Development of Integrated Analysis Technique for Plant Phenome

• Project/Area Number: 16K18562
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: The University of Tokyo
• Principal Investigator: Kutsuna Natsumaro 東京大学, 大学院新領域創成科学研究科, 特任准教授 (70578559)
• Research Collaborator: Hasezawa Seiichiro ; Higaki Takumi ; Akita Kae ; Kojo Kei H ; Shimahara Yuki ; Miura Takashi
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 植物細胞 / オルガネラ / 細胞骨格 / 顕微鏡画像 / 画像解析 / 植物 / 細胞・組織 / 解析・評価 / 共焦点顕微鏡 / 生態生命情報学 / 生体生命情報学 / 発生・分化

Outline of Final Research Achievements

Plant cells have variety of organelle and cytoskeletal structures. To perform cellular level phenome analysis based on their microscopic images, integrated image processing software was developed in this research. Additionally, simulating software of cytoskeletal dynamics in plant cell was also developed. To collect imaging data, mainly tobacco culture cells BY-2 and transformant of BY-2 cells were observed, in addition to the microscopic images provided by other research institutions.

Academic Significance and Societal Importance of the Research Achievements

研究の結果、光学的特性等が自ずと異なる複数の顕微鏡撮影系に対して、オルガネラ等を認識し個数や面積を測定する、といった細胞レベルのフェノーム解析を高精度高効率に実施するソフトウェアを開発することができた。その基礎を形づくる画像解析ソフトウェア群については国内企業によるユーザインタフェイス等の改良等を受け、アップデートと提供を続けていけるような体制を整えている。

