Digital Commons Network^™

Session C-1: Modeling Stem Activities Into Classroom Practice, Sowmya Anjur

Professional Learning Day

Students understand concepts better when they have had a chance to work hands on with relevant material. Examples will be presented from my classroom where difficult concepts have been modeled into simple experiments with considerable success in enhancing student understanding. Special focus will be given to selected topics that students seem to have the most difficulty grasping. The objective is to enable students to transfer their understanding to solve complex problems with considerable ease and apply their understanding to real world scenarios on assessments. Suggestions will also be provided for implementation of various concepts into the high school classroom.

Designing Proteins For Biomechanical And Molecular Biological Studies, Momoko Tajiri

TechTalks

Proteins are large biomolecules consisting one or more long chain of amino acid residues. Proteins perform a wide variety of functions within organisms including catalyzing metabolic activities, signal transduction, and transportation of molecules. They function differently from one another as their sequences of amino acids and also due to a variation of modification placed on residues. Change in modification patterns will impact protein interaction with other molecules, thus influence normal cell activities and may lead to disease development. In order to study the consequences of modification, we have a method to prepare proteins with desired modification patterns. Using the technique, …

Mechanism And Catalytic Strategy Of The Prokaryotic Specific Gtp Cyclohydrolase Ib, Naduni Paranagama, Shilah A. Bonnett, Jonathan Alvarez, Amit Luthra, Boguslaw Stec, Andrew Gustafson, Dirk Iwata-Reuyl, Manal A. Swairjo

Chemistry Faculty Publications and Presentations

GTP cyclohydrolase I catalyzes the first step in folic acid biosynthesis in bacteria and plants, biopterin biosynthesis in mammals, and the biosynthesis of 7-deazaguanosine modified tRNA nucleosides in bacteria and archaea. The type IB GTP cyclohydrolase (GCYH-IB) is a prokaryotic-specific enzyme found in a number of pathogens. GCYH-IB is structurally distinct from the canonical type IA GTP cyclohydrolase involved in biopterin biosynthesis in humans and animals, and thus is of interest as a potential antibacterial drug target. We report kinetic and inhibition data of Neisseria gonorrhoeae GCYH-IB, and two high-resolution crystal structures of the enzyme; one in complex with the …

Protection Of The Queuosine Biosynthesis Enzyme Quef From Irreversible Oxidation By A Conserved Intramolecular Disulfide, Adeba Mohammad, Adriana Bon Ramos, Bobby W.K. Lee, Spencer William Cohen, Maryam K. Kiani, Dirk Iwata-Reuyl, Boguslaw Stec, Manal A. Swairjo

Chemistry Faculty Publications and Presentations

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site. This structure is more symmetric than the substrate-bound structure and exhibits major rearrangement of …

An Investigation In The Performance Of Lithium Sulfur Battery With A Tic Coated Separator, Jian-Hua Fang, Yong Cao, Mao-Ping Yang, Ming-Sen Zheng, Quan-Feng Dong

Journal of Electrochemistry

To improve the specific capacity and cycle stability of lithium-sulfur (Li-S) battery, a TiC/Celgard coating separator was developed and its performance in Li-S battery was investigated. The electrochemical test results confirmed that the TiC coating layer could significantly increase the capacity and cycle stability. At a high rate of 2C, it still delivered the capacity of 650 mAh·g^-1. At 0.5C, the specific capacity was maintained at 841.3 mAh·g^-1 after 100 cycles.

Application Of Adamantane Schiff Base Nickel Complexes/Graphene Oxide/Glassy Carbon Modified Electrode In Detection Of Carmine, Peng Guo, Zheng Liu, Hai-Ying Li, Li-Ming Ma

Journal of Electrochemistry

The Schiff base nickel complexes/graphene oxide/glassy carbon electrodes were prepared by embedded method and electrodeposition on which were used to quantitatively detect the contents of carmine. Cyclic voltammetry, chronoamperometry, scanning electron microscopy (SEM) and other methods were employed to characterize properties and morphologies of the modified electrodes. The results show that the adamantane double Schiff base nickel complexes/graphene oxide/glassy carbon electrode had high electric catalytic activity toward carmine oxidation reaction, and might provide an easy and quick way to detect carmine content with good reproducibility.

