Chemistry Commons^™

A Turn-On Split-Luciferase Sensor For The Direct Detection Of Poly(Adp-Ribose) As A Marker For Dna Repair And Cell Death, Jennifer L. Furman, Pui-Wing Mok, Shengyi Shen, Cliff I. Stains, Indraneel Ghosh

Cliff Stains Publications

Designed sensors comprising split-firefly luciferase conjugated to tandem poly(ADP-ribose) binding domains allow for the direct solution phase detection of picogram quantities of PAR and for monitoring temporal changes in poly(ADP-ribosyl)ation events in mammalian cells.

Includes Supplementary Material.

Searching The Protein Structure Database For Ligand-Binding Site Similarities Using Cpass V.2, Robert Powers, Jennifer C. Copeland, Jaime L. Stark, Adam Caprez, Ashu Guru, David R. Swanson

Robert Powers Publications

Background: A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as “hypothetical” or “uncharacterized” protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number …

Electronic Excitations In Branched Conjugated Oligomers: A Quasiparticle View And Tight-Binding Models, Hao Li

Wayne State University Dissertations

This dissertation focuses on the theoretical understanding and simulation of the excited state electronic structures of organic conjugated molecules. The exciton scattering (ES) approach has been extended for efficient calculation of optical spectra of large branched conjugated oligomers. The methodology of tight-binding (lattice) model, originally developed in condensed matter theory, has been extended to the building block structure of conjugated molecules for explicit description of the electronic excitations.

Within the ES approach, the electronic excitations in quasi-1D molecular structures are attributed to standing waves that represent quantum quasiparticles (excitons) scattered at the molecular vertices. Excitation energies can be found by …

New Macrocyclic Glycopeptide Antibiotic For Chiral Hplc Stationary Phases And Ionic Liquids In Analytical Chemistry, Xiaotong Zhang

Chemistry & Biochemistry Dissertations - Archive

The main focus of this dissertation is on the development of new chiral stationary phases for HPLC and GC and the application of ionic liquids in analytical chemistry. They will be discussed separately in two parts. Enantiomeric separations continue to be of great interest to the pharmaceutical industry. It is because drug molecules of opposite chirality often possess distinctive effects in biological environments. Direct chromatography is one of the major techniques used to address the challenge of enantiomeric analysis. Macrocyclic glycopeptides are a very useful class of chiral selectors for HPLC stationary phases because of their broad enantioselectivity. A study …

The Development Of The Catalytic Wittig Reaction, Zachary S. Nixon

Chemistry & Biochemistry Dissertations - Archive

The formation of carbon-carbon double bonds with stereocontrol is of great importance to synthetic chemistry. The Wittig olefination involves the treatment of an aldehyde or ketone with a phosphonium ylide; yielding an alkene product with concomitant phosphine oxide byproduct. Mechanistic studies have shown that structural and electronic properties of the phosphine and halide reagent greatly influence the stereochemical outcome (E:Z) of the olefination. However, a significant limitation of the reaction is the difficulty of removing the phosphine oxide. A process catalytic in phosphine would alleviate the aforementioned concern and allow enhanced stereocontrol. Preliminary results led to the development of the …

Slowing Dna Translocation In A Biological Protein Α-Hemolysin Ion Channel, R. Samanthi S. De Zoysa

Chemistry & Biochemistry Dissertations - Archive

During the past decade, nanopore DNA sequencing has emerged as a revolutionary prospect towards a "$1000 genome" goal set by U.S. National Institute of Health. In the nanopore approach, electrophoretic movement of polynucleotide molecules through a nanopore would provide transient current blockades that are unique to each molecule. Since kilobase length DNA can be read directly without amplification or use of costly reagents such as enzymes and fluorescent tags, the nanopore approach can significantly reduce the sequencing cost. However, due to the rapid DNA translocation velocity through the nanopore, accurate detection of single nucleotide bases via the electrophoretically driven approach …

Ion Exchanger Based Ion Generation And Removal Devices. Behavior And Applications, Yongjing Chen

