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Unusual Acylation Of Chloramphenicol In Lysobacter Enzymogenes, A Biocontrol Agent With Intrinsic Resistance To Multiple Antibiotics, Wei Zhang, Justin Huffman, Shengying Li, Yuemao Shen, Liangcheng Du

Liangcheng Du Publications

Background: The environmental gliding bacteria Lysobacter are emerging as a new group of biocontrol agents due to their prolific production of lytic enzymes and potent antibiotic natural products. These bacteria are intrinsically resistant to many antibiotics, but the mechanisms behind the antibiotic resistance have not been investigated.

Results: Previously, we have used chloramphenicol acetyltransferase gene (cat) as a selection marker in genetic manipulation of natural product biosynthetic genes in Lysobacter, because chloramphenicol is one of the two common antibiotics that Lysobacter are susceptible to. Here, we found L. enzymogenes, the most studied species of this genus, could …

A Redox-Neutral Catechol Synthesis, Q. Wu, D. Yan, Y. Chen, T. Wang, F. Xiong, W. Wei, Y. Lu, W. Sun, Jie Jack Li, J. Zhao

Chemistry Faculty Publications

Ubiquitous tyrosinase catalyses the aerobic oxidation of phenols to catechols through the binuclear copper centres. Here, inspired by the Fischer indole synthesis, we report an iridium-catalysed tyrosinase-like approach to catechols, employing an oxyacetamide-directed C–H hydroxylation on phenols. This method achieves one-step, redox-neutral synthesis of catechols with diverse substituent groups under mild conditions. Mechanistic studies confirm that the directing group (DG) oxyacetamide acts as the oxygen source. This strategy has been applied to the synthesis of different important catechols with fluorescent property and bioactivity from the corresponding phenols. Finally, our method also provides a convenient route to ¹⁸O-labelled catechols using …

Special Topic 3, Part 1: Pesticides: Natural And Manmade Pesticides, Gordon Gribble

Chemistry 52, Gordon Gribble lectures on Special Topics

No abstract provided.

Synthesis And Reactivity Of Sydnone Derived 1,3,4-Oxadiazol-2(3h)-Ones, Jonathan Michael Tumey

Browse all Theses and Dissertations

5-(Bromomethyl)- and 5-(trichloromethyl)-3-phenyl-1,3,4-oxadiazol-2(3H)-ones were synthesized from bromocarbonyl hydrazine intermediate salts and acid halides to provide further evidence for our proposed mechanism for the formation of oxadiazolone ring systems from sydnones. 5-(Bromomethyl)-3-phenyl-1,3,4-oxadiazol-2(3H)-one was a compound of interest due to its SN2 possibilities and three potential sites of diversification. The procedure to synthesize 5-(bromomethyl)-3-phenyl-1,3,4-oxadiazol-2(3H)-one was developed originally by Madaram in the Turnbull lab, but was further optimized in the present work by altering the time, temperature and stoichiometric equivalents of the acid halide to provide high purity and excellent yields of the product. While this compound of interest had been isolated and …

Flipped Learning In Synchronously-Delivered, Geographically-Dispersed General Chemistry Classrooms, Michael A. Christiansen, Louis Nadelson, Lianna K. Etchberger, Marilyn M. Cuch, Trish A. Kingsford, Leslie O. Woodward

Chemistry and Biochemistry Faculty Publications

In synchronously-delivered, multi-site classrooms, the physical separation between distance students and instructors may create a perceived divide that negatively affects learning. Building on prior experience in flipping organic chemistry in single-site face-to-face (F2F) classes, we decided to extend our approach to multi-site, synchronously-delivered general chemistry courses. Our thought was to narrow the perceived instructor-student divide in distance teaching by using the flexible in-class time that flipping affords to increase the number of positive teacher/distance-student interactions. In this effort, we gradually developed a technique called “bridging questions,” through which the instructor becomes more familiar with student interests and then connects those …

Quantification Of Airborne Fungal Spores Comparing Molecular Tracers Via Ion Chromatography And Uv-Lif Methods, Marie Ila Gosselin

