Matching Items (118)
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Description
This work advances structural and biophysical studies of three proteins important in disease. First protein of interest is the Francisella tularensis outer membrane protein A (FopA), which is a virulence determinant of tularemia. This work describes recombinant expression in Escherichia coli and successful purification of membrane translocated FopA. The purified

This work advances structural and biophysical studies of three proteins important in disease. First protein of interest is the Francisella tularensis outer membrane protein A (FopA), which is a virulence determinant of tularemia. This work describes recombinant expression in Escherichia coli and successful purification of membrane translocated FopA. The purified protein was dimeric as shown by native polyacrylamide gel electrophoresis and small angle X-ray scattering (SAXS) analysis, with an abundance of β-strands based on circular dichroism spectroscopy. SAXS data supports the presence of a pore. Furthermore, protein crystals of membrane translocated FopA were obtained with preliminary X-ray diffraction data. The identified crystallization condition provides the means towards FopA structure determination; a valuable tool for structure-based design of anti-tularemia therapeutics.

Next, the nonstructural protein μNS of avian reoviruses was investigated using in vivo crystallization and serial femtosecond X-ray crystallography. Avian reoviruses infect poultry flocks causing significant economic losses. μNS is crucial in viral factory formation facilitating viral replication within host cells. Thus, structure-based targeting of μNS has the potential to disrupt intracellular viral propagation. Towards this goal, crystals of EGFP-tagged μNS (EGFP-μNS (448-605)) were produced in insect cells. The crystals diffracted to 4.5 Å at X-ray free electron lasers using viscous jets as crystal delivery methods and initial electron density maps were obtained. The resolution reported here is the highest described to date for μNS, which lays the foundation towards its structure determination.

Finally, structural, and functional studies of human Threonine aspartase 1 (Taspase1) were performed. Taspase1 is overexpressed in many liquid and solid malignancies. In the present study, using strategic circular permutations and X-ray crystallography, structure of catalytically active Taspase1 was resolved. The structure reveals the conformation of a 50 residues long fragment preceding the active side residue (Thr234), which has not been structurally characterized previously. This fragment adopted a straight helical conformation in contrast to previous predictions. Functional studies revealed that the long helix is essential for proteolytic activity in addition to the active site nucleophilic residue (Thr234) mediated proteolysis. Together, these findings enable a new approach for designing anti-cancer drugs by targeting the long helical fragment.
ContributorsNagaratnam, Nirupa (Author) / Fromme, Petra (Thesis advisor) / Johnston, Stephen (Thesis advisor) / Van Horn, Wade (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2020
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Description
Disasters represent disruptions to stability and offer lessons about how climate adaptation is negotiated and acted on. Viewing adaptation as a negotiation helps understand recovery not just as actions taken to minimize harm, but a reflection of values and motivations surrounding adaptation. This research elicits these perspectives and considers them

Disasters represent disruptions to stability and offer lessons about how climate adaptation is negotiated and acted on. Viewing adaptation as a negotiation helps understand recovery not just as actions taken to minimize harm, but a reflection of values and motivations surrounding adaptation. This research elicits these perspectives and considers them as part of an ongoing agreement for disaster recovery and adaptation in Puerto Rico. Previous research has characterized recovery as an opportunity for rethinking societal arrangements for climate adaptation and highlights the importance of how adaptation is conceptualized across actors. This study builds on past research by using distinct perspectives to understand recovery as an adaptation process and a co-production of a new ‘social contract’ after Hurricane Maria. Community interviews and government documents are analyzed to understand who is involved, where change is happening, and what resources are necessary for success. The purpose of this is to consider distinct framings of recovery and adaptation, and what these contribute to long-term change. Community interviews give a perspective of local stability and show capacities for immediate and long-term recovery. Similarly, government documents discuss managing foundational vulnerabilities like infrastructure, while navigating recovery given geographical and economic obstacles. Findings show that self-organization and harnessing social capital are crucial components of recovery in the Corcovada community after Maria. They rely on bonding and bridging social capital to mobilize resources and reduce vulnerabilities for future threats. This transformative approach was also present in official recovery documents, though political and economic change were stressed as necessary for stability, along with modernizing infrastructure. While recovery documents suggest connecting physical and social resilience, community residents have cultivated this connection long before Maria. Unlike in Corcovada, the government of Puerto Rico is only starting to view disruptions as windows of opportunity and therefore mention plans for transformation but don’t present actions taken. Further, the reality of vulnerable infrastructural, political and economic systems greatly affects recovery both in Corcovada and across the island. Both perspectives will likely affect actions taken in Puerto Rico and recognizing these unique framings of stability can help design transformative, adaptive social contracts for facing future threats.
ContributorsOrtiz, Jessica (Author) / Manuel-Navarrete, David (Thesis advisor) / Klinsky, Sonja (Thesis advisor) / Muñoz-Erickson, Tischa (Committee member) / Brundiers, Katja (Committee member) / Arizona State University (Publisher)
Created2019
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Description

