Digital Commons Network^™

The Analysis Of 2-Amino-2-Thiazoline-4-Carboxylic Acid In The Plasma Of Smokers And Non-Smokers, Brian A. Logue, Wendy K. Maserek, Gary A. Rockwood, Michael W. Keebaugh, Steven I. Baskin

Chemistry and Biochemistry Faculty Publications

ATCA (2-amino-2-thiazoline-4-carboxylic acid) is a promising marker to assess cyanide exposure because of several advantages of ATCA analysis over direct determination of cyanide and alternative cyanide biomarkers (i.e. stability in biological matrices, consistent recovery, and relatively small endogenous concentrations). Concentrations of ATCA in the plasma of smoking and non-smoking human volunteers were analyzed using gaschromatography mass-spectrometry to establish the feasibility of using ATCA as a marker for cyanide exposure. The levels of ATCA in plasma of smoking volunteers, 17.2 ng/ml, were found to be significantly (p < 0.001) higher than that of non-smoking volunteers, 11.8 ng/ml. Comparison of ATCA concentrations of smokers relative to nonsmokers in both urine and plasma yielded relatively similar results. The concentration ratio of ATCA for smokers versus non-smokers in plasma and urine was compared to similar literature studies of cyanide and thiocyanate, and correlations are discussed. This study supports previous evidence that ATCA can be used to determine past cyanide exposure and indicates that further studies should be pursued to validate the use of ATCA as a marker of cyanide exposure.

Assessment Of Methylthioadenosine/S-Adenosylhomocysteine Nucleosidases Of Borrelia Burgdorferi As Targets For Novel Antimicrobials Using A Novel High-Throughput Method, Kenneth Cornell, Shekerah Primus, Jorge A. Martinez, Nikhat Parveen

Chemistry and Biochemistry Faculty Publications and Presentations

Background: Lyme disease is the most prevalent tick-borne disease in the USA with the highest number of cases (27444 patients) reported by CDC in the year 2007, representing an unprecedented 37% increase from the previous year. The haematogenous spread of Borrelia burgdorferi to various tissues results in multisystemic disease affecting the heart, joints, skin, musculoskeletal and nervous system of the patients.

Objectives: Although Lyme disease can be effectively treated with doxycycline, amoxicillin and cefuroxime axetil, discovery of novel drugs will benefit the patients intolerant to these drugs and potentially those suffering from chronic Lyme disease that is refractory to these …

Beta-Peptides With Improved Affinity For Hdm2 And Hdmx, Elizabeth A. Harker, Douglas S. Daniels, Danielle A. Guarracino, Alanna S. Schepartz

Chemistry Faculty Publications

We previously described a series of 314-helical β-peptides that bind the hDM2 protein and inhibit its interaction with a p53-derived peptide in vitro. Here we present a detailed characterization of the interaction of these peptides with hDM2 and report two new β-peptides in which non-natural side chains have been substituted into the hDM2-recognition epitope. These peptides feature both improved affinity and inhibitory potency in fluorescence polarization and ELISA assays. Additionally, one of the new β-peptides also binds the hDM2-related protein, hDMX, which has been identified as another key therapeutic target for activation of the p53 pathway in tumors.

Development Of Microbial And Enzymatic Fuel Cells For Bio-Inspired Power Sources, Fatih Dogan, Shelley Minteer

Materials Science and Engineering Faculty Research & Creative Works

This report is based on some of the revolutionary concepts described in the Road Map on Bioinspired Power Systems within the AFRLRW Campus Challenge II. Development of biofuel cell concepts integrated with fuel regeneration and energy storage capabilities are proposed to create a compact and self-sustaining power system. The first part of this work identified a sediment based microbial fuel cell that could power small electronics and maintain electrical activity over long periods of time. AFRLRW does not feel that this work adequately addresses the original scope nor does it provide a basis on which to continue work. The second …