Electronic Theses and Dissertations

Fungal spores represent an understudied subcategory of bioaerosols that can impact human health as pathogenic and allergenic particles. Fungal spores also have been shown to act as effective ice nuclei and giant cloud condensation nuclei in some cases. This has implications on the hydrological cycle on local and regional scales by impacting the formation and evolution of clouds and precipitation. The quantification of fungal spores has been limited in the past due to methods that were costly and that suffered from poor time resolution. The most commonly applied methods for airborne fungal spore analysis have traditionally included microscopy and culturing, …

Mechanistic Insights Into The Radical S-Adenosyl L-Methionine Enzyme Mftc, Bulat Khaliullin

Electronic Theses and Dissertations

Mycofactocin is a putative peptide-derived redox cofactor in Mycobacterium family. Its putative biosynthetic pathway is encoded by the operon mftABCDEF. The initial step of this pathway is a posttranslational modification of a peptide precursor MftA, which is catalyzed by MftC enzyme. This modification only occurs in the presence of chaperone MftB. Here, we demonstrate that MftC is a radical S-adenosyl L-methionine (SAM) enzyme and we examine its catalytic mechanism. We show that the modification of MftA requires two equivalents of SAM and is implemented in two steps: (i) the decarboxylation of a C-terminal tyrosine, resulting in formation of an …

A Bioinspired And Biocompatible Ortho-Sulfiliminyl Phenol Synthesis, Feng Xiong, Liang Lu, Tian-Yu Sun, Qian Wu, Dingyuan Yan, Ying Chen, Xinhao Zhang, Wei Wei, Yi Lu, Wei-Yin Sun, Jie Jack Li, Jing Zhao

Chemistry Faculty Publications

Synthetic methods inspired by Nature often offer unique advantages including mild conditions and biocompatibility with aqueous media. Inspired by an ergothioneine biosynthesis protein EgtB, a mononuclear non-haem iron enzyme capable of catalysing the C–S bond formation and sulfoxidation, herein, we discovered a mild and metal-free C–H sulfenylation/intramolecular rearrangement cascade reaction employing an internally oxidizing O–N bond as a directing group. Our strategy accommodates a variety of oxyamines with good site selectivity and intrinsic oxidative properties. Combining an O–N bond with an X–S bond generates a C–S bond and an S¼N bond rapidly. The newly discovered cascade reaction showed excellent chemoselectivity …

Paper-Based Diagnostic Devices, Spencer A. Schultz, Isabelle C. Noxon, Tyler A. Sisley, Andres W. Martinez

Chemistry and Biochemistry

This chapter will provide an overview of existing diagnostic devices made primarily out of paper and then focus on paper-based microfluidic devices, the next generation of paper-based diagnostic devices that promises to extend the use of paper as a material for fabricating diagnostic devices well into the future.

Chapter Contents:

• 2.1 Introduction
• 2.2 Current paper-based diagnostic devices
• 2.2.1 Dipstick devices
• 2.2.2 Lateral-flow devices
• 2.2.2.1 Vertical-flow devices
• 2.2.3 Paper-based arrays
• 2.3 Paper-based microfluidic devices
• 2.3.1 Fabrication of paper-based microfluidic devices
• 2.3.2 Applications of paper-based microfluidic devices
• 2.4 Conclusions
• References

Chemical Applications In Techniques Of Emerging Significance: Nanoparticle Transformation In Mitochondria And Relative Tautomer Populations In Cellular Automata, Gregory Arland Bowers

Browse all Theses and Dissertations

Two techniques of emerging importance were used to study different biochemical phenomena: the fate of silver nanoparticles in Vero 76 African green monkey kidney cell mitochondria, and the effect of pH on tautomer ratios using cellular automata. In the first area of research Vero 76 Africa green monkey kidney cells were incubated with silver nanoparticles (AgNP) and ionic silver (Ag+). After 24 hours the cell mitochondria were harvested, then processed with CPE-TFF and ICP-OES. The initial AgNP incubation formed 52.9% ± 15.5% AgNP and 29.9% ± 4.0% Ag+, while the ionic silver incubation formed 9.5% ± 0.9% AgNP and 60.6% …

