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: Alford, Eddie
- Creators: Wang, Xiao
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
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
Grassland habitat restoration activities are occurring within the semi-arid grasslands of the Agua Fria National Monument located 65 km north of Phoenix, AZ. The goal of these restoration activities is to reduce woody species encroachment, remove lignified plant materials and recycle nutrients within the ecosystem thus improving range conditions for both wildlife species and livestock. Broadcast burning, juniper thinning and slash pile burns are the principle tools used to accomplish resource objectives. Line cover, belt transect, densities, heights and biomass of vegetation data were collected to determine the response of the vegetative community to habitat restoration activities. Principal Component Analysis (PCA) was used to reduce data analysis to the more influential factors. Regression analysis was conducted for statistically significant response variables. Quadratic regression analysis found low predictive values. In broadcast burn treatment units, all important factors as identified by PCA had low predictive factors but significantly differed (R2 <0.01, p<0.05) between unburned and the years post treatment. Regression analysis found significant, albeit weak, relationships between time since treatment and independent variables. In pile burn treatment units, data reduction by PCA was not possible in a biologically meaningful way due to the high variability within treatment units. This suggests the effect of juniper encroachment on grassland vegetation persists long after junipers have been cut and burned. This study concluded that broadcast burning of the central Arizona grasslands does significantly alter many components of the vegetative community. Fuels treatments generally initially reduced both perennial woody species and grasses in number and height for two year post fire. However, palatable shrubs, in particular shrubby buckwheat, were not significantly different in broadcast burn treatment areas. The vegetative community characteristics of juniper encroached woodlands of central Arizona are unaffected by the removal and burning of junipers aside from the removal of hiding cover for predators for multiple years. It is recommended that habitat restoration activities continue provided the needs of wildlife are considered, especially pronghorn, with the incorporation of state and transition models specific to each of the respective ecological site descriptions and with the consideration of the effects of fire to pronghorn fawning habitat.
ContributorsSitzmann, Paul Roman (Author) / Miller, William (Thesis advisor) / Alford, Eddie (Committee member) / Green, Douglas (Committee member) / Arizona State University (Publisher)
Created2014
Description
There has been considerable advancement in the algae research field to move algae production for biofuels and bio-products forward to become commercially viable. However, there is one key element that humans cannot control, the natural externalities that impact production. An algae cultivation system is similar to agricultural crop farming practices. Algae are grown on an area of land for a certain time period with the aim of harvesting the biomass produced. One of the advantages of using algae biomass is that it can be used as a source of energy in the form of biofuels. Major advances in algae research and development practices have led to new knowledge about the remarkable potential of algae to serve as a sustainable source of biofuel. The challenge is to make the price of biofuels from algae cost-competitive with the price of petroleum-based fuels. The scope of this research was to design a concept for an automated system to control specific externalities and determine if integrating the system in an algae cultivation system could improve the algae biomass production process. This research required the installation and evaluation of an algae cultivation process, components selection and computer software programming for an automated system. The results from the automated system based on continuous real time monitored variables validated that the developed system contributes insights otherwise not detected from a manual measurement approach. The implications of this research may lead to technology that can be used as a base model to further improve algae cultivation systems.
ContributorsPuruhito, Emil (Author) / Sommerfeld, Milton (Thesis advisor) / Gintz, Jerry (Thesis advisor) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Two nearly homogenous 60 acre watersheds near Heber, Arizona, within the Apache-Sitgreaves National Forest, were burned at moderate and high severities during the 2002 Rodeo-Chediski wildfire. Each watershed had 30 permanent plots located on it from earlier studies. In 2011, nearly 10 years following the fire, the plots were re-measured to determine how fire severity affects the long term vegetative recovery of this ecosystem; specifically herbaceous production and tree regeneration and density. Canopy cover, litter depth, herbaceous weight, herbaceous cover and shrub cover are vital indicators of herbaceous production, and were found to be significantly different between the sites. Canopy cover and litter depth were found to be significantly higher on the moderate site while herbaceous weight, herbaceous cover and shrub cover were found to be significantly higher on the high site. Tree densities of the three present tree species, ponderosa pine, alligator juniper, and gambel oak, were measured and divided into five size classes to distinguish the diversity of the communities. The mean densities for each species and size class were analyzed to determine if there were any statistically significant differences between the sites. Ponderosa pine saplings (regeneration) were found to have no significant differences between the sites. Juniper and oak saplings were found to be significantly higher on the high site. The remaining four ponderosa pine size classes were found to be significantly higher on the moderate site while the remaining four size classes for juniper and oak were found to have no statistical differences between the sites. Further analysis of the tree proportions revealed that the ponderosa pine species was significantly higher on the moderate site while juniper and oak were significantly higher on the high site. Species specific proportion analysis showed that the ponderosa pine size classes were significantly different across the sites while the juniper and oak size classes showed no significant differences between the sites. Within the ponderosa pine size classes, saplings were found to be significantly higher on the high site while the remaining four classes were significantly higher on the moderate site.
