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Cationic Amphiphilic Synthetic Macromolecules With Superior Antibacterial Activity, Ashish Punia

Dissertations, Theses, and Capstone Projects

The increasing prevalence of antibiotic resistant bacteria (superbugs) has created a pressing need for new systems of antimicrobial agents. In this dissertation, I report on my extensive research on the design, synthesis, and development of synthetic amphiphilic macromolecules with antimicrobial activity and very low hemolytic impact. Synthetic amphiphilic polymers attack bacteria directly to rupture the cell membrane through electrostatic and hydrophobic interactions. However, the toxicity of such synthetic amphiphilic polymers against mammalian cells have impeded their therapeutic applications. We investigated the systematic structure/activities relationships for antibacterial and hemolytic activities of amphiphilic polyacrylates and poly(vinyl esters). Acrylate homopolymers with various lengths …

Biomolecule Mediating Synthesis Of Inorganic Nanoparticles And Their Applications, Zengyan Wei

Dissertations, Theses, and Capstone Projects

Project 1.

The conventional phage display technique focuses on screening peptide sequences that can bind on target substrates, however the selected peptides are not necessary to nucleate and mediate the growth of the target inorganic crystals, and in many cases they only show moderate affinity to the targets. Here we report a novel phage display approach that can directly screen peptides catalytically growing inorganic nanoparticles in aqueous solution at room temperature. In this study, the phage library is incubated with zinc precursor at room temperature. Among random peptide sequences displayed on phages, those phages that can grow zinc oxide (ZnO) …

Synthetic Approaches To The Understanding Of Dna Nucleobase Methylation, Jagruti Rana

Dissertations

DNA methylation is a major source of genetic variation and cancer. Methylation occurs when nucleophilic DNA bases react with methylating agent methyl methanesulfonate (MMS), dimethyl sulfate (DMS), N-methyl-N-nitrosourea (MNU), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), etc. N7-methyl-2'-deoxyguanosine (N7-methyl-dG, or ^7MedG) adduct is the most abundant DNA methylation products for most methylating agents. DNA polymerase actions on ^7MedG are difficult to study due to its instability against ring- opening hydrolysis and deglycosyl ati on. Oligonucleotides containing a single chemical adduct of ^7MedG cannot be chemically synthesized. In addition, ^7MedG is unstable in vivo …

Synthesis Of Dinucleoside Acylphosphonites By Phosphonodiamidite Chemistry And Investigation Of Phosphorus Epimerization, William H. Hersh

Publications and Research

The reaction of the diamidite, (iPr2N)2PH, with acyl chlorides proceeds with the loss of HCl to give the corresponding acyl diamidites, RC(O)P(N(iPr)2)2 (R = Me (7), Ph (9)), without the intervention of sodium to give a phosphorus anion. The structure of 9 was confirmed by single-crystal X-ray diffraction. The coupling of the diamidites 7 and 9 with 5′-O-DMTr-thymidine was carried out with N-methylimidazolium triflate as the activator to give the monoamidites 3′-O-(P(N(iPr)2)C(O)R)-5′-O-DMTr-thymidine, and further coupling with 3′-O-(tert-butyldimethylsilyl)thymidine was carried out with activation by pyridinium trifluoroacetate/Nmethylimidazole. The new dinucleoside acylphosphonites could be further oxidized, hydrolyzed to the H-phosphonates, and sulfurized to …

Characterization Of Biomass Burning Emissions From Cooking Fires, Peat, Crop Residue, And Other Fuels With High-Resolution Proton-Transfer-Reaction Time-Of-Flight Mass Spectrometry, C. Stockwell, P. Veres, J. Williams

