Gene expression analyses in the mouse digital brain for understanding molecular bases of higher motor disfunction

• Project/Area Number: 26280110
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Okamura-Oho Yuko 国立研究開発法人理化学研究所, 光量子工学研究領域, 客員研究員 (60381571)
• Co-Investigator(Kenkyū-buntansha): 横田 秀夫 国立研究開発法人理化学研究所, 光量子工学研究領域, チームリーダー (00261206) ; 太田 聡史 国立研究開発法人理化学研究所, バイオリソースセンター, 専任研究員 (30391890)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥15,990,000 (Direct Cost: ¥12,300,000、Indirect Cost: ¥3,690,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000); Fiscal Year 2014: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
• Keywords: 遺伝子発現 / 随意運動 / モーションキャプチャー / ハンチントン病 / 逆運動学解析 / データベース / ３D 発現地図

Outline of Final Research Achievements

More than 85% of genes are expressed in the brain and maintain the structure and execute neural function. We have invented a TT method for profiling gene expression patterns of the whole brain in the three-dimensional coordinate. We have also developed a high-resolution motion capture method and detected subtle changes of walking motion and describe them with parameters of biomechanics. Using these methods, we analyzed a neuronal inherited disease model mouse with abnormal motion. Then, we found parameter changes in motion of abnormal mice and expression-area changes in gene expression of a group of genes in the beginning stages of the disease.

