Researcher basic information

• Doctor of Philosophy, The Graduate University for Advanced Studies, Mar. 2017

• https://researchmap.jp/kzyamamoto?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=201401034745930883
• https://orcid.org/0000-0001-5539-1203
• https://sites.google.com/view/kait-cellmech

• 00801937

• https://orcid.org/0000-0001-5539-1203

• 201401034745930883

• 細胞極性
• Force measurement
• Comparative embryology

• Life Science, Biophysics
• Life Science, Developmental biology

Research activity information

• Mar. 2017, National Institute of Genetics, Morishima Award
  A study on inter-cellular forces for blastomere configurations in developing embryos

• Spatiotemporal mapping of the contractile and adhesive forces sculpting early C. elegans embryos
  Kazunori Yamamoto; Sacha Ichbiah; Matthieu Perez; Joana Borrego-Pinto; Fabrice Delbary; Nathan W. Goehring; Paul Northrop; Hervé Turlier; Guillaume Charras
  Developmental Cell, Elsevier BV, May 2026, [Peer-reviewed], [Lead author]
  Scientific journal, 36410928
• Long-range viscosity of the plasma membrane of a living cell measured by a shear-driven flow method
  Yuka Sakuma; Kazunori Yamamoto; Saya Ichihara; Toshihiro Kawakatsu; Kenya Haga; Masayuki Imai; Akatsuki Kimura
  Biophysical Journal, Elsevier BV, Sep. 2025, [Peer-reviewed]
  Scientific journal
• Switching from weak to strong cortical attachment of microtubules accounts for the transition from nuclear centration to spindle elongation in metazoans
  Shohei Tada; Yoshitaka Yamazaki; Kazunori Yamamoto; Ken Fujii; Takahiro G. Yamada; Noriko F. Hiroi; Akatsuki Kimura; Akira Funahashi
  Heliyon, 10, 3, e25494, e25494, Elsevier BV, Feb. 2024, [Peer-reviewed]
  Scientific journal
• Cell polarity: Adapting the PAR cascade to diverse cellular contexts
  Kazunori Yamamoto; Fumio Motegi
  Current Biology, 33, 20, R1047, R1049, Elsevier BV, Oct. 2023
  Scientific journal
• Dissecting the subcellular forces sculpting earlyC. elegansembryos
  Kazunori Yamamoto; Sacha Ichbiah; Joana Pinto; Fabrice Delbary; Nate Goehring; Hervé Turlier; Guillaume Charras
  bioRxiv, Cold Spring Harbor Laboratory, 09 Mar. 2023, [Lead author]
  Summary
  
  Embryo shape is governed by the mechanics of individual cells, the strength of intercellular interactions, and geometrical constraints. Models in which cells interact through surface tensions successfully predict cell arrangement within aggregates. However, predicting cell shape dynamics remains challenging because of difficulties in measuring temporal changes in tensions. Here, we dissect the spatiotemporal changes in cellular surface tensions that sculpt the early nematode embryo, using AFM measurements and inverse modeling. We validate a hybrid tension inference pipeline that combines dynamic information from cell geometry and cortical myosin enrichment. The inferred spatiotemporal tensions allow prediction of morphogenesis in wild-type embryos as well as phenotypic changes arising from protein depletion. We further uncover a direct and non-affine contribution of cadherins to cell contact tensions, whose magnitude is comparable to cadherins’ indirect contribution via actomyosin regulation. Overall, our inference pipeline allows characterization of the forces underlying morphogenesis and their relationship to molecular processes.
  
  Highlights
  
  P lineage cells have lower cortical tensions than AB lineage cells
  
  The balance between cortical and cell-cell interfacial tensions determines, together with the confinement within the eggshell, the shape of theC. elegansembryo.
  
  Abundance of Myosin-II is a good predictor of cortical tension but is not sufficient to determine tension at cell-cell contacts.
  
  Myosin-informed tension inference allows determination of the spatiotemporal evolution of all surface tensions within the embryo.
  
  Cadherins contribute non-linearly to tension at cell-cell contacts.
  
