotic resistance is primarily due to the misuse and overuse of antibiotics. ^[1] To counter the increase in antibiotic resistance, infection control mechanisms have been aggressively researched in recent years. In particular, drug delivery has become a focal point to fight antibiotic resistant infections.^[2] Amphiphiles have a wide range of applications in the clinical setting, including the ability to inhibit bacterial transference because of their bactericidal activity. ^[3] Bolaamphiphiles are a subclass of amphiphiles that possess two or more hydrophilic …

Analysis Of Anacardic Acid On The Surface Of Pelargonium × Hortorum Using Matrix Assisted Laser Desorptoin Ionization Mass Spectrometry Imaging., Bryan Edward Wessel 1989-

Electronic Theses and Dissertations

The biosynthetic pathway leading to the production of anacardic acids (AnAcs) in glandular trichomes on the surface of geranium plants remains unclear. Anacardic acids are salicylic acid derivatives known to possess various medicinal benefits. Gene silencing techniques, such as RNA interference, could be useful in determining specific enzymes involved in the synthesis of AnAcs. However, it is first necessary to develop methodologies to image AnAcs. In this project, both fluorescence (FL) and mass spectral imaging (MSI) were tested. Our results indicate that cellular imaging of AnAcs, via FL, is not suitable because the spectral ranges of absorption and emission of …

Mentoring Undergraduates Via Organic Synthesis, Steven L. Castle

Journal of Undergraduate Research

This report summarizes the results that were generated under the auspices of the mentoring environment in my laboratory from January 2013 to the present. A total of eight undergraduates participated in the mentoring environment during this period.

Sulfidic Spring In The Gypsum Karst System Of Monte Conca (Italy): Chemistry And Microbiological Evidences, Marianna Messina, Tiziana Grech, Fiorenzo Fiorenza, Alessandro Marlettta, Pietro Valenti, Salvatore Petralia

International Journal of Speleology

Monte Conca Cave is a karst system placed in Messinian evaporites, consisting of an active cave and a resurgence located on the massif of Monte Conca, Campofranco within the "Riserva Naturale Integrale di Monte Conca". A sulfidic spring is located in the terminal gallery of the cave. To characterize the physical and chemical parameters of the Monte Conca cave and of the sulfidic spring, air temperature, relative humidity, water pH, and concentrations of dissolved sulfides, nitrates and sulfates were monitored. The high sulfide consumption rate in the sulfidic spring, evaluated by a kinetic study, suggests that biotic consumption is dominant. …

Design And Synthesis Of Bioactive Peptidomimetics, Yaogang Hu

USF Tampa Graduate Theses and Dissertations

Protein-Protein Interactions (PPIs) play a very important role in biological functions and therefore the inhibition of specific Protein-Protein Interactions has a huge therapeutic value. The most successful small molecular PPIs inhibitors do not fit with the prevalent `Rule of Five' drug profile. To overcome the disadvantages of small molecular PPIs inhibitors, peptide based PPIs inhibitors were developed. Herein we describe the development of a new class of peptidomimetics AA-peptides. The AApeptides were designed based on chiral PNA backbone. Substitution of nucleobases yields AApeptides that are resistant to proteolysis and capable of mimicking peptides. Two types of AApeptides were discussed in …

Biological Evaluation Of The Vaccine Candidate Tf-Ps A1 And A One-Pot Multicomponent Coupling/Cyclization For Natural Product Herbicide (±)-Thaxtomin A, Jean Paul Bourgault

Wayne State University Dissertations

ABSTRACT

BIOLOGICAL EVALUATION OF THE VACCINE CANDIDATE TF-PS A1 AND A ONE-POT MULTICOMPONENT COUPLING/CYCLIZATION FOR NATURAL PRODUCT HERBICIDE (±)-THAXTOMIN A

By

JEAN PAUL BOURGAULT

August 2015

Advisor: Prof. Peter R. Andreana

Major: Chemistry (Organic)

Degree: Doctor of Philosophy

The -aminooxy derivative of the Thomsen–Friedenreich tumor associated carbohydrate antigen has been synthesized in 11 steps utilizing a D-GalN3 acceptor carrying a pre-installed -N-hydroxysuccinimidyl moiety. The natural  linkage was prepared in high selectivity employing a suitably protected D-GalN3-thioglycoside donor with N-hydroxysuccinimide. With access to -TF-ONH2, the preparation of the TF-PS A1 vaccine candidate ensued smoothly through oxime bond formation. This construct …