Chemistry and Biochemistry Faculty Publications

We deployed a high-resolution proton-transferreaction time-of-flight mass spectrometer (PTR-TOF-MS) to measure biomass-burning emissions from peat, crop residue, cooking fires, and many other fire types during the fourth Fire Lab at Missoula Experiment (FLAME-4) laboratory campaign. A combination of gas standard calibrations and composition sensitive, mass-dependent calibration curves was applied to quantify gas-phase non-methane organic compounds (NMOCs) observed in the complex mixture of fire emissions. We used several approaches to assign the best identities to most major “exact masses”, including many high molecular mass species. Using these methods, approximately 80–96% of the total NMOC mass detected by the PTR-TOFMS and Fourier …

Repressive Mutations Restore Function-Loss Caused By The Disruption Of Trimerization In Escherichia Coli Multidrug Transporter Acrb, Zhaoshuai Wang, Meng Zhong, Wei Lu, Qian Chai, Yinan Wei

Chemistry Faculty Publications

AcrAB-TolC and their homologs are major multidrug efflux systems in Gram-negative bacteria. The inner membrane component AcrB functions as a trimer. Replacement of Pro223 by Gly in AcrB decreases the trimer stability and drastically reduces the drug efflux activity. The goal of this study is to identify suppressor mutations that restore function to mutant AcrB_P223G and explore the mechanism of function recovery. Two methods were used to introduce random mutations into the plasmid of AcrB_P223G. Mutants with elevated drug efflux activity were identified, purified, and characterized to examine their expression level, trimer stability, interaction with AcrA, and …

Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

This letter reports a chemical analysis of vapor from electronic cigarettes that shows high levels of formaldehyde, a known carcinogen. The authors project that the associated incremental lifetime risk of cancer could be higher than that from long-term smoking.

Observations And Analysis Of Organic Aerosol Evolution In Some Prescribed Fire Smoke Plumes, A. A. May, T. Lee, G. R. Mcmeeking, Sheryl Kashi Akagi, A. P. Sullivan, S. P. Urbanski, Robert Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Open biomass burning is a significant source of primary air pollutants such as particulate matter and non-methane organic gases. However, the physical and chemical atmospheric processing of these emissions during transport is poorly understood. Atmospheric 5 transformations of biomass burning emissions have been investigated in environmental chambers, but there have been limited opportunities to investigate these transformations in the atmosphere. In this study, we deployed a suite of real-time instrumentation on a Twin Otter aircraft to sample smoke from prescribed fires in South Carolina, conducting measurements at both the source and downwind to character10 ize smoke evolution with atmospheric aging. …

Long-Range Pcr Amplification Of Dna By Dna Polymerase Iii Holoenzyme From Thermus Thermophilus, Wendy Ribble, Shawn D. Kane, James M. Bullard

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

DNA replication in bacteria is accomplished by a multicomponent replicase, the DNA polymerase III holoenzyme (pol III HE). The three essential components of the pol III HE are the α polymerase, the β sliding clamp processivity factor, and the DnaX clamp-loader complex. We report here the assembly of the functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme capable of DNA synthesis consists of α, β and DnaX ( and γ), and components of the clamp-loader complex. The proteins were each cloned and expressed in a native form. Each component of the system was purified extensively. The …

Multiple-Time Step Ab Initio Molecular Dynamics Based On Two-Electron Integral Screening, Shervin Fatehi, Ryan P. Steele

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

A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree–Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

Enzymatic Control Of The Related Pathways Of Fatty Acid And Undecylprodiginine Biosynthesis In Streptomyces Coelicolor, Renu Singh

Dissertations and Theses

Streptomyces coelicolor produces fatty acids for both primary metabolism and for production of the components of natural products such as undecylprodiginine. Primary metabolism makes the longer and predominantly branched-chain fatty acids, while undecylprodiginine utilizes shorter and almost exclusively straight chain fatty acids. The first step in fatty acid biosynthetic process is catalyzed by FabH (β-ketoacyl synthase III), which catalyzes a decarboxylative condensation of an acyl-CoA primer with malonyl-acyl carrier protein (ACP). The resulting 3-ketoacyl-ACP product is reduced by NADPH-dependent FabG into 3-hydroxyacyl-ACP, which is dehydrated by FabA to form enoyl-ACP. The NADH-dependent FabI (InhA) completes the cycle. Subsequent rounds of …

