2024, 第6回物質・デバイス共同研究賞 基盤共同研究　　　　　　　　　　　　　　　
リザリア生物を用いた微小管系アメーバ運動の解析
野村真未;中垣 俊之;佐藤 勝彦;西上 幸範

Oct. 2018, 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　　　　　　　　　　　　　　　
西上 幸範

Nov. 2014, 日本原生生物学会, 奨励賞　　　　　　　　　　　　　　　
西上 幸範

Measurement of protoplasmic streaming over the entire body of <i>Physarum</i> plasmodium, and estimation of the transport and mixing of protoplasma through the intricate vein network
Yo Sato, Charles Fosseprez, Yukinori Nishigami, Katsuhiko Sato, Hiroshi Orihara, Toshiyuki Nakagaki
Biophysics and Physicobiology, Jan. 2025
English, Scientific journal

Cellular Ethological Dynamics in Diorama Environments
Yukinori Nishigami, Itsuki Kunita, Katsuhiko Sato, Toshiyuki Nakagaki
Journal of the Physical Society of Japan, 15 Dec. 2023, [Peer-reviewed], [Invited]
Scientific journal

Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora
Mami Nomura, Keisuke Ohta, Yukinori Nishigami, Takuro Nakayama, Kei-Ichiro Nakamura, Kenjiro Tadakuma, Josephine Galipon
Frontiers in Cell and Developmental Biology, 11, Frontiers Media SA, 04 Sep. 2023, [Peer-reviewed]
Scientific journal, Unicellular euglyphid testate amoeba Paulinella micropora with filose pseudopodia secrete approximately 50 siliceous scales into the extracellular template-free space to construct a shell isomorphic to that of its mother cell. This shell-constructing behavior is analogous to building a house with bricks, and a complex mechanism is expected to be involved for a single-celled amoeba to achieve such a phenomenon; however, the three-dimensional (3D) structure of the shell and its assembly in P. micropora are still unknown. In this study, we aimed to clarify the positional relationship between the cytoplasmic and extracellular scales and the structure of the egg-shaped shell in P. micropora during shell construction using focused ion beam scanning electron microscopy (FIB-SEM). 3D reconstruction revealed an extensive invasion of the electron-dense cytoplasm between the long sides of the positioned and stacked scales, which was predicted to be mediated by actin filament extension. To investigate the architecture of the shell of P. micropora, each scale was individually segmented, and the position of its centroid was plotted. The scales were arranged in a left-handed, single-circular ellipse in a twisted arrangement. In addition, we 3D printed individual scales and assembled them, revealing new features of the shell assembly mechanism of P. micropora. Our results indicate that the shell of P. micropora forms an egg shape by the regular stacking of precisely designed scales, and that the cytoskeleton is involved in the construction process.

Caenorhabditis elegans transfers across a gap under an electric field as dispersal behavior
Takuya Chiba, Etsuko Okumura, Yukinori Nishigami, Toshiyuki Nakagaki, Takuma Sugi, Katsuhiko Sato
Current Biology, 33, 13, 2668, 2677.e3, Elsevier BV, Jul. 2023, [Peer-reviewed]
Scientific journal

Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion
Atsushi Taniguchi, Yukinori Nishigami, Hiroko Kajiura-Kobayashi, Daisuke Takao, Daisuke Tamaoki, Toshiyuki Nakagaki, Shigenori Nonaka, Seiji Sonobe
Biology Open, 12, 2, 10.1242/bio.059671, The Company of Biologists, 15 Feb. 2023, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal, ABSTRACT

Amoebae are found all around the world and play an essential role in the carbon cycle in the environment. Therefore, the behavior of amoebae is a crucial factor when considering the global environment. Amoebae change their distribution through amoeboid locomotion, which are classified into several modes. In the pressure-driven mode, intracellular hydrostatic pressure generated by the contraction of cellular cortex actomyosin causes the pseudopod to extend. During amoeboid locomotion, the cellular surface exhibits dynamic deformation. Therefore, to understand the mechanism of amoeboid locomotion, it is important to characterize cellular membrane dynamics. Here, to clarify membrane dynamics during pressure-driven amoeboid locomotion, we developed a polkadot membrane staining method and performed light-sheet microscopy in Amoeba proteus, which exhibits typical pressure-driven amoeboid locomotion. It was observed that the whole cell membrane moved in the direction of movement, and the dorsal cell membrane in the posterior part of the cell moved more slowly than the other membrane. In addition, membrane complexity varied depending on the focused characteristic size of the membrane structure, and in general, the dorsal side was more complex than the ventral side. In summary, the membrane dynamics of Amoeba proteus during pressure-driven locomotion are asymmetric between the dorsal and ventral sides.

