Digital Commons Network^™

Structural Dynamics Of A Single-Stranded Rna–Helix Junction Using Nmr, Catherine D. Eichhorn, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for …

Combining Experiment And Theory To Elucidate The Role Of Supercritical Water In Sulfide Decomposition, Yuko Kida, Caleb A. Class, Anthony J. Concepcion, Michael T. Timko, William H Green

Scholarship and Professional Work – COPHS

The cleavage of C–S linkages plays a key role in fuel processing and organic geochemistry. Water is known to affect these processes, and several hypotheses have been proposed, but the mechanism has been elusive. Here we use both experiment and theory to demonstrate that supercritical water reacts with intermediates formed during alkyl sulfide decomposition. During hexyl sulfide decomposition in supercritical water, pentane and CO + CO2 were detected in addition to the expected six carbon products. A multi-step reaction sequence for hexyl sulfide reacting with supercritical water is proposed which explains the surprising products, and quantum chemical calculations provide quantitative …

Field Measurements Of Trace Gases Emitted By Prescribed Fires In Southeastern Us Pine Forests Using An Open-Path Ftir System, S. K. Akagi, I. R. Burling, A. Mendoza, T. J. Johnson, M. Cameron, David W. T. Griffith, C. Paton-Walsh, D. R. Weise, J. Reardon, Robert Yokelson

Chemistry and Biochemistry Faculty Publications

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, US measured during the fall of 2011. The fires were more intense than many prescribed burns because the fuels included mature pine stands not subjected to prescribed fire in decades that were lit following an extended drought. Emission factors were measured with a fixed open-path Fourier transform infrared (OP-FTIR) system that was deployed on the fire control lines. We compare these emission factors to those measured with a roving, point sampling, land-based FTIR and an airborne FTIR deployed on the same fires. We also compare to emission …

Aerosol Single Scattering Albedo Dependence On Biomass Combustion Efficiency: Laboratory And Field Studies, Shang Liu, Allison C. Aiken, Caleb Arata, Manvendra K. Dubey, C. Stockwell, Robert Yokelson, Elizabeth A. Stone, Thilina Jayarathne, Allen L. Robinson, Paul J. Demott, Sonia M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Single scattering albedo (ω) of fresh biomass burning (BB) aerosols produced from 92 controlled laboratory combustion experiments of 20 different woods and grasses was analyzed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCE_FI)—higher MCE_FI results in lower ω values and greater spectral dependence of ω. A parameterization of ω as a function of MCE_FI for fresh BB aerosols is derived from the laboratory data and is evaluated by field observations from two wildfires. The parameterization suggests that MCE_FI explains 60% of …

The Periodical Winter 2014, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 1, issue 1 of the Periodical includes articles about Rhonda Scott's time as chair of the department, faculty news, a pictorial directory of 2014 graduates, an alumni spotlight, and Chemistry Club news.

The Role Of Platelets In Hyaluronan Degradation, Sami Albeiroti

ETD Archive

Following tissue injury, platelets rapidly interact with the exposed extracellular matrix (ECM) of blood vessel wall and the surrounding tissues. Hyaluronan (HA) is a major polysaccharide component of the ECM and plays a significant role in regulating inflammation. Human platelets can degrade HA from the surfaces of activated endothelial cells into fragments capable of inducing immune responses by monocytes. In addition, platelets contain the enzyme hyaluronidse-2 (HYAL2), one of two major hyaluronidases that digest HA in somatic tissues. The deposition of HA increases in the inflamed tissues in several inflammatory diseases, including Inflammatory Bowel Disease (IBD). This study provides evidence …

Hyaluronan Rafts On Airway Epithelial Cells, Amineh M. Abbadi

ETD Archive

Many cells, including murine airway epithelial cells, respond to a variety of inflammatory stimuli by synthesizing leukocyte-adhesive hyaluronan cables that remain attached to their cell surfaces. This study shows that air-liquid interface cultures of murine airway epithelial cells (AECs) also actively synthesize and release a majority of their HA onto their ciliated apical surfaces to form a heavy chain-hyaluronan (HC-HA) matrix in the absence of inflammatory stimuli. These matrices do not resemble the rope-like HA cables, but occur in distinct sheets, or rafts, that can capture and embed leukocytes from cell suspensions. The HC-HA modification involves the transfer of heavy …

