Chemistry Commons^™

2-Acylamido Analogues Of N-Acetylglucosamine Prime Formation Of Chitin Oligosaccharides By Yeast Chitin Synthase 2, Jacob Gyore, Archana Parameswar, Carleigh Hebbard, Younghoon Oh, Erfei Bi, Alexei Demchenko, Neil Price, Peter Orlean

Chemistry & Biochemistry Faculty Works

Chitin, a homopolymer of β1,4-linked N-acetylglucosamine (GlcNAc) residues, is a key component of the cell walls of fungi and the exoskeletons of arthropods. Chitin synthases transfer GlcNAc from UDP-GlcNAc to preexisting chitin chains in reactions that are typically stimulated by free GlcNAc. The effect of GlcNAc was probed by using a yeast strain expressing a single chitin synthase, Chs2, by examining formation of chitin oligosaccharides (COs) and insoluble chitin, and by replacing GlcNAc with 2-acylamido analogues of GlcNAc. Synthesis of COs was strongly dependent on inclusion of GlcNAc in chitin synthase incubations, and N,N′-diacetylchitobiose (GlcNAc2) was the major reaction product. …

Determination Of Pore Size Distribution In Capillary-Channeled Polymer (C-Cp) Fiber Stationary Phases By Inverse Size-Exclusion Chromatography (Isec) And The Study Of The Role Of Interstitial Fraction On C-Cp Fibers On Protein Binding Capacity, Zhengxin Wang

All Theses

ABSTRACT High performance liquid chromatography (HPLC), first used in the 1960's, is a rapidly evolving analytical technique, widely employed for identification, separation, and purification in biotechnology and pharmaceutical industries. The development of the stationary phases has played an important role in improving this technique. Each stationary phase will have its own disadvantages. Polysaccharide-based stationary phases such as cross-linked dextran cannot tolerate high pressures and linear velocities; silica stationary phases are rigid enough but slow mass transfer in the pores on the surface causes another problem; with the introduction of non-porous and small bead packing materials, the low surface area and …

The Role Of Stress-Activated Protein Kinases In Parasites, Tamara Kreiss

Theses, Dissertations and Culminating Projects

Lymphatic filariasis and leishmaniasis are neglected tropical diseases that are caused by nematode and protozoal parasites. These diseases cause disfiguration, leaving their host socially marked, and in some cases cause more severe disease that can lead to death. These infections, which tend to persist for long periods of time, also lead to bacterial and fungal co-infections, which further exacerbate the disease. Currently there are insufficient treatment options. Current therapies are often too expensive, have toxicity associated with them and are subjected to growing resistance amongst parasite populations. In this thesis I investigated two potential drug targets. The first, is the …

Porphyrin Cross-Linkers For Generating Soluble Molecularly Imprinted Polymers From Polyethyleneimine, Mohammed R. Elshaer

Seton Hall University Dissertations and Theses (ETDs)

Molecular recognition is vital to many biochemical processes and is at the heart of promising bio-medically related technologies. Molecular imprinting has a long-standing history as a successful method for mimicking the molecular recognition phenomena exhibited by nature, whereby artificial receptors are prepared for a given target molecule based on synthetic polymers. The molecularly imprinted polymer (MIP) contains a three dimensional network with a memorized cavity specific to the shape and functionality of the templated target molecule. The utility of traditional MIPs has been limited due to an inherent lack of solubility. We have worked toward developing a system that allows …

Redox Active Motifs In Selenoproteins, Fei Li, Yuliya Pepelyayeva, Elias S. J. Arner, Craig A. Bayse, Sharon Rozovsky

Chemistry & Biochemistry Faculty Publications

Selenoproteins use the rare amino acid selenocysteine (Sec) to act as the first line of defense against oxidants, which are linked to aging, cancer, and neurodegenerative diseases. Many selenoproteins are oxidoreductases in which the reactive Sec is connected to a neighboring Cys and able to form a ring. These Sec-containing redox motifs govern much of the reactivity of selenoproteins. To study their fundamental properties, we have used Se-77 NMR spectroscopy in concert with theoretical calculations to determine the conformational preferences and mobility of representative motifs. This use of Se-77 as a probe enables the direct recording of the properties of …