Chemistry & Biochemistry Dissertations - Archive

Ion exchangers have many important applications. In Ion chromatography (IC), ion exchangers are used as stationary phase and used in some of the key components. The innovations that make the modern IC the most popular techniques for ion analysis are closely related to ion exchangers. Using the ion exchangers and inspired by some of the innovations in electrolytic devices of IC, the research in this dissertation mainly consists of four parts: A charge detector (ChD) is a flow-through device where a cation exchange membrane (CEM) and anion exchange membrane (AEM) separating three channels. One electrode is disposed in each of …

Mixed Lineage Luekemia Histone Methyltransferases In Hormonal Regulation Of Hoxb9 And Target Gene Regulation, Bishakha Shrestha

Chemistry & Biochemistry Dissertations - Archive

Homeobox gene (HOX) genes are evolutionary conserved genes that play important roles in cell differentiation, cell proliferation and embryogenesis. HOX genes bind to the DNA via their homeodomain and act as transcription factors. Of the 39 HOX genes present in human, HOXB9 is known to be a critical player in skeletal and mammary gland development. HOXB9 also regulates renin gene expression which is a critical player in Renin-Angiotensin system. Recent studies also demonstrate that HOXB9 is critical for angiogenesis. I have investigated transcriptional regulation of HOXB9 and its potential biochemical function during cell cycle progression and tumorigenesis. My studies demonstrate …

Solid State Light Source Based Analytical Measurement Systems For Atmospheric Particles, Shilpa Rashinkar

Chemistry & Biochemistry Theses - Archive

Solid-state light sources such as light-emitting diodes, use a solid semiconductor block instead of a conventional heated filament or discharge source. Such light sources are preferred in analytical instrumentation because of various environmental benefits, cost benefits and most importantly performance benefits due to their characteristic features. This thesis deals with the fabrication of solid-state light source based analytical instrumentation for measuring size distribution and spectral absorption characteristics of ambient aerosol particles and provides insights into the behavior of aerosol organic carbon concentrations determined in a continuous and automated manner. Various analytical instruments are commercially available for either measuring the particle …

A Diffusionless Transformation Path Relating Th₃P₄ And Spinel Structure Opportunities To Synthesize Ceramic Materials At High Pressures, Arindom Goswami

Chemistry & Biochemistry Theses - Archive

Physical properties of solids at high pressure hold the key to many interesting questions in earth and planetary sciences, as well as in applied sciences. At high pressure, most ambient-pressure materials become unstable and transform into new and denser phases. In recent years, many solids with new structure types have been realized at high pressure through experiments and predicted in numerical simulations. Some of these structures are novel and had not been seen at ambient pressure. Some possess a variety of electronic states, i.e., metallic, superconducting, or super-hard states [YAO08]. These discoveries are of high interests both for their potential …

A Survey Of The Chemical Content And Medicinal Activity Of Shrub-Steppe Plants Of The Pacific Northwest, Aaron M. John

Undergraduate Honors Theses

A need for new modes of antibiotic therapy has resulted from the increasing incidence of bacterial resistance to drugs. One approach to this problem involves the search for plant compounds that may help to overcome multi-drug resistance. Many plant genera have been utilized in Native American traditional medicine for their beneficial properties. Such plants include the shrub-steppe genera, Eriogonun and Collomia, which have been used as cold remedies, pain relievers, and for antibiotic-related uses. Limited chemical studies of these genera have revealed medicinally useful compounds such as flavonoids and terpenoids, and further research may result in the identification of …

Variations In Concentrations And Compositions Of Polycyclic Aromatic Hydrocarbons (Pahs) In Coals Related To The Coal Rank And Origin, Susanne Laumann, Vesna Micic Batka, Michael A. Kruge, Christine Achten, Reinhard Sachsenhofer, Jan Schwarzbauer, Thilo Hofmann

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The release of unburnt coal particles and associated polycyclic aromatic hydrocarbons (PAHs) may cause adverse impacts on the environment. This study assessed variations in the concentration and composition of PAHs in a set of fifty coal samples from eleven coal basins worldwide. The maximum PAH concentrations at high volatile bituminous rank were recorded in samples from a single basin. Considering the entire sample, the highest PAH concentrations were in fact found outside of this rank range, suggesting that the maceral composition and thus the coal's origin also influenced PAH concentrations. The examination of the PAH compositions revealed that alkylated 2-3 …

