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van der Schot G, Svenda M, Maia FRNC, Hantke MF, DePonte DP, Seibert MM, Aquila A, Schulz J, Kirian RA, Liang M, Stellato F, Bari S, Iwan B, Andreasson J, Timneanu N, Bielecki J, Westphal D, Nunes de Almeida F, Odić D, Hasse D, Carlsson GH, Larsson DSD, Barty A, Martin AV, Schorb S, Bostedt C, Bozek JD, Carron S, Ferguson K, Rolles D, Rudenko A, Epp SW, Foucar L, Rudek B, Erk B, Hartmann R, Kimmel N, Holl P, Englert L, Loh ND, Chapman HN, Andersson I, Hajdu J, Ekeberg T. Open data set of live cyanobacterial cells imaged using an X-ray laser. Sci Data 2016; 3:160058. [PMID: 27479514 PMCID: PMC4968219 DOI: 10.1038/sdata.2016.58] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/18/2016] [Indexed: 01/20/2023] Open
Abstract
Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
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Affiliation(s)
- Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Joachim Schulz
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Richard A Kirian
- Arizona State University, Physics Department, PO Box 871504, Tempe, Arizona 85287-1504, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sadia Bari
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 18221 Prague, Czech Republic
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, SE-751 20 Uppsala, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | | | - Duško Odić
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Center for Technology Transfer and Innovation, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Sebastian Schorb
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- Synchrotron SOLEIL, L'orme des Merisiers roundabout of St Aubin, 91190 Saint Aubin, France
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany.,Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Peter Holl
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 Munich, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany.,Ultrafast Coherent Dynamics Group, University Oldenburg, Carl-von-Ossietzky Strasse 9-11, 26129 Oldenburg, Germany
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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