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: Sabo, John
- Creators: Wang, Xuan
Description
The southwestern willow flycatcher (Empidonax traillii extimus) is listed as an endangered species throughout its range in the southwestern United States. Little is known about its sub-population spatial structure and how this impacts its population viability. In conjunction with being listed as endangered, a recovery plan was produced by the US Fish and Wildlife Service, with recovery units (sub-populations) roughly based on major river drainages. In the interest of examining this configuration of sub-populations and their impact on the measured population viability, I applied a multivariate auto-regressive state-space model to a spatially extensive time series of abundance data for the southwestern willow flycatcher over the period spanning 1995-2010 estimating critical growth parameters, correlation in environmental stochasticity or "synchronicity" between sub-populations (recovery units) and extinction risk of the sub-populations and the whole. The model estimates two parameters, the mean and variance of annual growth rate. Of the models I tested, I found the strongest support for a population model in which three of the recovery units were grouped (the Lower Colorado, Gila Basin, and Rio Grande recovery units) while keeping all others separate. This configuration has 6.6 times more support for the observed data than a configuration assigning each recovery unit to a separate sub-population, which is how they are circumscribed in the recovery plan. Given the best model, the mean growth rate is -0.0234 (CI95 -0.0939, 0.0412) with a variance of 0.0597 (CI95 0.0115, 0.1134). This growth rate is not significantly different from zero and this is reflected in the low potential for quasi-extinction. The cumulative probability of the population experiencing at least an 80% decline from current levels within 15 years for some sub-populations were much higher (range: 0.129-0.396 for an 80% decline). These results suggest that the rangewide population has a low risk of extinction in the next 15 years and that the formal recovery units specified by the original recovery plan do not correspond to proper sub-population units as defined by population synchrony.
ContributorsDockens, Patrick E. T. (Author) / Sabo, John (Thesis advisor) / Stromberg, Juliet (Committee member) / Fenichel, Eli (Committee member) / Arizona State University (Publisher)
Created2012
Description
Land management practices such as domestic animal grazing can alter plant communities via changes in soil structure and chemistry, species composition, and plant nutrient content. These changes can affect the abundance and quality of plants consumed by insect herbivores with consequent changes in population dynamics. These population changes can translate to massive crop damage and pest control costs. My dissertation focused on Oedaleus asiaticus, a dominant Asian locust, and had three main objectives. First, I identified morphological, physiological, and behavioral characteristics of the migratory ("brown") and non-migratory ("green") phenotypes. I found that brown morphs had longer wings, larger thoraxes and higher metabolic rates compared to green morphs, suggesting that developmental plasticity allows greater migratory capacity in the brown morph of this locust. Second, I tested the hypothesis of a causal link between livestock overgrazing and an increase in migratory swarms of O. asiaticus. Current paradigms generally assume that increased plant nitrogen (N) should enhance herbivore performance by relieving protein-limitation, increasing herbivorous insect populations. I showed, in contrast to this scenario, that host plant N-enrichment and high protein artificial diets decreased the size and viability of O. asiaticus. Plant N content was lowest and locust abundance highest in heavily livestock-grazed fields where soils were N-depleted, likely due to enhanced erosion and leaching. These results suggest that heavy livestock grazing promotes outbreaks of this locust by reducing plant protein content. Third, I tested for the influence of dietary imbalance, in conjunction with high population density, on migratory plasticity. While high population density has clearly been shown to induce the migratory morph in several locusts, the effect of diet has been unclear. I found that locusts reared at high population density and fed unfertilized plants (i.e. high quality plants for O. asiaticus) had the greatest migratory capacity, and maintained a high percent of brown locusts. These results did not support the hypothesis that poor-quality resources increased expression of migratory phenotypes. This highlights a need to develop new theoretical frameworks for predicting how environmental factors will regulate migratory plasticity in locusts and perhaps other insects.
ContributorsCease, Arianne (Author) / Harrison, Jon (Thesis advisor) / Elser, James (Thesis advisor) / DeNardo, Dale (Committee member) / Quinlan, Michael (Committee member) / Sabo, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used to research the protein-protein interactions in SlyA, MprA, and PhoP as heterodimers and homodimers in vivo. Two fragments, T25 and T18, that lack endogenous adenylate cyclase activity, were used for construction of chimeric proteins and reconstruction of adenylate cyclase activity was tested. The significant adenylate cyclase activities has proved that SlyA is able to form homodimers. However, weak adenylate cyclase activities in this study has proved that MprA and PhoP are not likely to form homodimers, and no protein-protein interactions were detected in between SlyA, MprA and PhoP, which no heterodimers have formed in between three transcriptional regulators.
