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 - 8 of 8
Filtering by
- All Subjects: Biology
- Creators: Buetow, Kenneth
- Creators: Bateman, Heather
Description
Human recreation on rangelands may negatively impact wildlife populations. Among those activities, off-road vehicle (ORV) recreation carries the potential for broad ecological consequences. A study was undertaken to assess the impacts of ORV on rodents in Arizona Uplands Sonoran Desert. Between the months of February and September 2010, rodents were trapped at 6 ORV and 6 non-ORV sites in Tonto National Forest, AZ. I hypothesized that rodent abundance and species richness are negatively affected by ORV use. Rodent abundances were estimated using capture-mark-recapture methodology. Species richness was not correlated with ORV use. Although abundance of Peromyscus eremicus and Neotoma albigula declined as ORV use increased, abundance of Dipodomys merriami increased. Abundance of Chaetodipus baileyi was not correlated with ORV use. Other factors measured were percent ground cover, percent shrub cover, and species-specific shrub cover percentages. Total shrub cover, Opuntia spp., and Parkinsonia microphylla each decreased as ORV use increased. Results suggest that ORV use negatively affects rodent habitats in Arizona Uplands Sonoran Desert, leading to declining abundance in some species. Management strategies should mitigate ORV related habitat destruction to protect vulnerable populations.
ContributorsReid, John Simon (Author) / Brady, Ward (Thesis advisor) / Miller, William (Committee member) / Bateman, Heather (Committee member) / Arizona State University (Publisher)
Created2012
Description
Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in knowledge. This investigation highlights how contextual factors from the language and social context of the microbiome are related to changes in the usage, meaning, and scientific knowledge on the microbiome. Two interconnected studies integrating qualitative and quantitative evidence examine the variation and change of the microbiome evidence are presented. First, the concepts microbiome, metagenome, and metabolome are compared to determine the boundaries of the microbiome concept in relation to other concepts where the conceptual boundaries have been cited as overlapping. A collection of publications for each concept or corpus is presented, with a focus on how to create, collect, curate, and analyze large data collections. This study concludes with suggestions on how to analyze biomedical concepts using a hybrid approach that combines results from the larger language context and individual words. Second, the results of a systematic review that describes the variation and change of microbiome research, funding, and knowledge are examined. A corpus of approximately 28,000 articles on the microbiome are characterized, and a spectrum of microbiome interpretations are suggested based on differences related to context. The collective results suggest the microbiome is a separate concept from the metagenome and metabolome, and the variation and change to the microbiome concept was influenced by contextual factors. These results provide insight into how concepts with extensive resources behave within biomedicine and suggest the microbiome is possibly representative of conceptual change or a preview of new dynamics within science that are expected in the future.
ContributorsAiello, Kenneth (Author) / Laubichler, Manfred D (Thesis advisor) / Simeone, Michael (Committee member) / Buetow, Kenneth (Committee member) / Walker, Sara I (Committee member) / Arizona State University (Publisher)
Created2018
Description
In most diploid cells, autosomal genes are equally expressed from the paternal and maternal alleles resulting in biallelic expression. However, as an exception, there exists a small number of genes that show a pattern of monoallelic or biased-allele expression based on the allele’s parent-of-origin. This phenomenon is termed genomic imprinting and is an evolutionary paradox. The best explanation for imprinting is David Haig's kinship theory, which hypothesizes that monoallelic gene expression is largely the result of evolutionary conflict between males and females over maternal involvement in their offspring. One previous RNAseq study has investigated the presence of parent-of-origin effects, or imprinting, in the parasitic jewel wasp Nasonia vitripennis (N. vitripennis) and its sister species Nasonia giraulti (N. giraulti) to test the predictions of kinship theory in a non-eusocial species for comparison to a eusocial one. In order to continue to tease apart the connection between social and eusocial Hymenoptera, this study proposed a similar RNAseq study that attempted to reproduce these results in unique samples of reciprocal F1 Nasonia hybrids. Building a pseudo N. giraulti reference genome, differences were observed when aligning RNAseq reads to a N. vitripennis reference genome compared to aligning reads to a pseudo N. giraulti reference. As well, no evidence for parent-of-origin or imprinting patterns in adult Nasonia were found. These results demonstrated a species-of-origin effect. Importantly, the study continued to build a repository of support with the aim to elucidate the mechanisms behind imprinting in an excellent epigenetic model species, as it can also help with understanding the phenomenon of imprinting in complex human diseases.
