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Open Access Publications from the University of California

UC Riverside Electronic Theses and Dissertations

Cover page of Charge Transport, Spin Transport and Magneto-Optics of Solid-State Topological Memory Devices

Charge Transport, Spin Transport and Magneto-Optics of Solid-State Topological Memory Devices

(2019)

Topological spin textures such as skyrmions are strong candidates for next-generation

storage units and spintronic devices. Skyrmions formed on the surface of Topological Insu-

lators (TIs) give rise to additional device functionalities. The skyrmion-TI heterostructure

system shows quantized topological Hall effect (QTHE) without any external magnetic eld.

This shows that the topological properties of the skyrmion spin texture can be imprinted

on the Dirac electrons of the topological insulator. We also predict such a skyrmion-TI

heterostructure will give rise to high gure-of-merit magneto-optic Kerr effects (MOKE).

Optical dielectric tensor elements are calculated using a tight-binding model and the Kubo

formula. We show that the Fermi level dependence of the MOKE signatures is distinct

for the different magnetic textures. Based on this, a skyrmion optical memory device is

proposed. Next, we investigate antiferromagnetic (AFM) skyrmion since it offers couple of

advantages in terms of speed and stability compared to its ferromagnetic counterpart. We

investigate how AFM skyrmions can be manipulated using temperature gradient to realize

novel spintronic device. The effect of temperature gradients on AFM skyrmion dynamics

is predicted using a numerical Landau Lifshitz Gilbert (LLG) model.

Cover page of Metabolite Assignment and Profiling of Environmental Stressors in Earthworms (Eisenia fetida), Coelomic Fluid, and Coelomocytes

Metabolite Assignment and Profiling of Environmental Stressors in Earthworms (Eisenia fetida), Coelomic Fluid, and Coelomocytes

(2019)

Earthworms (Eisenia fetida) are abundant and vital members of the soil environment and monitoring their metabolism may be a useful indicator of soil health and ecotoxicity. This dissertation aimed to expand the analysis of nonlethal and noninvasive earthworm metabolite pools to probe their usefulness in environmental monitoring. Coelomic fluid (CF) is a biofluid that fills the body cavity of the worm and contains free-moving liver-like and immune cells called coelomocytes (CC). 1H NMR, GC-MS, and LC-MS were used to identify metabolites in earthworm, CF, and CC extracts. Fifty-four metabolites were detected in earthworm extracts, 47 in CF, and 41 in CC using 1H NMR. GC-MS was only employed with CF extracts, where 44 metabolites were detected. Targeted LC-MS analyses detected 97 metabolites in earthworm extracts, 82 in CF, and 67 in CC. Significantly, assignment of the earthworm metabolomes led to the identification of a new metabolite: (-)-beta-ʟ-malyl-ʟ-glutamate. Malylglutamate was detected in several invertebrate species at concentrations in the mM - uM range, and it was elucidated as a chelator and potential store for malate and glutamate. This dissertation also sought to explore the response of earthworm metabolism to environmental stressors. CF of earthworms exposed to six chloroacetanilide herbicides (acetochlor, alachlor, butachlor, metolachlor, S-metolachlor, and propachlor) were collected and analyzed using 1H NMR and GC-MS. Perturbations in lipid metabolism and beta-oxidation were observed, suggesting that chloroacetanilide herbicides affected earthworms in a manner similar to the herbicidal mode of action. Exposure to chlorothalonil was used to compare the impact of metabolites in earthworm, CF, and CC extracts using 1H NMR and LC-MS. CF extracts were the most sensitive matrix to detect the effects of chlorothalonil exposure, where increased glutamine levels was the only biomarker detected at both doses. Chemometrics revealed N-acetylserine and ophthalmic acid as strong biomarkers in the high dose group of CF extracts, which may indicate increased oxidative stress. ADP ribose was the only metabolite consistently affected and its increase could be a response to chlorothalonil-induced DNA damage. This work supports metabolic profiling in earthworm and CF extracts to determine which matrix is most sensitive for detecting environmental stress.

Cover page of A Stochastic Restricted Maximum Likelihood Method for Genomic Selection and Genome-Wide Association Studies

A Stochastic Restricted Maximum Likelihood Method for Genomic Selection and Genome-Wide Association Studies

(2019)

Genomic selection is a marker-assisted methodology that dramatically decreases the cost of measuring phenotypes by using the whole-genome information to predict and select desirable individuals. In plant breeding, it plays an important role to speed up the breeding cycles. Modern techniques make obtaining marker information from the entire genome feasible. However, it results in high dimensionality of predictors when we implement a mathematical model to estimate the parameters and predict future crosses. Many statistical models including variable selection models can address this problem and have been applied in genomic selection. Variable selection models can also be applied in GWAS which is a powerful tool to discover the association between genetic variation and variation in quantitative traits.

