Self-organization of elaborate digestive tract in the simple chordate

• Project/Area Number: 17KT0023
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Multi-year Fund
• Section: 特設分野
• Research Field: Constructive Systems Biology
• Research Institution: Osaka University
• Principal Investigator: Nishida Hiroki 大阪大学, 理学研究科, 教授 (60192689)
• Co-Investigator(Kenkyū-buntansha): 小沼 健 大阪大学, 理学研究科, 助教 (30632103)
• Project Period (FY): 2017-07-18 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000); Fiscal Year 2019: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2018: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2017: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
• Keywords: 器官形成 / 消化器官 / 形態形成 / 口形成 / カドヘリン / 走査型電子顕微鏡 / オタマボヤ / 脊索動物 / 自己組織化 / 消化管

Outline of Final Research Achievements

Analyses of mechanisms on how intricate 3D structures of body and organs would contribute to our understanding of developmental processes. To this purpose, live imaging of developing animal with cellular resolution would provide crucial information. In this project, we used larvaceans with various advantages as a model system. First, each constitutive cell was mapped in 3D reconstruction of whole body and each organ with aid of serial block face scanning electron microscopy. Then, processes of mouth opening and formation of associated sensory organs were monitored using 4D fluorescence time-lapse recording. Genome browser was established and every cadherin gene in the genome were listed up. Their gene expression was analyzed during formation of tissue boundaries in the trunk.

Academic Significance and Societal Importance of the Research Achievements

複雑な形態が個体差なく形作られるしくみの理解は遅れており、発生生物学の中でも、フロンティアとして位置づけられている。研究を実りあるものにするためには利点に富んだ適切な系の選択が研究の推進に重要となる。本研究により、オタマボヤはライブイメージングのための多くの利点を備えていることがわかった。オタマボヤは体幹部で起こる形態形成を容易かつ包括的に記録できるユニークな系を提供する。本研究は我々のオタマボヤの継代飼育技術と実験手法等の積み重ねを元に遂行したものであり、オタマボヤが3D形態形成のしくみを解明するのに多くの利点を持った系であることを広く示すことができたという点で学術的な意義は大きい。

Research Products

• [Int'l Joint Research] バルセロナ大学(スペイン)
• [Int'l Joint Research] パドバ大学(イタリア)
• [Int'l Joint Research] 上海交通大学(中国)
• [Int'l Joint Research] パドバ大学(イタリア)
• [Int'l Joint Research] モンパリエ大学(フランス)
• [Int'l Joint Research] 上海交通大学(中国)
• [Int'l Joint Research] パドバ大学(イタリア)
• [Int'l Joint Research] モンパリエ大学(フランス)
• [Int'l Joint Research] 上海交通大学(中国)
• [Int'l Joint Research] パドヴァ大学(イタリア)
• [Int'l Joint Research] モンパリエ大学(フランス)
• [Journal Article] Germline development during embryogenesis of the larvacean, Oikopleura dioica. (2022)
  • Author(s): Nishida, H., Matsuo, M., Konishi, S., Ohno, N., Manni, L., and Onuma T.A.
  • Journal Title: Devevalopmental Biology Volume: 481 Pages: 188-200
  • DOI: 10.1016/j.ydbio.2021.10.009
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Developmental biology of the larvacean Oikopleura dioica : Genome resources, functional screening, and imaging (2022)
  • Author(s): Onuma, T. A. and Nishida, H.
  • Journal Title: Dev. Growth Differ. Volume: 64 Issue: 1 Pages: 67-82
  • DOI: 10.1111/dgd.12769
  • Peer Reviewed / Open Access
• [Journal Article] Expression and functional analyses of ectodermal transcription factors FoxJ-r, SoxF, and SP8/9 in early embryos of the ascidian Halocynthia roretzi (2021)
  • Author(s): Shih, Y., Wang, K., Kumano, G., and Nishida, H.
