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Aerobic Biodegradation Of Alternative Fuel Oxygenates In Unsaturated Soil Columns, Kevin A. Mares

Theses and Dissertations

Groundwater contamination problems caused by methyl-tertiary butyl ether (MTBE) in subsurface waters have prompted the search for a gasoline oxygenate replacement. In order to avoid the problems encountered with MTBE, it is prudent to evaluate the fate and transport in the subsurface of proposed replacements, such as ethanol. In this study, ethanol transport and degradation in unsaturated soil was investigated using a series of eight soil columns. This preliminary study was to see if the soil column system components functioned properly, how similarly the eight soil columns performed, and if soil oxygen concentration affected degradation of ethanol. Tracer tests, using …

Magnetoelastic Sensor For Characterizing Properties Of Thin-Film/Coatings, Leonidas G. Bachas, Gary Barrett, Craig A. Grimes, Dimitris Kouzoudis, Stephan Schmidt

Chemistry Faculty Patents

An apparatus for determining elasticity characteristics of a thin-film layer. The apparatus comprises a sensor element having a base magnetostrictive element at least one surface of which is at least partially coated with the thin-film layer. The thin-film layer may be of a variety of materials (having a synthetic and/or bio-component) in a state or form capable of being deposited, manually or otherwise, on the base element surface, such as by way of eye-dropper, melting, dripping, brushing, sputtering, spraying, etching, evaporation, dip-coating, laminating, etc. Among suitable thin-film layers for the sensor element of the invention are fluent bio-substances, thin-film deposits …

Substituted Pentacenes And Electronic Devices Made With Substituted Pentacenes, John E. Anthony, David L. Eaton, Sean Parkin

Chemistry Faculty Patents

Novel substituted pentacenes and electronic devices made with those substituted pentacenes are disclosed.

Human Glutaminyl Cyclase And Bacterial Zinc Aminopeptidase Share A Common Fold And Active Site, Rachell E. Booth, Simon C. Lovell, Stephanie A. Misquitta, Robert C. Bateman Jr.

Faculty Publications

Background: Glutaminyl cyclase (QC) forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP) and mutated the apparent active site residues to assess their role in QC catalysis.

Results: The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence …

Extending The Oniom Integrated Mo/Mo Approach To Hydrogen Bonding In Biologic Systems: Serine-Water And Threonine-Water Dimers, Brian W. Hopkins, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

A series of two-layer ONIOM (MO:MO) methods have been systematically applied to two biologically important hydrogen-bonded dimers. Single conformations of the serine-water dimer and of the threonine-water dimer were optimized with the MP2 technique and a DZP++ basis set. The counterpoise corrected and uncorrected dissociation energies of the dimers were then computed with RHF, B3LYP, MP2, and CCSD(T) electronic structure techniques with 3-21G, 6-31+G(d), and DZP++ basis sets as well as every possible two-layer ONIOM permutation using either CCSD(T)/DZP++ or MP2/DZP++ as the high-level method. To judge the performance of each technique, the data are compared to results obtained with …

Systems-Based Design Of Bi-Ligand Inhibitors Of Oxidoreductases: Filling The Chemical Proteomic Toolbox, Daniel S. Sem, Bonnie Bertolaet, Brian Baker, Edcon Chang, Aurora Demertrina Costache, Stephen Coutts, Qing Dong, Mark Hansen, Victor Hong, Xuemei Huang, Richard M. Jack, Richard Kho, Henk Lang, Chen-Ting Ma, David Meininger, Maurizio Pellacchia, Fabrice Pierre, Hugo Villar, Lin Yu

Chemistry Faculty Research and Publications

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. …

Thermochemical Properties Of Small Oxygenated Sulfur Hydrocarbons And Kinetics - Reaction Pathways Of Methylthiomethyl Radical With Oxygen, Fei Jin

Theses

The thermochemical properties on CH₃SCH₂OOH and the corresponding two radicals resulting from loss of H atom: CH₃SCH₂OO and CH₂SCH₂OOH are important to understand the stability, reaction paths and kinetics of reactions of dimethyl sulfide and other sulfur hydrocarbons (sulfides) in the atmosphere and combustion processes. Thermochemical properties for species and transition states in the methylthiomethyl radical (CH₃SCH₂) + O₂ reaction system are analyzed to evaluate reaction paths and kinetics under these conditions. Isodesmic working reaction are employed to determine the enthalpies of formation …

Comprehensive Laboratory Measurements Of Biomass-Burning Emissions: 2. First Intercomparison Of Open-Path Ftir, Ptr-Ms, And Gc-Ms/Fid/Ecd, Ted J. Christian, B. Kleiss, Robert J. Yokelson, R. Holzinger, P. J. Crutzen, Wein Min Hao, T. Shirai, Donald R. Blake

Chemistry and Biochemistry Faculty Publications

No abstract provided.

