研究者データベース

西上 幸範(ニシガミ ユキノリ)
電子科学研究所 附属社会創造数学研究センター
助教

基本情報

所属

  • 電子科学研究所 附属社会創造数学研究センター

職名

  • 助教

学位

  • 博士(理学)(兵庫県立大学)

論文上での記載著者名

  • Yukinori Nishigami
  • Y. Nishigami
  • 西上 幸範
  • Nishigami Yukinori
  • Nishigami Y.

ホームページURL

科研費研究者番号

  • 80639021

ORCID ID

J-Global ID

研究分野

  • ライフサイエンス / 生物物理学

所属学協会

  • 日本原生生物学会   日本生物物理学会   

研究活動情報

論文

  • Daniel Schenz, Yukinori Nishigami, Katsuhiko Sato, Toshiyuki Nakagaki
    Current Opinion in Genetics and Development 57 78 - 83 2019年08月 [査読有り][通常論文]
     
    © 2019 Elsevier Ltd Single-celled organisms show a fascinating faculty for integrating spatial information and adapting their behaviour accordingly. As such they are of potential interest for elucidating fundamental mechanisms of developmental biology. In this mini-review we highlight current research on two organisms, the true slime mould Physarum polycephalum and the ciliates Paramecium and Tetrahymena. For each of these, we present a case study how applying physical principles to explain behaviour can lead to the understanding of general principles possibly relevant to developmental biology.
  • Nishigami, Y., Ohmura, T., Taniguchi, A., Nonaka, S., Manabe, J., Ishikawa, T., Ichikawa, M.
    Communicative and Integrative Biology 11 4 2018年 [査読有り][通常論文]
     
    © 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Some types of ciliates accumulate on solid/fluid interfaces. This behavior is advantageous to survival in nature due to the presence of sufficient nutrition and stable environments. Recently, the accumulating mechanisms of Tetrahymena pyriformis at the interface were investigated. The synergy of the ellipsoidal shape of the cell body and the mechanosensing feature of the cilia allow for cells to slide on interfaces, and the sliding behavior leads to cell accumulation on the interfaces. Here, to examine the generality of the sliding behavior of ciliates, we characterized the behavior of Paramecium caudatum, which is a commonly studied ciliate. Our experimental and numerical results confirmed that P. caudatum also slid on the solid/fluid interface by using the same mechanism as T. pyriformis. In addition, we evaluated the effects of cellular ellipticity on their behaviors near the wall with a phase diagram produced via numerical simulation.
  • Ohmura, T., Nishigami, Y., Taniguchi, A., Nonaka, S., Manabe, J., Ishikawa, T., Ichikawa, M.
    Proceedings of the National Academy of Sciences of the United States of America 115 13 3231 - 3236 2018年 [査読有り][通常論文]
     
    © 2018 National Academy of Sciences. All Rights Reserved. An important habit of ciliates, namely, their behavioral preference for walls, is revealed through experiments and hydrodynamic simulations. A simple mechanical response of individual ciliary beating (i.e., the beating is stalled by the cilium contacting a wall) can solely determine the sliding motion of the ciliate along the wall and result in a wall-preferring behavior. Considering ciliate ethology, this mechanosensing system is likely an advantage in the single cell’s ability to locate nutrition. In other words, ciliates can skillfully use both the sliding motion to feed on a surface and the traveling motion in bulk water to locate new surfaces according to the single “swimming” mission.
  • The neck deformation of Lacrymaria olar depending upon cell states
    Ryuji Yanase, Yukinori Nishigami, Masatoshi Ichikawa, Tohru Yoshihisa, Seiji Sonobe
    Journal of Protistology 51 1 - 6 2018年 [査読有り][通常論文]
  • Active materials integrated with actomyosin
    Hiroaki Ito, Masahiro Makuta, Yukinori Nishigami, Masatoshi Ichikawa
    Journal of the Physical Society of Japan 86 101001  2017年 [査読有り][通常論文]
  • Dorota Buczek, Malgorzata Wojtkowska, Yutaka Suzuki, Seiji Sonobe, Yukinori Nishigami, Monika Antoniewicz, Hanna Kmita, Wojciech Makalowski
    BMC GENOMICS 17 2016年02月 [査読有り][通常論文]
     
    Background: An ancestral trait of eukaryotic cells is the presence of mitochondria as an essential element for function and survival. Proper functioning of mitochondria depends on the import of nearly all proteins that is performed by complexes located in both mitochondrial membranes. The complexes have been proposed to contain subunits formed by proteins common to all eukaryotes and additional subunits regarded as lineage specific. Since Amoebozoa is poorly sampled for the complexes we investigated the outer membrane complexes, namely TOM, TOB/SAM and ERMES complexes, using available genome and transcriptome sequences, including transcriptomes assembled by us. Results: The results indicate differences in the organization of the Amoebozoa TOM, TOB/SAM and ERMES complexes, with the TOM complex appearing to be the most diverse. This is reflected by differences in the number of involved subunits and in similarities to the cognate proteins of representatives from different supergroups of eukaryotes. Conclusions: The obtained results clearly demonstrate structural variability/diversity of these complexes in the Amoebozoa lineage and the reduction of their complexity as compared with the same complexes of model organisms.
  • Yukinori Nishigami, Hiroaki Ito, Seiji Sonobe, Masatoshi Ichikawa
    SCIENTIFIC REPORTS 6 2016年01月 [査読有り][通常論文]
     
