UMD Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/3
New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.
More information is available at Theses and Dissertations at University of Maryland Libraries.
Browse
10 results
Search Results
Item CHARACTERIZATION OF SEPTIC SYSTEM WASTEWATER AND MUNICIPAL SOLID WASTE LANDFILL LEACHATE(2021) Martin, Katherine; Gonsior, Michael; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The growing United States population means increasing waste production and a corresponding increase in the use and release of contaminants of emerging concern (CECs). The increasing volume and changing composition of waste poses new challenges for waste management and the protection of ecosystem, surface water, and groundwater resources. In the U.S., most domestic solid waste is disposed of in landfills, and domestic wastewater is treated by wastewater treatment plants (WWTPs) or onsite wastewater treatment systems (OWTSs). While OWTSs, the majority of which are conventional septic systems, account for the minority of wastewater treatment in the U.S., they present a significant pollution risk because they are not subject to the same treatment level or discharge regulatory standards as municipal WWTPs. Landfill leachate is also an important source of environmental contamination because most existing landfills in the U.S. are closed, unlined landfills that lack engineered systems to enhance refuse degradation or collect leachate. To mitigate the pollution risks of these effluents, it is important to understand initial wastewater composition and how to identify and trace environmental contamination.In this study, I generated background molecular composition data for landfill leachate and domestic wastewater effluents and developed chemical tracers for septic system impacted streams. I used ultrahigh resolution, Fourier-transform ion cyclotron resonance mass spectrometry, to molecularly characterize the dissolved organic matter (DOM) of septic system wastewater and septic system wastewater-impacted surface waters. I also analyzed traditional water quality markers such as CECs, chloride, nitrate isotopic signatures, and nutrients. Additionally, I molecularly characterized landfill leachate DOM and analyzed similar chemical markers to those used in the septic system study to understand composition. The goals in the main septic system study were to better understand the composition and natural processing of septic system wastewater and to develop new chemical wastewater tracers while assessing traditionally used tracers. The landfill leachate study addressed the lack of nontargeted leachate composition data. Determining initial molecular composition is necessary to understand the consequences of discharge to the environment and to design leachate treatments.Item Epigenetics of Neurodegeneration: Quantification of Histone Deacetylase Isoforms and Post-translational Modifications of Histones in Alzheimer’s Disease(2015) Anderson, Kyle; Fenselau, Catherine; Turko, Illarion V; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Histone post-translational modifications have been implicated in many biological functions and diseases and serve an important role in epigenetic regulation of gene expression. Aberrant modulations in histone post-translational have been suggested to occur in the brain as part of Alzheimer’s disease (AD) pathology, consistent with the epigenetic blockade of neurodegeneration. This dissertation details the development and optimization of unique protein standards for quantification, called quantification concatamers, for the absolute quantification of histone deacetylase isoforms in human frontal cortex with AD, human neural retina with AD and age-related macular degeneration, and whole brain hemisphere of a 5XFAD mouse model of AD. Histone deacetylases are enzymes responsible for the deacetylation of histones, which can directly regulate transcription, and have been implicated in AD pathology. In addition to measuring isoforms of histone-modifying enzymes, measurements of post-translational modifications on histones were also obtained for whole hemispheres of brain from 5XFAD mice and frontal cortex from human donors affected with AD. For the changes in post-translational modifications observed, structural mechanisms were proposed to explain alterations in the DNA-histone affinity in the nucleosome, which can modulate gene expression. Measurements and structural mechanisms were consistent with the global decrease in gene expression observed in AD, which supports the data. This body of work aims to better elucidate the epigenetic pathology of AD and to aid in identification of histone-modifying enzymes involved in AD pathology for drug targets and treatment options. Currently, there are no treatments that prevent, delay, or ameliorate AD, stressing the crucial importance of AD pathology research and the promise of epigenetics as the solution.Item A Deuterium Labeling Method for the