Chemistry Commons^™

Structural And Functional Study Of The Diheme Cytochrome C Subunit Of The Cytochrome Bc Complex In Heliobacterium Modesticaldum, Hair Yue

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation is focused on the structural and functional study of the unique diheme cytochrome c subunit of the cytochrome bc complex in H. modesticaldum, and its application in determining the stoichiometry between H. modesticaldum's cytochrome bc complex and its reaction center. Heliobacterium modesticaldum is a gram positive, anaerobic, anoxygenic photoheterotrophic bacterium. Its cytochrome bc complex (Rieske/cyt b complex) has some similarities to cytochrome b6f complexes from cyanobacteria and chloroplasts, and also shares some characteristics of typical bacterial cytochrome bc1 complexes. One of the unique features of the heliobacterial cytochrome bc complex is the presence of a diheme cytochrome c …

A Study On The Structure And Photodetachment Dynamics Of Copper Based Molecular Anions Using Photoelectron Spectroscopy, Nicholas Stephen Holtgrewe

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation represents a study of the effects of electron molecule interactions in the detachment and dissociation dynamics of copper based molecular anions. Results are presented on the photodetachment of small copper oxide CuO_n⁻ (n = 1, 2) and copper fluoride CuF _n⁻ (n = 1, 2) molecular anions. Effects of different resonances are explored using the photoelectron angular distributions (PADs) and the relative intensity variations in vibrational channel cross sections. The specific resonances studied include dipole bound resonances, in which the electric dipole moment of the neutral molecule captures the outgoing electron, and electronic Feshbach resonances, …

Photosynthetic Chromophore Analogs And Biohybrid Antenna For Light Harvesting, Joseph William Springer

Arts & Sciences Graduate Student Theses and Dissertations

Photosynthetic chromophore analogs are studied, starting with simplified structures and systematically building complexity to elucidate overarching design principles. The general goals are to achieve an artificial light-harvesting system that exhibits broad spectral coverage, including extension well into the photon rich red and near-infrared portions of the solar spectrum. For example, the spectral properties of chlorophylls are primarily a consequence of the 13¹-oxophorbine base macrocycle, with further tuning provided by the dramatic difference in auxochromic effects of a given substituent at the 7- versus 3-position, consistent with Gouterman's four-orbital model. While light-harvesting antennas in photosynthetic bacteria generally have near-quantitative …

Assessing Optic Neuritis In A Mouse Model Of Multiple Sclerosis With Diffusion Mr Imaging, Chia-Wen Chiang

Arts & Sciences Graduate Student Theses and Dissertations

Optic neuritis (ON) is an early manifestation in patients of multiple sclerosis (MS), typically resulting in visual dysfunction. The inflammatory demyelination of the optic nerve in ON closely resembles pathologies of the rest of central nervous system (CNS) white matter in MS. Since accumulated axonal degeneration in MS was considered as the potential cause leading to permanent disability, correlating optic nerve pathology and visual function in ON could be a model system to investigate the relationship between functional outcome and neuropathology. It may also present a new way to reflect the disease progression in MS. Various MR techniques have been …

Source Assessment Of Deposited Particles In A Slovenian Show Cave (Postojnska Jama): Evidence Of Long-Lasting Anthropogenic Impact, Gregor Muri, Aleksandra Jovičić, Andrej Mihevc

International Journal of Speleology

Postojnska jama (Postojna Cave) is one of the most famous karst caves in the world and has been a well-known tourist attraction for nearly 200 years. It is particularly famous for its unique double-track railway. Eight heavy metals – aluminium (Al), chromium (Cr), copper (Cu), iron (Fe), lead (Pb), manganese (Mn), strontium (Sr), and zinc (Zn) – were determined in dust deposits by ICP-MS in order to assess sources of deposited particles on the cave walls. The samples were collected along the main passage in the cave, at different horizontal and vertical levels, in order to test horizontal homogeneity and …

The Role Of Fcγ Receptor In Activation Of Nf-Κb In Follicular Dentritic Cells, Jonathan Scoville, Dr. Gregory F. Burton