Research Products

• [Journal Article] Three-Dimensional Observation of Microstructure of Bone Tissue Using High-Precision Machining (2017)
  • Author(s): Furushiro Naomichi、Yokota Hideo、Nakamura Sakiko、Fujisaki Kazuhiro、Yamagata Yutaka、Kokubo Mitsunori、Himeno Ryutaro、Makinouchi Akitake、Higuchi Toshiro、
  • Journal Title: International Journal of Automation Technology Volume: 11 Issue: 6 Pages: 883-894
  • DOI: 10.20965/ijat.2017.p0883
  • NAID: 130007505912
  • ISSN: 1881-7629, 1883-8022
  • Year and Date: 2017-11-05
  • Peer Reviewed / Open Access
• [Journal Article] Immobility responses are induced by photoactivation of single glomerular species responsive to fox odour TMT (2017)
  • Author(s): H. Saito, H. Nishizumi, S. Suzuki, H. Matsumoto, N. Ieki, T. Abe, H. Kiyonari, M. Morita, H. Yokota, N. Hirayama, T. Yamazaki, T. Kikusui, K. Mori, H. Sakano
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 16011-16011
  • DOI: 10.1038/ncomms16011
  • Peer Reviewed / Open Access
• [Journal Article] Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates (2015)
  • Author(s): Sergejeva, M, Papp, E. A., Bakker, R., Gaudnek, M. A., Okamura-Oho, Y., Boline, J., Bjaalie, J. G., Hess, A.
  • Journal Title: J. Neurosci. Methods Volume: 240 Pages: 161-169
  • DOI: 10.1016/j.jneumeth.2014.11.005
  • Peer Reviewed
• [Journal Article] Numerical simulation of airflow and microparticle deposition in a synchrotron micro-CT-based pulmonary acinus model (2015)
  • Author(s): T. Sera, K. Uesugi, N. Yagi, and H. Yokota
  • Journal Title: Computer Methods in Biomechanics and Biomedical Engineering Volume: 18 Issue: 13 Pages: 1427-1435
  • DOI: 10.1080/10255842.2014.915030
  • Peer Reviewed
• [Journal Article] Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain (2014)
  • Author(s): Okamura-Oho Y, Shimokawa K, Nishimura M, Takemoto S, Sato A, Furuichi T, Yokota H.
  • Journal Title: Scientific Report Volume: 4 Issue: 1 Pages: 6969-6969
  • DOI: 10.1038/srep06969
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Solvable model for chemical oscillations (2014)
  • Author(s): E. Chikayama, Y. Sunaga, S. Noda, H. Yokota
  • Journal Title: Journal of Mathematical Chemistry Volume: 52 Issue: 2 Pages: 399-406
  • DOI: 10.1007/s10910-013-0275-z
  • Peer Reviewed
• [Journal Article] Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. (2014)
  • Author(s): Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R. Ueda
  • Journal Title: Cell Volume: 157 Issue: 3 Pages: 726-739
  • DOI: 10.1016/j.cell.2014.03.042
  • Peer Reviewed
• [Journal Article] Prediction of open urinary tract in laparoscopic partial nephrectomy by virtual resection plane visualization (2014)
  • Author(s): D. Ueno, K. Makiyama, H. Yamanaka, T. Ijiri, H. Yokota, and Y. Kubota
  • Journal Title: BMC Urology Volume: 14 Issue: 1 Pages: 47-47
  • DOI: 10.1186/1471-2490-14-47
  • Peer Reviewed / Open Access
• [Journal Article] Communication Platform for Image Analysis and Sharing in Biology (2014)
  • Author(s): M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota
  • Journal Title: International Journal of Networking and Computing Volume: 4 Issue: 2 Pages: 369-391
  • DOI: 10.15803/ijnc.4.2_369
  • NAID: 130004709094
  • ISSN: 2185-2839, 2185-2847
  • Peer Reviewed / Open Access
• [Journal Article] Flower Modeling via X-ray Computed Tomography (2014)
  • Author(s): T. Ijiri, S. Yoshizawa, H. Yokota, and T. Igarashi
  • Journal Title: ACM Transactions on Graphics Volume: 33 Issue: 4 Pages: 1-10
  • DOI: 10.1145/2601097.2601124
  • Peer Reviewed
• [Journal Article] Efficient parallel LOD-FDTD method for Debye-dispersive media (2014)
  • Author(s): Tadashi Hemmi, Fumie Costen, Salvador Garcia, Ryutaro Himeno, Hideo Yokota, Mehshan Mustafa
  • Journal Title: IEEE Transactions on Antennas and Propagation Volume: 62 Issue: 3 Pages: 1330-1338
  • DOI: 10.1109/tap.2013.2294860
  • Peer Reviewed
• [Journal Article] オーダーメ─ド再生医療に向けたコンピュータサイエンス (2014)
  • Author(s): 横田秀夫
  • Journal Title: 四国医学雑誌 Volume: 70 Pages: 208-218
• [Presentation] Differential and tissue-specific gene expression in the mouse brain (2017)
  • Author(s): Yuko Okamura-Oho
  • Organizer: AINI (Advances in Neuroinformatics) 2017
  • Int'l Joint Research / Invited
• [Presentation] ViBrism database for gene expression maps and co-expression networks analysis on the 3D brain (2017)
  • Author(s): Kazuro Shimokawa, Masahiko Morita, Masaomi Nishimura, Hideo Yokota, Shuhei Wemler, Yoshihiro Okumura, Yoko Yamaguchi, Yuko Okamura-Oho
  • Organizer: Annual meeting of Society of Neuroscience 2017
  • Int'l Joint Research
• [Presentation] 3次元Ex Vivo 空間での遺伝子発現分布の測定～TT法で全脳を網羅解析～ (2016)
  • Author(s): 於保祐子
  • Organizer: nano tech 2016（国際ナノテクノロジー総合展・技術会議）理研ブース
