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Researcher Information

last modified:2024/01/08

Associate Professor Nakayama Takahiro

Mail Laboratory Website

Faculty, Affiliation

WPI Nano Life Science Institute
Associate Professor

College and School Educational Field

Division of Natural Sciences, Graduate School of Natural Science and Technology
Division of Natural System, Graduate School of Natural Science and Technology
Course in Biosystems, School of Biological Science and Technology, College of Science and Engineering


Academic Background

【Academic background(Doctoral/Master's Degree)】
Tokyo Institute of Technology Doctor 200803 Completed
【Academic background(Bachelor's Degree)】
Hiroshima University
Doctor of Science


Bio-AFM Frontier Research Center, Kanazawa University
Tokyo Institute of Technology Postdoctoral Researcher(2008/04/01-2012/03/31)
Japan Science and Technology Agency(2004/04/01-2005/03/01)
Tokyo Institute of Technology Chemical Resources Laboratory(2003/04/01-2004/03/30)

Year & Month of Birth

Academic Society



Speciality Keywords

Single molecule observation, Atomic force microscopy

Research Themes


  •  Watanabe-Nakayama T, Machida S, Saito M, Afrin R, Ikai A. Cells, Forces, and the Microenvironment CRC Press 2015/03/02
  •  Ikai A, Afrin R, Watanabe-Nakayama T, Machida S. Atomic Force Microscopy in Liquid: Biological Applications Wiley Online Library 2012/04/10


  •  A cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and an antagonist for amylin fibrillation Sahoo BR, Genjo T, Watanabe-Nakayama T, Stoddard AK, Ando T, Yasuhara K, Fierkead CA, Ramamoorthy A Chem Sci 10 3976-3986 2019
  •  High molecular weight amyloid β1-42 oligomers induce neurotoxicity via plasma membrane damage. Yasumoto T, Takamura Y, Tsuji M, Watanabe-Nakayama T, Imamura K, Inoue H, Nakamura S, Inoue T, Kimura A, Yano S, Nishijo H, Kiuchi Y, Teplow DB, Ono K. FASEB J. 2019/08
  •  Intramolecular interaction suggests an autosuppression mechanism for the innate immune adaptor protein MyD88. Uno M, Watanabe-Nakayama T, Konno H, Akagi KI, Tsutsumi N, Fukao T, Shirakawa M, Ohnishi H, Tochio H Chem Commun (Camb) 54 87 12318-12321 2018/10/30
  •  High-Speed Atomic Force Microscopy of Individual Amyloidogenic Protein Assemblies Watanabe-Nakayama T, Ono K Methods Mol Biol 1814 201-212 2018
  •  Membrane wound healing at single cellular level Afrin R, Saito M, Watanabe-Nakayama T, Ikai A. Nanomedicine 13 7 2351-2357 2017/07/26

