Chemistry Commons^™

Functional Variants Of Metal-Binding Domains 5 And 6 Of The Human Wilson Protein, Sandra Weitzner

Honors Theses

Wilson's disease is caused by mutations in atp7b, a gene that encodes a copper-transporting P_1B-type ATPase, otherwise known as the Wilson protein. Over 300 different mutations cause Wilson's disease, and we focused on missense mutations occurring in the 650 amino acid N-terminus of the Wilson protein. This portion of the protein includes six metal-binding domains that function to azquire Cu(I) from the cytosol, prior to passing it through the ATP-driven membrane-spanning pump. Of particular interest are metal-binding domains 5 and 6 (WLN5-6) since we know that they are absolutely required for function of the enzyme. Several missense mutations …

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. …

Mapping Posttranscriptional Regulation Of The Human Glycome Uncovers Microrna Defining The Glycocode, Praveen Agrawal, Tomasz Kurcon, Kanoelani T. Pilobello, John F. Rakus, Sujeethraj Koppolu, Zhongyin Liu, Bianca S. Batista, William S. Eng, Ku-Lung Hsu, Yaxuan Liang, Lara K. Maha

Chemistry Faculty Research

Cell surface glycans form a critical interface with the biological milieu, informing diverse processes from the inflammatory cascade to cellular migration. Assembly of discrete carbohydrate structures requires the coordinated activity of a repertoire of proteins, including glycosyltransferases and glycosidases. Little is known about the regulatory networks controlling this complex biosynthetic process. Recent work points to a role for microRNA (miRNA) in the regulation of specific glycan biosynthetic enzymes. Herein we take a unique systems-based approach to identify connections between miRNA and the glycome. By using our glycomic analysis platform, lectin microarrays, we identify glycosylation signatures in the NCI-60 cell panel …

Epigenetic Modification, Dehydration, And Molecular Crowding Effects On The Thermodynamics Of I-Motif Structure Formation From C-Rich Dna, Yogini P. Bhavsar-Jog, Eric Van Dornshuld, Tracy A. Brooks, Gregory S. Tschumper, Randy M. Wadkins

Chemistry Faculty Research & Creative Works

DNA sequences with the potential to form secondary structures such as i-motifs (iMs) and G-quadruplexes (G4s) are abundant in the promoters of several oncogenes and, in some instances, are known to regulate gene expression. Recently, iM-forming DNA strands have also been employed as functional units in nanodevices, ranging from drug delivery systems to nanocircuitry. To understand both the mechanism of gene regulation by iMs and how to use them more efficiently in nanotechnological applications, it is essential to have a thorough knowledge of factors that govern their conformational states and stabilities. Most of the prior work to characterize the conformational …

Optimization Of Microwave-Enhanced Williamson Ether Synthesis Of 1-Ethoxydodecane, Kevin Hess, Linda Farber

Chemistry Undergraduate Publications

1-ethoxydodecane is an asymmetrical ether used in production of sunscreen and moisturizing due to its nonpolar properties. One of the standard protocols for synthesizing both asymmetrical and symmetrical ethers is via the Williamson Ether Synthesis. The standard synthesis requires a 60-70 minute reflux time frame to allow for this reaction to run until completion; however, the ability to reduce this reaction time via microwave radiation has become increasingly prominent in organic synthesis. The conventional means of Williamson Ether Synthesis is also not ideal for optimal purity or speed, thus microwave synthesis of this compound was investigated. In order to obtain …

Choosing A Thesis Advisor: Surprise And Success, Kermin Martinez-Hernandez

Chemistry Faculty/Staff Publications

One of the most daunting and yet important decisions in graduate school is the selection of your thesis advisor. Inviting an advisor into your graduate thesis process is like hiring a ship navigator who will help guide your graduate study through the sometimes choppy waters of data research and thesis writing and into the safe harbor of graduation and a good job. Although you remain the captain of your own career, your graduate advisor teaches you how to use the charts and equipment that will bring you to the completion of your graduate degree.

