Physical Sciences and Mathematics Commons^™

Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams

Senior Theses

Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such …

Synthesis And Design Of Novel Polymer Grafted Nanoparticles Relevant To Drug Delivery Vehicles For Biomedical Applications, Maan Abduldiyem Hassan Al-Ali

Theses and Dissertations

The modification of inorganic nanoparticles with organic polymer chains has become a significant field of study for the engineering of advanced nanocomposite materials. This dissertation presents the design, synthesis, and characterization of novel polymer grafted silica nanoparticles as new strategies to combat bacterial resistance. Described herein is the synthesis of monomers that have been graft polymerized onto silica nanoparticles that can be used as a delivery drug vehicle for biomedical applications. The polymerization of these monomers was performed via reversible addition-fragmentation chain transfer (RAFT) polymerization. The molecular design of the RAFT agents that are attached to the surfaces of the …

Synthesis And Design Of Novel Polymer Grafted Nanoparticles Relevant To Drug Delivery Vehicles For Biomedical Application, Maan Abduldiyem Hassan Al-Ali

Theses and Dissertations

The modification of inorganic nanoparticles with organic polymer chains has become a significant field of study for the engineering of advanced nanocomposite materials. This dissertation presents the design, synthesis, and characterization of novel polymer grafted silica nanoparticles as new strategies to combat bacterial resistance. Described herein is the synthesis of monomers that have been graft polymerized onto silica nanoparticles that can be used as a delivery drug vehicle for biomedical applications. The polymerization of these monomers was performed via reversible addition-fragmentation chain transfer (RAFT) polymerization. The molecular design of the RAFT agents that are attached to the surfaces of the …

Interfacial Ligand Dynamics And Chemistry On Highly Curved Nanoparticle Surfaces: A Plasmon-Enhanced Spectroscopic Study, Esteban Villarreal

Theses and Dissertations

The dynamic interactions between capping ligands and nanoparticle surfaces play a critical role in guiding shape-controlled nanocrystalline growth, imparting unique physical and chemical properties to the nanoparticles. It has been well established that nanoparticles within the size regime of sub 5 nm possess unique heterogeneous catalytic properties, while sub wavelength metallic nanoparticles exhibit tunable plasmonic activity, when these properties are integrated into a single nanoparticle, it presents a significant opportunity to monitor, in real time, the molecular transformations associated with interfacial interactions at the nanoparticle surface. Using plasmon-enhanced Raman scattering as an ultrasensitive spectroscopic tool combining molecular fingerprinting with time …

Coordination Chemistry Of Carboranes And Furan Ligands On Transition Metal Cluster Complexes, Emmanuel Joseph Kiprotich

Theses and Dissertations

Chapter 1 presents the most relevant literature in the field of carborane chemistry. The focus is on icosahedral carboranes and the different methods of boron or carbon atoms substitution and functionalization. The direct addition of transition metal to boron atoms is covered in detail as well as strategies for cage opening of icosahedral carboranes.

Chapter 2 reports the preparation of some of the first polynuclear metal carbonyl cluster complexes where the closo-carborane cage: o-C₂B₁₀H₁₂ serves as a ligand on the face of one (Os₃(CO)₉(µ₃-4,5,9-C₂B₁₀H_{10 …}

Iron Uptake And Accumulation Is A Target Of Nickel Toxicity During The Lag Phase In Escherichia Coli, Geoffrey Tuttle Ford

Theses and Dissertations

Various transition metals are essential to all forms of life, and are only required in trace amounts. But this dependence comes as a double-edged sword. All organisms must maintain a careful intracellular quota that does not traverse outside an acceptable range. One transition metal in particular is nickel. The importance of this transition metal has been debated widely and its function varies greatly between organisms, including bacteria. However, the adverse effects caused by over exposure to this metal have been the center of much experimentation in recent years. Still, the mechanisms of nickel toxicity and the subsequent effects on cellular …

