Nanometer-resolution structural analysis of eukaryotic cells by coherent X-ray diffraction microscopy

• Project/Area Number: 25891033
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: Cell biology
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: TAKAYAMA Yuki 独立行政法人理化学研究所, 放射光科学総合研究センター, 基礎科学特別研究員 (40710132)
• Project Period (FY): 2013-08-30 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000); Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: X線回折イメージング / 凍結水和試料 / 細胞・オルガネラ / 構造解析 / X線自由電子レーザー

Outline of Final Research Achievements

Biological cells and organelles are essential for lives. An understanding of their physicochemical functions requires visualization of internal structures of whole cells and/or organelles as close to the native state as possible at high resolution. In this study, we conducted structural study of chloroplasts with a size of 1 micron by cryogenic coherent X-ray diffraction microscopy using X-ray free electron laser. Development of a sample preparation method and a measurement scheme allows efficient diffraction data collection, and we have succeeded in visualization of internal structures of chloroplasts at a resolution of 70 nm. We have also proposed a method to enhance weak diffraction signals from biological samples and to achieve robust phasing, and demonstrated that resolution can be improved by a factor of two or more from a set of calculation based on current experiments.

Research Products

• [Journal Article] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser. (2015)
  • Author(s): Takayama, Y., Inui, Y., Sekiguchi, Y., Kobayashi, A., Oroguchi, T., Yamamoto, M., Matsunaga, S., and Nakasako, M.
  • Journal Title: PLANT AND CELL PHYSIOLOGY Volume: 未定 Issue: 7 Pages: 1-15
  • DOI: 10.1093/pcp/pcv032
  • Peer Reviewed / Open Access
• [Journal Article] Signal-enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects (2015)
  • Author(s): Y. Takayama, S. Maki-Yonekura, T. Oroguchi, M. Nakasako and K. Yonekura
  • Journal Title: Sci. Rep. Volume: 5 Issue: 1 Pages: 8074-8074
  • DOI: 10.1038/srep08074
  • Peer Reviewed / Open Access
• [Journal Article] Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging (2014)
  • Author(s): 2.Kobayashi, A., Y. Sekiguchi, Y. Takayama, T. Oroguchi and M. Nakasako
  • Journal Title: Optics Express Volume: 22 Issue: 23 Pages: 27892-27909
  • DOI: 10.1364/oe.22.027892
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA (2014)
  • Author(s): 3.Sekiguchi, Y., M. Yamamoto, T. Oroguchi, Y. Takayama, S. Suzuki, and M. Nakasako
  • Journal Title: J. Synchrotron Radiation Volume: 21 Issue: 6 Pages: 1378-1383
  • DOI: 10.1107/s1600577514017111
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Single shot three-dimensional imaging of high-index-faceted nanocrystals with femtosecond X-ray free electron laser pulses (2014)
  • Author(s): R. Xu, H. Jiang, C. Song, Z. Huang, J. A. Rodriguez, C-C. Chen, D. Nam, J. Park, M. Gallagher-Jones, S. Kim, S. Kim, A. Suzuki, Y. Takayama, T. Oroguchi, Y. Takahashi, J. Fan, Y. Zou, T. Hatsui, Y. Inubushi, T. Kameshima, K. Yonekura et al.
