Development of electron microscopy atlas: Fusion with omics and electron microscopic data

• Project/Area Number: 23657051
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Morphology/Structure
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: TOYOOKA Kiminori 独立行政法人理化学研究所, 機能開発研究グループ, 上級研究員 (10360596)
• Co-Investigator(Renkei-kenkyūsha): NISHIKAWA Mayuko 独立行政法人理化学研究所, 機能開発研究グループ, 技師 (80550376) ; MOCHIDA Keiichi 独立行政法人理化学研究所, バイオマス研究基盤チーム, 上級研究員 (90387960)
• Research Collaborator: 永田 典子 日本女子大学, 理学部, 准教授 ; 朽名 夏麿 東京大学, 大学院・新領域創成科学研究科, 助教 ; 桧垣 匠 東京大学, 大学院・新領域創成科学研究科, 助教 ; 吉田 拓広 独立行政法人理化学研究所, ゲノム情報統合ユニット, テクニカルスタッフ ; 櫻井 哲也 独立行政法人理化学研究所, ゲノム情報統合ユニット, ユニットリーダー ; 若崎 眞由美 独立行政法人理化学研究所, 機能開発研究グループ, テクニカルスタッフ
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 電子顕微鏡 / 高圧凍結技法 / 電子地図 / オルガネラ / 超微形態

Research Abstract

Transmission electron microscopy (TEM) is important for high-resolution ultrastructure observation for organelles, cell and tissues. However, it is unsuitable for comprehensive analyses. I constructed TEM atlas to achieve an exhaustive ultrastructural analysis of organelles in model plants by using high-pressure freezing (HFP) and TEM techniques. To take wide and high-resolution TEM pictures, Arabidopsis roots and BY2 cells were frozen by HFP machine and then fix. After embedded in resin, large ultrathin sections were put on a hole grid. Then we took TEM pictures by auto-digital TEM recoding system. I succeed in records more than 30 thousand images. We developed auto-photomerge program for TEM pictures and several thousands of pictures were automatically merged. Using these wide-high resolution pictures, I have developed a web-based 2D map that can be zoomed and searched.

