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Elucidation of the working principle of cells based on high dimensional phenotyping

Research Project

Project/Area Number 15H04402
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Chromosome dynamics
Research InstitutionThe University of Tokyo

Principal Investigator

Ohya Yoshikazu  東京大学, 大学院新領域創成科学研究科, 教授 (20183767)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Fiscal Year 2017: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2016: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2015: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
KeywordsSaccharomyces cerevisiae / morphology / CalMorph / phenotyping / 出芽酵母 / 遺伝子機能 / 形態表現型 / 必須遺伝子 / 形態プロファイル / 形態異常度 / 画像解析 / 遺伝子ネットワーク / 細胞形態 / ケミカルゲノミクス / 高次元表現型解析 / カルシウム / 遺伝的相互作用 / 形態表現型解析 / 遺伝学 / 大規模解析 / ハプロ不全性
Outline of Final Research Achievements

It is one of the central issues of genetics to unravel the principle of motion of an organism by genetic information, that is, the principle of how genotype "cause" is linked to phenotype "result". In order to clarify the relationship between genotype and phenotype, we used the excellent genetic tool of unicellular eukaryotic budding yeast (S. cerevisiae) and used cell images obtained with fluorescence microscope. We analyzed the images with image processing system CalMorph and found that there is a close relationship between gene function and morphological phenotype. This was achieved by quantitatively analyzing high dimensional phenotype from two viewpoints including morphological profiling and morphological abnormality. Using that relationship, we succeeded in identifying intracellular targets of drugs.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (43 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (20 results) (of which Int'l Joint Research: 14 results,  Peer Reviewed: 20 results,  Open Access: 9 results,  Acknowledgement Compliant: 9 results) Presentation (16 results) (of which Int'l Joint Research: 8 results,  Invited: 13 results) Book (2 results) Remarks (1 results)

  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] SUNY/ミネソタ大学/プリンストン大学(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] リオン大学/ストラスブルグ大学(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] EMBL(ドイツ)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae2018

    • Author(s)
      Suzuki G, Wang Y, Kubo K, Hirata E, Ohnuki S, Ohya Y
    • Journal Title

      BMC Genomics

      Volume: 19 Issue: 1 Pages: 149-149

    • DOI

      10.1186/s12864-018-4526-z

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Testing the neutral hypothesis of phenotypic evolution2018

    • Author(s)
      Ho WC, Ohya Y, Zhang J
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 114 Issue: 46 Pages: 12219-12224

    • DOI

      10.1073/pnas.1710351114

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional annotation of chemical libraries across diverse biological processes.2017

    • Author(s)
      Piotrowski JS, Li SC, Deshpande R.......Shirahige K,......Boone C.
    • Journal Title

      Nat Chem Biol.

      Volume: 13 Issue: 9 Pages: 982-993

    • DOI

      10.1038/nchembio.2436

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Phenotypic diagnosis of lineage and differentiation during sake yeast breeding2017

    • Author(s)
      Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya
    • Journal Title

      G3 (Bethesda)

      Volume: 7 Issue: 8 Pages: 2807-2820

    • DOI

      10.1534/g3.117.044099

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Systematic analysis of Ca2+ homoeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles2017

    • Author(s)
      Farzan Ghanegolmohammadi, Mitsunori Yoshida, Shinsuke Ohnuki, Yuko Sukegawa, Hiroki Okada, Keisuke Obara, Akio Kihara, Kuninori Suzuki, Tetsuya Kojima, Nozomu Yachie, Dai Hirata, Yoshikazu Ohya
    • Journal Title

      Mol. Biol. Cell

      Volume: 28 Issue: 23 Pages: 3415-3427

    • DOI

      10.1091/mbc.e17-04-0216

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Dual Activity Responsible for the Elongation and Branching of β-(1,3)-Glucan in the Fungal Cell Wall.2017

    • Author(s)
      Aimanianda V, Simenel C, Garnaud C, Clavaud C, Tada R, Barbin L, Mouyna I, Heddergott C, Popolo L, Ohya Y, Delepierre M, Latge JP
    • Journal Title

      MBio

      Volume: 8 Issue: 3

    • DOI

      10.1128/mbio.00619-17

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Promoter engineering of the Saccharomyces cerevisiae RIM15 gene for improvement of alcoholic fermentation rates under stress conditions.2017

    • Author(s)
      Watanabe D, Kaneko A, Sugimoto Y, Ohnuki S, Takagi H, Ohya Y
    • Journal Title

      J Biosci Bioeng.

