Chemistry Commons^™

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri Edwards, Thomas Vidmar, Kevin Koeller, James Bashkin, Chris Fisher

Chemistry & Biochemistry Faculty Works

DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers …

Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta M. Gillner, Daniel P. Becker Ph.D., Richard C. Holz

Chemistry: Faculty Publications and Other Works

In this review, we summarize the recent literature on dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.

Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark

Department of Chemistry: Dissertations, Theses, and Student Research

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will …

Metallization Of Dna And Dna Origami Using A Pd Seeding Method, Yanli Geng

Theses and Dissertations

In this dissertation, I developed a Pd seeding method in association with electroless plating, to successfully metallize both lambda DNA and DNA origami templates on different surfaces. On mica surfaces, this method offered a fast, simple process, and the ability to obtain a relatively high yield of metallized DNA nanostructures. When using lambda DNA as the templates, I studied the effect of Pd(II) activation time on the seed height and density, and an optimal activation time between 10 and 30 min was obtained. Based on the Pd seeds formed on DNA, as well as a Pd electroless plating solution, continuous …

Psychosine, The Cytotoxic Sphingolipid That Accumulates In Globoid Cell Leukodystrophy, Alters Membrane Architecture, Jacqueline Hawkins-Salsbury, Archana Parameswar, Xuntian Jiang, Paul Schlesinger, Ernesto Bongarzone, Daniel Ory, Alexei Demchenko, Mark Sands

Chemistry & Biochemistry Faculty Works

Globoid cell leukodystrophy (GLD) is a neurological disease caused by deficiency of the lysosomal enzyme galactosylceramidase (GALC). In the absence of GALC, the cytotoxic glycosphingolipid, psychosine (psy), accumulates in the nervous system. Psychosine accumulation preferentially affects oligodendrocytes, leading to progressive demyelination and infiltration of activated monocytes/macrophages into the CNS. GLD is characterized by motor defects, cognitive deficits, seizures, and death by 2–5 years of age. It has been hypothesized that psychosine accumulation, primarily within lipid rafts, results in the pathogenic cascade in GLD. However, the mechanism of psychosine toxicity has yet to be elucidated. Therefore, we synthesized the enantiomer of …

Paper And Toner Three-Dimensional Fluidic Devices: Programming Fluid Flow To Improve Point-Of-Care Diagnostics, Kevin M. Schilling, Daisy Jauregui, Andres W. Martinez

Chemistry and Biochemistry

We present a new method for fabricating three-dimensional paper-based fluidic devices that uses toner as a thermal adhesive to bond multiple layers of patterned paper together. The fabrication process is rapid, involves minimal equipment (a laser printer and a laminator) and produces complex channel networks with dimensions down to 1 mm. The devices can run multiple diagnostic assays on one or more samples simultaneously, can incorporate positive and negative controls and can be programmed to display the results of the assays in a variety of patterns. The patterns of the results can encode information, which could be used to identify …

Single-Molecule Studies Of Local And Global Nucleic-Acid Dynamics, Eric Muthuri Patrick

Wayne State University Dissertations

Nucleic acids undergo both global and local conformational changes that are important for their function. Structural studies have over the decades been invaluable in elucidation of various biomolecular mechanisms, hence contributing significantly to the understanding of biological events. However, a clear understanding of how molecules function in the cellular context requires investigation of their interconversion between multiple conformations, including mapping the folding landscape and any coupled changes in conformation. Work in this thesis focuses on fluorescence experiments, mainly at a single-molecule level to investigate such processes.

First, a novel single-molecule approach is described focusing on local dynamics within nucleic acids …

Investigating Hfq-Mrna Interactions In Bacteria, Martha Audra Faner

Wayne State University Dissertations

Regulatory RNAs (sRNAs) are essential for bacteria to thrive in diverse environments and they also play a key role in virulence [11]. Trans-sRNAs affect the stability and/or translation of their target mRNAs through complementary base-pairing. The base-pairing interaction is not perfect and requires the action of an RNA binding protein, Hfq. Hfq facilitates these RNA-RNA interactions by stabilizing duplex formation, aiding in structural rearrangements, increasing the rate of structural opening, and/or by increasing the rate of annealing [18-21]. Hfq has two well characterized binding surfaces: the proximal surface, which binds AU rich stretches typical of sRNAs, and the distal surface, …

Toward A Comprehensive Model Of Photosystem Ii Oxygen Evolving Complex Photoassembly, James Scott Board Ii