Mechanochemical Synthesis Of Fuels From Sustainable Sources Utilizing Solid Catalysts, Jacob Todd

Electronic Theses and Dissertations

Mechanochemistry requires less solvents which results in less waste generation. The question becomes can we apply mechanochemistry to current chemical reactions and reduce the generation of waste. This process can be simple or can be very extensive resulting in the generation of large amounts of waste and very little product. A significant advantage of mechanochemistry is the reduced need for solvents that would be common place for reactions. Mechanochemistry transfers energy to reagents via impacts from milling media. Energy can be transferred to the reagents no matter their state-of-matter. Much of the current studies in mechanochemistry today are done using …

Relative Properties And Relative Potency Of Various Hydrazide Compounds That Inhibit Growth Of Mycobacterium Tuberculosis, Ronald Bartzatt

Chemistry Faculty Publications

The molecular properties of compounds expressing growth inhibition of Mycobacterium tuberculosis are determined and examined for underlying relationships by pattern recognition methods. Pattern recognition methods such as hierarchical cluster analysis will show relationships between compounds. Descriptive statistical analysis of molecular properties reveal commonality among bacteriostatic compounds. Outliers within any category of descriptor is identified by Grubb’s test. Potency of growth inhibition measured as MIC (minimum inhibitory concentration) after in vitro evaluation will be compared and analyzed. Structure moieties and their effect on activity is identified. All compounds analyzed showed substantial growth inhibition of Mycobacterium tuberculosis, having MIC values ranging from …

Mass Loading And Removal Of Pharmaceuticals And Personal Care Products Including Psychoactives, Antihypertensives, And Antibiotics In Two Sewage Treatment Plants In Southern India, Bikram Subedi, Keshava Balakrishna, Derrick Ian Joshua, Kurunthachalam Kannan

Faculty & Staff Research and Creative Activity

Environmental contamination by pharmaceuticals and personal care products (PPCPs) is barely studied in India despite being one of the largest global producers and consumers of pharmaceuticals. In this study, 29 pharmaceuticals and six metabolites were determined in sewage treatment plants (STPs) in Udupi (STP_U: population served ~150,000) and Mangalore (STP_M: population served ~450,000); the measured mean concentrations ranged from 12 to 61,000 ng/L and 5.0 to 31,000 ng/L, respectively. Atorvastatin (the most prescribed antihypercholesterolemic in India), mefenamic acid, and paraxanthine were found for the first time in wastewater in India at the mean concentrations of 395 …

Fluorogenic Protein Labeling Using A Genetically Encoded Unstrained Alkene, Xin Shang, X. Song, C. Faller, R. Lai, H. Li, R. Cerny, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.

Isotopes And Horses, Evyjo M. Compton

Natural Sciences Student Research Presentations

This presentation for the Natural Sciences Poster Session at Parkland College defines isotopes and summarizes an experiment conducted on a modern horse to examine the seasonal shifts of trace elements by measuring the oxygen and carbon isotopes in tooth enamel.

Airborne Measurements Of Western U.S. Wildfire Emissions: Comparison With Prescribed Burning And Air Quality Implications, Xiaoxi Liu, L. Gregory Huey, Robert J. Yokelson, Vanessa Selimovic, Isobel J. Simpson, Markus Müller, Jose L. Jimenez, Pedro Campuzano-Jost, Andreas J. Beyersdorf, Donald R. Blake, Zachary Butterfield, Yonghoon Choi, John D. Crounse, Douglas A. Day, Glenn S. Diskin, Manvendra K. Dubey, Edward Fortner, Thomas F. Hanisco, Weiwei Hu, Laura E. King, Lawrence Kleinman, Simone Meinardi, Tomas Mikoviny, Timothy B. Onasch, Brett B. Palm, Jeff Peischl, Ilana B. Pollack, Thomas B. Ryerson, Glen W. Sachse, Arthur J. Sedlacek, John E. Shilling, Stephen Springston, Jason M. St. Clair