Ligand-Induced Magnetic Changes In Metal Thin Films, Fiona Senta Oberbeck-Oxsher

Theses and Dissertations

The investigation of magnetic properties of thin films whose surfaces were modified by organic molecules shows that the addition of any functional group to the surface measurably changes the magnetic properties. The effect often scales with ligand strength and is not limited to surfaces with ferromagnetic properties. Improving upon the technique developed by Knaus et al. [1], a stable and sensitive device was developed to measure this magnetic effect using the planar Hall effect (PHE) in order to shed light onto controversial questions of purported paramagnetism of thiolated gold. There is a measureable non-diamagnetic response of thin gold layers when …

Structural And Functional Studies Of Nicotinamide Adenine Dinucleotide And Streptolysin S Biosynthesis Proteins From Streptococcus Pyogenes, William T. Booth

Theses and Dissertations

Invasive infections caused by Streptococcus pyogenes, also known as Group A Strep (GAS), results in approximately 600,000 deaths annually. With evidence of antibiotic-resistant strains of this bacterium on the rise, there is a need for the identification of new drug targets to control these infections. In our approach we target the quinolinate-salvage pathway (QSP) and the streptolysin S (SLS) biosynthesis pathway. The QSP provides a secondary pathway for NAD+ biosynthesis within this organism; the SLS pathway leads to the formation of a quorum sensing molecule (SLS). We hypothesize that inhibition of the pathways will lead to GAS cell death or …

The Development Of A High Resolution Deep-Uv Spatial Heterodyne Raman Spectrometer, Nirmal Lamsal

Theses and Dissertations

Raman spectroscopy is a light scattering technique that has a huge potential for standoff measurements in applications such as planetary exploration because a Raman spectrum provides a unique molecular fingerprint that can be used for unambiguous identification of target molecules. For this reason, NASA has selected a Raman spectrometer as one of the major instruments for its new Mars lander mission, Mars 2020, in the search for biomarkers that would be the indicators of past or present life. Raman scattering is strongest at UV wavelengths because of the inherent increase in the Raman cross section at shorter wavelengths and because …

The Chemistry Of Photography, Nichole Marie Witten

Senior Theses

People nowadays are used to instant gratification when it comes to taking photographs. They look at a digital display, click a button, and get a perfectly focused and lighted picture that they can see right away. New technologies enable people to have pocket-sized digital cameras, their smart phones, with them at all times, and they’re easy convenient, and fast. Behind a single lens reflex (SLR) film camera, the scenario is much different. More time is needed in framing the image and adjusting the aperture and shutter speed to get the correct exposure, and the film must be processed darkroom before …

Impact Of Ocean Acidification On Aphotic Biogeochemical Production Of Reactive Oxygen Species, Sarah Ann Murphy

Theses and Dissertations

Reactive oxygen species (ROS) are critical to global maintenance of the global organic carbon cycle, sulfur cycle, oxygen cycle, and transition metal cycles. The primary source of ROS is commonly considered to be photolysis or photochemically driven reactions, however ROS also exist in aphotic zones. A geochemical mechanism for the same in dark environments based on the tidally driven, episodic movement of anoxic groundwaters through oxidized, Fe(III) rich sediments is shown. Predictive models were developed based on in vitro experiments and tested using sediment samples collected from a saline tidal creek in the estuary at Murrell’s Inlet, South Carolina. These …

Facile Method For Large Scale Alignment Of One Dimensional Nanoparticles And Its Biomedical Application, Sheng Feng

Theses and Dissertations

Topographical cues can profoundly affect cellular behaviors. This thesis investigate how to utilize the topographical cues generated by two techniques, flow assembly and electrospinning, to regulate cellular behaviors.

First of all, a facile and robust method to align one-dimensional (1D) nanoparticles (NPs) in large scale has been developed. Using flow assembly, representative rod-like nanoparticles, including tobacco mosaic virus (TMV), gold nanorods and bacteriophage M13, have been aligned inside capillaries by controlling flow rate and substrate surface properties. The properties of 1D NPs, such as stiffness and aspect ratio, play a critical role in the alignment. Furthermore, these hierarchically organized structures …

Metals On Titania/Hopg As Models For Heterogeneous Catalysts, Randima Piyumalie Galhenage

