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Analysis of biological responses tol toxicity in model organisms using environmental RNA.

Research Project

Project/Area Number 19K22934
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 64:Environmental conservation measure and related fields
Research InstitutionUniversity of Hyogo

Principal Investigator

Hideyuki Doi  兵庫県立大学, シミュレーション学研究科, 准教授 (80608505)

Co-Investigator(Kenkyū-buntansha) 坂本 正樹  富山県立大学, 工学部, 准教授 (20580070)
Project Period (FY) 2019-06-28 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2019: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords環境RNA / 環境DNA / 毒性 / 遺伝子発現 / RNAseq / RNシークエンス / トランスクリプトーム / 毒性試験 / 生態毒性
Outline of Research at the Start

本研究では、水中において存在している“環境RNA“を用いて、遺伝子発現を解析する革新的手法を開発する。標準試験生物であり、全ゲノムの記載があるオオミジンコの生態毒性試験において、環境RNAを回収、シークエンス解析する手法を開発する。本研究で開発する環境RNAを用いた解析と、生物から直接取り出したRNAを用いた従来の解析との比較を行い、環境RNA手法による解析を確立する。

Outline of Final Research Achievements

We conducted this project toto establish an innovative technology for continuous measurement of gene expression responses of organisms using environmental RNA (eRNA), especially for applying to capture biological responses to toxicity over time. We developed a novel method to collect and sequence environmental RNA for using Daphnia magna, a toxic-standard test organism whose whole genome has been published. Daphnia magna was reared in a bottle exposed to dissolved copper, and the RNA was extracted from the water and the organism. The RNAseq was performed by RNA sequencing for ultra-low RNA concentration. The results were compared with RNAseq from the organisms, and the differences and similar in gene expressions were observed in the eRNA extracted from the water, depending on the presence or absence of copper toxicity.

Academic Significance and Societal Importance of the Research Achievements

本研究で開発した、環境RNAの解析では試験個体を分析に供するため、生きたまま連続的に関連遺伝子の発現量を追うことが不可能である。この問題を解決することができれば、現行の生態毒性試験で生物の生死や成長、増殖などの挙動を追うと同時に、関連遺伝子の発現量の変化をとらえることが可能となる。そこで、本研究では、水中において存在している“環境RNA“を用いて、遺伝子発現を解析する革新的手法を開発した。この”環境RNAにより生物の遺伝子発現反応を連続測定できる革新的技術”を確立により、毒性への生物応答を継時的に捉えるために応用することができると考えらえっる

Report

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

    (13 results)

All 2021 2020 2019

All Journal Article (10 results) (of which Peer Reviewed: 10 results,  Open Access: 9 results) Presentation (2 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Book (1 results)

  • [Journal Article] Taxonomic, functional, and phylogenetic diversity of fungi in a forest-tundra ecotone in Qu?bec2021

    • Author(s)
      Matsuoka Shunsuke、Doi Hideyuki、Masumoto Shota、Kitagawa Ryo、Nishizawa Keita、Tanaka Kaho、Hasegawa Motohiro、Hobara Satoru、Osono Takashi、Mori Akira S.、Uchida Masaki
    • Journal Title

      Polar Science

      Volume: 27 Pages: 100594-100594

    • DOI

      10.1016/j.polar.2020.100594

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique.2021

    • Author(s)
      Hoshino T, Nakao R, Doi H, Minamoto T
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 4372-4372

    • DOI

      10.1038/s41598-021-83318-6

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Suppression of environmental DNA degradation in water samples associated with different storage temperature and period using benzalkonium chloride2020

    • Author(s)
      Takahara Teruhiko、Taguchi Junya、Yamagishi Satoshi、Doi Hideyuki、Ogata Shigeki、Yamanaka Hiroki、Minamoto Toshifumi
    • Journal Title

      Limnology and Oceanography: Methods

      Volume: 18 Issue: 8 Pages: 437-445

    • DOI

      10.1002/lom3.10374

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sedimentary DNA tracks decadal-centennial changes in fish abundance2020

    • Author(s)
      Kuwae Michinobu、Tamai Hiromichi、Doi Hideyuki、Sakata Masayuki K.、Minamoto Toshifumi、Suzuki Yoshiaki
    • Journal Title

      Communications Biology

      Volume: 3 Issue: 1 Pages: 1-12

    • DOI

      10.1038/s42003-020-01282-9

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Broad-scale detection of environmental DNA for an invasive macrophyte and the relationship between DNA concentration and coverage in rivers2020

    • Author(s)
      Doi Hideyuki、Akamatsu Yoshihisa、Goto Masuji、Inui Ryutei、Komuro Takashi、Nagano Mariko、Minamoto Toshifumi
    • Journal Title

      Biological Invasions

      Volume: 23 Issue: 2 Pages: 507-520

    • DOI

      10.1007/s10530-020-02380-9

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exploring a legendary giant squid: An environmental DNA approach.2020

    • Author(s)
      Wada T, Doi H, Togaki D, Kaida R, Nagano M, Katano I, Suzuki M, Ohtani T, Mitsuhashi H.
    • Journal Title

      Marine Biology

      Volume: 167 Issue: 11 Pages: 1-7

    • DOI

      10.1007/s00227-020-03773-z

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols2020

    • Author(s)
      Minamoto Toshifumi、Miya Masaki、Sado Tetsuya、Seino Satoquo、Doi Hideyuki、Kondoh Michio、Nakamura Keigo、Takahara Teruhiko、Yamamoto Satoshi、Yamanaka Hiroki、Araki Hitoshi、Iwasaki Wataru、Kasai Akihide、Masuda Reiji、Uchii Kimiko
    • Journal Title

      Environmental DNA

      Volume: 3 Issue: 1 Pages: 8-13

    • DOI

      10.1002/edn3.121

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation2020

    • Author(s)
      Oka Shin‐ichiro、Doi Hideyuki、Miyamoto Kei、Hanahara Nozomi、Sado Tetsuya、Miya Masaki
    • Journal Title

      Environmental DNA

      Volume: 3 Issue: 1 Pages: 55-69

    • DOI

      10.1002/edn3.132

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA.2019

    • Author(s)
      Uchii K, Doi H, Okahashi T, Katano I, Yamanaka H, Sakata KM, Minamoto T.
    • Journal Title

      Environmental DNA

      Volume: 1 Issue: 4 Pages: 359-367

    • DOI

      10.1002/edn3.37

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The detection of aquatic macroorganisms using environmental DNA analysis?A review of methods for collection, extraction, and detection2019

    • Author(s)
      Tsuji Satsuki、Takahara Teruhiko、Doi Hideyuki、Shibata Naoki、Yamanaka Hiroki
    • Journal Title

      Environmental DNA

      Volume: 1 Issue: 2 Pages: 99-108

    • DOI

      10.1002/edn3.21

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 環境中に漂うDNAの情報から何がわかってきたか?2021

    • Author(s)
      土居秀幸
    • Organizer
      第68回日本生態学会 公開講演会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Environmental DNA methods for macroorganism populations2021

    • Author(s)
      Hideyuki Doi
    • Organizer
      The 1st DNAqua-Net international conference
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 環境DNA2021

    • Author(s)
      一般社団法人 環境DNA学会、土居 秀幸、近藤 倫生
    • Total Pages
      300
    • Publisher
      共立出版
    • ISBN
      9784320058163
    • Related Report
      2020 Annual Research Report

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Published: 2019-07-04   Modified: 2022-01-27  

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