Other Chemistry Commons^™

Ccpa Regulates Arginine Biosynthesis In Staphylococcus Aureus Through Repression Of Proline Catabolism, Austin S. Nuxoll, Steven M. Halouska, Marat R. Sadykov, Mark L. Hanke, Kenneth W. Bayles, Tammy Kielian, Robert Powers, Paul D. Fey

Department of Chemistry: Faculty Publications

Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, …

Unraveling The Structural Complexity In A Single-Stranded Rna Tail: Implications For Efficient Ligand Binding In The Prequeuosine Riboswitch, Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks Iii, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an …

Crystalline Nano Structures, Barry Chin Li Cheung, Joseph Reese Brewer, Nirmalendu Deo

Department of Chemistry: Faculty Publications

The present invention comprises nano obelisks and nanostructures and methods and processes for same. The nano obelisks of the present invention are advantageous structures for use as electron source emitters. For example, the ultra sharp obelisks can be used as an emitter source to generate highly coherent and high energy electrons with high current.

Biosynthesis Of Marineosin, A Spiroaminal Undecylprodiginine Natural Product, Shaimaa Mohamed Salem

Dissertations and Theses

Marineosins A and B are two spiroaminal-ring containing tripyrrole compounds isolated from the marine actinomycete, Streptomyces CNQ-617, and were found to possess potent and selective cytotoxic activity against leukemia and melanoma. Marineosins belong to the prodiginines class of natural products, examples of which are undecylprodiginine and streptorubin B. Unlike marineosins, prodiginines structures are characterized by the presence of fully conjugated tripyrrole nucleus linked to an alkyl chain (that lacks any oxygen). Cyclic prodiginines arise from an oxidative cyclization of the alkyl chain onto the tripyrrole, a step catalyzed by Rieske-oxygenase like enzymes such as RedG. The biosynthesis of prodiginines is …

Understanding The Emission From Semiconductor Nanoparticles, Beth Ann Manhat

Dissertations and Theses

This dissertation describes the synthesis and characterization of fluorescent semiconductor nanoparticles (NPs) in order to optimize their biomedical utility for imaging and sensing applications. While both direct and indirect bandgap semiconductor NPs have been studied, control over their emission properties vary. Quantum confinement (QC), which primarily controls the emission wavelength of nanosized semiconductors, dictates that as the size of semiconductor NPs decrease, the magnitude of the bandgap increases, resulting in changes in the observed emission wavelength: smaller NPs have a larger bandgap, and thus a bluer emission. However, surface, interfacial, or shell defects can act as non-radiative or radiative recombination …

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …

Use And Development Of Computational Tools In Drug Discovery: From Small Molecules To Cyclic Peptides, Daniel Navarrete Santiago

USF Tampa Graduate Theses and Dissertations

The scope of this work focuses on computationally modeling compounds with protein structures. While the impetus of drug discovery is the innovation of new therapeutic molecules, it also involves distinguishing molecules that would not be an effective drug. This can be achieved by inventing new tools or by refining old tools. Virtual screening (VS, also called docking), the computational modeling of a molecule in a receptor structure, is a staple in predicting a molecule's affinity for an intended target. In our Virtual Target Screening system (also called inverse-docking), VS is used to find high-affinity targets, which can potentially explain absorption, …

The Tetrafluoroborate Salt Of 4-Methoxybenzyl N-2-(Dimethylamino)Ethyl-N-Nitrosocarbamate: Synthesis, Crystal Structure And Dft Calculations, Helene Hedian, Vladimir Benin

Chemistry Faculty Publications

The tetrafluoroborate salt of 4-methoxybenzyl N-2-(dimethylamino)ethyl-N-nitrosocarbamate was prepared in two steps, via the corresponding carbamate. Its crystal structure is monoclinic, space group P21/c. The unit cell dimensions are: a = 19.499(8) Å, b = 5.877(3) Å, c = 15.757(7) Å, α = 90°, β = 110.019(7)°, γ = 90°, V = 1696.5(12) Å3, Z = 4. The structure exhibits an unexpected, pseudo-gauche conformation with respect to the C2–C3 bond, due to a stabilizing hydrogen bond between the carbonyl oxygen (O1) and the hydrogen atom at the trialkylammonium center (H3n), with a distance between them of …

A Modified Surface On Titanium Deposited By A Blasting Process, Caroline O' Sullivan, Peter O'Hare, Greg Byrne, Liam O'Neill, Katie B. Ryan, Abina M. Crean

Publications

Abstract

: Hydroxyapatite (HA) coating of hard tissue implants is widely employed for its biocompatible and osteoconductive properties as well as its improved mechanical properties. Plasma technology is the principal deposition process for coating HA on bioactive metals for this application. However, thermal decomposition of HA can occur during the plasma deposition process, resulting in coating variability in terms of purity, uniformity and crystallinity, which can lead to implant failure caused by aseptic loosening. In this study, CoBlast™, a novel blasting process has been used to successfully modify a titanium (V) substrate with a HA treatment using a dopant/abrasive regime. …

Application Of Raman Spectroscopy To Lubricants, Lubricated Surfaces And Lubrication Phenomena, David W. Johnson

Chemistry Faculty Publications

Recent advances in lasers and detector technologies and the development of low-cost instruments and fiber-optic probes have brought about an explosion in the lubrication systems being studied by Raman spectroscopy. This article provides examples of the use of Raman spectroscopy in the study of lubrication phenomena, including the characterization of liquid lubricants, lubricant additives, and solid lubricants; the study of vapor-phase lubrication; and the use of coated nanoparticles as lubricants.

