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Visualization on the distribution of nucreic acids in yeast nucleus by using coherent X-ray diffraction

Research Project

Project/Area Number 16H02218
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionKeio University

Principal Investigator

Nakasako Masayoshi  慶應義塾大学, 理工学部(矢上), 教授 (30227764)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥45,890,000 (Direct Cost: ¥35,300,000、Indirect Cost: ¥10,590,000)
Fiscal Year 2018: ¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2017: ¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000)
Fiscal Year 2016: ¥11,570,000 (Direct Cost: ¥8,900,000、Indirect Cost: ¥2,670,000)
KeywordsX線回折イメージング / 放射光 / X線自由電子レーザー / 低温X線回折実験 / 位相回復 / 三次元再構成 / 細胞核 / 細胞非侵襲イメージング / 低温X線回折イメージング / 非侵襲イメージング / 細胞核構造 / バクテリア構造 / X線トモグラフィー / 三次元構造 / 生物物理 / コヒーレントX線回折イメージング / 細胞イメージング / 低温X線回折 / 細胞周期 / 干渉性 / 凍結水和 / 低温構造解析 / シンクロトロン放射光 / コヒーレント回折イメージング / 非結晶生体粒子 / X線ナノイメージング
Outline of Final Research Achievements

In this project, we improved fundamental techniques including automatic control procedures of diffraction apparatuses, preparation of frozen-hydrated biological specimens, and measurement of spatial coherence of X-ray beam, in cryogenic X-ray diffraction imaging tomography using synchrotron X-rays and cryogenic X-ray diffraction using X-ray free electron laser pulses. In addition, we developed methods to obtain reliable electron density maps in phase retrieval calculation in structure analyses including the utilization of manifold learning. Based on these developments, we successfully established X-ray diffraction imaging technique for non-crystalline biological specimens, such as cells and organelles, through the visualization of common structures in yeast nucleus and cyanobacterium cell as well as the three-dimensional structures of yeast and bacteria cells without sectioning and chemical labeling necessary in other imaging techniques.

Academic Significance and Societal Importance of the Research Achievements

低温X線回折イメージング・トモグラフィー実験では、細胞個々の特性や細胞周期に応じた物質分布の変化を、一方、XFELを用いるX線回折イメージング実験では、大量の細胞試料の投影電子密度を得ることが可能となった。本課題の研究成果は、シンクロトロン放射光とX線自由電子レーザーを相補的利用によって、細胞の個性と多様性を見ることにつながり、他のイメージング手法では成しえない非侵襲的イメージングの大きな進展につながることが期待できる。今後、本手法が細胞イメージングの重要な柱の一つとなるだけでなく、非結晶金属ナノ材料試料の構造研究にも裾野を広げていくと期待できる。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (42 results)

All 2019 2018 2017 2016 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 2 results,  Acknowledgement Compliant: 3 results) Presentation (25 results) (of which Int'l Joint Research: 5 results,  Invited: 9 results) Book (3 results) Remarks (3 results)

  • [Journal Article] Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation2018

    • Author(s)
      Amane Kobayashi, Yuki Takayama, Koji Okajima, Mao Oide, Takahiro Yamamoto, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Yoshiki Kohmura, Masaki Yamamoto, Takahiko Hoshi, Yasufumi Torizuka
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 25 Issue: 6 Pages: 1803-1818

    • DOI

      10.1107/s1600577518012687

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser2018

    • Author(s)
      Tomotaka Oroguchi, Takashi Yoshidome, Takahiro Yamamoto, Masayoshi Nakasako
    • Journal Title

      Nano Letters

      Volume: 18 Issue: 8 Pages: 5192-5197

    • DOI

      10.1021/acs.nanolett.8b02153

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Classification of ab initio models of proteins restored from small-angle X-ray scattering2018

    • Author(s)
      Mao Oide, Yuki Sekiguchi, Asahi Fukuda, Koji Okajima, Tomotaka Oroguchi, Masayoshi Nakasako
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 25 Issue: 5 Pages: 1379-1388

