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.

Displaying 1 - 10 of 11
Filtering by

Clear all filters

130284-Thumbnail Image.png
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

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
130335-Thumbnail Image.png
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

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
130320-Thumbnail Image.png
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

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
130313-Thumbnail Image.png
Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the

Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
130308-Thumbnail Image.png
Description
Serial femtosecond crystallography (SFX) has opened a new era in crystallo­graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption.

Serial femtosecond crystallography (SFX) has opened a new era in crystallo­graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.
ContributorsConrad, Chelsie (Author) / Basu, Shibom (Author) / James, Daniel (Author) / Wang, Dingjie (Author) / Schaffer, Alexander (Author) / Roy Chowdhury, Shatabdi (Author) / Zatsepin, Nadia (Author) / Aquila, Andrew (Author) / Coe, Jesse (Author) / Gati, Cornelius (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Kupitz, Christopher (Author) / Nelson, Garrett (Author) / Subramanian, Ganesh (Author) / White, Thomas A. (Author) / Zhao, Yun (Author) / Zook, James (Author) / Boutet, Sebastien (Author) / Cherezov, Vadim (Author) / Spence, John (Author) / Fromme, Raimund (Author) / Weierstall, Uwe (Author) / Fromme, Petra (Author) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor)
Created2015-06-30
130306-Thumbnail Image.png
Description
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.
ContributorsFromme, Raimund (Author) / Ishchenko, Andrii (Author) / Metz, Markus (Author) / Roy Chowdhury, Shatabdi (Author) / Basu, Shibom (Author) / Boutet, Sebastien (Author) / Fromme, Petra (Author) / White, Thomas A. (Author) / Barty, Anton (Author) / Spence, John (Author) / Weierstall, Uwe (Author) / Liu, Wei (Author) / Cherezov, Vadim (Author) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2015-08-04
130302-Thumbnail Image.png
Description
Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic

Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.
ContributorsKupitz, Christopher (Author) / Olmos, Jose L. (Author) / Holl, Mark (Author) / Tremblay, Lee (Author) / Pande, Kanupriya (Author) / Pandey, Suraj (Author) / Oberthur, Dominik (Author) / Hunter, Mark (Author) / Liang, Mengning (Author) / Aquila, Andrew (Author) / Tenboer, Jason (Author) / Calvey, George (Author) / Katz, Andrea (Author) / Chen, Yujie (Author) / Wiedorn, Max O. (Author) / Knoska, Juraj (Author) / Meents, Alke (Author) / Majriani, Valerio (Author) / Norwood, Tyler (Author) / Poudyal, Ishwor (Author) / Grant, Thomas (Author) / Miller, Mitchell D. (Author) / Xu, Weijun (Author) / Tolstikova, Aleksandra (Author) / Morgan, Andrew (Author) / Metz, Markus (Author) / Martin Garcia, Jose Manuel (Author) / Zook, James (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Nagaratnam, Nirupa (Author) / Meza-Aguilar, Domingo (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Frank, Matthias (Author) / White, Thomas (Author) / Barty, Anton (Author) / Bajt, Sasa (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Zatsepin, Nadia (Author) / Nelson, Garrett (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Schwander, Peter (Author) / Pollack, Lois (Author) / Fromme, Petra (Author) / Ourmazd, Abbas (Author) / Phillips, George N. (Author) / Schmidt, Marius (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor)
Created2016-12-15
130396-Thumbnail Image.png
Description

Aim
To establish a chronology for late Quaternary avian extinction, extirpation and persistence in the Bahamas, thereby testing the relative roles of climate change and human impact as causes of extinction.
Location
Great Abaco Island (Abaco), Bahamas, West Indies.
Methods
We analysed the resident bird community as sampled by Pleistocene (> 11.7 ka) and Holocene