  • Journal Title: Zoological Science Volume: 38 Issue: 1 Pages: 26-35
  • DOI: 10.2108/zs200128
  • NAID: 210000177228
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM (2021)
  • Author(s): Nishida H., Ohno N., Caicci F., Manni L.
  • Journal Title: Scientific Reports Volume: 11 Issue: 1 Pages: 4833-4833
  • DOI: 10.1038/s41598-021-83706-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Massive gene loss and function shuffling in appendicularians stretch the boundaries of chordate Wnt family evolution (2021)
  • Author(s): Marti-Solans, J., Godoy, H., Diaz-Gracia, M., Onuma, T., Nishida, H., Albalat R., and Canestro, C.
  • Journal Title: Frontiers Cell Dev. Biol. Volume: 9 Pages: 700827-700827
  • DOI: 10.3389/fcell.2021.700827
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. (2020)
  • Author(s): Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse M, Louis A, Nitta N, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Gueroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan J, Davidson B, Nishida H, Dantec C and Lemaire P
  • Journal Title: Nucleic Acids Research. Volume: 48(D1)
  • DOI: 10.1093/nar/gkz955
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica. (2020)
  • Author(s): Matsuo M, Onuma TA, Omotezako T and Nishida N
  • Journal Title: Developmental Biology. Volume: 460(2) Issue: 2 Pages: 155-163
  • DOI: 10.1016/j.ydbio.2019.12.005
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning. (2020)
  • Author(s): Onuma, T.A., Hayashi, M., Gyoja, F., Kishi, K., Wang, K., Nishida, H.
  • Journal Title: Proc. Natl. Acad. Sci. USA. Volume: 117 Issue: 8 Pages: 4188-4198
  • DOI: 10.1073/pnas.1916858117
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A genome database for a Japanese population of the larvacean Oikopleura dioica. (2020)
  • Author(s): Wang, K., Tomura, R., Chen, W., Kiyooka, M., Ishizaki, H., Aizu, T., Minakuchi, Y., Seki, Yutaka Suzuki, M., Omotezako, T., Suyama, R., Masunaga, A., Plessy, C., Luscombe, N.M., Dantec, C., Lemaire, P., Itoh, T., Toyoda, A., Nishida, H., and Onuma, T.A.
  • Journal Title: Dev. Growth Differ. Volume: 62 Issue: 6 Pages: 450-461
  • DOI: 10.1111/dgd.12689
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mouth opening is mediated by separation of dorsal and ventral daughter cells of the lip precursor cells in the larvacean, Oikopleura dioica. (2020)
  • Author(s): Morita, R., Onuma, T.A., Manni, L., Ohno, N., Nishida, H.
  • Journal Title: Dev. Genes Evol. Volume: 230 Issue: 5-6 Pages: 315-327
  • DOI: 10.1007/s00427-020-00667-4
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. (2020)
  • Author(s): Coulcher, J. F., Roure, A., Chowdhury, R., Robert, M., Lescat, L., Bouin, A., Cadavid, J. C., Nishida, H., and Darras, S.
  • Journal Title: eLIFE Volume: 9
  • DOI: 10.7554/elife.59157
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Wavy movements of epidermis monocilia drive the neurula rotation that determines left-right asymmetry in ascidian embryos. (2019)
  • Author(s): Yamada, S., Tanaka, Y., Imai, K.S., Saigou, M., Onuma, T.A., and Nishida, H.
  • Journal Title: Dev. Biol. Volume: 印刷中 Issue: 2 Pages: 173-182
  • DOI: 10.1016/j.ydbio.2018.07.023
  • Peer Reviewed
• [Journal Article] Vitelline membrane proteins promote left-sided nodal expression after neurula rotation in the ascidian, Halocynthia roretzi. (2019)
  • Author(s): Tanaka, Y., Yamada, S., Connop, S. L., Hashii, N., Sawada, H., Shih, Y., and Nishida, H.
  • Journal Title: Dev. Biol. Volume: 449 Issue: 1 Pages: 52-61
  • DOI: 10.1016/j.ydbio.2019.01.016
  • Peer Reviewed
• [Journal Article] Control of Pem protein level by localized maternal factors for transcriptional regulation in the germline of the ascidian, Halocynthia roretzi. (2018)
  • Author(s): Miyaoku, K., Nakamoto, A., Nishida, H., and Kumano, G.