Research Products

• [Journal Article] The Ets Transcription Factor Spi-B Is Essential for the Differentiation of Intestinal Microfold (M) Cells (2012)
  • Author(s): Kanaya T, Hase K, Takahashi D, Fukuda S, Hoshino K, Sasaki I, Hemmi H, Knoop KA, Kumar N, Sato M, Katsuno T, Yokosuka O, Toyooka K, Nakai K, Sakamoto A, Kitahara Y, Jinnohara T, McSorley SJ, Kaisho T, Williams IR, Ohno H
  • Journal Title: Nature Immunology Volume: 13 Pages: 832-842
  • Peer Reviewed
• [Journal Article] Lysine Decarboxylases Involved in the First Step of Quinolizidine Alkaloid Biosynthesis in Leguminosae Plants (2012)
  • Author(s): Bunsupa S, Katayama K, Ikeura E,Oikawa A, Toyooka K, Saito K, Yamazaki M
  • Journal Title: Plant Cell Volume: 24 Pages: 1202-1216
  • Peer Reviewed
• [Journal Article] Regulation of Root Greening by Light and Auxin/Cytokinin Signaling in Arabidopsis (2012)
  • Author(s): Kobayashi K, Baba S, Obayashi T, Sato M, Toyooka K, Keranen M, Aro E, Fukaki H, Ohta H, Sugimoto K, Masuda T
  • Journal Title: Plant Cell Volume: 24 Pages: 1081-1095
  • Peer Reviewed
• [Journal Article] Ultrastructure of the rickettsial endosymbiont "MIDORIKO"in the green alga Carteria cerasiformis as revealed by high-pressure freezing and freeze-substitution fixation. (2012)
  • Author(s): Kawafune, K. , Sato, M., Toyooka, K. Nozaki, H
  • Journal Title: Protoplasma Volume: (印刷中) Issue: 4 Pages: 949-953
  • DOI: 10.1007/s00709-012-0469-4
  • Peer Reviewed
• [Journal Article] Micro-CT observations of the 3D distribution of calcium oxalate crystals in cotyledons during maturation and germination in Lotus miyakojimae seeds. (2012)
  • Author(s): Yamauchi, D., Tamaoki, D., Hayami, M., Takeuchi, M., Karahara, I., Sato, M., Toyooka, K., Nishioka, H., Terada, Y., Uesugi, K., Takano, H., Kagoshima, Y., Mineyuki, Y.
  • Journal Title: Journal of Electron Microscopy Volume: (印刷中) Issue: 3 Pages: 353-361
  • DOI: 10.1093/jmicro/dfs079
  • Peer Reviewed
• [Journal Article] a plant homolog of CtBP/BARS, functions outside the nucleus. (2011)
  • Author(s): Minamisawa, N., M. Sato, K.H. Cho, H. Ueno, K. Takechi, M. Kajikawa, K.T. Yamato, K. Ohyama, K. Toyooka, G.T. Kim, G. Horiguchi, H. Takano, T. Ueda, and H. Tsukaya
  • Journal Title: Plant J Volume: 68 Pages: 788-799
  • Peer Reviewed
• [Journal Article] Characterization of Arabidopsis CTP:3-deoxy-D-manno-2-octulosonate cytidylyltransferase (CMP-KDO synthetase), the enzyme that activates KDO during rhamnogalacturonan II biosynthesis. (2011)
  • Author(s): Kobayashi, M., N. Kouzu, A. Inami, K. Toyooka, Y. Konishi, K. Matsuoka, and T. Matoh
  • Journal Title: Plant Cell Physiol Volume: 52 Pages: 1832-1843
  • NAID: 10030304814
  • Peer Reviewed
• [Journal Article] Immunohistochemical observation of indole-3-acetic acid at the IAA synthetic maize coleoptile tips (2011)
  • Author(s): Nishimura,T., Toyooka, K, Sato, M., Matsumoto, S. Lucas,M.M., Strnad,M., Balu?ka, F., Koshiba, T
  • Journal Title: Plant Signaling & Behavior Volume: 6 Pages: 2013-2022
  • Peer Reviewed
• [Journal Article] Plasma membrane aquaporin AqpZ protein is essential for glucose metabolism during photomixotrophic growth of Synechocystis sp. PCC 6803 (2011)
  • Author(s): Akai M, Onai K, Kusano M, Sato, M., Redestig H, Toyooka, K, Morishita M, Miyake H, Hazama A, Checchetto V, Szabo I, Matsuoka K, Saito K, Yasui M, Ishiura M, Uozumi N
  • Journal Title: J. Biol. Chem Volume: 286 Pages: 25224-35
  • Peer Reviewed
• [Journal Article] Plasma membrane aquaporin AqpZ protein is essential for glucose metabolism during photomixotrophic growth of Synechocystis sp. PCC 6803 (2011)
  • Author(s): Akai M, Onai K, Kusano M, Sato, M., Redestig H, Toyooka, K, Morishita M, Miyake H, Hazama A, Checchetto V, Szabò I, Matsuoka K, Saito K, Yasui M, Ishiura M, Uozumi N
  • Journal Title: J. Biol. Chem. Volume: 286 Pages: 25224-25235
  • Peer Reviewed
• [Journal Article] ANGUSTIFOLIA, a plant homolog of CtBP/BARS, functions outside the nucleus. (2011)
  • Author(s): Minamisawa N, Sato, M., Cho KH, Ueno H, Takechi K, Kajikawa M, Yamato KT, Ohyama K, Toyooka, K, Kim GT, Horiguchi G, Takano H, Ueda T, Tsukaya H.