Functional Layer-By-Layer Design Of Xerogel-Based 1st Generation Amperometric Glucose Biosensors, Nicholas G. Poulos, Jackson R. Hall, Michael C. Leopold

Chemistry Faculty Publications

Xerogel-based first-generation amperometric glucose biosensors, constructed through specific layer-by-layer assembly of films featuring glucose oxidase doped xerogel, a diffusion-limiting xerogel layer, and capped with both electropolymerized polyphenol and blended polyurethane semipermeable membranes, are presented. The specific combination of xerogels formed from specific silane precursors, including propyl-trimethoxysilane, isobutyl-trimethoxysilane, octyl-trimethoxysilane, and hydroxymethyl-triethoxysilane, exhibit impressive dynamic and linear ranges of detection (e.g., ≥24–28 mM glucose) and low response times, as well as significant discrimination against common interferent species such as acetaminophen, ascorbic acid, sodium nitrite, oxalic acid, and uric acid as determined by selectivity coefficients. Additionally, systematic electrochemical and contact angle studies of …

Chloroamino Acids As A Chemical Explanation For Viking Labeled Release Soil Activity On Mars, John C. Hironimus

STAR Program Research Presentations

The Viking missions to Mars, which took place in the 1970’s, performed several experiments on martian soil in an attempt to discern if there was microbial life present. In one set of experiments, a nutrient solution containing amino acids and organic substrates tagged with carbon-14 was injected into sample cells containing martian soil, and the evolution of labeled CO2 was monitored. The evolution of labeled CO2 indicated that there was a process occurring that broke down the nutrients in solution and released CO2 as a byproduct. Cellular metabolism releases CO2, so this result supported the idea of microbial life on …

The Health Risks Of Chemicals In Personal Care Products And Their Fate In The Environment, Lisa Paulsen

Chemistry Honors Papers

Personal care products are everyday consumer products used to cleanse, enhance, or alter the appearance of the body, including, but not limited to, shampoos, body washes, lotions, and cosmetics. The regulations and safety information surrounding personal care products are severely lacking. The laws regulating the environmental fate of these chemicals and the harmful effects they can have on environmental ecosystems or organisms that are exposed to them are even more limited. However, studies have shown that the chemicals can have a dizzying array of health risks, including diseases on the rise in human populations such as diabetes, obesity, autism, ADHD, …

The Contribution Of Methionine To The Stability Of The Escherichia Coli Metniq Abc Transporter-Substrate Binding Protein Complex, P. Nguyen, N. Kadaba, J. Y. Lai, Janet G. Yang, D. C. Rees

Chemistry Faculty Publications

Despite the ubiquitous role of ATP-binding cassette (ABC) importers in nutrient uptake, only the Escherichia coli maltose and vitamin B₁₂ ABC transporters have been structurally characterized in multiple conformations relevant to the alternating access transport mechanism. To complement our previous structure determination of the E. coli MetNI methionine importer in the inward facing conformation (Kadaba et al. (2008) Science 321, 250–253), we have explored conditions stabilizing the outward facing conformation. Using two variants, the Walker B E166Q mutation with ATP+EDTA to stabilize MetNI in the ATP-bound conformation and the N229A variant of the binding protein MetQ, shown in …

The Allosteric Regulatory Mechanism Of The Escherichia Coli Metni Methionine Atp Binding Cassette (Abc) Transporter, Janet G. Yang, D. C. Rees

Chemistry Faculty Publications

The MetNI methionine importer of Escherichia coli, an ATP binding cassette (ABC) transporter, uses the energy of ATP binding and hydrolysis to catalyze the high affinity uptake of d- and l-methionine. Early in vivo studies showed that the uptake of external methionine is repressed by the level of the internal methionine pool, a phenomenon termed transinhibition. Our understanding of the MetNI mechanism has thus far been limited to a series of crystal structures in an inward-facing conformation. To understand the molecular mechanism of transinhibition, we studied the kinetics of ATP hydrolysis using detergent-solubilized MetNI. We find that transinhibition is …

2015 Oklahoma Research Day Full Program, Northeastern State University

Oklahoma Research Day Abstracts

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University.

