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A Dft Study Of Vibrational Spectra And Mutagenicity Predictions Of Mononitrated Fluoranthenes [Abstract], Kefa Karimu Onchoke, Jorge Ojeda

Faculty Publications

No abstract provided.

Ammonium Sulfate Precipitation Combined With Liquid Chromatography Is Sufficient For Purification Of Bovine Serum Albumin That Is Suitable For Most Routine Laboratory Applications, Odutayo O. Odunuge, Alina Shazhko

Faculty Publications

The use of bovine serum albumin (BSA) in routine biochemical assays such as restriction enzyme digestion and immunodetection is plagued largely by two common contaminants, DNase and immunoglobulins G (IgGs). Acetylation of BSA to inactivate DNase limits its use as a protein standard due to interference with color development in assays such as Lowry’s. In spite of the availability of inexpensive BSA, its purification involves several cumbersome and time-consuming steps. In this work, we employed a modified strategy of ammonium sulfate precipitation coupled with liquid chromatography to purify BSA that is free of DNase and IgGs. Purified BSA tested negative …

Hydraphiles: A Rigorously Studied Class Of Synthetic Channel Compounds With In Vivo Activity, Saeedeh Negin, Bryan Smith, Alexandra Unger, W. Leevy, George Gokel

Chemistry & Biochemistry Faculty Works

No abstract provided.

Insights Into Forest Soil Carbon Dynamics From Nuclear Magnetic Resonance Spectroscopy, Chris E. Johnson

Civil and Environmental Engineering - All Scholarship

No abstract provided.

Role Of Resonance-Enhanced Multiphoton Excitation In High-Harmonic Generation Of N-2: A Time-Dependent Density-Functional-Theory Study, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

A minimum at similar to 39 eV is observed in the high-harmonic-generation spectra of N-2 for several laser intensities and frequencies. This minimum appears to be invariant for different molecular orientations. We reproduce this minimum for a set of laser parameters and orientations in time-dependent density-functional-theory calculations, which also render orientation-dependent maxima at 23-26 eV. Photon energies of these maxima overlap with ionization potentials of excited states observed in photoelectron spectra. Time profile analysis shows that these maxima are caused by resonance-enhanced multiphoton excitation. We propose a four-step mechanism, in which an additional excitation step is added to the well-accepted …

Coupling Field And Laboratory Measurements To Estimate The Emission Factors Of Identified And Unidentified Trace Gases For Prescribed Fires, Robert J. Yokelson, I. R. Burling, J. Gilman, C. Warneke, C. Stockwell, J. De Gouw, S. K. Akagi, S. P. Urbanski, P. Veres, J. M. Roberts, W. C. Kuster, J. Reardon, David W. T. Griffith, T. J. Johnson, S. Hosseini, J. W. Miller, D. R. Cocker Iii, H. Jung, D. R. Weise

Chemistry and Biochemistry Faculty Publications

An extensive program of experiments focused on biomass burning emissions began with a laboratory phase in which vegetative fuels commonly consumed in prescribed fires were collected in the southeastern and southwestern US and burned in a series of 71 fires at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. The particulate matter (PM2.5) emissions were measured by gravimetric filter sampling with subsequent analysis for elemental carbon (EC), organic carbon (OC), and 38 elements. The trace gas emissions were measured by an open-path Fourier transform infrared (OP-FTIR) spectrometer, proton-transfer-reaction mass spectrometry (PTRMS), proton-transfer ion-trap mass spectrometry (PIT-MS), negative-ion proton-transfer …

Measurements Of Reactive Trace Gases And Variable O-3 Formation Rates In Some South Carolina Biomass Burning Plumes, S. K. Akagi, Robert J. Yokelson, I. R. Burling, S. Meinardi, Isobel J. Simpson, Donald R. Blake, G. R. Mcmeeking, A. Sullivan, T. Lee, S. Kreidenweis, S. P. Urbanski, J. Reardon, David W. T. Griffith, T. J. Johnson, D. R. Weise

