Chemistry Commons^™

Single Molecule Studies Of Rna-Target Interactions, Sharla Leann Wood

Wayne State University Dissertations

We have used FRET, single molecule spectroscopy, and several other biophysical techniques to study how the folding of RNA allows it to perform its various functions by recognizing and binding a target ligand. We have shown that the c-di-GMP riboswitch undergoes a large, global conformational change upon binding of the ligand. The folding dynamics of the c-di-GMP riboswitch upon Mg2+ binding help to pre-organize the aptamer for efficient ligand binding and ultimately efficient gene expression. We have also investigated two instances, a fluorophore-binding aptamer and molecular beacon, where the folding of RNA can be used to detect an analyte. We …

Synthesis Of Oligosaccharide Mimetics By The Desulfurative Rearrangement Of Allylic Disulfides And Stereoelectronic Influence Of C-O Bonds On C- And O-Glycosylation, Myriame Moume-Pymbock

Wayne State University Dissertations

This dissertation focuses on two different problems. The first part of this manuscript presents the application of a novel methodology to access the synthesis of oligosaccharide mimetics while the second part focuses on the study of the stereoelectronic effects of proximal C-O bonds in C- and O-glycosylation reactions.

The first chapter provides a brief overview of the important roles that oligosaccharides and glycoconjugates play in biological processes and sets out the major advances that have been made in the past few decades in the synthesis of such complex structures while bringing out the ongoing challenges and the limitations that impede …

Publish And Flourish, Stephen K. Taylor

Faculty Publications

At primarily undergraduate institutions (PUIs), teaching is usually the primary responsibility, and many PUI professors do not regularly produce publications, even if they were hired to include research as an important responsibility. Most instructors at these schools are busy enough with just teaching and other academic responsibilities. It can seem intimidating to think of doing research, writing a research proposal, then a publication, and so on. Perhaps the sum of these duties may seem like a daunting set of tasks, and a "fear factor," consciously or subconsciously, may slow or even stop the research initiative. But at PUIs, it is …

Synthesis And Characterization Of Novel Pyridyl Silver (I) Lipid Complexes, Luis J. Andujo

Open Access Theses & Dissertations

Cationic surfactants are being used in many applications in industrial manufacture and medical technologies. Pyridinium salts come under the category of cationic surfactants. Surfactants have two distinct regions in their chemical structure, one of which is water-linking or hydrophilic and the other of which water-avoiding or hydrophobic. These molecules are referred to as amphiphilic or amiphipathic molecules or simply as surfactants or surface active agents. Depending on their charge the characteristics of the surface-active molecules may be anionic, cationic, zwitterionic (ampholytic) or non-ionic. These surfactants are used less for their wetting abilities than for their pronounced germicidal properties and their …

The Driving Forces Of Change In Energy-Related Co2 Emissions In Ireland: A Multi-Sectoral Decomposition From 1990 To 2007, Tadhg O'Mahony, Peng Zhou, John Sweeney

Articles

Ireland recorded significant growth in energy-related carbon emissions from 1990 to 2007 as the country underwent rapid economic development. Using the LMDI decomposition analysis method, this paper aims to identify and analyse the driving forces of CO2 emissions in eleven final energy consuming sectors. This multi-sectoral analysis is based on four economic sectors, the residential sector and gives a detailed representation of transport in keeping with UNFCCC recommendations. Scale, structure and intensity effects are explored and substantial heterogeneity in sectoral performance is observed. Scale growth in economic and transport activity was considerable. Some improvements in energy intensity were recorded in …

Crystal Structure Of Bacillus Subtilis Gabr, An Autorepressor And Transcriptional Activator Of Gabt, Raji Edayathumangalam, Rui Wu, Roman Garcia, Yuguang Wang, Wei Wang

Chemistry: Faculty Publications and Other Works

Bacillus subtilis GabR is a transcription factor that regulates gamma-aminobutyric acid (GABA) metabolism. GabR is a member of the understudied MocR/GabR subfamily of the GntR family of transcription regulators. A typical MocR/GabR-type regulator is a chimeric protein containing a short N-terminal helix-turn-helix DNA-binding domain and a long C-terminal pyridoxal 5′-phosphate (PLP)-binding putative aminotransferase domain. In the presence of PLP and GABA, GabR activates the gabTD operon, which allows the bacterium to use GABA as nitrogen and carbon sources. GabR binds to its own promoter and represses gabRtranscription in the absence of GABA. Here, we report two crystal structures of …