    Active force generation in living organisms, which is mainly involved in actin cytoskeleton and myosin molecular motors, plays a crucial role in various biological processes. Although the contractile properties of actomyosin have been extensively investigated, their dynamic contribution to a deformable membrane remains unclear because of the cellular complexities and the difficulties associated with in vitro reconstitution. Here, by overcoming these experimental difficulties, we demonstrate the dynamic deformation of a reconstituted lipid interface coupled with self-organized structure of contractile actomyosin. Therein, the lipid interface repeatedly oscillates without any remarkable periods. The oscillatory deformation of the interface is caused by the aster-like three-dimensional hierarchical structure of actomyosin inside the droplet, which is revealed that the oscillation occurs stochastically as a Poisson process.
  • ブレブ駆動型アメーバ運動機構
    西上幸範, 伊藤弘明, 市川正敏
    原生動物学雑誌 49 17 - 25 2016年 [査読有り][通常論文]
  • Hiroaki Ito, Yukinori Nishigami, Seiji Sonobe, Masatoshi Ichikawa
    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 92 6 2015年12月21日 [査読有り][通常論文]
     
    Actomyosin actively generates contractile forces that provide the plasma membrane with the deformation stresses essential to carry out biological processes. Although the contractile property of purified actomyosin has been extensively studied, to understand the physical contribution of the actomyosin contractile force on a deformable membrane is still a challenging problem and of great interest in the field of biophysics. Here, we reconstitute a model system with a cell-sized deformable interface that exhibits anomalous curvature-dependent wrinkling caused by the actomyosin cortex underneath the spherical closed interface. Through a shape analysis of the wrinkling deformation, we find that the dominant contributor to the wrinkled shape changes from bending elasticity to stretching elasticity of the reconstituted cortex upon increasing the droplet curvature radius of the order of the cell size, i.e., tens of micrometers. The observed curvature dependence is explained by the theoretical description of the cortex elasticity and contractility. Our present results provide a fundamental insight into the deformation of a curved membrane induced by the actomyosin cortex.
  • Hiroaki Ito, Yukinori Nishigami, Seiji Sonobe, Masatoshi Ichikawa
    PHYSICAL REVIEW E 92 6 062711/1 - 062711/8 2015年12月 [査読有り][通常論文]
     
    Actomyosin actively generates contractile forces that provide the plasma membrane with the deformation stresses essential to carry out biological processes. Although the contractile property of purified actomyosin has been extensively studied, to understand the physical contribution of the actomyosin contractile force on a deformable membrane is still a challenging problem and of great interest in the field of biophysics. Here, we reconstitute a model system with a cell-sized deformable interface that exhibits anomalous curvature-dependent wrinkling caused by the actomyosin cortex underneath the spherical closed interface. Through a shape analysis of the wrinkling deformation, we find that the dominant contributor to the wrinkled shape changes from bending elasticity to stretching elasticity of the reconstituted cortex upon increasing the droplet curvature radius of the order of the cell size, i.e., tens of micrometers. The observed curvature dependence is explained by the theoretical description of the cortex elasticity and contractility. Our present results provide a fundamental insight into the deformation of a curved membrane induced by the actomyosin cortex.
  • 試験管内再構築系を用いたブレブ駆動型アメーバ運動機構の研究
    西上幸範, 伊藤弘明, 市川正敏
    植物科学最前線 6 82 - 91 2015年 [査読有り][通常論文]
  • Yukinori Nishigami, Masatoshi Ichikawa, Toshiya Kazama, Ryo Kobayashi, Teruo Shimmen, Kenichi Yoshikawa, Seiji Sonobe
    PLoS ONE 8 8 2013年08月05日 [査読有り][通常論文]
     
    Amoeboid locomotion is one of the typical modes of biological cell migration. Cytoplasmic sol-gel conversion of an actomyosin system is thought to play an important role in locomotion. However, the mechanisms underlying sol-gel conversion, including trigger, signal, and regulating factors, remain unclear. We developed a novel model system in which an actomyosin fraction moves like an amoeba in a cytoplasmic extract. Rheological study of this model system revealed that the actomyosin fraction exhibits shear banding: the sol-gel state of actomyosin can be regulated by shear rate or mechanical force. Furthermore, study of the living cell indicated that the shear-banding property also causes sol-gel conversion with the same order of magnitude as that of shear rate. Our results suggest that the inherent sol-gel transition property plays an essential role in the self-regulation of autonomous translational motion in amoeba. © 2013 Nishigami et al.

その他活動・業績

  • Anomalous swimming of a ciliary microorganism adjacent to wall
    Takuya Ohmura, Yukinori Nishigami, Junichi Manabe, Takuji Ishikawa, Masatoshi Ichikawa APS March Meeting 2018, Abstract K46.00001 2018年03月 [査読無し][通常論文]

受賞

  • 2018年10月 日本原生生物学会 第51回日本原生生物学会大会ベストプレゼンテーション賞
     
    受賞者: 西上 幸範
  • 2014年11月 日本原生生物学会 奨励賞
     
    受賞者: 西上 幸範

大学運営

委員歴

  • 2019年04月 - 現在   ナショナルバイオリソースプロジェクト ゾウリムシ   運営委員会委員
  • 2018年10月 - 現在   日本原生生物学会   評議委員
  • 2014年11月 - 現在   日本原生生物学会   編集委員


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