Revisiting The Biodesulfurization Capability Of Hyperthermophilic Archaeon Sulfolobus Solfataricus P2 Revealed Dbt Consumption By The Organism In An Oil/Water Two-Phase Liquid System At High Temperatures, Gökhan Gün, Yuda Yürüm, Gi̇zem Di̇nler Doğanay

Turkish Journal of Chemistry

The ability of the hyperthermophilic archaeon Sulfolobus solfataricus P2 to grow on organic and inorganic sulfur sources was investigated. A sulfur-free mineral medium was employed with different sources of carbon. The results showed that inorganic sulfur sources display growth curve patterns significantly different from the curves obtained with organic sulfur sources. Solfataricus has the ability to utilize DBT and its derivatives, but it lacks BT utilization. Solfataricus} utilizes DBT at a rate of 1.23 \mu mol 2-HBP h^{-1} g DCW^{-1} even at 78 °C, at which DBT is known to be unstable. After enabling DBT stabilization using a two-phase culture …

Synthesis, Characterization, Biological Studies, And Molecular Modeling Of Mixed Ligand Bivalent Metal Complexes Of Schiff Bases Based On $N$-Aminopyrimidine-2-One/2-Thione, Hati̇ce Gamze Soğukömeroğullari, Tuğba Taşkin Tok, Feyza Yilmaz, İsmet Berber, Mehmet Sönmez

Turkish Journal of Chemistry

New mixed Schiff bases, Cu(II), Co(II), Ni(II), and Mn(II) complexes, were synthesized derived from 5-chloro-2-hydroxyacethophenone and 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-one/thione. These complexes were characterized by elemental analysis, magnetic measurements, molar conductivity, IR, electronic, NMR, and mass spectral studies. All the complexes showed nonelectrolytic behavior. Moreover, the newly synthesized mixed ligand complexes were evaluated for their in vitro antimicrobial efficiency against bacteria and yeast. The compound named Co(L$_{1}$L) had good antifungal activity against Candida species, but no profound antibacterial effect against bacterial strains. In addition, the ground state geometries of the complexes were optimized using a semi-empirical method at PM6 level, which is a …

A New Series Of Cu(Ii) And Ni(Ii) Complexes Of No Bidentate 4-No$_{2}$-Benzoylhydrazones: Synthesis, Characterization, And Biological Studies, Hati̇ce Başpinar Küçük, Emel Mataraci Kara, Berna Özbek Çeli̇k

Turkish Journal of Chemistry

A series of new nickel(II) and copper(II) hydrazone complexes \textbf{1--14}, containing a bidentate NO-donor hydrazone ligand, derived from 4-nitrobenzoylhydrazide and several aliphatic and aromatic aldehydes were synthesized, and their chemical structures were confirmed by means of FT-IR, UV-Vis, $^{1}$H and $^{13}$C NMR, mass spectral data, conductance measurements, and elemental analyses. The spectral data of the newly synthesized complexes show the formation of a 1:2 [metal:ligand] ratio. The ligands and their complexes were also investigated for their possible in vitro antimicrobial activities against \textit{S. aureus}, \textit{S. epidermidis}, \textit{E. coli}, \textit{K. pneumonia}, \textit{P. aeruginosa}, \textit{P. mirabilis}, \textit{E. faecalis}, and \textit{C. albicans}. Among …

Versatility Of N-Peptidyl And N-Glycopeptidyl Nitroindolines For The Formation Of Peptide/Glycopeptide Acids, Amides, And Thioesters, Luis Alfonso Barrera

Open Access Theses & Dissertations

N-acyl-7-nitroindolines are photoreactive compounds that are known to acylate a number of nucleophiles in inert aprotic solvents under neutral conditions when illuminated at 350 nm. We have assembled a MUC1-derived peptide and Tn or STn-containing MUC1 glycopeptides with a C-terminal photoreactive 7-nitroindoline linker attached to Sieber amide resin by solid phase peptide synThesis using the Fmoc strategy. This type of construction allows for the cleavage of fully protected photoreactive peptides/glycopeptides from the resin with dilute trifluoroacetic acid, or for the direct photorelease of protected peptide/glycopeptide derivatives. Here we demonstrate that N-peptidyl and N-glycopeptidyl 7-nitrindolines can be photochemically converted into their …

The Dimerization Kinetics Of Ncad12 With A Mutated Cis-X-Pro Bond, Victoria Mcclearn

