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Microbial Pretreatment Of Waste For Anaerobic Digestion, Braden Myers, Jaron Hansen

Journal of Undergraduate Research

This project will demonstrate the technical feasibility of microbial pretreatment of lignocellulose for enhanced production of biogas when coupled with secondary anaerobic digestion as well as optimize the entire process.

Mitochondrial Membrane Lipids Regulator In B-Cll Leukemia Research, Brooke Keeton, Dr. John Prince

Journal of Undergraduate Research

B-cell chronic lymphocytic leukemia (B-CLL) is the most common type of leukemia in adults.1 Over 75% of patients diagnosed with B-CLL are over the age of 50 years old, and have a median survival between 18 months and 3 years.2 B-CLL originates from a mutation in the DNA of white blood cells, the potent infection fighters of the body. This genetic mutation produces abnormal white blood cells, rendering them nonfunctional and resulting in a weak immune system. While this mutation originally occurs in the bone marrow, it slowly invades other parts of the body, including the lymph nodes, liver, and …

Non-Covalent Affinity Materials For Protein Structure Determination Via Single Particle Reconstruction Analysis Cryo-Electron Microscopy, Minji Ha

Open Access Theses

Single particle analysis (SPA) by cryogenic electron microscopy (Cryo-EM) is one of the powerful tools for determining biological macromolecule structure, particularly when combined with computational methods or X-ray crystallography. However, the SPA is challenged by sample processing efficiency. In this work, polyrotaxane (PRTx) was designed and synthesized such that laterally and rotationally mobile lysine nitrolicacetic acid (Lys-NTA) modified α-cyclodextrins (α-CD) were threaded onto a polyethylene glycol (PEG) core. Polyrotaxanes threaded with amine modified α-CD were also designed and synthesized for stoichiometric control of His-tagged protein capture by PRTx. For higher efficiency of single particle analysis along a single strand of …

Assessment Of Silk Degradation Using Pyrolysis, Conor Makepeace

Honors Projects in Science and Technology

The purpose of this research is to investigate the molecular constitution of silk and the specific causes of post-production degradation in silk material. This capstone project focused specifically on the conditions and degradation of ancient Chinese silk products provided by the Chinese National Silk Museum. Modern silk products were artificially degraded and compared to the ancient silk using Py-GC-MS and comparative analytic techniques. This investigation revealed that the ancient silk products most likely underwent degradation in elevated temperatures while in the presence of moisture and the absence of sunlight or UV radiation during long term burial.

Structural Changes In Dna Upon Binding In A 2:1 Motif To A Polyamide Minor Groove Binder: F -Ipp In 5'-Tagcta-3', Alexandra Kwit

Senior Honors Projects

Polyamide minor groove binders are known to disrupt cellular function when bound to DNA. In this project, the structural changes of the sequence 5'-TAGCTA-3', an important binding site for regulatory proteins in the EGFR pathway, were investigated when bound to f-IPP using molecular dynamics simulations. Changes in base-pair and base-pair-step parameters of slide, twist, and roll varied when f-IPP was added to the 5'-TAGCTA-3' system, causing the DNA backbone to stretch and increase in flexibility. Additionally, changes in dihedral angles of the DNA phosphate backbone upon binding impacted global features of the DNA in that the minor groove narrowed following …

Laboratory Studies On The Production Of Alpha-Pinene-Derived Organic Nitrates And Their Atmospheric Fate, Joel David Rindelaub

Open Access Dissertations

Currently, the formation yields of organic nitrates from the oxidation of biogenic volatile organic compounds, such as α-pinene, is highly uncertain, negatively impacting our knowledge on tropospheric ozone production and the fate of atmospheric NO_x. To lower this uncertainty, we quantified the organic nitrate yield from the OH radical oxidation of α-pinene under high NO_x conditions. The α-pinene- derived nitrates created in chamber experiments readily partitioned to the aerosol phase and underwent particle phase hydrolysis, indicating that these processes are likely a sink for atmospheric NO_x. The hydrolysis of organic nitrates was found to be …