Composition And Antimicrobial Activity Of The Essential Oil Of Hyssopus Seravschanicus Growing Wild In Tajikistan, Rachel M. Thompson, Prabodh Satyal

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

"The Study Of Natural Products For Drug Discovery Is A Vital Field In Pharmaceutical Research…", Leah E. Woodall

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Natural Antiparasitic Coumarins: An In Silico Study, William R. Erwin

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

A Chemical Ecological Investigation Of The Allelophatic Potential Of Lamium Amplexcaule And Lamiun Purpureum, Chelsea D. Jones, Katherine E. Woods

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Dc Slice Imaging, Crossed Beam Reaction Of Chlorine Radical With Butane, Tarek Oussama Abdul Ghani

Wayne State University Theses

We present an investigation of the reaction dynamics of Cl radicals with

Butane using crossed molecular beams, at two collision energies: ~ 6.5 and 9 kcal/mol. The product butyl radical was ionized using a 157 nm probe laser, and detection was through a dc slice detection setup. The translational energy distributions looked similar for both collision energies. The angular distribution shows that at the high collision energy there is a sharp increase in the forward scattering. At low collision energy there is more backscattering. The results show that the different scattering angles give different translational energy distribution. The forward scattered …

Catalytic Effects Of Period Iv Transition Metal In The Oxidation Of Biodiesel, Bradley Clark

Wayne State University Theses

CATALYTIC EFFECTS OF PERIOD IV TRANSITION METALS IN THE OXIDATION OF BIODIESEL

BRADLEY R CLARK

December 2011

Advisors: Dr. Steve Salley, Dr. Simon Ng, Dr. Naiem Henien

Major: Alternative Energy Technology

Degree: Masters of Science

Transition metals have the ability to catalyze free radical autoxidation of unsaturated fatty acid methyl esters (i.e., biodiesel). The catalytic effects of the eight period IV transition metals: V, Cr, Mn, Fe, Co Ni, Cu and Zn in soybean oil and cottonseed oil-based biodiesel are investigated. All metals produced a reduction of the induction period of biodiesel, although there are considerable differences in their catalytic …

The Spliceosomal Protein Prp8 Stabilizes A Compact Conformation Of The U2-U6 Complex, Subasinghe Appuhamilage Lemintha Imali Subasinghe

Wayne State University Theses

The spliceosome is a large, RNA-protein complex that catalyzes pre-mRNA splicing during mRNA maturation. The RNA components (small nuclear RNA; snRNAs) of the spliceosome have been well studied and are believed to be involved in the splicing catalysis. Although proteins are essential for splicing, they may not be directly involved in catalysis. Among hundreds of proteins, Prp8 is the only protein that interacts with all of the catalytically important snRNAs. Therefore, it is hypothesized that Prp8 may catalyze splicing either by directly participating in catalysis or by stabilizing the conformation of the catalytically active spliceosome. In order to test whether …

Effect Of Low Endogenous Brain-Derived Neurotrophic Factor Levels On Striatal Dopamine Dynamics, Francis Kabui Maina

Wayne State University Dissertations

Many neurological diseases and disorders are a result of alterations with neurotransmitters, neuromodulators, and/or proteins. Specifically, one protein that has been linked to numerous neurological diseases and disorders such as Parkinson's disease, Huntington's disease, addiction, attention deficit hyperactivity disorder (ADHD), and depression is brain-derived neurotrophic factor (BDNF). As a trophic factor, BDNF role is to assist in the growth, survival, and differentiation of neurons. However, there is increasing evidence that BDNF may mediate neurotransmitter dynamics. Our goals were to understand how endogenous BDNF levels and aging modulate the dopamine (DA) dynamics in the mouse striatum. Two complementary neurochemical techniques, slice …

Determination Of Descriptors By Liquid-Liquid Partition And Chromatographic Methods, Thushara Namal Karunasekara