ContributorsUnderwood, Avery Elizabeth (Author) / Wilson, Melissa (Thesis advisor) / Buetow, Kenneth (Committee member) / Gile, Gillian (Committee member) / Arizona State University (Publisher)
Created2019
Description
Human-inhabited or -disturbed areas pose many unique challenges for wildlife, including increased human exposure, novel challenges, such as finding food or nesting sites in novel structures, anthropogenic noises, and novel predators. Animals inhabiting these environments must adapt to such changes by learning to exploit new resources and avoid danger. To my knowledge no study has comprehensively assessed behavioral reactions of urban and rural populations to numerous novel environmental stimuli. I tested behavioral responses of urban, suburban, and rural house finches (Haemorhous mexicanus) to novel stimuli (e.g. objects, noises, food), to presentation of a native predator model (Accipiter striatus) and a human, and to two problem-solving challenges (escaping confinement and food-finding). Although I found few population-level differences in behavioral responses to novel objects, environment, and food, I found compelling differences in how finches from different sites responded to novel noise. When played a novel sound (whale call or ship horn), urban and suburban house finches approached their food source more quickly and spent more time on it than rural birds, and urban and suburban birds were more active during the whale-noise presentation. In addition, while there were no differences in response to the native predator, rural birds showed higher levels of stress behaviors when presented with a human. When I replicated this study in juveniles, I found that exposure to humans during development more accurately predicted behavioral differences than capture site. Finally, I found that urban birds were better at solving an escape problem, whereas rural birds were better at solving a food-finding challenge. These results indicate that not all anthropogenic changes affect animal populations equally and that determining the aversive natural-history conditions and challenges of taxa may help urban ecologists better understand the direction and degree to which animals respond to human-induced rapid environmental alterations.
ContributorsWeaver, Melinda (Author) / McGraw, Kevin J. (Thesis advisor) / Rutowski, Ronald (Committee member) / Pratt, Stephen (Committee member) / Bateman, Heather (Committee member) / Deviche, Pierre (Committee member) / Arizona State University (Publisher)
Created2018
Description
When most people think of Phoenix, Arizona, they think of sprawling cityscapesand hot desert mountains full of saguaros and other cacti. They rarely think of water and
fish, and yet, the Arizona landscape is home to many lakes, ponds, rivers and streams,
full of both native fish and sportfish, including in the urban areas. According to the report
by DeSemple in 2006, between the years 2001 and 2006, the Rio Salado Environmental
Restoration Project worked to revitalize the dry river bed that runs through Phoenix, that
included the construction of two urban ponds, the Demonstration Pond and the Reservoir
Pond. At the start of this study, it was unknown what vertebrate species inhabited these
ponds, but it was known that these urban ponds have been used to dump unwanted
aquatic pets. The bluegill Lepomis macrochirus was found to reside in both ponds, and as
it is such an important sportfish species, it was chosen as the focal species for these
studies, which took place over periods in March, May, July, and September of 2021.
Single-season occupancy models were used to attempt to determine how L. macrochirus,
use the microhabitats within the system, and a multi-season model was used to estimate
their recruitment, and seasonal changes in occupancy. In addition, this study also
attempts to understand the size structures of the L. macrochirus population in the
Reservoir Pond and the population in the Demonstration Pond, and if that size structure
varies from March to September. As the populations of these ponds are physically
isolated from one another, statistical tests were also done to determine if the size
structures of the two populations of L. macrochirus differ from one another and found
that the two populations do indeed differ from one another, but only during two of the
sampling periods.
ContributorsKeister, Emily Jan (Author) / Saul, Steven (Thesis advisor) / Bateman, Heather (Committee member) / Suzart de Albuquerque, Fabio (Committee member) / Arizona State University (Publisher)
Created2022
Description
While only the sixth most common cancer globally, liver cancer is the third most deadly. Despite the importance of accurate diagnosis and effective treatment, standard diagnostic tests for most solid organ neoplasms are not required for the most common type of liver cancer, Hepatocellular Carcinoma (HCC). In addition, major discrepancies in the practices currently in place limits the ability to develop more precise oncological treatment and prognosis. This study aimed to identify biomarkers, with potential to more accurately diagnose how far cancer has advanced within a patient and determine prognosis. It is the hope that pathways provided by this study form the basis for future research into more standardized practices and potential treatment based on specific affected biological processes. The PathOlogist tool was utilized to calculate activity metrics for 1,324 biological pathways in 374 The Cancer Genome Atlas (TCGA) hepatocellular carcinoma donors. Further statistical analysis was done on two datasets, formed to identify grade or stage at time of diagnosis for the activity levels calculated by PathOlogist. The datasets were evaluated individually. Based on the variance and normality of each pathway’s activity levels in the respective data sets analysis of variance, Tukey-Kramer, Kruskal-Wallis, and Mann-Whitney-Wilcox tests were performed, when appropriate, to determine any statistically significant differences in pathway activity levels. Pathways were identified in both stage and grade data analyses that show significant differences in activity levels across designation. While some overlap is seen, there was a significant number of pathways unique to either stage or grade. These pathways are known to affect the cell cycle, cellular transport, disease, immune system, and metabolism regulation.