Biogeochemistry Of Trace Elements In The Mixing Zone Of The Mississippi And Atchafalaya Rivers And Chemical Distributions As Affected By The Deepwater Horizon Blowout, Dongjoo Joung

Dissertations

Selected trace elements (TEs), dissolved organic carbon, and nutrients were studied in Louisiana Shelf waters including the Mississippi (MR) and Atchafalaya (AR) River plumes during periods of high, intermediate, and low river discharges. Seasonal variations in TEs were observed at low salinity, reflecting seasonal changes in the river water endmembers. Shelf surface water dissolved Mo, Cs, U, Ni, and Cu showed conservative behavior with minor scattering in some high salinity waters. Based on associated mixing experiments, nutrient and chlorophyll distributions, as well as surface-bottom concentration contrasts, the non-conservative behavior of TEs was variously related to colloidal flocculation (Fe, Cr), biological …

Metal Stopping Reagents Facilitate Discontinuous Activity Assays Of The De Novo Purine Biosynthesis Enzyme Pure, Kelly L. Sullivan, Loredana C. Huma, Elwood Mullins, Michael E. Johnson, T. Joseph Kappock

Department of Biochemistry Faculty Publications

The conversion of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-AIR (CAIR) represents an unusual divergence in purine biosynthesis: microbes and nonmetazoan eukaryotes use class I PurEs while animals use class II PurEs. Class I PurEs are therefore a potential antimicrobial target; however, no enzyme activity assay is suitable for high throughput screening (HTS). Here we report a simple chemical quench that fixes the PurE substrate/product ratio for 24 h, as assessed by the Bratton-Marshall assay (BMA) for diazotizable amines. The ZnSO₄ stopping reagent is proposed to chelate CAIR, enabling delayed analysis of this acid-labile product by BMA or other HTS methods

Monitoring Citrus Nutrition In The Rio Grande Valley For Fertilizer Recommendations, Iram Lopez

Theses and Dissertations - UTB/UTPA

Soil fertility and plant nutrition is crucial for a better yield and consistent harvest in the Rio Grande Valley for local farmers growing citrus trees. A field of oranges and a field of grapefruits were monitored and nutrition deficiencies were noticed that played an important role during fruit set. Soil samples that were taken throughout the year were analyzed via a carbon dioxide extraction method that mimics the way plants naturally take up nutrients or extract nutrients from every soil type. Macronutrients such as the N, P, K, Na, Ca, Mg and some of the micronutrients (Zn, Fe, Mn, and …

Initial Characterization Of A Conserved Active Site Residue For The Cdc34 Ubiquitin Conjugating Enzyme, Arvin Akoopie

Honors College Theses

Ubiquitin-conjugating enzymes (E2s) covalently modify protein substrates with ubiquitins. The active site cysteine residues on E2s are essential for catalyzing the transfer of ubiquitin from the E2 active site onto the protein substrate, however there is a limited amount of information available concerning additional active site residues for E2s that may also participate in catalysis. Cdc34 is an essential E2 that has merited the lion’s share of attention for biochemical analysis of the E2 family. Previous phylogenetic analysis of Cdc34 amino acid sequences has identified an invariably conserved histidine residue close to the active site cysteine in the primary structure, …

Effect Of Microwave Heating On The Migration Of Additives From Ps, Pp And Pet Container Into Food Simulants, Ruoyin Cai, Kereilemang Khana Mokwena Nthoiwa, Changfeng Ge

Journal of Applied Packaging Research

The main objective of this thesis is to test three different microwaving packaging materials that are the most common material in the market, viz. polystyrene (PS), polypropylene (PP), and polyethylene terephthalate (PET), migrated into four food simulant solutions. Four different simulant solutions were used based on the food type and FDA recommendations and regulations. These food simulants include vegetable pure oil, 3% (v/v) aqueous acetic acid, 15% (v/v) ethanol, and olive oil in the temperature of 100°C.Headspace gas chromatography with mass spectrometric detection (GC/MS) was used to determine the relative migration values from packaging materials into food by putting the …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Combination Of The Computational Methods: Molecular Dynamics, Homology Modeling And Docking To Design Novel Inhibitors And Study Structural Changes In Target Proteins For Current Diseases, Katherine Cristina Parra

