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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Description
Infectious diseases have emerged as a significant threat to wildlife. Environmental change is often implicated as an underlying factor driving this emergence. With this recent rise in disease emergence and the acceleration of environmental change, it is important to identify the environmental factors that alter host-pathogen dynamics and their underlying mechanisms. The emerging pathogen Batrachochytrium dendrobatidis (Bd) is a clear example of the negative effects infectious diseases can have on wildlife. Bd is linked to global declines in amphibian diversity and abundance. However, there is considerable variation in population-level responses to Bd, with some hosts experiencing marked declines while others persist. Environmental factors may play a role in this variation. This research used populations of pond-breeding chorus frogs (Pseudacris maculata) in Arizona to test if three rapidly changing environmental factors nitrogen (N), phosphorus (P), and temperature influence the presence, prevalence, and severity of Bd infections. I evaluated the reliability of a new technique for detecting Bd in water samples and combined this technique with animal sampling to monitor Bd in wild chorus frogs. Monitoring from 20 frog populations found high Bd presence and prevalence during breeding. A laboratory experiment found 85% adult mortality as a result of Bd infection; however, estimated chorus frog densities in wild populations increased significantly over two years of sampling despite high Bd prevalence. Presence, prevalence, and severity of Bd infections were not correlated with aqueous concentrations of N or P. There was, however, support for an annual temperature-induced reduction in Bd prevalence in newly metamorphosed larvae. A simple mathematical model suggests that this annual temperature-induced reduction of Bd infections in larvae in combination with rapid host maturation may help chorus frog populations persist despite high adult mortality. These results demonstrate that Bd can persist across a wide range of environmental conditions, providing little support for the influence of N and P on Bd dynamics, and show that water temperature may play an important role in altering Bd dynamics, enabling chorus frogs to persist with this pathogen. These findings demonstrate the importance of environmental context and host life history for the outcome of host-pathogen interactions.
ContributorsHyman, Oliver J. (Author) / Collins, James P. (Thesis advisor) / Davidson, Elizabeth W. (Committee member) / Anderies, John M. (Committee member) / Elser, James J. (Committee member) / Escalante, Ananias (Committee member) / Arizona State University (Publisher)
Created2012
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
The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life.
ContributorsMathis, Cole (Nicholas) (Author) / Walker, Sara I (Thesis advisor) / Davies, Paul CW (Committee member) / Chamberlin, Ralph V (Committee member) / Lachmann, Michael (Committee member) / Arizona State University (Publisher)
Created2018
Description
The complex life cycle and widespread range of infection of Plasmodium parasites, the causal agent of malaria in humans, makes them the perfect organism for the study of various evolutionary mechanisms. In particular, multigene families are considered one of the main sources for genome adaptability and innovation. Within Plasmodium, numerous species- and clade-specific multigene families have major functions in the development and maintenance of infection. Nonetheless, while the evolutionary mechanisms predominant on many species- and clade-specific multigene families have been previously studied, there are far less studies dedicated to analyzing genus common multigene families (GCMFs). I studied the patterns of natural selection and recombination in 90 GCMFs with diverse numbers of gene gain/loss events. I found that the majority of GCMFs are formed by duplications events that predate speciation of mammal Plasmodium species, with many paralogs being neutrally maintained thereafter. In general, multigene families involved in immune evasion and host cell invasion commonly showed signs of positive selection and species-specific gain/loss events; particularly, on Plasmodium species is the simian and rodent clades. A particular multigene family: the merozoite surface protein-7 (msp7) family, is found in all Plasmodium species and has functions related to the erythrocyte invasion. Within Plasmodium vivax, differences in the number of paralogs in this multigene family has been previously explained, at least in part, as potential adaptations to the human host. To investigate this I studied msp7 orthologs in closely related non-human primate parasites where homology was evident. I also estimated paralogs’ evolutionary history and genetic polymorphism. The emerging patterns where compared with those of Plasmodium falciparum. I found that the evolution of the msp7 multigene family is consistent with a Birth-and-Death model where duplications, pseudogenization and gene lost events are common. In order to study additional aspects in the evolution of Plasmodium, I evaluated the trends of long term and short term evolution and the putative effects of vertebrate- host’s immune pressure of gametocytes across various Plasmodium species. Gametocytes, represent the only sexual stage within the Plasmodium life cycle, and are also the transition stages from the vertebrate to the mosquito vector. I found that, while male and female gametocytes showed different levels of immunogenicity, signs of positive selection were not entirely related to the location and presence of immune epitope regions. Overall, these studies further highlight the complex evolutionary patterns observed in Plasmodium.
ContributorsCastillo Siri, Andreina I (Author) / Rosenberg, Michael (Thesis advisor) / Escalante, Ananias (Committee member) / Taylor, Jesse (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2016