  Open Access
  
  For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.
• The extra-embryonic space and the local contour are crucial geometric constraints regulating cell arrangement
  Sungrim Seirin-Lee; Kazunori Yamamoto; Akatsuki Kimura
  Development, 149, 9, The Company of Biologists, 01 May 2022, [Peer-reviewed]
  English, Scientific journal, ABSTRACT
  
  In multicellular systems, cells communicate with adjacent cells to determine their positions and fates, an arrangement important for cellular development. Orientation of cell division, cell-cell interactions (i.e. attraction and repulsion) and geometric constraints are three major factors that define cell arrangement. In particular, geometric constraints are difficult to reveal in experiments, and the contribution of the local contour of the boundary has remained elusive. In this study, we developed a multicellular morphology model based on the phase-field method so that precise geometric constraints can be incorporated. Our application of the model to nematode embryos predicted that the amount of extra-embryonic space, the empty space within the eggshell that is not occupied by embryonic cells, affects cell arrangement in a manner dependent on the local contour and other factors. The prediction was validated experimentally by increasing the extra-embryonic space in the Caenorhabditis elegans embryo. Overall, our analyses characterized the roles of geometrical contributors, specifically the amount of extra-embryonic space and the local contour, on cell arrangements. These factors should be considered for multicellular systems.
• Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis.
  Hitoshi Sawada; Kazunori Yamamoto; Akira Yamaguchi; Lixy Yamada; Arata Higuchi; Haruhiko Nukaya; Masashi Fukuoka; Tetsushi Sakuma; Takashi Yamamoto; Yasunori Sasakura; Maki Shirae-Kurabayashi
  Scientific reports, 10, 1, 2514, 2514, 13 Feb. 2020, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Many hermaphroditic organisms possess a self-incompatibility system to avoid inbreeding. Although the mechanisms of self-incompatibility in flowering plants are well known, little is known about the mechanisms of self-sterility in hermaphroditic marine invertebrates. Ascidians are hermaphroditic sessile marine invertebrates that release sperm and eggs into the surrounding seawater. Several species, including Ciona intestinalis type A (Ciona robusta), exhibit strict self-sterility. In a previous study, we found that the candidate genes responsible for self-sterility in Ciona reside in chromosome 2q (locus A) and chromosome 7q (locus B). Two pairs of multi-allelic genes, named s(sperm)-Themis-A and v(vitelline-coat)-Themis-A in locus A and s-Themis-B and v-Themis-B in locus B, are responsible for self-sterility. In this study, we identified a third multi-allelic gene pair, s-Themis-B2 and v-Themis-B2, within locus B that is also involved in this system. Genetic analysis revealed that the haplotypes of s/v-Themis-A, s/v-Themis-B and s/v-Themis-B2 play essential roles in self-sterility. When three haplotypes were matched between s-Themis and v-Themis, fertilization never occurred even in nonself crossing. Interestingly, gene targeting of either s/v-Themis-B/B2 or s/v-Themis-A by genome editing enabled self-fertilization. These results indicate that s/v-Themis-A, -B and -B2 are S-determinant genes responsible for self-sterility in the ascidian C. intestinalis type A.
• An asymmetric attraction model for the diversity and robustness of cell arrangement in nematodes.
  Kazunori Yamamoto; Akatsuki Kimura
  Development (Cambridge, England), 144, 23, 4437, 4449, 01 Dec. 2017, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, During early embryogenesis in animals, cells are arranged into a species-specific pattern in a robust manner. Diverse cell arrangement patterns are observed, even among close relatives. In the present study, we evaluated the mechanisms by which the diversity and robustness of cell arrangements are achieved in developing embryos. We successfully reproduced various patterns of cell arrangements observed in various nematode species in Caenorhabditis elegans embryos by altering the eggshell shapes. The findings suggest that the observed diversity of cell arrangements can be explained by differences in the eggshell shape. Additionally, we found that the cell arrangement was robust against eggshell deformation. Computational modeling revealed that, in addition to repulsive forces, attractive forces are sufficient to achieve such robustness. The present model is also capable of simulating the effect of changing cell division orientation. Genetic perturbation experiments demonstrated that attractive forces derived from cell adhesion are necessary for the robustness. The proposed model accounts for both diversity and robustness of cell arrangements, and contributes to our understanding of how the diversity and robustness of cell arrangements are achieved in developing embryos.