The biological pathways named by this research depict prospective biomarkers for progression of hepatocellular carcinoma per subdivision within both stage and grade. These findings may be instrumental to new methods of early and more accurate diagnosis. The distinct differences in identified pathways in grade and stage illustrate the need for these new methods to not only look at stage but also grade when determining prognosis. Furthermore, the pathways identified herein have potential to aid in the development of targeted treatment based on the affected biological processes.
ContributorsGarrison, Alyssa Cameron (Author) / Buetow, Kenneth (Thesis advisor) / Hinde, Katie (Committee member) / Wilson, Melissa (Committee member) / Arizona State University (Publisher)
Created2022
Description
Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide and exhibits a male-bias in occurrence and mortality. Previous studies have provided insight into the role of inherited genetic regulation of transcription in modulating sex-differences in HCC etiology and mortality. This study uses pathway analysis to add insight into the biological processes that drive sex-differences in HCC etiology as well as a provide additional framework for future studies on sex-biased cancers. Gene expression data from normal, tumor adjacent, and HCC liver tissue were used to calculate pathway scores using a tool called PathOlogist that not only takes into consideration the molecules in a biological pathway, but also the interaction type and directionality of the signaling pathways. Analysis of the pathway scores uncovered etiologically relevant pathways differentiating male and female HCC. In normal and tumor adjacent liver tissue, males showed higher activity of pathways related to translation factors and signaling. Females did not show higher activity of any pathways compared to males in normal and tumor adjacent liver tissue. Work suggest biologic processes that underlie sex-biases in HCC occurrence and mortality. Both males and females differed in the activation of pathways related apoptosis, cell cycle, signaling, and metabolism in HCC. These results identify clinically relevant pathways for future research and therapeutic targeting.
ContributorsRehling, Thomas E (Author) / Buetow, Kenneth (Thesis advisor) / Wilson, Melissa (Committee member) / Maley, Carlo (Committee member) / Arizona State University (Publisher)
Created2021
Description
Evolutionary theory provides a rich framework for understanding cancer dynamics across scales of biological organization. The field of cancer evolution has largely been divided into two domains, comparative oncology - the study of cancer across the tree of life, and tumor evolution. This work provides a theoretical framework to unify these subfields with the intent that an understanding of the evolutionary dynamics driving cancer risk at one scale can inform the understanding of the dynamics on another scale. The evolution of multicellular life and the unique vulnerabilities in the cellular mechanisms that underpin it explain the ubiquity of cancer prevalence across the tree of life. The breakdown in cellular cooperation and communication that were required for multicellular life define the hallmarks of cancer. As divergent life histories drove speciation events, it similarly drove divergences in fundamental cancer risk across species. An understanding of the impact that species’ life history theory has on the underlying network of multicellular cooperation and somatic evolution allows for robust predictions on cross-species cancer risk. A large-scale veterinary cancer database is utilized to validate many of the predictions on cancer risk made from life history evolution. Changing scales to the cellular level, it lays predictions on the fate of somatic mutations and the fitness benefits they confer to neoplastic cells compared to their healthy counterparts. The cancer hallmarks, far more than just a way to unify the many seemingly unique pathologies defined as cancer, is a powerful toolset to understand how specific mutations may change the fitness of somatic cells throughout carcinogenesis and tumor progression. Alongside highlighting the significant advances in evolutionary approaches to cancer across scales, this work provides a lucid confirmation that an understanding of both scales provides the most complete portrait of evolutionary cancer dynamics.
ContributorsCompton, Zachary Taylor (Author) / Maley, Carlo C. (Thesis advisor) / Aktipis, Athena (Committee member) / Buetow, Kenneth (Committee member) / Nedelcu, Aurora (Committee member) / Compton, Carolyn (Committee member) / Arizona State University (Publisher)
Created2023