Enzyme-Based Nitric Oxide Releasing Thin Films And Scaffolds, Mutha Merenna Nuwan Bhagya Gunasekera

ETD Archive

Nitric oxide synthase enzyme (NOS) embedded in thin films and scaffolds, when exposed to a solution of its substrate arginine, a source of reducing equivalents, and other required ingredients of the NOS reaction, can release fluxes of nitric oxide (NO). The latter is a molecule known to counteract platelet aggregation, and thus can prevent the thrombosis cascade on the surfaces of implantable medical devices. Therefore NO antithrombogenic regimens such as active coatings and embedded scaffolds have the potential to increase the lifespan of implantable biomaterials. Layer-by-layer electrostatic adsorption allows for assembly of multi-component protein/polyelectrolytes nanostructured films. Electrospun fiber matrices may …

Magnesium As A Regulator Of Hepatic Nadph In The Hepatocyte :;Prospective Roles Of Magnesium In Diabetes And Obesity Onset, Chesinta B. Voma

ETD Archive

No abstract provided.

The Role Of Rnase L In Thymic Homeostasis And Humoral Responses, Lin Zhang

ETD Archive

RNase L is highly expressed in the spleen, thymus, and multiple immune cells, suggesting that it may play an important role in the immune system against microbes. Previous studies in the lab have shown that deficiency of RNase L results in enlarged thymuses in mice at young age. However, relatively little is known about its influence on the thymic development and adaptive immunogenicity. The present Ph.D. study focuses on investigating the role of RNase L in the thymic homeostasis and humoral immune responses, thereby gaining new insights into the molecular aspects in thymocyte development, maturation and adaptive immunity.By using RNase …

Effects Of Shear Stress On The Distribution Of Kindlins In Endothelial Cells, Sidney V. Jones

ETD Archive

Endothelial cells (ECs) are exposed to changes in shear stress under a variety of physiological and pathological circumstances and respond by changing their shape, gene expression and cytoskeletal arrangement. Integrins are central mediators of these mechanotransduction responses of ECs and integrin function is in turn controlled by interaction of their short cytoplasmic tails with cytoplasmic binding partners. Recent studies have demonstrated the importance of the kindlin family members, known cytoplasmic tail binding proteins, as regulators of integrin function. Our lab has previously shown that kindlin-2 (K2) and kindlin-3 (K3) are both expressed and functionally significant for integrin mediated cellular events …

Assembly And Function Of Macromolecular Complexes For Accurate Trna Aminoacylation In Helicobacter Pylori, Gayathri Niroshani Silva

Wayne State University Dissertations

ABSTRACT

ASSEMBLY AND FUNCTION OF MACROMOLECULAR COMPLEXES FOR ACCURATE TRNA AMINOACYLATION IN HELICOBACTER PYLORI

by

GAYATHRI SILVA

January 2014

Advisor: Dr. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Abstract

The aminoacylation of tRNA is a critical step in maintaining the accuracy of the genetic code. Many microorganisms are missing one or more aminoacyl tRNA synthetases (aaRSs) and rely on indirect pathways to produce certain aa–tRNAs. In Helicobacter pylori (H. pylori), the genes encoding both asparaginyl tRNA synthetase (AsnRS) and glutaminyl tRNA synthetase (GlnRS) are missing and the organism consequently relies on the indirect pathway for …

Experimental And Theoretical Studies Of Binding Interactions In Divalent Transition Metal Cation-N-Donor Ligand Complexes: Structures, Sequential Bond Dissociation Energies, Mechanisms And Energetics Of Collision-Induced Dissociation, Holliness Nose

Wayne State University Dissertations

The thesis research described here involves a series of experiments that have been designed to probe the influence of the electronic structure of the metal cation, the nature and number of ligands, as well as the effects of chelation and steric interactions on the geometry and binding strength of transition metal cation-ligand complexes. The experimental studies make use of energy-resolved collision-induced dissociation (CID) techniques that are carried out in a custom-built guided ion beam tandem mass spectrometer (GIBMS) to probe the structures, energetics, and fragmentation behavior of the complexes of interest. Electronic structure theory calculations including several density functional theory …

