Physical Sciences and Mathematics Commons^™

Hypothesis Driven Single Nucleotide Polymorphism Search (Hydn-Snp-S), Rebecca J. Swett, Angela Elias, Jeffrey A. Miller, Gregory E. Dyson, G. AndréS Cisneros

Chemistry Faculty Research Publications

The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome genotyping data for SNPs that link genetic locations …

Carcinogenic Adducts Induce Distinct Dna Polymerase Binding Orientations, Kyle B. Vrtis, Radoslaw P. Markiewicz, Louis J. Romano, David Rueda

Chemistry Faculty Research Publications

DNA polymerases must accurately replicate DNA to maintain genome integrity. Carcinogenic adducts, such as 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF), covalently bind DNA bases and promote mutagenesis near the adduct site. The mechanism by which carcinogenic adducts inhibit DNA synthesis and cause mutagenesis remains unclear. Here, we measure interactions between a DNA polymerase and carcinogenic DNA adducts in real-time by single-molecule fluorescence. We find the degree to which an adduct affects polymerase binding to the DNA depends on the adduct location with respect to the primer terminus, the adduct structure and the nucleotides present in the solution. Not only do the …

A Combined Radio- And Stable-Isotopic Study Of A California Coastal Aquifer System, Peter W. Swarzenski, Mark Baskaran, Robert J. Rosenbauer, Brian D. Edwards, Michael Land

Environmental Science and Geology Faculty Research Publications

Stable and radioactive tracers were utilized in concert to characterize geochemical processes in a complex coastal groundwater system and to provide constraints on the kinetics of rock/water interactions. Groundwater samples from wells within the Dominguez Gap region of Los Angeles County, California were analyzed for a suite of major cations (Na⁺, K⁺, Mg²⁺, Ca²⁺) and anions (Cl⁻, SO₄²⁻), silica, alkalinity, select trace elements (Ba, B, Sr), dissolved oxygen, stable isotopes of hydrogen (δD), oxygen (δ¹⁸O), dissolved inorganic carbon (δ¹³C_DIC), and radioactive …

Methodologies For Attaching Polypyridyl Ligands Into Amino Acids And Synthesis And Biological Evaluation Of Novel Light Activated Peptidomimetic Cysteine Protease Inhibitors Caged By Ruii(Bpy)2, Tomasz Respondek

Wayne State University Dissertations

Two separate subjects are described in this dissertation. The first part describes novel methodologies for attaching polypyridyl ligands into unnatural amino acids. The first chapter describes the different possibilities for attaching metal ligands to peptides and their applications as potential imaging and therapeutic agents covered so far in the literature. It is followed in the second chapter by the description of a new method for the construction of metal-peptide conjugates through the use of three unnatural amino acids, and their adaptation to solid phase synthesis. The third chapter describes the synthesis of a novel, "optimal" substrate for the enantioselective alkylation …

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, …

Design, Synthesis, And Luminescence Properties Of Bridged Dimetallic Lanthanide Coordination Compounds, Jeremiah David Moore

Wayne State University Dissertations

I synthesized and characterized new homo- and heterodimetallic Eu3+- and Tb3+-containing complexes. Solution-phase luminescence measurements and density functional theory (DFT)-optimized structures indicated that all complexes were nearly isostructural and contained a dimetallic lanthanide core bridged by three oxygen atoms that are covalently bound to the ligand backbone. The homodimetallic Eu3+ complex behaved as a concentration-independent pH sensor that correlates the luminescence-decay rate of the complex to pH. The probable mechanism of pH sensing was attributed to the modulation of a hydroxyl oscillator in the Eu3+ coordination sphere, which was a previously unreported method to sense pH. The heterodimetallic Tb3+/Eu3+ complex …

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 …

Exergetic Analysis Of Hydrogen Combustion Involving Electronically Excited Species, Devon Alan Washington

Wayne State University Dissertations

Plasma-assisted combustion (PAC) is a growing field of research that involves using nonthermal plasma (NTP) to enhance combustion. PAC research involves modeling reaction mechanisms and chemical kinetics. Exergy analysis of combustion devices focuses on combustion irreversibility, including mixing, internal heat transfer, and oxidation. This novel research project merges these two branches of research.

The focus of this work is the application of exergy analysis to PAC systems, to analyze the effect introducing NTP has on trends in exergy destruction associated with oxidation during hydrogen combustion. This was accomplished by developing a plug flow reactor model using the chemical simulation tool …

Synthesis And Characterization Of Biodegradable Poly(Vinyl Esters) With Hdac Inhibitory Activity, Kyle Lawrence Horton

Wayne State University Theses

HDAC inhibitors are known to have anti-inflammatory properties. HDAC inhibitors are used in combination with Oct4 to generate induced pluripotent stem cells. I hypothesized that polyesters based on simple aliphatic HDAC inhibitors like valproic acid (VPA) and phenylbutyric acid (PBA) can serve as alternatives to existing polyester biomaterials with improved anti-inflammatory properties and as scaffolds for generation of iPSCs when used in combination with layer-by-layer thin films delivering reprogramming transcription factors. Vinyl ester of phenylbutyric acid (VEPA) and vinyl ester of valproic acid (VEVA) were synthesized from their carboxylic acid precursors using an iridium complex catalyst at yields as high …

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 …

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] …

Studies On The Physicochemical Properties Of Eu2+ Cryptates: Implications To Contrast Agents For Magnetic Resonance Imaging, Joel Garcia