Theses, Dissertations and Capstones

Elucidating the mechanism of photoassembly of the oxygen-evolving complex (OEC) will lead to a better understanding of how nature catalyzes water oxidation. Although the temperature dependence of oxygen evolution has been described in the literature [1,2], we have performed a comprehensive study that covers Photosystem II (PSII) activity oxygen evolution in the presence and absence of 2,6-dichloro-1,4benzoquinone (DCBQ) from 5–45°C. In addition, we performed similar measurements for OEC photoassembly in the absence of DCBQ. PSIIenriched particles used for our measurements were prepared according to Berthold, Babcock, and Yocum[3], with modifications from Kolling, et al.[4] The oxygen-evolution of intact BBY particles …

Using Stable Isotope Analysis Of Zooplankton To Document Trophic And Biogeochemical Changes In The San Francisco Estuary, Steven C. Westbrook, Julien Moderan

STAR Program Research Presentations

Zooplankton represent a vital link between phytoplankton and fish, like the endangered Delta Smelt. Human interferences (nitrates from waste water, flow alteration, invasive species introduction…) have altered the structure of the San Francisco Estuary (SFE) ecosystem. We use stable isotope analysis to improve our knowledge of the planktonic food web in the SFE and gain insights into its evolution over the past decades. We use the ratios of certain isotopes (Nitrogen, Carbon, Sulfur, etc.) in different species of zooplankton to tell us what it is feeding on as well as the trophic level it feeds in. My research focused on …

X-Band Rapid-Scan Epr, Deborah Gale Mitchell

Electronic Theses and Dissertations

The advantages of rapid-scan EPR relative to CW and pulse techniques for samples with long longitudinal relaxation time T₁ (N_s⁰ defects in diamond, N@C₆₀, and amorphous hydrogenated silicon), heterogeneous samples (crystalline 1:1 α,γ-bisdiphenylene-β-phenylallyl (BDPA):benzene), lossy samples (aqueous nitroxyl radicals), and transient radicals (5-tert-butoxycarbonyl-5-methyl-1-pyrroline-N-oxide (BMPO)-superoxide adduct) were studied.

For samples with long relaxation times, CW (continuous wave) EPR is challenging due to power saturation and distortions from passage effects. In rapid-scan EPR, the field is swept through resonance in a time that is short relative to T₂. In rapid-scan EPR, the magnetic field is …

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 …

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 …

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 …

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 …

Computational Approaches To Anti-Toxin Therapies And Biomarker Identification, Rebecca Jane Swett

Wayne State University Dissertations

This work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data.

Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and …

Revisiting The Fundamentals In The Design And Control Of Nanoparticulate Colloids In The Frame Of Soft Chemistry, Vuk Uskoković

Pharmacy Faculty Articles and Research

This review presents thoughts on some of the fundamental features of conceptual models applied in the design of fine particles in the frames of colloid and soft chemistry. A special emphasis is placed on the limitations of these models, an acknowledgment of which is vital in improving their intricacy and effectiveness in predicting the outcomes of the corresponding experimental settings. Thermodynamics of self-assembly phenomena illustrated on the examples of protein assembly and micellization is analyzed in relation to the previously elaborated thesis that each self-assembly in reality presents a co-assembly, since it implies a mutual reorganization of the assembling system …

Membrane Surface Charges Attracted Protons Are Not Relevant To Proton Motive Force, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

[First Paragraph] Only a half-century ago, British scientist Peter Mitchell proposed the conceptual scheme known as "chemiosmotic theory" that identified the role of proton coupling in the formation of ATP in cells [1,2]. Mitchell's delocalized proton-coupling chemiosmotic theory was initially quite controversial. But it would win for him the Nobel Prize in Chemistry in 1978. However, questions about Mitchell's chemiosmotic hypothesis have never gone away and a number of credible studies indicated the full extent of Mitchell's idea didn't always hold up to experience.

Development Of Peptide Inhibitors Targeting Clostridium Difficile Toxins A/B And Characterizing The Regulatory Role Of A Putative Negative Regulator Tcdc In Clostridium Difficile Toxin Gene Expression, Sanofar Jainul Abdeen

Wayne State University Dissertations

Clostridium difficile infections cause one of the most common and vital hospitalacquired

diseases often associated with broad-spectrum antibiotic usage. TcdA and TcdB

are the key virulence factors involved in major patho-physiology. While standard

antibiotics provide some respite, due to the high relapse rates and the emergence of more

severe disease presentations, antibiotics alone have often proven to be suboptimal.