  • Place of Presentation: 東京ビッグサイト 東ホール
  • Year and Date: 2016-01-27
  • Invited
• [Presentation] Integrated analysis of anatomical and topological maps of gene expression in the mouse brain (2016)
  • Author(s): Yuko Okamura-Oho
  • Organizer: 3rd Japan-EU WS on Neurorobotics
  • Int'l Joint Research / Invited
• [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis (2016)
  • Author(s): Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
  • Organizer: NI(Neuroinformatics)2016
• [Presentation] ViBrism DB Platform (2016)
  • Author(s): 2.Yuko Okamura-Oho, Masahiko Morita, Masaomi Nishimura, Takahiro Tawara, Shuhei Wemler, Kazuro Shimokawa, Hideo Yokota
  • Organizer: AINI2016 and INCF Nodes Workshop
• [Presentation] Integration of anatomical and topological maps for functional analysis of the brain (2015)
  • Author(s): Yuko Okamura-Oho
  • Organizer: AINI (Advances in Neuroinformatics) 2015
  • Place of Presentation: 東京大学先端科学技術研究センター エネオスホール、東京 駒場
  • Year and Date: 2015-11-26
  • Int'l Joint Research / Invited
• [Presentation] The homology mapping: interspecies functional morphing (2015)
  • Author(s): Satoshi Oota, Yosuke Ikegami, Koh Ayusawa, Nobunori Kakusho, Atsushi Yoshiki,, Hideo Yokota, Yuko Okamura-Oho, Yoshihiko Nakamura
  • Organizer: AINI (Advances in Neuroinformatics) 2015
  • Place of Presentation: 東京大学先端科学技術研究センター エネオスホール、東京 駒場
  • Year and Date: 2015-11-26
  • Int'l Joint Research / Invited
• [Presentation] An automatic registration method for ISH images into the 3D standard brain atlas (2015)
  • Author(s): Daisuke Miyamoto, Yuko Okamura-Oho, Teiichi Furuichi, Ryohei Kanzaki, Hidetoshi Ikeno
  • Organizer: AINI (Advances in Neuroinformatics) 2015
  • Place of Presentation: 東京大学先端科学技術研究センター エネオスホール、東京 駒場
  • Year and Date: 2015-11-26
  • Int'l Joint Research / Invited
• [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis (2015)
  • Author(s): Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
  • Organizer: Neuroinformatics 2015
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2015-08-20 – 2015-08-22
• [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis (2015)
  • Author(s): Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
  • Organizer: NI(Neuroinformatics)2015
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2015-08-20
  • Int'l Joint Research
• [Presentation] Network analysis of 3D gene expression pattern, using microtomy based transcriptomic data sets in ViBrism DB (2015)
  • Author(s): Kazuro Shimokawa, Masahiko Morita, Masaomi Nishimura, Hideo Yokota, Yuko Okamura-Oho
  • Organizer: NI(Neuroinformatics)2015
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2015-08-20
  • Int'l Joint Research
• [Presentation] Neuromuscular Modeling by Bridging Mouse and Human (2015)
  • Author(s): Satoshi Oota
  • Organizer: Japan-EU Workshop on Neurorobotics
  • Place of Presentation: Ichijyo Hall, Yayoi Auditorium, The University of Tokyo,Tokyo
  • Year and Date: 2015-04-18
  • Int'l Joint Research / Invited
• [Presentation] 3次元内部構造顕微鏡による3次元計測の生物・材料分野への挑戦と展開 (2015)
  • Author(s): 於保祐子
  • Organizer: RIKENシンポジウム
  • Place of Presentation: 理化学研究所 仁科センター 大会議室、和光市、埼玉県
  • Year and Date: 2015-02-06
  • Invited
• [Presentation] Transcriptome tomography: mapping genes onto 3D brain structures (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Sakiko Nakamura, Yuki Tsujimura, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Takashi Ijiri, Takehiro Tawara, Hideo Yokota
  • Organizer: Annual meeting of Society of Neuroscience 2014
  • Place of Presentation: Washington DC, USA
  • Year and Date: 2014-11-15 – 2014-11-19
• [Presentation] Integrated Analysis of Expression Maps and Co-Expression Networks Using a Dataset of ViBrism DB (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Hideo Yokota
  • Organizer: AINI2014
  • Place of Presentation: Wako, Japan
  • Year and Date: 2014-09-25 – 2014-09-26
• [Presentation] Novel genes located in the co-expression networks detected with Transcriptome Tomography (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Akira Sato, Teiichi Furuichi, Hideo Yokota
  • Organizer: Neuroinformatics 2014
  • Place of Presentation: Leiden, Nederland
  • Year and Date: 2014-08-25 – 2014-08-27
• [Presentation] ﾄﾗﾝｽｸﾘﾌﾟﾄｰﾑ･ﾄﾓｸﾞﾗﾌｨｰを用いた遺伝子発現に基づく全脳地図作成 (2014)
  • Author(s): 於保祐子
  • Organizer: 科学技術振興機構主催 理化学研究所新技術説明会
  • Place of Presentation: JST 東京本部別館ホール、市ヶ谷、東京
  • Year and Date: 2014-06-12 – 2014-06-13
  • Invited
• [Book] バイオ画像解析手取り足取りガイド,第3章,５） (2014)
  • Author(s): 森田正彦,西村将臣,横田秀夫
  • Publisher: 羊土社
• [Book] ビッグデータ時代のゲノミクス情報処理 (2014)
  • Author(s): 北上始, 斉藤成也, 太田聡史
  • Total Pages: 226
  • Publisher: コロナ社
• [Remarks] ViBrism DB
  • URL: https://vibrism.neuroinf.jp/
• [Remarks] ViBrism DB
  • URL: http://vibrism.neuroinf.jp/