Chemistry and Biochemistry Faculty Publications

Wildfires emit significant amounts of pollutants that degrade air quality. Plumes from three wildfires in the western U.S. were measured from aircraft during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Biomass Burning Observation Project (BBOP), both in summer 2013. This study reports an extensive set of emission factors (EFs) for over 80 gases and 5 components of submicron particulate matter (PM1) from these temperate wildfires. These include rarely, or never before, measured oxygenated volatile organic compounds and multifunctional organic nitrates. The observed EFs are compared with previous measurements of temperate …

A Dual-Chamber Method For Quantifying The Effects Of Atmospheric Perturbations On Secondary Organic Aerosol Formation From Biomass Burning Emissions, Daniel S. Tkacik, Ellis S. Robinson, Adam Ahern, Rawad Saleh, Chelsea Stockwell, Patrick Veres, Isobel J. Simpson, Simone Meinardi, Donald R. Blake, Robert J. Yokelson, Albert A. Presto, Ryan C. Sullivan, Neil M. Donahue, Allen L. Robinson

Chemistry and Biochemistry Faculty Publications

Biomass burning (BB) is a major source of atmospheric pollutants. Field and laboratory studies indicate that secondary organic aerosol (SOA) formation from BB emissions is highly variable. We investigated sources of this variability using a novel dual-smog-chamber method that directly compares the SOA formation from the same BB emissions under two different atmospheric conditions. During each experiment, we filled two identical Teflon smog chambers simultaneously with BB emissions from the same fire. We then perturbed the smoke with UV lights, UV lights plus nitrous acid (HONO), or dark ozone in one or both chambers. These perturbations caused SOA formation in …

In Situ Measurements Of Water Uptake By Black Carbon-Containing Aerosol In Wildfire Plumes, Anne E. Perring, Joshua P. Schwarz, Milos Z. Markovic, David W. Fahey, Jose L. Jimenez, Pedro Campuzano-Jost, Brett D. Palm, Armin Wisthaler, Tomas Mikoviny, Glenn Diskin, Glen Sachse, Luke Ziemba, Bruce Anderson, Taylor Shingler, Ewan Crosbie, Armin Sorooshian, Robert Yokelson, Ru Shan Gao

Chemistry and Biochemistry Faculty Publications

Water uptake by black carbon (BC)-containing aerosol was quantified in North American wildfire plumes of varying age (1 to ~40 h old) sampled during the SEAC4RS mission (2013). A Humidified Dual SP2 (HD-SP2) is used to optically size BC-containing particles under dry and humid conditions from which we extract the hygroscopicity parameter, κ, of materials internally mixed with BC. Instrumental variability and the uncertainty of the technique are briefly discussed. An ensemble average κ of 0.04 is found for the set of plumes sampled, consistent with previous estimates of bulk aerosol hygroscopicity from biomass burning sources. The temporal evolution of …

The Periodical Winter 2017, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 4, issue 2 of the Periodical includes articles about the Chemistry Club's service activities, a student missions feature, student research at N.C. State, a pictorial directory of May 2017 graduates, and an alumni spotlight.

Using Nucleotide Analogs As Biochemical Probes To Evaluate The Mechanisms Involved In Translesion Replication By A High Fidelity Dna Polymerase, Anvesh Dasari

ETD Archive

Translesion DNA synthesis (TLS) allows DNA polymerases to incorporate nucleotides opposite and beyond damaged DNA. This activity is an important risk factor for the initiation and progression of genetic diseases including cancer. My study evaluates the ability of a high-fidelity DNA polymerase to perform TLS with 8-oxo-guanine, a pro-mutagenic DNA lesion formed by reactive oxygen species. Using modified purine and non-natural indole analogs as biochemical probes, I have evaluated the influence of desolvation, hydrogen bonding interactions, and shape complementarity towards nucleotide binding and incorporation opposite the miscoding lesion 8-oxo-guanine by the high fidelity gp43exo- DNA polymerase. In Chapter II, I …