Polyurethane Research For Applications In The Field Of Dentistry: Limiting Side Reactions In Monomer Development And Synthesizing N-Capped Polymenthide, Ellen M. (Ellie) Black

Honors Theses, 1963-2015

Modern dentistry has found uses for polyurethanes in both dental arch models and removable dental appliances. In an attempt to make polyurethanes from renewable resources, both naturally derived menthone and dihydrocarvone were oxidized in order to form menthide and dihydrocarvide, respectively. The resulting ester, if copolymerized could be modified to form a polyuria; however, dihydrocarvide synthesis was complicated by epoxidation. Different reaction environments with varying salts showed no positive effect on limiting epoxide products. A homopolymerization of menthide resulted in a polymenthide chain that was reacted in the presence of N,N'-Dicyclohexylcarbodiimide (DCC) in order to form an N-capped polymenthide chain. …

Investigations Into Uncharacterized Radical S-Adenosylmethionine Enzymes, Melissa Quintanilla

Honors Theses, 1963-2015

Radical S-adenosylmethionine (SAM) enzymes are a superfamily of enzymes that require the cofactor SAM for catalysis. These enzymes have diverse functions across all 3 domains of life, and are known to play roles in many biological pathways, including vitamin biosynthesis, synthesis of complex metal clusters, posttranslational RNA modification,DNA repair, and development of antibiotic resistance, among others. Radical SAM enzymes are characterized by the CX₃CX₂C motif, which is conserved throughout most members of the family. A number of genes have been identified which contain the CX₃CX₂C motif and other amino acid sequences …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Eagles Fly to Denver for Chemistry Presentations

Perspectives On Science Literacy: A Comparative Study Of United States And Kenya, Kermin Martinez-Hernandez, Chinwe Ikpeze, Irene Kimaru

Chemistry Faculty/Staff Publications

Results from a science literacy survey administered to the American and Kenyan educators are presented. Sixty-three educators from the U.S. and Kenya responded to a survey about their perspectives on science literacy. The research questions were designed to examine the factors that affect students’ performance in science, the skills required for students to be successful in science, and the challenges of teaching science and recommendations for improving scientific literacy in both countries. Results indicate that educators from both countries have similar concerns about science teaching and learning but they also face some unique problems. The participants were all in agreement …

A Bracketing Method For Proton Affinity Measurements Of Dehydro-And Didehydropyridines, Guannan Li

Open Access Theses

Proton affinity (PA) is a fundamental property that is related to the structure and reactivity of a molecule. Currently, very few experimental PA values are available for organic radicals and none for biradicals. Equilibrium methods cannot be used for these measurements. The traditional bracketing method is based on monitoring reactions of different reference bases with known proton affinities with the protonated analyte for the occurrence of exothermic proton transfer to determine the upper and lower limits of proton affinity. However, the energy deposited into the precursor ions upon CAD when forming protonated radicals may cause endothermic proton transfer reactions occur …

Development Of Experimental And Instrumental Systems To Study Biological Systems, Amanda J Hemphill

Open Access Dissertations

Chapters 1-4 of this thesis describes the development of an experimental system to measure diffusion-limited reaction kinetics in a biological environment. About 100 years ago, the relationship between reaction rate and diffusion in homogenous solution, ie water or buffer, was described as a linear relationship by Smoluchowski. Applying this theory naively would suggest that since the diffusion coefficients drop by factors of 4-100 then the rates of reaction would drop by the same amount. However, recent theory and simulations suggest that this does not hold. Even though biological diffusion coefficients drop to 0.1-20% of that in buffer, these recent studies …

Molecular Diagnosis Of Cancer Using Ambient Ionization Mass Spectrometry, Kevin S Kerian