Theses and Dissertations

The work done in this thesis is mainly focused on understanding the nanoscale morphology and activity of model heterogeneous catalysts. In order to do this we design and prepare model catalytic surfaces in ultrahigh vacuum (UHV) and study these surfaces using electron and ion based microscopies and spectroscopies. The nucleation, growth and chemical activity of mono and bimetallic clusters on TiO₂(110) were investigated in order to understand how activity is influenced by cluster sizes, interactions with the oxide support and surface compositions of the bimetallic clusters. For example, Au-based and Pt-based bimetallic clusters such as Co-Au, Co-Pt, and …

Self-Assembly And Ring-Opening Metathesis Polymerization Of A Bifunctional Carbonate–Stilbene Macrocycle, Yuewen Xu, Weiwei L. Xu, Mark D. Smith, Linda S. Shimizu

Faculty Publications

No abstract provided.

Advancements In The Design, Synthesis, And Application Of Polybenzimidazoles, Alexander Lanier Gulledge

Theses and Dissertations

The overall goal of the work presented within this thesis is to investigate, understand, and develop structure-property relationships in regards to polymer structure, membrane stability, and device performance. Previous work has shown that material properties such as acid loading, proton conductivity, mechanical integrity, and device performance can be attributed to polymer structure, chemical functionality, and polymer architecture (homo, random, co-polymer etc.). Developing and understanding these relationships is critical to the advancement of fuel cell technology. Within this thesis, several of these relationships are investigated and reported.

Novel polymers and copolymer systems have been developed in this research and have significantly …

Short, Strong Halogen Bonding In Co-Crystals Of Pyridyl Bis-Urea Macrocycles And Iodoperfluorocarbons, Michael F. Geer, James Mazzuca, Mark D. Smith, Linda S. Shimizu

Faculty Publications

No abstract provided.

Programmable Polymers Preparation Optimization And Applications On Solute Templates, Yinyan He

Theses and Dissertations

Programmable polymer is a type of stimuli-responsive polymer which can keep their induced properties after removal of the stimulu, as well as programmable polymers maintain the general properties as stimuli-responsive polymers, such as recognize and respond to the stimulus. The previous reported solvent Caryl-Nimide bonds based programmable polymers (SPP-1) can freely rotate and change the carboxylic acid recognition group orientation in response to templates. Solvent templates were used in the SPP-1. One potential application for SPPs is using their recognition and memory properties for the identification and separation of mixture solutions of various analytes. In my first project, I wanted …

New Ruthenium And Osmium Carbonyl Cluster Complexes With Main Group Bridging Ligands Having Unusual Structures And Bonding, Yuwei Kan

Theses and Dissertations

The reaction of IrRu3(CO)13(µ-H), 2.1 with HSnPh3 in hexane solvent at reflux has provided the new mixed metal cluster compounds Ir2Ru2(CO)11(SnPh3)(µ-H)3, 2.2 and IrRu3(CO)11(SnPh3)3(µ-H)¬4, 2.3 containing SnPh3 ligands. Compound 2.2 which was obtained in low yield (3%) contains a closed cluster having two iridium and two ruthenium atoms, one SnPh3 ligand and three bridging hydride ligands. Compound 2.3 has a butterfly structure for the four metal atoms with three SnPh3 ligands and four bridging hydride ligands around the periphery of the cluster. When compound 2.3 was heated to 97 oC for 30min, IrRu3(CO)9(μ-η2-C6H5)(μ4-SnPh)2(μ-SnPh2), 2.4 was formed by cleavage of phenyl …

Investigations Of The Non-Covalent Ch-Π Interactions Using Molecular Torsional Balances, Chen Zhao

Theses and Dissertations

Several bicycle N-arylimide based molecular balances were designed to study aliphatic CH-pi interactions and aromatic CH-pi interactions (edge-to-face arene-arene interactions). In each case, the geometries of the interactions were characterized in the solid-state via X-ray analysis, and the strengths of interactions were characterized in solution by their folded/unfolded ratios, as measured by integration of their 1H NMR spectra.