Design, Synthesis And Biological Evaluation Of Histone Deacetylase (Hdac) Inhibitors: Saha (Vorinostat) Analogs And Biaryl Indolyl Benzamide Inhibitors Display Isoform Selectivity, Ahmed Negmeldin

Wayne State University Dissertations

HDAC proteins have emerged as interesting targets for anti-cancer drugs due to their involvement in cancers, as well as several other diseases. Several HDAC inhibitors have been approved by the FDA as anti-cancer drugs, including SAHA (suberoylanilide hydroxamic acid, Vorinostat). Unfortunately, SAHA inhibits most HDAC isoforms, which limit its use as a pharmacological tool and may lead to side effects in the clinic. In this work we were interested in developing isoform selective HDAC inhibitors, which may decrease or eliminate the side effects associated with non-selective inhibitors treatment. In addition, isoform selective HDAC inhibitors can be used as biological tools …

Development Of Chemical Tools To Investigate Protein S-Glutathionylation In Response To Metabolic Alteration, Kusal Theekshana Gayan Samarasinghe

Wayne State University Dissertations

Oxidative stress is a common characteristic of age-related diseases such as vascular diseases, diabetes and cancer. Many diseases are known to be regulated by glutathionylation. Glutathionylation is referred to as the formation of disulfide bond between a protein cysteine and a glutathione. To understand the molecular mechanisms behind the disease initiation and progression, identification of such glutathionylated proteins is important. Even though existing methods have been widely used, several limitations of these methods hinder the identification of such proteins in disease conditions. Therefore, we developed a versatile chemical method that generates clickable glutathione inside the cells. In this method, we …

Ligand Binding Studies Of A Peptide Targeting Helix 69 Of 23s Rrna In Bacterial Ribosomes, Hyosuk Seo

Wayne State University Dissertations

In the development of finding a peptide targeting H69 of 23S rRNA in bacterial ribosomes, phage display was employed at pH 5.5, a buffer condition previously reported of H69 preferring a closed conformation. After sequencing, several peptides were chosen through sequence alignment, followed by preparation using solid-phase peptide synthesis. The peptides were characterized using MALDI-TOF and purified with HPLC. A truncated peptide TARHIY was selected from FID assay. Through binding studies using ESI-MS, SPR, BLItz, and NMR, the binding properties of the peptide to H69 were determined, such as binding affinity, stoichiometry, and interaction site. The peptide exhibited moderate binding …

The Development Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog-Dependent Kinase-Catalyzed Phosphorylation, Dissanayaka Mudiyanselage Maheeka Madhubashini Embogama

Wayne State University Dissertations

Kinase-catalyzed phosphorylation plays an important role in cell physiology by regulating a myriad of cellular functions. Thus aberrant kinase activity is implicated in various diseases. Methods are needed to discover kinase substrates and map signaling pathways to explore biology and to help drug discovery. A few techniques are currently available to discover kinase substrate and map cell signaling. However, to augment kinase substrate discovery approaches, it is essential to develop alternative techniques. Pflum has recently discovered cosubstrate promiscuity of protein kinases with gamma-modified ATP analogs. Here, kinase-catalyzed biotinylation with ATP-biotin was used to develop novel tools to discover kinase substrates …

Gas-Phase Ion Spectroscopy Of Nucleobases And Mononucleotides: Models For Higher Order Nucleic Acids, Yuan-Wei Nei

Wayne State University Dissertations

Experiments examining the structures and stabilities of protonated and sodium cationized nucleobases, and deprotonated DNA and RNA mononucleotides are presented and discussed in this dissertation. These studies were carried out using the infrared multiple photon dissociation (IRMPD) action spectroscopy technique that utilizes a Fourier transform ion cyclotron mass spectrometer (FT-ICR MS) coupled to a free electron laser (FEL) located at the Radboud University Nijmegen. Ionic species of these biologically important complexes were generated using an electrospray ionization source and then mass isolated to have their infrared (IR) spectra measured by the experimental apparatus. Detailed analysis of the IR spectra measured …