Open Access Dissertations

My dissertation focuses on advancing the development and application of ambient ionization mass spectrometry methodology and technology to the biomedical field. The primary ambient ionization method used in my studies is desorption electrospray ionization mass spectrometry (DESI-MS) imaging, which has been previously used to analyze and differentiate disease state (i.e. tumor and normal) and in some cases tumor subtype of human liver, kidney, bladder, testicular, prostate, and brain cancers. DESI-MS imaging is an ideal method for disease diagnosis, because it can be used to directly correlate disease state with histopathology to develop and validate MS libraries built using the molecular …

Polarization-Dependent Nonlinear Optical Microscopy Methods For The Analysis Of Crystals And Biological Tissues, Emma L. Kerian

Open Access Dissertations

The ability to solve a high-resolution protein structure is largely dependent on the successful generation and identification of protein crystals prior to X-ray diffraction (XRD). For novel protein targets, high-throughput crystallography often involves generation of multiple targets and thousands of crystallization trials per target to generate diffraction-quality crystals. Second harmonic generation (SHG) imaging has been developed as a fast, non-destructive and sensitive method for the selective identification of protein crystals, even in highly scattering environments. Polarization-dependent SHG microscopy methods were developed to assess the presence of multidomain crystals to provide a handle on crystal quality. In addition, polarization-dependent two-photon excited …

Studies Of The Interaction Of Biogenic Volatile Organic Compounds And Nox In Forest Environments, Kevin M. Mcavey

Open Access Dissertations

Ozone is a pollutant that causes crop damage, adverse health effects, and is a contributor to global climate change. Ozone concentrations are predicted to rise over the next half-century along with global temperature. Ozone production is controlled by the chemistry between biogenic volatile organic compounds and NO_x (NO + NO₂), and therefore, a greater understanding of NO_x + BVOC chemistry along with their sources and sinks is needed. One large uncertainty in understanding NO_x + BVOC chemistry is the production of organic nitrates (RONO₂), which act as a radical termination step in the …

Quantification Of Molecular Aggregation Equilibria Using Spectroscopic Measurements And Random Mixing Modeling, Blake M. Rankin

Open Access Dissertations

Molecular aggregation equilibria, such as the binding of ligands to a central solute molecule, are prevalent throughout biological processes and energy storage devices. However, both the sign and magnitude of hydrophobic and ionic interactions remains a subject of theoretical debate, and has yet to be experimentally determined. Here, Raman vibrational spectroscopy is combined with multivariate curve resolution (Raman-MCR) to experimentally quantify both the number of hydrophobic contacts between alcohol molecules in water and the affinity of ions for molecular hydrophobic interfaces. Furthermore, a generalized theoretical model is developed based on random statistics in which it is assumed that the concentration …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Effect Of Maleic Acid On The Selectivity Of Glucose And Fructose Dehydration And Degradation, Ximing Zhang

Open Access Dissertations

5-Hydroxymethyfurfural (HMF), a platform chemical can upgrade to a variety of fuels and polymers, can be manufactured from lignocellulose. This study focuses on the Lewis and Brønsted acid effect on hexose dehydration for HMF production. We report the positive effect of maleic acid, a dicarboxylic acid used as Brønsted acid, on the selectivity of hexose dehydration to 5-hydroxymethyfurfural (HMF), and subsequent hydrolysis to levulinic and formic acids. We also describe the kinetic analysis of a Lewis acid (AlCl ₃) alone and in combination with HCl or maleic acid to catalyze the isomerization of glucose to fructose, dehydration of fructose …

Novel Methods For Manipulating Ion Types In The Solution And Gas Phases For The Structural Analysis Of Biomolecules Using Mass Spectrometry, Christine M Fisher

Open Access Dissertations

Mass Spectrometry has become a valuable tool for the analysis of a variety of molecules, making it applicable to many fields. The advent of nanoelectrospray ionization (nESI) as a soft/low energy ionization technique has enabled the analysis of large, intact biomolecules. Most mass spectrometry experiments consist of three main steps: ionization, probe step(s), and mass analysis. The present work focuses on a variety of methods for altering ion types at various stages of the mass spectrometry experiment to affect ion fragmentation. Ion types can be manipulated in the solution/droplet phases using novel nESI emitters, generated from borosilicate theta capillaries. These …

