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
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
Once considered an abundant species in the eastern United States, local populations of red-shouldered hawks, Buteo lineatus, have declined due to habitat destruction. This destruction has created suitable habitat for red-tailed hawks, Buteo jamaicensis, and therefore increased competition between these two raptor species. Since suitable habitat is the main limiting factor for raptors, a computer model was created to simulate the effect of habitat loss in central Maryland and the impact of increased competition between the more aggressive red-tailed hawk. These simulations showed urban growth contributed to over a 30% increase in red-tailed hawk habitat as red-shouldered hawk habitat decreased 62.5-70.1% without competition and 71.8-76.3% with competition. However there was no significant difference seen between the rate of available habitat decline for current and predicted development growth.
ContributorsMurillo, Crystal (Author) / Whysong, Gary (Thesis advisor) / Alford, Eddie (Committee member) / Miller, William (Committee member) / Arizona State University (Publisher)
Created2011
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
ABSTRACT The elephant tree, Bursera microphylla, is at the northern limit of its range in central Arizona. This species is sensitive to frost damage thus limiting its occurrence in more northern areas of the southwest. Marginal populations of B. microphylla are found in mountain ranges of Central Arizona and are known to occur in the rugged mountain range system of the South Mountain Municipal Park (SMMP). Little is known of the distribution of this species within the park and details relevant to the health of both individual plants and the population such as diameter and number of trunks, height, and presence of damage have not been examined. This study was designed, in part, to test the hypothesis that favorable microhabitats at SMMP are created by particular combinations of abiotic features including aspect, slope, elevation and solar radiation. Data on abiotic factors, as well as specific individual plant locations and characteristics were obtained for 100 individuals. Temperature data was collected in vertical transects at different altitudinal levels. Some of these data were used in spatial analyses to generate a habitat suitability model using GIS software. Furthermore, collected data was analyzed using Matlab© software to identify potential trends in the variation of morphological traits. In addition, for comparative purposes similar information at one hundred computer-generated randomly chosen points throughout SMMP was obtained. The GIS spatial analyses indicated that aspect, slope, elevation, and relative solar radiance are strongly associated as major climatic components of the microhabitat of B. microphylla. Temperature data demonstrated that there are significant differences in ambient temperature among different altitudinal gradients with middle elevations being more favorable. Furthermore, analyses performed using Matlab© to explore trends of elevation as a factor indicated that multiple trunk plants are more commonly found at higher elevations than single trunk plants, there is a positive correlation of trunk diameter with elevation, and that canopy volume has a negative correlation with respect to elevation. It was concluded that microhabitats where B. microphylla occurs at the northern limit of its range require a particular combination of abiotic features that can be easily altered by climatic changes.
ContributorsCordova, Cesar, M.S (Author) / Steele, Kelly P. (Thesis advisor) / Tridane, Abdessaman (Committee member) / Miller, William (Committee member) / Brady, Ward (Committee member) / Arizona State University (Publisher)
Created2011
Description
Advances in sequencing technology have generated an enormous amount of data over the past decade. Equally advanced computational methods are needed to conduct comparative and functional genomic studies on these datasets, in particular tools that appropriately interpret indels within an evolutionary framework. The evolutionary history of indels is complex and often involves repetitive genomic regions, which makes identification, alignment, and annotation difficult. While previous studies have found that indel lengths in both deoxyribonucleic acid and proteins obey a power law, probabilistic models for indel evolution have rarely been explored due to their computational complexity. In my research, I first explore an application of an expectation-maximization algorithm for maximum-likelihood training of a codon substitution model. I demonstrate the training accuracy of the expectation-maximization on my substitution model. Then I apply this algorithm on a published 90 pairwise species dataset and find a negative correlation between the branch length and non-synonymous selection coefficient. Second, I develop a post-alignment fixation method to profile each indel event into three different phases according to its codon position. Because current codon-aware models can only identify the indels by placing the gaps between codons and lead to the misalignment of the sequences. I find that the mouse-rat species pair is under purifying selection by looking at the proportion difference of the indel phases. I also demonstrate the power of my sliding-window method by comparing the post-aligned and original gap positions. Third, I create an indel-phase moore machine including the indel rates of three phases, length distributions, and codon substitution models. Then I design a gillespie simulation that is capable of generating true sequence alignments. Next I develop an importance sampling method within the expectation-maximization algorithm that can successfully train the indel-phase model and infer accurate parameter estimates from alignments. Finally, I extend the indel phase analysis to the 90 pairwise species dataset across three alignment methods, including Mafft+sw method developed in chapter 3, coati-sampling methods applied in chapter 4, and coati-max method. Also I explore a non-linear relationship between the dN/dS and Zn/(Zn+Zs) ratio across 90 species pairs.