The specific steps involved in choosing …

Design, Synthesis, And Biological Evaluation Of Non-Symmetric Smal, Himabindu Anumala

Master's Theses and Doctoral Dissertations

Plasminogen activator inhibitor-1 (PAI-1) is a member of the serpin family of proteins, a primary inhibitor of both tissue-type and urokinase-type plasminogen activators in plasma, and is a well-established risk factor in various disease conditions. Increased levels of active PAI-1 in plasma are correlated with the development of atherosclerosis, diabetes, stroke, and other maladies. In the present study, we describe the synthesis of two new series of compounds that aim to reduce physiologically active PAI-1 levels. These molecules are related to a series of bis-arylsulfonimides and arylsulfonamides connected by short linking diamines, and to a series of hydrazine-based analogues. These …

Tcr Scanning Of Peptide/Mhc Through Complementary Matching Of Receptor And Ligand Molecular Flexibility, William F. Hawse, Soumya De, Alexander I. Greenwood, Linda K. Nicholson, Jaroslav Zajicek, Evgeni L. Kovrigin, David M. Kranz, K. Chrisopher Garcia, Brian M. Baker

Chemistry Faculty Research and Publications

Although conformational changes in TCRs and peptide Ags presented by MHC protein (pMHC) molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. In this study, we used nuclear magnetic resonance to study TCR–pMHC binding, examining recognition of the QL9/H-2L^d complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR–pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR–pMHC complex. …

Ultraviolet Light Emitting Diode Use In Advanced Oxidation Processes, Kelsey L. Duckworth

Theses and Dissertations

Cleanup from a hazardous chemical release can result in large volumes of water containing hazardous materials, such as organophosphates. Unfortunately, this water cannot be treated in a municipal wastewater treatment plant without adversely affecting the performance of the plant. A known method for pretreating this water to prepare it for processing in a traditional treatment plant includes the addition of hydrogen peroxide, followed by ultraviolet (UV) light exposure to form reactive hydroxyl radicals which oxidize the chemical. Light emitting diodes (LEDs) are explored as a UV source as they are durable; compact; can be powered by low voltage, direct current …

Atmospheric Peroxyacetyl Nitrate (Pan): A Global Budget And Source Attribution, E. V. Fischer, D. J. Jacob, R. M. Yantosca, M. P. Sulprizio, D. B. Millet, J. Mao, F. Paulot, H. B. Singh, A. Roiger, L. Ries, R. W. Talbot, K. Dzepina, S. Pandey Deolal

Michigan Tech Publications, Part 1

Peroxyacetyl nitrate (PAN) formed in the atmospheric oxidation of non-methane volatile organic compounds (NMVOCs) is the principal tropospheric reservoir for nitrogen oxide radicals (NOx =NO+NO2). PAN enables the transport and release of NOx to the remote troposphere with major implications for the global distributions of ozone and OH, the main tropospheric oxidants. Simulation of PAN is a challenge for global models because of the dependence of PAN on vertical transport as well as complex and uncertain NMVOC sources and chemistry. Here we use an improved representation of NMVOCs in a global 3-D chemical transport model (GEOS-Chem) and show that it …

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 …

Synergism Between Airborne Singlet Oxygen And A Trisubstituted Olefin Sulfonate For The Inactivation Of Bacteria, Rajib Choudhury, Alexander Greer

Publications and Research

The reactivity of a trisubstituted alkene surfactant (8-methylnon-7-ene-1 sulfonate, 1) to airborne singlet oxygen in a solution containing E. coli was examined. Surfactant 1 was prepared by a Strecker-type reaction of 9-bromo-2-methylnon-2-ene with sodium sulfite. Submicellar concentrations of 1 were used that reacted with singlet oxygen by an “ene” reaction to yield two hydroperoxides (7-hydroperoxy-8-methylnon-8-ene-1 sulfonate and (E)-8-hydroperoxy-8-methylnon-6-ene-1 sulfonate) in a 4:1 ratio. Exchanging the H₂O solution for D₂O where the lifetime of solution-phase singlet oxygen increases by 20-fold led to an ∼2-fold increase in the yield of hydroperoxides pointing to surface activity …

Thermal Denaturation Of Mycobacterium Tuberculosis Protein Rv0045c Monitored By Intrinsic Tryptophan Fluorescence, Lindsey Renee Drake

Undergraduate Honors Thesis Collection

The aim of my project was to use intrinsic tryptophan fluorescence to monitor the denaturation pathway of a protein, specifically the Mycobacterium tuberculosis enzyme Rv0045c. The larger scientific goal and inspiration for this honors thesis was to use the amino acid residues of a protein to map it's unfolding by thermal denaturation.

Hitting Pause On Organic Chemistry, Jenny B. Vu

Interdisciplinary STEM Teaching & Learning Conference (2012-2019) (Archived)

Written procedures for performing organic chemistry experiments are replaced by visual demonstrations that allow students to watch these videos at home and/ or in the laboratory. These previously recorded demonstrations allow students to watch, pause, and rewind the video to better understand laboratory techniques.

