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
- Creators: Bateman, Heather L
- Creators: Maley, Carlo C
Description
Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of five AWS and five paired control sites (treatments) in the surrounding Sonoran desert from October 2011 to May 2012. I measured plant species richness, density, and percent cover in the spring of 2012. A Multi-response Permutation Procedure was used to identify differences in small mammal community abundance, biomass, and species richness by season and treatment. I used Principle Component Analysis to reduce 11 habitat characteristics to five habitat factors. I related rodent occurrence to habitat characteristics using multiple and logistic regression. A total of 370 individual mammals representing three genera and eight species of rodents were captured across 4800 trap nights. Desert pocket mouse (Chaetodipus penicillatus) was the most common species in both seasons and treatments. Whereas rodent community abundance, biomass, and richness were similar between seasons, community variables of AWS were greater than CS. Rodent diversity was similar between treatments. Desert pocket mouse abundance and biomass were twice as high at AWS when compared to controls. Biomass of white-throated woodrat (Neotoma albigula) was five times greater at AWS. Habitat characteristics were similar between treatments. Neither presence of water nor distance to water explained substantial habitat variation. Occurrence of rodent species was associated with habitat characteristics. Desert rodent communities are adapted for arid environments (i.e. Heteromyids) and are not dependent on "free water". Higher abundances of desert pocket mouse at AWS were most likely related to increased disturbance and debris and not the presence of water. The results of this study and previous studies suggest that more investigation is needed and that short term studies may not be able to detect interactions (if any) between AWS and desert small mammal communities.
ContributorsSwitalski, Aaron (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires an understanding of the life history and ecology of each population. I looked at one physiological and one behavioral aspect of a population of tortoises at the Sugarloaf Mountain (SL) study site in central Arizona, USA. I used 21 years of capture-recapture records to estimate growth parameters of the entire population. I investigated habitat selection of juvenile tortoises by selecting 117 locations of 11 tortoises that had been tracked by radio-telemetry one to three times weekly for two years, selecting locations from both summer active season and during winter hibernation. I compared 22 microhabitat variables of tortoise locations to random SL locations to determine habitat use and availability. Male tortoises at SL reach a greater asymptotic length than females, and males and females appear to grow at the same rate. Juvenile tortoises at the SL site use steep rocky hillsides with high proportions of sand and annual vegetation, few succulents, and enclosed shelters in summer. They use enclosed shelters on steep slopes for winter hibernation. An understanding of these features can allow managers to quantify Sonoran desert tortoise habitat needs and life history characteristics and to understand the impact of land use policies.
ContributorsBridges, Andrew (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Ulrich, Jon (Committee member) / Arizona State University (Publisher)
Created2012
Description
The immune system plays a dual role during neoplastic progression. It can suppress tumor growth by eliminating cancer cells, and also promote neoplastic expansion by either selecting for tumor cells that are fitter to survive in an immunocompetent host or by establishing the right conditions within the tumor microenvironment. First, I present a model to study the dynamics of subclonal evolution of cancer. I model selection through time as an epistatic process. That is, the fitness change in a given cell is not simply additive, but depends on previous mutations. Simulation studies indicate that tumors are composed of myriads of small subclones at the time of diagnosis. Because some of these rare subclones harbor pre-existing treatment-resistant mutations, they present a major challenge to precision medicine. Second, I study the question of self and non-self discrimination by the immune system, which is fundamental in the field in cancer immunology. By performing a quantitative analysis of the biochemical properties of thousands of MHC class I peptides, I find that hydrophobicity of T cell receptors contact residues is a hallmark of immunogenic epitopes. Based on these findings, I further develop a computational model to predict immunogenic epitopes which facilitate the development of T cell vaccines against pathogen and tumor antigens. Lastly, I study the effect of early detection in the context of Ebola. I develope a simple mathematical model calibrated to the transmission dynamics of Ebola virus in West Africa. My findings suggest that a strategy that focuses on early diagnosis of high-risk individuals, caregivers, and health-care workers at the pre-symptomatic stage, when combined with public health measures to improve the speed and efficacy of isolation of infectious individuals, can lead to rapid reductions in Ebola transmission.
