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Pages
- Title
- The Owl Sensor: a smart nanostructure for single nucleotide variation analysis.
- Creator
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Karadeema, Rebekah, Kolpashchikov, Dmitry, Chumbimuni Torres, Karin, Harper, James, University of Central Florida
- Abstract / Description
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Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5(&)deg;C-32(&)deg;C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and...
Show moreAnalysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5(&)deg;C-32(&)deg;C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and synthetic biology to self-assemble a fluorescent DNA nanostructure called a Double Crossover, or DX Tile, capable of differentiating SNVs in a large temperature range, including ambient temperature. In the presence of fully matched nucleic acid analytes, a stable complex is formed with high fluorescent signal; however in the presence of a single base variation in the analyte, unfavourable helicity results in little-to-no observed complex formation. The novelty of the approach is that selectivity of analyte recognition is, at least in part, determined by the structural rigidity of the entire nanostructure rather than by the stability of analyte-probe hybrid, as is the case for conventional hybridization probes. The rigid nanostructure collapses if a minor imperfection, e.g. if a single-base mispairing, is present. Owl Sensor differentiates fully matched analyte from mismatched in a wide temperature range, with mismatched analyte producing only the background fluorescence, selectivity that is hard to achieve by conventional hybridization probes. Owl Sensor therefore promises to add to the toolbox for diagnosis of genetic disorders and infectious diseases at ambient temperatures.
Show less - Date Issued
- 2016
- Identifier
- CFE0006691, ucf:51916
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006691
- Title
- Synthetic Design and Characterization of Polycyclic Aromatic Compounds in Molecular and Extended System.
- Creator
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Pour, Gavin, Belfield, Kevin, Frazer, Andrew, Elsheimer, Seth, University of Central Florida
- Abstract / Description
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The work presented herein focuses on the synthesis and characterization of polycyclic aromatic compounds for a wide variety of toxicological, analytical, and electronic applications. First, the modular synthesis of 12 dibenzo- and naphtho- fluoranthene polycyclic aromatic hydrocarbons (PAHs) via a Pd-catalyzed five-membered ring closing procedure is discussed. By understanding the various modes through which the Pd migrates during transformation, structural rearrangements were bypassed,...
Show moreThe work presented herein focuses on the synthesis and characterization of polycyclic aromatic compounds for a wide variety of toxicological, analytical, and electronic applications. First, the modular synthesis of 12 dibenzo- and naphtho- fluoranthene polycyclic aromatic hydrocarbons (PAHs) via a Pd-catalyzed five-membered ring closing procedure is discussed. By understanding the various modes through which the Pd migrates during transformation, structural rearrangements were bypassed, obtaining regioselectivity through various redesigns in the synthetic route. Each compound in the serious was rigorously characterized via 1D/2D NMR, absorption and emission spectroscopy as well as cyclic voltammetry, which shows vast differences due to small structural changes between these constitutional isomers. Next, a series of polyphenylated organic ligands for zirconium metal organic frameworks is presented as materials for post-synthetic Scholl cyclodehydrogenation. Lastly, a series of organic linkers featuring covalently anchored redox-active pendants is explored for tuneable redox activity in Zr-based metal-organic frameworks. Thin-films were grown onto fluorine-doped tin-oxide glass electrodes and analyzed by cyclic voltammetry. This is the first reported pre-synthetic incorporation of covalently-bound ferrocenyl pendants into such a system. By attenuating the proportions of redox active and inactive links the oxidative peak currents could be tuned. This body of work represents a contribution toward the practical design and synthesis of polycyclic aromatic for a wide variety of analytical and electrochemical applications.
Show less - Date Issued
- 2019
- Identifier
- CFE0007512, ucf:52647
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007512
- Title
- Chemistry and dissipation at mineral surfaces in the space environment.
- Creator
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Tucker, William, Schelling, Patrick, Britt, Daniel, Kara, Abdelkader, Coffey, Kevin, University of Central Florida
- Abstract / Description
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The composition and morphology of mineral surfaces is known to play an important role in various phenomena relevant to planetary science. For example, the synthesis and processing of complex organics likely occurs at mineral surfaces strongly affected by the space environment. Furthermore, the dissipative and adhesive properties of dust grains may depend strongly on the chemical state of the surface including the presence of dangling bonds, adsorbates, and radicals. In this dissertation,...