ContributorsTao, Zenan (Author) / Shi, Yixin (Thesis advisor) / Wang, Xuan (Committee member) / Bean, Heather (Committee member) / Arizona State University (Publisher)
Created2018
Description
Lignocellulosic biomass represents a renewable domestic feedstock that can support large-scale biochemical production processes for fuels and specialty chemicals. However, cost-effective conversion of lignocellulosic sugars into valuable chemicals by microorganisms still remains a challenge. Biomass recalcitrance to saccharification, microbial substrate utilization, bioproduct titer toxicity, and toxic chemicals associated with chemical pretreatments are at the center of the bottlenecks limiting further commercialization of lignocellulose conversion. Genetic and metabolic engineering has allowed researchers to manipulate microorganisms to overcome some of these challenges, but new innovative approaches are needed to make the process more commercially viable. Transport proteins represent an underexplored target in genetic engineering that can potentially help to control the input of lignocellulosic substrate and output of products/toxins in microbial biocatalysts. In this work, I characterize and explore the use of transport systems to increase substrate utilization, conserve energy, increase tolerance, and enhance biocatalyst performance.
ContributorsKurgan, Gavin (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Misra, Rajeev (Committee member) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2018
Description
Emergence of multidrug resistant (MDR) bacteria is a major concern to global health. One of the major MDR mechanisms bacteria employ is efflux pumps for the expulsion of drugs from the cell. In Escherichia coli, AcrAB-TolC proteins constitute the major chromosomally-encoded drug efflux system. AcrB, a trimeric membrane protein is well-known for its substrate promiscuity. It has the ability to efflux a broad spectrum of substrates alongside compounds such as dyes, detergent, bile salts and metabolites. Newly identified AcrB residues were shown to be functionally relevant in the drug binding and translocation pathway using a positive genetic selection strategy. These residues—Y49, V127, D153, G288, F453, and L486—were identified as the sites of suppressors of an alteration, F610A, that confers a drug hypersensitivity phenotype. Using site-directed mutagenesis (SDM) along with the real-time efflux and the classical minimum inhibitory concentration (MIC) assays, I was able to characterize the mechanism of suppression.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
Three approaches were used for the characterization of these suppressors. The first approach focused on side chain specificity. The results showed that certain suppressor sites prefer a particular side chain property, such as size, to overcome the F610A defect. The second approach focused on the effects of efflux pump inhibitors. The results showed that though the suppressor residues were able to overcome the intrinsic defect of F610A, they were unable to overcome the extrinsic defect caused by the efflux pump inhibitors. This showed that the mechanism by which F610A imposes its effect on AcrB function is different than that of the efflux pump inhibitors. The final approach was to determine whether suppressors mapping in the periplasmic and trans-membrane domains act by the same or different mechanisms. The results showed both overlapping and distinct mechanisms of suppression.
To conclude, these approaches have provided a deeper understanding of the mechanisms by which novel suppressor residues of AcrB overcome the functional defect of the drug binding domain alteration, F610A.
ContributorsBlake, Mellecha (Author) / Misra, Rajeev (Thesis advisor) / Stout, Valerie (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
There is considerable recent interest in the dynamic nature of immune function in the context of an animal’s internal and external environment. An important focus within this field of ecoimmunology is on how availability of resources such as energy can alter immune function. Water is an additional resource that drives animal development, physiology, and behavior, yet the influence hydration has on immunity has received limited attention. In particular, hydration state may have the greatest potential to drive fluctuations in immunity and other physiological functions in species that live in water-limited environments where they may experience periods of dehydration. To shed light on the sensitivity of immune function to hydration state, I first tested the effect of hydration states (hydrated, dehydrated, and rehydrated) and digestive states on innate immunity in the Gila monster, a desert-dwelling lizard. Though dehydration is often thought to be stressful and, if experienced chronically, likely to decrease immune function, dehydration elicited an increase in immune response in this species, while digestive state had no effect. Next, I tested whether dehydration was indeed stressful, and tested a broader range of immune measures. My findings validated the enhanced innate immunity across additional measures and revealed that Gila monsters lacked a significant stress hormone response during dehydration (though results were suggestive). I next sought to test if life history (in terms of environmental stability) drives these differences in dehydration responses using a comparative approach. I compared four confamilial pairs of squamate species that varied in habitat type within each pair—four species that are adapted to xeric environments and four that are adapted to more mesic environments. No effect of life history was detected between groups, but hydration was a driver of some measures of innate immunity and of stress hormone concentrations in multiple species. Additionally, species that exhibited a stress response to dehydration did not have decreased innate immunity, suggesting these physiological responses may often be decoupled. My dissertation work provides new insight into the relationship between hydration, stress, and immunity, and it may inform future work exploring disease transmission or organismal responses to climate change.