ContributorsChowell-Puente, Diego (Author) / Castillo-Chavez, Carlos (Thesis advisor) / Anderson, Karen S (Thesis advisor) / Maley, Carlo C (Committee member) / Wilson Sayres, Melissa A (Committee member) / Blattman, Joseph N (Committee member) / Arizona State University (Publisher)
Created2016
Description
The built environment increases radiant heat exchange in urban areas by several degrees hotter compared to non-urban areas. Research has investigated how urbanization and heat affect human health; but there is scant literature on the effects of urban heat on wildlife. Animal body condition can be used to assess overall health. This parameter estimates the storage of energy-rich fat, which is important for growth, survival, and reproduction. The purpose of my research was to examine the Urban Heat Island effect on wild rodents across urban field sites spanning three strata of land surface temperature. Site level surface temperatures were measured using temperature data loggers and I captured 116 adult pocket mice (Chaetodipus spp. and Perognathus spp.) and Merriam’s kangaroo rats (Dipodomys merriami) to measure their body condition using accurate and noninvasive quantitative magnetic resonance. I used baited Sherman live traps from mid-May to early September during 2019 and 2020 in mountainous urban parks and open spaces over two summers. Rodents were captured at seven sites near the Phoenix metropolitan area; an ideal area for examining the effect of extreme heat experienced by urban wildlife. Results supported the prediction that rodent body condition was greatest in the cooler temperature stratas compared to the hottest temperature strata. I related rodent body condition to environmental predictors to dispute to environmental predictors to dispute alternative hypotheses; such as vegetation cover and degree of urbanization. Results based on measures of body fat and environmental predictors show pocket mice have more fat where vegetation is higher, nighttime temperatures are lower, surface temperatures are lower, and urbanization is greater. Kangaroo rats have more fat where surface temperature is lower. My results contribute to understanding the negative effects of extreme heat on body condition and generalized health experienced by urban wildlife because of the built environment. This research shows a need to investigate further impacts of urban heat on wildlife. Management suggestions for urban parks and open spaces include increasing vegetation cover, reducing impervious surface, and building with materials that reduce radiant heat.
ContributorsAllen, Brittany D'Ann (Author) / Bateman, Heather L (Thesis advisor) / Moore, Marianne S (Committee member) / Hondula, David M (Committee member) / Arizona State University (Publisher)
Created2021
Description
The Arizona toad (Anaxyrus microscaphus) is unique among bufonids because they primarily breed in streams of Arizona, New Mexico, Utah, and Nevada. Arizona toad is a species of conservation concern throughout their range. The non-native northern crayfish (Orconectes virilis) are opportunistic omnivores implicated in the declines of other native aquatic species. I wanted to determine occupancy, habitat use, and species interactions of the Arizona toad throughout its range Visual encounter surveys (VES) were completed by ASU and natural resource agency partners in the summers of 2021 and 2022 (n = 232) throughout Arizona toad range in Arizona. I used VES data and crayfish occurrence records, to determine interactions between the two species. I used broadscale environmental variables (1 km resolution) from WorldClim and EarthEnv to evaluate a relationship with Arizona toad occupancy across transects. These broadscale variables included bioclimatic variables, measures of habitat heterogeneity, measures of solar radiation, and topographic variables. In 2022 I collected fine-scale habitat data evaluating available vegetation cover and substrate composition within paired habitat plots. Fine-scale variables included canopy cover, substrate type, vegetation cover, and water depth. I applied multiple occupancy modeling approaches. Single-species model results found low toad occupancy, but high detection, as this is a rare species. Multi-species results showed no positive or negative relationship between Arizona toad and northern crayfish for both seasons. Two principal component analyses (PCA) were run on broadscale environmental variables and fine-scale habitat variables for 2021 and 2022, respectively, creating new synthetic variables for use in analysis. In 2021, the broadscale components were added to the single-species occupancy models and the top model included bioclimatic variables related to annual temperature range and precipitation. Arizona toad occupancy is lower with extreme hot temperatures and less precipitation. A logistic regression was run with the fine-scale habitat variables and the top model included PC1 and PC3. PC1 described elements related to riparian complexity, while PC3 described elements related to algae presence, including attached to cobble substrate. Arizona Toad select for certain habitats including canopy cover, shallow water, algae cover, and pebble cover. It is important to maintain riparian area habitat complexity and conserve habitat for the Arizona toad, a riparian stream specialist.