Characterization of (Chromophoric) Dissolved Organic Matter Using Ultrahigh Resolution Electrospray Ionization Mass Spectrometry(2015) Baluha, Daniel Robert; Blough, Neil; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Dissolved organic matter (DOM) is a complex ensemble of naturally occurring organic compounds found in virtually all aquatic environments. The overwhelming diversity of DOM makes it extremely difficult to understand the relationship between its bulk physicochemical properties and its molecular structure and composition. This dissertation describes the development of a novel method to identify ketone/aldehyde-containing species within DOM, which are known to contribute substantially to the ultraviolet/visible (UV-vis) absorption and emission of chromophoric DOM. In this method, an aqueous sample is treated with sodium borodeuteride (NaBD4) and is analyzed via ultrahigh resolution electrospray ionization (ESI) mass spectrometry. Ketone/aldehyde-containing species (at mass m) in the untreated sample are identified by searching the mass spectrum of the reduced sample for peaks corresponding to deuterated derivatives (at mass m+3.021927n). Initial experiments demonstrated that this method reliably discriminates among mass spectral peaks in an untreated DOM sample that comprise species with zero, one, and/or two reducible moieties. The reactivity and optical properties of reducible species within Suwannee River fulvic acid (SRFA) were studied by treating an aqueous sample with several amounts of NaBD4. This study demonstrated that most species with at least one ketone/aldehyde moiety were reduced a single time under low [NaBD4], while higher [NaBD4] resulted primarily in additional reductions on multi-ketone/aldehyde species. Furthermore, the changes in UV-vis absorption and emission of the reduced aliquots relative to that of the untreated were correlated with the number of ketone/aldehyde-containing species reduced and identified by this method. The fully developed protocol was used to compare DOM extracted from several aquatic environments. Two pools of ketone/aldehyde-containing species were tentatively identified: A terrestrially-produced group of lignin/tannin-derivatives and a microbially-produced group of carboxyl-rich alicyclic molecules. While the first pool has previously been shown to contribute substantially to the absorption/emission of chromophoric DOM, the second pool most likely would not. The mass labeling method developed here revealed compositional features that are not observable by common ESI mass spectrometric analyses and may serve as a useful way to link the physicochemical properties of DOM to its structure and composition.Item Ultrasensitive CITP-MS based targeted proteomics technologies for protein identification and quantification(2014) Wang, Chenchen; Lee, Cheng S; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Mass Spectrometry (MS) based technologies have enabled efficient and comprehensive proteomic profiling for biomarker discovery. However, due to sample complexity and large concentration variation, the obtained data is usually biased to endogeneous high abundance proteins while the important disease-related information went missing. Targeted proteomics enables the delivery of precise and sensitive qualitative/quantitative data of interest to researchers by focusing analysis on a preselected population of cells or proteins. This project aims to develop targeted proteomic technologies through capillary isotachophoresis (CITP)-based technique which is capable of selectively enriching trace compounds for a further improved sensitivity in both discovery and validation studies. By employing tissue microdissection and a CITP-based multidimensional separation platform, homogeneous glioma cells were isolated from unwanted cells and analyzed in search of glioblastoma biomarker. Comparative proteomic profiling of pure tumor cells from different grades of infiltrative astrocytomas revealed disease specific protein expression variation among grades. Further validation using immunohistochemistry demonstrated consistent results. This targeted tissue analyzing platform provided a sensitive and confident methodology for biomarker discovery within minute amount of samples. With the demonstrated outstanding analyzing capacity on targeted biomarker discovery, we moved on to developing ultrasensitive targeted quantitation techniques. We demonstrated online coupling of transient-CITP/CZE (capillary zone electrophoresis) with selective reaction monitoring (SRM) MS for the first time via a sheathliquid interface for improved sensitivity and selectivity. Ultrasensitive targeted quantitation was achieved through the incorporation of the selective enrichment capability of CITP/CZE with SRM MS, giving a limit of quantitation (LOQ) of 50 pM with a total sample loading of 50 attomoles. In order to further improve the sensitivity, we developed a novel sheathless interface which enables increased