• 海外だより～国際色豊かなロンドンでの研究生活～
  山本一徳
  生物物理/60 巻 (2020) 5 号, 2020, 36410928, [Single work]
• Sexual Reproduction in Animals and Plants
  Hitoshi Sawada; Kazunori Yamamoto; Kei Otsuka; Takako Saito; Akira Yamaguchi; Masako Mino; Mari Akasaka; Yoshito Harada; Lixy Yamada, Allorecognition and Lysin Systems During Ascidian Fertilization
  Springer, 2014, [Joint work]

• 線虫C. elegansの孵化過程の観察
  山本一徳
  日本動物学会 第93回 早稲田大会, 08 Sep. 2022, Japanese, Oral presentation
  08 Sep. 2022 - 10 Sep. 2022
• Measurement of the surface tension of the cells in C. elegans early embryo using Atomic Force Microscopy
  K Yamamoto; G Charras
  Physics of Living Matter 13th (Marseille, France), Sep. 2018, English, Poster presentation
  Sep. 2018 - Sep. 2018
• Shapes of eggshell and inter-cellular forces contribute to arrangements of the cells in early worms embryo
  K Yamamoto
  IPLS Meet-Up (UCL, LMCB, London), Jun. 2018, English, Oral presentation
  Jun. 2018 - Jun. 2018
• A possible impact of oocyte shapes on cell arrangement patterns during embryogenesis in C. elegans and their diversity among nematode species
  K Yamamoto; A Kimura
  The International Research Symposium on Regulation of Germ Cell Development in vivo and in vitro, Jun. 2017, English, Poster presentation
  Jun. 2017 - Jun. 2017
• A novel mechanistic model that accounts for the diversity and robustness of blastomere configurations against embryo deformations in nematodes
  K Yamamoto; A Kimura
  50th Annual Meeting of the JSDB, May 2017, English, Poster presentation
  May 2017 - May 2017
• Inter-cellular forces contribute to pattern formation of cell arrangement
  K Yamamoto; A Kimura
  JSDB Autumn symposium, Oct. 2016, Japanese, Oral presentation
  Oct. 2016 - Oct. 2016
• The eggshell shape contributes to generate multiple patterns of cell alignment
  K Yamamoto; A Kimura
  Japan Q-Bio Week Tokyo Symposium, Jan. 2016, Japanese, Poster presentation
  Jan. 2016 - Jan. 2016
• The mechanical effect of eggshell shape on the pattern of cell alignment during C. elegans embryogenesis
  Yamamoto K; Kimura A
  BMB2015, Dec. 2015, Japanese, Poster presentation
  Dec. 2015 - Dec. 2015
• Diversity of cleavage pattern during embryogenesis in Nematodes(small worm)
  Yamamoto K; Kimura A
  Life Science retreat, Oct. 2014, English, Oral presentation
  Oct. 2014 - Oct. 2014
• Watching variable cleavage patterns in Nematodes standing from the viewpoint of mechanics
  Yamamoto K; Kimura A
  NIG retreat, Jul. 2014, English
  Jul. 2014 - Jul. 2014
• Self-sterile mechanism in an ascidian (primitive chordate) Ciona intestinalis: Its reproductive tactics shared with flowering plants
  Sawada H; Yamamoto K; Yamaguchi A; Otsuka K; Yamada L
  Gordon research conference, Jul. 2013, English, Oral presentation
  Jul. 2013 - Jul. 2013
• Genetic analysis of novel candidates involved in the self-incompatibility system of ascidian
  Yamamoto K; Yamada L; Sawada H
  46th Annual Meeting of JSDB, May 2013, English, Poster presentation
  May 2013 - Jun. 2013
• s/v-Themis and novel allorecognition candidates for the self-incompatibility system in the ascidian Ciona intestinalis
  Yamamoto K; Yamada L; Sawada H
  International Symposium on the Mechanism of Sexual Reproduction in Animals and Plants, Nov. 2012, English, Poster presentation
  Nov. 2012

