Scientist & Research
Home > Scientist & Research > Scientists > Masashi Yamaguchi

Masashi Yamaguchi

Position Grand Fellow,Visiting Lecturer
Research Projects Candida Phenome Project
Division Division of Molecular Biology
FAX +81 43 226 2486
E-mail yama[at]


Ultrastructural study of microorganisms

Main topics of research

Ultrastructural studies on pathogenic fungi, Examining evolution through cellular structures of deep-sea microorganisms

Main publications

  1. Okamoto M, Takahashi-Nakaguchi A, Tejima K, Sasamoto K, Yamaguchi M, Aoyama T, Nagi M, Tanabe K, Miyazaki Y, Nakayama H, Sasakawa C, Kajiwara S, Brown AJP, Teixeira MC, Chibana H: Erg25 Controls Host-Cholesterol Uptake Mediated by Aus1p-Associated Sterol-Rich Membrane Domains in Candida glabrata. Front Cell Dev Biol, 24;10:820675, 2022.
  2. Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Naito K,Sato-Okamoto M, Ishiwata K, Naraoka S, Chibana H: Electron microscopy of mouse tissues by sandwich freezing and freeze-substitution. Cytologia 87: 149-155, 2022.
  3. Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Yamada H, Sato-Okamoto M, Chibana H: Ultrastructural examination of mouse glomerular capillary loop by sandwich freezing and freeze-substitution, Microscopy (Oxf) , 00010.R2, 2022.
  4. Yamaguchi M, Taguchi M, Uematsu K, Takahashi-Nakaguchi A, Sato-Okamoto M, Chibana H: Sandwich freezeng device for rapid freezing of virus, bacteria, yeast, cultured cells, and animal and human tissues in electron microscopy. Microscopy 70: 215-223, 2021.
  5. Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Taguchi M, Sato-Okamoto M, Chibana H: Rapid freezing using Sandwich Freezing Device for good ultrastructural preservation of 4 viruses, yeast, and animal tissues in electron microscopy. Journal of Visualized Experiments, 2021.
  6. Yamaguchi M, Yamada H, Chibana H: Deep-sea bacteria harboring bacterial endosymbionts in a cytoplasm? 3D electron microscopy by serial ultrathin sectioning of freeze-substituted specimen. Cytologia, 85(3) 209-211, 2020.
  7. Nishimura K, Okamoto M, Shibue R, Mizuta T, Shibayama T, Yoshino T, Murakami T, Yamaguchi M, Tanaka S, Toida T, Igarashi K: KLF4 is required for suppression of histamine synthesis by polyamines during bone marrow-derived mast cell differentiation. PLoS ONE, 15, e0229744, 2020.
  8. Yamaguchi M, Wakabayashi S, Nakamura Y, Matsue H, Hirao T, Aoki S, Yamashina S, Yamada H, Mamizu N, Furukawa H, Chibana H: Good ultrastructural preservation of human tissues and cultured cells by glutaraldehyde fixation, sandwich freezing, and freeze-substitution. Cytologia, 85: 15-26, 2020.
  9. Horinouchi Y, Yamaguchi M, Chibana H, Togashi T: Nuclear behavior and roles indicate that Codiolum phase is a sporophyte in Monostroma angicava (Ulotrichales, Ulvophyceae). J Phycology, 55: 534-542, 2019.
  10. Ikezaki S, Cho T, Nagao J, Tasaki S, Yamaguchi M, Arita-Morioka K, Yasumatsu K, Chibana H, Ikebe T, Tanaka Y: Mild heat stress affects the cell wall structure in Candida albicans biofilm. Med Mycol J, 60: 29-37, 2019.
  11. Takeuchi N, Ohkusu M, Wada N, Kurosawa S, Miyabe A, Yamaguchi M, Nahm MH, Ishiwada N: Molecular typing, antibiotic susceptibility, and biofilm production in nonencapsulated Streptococcus pneumoniae isolated from children in Japan. J Infect Chemother, 25: 750-757, 2019.
  12. Stepanova A, Vasilyeva NV, Yamaguchi M, Chibana H, Chilina GA, Bogomolova TS: The peculiarityof Aspergillus tubigensis micromorphology: scanning electron microscopy. Problems in Medical Mycology, 21: 23-26, 2019.
  13. Shiratori R, Furuichi K, Yamaguchi M, Miyazaki N, Aoki H, Chibana H, Ito K, Aoki S: Glycolytic suppression dramatically changes the intracellular metabolic profile of multiple cancer cell lines in a mitochondrial metabolism-dependent manner. Scientfic Reports, 9: 18699, 2019.
