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Description
Safe, readily available, and reliable sources of water are an essential component of any municipality’s infrastructure. Phoenix, Arizona, a southwestern city, has among the highest per capita water use in the United States, making it essential to carefully manage its reservoirs. Generally, municipal water bodies are monitored through field sampling. However, this approach is limited spatially and temporally in addition to being costly. In this study, the application of remotely sensed reflectance data from Landsat 7’s Enhanced Thematic Mapper Plus (ETM+) and Landsat 8’s Operational Land Imager (OLI) along with data generated through field-sampling is used to gain a better understanding of the seasonal development of algal communities and levels of suspended particulates in the three main terminal reservoirs supplying water to the Phoenix metro area: Bartlett Lake, Lake Pleasant, and Saguaro Lake. Algal abundances, particularly the abundance of filamentous cyanobacteria, increased with warmer temperatures in all three reservoirs and reached the highest comparative abundance in Bartlett Lake. Prymnesiophytes (the class of algae to which the toxin-producing golden algae belong) tended to peak between June and August, with one notable peak occurring in Saguaro Lake in August 2017 during which time a fish-kill was observed. In the cooler months algal abundance was comparatively lower in all three lakes, with a more even distribution of abundance across algae classes. In-situ data from March 2017 to March 2018 were compared with algal communities sampled approximately ten years ago in each reservoir to understand any possible long-term changes. The findings show that the algal communities in the reservoirs are relatively stable, particularly those of the filamentous cyanobacteria, chlorophytes, and prymnesiophytes with some notable exceptions, such as the abundance of diatoms, which increased in Bartlett Lake and Lake Pleasant. When in-situ data were compared with Landsat-derived reflectance data, two-band combinations were found to be the best-estimators of chlorophyll-a concentration (as a proxy for algal biomass) and total suspended sediment concentration. The ratio of the reflectance value of the red band and the blue band produced reasonable estimates for the in-situ parameters in Bartlett Lake. The ratio of the reflectance value of the green band and the blue band produced reasonable estimates for the in-situ parameters in Saguaro Lake. However, even the best performing two-band algorithm did not produce any significant correlation between reflectance and in-situ data in Lake Pleasant. Overall, remotely-sensed observations can significantly improve our understanding of the water quality as measured by algae abundance and particulate loading in Arizona Reservoirs, especially when applied over long timescales.
ContributorsRussell, Jazmine Barkley (Author) / Neuer, Susanne (Thesis advisor) / Fox, Peter (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2018
Description
Amongst the most studied of the social insects, the honey bee has a prominent place due to its economic importance and influence on human societies. Honey bee colonies can have over 50,000 individuals, whose activities are coordinated by chemical signals called pheromones. Because these pheromones are secreted from various exocrine glands, the proper development and function of these glands are vital to colony dynamics. In this thesis, I present a study of the developmental ontogeny of the exocrine glands found in the head of the honey bee. In Chapter 2, I elucidate how the larval salivary gland transitions to an adult salivary gland through apoptosis and cell growth, differentiation and migration. I also explain the development of the hypopharyngeal and the mandibular gland using apoptotic markers and cytoskeletal markers like tubulin and actin. I explain the fundamental developmental plan for the formation of the glands and show that apoptosis plays an important role in the transformation toward an adult gland.