USF Tampa Graduate Theses and Dissertations

In this thesis, molecular dynamics simulations, molecular docking, and homology modeling methods have been used in combination to design possible inhibitors as well as to study the structural changes and function of target proteins related to diseases that today are in the spotlight of drug discovery. The inwardly rectifying potassium (Kir) channels constitute the first target in this study; they are involved in cardiac problems. On the other hand, tensin, a promising target in cancer research, is the second target studied here.

The first chapter includes a brief update on computational methods and the current proposal of the combination of …

Volume 06, Kristen Gains, Amanda Willis, Holly Backer, Monika Gutierrez, Cara O'Neal, Sara Nelson, Sasha Silberman, Jessica Beardsley, Jamie Gardner, Edward Peeples, Matthew Sakach, Tess Lione, Emily Wilkins, Kelsey Holt, Jessica Page, Jamie Clift, Charles Vancampen, Gilbert Hall, Jenny Nehrt, Kasey Dye, Amanda Tharp, Jamie Leeuwrik, Ashley Mcgee, Emily Poulin, Michael Kropf, Nick Pastore, Austin Polasky, Morgan Glasco, Laura L. Kahler, Melinda L. Edwards, Brandon C. Smith, Mariah Asbell, Cabell Edmunds, Amelia D. Perry, Alyssa Hayes, Irina Boothe, Perry Bason, James Early

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Caught Between Folklore and the Cold War: The Americanization of Russian Children's Literature by Kristen Gains

Graphic Design by Amanda Willis

Graphic Design by Holly Backer

Prejudices in Swiss German Accents by Monika Gutierrez

Photography by Cara O'Neal

Photography by Sara Nelson

Edmund Tyrone's Long Journey through Night by Sasha Silberman

Photography by Jessica Beardsley

Photography by Jamie Gardner and Edward Peeples

The Republican Razor: The Guillotine as a Symbol of Equality by Jamie Clift

Graphic Design by Matthew Sakach

Genocide: The Lasting Effects of Gender Stratification in Rwanda By Tess Lione and Emily …

Prepubertal Exposure To Arsenic(Iii) Suppresses Circulating Insulin-Like Growth Factor-1 (Igf-1) Delaying Sexual Maturation In Female Rats, Michael P. Reilly, James C. Saca, Alina Hamilton, Rene F. Solano, Jesse R. Rivera, Wendy Innis-Whitehouse, Jason Parsons, Robert K. Dearth

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Arsenic (As) is a prevalent environmental toxin readily accessible for human consumption and has been identified as an endocrine disruptor. However, it is not known what impact As has on female sexual maturation. Therefore, in the present study, we investigated the effects of prepubertal exposure on mammary gland development and pubertal onset in female rats. Results showed that prepubertal exposure to 10 mg/kg of arsenite (As(III)) delayed vaginal opening (VO) and prepubertal mammary gland maturation. We determined that As accumulates in the liver, disrupts hepatocyte function and suppresses serum levels of the puberty related hormone insulin-like growth factor 1 (IGF-1) …

Isolation Of Antibacterial Compounds From Artemisia Californica, Jae Eun Min

Seaver College Research And Scholarly Achievement Symposium

The Chumash Native Americans of Southern California have well-documented traditions of using plants for medicinal purposes. If a specific plant has traditionally been used by Chumash for the treatment of cuts, wounds and infections, it may contain chemicals with anti-bacterial properties. One plant that fits these criteria is Artemisia californica (coastal sage). Because of the widespread use of antibiotics over the past sixty years bacteria are evolving greater resistance to known antibiotics, but unfortunately the rate of antibiotic discovery has diminished during the past twenty years. Therefore, novel and effective antibiotics are essential for the continued treatment of bacterial infections. …

Desorption Electrospray Ionization Mass Spectrometry Imaging: Instrumentation, Optimization And Capabilities, Manan Dhunna