ContributorsNeeley, Heidi L (Author) / Alford, Eddie (Thesis advisor) / Pyne, Stephen (Committee member) / Brady, Ward (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
The introduction of livestock to the vast majority of public lands may be used to simulate the conditions provided by herbivorous grazers in the past, however little data has been collected on the effects of livestock grazing in Sonoran desert habitats. Vegetative species that are characteristic of the Arizona Upland subdivision of the Sonoran desert did not evolve with extensive grazing by large ungulate populations, and therefore the response to livestock grazing is of particular interest. Four historic Parker 3-step clusters in south-central Arizona were sampled in three cohorts between 1953 and 2016 to interpret changes in rangeland health using soil coverage data, species richness and frequency, and long-term photo point comparisons. Cattle grazing was active across the allotment until 1984, allowing approximately 30 years of rest before the third and final cohort was measured. Over the entirety of this study, there was a 66.67% increase in perennial basal hits, a 56.29% increase in rock, and a 44.55% increase of forage basal hits. Decreases were seen in litter (-57.69%) and bare soil hits (-8.76%). Cluster 3 consistently had a lower percent of cover across all classes of vegetation in the 2014 cohort
(-81.61%), however the average percent of cover increased by 63.16% (40 hits) across the allotment. Available species richness data from 1971 and 2014 cohorts indicates a 112% increase in unique species; however, species richness increases in the 2014 cohort are largely based on recruitment of non-palatable species (71%). Although the status of some species were undetermined, all individuals identified to species in the invader class (non-palatable) were determined to be native to the study site. Perennial grass frequency became less abundant over the duration of this study, while growth was predominantly observed in shrubs. Increases in species frequency was detected on two of the four clusters measured in the 2014 cohort; the growth was primarily observed in jojoba (Simmondsia chinensis), oak (Quercus spp.), and catclaw acacia (Senegalia greggii) in C4, and hopseed bush (Dodonaea viscosa) in C2.
(-81.61%), however the average percent of cover increased by 63.16% (40 hits) across the allotment. Available species richness data from 1971 and 2014 cohorts indicates a 112% increase in unique species; however, species richness increases in the 2014 cohort are largely based on recruitment of non-palatable species (71%). Although the status of some species were undetermined, all individuals identified to species in the invader class (non-palatable) were determined to be native to the study site. Perennial grass frequency became less abundant over the duration of this study, while growth was predominantly observed in shrubs. Increases in species frequency was detected on two of the four clusters measured in the 2014 cohort; the growth was primarily observed in jojoba (Simmondsia chinensis), oak (Quercus spp.), and catclaw acacia (Senegalia greggii) in C4, and hopseed bush (Dodonaea viscosa) in C2.
ContributorsDunn, Kellie Ann (Author) / Alford, Eddie (Thesis advisor) / Cunningham, Stanley (Committee member) / Stutz, Jean (Committee member) / Arizona State University (Publisher)
Created2018
Description
Synthetic gene networks have evolved from simple proof-of-concept circuits to
complex therapy-oriented networks over the past fifteen years. This advancement has
greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a
mechanism that cells use to achieve a discrete number of mutually exclusive states in
response to environmental inputs. However, complex contextual connections of gene
regulatory networks in natural settings often impede the experimental establishment of
the function and dynamics of each specific gene network.
In this work, diverse synthetic gene networks are rationally designed and
constructed using well-characterized biological components to approach the cell fate
determination and state transition dynamics in multistable systems. Results show that
unimodality and bimodality and trimodality can be achieved through manipulation of the
signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to
communicate with each other.
Moreover, a synthetic quadrastable circuit is also built and experimentally
demonstrated to have four stable steady states. Experiments, guided by mathematical
modeling predictions, reveal that sequential inductions generate distinct cell fates by
changing the landscape in sequence and hence navigating cells to different final states.
Circuit function depends on the specific protein expression levels in the circuit.
We then establish a protein expression predictor taking into account adjacent
transcriptional regions’ features through construction of ~120 synthetic gene circuits
(operons) in Escherichia coli. The predictor’s utility is further demonstrated in evaluating genes’ relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks.
