ASU Regents' Professors Open Access Works
The title “Regents’ Professor” is the highest faculty honor awarded at Arizona State University. It is conferred on ASU faculty who have made pioneering contributions in their areas of expertise, who have achieved a sustained level of distinction, and who enjoy national and international recognition for these accomplishments. This collection contains primarily open access works by ASU Regents' Professors.
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- Creators: Weierstall, Uwe
- Creators: School of Geographical Sciences and Urban Planning
Description
The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
ContributorsAbdallah, Bahige (Author) / Zatsepin, Nadia (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Conrad, Chelsie (Author) / Dorner, Katerina (Author) / Sierra, Raymond G. (Author) / Stevenson, Hilary P. (Author) / Camacho Alanis, Fernanda (Author) / Grant, Thomas D. (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Calero, Guillermo (Author) / Wachter, Rebekka (Author) / Spence, John (Author) / Weierstall, Uwe (Author) / Fromme, Petra (Author) / Ros, Alexandra (Author) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-08-19
Description
Precipitation and temperature enact variable influences on vegetation, impacting the type and condition of land cover, as well as the assessment of change over broad landscapes. Separating the influence of vegetative variability independent and discrete land cover change remains a major challenge to landscape change assessments. The heterogeneous Lerma-Chapala-Santiago watershed of central Mexico exemplifies both natural and anthropogenic forces enacting variability and change on the landscape. This study employed a time series of Enhanced Vegetation Index (EVI) composites from the Moderate Resolution Imaging Spectoradiometer (MODIS) for 2001–2007 and per-pixel multiple linear regressions in order to model changes in EVI as a function of precipitation, temperature, and elevation. Over the seven-year period, 59.1% of the variability in EVI was explained by variability in the independent variables, with highest model performance among changing and heterogeneous land cover types, while intact forest cover demonstrated the greatest resistance to changes in temperature and precipitation. Model results were compared to an independent change uncertainty assessment, and selected regional samples of change confusion and natural variability give insight to common problems afflicting land change analyses.
ContributorsChristman, Zachary (Author) / Rogan, John (Author) / Eastman, J. Ronald (Author) / Turner II, B. L. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor)
Created2016-06-07
Description
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
ContributorsLee, Ho-Hsien (Author) / Cherni, Irene (Author) / Yu, HongQi (Author) / Fromme, Raimund (Author) / Doran, Jeffrey (Author) / Grotjohann, Ingo (Author) / Mittman, Michele (Author) / Basu, Shibom (Author) / Deb, Arpan (Author) / Dorner, Katerina (Author) / Aquila, Andrew (Author) / Barty, Anton (Author) / Boutet, Sebastien (Author) / Chapman, Henry N. (Author) / Doak, R. Bruce (Author) / Hunter, Mark (Author) / James, Daniel (Author) / Kirian, Richard (Author) / Kupitz, Christopher (Author) / Lawrence, Robert (Author) / Liu, Haiguang (Author) / Nass, Karol (Author) / Schlichting, Ilme (Author) / Schmidt, Kevin (Author) / Seibert, M. Marvin (Author) / Shoeman, Robert L. (Author) / Spence, John (Author) / Stellato, Francesco (Author) / Weierstall, Uwe (Author) / Williams, Garth J. (Author) / Yoon, Chun Hong (Author) / Wang, Dingjie (Author) / Zatsepin, Nadia (Author) / Hogue, Brenda (Author) / Matoba, Nobuyuki (Author) / Fromme, Petra (Author) / Mor, Tsafrir (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Biodesign Institute (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Department of Physics (Contributor)
Created2014-08-20
Description
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A[subscript 2A] adenosine receptor (A[subscript 2A]AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A[subscript 2A]AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A[subscript 2A]AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
ContributorsMartin Garcia, Jose Manuel (Author) / Conrad, Chelsie (Author) / Nelson, Garrett (Author) / Stander, Natasha (Author) / Zatsepin, Nadia (Author) / Zook, James (Author) / Zhu, Lan (Author) / Geiger, James (Author) / Chun, Eugene (Author) / Kissick, David (Author) / Hilgart, Mark C. (Author) / Ogata, Craig (Author) / Ishchenko, Andrii (Author) / Nagaratnam, Nirupa (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Subramanian, Ganesh (Author) / Schaffer, Alexander (Author) / James, Daniel (Author) / Ketwala, Gihan (Author) / Venugopalan, Nagarajan (Author) / Xu, Shenglan (Author) / Corcoran, Stephen (Author) / Ferguson, Dale (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Cherezov, Vadim (Author) / Fromme, Petra (Author) / Fischetti, Robert F. (Author) / Liu, Wei (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2017-05-24
Description
Fire is one of the earliest and most common tools used by humans to modify the earth surface. Landscapes in the Yucatán Peninsula are composed of a mosaic of old growth subtropical forest, secondary vegetation, grasslands, and agricultural land that represent a well-documented example of anthropogenic intervention, much of which involves the use of fire. This research characterizes land use systems and land cover changes in the Yucatán during the 2000–2010 time period. We used an active fire remotely sensed data time series from the Moderate Resolution Imaging Spectroradiometer (MODIS), in combination with forest loss, and anthrome map sources to (1) establish the association between fire and land use change in the region; and (2) explore links between the spatial and temporal patterns of fire and specific types of land use practices, including within- and between-anthromes variability. A spatial multinomial logit model was constructed using fire, landscape configuration, and a set of commonly used control variables to estimate forest persistence, non-forest persistence, and change. Cross-tabulations and descriptive statistics were used to explore the relationships between fire occurrence, location, and timing with respect to the geography of land use. We also compared fire frequencies within and between anthrome groups using a negative binomial model and Tukey pairwise comparisons. Results show that fire data broadly reproduce the geography and timing of anthropogenic land change. Findings indicate that fire and landscape configuration is useful in explaining forest change and non-forest persistence, especially in fragmented (mosaicked) landscapes. Absence of fire occurrence is related usefully to the persistence of spatially continuous core areas of older growth forest. Fire has a positive relationship with forest to non-forest change and a negative relationship with forest persistence. Fire is also a good indicator to distinguish between anthrome groups (e.g., croplands and villages). Our study suggests that active fire data series are a reasonable proxy for anthropogenic land persistence/change in the context of the Yucatán and are useful to differentiate quantitatively and qualitatively between and within anthromes.