This article has an associated interview with the co-first authors of the paper.

Switching of behavioral modes and their modulation by a geometrical cue in the ciliate Stentor coeruleus
Echigoya, S., Sato, K., Kishida, O., Nakagaki, T., Nishigami, Y.
Frontiers in Cell and Developmental Biology, 10, 1021469, 01 Nov. 2022, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
Scientific journal

Simple dynamics underlying the survival behaviors of ciliates
Takuya Ohmura, Yukinori Nishigami, Masatoshi Ichikawa
Biophysics and Physicobiology, 19, e190026, Biophysical Society of Japan, Aug. 2022, [Peer-reviewed], [Invited], ［Internationally co-authored］, [Domestic magazines]
Scientific journal

Dynamic control of microbial movement by photoswitchable ATP antagonists
Sampreeth Thayyil, Yukinori Nishigami, Md. Jahirul Islam, P. K. Hashim, Ken{\textquotesingle}ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, Nobuyuki Tamaoki
Chemistry – A European Journal, 28, 30, e2022008, Wiley, 25 Mar. 2022, [Peer-reviewed], [Lead author], [International Magazine]
English, Scientific journal

Binocular stereo-microscopy for deforming intact amoeba
Kenji Matsumoto, Yukinori Nishigami, Toshiyuki Nakagaki
Optics Express, 30, 2, 2424, The Optical Society, 17 Jan. 2022, [Peer-reviewed], [International Magazine]
Scientific journal

Accumulation of Tetrahymena pyriformis on Interfaces
Kohei Okuyama, Yukinori Nishigami, Takuya Ohmura, Masatoshi Ichikawa
Micromachines, 12, 11, 1339, 1339, MDPI AG, 30 Oct. 2021, [Peer-reviewed]
Scientific journal, The behavior of ciliates has been studied for many years through environmental biology and the ethology of microorganisms, and recent hydrodynamic studies of microswimmers have greatly advanced our understanding of the behavioral dynamics at the single-cell level. However, the association between single-cell dynamics captured by microscopic observation and pattern dynamics obtained by macroscopic observation is not always obvious. Hence, to bridge the gap between the two, there is a need for experimental results on swarming dynamics at the mesoscopic scale. In this study, we investigated the spatial population dynamics of the ciliate, Tetrahymena pyriformis, based on quantitative data analysis. We combined the image processing of 3D micrographs and machine learning to obtain the positional data of individual cells of T. pyriformis and examined their statistical properties based on spatio-temporal data. According to the 3D spatial distribution of cells and their temporal evolution, cells accumulated both on the solid wall at the bottom surface and underneath the air–liquid interface at the top. Furthermore, we quantitatively clarified the difference in accumulation levels between the bulk and the interface by creating a simple behavioral model that incorporated quantitative accumulation coefficients in its solution. The accumulation coefficients can be compared under different conditions and between different species.

Near-wall rheotaxis of the ciliate Tetrahymena induced by the kinesthetic sensing of cilia
Takuya Ohmura, Yukinori Nishigami, Atsushi Taniguchi, Shigenori Nonaka, Takuji Ishikawa, Masatoshi Ichikawa
Science Advances, 7, 43, abi5878, American Association for the Advancement of Science ({AAAS}), 22 Oct. 2021, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal, Kinesthetic sensing of cilia results in upstream motility for Tetrahymena pyriformis , a typical freshwater microorganism.

Uni-cellular integration of complex spatial information in slime moulds and ciliates
Schenz, D., Nishigami, Y., Sato, K., Nakagaki, T.
Current Opinion in Genetics and Development, 57, 78, 83, Aug. 2019, [Peer-reviewed]
English, Scientific journal, © 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.