An Investigation Of The Effect Of Mn2+ On The Fth1 Ire-Irp Complex, Eric Thomas Mendenhall

Theses, Dissertations and Capstones

Iron is a widely distributed metal found in almost every physiological system in nature, thus being an essential part of life. Iron homeostasis in the human body must be tightly regulated as iron is both beneficial and harmful to different cellular processes. Ferritin is a protein that has a prominent role in maintaining iron homeostasis via iron sequestration. Additionally, this protein itself is regulated by the Iron Responsive Element (IRE) and its interaction with an apoaconitase protein or the Iron Regulatory Protein (IRP). The binding of the IRP to this IRE, located on the 5’ untranslated stem loop region of …

Glycation Of Lysozyme, Wisam Talib Joudah

Theses, Dissertations and Capstones

For this research project, I propose a method for the analysis of glycated lysozyme using Matrix Associated Laser Desorption / Ionization-Time of Flight Mass spectrometry (MALDI-TOF MS). Glycation or "Maillard reaction" is a non-enzymatic reaction that occurs between amino acid residues, usually primary and secondary amines, of proteins and the carbonyl group of reducing sugars to yield Schiff bases. The glycation mechanism occurs between the carbonyl group of the reducing sugars and a primary amine by nucleophilic addition, resulting in the formation of a Schiff base. The Schiff base can then rearrange into the more stable Amadori product which is …

Investigation Into The Biological Importance And Function Of Proinsulin C-Peptide, Christina L. Newsome

Theses, Dissertations and Capstones

The C-peptide of insulin was thought to be biologically inactive, but recent studies have shown that the C-peptide causes multiple molecular and physiological effects. Evidence has shown that C-peptide binds to a cell surface receptor, probably a G-protein coupled receptor, and that the COOH-terminal pentapeptide is essential for binding and constitutes an active site. For a further understanding of the detailed nature of the physiological effects of C-peptide, the receptor structure needs to be determined. We designed an affinity column using C-peptide to try and gain a better understanding of the biological effects by examining what proteins the affinity column …

Determination Of The Optical Properties Of Secondary Organic Aerosol Particles, Matthew E. Wise, John Shilling, Felisha Imholt, Ryan Caylor

CUP Faculty Research

The enhanced greenhouse effect is currently considered to be our most important global environmental problem. While the magnitude of radiation absorbed by greenhouse gases is known to a high certainty, the absorption of radiation by atmospheric aerosol particles is not. In the initial Visiting Faculty Program application, we proposed the use of an ultraviolet-visible (UV/Vis) spectrometer equipped with a liquid waveguide capillary flow cell to determine the extent to which secondary organic aerosol particles (SOA) absorb visible light. Early in the research period, the UV/Vis technique was optimized for three solvent systems (methanol, water and 0.1 M hydrochloric acid). Using …

Proxy-Pet Building Blocks As A Design Element For Library Synthesis, Lainey Jo Mallin

Browse all Theses and Dissertations

In exploring radioligands for positron emission tomography (PET) imaging, it is not unusual to synthesize a library of compounds around some targeting scaffold, screen for optimal binding to a relevant diagnostic cellular target, remove some portion of optimized molecule so as to append the requisite reporter group, and then re-evaluate. To this end, the use of "click labeling" in radiochemistry is proving an increasingly attractive means of conjugating a 18F-reporter group, wherein the targeting scaffold bearing a terminal alkyne is allowed to react with a 2-[18F]-fluoroethylazide to forge a linkage as a 1,2,3-triazole substituent. Since the triazole linked prosthetic group …