ContributorsNath, Rachna (Author) / Gadau, Juergen (Thesis advisor) / Rawls, Alan (Committee member) / Harrison, Jon (Committee member) / Arizona State University (Publisher)
Created2018
Description
Synthetic manipulation of chromatin dynamics has applications for medicine, agriculture, and biotechnology. However, progress in this area requires the identification of design rules for engineering chromatin systems. In this thesis, I discuss research that has elucidated the intrinsic properties of histone binding proteins (HBP), and apply this knowledge to engineer novel chromatin binding effectors. Results from the experiments described herein demonstrate that the histone binding domain from chromobox protein homolog 8 (CBX8) is portable and can be customized to alter its endogenous function. First, I developed an assay to identify engineered fusion proteins that bind histone post translational modifications (PTMs) in vitro and regulate genes near the same histone PTMs in living cells. This assay will be useful for assaying the function of synthetic histone PTM-binding actuators and probes. Next, I investigated the activity of a novel, dual histone PTM binding domain regulator called Pc2TF. I characterized Pc2TF in vitro and in cells and show it has enhanced binding and transcriptional activation compared to a single binding domain fusion called Polycomb Transcription Factor (PcTF). These results indicate that valency can be used to tune the activity of synthetic histone-binding transcriptional regulators. Then, I report the delivery of PcTF fused to a cell penetrating peptide (CPP) TAT, called CP-PcTF. I treated 2D U-2 OS bone cancer cells with CP-PcTF, followed by RNA sequencing to identify genes regulated by CP-PcTF. I also showed that 3D spheroids treated with CP-PcTF show delayed growth. This preliminary work demonstrated that an epigenetic effector fused to a CPP can enable entry and regulation of genes in U-2 OS cells through DNA independent interactions. Finally, I described and validated a new screening method that combines the versatility of in vitro transcription and translation (IVTT) expressed protein coupled with the histone tail microarrays. Using Pc2TF as an example, I demonstrated that this assay is capable of determining binding and specificity of a synthetic HBP. I conclude by outlining future work toward engineering HBPs using techniques such as directed evolution and rational design. In conclusion, this work outlines a foundation to engineer and deliver synthetic chromatin effectors.
ContributorsTekel, Stefan (Author) / Haynes, Karmella (Thesis advisor) / Mills, Jeremy (Committee member) / Caplan, Michael (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2019
Description
The Western Continental United States has a rapidly changing and complex ecosystem that provides valuable resources to a large portion of the nation. Changes in social and environmental factors have been observed to be significantly correlated to usable ground and surface water levels. The assessment of water level changes and their influences on a semi-national level is needed to support planning and decision making for water resource management at local levels. Although many studies have been done in Ground and Surface Water (GSW) trend analysis, very few have attempted determine correlations with other factors. The number of studies done on correlation factors at a semi-national scale and near decadal temporal scale is even fewer. In this study, freshwater resources in GSW changes from 2004 to 2017 were quantified and used to determine if and how environmental and social variables are related to GSW changes using publicly available remotely sensed and census data. Results indicate that mean annual changes of GSW of the study period are significantly correlated with LULC changes related to deforestation, urbanization, environmental trends, as well as social variables. Further analysis indicates a strong correlation in the rate of change of GSW to LULC changes related to deforestation, environmental trends, as well as social variables. GSW slope trend analysis also reveals a negative trend in California, New Mexico, Arizona, and Nevada. Whereas a positive GSW trend is evident in the northeast part of the study area. GSW trends were found to be somewhat consistent in the states of Utah, Idaho, and Colorado, implying that there was no GSW changes over time in these states.
ContributorsReynolds, Ryan (Author) / Myint, Soe (Thesis advisor) / Werth, Susanna (Committee member) / Brazel, Anthony (Committee member) / Arizona State University (Publisher)
Created2018
Description
Soil moisture (θ) is a fundamental variable controlling the exchange of water and energy at the land surface. As a result, the characterization of the statistical properties of θ across multiple scales is essential for many applications including flood prediction, drought monitoring, and weather forecasting. Empirical evidences have demonstrated the existence of emergent relationships and scale invariance properties in θ fields collected from the ground and airborne sensors during intensive field campaigns, mostly in natural landscapes. This dissertation advances the characterization of these relations and statistical properties of θ by (1) analyzing the role of irrigation, and (2) investigating how these properties change in time and across different landscape conditions through θ outputs of a distributed hydrologic model. First, θ observations from two field campaigns in Australia are used to explore how the presence of irrigated fields modifies the spatial distribution of θ and the associated scale invariance properties. Results reveal that the impact of irrigation is larger in drier regions or conditions, where irrigation creates a drastic contrast with the surrounding areas. Second, a physically-based distributed hydrologic model is applied in a regional basin in northern Mexico to generate hyperresolution θ fields, which are useful to conduct analyses in regions and times where θ has not been monitored. For this aim, strategies are proposed to address data, model validation, and computational challenges associated with hyperresolution hydrologic simulations. Third, analyses are carried out to investigate whether the hyperresolution simulated θ fields reproduce the statistical and scaling properties observed from the ground or remote sensors. Results confirm that (i) the relations between spatial mean and standard deviation of θ derived from the model outputs are very similar to those observed in other areas, and (ii) simulated θ fields exhibit the scale invariance properties that are consistent with those analyzed from aircraft-derived estimates. The simulated θ fields are then used to explore the influence of physical controls on the statistical properties, finding that soil properties significantly affect spatial variability and multifractality. The knowledge acquired through this dissertation provides insights on θ statistical properties in regions and landscape conditions that were never investigated before; supports the refinement of the calibration of multifractal downscaling models; and contributes to the improvement of hyperresolution hydrologic modeling.