Chemistry and Biochemistry Faculty Publications

In October-November 2011 we measured trace gas emission factors from seven prescribed fires in South Carolina (SC), US, using two Fourier transform infrared spectrometer (FTIR) systems and whole air sampling (WAS) into canisters followed by gas-chromatographic analysis. A total of 97 trace gas species were quantified from both airborne and ground-based sampling platforms, making this one of the most detailed field studies of fire emissions to date. The measurements include the first emission factors for a suite of monoterpenes produced by heating vegetative fuels during field fires. The first quantitative FTIR observations of limonene in smoke are reported along with …

Development Of Matrix Assisted Ionization Methods For Characterization Of Soluble And Insoluble Proteins From Native Environments By Mass Spectrometry, Ellen Dela Victoria Inutan

Wayne State University Dissertations

Matrix-assisted laser/desorption ionization (MALDI) and electrospray ionization (ESI) have made a huge impact in the analysis of biological materials. ESI has gained its popularity involving liquid based analysis, efficient fragmentation, chromatographic and electrophoretic separations but has a limitation for solubility restricted materials and surface analysis. MALDI is applicable to large biomolecule analysis and for surface methods useful for tissue imaging but is limited for structural characterization due to poor fragmentation and is ill suited for liquid based separation methods. The research presented here relates to new ionization methods that encompass the benefits of ESI and MALDI. These novel ionization methods …

Development Of Quantitative Bioanalytical Methods For The Pharmacological Studies Of Anti-Cancer Drugs, Ye Feng

ETD Archive

In the anticancer drug discovery and therapy development, it is essential to understand the pharmacological properties of the drugs. Today, pharmaceutical analysis is employed throughout the whole drug discovery and development process. Pharmacokinetic-pharmacodynamic relationships are playing an increasingly important role in decisions on the rational development and use of new drugs and they can provide a detailed knowledge of the mechanism of the drug and a better understanding of the molecular targets on which they act. Due to the significance of pharmacological analysis, sensitive analytical methods are critically needed for pharmacological studies. Therefore, our long-term goal is to provide guidelines …

Optimization Of Gradient Chromatofocusing For The Protein Separation And Lc-Ms/Ms Determination Of Ngp1-01 In Mouse Serum, Brain, And Retina, Harini Jogiraju

ETD Archive

No abstract provided.

Gradient Chromatofocusing And Reversed Phase Hplc In Protein Analysis And Lc-Ms/Ms Determination Of Thiazolidinedione Nl-1 In Mouse Serum And Brain, Kiran K. Pedada

ETD Archive

No abstract provided.

Development Of Lc-Ms/Ms Methods For Quantitative Analysis Of Plant-Derived Anticancer Agent And Synthetic Estrogen In Complex Matrices, Simuli Lindah Wabuyele

ETD Archive

No abstract provided.

Automated Spectral Identification Of Materials Using Spectral Identity Mapping, Robert William Cannon

ETD Archive

With increased use of Raman spectroscopic instrumentation for material analysis there has also been an increase in the amount of acquired Raman spectral data. Because of this, there is a clear need to develop and implement advanced spectral analysis techniques. This is especially true in cases where limited reference data may be available and large data sets need to be interpreted. Raman spectral analysis and standardization techniques, along with a foundation for a comprehensive repository of Raman spectral data, will be described in this thesis. The main focus will be automated analysis and standardization of Raman spectral data using spectral …

Nos Oxygenase-Mediated Nitroalkane Catalytic Reduction: Impact On Nos Reaction, Praneeth Ivan Joel Fnu

ETD Archive

Organic nitroalkanes are used in many industries and for a variety of purposes. Their use is expanding and is steadily claiming new territories in our immediate environment. Some nitroalkanes, when they enter the human body, can be harmful as such or can be activated to generate reactive intermediates with known detrimental effects. P450 enzymes are known for metabolizing a variety of drugs and substances including organic nitroalkanes. Nitric oxide synthases (NOS) exhibit some similarities to P450 metalloenzymes and their potential interaction with nitroalkanes as xenobiotics is not well known. The present study investigates the effect of nitroalkanes on the catalytic …

Development Of Kinase Catalyzed Biotinylation To Study Phosphoproteomics, Kona Arachchilage Chamara Indunil Bandara Senevirathne