ContributorsZhu, Ziqi (Author) / Cartwright, Reed A (Thesis advisor) / Taylor, Jay (Committee member) / Wideman, Jeremy (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2022
Description
Cocaine induces long-lasting changes in mesolimbic ‘reward’ circuits of the brain after cessation of use. These lingering changes include the neuronal plasticity that is thought to underlie the chronic relapsing nature of substance use disorders. Genes involved in neuronal plasticity also encode circular RNAs (circRNAs), which are stable, non-coding RNAs formed through the back-splicing of pre-mRNA. The Homer1 gene family, which encodes proteins associated with cocaine-induced plasticity, also encodes circHomer1. Based on preliminary evidence from shows cocaine-regulated changes in the ratio of circHomer1 and Homer1b mRNA in the nucleus accumbens (NAc), this study examined the relationship between circHomer1 and incentive motivation for cocaine by using different lengths of abstinence to vary the degree of motivation. Male and female rats were trained to self-administer cocaine (0.75 mg/kg/infusion, IV) or received a yoked saline infusion. Rats proceeded on an increasingly more difficult variable ratio schedule of lever pressing until they reached a variable ratio 5 schedule, which requires an average of 5 lever presses, and light and tone cues were delivered with the drug infusions. Rats were then tested for cocaine-seeking behavior in response to cue presentations without drug delivery either 1 or 21 days after their last self-administration session. They were sacrificed immediately after and circHomer1 and Homer1b expression was then measured from homogenate and synaptosomal fractions of NAc shell using RT-qPCR. Lever pressing during the cue reactivity test increased from 1 to 21 days of abstinence as expected. Results showed no group differences in synaptic circHomer1 expression, however, total circHomer1 expression was downregulated in 21d rats compared to controls. Lack of change in synaptic circHomer1 was likely due to trends toward different temporal changes in males versus females. Total Homer1b expression was higher in females, although there was no effect of cocaine abstinence. Further research investigating the time course of circHomer1 and Homer1b expression is warranted based on the inverse relationship between total circHomer1and cocaine-seeking behavior observed in this study.