  • Journal Title: Plant J. Volume: 68 Pages: 788-799
  • Peer Reviewed
• [Journal Article] Characterization of Arabidopsis CTP:3-deoxy-D-manno-2-octulosonate cytidylyltransferase (CMP-KDO synthetase), the enzyme that activates KDO during rhamnogalacturonan II biosynthesis. (2011)
  • Author(s): Kobayashi M, Kouzu N, Inami A, Toyooka, K, Konishi Y, Matsuoka K, Matoh T.
  • Journal Title: Plant Cell Physiol. Volume: 52 Pages: 1832-1834
  • NAID: 10030304814
  • Peer Reviewed
• [Journal Article] Ultrastructure of the rickettsial endosymbiont "MIDORIKO" in the green alga Carteria cerasiformis as revealed by high-pressure freezing and freeze-substitution fixation
  • Author(s): Kawafune, K., Sato, M. Toyooka, K., Nozaki, H
  • Journal Title: Protoplasma Volume: (in press)
  • Peer Reviewed
• [Journal Article] Micro-CT observations of the 3D distribution of calcium oxalate crystals in cotyledons during maturation and germination in Lotus miyakojimae seeds
  • Author(s): Yamauchi, D., Tamaoka, D., Hayami, M., Takeuchi, M., Karahara, I., Sato, M., Toyooka, K., Nishioka, H., Terada, Y., Uesugi, K., Takano, H., Kagoshima, Y., Mineyuki, Y
  • Journal Title: J. Electron Microscopy Volume: (in press)
  • Peer Reviewed
• [Presentation] 電顕アトラス:高圧凍結技法を取り入れた広域電顕像撮影システムの開発 (2013)
  • Author(s): 佐藤繭子、朽名夏麿、澤木史江、若崎眞由美、桧垣匠、吉田拓弘、櫻井哲也、馳澤盛一郎、持田恵一、永田典子、豊岡公徳
  • Organizer: 第54回日本植物生理学会年会
  • Place of Presentation: 岡山
  • Year and Date: 2013-03-21
• [Presentation] 電顕アトラス：高圧凍結技法を取り入れた広域電顕像撮影システムの開発 (2013)
  • Author(s): 豊岡公徳
  • Organizer: 第54回日本植物生理学会年会
  • Place of Presentation: 岡山県岡山市
• [Presentation] V-PPaseの細胞内局在から見るタバコ根端分裂組織の液胞形成 (2012)
  • Author(s): 佐藤繭子、後藤友美、松岡健、豊岡公徳
  • Organizer: 第68回日本顕微鏡学会年会
  • Place of Presentation: つくば
  • Year and Date: 2012-05-15
• [Presentation] 生体顕微マルチスケールマッピングシステム:小胞クラスターの分布と構造 (2012)
  • Author(s): 豊岡公徳、若崎眞由美、朽名夏麿、桧垣匠、永田典子、松岡健、持田恵一、佐藤繭子
  • Organizer: 第68回日本顕微鏡学会年会
  • Place of Presentation: つくば
  • Year and Date: 2012-05-15
• [Presentation] 小胞輸送系での物質合成・輸送関連タンパク質と脂質膜ドメイン (2012)
  • Author(s): 松岡健, 豊岡公徳
  • Organizer: 日本植物生理学会第53回大会 シンポジウム 生化学と細胞生物学の融合による低分子集積生物学の構築に向けて
  • Place of Presentation: 京都
  • Year and Date: 2012-03-17
• [Presentation] タバコ根端組織における液胞型プロトンピロホスファターゼの細胞内局在 (2012)
  • Author(s): 佐藤繭子, 後藤友美, 松岡健, 豊岡公徳
  • Organizer: 日本植物生理学会第53回大会
  • Place of Presentation: 京都
  • Year and Date: 2012-03-17
• [Presentation] 生体顕微マルチスケーリングマッピングシステムを用いた小胞クラスターの分布と超微形態解析 (2012)
  • Author(s): 豊岡公徳, 若崎眞由美, 吉田拓弘, 朽名夏麿, 桧垣匠, 永田典子, 松岡健, 櫻井哲也, 持田恵一, 佐藤繭子
  • Organizer: 日本植物生理学会第53回大会
  • Place of Presentation: 京都
  • Year and Date: 2012-03-17
• [Presentation] Electron microscopy atlas : The ultrastructure and distribution of vesicle clusters (2012)
  • Author(s): K. Toyooka, M. Wakazaki, N. Kutsuna, T. Higaki, N. Nagata, K. Mochida, K. Matsuoka, K. Shinozaki, M. Sato
  • Organizer: The 1st International Symposium on Plant Environmental Sensing
  • Place of Presentation: Nara, Japan
• [Presentation] V-PPaseの細胞内局在から見るタバコ根端分裂組織の液胞形成 (2012)
  • Author(s): 佐藤繭子
  • Organizer: 第68回日本顕微鏡学会年会
  • Place of Presentation: 茨城県つくば市
• [Presentation] 生体顕微マルチスケールマッピングシステム：小胞クラスターの分布と構造 (2012)
  • Author(s): 豊岡公徳
  • Organizer: 第68回日本顕微鏡学会年会
  • Place of Presentation: 茨城県つくば市
• [Presentation] 生体顕微マルチスケーリングマッピングシステムを用いた小胞クラスターの分布と超微形態解析 (2012)
  • Author(s): 豊岡公徳、若崎眞由美、吉田拓広、朽名夏麿、桧垣匠、永田典子、櫻井哲也、松岡健、持田恵一、佐藤繭子
  • Organizer: 第53回日本植物生理学会年会
  • Place of Presentation: 京都産業大学(京都)
• [Presentation] 物質輸送装置を捉える:ゴルジ以降の分泌に関与する小胞クラスターSVC (2011)
  • Author(s): 豊岡公徳、後藤友美、佐藤繭子、松岡健
  • Organizer: 第67回日本顕微鏡学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2011-05-17
• [Presentation] 高圧凍結技法を用いた植物液胞形成過程の微細構造解析 (2011)
  • Author(s): 佐藤繭子、後藤友美、豊岡公徳
  • Organizer: 第67回日本顕微鏡学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2011-05-17
• [Remarks]
  • URL: http://labs.psc.riken.jp/gdrg/Research1/PSC_bioimaging/Top.html
• [Remarks] 理化学研究所植物科学研究センター基盤研究
  • URL: http://labs.psc.riken.jp/gdrg/Research1
• [Remarks]
  • URL: http://labs.psc.riken.jp/gdrg/research1.html