Climate Change: The Fork At The End Of Now, Micha Tomkiewicz

Publications and Research

There are many books on global warming written entirely from a layman's perspective, and there is a great deal of scientific literature on this subject. But few if any books attempt to bridge the science to those who lack a rigorous background in mathematics, physics and chemistry-but who may be working on careers in environmental science and policy. The new text is designed to introduce the field of global climate change from a scientific perspective-but written in a way that is accessible to students with some or little science background. It reviews the basic principles of climatic thermodynamics and atmospheric …

Synthesis Of Peptide-Ligand Conjugates And Their Applications, Nitinkumar Dilipkumar Jabre

Wayne State University Dissertations

Three research areas pertaining to this dissertation, (i) synthesis strategies of peptide-ligand conjugates, (ii) their applications and (iii) chemistry of ferryls were surveyed in the introduction chapter. Next, the divergent and dual divergent strategies for the synthesis of non-heme ligand-peptide conjugates were developed. Using these strategies various peptide-ligand conjugates were synthesized via solution as well as solid phase synthesis. The scope and the functional group compatibility of these strategies were also established. The utility of the dual divergent strategy has been demonstrated by synthesizing a small library of metal-binding LHRH analogues. This work showcased the ability of the dual divergent …

Crystallization And Preliminary X-Ray Crystallographic Analysis Of Ligand-Free And Arginine-Bound Forms Of Thermotoga Maritima Arginine-Binding Protein, Alessia Ruggiero, Jonathan D. Dattelbaum, Anna Pennacchio, Luisa Iozzion, Maria Staiano, Matthew S. Luchansky, Bryan S. Der, Rita Berisio, Sabato D'Auria, Luigi Vitagliano

Chemistry Faculty Publications

The arginine-binding protein from Thermotoga maritima (TmArgBP) is an arginine-binding component of the ATP-binding cassette (ABC) transport system in this hyperthermophilic bacterium. This protein is endowed with an extraordinary stability towards thermal and chemical denaturation. Its structural characterization may provide useful insights for the clarification of structure– stability relationships and for the design of new biosensors. Crystallization trials were set up for both arginine-bound and ligand-free forms of TmArgBP and crystals suitable for crystallographic investigations were obtained for both forms. Ordered crystals of the arginine adduct of TmArgBP could only be obtained by using the detergent LDAO as an additive …

Dynamic Light Scattering And Zeta Potential Of Colloidal Mixtures Of Amelogenin And Hydroxyapatite In Calcium And Phosphate Rich Ionic Milieus, Vuk Uskoković, Roselyn Odsinada, Sonia Djordjevic, Stefan Habelitz

Pharmacy Faculty Articles and Research

The concept of zeta-potential has been used for more than a century as a basic parameter in controlling the stability of colloidal suspensions, irrespective of the nature of their particulate ingredients – organic or inorganic. There are prospects that self-assembly of peptide species and the protein-mineral interactions related to biomineralization may be controlled using this fundamental physicochemical parameter. In this study, we have analyzed the particle size and zeta-potential of the full-length recombinant human amelogenin (rH174), the main protein of the developing enamel matrix, in the presence of calcium and phosphate ions and hydroxyapatite (HAP) particles. As calcium and phosphate …

Optimization And Validation Of Direct Analysis In Real Time Mass Spectrometry (Dart-Ms) For Quantitation Of Sugars To Advance Biofuel Production, Daudi Sayialel Saang'onyo

Online Theses and Dissertations

A direct analysis in real time mass spectrometry method was developed and validated for the analysis and quantitation of sugars that would be generated from pretreated and hydrolyzed switchgrass. This research aspect can be divided into two sections:

i) Literature Review: A review is presented on the status of energy security and how biomass and biofuels can be utilized as a source of transportation fuel. To this end, biomass (specifically switchgrass) can be broken down by pretreatment methods and then enzymatically hydrolyzed to simple sugars. These sugars can assist with algae growth that can eventually be converted into biofuels. …