  14. Takahashi-Nakaguchi A, Sakai K, Takahashi H, Hagiwara D, Toyotome T, Chibana H, Watanabe A, Yaguchi T, Yamaguchi M, Kamei K, Gonoi T: Aspergillus fumigatus adhesion factors in dormant conidia revealed through comparative phenotypic and transcriptomic analyses. Cell Microbiol, 20: e12802, 2018
  15. Hirao T, Yamaguchi M, Kikuya M, Chibana H, Ito K, Aoki S: Altered intracellular signaling by imatinib increases the anticancer effects of tyrosine kinase inhibitors in chronic myelogenous leukemia cells. Cancer Science, 109: 212-131, 2018.
  16. Stepanova A, Vasilyeva NV, Yamaguchi M, Chibana H, Bosak, Filippova L: Ultrastructural patterns of interactions between murine lung macrophages and yeast cells of Cryptococcus neoformans strains with different virulence. Med Mycol J, 59E: E1-E6, 2018.
  17. Yamaguchi M, Chibana H: A method for obtaining serial ultrathin sections of microorganisms in transmission electron microscopy. J Vis Exp, 131, e56235, 2018.
  18. Fujimoto Y, Kobayashi Y, Kato K, Yamaguchi M: Delamination of novel ultrathin bioabsorbable abluminal polymerof platinum chromium everolimus-eluting stent. Cardiovasc Interv and Ther, 33: 97-98, 2018.
  19. Yamaguchi M, Yamada H, Uematsu K, Horinouchi Y, Chibana H: Electron microscopy and structome analysis of unique amorphous bacteria from the deep sea in Japan. Cytologia, 83 (3): 337-342, 2018.
  20. Stepanova A, Vasilyeva NV, Yamaguchi M, Chibana H, Chilina GA, Bosak LA: Cytological investigations of cell components migration dynamics during budding in the yeast Cryptococcus neoformans. Problems in Medical Mycology, 20: 34-39, 2018.
  21. Yamaguchi M, Takahashi-Nakaguchi A, Aida Y, Sato-Okamoto M, Chibana H: Convenient method for better preservation of fine structures of cultured macrophages and engulfed yeast cells by freeze-substitution fixation. Microscopy, 66: 209-211, 2017.
  22. Yamada H, Yamaguchi M, Shimizu K, Murayama SY, Mitarai S, Sasakawa C, Chibana H: Structome analysis of Escherichia coli cells by serial ultrathin sectioning reveals the precise cell profiles and the ribosome density. Microscopy, 66: 283-294, 2017.
  23. Stepanova A, Vasilyeva NV, Yamaguchi M, Chibana H, Bosak A: Ultrastructural investigations of early stages of transformation of yeast from hyphal in Cryptococcus neoformans var. grubii in vivo. Problems in Medical Mycology, 19 (2): 19-24, 2017.
  24. Toh-e A, Ohkusu M, Shimizu K, Yamaguchi M, Ishiwada N, Watanabe A, Kamei K: Creation, characterization, and utilization of Cryptococcus neoformans mutants sensitive to micafungin. Current Genetics, 63: 1093-1104, 2017.
  25. Aoki S, Morita M, Hirao T, Yamaguchi M, Shiratori R, Kikuya M, Chibana H, Ito K: Shift in energy metabolism caused by glucocorticoids enhances the effect of cytotoxic anti-cancer drugs against acute lymphoblastic leukemia cells. Oncotarget, 8: 94271-94285, 2017.
  26. Stepanova A, Yamaguchi M, Chibana H, Vasilyeva NV, Shulgina MV: Comparative ultrastructural analysis of the in vitro growing hyphal cells of Scedosporium aurantiacum. Problems of Medical Mycology, 19: 18-25, 2017.
  27. Stepanova A, Vasilyeva NV, Yamaguchi M, Chibana H: Ultrastructure of senescent and desiccated cells of Cryptococcus neoformans. Problems in Medical Mycology, 18 (4): 47-52, 2016.
  28. Stepanova A, Vasilyeva NV, Yamaguchi M: Cellular pattern of morphogenesis, ultrastructure of senescent and desiccated in vitro growing yeast cells of Cryptococcus neoformans. Problems in Med Mycol 18: 47-51,2016.
  29. Yamaguchi M, Aoyama T, Yamada N, Chibana H: Quantitative measurement of hydrophilicity/hydrophobicity of the plasma-polymerized naphthalene film (Super Support Film) and other support films and grids in electron microscopy. Microscopy. 65(5), 444-450, 2016.