  • Journal Title: PLOS ONE Volume: 13 Issue: 4 Pages: e0196500-e0196500
  • DOI: 10.1371/journal.pone.0196500
  • Peer Reviewed / Open Access
• [Journal Article] Wnt evolution and function shuffling in liberal and conservative chordate genomes. (2018)
  • Author(s): Somorjai, I. M. L., Marti-Solans, J., Diaz-Gracia, M., Nishida, H., Imai, K. S., Escriva, H., Canestro, C., and Albalat, R.
  • Journal Title: Genome Biology Volume: 19 Issue: 1 Pages: 9-9
  • DOI: 10.1186/s13059-018-1468-3
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets (2017)
  • Author(s): Brozovic Matija、Dantec Christelle、,,,,,,, Nishida Hiroki、,,,,,,, Lemaire Patrick
  • Journal Title: Nucleic Acids Res. Volume: 46 Issue: D1 Pages: D718-D725
  • DOI: 10.1093/nar/gkx1108
  • NAID: 120006401706
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Asymmetric and Unequal Cell Divisions in Ascidian Embryos (2017)
  • Author(s): Negishi Takefumi、Nishida Hiroki
  • Journal Title: Results and Problems in Cell Differentiation Volume: 61 Pages: 261-284
  • DOI: 10.1007/978-3-319-53150-2_12
  • ISBN: 9783319531496, 9783319531502
  • Peer Reviewed
• [Journal Article] Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi (2017)
  • Author(s): Wang Kai、Dantec Christelle、Lemaire Patrick、Onuma Takeshi A.、Nishida Hiroki
  • Journal Title: BMC Genomics Volume: 18 Issue: 1 Pages: 314-314
  • DOI: 10.1186/s12864-017-3707-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Patterning and morphogenesis of the intricate but stereotyped oikoplastic epidermis of the appendicularian, Oikopleura dioica (2017)
  • Author(s): Kishi Kanae、Hayashi Momoko、Onuma Takeshi A.、Nishida Hiroki
  • Journal Title: Developmental Biology Volume: 428 Issue: 1 Pages: 245-257
  • DOI: 10.1016/j.ydbio.2017.06.008
  • Peer Reviewed
• [Journal Article] Modified whole-mount in situ hybridisation and immunohistochemistry protocols without removal of the vitelline membrane in the appendicularian Oikopleura dioica (2017)
  • Author(s): Onuma Takeshi A.、Matsuo Masaki、Nishida Hiroki
  • Journal Title: Development Genes and Evolution Volume: 227 Issue: 5 Pages: 367-374
  • DOI: 10.1007/s00427-017-0588-1
  • Peer Reviewed
• [Presentation] Transcriptomic analyses of the fast-developing chordate, Oikopleura dioica, uncover re-organization of transcription factors functioning in early embryos and the animal-vegetal axis specification (2021)
  • Author(s): Kai Wang, Ritsuko Suyama, Nakako Mizutani, Masaki Matsuo, Yu Peng, Masahide Seki, Yutaka Suzuki, Nicholas M. Luscombe, Christelle Dantec, Patrick Lemaire, Atsushi Toyoda, Hiroki Nishida and Takeshi A. Onuma
  • Organizer: 日本発生生物学会
• [Presentation] マボヤの原腸陥入と単離内胚葉割球のブレブ形成 (2021)
  • Author(s): 濵田 果歩、西田 遥香、児下 未佳、西田 宏記
  • Organizer: 日本動物学会
