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Intra-nucleic and genomic distributions of liquid droplets formed by liquid-liquid phase separations

Research Project

Project/Area Number 18K19297
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionKyoto University

Principal Investigator

Shirakawa Masahiro  京都大学, 工学研究科, 教授 (00202119)

Project Period (FY) 2018-06-29 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2020: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2019: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords量子センシング / 光検出磁気共鳴 / 1分子観察 / ナノ粒子 / 光検出磁気共鳴法 / ナノダイヤモンド / 細胞内温度計測 / 細胞内粘度計測 / 高分解能イメージング / 液滴様構造体 / ODMR-FIONA / エピジェネティックス / 液液相分離 / 細胞分化
Outline of Final Research Achievements

The aim of this study was establish the method to measure several physicoochemical parameters inside living cells by using optical detection of magnetic resonance (ODMR) of Nitrogen Vacancy Centers (NVCs) in nanodiamonds (NDs) at nanometer space resolution. For the preparation of quantum molecular sensors, we irradiated NDs (φ5-20 nm) by electron beams in order to generate NVCs. We then coated the surfaces of FNDs by polymers in order to avoid self-aggregations. We further modified the surfaces by several functional groups so that we can measure diffusion rates, temperatures, pH and so on by ODMR spectra of FNDs at space resolution of 10 nm orders. We also measured temperatures inside living cells, and analyzed movements of actin fibers ic cytoskeletons.

Academic Significance and Societal Importance of the Research Achievements

FNDの光検出磁気共鳴法(ODMR)によって、生細胞内の高分子の動態、拡散性、温度、pHなどの様々な物理パラメータを高い空間分解能で量子センシングするという手法の開発を進めた。その達成には、窒素空孔センターが持つの光三重項電子のを用いた光超偏極技術と光学検出装置の作成といった電子・光工学技術に始まって、ソフトウェア技術、nmオーダーのFNDの調製や官能基の導入といった化学的技術、さらに物理学的理論、分子・細胞生物学の技術、といった広範な学問分野を要する。このような分野横断的な新規技術を開発したことは、学術的意義が高い。更に生物、医学的分野に適用が進めば、その社会的意義は計り知れない。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (11 results)

All 2021 2020 2019

All Journal Article (11 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 10 results,  Open Access: 3 results)

  • [Journal Article] Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel2021

    • Author(s)
      Iwakawa Naoto、Morimoto Daichi、Walinda Erik、Leeb Sarah、Shirakawa Masahiro、Danielsson Jens、Sugase Kenji
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Issue: 10 Pages: 2521-2532

    • DOI

      10.1021/acs.jpcb.0c11162

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural Dynamic Heterogeneity of Polyubiquitin Subunits Affects Phosphorylation Susceptibility2021

    • Author(s)
      Morimoto Daichi、Walinda Erik、Takashima Shingo、Nishizawa Mayu、Iwai Kazuhiro、Shirakawa Masahiro、Sugase Kenji
    • Journal Title

      Biochemistry

      Volume: 60 Issue: 8 Pages: 573-583

    • DOI

      10.1021/acs.biochem.0c00619

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chain-length dependent physical properties and degradation of ubiquitin chains2020

    • Author(s)
      森本 大智、白川 昌宏
    • Journal Title

      生化学

      Volume: 92 Issue: 1 Pages: 7-13

    • DOI

      10.14952/SEIKAGAKU.2020.920007

    • ISSN
      0037-1017
    • Year and Date
      2020-02-25
    • Related Report
      2019 Research-status Report
  • [Journal Article] Quantitative monitoring of ubiquitination/deubiquitination reaction cycles by 18O-incorporation2020

    • Author(s)
      Tanaka Yuka、Morimoto Daichi、Walinda Erik、Sugase Kenji、Shirakawa Masahiro
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 529 Issue: 2 Pages: 418-424

    • DOI

      10.1016/j.bbrc.2020.06.008

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nanodiamonds for bioapplications?specific targeting strategies2020

    • Author(s)
      Terada Daiki、Genjo Takuya、Segawa Takuya F.、Igarashi Ryuji、Shirakawa Masahiro
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129354-129354

    • DOI

      10.1016/j.bbagen.2019.04.019

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Visualizing protein motion in Couette flow by all-atom molecular dynamics2020

    • Author(s)
      Walinda Erik、Morimoto Daichi、Shirakawa Masahiro、Scheler Ulrich、Sugase Kenji
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129383-129383

    • DOI

      10.1016/j.bbagen.2019.06.006

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] High resolution protein 3D structure determination in living eukaryotic cells2019

    • Author(s)
      Tanaka, T., Ikeya, T., Kamoshida, H., Suemoto, Y., Mishima, M., Shirakawa, M., Guentert, P., Ito, Y.
    • Journal Title

      Angewandte Chemie International Edition

      Volume: in press Issue: 22 Pages: 1-7

    • DOI

      10.1002/anie.201900840

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An innate interaction between IL-18 and the propeptide that inactivates its precursor form2019

    • Author(s)
      Naotaka Tsutsumi, Ayumi Yokota, Takeshi Kimura, Zenichiro Kato, Toshiyuki Fukao, Masahiro Shirakawa, Hidenori Ohnishi & Hidehito Tochio
    • Journal Title

      Scientific Reportsvolume

      Volume: 9 Issue: 1 Pages: 6160-6160

    • DOI

      10.1038/s41598-019-42661-5

    • NAID

      120007006235

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Monodisperse Five-Nanometer-Sized Detonation Nanodiamonds Enriched in Nitrogen-Vacancy Centers2019

    • Author(s)
      Terada Daiki、Segawa Takuya F.、Shames Alexander I.、Onoda Shinobu、Ohshima Takeshi、O?sawa Eiji、Igarashi Ryuji、Shirakawa Masahiro
    • Journal Title

      ACS Nano

      Volume: 13 Issue: 6 Pages: 6461-6468

    • DOI

      10.1021/acsnano.8b09383

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Contribution of Coiled-Coil Assembly to Ca2+/Calmodulin-Dependent Inactivation of TRPC6 Channel and its Impacts on FSGS-Associated Phenotypes2019

    • Author(s)
      Polat Onur K.、Uno Masatoshi、Maruyama Terukazu、Tran Ha Nam、Imamura Kayo、Wong Chee Fah、Sakaguchi Reiko、Ariyoshi Mariko、Itsuki Kyohei、Ichikawa Jun、Morii Takashi、Shirakawa Masahiro、Inoue Ryuji、Asanuma Katsuhiko、Reiser Jochen、Tochio Hidehito、Mori Yasuo、Mori Masayuki X.
    • Journal Title

      Journal of the American Society of Nephrology

      Volume: 30 Issue: 9 Pages: 1587-1603

    • DOI

      10.1681/asn.2018070756

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] pH Nanosensor Using Electronic Spins in Diamond2019

    • Author(s)
      Fujisaku Takahiro、Tanabe Ryotaro、Onoda Shinobu、Kubota Ryou、Segawa Takuya F.、So Frederick T.-K.、Ohshima Takeshi、Hamachi Itaru、Shirakawa Masahiro、Igarashi Ryuji
    • Journal Title

      ACS Nano

      Volume: 13 Issue: 10 Pages: 11726-11732

    • DOI

      10.1021/acsnano.9b05342

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access

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Published: 2018-07-25   Modified: 2022-01-27  

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