ContributorsMoeller, Karla T (Author) / DeNardo, Dale (Thesis advisor) / Angilletta, Michael (Committee member) / French, Susannah (Committee member) / Rutowski, Ronald (Committee member) / Sabo, John (Committee member) / Arizona State University (Publisher)
Created2016
Description
Desert environments provide considerable challenges to organisms because of high temperatures and limited food and water resources. Accordingly, desert species have behavioral and physiological traits that enable them to cope with these constraints. However, continuing human activity as well as anticipated further changes to the climate and the vegetative community pose a great challenge to such balance between an organism and its environment. This is especially true in the Arabian Desert, where climate conditions are extreme and environmental disturbances substantial. This study combined laboratory and field components to enhance our understanding of dhub (Uromastyx aegyptius) ecophysiology and determine whether habitat protection influences dhub behavior and physiology.
Results of this study showed that while body mass and body condition consistently diminished as the active season progressed, they were both greater in protected habitats compared to non-protected habitats, regardless of season. Dhubs surface activity and total body water decreased while evaporative water loss and body temperature increased as the active season progressed and ambient temperature got hotter. Total body water was also significantly affected by habitat protection.
Overall, this study revealed that, while habitat protection provided more vegetation, it had little effect on seasonal changes in surface activity. While resource availability in protected areas might allow for larger dhub populations, unprotected areas showed similar body morphometrics, activity, and body temperatures. By developing an understanding of how different coping strategies are linked to particular ecological, morphological, and phylogenetic traits, we will be able to make more accurate predictions regarding the vulnerability of species. By combining previous studies pertaining to conservation of protected species with the results of my study, a number of steps in ecosystem management are recommended to help in the preservation of dhubs in the Kuwaiti desert.
Results of this study showed that while body mass and body condition consistently diminished as the active season progressed, they were both greater in protected habitats compared to non-protected habitats, regardless of season. Dhubs surface activity and total body water decreased while evaporative water loss and body temperature increased as the active season progressed and ambient temperature got hotter. Total body water was also significantly affected by habitat protection.
Overall, this study revealed that, while habitat protection provided more vegetation, it had little effect on seasonal changes in surface activity. While resource availability in protected areas might allow for larger dhub populations, unprotected areas showed similar body morphometrics, activity, and body temperatures. By developing an understanding of how different coping strategies are linked to particular ecological, morphological, and phylogenetic traits, we will be able to make more accurate predictions regarding the vulnerability of species. By combining previous studies pertaining to conservation of protected species with the results of my study, a number of steps in ecosystem management are recommended to help in the preservation of dhubs in the Kuwaiti desert.
ContributorsAl-Sayegh, Mohammed (Author) / DeNardo, Dale (Thesis advisor) / Angilletta, Michael (Committee member) / Smith, Andrew (Committee member) / Sabo, John (Committee member) / Majeed, Qais (Committee member) / Arizona State University (Publisher)
Created2017
Description
Introduction: Often it is presumed that in high-income countries, like the United States, water insecurity is not an issue. Yet, more than 2 million individuals in the United States are affected by water insecurity. Experiencing the effects of water insecurity are informal settlements and impoverished communities termed as “colonias”, characterized by the lack of possessing basic infrastructures and services, including water systems and wastewater disposal amongst many. Purpose: To critically analyze how water insecurity manifests in the colonias and the impacts it has on the health and well-being of the community members.
Methods: An extensive systematic literature review was conducted in the effort to bring a meaningful framework of existing challenges and potential resolutions and theorize water insecurity in colonias.
Results: The effects of water insecurity due to water scarcity and water contamination in the colonias led to health complications, unsanitary living conditions and mental distress for residents. The causes of water insecurity in the colonias were because of political exclusion, municipal underbounding and the failure to monitor water quality.
Conclusion: The dire consequences of household water insecurity to an individual, no less an entire population, are detrimental to health and well-being. Despite this acknowledgement of a critical and basic human necessity, literature reveals a robust water governance infrastructure is much needed for the people in colonias. For meaningful progress and developments to be made in addressing water insecurity for the people of colonias, this review was approached through a transdisciplinary lens - one that achieves convergence.