  30. Yamaguchi M, Yamada H, Higuchi K, Yamamoto Y, Arai S, Murata K, Mori Y, Furukawa H, Uddin MS, Chibana H: High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea. Microscopy, 65(4), 363-369, 2016.
  31. Stepanova AA, Vasilyeva NV, Yamaguchi M, Chibana H, Bosak IA: Ultrastructural aspects of the interactions between the murine lung macrophages and the Aspergillus fumigatus hyphal cells. Problems in Medical Mycology 18: 20-25, 2016.
  32. Stepanova AA, Yamaguchi M, Chibana H, Vasilyeva NV: Ultrastructural aspects of cell components migration during budding in the yeast Cryptococcus leurentii. Problems in Medical Mycology 18 (No. 3): 24-29, 2016.
  33. Kopecka M, Yamaguchi M, Kawamoto S: The effects of the F-actin inhibitor latrunculin A on the budding yeast Saccharomyces cerevisiae. Microbiology 161: 1348-1355, 2015.
  34. Yamaguchi M: An electron microscopic study of microorganisms: from influenza virus to deep-sea microorganisms. JSM Mycotoxins 65: 81-99, 2015.
  35. Yamada H, Yamaguchi M, Chikamatsu, Aono A, Mitarai S: Structome analysis of virulent Mycobacterium tuberculosis, which survives with only 700 ribosomes at density per 0.1 fl cytoplasm. PLoS ONE 10: e0117109, 2015.
  36. Stepanova AA, Vasilyeva NV, Yamaguchi M, Shimizu K, Kawamoto S: Electron microscopy of autopsy material from the human brain Cryptococcosis and AIDS. Problems in Medical Mycology 17: 35-40, 2015.
  37. Yamaguchi M, Shimizu K, Kawamoto S, Stepanova AA, Vasiyeva NV: Dynamics of cell components during budding of Cryptococcus albidus yeast cells. Problems in Medical Mycology 16: 29-35, 2014.
  38. Yamaguchi M, Shimizu K, Kawamoto S, Stepanova AA, Vasiyeva NV: Ultrastructural observation of cell components during budding in yeast Malassezia pachydermatis. Problems in Medical Mycology Vol. 16, No. 4: 13-18, 2014.
  39. Yamaguchi M., Shimizu K., Kawamoto S., Stepanova A.A., Vasilyeva N.V. Electronmicroscopic investigation of the mother cell of the Rhodotorula minuta // VII Kashkin Reading, Saint-Petersburg, 2014, 9-11 April, in Probl. Med. Mycol. 2014. Vol.16, No.2. P.153.
  40. Yamaguchi M, Worman CO: Deep-sea microorganisms and the origin of the eukaryotic cell. Jpn J Protozool 47: 29-48, 2014.
  41. Kopecka M, Yamaguchi M, Kawamoto S: The effect of the F-actin inhibitor latrunculin A on the pathogenic yeast Cryptococcus neoformans. Chemotherapy 60: 185-190, 2014.
  42. Kopecka M, Kawamoto S, Yamaguchi M: A new F-actin structure in fungi: actin ring formation around the cell nucleus of Cryptococcus neoformans. Microscopy 62: 295-301, 2013.
  43. Yoshimi A, Sano M, Inaba A, Kokubun Y, Fujioka T, Mizutani O, Hagiwara D, Fujikawa T, Nishimura M, Yano S, Kasahara S, Shimizu K, Yamaguchi M, Kawakami K, Abe K: Functional analysis of the α-1,3-glucan synthase genes agsA and agsB in Aspergillus nidulans: agsB is the majorα-1,3-glucan synthase in this fungus. PLoS One. 2013; 8 (1): e54893.
  44. Tomita M, Kikuchi A, Kobayashi M, Yamaguchi M, Ifuku S, Yamashoji S, Ando A, Saito A: Chracterization of antifungal activity of the GH-46 subclass III chitosanase from Bacillus circulans MH-K1. Antonie van Leeuwenhoek J Microbiol, 104: 737-748, 2013.
  45. Kozubowski L, Yadav V, Chatterjee G, Sridhar S, Yamaguchi M, Kawamoto S, Bose I, Heitman J, Sanyal K: Ordered kinetochore assembly in the human pathogenic basidiomycetous yeast, Cryptococcus neoformans. mBio 4():e00614-13. doi:10.1128/mBio.00614-13, 2013.
  46. Yamaguchi M: Ultrathin sectioning of the Myojin parakaryote discovered in the deep sea. Cytologia 78: 333-334, 2013.
  47. Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman C, Yokoyama K: Prokaryote or eukaryote? A unique microorganism from the deep-sea. J Electron Microsc, 61: 423-431, 2012.