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  •  Atomic force microscope as a nano- and micrometer scale biological manipulator: a short review Ikai A, Afrin R, Saito M, Watanabe-Nakayama T. Semin Cell Dev Biol pii: S1084-9521(17) 30326-9 2017/07/21
  •  High-Speed Atomic Force Microscopy Reveals Loss of Nuclear Pore Resilience as a Dying Code in Colorectal Cancer Cells Mohamed M, Kobayashi A, Taoka A, Watanabe-Nakayama T, Kikuchi Y, Hazawa M, Minamoto T, Fukumori Y, Kodera N, Uchihashi T, Ando T, Wong RW. ACS Nano 11 6 5567-5578 2017/06/27
  •  High-speed atomic force microscopy reveals strongly polarized movement of clostridial collagenase along collagen fibrils Watanabe-Nakayama T, Itami M, Kodera N, Ando T, Konno H Scientific Reports 6 28975 2016/07/04
  •  High-speed atomic force microscopy reveals structural dynamics of amyloid β1-42 aggregates Watanabe-Nakayama T, Ono K, Itami M, Takahashi R, Teplow DB, Yamada M Proceedings of the National Academy of Sciences of the United States of America 113 21 5835-40 2016/05/24
  •  Spectrin-ankyrin interaction mechanics: A key force balance factor in the red blood cell membrane skeleton Saito M, Watanabe-Nakayama T, Machida S, Osada T, Afrin R, Ikai A Biophysical Chemistry 200-201 1-8 2015/03/28
  •  Fabrication of electron beam deposited tip for atomic-scale atomic force microscopy in liquid Miyazawa K, Izumi H, Watanabe-Nakayama T, Asakawa H, Fukuma T Nanotechnology 26 10 105707 2015/03/13
  •  Significant improvements in stability and reproducibility of atomic-scale atomic force microscopy in liquid Akrami SM, Nakayachi H, Watanabe-Nakayama T, Asakawa H, Fukuma T Nanotechnology 25 45 455701 2014/11/14
  •  Requirement of LIM domains for the transient accumulation of paxillin at damaged stress fibres Watanabe-Nakayama T, Saito M, Machida S, Kishimoto K, Afrin R, Ikai A. Biology Open 2 7 667-674 2013/05/23
  •  Fabricated cantilever for AFM measurements and manipulations: Pre-stress analysis of stress fibers Machida S, Watanabe-Nakayama T, Saito M, Afrin R, Ikai A. Micron 43 12 1380-9 2012/04/21
  •  Thermodynamic efficiency and mechanochemical coupling of F1-ATPase Toyabe S, Watanabe-Nakayama T, Okamoto T, Kudo S, Muneyuki E. Proceedings of the National Academy of Sciences of the United States of America 108 44 17951-6 2011/11/01
  •  Mechanics of Intracellular Stress Fibers: A Short Review. Ikai A, Watanabe-Nakayama T, Machida S, Saito M, Afrin R. Japanese Journal of Applied Physics 50 8 08LA04-08LA04-8 2011/08/22
  •  Direct detection of cellular adaptation to local cyclic stretching at the single cell level by atomic force microscopy. Watanabe-Nakayama T, Machida S, Harada I, Sekiguchi H, Afrin R, Ikai A. Biophysical Journal 100 3 564-72 2011/02/02
  •  Microscoop for manipulation of micro-objects: use of fabricated cantilever with atomic force microscope. Watanabe-Nakayama T, Machida S, Afrin R, Ikai A. Small 6 24 2853-7 2010/12/20
  •  Direct manipulation of intracellular stress fibres using a hook-shaped AFM probe. Machida S, Watanabe-Nakayama T, Harada I, Afrin R, Nakayama T, Ikai A. Nanotechnology 21 38 385102 2010/09/24
  •  Nonequilibrium energetics of a single F1-ATPase molecule. Toyabe S, Okamoto T, Watanabe-Nakayama T, Taketani H, Kudo S, Muneyuki E. Physical Review Letters 104 19 198103 2010/05/14
  •  Atomic force microscopy for cellular level manipulation: imaging intracellular structures and DNA delivery through a membrane hole. Afrin R, Zohora US, Uehara H, Watanabe-Nakayama T, Ikai A. Journal of Molecular Recognition 22 5 363-72 2009/07/21
  •  Effect of external torque on the ATP-driven rotation of F1-ATPase. Watanabe-Nakayama T, Toyabe S, Kudo S, Sugiyama S, Yoshida M, Muneyuki E.  Biochemical and Biophysical Research Communications 366 4 951-7 2008/02/22
  •  Single molecule energetics of F1-ATPase motor. Muneyuki E, Watanabe-Nakayama T, Suzuki T, Yoshida M, Nishizaka T, Noji H. Biophysical Journal 92 5 1806-12 2007/03/01
  •  Probing the ubiquinol-binding site in cytochrome bd by site-directed mutagenesis. Mogi T, Akimoto S, Endou S, Watanabe-Nakayama T, Mizuochi-Asai E, Miyoshi H. Biochemistry 45 25 7924-30 2006/06/27
  •  VanabinP, a novel vanadium-binding protein in the blood plasma of an ascidian, Ascidia sydneiensis samea. Yoshihara M, Ueki T, Watanabe T, Yamaguchi N, Kamino K, Michibata H. Biochimica et Biophysica Acta 1730 3 206-14 2005/09/25

Conference Presentations

  • Nano-space video imaging of amyloidogenic protein aggregation(conference:International Symposium on Pathomechanisms of Amyloid Diseases)(2018/12/20)
  • Video-imaging of Structural Dynamics of Protein Assemblies(conference:International Symposium on Atomic Force Microscopy at Solid-Liquid Interfaces)(2017/11/09)
  • NANOMETER RESOLUTION VIDEO IMAGING REVEALS STRUCTURAL DYNAMICS OF SINGLE AMYLOIDOGENIC PROTEIN ASSEMBLIES(conference:The 5th Asia Pacific Protein Association Conference / The 12th International Symposium of The Protein Society of Thailand)(2017/07/13)
  • High-speed atomic force microscopy directly visualizes amyloidogenic protein structural dynamics(conference:The 39th annual meeting of the Molecular Biology Society of Japan)(2016/11/30)

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  • Nano-space video imaging of fibrous assembly of protein and relevant enzyme molecule dynamics(conference:The 4th Kanazawa Bio-AFM Workshop)(2016/10/06)
  • Video imaging of structural dynamics in amyloid fibril polymorphism(conference:The 72nd annual meeting of Japanese Society of Microscopy)(2016/06/14)
  • Nano-space video imaging of collagen degradation with collagenases(conference:The 72nd annual meeting of Japanese Society of Microscopy)(2016/06/14)


Arts and Fieldwork


Theme to the desired joint research

Grant-in-Aid for Scientific Research


Competitive research funding,Contribution

Collaborative research,Consignment study

Classes (Bachelors)

○Plant Physiology Lab(2019)
○Research Work in Biology(1)(2019)
○Research Work in Biology(2)(2019)
○Research Seminar in Biology (1)(2019)
○Research Seminar in Biology (2)(2019)
○Guide to Biology and Bioengineering A(2018)
○Plant Physiology Lab(2018)
○Research Work in Biology(1)(2018)
○Research Work in Biology(2)(2018)
○Research Seminar in Biology (1)(2018)
○Research Seminar in Biology (2)(2018)
○Plant Physiology Lab(2017)
○Research Work in Biology(2)(2017)
○Plant Physiology Lab(2017)
○Research Seminar in Biology (1)(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Research Work in Biology(1)(2017)
○Research Seminar in Biology (2)(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Freshman Seminar I(2017)
○Research Work in Biology(2)(2016)
○Research Seminar in Biology (2)(2016)
○Research Work in Biology(1)(2016)
○Research Seminar in Biology (1)(2016)
○Plant Physiology Lab(2016)

Classes (Graduate Schools)

International Project

International Students

Lecture themes

Others (Social Activities)

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