Effects Of Cisplatin On Mitochondrial Function In Jurkat Cells, Kirk Tacka, James C. Dabrowiak, Jerry Goodisman, Harvey S. Penefsky, Abdul Kader Souid

Chemistry - All Scholarship

In this work, we measured the effects of pharmacological concentrations of cisplatin (cis-diaminedichloroplatinum II) on mitochondrial function, cell viability, and DNA fragmentation in Jurkat cells. The exposure of cells to 0-25 microM cisplatin for 3 h had no immediate effect on cellular mitochondrial oxygen consumption, measured using a palladium-porphyrin oxygen sensing phosphor. Similarly, the cell viability as measured by trypan blue staining was unchanged immediately following exposure to the drug, and no small DNA fragments, characteristic of drug-induced apoptosis, appeared. At 24 h after exposure to cisplatin, cellular respiration and viability decreased relative to controls and the amount of small …

The Contribution Of Amino Acid Region Asp695-Tyr698 Of Factor V To Procofactor Activation And Factor Va Function, Daniel O. Beck, Michael A. Bukys, Lisam S. Singh, Katalin A. Szabo, Michael Kalafatis

Chemistry Faculty Publications

There is strong evidence that a functionally important cluster of amino acids is located on the COOH-terminal portion of the heavy chain of factor Va, between amino acid residues 680 and 709. To ascertain the importance of this region for cofactor activity, we have synthesized five overlapping peptides representing this amino acid stretch (10 amino acids each, HC1-HC5) and tested them for inhibition of prothrombinase assembly and function. Two peptides, HC3 (spanning amino acid region 690-699) and HC4 (containing amino acid residues 695-704), were found to be potent inhibitors of prothrombinase activity with IC(50) values of approximately 12 and approximately …

Energy Conserving Approximations To The Quantum Potential: Dynamics With Linearized Quantum Force, Sophya Garashchuk, Vitaly A. Rassolov

Faculty Publications

Solution of the Schrödinger equation within the de Broglie–Bohm formulation is based on propagation of trajectories in the presence of a nonlocal quantum potential. We present a new strategy for defining approximate quantum potentials within a restricted trial function by performing the optimal fit to the log-derivatives of the wave function density. This procedure results in the energy-conserving dynamics for a closed system. For one particular form of the trial function leading to the linear quantum force, the optimization problem is solved analytically in terms of the first and second moments of the weighted trajectory distribution. This approach gives exact …

Altered Phosphorylation Of [Beta]-Catenin In Glucocorticoid Treated 235-1 Rat Pituitary Tumor Cells, Susie K. Saunders

Theses, Dissertations and Capstones

Beta-catenin is an essential cell adhesion and signaling protein, associated with high prolactin levels in rat pituitary tumor cells. It has been shown that phosphorylation affects the location and activity of b-catenin. Glycogen synthase kinase (GSK3-b) is a serine-threonine kinase that phosphorylates b-catenin on N-terminal residues, targeting it for proteasomal degradation. Studies have shown that C-terminal tyrosine phosphorylation decreases the association of b-catenin with cadherin. In 235-1 rat pituitary tumor cells, our lab has shown that the glucocorticoid analog dexamethasone (Dex) decreases the half- life of b-catenin while increasing the activity of GSK3-b. The current study was undertaken to examine …

Semi-Biosynthesis Of Dna Nanostructures, Aoune Barhoumi

Theses, Dissertations and Capstones

Nanotechnology refers to all technologies aiming to build objects, make measurements, and carry out processes on the nanometer length scale. In particular molecular nanotechnology exemplifies the so-called "bottom up" approach, which is briefly defined as the ability to build useful nanostructures with molecular precision, such as molecular machinery. Such capability for controlling matter at the molecular scale has always been the dream of scientists.