Wayne State University Dissertations

ABSTRACT

DETERMINATION OF DESCRIPTORS BY LIQUID-LIQUID PARTITION AND CHROMATOGRAPHIC METHODS

by

THUSHARA KARUNASEKARA

September 2012

Advisor: Prof. Colin F. Poole

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

Partition coefficients for varied compounds were determined for several totally organic biphasic systems using formamide, propylene carbonate, ethylene glycol or dimethyl sulfoxide as the base solvent and n-heptane, 1,2-dichloroethane, 1-octanol or isopentyl ether as the counter solvent. These partition coefficient databases are analyzed using the solvation parameter model facilitating a quantitative comparison of these systems with other totally organic and water-based partition systems. These totally organic biphasic solvent systems offer a complementary approach …

Synthesis, Characterization, And Antioxidant Activities Of New Trisubstituted Triazoles, Kemal Sancak, Yasemi̇n Ünver, Di̇lek Ünlüer, Esra Düğdü, Gülcan Kör, Fati̇h Çeli̇k, Emrah Bi̇ri̇nci̇

Turkish Journal of Chemistry

A series of new 4-(3,4dimethoxyphenethyl)-3,5-akyl/aryl-4H- 1,2,4-triazoles (3a-g) were obtained by reaction of ethyl N'-(alkylidene/arylidene)hydrazonate (1) and 2-(3,4-dimethoxy phenyl)ethanamine (2). Compounds 4d, e, and g were synthesized from the reaction of corresponding compounds 3d, e, and g with BBr_3, respectively. The 10 new compounds synthesized were characterized by elemental analyses, IR, ^1H-NMR, and ^{13}C-NMR spectral data. The structure of compound 3g was inferred through IR, ^1H-, ^{13}C-NMR, elemental analyses, and X-ray spectral techniques. In addition, the newly synthesized chemicals were screened for their antioxidant properties. Among the chemicals tested, 4d, e, and g exhibited the highest degree of antioxidant activity.

Evaluation Of A Wide Rim Phosphorylated Calix[4]Arene's Properties As A Sensory Molecule In An Er(Iii)-Pvc Membrane Sensor, Abbas Ali Zamani, Massoumeh Parinejad, Fataneh Jamali, Mohammad Reza Yaftian, Dominique Matt

Turkish Journal of Chemistry

This study concerns the evaluation of ionophoric properties of a functionalized calix[4]arene, named 5,17-bis(diphenylphosphinoyl)- 25,26,27,28-tetrapropoxycalix[4]arene (Calix), by its application as a sensing material in an erbium(III)-PVC membrane potentiometric sensor. A membrane formed by 30% PVC, 65% dioctyl phthalate (DOP) as plasticizing solvent mediator, 2% sodium tetraphenyl borate (NaTPB) as ion excluder, and 3% of Calix as ionophore shows the best performance of the sensor. The prepared sensor presents a nearly Nernstian response (a slope of 20.0 \pm 0.5 mV/decade) over a concentration range of 1 \times 10^{-7}--1 \times 10^{-3} M of erbium ions, with a limit of detection of 3.8 …

Ultraviolet Resonance Raman Spectroscopy For Characterization Of Rna Structure And Thermodynamics, Joseph Dustin Handen

Legacy Theses & Dissertations (2009 - 2024)

Raman spectroscopy is a technique well suited for the study of biological molecules such as proteins, peptides, or RNAs. By utilizing an ultraviolet resonance Raman (UVRR) instrument, we are afforded a tremendous increase in sensitivity because of resonance enhancement. Additionally, this technique does not require any labeling. Moreover, this technique is better suited for studying biological systems than infrared absorption due to reduced interference from water. In this study, we apply techniques we have developed for the study of protein and peptide fibrillation to a model RNA homodimer. We demonstrate that UVRR spectroscopy is uniquely suited to monitoring the free …

An Application Of Camx Process Analysis Tools : Exploring Process Contributions To Extreme Ozone, Nitrogen Oxides And Sulfur Dioxide, David-Anthony Murray

Legacy Theses & Dissertations (2009 - 2024)