Influence of cellular shape on sliding behavior of ciliates
Nishigami, Y., Ohmura, T., Taniguchi, A., Nonaka, S., Manabe, J., Ishikawa, T., Ichikawa, M.
Communicative and Integrative Biology, 11, 4, 2018, [Peer-reviewed], [Lead author]
Scientific journal, © 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.

Simple mechanosense and response of cilia motion reveal the intrinsic habits of ciliates
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, [Peer-reviewed], [Lead author]
Scientific journal, © 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 olor depending upon cell states
Yukinori Nishigami
Journal of Protistology, 51, 1, 6, 2018, [Peer-reviewed], [Lead author]
English, Scientific journal

Active Materials Integrated with Actomyosin
Hiroaki Ito, Masahiro Makuta, Yukinori Nishigami, Masatoshi Ichikawa
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 86, 10, 101001, PHYSICAL SOC JAPAN, Oct. 2017, [Peer-reviewed]
English, Scientific journal, Muscles are the engine of our body, and actomyosin is the engine of a cell. Both muscle and the actomyosin use the same proteins, namely, actin, and myosin, which are the pair of cytoskeleton and motor proteins generating a force to realize deformation. The properties of force generation by actomyosin at a single-molecule level have been studied for many years. Moreover, the active properties of higher-order structures integrated by actomyosin are attracting the attention of researchers. Here, we review the recent progress in the study of reconstituted actomyosin systems in vitro toward real-space models of nonequilibrium systems, collective motion, biological phenomena, and active materials.

Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives
Dorota Buczek, Malgorzata Wojtkowska, Yutaka Suzuki, Seiji Sonobe, Yukinori Nishigami, Monika Antoniewicz, Hanna Kmita, Wojciech Makalowski
BMC GENOMICS, 17, BIOMED CENTRAL LTD, Feb. 2016, [Peer-reviewed]
English, Scientific journal, 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.

Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface
Yukinori Nishigami, Hiroaki Ito, Seiji Sonobe, Masatoshi Ichikawa
SCIENTIFIC REPORTS, 6, NATURE PUBLISHING GROUP, Jan. 2016, [Peer-reviewed], [Lead author]
English, Scientific journal, 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.

Wrinkling of a spherical lipid interface induced by actomyosin cortex
Hiroaki Ito, Yukinori Nishigami, Seiji Sonobe, Masatoshi Ichikawa
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 92, 6, American Physical Society, 21 Dec. 2015, [Peer-reviewed], [Lead author]
English, Scientific journal, 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.

Reconstruction of Active Regular Motion in Amoeba Extract: Dynamic Cooperation between Sol and Gel States
Yukinori Nishigami, Masatoshi Ichikawa, Toshiya Kazama, Ryo Kobayashi, Teruo Shimmen, Kenichi Yoshikawa, Seiji Sonobe
PLoS ONE, 8, 8, 05 Aug. 2013, [Peer-reviewed], [Lead author]
English, Scientific journal, 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.

Amoeboid movement utilizes the shape coupled bifurcation of an active droplet to boost ballistic motion
H. Ebata, Y. Nishigami, H. Fujiwara, S. Kidoaki, M. Ichikawa, 06 Feb. 2024
One of the essential functions of living organisms is spontaneous migration
through the deformation of their body, such as crawling, swimming, and walking.
Depending on the size of the object, the efficient migratory mode should be
altered because the contribution from the inertial and frictional forces acting
on the object switches. Although the self-propelling motion characterizing
active matter has been extensively studied, it is still elusive how a living
cell utilizes the mode switching of the self-propulsion. Here, we studied the
migration dynamics of amoeboid movement of free-living amoeba, Amoeba proteus,
for starved and vegetative phases, as typified by dynamic and stationary
states, respectively. Fourier-mode analysis on the cell shape and migration
velocity extracted two characteristic migration modes, which makes a
coexistence of amoeboid-swimmer like random motion and the active-droplet like
ballistic motion. While the amoeboid-swimmer mode governs random motion, the
active-droplet mode performs non-negligible contribution on the migration
strength. By employing the symmetry argument of the active-droplet, we discover
the supercritical pitchfork bifurcation of the migration velocity due to the
symmetry breaking of the cell shape represents the switching manner from the
motionless state to the random and the ballistic motions. Our results suggest
that sub-mm sized A. proteus utilizes both shape oscillatory migration of
deformed-swimmer driven by surface wave and convection based mass transfer,
called blebbing, as like as cm-sized active droplet to optimize the movement
efficiency.