• Midbodyはシグナル因子のハブとして細胞極性を能動的に制御するか
  科学研究費助成事業
  Apr. 2026 - Mar. 2029
  山本 一徳
  日本学術振興会, 基盤研究(C), 北海道大学, 26K09299
• Boundary between non-living and living matter revealed by measuring the fluidity of "living" cell membranes
  Grants-in-Aid for Scientific Research
  01 Apr. 2023 - 31 Mar. 2027
  佐久間 由香; 山本 一徳
  細胞膜における膜流動性は、生体機能の発現を制御する重要な因子であり、これまでに脂質のみから成るモデル細胞膜を用いて盛んに研究されてきた。一方、生きた細胞膜は糖鎖などによる膜表面の修飾や脂質分布の非対称性，膜内外での溶液粘度の非対称性など複雑な構造を持つ。さらに、細胞骨格から力学的揺動を受けた非平衡状態にあり、細胞の生死によってその流動特性に大きな違いがあることが予想される。本研究では「生きている細胞膜と無生物であるモデル細胞膜の流動性は何が違うのか」を明らかにするため、モデル細胞膜に糖鎖に見立てた高分子をグラフトし、膜粘度への影響を調べた。その結果、膜にグラフトする高分子濃度が高くなると膜粘度は高分子をグラフトしない膜の8倍程度まで大きくなることがわかった。さらに、グラフトした高分子同士の相互作用が膜粘度上昇に寄与していることを理論的な観点から明らかにした. この成果は専門誌Biophysical Journalに発表した [Sakuma et al., Biophys. J. (2024]]. また、生きている細胞膜と細胞骨格の相互作用について実験的に明らかにし、細胞骨格の状態がの膜流動性に大きく影響することを明らかにした。さらに、モデル細胞膜と細胞膜のギャップをつなぐために細胞から細胞表層のみを単離したGiant Plasma Membrane Vesicle (GPMV)の作製技術を習得した。これによって、今後は細胞, GPMV, モデル細胞膜のそれぞれの膜粘度測定をすることで、その差異から生物と無生物の違いについて膜流動性の観点から明らかにする足掛かりができた。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Tohoku University, 23K25834
• 「生きている」細胞膜の流動性測定から解明する非生命と生命の境界
  科学研究費助成事業 基盤研究(B)
  Apr. 2023 - Mar. 2027
  佐久間 由香
  日本学術振興会, 基盤研究(B), 東北大学, Coinvestigator, 23H01137
• 細胞極性の反転：自律的極性化の環境応答性を司る分子機構の解明
  科学研究費助成事業
  01 Apr. 2024 - 31 Mar. 2026
  山本 一徳
  日本学術振興会, 若手研究, 北海道大学, 24K18103
• Measurement of cellular cortical forces and their comparison in invertebrate embryos
  NIG-JOINT (A)
  Apr. 2021 - Mar. 2022
  Akatsuki Kimura
  National Institute of Genetics, National Institute of Genetics, Principal investigator, NIG-JOINT83A2021
• 多細胞体の形態を規定する細胞表層張力・曲げ弾性率・細胞間接着力の動物種間比較
  笹川科学研究助成
  Apr. 2021 - Mar. 2022
  日本科学協会, Principal investigator
• C. elegans初期胚を用いた細胞力学特性の測定
  海外留学助成 ポストドクトラルフェローシップ
  Apr. 2018 - Mar. 2019
  上原生命科学財団
• 卵割期の細胞配置パターンの定量計測と数理モデルの構築
  科学研究費助成事業 特別研究員奨励費
  Apr. 2016 - Mar. 2018
  山本 一徳
  H29年度は、これまでに得られた実験結果をまとめて論文を作成し、海外の学術雑誌への掲載を目指した。特別研究員が筆頭著者として受け入れ研究者と共に論文を執筆した。Development誌においてリバイスを受け、追加の実験を行ない論文掲載に至った。追加の実験では、２細胞期から４細胞期にかけての細胞の分裂方向のパターンが野生型とは異なる場合に卵殻形状の違いとともに細胞がどのように配置するのかを調べた。そして、構築した数理モデルが分裂方向のパターンが異なる場合においても有用かどうか検討した。本研究で提唱された数理モデルは細胞の分裂パターンが異なる条件でも実際の観察結果を再現することがある程度できているため、他線虫種を含めた様々な細胞配置パターンを再現・予測することができると考えられた。これまでは胚発生の初期段階における多様な細胞配置パターン形成の力学的な機構はほとんど分かっていなかったが、本研究により、細胞の周囲を覆う空間的な制約の形状と細胞間力(細胞同士の押し合う力や引き合う力)の二つの要素の違いによって線虫胚における多様な細胞配置形成が決まることが明らかとなった。
  次の課題として、数理モデルで仮定した細胞間力が実際のC. elegans初期胚でどう働いているのかは明らかではなかった。そのため、細胞間力の大きさと細胞間距離の関係を実際に測定することを目的として、Atomic Force Microscopy(AFM)を用いた実験を新たに計画した。JSPSとERCとの協力による特別研究員の海外渡航支援事業を利用してCell mechanicsが専門のUniversity College London(UCL)のGuillaume Charras教授にコンタクトをとった。５ヶ月間の滞在でAFMの使い方を習得し、細胞表層のアクトミオシンの細胞間力への寄与について知見を得ることもできた。
  日本学術振興会, 特別研究員奨励費, 16J09469