From Gene Mutation To Protein Characterization, David A. Moffet

Chemistry and Biochemistry Faculty Works

A seven-week “gene to protein” laboratory sequence is described for an undergraduate biochemistry laboratory course. Student pairs were given the task of introducing a point mutation of their choosing into the well studied protein, enhanced green fluorescent protein (EGFP). After conducting literature searches, each student group chose the mutation they wanted to introduce into EGFP. Students designed their sequence-specific mutagenic primers and constructed their desired mutation. The resulting EGFP mutant proteins were expressed in E. coli, purified and characterized. This laboratory sequence connected the major concepts of molecular biology and biochemistry, while incorporating the thrill of novel discovery in …

Synthesis And Evaluation Of Lanthanide Ion Dota-Tetraamide Complexes Bearing Peripheral Hydroxyl Groups, Azhar Pasha, Mai Lin, Gyula Tircso, Cynthia L. Rostollan, Mark Woods, Garry Kiefer, A. Dean Sherry, Xiankai Sun

Chemistry Faculty Publications and Presentations

The use of lanthanide-based contrast agents for magnetic resonance imaging has become an integral component of this important diagnostic modality. These inert chelates typically possess high thermodynamic stability constants that serve as a predictor for in vivo stability and low toxicity. Recently, a new class of contrast agents was reported having a significantly lower degree of thermodynamic stability while exhibiting biodistribution profiles indicative of high stability under biological conditions. These observations are suggestive that the nature of contrast agent stability is also dependent upon the kinetics of complex dissociation, a feature of potential importance when contemplating the design of new …

Polymer Microfluidic Devices For Bioanalysis, Xuefei Sun

Theses and Dissertations

Polymeric microchips have received increasing attention in chemical analysis because polymers have attractive properties, such as low cost, ease of fabrication, biocompatibility and high flexibility. However, commercial polymers usually exhibit analyte adsorption on their surfaces, which can interfere with microfluidic transport in, for example, chemical separations such as chromatography or electrophoresis. Usually, surface modification is required to eliminate this problem. To perform stable and durable surface modification, a new polymer, poly(methyl methacrylate-co-glycidyl methacrylate) (PGMAMMA) was prepared for microchip fabrication, which provides epoxy groups on the surface. Whole surface atom transfer radical polymerization (ATRP) and in-channel ATRP approaches were employed to …

Isolation And Characterization Of Aromatase Inhibitors From Brassaiopsis Glomerulata (Araliaceae), Marcy J. Balunas, Bin Su, Soedarsono Riswan, Harry H.S. Fong, Robert W. Brueggemeier, John M. Pezzuto, A. Douglas Kinghorn

Chemistry Faculty Publications

The hexane- and ethyl acetate-soluble extracts of the leaves of Brassaiopsis glomerulata (Blume) Regel (Araliaceae), collected in Indonesia, were found to inhibit aromatase, the rate-limiting enzyme in the production of estrogens from androgens, in both enzyme- and cell-based aromatase inhibition (AI) assays. Bioassay-guided fractionation led to the isolation of six known compounds of the steroid and triterpenoid classes (1–6) from the hexane extract, of which 6β-hydroxystimasta-4-en-3-one (5), was moderately active in the cell-based AI assay. Fractionation of the ethyl acetate extract afforded seven pure isolates (7–13) of the modified peptide, fatty acid, monoterpenoid, and benzenoid types, including six known compounds …

Multivalent Recognition Of Peptides By Modular Self-Assembled Receptors, Joseph J. Reczek, Aimee A. Kennedy, Brian T. Halbert, Adam R. Urbach

Chemistry Faculty Research

Developing nontraditional approaches to the synthesis and characterization of multivalent compounds is critical to our efforts to study and interface with biological systems and to build new noncovalent materials. This paper demonstrates a biomimetic approach to the construction of discrete, modular, multivalent receptors via molecular self-assembly in aqueous solution. Scaffolds presenting 1−3 viologen groups recruit a respective 1−3 copies of the synthetic host, cucurbit[8]uril, in a noncooperative manner and with a consistent equilibrium association constant (K_a) value of 2 × 10⁶ M⁻¹ per binding site. The assembled mono-, di-, and trivalent receptors bind to their …