loading capacity and nanoflow operation by assembling a large size separation capillary and a small size porous emitter. LOQ was improved 5 times comparing to using the first sheathliquid interface, giving a LOQ of 10 pM with a total sample loading of 25 attomoles. This novel interface optimally preserved the high resolution and efficiency of CITP/CZE while improving the limited sample loading capacity, demonstrating a powerful analytic platform for targeted proteomic quantitation and validation.Item Probing the Dynamics of Ultra-Fast Condensed State Reactions in Energetic Materials(2012) Piekiel, Nicholas William; Zachariah, Michael R; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Energetic materials (EMs) are substances with a high amount of stored energy and the ability to release that energy at a rapid rate. Nanothermites and green organic energetics are two classes of EMs which have gained significant interest as they each have desirable properties over traditional explosives. These systems also possess downfalls, which could potentially be overcome if more were understood about the nature of their reactions. However, ultra-fast reactions are prominent during ignition and combustion, and increase the difficulty in probing the initial and intermediate reaction steps. The goal of this study is to probe the early phases of reaction in nanothermites and green EMs, and to do so we have developed a Temperature-Jump/Time-of-Flight Mass Spectrometer (T-Jump/TOFMS) capable of rapid sampling and heating rates. Various nanothermites have been investigated with this system, and analysis has shown that nanothermite ignition is dependent on the decomposition of the metal oxide, and in certain systems there is distinct evidence of condensed phase initiation. Carbon/metal oxide mixtures, which have application to chemical looping combustion, were also investigated and further demonstrate condensed phase reaction. Aside from mass spectrometry, complementary high heating rate SEM/TEM, pressure cell, and optical experiments were also performed. Many organic energetics including a variety of tetrazole containing ionic salts have also been examined. To investigate the breakdown of the tetrazole ring, a common substructure in green organic energetics, several tetrazole containing salts with minor variations in either functional group or anion composition were studied. Two main tetrazole decomposition pathways were identified and are affected by the placement of functional groups along the tetrazole ring. Many differences were also observed in comparison to previous works at slow heating rates due to either different reaction processes or the presence of secondary reactions in the previous studies. A μ-DSC experiment showed a decrease in activation energy for tetrazole containing materials under high heating rates, further suggesting different mechanistic processes are at play.Item IDENTIFYING AND TRACKING MARINE PROTEIN AND ITS IMPORTANCE IN THE NITROGEN CYCLE USING PROTEOMICS(2011) Moore, Eli Kelly; Harvey, H. Rodger; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Protein comprises the largest compartment of organic nitrogen in the ocean, and makes up a major portion of organic carbon in phytoplankton. Protein has long been thought to be highly labile in the environment and rapidly lost during diagenesis. However, the analysis of dissolved and particulate organic matter with NMR has revealed that much of dissolved and particulate marine organic nitrogen is linked by amide bonds, the very bonds that join amino acids in proteins. Throughout the global ocean, total hydrolysable amino acids (THAAs, the building blocks of proteins) can be measured in the water column and sediments, yet their biosynthetic source has remained elusive. Here, analytical techniques were developed combining protein solubilizing buffer extractions, gel electrophoresis, and proteomic mass spectrometry in order to investigate the biogeochemical significance of marine protein from primary production during transport and incorporation in sediments. These techniques enabled the detection and classification of previously unidentified marine sedimentary proteins. Specific proteins were tracked through the water column to continental shelf and deeper basin (3490 m) sediments of the Bering Sea, one of the world's most productive ecosystems. Diatoms were observed to be the principal source of identifiable protein in sediments. In situ shipboard phytoplankton degradation experiments were conducted to follow protein degradation, and it was observed that individual proteins remained identifiable even after 53 days of microbial recycling. These studies show that proteins can be identified from complex environmental matrices, and the methods developed here can be applied to investigate and identify proteins in degraded organic matter from a broad range of sources. The longevity of some fraction of algal proteins indicates that carbon and nitrogen sources can be