Keisuke Shimizu

Profile

Yasuhiro Hoshiba

Marine Ecosystem Research Group
Researcher

Address

Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Earth Surface System Research Center　(ESS)
2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan

Research interest

  • Molecular mechanisms of biomineralization
  • Effect of shell formation on ocean acidification
  • Molecular phylogeography of zooplankton

Education

  • Ph.D, The University of Tokyo, Japan, 2014
  • M.S., Tsukuba University, Japan, 2011
  • B.S., Shinshu University, Japan, 2008

Work Experience

2023/4 Contract staff, Waseda University
2021/7 Project Assistant Professor, The University of Tokyo
2019/12 Project Assistant Professor, The University of Tokyo
2017/12 Overseas Research Fellowships (JSPS), University of Exeter (UK)
2015/4 Postdoctoral researcher, JAMSTEC
2014/6 Postdoctoral researcher, University of Kyoto
2014/4 Postdoctoral researcher, The University of Tokyo

Publications (Peer-reviewed)

  • 1) Shimizu K, Sarashina I, Kagi H, Endo K (2011) Possible functions of Dpp in gastropod shell formation and shell coiling. Development Genes and Evolution 221: 59–68. DOI: 10.1007/s00427-011-0358-4.
  • 2) Setiamarga DHE & Shimizu K, Kuroda J, Inamura K, Sato K, et al. (2013) An in-silico survey for genes coding for early development signaling molecules in the pearl oyster Pinctada fucata. Zoological Science 30: 877-888. DOI: 10.2108/zsj.30.877.
  • 3) Shimizu K, Iijima M, Setiamarga DHE, Sarashina I, Kudoh T, Asami T, Gittenberger E, Endo K (2013) Left-right asymmetric expression of dpp in the mantle of gastropod correlate to the asymmetric shell coiling. EvoDevo 4: 15. DOI:10.1186/2041-9139-4-15.
  • 4) Shimizu K, Endo K (2015) Evo-Devo of spiral shell growth in gastropods. Proceeding of the 3rd International Symposium on Biological Shape Analysis pp. 130-137. DOI:10.1142/9789814704199_0009.
  • 5) Noshita K, Shimizu K, Sasaki T (2016) Geometric analysis and estimation of the growth rate gradient on gastropod shells. Journal of Theoretical Biology 389: 1–19.　DOI:10.1016/j.jtbi.2015.10.011.
  • 6) Shimizu K, Luo Y-J, Satoh N, Endo K (2017) Possible co-option of engrailed during brachiopod and mollusc shell development. Biology Letters 13: 20170254. DOI:10.1098/rsbl.2017.0254.
  • 7) Shimizu K, Kimoto K, Noshita K, Wakita M, Fujiki T, Sasaki T (2018) Phylogeography of the pelagic snail Limacina helicina (Gastropoda: Thecosomata) in the subarctic western North Pacific. Journal of Molluscan Studies 84: 30-37. DOI:10.1093/mollus/eyx040.
  • 8) Shimizu K, Kimura K, Isowa Y, Oshima K, Ishikawa M, Kagi H, Kito K, Hattori M, Chiba S, Endo K (2019) Insights into the evolution of shell and love dart of land snail revealed from their matrix proteins. Genome Biology and Evolution 11: 380-397. DOI:10.1093/gbe/evy242.
  • 9) Ishikawa A, Shimizu K, Isowa Y, Takeuchi T, Zhao R, Kito K, Fujie M, Satoh N, Endo K (2020) Asymmetric shell morphology of snails allows identification of potentially operational shell matrix proteins. Scientific Reports 10: 9768. DOI:10.1038/s41598-020-66021-w.
  • 10) Iwamoto S & Shimizu K, Negishi L, Suzuki N, Nagata K, Suzuki M (2020) Characterization of the chalky layer-derived EGF-like domain-containing protein (CgELC) in the pacific oyster, Crassostrea gigas. Journal of Structural Biology 212: 107594. DOI: 10.1016/j.jsb.2020.107594.
  • 11) Shimizu K, Kintsu H, Awaji M, Matumoto T, Suzuki M (2020) Evolution of biomineralization genes in the prismatic layer of the pen shell Atrina pectinata. Journal of Molecular Evolution 88: 742–758. DOI:10.1007/s00239-020-09977-7.
  • 12) Shimizu K, Noshita K, Kimoto K, Sasaki T (2021) Phylogeography and shell morphology of the pelagic snail Limacina helicina in the Okhotsk Sea and western North Pacific. Marine Biodiversity 51: 22. DOI:10.1007/s12526-021-01166-z.
  • 13) Setiamarga DHE, Hirota K, Yoshida M, Takeda Y, Kito K, Shimizu K, Isowa Y, Ikeo K, Sasaki T, Endo K (2021) Hydrophilic shell matrix proteins of Nautilus pompilius and the identification of a core set of Conchiferan domains. Genes 12(12), 1925. DOI:10.1101/2020.11.14.382804
  • 14) Sentoku A, Shimizu K, Naka T, Tokuda Y (2022) Dimorphic life cycle through transverse division in burrowing hard coral Deltocyathoides orientalis. Scientific Reports 12: 9359. DOI: https://doi.org/10.1038/s41598-022-13347-2
  • 15) Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M (2022) Evolution of Epidermal Growth Factor (EGF)-like and zona pellucida domains containing shell matrix proteins in Mollusks. Molecular Biology and Evolution 39: msac148. DOI:10.1093/molbev/msac148
  • 16) Shimizu K, Negishi L, Ito T, Touma S, Matsumoto T, Awaji M, Kurumizaka H, Yoshitake K, Kinoshita S, Asakawa S, Suzuki M (2022) Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata. Comparative Biochemistry and Physiology PartD: Genomics and Proteomics 44:101025. DOI:10.1016/j.cbd.2022.101025
  • 17) Zhu L, Shimizu K, Kintsu H, Negishi L, Zheng Z, et al. (2023) Structural and functional analyses of chitinolytic enzymes in the nacreous layer of Pinctada fucata. Biochemical Engineering Journal 191: 108780. DOI:10.1016/j.bej.2022.108780
  • 18) Shimizu K, Negishi L, Kurumizaka H, Suzuki M (accept) Diversification of von Willebrand factor A and chitin-binding domains in Pif/BMSPs among mollusks. Journal of Molecular Evolution.

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