Rapid Scan Electron Paramagnetic Resonance (Epr) And Digital Epr Development, Zhelin Yu

Electronic Theses and Dissertations

Rapid scan electron paramagnetic resonance (EPR) was developed in the Eaton laboratory at the University of Denver. Applications of rapid scan to wider spectra, such as for immobilized nitroxides, spin-labeled proteins, irradiated tooth and fingernail samples were demonstrated in this dissertation. The scan width has been increased from 55 G to 160 G. The signal to noise (S/N) improvement for slowly tumbling spin-labeled protein samples that is provided by rapid scan EPR will be highly advantageous for biophysical studies. With substantial improvement in S/N by rapid scan, the dose estimation for irradiated tooth enamels became more reliable than …

Computational Estimation Of The Pka's Of Purines And Related Compounds, Kara L. Geremia

Browse all Theses and Dissertations

The acid dissociation value pKa of a compound provides important information regarding the neutral and ionic forms of the compound present under different conditions. However, for many compounds experimental pKa values are not available, and for others the measured values are sometimes uncertain. Consequently, having a computational means for estimating pKa values can be of benefit for biochemical, pharmaceutical, polymer, and many other studies. Purines form a key group of bioactive compounds whose acid/base activities are of considerable interest. The purine class includes such diverse compounds as the nucleic acid bases adenine and guanine, the gout-related compound uric acid, the …

Ua66 Ogden College Of Science & Engineering Newsletter, Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

The Effects Of Clay On Glycerol/Carboxylic Acid Polymerization: Implications Of Mineral Controls In Prebiotic Chemistry, Joseph T. Romero

Geology: Student Scholarship & Creative Works

Proto-enzymatic catalysis on early Earth is an important consideration in prebiotic chemistry research as it leads to the understanding of the emergence of the metabolic reaction networks. Contemporary enzymes are comprised of either organic or inorganic factors scaffolded by globular protein structure whereas we consider hyperbranched polyesters as a possible extant scaffold that is easier assembled than the peptide one. The goals of this project are to consider prebiotically plausible starting materials for such structure formation utilizing a subset of conditions for polymer synthesis involving the presence of mineral surfaces as well as temperature and hydration differential. As likely candidates …

Probing A Complex Dissociation Energy Surface With Experimental And Theoretical Methods, Hannah Elizabeth Bott

Theses, Dissertations and Capstones

Dendrimers are hyperbranched polymers with a tree-like structure that can be tuned for size, shape, and functionality. Dendrimers have exhibited numerous possibilities in chemical and biochemical processes as their use in host-guest systems and controlled gene and drug delivery vehicles. Distinct properties of dendrimers, such as well-defined architecture and high ratio of functional moieties to molecular volume, make these polymers substantially useful for the development of nanomaterials and medicines. It has recently been demonstrated that polypropylene-imine (PPI) dendrimers have specific physical properties that are well suited for many applications. More specifically, the nitrile-terminated dendrimer creates a unique environment that is …

Ua94/6/15 Student / Alumni Personal Papers Wku Dorris Hutchinson, Wku Archives

WKU Archives Collection Inventories

Correspondence and publications created by and about the Dorris Hutchison during her time at Sloan-Kettering Institute.

The Coastal Monitor: Vol. 1, No. 1, John Tanacredi Ph.D.

The Coastal Monitor

The Center for Environmental Research and Coastal Oceans Monitoring (CERCOM) is a scientific coastal research center and field station dedicated to exploring our global coastal environments and near-shore oceans. CERCOM is the field station support facility for all sciences at Molloy College and services the degree programs of Biology, Chemistry, and Environmental Studies, with special attention to a B.S. degree in Earth and Environmental Studies. Located at the West Sayville Boat Basin on the Great South Bay, CERCOM is a 2,500 sq. ft. field station estuarine/ marine science laboratory where environmental monitoring and analysis is conducted 365 days a year.