    • DOI

      10.1107/s1600577518010342

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 生物細胞の低温X線回折イメージング2018

    • Author(s)
      中迫雅由,高山裕貴,小林周,山本隆寛,大出真央,岡島公司,苙口友隆,山本雅貴
    • Journal Title

      放射光

      Volume: 31 Pages: 189-201

    • NAID

      40021599633

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Shot-by-shot characterization of focused X-ray free electron laser pulses2018

    • Author(s)
      A. Kobayashi, Y. Sekiguchi, T. Oroguchi, M. Yamamoto and M. Nakasako
    • Journal Title

      Shot-by-shot characterization of focused X-ray free electron laser pulses

      Volume: 8 Issue: 1 Pages: 831-831

    • DOI

      10.1038/s41598-018-19179-3

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Blue-light excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis2018

    • Author(s)
      Oide, K. Okajima, H. Nakagami, T. Kato, Y. Sekiguchi, T. Oroguchi, T. Hikima, M. Yamamoto, and M. Nakasako
    • Journal Title

      Journal of Biological Chemistry

      Volume: 293 Pages: 963-972

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 生物細胞の低温X線回折イメージング2018

    • Author(s)
      中迫雅由,高山裕貴,小林周,関口優希,大出真央,山本隆寛,岡島公司,苙口友隆,山本雅貴
    • Journal Title

      放射光

      Volume: 31

    • NAID

      40021599633

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A protocol for searching most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting relationship between convergence of retrieved phase and success of calculation2017

    • Author(s)
      Y. Sekiguchi, S. Hashimoto, A. Kobayashi, T. Oroguchi and M. Nakasako
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 24 Issue: 5 Pages: 1024-1038

    • DOI

      10.1107/s1600577517008396

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging2017

    • Author(s)
      H. Kameda, S. Usugi, M. Kobayashi, N. Fukui, S. Lee, K. Hongo, T. Mizobata, Y. Sekiguchi, Y. Masaki, A. Kobayashi, T. Oroguchi, M. Nakasako, Y. Takayama, M. Yamamoto, and Y. Kawata
    • Journal Title

      Journal of Biochemistry (Tokyo)

      Volume: 161 Issue: 1 Pages: 55-65

    • DOI

      10.1093/jb/mvw052

    • NAID

      40021091513

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and organelles using X-ray free-electron laser at SACLA2016

    • Author(s)
      A. Kobayashi, Y. Sekiguchi, T. Oroguchi, K. Okajima, A. Fukuda, M. Oide, M. Yamamoto and M. Nakasako
    • Journal Title

      Journal of Synchrotron Radiation

      Volume: 23 Issue: 4 Pages: 975-989

    • DOI

      10.1107/s1600577516007736

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA2016

    • Author(s)
      A. Kobayashi, Y. Sekiguchi, Y. Takayama, T. Oroguchi, K. Shirahama, Y. Torizuka, M. Manoda, M. Nakasako* and M. Yamamoto
    • Journal Title

      Review of Scientific Instruments

      Volume: 87 Issue: 5 Pages: 053109-053109

    • DOI

      10.1063/1.4948317

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] XFEL回折イメージングの空間分解能向上に向けた金ピラーパターニング試料基盤の開発2019

    • Author(s)
      高山裕貴、小林周、大出真央、山本隆寛、溝口陽太、岡島公司、苙口友隆、山本雅貴、中迫雅由、米倉功治
    • Organizer
      第32回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 酵母核内核酸分布の多様性と普遍性:XFEL-低温X線回折イメージングによる構造解析2019

    • Author(s)
      山本隆寛、小林周、大出真央、岡島公司、溝口陽太、高山裕貴、苙口友隆、山本雅貴、中迫雅由
    • Organizer
      第32回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 低温X線回折イメージング・トモグラフィーによる酵母細胞の三次元構造解析2019

    • Author(s)
      朝倉健太、小林周、高山裕貴、大出真央、岡島公司、山本隆寛、溝口陽太、大野哲、苙口友隆、香村芳樹、山本雅貴、中迫雅由
    • Organizer
      第32回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 細胞の低温コヒーレントX線回折イメージングトモグラフィー実験における計測手法の高度化2019

    • Author(s)
      小林周、高山裕貴、山本隆寛、朝倉健太、大出真央、大野哲、溝口陽太、岡島公司、苙口友隆、香村芳樹、山本雅貴、中迫雅由
    • Organizer
      第32回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 量子ビームを用いる細胞の空間階層イメージング2018