Computational Studies Of Enzymatic Reactions And Inorganic Compounds, Dong Fang

Wayne State University Dissertations

Quantum mechanics (QM) calculations have been demonstrated to give very accurate results in studying a variety of chemical reactions. However, the current computing resources limits its use in large-size systems such as enzymes. Compared to QM, Molecular Mechanics (MM) have an advantage in computing time but disadvantage in accuracy, and MM cannot be used in reactions involving bonding forming and breaking. To combine the advantages of these two types of methods, QM/MM has been introduced to study reactions and processes in large-size systems, and it has been proven to give accurate results with moderate computational expense. When studying enzymatic reactions, …

Theoretical And Experimental Studies Of Noncovalent Metal Cation Binding And Base Pairing Interactions Of Cytosine And Modified Cytosines, Bo Yang

Wayne State University Dissertations

ABSTRACT

THEORETICAL AND EXPERIMENTAL STUDIES OF NONCOVALENT METAL CATION BINDING AND BASE PARING INTERACTIONS OF CYTOSINE AND MODIFIED CYTOSINES

by

BO YANG

December 2014

Advisor: Professor Mary T. Rodgers

Major: Analytical Chemistry

Degree: Doctor of Philosophy

Binding of metal cations to the nucleobases can lead to formation of rare tautomers of the nucleobases. The infrared multiple photon dissociation (IRMPD) action spectroscopy of five alkali metal cation-cytosine complexes, M⁺(cytosine), where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺, are examined using a Fourier transform ion cyclotron resonance mass …

Structural And Functional Characterization Of Proteins Of Unknown Function (Hp0495, Hp0100 And Hp1259) In Helicobacter Pylori, Shirin Fatma

Wayne State University Dissertations

H. pylori is missing the glutaminyl- and asparaginyl-tRNA synthetases (GlnRS and AsnRS, respectively). Consequently, H. pylori uses an indirect aminoacylation pathway to generate Gln-tRNAGln and Asn-tRNAAsn. Within this process, Asn-tRNAAsn is produced by misacylation of tRNAAsn with aspartate by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS). Next, the heterotrimeric, glutamine-dependent amidotransferase (called AdT or GatCAB) converts the misacylated Asp-tRNAAsn into Asn-tRNAAsn. A parallel pathway exists for the synthesis of Gln-tRNAGln, wherein misacylation of tRNAGln with glutamate is catalyzed by a tRNAGln-specific glutamyl-tRNA synthetase (GluRS2) to generate Glu-tRNAGln; this misacylated intermediate is converted to Gln-tRNAGln by the same AdT. This dependence on misacylated …

Design, Synthesis And Applications Of Fluorescent And Electrochemical Probes, Giri K. Vegesna

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

“Seeing is believing” the proverb well suits for fluorescent imaging probes. Since we can selectively and sensitively visualize small biomolecules, organelles such as lysosomes, neutral molecules, metal ions, anions through cellular imaging, fluorescent probes can help shed light on the physiological and pathophysiological path ways. Since these biomolecules are produced in low concentrations in the biochemical pathways, general analytical techniques either fail to detect or are not sensitive enough to differentiate the relative concentrations. During my Ph.D. study, I exploited synthetic organic techniques to design and synthesize fluorescent probes with desirable properties such as high water solubility, high sensitivity and …

Using Spe And Hplc-Ms To Quantify And Identify Pharmaceutical Compounds In St. John's University Wastewater, Melissa E. Stuckey

Honors Theses, 1963-2015

Pharmaceuticals in wastewater have become a concern of environmental toxicologists. An efficient method of discovering the concentrations of these pharmaceuticals in wastewater has not yet been produced. The method we developed includes an automated Solid Phase Extraction (SPE) procedure prior to injecting a sample of wastewater into the High Performance Liquid Chromatograph (HPLC) and Mass Spectrometer – Electrospray Ionization (MS-ESI). Three unknown peaks were identified on the HPLC and MS from wastewater obtained from the St. John’s Wastewater Treatment Plant in June 2013. Methods of analysis including NMR, GC-MS and IR have been used to determine the composition of these …

Probing Proteasome Inhibition By Metal Copmplexes As A New Route For Anticancer Therapy, Dajena Tomco