Theses and Dissertations

Desorption Electrospray Ionization Mass spectrometry Imaging (DESI-MSI) is an area of great interest and a promising tool in the field of chemical imaging. It is a powerful, label-free technique, which can determine, map and visualize different molecular compounds on a sample surface. The amount of information acquired in a single DESI-MSI experiment is enormous compared to other techniques, as it can simultaneously detect different compounds with their spatial distribution on the surface. The experiment can be used to produce two-dimensional and three-dimensional images. Chapter 2 focuses on the design and optimization of the setup for performing DESI-MS imaging on various …

Facile Synthesis And Characterization Of A Thermally Stable Silica-Doped Alumina With Tunable Surface Area, Porosity, And Acidity, Maryam Khosravi Mardkhe

Theses and Dissertations

Mesoporous γ-Al2O3 is one of the most widely used catalyst supports for commercial catalytic applications. The performance of a catalyst strongly depends on the combination of textural, chemical and physical properties of the support. Pore size is essential since each catalytic system requires a unique pore size for optimal catalyst loading, diffusion and selectivity. In addition, high surface area and large pore volume usually result in higher catalyst loading, which increases the number of catalytic reaction sites and decreases reaction time. Therefore, determination of surface area and porosity of porous supports is critical for the successful design and optimization of …

Structural Insights Into The Interaction Between A Potent Anti-Inflammatory Protein, Viral Cc Chemokine Inhibitor (Vcci), And The Human Cc Chemokine, Eotaxin-1, Nai-Wei Kuo, Yong-Guang Gao, Megan Schill, Nancy Isern, Cynthia Dupureur, Patricia Liwang

Chemistry & Biochemistry Faculty Works

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N …

Structural Insights Into The Interaction Between A Potent Anti-Inflammatory Protein, Viral Cc Chemokine Inhibitor (Vcci), And The Human Cc Chemokine, Eotaxin-1*, Nai-Wei Kuo, Yong-Guang Gao, Megan S. Schill, Nancy Isern, Cynthia M. Dupureur, Patricia J. Liwang

Educator Preparation & Leadership Faculty Works

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β …

Strad Pseudokinases Regulate Axogenesis And Lkb1 Stability, Biliana O. Veleva-Rotse, James L. Smart, Annette F. Baas, Benjamin Edmonds, Zi-Ming Zhao, Allyson Brown, Lillian R. Klug, Kelly Hansen, Gabrielle Rielly, Alexandria P. Gardner, Krishnaveni Subbiah, Eric A. Gaucher, Hans Clevers, Anthony P. Barnes

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can …

Deconstructing A Plant Macromolecular Assembly: Chemical Architecture, Molecular Flexibility, And Mechanical Performance Of Natural And Engineered Potato Suberins, Olga Serra, Subhasish Chatterjee, Merce Figueras, Marisa Molinas, Ruth E. Stark

Publications and Research

Periderms present in plant barks are essential protective barriers to water diffusion, mechanical breakdown, and pathogenic invasion. They consist of densely packed layers of dead cells with cell walls that are embedded with suberin. Understanding the interplay of molecular structure, dynamics, and biomechanics in these cell wall-associated insoluble amorphous polymeric assemblies presents substantial investigative challenges. We report solid-state NMR coordinated with FT-IR and tensile strength measurements for periderms from native and wound-healing potatoes and from potatoes with genetically modified suberins. The analyses include the intact suberin aromatic; aliphatic polymer and cell-wall polysaccharides, previously reported soluble depolymerized transmethylation products, and undegraded …

On Chip Preconcentration And Labeling Of Protein Biomarkers Using Monolithic Columns, Device Fabrication, Optimization, And Automation, Rui Yang

Theses and Dissertations

Detection of disease specific biomarkers is of great importance in diagnosis and treatment of diseases. Modern bioanalytical techniques, such as liquid chromatography with mass spectrometry (LC-MS), have the ability to identify biomarkers, but their cost and scalability are two main drawbacks. Enzyme-linked immunosorbent assay (ELISA) is another potential tool, but it works best for proteins, rather than peptide biomarkers. Recently, microfluidics has emerged as a promising technique due to its small fluid volume consumption, rapidness, low fabrication cost, portability and versatility. Therefore, it shows prominent potential in the analysis of disease specific biomarkers. In this thesis, microfluidic systems that integrate …

