ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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Metal hydride materials have been intensively studied for hydrogen storage applications. In addition to potential hydrogen economy applications, metal hydrides offer a wide variety of other interesting properties. For example, hydrogen-dominant materials, which are hydrides with the highest hydrogen content for a particular metal/semimetal composition, are predicted to display high-temperature superconductivity. On the other side of the spectrum are hydrides with small amounts of hydrogen (0.1 - 1 at.%) that are investigated as viable magnetic, thermoelectric or semiconducting materials. Research of metal hydride materials is generally important to gain fundamental understanding of metal-hydrogen interactions in materials. Hydrogenation of Zintl phases, which are defined as compounds between an active metal (alkali, alkaline earth, rare earth) and a p-block metal/semimetal, were attempted by a hot sintering method utilizing an autoclave loaded with gaseous hydrogen (< 9 MPa). Hydride formation competes with oxidative decomposition of a Zintl phase. The oxidative decomposition, which leads to a mixture of binary active metal hydride and p-block element, was observed for investigated aluminum (Al) and gallium (Ga) containing Zintl phases. However, a new phase Li2Al was discovered when Zintl phase precursors were synthesized. Using the single crystal x-ray diffraction (SCXRD), the Li2Al was found to crystallize in an orthorhombic unit cell (Cmcm) with the lattice parameters a = 4.6404(8) Å, b = 9.719(2) Å, and c = 4.4764(8) Å. Increased demand for materials with improved properties necessitates the exploration of alternative synthesis methods. Conventional metal hydride synthesis methods, like ball-milling and autoclave technique, are not responding to the demands of finding new materials. A viable alternative synthesis method is the application of high pressure for the preparation of hydrogen-dominant materials. Extreme pressures in the gigapascal ranges can open access to new metal hydrides with novel structures and properties, because of the drastically increased chemical potential of hydrogen. Pressures up to 10 GPa can be easily achieved using the multi-anvil (MA) hydrogenations while maintaining sufficient sample volume for structure and property characterization. Gigapascal MA hydrogenations using ammonia borane (BH3NH3) as an internal hydrogen source were employed in the search for new hydrogen-dominant materials. Ammonia borane has high gravimetric volume of hydrogen, and additionally the thermally activated decomposition at high pressures lead to a complete hydrogen release at reasonably low temperature. These properties make ammonia borane a desired hydrogen source material. The missing member Li2PtH6 of the series of A2PtH6 compounds (A = Na to Cs) was accessed by employing MA technique. As the known heavier analogs, the Li2PtH6 also crystallizes in a cubic K2PtCl6-type structure with a cell edge length of 6.7681(3) Å. Further gigapascal hydrogenations afforded the compounds K2SiH6 and Rb2SiH6 which are isostructural to Li2PtH6. The cubic K2SiH6 and Rb2SiH6 are built from unique hypervalent SiH62- entities with the lattice parameters of 7.8425(9) and 8.1572(4) Å, respectively. Spectroscopic analysis of hexasilicides confirmed the presence of hypervalent bonding. The Si-H stretching frequencies at 1550 cm-1 appeared considerably decreased in comparison with a normal-valent (2e2c) Si-H stretching frequencies in SiH4 at around 2200 cm-1. However, the observed stretching modes in hypervalent hexasilicides were in a reasonable agreement with Ph3SiH2- (1520 cm-1) where the hydrogen has the axial (3e4c bonded) position in the trigoal bipyramidal environment.