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 …

[M3(Μ3-O)(O2cr)6] And Related Trigonal Prisms: Versatile Molecular Building Blocks For 2-Step Crystal Engineering Of Functional Metal-Organic Materials, Alexander Schoedel

USF Tampa Graduate Theses and Dissertations

Metal-organic materials (MOMs) assembled from metal-based building blocks and organic linkers have attracted much interest due to their large pore dimensions and their enormous structural diversity. In comparison to their inorganic counterparts (zeolites), these crystalline materials can be easily modified to tailor pore dimensions and functionality for specifically targeted properties.

The work presented herein encompasses the development of a synthetic 2-step process for the construction of novel families of MOMs or 'platforms' and allow us exquisite design and control over the resulting network topologies. Examples of cationic mesoporous structures were initially exploited, containing carboxylate based centers connected by metal-pyridine bonds. …

Capping Amyloid Β‑Sheets Of The Tau-Amyloid Structure Vqivyk With Hexapeptides Designed To Arrest Growth. An Oniom And Density Functional Theory Study, Joshua A. Plumley, Jorge Ali-Torres, Gabor Pohl, J. J. Dannenberg

Publications and Research

We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer’s disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of a parallel sheet, using all-D residues to form rippled interactions at the edge of the sheet, and replacing the H-bond donor N−H’s that inhibit further growth) that can be used individually and in combination to design such peptides that will …

Etherification Reactions Of Propargylic Alcohols Catalyzed By A Cationic Ruthenium Allenylidene Complex, Doaa F. Alkhaleeli, Kevin J. Baum, Jordan M. Rabus, Eike B. Bauer

Educator Preparation & Leadership Faculty Works

The cationic ruthenium allenylidene complex RRuRax −[Ru(indenyl)L(PPh3)CCCPh2]+PF6 catalyzes the etherification of secondary and tertiary propargylic alcohols in a formal nucleophilic substitution reaction utilizing primary and secondary alcohols as the nucleophiles. At a catalyst loading of only 1.1 mol%, the corresponding propargylic ether products were obtained in 9 to 73% isolated yields (18 h reaction time at 100 °C); no further additives are required. The reaction exhibits an induction period; as shown by a control reaction, the high reaction temperature may chemically change the allenylidene complex to be employed as the catalyst but does not lead to …

Characterization Of The Potential Energy Surfaces Of Two Small But Challenging Noncovalent Dimers: P2)2 And (Pccp) 2, Eric Van Dornshuld, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

This work characterizes eight stationary points of the P2 dimer and six stationary points of the PCCP dimer, including a newly identified minimum on both potential energy surfaces. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with the second-order Møller-Plesset (MP2) electronic structure method and six different basis sets: aug-cc-pVXZ, aug-cc-pV(X+d)Z, and aug-cc-pCVXZ where X = T, Q. A new L-shaped structure with C₂ symmetry is the only minimum for the P₂ dimer at the MP2 level of theory with these basis sets. The previously reported parallel-slipped structure with C_2h symmetry and a newly identified …

Systems And Methods For Diagnosis And Monitoring Of Bacteria-Related Conditions, Sylvia Daunert, Sapna K. Deo, Patrizia Pacini, Anjali Kumari Struss, Harohalli Shashidhar, Deborah R. Auer Flomenhoft, Nilesh Raut

Chemistry Faculty Patents

The presently-disclosed subject matter provides systems, methods, and kits for diagnosing and/or monitoring a bacteria-related condition of interest in a subject by providing a cell sensing system, each system containing a reporter molecule capable of detecting binding of a quorum sensing molecule and capable of generating a detectable signal.

A Semi-Lagrangian View Of Ozone Production Tendency In North American Outflow In The Summers Of 2009 And 2010, B. Zhang, R. C. Owen, J A Perlinger, A. Kumar, S. Wu, M. Val Martin, L. Kramer, D. Helmig, R. E. Honrath

Michigan Tech Publications, Part 1

The Pico Mountain Observatory, located at 2225 m a.s.l. in the Azores Islands, was established in 2001 to observe long-range transport from North America to the central North Atlantic. In previous research conducted at the observatory, ozone enhancement (> 55 ppbv) in North American outflows was observed, and efficient ozone production in these outflows was postulated. This study is focused on determining the causes for high d[O3] / d[CO] values (~1 ppbv ppbv−1) observed in the summers of 2009 and 2010. The folded retroplume technique, developed by Owen and Honrath (2009), was applied to combine upwind FLEXPART transport …

Multivariate Factor Analysis Of A Rocky Mountain Lichen Set, S. Aaron Ross, Dr. Nolan F. Mangelson

Journal of Undergraduate Research

Lichens are a symbiotic relationship between a fungus and an alga. They have no root system, so although they grow off rocks and trees, they need to gather their nutrients from the air. Their great dependence on the atmosphere makes them very susceptible to changes in the air. For instance, a high ambient level of pollution particulates could cause the lichens to collect an increased amount of those particles. Because of this sensitivity to the environment, lichens have become a focus point of scientists to determine ambient pollution levels.1