原生生物の行動と運動 ー単細胞真核生物の生存戦略ー　　　　　　　　　　　　　　　
西上幸範, 可視化情報, 44, 169, 11, 14, 01 Jan. 2024, [Invited], [Lead author, Last author, Corresponding author]

Voltage Response of STM Tunneling Currents on Microtubules: Proposal of a New Neural Model by Quantum Reduction with Entanglement
Yutaro Teranishi, Keiji Nakatsugawa, Yukinori Nishigami, Toshiyuki Nakagaki, Koichi Ichimura, Yuta Fukuda, Satoshi Tanda, Proceedings of the 29th International Conference on Low Temperature Physics (LT29), 22 May 2023
Journal of the Physical Society of Japan

First person – Atsushi Taniguchi and Yukinori Nishigami
Biology Open, 12, 2, 15 Feb. 2023
ABSTRACT

First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping researchers promote themselves alongside their papers. Atsushi Taniguchi and Yukinori Nishigami are co-first authors on ‘ Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion’, published in BiO. Atsushi is a postdoc in the lab of Toshiyuki Nakagaki at Research Institute for Electronic Science, Hokkaido University, Kita-Ward Sapporo, Japan, investigating algorithms for collective space exploration and use in ciliates and amoebae. Yukinori is an assistant professor in the lab of Toshiyuki Nakagaki at the Research Institute for Electronic Science, Hokkaido University, Kita-Ward Sapporo, Japan, investigating the behavior of protists., The Company of Biologists

Linear contraction of stress fibers generates cell body rotation
Chika Okimura, Syu Akiyama, Yukinori Nishigami, Ryota Zaitsu, Tatsunari Sakurai, Yoshiaki Iwadate, 07 Jan. 2023
Abstract

Wounds are healed by crawling migration of the epidermal cells around the injured area. Fish epidermal keratocytes that rapidly repair wounds comprise a frontal crescent-shaped lamellipodium and a rear rugby ball-shaped cell body. The cell body rotates like a wheel during migration. Stress fibers, which are bundles of contractile actomyosin filaments, are arranged along the seams of the rugby ball. Here we show the linear contraction of stress fibers to be the driving force for rotation. We constructed a mechanical model of the cell body that consisted of a soft cylinder with a contractile coil. From the motion of the model, it was predicted that contraction of the stress fibers would deform the soft cell body, as a result of which the deformed cell body would push against the substrate to generate torque. This prediction was confirmed by the observation of stress fiber dynamics in migrating cells. Linear-to-rotation conversion in migrating keratocytes is realized by simple soft-body mechanics. Conversion from linear motion to rotation is widely used in machines with moving parts, but requires somewhat complicated mechanics. An understanding of linear-to-rotation conversion in keratocytes has potential for use in the design of biomimetic soft robots., Cold Spring Harbor Laboratory

Environment-adaptive transport network in Physarum plasmodium
中垣俊之, 佐藤勝彦, 西上幸範, BSJ-Review, 13, 151, Aug. 2022, [Peer-reviewed], [Invited], [International Magazine]
Japanese

Fluid Dynamic Model Reveals a Mechano-sensing System Underlying the Behavior of Ciliates
Takuya OHMURA, Yukinori NISHIGAMI, Masatoshi ICHIKAWA, Seibutsu Butsuri, 61, 1, 016, 019, Jan. 2021, [Peer-reviewed], [Invited]
Ciliates are microorganisms found in water environments that feed by accumulating close to solid-liquid interfaces such as pond bottom and waterweed surface. The ability of swimming ciliates to remain near surfaces is crucial for efficient nutrient acquisition. Here, we investigated the dynamics of the near-surface swimming behavior. In our experiments, the cilia of these ciliates lost their propelling activity when encountering a surface, suggesting they have a mechano-sensing system, and the ciliate slid along the surface. Our simulations revealed that not only the loss of ciliary activity but also the cell body aspect ratio was critical for this sliding motion., Biophysical Society of Japan, Japanese

