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Title: Capillary Electrophoresis Separation of Formaldehyde Cross-Linked Aptamer-Protein Complexes.
Creator: Duren, Joseph, Biochemistry
Abstract/Description: An Immunoglobulin-E (IgE) DNA aptamer was covalently bound to IgE using a formaldehyde cross-linking method. The resulting complex was then separated from free aptamer by capillary electrophoresis (CE). The bound-to-free peak area ratios were preserved as a result of the cross-linking, which acted as a "freeze-frame" of the reaction in equilibrium. Elevated temperature occurring during CE separations can cause dissociation of non-covalently bound molecules and their targets, decreasing the...
Show moreAn Immunoglobulin-E (IgE) DNA aptamer was covalently bound to IgE using a formaldehyde cross-linking method. The resulting complex was then separated from free aptamer by capillary electrophoresis (CE). The bound-to-free peak area ratios were preserved as a result of the cross-linking, which acted as a "freeze-frame" of the reaction in equilibrium. Elevated temperature occurring during CE separations can cause dissociation of non-covalently bound molecules and their targets, decreasing the usefulness of the information obtained. Due to the formaldehyde cross-linking performed, the bound-to-free ratio was preserved over that of the uncross-linked control, which showed a decreased bound-to-free ratio upon heating. Additional trials were run on bovine serum albumin (BSA), anti-BSA, glucagon, and anti-glucagon using the formaldehyde cross-linking method. The results for this section were not conclusive due to difficulties in the separation and mechanistic issues with formaldehyde cross-linking. With the use of formaldehyde cross-linking, complexes that easily dissociate, under stringent separation conditions, can be covalently linked to prevent dissociation and allow for more sensitive analyses to be performed. Keywords:
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Date Issued: 2011
Identifier: FSU_migr_uhm-0012
Format: Thesis

Title: Carbohydrate conformation modeling in human chorionic gonadotropin.
Creator: O'Neil, Erika Rose
Date Issued: 2007-07-13
Identifier: 160767, FSDT160767, fsu:19065
Format: Document (PDF)

Title: Design and Synthesis of a Chiral, Amino Acid Derived, Six-Membered N-Heterocyclic Carbene Copper(I) Complex.
Creator: Fleming, Jeffrey, Department of Chemistry and Biochemistry
Abstract/Description: A catalyst is any species that increases the reaction rate of a chemical reaction by decreasing activation energy without being consumed. Catalysts are used in organic synthesis to increase reaction rates and to enable the synthesis of optically pure products. Asymmetric catalysis is crucial to the synthesis of pharmaceutical intermediates and novel catalysts are needed to synthesize the intermediates of future medicines. The study of N-heterocyclic carbene (NHC) metal complexes is a growing...
Show moreA catalyst is any species that increases the reaction rate of a chemical reaction by decreasing activation energy without being consumed. Catalysts are used in organic synthesis to increase reaction rates and to enable the synthesis of optically pure products. Asymmetric catalysis is crucial to the synthesis of pharmaceutical intermediates and novel catalysts are needed to synthesize the intermediates of future medicines. The study of N-heterocyclic carbene (NHC) metal complexes is a growing field that has provided many selective catalysts. NHC ligands with tunable properties enable rapid development of new synthetic methods. Building off previous work in the McQuade research group, a novel six-membered NHC copper(I) catalyst has been designed using a modular approach to tunable NHCs. Interchangeable amino acid-based starting materials provide a readily accessible source of chirality to control the steric and electronic environment surrounding the metal atom bound to the NHC. The synthesis of several complexes enables relative catalytic ability to be tested and provides increased insight into catalyst design.
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Date Issued: 2014
Identifier: FSU_migr_uhm-0306
Format: Thesis