These combined results illustrate applications of synthetic gene networks to
understand the cell fate determination and state transition dynamics in multistable
systems. A protein-expression predictor is also developed to evaluate and tune circuit
dynamics.
complex therapy-oriented networks over the past fifteen years. This advancement has
greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a
mechanism that cells use to achieve a discrete number of mutually exclusive states in
response to environmental inputs. However, complex contextual connections of gene
regulatory networks in natural settings often impede the experimental establishment of
the function and dynamics of each specific gene network.
In this work, diverse synthetic gene networks are rationally designed and
constructed using well-characterized biological components to approach the cell fate
determination and state transition dynamics in multistable systems. Results show that
unimodality and bimodality and trimodality can be achieved through manipulation of the
signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to
communicate with each other.
Moreover, a synthetic quadrastable circuit is also built and experimentally
demonstrated to have four stable steady states. Experiments, guided by mathematical
modeling predictions, reveal that sequential inductions generate distinct cell fates by
changing the landscape in sequence and hence navigating cells to different final states.
Circuit function depends on the specific protein expression levels in the circuit.
We then establish a protein expression predictor taking into account adjacent
transcriptional regions’ features through construction of ~120 synthetic gene circuits
(operons) in Escherichia coli. The predictor’s utility is further demonstrated in evaluating genes’ relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks.
These combined results illustrate applications of synthetic gene networks to
understand the cell fate determination and state transition dynamics in multistable
systems. A protein-expression predictor is also developed to evaluate and tune circuit
dynamics.
ContributorsWu, Fuqing (Author) / Wang, Xiao (Thesis advisor) / Haynes, Karmella (Committee member) / Marshall, Pamela (Committee member) / Nielsen, David (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2017
Description
Fusion proteins that specifically interact with biochemical marks on chromosomes represent a new class of synthetic transcriptional regulators that decode cell state information rather than deoxyribose nucleic acid (DNA) sequences. In multicellular organisms, information relevant to cell state, tissue identity, and oncogenesis is often encoded as biochemical modifications of histones, which are bound to DNA in eukaryotic nuclei and regulate gene expression states. In 2011, Haynes et al. showed that a synthetic regulator called the Polycomb chromatin Transcription Factor (PcTF), a fusion protein that binds methylated histones, reactivated an artificially-silenced luciferase reporter gene. These synthetic transcription activators are derived from the polycomb repressive complex (PRC) and associate with the epigenetic silencing mark H3K27me3 to reactivate the expression of silenced genes. It is demonstrated here that the duration of epigenetic silencing does not perturb reactivation via PcTF fusion proteins. After 96 hours PcTF shows the strongest reactivation activity. A variant called Pc2TF, which has roughly double the affinity for H3K27me3 in vitro, reactivated the silenced luciferase gene by at least 2-fold in living cells.
ContributorsVargas, Daniel A. (Author) / Haynes, Karmella (Thesis advisor) / Wang, Xiao (Committee member) / Mills, Jeremy (Committee member) / Arizona State University (Publisher)
Created2019
Description
A notable challenge when assembling synthetic gene circuits is that modularity often fails to function as intended. A crucial underlying reason for this modularity failure is the existence of competition for shared and limited gene expression resources. By designing a synthetic cascading bistable switches (Syn-CBS) circuit in a single strain with two coupled self-activation modules to achieve successive cell fate transitions, nonlinear resource competition within synthetic gene circuits is unveiled. However, in vivo it can be seen that the transition path was redirected with the activation of one switch always prevailing over that of the other, contradictory to coactivation theoretically expected. This behavior is a result of resource competition between genes and follows a ‘winner-takes-all’ rule, where the winner is determined by the relative connection strength between the two modules. Despite investigation demonstrating that resource competition between gene modules can significantly alter circuit deterministic behaviors, how resource competition contributes to gene expression noise and how this noise can be controlled is still an open issue of fundamental importance in systems biology and biological physics. By utilizing a two-gene circuit, the effects of resource competition on protein expression noise levels can be closely studied. A surprising double-edged role is discovered: the competition for these resources decreases noise while the constraint on resource availability adds its own term of noise into the system, denoted “resource competitive” noise. Noise reduction effects are then studied using orthogonal resources. Results indicate that orthogonal resources are a good strategy for eliminating the contribution of resource competition to gene expression noise.
Noise propagation through a cascading circuit has been considered without resource competition. It has been noted that the noise from upstream genes can be transmitted downstream. However, resource competition’s effects on this cascading noise have yet to be studied. When studied, it is found that resource competition can induce stochastic state
switching and perturb noise propagation. Orthogonal resources can remove some of the resource competitive behavior and allow for a system with less noise.
ContributorsGoetz, Hanah Elizabeth (Author) / Tian, Xiaojun (Thesis advisor) / Wang, Xiao (Committee member) / Lai, Ying-Cheng (Committee member) / Arizona State University (Publisher)
Created2022