    • Author(s)
      中迫雅由
    • Organizer
      平成30年度 東北大学多元物質科学研究所 附属先端計測開発センター講演会 第2回「計測とデータ科学の協奏」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Structural analyses of yeast nuclei in different cell phases by X-ray diffraction imaging at cryogenic temperature using XFEL2018

    • Author(s)
      T. Yamamoto, A. Kobayashi, M. Oide,K. Okajima, T. Oroguchi, M. Yamamtoto and M. Nakasako
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] X-ray diffraction imaging of biological cells2018

    • Author(s)
      M. Nakasako
    • Organizer
      Microbiology and Environment
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] XFEL低温コヒーレント回折イメージングによる 異なる細胞周期における酵母細胞核の構造解析2018

    • Author(s)
      山本隆寛、関口優希、小林周、大出真央、福田朝陽、岡島公司、苙口友隆 、山本雅貴、中迫雅由
    • Organizer
      第31回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] 低温コヒーレントX線回折イメージング・ トモグラフィー実験による細胞試料の三次元構造解析2018

    • Author(s)
      小林 周、高山裕貴、関口優希、大出真央、福田朝陽、山本隆寛、岡島公司、苙口友隆、香村芳樹、山本雅貴、中迫雅由
    • Organizer
      第31回日本放射光学会年会・放射光科学合同シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] 細胞のコヒーレントX線回折イメージング2017

    • Author(s)
      中迫雅由
    • Organizer
      バイオイメージング学会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 生体及び材料非結晶粒子のコヒーレントX線回折イメージング2017

    • Author(s)
      中迫雅由
    • Organizer
      第一回マテリアルズインフォマティクス基礎研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 3D structural analysis of yeast nucleus in different cell phases by coherent X-ray diffraction imaging using X-ray free electron laser2017

    • Author(s)
      T. Yamamoto, Y. Sekiguchi, A. Kobayashi, M. Oide, A. Fukuda, K. Okajima, T. Oroguchi, M. Yamamoto, M. Nakasako
    • Organizer
      第55回生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Three-dimensional structure of Cyanidioschyzon merolae by using coherent X-ray diffraction imaging tomography at cryogenic temperature2017

    • Author(s)
      A. Kobayashi, Y. Takayama, Y. Sekiguchi, M. Oide, A. Fukuda, T. Yamamoto, K. Okajima, T. Oroguchi, S. Matsunaga, Y. Kohmura, M. Yamamoto, M. Nakasako
    • Organizer
      第55回生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ありのままの細胞の姿を探るシン・顕微鏡2017

    • Author(s)
      中迫雅由
    • Organizer
      第30回日本放射光学会年会・放射光科学合同シンポジウム市民講座
    • Place of Presentation
      神戸芸術劇場(兵庫県神戸市)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生命科学におけるコヒーレントX線回折イメージングの展開2017

    • Author(s)
      中迫雅由
    • Organizer
      平成28年度第2回生物構造学研究会
    • Place of Presentation
      研究社英語センター(東京都新宿区神楽坂)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] XFEL コヒーレント回折イメージングによるシアノバクテリアの三次元構造解析2017

    • Author(s)
      小林周, 関口優希, 岡島公司, 苙口友隆, 中迫雅由, 乾弥生, 平川健, 松永幸大, 山本雅貴
    • Organizer
      第30回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      神戸芸術劇場(兵庫県神戸市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] XFEL コヒーレント回折イメージング実験におけるデータ解析の高度化と酵母細胞核の三次元構造解析への適用2017

    • Author(s)
      関口優希, 小林周, 岡島公司, 苙口友隆, 中迫雅由, 山本雅貴
    • Organizer
      第30回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      神戸芸術劇場(兵庫県神戸市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] XFELコヒーレント低温X線回折イメージングによる磁性細菌の構造解析2017

    • Author(s)
      山本隆寛,関口優希,小林周,岡島公司,苙口友隆,中迫雅由,山本雅貴,加藤貴之、難波啓一
    • Organizer
      第30回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      神戸芸術劇場(兵庫県神戸市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] ソフトウェア「閻魔」を用いた銅キューブのコヒーレントX線回折イメージングデータの分類2017