A novel statistical approach based on BLUP was proposed to be implemented in both genomic selection and GWAS. The general idea of the proposed approach is using an algorithm to divide markers into the small effect group and the large effect group. Markers within the large effect group can be potentially significant markers associated with the analyzed phenotypic trait. In Chapter 3, we used simulated data and two real-world data sets to demonstrate the distinctions among six statistical methods for genomic selection. In addition, the proposed model was applied in GWAS based on another simulated data, and the proposed model is superior to the other two variable selection models.

Cover page of Regulation of Gene Expression in the Drosophila Olfactory System Varies Widely With Stimulus, Duration, Age, and Development

Regulation of Gene Expression in the Drosophila Olfactory System Varies Widely With Stimulus, Duration, Age, and Development

(2019)

The Drosophila olfactory system is an ideal model for the investigation of

principles of gene regulation in the nervous system. Within this system, we characterize

gene expression changes in response to short-term and long-term exposure to odorants.

Additionally, we examine the contributions of two transcription factors to the

development of this chemosensory system. Short-term exposure to odorants and light

leads to neural activation and induction of activity regulated genes (ARGs). ARG

induction in neurons in can lead to long-term changes at the level of the synapse. Such

alterations in synaptic structure/function are thought to underlie important cellular

processes such as synaptic plasticity and long-term memory formation. We have

conducted a genome-wide study of genes in the Drosophila central nervous system

induced after brief periods of sensory stimulation and have identified 352 genes whose

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expression increases in response to neural activity. The regulation of these genes is

altered with increasing age. Furthermore, we demonstrate that loss of a histone

deacetylase alters neuronal response to sensory stimuli, suggesting a mechanism of

epigenetic regulation. We extended our transcriptome analysis to the fly antenna and

found that the genes increased in response to fruit odorants differ significantly from the

genes induced by the repellent DEET. In response to long-term exposure to the odorant

diacetyl, we find that dramatic changes in gene expression can, in part, be attributed to

inhibition of histone deacetylases. This non-traditional action of diacetyl slows

neurodegeneration in the fly model for Huntington’s Disease. We conclude with an

analysis of two transcription factors acj6 and pdm3 and find they regulated proper

chemosensory receptor and axon guidance gene expression in the developing

Drosophila olfactory system.

Cover page of An ‘Omics Investigation into the Effects of Aluminum Toxicity on Arabidopsis Thaliana

An ‘Omics Investigation into the Effects of Aluminum Toxicity on Arabidopsis Thaliana

(2019)

Aluminum (Al) toxicity is a global problem that leads to stoppage of root growth, overall smaller plant size and lower crop yields. Previous research has shown the molecular response of plants to Al toxicity occurs through a DNA damage response pathway involving ATR and SOG1 genes. To explore this phenomenon further both transcriptomic and genomic experiments were performed using Arabidopsis Thaliana. The goal of the transcriptomics was to determine a gene or suite of genes that were deferentially expressed with Al3+ exposure that could potentially confer Al tolerance to crop plants. While a companion genomics study aimed to understand what type of genomic damage was occurring following Al exposure. Arabidopsis seedlings were grown on gel soaked media plates in the absences or presence of Al3+, before nucleic acids were harvested for Illumina short read sequencing. Transcriptionally, a suite of genes that included known Al response factors and some novel genes were identified using a cut off of 2 fold change and a false discover rate of 1%, 10 of the genes had their expression validated using quantitative real time PCR. In addition, it was identified genetically that Al toxicity leads to the generation of one and two base pair insertions and deletions, which were determined to be statistically significant. With this knowledge future experiments can be performed with the promise of finding the molecular critical to responding to Al exposure and how to use this response to confer Al tolerance to crop plants. Such experiments should include testing Arabidopsis mutants that have reactive oxygen species related genes knocked out or overexpressed to evaluate the level of genomic damage in the presence Al3+. Additionally, genes identified from this transcriptional study should have their expression modified to further understand their role in Al toxicity. Pathway interaction studies with these factors could highlight the full molecular pathway of the plants response to Al exposure.

Cover page of Air Pollution Research in SoCal - From Mobile Laboratory Atmospheric Contaminant Measurements to In-Vivo Health Investigations Using a Newly Constructed Environmental Chamber

Air Pollution Research in SoCal - From Mobile Laboratory Atmospheric Contaminant Measurements to In-Vivo Health Investigations Using a Newly Constructed Environmental Chamber

(2019)

Air pollution is the presence of toxic chemicals or compounds emitted into the air at a level that poses a threat to the environment and human health. This Ph.D. thesis provides construction of two energy self-supported mobile laboratories and an environmental chamber for animal exposure experiments to target on real-time on-road measurement of atmospheric contaminants and in-depth health investigations of multiple air pollutants.