ContributorsPuhakainen, Kati (Author) / Häussermann, Ulrich (Thesis advisor) / Seo, Dong (Thesis advisor) / Kouvetakis, John (Committee member) / Wolf, George (Committee member) / Arizona State University (Publisher)
Created2013
Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
Description
Speciation is the fundamental process that has generated the vast diversity of life on earth. The hallmark of speciation is the evolution of barriers to gene flow. These barriers may reduce gene flow either by keeping incipient species from hybridizing at all (pre-zygotic), or by reducing the fitness of hybrids (post-zygotic). To understand the genetic architecture of these barriers and how they evolve, I studied a genus of wasps that exhibits barriers to gene flow that act both pre- and post-zygotically. Nasonia is a genus of four species of parasitoid wasps that can be hybridized in the laboratory. When two of these species, N. vitripennis and N. giraulti are mated, their offspring suffer, depending on the generation and cross examined, up to 80% mortality during larval development due to incompatible genic interactions between their nuclear and mitochondrial genomes. These species also exhibit pre-zygotic isolation, meaning they are more likely to mate with their own species when given the choice. I examined these two species and their hybrids to determine the genetic and physiological bases of both speciation mechanisms and to understand the evolutionary forces leading to them. I present results that indicate that the oxidative phosphorylation (OXPHOS) pathway, an essential pathway that is responsible for mitochondrial energy generation, is impaired in hybrids of these two species. These results indicate that this impairment is due to the unique evolutionary dynamics of the combined nuclear and mitochondrial origin of this pathway. I also present results showing that, as larvae, these hybrids experience retarded growth linked to the previously observed mortality and I explore possible physiological mechanisms for this. Finally, I show that the pre-mating isolation is due to a change in a single pheromone component in N. vitripennis males, that this change is under simple genetic control, and that it evolved neutrally before being co-opted as a species recognition signal. These results are an important addition to our overall understanding of the mechanisms of speciation and showcase Nasonia as an emerging model for the study of the genetics of speciation.
ContributorsGibson, Joshua D (Author) / Gadau, Jürgen (Thesis advisor) / Harrison, Jon (Committee member) / Pratt, Stephen (Committee member) / Verrelli, Brian (Committee member) / Willis, Wayne (Committee member) / Arizona State University (Publisher)
Created2013
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips respectively. In this work, peptide microarray fabrication based on the abovementioned techniques were optimized. In addition, MALDI mass spectrometry based peptide synthesis characterization on semiconductor microchips was developed and novel applications of a CombiMatrix (CBMX) platform for electrochemically controlled synthesis were explored. We have investigated performance of 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) derivatives as photo-labile protecting group. Specifically, influence of substituents on 4 and 5 positions of phenyl ring of NPPOC group on the rate of photolysis and the yield of the amine was investigated. The results indicated that substituents capable of forming a π-network with the nitro group enhanced the rate of photolysis and yield. Once such properly substituted NPPOC groups were used, the rate of photolysis/yield depended on the nature of protected amino group indicating that a different chemical step during the photo-cleavage process became the rate limiting step. We also focused on electrochemically-directed parallel synthesis of high-density peptide microarrays using the CBMX technology referred to above which uses electrochemically generated acids to perform patterned chemistry. Several issues related to peptide synthesis on the CBMX platform were studied and optimized, with emphasis placed on the reactions of electro-generated acids during the deprotection step of peptide synthesis. We have developed a MALDI mass spectrometry based method to determine the chemical composition of microarray synthesis, directly on the feature. This method utilizes non-diffusional chemical cleavage from the surface, thereby making the chemical characterization of high-density microarray features simple, accurate, and amenable to high-throughput. CBMX Corp. has developed a microarray reader which is based on electro-chemical detection of redox chemical species. Several parameters of the instrument were studied and optimized and novel redox applications of peptide microarrays on CBMX platform were also investigated using the instrument. These include (i) a search of metal binding catalytic peptides to reduce overpotential associated with water oxidation reaction and (ii) an immobilization of peptide microarrays using electro-polymerized polypyrrole.