The balances are very sensitive to variations in the strengths of weak non-covalent interactions. Several different aspects of the CH-pi interactions were studied, such as sterics, conformational entropy, cooperativity, deuterium isotope effect, substitution effects, and solvent effects. It showed that due to …

Il-6 Regulation On Skeletal Muscle Mitochondrial Remodeling During Cancer Cachexia In The ApcMin/+ Mouse, James P. White, Melissa J. Puppa, Shuichi Sato, Song Gao, Robert L. Price, John W. Baynes, Matthew C. Kostek, Lydia E. Matesic, James A. Carson

Faculty Publications

BACKGROUND:

Muscle protein turnover regulation during cancer cachexia is being rapidly defined, and skeletal muscle mitochondria function appears coupled to processes regulating muscle wasting. Skeletal muscle oxidative capacity and the expression of proteins regulating mitochondrial biogenesis and dynamics are disrupted in severely cachectic Apc^Min/+ mice. It has not been determined if these changes occur at the onset of cachexia and are necessary for the progression of muscle wasting. Exercise and anti-cytokine therapies have proven effective in preventing cachexia development in tumor bearing mice, while their effect on mitochondrial content, biogenesis and dynamics is not well understood. The purposes of …

The Regulation Of Skeletal Muscle Protein Turnover During The Progression Of Cancer Cachexia In The ApcMin/+ Mouse, James P. White, John W. Baynes, Stephen L. Welle, Matthew C. Kostek, Lydia E. Matesic, Shuichi Sato, James A. Carson

Faculty Publications

Muscle wasting that occurs with cancer cachexia is caused by an imbalance in the rates of muscle protein synthesis and degradation. The Apc(Min/+) mouse is a model of colorectal cancer that develops cachexia that is dependent on circulating IL-6. However, the IL-6 regulation of muscle protein turnover during the initiation and progression of cachexia in the Apc(Min/+) mouse is not known. Cachexia progression was studied in Apc(Min/+) mice that were either weight stable (WS) or had initial (≤5%), intermediate (6-19%), or extreme (≥20%) body weight loss. The initiation of cachexia reduced %MPS 19% and a further ∼50% with additional weight …

Efficient Quantum Trajectory Representation Of Wavefunctions Evolving In Imaginary Time, Sophya V. Garashchuk, James Mazzuca, Tijo Vazhappilly

Faculty Publications

The Boltzmann evolution of a wavefunction can be recast as imaginary-time dynamics of the quantum trajectory ensemble. The quantum effects arise from the momentum-dependent quantum potential – computed approximately to be practical in high-dimensional systems – influencing the trajectories in addition to the external classical potential [S. Garashchuk, J. Chem. Phys.132, 014112 (2010)]. For a nodelesswavefunction represented as ψ(x, t) = exp ( − S(x, t)/ℏ) with the trajectory momenta defined by ∇S(x, t), analysis of the Lagrangian and Eulerian evolution shows that for bound potentials the former …

A Bis-Urea Naphthalene Macrocycle Displaying Two Crystal Structures With Parallel Ureas, Michael F. Geer, Mark D. Smith, Linda S. Shimizu

Faculty Publications

Herein we synthesized a bis-urea macrocycle from 2,7-dimethylnaphthalene that displays an unusual parallel urea conformation. The naphthalenes also adopt a bowl shape over the anticipated parallel planar orientation. Crystallization of the macrocycle from different solvent systems affords two solvated forms. 1·DMSO·(H₂O)₂ has an extended columnar structure where parallel macrocycles are linked by intervening hydrogen bonded water molecules. In 1·(MeOH)₂direct hydrogen-bonds link the macrocycles into chains, which hydrogen-bond with methanolmolecules to form a layered structure.

Guest Induced Transformations Of Assembled Pyridyl Bis-Urea Macrocycles, Kinkini Roy, Chun Wang, Mark D. Smith, Mahender B. Dewal, Arief C. Wibowo, Julius C. Brown, Shugo Ma, Linda S. Shimizu

Faculty Publications

Pyridine macrocycles with no cavities assembled into close packed columns yet absorbed guests including hydrogen, carbon dioxide, and iodine.