Concern has been raised that select atmospheric pollutants might adversely impact the performance of Honda’s fuel cell car due to the heavy air pollution in Southern California. Ammonium and sodium cations may displace hydrogen ions in the fuel cell’s Proton Exchange Membrane (PEM), while SO2 and NO2 may react with the platinum anode. Ammonia may attack the cathode directly and can be a potential source of additional ammonium cations. A short-period intensive study was performed to identify transient and average exposure levels to these species in Southern California and to compare these values to the closest local air monitoring station data. We found highly elevated NO2 and SO2 concentration in the industrial areas and similar concentration range for other target contaminants when comparing with available data from SCAQMD.

The negative impact of air pollution also prompts the development of health research. Most in-vivo health studies conducted regarding air pollutants have been either through traditional medical intranasal treatment or using a tiny chamber, which limit animal activities. In this study, we designed and tested a large, whole-body, multiple animal exposure chamber that simultaneously controls particle size distribution and PM mass concentration. We demonstrate that the chamber system provides well controlled and characterized whole animal exposures, where dosage is by inhalation of particulate matter. We found inhalation exposure to a natural fungal allergen sufficient to induce lung inflammation and surprisingly caused reductions in baseline expression of select innate immune molecules in the region of the CNS controlling respiration.

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Cover page of Mathematical Model for Studying Combined Effect of Individual Cell Behavior on Developing Tissue Shape in Plants

Mathematical Model for Studying Combined Effect of Individual Cell Behavior on Developing Tissue Shape in Plants

(2019)

The development of an organ or organism is a complex process that includes many interact- ing components. Scientific inquiries in developmental biology have motivated the creation of novel mathematical tools to better understand how distributions of cellular identities and phenotypes are attained through spatiotemporal regulation of cell behaviors and gene regulation. One of the central problems in animal and plant developmental biology is de- ciphering how chemical and mechanical signals interact within a tissue to produce organs of defined size, shape, and function. Plant development is much different from animals since the majority of organs are continually produced throughout the life of the plant and the presence of the cell wall imposes a unique constraint on cell behaviors. How exactly cell wall mechanical properties influence cell behaviors that lead to stem cell maintenance and correct organ formation is still largely unknown. To address this problem, a novel, subcellular element computational model of growth of stem cells within the multilayered shoot apical meristem (SAM) of Arabidopsis thaliana is developed and calibrated using experimental data. Novel features of the model include separate, detailed descriptions of cell wall extensibility and mechanical stiffness, deformation of the middle lamella, and in- crease in cytoplasmic pressure generating internal turgor pressure. The model is used to test novel hypothesized mechanisms of formation of the shape and structure of the growing, multilayered SAM based on WUS concentration of individual cells controlling cell growth rates and layer-dependent anisotropic mechanical properties of subcellular components of individual cells determining anisotropic cell expansion directions. Model simulations also provide a detailed prediction of distribution of stresses in the growing tissue which can be tested in future experiments.

Cover page of Combining Seismology and Geodesy to Better Constrain Earthquake Source Parameters and Shallow Fault Behavior

Combining Seismology and Geodesy to Better Constrain Earthquake Source Parameters and Shallow Fault Behavior

(2019)

Our current understanding of the Earth’s interior structure and processes is limited to observations made at the surface that are mapped to the subsurface using inverse methods. The complexity of geophysical inverse problems mainly arises from the existence of many free parameters that sometimes have traded off with each other. This can cause inaccuracies, low resolution and non-uniqueness problems in geophysical models. The main focus of my dissertation is on how we can use two independent geophysical data types – geodesy and seismology – to increase knowledge, resolution and accuracy of Earth’s structure, and of interseismic and coseismic processes in the earthquake cycle.

For example, in my first project (Chapter 2) I search for repeating earthquakes (REs) using similarity search on recorded seismic waveforms from the northern San Francisco Bay Area. Evidence from the San Andreas fault and elsewhere indicates that REs are correlated with, and likely driven by, aseismic slip (creep) at depth. This is complementary knowledge to the geodetic observation of creep at the surface. The source information of REs can also be used to constrain the interseismic slip models inverted from geodetic data such as GPS and InSAR.

By using a new fast similarity search algorithm, that I developed specifically for probing big seismic data sets (described in Chapter 3), we found 198 RE groups, including periodic and nonperiodic repeating earthquake 'families', and repeating event pairs. Our results can not only help us to map the depth and extent of creep on several major faults but also reveal previously unknown structural complexity – e.g. that subparallel strands of the Maacama fault are active and creep simultaneously. Source parameters and locations of these REs can be used to update seismic hazard models, by better constraining the creeping areas of faults in the region, and to improve community models of fault geometry.