Wayne State University Dissertations

Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to identify phosphoproteins in normal and diseased states is critical to fully characterize cell biology. Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag. To explore kinase-catalyzed biotinylation, kinetic measurements were obtained with various kinases and the data indicated that kinase-catalyzed biotinylation occurs with catalytic efficiency appropriate for phosphoproteomics application. Next, the susceptibility of the biotin tag to phosphatases was characterized and found that the phosphorylbiotin group was relatively insensitive to protein phosphatases. …

Exploring Molecular Systems From Chemical Physics To Biochemistry Using Classical And Quantum Mechanics, Brian Thomas Psciuk

Wayne State University Dissertations

Six topic are considered in this dissertation. Chapter 2 is an investigation into the role of ultra-fast hydrogen dynamics in determining fragmentation products of C3H4 following exposure to intense laser fields. Classical dynamics simulations were performed starting from C3H4 isomers with 190 - 240 kcal/mol excess energy distributed randomly as nuclear momenta. Deprotonation events were seen in ca. 50 - 75 % of all trajectories. Roughly one third of all trajectories showed fragmentation involving internal isomerization prior to dissociation. Chapter 3 is a survey of currently popular density functional methods and their ability to calculate accurate excitation energies and intensities …

Investigation Of Dopamine Dynamics In Bdnf+/- Mice Using In Vivo Microdialysis And Electrochemical Analysis Of Purine And Monoamine Molecules Using A Boron-Doped Diamond Electrode, Johnna A. Birbeck

Wayne State University Dissertations

The goal of the first study was to determine if a reduction in brain-derived neurotrophic factor (BDNF) levels in female mice lead to a dysregulation in their dopaminergic system. Through a series of in vivo microdialysis and slice voltammetry experiments, we have discerned that female BDNF^+/- mice are hyperdopaminergic similar to their male BDNF^+/- counterparts. The in vivo microdialysis method zero-net flux highlighted that female BDNF^+/- mice had increased extracellular dopamine (DA) levels, while stimulated regional release by high potassium potentiated DA release from vesicular mediated depolarization. Using the complementary technique of fast scan cyclic voltammetry, electrical …

Striatal Dopamine Dynamics Upon Manganese Accumulation, Madiha Khalid

Wayne State University Dissertations

STRIATAL DOPAMINE DYNAMICS UPON MANGANESE ACCUMULATION

by MADIHA KHALID

August 2013

Advisor: Dr. Tiffany Mathews

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

Although manganese (Mn) is fundamental for many biological processes, exposure to excess amounts leads to a neurological disorder termed manganism. Due to its symptomatic similarity to Parkinson's disease, as well its preferential accumulation in dopamine rich brain regions, alterations in the dopamine system are implicated in the onset of manganism. In my research, Mn overexposure is mimicked via subcutaneous administration of manganese chloride to C57BL/6 mice over the course of seven days using a protocol that has been …

Synthesis And Application Of Atp Analogs For Phosphorylation-Dependent Kinase-Substrate Crosslinking, Satish Kumar Garre Venkata Raghavendra

Wayne State University Dissertations

Phosphorylation is an important post-translational modification that plays a key role in a variety of signaling cascades and cellular functions. Kinases phosphorylate protein substrates in a highly regulated manner and are promiscuous. Understanding kinase-substrate specificity has been challenging and there is a need for new chemical tools. To this end we developed -phosphate modified ATP photocrosslinking analogs ATP-ArN3 and ATP-BP, that crosslink substrate and kinase in a phosphorylation dependent manner. We have successfully demonstrated that ATP-ArN3 and ATP-BP can be used with natural kinase and substrates using cell lysates in vitro. We used our approach to identify novel kinases of …

Synthesis And Characterization Of A Biometric Model Of The Tricopper Binding Site Of Multicopper Oxidases, Haosen Wang

Honors Theses, 1963-2015

This research employs the principles of bioinorganic modeling, simplifying the extraneous structures of the molecule being mimicked and focusing only on the active components of the large biological molecules. Specifically, this project attempts to mimic the structure and reactivity of tri-copper active sites found in Multi-copper Oxidises, such as Laccase and Ceruloplasmin, that bind with oxygen and reduce it to water. After experimenting with various other structures that failed to mimic the active sites, we selected another potential ligand, 1,3,5-tri(2-pyridylmethyltriazole)-2,4,6-triethyl benzene, abbreviated L_tapma, to be the substrate for this research to bind with three Cu(I) ions and then …

