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.
Displaying 1 - 10 of 269
Filtering by
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
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
After a decade of efforts, accurate and affordable DNA sequencing continues to remain an important goal in current research landscape. This thesis starts with a brief overview of the recent updates in the field of DNA sequencing technologies followed by description of the nanofluidics route to single molecule DNA detection. Chapter 2 presents discusses carbon nanotube(CNT) based nanofluidics. The fabrication and DNA sensing measurements of CNT forest membrane devices are presented. Chapter 3 gives the background for functionalization and recognition aspects of reader molecules. Chapter 4 marks the transition to solid state nanopore nanofluidics. The fabrication of Imidazole functionalized nanopores is discussed. The Single Molecule detection results of DNA from Palladium nanopore devices are presented next. Combining chemical recognition to nanopore technology, it has been possible to prolong the duration of single molecule events from the order of a few micro seconds to upto a few milliseconds. Overall, the work presented in this thesis promises longer single molecule detection time in a nanofludic set up and paves way for novel nanopore- tunnel junction devices that combine recognition chemistry, tunneling device and nanopore approach.
ContributorsKrishnakumar, Padmini (Author) / Lindsay, Stuart (Thesis advisor) / He, Jin (Committee member) / Vaiana, Sara (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2013
Description
The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk Ge, dominated by indirect gap emission, and the PL spectrum of Ge-on-Si films, dominated by direct gap emission. It was found that the difference is due to the supression of self-absorption effects in Ge films, combined with a deviation from quasi-equilibrium conditions in the conduction band of undoped films. The latter is confirmed by a model suggesting that the deviation is caused by the shorter recombination lifetime in the films relative to bulk Ge. The knowledge acquired from this work was then utilized to study the PL properties of n-type Ge1-ySny/Si (y=0.004-0.04) samples grown via chemical vapor deposition of Ge2H6/SnD4/P(GeH3)3. It was found that the emission intensity (I) of these samples is at least 10x stronger than observed in un-doped counterparts and that the Idir/Iind ratio of direct over indirect gap emission increases for high-Sn contents due to the reduced gamma-L valley separation, as expected. Next the PL investigation was expanded to samples with y=0.05-0.09 grown via a new method using the more reactive Ge3H8 in place of Ge2H6. Optical quality, 1-um thick Ge1-ySny/Si(100) layers were produced using Ge3H10/SnD4 and found to exhibit strong, tunable PL near the threshold of the direct-indirect bandgap crossover. A byproduct of this study was the development of an enhanced process to produce Ge3H8, Ge4H10, and Ge5H12 analogs for application in ultra-low temperature deposition of Group-IV semiconductors. The thesis also studies synthesis routes of an entirely new class of semiconductor compounds and alloys described by Si5-2y(III-V)y (III=Al, V= As, P) comprising of specifically designed diamond-like structures based on a Si parent lattice incorporating isolated III-V units. The common theme of the two thesis topics is the development of new mono-crystalline materials on ubiquitous silicon platforms with the objective of enhancing the optoelectronic performance of Si and Ge semiconductors, potentially leading to the design of next generation optical devices including lasers, detectors and solar cells.
