1
|
Takayama Y, Nakasako M. Similarity score for screening phase-retrieved maps in X-ray diffraction imaging - characterization in reciprocal space. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:95-112. [PMID: 38054944 PMCID: PMC10833420 DOI: 10.1107/s1600577523009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.
Collapse
Affiliation(s)
- Yuki Takayama
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Synchrotron Radiation Research Center, Hyogo Science and Technology Association, 1-490-2 Kouto, Shingu, Tatsuno, Hyogo 679-5148, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Masayoshi Nakasako
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
2
|
Yoshida S, Harada K, Uezu S, Takayama Y, Nakasako M. Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:113-128. [PMID: 38054945 PMCID: PMC10833425 DOI: 10.1107/s1600577523009864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad. 24, 1024-1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses.
Collapse
Affiliation(s)
- Syouyo Yoshida
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - Kosei Harada
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - So Uezu
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - Yuki Takayama
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| |
Collapse
|
3
|
Uezu S, Yamamoto T, Oide M, Takayama Y, Okajima K, Kobayashi A, Yamamoto M, Nakasako M. Ultrastructure and fractal property of chromosomes in close-to-native yeast nuclei visualized using X-ray laser diffraction. Sci Rep 2023; 13:10802. [PMID: 37407674 DOI: 10.1038/s41598-023-37733-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Genome compaction and activity in the nucleus depend on spatiotemporal changes in the organization of chromatins in chromosomes. However, the direct imaging of the chromosome structures in the nuclei has been difficult and challenging. Herein, we directly visualized the structure of chromosomes in frozen-hydrated nuclei of budding yeast in the interphase using X-ray laser diffraction. The reconstructed projection electron density maps revealed inhomogeneous distributions of chromosomes, such as a 300 nm assembly and fibrous substructures in the elliptic-circular shaped nuclei of approximately 800 nm. In addition, from the diffraction patterns, we confirmed the absence of regular arrangements of chromosomes and chromatins with 400-20 nm spacing, and demonstrated that chromosomes were composed of self-similarly assembled substructural domains with an average radius of gyration of 58 nm and smooth surfaces. Based on these analyses, we constructed putative models to discuss the organization of 16 chromosomes, carrying DNA of 4.1 mm in 800 nm ellipsoid of the nucleus at the interphase. We anticipate the structural parameters on the fractal property of chromosomes and the experimental images to be a starting point for constructing more sophisticated 3D structural models of the nucleus.
Collapse
Grants
- XFEL key technology and the X-ray Free Electron Laser Priority Strategy Program the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp23120525 the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp25120725 the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp15H01647 the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp24113723 the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp26104535 the Ministry of Education, Culture, Sports, Science and Technology, Japan
- jp24654140 the Japan Society for the Promotion of Science
- jp1920402 the Japan Society for the Promotion of Science
- jp16H02218 the Japan Society for the Promotion of Science
Collapse
Affiliation(s)
- So Uezu
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
| | - Takahiro Yamamoto
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
- PRESTO, Japan Science and Technology Agency, Chiyoda-Ku, Tokyo, 102-0076, Japan
| | - Yuki Takayama
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-Cho, Ako-Gun, Hyogo, 678-1297, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan
- CRESTO, Japan Science and Technology Agency, Chiyoda-Ku, Tokyo, 102-0076, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
| | - Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN, Spring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayogun, Hyogo, 679-5148, Japan.
| |
Collapse
|
4
|
Kobayashi A, Takayama Y, Hirakawa T, Okajima K, Oide M, Oroguchi T, Inui Y, Yamamoto M, Matsunaga S, Nakasako M. Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser. Sci Rep 2021; 11:3877. [PMID: 33594220 PMCID: PMC7886902 DOI: 10.1038/s41598-021-83401-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/02/2021] [Indexed: 11/24/2022] Open
Abstract
Visualization 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.
Collapse
Affiliation(s)
- Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Takeshi Hirakawa
- Department of Applied Biological Science Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yayoi Inui
- Department of Applied Biological Science Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
| |
Collapse
|
5
|
Nakasako M, Kobayashi A, Takayama Y, Asakura K, Oide M, Okajima K, Oroguchi T, Yamamoto M. Methods and application of coherent X-ray diffraction imaging of noncrystalline particles. Biophys Rev 2020; 12:541-567. [PMID: 32180121 DOI: 10.1007/s12551-020-00690-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/05/2020] [Indexed: 11/26/2022] Open
Abstract
Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan.
Collapse
Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan.
| | - Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Kenta Asakura
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| |
Collapse
|