Matching Items (47)
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Description

Course-based undergraduate research experiences (CUREs) meet national recommendations for integrating research experiences into life science curricula. As such, CUREs have grown in popularity and many research studies have focused on student outcomes from CUREs. Institutional change literature highlights that understanding faculty is also key to new pedagogies succeeding. To begin

Course-based undergraduate research experiences (CUREs) meet national recommendations for integrating research experiences into life science curricula. As such, CUREs have grown in popularity and many research studies have focused on student outcomes from CUREs. Institutional change literature highlights that understanding faculty is also key to new pedagogies succeeding. To begin to understand faculty perspectives on CUREs, we conducted semi-structured interviews with 61 faculty who teach CUREs regarding why they teach CUREs, what the outcomes are, and how they would discuss a CURE with a colleague. Using grounded theory, participant responses were coded and categorized as tangible or intangible, related to both student and faculty-centered themes. We found that intangible themes were prevalent, and that there were significant differences in the emphasis on tangible themes for faculty who have developed their own independent CUREs when compared with faculty who implement pre-developed, national CUREs. We focus our results on the similarities and differences among the perspectives of faculty who teach these two different CURE types and explore trends among all participants. The results of this work highlight the need for considering a multi-dimensional framework to understand, promote, and successfully implement CUREs.

ContributorsShortlidge, Erin (Author) / Bangera, Gita (Author) / Brownell, Sara (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-05-26
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Description

We recommend using backward design to develop course-based undergraduate research experiences (CUREs). The defining hallmark of CUREs is that students in a formal lab course explore research questions with unknown answers that are broadly relevant outside the course. Because CUREs lead to novel research findings, they represent a unique course

We recommend using backward design to develop course-based undergraduate research experiences (CUREs). The defining hallmark of CUREs is that students in a formal lab course explore research questions with unknown answers that are broadly relevant outside the course. Because CUREs lead to novel research findings, they represent a unique course design challenge, as the dual nature of these courses requires course designers to consider two distinct, but complementary, sets of goals for the CURE: 1) scientific discovery milestones (i.e., research goals) and 2) student learning in cognitive, psychomotor, and affective domains (i.e., pedagogical goals). As more undergraduate laboratory courses are re-imagined as CUREs, how do we thoughtfully design these courses to effectively meet both sets of goals? In this Perspectives article, we explore this question and outline recommendations for using backward design in CURE development.