Mechanism of bleb-driven amoeboid locomotion　　　　　　　　　　　　　　　
Yukinori Nishigami, Hiroaki Ito, Masatoshi Ichikawa, Japanese Journal of Protozoology, 49, 17, 25, 2016, [Peer-reviewed], [Lead author]
Japanese

Studies on bleb-driven cell locomotion using reconstituted systems　　　　　　　　　　　　　　　
Yukinori Nishigami, Hiroaki Ito, Masatoshi Ichikawa, BSJ-Review, 6, 82, 91, 2015, [Peer-reviewed], [Lead author]
Japanese

原生生物学事典
梁瀬隆二, 西上幸範, 3-7 運動関連装置
朝倉書店, May 2023, 9784254171815, viii, 446p, 図版 [4] p, Japanese, [Contributor]

原生生物学事典
谷口篤史, 西上幸範, 2-2-2 ツブリネア
朝倉書店, May 2023, 9784254171815, viii, 446p, 図版 [4] p, Japanese, [Contributor]

原生生物学事典
谷口篤史, 西上幸範, 2-2-1 ディスコセア
朝倉書店, May 2023, 9784254171815, viii, 446p, 図版 [4] p, Japanese, [Contributor]

原生生物学事典
谷口篤史, 西上幸範, 2-2 アメーボゾア
朝倉書店, May 2023, 9784254171815, viii, 446p, 図版 [4] p, Japanese, [Contributor]

生物系のための物理学　　　　　　　　　　　　　　　
北海道大学
2024 - Present

Soft Matter Physics Nonlinear Phenomenon　　　　　　　　　　　　　　　
Hokkaido University
2020 - 2024

Functional and Regulatory Life Science Nonlinear Phenomenon　　　　　　　　　　　　　　　
Hokkaido University
2020 - 2024

Freshman Seminar Science in our daily life　　　　　　　　　　　　　　　
Hokkaido University
2019 - 2024

数学総合講義Ⅰ「数理で読み解く生物行動学」　　　　　　　　　　　　　　　
北海道大学
2024

大学院共通授業科目（一般科目）：自然科学・応用科学：ナノテクノロジー・ナノサイエンス概論Ⅰ 「細胞内の運動性ナノ構造物」　　　　　　　　　　　　　　　
北海道大学
2023

数学総合講義Ⅰ「数理で読み解く生物行動学」　　　　　　　　　　　　　　　
北海道大学
2022

Special Lecture in Biology　　　　　　　　　　　　　　　
Konan University
2019

Karenia属赤潮原因藻の遊泳および接着機構の解明
科学研究費助成事業
01 Apr. 2024 - 31 Mar. 2027
西上 幸範
日本学術振興会, 基盤研究(C), 北海道大学, 24K09388

環境連成力学を基盤とした微生物行動シミュレータの開発
科学研究費助成事業
10 Sep. 2021 - 31 Mar. 2026
石川 拓司, 上野 裕則, 西上 幸範
本年度は研究の立ち上げを行い、大型計算機を入札により導入した。主要な研究実績は以下の通りである。
１．クラミドモナスが流れに逆らって泳ぐ性質（走流性）を示すことを発見した。実験と理論、数値シミュレーションを融合し、そのメカニズムが遊泳の非定常性からくることを明らかにした（Omori, et al., J. Fluid Mech. 2021）。 ２．さまざまな遊泳モードを持つ微生物の2体干渉の解析を行い、干渉運動の相図を作成した。これにより、微生物干渉の体系的な理解が進んだ（Darveniza, et al., Phys. Rev. Fluids,2022）。 ３．数値解析手法の高度化にも取り組み、汎用性の高い境界要素法と近接場が得意な潤滑理論を融合させたLT-BEMを開発した。この手法を用いることで、微生物運動の解析精度が大幅に改善することを示した（Ishikawa, J. Comp. Phys., 2022）。 ４．開発した微生物行動シミュレータをバイオフィルムの形成過程へと展開した。複雑流路内に形成されるストリーマーの形成過程を、細胞スケールからメゾスケールで計算した。そして、マクロなレオロジー特性とストリーマー形状の関係を解明した（Kitamura, et al., J. R. Soc. Interface, 2021）。 ５．開発した微生物行動シミュレータを酵母の発酵過程へと展開し、培養時の輸送現象を定量的に調べた。培養容器内にプラスチックごみを模擬した物体を混入させると、ブラジルナッツ効果が現れることを発見した。この成果はSoft Matter誌の背表紙を飾り、プレスリリースされた（Srivastava, et al., Soft Matter, 2021）。
日本学術振興会, 学術変革領域研究(A), 東北大学, 21H05308