The objective of articulating sustainability visions through modeling is to enhance the outcomes and process of visioning in order to successfully move the system toward a desired state. Models emphasize approaches to develop visions that are viable and resilient and are crafted to adhere to sustainability principles. This approach is

The objective of articulating sustainability visions through modeling is to enhance the outcomes and process of visioning in order to successfully move the system toward a desired state. Models emphasize approaches to develop visions that are viable and resilient and are crafted to adhere to sustainability principles. This approach is largely assembled from visioning processes (resulting in descriptions of desirable future states generated from stakeholder values and preferences) and participatory modeling processes (resulting in systems-based representations of future states co-produced by experts and stakeholders). Vision modeling is distinct from normative scenarios and backcasting processes in that the structure and function of the future desirable state is explicitly articulated as a systems model. Crafting, representing and evaluating the future desirable state as a systems model in participatory settings is intended to support compliance with sustainability visioning quality criteria (visionary, sustainable, systemic, coherent, plausible, tangible, relevant, nuanced, motivational and shared) in order to develop rigorous and operationalizable visions. We provide two empirical examples to demonstrate the incorporation of vision modeling in research practice and education settings. In both settings, vision modeling was used to develop, represent, simulate and evaluate future desirable states. This allowed participants to better identify, explore and scrutinize sustainability solutions.

ContributorsIwaniec, David (Author) / Childers, Dan (Author) / VanLehn, Kurt (Author) / Wiek, Arnim (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor)
Created2014-07-01
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It has become common for sustainability science and resilience theory to be considered as complementary approaches. Occasionally the terms have been used interchangeably. Although these two approaches share some working principles and objectives, they also are based on some distinct assumptions about the operation of systems and how we can

It has become common for sustainability science and resilience theory to be considered as complementary approaches. Occasionally the terms have been used interchangeably. Although these two approaches share some working principles and objectives, they also are based on some distinct assumptions about the operation of systems and how we can best guide these systems into the future. Each approach would benefit from some scholars keeping sustainability science and resilience theory separate and focusing on further developing their distinctiveness and other scholars continuing to explore them in combination. Three areas of research in which following different procedures might be beneficial are whether to prioritize outcomes or system dynamics, how best to take advantage of community input, and increasing the use of knowledge of the past as a laboratory for potential innovations.

Created2013-11-30
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Description

The context in which many self-governed commons systems operate will likely be significantly altered as globalization processes play out over the next few decades. Such dramatic changes will induce some systems to fail and subsequently to be transformed, rather than merely adapt. Despite this possibility, research on globalization-induced transformations of

The context in which many self-governed commons systems operate will likely be significantly altered as globalization processes play out over the next few decades. Such dramatic changes will induce some systems to fail and subsequently to be transformed, rather than merely adapt. Despite this possibility, research on globalization-induced transformations of social-ecological systems (SESs) is still underdeveloped. We seek to help fill this gap by exploring some patterns of transformation in SESs and the question of what factors help explain the persistence of cooperation in the use of common-pool resources through transformative change. Through the analysis of 89 forest commons in South Korea that experienced such transformations, we found that there are two broad types of transformation, cooperative and noncooperative. We also found that two system-level properties, transaction costs associated group size and network diversity, may affect the direction of transformation. SESs with smaller group sizes and higher network diversity may better organize cooperative transformations when the existing system becomes untenable.