Excited-State Dynamics Of The Thiopurine Prodrug 6-Thioguanine: Can N9-Glycosylation Affect Its Phototoxic Activity?, Brennan Ashwood, Carlos E. Crespo-Hernández

Faculty Scholarship

6-Thioguanine, an immunosuppressant and anticancer prodrug, has been shown to induce DNA damage and cell death following exposure to UVA radiation. Its metabolite, 6-thioguanosine, plays a major role in the prodrug's overall photoreactivity. However, 6-thioguanine itself has proven to be cytotoxic following UVA irradiation, warranting further investigation into its excited-state dynamics. In this contribution, the excited-state dynamics and photochemical properties of 6-thioguanine are studied in aqueous solution following UVA excitation at 345 nm in order to provide mechanistic insight regarding its photochemical reactivity and to scrutinize whether N9-glycosylation modulates its phototoxicity in solution. The experimental results are complemented with time-dependent …

Hydroalkynylation Of Oxocarbenium Intermediates Via Au(I) Catalysis, Courtney Smith Smith

USF Tampa Graduate Theses and Dissertations

Au(I) catalysis has recently emerged as a powerful tool for the realization of a broad range of organic transformations. Despite this rapid development, attaining selectivity and maintaining catalyst stability remain significant challenges. Rational ligand design, such as the employment of NHC or TA ligands, has been used to confront these issues. This thesis focuses on the use of Au(I) catalysts bearing these ligands for the selective hydroalkynylation of enol ethers. By employing a TA-Au stabilized catalyst, [(OAr)₃PAu(TA-H)]OTf, the intermolecular hydroalkynylation of enol ethers, a substrate that is well-known to promote decomposition of the gold cation, was efficiently achieved. …

Scitech News Volume 71, No. 1 (2017)

Sci-Tech News

Columns and Reports

• From the Editor 3

Division News

• Science-Technology Division 5
• Chemistry Division 8
• Engineering Division
• Aerospace Section of the Engineering Division 9
• Architecture, Building Engineering, Construction and Design Section of the Engineering Division 11

Reviews

• Sci-Tech Book News Reviews 12

Advertisements

• IEEE 4

Pd-Catalyzed Conversion Of Aryl Iodides To Sulfonyl Fluorides Using So2 Surrogate Dabso And Selectfluor, Nicholas Ball, Ariana L. Tribby, Ismerai Rodríguez, Shamira Shariffudin

Pomona Faculty Publications and Research

A one-pot Pd-catalyzed conversion of aryl iodide to aryl sulfonyl fluorides using DABSO and Selectfluor has been developed generating aryl sulfonyl fluorides in good to excellent yields. The reaction results in the generation of electronically and sterically diverse sulfonyl fluorides. Additionally, sulfonyl fluorides can be converted to aryl sulfonamides and sulfonic esters using Cs₂CO₃ under mild conditions.

Dual-Functional-Tag-Facilitated Protein Labeling And Immobilization, Xinyi Zhang, Wei Lu, Kevin Kwan, Dibakar Bhattacharyya, Yinan Wei

Chemistry Faculty Publications

An important strategy in the construction of biomimetic membranes and devices is to use natural proteins as the functional components for incorporation in a polymeric or nanocomposite matrix. Toward this goal, an important step is to immobilize proteins with high efficiency and precision without disrupting the protein function. Here, we developed a dual-functional tag containing histidine and the non-natural amino acid azidohomoalanine (AHA). AHA is metabolically incorporated into the protein, taking advantage of the Met-tRNA and Met-tRNA synthetase. Histidine in the tag can facilitate metal-affinity purification, whereas AHA can react with an alkyne-functionalized probe or surface via well-established click chemistry. …

Modeling Of S‐Nitrosothiol–Thiol Reactions Of Biological Significance: Hno Production By S‐Thiolation Requires A Proton Shuttle And Stabilization Of Polar Intermediates, Lena V. Ivanova, Daniel Cibich, Gregory Deye, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S‐thiolation reaction between thiols and S‐nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S‐thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge‐separated zwitterionic intermediate structure RSS⁺(R)N(H)O⁻ (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S−S …

Enzyme–Free Uric Acid Electrochemical Sensors Using Β–Cyclodextrin Modified Carboxylic Acid Functionalized Carbon Nanotubes, Mulugeta B. Wayu, Margaret A. Schwarzmann, Samuel D. Gillespie, Michael C. Leopold