ContributorsKo, Ara (Author) / Mascaro, Giuseppe (Thesis advisor) / Vivoni, Enrique R. (Thesis advisor) / Myint, Soe (Committee member) / Wang, Zhihua (Committee member) / Muenich, Rebecca (Committee member) / Arizona State University (Publisher)
Created2018
Description
Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, or amyotrophic lateral sclerosis are defined by the loss of several types of neurons and glial cells within the central nervous system (CNS). Combatting these diseases requires a robust population of relevant cell types that can be employed in cell therapies, drug screening, or patient specific disease modeling. Human induced pluripotent stem cells (hiPSC)-derived neural progenitor cells (hNPCs) have the ability to self-renew indefinitely and differentiate into the various neuronal and glial cell types of the CNS. In order to realize the potential of hNPCs, it is necessary to develop a xeno-free scalable platform for effective expansion and differentiation. Previous work in the Brafman lab led to the engineering of a chemically defined substrate—vitronectin derived peptide (VDP), which allows for the long-term expansion and differentiation of hNPCs. In this work, we use this substrate as the basis for a microcarrier (MC)-based suspension culture system. Several independently derived hNPC lines were cultured on MCs for multiple passages as well as efficiently differentiated to neurons. Finally, this MC-based system was used in conjunction with a low shear rotating wall vessel (RWV) bioreactor for the integrated, large-scale expansion and neuronal differentiation of hNPCs. Finally, VDP was shown to support the differentiation of hNPCs into functional astrocytes. Overall, this fully defined and scalable biomanufacturing system will facilitate the generation of hNPCs and their derivatives in quantities necessary for basic and translational applications.
ContributorsMorgan, Daylin (Author) / Brafman, David (Thesis advisor) / Stabenfeldt, Sarah (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2018
Description
Calcium imaging is a well-established, non-invasive or minimally technique designed to study the electrical signaling neurons. Calcium regulates the release of gliotransmitters in astrocytes. Analyzing astrocytic calcium transients can provide significant insights into mechanisms such as neuroplasticity and neural signal modulation.
In the past decade, numerous methods have been developed to analyze in-vivo calcium imaging data that involves complex techniques such as overlapping signals segregation and motion artifact correction. The hypothesis used to detect calcium signal is the spatiotemporal sparsity of calcium signal, and these methods are unable to identify the passive cells that are not actively firing during the time frame in the video. Statistics regarding the percentage of cells in each frame of view can be critical for the analysis of calcium imaging data for human induced pluripotent stem cells derived neurons and astrocytes.
The objective of this research is to develop a simple and efficient semi-automated pipeline for analysis of in-vitro calcium imaging data. The region of interest (ROI) based image segmentation is used to extract the data regarding intensity fluctuation caused by calcium concentration changes in each cell. It is achieved by using two approaches: basic image segmentation approach and a machine learning approach. The intensity data is evaluated using a custom-made MATLAB that generates statistical information and graphical representation of the number of spiking cells in each field of view, the number of spikes per cell and spike height.
