Updated on 2025/03/08

写真a

 
SUGA Michi
 
Organization
Research Institute for Interdisciplinary Science Professor
Position
Professor
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Degree

  • 博士(理学) ( 大阪大学 )

Research Areas

  • Life Science / Structural biochemistry

Education

  • 大阪大学理学研究科    

    2006 - 2009

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Research History

  • Okayama University   高等先鋭研究院 植物・光エネルギー開発拠点

    2024.10

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  • Okayama University   Research Institute for Interdisciplinary Science   Professor

    2022.4

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  • Japan Science and Technology Agency

    2018.10 - 2022.3

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Professional Memberships

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Committee Memberships

  •   岡山大学理学部生物学科長  

    2024.4 - 2025.3   

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  •   岡山大学国際構造生物学研究センター 副センター長  

    2023.4   

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  •   岡山大学環境生命自然科学研究科 異分野基礎科学学位プログラム長  

    2023.4 - 2025.3   

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  •   岡山大学自然科学研究科異分野基礎科学専攻長  

    2023.4 - 2025.3   

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  • SPRUC 放射光構造生物学研究会   幹事  

    2022.5   

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    Committee type:Other

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Papers

  • Oxygen-evolving photosystem II structures during S1-S2-S3 transitions. International journal

    Hongjie Li, Yoshiki Nakajima, Eriko Nango, Shigeki Owada, Daichi Yamada, Kana Hashimoto, Fangjia Luo, Rie Tanaka, Fusamichi Akita, Koji Kato, Jungmin Kang, Yasunori Saitoh, Shunpei Kishi, Huaxin Yu, Naoki Matsubara, Hajime Fujii, Michihiro Sugahara, Mamoru Suzuki, Tetsuya Masuda, Tetsunari Kimura, Tran Nguyen Thao, Shinichiro Yonekura, Long-Jiang Yu, Takehiko Tosha, Kensuke Tono, Yasumasa Joti, Takaki Hatsui, Makina Yabashi, Minoru Kubo, So Iwata, Hiroshi Isobe, Kizashi Yamaguchi, Michihiro Suga, Jian-Ren Shen

    Nature   2024.1

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

    DOI: 10.1038/s41586-023-06987-5

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  • Structural basis for high selectivity of a rice silicon channel Lsi1 Reviewed

    Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    Nature Communications   12 ( 1 )   2021.10

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.

    DOI: 10.1038/s41467-021-26535-x

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    Other Link: https://www.nature.com/articles/s41467-021-26535-x

  • An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser. Reviewed

    Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Hirata K, Umena Y, Yonekura S, Yu LJ, Murakami H, Nomura T, Kimura T, Kubo M, Baba S, Kumasaka T, Tono K, Yabashi M, Isobe H, Yamaguchi K, Yamamoto M, Ago H, Shen JR

    Science (New York, N.Y.)   366 ( 6463 )   334 - 338   2019.10

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S-0 to S-4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S-1, S-2, and S-3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S-2, but flipping of D1 Glu(189) upon transition to S-3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

    DOI: 10.1126/science.aax6998

    Web of Science

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  • Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Reviewed

    Michihiro Suga, Fusamichi Akita, Michihiro Sugahara, Minoru Kubo, Yoshiki Nakajima, Takanori Nakane, Keitaro Yamashita, Yasufumi Umena, Makoto Nakabayashi, Takahiro Yamane, Takamitsu Nakano, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, Taiki Motomura, Jing-Hua Chen, Yuki Kato, Takumi Noguchi, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Eriko Nango, Rie Tanaka, Hisashi Naitow, Yoshinori Matsuura, Ayumi Yamashita, Masaki Yamamoto, Osamu Nureki, Makina Yabashi, Tetsuya Ishikawa, So Iwata, Jian-Ren Shen

    NATURE   543 ( 7643 )   131 - +   2017.3

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC)(1-3). The structure of PSII has been analysed at 1.9 angstrom resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, `distorted-chair' form(4). This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the `radiation damage-free'(5) structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 angstrom using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 angstrom compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 angstrom from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique mu 4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 angstrom between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously(6,7.)

