Graduate School of Medicine / School of Medicine, Faculty of Medicine

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Biological Regulation


Neurons are connected via synapses to form neuronal circuits in the brain. The final goal of our laboratory is to understand how the brain works as a complex of neuronal network. Particularly, we are interested in the molecular mechanisms that govern synapse formation and elimination during development. We use state-of-the-art imaging technologies using both electron and light microscopy for describing the whole wiring diagram of the brain (connectome). We also put efforts on the development of new imaging tools. We use these newly-invented tools not only for the analysis of the brain but also for other organs to shed light on a new aspects of biological phenomena.

  • Staff
  • Research & education
  • Clinical Activities
  • Citizen Activities
  • Achievement
  • History


Professor Hirohide IWASAKI, Ph.D
Assosiate Professor Tohru MURAKAMI, MD,Ph.D
Lecturer Yuki TAJIKA, Ph.D
Assistant Professor Sotaro ICHINOSE, Ph.D

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Research & Education

Research content

1. Morphological analysis of neurons and glial cells
2. Molecular mechanism of synapse formation and elimination during development
3. Description of the whole wiring diagram of the neuronal network (Connectome)
4. Vesicle transport in skeletal muscle and other organs/tissues.
5. Exploration and functional analysis of novel cell adhesive molecules during early development in zebrafish
6. Development of the new system of anatomy education

Business education

(Undergraduate education)
1. Gross anatomy (Lecture and training)
2. Histology (Lecture and training)
(Graduate education)
1. Anatomy B
2. Anatomy (basic)
3. Anatomy Methodology
4. Anatomy Research
5. Department of Anatomy LectureⅠ
6. Department of Anatomy Seminar
7. Department of Anatomy Technical Course

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Clinical Activities

(No clinical assignments)

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Citizenship Activities

1. Providing postgraduate educational opportunities of anatomy course for medical doctors.
2. Providing opportunities to observe dissected human bodies for students of healthcare professionals.
3. Providing opportunities for high school students to experience research activity in the laboratory during Brain Awareness Week.

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1. Takahashi A, Parajuli LK, Iwasaki H, Tanaka S and Okabe S.: Ultrastructural observation of glutamatergic synapses by focused ion beam scanning electron microscopy (FIB/SEM).
Methods in Molecular Biology. Volume 1941: “Glutamate Receptors – Methods and Protocols”, Humana Press, 17-27, Humana Press, 2019

2. Iijima K, Tajika Y,Tanaka Y, Yorifuji H and Yoshimoto Y.: Microanatomy Around the Facial Nerve Pathway for Microvacular Decompression Surgery Investigated with Correlative Light Microscopy and Block-Face Imaging.118:e526-e533, 2018.

3. Ikezawa M, Tajika Y, Ueno H, Murakami T, Inoue N and Yorifuji H.: Loss of VAMP5 in mice results in duplication of the ureter and insufficient expansion of the lung. Devlopmental Dynamics. 247:754-762, 2018.

4. Chen S, Weitemier AZ, Zeng X, He L, Wang X, Tao Y, Huang AJY, Hashimotodani Y, Kano M, Iwasaki H, Parajuli LK, Okabe S, Tsutsui-Kimura I, Tanaka KF, Liu X. and McHugh TJ.: Near-infrared deep brain stimulation via upconversion nanoparticle-mediated optogenetics. Science. 359:679-684, 2018.

5. Koeberle S, Tanaka S, Kuriu T, Iwasaki H, Koeberle A, Schulz A, Helbing D, Yamagata Y, Morrison H and Okabe S.: Developmental stage-dependent regulation of spine formation by calcium-calmodulin dependent protein kinase IIα and Rap1. Scientific Reports. 7:13409, 2017.

6. Tajika Y, Murakami T, Iijima K, Gotoh H, Takahashi-Ikezawa M, Ueno H, Yoshimoto Y and Yorifuji H.: A novel imaging method for correlating 2D light microscopic data and 3D volume data based on block-face imaging. Scientific Reports. 7:3645, 2017.

7. Iriuchishima T, Ryu K, Murakami T and Yorifuji H.: The correlation between femoral sulcus morphology and osteoarthritic changes in the patellofemoral joint. Knee Surg. Sports Traumatol. Arthrosc. 25: 2715-2720, 2017.

8. Iwasaki H, Tanaka S and Okabe S.: Dendrites: Development and Disease, Chapter 15: Molecular Assembly of Excitatory Synapses, 359-385, Springer, 2016

9. Khairani AF, Tajika Y, Takahashi M, Ueno H, Murakami T, Soenggono A and Yorifuji H.: Filamentous structures in skeletal muscle: anchors for the subsarcolemmal space. Med Molec Morph. 48:1–12, 2015.

10. Tajika Y, Takahashi M, Ueno H, Murakami T and Yorifuji H.: Organization of organelles and VAMP-associated vesicular transport systems in differentiating skeletal muscle cells. Anat Sci Int. 90:33–39, 2015.

11. Dai X, Iwasaki H, Watanabe M and Okabe S.: Dlx1 transcription factor regulates dendritic growth and postsynaptic differentiation through inhibition of neuropilin-2 and PAK3 expression. Eur. J. Neurosci. 39: 531-547,2014.

12. Tajika Y, Takahashi M, Khairani AF, Ueno H, Murakami T and Yorifuji H.: Vesicular transport system in myotubes: ultrastructural study and signposting with SNARE proteins. Histochem Cell Biol 141:441-454,2014.

13. Murakami T, Tajika Y, Ueno H, Awata S, Hirasawa S, Sugimoto M, Kominato Y, Tsushima Y, Endo K and Yorifuji H.: Integrated education of gross anatomy and CT radiology for current advances in medicine. Anat Sci Educ, 7:438–449, 2014.