In the past decade, numerous methods have been developed to analyze in-vivo calcium imaging data that involves complex techniques such as overlapping signals segregation and motion artifact correction. The hypothesis used to detect calcium signal is the spatiotemporal sparsity of calcium signal, and these methods are unable to identify the passive cells that are not actively firing during the time frame in the video. Statistics regarding the percentage of cells in each frame of view can be critical for the analysis of calcium imaging data for human induced pluripotent stem cells derived neurons and astrocytes.
The objective of this research is to develop a simple and efficient semi-automated pipeline for analysis of in-vitro calcium imaging data. The region of interest (ROI) based image segmentation is used to extract the data regarding intensity fluctuation caused by calcium concentration changes in each cell. It is achieved by using two approaches: basic image segmentation approach and a machine learning approach. The intensity data is evaluated using a custom-made MATLAB that generates statistical information and graphical representation of the number of spiking cells in each field of view, the number of spikes per cell and spike height.
ContributorsBhandarkar, Siddhi Umesh (Author) / Brafman, David (Thesis advisor) / Stabenfeldt, Sarah (Committee member) / Tian, Xiaojun (Committee member) / Arizona State University (Publisher)
Created2019
Description
A global warming of two degrees Celsius is predicted to drive almost half the world's lizard populations to extinction. Currently, the Phoenix metropolitan region in Arizona, USA, is an average of 3 oC warmer than the surrounding desert. Using a bare lot as a control, I placed copper lizard models with data loggers in several vegetation and irrigation treatments that represent the dominant backyard landscaping styles in Phoenix (grassy mesic with mist irrigation, drip irrigated xeric, unirrigated native, and a hybrid style known as oasis). Lizard activity time in summer is currently restricted to a few hours in un-irrigated native desert landscaping, while heavily irrigated grass and shade trees allow for continual activity during even the hottest days. Maintaining the existing diversity of landscaping styles (as part of an ongoing mitigation strategy targeted at humans) will be beneficial for lizards.
Fourteen native lizard species inhabit the desert surrounding Phoenix, AZ, USA, but only two species persist within heavily developed areas. This pattern is best explained by a combination of socioeconomic status, land cover, and location. Lizard diversity is highest in affluent areas and lizard abundance is greatest near large patches of open desert. The percentage of building cover has a strong negative impact on both diversity and abundance. Despite Phoenix's intense urban heat island effect, which strongly constrains the potential activity and microhabitat use of lizards in summer, thermal patterns have not yet impacted their distribution and relative abundance at larger scales.
Fourteen native lizard species inhabit the desert surrounding Phoenix, AZ, USA, but only two species persist within heavily developed areas. This pattern is best explained by a combination of socioeconomic status, land cover, and location. Lizard diversity is highest in affluent areas and lizard abundance is greatest near large patches of open desert. The percentage of building cover has a strong negative impact on both diversity and abundance. Despite Phoenix's intense urban heat island effect, which strongly constrains the potential activity and microhabitat use of lizards in summer, thermal patterns have not yet impacted their distribution and relative abundance at larger scales.
ContributorsAckley, Jeffrey (Author) / Wu, Jianguo (Thesis advisor) / Sullivan, Brian (Thesis advisor) / Myint, Soe (Committee member) / DeNardo, Dale (Committee member) / Angilletta Jr., Michael (Committee member) / Arizona State University (Publisher)
Created2015
Description
This study uses the Weather Research and Forecasting (WRF) model to simulate and predict the changes in local climate attributed to the urbanization for five desert cities. The simulations are performed in the fashion of climate downscaling, constrained by the surface boundary conditions generated from high resolution land-use maps. For each city, the land-use maps of 1985 and 2010 from Landsat satellite observation, and a projected land-use map for 2030, are used to represent the past, present, and future. An additional set of simulations for Las Vegas, the largest of the five cities, uses the NLCD 1992 and 2006 land-use maps and an idealized historical land-use map with no urban coverage for 1900.