  48. Toyotome T, Yamaguchi M, Iwasaki A, Watanabe A, Taguchi H, Qin L, Watanabe H, Kamei K: Fetuin A, a serum component, promotes growth and biofilm formation by Aspergillus fumigatus. Int J Med Microbiol 302: 108-116, 2012.
  49. Kopecka M, Yoshida S, Yamaguchi M: Actin ring formation around the cell nucleus of long-neck yeast. J Electron Microsc. 61: 249-255, 2012.
  50. Kopecka M, Yamaguchi M: Ultrastructural disorder of actin mutant suggests uncoupling of actin-dependent pathway from microtubule-dependent pathway in budding yeast. J Electron Microsc. 60: 379-391. 2011.
  51. Yamaguchi M, Namiki Y, Okada H, Mori Y, Furukawa H, Wang J, Ohkusu M, Kawamoto S: Structome of Saccharomyces cerevisiae determined by freeze-substitution and serial ultrathin sectioning electron microscopy. J Electron Microsc. 60: 337-351, 2011.
  52. Kuriyama N, Kobayashi Y, Yamaguchi M, Shibata Y: Usefulness of rotational atherectomy preventing polymer damage of everolimus-eluting stent in calcified coronary artery. JACC: Cardiovascular Interventions 4: 588-589, 2011.
  53. Ueno K, Namiki Y, Mitani H, Yamaguchi M, Chibana H: Differential cell wall remodeling of two chitin synthase deletants Δchs3A and Δchs3B in the pathogenic yeast Candida glabrata. FEMS Yeast Res 11: 398-407, 2011.
  54. Namiki Y, Ueno K, Mitani H, Virtudazo EV, Ohkusu M, Shimizu K, Kawamoto S, Chibana H, Yamaguchi M: Scanning and negative staining electron microscopy of protoplast regeneration of a wild type and two chitin synthase mutants in the pathogenic yeast Candida glabrata. J Electron Microsc. 60: 157-165, 2011.
  55. Yamaguchi M, Namiki Y, Okada H, Uematsu K, Tame A, Maruyama T, Kozuka Y: Improved preservation of fine structure of deep-sea microorganisms by freeze-substitution after glutaraldehyde fixation. J Electron Microsc. 60: 283-287, 2011.
  56. Shimizu K, Li H-M, Virtudazo EV, Watanabe A, Kamei K, Yamaguchi M, Kawamoto S: Deletion of CnLIG4 DNA ligase gene in the fungal pathogen Cryptococcus neoformans elevates homologous recombination efficiency. Mycoscience 51: 28-33, 2010.
  57. Yamada H, Mitarai S, Chikamatsu K, Mizuno K, Yamaguchi M: Novel freeze-substitution electron microscopy provides new aspects of virulent Mycobacterium tuberculosis with visualization of the outer membrane and satisfying biosafety requirements. J Microbiol Method 80: 14-18, 2010.
  58. Kopecka M, Ilkovics L, Ramikova V, Yamaguchi M: Effect of cytoskeleton inhibitors on conidiogenesis and capsule in the long neck yeast Fellomyces examined by scanning electron microscopy. Chemotherapy 56: 197-202, 2010.
  59. Yamaguchi M, Ikeda R, Nishimura M, Kawamoto S: Localization by scanning immunoelectron microscopy of triosephosphate isomerase, the molecules responsible for contact-mediated killing of Cryptococcus, on the surface of Staphylococcus. Microbiol Immunol 54: 368-370, 2010.
  60. Yamaguchi M, Biswas SK, Kuwabara Y, Ohkusu M, Shimizu M, Takeo K: The spindle pole body of the pathogenic yeast Cryptococcus neoformans: variation in morphology and positional relationship to the nucleolus and the bud in interphase cells. J Electron Microsc. 59: 165-172, 2010.
  61. Yamaguchi M, Kopecka M: Ultrastructural disorder of the secretory pathway in temperature-sensitive actin mutants of Saccharomyces cerevisiae. J Electron Microsc. 59: 141-152, 2010.
  62. Yamaguchi M, Okada H, Namiki Y: Smart specimen preparation for freeze-substitution and serial ultrathin sectioning of yeast cells. J Electron Microsc 58: 261-266, 2009.
  63. Yamaguchi M, Biswas SK, Ohkusu M, Takeo K: Dynamics of the spindle pole body of the pathogenic yeast Cryptococcus neoformans examined by freeze-substitution electron microscopy. FEMS Microbiol Lett 296: 257-265, 2009
  64. Yamaguchi M, Danev R, Nishiyama K, Sugawara K, Nagayama K: Zernike phase contrast electron microscopy of ice-embedded influenza A virus. J Struct Biol 162: 271-276, 2008.