In a second major project (Chapter 4), I aim to reconcile earthquake source parameters and locations determined by long-period teleseismic source inversions with those obtained from InSAR data. The latter observes earthquakes in situ and thus, we presume, accurately locates them. Previous studies suggest that the discrepancies between these two catalogs arise from the existing inaccuracy in Earth models and are caused by the historic (and circular) problem that earthquake locations estimated using inaccurate velocity models are themselves inaccurate, and vice-versa.

In several case studies of various locations (e.g. California, Iceland, central Italy) we observe and quantify the biases of the S40RTS Earth velocity model that cause a delay or early arrival of the predicted seismic waves to the seismic stations at certain azimuths. We gather these misestimations of predicted seismic wave arrivals as corrections that can be applied to teleseismic source inversions in order to improve location accuracy. The similarity of corrections that we observe for events in the same region suggests they could be used as regional corrections. We also show that these corrections not only can be used to accurately locate global events but also can help us to accurately obtain the source mechanisms of these events. In future, by gathering these corrections for all the events with existing InSAR source models (i.e. more than 120 global events so far) we might be able to increase accuracy of velocity models of the upper mantle, e.g. by using finite-frequency tomography.

Cover page of Disrupting Suburban Religion: The Great Recession, Suburban Poverty, and Reframing Evangelical Narratives

Disrupting Suburban Religion: The Great Recession, Suburban Poverty, and Reframing Evangelical Narratives

(2019)

The Great Recession that started in 2007 was one of the worst economic downturns in United States history. Unemployment hit record highs and home foreclosures became a normal part of the national landscape. The suburban middle-class population in America saw a rise in poverty unlike anything before. More people in suburbs living under the federal poverty limit compared to urban areas. Suburban evangelical Christians were among those who lost homes, jobs, assets, and savings. They turned to their local churches for financial assistance and pastoral care as they tried to make sense of their circumstances. Pastors had to evaluate their perspectives on poverty and benevolence as a new demographic of people sought financial assistance.

This dissertation examines how evangelical pastors and leaders ministered to congregants that were affected by the recession in the Inland Empire of Southern California. The recession caused pastors and ministry leaders to challenge their congregants to change their worldviews from a consumerist narrative of the American Dream and towards a worldview based on biblical teachings focused on stewardship, living within one’s financial means, and grounding individual identity in the person of Jesus Christ. Using narrative analysis and a theory of worldview transformation, this project looks at reflections about pastoral care and counseling, sermons, and financial religious educational curriculum, to explore how pastors challenged their congregants to rethink their views about socio-economic status, wealth, materiality, and how these things related to their faith. Pastors encouraged their congregants to get out of debt and explained to them how to view money as a tool to build God’s Kingdom. These pastors were not just helping people work through their hardships during the recession – they changed the narrative of how evangelical faith ought to relate with the American Dream. Evangelicals were challenged to be stewards and managers of God's resources rather than consumers. This new narrative focused on financial freedom through debt elimination and generosity as the vehicle to experience God’s blessings and to build his kingdom.

Cover page of Using Telepresence Robots to Improve Disruptive Behavior in Students with Emotional Disturbance

Using Telepresence Robots to Improve Disruptive Behavior in Students with Emotional Disturbance

(2019)

Problem-solving consultation in school settings has been found to be an effective service delivery method to support educators struggling to address behavioral concerns for students with Emotional Disturbance (ED). Despite the benefits, many barriers to service providers, such as lack of time and competing obligations, restrict opportunities to offer problem solving-consultation to high-need schools that are otherwise unable to receive services. The caseload of a typical school psychologist often exceeds the levels specified in best practices, suggesting that it can be highly challenging for professionals to offer behavioral services to educators outside their necessary role for assessing special education eligibility. The purpose of this study is to evaluate the effectiveness and acceptability of telepresence robot problem-solving consultation (TRPSC) for reducing disruptive behaviors for the ED population. Using a randomized multiple baseline design, the proposed study will examine behavior outcomes of four middle school students as well as the effectiveness and acceptability ratings by educators of the TRPSC process in self-contained ED classrooms. Educators will be involved in the consultation process and implement a behavior intervention plan (BIP) generated through teleconsultation for students with ED engaging in disruptive behaviors. It is hypothesized that implementing a BIP using TRPSC will result in (a) a decrease in students’ disruptive behaviors, (b) acceptable ratings of the teleconsultation process by teachers, and (c) ratings by educators of the consultant and BIP as effective.