Single-Cell Imaging And Spectroscopic Analyses Of Cr(Vi) Reduction On The Surface Of Bacterial Cells, Yuanmin Wang, Papatya C. Sevinc, Sara M. Belchik, Jim Fredrickson, Liang Shi, H. Peter Lu

Chemistry Faculty Publications

We investigate the single-cell reduction of toxic Cr(VI) by the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), an important bioremediation process, using Raman spectroscopy and scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDX). Our experiments indicate that the toxic, highly soluble Cr(VI) can be efficiently reduced to less toxic, nonsoluble Cr2O3 nanoparticles by MR-1. Cr2O3 is observed to emerge as nanoparticles adsorbed on the cell surface and its chemical nature is identified by EDX imaging and Raman spectroscopy. Co-localization of Cr2O3 and cytochromes by EDX imaging and Raman spectroscopy suggests a terminal reductase role for MR-1 surface-exposed cytochromes …

1. Chromium(0)- Promoted Higher Order Cycloaddition Reactions: Studies Toward The Total Synthesis Of The Cyclocitrinols And Echinopines A And B 2. Total Synthesis Of (±)-Debromoflustramine B Via [4+1] Cyclization Of An Indole Isocyanate And A Bis(Alkylthio)Carbene, Saptarshi De

Wayne State University Dissertations

A facile and short stereoselective synthesis of the functionalized tetracyclic core structure of the cyclocitrinols, a family of unusual C25 steroid isomers, has been accomplished. The key structural unit, the bicyclo[4.4.1]A/B ring system, was constructed by a regioselective Cr(0)-promoted [6π + 4π] photochemical cycloaddition reaction.

A Bronsted acid catalyzed rearrangement of the 11-trimethylsilyl-tetracyclo[8.1.0.03,7.04,11]undeca-5,8-diene ring system to the unusual homotriquinacene ring system. The trimethylsilyl substitution on the cyclopropane moiety was found to be crucial for the rapid transformation which is believed to proceed via carbocation intermediates.

A short concise formal synthesis of Echinopines A and B is reported. The key [5.5.7] …

Protein-Protein Interactions In The Neocortex: Emx2 And Its Binding Partners, Cierra Miller

Undergraduate Honors Theses

The mammalian neocortex is divided into discrete functional areas that are marked by distinct boundaries and whose positions are assigned through a process called neocortical arealization. One of the proteins involved in this process is Emx2, a transcription factor (protein that turns genes on and off) that is expressed, or made, in a gradient along the axis of the neocortex and determines the positions of these areal boundaries. In order to determine how Emx2 carries out this function of assigning areas, we have identified the proteins QKl-7 and Cnot61 as binding partners of Emx2.

Current research involves confirming the interactions …

Studies Of Mercury In Water, Sediment, And Fish In Mississippi: Concentrations, Speciation, Cycling, And Isotopic Composition, Garry Brown

Electronic Theses and Dissertations

The goal of this project is to better understand the biogeochemical cycle of mercury (Hg) in Mississippi to aid those managing the resources and developing related policy. To that end, Hg levels were determined in a total of 202 fish from Enid, Sardis and Grenada Lakes; Enid and Grenada have fish consumption advisories due to Hg. In addition, total-Hg and methylmercury (MeHg) levels were determined in the inflow and outflows from Enid and Sardis Lakes and in bottom sediment and suspended solids in Enid Lake. Potential sources of Hg to Enid Lake were investigated, including precipitation and runoff from urban, …

Online Learning In A Chemical Perceptron, Peter Banda, Christof Teuscher, Matthew R. Lakin

Computer Science Faculty Publications and Presentations

Autonomous learning implemented purely by means of a synthetic chemical system has not been previously realized. Learning promotes reusability and minimizes the system design to simple input-output specification. In this article we introduce a chemical perceptron, the first full-featured implementation of a perceptron in an artificial (simulated) chemistry. A perceptron is the simplest system capable of learning, inspired by the functioning of a biological neuron. Our artificial chemistry is deterministic and discrete-time, and follows Michaelis-Menten kinetics. We present two models, the weight-loop perceptron and the weight-race perceptron, which represent two possible strategies for a chemical implementation of linear integration and …