Parkinson Disease-Associated Mutation R1441h In Lrrk2 Prolongs The “Active State” Of Its Gtpase Domain, Jingling Liao, Chun-Xiang Wu, Christopher Burlak, Sheng Zhang, Dali Liu

Chemistry: Faculty Publications and Other Works

Mutation in leucine-rich-repeat kinase 2 (LRRK2) is a common cause of Parkinson disease (PD). A disease-causing point mutation R1441H/G/C in the GTPase domain of LRRK2 leads to overactivation of its kinase domain. However, the mechanism by which this mutation alters the normal function of its GTPase domain [Ras of complex proteins (Roc)] remains unclear. Here, we report the effects of R1441H mutation (Roc_R1441H) on the structure and activity of Roc. We show that Roc forms a stable monomeric conformation in solution that is catalytically active, thus demonstrating that LRRK2 is a bona fide self-contained GTPase. We further show …

Lysine Deacetylase (Kdac) Regulatory Pathways: An Alternative Approach To Selective Modulation, Michael W. Van Dyke

Faculty Articles

Protein lysine deacetylases (KDACs), including the classic Zn2+-dependent histone deacetylases (HDACs) and the nicotinamide adenine dinucleotide (NAD+)-requiring sirtuins, are enzymes that play critical roles in numerous biological processes, particularly the epigenetic regulation of global gene expression programs in response to internal and external cues. Dysregulation of KDACs is characteristic of several human diseases, including chronic metabolic, neurodegenerative, and cardiovascular diseases and many cancers. This has led to the development of KDAC modulators, two of which (HDAC inhibitors vorinostat and romidepsin) have been approved for the treatment of cutaneous T cell lymphoma. By their nature, existing KDAC modulators are relatively nonspecific, …

Photoassisted Access To New Polyheterocycles, Teresa M. Cowger

Electronic Theses and Dissertations

Photoassisted diversity-oriented synthesis holds great promise in its ability to provide rapid access to complex and diverse molecular scaffolds. As it stands, while photochemical techniques have this potential, their implementation in the field of synthetic organic chemistry is very limited. The main goal of this project was to utilize photochemically assisted techniques in the synthesis of a variety of novel polyheterocycles.

Initially, we explored the how the strain installed in these polycycles could be harnessed to trigger cationic rearrangements in the framework of the system. This was achieved via the high yield and rapid assembly of a highly strained system …

2,9-Bis(5-Sulfanylidene-4,5-Di­Hydro-1,3,4-Oxa­Diazol-2-Yl)-1,10-Phenanthroline Dimethyl Sulfoxide Disolvate, Mohammad A. Rahman, Mohammad R. Karim, Md Arifuzzaman, Tasneem Siddiquee, Lee M. Daniels

Chemistry Faculty Research

In the title compound, C₁₆H₈N₆O₂S₂·2C₂H₆OS, the phenanthroline mol­ecule resides on a twofold axis, and the asymmetric unit also contains a slightly disordered [occupancy ratio for S atom of 0.95 (3):0.047 (3)] mol­ecule of dimethyl sulfoxide. The O atoms of the solvent mol­ecule accept hydrogen bonds from the N-H groups of the five-membered 2,3-di­hydro-1,3,4-oxa­diazole-2-thione ring. This ring is nearly coplanar with the phenanthroline ring, with a dihedral angle between their least-squares planes of 8.86 (6)°. In the crystal, the mol­ecules are linked by C-HO inter­actions.

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.

Extracellular Gluco-Oligosaccharide Degradation By Caulobacter Crescentus, Gerald Presley, Matthew Payea, Logan Hurst, Annie Egan, Brandon Martin, Gopal Periyannan

Faculty Research and Creative Activity

The oligotrophic bacterium Caulobacter crescentus has the ability to metabolize various organic molecules, including plant structural carbohydrates, as a carbon source. The nature of β-glucosidase (BGL)-mediated gluco-oligosaccharide degradation and nutrient transport across the outer membrane in C. crescentus was investigated. All gluco-oligosaccharides tested (up to celloheptose) supported growth in M2 minimal media but not cellulose or CM-cellulose. The periplasmic and outer membrane fractions showed highest BGL activity, but no significant BGL activity was observed in the cytosol or extracellular medium. Cells grown in cellobiose showed expression of specific BGLs and TonB-dependent receptors (TBDRs). Carbonyl cyanide 3-chlorophenylhydrazone lowered the rate of …