Public Understanding Of Chemistry Research In Print News, Michael D. Hands

Open Access Dissertations

Despite numerous calls for improving scientific literacy, many American adults show a lack of understanding of experiments, scientific study, and scientific inquiry. News media is one important avenue for science learning, but previous research investigating health and/or environmental science news has shown that it is inconsistent in the presentation of scientific research limitations, potentially impacting reader understanding. In the first phase of this dissertation, seventeen news articles reporting on a single chemistry research article, along with associated press releases and research articles, were analyzed using move analysis to determine the structure of each type of text. It was found that …

Synthesis And Screen Of A Proline-Rich Combinatorial Library Towards The Identification Of Sickle Cell Hemoglobin Polymerization Inhibitors, Laura Steenberge

Honors Projects

Sickle cell disease is a genetic disorder that affects the hemoglobin within red blood cells. A point mutation in the gene coding for the β-subunit of hemoglobin allows the mutant chain to interact with a hydrophobic pocket of another hemoglobin in a deoxygenated environment, causing polymerization of the proteins. This creates the characteristic sickle-shape of the diseased blood cells that can clog capillaries, leading to tissue damage and cell death. Currently, there are limited options for those affected with sickle cell disease. The research to be presented is focused on discovering peptides that can interact with the mutated hemoglobin and …

Exploration Of Protein-Protein Interactions Involving Deinococcus Radiodurans Pria, Dnab And Ssb, Christopher S. Morrow

Honors Theses

Deinococcus radiodurans is a species of bacteria that has sparked a lot of interest since its discovery due to its incredible resistance to ionizing radiation. When exposed to ionizing radiation the genome of D. radiodurans will sustain over one hundred double stranded breaks. D. radiodurans demonstrates the ability to repair its genome and restart replication after sustaining, typically lethal, DNA damage. This project examined the mechanism of replication restart in D. radiodurans by investigating primosome protein PriA interacting with replicative helicase DnaB and single stranded binding protein. Many different types of gel electrophoresis were employed to investigate potential protein complex …

Computational Study Of The Visible Spectrum Of Curcumin's Protonation States, Peter Braegelmann, Joseph D. Alia

Chemistry Publications

Curcumin, the main dye in the important Indian spice turmeric, has received much attention recently for its potential anti-cancer and anti-Alzheimer properties.1 Our study computes the thermodynamics and spectroscopic properties of curcumin’s various protonation states using several methods and compares the results to experiment. M06/3-21G* gave the best thermodynamic results, while M06 with 3-21G* and 6-31G* gave good spectroscopic results for the neutral and dianionic forms of curcumin. However, applying diffuse functions appears to be necessary for the trianionic form. Interestingly, M06 and B3LYP with 6-31+G* gave good spectroscopic results for the singly anionic form.

Toward An Expanded Role For Collision-Induced Dissociation In Glycoproteomic Analysis, Venkata Kolli

Department of Chemistry: Dissertations, Theses, and Student Research

This thesis begins with an overview of the state-of-the-art in tandem mass spectrometry (MS/MS) analysis of glycopeptides. In this introduction, the primary focus is on utilization of different ion dissociation techniques for MS/MS to obtain structural information of N-glycopeptides. This includes a discussion of the importance of complementary MS/MS methods to attain complete structural characterization of N-glycopeptides. Emerging methods involving the use of a single ion dissociation technique for complete glycopeptide connectivity analysis were also presented. Next, the application of collision-induced dissociation (CID) to provide both amino acid sequence and monosaccharide connectivity for model N-glycopeptides was discussed in detail. Implementation …

Synthetic And Mechanistic Studies Of Catalytic Oxidations By Manganese(Iii) Porphyrin And Iodobenzene Diacetate, Kawai Kwong