Wayne State University Dissertations

The scope of this thesis is focused towards the development of metal-containing coordination compounds as potential therapeutic agents. Efforts of this research involve the design, synthesis, and purification of these complexes, as well as their evaluation by spectroscopic, spectrometric, and electrochemical characterization. The antineoplastic properties of these metal-containing pro-drugs are tested against the inhibition activity of the 26S proteasome. Selected metal ions ranging from transition to main group elements have been incorporated in various ligand systems containing phenolate and pyridyl donor sets. The mechanistic behavior of these complexes in solution has been thoroughly investigated along with their in vitro anticancer …

Alterations In The Mouse Striatum Following Acute And Repeated Ethanol Exposure, Brooke D. Newman

Wayne State University Dissertations

Brain-derived neurotrophic factor (BDNF) is an important neuromodulator that has implicated in regard to several neurological disorders, including alcohol addiction. BDNF is also an important modulator of dopamine (DA), a neurotransmitter that is heavily implicated in addiction with one of the DA rich brain regions being referred to as the reward center of the brain. One of the focuses in alcohol dependence research includes determining risk factors that make an individual more susceptible to becoming dependent. BDNF has been of interest as a risk factor due to its involvement in ethanol consumption and addiction evidenced in a vast number of …

Investigation Into The Binding Interactions Of Klenow Fragment To Dna Modified With Carcinogens Af And Aaf Using Surface Plasmon Resonance, Ashley M. Floyd

Wayne State University Dissertations

The two major forms of DNA adducts from the carcinogen N-acetoxyacetyl-2-aminofluorene, N-(deoxygunanonsin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) and N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), are both known to impede replication, though in different ways. AAF is a strong block to replication leading to frameshift mutations, while the AF adduct is more easily bypassed, causing base substitutions. Surface plasmon resonance (SPR) was used to study the binding of exonuclease deficient E. coli polymerase I, Klenow fragment (KF), to DNA modified with AF or AAF at two locations: as a templating base or in the last formed base pair. KF binding to the modified DNA bases was also monitored to …

New Carbohydrate-Based Anti-Cancer And Anti-Bacterial Vaccines, Zhifang Zhou

Wayne State University Dissertations

The unique carbohydrates expressed on the surface of cancer, bacterial, viral and fungal cells are excellent target antigens for the design of therapeutic or preventive vaccines. However, as antigens carbohydrates have problems. First, carbohydrates usually have low immunogenicity. Second, even if immunogenic, carbohydrates typically elicit T cell-independent immune responses. To overcome these problems and design useful vaccines based on carbohydrate antigens, they are usually coupled with carrier proteins to form conjugates to enhance the immunogenicity of the antigens. However, there are still some issues existing in glycoprotein vaccines, such as poor reproducibility of the conjugates, difficulties in quality control and …

Lanthanide-Based Precatalysts For Carbon-Carbon Bond-Forming Reactions In Aqueous Media, Derek James Averill

Wayne State University Dissertations

The formation of carbon-carbon bonds is of great interest to synthetic chemists because these bonds make up the majority of biologically active compounds. The Mukaiyama aldol reaction is a Lewis-acid-catalyzed carbon-carbon bond-forming reaction that has the ability to produce optically active β-hydroxy carbonyls which can be found in many pharmaceuticals and natural products. Because of precatalyst instability towards hydrolysis, anhydrous solvents are commonly used. Recent efforts have focused on water-tolerant versions of enantioselective Mukaiyama aldol reactions because of the financial and environmental benefits of using aqueous media. Consequently, the Lewis-acidic and water-tolerant features of Ln³⁺ ions have aroused great …

Synthesis And Characterization Of Discrete Fexni2-Xp Nanoparticles; Assembly Of Phosphide Nanoparticles Into Porous Networks, Asha Hitihami Mudiyanselage

Wayne State University Dissertations

This dissertation research is focused on synthesis, characterization and assembly of metal phosphide nanoparticles of relevance to catalysis, magnetism, and optoelectronic applications. These include (1) synthesis of discrete FexNi2-xP ternary nanocrystals of relevance to hydrodesulfurization (HDS) catalysis and magnetism, and (2) 3-dimensional nanostructures (gels and aerogels) of InP and Ni2P.