The University at Albany Air Quality Forecasting Modeling System (AQFMS) is a state-of-the-art model that generates reliable daily and "day-ahead" air quality forecasts for the Northeastern United States. The three major categories of processes which dictate regional air quality are production from emission sources, horizontal and vertical transport driven by the prevailing meteorology, and chemical transformations. The Advanced Research WRF (ARW) produces meteorological fields. The Sparse Matrix Operator for Kernel Emissions (SMOKE) processes available emission inventories for air quality modeling. The Comprehensive Air Quality Model with extension (CAMx) handles both chemical processes and the integration of ARW-WRF and SMOKE in …

Short-Term Associations Between Pm2.5, Black Carbon, Delta-C, And Cardiovascular Diseases In A Large Developing Megacity, Daniel Malashock

Legacy Theses & Dissertations (2009 - 2024)

Introduction: Association between ambient air pollution and cardiovascular disease (CVD) have been demonstrated by many epidemiological studies in developed countries, however few studies have been performed in developing countries of Asia.

Selection Of Chemically Modified Rna Aptamers Against The Glua2q Flop Ampa Receptor, Hyojung Seo

Legacy Theses & Dissertations (2009 - 2024)

The á-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors play an important role in neurotransmission and synaptic plasticity in the central nervous system. Excessive activity of these receptors has been implicated in some neurodegenerative diseases, such as Parkinson's disease, ischemic stroke and amyotrophic lateral sclerosis (ALS). AMPA receptor inhibitors are therefore drug candidates for potential treatment of these neurological disorders and diseases. The objective of my MS thesis work is to develop a stable aptamer so that it can be tested and used in vivo where the aptamer must be exposed to ribonucleases. To do this, I prepared a library containing RNAs with 2'-Fluoro …

Trace Element Analysis Of Environmental And Clinical Materials Using Novel Instrumentation Based On X-Ray Fluorescence Spectrometry : New Capabilities For Public Health Laboratories, Kathryn G. Mcintosh

Legacy Theses & Dissertations (2009 - 2024)

X-ray fluorescence (XRF) spectrometry is a well-established analytical technique for determining the elemental content of many different materials. XRF has long been used for public health applications, particularly for identifying lead-based paint hazards. The primary advantage of XRF over other atomic spectrometric techniques is that it is nondestructive. In addition, little sample preparation is required, so results are obtained rapidly and at low cost. The principal aim of this study was to characterize the utility and reliability of current XRF instrumentation for use in the environmental health sciences. Interest in the use of XRF for detecting lead in children's toys …

The Analytic Reconciliation Of Classic Mayan Elite Pottery : Squaring Pottery Function With Form, Adornment, And Residual Contents, Jennifer Ann Loughmiller-Newman

Legacy Theses & Dissertations (2009 - 2024)

This dissertation presents a multidisciplinary means of determining the actual content (foodstuff, non-foodstuff, or lack of contents) of Classic Mayan (A.D. 250-900) vessels. Based on previous studies that have identified the residues of foodstuffs named in hieroglyphic texts (e.g. cacao), this study is designed to further investigate foodstuff residues in the elite vessels indicated by text or image to contain those residues, and the methods employed for residue characterization. Prior to studies utilizing residue analysis, the content of Classic Maya vessels largely had long been inferred largely by ethnographic analogy, associating specific vessel forms with specific uses based on ethnographic …

Inhibition Of Glutamate Receptors By Constructing Bipartite Rna Aptamers, Jeffrey Hebert

Legacy Theses & Dissertations (2009 - 2024)

The relationship of excessive activity of AMPA-type glutamate receptors, and cell death, has long provided researchers a means of investigating neurodegenerative disorders, such as Parkinson's Disease (PD) and amyotrophic lateral sclerosis (ALS). Inhibitors of AMPA receptor channels, including chemical and nucleic acid molecules such as RNA aptamers, have served as potential therapeutic agents and treatment of neurodegenerative disorders. In this study, building bipartite aptamers to enhance inhibitory potency, as compared with a monomeric aptamer of AMPA receptor, is described. An enhanced potency is due, at least in part; to the proximity effect in bipartite structures or binding of a monomeric …

A Novel Fabrication Technique For Three-Dimensional Nanostructures, Ravi Kiran Bonam

Legacy Theses & Dissertations (2009 - 2024)

Three dimensional micro- and nano-structures are commonly used in the field of Photonics, Optoelectronics, Sensors and Biological applications. Although numerous physical models are developed, a major challenge has been in their fabrication which is commonly limited to conventional layer-by-layer techniques. In this dissertation, a novel method for fabricating three dimensional structures using Electron Beam Lithography (EBL) will be presented.