tracked down the marine water column to sediments in diatom dominated systems as well as other types of phytoplankton. Using proteomic techniques to understand the marine carbon and nitrogen cycles will become increasingly important as climate change influences the timing, location, and phylogeny of those organisms responsible for oceanic primary production.Item Top-Down Analysis of Bacterial Proteins by High-Resolution Mass Spectrometry(2010) Wynne, Colin Michael; Fenselau, Catherine; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In the biodefense and medical diagnostic fields, MALDI mass spectrometry-based systems are used for rapid characterization of microorganisms generally by detecting and discriminating the highly abundant protein mass-to-charge peaks. It is important that these peaks eventually are identified, but few bacteria have publicly available, annotated genome or proteome from which this identification can be made. This dissertation proposes a method of top-down proteomics using a high-resolution, high mass accuracy analyzer coupled with bioinformatics tools to identify proteins from bacteria with unavailable genome sequences by comparison to protein sequences from closely-related microorganisms. Once these proteins are identified and a link between the unknown target bacteria and the annotated related bacteria is established, phylogenetic trees can be constructed to characterize where the target bacteria relates to other members of the same phylogenetic family. First, the top-down proteomic approach using an Orbitrap mass analyzer is tested using a well known, well studied single protein. After this is demonstrated to be successful, the approach is demonstrated on a bacterium without a sequenced genome, only matching proteins from other organisms which are thought to have 100% homology with the proteins studied by the top-down approach. Finally, the proposed method is changed slightly to be more inclusive and the proteins from two other bacteria without publicly available genomes or proteomes are matched to known proteins that differ in mass and may not be 100% homologous to the proteins of the studied bacteria. This more inclusive method is shown to also be successful in phylogenetically characterizing the bacteria lacking sequence information. Furthermore, some of the mass differences are localized to a small window of amino acids and proposed changes are made that increase confidence in identification while lowering the mass difference between the studied protein and the matched, homologous, known protein.Item Design, Fabrication and Testing of Micronozzles for Gas Sensing Applications(2006-04-03) Li, Sheng; Ghodssi, Reza; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Real-time identification and quantitative analysis of volatile and semi-volatile chemical vapors are critical for environmental monitoring. Currently available portable instruments lack the sensitivity for routine air quality monitoring, so preconcentrators are employed as front-ends for miniaturized chemical sensors. However, commonly used techniques for sensitivity enhancement have a time constant associated with adsorption/desorption or permeation of gas molecules being concentrated. Little work has been reported on fast-response concentrating techniques for gas sensing applications. This research is devoted to the development of a fast-response microfluidic gas concentrating device with appropriate flow dynamic shapes and pressure gradients based on the separation nozzle method. It is capable of concentrating heavy gas molecules diluted in light ones when they are flowing at high speeds, thus maintaining the measurement system response time. This is promising for developing real-time preconcentrators to improve the sensitivity of miniature chemical sensors. In the initial phase of this work, linear test structures were used to characterize viscous effects in microfluidic devices. Unit processes were developed to fabricate encapsulated micronozzles with through-hole inlets and outlets. The mass flow efficiency of the test structures was measured to be in the range of 0.36-0.81, increasing with rising Reynolds number as a result of the decreasing influence of boundary layers. Single-stage gas concentration devices were designed and fabricated on the basis of the test structures. A gas separation experimental setup and a mass spectrometric analysis apparatus were developed to evaluate the performance of the devices. Analytical and finite element analyses were conducted to better understand and verify the experimental results. As a proof-of-concept, gas separation experiments with two different inert gas mixtures were carried out in conjunction with mass spectrometric analysis. More than two-fold enrichment of SF6 molecules with a response time on the order of 0.01 ms was demonstrated through the device. The effects of design parameters and operating conditions on the separation factor were determined experimentally and