ContributorsMontgomery, Brett Joseph (Author) / Bateman, Heather L (Thesis advisor) / Albuquerque, Fabio S (Committee member) / Bogan, Michael T (Committee member) / Arizona State University (Publisher)
Created2023
Description
Resistance to existing anti-cancer drugs poses a key challenge in the field of medical oncology, in that it results in the tumor not responding to treatment using the same medications to which it responded previously, leading to treatment failure. Adaptive therapy utilizes evolutionary principles of competitive suppression, leveraging competition between drug resistant and drug sensitive cells, to keep the population of drug resistant cells under control, thereby extending time to progression (TTP), relative to standard treatment using maximum tolerated dose (MTD). Development of adaptive therapy protocols is challenging, as it involves many parameters, and the number of parameters increase exponentially for each additional drug. Furthermore, the drugs could have a cytotoxic (killing cells directly), or a cytostatic (inhibiting cell division) mechanism of action, which could affect treatment outcome in important ways. I have implemented hybrid agent-based computational models to investigate adaptive therapy, using either a single drug (cytotoxic or cytostatic), or two drugs (cytotoxic or cytostatic), simulating three different adaptive therapy protocols for treatment using a single drug (dose modulation, intermittent, dose-skipping), and seven different treatment protocols for treatment using two drugs: three dose modulation (DM) protocols (DM Cocktail Tandem, DM Ping-Pong Alternate Every Cycle, DM Ping-Pong on Progression), and four fixed-dose (FD) protocols (FD Cocktail Intermittent, FD Ping-Pong Intermittent, FD Cocktail Dose-Skipping, FD Ping-Pong Dose-Skipping). The results indicate a Goldilocks level of drug exposure to be optimum, with both too little and too much drug having adverse effects. Adaptive therapy works best under conditions of strong cellular competition, such as high fitness costs, high replacement rates, or high turnover. Clonal competition is an important determinant of treatment outcome, and as such treatment using two drugs leads to more favorable outcome than treatment using a single drug. Switching drugs every treatment cycle (ping-pong) protocols work particularly well, as well as cocktail dose modulation, particularly when it is feasible to have a highly sensitive measurement of tumor burden. In general, overtreating seems to have adverse survival outcome, and triggering a treatment vacation, or stopping treatment sooner when the tumor is shrinking seems to work well.
ContributorsSaha, Kaushik (Author) / Maley, Carlo C (Thesis advisor) / Forrest, Stephanie (Committee member) / Anderson, Karen S (Committee member) / Cisneros, Luis H (Committee member) / Arizona State University (Publisher)
Created2023
Description
Human land use and land cover change alter key features of the landscape that may favor habitat selection by some species. Lizards are especially sensitive to these alterations because they rely on their external environment for regulating their body temperature. However, because of their diverse life-history traits and strategies, some are able to respond well to disturbance by using their habitat in various ways. To understand how they use their habitat and how human modifications may impact their ability to do this, biologists must identify where they occur and the habitat characteristics on which they depend. Therefore, I used species occupancy modeling to determine (1) whether disturbance predicts the presence of two sympatric congeneric (species of the same genus) lizard species Sceloporus grammicus and S. torquatus, and (2) which habitat characteristics are essential for predicting their occupancy and detection. I focused my study in central Mexico, a region of prevalent land use and land cover change. Here, I conducted visual encounter and habitat surveys at 100 1-hectare sites during the spring of 2019. I measured vegetation and ground cover, average tree diameter, and abundance of refuges. I recorded air temperature, relative humidity, and elevation. I summarized sites as either undisturbed or disturbed, based on the presence of human development. I also summarized sites by ecosystem type, desert or forest, based on vegetation composition (i.e., desert-adapted vs. non-desert-adapted plants), evidence of remnant forest, air temperature, and relative humidity. I found that S. torquatus was more likely to be present in disturbed habitat, whereas S. grammicus was more likely to be present in areas with leaf litter, tree cover, and woody debris. S. torquatus was twice as likely to be detected in forests than deserts, and S. grammicus was more likely to be detected at sites with high elevation and high relative humidity, low temperature, and herbaceous and grass cover. These results emphasize the utility of species occupancy modeling for estimating detection and occupancy in dynamic landscapes.
