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Open data set of live cyanobacterial cells imaged using an X-ray laser
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed) Published
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Text
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 3, article id 160058
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-300201DOI: 10.1038/sdata.2016.58ISI: 000390225400003OAI: oai:DiVA.org:uu-300201DiVA, id: diva2:951087
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Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
In thesis
1. Imaging Living Cells with an X-ray Laser
Open this publication in new window or tab >>Imaging Living Cells with an X-ray Laser
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Imaging living cells at a resolution higher than the resolution of optical microscopy is a significant challenge. Fluorescence microscopy can achieve a degree of super-resolution via labeling cellular components with a fluorescent dye. Reaching nanometer or sub-nanometer resolution requires high-energy radiation with significantly shorter wavelength than that of optical light. X-rays and electrons have the requisite wavelengths and could be suitable for such studies; however, these probes also cause significant radiation damage. A dose in excess of 100,000,000 Gray (Gy, J/kg) would be required to reach nanometer resolution on a cell, and no cell can survive this amount of radiation. As a consequence, much of what we know about cells at high resolution today comes from dead material.

Theory predicts that an ultra-short and extremely bright coherent X-ray pulse from an X-ray free-electron laser can outrun key damage processes to deliver a molecular-level snapshot of a cell that is alive at the time of image formation. The principle of ‘diffraction before destruction’ exploits the difference between the speed of light (the X-ray pulse) and the much slower speed of damage formation. The femtosecond pulse ‘freezes’ motion in the cell at physiological temperatures on the time scale of atomic vibrations, offering unprecedented time resolution and a plethora of new experimental possibilities.

This thesis describes the first test experiments on imaging living cells with an X-ray laser. I present results in three essential areas of live cell imaging. (i) We have used an aerosol injector to introduce live cyanobacteria into the X-ray focus, and recorded diffraction patterns with extremely low background at very high hit rates. (ii) We demonstrated scattered signal beyond 4 nm resolution in some of these experiments. (iii) The thesis also describes image reconstruction, using a new fully automated pipeline that I developed during my studies. The reconstruction of diffraction patterns was successful for all patterns that did not have saturated pixels. The new software suite, called RedFlamingo, selects exposures with desired properties, can sort them according to sample size, shape, orientation, exposure, the number and type of objects in the beam during the exposure, their distance from each other, and so forth. The software includes validation tools to assess the quality of the reconstructions.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 79
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1625
Keyword
Coherent diffractive X-ray imaging, flash X-ray imaging, lensless imaging, single particle imaging, cyanobacteria, phasing, image classification, substrate-free sample delivery, X-ray free-electron laser, XFEL, FEL, CDXI, CDI, CXI, FXI
National Category
Biophysics Atom and Molecular Physics and Optics Cell Biology
Research subject
Chemistry with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-334219 (URN)978-91-513-0217-1 (ISBN)
Public defence
2018-03-12, B/A1:111a, BMC, Husargatan 3, Uppsala, 09:00 (English)
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Supervisors
Available from: 2018-02-19 Created: 2017-11-21 Last updated: 2018-03-07

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van der Schot, GijsSvenda, MartinMaia, Filipe R.N.C.Hantke, Max F.Seibert, M. MarvinAndreasson, JakobTimneanu, NicusorBielecki, JohanWestphal, DanielHasse, DirkCarlsson, Gunilla H.Larsson, Daniel S.D.Andersson, IngerHajdu, JanosEkeberg, Tomas

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van der Schot, GijsSvenda, MartinMaia, Filipe R.N.C.Hantke, Max F.Seibert, M. MarvinAndreasson, JakobTimneanu, NicusorBielecki, JohanWestphal, DanielHasse, DirkCarlsson, Gunilla H.Larsson, Daniel S.D.Andersson, IngerHajdu, JanosEkeberg, Tomas
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