    DOI: 10.1038/nature21400

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  • Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex Reviewed

    Xiaochun Qin, Michihiro Suga, Tingyun Kuang, Jian-Ren Shen

    SCIENCE   348 ( 6238 )   989 - 995   2015.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors-especially within LHCI-as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.

    DOI: 10.1126/science.aab0214

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Books

  • Ultrafast Electronic and Structural Dynamics

    Allen M. Orville, Eriko Nango, So Iwata, Sandra Mous, Joerg Standfuss, Przemyslaw Nogly, Michihiro Suga, Jian-Ren Shen, Minoru Kubo( Role: Joint author ,  Chaptor 15. Time-Resolved Studies of Protein Structural Dynamics)

    Springer Nature Singapore  2024 

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  • Structure, Electron Transfer Chain of Photosystem II and the Mechanism of Water Splitting

    Jian-Ren Shen, Yoshiki Nakajima, Fusamichi Akita, Michihiro Suga( Role: Contributor)

    Springer, Cham  2021.9 

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  • 光エネルギー変換における分子触媒の新展開 : 天然光合成を凌駕する反応系の構築を目指して

    日本化学会( Role: Joint author ,  光合成光化学系IIの構造と触媒機能)

    化学同人  2020.9  ( ISBN:9784759813982

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    Total pages:v, 176p, 図版 [4] p   Language:Japanese

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MISC

  • 光合成水分解反応機構の解明 Invited Reviewed

    沈 建仁, 菅 倫寛

    光アライアンス   2024.9

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    Authorship:Last author  

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  • 光合成の酸素発生触媒が水分子を取り込む瞬間を捉えた Invited Reviewed

    79 ( 9 )   12 - 16   2024.8

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    Authorship:Lead author, Corresponding author  

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  • 光合成の水分解反応機構の解明 Invited Reviewed

    菅 倫寛, 沈 建仁

    生体の科学   75 ( 3 )   263 - 268   2024.6

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    Authorship:Lead author, Corresponding author  

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  • Structure and Function of a plant silicic acid channel Invited Reviewed

    Yasunori Saitoh, Michihiro Suga

    64   1 - 2   2022.12

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    Authorship:Last author  

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  • 光環境に適応する光化学系I-アンテナ超複合体の多彩な構造 Invited Reviewed

    菅倫寛, 沈建仁

    光合成研究   32   77 - 85   2022

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Presentations

  • (基調講演)光化学系IIのS-状態遷移における立体構造ダイナミクス

    菅 倫寛

    第57回酸化反応討論会  2024.11.17 

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    Event date: 2024.11.16 - 2024.11.17

    Presentation type:Oral presentation (keynote)  

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  • Real-time structural changes during the S1-S2-S3 state transitions of the Kok cycle of Photosystem II caught by time-resolved crystallography Invited

    Michi Suga

    2nd Asia-Oceania International Congress on Photosynthesis (AOICP)  2024.9.18 

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    Event date: 2024.9.18 - 2024.9.21

    Presentation type:Oral presentation (keynote)  

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  • Statistical insights into the significance of collective motion within the primary coordination sphere of the Mn4CaO5 cluster in determining the catalytic progresson for O2 evolution Invited

    Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

    2nd Asia-Oceania International Congress on Photosynthesis (AOICP) 

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    Event date: 2024.9.18 - 2024.9.21

    Language:English   Presentation type:Oral presentation (general)  

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  • Real-Time Structural Changes during the S1-S2-S3 state transitions of the Kok cycle of Photosystem II Caught by Time-Resolved Crystallography Invited

    Michi Suga

    IUPB-MESPA World Congress 2024, the 18th International Congress of Photobiology  2024.8 

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    Event date: 2024.8.25 - 2024.8.30

    Presentation type:Oral presentation (invited, special)  

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  • Real-Time Structural Changes during the Light-induced photosynthetic water oxidation of Photosystem II. Invited

    Michi Suga

    UK-Japan symposium on Frontiers of Structural Biology  2024 

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    Event date: 2024.6.18 - 2024.6.19