• [Presentation] The larvacean Oikopleura dioica lacks Nodal and utilizes calcium oscillation and Bmp expression for left-right patterning. (2020)
  • Author(s): Takeshi A. Onuma, Momoko Hayashi, Fuki Gyoja, Kanae Kishi, Kai Wang and Hiroki Nishida
  • Organizer: 日本発生生物学会
• [Presentation] 脊索動物オタマボヤをもちいて左右形成の新しい領域を開拓する (2020)
  • Author(s): 小沼健、西田宏記
  • Organizer: 第５回ホヤ研究会
• [Presentation] マボヤの原腸陥入と単離内胚葉割球のブレブ形成活性について (2020)
  • Author(s): 西田宏記、西田遥香、児下未佳
  • Organizer: 第５回ホヤ研究会
• [Presentation] 動物繊維をもちいたオタマボヤの「ハウス」建築 (2020)
  • Author(s): 小沼 健、秋山 正和、山崎 慎太郎、近藤 滋、西田 宏記
  • Organizer: 日本分子生物学会
  • Invited
• [Presentation] 複雑で規則性のないパターンを個体差なく作り出すしくみ：オタマボヤの幼生発生にける表皮細胞のパターン形成 (2019)
  • Author(s): 岸香苗, 林桃子, 小沼健, 西田宏記
  • Organizer: 日本動物学会
  • Invited
• [Presentation] Nodal遺伝子を持たない脊索動物オタマボヤにおける左右非対称形成 (2019)
  • Author(s): 小沼 健、林 桃子、行者 蕗、岸 香苗、王 凱、西田 宏記
  • Organizer: 日本動物学会
• [Presentation] オタマボヤ綱ミトコンドリアゲノムの進化 (2019)
  • Author(s): 笠原 享祐、足立 千尋、望月 遊 、大塚 玄航、西野 敦雄、小沼 健、西田 宏記 、横堀 伸一
  • Organizer: 日本動物学会
• [Presentation] SBF-SEM：70 nmごとの電顕連続切片からオタマボヤの3D像を立体構築する実験の紹介 (2019)
  • Author(s): 西田宏記
  • Organizer: ホヤ研究会
  • Invited
• [Presentation] Neurula rotation and left-right asymmetry in ascidian embryos: Ciliarymovements and the vitelline membrane signal (2019)
  • Author(s): hiori Yamada, Yuka Tanaka, Kaoru S. Imai, Motohiko Saigo1, Takeshi A. Onuma, Samantha L. Connop, Noritaka Hashii, Hitoshi Sawada, Hiroki Nishida
  • Organizer: 10th INTERNATIONAL TUNICATE MEETING
  • Int'l Joint Research / Invited
• [Presentation] A CHORDATE SPECIES LACKING NODAL UTILIZES CALCIUM OSCILLATION AND BMP4 FOR LEFT-RIGHT PATTERNING (2019)
  • Author(s): akeshi A. Onuma, Momoko Hayashi, Fumi Gyojya, Kanae Kishi, Kai Wang and Hiroki Nishida
  • Organizer: 10th INTERNATIONAL TUNICATE MEETING
  • Int'l Joint Research
• [Presentation] Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica (2019)
  • Author(s): Masaki Matsuo, Takeshi A. Onuma, and Hiroki Nishida
  • Organizer: 10th INTERNATIONAL TUNICATE MEETING
  • Int'l Joint Research
• [Presentation] XPRESSION AND FUNCTIONAL ANALYSES OF THE FOUR ECTODERMAL TRANSCRIPTION FACTORS IN THE ASCIDIAN, HALOCYNTHIA EMBRYOS (2019)
  • Author(s): Shih Yu, Wang Kai, and Nishida Hiroki
  • Organizer: 10th INTERNATIONAL TUNICATE MEETING
  • Int'l Joint Research
• [Presentation] COMPARATIVE GENOMIC ANALYSIS : IDENTIFICATIONOF NOVEL GENES IN ASCIDIANS (2019)
  • Author(s): Christelle Dantec, Paul Simion, Magali Naville, Justine Dardaillon, Remo Sanges, Celine Scornavacca , Frederic Delsuc, Jean-Nicolas Volff, Hiroki Nishida, Emmanuel Douzery and Patrick Lemaire
  • Organizer: 10th INTERNATIONAL TUNICATE MEETING
  • Int'l Joint Research
• [Presentation] A new chordate model animal with short life cycle of five days: The Appendicularian, Oikopleura dioica (2019)
  • Author(s): Hiroki Nishida