Show moreThe composition and morphology of mineral surfaces is known to play an important role in various phenomena relevant to planetary science. For example, the synthesis and processing of complex organics likely occurs at mineral surfaces strongly affected by the space environment. Furthermore, the dissipative and adhesive properties of dust grains may depend strongly on the chemical state of the surface including the presence of dangling bonds, adsorbates, and radicals. In this dissertation, experimental results are first presented which demonstrate that mineral grains subjected to high temperatures in a reducing environment lead to iron nanoparticles which are strongly catalytic for the formation of complex organic species. Next, results obtained using molecular-dynamics simulations demonstrate that uncoordinated surface atoms in metallic nanoparticles result in plastic deformation, strong dissipation and adhesion during collisions. This can be contrasted with previous simulations which demonstrate significantly weaker dissipation when surface atoms are passivated. Calculations of critical sticking velocities demonstrate that simple coarse- grain models are insufficient for predicting the adhesive behavior of sub-micron sized grains. Next, results are presented describing a computational study illuminating the role of surface chemistry on adhesion and dissipation for iron nanoparticle collisions, which in the case of free radical adsorbates may also contribute to the creation of more complex species. Lastly, to further elucidate dissipation, the direct coupling of harmonic vibrational modes in the dissipation process is established. The results demonstrate broad participation of low and high-frequency modes during a collision during a timescale less than time required for particles to rebound. Hence, our results demonstrate extremely strong likelihood of adhesion during collisions. This approach provides a way to use density-functional theory calculations to directly compute dissipative couplings at mineral interfaces.
Show less - Date Issued
- 2019
- Identifier
- CFE0007545, ucf:52592
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007545
- Title
- THEORETICAL TAILORING OF PERFORATED THIN SILVER FILMS FOR AFFINITY SURFACE PLASMON RESONANCE BIOSENSOR APPLICATIONS.
- Creator
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Gongora Jr., Renan, Zou, Shengli, University of Central Florida
- Abstract / Description
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Metallic films, in conjunction with biochemical-targeted probes, are expected to provide early diagnosis, targeted therapy and non-invasive monitoring for epidemiology applications. The resonance wavelength peaks, both plasmonic and Wood-Rayleigh Anomalies (WRAs), in the scattering spectra are affected by the metallic architecture. As of today, much research has been devoted to extinction efficiency in the plasmonic region. However, Wood Rayleigh Anomalies (WRAs) typically occur at...
Show moreMetallic films, in conjunction with biochemical-targeted probes, are expected to provide early diagnosis, targeted therapy and non-invasive monitoring for epidemiology applications. The resonance wavelength peaks, both plasmonic and Wood-Rayleigh Anomalies (WRAs), in the scattering spectra are affected by the metallic architecture. As of today, much research has been devoted to extinction efficiency in the plasmonic region. However, Wood Rayleigh Anomalies (WRAs) typically occur at wavelengths associated with the periodic distance of the structures. A significant number of papers have already focused on the plasmonic region of the visible spectrum, but a less explored area of research was presented here; the desired resonance wavelength region was 400-500nm, corresponding to the WRA for the silver film with perforated hole with a periodic distance of 400nm. Simulations obtained from the discrete dipole approximation (DDA) method, show sharp spectral bands (either high or low scattering efficiencies) in both wavelength regions of the visible spectrum simulated from Ag film with cylindrical hole arrays In addition, surprising results were obtained in the parallel scattering spectra,where the electric field is contained in the XY plane, when the angle between the metallic surface and the incident light was adjusted to 14 degrees; a bathochromic shift was observed for the WRA peak suggesting a hybrid resonance mode. Metallic films have the potential to be used in instrumental techniques for use as sensors, i.e. surface plasmon resonance affinity biosensors, but are not limited to such instrumental techniques. Although the research here was aimed towards affinity biosensors, other sensory designs can benefit from the optimized Ag film motifs. The intent of the study was to elucidate metal film motifs, when incorporated into instrumental analysis, allowing the quantification of genetic material in the visible region. Any research group that routinely benefits from quantification of various analytes in solution matrices will also benefit from this study, as there are a bewildering number of instrumental sensory methods and setups available.