All living things are nanofoundries. Billions of years ago, nature perfectly provided all living things with the most accurate biological nanotechnology systems. Cellular internal dynamics, communicative resonance in protein conformational states, viruses as microreplicators, nanoscale life …

Synthesis Of The Novel Crown Ether 1 ,9-Dioxa-4,6-Dithiacycloundecane, Cassie Booth

Capstone Research Projects

Attempts to produce novel crowns, incorporating a thioacetal fragment, were made via two synthetic pathways. Despite the well-established reactions found in path A (see figure 3), this method failed to produce the desired crown. Path B, a one-pot reaction originally designed to close rings via the addition of a thioacetal fragment, yielded an oily product that was purified with a silica gel column (48.3% yield). Initial analysis by 1H NMR showed a structure consistent with that of the desired crown (figure 2). Mass spectroscopy was used to verify product identity, confirming the creation of our target molecule 1 ,9-dioxa-4,6-dithiacycloundecane.

Cloning, Expression, And Purification Of Glyoxysomal 3-Oxoacyl-Coa Thiolase From Sunflower Cotyledons, Anke C. Schiedel, Silke Oeljeklaus, Patricia Minihan, Jim Dyer

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The glyoxysomal β-oxidation system in sunflower (Helianthus annuus L.) cotyledons is distinguished by the coexistence of two different thiolase isoforms, thiolase I and II. So far, this phenomenon has only been described for glyoxysomes from sunflower cotyledons. Thiolase I (acetoacetyl-CoA thiolase, EC 2.3.1.9) recognizes acetoacetyl-CoA only, while thiolase II (3-oxoacyl-CoA thiolase, EC 2.3.1.16) exhibits a more broad substrate specificity towards 3-oxoacyl-CoA esters of different chain length. Here, we report on the cloning of thiolase II from sunflower cotyledons. The known DNA sequence of Cucumis sativus 3-oxoacyl-CoA thiolase was used to generate primers for cloning the corresponding thiolase from sunflower cotyledons. …

Distributions Of Z-Dna And Nuclear Factor I In Human Chromosome 22: A Model For Coupled Transcriptional Regulation, P. Christoph Champ, Sandor Maurice, Jeff Vargason, Tracy Camp, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcriptional start sites of the known genes. Thus, the occurrence of Z-DNA across human genomic sequences mirrors that of a known eukaryotic transcription factor. In addition, 43 of the 383 fully annotated chromosomal genes have ZDRs within 2 nucleosomes upstream of strong NFIs. This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism …

Development Of A Gene Transfer System In Clostridium Scindens Vpi 12708, Rashmi Ramasubbaiah

Masters Theses & Specialist Projects

Clostridium scindens VPI 12708 (previously known as Eubacterium sp. VPI 12708) is a bile-acid dehydroxylating bacterium originally isolated from the feces of a colon cancer patient. Many genes required for bile acid 7-a dehydroxylation are found on a large bile acid inducible operon (bai) that has been extensively studied. However the bai promoter, which directs expression of the bai operon, has yet to be characterized due, in part, to a lack of a functional genetic transfer system for this strain. A spontaneous rifampinresistant Clostridium scindens VPI 12708 mutant was used as a recipient to determine the efficacy of conjugation as …

Lanthanide Spectroscopic Studies Of The Dinuclear And Mg(Ii)-Dependent Pvuii Restriction Endonuclease, Gilles Muller, L. M. Bowen, J. P. Riehl, C. M. Dupureur

Faculty Publications, Chemistry

Type II restriction enzymes are homodimeric systems that bind four to eight base pair palindromic recognition sequences of DNA and catalyze metal ion-dependent phosphodiester cleavage. While Mg(II) is required for cleavage in these enzymes, in some systems Ca(II) promotes avid substrate binding and sequence discrimination. These properties make them useful model systems for understanding the roles of alkaline earth metal ions in nucleic acid processing. We have previously shown that two Ca(II) ions stimulate DNA binding by PvuII endonuclease and that the trivalent lanthanide ions Tb(III) and Eu(III) support subnanomolar DNA binding in this system. Here we capitalize on this …

"A New Phase Of The Complex Trinitratotris(Triphenylphosphineoxide)Neodymium(Lll), J. Brannon Gary

Faculty Publications

There has been considerable interest in the complexes formed by the lanthanides with various monodentate neutral ligands with O as the donor atom. Phosphine oxides, in particular, have proven useful in complexing to lanthanide metal ions and have found practical application in the solvent extraction and separation of lanthanides.1 Several lanthanide(III) nitrate complexes with triphenylphosphine oxide (OPPh3) have been prepared resulting in complexes having as few as two and as many as four OPPh3 groups per lanthanide center.2−4 An earlier study by Cousins and Hart5 identified the complex [Nd(OPPh3)3(NO3)3]. Two crystal phases of this same complex were briefly reported later …

