Imaging live cell in micro-liquid enclosure by X-ray laser diffraction

Kimura, Takashi; Joti, Yasumasa; Shibuya, Akemi; Song, Changyong; Kim, Sang Soo; Tono, Kensuke; Yabashi, Makina; Tamakoshi, Masatada; Moriya, Toshiyuki; Oshima, Tairo; Ishikawa, Tetsuya; Bessho, Yoshitaka; Nishino, Yoshinori

doi:10.1038/ncomms4052

Cited by 192 publications

(134 citation statements)

References 43 publications

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“…Typically, SFC data will contain extraneous photons scattered from upstream optics, solvent and/or carrier gases [33]. This presents two important consequences to SFC.…”

Section: Extraneous Photonsmentioning

confidence: 99%

A minimal view of single-particle imaging with X-ray lasers

Loh

2014

Phil. Trans. R. Soc. B

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One contribution of 27 to a Discussion Meeting Issue 'Biology with free-electron X-ray lasers'. Subject Areas: computational biology, biophysicsKeywords: X-ray free-electron laser, coherent diffraction, single particle imaging, bioimaging The ability to serially interrogate single biomolecules with femtosecond X-ray pulses from free-electron lasers has ushered in the possibility of determining the three-dimensional structure of biomolecules without crystallization. However, the complexity of imaging a sample's structure from very many of its noisy and incomplete diffraction data can be daunting. In this review, we introduce a simple analogue of this imaging workflow, use it to describe a structure reconstruction algorithm based on the expectation maximization principle, and consider the effects of extraneous noise. Such a minimal model can aid experiment and algorithm design in future studies.

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“…Typically, SFC data will contain extraneous photons scattered from upstream optics, solvent and/or carrier gases [33]. This presents two important consequences to SFC.…”

Section: Extraneous Photonsmentioning

confidence: 99%

A minimal view of single-particle imaging with X-ray lasers

Loh

2014

Phil. Trans. R. Soc. B

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“…This will certainly be the case for fast timeresolved studies of excited states. The potential for imaging larger objects using coherent FEL experiments becomes obvious in the imaging of living cells inside micro-liquid enclosures (Kimura et al, 2014) and by the combination of CDI at a SR source and a FEL for the determination of the structure of macromolecular nanostructures (Gallagher-Jones et al, 2014). All the crystallographic experiments described above used the ultra-short FEL pulses only to minimize radiation damage.…”

Section: Free-electron Lasersmentioning

confidence: 99%

The potential of future light sources to explore the structure and function of matter

Weckert¹

2014

Acta Cryst Sect A

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Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Lowemittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.

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“…XFELs can significantly relax the resolution barrier imposed by radiation damage by recording the diffraction pattern before specimen destruction, due to femtosecond-short pulse duration (Neutze et al, 2000;Chapman et al, 2011;Hirata et al, 2014;Suga et al, 2014). XFEL experimental data are becoming increasingly available and several low-resolution structures from single-particle approaches have been reported Gallagher-Jones et al, 2014;Kimura et al, 2014;Xu et al, 2014;Ekeberg et al, 2015;Takayama et al, 2015;. It has also been shown, theoretically, that high-resolution 3D structures could be obtained using millions of diffraction patterns (Loh & Elser, 2009;Tegze & Bortel, 2012;Tokuhisa et al, 2012;Hosseinizadeh et al, 2014) and that dynamics could be directly extracted from two-dimensional (2D) data (Tokuhisa et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

Nakano

Miyashita

Jonić

et al. 2017

J Synchrotron Radiat

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The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

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Imaging live cell in micro-liquid enclosure by X-ray laser diffraction

Cited by 192 publications

References 43 publications

A minimal view of single-particle imaging with X-ray lasers

A minimal view of single-particle imaging with X-ray lasers

The potential of future light sources to explore the structure and function of matter

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

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