Title: The Effects of Nicotine on Neurotrophic Factor Expression in the Adult Male Zebra Finch.
Creator: Peoples, Jessica, Chemistry and Biochemistry
Abstract/Description: This thesis examines the effects of nicotine on the expression of Brain- Derived Neurotrophic Factor (BDNF) in the brain of adult male zebra finches (Taeniopygia guttata) under isolated and social housing conditions. BDNF, which is essential for survival, growth, and neuroplasticity of neurons, is significantly decreased in patients with affective disorders, such as depression and schizophrenia. A significant number of these patients use tobacco products, which induce an increase in plasma...
Show moreThis thesis examines the effects of nicotine on the expression of Brain- Derived Neurotrophic Factor (BDNF) in the brain of adult male zebra finches (Taeniopygia guttata) under isolated and social housing conditions. BDNF, which is essential for survival, growth, and neuroplasticity of neurons, is significantly decreased in patients with affective disorders, such as depression and schizophrenia. A significant number of these patients use tobacco products, which induce an increase in plasma BDNF levels. Isolated rodents exposed to nicotine showed an increase in central BDNF levels. The zebra finch is an established model to study cognitive functioning, and as such we examined how nicotine interacts with BDNF expression in zebra finch brain areas involved in cognitive functioning such as the song nuclei and the hippocampal area. Adult male zebra finches were exposed to nicotine and the expression of BDNF was examined between isolated and social housed male zebra finches, using immunocytochemistry. The results show that the housing conditions did not have an effect on the expression of BDNF in the examined song nuclei or the hippocampal area. However, nicotine induced an increased expression of BDNF in the song nuclei HVC, RA (Robust Nucleus of the Archistriatum), and Area X. The HVC and RA contain nicotinic acetylcholinergic receptors, which could explain our finding. Area X is involved in song learning, which is not applicable to our animals, as adult animals have a crystallized pattern. The results could be explained by the fact that Area X might be under direct control of the HVC.
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Date Issued: 2012
Identifier: FSU_migr_uhm-0069
Format: Thesis

Title: The Evaluation of Industrial Methods of Size-Exclusion Chromatography (SEC) of Difficult-to-Dissolve Polymers.
Creator: McNeel, Kelsey, Chemistry
Abstract/Description: In experiments presented here, well-characterized polystyrene and poly(methyl methacrylate) standards were analyzed using size-exclusion chromatography and an approach in which the mobile phase differed from the solvent in which the polymer was dissolved. Solvent combinations included a mobile phase in which the polymer was insoluble and a mobile phase that was immiscible with the solvent. It is important to determine the accuracy of molar mass averages and distributions obtained from such...
Show moreIn experiments presented here, well-characterized polystyrene and poly(methyl methacrylate) standards were analyzed using size-exclusion chromatography and an approach in which the mobile phase differed from the solvent in which the polymer was dissolved. Solvent combinations included a mobile phase in which the polymer was insoluble and a mobile phase that was immiscible with the solvent. It is important to determine the accuracy of molar mass averages and distributions obtained from such experiments because the averages and distributions are frequently used in industry to give information about physical properties of the analyte. It is often expensive and time consuming to determine the ideal solvent in which to analyze a polymer, and even more so to purge the system of the previous solvent and condition it with the new one. To circumnavigate these problems, polymers are sometimes dissolved in a known solvent and injected into an instrument containing a chemically different mobile phase, a mobile phase that is already in the instrument. We found that performing experiments using this industrial approach needs to be done with caution. The molar mass averages and distributions can be determined accurately when the mobile phase is a solvent for the polymer and miscible with the solvent, but other cases were less conclusive. Using a mobile phase that is not a solvent for the polymer appears to yield accurate results for low molar mass polymers (<20,000 g/mol) but, in some solvent combinations, yields exclusively solvent peaks. It is likely that the larger polymers precipitate when the miscible solvent and mobile phase mix and the polymers are adsorbed onto the column. Experiment set 5, in which the mobile phase was a solvent for the polymer but was immiscible with the solvent in which the polymer was dissolved, yielded no peaks in these experiments. It is hypothesized that this lack of peaks is a result of enthalpic interactions between the stationary phase, sample solution, and mobile phase. It appears that the elution of the polymer may not be driven by entropic interactions, as is the case in a size-exclusion mechanism, resulting in the co-elution of the polymer and the solvent.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0026
Format: Thesis