Honors Theses

VICTORIA RAE McCLEARN: DIMERIZATION KINECTICS OF NCAD12 P16A (Under the direction Dr. Susan Pedigo) Calcium binding causes a conformational change into a strand swapped dimer for the cadherins. However, regardless of the sequence similarity for Epithelial Cadherin (ECAD) and Neural Cadherin (NCAD), they respond to the presence of calcium differently. For NCAD, the rate of assembly and disassembly depends upon the presence of calcium, whereas for ECAD the rate of exchange is independent of calcium. Studies into a kinetic model to explain the differences between the rates have been recently conducted. It is believed that ECAD uses an X-dimer intermediate …

Synthetic Oligodeoxynucleotide Purification Via Catching By Polymerization, Suntara Fueangfung

Dissertations, Master's Theses and Master's Reports - Open

Large quantities of pure synthetic oligodeoxynucleotides (ODNs) are important for preclinical research, drug development, and biological studies. These ODNs are synthesized on an automated synthesizer. It is inevitable that the crude ODN product contains failure sequences which are not easily removed because they have the same properties as the full length ODNs. Current ODN purification methods such as polyacrylamide gel electrophoresis (PAGE), reversed-phase high performance liquid chromatography (RP HPLC), anion exchange HPLC, and affinity purification can remove those impurities. However, they are not suitable for large scale purification due to the expensive aspects associated with instrumentation, solvent demand, and high …

Mercury Methylation Potentials In Sediments An Ancient Cypress Wetland Using Species-Specific Isotope Dilution-Gc-Icp-Ms: Analytical Method Development And The Effect Of Sorbent Amendments, Derek Davin Bussan

Electronic Theses and Dissertations

A novel method was developed to measure mercury (Hg) directly in environmental solids using inductively coupled plasma mass spectrometry (ICP-MS) with online sample ashing. The method combines a direct mercury analyzer (DMA) that is based on sample combustion, Hg pre-concentration by amalgamation with gold, and atomic absorption spectrometry (AAS), with a high resolution ICP-MS. Unlike AAS, the ICP-MS is capable of individual isotope measurements allowing for accurate quantitation by isotope dilution mass spectrometry (IDMS) and for isotope tracer experiments. The method was validated using certified reference materials including sediment (NIST 2709), leaves (NIST 1547), and fish-muscle (DORM-3), with recoveries within …

The Electronic Structure Of Environmentally Persistent Free Radicals Formed On Metal Oxide Surfaces, Chad Allen Thibodeaux

LSU Doctoral Dissertations

We have investigated the electronic structure of environmentally persistent free radicals (EPFRs) formed on two different metal oxides: Cu(II)O and ZnO. Cu(II)O is known to be one of the most active metal oxides to form EPFRs. ZnO, however, forms the longest-lived EPFRs. First, we examined the adsorption of phenol on different crystal faces of ZnO. Ultraviolet photoelectron spectroscopy (UPS) shows direct evidence of charge transfer away from the ZnO to the phenol. This differs from the hypothesized mechanism of EPFR formation that says that an electron is transferred to the metal oxide. UPS difference spectra also shows that the phenol …

I. Synthesis Of Ascarosides For Chemical Biology Studies In Caenorhabditis Elegans, Ii. A Photochemical Approach To Delavayine, And Iii. Remote Hydroxylation By Radical Translocation And Polar Crossover, Kyle Allen Hollister

LSU Doctoral Dissertations

The foci of this dissertation are the synthesis of analogs for chemical biology studies, synthetic chemistry method development (with an emphasis on photochemistry), and the application of these methods toward total synthesis. Chapter 1 outlines the synthesis of an array of pheromone analogs that are derivatives of the dideoxy sugar ascarylose. Referred to as ascarosides, such compounds have recently been shown to influence important biological processes in the model organism Caenorhabditis elegans. C. elegans secretes ascarosides into its environment, where the compounds then act as signaling molecules by providing information on factors like population density. Chapter 2 describes the biological …

Nanoscale Gumbos: Size-Control, Characterization, And Applications As Enantioselective Molecularly Imprinted Polymers And Fluorescent Materials, Suzana Hamdan