Aim
To establish a chronology for late Quaternary avian extinction, extirpation and persistence in the Bahamas, thereby testing the relative roles of climate change and human impact as causes of extinction.
Location
Great Abaco Island (Abaco), Bahamas, West Indies.
Methods
We analysed the resident bird community as sampled by Pleistocene (> 11.7 ka) and Holocene (< 11.7 ka) fossils. Each species was classified as extinct (lost globally), extirpated (gone from Abaco but persists elsewhere), or extant (still resident on Abaco). We compared patterns of extinction, extirpation and persistence to independent estimates of climate and sea level for glacial (late Pleistocene) and interglacial (Holocene) times.
Results
Of 45 bird species identified in Pleistocene fossils, 25 (56%) no longer occur on Abaco (21 extirpated, 4 extinct). Of 37 species recorded in Holocene deposits, 15 (14 extirpated, 1 extinct; total 41%) no longer exist on Abaco. Of the 30 extant species, 12 were recovered as both Pleistocene and Holocene fossils, as were 9 of the 30 extirpated or extinct species. Most of the extinct or extirpated species that were only recorded from Pleistocene contexts are characteristic of open habitats (pine woodlands or grasslands); several of the extirpated species are currently found only where winters are cooler than in the modern or Pleistocene Bahamas. In contrast, most of the extinct or extirpated species recorded from Holocene contexts are habitat generalists.
Main conclusions
The fossil evidence suggests two main times of late Quaternary avian extirpation and extinction in the Bahamas. The first was during the Pleistocene–Holocene transition (PHT; 15–9 ka) and was fuelled by climate change and associated changes in sea level and island area. The second took place during the late Holocene (< 4 ka, perhaps primarily < 1 ka) and can be attributed to human impact. Although some species lost during the PHT are currently found where climates are cooler and drier than in the Bahamas today, a taxonomically and ecologically diverse set of species persisted through that major climate change but did not survive the past millennium of human presence.

Created2015-03-01
130391-Thumbnail Image.png
Description
Estimating and projecting population trends using population viability analysis (PVA) are central to identifying species at risk of extinction and for informing conservation management strategies. Models for PVA generally fall within two categories, scalar (count-based) or matrix (demographic). Model structure, process error, measurement error, and time series length all have

Estimating and projecting population trends using population viability analysis (PVA) are central to identifying species at risk of extinction and for informing conservation management strategies. Models for PVA generally fall within two categories, scalar (count-based) or matrix (demographic). Model structure, process error, measurement error, and time series length all have known impacts in population risk assessments, but their combined impact has not been thoroughly investigated. We tested the ability of scalar and matrix PVA models to predict percent decline over a ten-year interval, selected to coincide with the IUCN Red List criterion A. 3, using data simulated for a hypothetical, short-lived organism with a simple life-history and for a threatened snail, Tasmaphena lamproides. PVA performance was assessed across different time series lengths, population growth rates, and levels of process and measurement error. We found that the magnitude of effects of measurement error, process error, and time series length, and interactions between these, depended on context. We found that high process and measurement error reduced the reliability of both models in predicted percent decline. Both sources of error contributed strongly to biased predictions, with process error tending to contribute to the spread of predictions more than measurement error. Increasing time series length improved precision and reduced bias of predicted population trends, but gains substantially diminished for time series lengths greater than 10-15 years. The simple parameterization scheme we employed contributed strongly to bias in matrix model predictions when both process and measurement error were high, causing scalar models to exhibit similar or greater precision and lower bias than matrix models. Our study provides evidence that, for short-lived species with structured but simple life histories, short time series and simple models can be sufficient for reasonably reliable conservation decision-making, and may be preferable for population projections when unbiased estimates of vital rates cannot be obtained.
Created2015-07-15
130421-Thumbnail Image.png
Description
Tree and shrub abundance has increased in many grasslands causing changes in ecosystem carbon and nitrogen pools that are related to patterns of woody plant distribution. However, with regard to spatial patterns of shrub proliferation, little is known about how they are influenced by grazing or the extent to which

Tree and shrub abundance has increased in many grasslands causing changes in ecosystem carbon and nitrogen pools that are related to patterns of woody plant distribution. However, with regard to spatial patterns of shrub proliferation, little is known about how they are influenced by grazing or the extent to which they are influenced by intraspecific interactions. We addressed these questions by quantifying changes in the spatial distribution of Prosopis velutina (mesquite) shrubs over 74 years on grazed and protected grasslands. Livestock are effective agents of mesquite dispersal and mesquite plants have lateral roots extending well beyond the canopy. We therefore hypothesized that mesquite distributions would be random on grazed areas mainly due to cattle dispersion and clustered on protected areas due to decreased dispersal and interspecific interference with grasses; and that clustered or random distributions at early stages of encroachment would give way to regular distributions as stands matured and density-dependent interactions intensified. Assessments in 1932, 1948, and 2006 supported the first hypothesis, but we found no support for the second. In fact, clustering intensified with time on the protected area and the pattern remained random on the grazed site. Although shrub density increased on both areas between 1932 and 2006, we saw no progression toward a regular distribution indicative of density-dependent interactions. We propose that processes related to seed dispersal, grass–shrub seedling interactions, and hydrological constraints on shrub size interact to determine vegetation structure in grassland-to-shrubland state changes with implications for ecosystem function and management.
Created2014-09-01