Tetraaquabis(3-Fluoropyridine-4-Carboxylato-Κn)Zinc(Ii) Dihydrate, Jonetha Fleming, Jennifer Kelley, Leroy Peterson Jr., Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, [Zn(C₆H₃FNO₂)₂(H₂O)₄]·2H₂O, the Zn^II atom is octahedrally coordinated in a ZnO₄N₂ environment by two 3-fluoropyridine-4-carboxylate (3-fpy4-cbx) ligands and four water molecules. The [Zn(3-fpy4-cbx)₂(H₂O)₄] molecules form a three-dimensional network through strong O-HO and weak O-HF hydrogen bonds between 3-fpy4-cbx and water molecules. The crystal used for data collection was a twin, with the twin law corresponding to a 180° rotation about the real-space [001] axis. The major twin fraction refined to 0.795 (1).

Poly[[(Μ-2,2'-Bipyrimidine-Κ4N1,N1':N3,N3')(Μ-Sulfato-Κ2O:O')Zinc(Ii)] Monohydrate], Aaron Oxendine, Jennifer Kelley, Leroy Peterson Jr., Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, {[Zn(SO₄)(C₈H₆N₄)]·H₂O}_n, the Zn^II atom is in a distorted octahedral environment. The Zn^II atoms are bridged by both 2,2'-bipyrimidine and sulfate ligands, thus forming a three-dimensional polymeric metal-organic solid that contains uncoordinated water molecules in the interstitial space. O-HO hydrogen bonding consolidates the crystal structure.

A Dielectric Affinity Microbiosensor, Xian Huang, Siqi Li, Jerome S. Schultz, Qian Wang, Qiao Lin

Faculty Publications

We present an affinity biosensing approach that exploits changes in dielectric properties of a polymer due to its specific, reversible binding with an analyte. The approach is demonstrated using a microsensor comprising a pair of thin-film capacitive electrodes sandwiching a solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid), a synthetic polymer with specific affinity to glucose. Binding with glucose induces changes in the permittivity of the polymer, which can be measured capacitively for specific glucose detection, as confirmed by experimental results at physiologically relevant concentrations. The dielectric affinity biosensing approach holds the potential for practical applications such as long-term continuous glucose monitoring.

Quantum Trajectory Dynamics In Imaginary Time With The Momentum-Dependent Quantum Potential, Sophya Garashchuk

Faculty Publications

The quantum trajectory dynamics is extended to the wave function evolution in imaginary time. For a nodeless wave function a simple exponential form leads to the classical-like equations of motion of trajectories, representing the wave function, in the presence of the momentum-dependent quantum potential in addition to the external potential. For a Gaussian wave function this quantum potential is a time-dependent constant, generating zero quantum force yet contributing to the total energy. For anharmonic potentials the momentum-dependent quantum potential is cheaply estimated from the global Least-squares Fit to the trajectory momenta in the Taylor basis. Wave functions with nodes are …

Rfx2 Is A Candidate Downstream Amplifier Of A-Myb Regulation In Mouse Spermatogenesis, Gary C. Horvath, Malathi K. Kistler, Wilson Stephen Kistler

Faculty Publications

Background: Mammalian spermatogenesis involves formation of haploid cells from the male germline and then a complex morphological transformation to generate motile sperm. Focusing on meiotic prophase, some tissue-specific transcription factors are known (A-MYB) or suspected (RFX2) to play important roles in modulating gene expression in pachytene spermatocytes. The current work was initiated to identify both downstream and upstream regulatory connections for Rfx2.

Results: Searches of pachytene up-regulated genes identified high affinity RFX binding sites (X boxes) in promoter regions of several new genes: Adam5, Pdcl2, and Spag6. We confirmed a strong promoter-region X-box for Alf, a germ cell-specific variant of …

Wavepacket Approach To The Cumulative Reaction Probability Within The Flux Operator Formalism, Sophya Garashchuk, Tijo Vazhappilly

Faculty Publications

Expressions for the singular flux operator eigenfunctions and eigenvalues are given in terms of the Dirac δ-function representable as a localized Gaussian wavepacket. This functional form enables computation of the cumulative reaction probability N(E) from the wavepacket time-correlation functions. The Gaussian based form of the flux eigenfunctions, which is not tied to a finite basis of a quantum-mechanical calculation, is particularly useful for approximate calculation of N(E) with the trajectory based wavepacket propagation techniques. Numerical illustration is given for the Eckart barrier using the conventional quantum-mechanical propagation and the quantum trajectory dynamics with the approximate quantum potential. N(E) converges with …