Title: Fluorescent staining of biotinylated lambda DNA attached to streptavidin-coated paramagnetic particles.
Creator: Pepper, Nora A.
Date Issued: 2005-08-30
Identifier: 160349, FSDT160349, fsu:18870
Format: Document (PDF)

Title: Isolating and Crystallizing the Permuted HD Domain of CRISPR.
Creator: Hubert, Joshua, Li, Hong, Ramia, Nancy, Department of Chemistry and Biochemistry
Abstract/Description: CRISPR-cas systems have been found to confer RNA guided immunity in prokaryotes comparable to the eukaryotic RNA interference. These Clustered Regularly Interspaced Short Palindromic Repeats, as their name entails, are repeated sequences varying from 25 to 45 nucleotides in length separated by variable spacers. The CRISPR system has been found in many different bacteria and Archaea. Associated with the CRISPR locus are cas genes, which are thought to encode for nucleases, helicases, and...
Show moreCRISPR-cas systems have been found to confer RNA guided immunity in prokaryotes comparable to the eukaryotic RNA interference. These Clustered Regularly Interspaced Short Palindromic Repeats, as their name entails, are repeated sequences varying from 25 to 45 nucleotides in length separated by variable spacers. The CRISPR system has been found in many different bacteria and Archaea. Associated with the CRISPR locus are cas genes, which are thought to encode for nucleases, helicases, and polymerases involved in the CRISPR defense mechanism. The mechanism involved with the defense occurs when the CRISPR locus is transcribed into a long RNA that will be processed into short sequences used as a guide to target and cleave the invader genome sequences through base pairing. Together, the CRISPR-cas systems are able to protect the bacteria or archaea from invading DNA or RNA. Cas 10 is the signature protein of type III CRISPR systems and is characterized by a permuted Histidine-Aspartic acid (HD) domain predicted to possess a nuclease activity. The presence of the permuted HD and the presence of a nucleotidyl cylcase-like have guided the belief that the permuted HD domain may be the activity site. After several attempts, it was found that the HD domain protein from both PF1129 and TTHB147 is insoluble in water and is consistently lost in the pellet during centrifugation. However, there is still a small concentration of the domain collected in the elution, showing that some of the HD domain can be purified to the last step. The max concentration collected of the permuted HD domain from the TTHB147 was found to be 2.45 mg/mL.
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Date Issued: 2014
Identifier: FSU_migr_uhm-0317
Format: Thesis

Title: Lipid Profiling of Algae Biofuel Feedstock Grown in Wastewater.
Creator: Baxter, Alexis, Chemistry and Biochemistry
Abstract/Description: Algae represent a carbon neutral feedstock for biofuel production. However, to fully realize the benefits of coupling algae production with nutrient reduction of wastewater, maximum usable biofuel output must be achieved. Indeed, identification of appropriate algal strains, understanding biochemical pathways, and optimization of production of fuel precursors (i.e. lipids) have been identified as some of the most important challenges that need to be addressed before this technology becomes...
Show moreAlgae represent a carbon neutral feedstock for biofuel production. However, to fully realize the benefits of coupling algae production with nutrient reduction of wastewater, maximum usable biofuel output must be achieved. Indeed, identification of appropriate algal strains, understanding biochemical pathways, and optimization of production of fuel precursors (i.e. lipids) have been identified as some of the most important challenges that need to be addressed before this technology becomes economically feasible. Prospective biofuels originate from the medium-chain fatty acids encased in algal cell membranes. Under ideal conditions, algae synthesize primarily proteins and carbohydrates that are necessary for cell growth. However, when stressed, algae will synthesize large quantities of triacylglycerols (TAGs) that are comprised of mid- to long-chain fatty acids (FAs) bound to glycerol, and these FAs are the primary source of biodiesel. By manipulating growth conditions (e.g. temperature, light, nutrients, pH etc.) the concentration and composition of the FAs can be altered. In this work, various species of freshwater algae grown on domestic wastewater were harvested to determine their potential as a source of combustible biofuels. The goal was to determine which algal strains and stress conditions optimize lipid composition. Total lipid content in dried algal pellets was screened with UV-Vis spectroscopy after derivatization of free fatty acids. Since the quality of the lipids produced is also important in determining biofuel conversion efficiency, the composition of individual lipids (e.g. carbon chain length, number and position of double bonds) was characterized by capillary gas chromatography.
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Date Issued: 2012
Identifier: FSU_migr_uhm-0102
Format: Thesis