Using Nanotechnology To Detect Nerve Agents, Mark N. Goltz, Dong-Shik Kim, Leeann Racz

Faculty Publications

Nanotechnology has opened a wide range of opportunities having potential impacts in areas as diverse as medicine and consumer products. In collaboration with researchers at the University of Toledo UT, Air Force Institute of Technology AFIT scientists are exploring the possibility of using a nanoscale organic matrix to detect organophosphate OP nerve agents. Current techniques for detecting OP compounds are expensive and time consuming. Developing a nanoscale organic matrix sensor would allow for direct, real-time sensing under field conditions. This article describes the science behind such a sensor and its possible applications. High-performance sensors are needed to protect Soldiers and …

Communication: Bubbles, Crystals, And Laser-Induced Nucleation, Brandon C. Knott, Jerry L. Larue, Alec M. Wodtke, Michael F. Doherty, Baron Peters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Short intense laser pulses of visible and infrared light can dramatically accelerate crystal nucleation from transparent solutions; previous studies invoke mechanisms that are only applicable for nucleation of ordered phases or high dielectric phases. However, we show that similar laser pulses induce CO₂bubblenucleation in carbonated water. Additionally, in water that is cosupersaturated with argon and glycine, argon bubbles escaping from the water can induce crystal nucleation without a laser. Our findings suggest a possible link between laser-induced nucleation of bubbles and crystals.

Quantum Dot Biofunctionalization, Nathaniel J. Miska

Renée Crown University Honors Thesis Projects - All

We have shown the efficacy of Quantum Dots (qdots), nano-scale fluorescent particles made of semi-conductive material, as versatile biologically functional research tools. This functionality depends upon a series of chemical transformations that produce stable, aqueous, biomolecule-bound qdots with high quantum yield. We utilize the metal binding and chelating properties of the amino acid histidine to displace hydrophobic surface ligands and to phase-transfer qdots from organic to aqueous media. The intermediate binding strength of histidine to qdot surface facilitates its exchange with a variety of strongly binding thiolated biomolecules. Ligand profiles are subsequently characterized via FTIR, NMR, and gel electrophoresis. Negatively-charged …

A Sodium Salt Of The Dimer Of Boronoterephthalic Acid Anhydride, Scott Simmons, Albert Fratini, Vladimir Benin

Chemistry Faculty Publications

The title compound, sodium bis­(6-carb­oxy-1-hy­droxy-3-oxo-1,3-dihydro-2,1-benzoxaborol-1-yl)oxidanium, Na+·C16H15B2O13-, was prepared in two steps from 2-bromo-p-xylene. Its crystal structure was determined at 140 K and has triclinic (P) symmetry. The compound presents a unique structural motif, including two units of the cyclic anhydride of boronoterephthalic acid, joined by a protonated, and thereby trivalent, oxonium center. Association in the crystal is realized by complementary hydrogen bonding of the carboxyl groups, as well as by coordination of the sodium cations to the oxygen centers on the five-membered rings.

Theoretical Investigation Of A Reported Antibiotic From The 'Miracle Tree' Moringa Oleifera, Michael Horwath, Vladimir Benin

Chemistry Faculty Publications

Moringa oleifera, sometimes called the “Miracle Tree,” has received international attention for its potential to improve health in impoverished tropical areas. In addition to high vitamin content in the leaves and pods, the tree contains compounds with antioxidant and antibacterial properties. This study focused on the theoretical investigation of the suggested structure of one antibacterial compound, “pterygospermin,” whose existence was proposed after some studies of the roots of M. oleifera. The structure of pterygospermin was first proposed by a research group working in the 1950s, but later studies have not found evidence of this compound and have instead …

A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers

Faculty Publications, Chemistry

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …

Structure Function Analysis Of An Adp-Ribosyltransferase Type Iii Effector And Its Rna-Binding Target In Plant Immunity, Byeong-Ryool Jeong, Yan Lin, Anna Joe, Ming Guo, Christin Korneli, Huirong Yang, Ping Wang, Min Yu, Ronald Cerny, Dorothee Staiger, James R. Alfano, Yanhui Xu

Ronald Cerny Publications

Background: HopU1 ADP-ribosylates GRP7, suppressing plant immunity.

Results: The HopU1 structure has two novel loops required for GRP7 recognition, and HopU1 ribosylates GRP7 at an arginine in position 49 disrupting its function.

Conclusion: HopU1 targets a conserved arginine in GRP7, disabling its ability to bind immunity-related RNA.

Significance: The mechanistic details of how HopU1 recognizes its substrate reveal how HopU1 contributes to pathogenesis.

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 …

The Impact Of Driving Conditions On Phev Battery Performance, Nathan Christensen, John Patten, Steven Srivastava, Gary P. Nola

Green Manufacturing Research Journal

The battery performance of a modified Prius with a 5 kWh plug-in battery was documented for a year to determine the impact of environmental conditions and user attributes on vehicle performance.  Both fuel economy and pure electrical efficiency were compared to ambient temperature.  The fuel economy has a positive relationship with ambient temperature until approximately 70˚F where the efficiency begins to drop.  Electrical performance has a positive linear relationship with ambient temperature.  With the emergence of electric vehicles (EVs) and PHEVs from a variety of automotive manufacturers, information on EV and PHEV performance for consumers will become more important.

Crystallisation And Phase Transition Characteristics Of Sol-Gel-Synthesized Zinc Titanates, Suresh Pillai, Michael Seery, Nicholas Nolan

Articles

No abstract provided.