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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- All Subjects: Biology
Description
What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory ought to be broad enough as to not be constrained to an Earth-based biochemistry. In this dissertation, the philosophy of studying living systems from the perspective of traditional physics is first explored as a motivating discussion for subsequent research. Traditionally, we have often thought of the physical world from a bottom-up approach: things happening on a smaller scale aggregate into things happening on a larger scale. In addition, the laws of physics are generally considered static over time. Research suggests that biological evolution may follow dynamic laws that (at least in part) change as a function of the state of the system. Of the three featured research projects, cellular automata (CA) are used as a model to study certain aspects of living systems in two of them. These aspects include self-reference, open-ended evolution, local physical universality, subjectivity, and information processing. Open-ended evolution and local physical universality are attributed to the vast amount of innovation observed throughout biological evolution. Biological systems may distinguish themselves in terms of information processing and storage, not outside the theory of computation. The final research project concretely explores real-world phenomenon by means of mapping dominance hierarchies in the evolution of video game strategies. Though the main question of how life differs from non-life remains unanswered, the mechanisms behind open-ended evolution and physical universality are revealed.
ContributorsAdams, Alyssa M (Author) / Walker, Sara I (Thesis advisor) / Davies, Paul CW (Committee member) / Pavlic, Theodore P (Committee member) / Chamberlin, Ralph V (Committee member) / Arizona State University (Publisher)
Created2017
Description
Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is αMβ2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.
ContributorsChristenson, Wayne B (Author) / Ros, Robert (Thesis advisor) / Beckstein, Oliver (Committee member) / Lindsay, Stuart (Committee member) / Ugarova, Tatiana (Committee member) / Arizona State University (Publisher)
Created2016
Description
Variation in living systems and how it cascades across organizational levels is central to biology. To understand the constraints and amplifications of variation in collective systems, I mathematically study how group-level differences emerge from individual variation in eusocial-insect colonies, which are inherently diverse and easily observable individually and collectively. Considering collective processes in three species where increasing degrees of heterogeneity are relevant, I address how individual variation scales to colony-level variation and to what degree it is adaptive. In Chapter 2, I introduce a Markov-chain decision model for stochastic individual quorum-based recruitment decisions of rock-ant workers during house hunting, and how they determine collective speed--accuracy balance. Differences in the average threshold-dependent response characteristics of workers between colonies cause collective differences in decision-making. Moreover, noisy behavior may prevent drastic collective cascading into poor nests. In Chapter 3, I develop an ordinary differential equation (ODE) model to study how cognitive diversity among honey-bee foragers influences collective attention allocation between novel and familiar resources. Results provide a mechanistic basis for changes in foraging activity and preference with group composition. Moreover, sensitivity analysis reveals that the main individual driver for foraging allocation shifts from recruitment (communication) to persistence (independent effort) as colony composition changes. This might favor specific degrees of heterogeneity that best amplify communication in wild colonies. Lastly, in Chapter 4, I consider diversity in size, age, and task for nest defense in stingless bees. To better understand how these dimensions of diversity interact to balance defensive demands with other colony needs, I study their effect on colony size and task allocation through a demographic Filippov ODE model. Along each dimension, variation is beneficial in a certain range, outside of which colony adaptation and survival are compromised. This work elucidates how variation in collective properties emerges from nonlinear interactions between varying components in eusocial insects, but it can be generalized to other biological systems with similar fundamental characteristics but less empirical tractability. Moreover, it has the potential of inspiring algorithms that capitalize on heterogeneity in engineered systems where simple components with limited information and no central control must solve complex tasks.