ContributorsGrzybowski, Gordon (Author) / Kouvetakis, John (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2013
Description
The work contained in this dissertation is focused on the optical properties of direct band gap semiconductors which crystallize in a wurtzite structure: more specifically, the III-nitrides and ZnO. By using cathodoluminescence spectroscopy, many of their properties have been investigated, including band gaps, defect energy levels, carrier lifetimes, strain states, exciton binding energies, and effects of electron irradiation on luminescence. Part of this work is focused on p-type Mg-doped GaN and InGaN. These materials are extremely important for the fabrication of visible light emitting diodes and diode lasers and their complex nature is currently not entirely understood. The luminescence of Mg-doped GaN films has been correlated with electrical and structural measurements in order to understand the behavior of hydrogen in the material. Deeply-bound excitons emitting near 3.37 and 3.42 eV are observed in films with a significant hydrogen concentration during cathodoluminescence at liquid helium temperatures. These radiative transitions are unstable during electron irradiation. Our observations suggest a hydrogen-related nature, as opposed to a previous assignment of stacking fault luminescence. The intensity of the 3.37 eV transition can be correlated with the electrical activation of the Mg acceptors. Next, the acceptor energy level of Mg in InGaN is shown to decrease significantly with an increase in the indium composition. This also corresponds to a decrease in the resistivity of these films. In addition, the hole concentration in multiple quantum well light emitting diode structures is much more uniform in the active region when Mg-doped InGaN (instead of Mg-doped GaN) is used. These results will help improve the efficiency of light emitting diodes, especially in the green/yellow color range. Also, the improved hole transport may prove to be important for the development of photovoltaic devices. Cathodoluminescence studies have also been performed on nanoindented ZnO crystals. Bulk, single crystal ZnO was indented using a sub-micron spherical diamond tip on various surface orientations. The resistance to deformation (the "hardness") of each surface orientation was measured, with the c-plane being the most resistive. This is due to the orientation of the easy glide planes, the c-planes, being positioned perpendicularly to the applied load. The a-plane oriented crystal is the least resistive to deformation. Cathodoluminescence imaging allows for the correlation of the luminescence with the regions located near the indentation. Sub-nanometer shifts in the band edge emission have been assigned to residual strain the crystals. The a- and m-plane oriented crystals show two-fold symmetry with regions of compressive and tensile strain located parallel and perpendicular to the ±c-directions, respectively. The c-plane oriented crystal shows six-fold symmetry with regions of tensile strain extending along the six equivalent a-directions.
ContributorsJuday, Reid (Author) / Ponce, Fernando A. (Thesis advisor) / Drucker, Jeff (Committee member) / Mccartney, Martha R (Committee member) / Menéndez, Jose (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microwave dielectrics are widely used to make resonators and filters in telecommunication systems. The production of thin films with high dielectric constant and low loss could potentially enable a marked reduction in the size of devices and systems. However, studies of these materials in thin film form are very sparse. In this research, experiments were carried out on practical high-performance dielectrics including ZrTiO4-ZnNb2O6 (ZTZN) and Ba(Co,Zn)1/3Nb2/3O3 (BCZN) with high dielectric constant and low loss tangent. Thin films were deposited by laser ablation on various substrates, with a systematical study of growth conditions like substrate temperature, oxygen pressure and annealing to optimize the film quality, and the compositional, microstructural, optical and electric properties were characterized. The deposited ZTZN films were randomly oriented polycrystalline on Si substrate and textured on MgO substrate with a tetragonal lattice change at elevated temperature. The BCZN films deposited on MgO substrate showed superior film quality relative to that on other substrates, which grow epitaxially with an orientation of (001) // MgO (001) and (100) // MgO (100) when substrate temperature was above 500 oC. In-situ annealing at growth temperature in 200 mTorr oxygen pressure was found to enhance the quality of the films, reducing the peak width of the X-ray Diffraction (XRD) rocking curve to 0.53o and the χmin of channeling Rutherford Backscattering Spectrometry (RBS) to 8.8% when grown at 800oC. Atomic Force Microscopy (AFM) was used to study the topography and found a monotonic decrease in the surface roughness when the growth temperature increased. Optical absorption and transmission measurements were used to determine the energy bandgap and the refractive index respectively. A low-frequency dielectric constant of 34 was measured using a planar interdigital measurement structure. The resistivity of the film is ~3×1010 ohm·cm at room temperature and has an activation energy of thermal activated current of 0.66 eV.