14. Takahashi M, Tajika Y, Khairani AF, Ueno H, Murakami T and Yorifuji H.: The localization of VAMP5 in skeletal and cardiac muscle. Histochem Cell Biol 139: 573-582, 2013.

15. Itoh M, Shimokawa N, Tajika Y, Murakami T, Aotsuka N, Lesmana R, Farenia R, Iwasaki T, Okada J, Yorifuji H and Koibuchi N.: Alterations of biochemical marker levels and myonuclear numbers in rat skeletal muscle after ischemia reperfusion. Mol Cell Biochem 373: 11-18, 2013.

16. Shin E, Kashiwagi Y, Kuriu T, Iwasaki H, Tanaka T, Koizumi H, Gleeson JG and Okabe S.: Doublecortin-like kinase enhances dendritic remodeling and negatively regulates synapse maturation. Nature Commun 4: 1440, 2013.

17. Tajika Y, Takahashi M, Hino M, Murakami and Yorifuji H.: VAMP2 marks quiescent satellite cells and myotubes, but not activated myoblast. Acta Histochem Cytochem 43: 107-114, 2010.

18. Hino M, Hamada N, Tajika Y, Funayama T, Morimura Y, Sakashita T, Yokota Y, Fukamoto K, Mutou Y, Kobayashi Y and Yorifuji H.: Heavy ion irradiation induces autophagy in irradiated C2C12 myoblasts and their bystander cells. J Electr Microsc: 59, 495-501, 2010.

19. Hino M, Hamada N, Tajika Y, Funayama T, Morimura Y, Sakashita T, Yokota Y, Fukamoto K, Kobayashi Y and Yorifuji H.: Insufficient membrane fusion in dysferlin-deficient muscle fibers after heavy-ion irradiation. Cell Sturct Funct 34:11-15, 2009.

20. Kabayama H, Nakamura T, Takeuchi M, Iwasaki H, Taniguchi M, Tokushige N and Mikoshiba K.: Ca2+ induces macropinocytosis via F-actin depolymerization during growth cone collapse. Mol. and Cellular Neurosci. 40: 27-38, 2009.

21. Okochi Y, Sasaki M, Iwasaki, H and Okamura Y.: Voltage-gated proton channel is expressed on phagosomes. Biochem. Biophys. Res. Commun. 382: 274-279, 2009.

22. Tajika Y, Murakami T, Sato M, Kubota F and Yorifuji H.: Expression of VAMP2 in muscular tissues during development. Devlopmental Dynamics 237:1886-1892, 2008.

23. Murakami T, Hijikata T and Yorifuji H.: Staging of disuse atrophy of skeletal muscles on immunofluorescence microscopy. Anat Sci Internat 83:68-76, 2008.

24. Iwasaki H, Murata Y, Kim Y, Hossain MI, Worby CA, Dixon JE, McCormack T, Sasaki T and Okamura Y.: A voltage-sensing phosphatase, Ci-VSP, which shares sequence identity with PTEN, dephosphorylates phosphatidylinositol 4, 5-bisphosphate. Proc. Nat. Acad. of Sci. 105: 7970-7975, 2008.

25. Kubota F, Murakami T, Tajika Y, and Yorifuji H.: Expression of protocadherin 18 in the CNS and pharyngeal arches of zebrafish embryos. Int J Dev Biol 52:397-405, 2008.

26. Hossain MI, Iwasaki H, Okochi Y, Chahine M, Higashijima S, Nagayama K and Okamura Y.: Enzyme Domain Affects the Movement of the Voltage Sensor in Ascidian and Zebrafish Voltage-sensing Phosphatases. J.Biol.Chem. 283:18248-18259, 2008.

27. Murakami T and Yorifuji H. Patent for kit to inspect skeletal muscle. 2005-070378.No.4150796, July,11.2008.

28. Hino M, Wada S, Tajika Y, Morimura Y, Hamada N, Funayama T, Sakashita T, Kakizaki T, Kobayashi Y and Yorifuji H.: Heavy ion microbeam irradiation induces ultrastructural change in isolated single fibers of skeletal muscle. Cell Struct Funct. 32:51-56, 2007.

29. Tajika Y, Sato M, Murakami T, Takata K and Yorifuji H.: VAMP2 is expressed in muscle satellite cells and up-regulated during muscle regeneration. Cell Tissue Res. 328: 573-581, 2007.

30. Zhou H, Iwasaki H, Nakamura T, Nakamura K, Maruyama T, Hamano S, Ozaki S, Mizutani A and Mikoshiba K.: 2-Aminoethyl diphenylborinate analogues: selective inhibition for store-operated Ca2+ entry. Biochem Biophys Res Commun. 352(2):277-282, 2007.

31. Shirahata E, Iwasaki H, Takagi M, Lin C, Bennett V, Okamura Y and Hayasaka K.: Ankyrin-G regulates inactivation of the neuronal sodium channel, Nav1.6. J.Neurophysiol., 96: 1347-1357, 2006

32. Murata Y#, Iwasaki H#,Sasaki M#, Inaba K and Okamura Y.: Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor. Nature, 435 (7046): 1239-1243, 2005 (#; equal contribution)

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Professor and Main Research Project

1. Prof. Akoyoshi Takisawa(1952-1983)
Gross anatomy

2. Prof. Harunori Ishikawa (1983-2001)
Cell biology of cytoskeletons.

3. Prof. Hiroshi Yorifuji (2002-2018)
Cell biology of skeletal muscle.

4. Prof. Hirohide Iwasaki (2018- )
Cell biology of the central nervous system and neuroanatomy.