LSU Doctoral Dissertations

Nanomaterials derived from a group of uniform materials based on organic salts (GUMBOS) have been introduced into the scientific literature through many analytical, biological, and technological applications. These nanomaterials, referred to as nanoGUMBOS, have been shown to display a number of interesting properties including fluorescence, magnetism, tumor targeting, and optoelectronic properties. Herein, we present major studies on nanoGUMBOS including synthesis and size-control, chiral molecular imprinting in polymers, as well as investigation of optical properties and quantum yield of fluorescent semiconductor-based nanoGUMBOS. Various strategies were introduced for production of well-defined nanoGUMBOS. Specifically, several methods based on sonochemistry, microwave, cyclodextrin, and surfactant-assisted …

Synthesis And Anti-Proliferative Activity Of N,N’-Bis(Arylmethyl)Benzimidazolium Salts, Travis M. Williams

Williams Honors College, Honors Research Projects

A series of N,N’-bis(arylmethyl)benzimidazolium salts with hydrophilic and lipophilic substituents have been synthesized, characterized, and tested against select non-small cell cancer cell lines. Substituent variations on the imidazole ring have shown that lipophilicity and hydrophilicity can influence the imidazolium salts’ anti-proliferative activity and aqueous solubility.

Development Of New Linking Chemistry With The Fac-{Re(Co)3}+ Core For Eventual Applications In Radiopharmaceuticals In Imaging And Therapy, Aponsu Meregngna Pramuditha Lakmi Abhayawardhana

LSU Doctoral Dissertations

The facile labeling of biomolecules with a radionuclide is a key goal in radiopharmaceutical development. This study explores two different ligand systems for fac-[Re(CO)3L]+ complexes, that could be used in bioconjugation. The first approach uses a tridentate ligand having a sulfonamide linkage and modeled on previously evaluated fac-[Re(CO)3(N(SO2R)dpa)]PF6 complexes. The present goal was to develop new related sulfonamide complexes with more hydrophilic ligands designed to avoid the bioavailability problems that would plague the N(SO2R)dpa ligand system. A series of fac-[Re(CO)3(N(SO2R)dien)]PF6 complexes with different R groups linked to the central nitrogen of a symmetric tridentate sulfonamides were synthesized with the aim …

I. Synthesis Of Ascarosides For Biological Evaluation And Ii. Development Of Visible Light-Promoted Selenofunctionalization And Grafting Of Aryl Iodides, Elizabeth Susan Conner Balapitiya

LSU Doctoral Dissertations

This dissertation focuses on analog synthesis for biological evaluation and visible light promoted method development. Chapter 1 centers upon the synthesis of Caenorhabditis elegans dauer pheromone analogs. C. elegans is a nematode which, in times of environmental stress, enters a dauer stage. Two highly conserved pathways, which play important roles in some diseases in higher organisms, monitor dauer formation: TGF-β and IGF-1. Dauer formation is triggered by the nematode’s chemosensation of the dauer pheromone, consisting of a group of previously-isolated ascarosides. These compounds differ in chain length, saturation, terminal functionality of side chain, ω vs. ω-1 oxygenation and presence of …

Evolution Of Acyl-Substrate Recognition By A Family Of Acyl-Homoserine Lactone Synthases, Quin H. Christensen, Ryan M. Brecht, Dastagiri Dudekula, E. Peter Greenberg, Rajesh Nagarajan

Chemistry and Biochemistry Faculty Publications and Presentations

Members of the LuxI protein family catalyze synthesis of acyl-homoserine lactone (acyl-HSL) quorum sensing signals from S-adenosyl-L-methionine and an acyl thioester. Some LuxI family members prefer acyl-CoA, and others prefer acyl-acyl carrier protein (ACP) as the acyl-thioester substrate. We sought to understand the evolutionary history and mechanisms mediating this substrate preference. Our phylogenetic and motif analysis of the LuxI acyl-HSL synthase family indicates that the acyl-CoA-utilizing enzymes evolved from an acyl-ACP-utilizing ancestor. To further understand how acyl-ACPs and acyl-CoAs are recognized by acyl-HSL synthases we studied BmaI1, an octanoyl-ACP-dependent LuxI family member from Burkholderia mallei, and BjaI, an …

Hydrolytically Stable Analogues Of Sugar Phosphates And A Miniaturized In Situ Enzymatic Screen, Xiang Fei

Department of Chemistry: Dissertations, Theses, and Student Research

The glmS riboswitch undergoes self-cleavage upon binding its metabolic product GlcN6P, thereby providing a negative feedback mechanism limiting translation of the glmS protein when GlcN6P is abundant. As a first step toward the development of novel antimicrobials, we have synthesized a series of GlcN6P analogues bearing phosphatase-inert surrogates in place of the natural phosphate ester functionality. The self-cleavage assay identified two such compounds that display significant riboswitch actuator activity; namely those bearing a 6-phosphonomethyl group or a 6-O-malonyl ether. These two analogues exhibit a 22-fold and a 27-fold higher catalytic efficiency, respectively, than does glucosamine. Docking experiments were …