ContributorsKumar, Pallav (Author) / Woodbury, Neal (Thesis advisor) / Allen, James (Committee member) / Johnston, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
Human breath is a concoction of thousands of compounds having in it a breath-print of physiological processes in the body. Though breath provides a non-invasive and easy to handle biological fluid, its analysis for clinical diagnosis is not very common. Partly the reason for this absence is unavailability of cost effective and convenient tools for such analysis. Scientific literature is full of novel sensor ideas but it is challenging to develop a working device, which are few. These challenges include trace level detection, presence of hundreds of interfering compounds, excessive humidity, different sampling regulations and personal variability. To meet these challenges as well as deliver a low cost solution, optical sensors based on specific colorimetric chemical reactions on mesoporous membranes have been developed. Sensor hardware utilizing cost effective and ubiquitously available light source (LED) and detector (webcam/photo diodes) has been developed and optimized for sensitive detection. Sample conditioning mouthpiece suitable for portable sensors is developed and integrated. The sensors are capable of communication with mobile phones realizing the idea of m-health for easy personal health monitoring in free living conditions. Nitric oxide and Acetone are chosen as analytes of interest. Nitric oxide levels in the breath correlate with lung inflammation which makes it useful for asthma management. Acetone levels increase during ketosis resulting from fat metabolism in the body. Monitoring breath acetone thus provides useful information to people with type1 diabetes, epileptic children on ketogenic diets and people following fitness plans for weight loss.
ContributorsPrabhakar, Amlendu (Author) / Tao, Nongjian (Thesis advisor) / Forzani, Erica (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2013
Description
Synechocystis sp PCC 6803 is a photosynthetic cyanobacterium that can be easily transformed to produce molecules of interest; this has increased Synechocystis’ popularity as a clean energy platform. Synechocystis has been shown to produce and excrete molecules such as fatty acids, isoprene, etc. after appropriate genetic modification. Challenges faced for large–scale growth of modified Synechocystis include abiotic stress, microbial contamination and high processing costs of product and cell material. Research reported in this dissertation contributes to solutions to these challenges. First, abiotic stress was addressed by overexpression of the heat shock protein ClpB1. In contrast to the wild type, the ClpB1 overexpression mutant (Slr1641+) tolerated rapid temperature changes, but no difference was found between the strains when temperature shifts were slower. Combination of ClpB1 overexpression with DnaK2 overexpression (Slr1641+/Sll0170+) further increased thermotolerance. Next, we used a Synechocystis strain that carries an introduced isoprene synthase gene (IspS+) and that therefore produces isoprene. We attempted to increase isoprene yields by overexpression of key enzymes in the methyl erythritol phosphate (MEP) pathway that leads to synthesis of the isoprene precursor. Isoprene production was not increased greatly by MEP pathway induction, likely because of limitations in the affinity of the isoprene synthase for the substrate. Finally, two extraction principles, two–phase liquid extraction (e.g., with an organic and aqueous phase) and solid–liquid extraction (e.g., with a resin) were tested. Two–phase liquid extraction is suitable for separating isoprene but not fatty acids from the culture medium. Fatty acid removal required acidification or surfactant addition, which affected biocompatibility. Therefore, improvements of both the organism and product–harvesting methods can contribute to enhancing the potential of cyanobacteria as solar–powered biocatalysts for the production of petroleum substitutes.
ContributorsGonzalez Esquer, Cesar Raul (Author) / Vermaas, Willem (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Nielsen, David (Committee member) / Arizona State University (Publisher)
Created2013
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.
ContributorsBergkamp, Jesse J (Author) / Moore, Ana L (Thesis advisor) / Mariño-Ochoa, Ernesto (Thesis advisor) / Gust, Devens J (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Developing a system capable of using solar energy to drive the conversion of an abundant and available precursor to fuel would profoundly impact humanity's energy use and thereby the condition of the global ecosystem. Such is the goal of artificial photosynthesis: to convert water to hydrogen using solar radiation as the sole energy input and ideally do so with the use of low cost, abundant materials. Constructing photoelectrochemical cells incorporating photoanodes structurally reminiscent of those used in dye sensitized photovoltaic solar cells presents one approach to establishing an artificial photosynthetic system. The work presented herein describes the production, integration, and study of water oxidation catalysts, molecular dyes, and metal oxide based photoelectrodes carried out in the pursuit of developing solar water splitting systems.
ContributorsSherman, Benjamin D (Author) / Moore, Thomas (Thesis advisor) / Moore, Ana (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2013