Characterization Of Putative Self-Resistance Genes In The Biosynthetic Gene Cluster Of Hygromycin A From Streptomyces Hygroscopicus Nrrl 2388, Vidya Dhote

Dissertations and Theses

Streptomyces hygroscopicus NRRL 2388 produces an aminocyclitol antibiotic called hygromycin A (HA), which targets bacterial protein synthesis by inhibiting the peptidyl transferase reaction. The hyg6, hygl9, hyg21, hyg28, and hyg29 genes in the biosynthetic gene cluster of HA are predicted to confer self-resistance to the producer strain by different mechanisms. Targeted gene disruptions and in vitro characterization of recombinant proteins were carried out to elucidate the functions of these genes. The hyg21 gene encodes an O-phosphotransferase with a proposed role in HA inactivation by phosphorylation. Disruption of hyg21 led to a significant decrease in HA production but did not …

Synthesis Of Aptamer-Porphyrin Conjugate For Photodynamic Therapy & Synthesis And Stability Of Mixed Thiol/Lipid Coated Gold Nanoparticles, Sarita Sitaula

Dissertations and Theses

An underlying problem in Photodynamic Therapy (PDT) is low selectivity of photosensitizers currently being used for the treatment of tumors. This thesis is focused on developing new PDT drugs and is divided into two parts. The first chapter describes a method for selective delivery of the photosensitizers to the tumor site by conjugating porphyrins to an aptamer for the targeted PDT. To achieve this, a novel synthesis of 2'-porphyrin-modified uridine was developed. The 3'-H-phosphonate derivatives of both 2'-porphyrin and 2'-dithiaporphyrin modified uridine were also synthesized. The 3'41-phosphonate derivative of 2'-porphyrin-modified uridine was conjugated to a 19-mer DNA and to a …

Development And Validation Of An Empirical Free Energy Function For Calculating Protein–Protein Binding Free Energy Surfaces, Joseph Audie

Chemistry & Physics Faculty Publications

In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein–protein complexes to within ≈1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free …

Ratiometric Single-Nanoparticle Oxygen Sensors For Biological Imaging, Changfeng Wu, Barbara Bull, Kenneth Christensen, Jason Mcneill

Publications

It makes sense: Conjugated polymer nanoparticles doped with a platinum porphyrin dye exhibit bright phosphorescence that is highly sensitive to the concentration of molecular oxygen. The small size, extraordinary brightness, excellent sensitivity, and ratiometric emission, together with the demonstration of single-particle sensing and cellular uptake, indicate the potential of the nanoparticle sensors for quantitative mapping of local molecular oxygen concentration.

Probing Single-Molecule Interfacial Electron Transfer Dynamics Of Porphyrin On Tio2 Nanoparticles, Yuanmin Wang, Xuefei Wang, Sujit Kumar Ghosh, H. Peter Lu

Chemistry Faculty Publications

Single-molecule interfacial electron transfer (ET) dynamics has been studied by using single-molecule fluorescence spectroscopy and microscopic imaging. For a single-molecule zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO2 nanoparticle system, the single-molecule fluorescence trajectories show strong fluctuation and blinking between bright and dark states. The intermittency and fluctuation of the single-molecule fluorescence are attributed to the variation of the reactivity of interfacial electron transfer. The nonexponential autocorrelation function and the power-law distribution of the probability density of dark times imply the dynamic and static inhomogeneities of the interfacial ET dynamics. On the basis of the power-law analysis, the variation of single-molecule interfacial ET reactivity …

Paramagnetic Resonance Studies Of Bistrispyrazolylborate Cobalt(Ii) And Related Derivatives, William K. Myers