Capillary Electrophoresis Separation Of Neutral Organic Compounds, Pharmaceutical Drugs, Enantiomers And Anions, Qing Feng

Chemistry & Biochemistry Theses - Archive

The focus of this thesis is on using capillary electrophoresis (CE) with on-column UV detection in achiral and chiral separations. Chapter 1 provides a brief introduction to the principle, mechanism, meaning and application of the CE method. Chapter 2 presents the CE separation of multivalent anions by using di- and tetracationic ion pairing reagents. Two newly developed UV transparent phosphonium-based cationic reagents were evaluated as additivesto the background electrolyte of CE for the separation of multiply charged anions, including several complex anions. These cationic reagents showed moderate suppression of the electroosmotic flow (EOF), interacted with the analytes to improve their …

Synthesis And Evaluation Of Multicationic Ionic Liquids As Gas Chromatographic Stationary Phases And Synthetic Polymers As Chiral Hplc Stationary Phases, Tharanga Payagala

Chemistry & Biochemistry Dissertations - Archive

Due to the characteristics unique to ionic liquids (ILs), they are found in a plethora of applications from simple liquid-liquid extractions to a proposed liquid medium for a lunar telescope. These applications require a thorough knowledge of the physical and chemical properties of ionic liquids and the knowledge to tune the structure to obtain the desired properties. In my dissertation I have described the systematical design and synthesis of a large number of dicationic, trigonal tricationic and linear tricationic ionic liquids. Their physicochemical properties are characterized and the structural variations attributing to the properties such as melting point, thermal stability, …

Synthesis, Co-Polymerisation And Electrochemical Evaluation Of Novel Ferrocene-Pyrrole Derivatives, Mary Deasy, Eithne Dempsey, Geok Hong Soon, Oliver Worsfold

Articles

New ferrocene derivatives, ((4-(1H-pyrrol-1-yl)phenoxy)carbonyl) ferrocene (4) and (6-(4-(1H-pyrrol-1-yl)phenoxy)hexyl) ferrocene (7) were synthesised, characterised and electrochemically evaluated as redox active films formed via anodic oxidation with pyrrole. Thin film studies were conducted and films formed from both compounds resulted in a stable Fe ^II/III redox couple with E^o = 0.04V and 0.36V vs. Ag/Ag⁺ for (7) and (4) respectively. Both potential sweeping and chronocoulometry were employed for film formation with the former resulting in controllable, reproducible film deposition. Growth conditions and solution concentrations were varied in the case of both compounds in order to assess …

Depositional Ice Nucleation Onto Hydrated Nacl Particles: A New Mechanism For Ice Formation In The Troposphere, M. E. Wise, K. J. Baustian, T. Koop, M. A. Freedman, E. J. Jensen, M. A. Tolbert

CUP Faculty Research

Sea-salt aerosol particles (SSA) are ubiquitous in the marine boundary layer and over coastal areas. Therefore SSA have ability to directly and indirectly affect the Earth’s radiation balance. The influence SSA have on climate is related to their water uptake and ice nucleation characteristics. In this study, optical microscopy coupled with Raman spectroscopy was used to detect the formation of an NaCl hydrate that could form under atmospheric conditions. NaCl_(s) particles deliquesced at the well established value of 75.7±2.5% RH. NaCl_(aq) particles effloresced to a mixture of hydrated and non-hydrated particles at temperatures between 236 and 252 K. …

Insulin Based Analogs Hlvealylv And Lvealylv To Inhibit The Formation Of Amyloid Fibrils In Beta Cells, Balakrishna Kurva

Master's Theses and Doctoral Dissertations

Human islet amyloid polypetide (hIAPP) is a 37 amino acid peptide, co-secreted along with insulin in the islets of Langerhans of pancreatic beta cells. Aggregation of hIAPP fibrils is believed to be toxic to beta cells and responsible for beta cell dysfunction and death associated with type 2 diabetes. Insulin has been found to act against the actions of hIAPP. The internal sequence of insulin, HLVEALYLV, recognizes and binds the 10-19 region of hIAPP. Since insulin reportedly blocks the formation of amyloid fibers, insulin analogs may protect cell membranes from damage. In an effort to study this effect, truncated analogs …