compared to the numerical simulation results. This study forms the basis for developing a cascade of the single-stage elements envisioned as a preconcentrator for miniature chemical sensors to realize real-time environmental monitoring.Item SOLUTION ISOELECTRIC FOCUSING AND ITS APPLICATION IN COMPARATIVE PROTEOMIC STUDIES OF NUCLEAR PROTEINS(2005-05-27) An, Yanming; Fenselau, Catherine C; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In proteomic research, experimental and computational approaches are combined to provide global analysis of the entire proteomes of cells and tissues. The identification and quantification of multiple proteins, which constitute a specific biological system, are important for understanding complex problems in biology. The coupling of highly efficient separations and mass spectrometry instrumentation is evolving rapidly and is being widely applied to problems ranging from biological function to drug development. Development of rapid and high-resolution separation technology is an important field in proteomics. In this study, a solution isoelectric focusing apparatus was modified and built into a two-dimensional separation method for peptides. Newly commercialized isoelectric membranes, which carry immobilized ampholytes, were integrated to establish the pH boundaries in this apparatus. High-performance liquid chromatography was employed as the second dimension, integrated with mass spectrometry. An insoluble nuclear protein fraction was used for optimization and evaluation of this method. The insoluble nuclear proteins were recovered from the nuclei of human MCF-7 human cancer cells and cleaved enzymatically. The resulting peptides were analyzed by the two-dimensional separation method, which coupled solution isoelectric focusing with reversed-phase liquid chromatography interfaced with mass spectrometry. A total of 281 peptides corresponding to 167 proteins were identified by this experiment. The high sample capacity and concentration effect of isoelectric focusing make it possible to detect relatively low abundance proteins in a complex mixture. This two-dimensional separation method dramatically improves peptide detection and identification compared with a single dimension LC-MS analysis. This method has been demonstrated to provide efficient and reproducible separation of both protein and peptides. The two-dimensional separation method was combined with proteolytic isotopic labeling for comparative analysis of protein expression in different cells. Abundances of nuclear proteins from three different drug resistant MCF-7 cancer cell lines were compared to those from the drug susceptible parent cell line using this combined strategy. The abundances of 19 proteins were found to be significantly changed. Their functions are considered in relation to potential mechanisms of in drug resistance.Item Proteomic Analysis of Plasma Membrane Proteins from Drug Susceptible and Drug Resistant Breast Cancer Cell Lines(2004-11-08) Rahbar, Amir Mikel; Fenselau, Catherine C; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Drug discovery is an important field of research in the biotechnology and pharmaceutical industries. Plasma membranes are rich in drug targets and other proteins responsible for cell signaling, transport, signal transduction, and other cellular functions. Information obtained about these proteins, and the pathways they participate in, helps to facilitate the drug discovery process. Although these plasma membrane proteins play important roles in cellular function, they are usually expressed in very low abundance and are therefore hard to identify and analyze. Comparative proteomic analysis of plasma membranes in different types of cells or different disease states of the same cell or tissue type can help to design targeted therapies specific to particular cell or tissue types and can be used in the identification of biomarkers for early disease detection. In order to be able to identify proteins in the plasma membrane it is important to start out with a plasma membrane fraction that is free of contamination from other more abundant proteins from other portions of the cell. 2D gel electrophoresis is the primary protein separation tool for use with proteomics and drug discovery, however, the inability of membrane proteins to be separated using isoelectric focusing, which is the first step in the 2D gel protocol, excludes 2D gel electrophoresis as a viable technique for the separation of membrane proteins. This thesis develops and evaluates a method to identify proteins found in the plasma membranes of mammalian cells using a modified form of the cationic colloidal silica technique for plasma membrane isolation combined with analysis of these proteins using mass spectrometry. This method is then used in combination with metabolic stable isotope labeling to identify protein expression changes between the mitoxantrone drug susceptible and drug resistant MCF-7 breast cancer cell lines.