ContributorsLi, You (Author) / Newman, Nathan (Thesis advisor) / Alford, Terry (Committee member) / Singh, Rakesh (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation is focused on material property exploration and analysis using computational quantum mechanics methods. Theoretical calculations were performed on the recently discovered hexahydride materials A2SiH6 (A=Rb, K) to calculate the lattice dynamics of the systems in order to check for structural stability, verify the experimental Raman and infrared spectrospcopy results, and obtain the theoretical free energies of formation. The electronic structure of the systems was calculated and the bonding and ionic properties of the systems were analyzed. The novel hexahydrides were compared to the important hydrogen storage material KSiH3. This showed that the hypervalent nature of the SiH62- ions reduced the Si-H bonding strength considerably. These hydrogen rich compounds could have promising energy applications as they link to alternative hydrogen fuel technology. The carbide systems Li-C (A=Li,Ca,Mg) were studied using \emph{ab initio} and evolutionary algorithms at high pressures. At ambient pressure Li2C2 and CaC2 are known to contain C22- dumbbell anions and CaC2 is polymorphic. At elevated pressure both CaC2 and Li2C2 display polymorphism. At ambient pressure the Mg-C system contains several experimentally known phases, however, all known phases are shown to be metastable with respect to the pure elements Mg and C. First principle investigation of the configurational space of these compounds via evolutionary algorithms results in a variety of metastable and unique structures. The binary compounds ZnSb and ZnAs are II-V electron-poor semiconductors with interesting thermoelectric properties. They contain rhomboid rings composed of Zn2Sb2 (Zn2As2) with multi-centered covalent bonds which are in turn covalently bonded to other rings via two-centered, two-electron bonds. Ionicity was explored via Bader charge analysis and it appears that the low ionicity that these materials display is a necessary condition of their multicentered bonding. Both compounds were found to have narrow, indirect band gaps with multi-valley valence and conduction bands; which are important characteristics for high thermopower in thermoelectric materials. Future work is needed to analyze the lattice properties of the II-V CdSb-type systems, especially in order to find the origin of the extremely low thermal conductivity that these systems display.
ContributorsBenson, Daryn Eugene (Author) / Häussermann, Ulrich (Thesis advisor) / Shumway, John (Thesis advisor) / Chamberlin, Ralph (Committee member) / Sankey, Otto (Committee member) / Treacy, Mike (Committee member) / Arizona State University (Publisher)
Created2013
Description
The purpose of the current study was to use structural equation modeling-based quantitative genetic models to characterize latent genetic and environmental influences on proneness to three discrete negative emotions in middle childhood, according to mother-report, father-report and in-home observation. One primary aim was to test the extent to which covariance among the three emotions could be accounted for by a single, common genetically- and environmentally-influenced negative emotionality factor. A second aim was to examine the extent to which different reporters appeared to be tapping into the same genetically- and environmentally-influenced aspects of each emotion. According to mother- and father-report, moderate to high genetic influences were evident for all emotions, with mother- and father-report of fear and father-report of anger showing the highest heritability. Significant common environmental influences were also found for mother-report of anger and sadness in both univariate and multivariate models. For observed emotion, anger was moderately heritable with no evidence for common environmental variance, but sadness, object fear and social fear all showed modest to moderate common environmental influences and no significant genetic variance. In addition, cholesky decompositions examining genetic and environmental influences across reporter suggested that despite considerable overlap between mother-report and father-report, there was also reporter-specific variance on anger, sadness, and fear. Specifically, there were significant common environmental influences on mother-report of anger- and sadness that were not shared with father-report, and genetic influences on father-report of sadness and fear that were not shared with mother-report. In-home observations were not highly correlated enough with parent-report to support multivariate analysis for any emotion. Finally, according to both mother- and father-report, a single set of genetic and environmental influences was sufficient to account for covariance among all three negative emotions. However, fear was primarily explained by genetic influences not shared with other emotions, and anger also showed considerable emotion-specific genetic variance. In both cases, findings support the value of a more emotion-specific approach to temperament, and highlight the need to consider distinctions as well as commonalities across emotions, reporters and situations.
ContributorsClifford, Sierra (Author) / Lemery, Kathryn (Thesis advisor) / Shiota, Michelle (Committee member) / Eisenberg, Nancy (Committee member) / Arizona State University (Publisher)
Created2013