Insulin Based Inhibitors Of Human Islet Amyloid Polypeptide (Hiapp) And Their Effect On Aggregation Of Hiapp In The Treatment Of Type Ii Diabetes, Ranadheer R. Pesaru

Master's Theses and Doctoral Dissertations

Human islet amyloid polypeptide protein (hIAPP) is secreted by the pancreas along with insulin and is assumed to play a role in pathological development of type II diabetes. It has 37 amino acids in its sequence. Amyloid is formed due to misfolding of the protein, which is cytotoxic to beta cells in the pancreas of type II diabetic patients. The presence of amyloid deposits is also a characteristic feature of a number of other diseases like Alzheimer’s disease and Parkinson’s disease. Since insulin has been reported to interact with hIAPP and block amyloid formation, fragments of insulin were synthesized and …

Characterizing The Oligomeric Structure And Catalytic Activity Of The Dihydroorotase And Aspartate Transcarbamoylase From The Bacterium, Bacillus Anthracis, Reshma Kankanala

Master's Theses and Doctoral Dissertations

Bacteremia refers to bacterial presence in the blood. Bacterial proliferation in the blood requires that the organism adapt its metabolism to available nutrients. Nucleotide precursors that could be used are present at low levels in the blood, and thus the invading bacteria must rely on de novo nucleotide biosynthesis for survival. The dihydroorotase domain is a key enzyme in pyrimidine biosynthesis and a promising drug target. The genes encoding the dihydroorotase (DHOase) and aspartate transcarbamoylase (ATCase) of Bacillus anthracis (B. anthracis) were cloned for expression in Escherichia coli (E. coli). The proteins were purified by affinity …

Investigation Of Synthetic Methods For Preparation Of 2O-Amino Derivatives Of 5-Amino- 1, 10-Phenanthroline: Applications To Cu+2 Based Impedance Sensors, Satish B. Chunchu

Master's Theses and Doctoral Dissertations

The main purpose of this project is to synthesize 2^o - derivatives of 5-amino-1, 10- phenanthroline (5-aphen) for application as self-assembled monolayers on gold interdigitated electrode array chips in standard impedance and impedance resonance-based Cu²⁺ sensors. Potential applications include monitoring Cu²⁺ leaching from anti-fouling coatings on ship hulls. The importance of the planned secondary alkyl amino derivatives will be to test their binding properties to the gold surface through dithiocarbamate linkages by monitoring the IDE impedance signal. Practical sensor development requires good impedance response, maximum binding to the gold IDE chip, and maximum long term stability of …

Investigation Of Occurrence, Elimination And Degradation Of Pharmaceutical And Personal Care Products In Drinking Water Using Liquid Chromatography-Tandem Mass Spectrometry, Chuan Wang

Doctoral Dissertations

"Pharmaceutical and personal care products have benefited humans and animals around the world. However, their presence in natural and treated water system as emerging contaminates may have potentially adverse effects on the aquatic environment and cause development of bacterial resistance. In this research project, a comprehensive liquid chromatography tandem mass spectrometry method has been developed and validated for the analysis of sixteen pharmaceutical compounds using solid phase extraction. Treated and untreated water samples collected across Missouri from water treatment facilities were analyzed to access the distribution of sixteen pharmaceutical compounds in both winter and summer seasons. The results of the …

The Importance Of Hydrogen Bonds In Dna, Ashley Mcentire

Natural Sciences Student Research Presentations

No abstract provided.

The Promising Future Of Dendrimers, Jaimie Sanders

Natural Sciences Student Research Presentations

No abstract provided.

Agriculture's Fascination With Fermentation, Micah Zehr

Natural Sciences Student Research Presentations

No abstract provided.

Electrochemical Fuel Cell Detectors: Not Just Another Battery, Somer Andries

Natural Sciences Student Research Presentations

No abstract provided.