Title: Medium Effects on the Photoisomerization of Trans, Trans-1, 4-Diphenyl-1, 3-Butadiene.
Creator: Redwood, Christopher, Chemistry
Abstract/Description: Photoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB) has been rigorously studied with the assumption that torsion about the excited state is the sole radiationless decay pathway in competition with fluorescence12, 13, 14. This assumption is questioned and tested as it disregards the many channels for photochemical radiationless deactivation of the excited state, which have been rigorously studied33. Irradiation of tt-DPB in acetonitrile, cyclohexane, decane, ethanol,...
Show morePhotoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB) has been rigorously studied with the assumption that torsion about the excited state is the sole radiationless decay pathway in competition with fluorescence12, 13, 14. This assumption is questioned and tested as it disregards the many channels for photochemical radiationless deactivation of the excited state, which have been rigorously studied33. Irradiation of tt-DPB in acetonitrile, cyclohexane, decane, ethanol, isopropyl alcohol, methanol, and methylcyclohexane was performed and monitored by UV-Vis spectroscopy. Notably, it is found that trans to cis photoisomerization is occurs faster than alcohol photoaddition from the excited state of tt-DPB. Additionally, methods for automatic baseline correction of degassed samples are discussed.
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Date Issued: 2011
Identifier: FSU_migr_uhm-0035
Format: Thesis

Title: Morphological changes in rat brains resulting from social defeat.
Creator: Moore, Steven
Date Issued: 2006-07-27
Identifier: 160809, FSDT160809, fsu:19086
Format: Document (PDF)

Title: Novel Carbon Nanotube Structures and Microcellular Foams.
Creator: Amrhein, Christina, Department of Biological Science
Abstract/Description: Structural foams reinforced with carbon nanotubes could prove to be beneficial in numerous industrial applications. High internal phase emulsion foams are emerging as new and important forms of microcellular foams. Microcellular foams, foams with a pores size of 0.1-10 μm, have numerous advantages, such as high impact strength. The dispersal of carbon nanofibers, as wall pore reinforcements, within microcellular foams promises to enhance the foams' mechanical properties. This research has...
Show moreStructural foams reinforced with carbon nanotubes could prove to be beneficial in numerous industrial applications. High internal phase emulsion foams are emerging as new and important forms of microcellular foams. Microcellular foams, foams with a pores size of 0.1-10 μm, have numerous advantages, such as high impact strength. The dispersal of carbon nanofibers, as wall pore reinforcements, within microcellular foams promises to enhance the foams' mechanical properties. This research has developed a novel method for creating such foam.
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Date Issued: 2014
Identifier: FSU_migr_uhm-0290
Format: Thesis

Title: Physical Models and Classroom Demonstrations based on Applying the Hydraulic Analogy to Chemical Equilibrium, Thermodynamics, and Kinetics.
Creator: Lev-Ran, Dana, Department of Chemistry and Biochemistry
Abstract/Description: The hydraulic analogy for electrical circuits is a well-known, if limited, model for understanding potential and current. The work described in this thesis extends this analogy to chemical reactions by constructing apparatuses that model chemical equilibrium and the dynamics of forming kinetic and thermodynamic products in a chemical reaction. The apparatuses were designed so that they could be constructed from readily available and affordable materials by middle or high school students under...
Show moreThe hydraulic analogy for electrical circuits is a well-known, if limited, model for understanding potential and current. The work described in this thesis extends this analogy to chemical reactions by constructing apparatuses that model chemical equilibrium and the dynamics of forming kinetic and thermodynamic products in a chemical reaction. The apparatuses were designed so that they could be constructed from readily available and affordable materials by middle or high school students under the supervision of a shop or science teacher. The resulting hydrodynamic models were evaluated qualitatively and quantitatively with respect to the well-established theories of chemical equilibria, kinetics, and thermodynamics. The effectiveness and utility of the hydrodynamic models to illustrate chemical behavior, as well as their limitations, are discussed.
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Date Issued: 2014
Identifier: FSU_migr_uhm-0417
Format: Thesis