The Cloning And Expression Of Histone Genes From The Archaeal Organisms Pyrococcus Furiosus And Methanobrevibacter Smithii In The Polycistronic Vector Pst44., Doha Abdullah Alqurashi

Electronic Theses & Dissertations

The Euryarcheota branch of the Archaea contains histone proteins that are highly homologous to eukaryotic histones. Virtually all species within this group have two histone proteins (designated H1A and H2B). These proteins contain a canonical histone fold motif that stabilizes homo- and perhaps hetero-dimeric interactions. Molecular modeling calculations previously carried out in our laboratory revealed that both homo and hetero-dimers of histones from two euryarchaeal organisms are equally plausible. We have also shown through molecular modeling that inter-species hetero-dimers are structurally identical to existing solution structures archaeal histones. An interesting question that needs to be addressed is whether homo- and …

Development And Optimization Of The First High Throughput In Vitro Fret Assay To Characterize The Saccharomyces Cerevisiae Gpi-T, Sandamali Amarasingha Ekanayaka

Wayne State University Dissertations

DEVELOPMENT AND OPTIMIZATION OF AN IN VITRO FRET ASSAY TO CHARACTERIZE THE SACCHAROMYCES CEREVISIAE GPI TRANSAMIDASE

By

SANDAMALI AMARASINGHA EKANAYAKA

December 2013

Advisor: Dr. Tamara L. Hendrickson

Major: Biochemistry

Degree: Doctor of Philosophy

The enzyme glycosylphosphatidylinositol transamidase (GPI-T) mediates the attachment of a glycosylphosphatidylinositol (GPI) anchor to the C-terminus of specific proteins to produce GPI anchored proteins. This post-translational modification is essential for viability of eukaryotic organisms. However, very little is known about GPI-T and its catalytic activity. Thus, the research described in this abstract was conducted to develop an in vitro assay to monitor GPI-T. A high-throughput assay for …

Characterization Of A Novel Fusion Protein Of Ipab And Ipad Of Shigella And Its Potential As A Pan-Shigella Vaccine, F. J. Martinez-Becerra, X. Chen, Nicholas E. Dickenson, S. P. Choudhari, K. Harrison, J. D. Clements, W. D. Picking, L. L. Van De Verg, R. I. Walker, W. L. Picking

Chemistry and Biochemistry Faculty Publications

Shigellosis is an important disease in the developing world, where about 90 million people become infected with Shigella spp. each year. We previously demonstrated that the type three secretion apparatus (T3SA) proteins IpaB and IpaD are protective antigens in the mouse lethal pulmonary model. In order to simplify vaccine formulation and process development, we have evaluated a vaccine design that incorporates both of these previously tested Shigella antigens into a single polypeptide chain. To determine if this fusion protein (DB fusion) retains the antigenic and protective capacities of IpaB and IpaD, we immunized mice with the DB fusion and compared …

The Magnitude And Mechanism Of Charge Enhancement Of Ch∙∙O H-Bonds, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations find that neutral methylamines and thioethers form complexes, with N-methylacetamide (NMA) as proton acceptor, with binding energies of 2–5 kcal/mol. This interaction is magnified by a factor of 4–9, bringing the binding energy up to as much as 20 kcal/mol, when a CH3+ group is added to the proton donor. Complexes prefer trifurcated arrangements, wherein three separate methyl groups donate a proton to the O acceptor. Binding energies lessen when the systems are immersed in solvents of increasing polarity, but the ionic complexes retain their favored status even in water. The binding energy is reduced when the methyl …

Characterization Of Flavonoid Reactivities And Degradation Products Using Online Continuous Flow Kinetic Measurements And Higher Order Mass Spectrometry, Jeremy S. Barnes

Chemistry & Biochemistry Dissertations - Archive

Epidemiological studies offer strong evidence that diets rich in fruits and vegetables provide a defense against cardiovascular disease, cancer and other physiological disorders. One theory suggests that these hazards are due in part to an imbalance of the body's oxidative load, caused by an increase in biologically-relevant free radicals, such as reactive oxygen species (ROS). Flavonoids, a family of plant metabolites, are associated with an antioxidant capacity which could reduce oxidative stress and aging. Quercetin, a flavonol with one of the highest rated antioxidant characteristic, was used as a model system to evaluate the reactivity of flavonoids in the presence …