Statistical Analysis Of Gasoline As An Accelerant Using Principal Component Analysis, Carolyn Frantz

Legacy Theses & Dissertations (2009 - 2024)

Arson is one of the most difficult crimes to investigate, as much of the physical evidence is destroyed by the fire. Evidence of an accelerant at a scene is often vital in determining whether a fire was intentional or accidental. Gasoline is one of the most commonly used accelerants, due to its wide availability and low cost. Neat gasoline samples were analyzed by gas chromatography/mass spectrometry (GC/MS) to identify the components present in each gasoline and differentiate between gasoline samples based on their seasonal blend and grade. Advanced distillations were executed to compare regular and premium grade gasolines and determine …

Mechanism Of Inhibition Of The Glua2 Receptors By N-3 Derivatives Of 2,3-Benzodiazepines With C-4 Methyl Group, Congzhou Wang

Legacy Theses & Dissertations (2009 - 2024)

α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are one of the three subtypes of ionotropic glutamate receptors. AMPA receptors mediate fast synaptic neurotransmission in the central nervous system (CNS). Over-activation of calcium permeable AMPA receptors causes intracellular calcium overload, which leads to neurodegeneration and cell death. As such, AMPA receptors have been implicated in a number of neurological disorders and diseases, such as epilepsy, amyotrophic lateral sclerosis (ALS), and Parkinson's disease. 2,3-Benzodiazepine derivatives (or GYKI compounds) are a group of structurally similar compounds synthesized as inhibitors of AMPA receptors, and they have been used as potential drug candidates for the treatment of various …

Structural And Thermodynamic Anaylsis Of Self-Assembled Dna Cross-Tiles, Lauren Hakker

Legacy Theses & Dissertations (2009 - 2024)

A thermodynamic and structural analysis of DNA nanostructures was performed, following the replacement of the unpaired thymine bases within a central loop to determine their effect on the self-assembly process. Specifically this study focused on DNA cross-tile nanostructures. Self-assembly of DNA cross-tiles occurs by means of Watson-crick base-pairing interactions between designed single-stranded DNAs from which lattice structures assemble through sticky-end cohesion. These cross-tile structures were constructed from nine single-stranded DNAs and consisted of a central loop containing 16 unpaired thymine bases, four shell strands, and four arms. Modifications were introduced to replace the central unpaired thymine base loop. The modifications …

Interactions Of The Human Immunodeficiency Virus Type 1 Nucleocapsid Protein With Non-Hiv-Derived Nucleic Acids : Implications For The Viral Replication Cycle, Abhijit Padmakar Jadhav

Legacy Theses & Dissertations (2009 - 2024)

During attempts to develop aptamers that bind to the nucleocapsid protein of HIV-1 (i.e. NCp7) with high affinity, a heretofore unreported property of the protein--the ability to mediate degradation of nucleic acids, was discovered. Using λ DNA as a model nucleic acid system, it was shown that NCp7-mediated degradation of nucleic acids is non-specific, depends on incubation time, the concentration of NCp7, and the presence of divalent and monovalent cations. It was further demonstrated that degradation can be abrogated if NCp7 is pre-incubated with NCp7-inhibitors. Lyophilization of NCp7 can induce irreversible changes in its secondary structure that result in loss …

Fractional Comparison Of Arson Accelerants Using Advanced Distillation, Sarah Clickner

Legacy Theses & Dissertations (2009 - 2024)

Detection of accelerants is often critical in proving a fire was intentional. Establishing a fire was intentionally set is not an easy task and hinges on the preservation of accelerant present in fire debris. Various accelerants have previously been studied using the advanced distillation method to get fractional composition information. The resulting fractions from advanced distillations were compared to evaporation and burn samples to determine if there were any similarities.