Title: Rhodamine B Thiohydrazide Tautomerization Chemistry and a New Class of Rhodamine-Spirolactam Indicators.
Creator: Barsoum, David, Zhu, Lei, Department of Chemistry and Biochemistry
Abstract/Description: While studying the various rhodamine spirolactam-based fluorescent indicators, evidence of important structural properties was observed. IR spectroscopic analysis leads one to conclude that rhodamine B thiohydrazide, the precursor for rhodamine B thiohydrazone, is misrepresented in literature as the incorrect tautomer. Correcting the literature with the proper tautomer should give insight and provide better guidelines for metal ion selectivity in rhodamine spirolactam-type indicator design....
Show moreWhile studying the various rhodamine spirolactam-based fluorescent indicators, evidence of important structural properties was observed. IR spectroscopic analysis leads one to conclude that rhodamine B thiohydrazide, the precursor for rhodamine B thiohydrazone, is misrepresented in literature as the incorrect tautomer. Correcting the literature with the proper tautomer should give insight and provide better guidelines for metal ion selectivity in rhodamine spirolactam-type indicator design. During synthesis a significant improvement of the notoriously low yielding thionation of rhodamine B derivatives with Lawesson's reagent was developed. Furthermore, a new class of rhodamine spirolactam-type indicators are proposed (rhodamine di-alkylated hydrazides) through the synthetic development of a counterintuitive, yet simple, asymmetric di-alkylation of hydrazine. This new class will increase the diversity of rhodamine spirolactam class of indicators for better control over metal ion selectivity.
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Date Issued: 2013
Identifier: FSU_migr_uhm-0259
Format: Thesis

Title: Spin-Crossover in Fe(II) Complexes with N4S2 Coordination Environments.
Creator: Arroyave, Alejandra, Department of Chemistry and Biochemistry
Abstract/Description: Spin crossover (SCO) is a phenomenon of magnetic switching in transition metal complexes that can exist in two different electronic configurations, depending on the splitting of d-orbitals by the surrounding ligand field. About 90% of known SCO compounds are represented by FeII complexes, which most commonly exhibit SCO in a {N6} coordination environment. In this work, we demonstrate that SCO in FeII complexes with {N4S2} coordination is also possible, despite the presence of the two...
Show moreSpin crossover (SCO) is a phenomenon of magnetic switching in transition metal complexes that can exist in two different electronic configurations, depending on the splitting of d-orbitals by the surrounding ligand field. About 90% of known SCO compounds are represented by FeII complexes, which most commonly exhibit SCO in a {N6} coordination environment. In this work, we demonstrate that SCO in FeII complexes with {N4S2} coordination is also possible, despite the presence of the two seemingly weak-field sulfur donor atoms. The three ligands synthesized were S′,S′-bis(2-pyridylmethyl)-1,2-thioethane (bpte), 2-[(methylsulfanyl)methyl]-pyridine (picSMe), and S′,S′-bis(2-pyridylmethyl)-1,3-thiopropane (bptp). All of them furnish the {N4S2} coordination environment when complemented with two NCX– co-ligands (X = S, Se, BH3). The variation in the geometry of the N,S-binding ligand affects the SCO significantly, either in the occurrence of the transition, its completeness, or the transition temperature. Furthermore, changing the co-ligands from NCS– to NCSe– to NCBH3–produces a shift in the SCO temperature, according to the increasing ligand field strength in this series of NCX– co-ligands. Magnetic susceptibility, MÃ¶ssbauer spectroscopy and crystallography studies were performed to fully characterize these complexes.
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Date Issued: 2015
Identifier: FSU_migr_uhm-0449
Format: Thesis

Title: The synthesis and characterization of a ruthenium-histamine complex.
Creator: Marshall, Kimberly
Date Issued: 2006-08-03
Identifier: 160790, FSDT160790, fsu:19076
Format: Document (PDF)

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