再構成アプローチで解明するダイナミンの膜切断機構とその破綻に起因する疾患発症機序
科学研究費助成事業
07 Oct. 2019 - 31 Mar. 2023
竹田 哲也, 内橋 貴之, 竹居 孝二, 西上 幸範, 谷 知己
今年度は，Dynamin 2の異常で起こる筋疾患である先天性ミオパチーについて，研究の進展があった．先天性ミオパチーの一つである中心核ミオパチー（Centronuclear Myopathy; CNM）の患者では，骨格筋の興奮収縮連関に必要な細胞膜の陥入構造（T管）の形成異常により，筋収縮が正常に起こらない．先行研究で，Dynamin 2の遺伝子上のSNV（一塩基変異）が，CNM発症に関与することが示されていた．そこで，CNM変異型のDynamin 2の膜リモデリング機能異常について，in vitro再構成系による分子レベルの解析と，筋芽細胞を用いた細胞レベルの解析を行った．その結果，①Dynamin 2は，T管構造の安定化に必要であること，②CNM変異型Dynamin 2は，膜切断に必要なGTPアーゼ活性が恒常的に亢進しており，T管構造の形成異常が起こることを明らかにした（Fujise et al., JBC 2021）．さらに，③CNM患者のコホート解析で同定された意義不明SNVから，in vitroおよび細胞レベルの解析法を用いて疾患責任SNVを同定することに成功した（Fujise et al., bioRxiv 2021）．
今年度は，新型コロナウィルスの影響もあり，イギリスへの渡航およびチームによるオンサイトミーティングを延期せざるをえなかった．しかし，研究代表者がオーガナイズした第58回日本生物物理学会年会のシンポジウム「膜のリモデリングと組織化の分子基盤」（web開催）に国際共同研究者のMcMahon博士（MRC分子生物学研究所）をゲストスピーカーとして招聘し，最新の知見についての講演をしていただき，その後チームメンバーとのディスカッションを行った．
日本学術振興会, 国際共同研究加速基金(国際共同研究強化(B)), 岡山大学, 19KK0180

Analysis of higher order F-actin structures in bleb-driven amoeboid locomotion using a reconstituted system
Grants-in-Aid for Scientific Research
26 Apr. 2017 - 31 Mar. 2020
西上 幸範
ブレブ駆動型アメーバ運動は組織中を移動する接着性真核細胞が一般に行う運動様式で、多くの生命現象において重要であることが示されている。生細胞を用いた研究からアクチン高次構造制御タンパク質がこの運動に重要であることが示唆されているが、このアクチン高次構造が細胞を構成するタンパク質や細胞膜などに対し具体的にどのように作用するのかは十分に理解されていない。そこで、本研究ではブレブ駆動型アメーバ運動を試験管内で再構築し、アクチン高次構造を任意に変化させることで、この構造と運動の関係を明らかにするとこを目的とする。
本年度は研究計画に従い前年度に作製、至適化したブレブ駆動型アメーバ運動試験管内再構築系に、数種類のアクチン高次構造を変化させるアクチン結合タンパク質を追加し、それぞれの運動に対する影響を調べた。アクチン結合タンパク質の追加によって、膜形状の非平衡揺らぎ特性や形状発展のモードが大きく影響を受けるということがわかった。また、これらの原因を調べるため、これらアクチン結合タンパク質を加えた際のアクチン溶液の粘弾性特性に関しても調べた。その結果、粘弾性特性が同等であっても膜形状の非平衡揺らぎや形状発展は異なるという状態が存在することを発見した。
本研究によって、アクチン結合タンパク質が膜の形状変化に大きな影響を与え、その際、粘弾性特性以外の要素の重要性が示唆された。次の目標は、その機構の詳細の解明である。そのためには、膜の粘弾性特性などを定量的に測定する必要がある。また、アクチン結合タンパク質の種類によって膜への封入可能な条件が異なるため、それぞれの状態を単純に比較することはできないということも問題点として挙げられる。今後、これらを改善することで本分野の大きな進歩があると期待される。
Japan Society for the Promotion of Science, Grant-in-Aid for JSPS Fellows, 17J06827