Show less - Date Issued
- 2014
- Identifier
- CFH0004538, ucf:45155
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH0004538
- Title
- GLIAL DIFFERENTIATION OF HUMAN UMBILICAL STEM CELLS IN 2D AND 3D ENVIRONMENTS.
- Creator
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Davis, Hedvika, Hickman, James, University of Central Florida
- Abstract / Description
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During differentiation stem cells are exposed to a range of microenvironmental chemical and physical cues. In this study, human multipotent progenitor cells (hMLPCs) were differentiated from umbilical cord into oligodendrocytes and astrocytes. Chemical cues were represented by a novel defined differentiation medium containing the neurotransmitter norepinephrine (NE). In traditional 2 dimensional (2D) conditions, the hMLPCs differentiated into oligodendrocyte precursors, but did not progress...
Show moreDuring differentiation stem cells are exposed to a range of microenvironmental chemical and physical cues. In this study, human multipotent progenitor cells (hMLPCs) were differentiated from umbilical cord into oligodendrocytes and astrocytes. Chemical cues were represented by a novel defined differentiation medium containing the neurotransmitter norepinephrine (NE). In traditional 2 dimensional (2D) conditions, the hMLPCs differentiated into oligodendrocyte precursors, but did not progress further. However, in a constructed 3 dimensional (3D) environment, the hMLPCs differentiated into committed oligodendrocytes that expressed MBP. When co-cultured with rat embryonic hippocampal neurons (EHNs), hMLPCs developed in astrocytes or oligodendrocytes, based on presence of growth factors in the differentiation medium. In co-culture, physical cues provided by axons were essential for complete differentiation of both astrocytes and oligodendrocytes. This study presents a novel method of obtaining glia from human MLPCs that could eliminate many of the difficulties associated with their differentiation from embryonic stem cells. In addition, it reveals the complex interplay between physical cues and biomolecules on stem cell differentiation.
Show less - Date Issued
- 2011
- Identifier
- CFE0003570, ucf:48894
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003570
- Title
- Novel Developments on the Extraction and Analysis of Polycyclic Aromatic Hydrocarbons in Environmental Samples.
- Creator
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Wilson, Walter, Campiglia, Andres, Belfield, Kevin, Rex, Matthew, Harper, James, Hoffman, Jay, University of Central Florida
- Abstract / Description
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This dissertation focuses on the development of analytical methodology for the analysis of polycyclic aromatic hydrocarbons (PAHs) in water samples. Chemical analysis of PAHs is of great environmental and toxicological importance. Many of them are highly suspect as etiological agents in human cancer. Among the hundreds of PAHs present in the environment, the U.S. Environmental Protection Agency (EPA) lists sixteen as "Consent Decree" priority pollutants. Their routine monitoring in...
Show moreThis dissertation focuses on the development of analytical methodology for the analysis of polycyclic aromatic hydrocarbons (PAHs) in water samples. Chemical analysis of PAHs is of great environmental and toxicological importance. Many of them are highly suspect as etiological agents in human cancer. Among the hundreds of PAHs present in the environment, the U.S. Environmental Protection Agency (EPA) lists sixteen as "Consent Decree" priority pollutants. Their routine monitoring in environmental samples is recommended to prevent human contamination risks.A primary route of human exposure to PAHs is the ingestion of contaminated water. The rather low PAH concentrations in water samples make the analysis of the sixteen priority pollutants particularly challenging. Current EPA methodology follows the classical pattern of sample extraction and chromatographic analysis. The method of choice for PAHs extraction and pre-concentration is solid-phase extraction (SPE). PAHs determination is carried out via high-performance liquid chromatography (HPLC) or gas chromatography/mass spectrometry (GC/MS). When HPLC is applied to highly complex samples, EPA recommends the use of GC/MS to verify compound identification and to check peak-purity of HPLC fractions. Although EPA methodology provides reliable data, the routine monitoring of numerous samples via fast, cost effective and environmentally friendly methods remains an analytical challenge. Typically, 1 L of water is processed through the SPE device in approximately 1 h. The rather large water volume and long sample processing time are recommended to reach detectable concentrations and quantitative removal of PAHs from water samples. Chromatographic elution times of 30 (-) 60 min are typical and standards must be run periodically to verify retention times. If concentrations of targeted PAHs are found to lie outside the detector's response range, the sample must be diluted (or concentrated), and the process repeated. In order to prevent environmental risks and human contamination, the routine monitoring of the sixteen EPA-PAHs is not sufficient anymore. Recent toxicological studies attribute a significant portion of the biological activity of PAH contaminated samples to the presence of high molecular weight (HMW) PAHs, i.e. PAHs with MW ? 300. Because the carcinogenic properties of HMW-PAHs differ significantly from isomer to isomer, it is of paramount importance to determine the most toxic isomers even if they are present at much lower concentrations than their less toxic isomers. Unfortunately, established methodology cannot always meet the challenge of specifically analyzing HMW-PAHs at the low concentration levels of environmental samples. The main problems that confront classic methodology arise from the relatively low concentration levels and the large number of structural isomers with very similar elution times and similar, possibly even virtually identical, fragmentation patterns. This dissertation summarizes significant improvements on various fronts. Its first original component deals with the unambiguous determination of four HMW-PAHs via laser-excited time-resolved Shpol'skii spectroscopy (LETRSS) without previous chromatographic separation. The second original component is the improvement of a relatively new PAH extraction method - solid-phase nanoextraction (SPNE) - which uses gold nanoparticles as extracting material for PAHs. The advantages of the improved SPNE procedure are demonstrated for the analysis of EPA-PAHs and HMW-PAHs in water samples via GC/MS and LETRSS, respectively.