Therefore there is a desperate need to develop an effective non-antimicrobial

therapeutics. Part of this work focuses on identification and further characterization of

peptide therapeutic that target the major virulence factor TcdA/TcdB. Towards

development of mechanistic-based anti-toxin agent, phage display was …

Decoration Of Graphene With Metal Nanoparticles And Its Application For Bioanalysis, Keun Soo Kwon

Theses, Dissertations and Culminating Projects

Graphene is a two-dimensional monolayer of tightly packed sp² hybridized Carbon atoms. Formed from graphite, the theoretical surface area of the monolayer is about 2630 m²/g, and the initial formation of graphene oxide from graphite oxide introduces a variety o f functional groups, such as -COOH, -C=0, and -OH, on its surface. The high surface area and the rich presence of functional groups, along with the potential formation o f sp² bonding networks within graphene oxide, all serve as critical factors allowing for additional chemical modifications. There are extensive research attempts being performed to explore and …

Molecular Biochemical Study Of The Cataract-Associated Mutants In Human Gammad-Crystallin, Cindy Yeung

Legacy Theses & Dissertations (2009 - 2024)

Cataract is a vision impairment disease that leads to light scattering and opacity of the eye lens. It is recognized as the most prevalent cause of blindness. Most cataracts occur due to aging, but those that occur in childhood or in young adults are typically of genetic origin. In the young (developing) eye, post–surgical complications such as glaucoma are common after cataract surgery. Hence there is a great need to develop non-surgical intervention strategies for the treatment of cataract. Here, two cataract-associated mutants of human γD-crystallin (HGD): i) Arg76 to Ser (R76S) and ii) a truncation mutation at Trp156 (W156X …

Structure-Activity Relationship Of 2,3-Benzodiazepin-4-Ones As Noncompetitive Ampa Receptor Antagonists, Mohammad Shaban Qneibi

Legacy Theses & Dissertations (2009 - 2024)

2,3-Benzodiazepin-4-one (BDZ-11) derivatives are a special group of 2,3-benzodiazepine compounds. These compounds have been previously synthesized as AMPA receptor inhibitors, and they are also potential drugs for the treatment of various neurological diseases involving excessive AMPA receptor activity. AMPA receptors are a subtype of glutamate ion channel proteins and are responsible for the majority of excitatory neurotransmission in the mammalian central nervous system. Specifically, they are critically involved in neuronal development and brain activities, including learning and memory. Overstimulation of AMPA receptors is associated with some neurological diseases such as ALS, stroke and Alzheimer's disease. Despite the fact that hundreds …

(S)-Trifluoroselenomethionine : A New Non-Natural Amino Acid With Enhanced Methioninase-Induced Cytotoxicity Toward Human Colon Cancer Cells, Stephene Nathele Lodge

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Voltage-Controlled Enzyme-Catalyzed Glucose–Gluconolactone Conversion Using A Field-Effect Enzymatic Detector, Siu Tung Yau, Yan Xu, Yang Song, Ye Feng, Jiapeng Wang

Chemistry Faculty Publications

The field-effect enzymatic detection (FEED) technique was used to control the kinetics of the enzymatic conversion of glucose to gluconolactone. The glucose–gluconolactone conversion occurring at an enzyme-immobilized electrode, a well-studied process, was confirmed using mass spectrometry. Electrochemical studies showed that the glucose oxidation current depends on the gating voltage VG and the ion concentration of the sample solution. Additionally, the depletion of glucose in the sample also showed a dependence on VG. FEED was used to detect H2O2 on the zepto-molar level in order to show the ultrasensitive detection capability of the technique. These results, while providing evidence for the …

Spliceosomal Prp24 Unwinds A Minimal U2/U6 Complex From Yeast, Chandani Manoja Warnasooriya

Wayne State University Theses

Splicing plays a major role in eukaryotic gene expression by processing pre-mRNA to form mature mRNA. Pre-mRNAs undergo splicing to remove introns, non–protein coding regions, and religate exons, protein coding regions. This process is catalyzed by the spliceosome, which consists of five small nuclear ribonucleoprotein particles (snRNPs: U1, U2, U4, U5 and U6) and numerous protein factors. Proper assembly of spliceosomal components is critical for function, and thus, defects in assembly can be lethal. Several spliceosomal proteins facilitate structural rearrangements important for spliceosomal assembly and function. Prp24 is an essential factor in U6 snRNP assembly, and it has been proposed …