ContributorsCooper, Katelyn (Author) / Soneral, Paula A. G. (Author) / Brownell, Sara (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-05-26
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Description
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
ContributorsReddy, Hemanth K. N. (Author) / Yoon, Chun Hong (Author) / Aquila, Andrew (Author) / Awel, Salah (Author) / Ayyer, Kartik (Author) / Barty, Anton (Author) / Berntsen, Peter (Author) / Bielecki, Johan (Author) / Bobkov, Sergey (Author) / Bucher, Maximilian (Author) / Carini, Gabriella A. (Author) / Carron, Sebastian (Author) / Chapman, Henry (Author) / Daurer, Benedikt (Author) / DeMirci, Hasan (Author) / Ekeberg, Tomas (Author) / Fromme, Petra (Author) / Hajdu, Janos (Author) / Hanke, Max Felix (Author) / Hart, Philip (Author) / Hogue, Brenda (Author) / Hasseinizadeh, Ahmad (Author) / Kim, Yoonhee (Author) / Kirian, Richard (Author) / Kurta, Ruslan P. (Author) / Larsson, Daniel S. D. (Author) / Loh, N. Duane (Author) / Maia, Filipe R. N. C. (Author) / Mancuso, Adrian P. (Author) / Muhlig, Kerstin (Author) / Munke, Anna (Author) / Nam, Daewoong (Author) / Nettelblad, Carl (Author) / Ourmazd, Abbas (Author) / Rose, Max (Author) / Schwander, Peter (Author) / Seibert, Marvin (Author) / Sellberg, Jonas A. (Author) / Song, Changyong (Author) / Spence, John (Author) / Svenda, Martin (Author) / van der Schot, Gijs (Author) / Vartanyants, Ivan A. (Author) / Williams, Garth J. (Author) / Xavier, P. Lourdu (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) / School of Life Sciences (Contributor) / Department of Physics (Contributor)
Created2017-06-27
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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
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Description
Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A[subscript 2A] adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
ContributorsBatyuk, Alexander (Author) / Galli, Lorenzo (Author) / Ishchenko, Andrii (Author) / Han, Gye Won (Author) / Gati, Cornelius (Author) / Popov, Petr A. (Author) / Lee, Ming-Yue (Author) / Stauch, Benjamin (Author) / White, Thomas A. (Author) / Barty, Anton (Author) / Aquila, Andrew (Author) / Hunter, Mark S. (Author) / Liang, Mengning (Author) / Boutet, Sebastien (Author) / Pu, Mengchen (Author) / Liu, Zhi-jie (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Li, Chufeng (Author) / Zhao, Yun (Author) / Spence, John (Author) / Liu, Wei (Author) / Fromme, Petra (Author) / Katritch, Vsevolod (Author) / Weierstall, Uwe (Author) / Stevens, Raymond C. (Author) / Cherezov, Vadim (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-09-23
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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
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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
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Description
X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
ContributorsFrank, Matthias (Author) / Carlson, David B. (Author) / Hunter, Mark S. (Author) / Williams, Garth J. (Author) / Messerschmidt, Marc (Author) / Zatsepin, Nadia (Author) / Barty, Anton (Author) / Benner, W. Henry (Author) / Chu, Kaiqin (Author) / Graf, Alexander T. (Author) / Hau-Riege, Stefan P. (Author) / Kirian, Richard A. (Author) / Padeste, Celestino (Author) / Pardini, Tommaso (Author) / Pedrini, Bill (Author) / Segelke, Brent (Author) / Seibert, M. Marvin (Author) / Spence, John (Author) / Tsai, Ching-Ju (Author) / Lane, Stephen M. (Author) / Li, Xiao-Dan (Author) / Schertler, Gebhard (Author) / Boutet, Sebastien (Author) / Coleman, Matthew (Author) / Evans, James E. (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-02-28
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Description

Summer bridge programs are designed to help transition students into the college learning environment. Increasingly, bridge programs are being developed in science, technology, engineering, and mathematics (STEM) disciplines because of the rigorous content and lower student persistence in college STEM compared with other disciplines. However, to our knowledge, a comprehensive

Summer bridge programs are designed to help transition students into the college learning environment. Increasingly, bridge programs are being developed in science, technology, engineering, and mathematics (STEM) disciplines because of the rigorous content and lower student persistence in college STEM compared with other disciplines. However, to our knowledge, a comprehensive review of STEM summer bridge programs does not exist. To provide a resource for bridge program developers, we conducted a systematic review of the literature on STEM summer bridge programs. We identified 46 published reports on 30 unique STEM bridge programs that have been published over the past 25 years. In this review, we report the goals of each bridge program and whether the program was successful in meeting these goals. We identify 14 distinct bridge program goals that can be organized into three categories: academic success goals, psychosocial goals, and department-level goals. Building on the findings of published bridge reports, we present a set of recommendations for STEM bridge programs in hopes of developing better bridges into college.

ContributorsAshley, Michael (Author) / Cooper, Katelyn (Author) / Cala, Jacqueline (Author) / Brownell, Sara (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-12-01
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Description

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

ContributorsCasadei, Cecilia M. (Author) / Tsai, Ching-Ju (Author) / Barty, Anton (Author) / Hunter, Mark S. (Author) / Zatsepin, Nadia (Author) / Padeste, Celestino (Author) / Capitani, Guido (Author) / Benner, W. Henry (Author) / Boutet, Sebastien (Author) / Hau-Riege, Stefan P. (Author) / Kupitz, Christopher (Author) / Messerschmidt, Marc (Author) / Ogren, John I. (Author) / Pardini, Tom (Author) / Rothschild, Kenneth J. (Author) / Sala, Leonardo (Author) / Segelke, Brent (Author) / Williams, Garth J. (Author) / Evans, James E. (Author) / Li, Xiao-Dan (Author) / Coleman, Matthew (Author) / Pedrini, Bill (Author) / Frank, Matthias (Author) / College of Liberal Arts and Sciences (Contributor)
Created2018-01