Chemistry and Chemical Biology ETDs

Herein, a systematic frozen solution electron-nuclear double resonance (ENDOR) study of high-spin Co(II) complexes is reported to demonstrate the efficacy of methyl substitutions as a means of separating dipolar and contact coupling, and further, to increase the utility of high-spin Co(II) as a spectroscopic probe for the ubiquitous, but spectroscopically-silent Zn(II) metalloenzymes. High-spin (hs) Co(II) has been subject of paramagnetic resonance studies for over 50 years and has been used as a spectroscopic probe for Zn metalloenzymes for over 35 years. However, as will be seen, the inherent complexity of the electronic properties of the cobaltous ion remains to be …

Gec1-Kappa Opioid Receptor Binding Involves Hydrophobic Interactions Gec1 Has Chaperone-Like Effect, Yong Chen, Chongguang Chen, Evangelia Kotsikorou, Diane L. Lynch, Patricia H. Reggio, Lee Yuan Liu-Chen

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

We demonstrated previously that the protein GEC1 (glandular epithelial cell 1) bound to the human κ opioid receptor (hKOPR) and promoted cell surface expression of the receptor by facilitating its trafficking along the secretory pathway. Here we showed that three hKOPR residues (Phe³⁴⁵, Pro³⁴⁶, and Met³⁵⁰) and seven GEC1 residues (Tyr⁴⁹, Val⁵¹, Leu⁵⁵, Thr⁵⁶, Val⁵⁷, Phe⁶⁰, and Ile⁶⁴) are indispensable for the interaction. Modeling studies revealed that the interaction was mediated via direct contacts between the kinked hydrophobic fragment in …

Dispersal And Establishment Both Limit Colonization During Primary Succession On A Glacier Foreland, Chad C. Jones, Roger Del Moral

Botany Faculty Publications

Plant colonization can be limited by lack of seeds or by factors that reduce establishment. The role of seed limitation in community assembly is being increasingly recognized, but in early primary succession, establishment failure is still considered more important. We studied the factors limiting colonization on the foreland of Coleman Glacier, Washington, USA to determine the importance of seed and establishment limitation during primary succession. We also evaluated the effects of seed predation, drought and existing vegetation on establishment. We planted seeds of seven species into plots of four different ages and found evidence that both seed and establishment limitation …

Structure Of Human Dna Polymerase Κ Inserting Datp Opposite An 8-Oxog Dna Lesion, Rodrigo Vasquez-Del Carpio, Timothy D. Silverstein, Samer Lone, Michael K. Swan, Jayati R. Choudhury, Robert E. Johnson, Satya Prakash, Louise Prakash, Aneel K. Aggarwal

Chemical Sciences Faculty Publications

Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polκ) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polκ's preference for insertion of an A opposite 8-oxoG lesion, …

Rationale For Studying Physical Chemistry, Carl W. David

Chemistry Education Materials

The various rationales for studying physical chemistry, and specifically the theoretical component thereof are presented in what is hoped in a coherent package.

Structural Investigation Of The Complex Of Filamin A Repeat 21 With Integrin Αiib And Β3 Cytoplasmic Tails – A Potential “Transmission” To Regulate Cell Migration, Jianmin Liu

ETD Archive

Cell functions in multi-cellular organisms are strongly depend on the dynamic cooperation between cell adhesion and cytoskeleton reorganization. Integrins, the major cell adhesion receptors, bind to extracellular matrix (ECM) and soluble ligands on the cell surface and link to the actin cytoskeleton inside the cell membrane. In this manner, integrins integrate cell adhesion and cytoskeleton reorganization by acting as a mechanical force transducer and a biochemical signaling hub (Zamir and Geiger 2001). Consequently, integrins are vital for development, immune responses, leukocyte traffic and hemostasis, and a variety of other cellular and physiological processes. Integrins are also are the focal point …

Hemeproteins Bathed In Ionic Liquids;Examining The Role Of Water And Protons In Redox Behavior And Catalytic Function, John Joseph Moran