Chemistry Faculty Publications

Carboxylic acid-functionalized multi-walled carbon nanotubes (COOH-MWCNT) were modified via ultrasonication with β-cyclodextrin (β-CD) to obtain a COOH-MWCNT:β-CD nanocomposite material for the purpose of developing an enzyme-free electrochemical sensor for uric acid—a clinically relevant molecule implemented in pregnancy-induced hypertension diagnosis. The nanocomposite material is deposited onto glassy carbon electrodes and subsequently capped with layers of Nafion and Hydrothane polyurethane. The surface morphology and electronic structure of the nanocomposite material were characterized using UV–Vis, TEM, and FTIR. The performance of the electrochemical sensor was measured through direct injection of UA during amperometry. With the high surface area of the COOH-MWCNT in concert …

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.

Strong Metal-Support Interactions: An Extra Layer Of Complexity, Bert D. Chandler

Chemistry Faculty Research

Strong interactions between oxide supports and catalytic metal particles can lead to inhibitive oxide layers forming over the active metal catalyst. Now, adsorbate-induced metal–support interactions have been shown to lead to a porous overlayer in the Rh/TiO₂ system that tunes catalyst activity, improving its selectivity for the partial reduction of CO₂.

Hmba Is A Putative Hsp70 Activator Stimulating Hexim1 Expression That Is Down-Regulated By Estrogen, Rati Lama, Chunfang Gan, Nethrie Idippily, Viharika Bobba, David Danielpour, Monica Montano, Bin Su Ph.D.

Chemistry Faculty Publications

Hexamethylene bis-acetamide inducible protein 1 (HEXIM1) is identified as a novel inhibitor of estrogen stimulated breast cell growth, and it suppresses estrogen receptor-a transcriptional activity. HEXIM1 protein level has been found to be downregulated by estrogens. Recently, HEXIM1 has been found to inhibit androgen receptor transcriptional activity as well. Researchers have used Hexamethylene bisacetamide (HMBA) for decades to stimulate HEXIM1 expression, which also inhibit estrogen stimulated breast cancer cell gene activation and androgen stimulated prostate cancer gene activation. However, the direct molecular targets of HMBA that modulate the induction of HEXIM1 expression in mammalian cells have not been identified. Based …

Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur

Dissertations, Theses, and Capstone Projects

Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 …

Iterative Non-Proteinogenic Residue Incorporation Yields Α/Β-Peptides With A Helix-Loop-Helix Tertiary Structure And High Affinity For Vegf, James W. Checco, Samuel H. Gellman

Department of Chemistry: Faculty Publications

Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (“α/β-peptides”) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix “mini-Z-domain” can be modified to contain β and other non-proteinogenic residues while retaining the target-binding epitope using iterative non-natural residue incorporation. …

Ozone Depletion, A Big Threat To Climate Change: What Can Be Done?, Sumera Aziz Ali, Savera Aziz Ali, Nadir Suhail

Community Health Sciences

Ozone in the stratosphere is very important as it acts as a safeguard for the earth and protects life from harmful ultraviolet radiations coming from the sun. Depletion of stratospheric ozone, resulting from atmospheric pollution has led to increased ultraviolet radiation at the earth’s surface as well as spectral shifts to the more biologically damaging shorter wavelengths. A decrease in the concentration of stratospheric ozone enhances the solar ultraviolet (UV) radiation, which is harmful to the growth of the plant and various other metabolic processes of the organisms and might cause changes in pigment concentrations, nucleic acids, and proteins. Multiple …

Multi-Instrument Comparison And Compilation Of Non-Methane Organic Gas Emissions From Biomass Burning And Implications For Smoke-Derived Secondary Organic Aerosol Precursors, Lindsay E. Hatch, Robert J. Yokelson, Chelsea E. Stockwell, Patrick R. Veres, Isobel J. Simpson, Donald R. Blake, John J. Orlando, Kelley C. Barsanti