Mahurin Honors College Capstone Experience/Thesis Projects

With iodobenzene diacetate [PhI(OAc)2] as the oxygen source, manganese(III) porphyrin complexes exhibit remarkable catalytic activity towards the selective oxidation of hydrocarbons. The readily soluble PhI(OAc)2 in the presence of small amount of water is more efficient oxygen source than the commonly used PhIO under the same conditions, leading to a potent catalytic system for the efficient oxidation of alkenes and activated hydrocarbons. When the reactions were carried out in the presence of a small amount of water at 50 oC, high selectivity for epoxides and excellent catalytic efficiency with up to 10,000 TON have been achieved in alkene epoxidations. In …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Eagles Fly to Denver for Chemistry Presentations

Using Planar Chiral Iron(0) Tricarbonyl Diene Complexes: A Focus On Azaspirocycles And The Use Of An Oxazolidinone Chiral Auxiliary, Julia S. Murphy , '15

Senior Theses, Projects, and Awards

For many years, the Paley laboratory has developed the use of planar chiral η⁴ iron(O) tricarbonyl complexes for use in directing the central chirality of adjacent centers. This work examines the use of dienes functionalized at C2 with a chiral auxiliary. The functionalization of a stereocontrolled [6,6]-azaspirocycle was taken on to great success. This sequence involved a 2-sulfinyl diene complex. The keystone Grignard addition to the cyclic imine was accomplished to afford a single diastereomer. Ring closing metathesis was used to form the final ring of the azaspirocycle framework. Two more sequences were attempted to form azaspirocycle centers. The first …

Synthesis And Characterization Of Low Valent Metalloporphyrins, Nagabhushanam Kundakarla

Master's Theses (2009 -)

Metalloporphyrins and metalloporphinones have been seen in a number of enzymes and involved in nitrogen metabolism, photosynthesis, and methanogenesis. The reduction of metalloporphyrins and metalloporphinones are achievable, but the site of reduction in either, the metal center or porphyrin core is still debatable. This prompted us to investigate the position of reduction in order to generate low valent metalloporphyrins and porphinones. The reduced porphyrins were characterized by spectroscopic and X-ray crystallographic methods. Previous work in our laboratory has generated low valent metalloporphyrins and porphinones by electrochemical reduction. In this work cobalt, manganese, and iron low valent metalloporphyrins were generated via …

Investigation Of The Potential For Algaenan To Produce Hydrocarbon Based Fuels From Algae By Hydrous Pyrolysis, Wassim Adel Obeid

Chemistry & Biochemistry Theses & Dissertations

The use of algae as a feedstock for hydrous pyrolysis has a high potential for producing biofuels. The non-food nature of algae in addition to the various advantages associated with the hydrous pyrolysis process makes this combination for the production of biofuels of high interest. However, current results from algae processing have alluded to some challenges: byproducts arising from the thermal transformation of carbohydrates and proteins, which become incorporated in the oil fraction, result in high oxygen and nitrogen contents of the oil. Accordingly, this produces an oil of low quality for refineries. This dissertation investigates use of a pretreatment …

Blue Carbon In Freshwater / Brackish Marshes On The Barrier Islands Of Virginia Aboveground Net Primary Productivity And Carbon Pools, Emily Caitlin Adams

Biological Sciences Theses & Dissertations

"Blue carbon" is a relatively new concept describing carbon distributed tidally and sequestered via net production within coastal ecosystems, including seagrass beds, mangrove forests, and salt-water marshes. These systems sequester carbon at least 10 times faster than terrestrial systems. Fresh to brackish wetlands that receive irregular tidal influence due to overwash and storm events have not been typically studied as blue carbon systems. My objective was to quantify carbon pools within four interdunal fresh to brackish marshes on Hog Island, Virginia to determine their blue carbon potential. Marshes 1 and 2 were farthest from the ocean, below and above a …