ContributorsJohnson, Michael Christian (Author) / Neisewander, Janet L (Thesis advisor) / Perrone-Bizzozero, Nora (Thesis advisor) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2022
Description
The partitioning of photosynthates between their sites of production (source) and their sites of utilization (sink) is a major determinant of crop yield and the potential of regulating this translocation promises substantial opportunities for yield increases. Ubiquitous overexpression of the plant type I proton pyrophosphatase (H+-PPase) in crops improves several valuable traits including salt tolerance and drought resistance, nutrient and water use efficiencies, and increased root biomass and yield. Originally, type I H+-PPases were described as pyrophosphate (PPi)-dependent proton pumps localized exclusively in vacuoles of mesophyll and meristematic tissues. It has been proposed that in the meristematic tissues, the role of this enzyme would be hydrolyzing PPi originated in biosynthetic reactions and favoring sink strength. Interestingly, this enzyme has been also localized at the plasma membrane of companion cells in the phloem which load and transport photosynthates from source leaves to sinks. Of note, the plasma membrane-localized H+-PPase could only function as a PPi-synthase in these cells due to the steep proton gradient between the apoplast and cytosol. The generated PPi would favor active sucrose loading through the sucrose/proton symporter in the phloem by promoting sucrose hydrolysis through the Sucrose Synthase pathway and providing the ATP required to maintain the proton gradient. To better understand these two different roles of type I H+-PPases, a series of Arabidopsis thaliana transgenic plants were generated. By expressing soluble pyrophosphatases in companion cells of Col-0 ecotype and H+-PPase mutants, impaired photosynthates partitioning was observed, suggesting phloem-localized H+-PPase could generate the PPi required for sucrose loading. Col-0 plants expressed with either phloem- or meristem-specific AVP1 overexpression cassette and the cross between the two tissue specific lines (Cross) were generated. The results showed that the phloem-specific AVP1-overexpressing plants had increased root hair elongation under limited nutrient conditions and both phloem- and meristem-overexpression of AVP1 contributed to improved rhizosphere acidification and drought resistance. It was concluded that H+-PPases localized in both sink and source tissues regulate plant growth and performance under stress through its versatile enzymatic functions (PPi hydrolase and synthase).
ContributorsLi, Lin (Author) / Park, Yujin (Thesis advisor) / Mangone, Marco (Committee member) / Roberson, Robert (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2022
Description
Glioblastoma (GBM), the most common and aggressive primary brain tumor affecting adults, is characterized by an aberrant yet druggable epigenetic landscape. The Histone Deacetylases (HDACs), a major family of epigenetic regulators, favor transcriptional repression by mediating chromatin compaction and are frequently overexpressed in human cancers, including GBM. Hence, over the last decade there has been considerable interest in using HDAC inhibitors (HDACi) for the treatment of malignant primary brain tumors. However, to date most HDACi tested in clinical trials have failed to provide significant therapeutic benefit to patients with GBM. This is because current HDACi have poor or unknown pharmacokinetic profiles, lack selectivity towards the different HDAC isoforms, and have narrow therapeutic windows. Isoform selectivity for HDACi is important given that broad inhibition of all HDACs results in widespread toxicity across different organs. Moreover, the functional roles of individual HDAC isoforms in GBM are still not well understood. Here, I demonstrate that HDAC1 expression increases with brain tumor grade and is correlated with decreased survival in GBM. I find that HDAC1 is the essential HDAC isoform in glioma stem cells and its loss is not compensated for by its paralogue HDAC2 or other members of the HDAC family. Loss of HDAC1 alone has profound effects on the glioma stem cell phenotype in a p53-dependent manner and leads to significant suppression of tumor growth in vivo. While no HDAC isoform-selective inhibitors are currently available, the second-generation HDACi quisinostat harbors high specificity for HDAC1. I show that quisinostat exhibits potent growth inhibition in multiple patient-derived glioma stem cells. Using a pharmacokinetics- and pharmacodynamics-driven approach, I demonstrate that quisinostat is a brain-penetrant molecule that reduces tumor burden in flank and orthotopic models of GBM and significantly extends survival both alone and in combination with radiotherapy. The work presented in this thesis thereby unveils the non-redundant functions of HDAC1 in therapy- resistant glioma stem cells and identifies a brain-penetrant HDACi with higher selectivity towards HDAC1 as a potent radiosensitizer in preclinical models of GBM. Together, these results provide a rationale for developing quisinostat as a potential adjuvant therapy for the treatment of GBM.
ContributorsLo Cascio, Costanza (Author) / LaBaer, Joshua (Thesis advisor) / Mehta, Shwetal (Committee member) / Mirzadeh, Zaman (Committee member) / Mangone, Marco (Committee member) / Paek, Andrew (Committee member) / Arizona State University (Publisher)
Created2022