The Effects Of Multiple Mutations In The Hydrophobic Core Upon The Stability Of Staphylococcal Nuclease, Rebecca L. Danforth

Inquiry: The University of Arkansas Undergraduate Research Journal

Previous work in the laboratory of my research advisor, Dr. Wesley Stites, has investigated the core packing of the protein staphylococcal nuclease. The core of a protein is critical in determining a protein's structure and stability. The hydrophobicity of the core has long been thought to be the principal driving force for folding, but recent work in the Stites lab has shown that optimization of van der Waals contacts and minimization of cavities, in our shorthand term, packing, is at least as energetically important. We are building upon this information in our attempt to better pack the protein core. If …

Development Of An Analytical Method For Distinguishing Ammonium Bicarbonate From The Products Of An Aqueous Ammonia Co2 Scrubber And The Characterization Of Ammonium Bicarbonate, Lingyu Meng

Masters Theses & Specialist Projects

The link between anthropogenic emissions of CO2 with increased atmospheric CO2 levels and, in turn, with increased global temperature has been well established and accepted. Using aqueous ammonia to capture CO2 and produce an inexpensive nitrogen fertilizer, ammonium bicarbonate (ABC) has been thought as a feasible approach to CO2 sequestration.

Due to the different concentrations of reactants and reaction conditions, different carbon-ammonium composites can be produced. In view of achieving a maximum of NH3 utilization in the capture of CO2, the product of ABC will be ideal. Hence the ABC in the products needs to be identified. Various analytical techniques …

Reduced Acetylcholine Receptor Density, Morphological Remodeling, And Butyrylcholinesterase Activity Can Sustain Muscle Function In Acetylcholinesterase Knockout Mice, Michael Adler, Heather A. Manley, Angela L. Purcell, Sharad S. Deshpande, Tracey A. Hamilton, Robert K. Kan, George Oyler, Oksana Lockridge, Ellen G. Duysen, Robert E. Sheridan

United States Army: Publications

The vertebrate neuromuscular junction is designed for rapid transmission of excitatory signals for initiation of muscle contraction.5 Among the features responsible for the high throughput of this synapse are the close proximity of the presynaptic and postsynaptic membranes,10 the direct coupling of acetylcholine (ACh) binding to the opening of the ion channel associated with the nicotinic acetylcholine receptor (nAChR),27 the brief open time of this channel,21,27 and the presence of cholinesterase (ChE) for hydrolysis of ACh.21,30 At the endplate, there are two distinct ChEs for transmitter hydrolysis: acetylcholinesterase (EC 3.1.1.7, AChE) and butyrylcholinesterase (EC 3.1.1.8, BChE).33 Both enzymes can …

Gated Electron Transfer As A Probe Of The Configurational Dynamics Of Peptide−Protein Complexes, Liu Liu, Jing Hong, Michael Y. Ogawa

Chemistry Faculty Publications

Gated electron-transfer measurements are used to probe the configurational dynamics of complexes formed between small metallopeptides and cytochrome c. The results show that that an apparently subtle chemical alteration of the metallopeptide produces significant changes to the dynamics of the peptide−protein complex.

Facile Synthesis Of Hydantoin Derivatives Under Microwave Irradiation, Khalil Faghihi, Khosrow Zamani, Akbar Mobinikhaledi

Turkish Journal of Chemistry

The rapid and highly efficient synthesis of hydantoin derivatives 3(a-f) was achieved under microwave irradiation by using a domestic microwave oven from the reactions of cyanohydrin derivatives 2(a-f) with ammonium carbonate. The reaction proceeded rapidly (2-5 min.), and as a result a series of hydantoin derivatives 3(a-f) were obtained in high yields. All of the synthesized compounds were fully characterized by their melting point, ^1H-NMR, FTIR spectroscopy and elemental analyses. Cyanohydrin derivatives 2(a-f) were also prepared from the ketone derivatives 1(a-f) with potassium cyanide in the presence of sodium metabisulfite in an additional reaction.

