scholarly journals Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amane Kobayashi ◽  
Yuki Takayama ◽  
Takeshi Hirakawa ◽  
Koji Okajima ◽  
Mao Oide ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Single Cells ◽  
Three Dimensional ◽  
Biological Functions ◽  
X Ray Diffraction ◽  
Characteristic Structure ◽  
X Ray ◽  
Diffraction Imaging ◽  
Diffraction Patterns

AbstractVisualization of intracellular structures and their spatial organization inside cells without any modification is essential to understand the mechanisms underlying the biological functions of cells. Here, we investigated the intracellular structure of cyanobacteria Prochlorococcus in the interphase by X-ray diffraction imaging using X-ray free-electron laser. A number of diffraction patterns from single cells smaller than 1 µm in size were collected with high signal-to-noise ratio with a resolution of up to 30 nm. From diffraction patterns, a set of electron density maps projected along the direction of the incident X-ray were retrieved with high reliability. The most characteristic structure found to be common among the cells was a C-shaped arrangement of 100-nm sized high-density spots, which surrounded a low-density area of 100 nm. Furthermore, a three-dimensional map reconstructed from the projection maps of individual cells was non-uniform, indicating the presence of common structures among cyanobacteria cells in the interphase. By referring to the fluorescent images for distributions of thylakoid membranes, nucleoids, and carboxysomes, we inferred and represented their spatial arrangements in the three-dimensional map. The arrangement allowed us to discuss the relevance of the intracellular organization to the biological functions of cyanobacteria.

scholarly journals Data processing software suiteSITENNOfor coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA

2014 ◽  
Vol 21 (3) ◽  
pp. 600-612 ◽  
Author(s):  
Yuki Sekiguchi ◽  
Tomotaka Oroguchi ◽  
Yuki Takayama ◽  
Masayoshi Nakasako
Keyword(s):  
Data Processing ◽  
Free Electron ◽  
Free Electron Laser ◽  
Single Shot ◽  
X Ray Diffraction ◽  
X Ray ◽  
Custom Made ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Ccd Detectors

Coherent X-ray diffraction imaging is a promising technique for visualizing the structures of non-crystalline particles with dimensions of micrometers to sub-micrometers. Recently, X-ray free-electron laser sources have enabled efficient experiments in the `diffraction before destruction' scheme. Diffraction experiments have been conducted at SPring-8 Angstrom Compact free-electron LAser (SACLA) using the custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors. In the experiments, ten thousands of single-shot diffraction patterns can be collected within several hours. Then, diffraction patterns with significant levels of intensity suitable for structural analysis must be found, direct-beam positions in diffraction patterns determined, diffraction patterns from the two CCD detectors merged, and phase-retrieval calculations for structural analyses performed. A software suite namedSITENNOhas been developed to semi-automatically apply the four-step processing to a huge number of diffraction data. Here, details of the algorithm used in the suite are described and the performance for approximately 9000 diffraction patterns collected from cuboid-shaped copper oxide particles reported. Using theSITENNOsuite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles.

scholarly journals Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA

2016 ◽  
Vol 23 (4) ◽  
pp. 975-989 ◽  
Author(s):  
Amane Kobayashi ◽  
Yuki Sekiguchi ◽  
Tomotaka Oroguchi ◽  
Koji Okajima ◽  
Asahi Fukuda ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
X Ray Diffraction ◽  
X Ray ◽  
Internal Structures ◽  
Thin Membranes ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Cellular Organelles

Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.

Incorporating particle symmetry into orientation determination in single-particle imaging

2018 ◽  
Vol 74 (5) ◽  
pp. 512-517
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Three Dimensional ◽  
Symmetric Case ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
Orientation Determination

In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.

scholarly journals 3P287 Approaches to cohherent X-ray diffraction imaging of single virus particle using X-ray free-electron laser(27. Bioimaging,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S259
Author(s):  
Akifumi Higashiura ◽  
Marina Murakami ◽  
Kenji Iwasaki ◽  
Eiki Yamashita ◽  
Kazuki Takeda ◽  
...  
Keyword(s):  
Virus Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging

scholarly journals Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy

2016 ◽  
Vol 72 (2) ◽  
pp. 179-189 ◽  
Author(s):  
Yuki Takayama ◽  
Koji Yonekura
Keyword(s):  
Light Microscopy ◽  
Biological Samples ◽  
Free Electron ◽  
Free Electron Laser ◽  
X Rays ◽  
X Ray Diffraction ◽  
Cell Organelles ◽  
X Ray ◽  
Electron And Light Microscopy ◽  
Diffraction Imaging

Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.

scholarly journals Coherent X-ray Diffraction Imaging of Non-Crystalline Particles using X-ray Free Electron Laser

2014 ◽  
Vol 56 (1) ◽  
pp. 27-35
Author(s):  
Masayoshi NAKASAKO ◽  
Tomotaka OROGUCHI ◽  
Yuki SEKIGUCHI ◽  
Amane KOBAYASHI ◽  
Saki HASHIMOTO ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging

Quantitative nanotomography of amorphous and polycrystalline samples using coherent X-ray diffraction

2019 ◽  
Vol 52 (3) ◽  
pp. 571-578 ◽  
Author(s):  
Y. Chushkin ◽  
F. Zontone ◽  
O. Cherkas ◽  
A. Gibaud
Keyword(s):  
Mass Density ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Better Than

This article presents a combined approach where quantitative forward-scattering coherent diffraction imaging (CDI) is supported by crystal diffraction using 8.1 keV synchrotron X-ray radiation. The method allows the determination of the morphology, mass density and crystallinity of an isolated microscopic specimen. This approach is tested on three homogeneous samples made of different materials with different degrees of crystallinity. The mass density and morphology are revealed using three-dimensional coherent diffraction imaging with a resolution better than 36 nm. The crystallinity is extracted from the diffraction profiles measured simultaneously with coherent diffraction patterns. The presented approach extends CDI to structural characterization of samples when crystallinity aspects are of interest.

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