Active bio & soft matters studied through interface-induced phenomena
Grants-in-Aid for Scientific Research
01 Apr. 2014 - 31 Mar. 2019
Ichikawa Masatoshi, Nishigami Yukinori
We conducted research on macroscopic transfer phenomena induced by nonequilibrium interfaces in soft-matters and bio-matters, and created various model experimental systems and clarified their driving mechanisms. In particular, the following results have been obtained: motion bifurcation between straight and rotational motions of droplets driven by thermal Marangoni effect under light-to-heat conversion; spontaneous structure formation of actomyosin emerged inside a water-in-oil droplet coated with a lipid monolayer to induce non-thermal fluctuation of the interface; cortex reconstruction that causes buckling deformation of the interface; induction of limit cycle oscillations by coherent resonance; and elucidation of the accumulation mechanism of swimming unicellular microorganisms Tetrahymena near a wall.
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (A), Kyoto University, 26707020

新規モデルシステムを用いたアメーバ運動機構の解明
科学研究費助成事業
2010 - 2012
西上 幸範
アメーバ運動の運動機構としては仮足先端部分でのアクチンの重合が重要であると考えられてきたが、近年、ブレブ依存的アメーバ運動と呼ばれるもう一つの機構が多種の細胞で確認されている。しかしながら、その機構に関しては不明な点が多い。その原因としては、ブレブ依存的アメーバ運動は細胞全体が関わる運動であるため、詳細な解析や生化学的研究などが困難であるということが挙げられる。私はこのような問題を解決するために、これまで独自に開発した試験管内再構築系を用いて研究を行ってきた。この系は「細胞抽出液中にアクトミオシン溶液を注入すると、アクトミオシン溶液がアメーバ運動様の動きを示す」という系である。
再構築系と生細胞が行うブレブ依存的アメーバ運動の類似性を示すため、運動中のアクチンを蛍光ファロイジンにより可視化した。その結果、運動を行うアクトミオシン溶液では運動に先立ち、表層部分にアクチンが局在し、さらに仮足様構造の伸長方向ではアクチンの破壊が起こることが確認された。この挙動はこれまで報告されている生細胞のブレブ依存的アメーバ運動におけるアクチンの挙動と等しい。次に、アクトミオシン溶液の収縮過程を詳細に観察し、その過程にMahadevan-Pomeau Model(1999)を適用したところ、収縮過程中にはアクトミオシン溶液の表層部分が収縮し表面力を上昇させていることが示唆された。また、仮足形成過程を観察し、表面収縮力の散逸と流体力学的散逸を考慮することで、仮足形成時における表面力の相対値を見積もった。その結果、アクトミオシン溶液と表面力の関係は正の相関を持つことが分かった。したがってこの系は、仮足様構造を形成する際、界面張力といった力ではなく表層部分の収縮力を用いて新たな仮足形成を行っていることが示唆された。以上の事からこの系がブレブ依存的アメーバ運動とよく似た機構で動いていることが示された。
日本学術振興会, 特別研究員奨励費, 兵庫県立大学, 10J10340

流れに逆らって泳ぐ微生物　　　　　　　　　　　　　　　
16 Jan. 2022
読売新聞
くらしサイエンス, [Paper]

下流に流されない微生物たちの、自動的に流れに逆らう仕組みを解明　　　　　　　　　　　　　　　
28 Oct. 2021
大学ジャーナルオンライン
https://univ-journal.jp/125014/, [Internet]

京大など、水生微生物が上流に向かって移動する仕組みを解明　　　　　　　　　　　　　　　
21 Oct. 2021
環境展望台
国内ニュース
https://tenbou.nies.go.jp/news/jnews/detail.php?i=32647, [Internet]