ContributorsFlores, Jennifer (Author) / Martins, Emília P. (Thesis advisor) / Bateman, Heather L (Thesis advisor) / Zuniga-Vega, J. Jaime (Committee member) / Arizona State University (Publisher)
Created2020
Modeling Spatial Competition and Adaptive Therapy Protocols in Three-Dimensional Vascularized Tumors
Description
In contrast to traditional chemotherapy for cancer which fails to address tumor heterogeneity, raises patients’ levels of toxicity, and selects for drug-resistant cells, adaptive therapy applies ideas from cancer ecology in employing low-dose drugs to encourage competition between cancerous cells, reducing toxicity and potentially prolonging disease progression. Despite promising results in some clinical trials, optimizing adaptive therapy routines involves navigating a vast space of combina- torial possibilities, including the number of drugs, drug holiday duration, and drug dosages. Computational models can serve as precursors to efficiently explore this space, narrowing the scope of possibilities for in-vivo and in-vitro experiments which are time-consuming, expensive, and specific to tumor types. Among the existing modeling techniques, agent-based models are particularly suited for studying the spatial inter- actions critical to successful adaptive therapy. In this thesis, I introduce CancerSim, a three-dimensional agent-based model fully implemented in C++ that is designed to simulate tumorigenesis, angiogenesis, drug resistance, and resource competition within a tissue. Additionally, the model is equipped to assess the effectiveness of various adaptive therapy regimens. The thesis provides detailed insights into the biological motivation and calibration of different model parameters. Lastly, I propose a series of research questions and experiments for adaptive therapy that CancerSim can address in the pursuit of advancing cancer treatment strategies.
ContributorsShah, Sanjana Saurin (Author) / Daymude, Joshua J (Thesis advisor) / Forrest, Stephanie (Committee member) / Maley, Carlo C (Committee member) / Arizona State University (Publisher)
Created2023
Description
Riparian ecosystems comprise less than 2% of the landscape in the arid western U.S. yet provide habitat and resources to over half of arid-land wildlife species, including a broad diversity of anurans (frogs and toads). I surveyed anurans using passive acoustic monitoring to capture spring advertisement calls in wilderness area tributaries of the Verde River, Arizona, USA. In the spring and summer of 2021 and 2022, 13-29 autonomous recording units (ARUs) were deployed along perennial, intermittent, and ephemeral reaches across eight headwater streams. I characterized stream reaches based on the percent of pool, riffle, run, and side channel habitat within 100 meters of each ARU. I quantified substrate, discharge at 95% exceedance probability, flow width, and canopy cover at each site. To relate anuran occupancy and relative habitat use to environmental and hydrological variables, I evaluated acoustic data using single-species occupancy and Royle-Nichols and N-mixture (relative habitat use) models. Four species were detected in this study: canyon treefrog (Hyla arenicolor), red-spotted toad (Anaxyrus punctatus), Woodhouse’s toad (Anaxyrus woodhousii), and non-native American bullfrog (Lithobates catesbeianus), with canyon treefrog being the most ubiquitous species observed. Occupancy of canyon treefrog was greater at perennial and intermittent sites compared to ephemeral sites, and presence of pool was the most important driver of canyon treefrog occupancy and relative habitat use. Notably, this study did not detect several species with historical records in the middle Verde River watershed, including Arizona toad (Anaxyrus microscaphus) and Northern leopard frog (Lithobates pipiens). Given climate change-related flow declines and intensifying demands for water in the Southwest, maintaining stream flows that provide consistent and suitable hydroregimes for anuran breeding and larval development is of increasing importance. Determining habitat use and flow regimes necessary to support anuran populations can aid in prioritization of conservation actions related to water management and predict how changes in water availability may impact stream-breeding anurans.
ContributorsHuck, Margaret (Author) / Bateman, Heather L (Thesis advisor) / Albuquerque, Fabio S (Thesis advisor) / Lewis, Jesse S (Committee member) / Arizona State University (Publisher)
Created2023