Synthesis Of Netilmicin And Apramycin Derivatives For The Treatment Of Multidrug-Resistant Infectious Diseases, Amr Sayed Motawi Sonousi

Wayne State University Dissertations

The ever-growing bacterial resistance to existing antibiotics is alarming to humanity. Many researchers decided to revisit aminoglycosides with renewed emphasis on chemical modification as they have long been used as highly potent antibiotics for treating severe bacterial infections. The bactericidal effect of aminoglycosides is mainly due to protein synthesis inhibition by binding to the A-site of the bacterial ribosomes. However, the high potency and the broad spectrum of aminoglycosides has been outweighed by their side effects, especially ototoxicity, and by the resistance of pathogens. The goal of this research was the modification of existing aminoglycosides to develop derivatives which are …

Exploring Potential Energy Surfaces Of Chemical Reactions Using Electronic Structure Methods, Bishnu Thapa

Wayne State University Dissertations

This dissertation includes three topics: molecular dynamics in strong laser fields, pKa’s and redox potential calculations of bio–organic molecules, and oxidative damage of the nucleobases. Electronic structure calculations are used to provide a deeper understanding of experimental observations as well as to predict new results.

Chapters 2, 3 and 4 investigate the fragmentation and isomerization reactions of small monocations in the presence of strong laser fields. In the presence of intense laser pulses with 800 nm wavelengths, Born-Oppenheimer classical trajectory simulations were performed to investigate the dynamics of methanol monocation on the ground state potential energy surface (Chapter 2). With …

Classical And Quantum Mechanical Simulations Of Condensed Systems And Biomolecules, Hedieh Torabifard

Wayne State University Dissertations

This work describes the fundamental study of two enzymes of Fe(II)/-KG super family enzymes (TET2 and AlkB) by applying MD and QM/MM approaches, as well as the development of multipolar-polarizable force field (AMOEBA/GEM-DM) for condensed systems (ionic liquids and water).

TET2 catalytic activity has been studied extensively to identify the potential source of its substrate preference in three iterative oxidation steps. Our MD results along with some experimental data show that the wild type TET2 active site is shaped to enable higher order oxidation. We showed that the scaffold stablished by Y1902 and T1372 is required for iterative oxidation. The …

Exploration Of Nanomaterials-Based Electrochemical Sensors For Peroxynitrite Detection, Ousama Al-Mahmoud, Haitham Kalil

Undergraduate Research Posters 2017

Peroxynitrite (PON, ONOO-) plays an essential role in several cardiovascular dysfunctions and other diseases triggered by oxidative stress. The precise detection of this analyte in biological systems is of paramount importance not only to understand the genesis and development of diseases, but also to design and assess efficient therapies. We fabricated highly sensitive and selective electrochemical sensors based on transition metal-decorated graphene nanocomposites as catalytic interfaces for peroxynitrite quantification. The interfaces of metal-decorated graphene nanostructures were immobilized on carbon electrodes by electro-grafting, electro- depositing, and drop-casting techniques. The morphology and surface chemistry of the nanostructured materials were characterized using Scanning …

Fidelity Of Implementation: An Overlooked Yet Critical Construct To Establish Effectiveness Of Evidence-Based Instructional Practices, Marilyne Stains, Trisha Vickrey

Department of Chemistry: Faculty Publications

The discipline-based education research (DBER) community has been invested in the research and development of evidence-based instructional practices (EBIPs) for decades. Unfortunately, investigations of the impact of EBIPs on student outcomes typically do not characterize instructors’ adherence to an EBIP, often assuming that implementation was as intended by developers. The validity of such findings is compromised, since positive or negative outcomes can be incorrectly attributed to an EBIP when other factors impacting implementation are often present. This methodological flaw can be overcome by developing measures to determine the fidelity of implementation (FOI) of an intervention, a construct extensively studied in …