Journal of Undergraduate Research

The purpose of this project was to determine the reason why the transcription factor NF-κB is not activated when immune complexes (especially those containing HIV) bind to its Fcγ-Receptor, but is activated in FDC’s when the same immune complex (IC) binds to its Fcγ-Receptor. We believed that certain molecules in B-cells bind to Fcγ-Receptor that are not present in the FDC to block activation of transcription. Our purpose was to successfully isolate these molecules in B cells, and then use them to perform the same function in CD 4 bearing T cells, HIV’s main target during infection. Our goal was …

Usage Of Csa-13 In The Antibiotic Lock Technique For Hemodialysis Catheters, Jonathan O. Wright, Dr. Paul Savage

Journal of Undergraduate Research

The projects that I have worked on this past year have been focused on a novel group of antibiotics developed Dr. Savage’s lab. The antibiotics, called ceragenins or cationic steroid antibiotics (CSA’s), are molecules synthesized from cholic acid and mimic the structure and functionality of antimicrobial peptides found in nature. Although the CSA’s are much smaller than the peptides, they have similar structural aspects, a hydrophobic side as well as a cationic side, and are believed to have a similar mechanism of action. They, like the antimicrobial peptides, have been found to be effective against a broad spectrum of bacteria, …

Hiv Tropism And The Germinal Center, Andrew Jay Thorne, Dr. Greg Burton

Journal of Undergraduate Research

Human immunodeficiency virus (HIV) infection and resultant development of autoimmune deficiency syndrome (AIDS) killed 1.8 million people and infected 2.2 million more just in 2009. Not only are those whose personal lifestyle choices put them at risk for HIV infection affected. As of 2009, there are 16.6 million orphaned children living whose parent(s) died from AIDS. These numbers are difficult to ignore, and show the need for further improvement of treatment and prevention.

Organic Synthesis Of Sulfonated Glycosphingolipids To Study Natural Killer T Cell Stimulation, Dylan Pratt, Brian Anderson, Dr. Paul B. Savage

Journal of Undergraduate Research

The body’s innate immune system is continuously checking our body for molecular structures of antigens on potential pathogens. The CD1d antigen-presenting cell presents glycolipid antigens to Natural Killer T (NKT) cells. NKT cells start a signaling pathway that produces an inflammatory response. 3’’-O-sulfo-Beta-galactosylceramide has been shown to produce a stimulatory response with NKT cells [1]. This project involves the organic synthesis of structural variations of 3’’-O-sulfo-Beta-galactosylceramide. All of these molecules will be tested on their ability to stimulate NKT cells.

The Role Of Inwardly-Rectifying Potassium Channels In Drosophila Development, Brandon Gassaway, Dr. Emily Bates

Journal of Undergraduate Research

Anderson-Tawil Syndrome (ATS) is characterized by morphological defects including clinodactyly (abnormal curvature of digits), syndactyly (fused digits), micrognathia (small jaw), cleft palate, and hypertelorism (wide-set eyes) as well as periodic paralysis and heart arrhythmia. Mutations in inwardly rectifying potassium (Irk) channels are found in patients with ATS. Expression of mutant Irk channels causes similar physiological and morphological defects in mice.

Covalent Solutions To Biofilm Formation: Incorporation Of Antimicrobial Ceragenins Into Polymer-Brush Coatings, Jeffrey Clark, Dr. Paul Savage

Journal of Undergraduate Research

The accumulation of biofilm on urinary catheters and endotracheal tubes is one of the leading causes of hospital-acquired infection1. A variety of techniques have been developed to help mitigate this problem. One of these techniques is to coat devices with a biofilm-resistant polymer brush coating. Although these coatings may prevent adhesion by bacteria, they do not actively kill invading bacteria.

Synthesis Of 2-Dos Mimic From Diacetone-D-Glucose, Susie Choi, Dr. Young Wan Ham

Journal of Undergraduate Research

2-deoxystreptamine (2-DOS) mimic was to be synthesized in several steps from commercially available diacetone-D-glucose in an effort to prepare novel amino acid residues for antiviral therapeutic development. The method presented in this paper was given up due to unexpected problems occurring at three of the 10 steps. A new method, which uses xylitol as the starting material and takes fewer steps, is to be used.