ContributorsYu, David (Author) / Anderies, John (Author) / Lee, Dowon (Author) / Perez, Irene (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor)
Created2013-11-30
Description

The effects of urbanization on ozone levels have been widely investigated over cities primarily located in temperate and/or humid regions. In this study, nested WRF-Chem simulations with a finest grid resolution of 1 km are conducted to investigate ozone concentrations O3 due to urbanization within cities in arid/semi-arid environments. First,

The effects of urbanization on ozone levels have been widely investigated over cities primarily located in temperate and/or humid regions. In this study, nested WRF-Chem simulations with a finest grid resolution of 1 km are conducted to investigate ozone concentrations O3 due to urbanization within cities in arid/semi-arid environments. First, a method based on a shape preserving Monotonic Cubic Interpolation (MCI) is developed and used to downscale anthropogenic emissions from the 4 km resolution 2005 National Emissions Inventory (NEI05) to the finest model resolution of 1 km. Using the rapidly expanding Phoenix metropolitan region as the area of focus, we demonstrate the proposed MCI method achieves ozone simulation results with appreciably improved correspondence to observations relative to the default interpolation method of the WRF-Chem system. Next, two additional sets of experiments are conducted, with the recommended MCI approach, to examine impacts of urbanization on ozone production: (1) the urban land cover is included (i.e., urbanization experiments) and, (2) the urban land cover is replaced with the region's native shrubland. Impacts due to the presence of the built environment on O3 are highly heterogeneous across the metropolitan area. Increased near surface O3 due to urbanization of 10–20 ppb is predominantly a nighttime phenomenon while simulated impacts during daytime are negligible. Urbanization narrows the daily O3 range (by virtue of increasing nighttime minima), an impact largely due to the region's urban heat island. Our results demonstrate the importance of the MCI method for accurate representation of the diurnal profile of ozone, and highlight its utility for high-resolution air quality simulations for urban areas.

ContributorsLi, Jialun (Author) / Georgescu, Matei (Author) / Hyde, Peter (Author) / Mahalov, Alex (Author) / Moustaoui, Mohamed (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor)
Created2014-11-01
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Description

There are growing demands for detailed and accurate land cover maps in land system research and planning. Macro-scale land cover maps normally cannot satisfy the studies that require detailed land cover maps at micro scales. In the meantime, applying conventional pixel-based classification methods in classifying high-resolution aerial imagery is ineffective

There are growing demands for detailed and accurate land cover maps in land system research and planning. Macro-scale land cover maps normally cannot satisfy the studies that require detailed land cover maps at micro scales. In the meantime, applying conventional pixel-based classification methods in classifying high-resolution aerial imagery is ineffective to develop high accuracy land-cover maps, especially in spectrally heterogeneous and complicated urban areas. Here we present an object-based approach that identifies land-cover types from 1-meter resolution aerial orthophotography and a 5-foot DEM. Our study area is Tippecanoe County in the State of Indiana, USA, which covers about a 1300 km[superscript 2] land area. We used a countywide aerial photo mosaic and normalized digital elevation model as input datasets in this study. We utilized simple algorithms to minimize computation time while maintaining relatively high accuracy in land cover mapping at a county scale. The aerial photograph was pre-processed using principal component transformation to reduce its spectral dimensionality. Vegetation and non-vegetation were separated via masks determined by the Normalized Difference Vegetation Index. A combination of segmentation algorithms with lower calculation intensity was used to generate image objects that fulfill the characteristics selection requirements. A hierarchical image object network was formed based on the segmentation results and used to assist the image object delineation at different spatial scales. Finally, expert knowledge regarding spectral, contextual, and geometrical aspects was employed in image object identification. The resultant land cover map developed with this object-based image analysis has more information classes and higher accuracy than that derived with pixel-based classification methods.