Show less - Date Issued
- 2014
- Identifier
- CFE0005443, ucf:50384
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005443
- Title
- Measuring and Modeling NMR and Emission Spectra to Gain New Insight into Challenging Organic Compounds.
- Creator
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Powell, Jacob, Harper, James, Campiglia, Andres, Beazley, Melanie, Richardson, David, Blair, Richard, University of Central Florida
- Abstract / Description
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The advancement of theoretical methods in recent years has allowed the calculation of highly accurate spectroscopic parameters. Comparing these values to the corresponding experimental data can allow molecular structures to be elucidated. This dissertation details the use of experimental and theoretical data from nuclear magnetic resonance (NMR) and fluorescence spectroscopy to determine structure. Herein the NMR focus is on measuring (&) modeling chemical shift anisotropy and one-bond carbon...
Show moreThe advancement of theoretical methods in recent years has allowed the calculation of highly accurate spectroscopic parameters. Comparing these values to the corresponding experimental data can allow molecular structures to be elucidated. This dissertation details the use of experimental and theoretical data from nuclear magnetic resonance (NMR) and fluorescence spectroscopy to determine structure. Herein the NMR focus is on measuring (&) modeling chemical shift anisotropy and one-bond carbon-carbon J-coupling constants (1JCC). The fluorescence analysis models vibrationally resolved fluorescence spectra.Chemical shift anisotropy techniques were used to study two conflicting crystal structures of the n-alkyl fatty acid, lauric acid. These two crystal structures differ only in their COOH conformation. Lattice-including density functional theory (DFT) refinements of each crystal structure failed to match experimental data leading to the proposal of a third crystal structure with a hydrogen disordered COOH moiety. This disorder strengthens the hydrogen bond providing a new rationalization to the long observed non-monotonic melting behavior of fatty acids having even and odd numbers of carbons.The INADEQUATE is a NMR experiment that directly establishes the skeleton of organic compounds by measuring the 1JCC throughout a molecule. The low occurrence of 13C-13C pairs (1 in 10,000) and breaks in connectivity due to the presence of heteroatoms causes challenges to INADEQUATE analysis. Here, the insensitivity problem is overcome using analysis software that automatically processes data and identifies signals, even when they are comparable in magnitude to noise. When combined with DFT 1JCC predictions,configuration and confirmations of the natural products 5-methylmellein and hydroheptelidic acid are elucidated.Vibrationally resolved fluorescence spectra of high molecular weight PAHs can be accurately calculated through time-dependent density functional theory (TD-DFT) methods. Here, the theoretical spectral profiles of certain PAHs are shown to match experimental high- resolution fluorescence spectra acquired at cryogenic temperatures. However, in all cases, theoretical spectra were systematically offset from experimental spectra. To decrease these uncertainties spectra were empirically corrected and an automated scheme employed to match theoretical spectra with all possible experimental spectra. In all cases the theoretical spectra were correctly matched to the experimental spectra.
Show less - Date Issued
- 2017
- Identifier
- CFE0006953, ucf:51680
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006953