Using Dip-Pen Nanolithography To Orient Dna Origami, Michael Lydiksen, Dr. Adam Woolley

Journal of Undergraduate Research

Imagine having the ability to control the placement of atoms with reasonable speed and accuracy. Having this capacity naturally brings with it incredible technological advancements in areas such as integrated circuits and biochemistry. An exciting process known as dip-pen nanolithography (DPN) that I have been actively perfecting over the past year gives researchers the ability to control the placement of individual atoms at a desired location on a substrate. I have presented some of my results last spring in BYU’s annual College of Physical and Mathematical Science Spring Research Conference.

Structure Of Octahedral Polyomavirus, Robert Swenson, Dr. David Belnap

Journal of Undergraduate Research

Polyomaviruses (PVs) are viruses that can cause tumors in mammals and fatal diseases in birds. Knowles et al. (2) estimated that over 90% of the human population is infected with a polyomavirus, but these infections are usually dormant, and only show symptoms in patients with compromised immune systems. PVs normally form a capsid with icosahedral symmetry whose structure is known (Figure 1). In this structure, the major capsid protein (VP1) forms a stable pentamer with the C-terminal arms of the proteins extending outwards. VP1 pentamers (filled pentagons, Figure 1) interact with five other pentamers on some vertices, and with six …

Temporally Overlapped But Uncoupled Motions In Dihydrofolate Reductase Catalysis, C. Tony Liu, Lin Wang, Nina Goodey, Philip Hanoian, Stephen J. Benkovic

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Temporal correlations between protein motions and enzymatic reactions are often interpreted as evidence for catalytically important motions. Using dihydrofolate reductase as a model system, we show that there are many protein motions that temporally overlapped with the chemical reaction, and yet they do not exhibit the same kinetic behaviors (KIE and pH dependence) as the catalyzed chemical reaction. Thus, despite the temporal correlation, these motions are not directly coupled to the chemical transformation, and they might represent a different part of the catalytic cycle or simply be the product of the intrinsic flexibility of the protein.

Substituent Effects On Reactivity And Allergenicity Of Benzoquinone, Wilbes Mbiya

Dissertations and Theses

Benzoquinone (BQ) is an extremely potent electrophilic contact allergen that haptenates endogenous proteins through Michael addition (MA). It is also hypothesized that BQ may haptenate proteins via free radical formation. The objective of this study was to assess the inductive effects (activating and deactivating) of substituents on BQ reactivity and the mechanistic pathway of covalent binding to nucleophilic thiols. The BQ binding by Cys34 on human serum albumin was studied, and for reactivity studies, nitrobenzenethiol (NBT) was used as a surrogate for protein binding of the BQ and benzoquinone derivatives (BQD). Stopped flow techniques were used to determine pseudo-first order …

Application Of Iron Complexes As Catalysts In C-O And C-C Bond Forming Reactions, Pushkar Sudhakar Shejwalkar

Dissertations

‘Green Chemistry’ is a philosophy that encourages chemists in research and industry to reduce toxic waste for cleaner and safer chemical production. Oxidation reactions are commonly used in industry and are traditionally achieved by methods that involve toxic metals (such as chromium) and solvents, generating considerable waste compared to the value of the final product. The Mukaiyama Aldol reaction is another organic reaction that utilizes metals as Lewis acid catalysts. The principles of Green Chemistry suggest that chemical reactions should be performed with a maximum of efficiency and with a minimum of side product formation, accompanied by a minimal use …

Sustainable Development Of Tajikistan: Perspectives For Tajik Aluminum Company (Talco), Tahmina Azizova

Capstone Collection

Energy efficiency is one the most pressing objectives of the XXI century. Energy efficiency is an intrinsic part of sustainable development of any country. But it is especially crucial for country like Tajikistan, which has an inefficient energy use pattern as a result of the legacy of Soviet era. Energy resources required for economic development can be obtained not only through increased extraction of raw materials, but also through improved energy efficiency at the demand side. Tajikistan imports about 35 percent of its energy needs, which makes the country extremely energy-dependent. That leads to an obvious inference that for Tajikistan …