Chemistry and Biochemistry Faculty Publications

Multiple trace-gas instruments were deployed during the fourth Fire Lab at Missoula Experiment (FLAME- 4), including the first application of proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOFMS) and comprehensive two-dimensional gas chromatography-time-offlight mass spectrometry (GC×GC-TOFMS) for laboratory biomass burning (BB) measurements. Open-path Fourier transform infrared spectroscopy (OP-FTIR) was also deployed, as well as whole-air sampling (WAS) with onedimensional gas chromatography-mass spectrometry (GCMS) analysis. This combination of instruments provided an unprecedented level of detection and chemical speciation. The chemical composition and emission factors (EFs) determined by these four analytical techniques were compared for four representative fuels. The results demonstrate that the instruments are …

Comparison Of Tetrel Bonds In Neutral And Protonated Complexes Of Pyridinetf3 And Furantf3 (T = C, Si, And Ge) With Nh3, Mingxiu Liu, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio calculations have been performed for the complexes H+–PyTX3⋯NH3 and H+–furanTF3⋯NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an F⋯H hydrogen bond to a C⋯N tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol−1. The tetrel bonding becomes stronger …

Evolution Of Complex Target Selex To Identify Aptamers Against Mammalian Cell-Surface Antigens, Prabodhika R. Mallikaratchy

Publications and Research

The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This …

Monofluorophosphate Blocks Internal Polysaccharide Synthesis In Streptococcus Mutans, Miguel Ballicora, Ana M. Demonte, Conrad Naleway, Matias D. Asencion Diez, Alberto A. Iglesias

Chemistry: Faculty Publications and Other Works

Streptococcus mutans is the leading cause of dental caries worldwide by accumulating a glycogen-like internal polysaccharide (IPS) that contributes to cariogenicity when sugars are in excess. Sodium monofluorophosphate (MFP) is an active anticariogenic compound in toothpastes. Herein, we show that MFP inhibits (with an I_0.5 of 1.5 mM) the S. mutans ADP-glucose pyrophosphorylase (EC 2.7.7.27), which catalyzes the key step in IPS biosynthesis. Enzyme inhibition by MFP is similar to orthophosphate (Pi), except that the effect caused by MFP is not reverted by fructose-1,6-bisP, as occurs with Pi. Inhibition was correlated with a decrease in acidogenesis and IPS …

One Ion To Rule Them All: Combined Antibacterial, Osteoinductive And Anticancer Properties Of Selenite-Incorporated Hydroxyapatite, Vuk Uskoković, Maheshwar Adiraj Iyer, Victoria M. Wu

Pharmacy Faculty Articles and Research

Although hydroxyapatite (HAp) has been doped with dozens of different ions, the quest for an ion imparting a combination of properties conducive to bone healing is still ongoing. Because of its protean potency and the similarity in size and shape to the phosphate tetrahedron, the selenite ion presents a natural ionic substitute in HAp. The incorporation of selenite into synthetic HAp using two different methods – co-precipitation and ion-exchange sorption – was studied for its effect on crystal properties and on a triad of biological responses: antibacterial, anticancer and osteoinductive. Co-precipitation yielded HAp with a higher selenite content than sorption …

Far-Red And Near-Infrared Seminaphthofluorophores For Targeted Pancreatic Cancer Imaging, Lei Wang, Connor W. Barth, Martha Sibrian-Vazquez, Jorge O. Escodedo, Mark Lowry, John Muschler, Haiyan Li, Summer L. Gibbs, Robert Strongin

Chemistry Faculty Publications and Presentations

Molecular probes that selectively highlight pancreatic cancer (PC) tissue have the potential to improve pancreatic ductal adenocarcinoma (PDAC) margin assessment through the selective highlighting of individual PC cells. Herein, we report a simple and unique family of systematically modified red and near-infrared fluorescent probes that exhibit a field-effect-derived redshift. Two of thirteen probes distributed to the normal mouse pancreas following systemic administration. One selectively accumulated in genetically modified mouse models of PDAC. The probe exhibited intracellular accumulation and enabled visualization of four levels of the structure, including the whole organ, resected tissue, individual cells, and subcellular organelles. In contrast to …

Safer Chemicals Design Diagrams, Longzhu Shen, Fjodor Melnikov, John Roethle, Aditya Gudibanda, Richard Judson, Julie Zimmerman, Paul Anastas