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Awards

  • 晝馬輝夫 光科学賞

    2025.3   光科学技術研究振興財団  

    菅 倫寛

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  • 研究奨励賞

    2024.5   量子生命科学会  

    菅 倫寛

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  • The Robin Hill Award

    2022.8   The international Society of Photosynthesis Research  

    Michihiro Suga

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  • Young Scientist Award from the Photobiology Association of Japan

    2020.8   Photobiology Association of Japan  

    Michi Suga

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  • The Japanese Society of Plant Physiology Young Investigator Award

    2017.3   The Japanese Society of Plant Physiology  

    Michi Suga

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Research Projects

  • 光合成ベシクルを用いた光エネルギー変換の統合的理解

    2024.10

    JST  創発研究 

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    Authorship:Principal investigator 

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  • Structural dynamics of anoxyogenic photosynthetic reaction centre - light-harvesting antenna protein supercomplexes

    Grant number:24K21948  2024.06 - 2026.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

    菅 倫寛

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    Grant amount:\6500000 ( Direct expense: \5000000 、 Indirect expense:\1500000 )

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  • Molecular basis and substrate selectivity of toxic metalloid channels and transporters

    Grant number:23H02450  2023.04 - 2026.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    菅 倫寛, 三谷 奈見季

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    Grant amount:\18720000 ( Direct expense: \14400000 、 Indirect expense:\4320000 )

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  • Elucidation of the mechanisms for light-induced water-splitting and light energy utilization in photosynthesis

    Grant number:22H04916  2022.04 - 2027.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Specially Promoted Research  Grant-in-Aid for Specially Promoted Research

    沈 建仁, 庄司 光男, 秋田 総理, 菅 倫寛, 山口 兆

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    Grant amount:\627640000 ( Direct expense: \482800000 、 Indirect expense:\144840000 )

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  • Ultrafast structural dynamics of light-harvesting complex I and the photosynthetic reaction center supercomplex

    Grant number:22H04754  2022.04 - 2024.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    菅 倫寛

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    Grant amount:\11180000 ( Direct expense: \8600000 、 Indirect expense:\2580000 )

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Class subject in charge

  • Advanced practice in scientific presentation (2024academic year) special  - その他

  • Protein Crystallography (2024academic year) Late  - 木3~4

  • Internship for advanced research (2024academic year) special  - その他

  • Basic Biology A (2024academic year) 1st and 2nd semester  - 金3~4

  • Basic Biology A1 (2024academic year) 1st semester  - 金3~4

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Social Activities

  • 第25回岡山県理数科理数系コース課題研究合同発表会

    Role(s):Lecturer

    高大連携理数科教育研究会  2025.1.31

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    Type:Research consultation

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  • 講師

    Role(s):Lecturer

    岡山県立城東高校 2年次生課題研究  2025.1.29

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    Type:Research consultation

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  • 講師

    Role(s):Lecturer

    岡山県立城東高校 2年次生課題研究  2024.10.16

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    Type:Research consultation

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  • ラジオ出演

    Role(s):Appearance

    RSKラジオ 朝耳らじお  2024.3.13

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    Type:TV or radio program

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  • ラジオ出演

    Role(s):Appearance

    RSKラジオ 朝耳らじお  2024.3.6

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    Type:TV or radio program

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Media Coverage

  • 晝馬輝夫光科学賞、24年度は岡山大・菅教授に贈呈 光合成の理解を深化 Internet

    中日BIZナビ  https://biz.chunichi.co.jp/news/article/10/101146/  2025.3

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  • 浜松ホトニクス系財団、晝馬輝夫光科学賞に岡山大の菅氏 Newspaper, magazine

    日経新聞  https://www.nikkei.com/article/DGXZQOCC05ALQ0V00C25A3000000/  2025.3

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  • 菅・岡山大教授「精進する」 晝馬輝夫光科学賞 浜松で贈呈式 Newspaper, magazine

    静岡新聞  https://news.at-s.com/article/1667286  2025.3

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  • 晝馬輝夫科学賞に岡山大の菅倫寛教授、光合成の理解深化に貢献 Internet

    中日BIZナビ  2025.1

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  • 第7回晝馬輝夫 光科学賞,岡山大 菅倫寛教授が受賞

    オプトニクスニュース  https://optronics-media.com/news/20250130/97353/  2025.1

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