ETD Archive

We investigate the changing behaviors of myoglobin and nitric oxide synthase (NOS) in the near-absence of bulk water and/or protons by using ionic liquid butyl methyl imidazolium tetrafluoroborate as a non-aqueous milieu. Through direct charge transfer and metalloprotein-mediated catalytic reduction of oxygen and nitric oxide, we shed light on diverging aspects on how the two hemeproteins face the scarcity of water and/or protons in bulk. Isotopic effect investigations using D2O further elucidates kinetic aspects of proton transfer. Finally, in the case of NOS oxygenase, pterin cofactor binding and NOS-mediated catalytic oxidation of L-arginine in ionic liquids interrogates proton and water …

Fabricating New Miniaturized Biosensors For The Detection Of Dna Damage And Dna Mismatches, N. Indika Perera

ETD Archive

A large number of genetic diseases and genetic disorders are simply caused by base alterations in the genome. Therefore, developing efficient and cost effective techniques for routine detection of these alterations is of great importance. Different methods involving gel electrophoresis and Polymerase Chain Reaction have been widely employed, but majority of these methods are costly, time consuming, and lack throughput, creating a fundamental gap between the current state-of-the-art and desired characteristics of low-cost, high-speed, simplicity, versatility, and potential for miniaturization. In this study, we attempt to bridge this gap by developing new sensing platforms to detect DNA base mismatches and …

Nitric Oxide Synthase In Confined Environments;Detection And Quantification Of Nitric Oxide Released From Cells And Modified Liposomes Using A Sensitive Metal Catalyst-Pedot Modified Carbon Fiber Electrode, P. A. Reshani H. Perera

ETD Archive

Nitric oxide (NO) is a freely diffusible, gaseous free radical, associated with many physiological and pathological processes that include neuronal signaling, immune response, and inflammatory response. NO is produced from L-arginine in an NADPH-dependent reaction catalyzed by a family of nitric oxide synthase (NOS) enzymes. A deficiency in NO plays a role in hypertension, hyperglycaemia, and arteriosclerosis, among other pathological states. Conversely, increased NO levels contribute to arthritis, septic shock, and hypotention. Therefore, measuring and quantifying NO production in biological systems and matrices may be vital in elucidating physiological and pathological processes. The goal of this work is to develop …

High Resolution Single Molecule Optical Localization Of Multiple Fluorophores On Dna Origami Constructs Fluorophores On Dna Origami Constructs, Anuradha Rajulapati

Theses, Dissertations and Capstones

An ongoing challenge in the development of nanoelectronics and nanophotonics is the nondestructive, high-resolution localization in space of single molecules and multi-molecular assemblies. The apparent barrier to the use of optical microscopy at the sub-100 nm scale is the well known Abbe Limit, the diffraction limit to resolution. This laboratory has adapted a technique called Single-molecule high resolution imaging with photobleaching (SHRIMP). We have developed methods for utilizing SHRIMP for the determination of the separation of two fluorophores in single DNA origami constructs.

DNA Origami is extremely useful because it can address nanocomponents down to 2nm separation. It should be …

The Transsulfuration Pathway Significantly Contributes To Glutathione Biosynthesis In Human Mammary Epithelial Cells, Andrea Del Pilar Belalcazar Maya

Theses, Dissertations and Capstones

Cellular methylation and antioxidant metabolism are linked by the transsulfuration pathway, which converts the methionine cycle intermediate homocysteine to cysteine, a precursor for glutathione biosynthesis, principally in hepatic cells. In mammals, the transsulfuration pathway has been identified in liver, kidney, pancreas and brain. To determine whether the pathway exists in mammary cells human breast adenocarcinoma cells (MCF-7) and normal mammary epithelial cells (HMEC) were labeled with ³⁵S-methionine for 24 hours following pre-treatment with a vehicle control, the cysteine biosynthesis inhibitor propargylglycine (PPG) or the gammaglutamyl cysteine synthesis inhibitor buthionine sulfoximine (BSO). Cell lysates were prepared and reacted with glutathione-S-transferase …