Yale Day of Data

The NRF2-ARE antioxidant pathway is an important biological sensing and regulating system that responds to chemical insults. At minute level, it protects a living species to go through hard environmental conditions. However, when the external disruption exceeds the inherent resilience, cellular damage can occur, eventually leading to cytotoxicity. Therefore, studying the likelihood of a chemical activating the NRF2-ARE pathway is interesting to discovering therapeutic agents and designing safer chemicals. In this research, we engaged a combination of computational chemistry, statistical learning and mechanistic toxicology to estimate the likelihood of a chemical to perturb this critical toxicological pathway and derive a …

Cyclipostins And Cyclophostin Analogs As Promising Compounds In The Fight Against Tuberculosis, Phuong Nguyen, Vincent Delorme, Anaïs Bénarouche, Benjamin Martin, Rishi Paudel, Giri Gnawali, Abdeldjalil Madani, Rémy Puppo, Valérie Landry, Laurent Kremer, Priscille Brodin, Christopher Spilling, Jean-François Cavalier, Stéphane Canaan

Chemistry & Biochemistry Faculty Works

A new class of Cyclophostin and Cyclipostins (CyC) analogs have been investigated against Mycobacterium tuberculosis H37Rv (M. tb) grown either in broth medium or inside macrophages. Our compounds displayed a diversity of action by acting either on extracellular M. tb bacterial growth only, or both intracellularly on infected macrophages as well as extracellularly on bacterial growth with very low toxicity towards host macrophages. Among the eight potential CyCs identified, CyC 17 exhibited the best extracellular antitubercular activity (MIC50 = 500 nM). This compound was selected and further used in a competitive labelling/enrichment assay against the activity-based probe Desthiobiotin-FP in order …

The Statistical Mechanics Of Solar Wind Hydroxylation At The Moon, Within Lunar Magnetic Anomalies, And At Phobos, W. M. Farrell, D. M. Hurley, Vincent J. Esposito, J. L. Mclain, M. I. Zimmerman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present a new formalism to describe the outgassing of hydrogen initially implanted by the solar wind protons into exposed soils on airless bodies. The formalism applies a statistical mechanics approach similar to that applied recently to molecular adsorption onto activated surfaces. The key element enabling this formalism is the recognition that the interatomic potential between the implanted H and regolith-residing oxides is not of singular value but possess a distribution of trapped energy values at a given temperature, F(U,T). All subsequent derivations of the outward diffusion and H retention rely on the specific properties of this distribution. We …

Palladium-Catalyzed Intramolecular Cross-Dehydrogenative Coupling: Synthesis Of Fused Imidazo[1,2‑A]Pyrimidines And Pyrazolo[1,5‑A]Pyrimidines, Siva K. Reddy Kotla, Jaya Kishore Vandavasi, Jeh-Jeh Wang, Keykavous Parang, Rakesh Tiwari

Pharmacy Faculty Articles and Research

A palladium-catalyzed intramolecular dehydrogenative coupling reaction was developed for the synthesis of fused imidazo[1,2-a]pyrimidines and pyrazolo[1,5-a]- pyrimidines. The developed protocol provides a practical approach for the synthesis of biologically important substituted pyrimidines from easily available substrates, with a broad substrate scope under mild reaction conditions.

Nitroxide-Based Macromolecular Contrast Agents With Unprecedented Transverse Relaxivity And Stability For Magnetic Resonance Imaging Of Tumors, Hung V.T. Nguyen, Qixian Chen, Joseph T. Paletta, Peter Harvey, Yivan Jiang, Hui Zhang, Michael Boska, M. Francesca Ottaviani, Alan Jasanoff, Andrzej Rajca, Jeremiah A. Johnson

Andrzej Rajca Publications

Metal-free magnetic resonance imaging (MRI) agents could overcome the established toxicity associated with metal-based agents in some patient populations and enable new modes of functional MRI in vivo. Herein, we report nitroxidefunctionalized brush-arm star polymer organic radical contrast agents (BASP-ORCAs) that overcome the low contrast and poor in vivo stability associated with nitroxide-based MRI contrast agents. As a consequence of their unique nanoarchitectures, BASP-ORCAs possess per-nitroxide transverse relaxivities up to ∼44-fold greater than common nitroxides, exceptional stability in highly reducing environments, and low toxicity. These features combine to provide for accumulation of a sufficient concentration of BASP-ORCA in murine subcutaneous …