The study finds that urbanization in Las Vegas produces a classic urban heat island (UHI) at night but a minor cooling during the day. A further analysis of the surface energy balance shows that the decrease in surface Albedo and increase effective emissivity play an important role in shaping the local climate change over urban areas. The emerging urban structures slow down the diurnal wind circulation over the city due to an increased effective surface roughness. This leads to a secondary modification of temperature due to the interaction between the mechanical and thermodynamic effects of urbanization.
The simulations for the five desert cities for 1985 and 2010 further confirm a common pattern of the climatic effect of urbanization with significant nighttime warming and moderate daytime cooling. This effect is confined to the urban area and is not sensitive to the size of the city or the detail of land cover in the surrounding areas. The pattern of nighttime warming and daytime cooling remains robust in the simulations for the future climate of the five cities using the projected 2030 land-use maps. Inter-city differences among the five urban areas are discussed.
The study finds that urbanization in Las Vegas produces a classic urban heat island (UHI) at night but a minor cooling during the day. A further analysis of the surface energy balance shows that the decrease in surface Albedo and increase effective emissivity play an important role in shaping the local climate change over urban areas. The emerging urban structures slow down the diurnal wind circulation over the city due to an increased effective surface roughness. This leads to a secondary modification of temperature due to the interaction between the mechanical and thermodynamic effects of urbanization.
The simulations for the five desert cities for 1985 and 2010 further confirm a common pattern of the climatic effect of urbanization with significant nighttime warming and moderate daytime cooling. This effect is confined to the urban area and is not sensitive to the size of the city or the detail of land cover in the surrounding areas. The pattern of nighttime warming and daytime cooling remains robust in the simulations for the future climate of the five cities using the projected 2030 land-use maps. Inter-city differences among the five urban areas are discussed.
ContributorsKamal, Samy (Author) / Huang, Huei-Ping (Thesis advisor) / Anderson, James (Thesis advisor) / Herrmann, Marcus (Committee member) / Calhoun, Ronald (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2015
Description
Several debilitating neurological disorders, such as Alzheimer's disease, stroke, and spinal cord injury, are characterized by the damage or loss of neuronal cell types in the central nervous system (CNS). Human neural progenitor cells (hNPCs) derived from human pluripotent stem cells (hPSCs) can proliferate extensively and differentiate into the various neuronal subtypes and supporting cells that comprise the CNS. As such, hNPCs have tremendous potential for disease modeling, drug screening, and regenerative medicine applications. However, the use hNPCs for the study and treatment of neurological diseases requires the development of defined, robust, and scalable methods for their expansion and neuronal differentiation. To that end a rational design process was used to develop a vitronectin-derived peptide (VDP)-based substrate to support the growth and neuronal differentiation of hNPCs in conventional two-dimensional (2-D) culture and large-scale microcarrier (MC)-based suspension culture. Compared to hNPCs cultured on ECMP-based substrates, hNPCs grown on VDP-coated surfaces displayed similar morphologies, growth rates, and high expression levels of hNPC multipotency markers. Furthermore, VDP surfaces supported the directed differentiation of hNPCs to neurons at similar levels to cells differentiated on ECMP substrates. Here it has been demonstrated that VDP is a robust growth and differentiation matrix, as demonstrated by its ability to support the expansions and neuronal differentiation of hNPCs derived from three hESC (H9, HUES9, and HSF4) and one hiPSC (RiPSC) cell lines. Finally, it has been shown that VDP allows for the expansion or neuronal differentiation of hNPCs to quantities (>1010) necessary for drug screening or regenerative medicine purposes. In the future, the use of VDP as a defined culture substrate will significantly advance the clinical application of hNPCs and their derivatives as it will enable the large-scale expansion and neuronal differentiation of hNPCs in quantities necessary for disease modeling, drug screening, and regenerative medicine applications.
ContributorsVarun, Divya (Author) / Brafman, David (Thesis advisor) / Nikkhah, Mehdi (Committee member) / Stabenfeldt, Sarah (Committee member) / Arizona State University (Publisher)
Created2016