Wayne State University Dissertations

Magnetic resonance imaging (MRI) is a powerful medical imaging technique that can be enhanced using metal complexes called contrast agents. Most clinically approved contrast agents contain Gd³⁺. However, the efficiency (also known as relaxivity) of these Gd³⁺-containing complexes decreases as field strength increases, and in the ultra-high field strength regime, the relaxivity of these complexes is decreased considerably. Because of the slow water-exchange rate of most Gd³⁺-containing complexes (∼;10⁶ s^-1), I used Eu²⁺ instead of Gd³⁺ and adapted the ligand modification strategies that have been used for Gd^{3+ …}

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 …

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. …

Synthesis And Characterization Of Transition Metal Arsenide Nanocrystals And The Metastability And Magneto-Structural Phase Transition Behavior Of Mnas Nanocrystals, Yanhua Zhang

Wayne State University Dissertations

This dissertation study focuses on (1) probing the magneto-structural phase transformation in nanoscale MnAs; (2) evaluation of the size-dependent phase stability of type-B MnAs (prepared by rapid injection); and (3) developing a general synthetic method for transition metal arsenide nanoparticles.

Discrete MnAs nanoparticles that adopt different structures at room temperature (type-A, α-structure and type-B, β-structure) have been prepared by the solution-phase arrested precipitation method. Atomic pair distribution and Rietveld refinement were employed on synchrotron data to explore the structural transitions of the bulk and nanoparticle samples, and these results were compared to AC magnetic susceptibility measurements of the samples. The …

Fundamental Studies And Applications Of Strong Field Ionization, Lu Yan

Wayne State University Dissertations

In an intense laser field, atoms and molecules experience tunneling ionization directly to the continuum. We used this method to study several aspects and applications of strong field ionization (SFI) in atoms and molecules. One study used SFI to probe the photofragments produced by photodissociation using DC sliced imaging. The photodissociation mechanism of two polyatomic molecules (sulfur dioxide and nitromethane) were investigated. In a second study, we show the strong field ionization rate depends on the sign of the magnetic number distribution. We detect the signal of sequential double ionization of argon dications by a pump-probe method to investigate the …

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 …

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 …

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 …

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 …

Single-Stranded Dna Scanning And Deamination With Single-Molecule Resolution, Padhuk Gamarala Senavirathne

Wayne State University Dissertations

SINGLE-STRANDED DNA SCANNING AND DEAMINATION WITH SINGLE-MOLECULE RESOLUTION

by

GAYAN SENAVIRATHNE

December 2013

Advisor: Dr. David Rueda & Dr.Ashok Bhagwat

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

APOBEC3G (Apo3G) and Activation-Induced cytidine Deaminase (AID) are the most notable members of APOBEC enzymes, a family of cytidine (C) deaminases with crucial functions in the immune system. In T cells, Apo3G deaminates C in viral cDNA to halt the replication of HIV 1 strains lacking viral infectivity factor (vif). In B cells, AID is required for the diversification of antibodies through initiation of somatic hypermutation (SHM), and class switch recombination (CSR), by …

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 …

Unveiling Dna Polymerase Synthesis And Proofreading Activities - One Molecule At A Time, Kyle Vrtis

Wayne State University Dissertations

DNA polymerases maintain the genome integrity from one generation to the next by faithfully synthesizing new DNA and by participating in DNA repair processes. The Klenow fragment of E. coli DNA polymerase I has served as a model polymerase for decades because it is straightforward to purify, well-characterized kinetically, and it is able to carry out DNA synthesis and proofreading. In 2009, Christian, et al. developed a single molecule Förster resonance energy transfer (smFRET) approach to monitor the polymerase position on the DNA with single base pair resolution.

We have worked to optimize nearly every aspect of that approach and …

Development Of Ruthenium/Terpyridine Complexes For Water Oxidation, Dakshika Chandrashani Wanniarachchi

Wayne State University Dissertations

The work presented in the dissertation is focused on developing catalysts for water oxidation. In this regard, a series of unsysmmetrical ruthenium complexes of type [Ru(terpy-R)(phen-X)Cl]PF6 where terpy-R= 4'-(4-methylmercaptophenyl)-2,2':6'2"-terpyridine and phen-X=H (1), X= 5-nitro (2), X=5,6-dimethyl (3), and X= 3,4,7,8-tretramethyl (4) was synthesized as precursors for self-assembled monolayers. Water oxidation properties of these complexes were evaluated in the presence of (NH4)2[Ce(NO3)6] as the sacrificial oxidant by measuring catalytic turnover number (TON) after 24 h of reaction time and rate of dioxygen evolution in solution during early stages of catalysis. The results revealed that all complexes 1 - 4 are catalytic …

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 …

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 …

Synthesis And Characterization Of Metal Complexes Containing Tetrazolate, Poly(Tetrazolyl)Borate, And Poly(Azolyl)Aluminate Ligands As High Energy Density Materials, Christopher James Snyder

Wayne State University Dissertations

A series of heavy alkaline earth metal tetrazolate complexes has been synthesized that contain metal ions saturated by aqua ligands. Tetrazolates with small ring-core carbon substituents favor formation of two dimensional polymers with u3-coordination of the tetrazolate to the metal centers. Tetrazolates with bulkier groups block coordination to the 1- and 4-nitrogen atoms, resulting in monomer formation. The first example of a trihydro(tetrazolyl)borate was prepared, and its bonding is heavily influenced by the basic BH3 moiety. 18-Crown-6 adducts of dihydrobis(tetrazolyl)borate complexes have been prepared that contain B-N bonding to the 2-nitrogen atoms, due to bulky ring-core atom substituents. A series …