Created2014-11-01
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Description

As part of an international collaboration to compare large-scale commons, we used the Social-Ecological Systems Meta-Analysis Database (SESMAD) to systematically map out attributes of and changes in the Great Barrier Reef Marine Park (GBRMP) in Australia. We focus on eight design principles from common-pool resource (CPR) theory and other key

As part of an international collaboration to compare large-scale commons, we used the Social-Ecological Systems Meta-Analysis Database (SESMAD) to systematically map out attributes of and changes in the Great Barrier Reef Marine Park (GBRMP) in Australia. We focus on eight design principles from common-pool resource (CPR) theory and other key social-ecological systems governance variables, and explore to what extent they help explain the social and ecological outcomes of park management through time. Our analysis showed that commercial fisheries management and the re-zoning of the GBRMP in 2004 led to improvements in ecological condition of the reef, particularly fisheries. These boundary and rights changes were supported by effective monitoring, sanctioning and conflict resolution. Moderate biophysical connectivity was also important for improved outcomes. However, our analysis also highlighted that continued challenges to improved ecological health in terms of coral cover and biodiversity can be explained by fuzzy boundaries between land and sea, and the significance of external drivers to even large-scale social-ecological systems (SES). While ecological and institutional fit in the marine SES was high, this was not the case when considering the coastal SES. Nested governance arrangements become even more important at this larger scale. To our knowledge, our paper provides the first analysis linking the re-zoning of the GBRMP to CPR and SES theory. We discuss important challenges to coding large-scale systems for meta-analysis.

Created2013-11-30
Description

Background: Cancer diagnosis in both dogs and humans is complicated by the lack of a non-invasive diagnostic test. To meet this clinical need, we apply the recently developed immunosignature assay to spontaneous canine lymphoma as clinical proof-of-concept. Here we evaluate the immunosignature as a diagnostic for spontaneous canine lymphoma at both

Background: Cancer diagnosis in both dogs and humans is complicated by the lack of a non-invasive diagnostic test. To meet this clinical need, we apply the recently developed immunosignature assay to spontaneous canine lymphoma as clinical proof-of-concept. Here we evaluate the immunosignature as a diagnostic for spontaneous canine lymphoma at both at initial diagnosis and evaluating the disease free interval following treatment.

Methods: Sera from dogs with confirmed lymphoma (B cell n = 38, T cell n = 11) and clinically normal dogs (n = 39) were analyzed. Serum antibody responses were characterized by analyzing the binding pattern, or immunosignature, of serum antibodies on a non-natural sequence peptide microarray. Peptides were selected and tested for the ability to distinguish healthy dogs from those with lymphoma and to distinguish lymphoma subtypes based on immunophenotype. The immunosignature of dogs with lymphoma were evaluated for individual signatures. Changes in the immunosignatures were evaluated following treatment and eventual relapse.

Results: Despite being a clonal disease, both an individual immunosignature and a generalized lymphoma immunosignature were observed in each dog. The general lymphoma immunosignature identified in the initial set of dogs (n = 32) was able to predict disease status in an independent set of dogs (n = 42, 97% accuracy). A separate immunosignature was able to distinguish the lymphoma based on immunophenotype (n = 25, 88% accuracy). The individual immunosignature was capable of confirming remission three months following diagnosis. Immunosignature at diagnosis was able to predict which dogs with B cell lymphoma would relapse in less than 120 days (n = 33, 97% accuracy).

Conclusion: We conclude that the immunosignature can serve as a multilevel diagnostic for canine, and potentially human, lymphoma.

ContributorsJohnston, Stephen (Author) / Thamm, Douglas H. (Author) / Legutki, Joseph Barten (Author) / Biodesign Institute (Contributor)
Created2014-09-08
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Description

Three studies examined the symbolic and self-presentational meaning of low-water-use residential landscaping in a desert city in the southwestern United States. We hypothesized that owners' water-intensive or water-conserving landscape choices would be seen to convey very different characteristics. Data indicated that these two types of residential landscapes led to substantially

Three studies examined the symbolic and self-presentational meaning of low-water-use residential landscaping in a desert city in the southwestern United States. We hypothesized that owners' water-intensive or water-conserving landscape choices would be seen to convey very different characteristics. Data indicated that these two types of residential landscapes led to substantially different attributions about homeowners and also that potential homeowners could use landscapes to convey an array of characteristics to a social audience. In general, water-intensive landscapes led to more positive attributions than did water-conserving landscapes. The results support the idea that landscaping choice may be guided by self-presentational considerations, and that such considerations might influence the adoption of high- or low-water-use landscapes.

ContributorsNeel, Rebecca (Author) / Sadalla, Edward (Author) / Berlin, Anna (Author) / Ledlow, Susan (Author) / Neufeld, Samantha (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor)
Created2014-12-01