A three-step solution-phase arrested precipitation method was employed for bimetallic nanocrystal synthesis. The synthesis of nanocrystals involves preparation of amorphous NixPy amorphous particles, introduction of the Fe precursor to form amorphous Fe-Ni-P particles, and high temperature conversion of Fe-Ni-P particles into crystalline ternary phosphide nanocrystals. Ternary FexNi2-xP nanocrystals crystalize in …

Synthesis And Evaluation Of Some New Aza-B-Homocholestane Derivatives As Anticancer Agents, Yanmin Huang, Jianguo Cui, Sijing Chen, Qifu Lin, Huacan Song, Chunfang Gan, Bin Su, Aimin Zhou

Chemistry Faculty Publications

Using analogues of some marine steroidal oximes as precursors, a series of aza-B-homocholestane derivatives possessing different substituted groups at the 3-position of the steroidal nucleus were synthesized. Their biological activity against cancer cell proliferation was determined with multiple cancer cell lines. Aza-B-homocholestane derivatives possessing 3-hydroxyl, 3-hydroximino and 3-thiosemicarbazone groups displayed remarkable cytotoxicity to cancer cells via apoptosis inducing mechanism. Compounds 5, 10, 12, 15 and 18 exhibited better potency to inhibit cancer cell proliferation. In addition, compound 15 was further evaluated with three dimensional (3D) multicellular spheroids assay to determine its potency against spheroid growth. The structure-activity relationship (SAR) generated …

Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original …

Upregulation Of Functional Kv11.1 Isoform Expression By Inhibition Of Intronic Polyadenylation With Antisense Morpholino Oligonucleotides, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The KCNH2 gene encodes the Kv11.1 potassium channel that conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative processing; intron 9 splicing leads to the formation of a functional, full-length Kv11.1a isoform, while polyadenylationwithin intron 9 generates a non-functional, Cterminally truncated Kv11.1a-USO isoform. The relative expression of Kv11.1 isoforms plays an important role in the regulation of Kv11.1 channel function and the pathogenesis of long QT syndrome. In this study,we identified cis-acting elements that are required for KCNH2 intron 9 poly(A) signal activity. Mutation of these elements decreased Kv11.1a-USO expression and increased the expression of …

Thio-Β-D-Glucosides: Synthesis And Evaluation As Glycosidase Inhibitors And Activators, Andrey V. Samoshin, Irina A. Dotsenko, Nataliya M. Samoshina, Andreas H. Franz, Vyacheslav V. Samoshin

College of the Pacific Faculty Articles

Structurally simple 1-thio-β-D-glucopyranosides were synthesized and tested as potential inhibitors toward several fungal glycosidases from Aspergillus oryzae and Penicillium canescens. Significant selective inhibition was observed for α- and β-glucosidases, while a weak to moderate activation for α- and β-galactosidases.

Convenient Synthesis Of 1,3-Dithiolane-2-Thiones: Cyclic Trithiocarbonates As Conformational Locks, Irina A. Dotsenko, Qinliang Zhao, Andreas H. Franz, Patrick Batoon, Nataliya M. Samoshina, Vyacheslav V. Samoshin

College of the Pacific Faculty Articles

A series of novel 1,3-dithiolane-2-thiones, or cyclic trithiocarbonates, has been prepared by a new simple procedure: a treatment of the corresponding epoxides with the commercially available potassium ethyl xanthogenate, KSC(S)OEt. The stereochemistry of the products was determined by 1 H NMR and in some cases by single-crystal X-ray data. Cyclohexane-based 1,3- dithiolane-2-thiones revealed a trans-fusion of the carbo- and hetero-cycles. The products obtained from the mono-substituted cyclohexene oxides demonstrated an axial position of the substituents. Thus the epoxide transformation into trithiocarbonate can be used as a method for locking cyclic compounds in unstable conformations.

Tailored Analytical Methods For Surveying Groundwater Quality In Areas Of Unconventional Drilling, Doug Dewayne Carlton Jr.

Chemistry & Biochemistry Dissertations - Archive

Many questions have been raised over the environmental impact of unconventional drilling techniques, especially on the groundwater of the extraction area. Analytical approaches and methods specific to hydraulic fracturing had to be developed due to the lack of available research at the time. The analytical approaches chosen for the extensive survey of groundwater quality included general groundwater measurements, bulk water characterization, and organic, inorganic, and ionic speciation. Some of the chosen targets included volatile and semivolatile ingredients in hydraulic fracturing fluid, metals associated with drilling fluids or formation waters, and total carbon and nitrogen measurements. These methods were developed and …