  • Journal Title: Nat. Commun. Volume: 5 Issue: 1 Pages: 4061-4061
  • DOI: 10.1038/ncomms5061
  • Peer Reviewed / Open Access
• [Journal Article] Data processing software suite SITENNO for coherent X-ray diffraction imaging using X-ray free electron laser SACLA (2014)
  • Author(s): Y. Sekiguchi, T. Oroguchi, Y. Takayama and M. Nakasako
  • Journal Title: Journal of Synchrotron Radiatio Volume: 21 Issue: 3 Pages: 600-612
  • DOI: 10.1107/s1600577514003439
  • Peer Reviewed
• [Journal Article] Coherent X-ray Diffraction Imaging of Non-Crystalline Particles using X-ray Free Electron Laser (2014)
  • Author(s): 中迫雅由、苙口友隆、関口優希、小林周、橋本早紀、白濱圭也、山本雅貴、高山裕貴、米倉功治、眞木さおり、引間孝明、高橋幸生、鈴木明大、松永幸大、乾弥生、登野健介、亀島敬、城地保昌、犬伏雄一、星貴彦
  • Journal Title: Nihon Kessho Gakkaishi Volume: 56 Issue: 1 Pages: 27-35
  • DOI: 10.5940/jcrsj.56.27
  • NAID: 130003395580
  • ISSN: 0369-4585, 1884-5576
  • Peer Reviewed
• [Journal Article] KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging (2013)
  • Author(s): M. Nakasako, Y. Takayama, T. Oroguchi, Y. Sekiguchi, A. Kobayashi, K. Shirahama, M. Yamamoto*, T. Hikima, K. Yonekura, S. Maki-Yonekura, Y. Kohmura, Y. Inubushi, Y. Takahashi*, A. Suzuki, S. Matsunaga, Y. Inui, K. Tono, T. Kameshima, Y. Joti, and T. Hoshi
  • Journal Title: Review of Scientific Instruments Volume: 84 Issue: 12 Pages: 93705-16
  • DOI: 10.1021/nl403247x
  • Peer Reviewed
• [Presentation] X線自由電子レーザーを利用した低温コヒーレントX線回折イメージング法による葉緑体内部構造の可視化 (2015)
  • Author(s): 高山裕貴、乾弥生、関口優希、小林周、苙口友隆、山本雅貴、米倉功治、松永幸大、中迫雅由
  • Organizer: 分子システム研究 第4回春季研究会
  • Place of Presentation: 静岡県伊東市、ラフォーレ倶楽部伊東温泉湯の庭
  • Year and Date: 2015-05-15
• [Presentation] Cryogenic coherent X-ray diffraction imaging of organelles at SACLA (2015)
  • Author(s): Yuki Takayama, Koji Yonekura, Masaki Yamamoto, Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Yayoi Inui, Sachihiro Matsunaga
  • Organizer: The 1st SACLA Workshop on Femtosecond Crystallography
  • Place of Presentation: Harima, Hyogo, Japan
  • Year and Date: 2015-03-26
• [Presentation] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser (2015)
  • Author(s): Yuki Sekiguchi, Amane Kobayashi, Tomotaka Oroguchi, Masayoshi Nakasako, Inui Yayoi, Sachihiro Matsunaga, Yuki Takayama and Masaki Yamamoto
  • Organizer: The 2nd International Symposium on Plant Environmental Sensing
  • Place of Presentation: Odaiba, Tokyo, Japan
  • Year and Date: 2015-03-14
• [Presentation] Patterson解析法を利用したサブミクロン粒子集団のコヒーレントX線回折イメージング (2015)
  • Author(s): 高山裕貴、眞木さおり、苙口友隆、中迫雅由、米倉功治
  • Organizer: 第28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: 滋賀県草津市、立命館大学びわこ・くさつキャンパス
  • Year and Date: 2015-01-12
• [Presentation] XFEL低温コヒーレントX線回折イメージングによるアミロイド繊維凝集体の構造研究 (2015)
  • Author(s): 真崎悠、小林周、関口優希、苙口友隆、中迫雅由、山口圭一、桑田一夫、亀田啓、福井直也、河田康志、高山裕貴、山本雅貴
  • Organizer: 第28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: 滋賀県草津市、立命館大学びわこ・くさつキャンパス
  • Year and Date: 2015-01-12
• [Presentation] XFEL低温コヒーレントX線回折イメージングによる細胞内小器官の構造研究 (2015)
  • Author(s): 関口優希、小林周、苙口友隆、中迫雅由、乾弥生、松永幸大、市川雄一、胡桃坂仁志、清水光弘、高山裕貴、山本雅貴
  • Organizer: 第28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: 滋賀県草津市、立命館大学びわこ・くさつキャンパス