  • Organizer: Kunming University Seminar
  • Int'l Joint Research / Invited
• [Presentation] Protein phosphatase 2A (PP2A) is essential for maintenance of meiotic arrest in the larvacean, Oikopleura dioica (2018)
  • Author(s): Masaki Matsuo, Takeshi A. Onuma, Hiroki Nishida
  • Organizer: 日本発生生物学会
• [Presentation] Direction of calcium waves is linked with the left-right axis of larvacean embryos (2018)
  • Author(s): Takeshi A Onuma, Hiroki Nishida
  • Organizer: 日本発生生物学会
• [Presentation] ワカレオタマボヤにおける2 本鎖DNA を介した新規の遺伝子抑制現象 は、小分子RNA の合成をともなう (2018)
  • Author(s): 塚田かすみ，小沼健，西田宏記
  • Organizer: 日本動物学会
• [Presentation] ワカレオタマボヤの幼生発生において複雑で規則性のない表皮細胞パターンを個体差なく作り出すしくみ (2018)
  • Author(s): 西田宏記，岸香苗，林桃子，小沼健
  • Organizer: 日本動物学会
• [Presentation] Eccentric position of the germinal vesicle and cortical flow during oocyte maturation specify the animal-vegetal axis of ascidian embryos (2017)
  • Author(s): Masumi Tokuhisa, Miyuki Muto, Hiroki Nishida
  • Organizer: 日本発生生物学会
  • Invited
• [Presentation] Whole-mount in situ hybridization and immunohistochemistry procedures without removal of the vitelline membrane of embryos in the appendicularian, Oikopleura dioica (2017)
  • Author(s): Takeshi Onuma, Masaki Matsuo, Hiroki Nishida
  • Organizer: 日本発生生物学会
• [Presentation] Functional screening of maternal factors and analysis of metaphase arrest of meiosis in the appendicularian, Oikopleura dioica (2017)
  • Author(s): Masaki Matsuo, Tatsuya Omotezako, Takeshi Onuma, Hiroki Nishida
  • Organizer: 日本発生生物学会
• [Presentation] オタマボヤにおける2 細胞期から開始する左右非対称な発生過程 (2017)
  • Author(s): 小沼健，林桃子，岸香苗，西田宏記
  • Organizer: 日本動物学会
  • Invited
• [Presentation] 神経胚回転によるマボヤの左右非対称性の決定には繊毛が関与している (2017)
  • Author(s): 田中 佑佳，山田 詩織，西田 宏記
  • Organizer: 日本動物学会
• [Presentation] 18S rRNA 遺伝子並びにミトコンドリアゲノムに基づくオタマボヤ綱の分子系統解析 (2017)
  • Author(s): 横堀 伸一，笠原 享祐，大塚 玄航，西野 敦雄，小沼 健，西田 宏記，山岸 明彦
  • Organizer: 日本動物学会
• [Presentation] Eccentric position of the germinal vesicle and cortical flow during oocyte maturation specify the animal-vegetal axis of ascidian embryos (2017)
  • Author(s): Nishida H, Tokuhisa M, Muto M
  • Organizer: 国際発生生物学会
  • Int'l Joint Research
• [Presentation] Patterning and morphogenesis of the intricate but stereotyped Oikoplastic epidermis of the appendicularian, Oikopleura dioica (2017)
  • Author(s): Kanae Kishi, Momoko Hayashi, Takeshi A. Onuma, and Hiroki Nishida
  • Organizer: 9th International Tunicate Meeting
  • Int'l Joint Research
• [Remarks] 研究室ホームページ
  • URL: https://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/nishida/index.html
• [Remarks] 研究室ホームページ
  • URL: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/nishida/index.html
• [Remarks] Hiroki NISHIDA's Laboratory
  • URL: http://www.bio.sci.osaka-u.ac.jp/bio_web/lab_page/nishida/index.html