Conformational Features Of The Human U2-U6 Snrna Complex, Ravichandra Bachu

Dissertations, Theses, and Capstone Projects

The splicing of precursor messenger (pre-m) RNA, during which noncoding intervening sequences are excised and flanking coding regions ligated, is an integral reaction of gene expression. In eukaryotes, it is carried out by a dynamic RNA-protein complex called the spliceosome, in which five small nuclear (sn) RNA components are actively involved in recognition and chemical aspects of the process. A complex formed between U2 and U6 snRNAs is implicated in the chemistry of pre-mRNA splicing. The catalytic activity of the U2-U6 snRNA complex is dependent on the presence of Mg2+ ions, and the complex has been shown to have several …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

Paper-Based Standard Addition Assays, Cory A. Chaplan, Haydn T. Mitchell, Andres W. Martinez

Chemistry and Biochemistry

Standard addition assays conducted on paper-based microfluidic devices are introduced as an alternative to external standards for calibrating quantitative tests. To demonstrate this technique, a colorimetric, paper-based, standard addition assay was optimized for the determination of glucose concentrations in the range of 0 to 5 mM. Comparable results were obtained from the assay via digital image colorimetry under three different lighting conditions.

Polymeric Monolithic Stationary Phases For Capillary Reversed-Phase Liquid Chromatography Of Small Molecules, Kun Liu

Theses and Dissertations

Highly cross-linked monoliths prepared from single cross-linking monomers were found to increase surface area and stability. Therefore, seven cross-linking monomers, i.e., 1,3-butanediol dimethacrylate (1,3-BDDMA), 1,4-butanediol dimethacrylate (1,4-BDDMA), neopentyl glycol dimethacrylate (NPGDMA), 1,5-pentanediol dimethacrylate (1,5-PDDMA), 1,6-hexanediol dimethacrylate (1,6-HDDMA), 1,10-decanediol dimethacrylate (1,10-DDDMA), and 1,12-dodecanediol dimethacrylate (1,12-DoDDMA), were used to synthesize highly cross-linked monolithic columns in 75-µm i.d. capillaries by one-step UV-initiated polymerization using dodecanol and methanol as porogens for reversed-phase liquid chromatography (RPLC) of small molecules. Selection of porogen type and concentration was investigated in detail. Isocratic elution of alkylbenzenes at a flow rate of 300 nL/min was conducted for all of …

Bsa–Boronic Acid Conjugate As Lectin Mimetics, Satya Nandana Narla, Poornima Pinnamaneni, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

We report bovine serum albumin (BSA)–boronic acid (BA) conjugates as lectin mimetics and their glyco-capturing capacity. The BSA–BA conjugates were synthesized by amidation of carboxylic acid groups in BSA with aminophenyl boronic acid in the presence of EDC, and were characterized by Alizarin Red S (ARS) assay and SDS–PAGE gel. The BSA–BA conjugates were immobilized onto maleimide-functionalized silica beads and their sugar capturing capacity and specificity were confirmed by ARS displacement assay. Further, surface plasmon resonance (SPR) analysis of the glyco-capturing activity of the BSA–BA conjugates was conducted by immobilizing BSA–BA onto SPR gold chip. Overall, we demonstrated a BSA–BA-based …

Collisional Dynamic Elements Of The Pyrazine - N2o System:Middle And Low J States, La Moyne Tyler Mix

Theses and Dissertations

Unimolecular reactions based on the Lindemann - Hinchelwood mechanism are important to understanding combustion and atmospheric processes. The main feature of this mechanism is the energy transfer probability distribution function, P(E',E). We have chosen to study P(E',E) through gas phase collisional dynamics probed with IR transient absorption spectroscopy. Post-collision absorption line widths for the pyrazine-N2O system are used to calculate lab frame translational temperatures. The translational temperatures reveal that collisions with large rotational energy transfer also transfer large amounts of translational energy. For J states >47 the relationship is linear indicating a constant impact parameter. Line widths for J=47 through …

06. Computer Science, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.