Part I: Evaluation Of Russian Synthetic Compounds As A Potential Source Of New Drug Leads Agains Breast And Colon Cancer Part Ii: Isolation Of Beta-Amyrin Formate From Eucalyptus Viminalis Labill And Investigation Of Its Colon Cancer Activity, Mihaela Cohanoschi

Electronic Theses and Dissertations

Although modern medicine made great steps toward curing most diseases considered deadliest, yet cancer remains one of the major public health problems. The first part of this thesis investigates a new source of selective compounds that are potential candidates against cancer. Fifteen Russian compounds were tested in order to establish their efficiency against two types of cancer: human breast SK-Br-3 and colorectal carcinoma HT-29. The bioassay results show that seven of the new synthetic Russian compounds can be considered new drug leads, based upon their low toxicity and efficacy in slowing the growth of human breast cancer and colon cancer …

Application Of Pyrolysis-Gc/Ms For Rapid Assessment Of Organic Contamination In Sediments From Barcelona Harbor, Michael A. Kruge, Albert Permanyer

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Pyrolysis-GC/MS is advantageous as a tool for rapid sediment contamination assessment because of the small sample size required, minimal sample preparation, and its ability to detect a wide variety of organic pollutants as well as naturally-occurring biological materials. Py-GC/MS was applied, together with determination of organic carbon, and major and minor element concentrations, to evaluate potentially contaminated sediments in the port of Barcelona (Spain) and the adjacent Llobregat River delta. Detected contaminant markers, most evident in the Old Port (Port Vell) area, included hopanes and alkylated PAHs (petroleum), sterenes (sewage), C₁₆-C₁₉ phenylalkanes (detergents) and parent …

Analysis Of Free Analyte Fractions By Rapid Affinity Chromatography, David S. Hage, William A. Clarke

Department of Chemistry: Faculty Publications

The invention is generally directed toward an analytical method to determine the concentration of the free analyte fraction in a sample. More particularly, the method encompasses applying a sample comprising a free and bound analyte fraction to an affinity column capable of selectively extracting the free fraction in the millisecond time domain. The signal generated by the free fraction is then quantified by standard analytical detection techniques. The concentration of the free fraction may then be determined by comparison of its signal with that of a calibration curve depicting the signal of known concentration of the same analyte.

Development Of Electrochemical Sensors For Monitoring Glucose, Michael Nesbitt

Theses

The thesis focuses on evaluating calcium alginate as an immobilisation matrix for the oxidase enzyme glucose oxidase for the amperometric determination of glucose. The basic principles of enzymology and enzyme immobilisation is discussed followed by a review of a variety of first, second and third generation type enzyme electrodes. Amperometry as governed by the Cottrell equation and mass transfer models relating to amperometric electrodes are also considered.

Bovine serum albumin (BSA / GOx) enzyme electrode system was employed as a model to evaluate a calcium alginate immobilisation technique for glucose oxidase. The principal methods employed for enzyme immobilisation were:

• …

Biologically Important Thiols In Various Vegetables And Fruits, Omca Demirkol, Craig D. Adams, Nuran Ercal

Chemistry Faculty Research & Creative Works

Biological thiols are important antioxidants, and recent studies showed that their contents vary depending on the groups of foodstuffs. Therefore, we investigated the levels of some biological thiols in various vegetables and fruits by using a sensitive high-performance liquid chromatography (HPLC) technique. Biological thiols measured in some vegetables and fruits include glutathione (L-glutamyl-L-cysteinly glycine, GSH), N-acetylcysteine (NAC), captopril [CAP (C9H15NO3S)], homocysteine (HCYS), cysteine (CYS), and -glutamyl cysteine (GGC). Our results show that biological thiol contents are between 3-349 nM/g wet weight in vegetables and 4-136 nM/g wet weight in fruits. CAP is only found in asparagus (28 nM/g wet weight). …

Attachment Of Oligonucleotide Probes To Polymer Biochips And Its Application For The Detection Of Point Mutations, Yun Wang

LSU Doctoral Dissertations

This dissertation is on the fabrication of polymer-based microfluidic arrays for the detection of genetic mutations. Poly(methyl methacrylate) was chosen as one of the polymer substrate materials due to its low background noise, low adsorption of biomolecules, and low assembly temperature. The surface modification of polymer substrates for covalent attachment of oligonucleotide probes, the construction of fluidic channels/arrays, and hybridization kinetics will be covered. As an example of the application, point mutation detection using immobilized arrays constructed in microfluidic devices will be demonstrated. The PMMA surface was derivatized with N-lithioethylenediamine solution to introduce amine groups, which were utilized for the …