ContributorsMillones, Marco (Author) / Rogan, John (Author) / Turner II, B. L. (Author) / Parmentier, Benoit (Author) / Clary Harris, Robert (Author) / Griffith, Daniel A. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2017-09-12
Description
A species’ response to climate change depends on the interaction of biotic and abiotic factors that define future habitat suitability and species’ ability to migrate or adapt. The interactive effects of processes such as fire, dispersal, and predation have not been thoroughly addressed in the climate change literature. Our objective was to examine how life history traits, short-term global change perturbations, and long-term climate change interact to affect the likely persistence of an oak species - Quercus engelmannii (Engelmann oak). Specifically, we combined dynamic species distribution models, which predict suitable habitat, with stochastic, stage-based metapopulation models, which project population trajectories, to evaluate the effects of three global change factors – climate change, land use change, and altered fire frequency – emphasizing the roles of dispersal and seed predation. Our model predicted dramatic reduction in Q. engelmannii abundance, especially under drier climates and increased fire frequency. When masting lowers seed predation rates, decreased masting frequency leads to large abundance decreases. Current rates of dispersal are not likely to prevent these effects, although increased dispersal could mitigate population declines. The results suggest that habitat suitability predictions by themselves may under-estimate the impact of climate change for other species and locations.
ContributorsConlisk, Erin (Author) / Lawson, Dawn (Author) / Syphard, Alexandra D. (Author) / Franklin, Janet (Author) / Flint, Lorraine (Author) / Flint, Alan (Author) / Regan, Helen M. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor)
Created2012-05-18
Description
Urban economic modeling and effective spatial planning are critical tools towards achieving urban sustainability. However, in practice, many technical obstacles, such as information islands, poor documentation of data and lack of software platforms to facilitate virtual collaboration, are challenging the effectiveness of decision-making processes. In this paper, we report on our efforts to design and develop a geospatial cyberinfrastructure (GCI) for urban economic analysis and simulation. This GCI provides an operational graphic user interface, built upon a service-oriented architecture to allow (1) widespread sharing and seamless integration of distributed geospatial data; (2) an effective way to address the uncertainty and positional errors encountered in fusing data from diverse sources; (3) the decomposition of complex planning questions into atomic spatial analysis tasks and the generation of a web service chain to tackle such complex problems; and (4) capturing and representing provenance of geospatial data to trace its flow in the modeling task. The Greater Los Angeles Region serves as the test bed. We expect this work to contribute to effective spatial policy analysis and decision-making through the adoption of advanced GCI and to broaden the application coverage of GCI to include urban economic simulations.
ContributorsLi, Wenwen (Author) / Li, Linna (Author) / Goodchild, Michael F. (Author) / Anselin, Luc (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Computational Spatial Science (Contributor)
Created2013-05-21
Description
Evolving Earth observation and change detection techniques enable the automatic identification of Land Use and Land Cover Change (LULCC) over a large extent from massive amounts of remote sensing data. It at the same time poses a major challenge in effective organization, representation and modeling of such information. This study proposes and implements an integrated computational framework to support the modeling, semantic and spatial reasoning of change information with regard to space, time and topology. We first proposed a conceptual model to formally represent the spatiotemporal variation of change data, which is essential knowledge to support various environmental and social studies, such as deforestation and urbanization studies. Then, a spatial ontology was created to encode these semantic spatiotemporal data in a machine-understandable format. Based on the knowledge defined in the ontology and related reasoning rules, a semantic platform was developed to support the semantic query and change trajectory reasoning of areas with LULCC. This semantic platform is innovative, as it integrates semantic and spatial reasoning into a coherent computational and operational software framework to support automated semantic analysis of time series data that can go beyond LULC datasets. In addition, this system scales well as the amount of data increases, validated by a number of experimental results. This work contributes significantly to both the geospatial Semantic Web and GIScience communities in terms of the establishment of the (web-based) semantic platform for collaborative question answering and decision-making.
ContributorsVadjunec, Jacqueline M. (Author) / Radel, Claudia (Author) / Turner II, B. L. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2016-10-25
Description
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.
ContributorsLi, Xuanxuan (Author) / Chiu, Chun-Ya (Author) / Wang, Hsiang-Ju (Author) / Kassemeyer, Stephan (Author) / Botha, Sabine (Author) / Shoeman, Robert L. (Author) / Lawrence, Robert (Author) / Kupitz, Christopher (Author) / Kirian, Richard (Author) / James, Daniel (Author) / Wang, Dingjie (Author) / Nelson, Garrett (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Hartman, Elisabeth (Author) / Jafarpour, Aliakbar (Author) / Foucar, Lutz M. (Author) / Barty, Anton (Author) / Chapman, Henry (Author) / Liang, Mengning (Author) / Menzel, Andreas (Author) / Wang, Fenglin (Author) / Basu, Shibom (Author) / Fromme, Raimund (Author) / Doak, R. Bruce (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Huang, Michael H. (Author) / Spence, John (Author) / Schlichting, Ilme (Author) / Hogue, Brenda (Author) / Liu, Haiguang (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / School of Life Sciences (Contributor)
Created2017-04-11
Description
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.
ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16