Siloles Bearing Coordination-Active 2,5-Substituents: Synthesis, Reactivity, Structural And Spectral Properties., James Bryan Carroll

Dissertations

Siloles, or silacyclopentadienes and other group 14 metalloles are structurally analogous to their all-carbon analogue, cyclopentadiene, except for the heavy group 14 element (i.e., Si, Ge, Sn, and Pb) in the 1-position. The placement of the heavy element in this position allows for unique properties, such as high electron affinity, mobility, and bathochromically shifted optical spectra, as compared to cyclopentadienes, and the relatively low-lying lowest-unoccupied molecular orbital (LUMO) helps to account for these properties. The substituents about the silole have a significant impact on the electronics and properties observed, with 2,5-substituents inducing the most substantive changes. Even as many 2,5-substituents …

Mechanism Of Ubiquitin Ligation And Lysine Prioritization By A Hect E3, Hari B. Kamadurai, Yu Qiu, Alan Deng, Joseph S. Harrison, Chris Macdonald, Marcelo Actis, Patrick Rodrigues, Darcie J. Miller, Judith Souphron, Steven M. Lewis, Igor Kurinov, Naoaki Fujii, Michal Hammel, Robert Piper, Brian Kuhlman, Brenda A. Schulman

College of the Pacific Faculty Articles

Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT …

Organic Wastewater Chemicals In Silver Bow Creek - Butte To Warm Springs Ponds, Heidi Reid, Katie Hailer, Ph.D., Steve Parker, Ph.D.

2013 Undergraduate Research

The purpose of this study is to detail and analyze the distribution, concentration, and loads of 5 organic compounds along Silver Bow Creek in Butte, Montana from the Municipal Wastewater treatment plant to the Warm Springs Ponds. The chemicals analyzed include Carbamazepine (pharmaceutical), Miconazole (fungicide) and three antibiotics – Sulfamethoxazole, Thiabendazole, and Ciprofloxacin.

This project begins a 2 year study to analyze 6 additional compounds (11 compounds total), to develop an effective method to detail and analyze OWCs using Mass Spectrometer/Liquid chromatography system, and to aid in assessment of aquatic health and ongoing restoration work. The EPA method 1694 was …

Type‐I Collagen Modeled As A Liquid Crystal, Alexander Thomas

Rose-Hulman Undergraduate Research Publications

Type-I collagen is found in numerous parts of the human body. This research has been focused on the macrostructures of type-I collagen and its implications on the physical properties of certain tissues. Furthermore, the self-assembly of the three α chains into the collagen triple helix has been studied in order to understand the biochemical pathway in which type-I collagen is produced.

Approaches For Improved Positional Proteomics, Yanjie Jiang

LSU New Orleans Theses and Dissertations

Positional proteomics is emerging as an attractive technique to characterize protein termini, which play important biological roles in cells. Even with the advances in past decades, there still are areas for improvement. This thesis focuses on improving data quality and assignment confidence in positional proteomics.

A novel workflow was designed for the large-scale identification of protein N-terminal sequences. 4-sulfophenyl isothiocyanate (SPITC) is used for N-termini sulfonation; Upon higher energy collisional dissociation (HCD), SPITC peptides in electrospray ionization ESI generate predominately y-type ion series; such simplification of spectra enables the identification of N-termini with high fidelity. The presence of b_{1 …}

In Situ Study Of The Photodegradation Of Carbofuran Deposited On Tio2 Film Under Uv Light, Using Atr-Ftir Coupled To Hs-Mcr-Als, Abderrahman Atifi, Kazimierz Czarnecki, Hafida Mountacer, Michael D. Ryan

Chemistry Faculty Research and Publications

The in situ study of the photodegradation of carbofuran deposited on a TiO₂ catalyst film under UV light was carried out using the ATR-FTIR technique. The data were analyzed using a Hard–Soft Multivariate Curve Resolution-Alternating Least Squares (HS-MCR-ALS) methodology. Using S-MCR-ALS, four factors were deduced from the evolving factor analysis of the data, and their concentrations and spectra were determined. These results were used to draw qualitative and quantitative analyses of the major products of carbofuran photodegradation. The results of this analysis were in good agreement with GC-MS results and with reported mechanisms. Hard-MCR-ALS was then used to refine …

2013 Annual Meeting Program

Journal of the South Carolina Academy of Science

No abstract provided.