Structural Determination Of The 5' Untranslated Regions Of Ire-Containing Mrnas, Chandra Sekhar Bathina

Theses, Dissertations and Capstones

The expression of ferritin and amyloid precursor protein (APP) is post-transcriptionally regulated by iron-regulating proteins via binding to a stem-loop structure known as an iron-responsive element in the 5’-untranslated region (5’UTR) of ferritin and APP mRNAs. In this study, we used atomic force microscopy (AFM) to visualize the conformation of the 5’UTRs of ferritin heavy chain (Ferritin-H), ferritin light chain (Ferritin-L), and APP mRNA transcripts from human and mouse, and determined the secondary RNA structures using selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE). The AFM imaging did not provide high resolution structural information about these RNAs, whereas the SHAPE …

Ethyl 1-Acetyl-1h-Indole-3-Carboxyl­Ate, Tasneem Siddiquee, Shahid Islam, Dennis Bennett, Matthias Zeller, Mahmun Hossain

Chemistry Faculty Research

The title compound, C₁₃H₁₃NO₃, was synthesized by acetyl­ation of ethyl 1H-indole-3-carboxyl­ate. The aromatic ring system of the mol­ecule is essentially planar, but the saturated ethyl group is also located within this plane and the overall r.m.s. deviation from planarity is only 0.034 Å. Pairs of C-HO inter­actions connect mol­ecules into chains along the diagonal of the unit cell. Mol­ecules also form weakly connected dimers via stacking inter­actions of the indole rings with centroid-centroid separations of 3.571 (1) Å. C-H inter­actions between methyl­ene and methyl groups and the indole and benzene ring complete …

"One-Pot" Oligomeric A2 + B3 Approach To Branched Poly(Arylene Ether Sulfone)S: Reactivity Ratio Controlled Polycondensation, Andrea M. Elsen

Browse all Theses and Dissertations

The synthesis of fully soluble branched poly(arylene ether)s via an oligomeric A2 + B3 system, in which the A2 oligomers are generated in situ, is presented. This approach takes advantage of the significantly higher reactivity toward nucleophilic aromatic substitution reactions, NAS, of B2, 4-Fluorophenyl sulfone, relative to B3, tris(4-Fluorophenyl) phosphine oxide. The A2 oligomers were synthesized by reaction of Bisphenol-A and B2, in the presence of the B3 unit, at temperatures between 100 and 160 °C, followed by an increase in the reaction temperature to 180 °C at which point the branching unit was incorporated. The presence of branching was …

Evaluation Of Silica Monoliths In Affinity Microcolumns For High-Throughput Analysis Of Drug–Protein Interactions, Michelle J. Yoo, David S. Hage

David Hage Publications

Silica monoliths in affinity microcolumns were tested for the high-throughput analysis of drug–protein interactions. HSA was used as a model protein for this work, while carbamazepine and R-warfarin were used as model analytes. A comparison of HSA silica monoliths of various lengths indicated columns as short as 1 to 3 mm could be used to provide reproducible estimates of retention factors or plate heights. Benefits of using smaller columns for this work included the lower retention times and lower back pressures that could be obtained versus traditional HPLC affinity columns, as well as the smaller amount of protein that …

Microscopic Dynamics Of The Orientation Of A Hydrated Nanoparticle In An Electric Field, C. D. Daub, D. Bratko, A. Towshif, A. Luzar

Chemistry Publications

We use atomistic simulations to study the orientational dynamics of a nonpolar nanoparticle suspended in water and subject to an electric field. Due to molecular-level effects we describe, the torque exerted on the nanoparticle exceeds continuum-electrostatics based estimates by about a factor of two. The reorientation time of a 16.2×16.2×3.35 ̊A3 nanoparticle in a field E > 0.015V/ ̊A is an order of magnitude less than the field-free orientational time (∼ 1 ns). Surprisingly, the alignment speed is nearly independent of the nanoparticle size in this regime. These findings are relevant for design of novel nanostructures and sensors and development of …