Research Products

• [Journal Article] Quantitative Evaluation of Stromule Frequency at Hourly Intervals in <i>Arabidopsis</i> Stomatal Guard Cell Chloroplasts (2019)
  • Author(s): Shimahara Y, Kutsuna N, Hasezawa S, Kojo KH.
  • Journal Title: CYTOLOGIA Volume: 84 Issue: 1 Pages: 31-35
  • DOI: 10.1508/cytologia.84.31
  • NAID: 130007628779
  • ISSN: 0011-4545, 1348-7019
  • Year and Date: 2019-03-25
  • Peer Reviewed
• [Journal Article] A cloud-based bioimage analysis platform for morphological analysis and image classification. (2019)
  • Author(s): Shimahara Y, Sugawara K, Kojo KH, Kawai H, Yoshida Y, Hasezawa S, Kutsuna N
  • Journal Title: PLOS ONE Volume: 14 Issue: 2 Pages: e0212619-e0212619
  • DOI: 10.1371/journal.pone.0212619
  • Peer Reviewed / Open Access
• [Journal Article] ROSA26 reporter mouse lines and image analyses reveal the distinct region-specific cell behaviors in the visceral endoderm (2018)
  • Author(s): Abe T, Kutsuna N, Kiyonari H, Furuta Y, Fujimori T
  • Journal Title: Development Volume: 145
  • DOI: 10.1242/dev.165852
  • Peer Reviewed / Open Access
• [Journal Article] Ultrafast confocal fluorescence microscopy beyond the fluorescence lifetime limit (2018)
  • Author(s): Mikami H, Harmon J, Kobayashi H, Hamad S, Wang Y, Iwata O, Suzuki K, Ito T, Aisaka Y, Kutsuna N, Nagasawa K, Watarai H, Ozeki Y, Goda K.
  • Journal Title: Optica Volume: 5 Issue: 2 Pages: 117-126
  • DOI: 10.1364/optica.5.000117
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Isolation of uracil auxotroph mutants of coral symbiont alga for symbiosis studies (2018)
  • Author(s): Ishii Yuu、Maruyama Shinichiro、Fujimura-Kamada Konomi、Kutsuna Natsumaro、Takahashi Shunichi、Kawata Masakado、Minagawa Jun
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 3237-3237
  • DOI: 10.1038/s41598-018-21499-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Label-free detection of aggregated platelets in blood by machine-learning-aided optofluidic time-stretch microscopy. (2017)
  • Author(s): Jiang Y, Lei C, Yasumoto A, Kobayashi H, Aisaka Y, Ito T, Guo B, Nitta N, Kutsuna N, Ozeki Y, Nakagawa A, Yatomi Y, Goda K.
  • Journal Title: Lab on a Chip Volume: 17 Issue: 14 Pages: 2426-2434
  • DOI: 10.1039/c7lc00396j
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Modification of growth anisotropy and cortical microtubule dynamics in Arabidopsis hypocotyls grown under microgravity conditions in space (2017)
  • Author(s): Soga K, Yamazaki C, Kamada M, Tanigawa N, Kasahara H, Yano S, Kojo KH, Kutsuna N, Kato T, Hashimoto T, Kotake T, Wakabayashi K, Hoson T
  • Journal Title: Phyiologia Plantarum Volume: 162 Issue: 1 Pages: 135-144
  • DOI: 10.1111/ppl.12640
  • Peer Reviewed
• [Journal Article] Exogenous cellulase switches cell interdigitation to cell elongation in a RIC1-dependent manner in Arabidopsis thaliana cotyledon pavement cells. (2017)
  • Author(s): Higaki T, Takigawa-Imamura H, Akita K, Kutsuna N, Kobayashi R, Hasezawa S, Miura T
  • Journal Title: Plant Cell Physiol Volume: 58 Pages: 106-119
  • DOI: 10.1093/pcp/pcw183
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] FIT: Statistical modeling tool for transcriptome dynamics under fluctuating field conditions (2017)
  • Author(s): Iwayama K., Aisaka Y., Kutsuna N., Nagano A.J.
  • Journal Title: Bioinformatics Volume: - Issue: 11 Pages: 1672-1680
  • DOI: 10.1093/bioinformatics/btx049
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] ブドウ挿し木苗および幼苗へのブドウ黒とう病菌噴霧接種による抵抗性評価法の開発 (2017)
  • Author(s): 河野淳, 朽名夏麿, 尾上典之, 伴雄介, 佐藤明彦
  • Journal Title: 園芸学研究 Volume: 印刷中
  • NAID: 130006300701
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Dopamine regulates body size in Caenorhabditis elegans (2016)
  • Author(s): Takashi Nagashima, Eitaro Oamia, Natsumaro Kutsuna, Shoichi Ishiura, Satoshi Suo
  • Journal Title: Developmenta Biology Volume: 412 Issue: 1 Pages: 128-138
  • DOI: 10.1016/j.ydbio.2016.02.021
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells (2016)
  • Author(s): Takumi Higaki, Natsumaro Kutsuna, Kae Akita, Hisako Takigawa-Imamura, Kenji Yoshimura, Takashi Miura
  • Journal Title: PLOS Computational Biology Volume: 12 Issue: 4 Pages: e1004833-e1004833
  • DOI: 10.1371/journal.pcbi.1004833
  • Peer Reviewed / Open Access
• [Journal Article] Detection of image manipulation and plagiarism in life sciences research. (2016)
  • Author(s): Shimahara Y, Kutsuna N
  • Journal Title: Editorial Office News Volume: 9 Issue: 4 Pages: 1-2
  • DOI: 10.18243/eon/2016.9.4.5
  • Peer Reviewed