ContributorsPatwoary, Nargish (Author) / Wutich, Amber (Thesis advisor) / Sabo, John (Thesis advisor) / Roque, Anais (Committee member) / Arizona State University (Publisher)
Created2021
Characterization and Manipulation of Microbiomes From Arid Landfills for Improved Methane Production
Description
Environmentally harmful byproducts from solid waste’s decomposition, including methane (CH4) emissions, are managed through standardized landfill engineering and gas-capture mechanisms. Yet only a limited number of studies have analyzed the development and composition of Bacteria and Archaea involved in CH4 production from landfills. The objectives of this research were to compare microbiomes and bioactivity from CH4-producing communities in contrasting spatial areas of arid landfills and to tests a new technology to biostimulate CH4 production (methanogenesis) from solid waste under dynamic environmental conditions controlled in the laboratory. My hypothesis was that the diversity and abundance of methanogenic Archaea in municipal solid waste (MSW), or its leachate, play an important role on CH4 production partially attributed to the group’s wide hydrogen (H2) consumption capabilities. I tested this hypothesis by conducting complementary field observations and laboratory experiments. I describe niches of methanogenic Archaea in MSW leachate across defined areas within a single landfill, while demonstrating functional H2-dependent activity. To alleviate limited H2 bioavailability encountered in-situ, I present biostimulant feasibility and proof-of-concepts studies through the amendment of zero valent metals (ZVMs). My results demonstrate that older-aged MSW was minimally biostimulated for greater CH4 production relative to a control when exposed to iron (Fe0) or manganese (Mn0), due to highly discernable traits of soluble carbon, nitrogen, and unidentified fluorophores found in water extracts between young and old aged, starting MSW. Acetate and inhibitory H2 partial pressures accumulated in microcosms containing old-aged MSW. In a final experiment, repeated amendments of ZVMs to MSW in a 600 day mesocosm experiment mediated significantly higher CH4 concentrations and yields during the first of three ZVM injections. Fe0 and Mn0 experimental treatments at mesocosm-scale also highlighted accelerated development of seemingly important, but elusive Archaea including Methanobacteriaceae, a methane-producing family that is found in diverse environments. Also, prokaryotic classes including Candidatus Bathyarchaeota, an uncultured group commonly found in carbon-rich ecosystems, and Clostridia; All three taxa I identified as highly predictive in the time-dependent progression of MSW decomposition. Altogether, my experiments demonstrate the importance of H2 bioavailability on CH4 production and the consistent development of Methanobacteriaceae in productive MSW microbiomes.
ContributorsReynolds, Mark Christian (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Wang, Xuan (Committee member) / Kavazanjian, Edward (Committee member) / Arizona State University (Publisher)
Created2022
Description
Biomass synthesis is a competing factor in biological systems geared towards generation of commodity and specialty chemicals, ultimately limiting maximum titer and yield; in this thesis, a widely generalizable, modular approach focused on decoupling biomass synthesis from the production of the phenylalanine in a genetically modified strain of E. coli BW25113 was explored with the use of synthetic trans-encoded small RNA (sRNA) to achieve greater efficiency. The naturally occurring sRNA MicC was used as a scaffold, and combined on a plasmid with a promoter for anhydrous tetracycline (aTc) and a T1/TE terminator. The coding sequence corresponding to the target binding site for fourteen potentially growth-essential gene targets as well as non-essential lacZ was placed in the seed region of the of the sRNA scaffold and transformed into BW25113, effectively generating a unique strain for each gene target. The BW25113 strain corresponding to each gene target was screened in M9 minimal media; decreased optical density and elongated cell morphology changes were observed and quantified in all induced sRNA cases where growth-essential genes were targeted. Six of the strains targeting different aspects of cell division that effectively suppressed growth and resulted in increased cell size were then screened for viability and metabolic activity in a scaled-up shaker flask experiment; all six strains were shown to be viable during stationary phase, and a metabolite analysis showed increased specific glucose consumption rates in induced strains, with unaffected specific glucose consumption rates in uninduced strains. The growth suppression, morphology and metabolic activity of the induced strains in BW25113 was compared to the bacteriostatic additives chloramphenicol, tetracycline, and streptomycin. At this same scale, the sRNA plasmid targeting the gene murA was transformed into BW25113 pINT-GA, a phenylalanine overproducer with the feedback resistant genes aroG and pheA overexpressed. Two induction times were explored during exponential phase, and while the optimal induction time was found to increase titer and yield amongst the BW25113 pINT-GA murA sRNA variant, overall this did not have as great a titer or yield as the BW25113 pINT-GA strain without the sRNA plasmid; this may be a result of the cell filamentation.
ContributorsHerschel, Daniel Jordan (Author) / Nielsen, David R (Thesis advisor) / Torres, César I (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016