Synthesis And Evaluation Of Sensitizer Drug Photorelease Chemistry: Micro-Optic Method Applied To Singlet Oxygen Generation And Drug Delivery, Goutam Ghosh

Dissertations, Theses, and Capstone Projects

This thesis summarizes a new micro-optic method for singlet oxygen generation and sensitizer drug delivery, which include i) synthesis and evaluation of a first generation device for drug delivery from native and fluorinated silica probe tips, ii) synthesis of PEG conjugated sensitizers to study phototoxicity in ovarian cancer cells, and iii) synthesis and evaluation of tris-PEGylated chlorin conjugated fluorinated silica for its future integration into the device to use as a 2nd generation device. A first generation micro-optic device was developed that works by sparging O2 gas and light generating cytotoxic singlet oxygen that cleaves the covalently attached drug (sensitizer) …

Passivation And Functionalization Of Conjugated Polymer Nanoparticles With Head Group Modified Phospholipids And Proteins, Prakash Kandel

All Dissertations

Conjugated polymer nanoparticles (CPNs) possess important characteristics such as high fluorescence brightness, reasonable photostability, and non-toxicity. These properties allow the use of CPNs in fluorescence based cellular and biological applications including cellular labeling, imaging, biosensing, and single particle tracking. To realize the broad applications of CPNs, it is required that CPNs possess functionality to conjugate a recognition moiety and maintain colloidal stability in biological media. In the following Dissertation, we have prepared functionalized CPNs by surface passivation with head group- functionalized poly (ethylene glycol) lipids and proteins. We studied the colloidal stability of CPNs in biological media and investigated their …

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new …

Synthesis Of N-Heterocycles Through Cyclization-Triggered Tandem Additions To Alkynes And The Study Of Promoters In Ionic Reactions., Junbin Han

Electronic Theses and Dissertations

Our research mainly focused on three parts related to the rapid construction of N-heterocycles and the search for ionic reaction promoters. First, N-heterocycles of different ring sizes and with different substitution patterns constitute extremely important structure classes (e.g., alkaloids) in the search for bioactivity. A contemporary challenge in organic synthesis is the mapping of new chemical spaces through tandem or cascade reactions in an atom economical fashion. Our strategy to access these biologically important heterocycles is through a cyclization-triggered tandem addition to alkynes catalyzed by readily available alkynophilic coinage metals like copper. In this manner, a variety of functional groups …

Understanding The Influence Of Interfacial Chemistry In Core, Core/Shell And Core/Shell/Shell Quantum Dots On Their Fluorescence Properties, Omondi Bernard Omogo

Graduate Theses and Dissertations

Colloidal semiconductor nanocrystals (quantum dots) have received a great deal of attention due to their superior size tunable properties and promising applications in many areas. Some of the most practical areas of their applications include light emitting diodes (LED), photovoltaic and biological studies. Synthetic methods of these crystals is becoming more established with new strategies being reported every now and then. However, quantitative studies connecting the processes at the interface, namely core-ligand, core-shell and shell-shells, to the overall quantum dots fluorescence properties are not well understood. Specifically for cores, relating surface-atoms interactions, solvents, ligands nature, density and functional groups on …

N-Methylmesoporphyrin Ix Fluorescence As A Reporter Of Strand Orientation In Guanine Quadruplexes, Navin C. Sabharwal , '14, V. Savikhin, Joshua R. Turek-Herman , '16, John Michael Nicoludis , '12, V. A. Szalai, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs invivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect …

Photochemical Elimination Reactions That Proceed Via Triplet Excited State Electrocyclic Ring Closures, Himali Devika Jayasekara

Master's Theses (2009 -)

Cage compounds have become an important tool for the study of biological processes. The research focuses on new cage compounds that can unmask functional groups present in biologically important molecules such as proteins, peptides, and oligonucleosides. The project focuses on certain functional groups that are often difficult to release photochemically. These are the thiolate groups present in cysteine residues of proteins and peptides. Thiolate groups are fairly basic leaving groups, unlike the more labile groups such as the carboxylates that are present in proteins and peptides, or the phosphate groups present in nucleosides. The research takes advantage of the ability …