• [Journal Article] Modulation of plant RAB GTPase-mediated membrane trafficking pathway at the interface between plants and obligate biotrophic pathogens. (2016)
  • Author(s): Inada, N., Betsuyaku, S., Shimada, T., Ebine, K., Ito, E., Kutsuna, N., Hasezawa, S., Takano, Y., Fukuda, H., Nakano, A., & Ueda, T.
  • Journal Title: Plant Cell Physiol. Volume: 57 Issue: 9 Pages: 1854-1864
  • DOI: 10.1093/pcp/pcw107
  • Peer Reviewed / Open Access
• [Journal Article] In vivo 3D analysis of systemic effects after local heavy-ion beam irradiation in an animal model (2016)
  • Author(s): Nagata K, Hashimoto C, Watanabe-Asaka T, Itoh K, Yasuda T, Ohta K, Oonishi H, Igarashi K, Suzuki M, Funayama T, Kobayashi Y, Nishimaki T, Katsumura T, Oota H, Ogawa M, Oga A, Ikemoto K, Itoh H, Kutsuna N, Oda S, and Mitani H
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 28691-28691
  • DOI: 10.1038/srep28691
  • Peer Reviewed / Open Access
• [Journal Article] Accumulation of fluorescent proteins derived from a trans-Golgi cisternal membrane marker and paramural bodies in interdigitated apoplastic space in Arabidopsis leaf epidermis (2016)
  • Author(s): Akita, K., Kobayashi, M., Sato, M., Kutsuna, N., Ueda, T., Toyooka, K., Nagata, N., Hasezawa, S., and Higaki, T.
  • Journal Title: Protoplasma Volume: in press Issue: 1 Pages: 367-377
  • DOI: 10.1007/s00709-016-0955-1
  • Peer Reviewed / Open Access
• [Presentation] Enteroendocrine peptides can regulate insect feeding behavior via controlling intestinal contraction. (2018)
  • Author(s): Matsumoto Sumihiro, Kutsuna Natsumaro, Nagata Shinji
  • Organizer: Asia and Oceania Society for Comparative Endocrinology Intercongress
  • Int'l Joint Research
• [Presentation] AIによる画像解析: 植物科学への応用 (2018)
  • Author(s): 朽名夏麿, 島原佑基, 馳澤盛一郎
  • Organizer: 日本農芸化学会2018年度大会
  • Invited
• [Presentation] Feedback regulation in secondary cell wall thickening in poplar (2018)
  • Author(s): Naoki Takata, Tatsuya Awano, Natsumaro Kutsuna, Toru Taniguchi
  • Organizer: 第59回日本植物生理学会年会
• [Presentation] 子葉表皮細胞壁の湾曲における微小管結合タンパク質RIC1の役割: 細胞形態計測と力学モデルによる解析 (2017)
  • Author(s): 桧垣匠, 今村寿子, 秋田佳恵, 朽名夏麿, 三浦岳, 馳澤 盛一郎
  • Organizer: 第58回日本植物生理学会年会
  • Place of Presentation: 鹿児島大学郡元キャンパス(鹿児島県鹿児島市)
  • Year and Date: 2017-03-16
• [Presentation] 非標識リアルタイムイメージング装置を用いた血小板凝集塊の検出法の確立 (2017)
  • Author(s): 安本篤史, Yiyue Jiang, Cheng Lei, 相坂有理, 伊藤卓朗, Baoshan Guo, 小林博文, 新田尚, 朽名夏麿, 小関泰之, 中川敦寛, 合田圭介, 矢冨裕
  • Organizer: 第39回日本血栓止血学会学術集会
• [Presentation] バイオメディカル画像の分類・評価のための人工知能によるアプローチ (2017)
  • Author(s): 朽名夏麿
  • Organizer: 先進歯科画像研究会第一回学術講演
  • Invited
• [Presentation] 生物画像自動分類を用いたシロイヌナズナ色素体におけるストロミュールの検出 (2017)
  • Author(s): 島原佑基, 湖城恵, 馳澤盛一郎, 朽名夏麿
  • Organizer: 日本植物学会第81回大会
• [Presentation] 人工知能による植物の効率的フェノタイピング (2017)
  • Author(s): 朽名夏麿
  • Organizer: 第35回日本植物細胞分子生物学会大会
  • Invited
• [Presentation] 宇宙の微小重力環境におけるシロイヌナズナ胚軸の成長と表層微小管動態 - Aniso Tubule 宇宙実験 (2017)
  • Author(s): 曽我康一, 山崎千秋, 鎌田源司, 谷川直樹, 笠原春夫, 矢野幸子, 湖城恵, 朽名夏麿, 加藤壮英, 橋本隆, 小竹敬久, 若林和幸, 保尊隆享
  • Organizer: 日本植物学会第81回大会
• [Presentation] 生物画像の自動評価工程をハイスループット化する能動学習技術 CARTA (2017)
  • Author(s): 朽名夏麿
  • Organizer: 定量生物学の会 第8回年会
  • Place of Presentation: 岡崎コンファレンスセンター(愛知県岡崎市)
  • Invited
• [Presentation] Mechanism of jigsaw-puzzle pattern formation in plant leaf epidermal cell: modeling single cell shape by interface equation and convolution kernel. (2016)
  • Author(s): Miura T, Higaki T, Akita K, Kutsuna N, Takigawa-Imamura H.
  • Organizer: The 2016 (26th) annual meeting of the Japanese Society for Mathematical Biology
  • Place of Presentation: 九州大学伊都新キャンパス(福岡県福岡市)
  • Year and Date: 2016-09-07
  • Int'l Joint Research
• [Presentation] 生物・医用画像の自動評価のための能動的機械学習法 CARTA (2016)
  • Author(s): 朽名夏麿
  • Organizer: 第20回 NMR マイクロイメージング研究会
  • Place of Presentation: 国立がん研究センター東病院(千葉県柏市)
  • Invited
• [Presentation] Radiomics 入門: 機械学習の基礎 (2016)
  • Author(s): 朽名夏麿
  • Organizer: 第44回 日本磁気共鳴医学会大会
  • Place of Presentation: 大宮ソニックシティ(埼玉県さいたま市)
  • Invited
• [Presentation] マウス着床後初期胚における細胞系譜解析 (2016)
  • Author(s): Takaya Abe, Natsumaro Kutsuna, Hiroshi Kiyonari, Yasuhide Furuta, and Toshihiko Fujimori
  • Organizer: 日本発生生物学会大会 秋季シンポジウム2016
  • Place of Presentation: 三島市民文化会館(静岡県三島市)
• [Presentation] 着床後マウス胚における細胞系譜解析 (2016)
  • Author(s): 阿部高也、朽名夏麿、清成寛、古田 泰秀、藤森 俊彦
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜(神奈川県横浜市)
• [Presentation] 植物表皮細胞の湾曲構造形成のメカニズム (2016)
  • Author(s): 三浦岳、桧垣匠、朽名夏麿、秋田佳恵、今村（滝川） 寿子、吉村 賢二
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜(神奈川県横浜市)
• [Remarks] 東京大学大学院新領域創成科学研究科植物全能性制御システム解析学分野ウェブページ
  • URL: http://hasezawa.ib.k.u-tokyo.ac.jp/zp/hlab/