Use Of Thermodynamic Models For Optimizing Fuel Treatment Processes, Shawn Pj Kirby, Andrew Guenthner

STAR Program Research Presentations

Dyes are often added to fuels for tax purposes, but they cause degradation of the fuels. It would be advantageous to remove the dyes prior to their use in critical aerospace applications. Current technologies vary in the efficiency with which they can remove unwanted dyes from fuel sources. We have used Hansen Solubility Parameters to develop an “ideal solvent” that can be used to extract these dyes from fuel. This will also be applied to removal of sulfur compounds from fuels. Sulfur compounds in fuels create sulfates during combustion, which in turn react with water to make sulfuric acid. Sulfuric …

The Influence Of Soil Organic Matter Stabilization Mechanisms On Carbon Mean Residence Time Within Various Ecosystems In The United States, Vicky Lynn Giese, Kate Heckman Phd

STAR Program Research Presentations

Some terrestrial ecosystems and soils serve as carbon sinks, partially offsetting rising atmospheric CO₂ levels. Physiochemical mechanisms of soil organic matter (SOM) stabilization affect how carbon stocks respond to global warming. In order to clarify the variance in SOM stabilization mechanisms across different soil types, SOM abundance, distribution and mean residence time (MRT) were compared for thirty-two soil samples from six ecosystems across the United States. Soils were previously described, collected and archived by the United States Geological Survey. Samples were processed by LLNL at the Center for Accelerator Mass Spectrometry (CAMS) using density fractionation to separate particulate organics …

Investigation Of Ozone In Urban And Rural Areas Of California, Mia J. Hiles, David Parrish

STAR Program Research Presentations

Ozone is the air pollutant about which we have probably heard the most. Two types of ozone exist: stratospheric and tropospheric. Stratospheric ozone absorbs most of the damaging ultra-violet sunlight and tropospheric ozone comes into direct contact with life-forms and is toxic at high levels. Ozone concentration in California has been studied for over five decades, and there is a long history of control efforts. During 2010, California Air Resources Board (CARB) and National Oceanic and Atmospheric Administration (NOAA) conducted a major climate and air quality study in California called CalNex 2010 (California Research at the Nexus of Air Quality …

Io3- And I- Sorption From Groundwater By Layered Double Hydroxides, Abbey Rickelmann, Emily Campbell, Natasha Pence, Tatiana Levitskaia, Sayandev Chatterjee, Frances Smith

STAR Program Research Presentations

Several subsurface water plumes are found at the Hanford U.S. DOE site. These plumes contain many different types of hazardous components including radioactive iodate (IO₃^-) and iodide (I^-), which may have deleterious health effects. To selectively uptake IO₃^- and I^-, inorganic layered double hydroxide (LDH) compounds were synthesized and tested. LDHs are mixed transition metal hydroxides that contain positively charged layers that undergo anion exchange. When LDHs are submerged in the plume water, they can selectively uptake IO₃^- and I^- and remove them from the plume. Raman spectroscopy …

Effects Of Composition And Separation Techniques On The Structure Of Aggregates In The Milk Fat Globular Membrane, Tristan Dilbeck, Jose Ibarra, Rafael Jimenez-Flores, Tracey Nguyen

STAR Program Research Presentations

The milk fat globular membrane (MFGM) is a complex structure composed mainly of phospholipids, sphingolipids, and membrane specific proteins. The composition and size of the MFGM differs based on the isolation, purification, and techniques used in analysis of the membrane as well as physiological, chemical, and mechanical factors present during its creation. The purpose of this experiment is to analyze the effects of separation techniques and composition of lipids and proteins on the structure of aggregates in the MFGM. The aggregates found in whey protein isolate (95% pure whey protein), whey buttermilk (whey protein and phospholipids), and sweet buttermilk (whey …