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: Biochemistry
- Creators: Anbar, Ariel D
Description
Biochemical reactions underlie all living processes. Their complex web of interactions is difficult to fully capture and quantify with simple mathematical objects. Applying network science to biology has advanced our understanding of the metabolisms of individual organisms and the organization of ecosystems, but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, I constructed biochemical networks using global databases of annotated genomes and metagenomes, and biochemical reactions. I uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals the observed biological scaling is not a product of chemistry alone, but instead emerges due to the particular structure of selected reactions commonly participating in living processes. I perform distinguishability tests across properties of individual and ecosystem-level biochemical networks to determine whether or not they share common structure, indicative of common generative mechanisms across levels. My results indicate there is no sharp transition in the organization of biochemistry across distinct levels of the biological hierarchy—a result that holds across different network projections.
Finally, I leverage these large biochemical datasets, in conjunction with planetary observations and computational tools, to provide a methodological foundation for the quantitative assessment of biology’s viability amongst other geospheres. Investigating a case study of alkaliphilic prokaryotes in the context of Enceladus, I find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a reference for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent. Taken together these results point to a deeper level of organization in biochemical networks than what has been understood so far, and suggests the existence of common organizing principles operating across different levels of biology and planetary chemistry.
Finally, I leverage these large biochemical datasets, in conjunction with planetary observations and computational tools, to provide a methodological foundation for the quantitative assessment of biology’s viability amongst other geospheres. Investigating a case study of alkaliphilic prokaryotes in the context of Enceladus, I find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a reference for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent. Taken together these results point to a deeper level of organization in biochemical networks than what has been understood so far, and suggests the existence of common organizing principles operating across different levels of biology and planetary chemistry.
ContributorsSmith, Harrison Brodsky (Author) / Walker, Sara I (Thesis advisor) / Anbar, Ariel D (Committee member) / Line, Michael R (Committee member) / Okie, Jordan G. (Committee member) / Romaniello, Stephen J. (Committee member) / Arizona State University (Publisher)
Created2018
Description
All known life requires three main metabolic components to grow: an energy source, an electron source, and a carbon source. For energy, an organism can use light or chemical reactions. For electrons, an organism can use metals or organic molecules. For carbon, an organism can use organic or inorganic carbon. Life has adapted to use any mixture of the endpoints for each of the three metabolic components. Understanding how these components are incorporated in a living bacterium on Earth in modern times is relatively straight forward. This becomes much more complicated when trying to determine what metabolisms may have been used in ancient times on Earth or potential novel metabolisms that exist on other planets. One way to examine these possibilities is by creating genetically modified mutant bacteria that have novel metabolisms or proposed ancient metabolisms to study. This thesis is the beginning of a broader study to understand novel metabolisms using Heliobacteria modesticaldum. H. modesticaldum was grown under different environmental conditions to isolate the impacts of energy, electron, and carbon sources on carbon and nitrogen isotope fractionation. Additionally, the wild type and a novel mutant H. modesticaldum were compared to measure the effects of specific enzymes on carbon and nitrogen isotope fractionation. By forcing the bacterium to adapt to different conditions, variation in carbon and nitrogen content and isotopic signature are detected. Specifically, by forcing the bacterium to fix nitrogen as opposed to nitrogen incorporation, the isotopic signature of the bacterium had a noticeable change. Themutant H. modesticaldum also had a different isotopic signature than the wild type. Without the enzyme citrate synthase, H. modesticaldum had to adapt its carbon metabolic cycle, creating a measurable carbon isotope fractionation. The results described here offer new insight into the effects of metabolism on carbon and nitrogen fractionation of ancient or novel organisms.
ContributorsElms, Nicholas (Author) / Hartnett, Hilairy E (Thesis advisor) / Redding, Kevin (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Anbar, Ariel D (Committee member) / Arizona State University (Publisher)
Created2021