  • Year and Date: 2015-01-11
• [Presentation] Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects (2014)
  • Author(s): Yuki Takayama, Saori Maki-Yonekura, Tomotaka Oroguchi, Masayoshi Nakasako, Koji Yonekura
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 北海道札幌市、札幌コンベンションセンター
  • Year and Date: 2014-09-27
• [Presentation] Dark-field phase-retrieval method under the constraint of Friedel’s symmetry for structure analyses in coherent X-ray diffraction imaging (2014)
  • Author(s): Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, Masayoshi Nakasako
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 北海道札幌市、札幌コンベンションセンター
  • Year and Date: 2014-09-27
• [Presentation] Cryogenic coherent X-ray diffraction imaging of cellular organelle particles (2014)
  • Author(s): Yuki Sekiguchi, Amane Kobayashi, Saki Hashimoto, Tomotaka Oroguchi, Masayoshi Nakasako, Yuki Takayama, Koji Yonekura, Masaki Yamamoto, Yayoi Inui, Sachihiro Matsunaga, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 北海道札幌市、札幌コンベンションセンター
  • Year and Date: 2014-09-26
• [Presentation] SPring-8・SACLAでの非結晶生体粒子低温コヒーレントX線回折イメージング (2014)
  • Author(s): 高山裕貴
  • Organizer: 放射光学会第6回若手研究会 コヒーレントX線が拓く構造可視化の新しい世界
  • Place of Presentation: 兵庫県播磨、SPring-8キャンパス
  • Year and Date: 2014-08-23
  • Invited
• [Presentation] Cryogenic coherent X-ray diffraction imaging of biological particles at SACLA (2014)
  • Author(s): Yuki Takayama, Masayoshi Nakasako, Tomotaka Oroguchi, Yuki Sekiguchi, Masaki Yamamoto, Koji Yonekura, Yukio Takahashi, Akihiro Suzuki, Sachihiro Matsunaga and Yayoi Tsujimoto-Inui
  • Organizer: 23rd Congress and General Assembly of the International Union of Crystallography
  • Place of Presentation: Montreal, Quebec, Canada
  • Year and Date: 2014-08-07
• [Presentation] 生体粒子の高分解能コヒーレントX線回折イメージングに向けた金属粒子による回折シグナル増幅及び位相決定法の開発 (2014)
  • Author(s): 高山裕貴、眞木さおり、苙口友隆、中迫雅由、米倉功治
  • Organizer: 「分子システム研究」第3回春季研究会
  • Place of Presentation: 滋賀県彦根市、かんぽの宿彦根
  • Year and Date: 2014-04-25
• [Presentation] 金属粒子混合による回折シグナル増強及びPatterson解析を用いた生体粒子高分解能コヒーレントX線回折イメージング
  • Author(s): 高山裕貴、眞木さおり、苙口友隆、中迫雅由、米倉功治
  • Organizer: X線自由電子レーザー重点課題「SACLAにおける低温X線回折イメージング実験の展開と標準化」 コヒーレントＸ線回折イメージングにおけるデータ収集と構造解析の現状と将来
  • Place of Presentation: 慶應義塾大学矢上キャンパス、横浜
• [Presentation] クライオ試料照射装置”壽壱号”を用いたSACLA でのコヒーレントＸ線回折イメージング実験の現状
  • Author(s): 中迫雅由、苙口友隆、関口優希、小林周、橋本早紀、山本雅貴、引間孝明、米倉功治、高山裕貴、眞木さおり、高橋幸生、鈴木明大、松永幸大、乾弥生、胡桃坂仁志、市川雄一、星 貴彦
  • Organizer: 第27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: 広島国際会議場、広島
• [Presentation] 生体粒子のコヒーレントX 線回折イメージングにおける金コロイド粒子を利用した回折シグナル増幅及び位相決定法の開発
  • Author(s): 高山裕貴、眞木さおり、苙口友隆、中迫雅由、米倉功治
  • Organizer: 第27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: 広島国際会議場、広島
• [Presentation] SACLAの高空間コヒーレンスX線ビームを用いた細胞イメージング
  • Author(s): 乾弥生、松永幸大、加藤翔一、高山裕貴、苙口友隆、関口優希、小林周、橋本早紀、米倉功治、山本雅貴、中迫雅由
  • Organizer: 東京理科大学総合研究機構イメージングフロンティア研究部門・第3回シンポジウム
  • Place of Presentation: 東京理科大学野田キャンパス、野田
• [Remarks] 生体試料の高分解能・高信頼度イメージング法を開発 -従来の測定条件で分解能が2倍以上向上-
  • URL: http://www.spring8.or.jp/ja/news_publications/press_release/2015/150129/