    • Author(s)
      吉留崇、関口優希、山本隆寛、苙口友隆、中迫雅由、池口満徳
    • Organizer
      第30回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      神戸芸術劇場(兵庫県神戸市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Cryogenic Coherent X-ray Diffraction Imaging of cells and cellular organelles at SACLA2016

    • Author(s)
      M. Nakasako
    • Organizer
      CLF-RCaH UK Bio-XFEL single particle imaging workshop
    • Place of Presentation
      STFC Rutherford Appleton Laboratory (Didcot, UK)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Diffraction apparatus TAKASAGO-6 for fast data collection in cryogenic coherent X-ray diffraction imaging at SACLA2016

    • Author(s)
      A. Kobayashi, M. Nakasako
    • Organizer
      CLF-RCaH UK Bio-XFEL single particle imaging workshop
    • Place of Presentation
      STFC Rutherford Appleton Laboratory (Didcot, UK)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cryogenic coherent diffraction imaging of biological samples with synchrotron and X-ray laser2016

    • Author(s)
      Y. Takayama, M. Yamamoto, K. Yonekura, Y. Sekiguchi, A. Kobayashi, K. Okajima, T. Oroguchi, M. Nakasako, Y. Inui, S. Matsunaga
    • Organizer
      13th International Conference on X-ray Microscopy (XRM2016)
    • Place of Presentation
      The Mathematical Institute, University of Oxford (Oxford, UK)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Reconstruction of three-dimensional structures of a protein with software ENMA and EMC algorithm: A simulation for XFEL-CXDI experiment2016

    • Author(s)
      T. Yoshidome, Y. Sekiguchi, T. Oroguchi, M. Nakasako, M. Ikeguchi
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくばコンファレンスセンター(茨城県つくば市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Three-dimensional structure of a cyanobacterium visualized by cryogenic coherent X-ray diffraction imaging using X-ray free-electron laser2016

    • Author(s)
      A. Kobayashi, Y. Sekiguchi, K. Okajima, T. Oroguchi, M. Nakasako, Y. Inui, T. Hirakawa, S. Matsunaga, M. Yamamoto
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくばコンファレンスセンター(茨城県つくば市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Automated data analyses for 3D structural reconstruction of yeast nuclei in coherent diffraction imaging using X-ray free-electron laser2016

    • Author(s)
      Y. Sekiguchi, A. Kobayashi, K. Okajima, T. Oroguchi, M. Nakasako, M. Yamamoto
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくばコンファレンスセンター(茨城県つくば市)
    • Related Report
      2016 Annual Research Report
  • [Book] X-ray diffraction imaging of biological cells2018

    • Author(s)
      M. Nakasako
    • Total Pages
      228
    • Publisher
      Springer
    • ISBN
      9784431566168
    • Related Report
      2018 Annual Research Report
  • [Book] X-ray diffraction imaging of biological cells (Springer Ser. Optic. Sciences Vol. 210)2018

    • Author(s)
      M. Nakasako
    • Total Pages
      228
    • Publisher
      Springer
    • ISBN
      9784431566168
    • Related Report
      2017 Annual Research Report
  • [Book] Coherent X-ray diffraction imaging of biological specimens2017

    • Author(s)
      M. Nakasako
    • Total Pages
      370
    • Publisher
      Springer
    • Related Report
      2016 Annual Research Report
  • [Remarks] 低温X線回折イメージング・トモグラフィー技術の確立-細胞丸ごと、内部構造を非侵襲的に可視化-

    • URL

      http://www.riken.jp/pr/press/2018/20181026_1/

    • Related Report
      2018 Annual Research Report
  • [Remarks] SACLAにより銅キューブ粒子の内部構造変化を可視化-金属ナノ粒子の成長機構の一端を解明-

    • URL

      http://www.riken.jp/pr/press/2018/20180731_2/

    • Related Report
      2018 Annual Research Report
  • [Remarks] X線自由電子レーザーによる非結晶試料からの高効率回折データ収集装置を実用化

    • URL

      https://www.keio.ac.jp/ja/press_release/2016/osa3qr000001ozih.html

    • Related Report
      2016 Annual Research Report

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Published: 2016-04-21   Modified: 2020-03-30  

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