ContributorsNavas Zuloaga, Maria Gabriela (Author) / Kang, Yun (Thesis advisor) / Smith, Brian H (Thesis advisor) / Pavlic, Theodore P (Committee member) / Arizona State University (Publisher)
Created2022
Description
Emerging pathogens present several challenges to medical diagnostics. Primarily, the exponential spread of a novel pathogen through naïve populations require a rapid and overwhelming diagnostic response at the site of outbreak. While point-of-care (PoC) platforms have been developed for detection of antigens, serologic responses, and pathogenic genomes, only nucleic acid diagnostics currently have the potential to be developed and manufactured within weeks of an outbreak owing to the speed of next-generation sequencing and custom DNA synthesis. Among nucleic acid diagnostics, isothermal amplification strategies are uniquely suited for PoC implementation due to their simple instrumentation and lack of thermocycling requirement. Unfortunately, isothermal strategies are currently prone to spurious nonspecific amplification, hindering their specificity and necessitating extensive empirical design pipelines that are both time and resource intensive. In this work, isothermal amplification strategies are extensively compared for their feasibility of implementation in outbreak response scenarios. One such technology, Loop-mediated Amplification (LAMP), is identified as having high-potential for rapid development and PoC deployment. Various approaches to abrogating nonspecific amplification are described including a novel in silico design tool based on coarse-grained simulation of interactions between thermophilic DNA polymerase and DNA strands in isothermal reaction conditions. Nonspecific amplification is shown to be due to stabilization of primer secondary structures by high concentrations of Bst DNA polymerase and a mechanism of micro-complement-mediated cross-priming is demonstrated as causal via nanopore sequencing of nonspecific reaction products. The resulting computational model predicts primer set background in 64% of 67 test assays and its usefulness is illustrated further by determining problematic primers in a West Nile Virus-specific LAMP primer set and optimizing primer 3’ nucleotides to eliminate micro-complements within the reaction, resulting in inhibition of background accumulation. Finally, the emergence of Orthopox monkeypox (MPXV) as a recurring threat is discussed and SimCycle is utilized to develop a novel technique for clade-specific discrimination of MPXV based on bridging viral genomic rearrangements (Bridging LAMP). Bridging LAMP is implemented in a 4-plex microfluidic format and demonstrates 100% sensitivity in detection of 100 copies of viral lysates and 45 crude MPXV-positive patient samples collected during the 2022 Clade IIb outbreak.
ContributorsKnappenberger, Mark Daniel (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Committee member) / Roberson, Robert (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2023
Description
The flexibility and robustness of social insect colonies, when they cope with challenges as integrated units, raise many questions, such as how hundreds and thousands of individual local responses are coordinated without a central controlling process. Answering such questions requires: 1. Quantifiable collective responses of colonies under specific scenarios; 2. Decomposability of the collective colony-level response into individual responses; and 3. Mechanisms to integrate the colony- and individual-level responses. In the first part of my dissertation, I explore coordinated collective responses of colonies in during the alarm response to an alarmed nestmate (chapter 2&3). I develop a machine-learning approach to quantitatively estimate the collective and individual alarm response (chapter 2). Using this methodology, I demonstrate that colony alarm responses to the introduction of alarmed nestmates can be decomposed into immediately cascading, followed by variable dampening processes. Each of those processes are found to be modulated by variation in individual alarm responsiveness, as measured by alarm response threshold and persistence of alarm behavior. This variation is modulated in turn by environmental context, in particular with task-related social context (chapter 3). In the second part of my dissertation, I examine the mechanisms responsible for colonial changes in metabolic rate during ontogeny. Prior studies have found that larger ant colonies (as for larger organisms) have lower mass-specific metabolic rates, but the mechanisms remain unclear. In a 3.5-year study on 25 colonies, metabolic rates of colonies and colony components were measured during ontogeny (chapter 4). The scaling of metabolic rate during ontogeny was fit better by segmented regression or quadratic regression models than simple linear regression models, showing that colonies do not follow a universal power-law of metabolism during the ontogenetic development. Furthermore, I showed that the scaling of colonial metabolic rates can be primarily explained by changes in the ratio of brood to adult workers, which nonlinearly affects colonial metabolic rates. At high ratios of brood to workers, colony metabolic rates are low because the metabolic rate of larvae and pupae are much lower than adult workers. However, the high colony metabolic rates were observed in colonies with moderate brood: adult ratios, because higher ratios cause adult workers to be more active and have higher metabolic rates, presumably due to the extra work required to feed more brood.
ContributorsGuo, Xiaohui (Author) / Fewell, Jennifer H (Thesis advisor) / Kang, Yun (Thesis advisor) / Harrison, Jon F (Committee member) / Liebig, Juergen (Committee member) / Pratt, Stephen C (Committee member) / Pavlic, Theodore P (Committee member) / Arizona State University (Publisher)
Created2021