      Volume: 123 Issue: 2 Pages: 183-189

    • DOI

      10.1016/j.jbiosc.2016.08.004

    • NAID

      40021112533

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.2016

    • Author(s)
      Jung PP, Sigwalt A, Ohnuki S, de Montigny J, Ohya Y, Schacherer J.
    • Journal Title

      G3

      Volume: 6 Issue: 4 Pages: 1063-71

    • DOI

      10.1534/g3.115.026682

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Identification of a mutation causing a defective spindle assembly checkpoint in high ethyl caproate-producing sake yeast strain K1801.2016

    • Author(s)
      Goshima T, Nakamura R, Kume K, Okada H, Ichikawa E, Tamura H, Hasuda H, Inahashi M, Okazaki N, Akao T, Shimoi H, Mizunuma M, Ohya Y, Hirata D.
    • Journal Title

      Biosci Biotechnol Biochem.

      Volume: 80 Issue: 8 Pages: 1657-62

    • DOI

      10.1080/09168451.2016.1184963

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects.2016

    • Author(s)
      Chuffart F, Richard M, Jost D, Burny C, Duplus-Bottin H, Ohya Y, Yvert G.
    • Journal Title

      PLOS Genetics

      Volume: 12 Issue: 8 Pages: e1006213-e1006213

    • DOI

      10.1371/journal.pgen.1006213

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Fluorescent Labeling of Yeast Cell Wall Components.2016

    • Author(s)
      Okada H, Ohya Y
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: 085241-085241

    • DOI

      10.1101/pdb.prot085241

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Assay for Spore Wall Integrity Using a Yeast Predator.2016

    • Author(s)
      Okada H, Neiman AM, Ohya Y.
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: pdb.prot085258-pdb.prot085258

    • DOI

      10.1101/pdb.prot085258

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Local and Acute Disruption of the Yeast Cell Surface2016

    • Author(s)
      Kono K, Okada H, Ohya Y
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: pdb.prot085266-pdb.prot085266

    • DOI

      10.1101/pdb.prot085266

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Examination and Disruption of the Yeast Cell Wall2016

    • Author(s)
      Okada H, Kono K, Neiman AM, Ohya Y
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: 078659-078659

    • DOI

      10.1101/pdb.top078659

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A global genetic interaction network maps a wiring diagram of cellular function2016

    • Author(s)
      Costanzo M, et al.
    • Journal Title

      Science

      Volume: 353

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Late S-Phase Transcription Factor Hcm1 Is Regulated through Phosphorylation by the Cell Wall Integrity Checkpoint.2016

    • Author(s)
      Negishi T, Veis J, Hollenstein D, Sekiya M, Ammerer G, Ohya Y.
    • Journal Title

      Mol Cell Biol.

      Volume: 36 Issue: 6 Pages: 941-953

    • DOI

      10.1128/mcb.00952-15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Single-cell phenomics in budding yeast.2015

    • Author(s)
      Ohya Y, Kimori Y, Okada H, Ohnuki S.
    • Journal Title

      Mol Biol of the Cell

      Volume: 26 Issue: 22 Pages: 3920-3925

    • DOI

      10.1091/mbc.e15-07-0466

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis.2015

    • Author(s)
      Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y
    • Journal Title

      FEMS Yeast Res

      Volume: 15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Plant-derived antifungal agent poacic acid targets β-1,3-glucan2015

    • Author(s)
      Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 112 Issue: 12

    • DOI

      10.1073/pnas.1410400112

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Quantification of Cell, Actin, and Nuclear DNA Morphology with High-Throughput Microscopy and CalMorph.2015

    • Author(s)
      Okada H, Ohnuki S, Ohya Y.
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2015 (4) Issue: 4 Pages: 408-412

    • DOI

      10.1101/pdb.prot078667

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Presentation] High-dimensional and single-cell phenotyping in Saccharomyces cerevisiae: Rational selection of the morphological parameters2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      CiFA Program Meeting (Tokyo, 2017.4.27)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The book of yeast morphology is written in the language of mathematics2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Gene, genome and beyond (South San Francisco, 2017.9.16)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 酵母の細胞壁研究の魅力2017

    • Author(s)
      大矢禎一
    • Organizer
      日本植物学会シンポジウム (野田、2017.9.8)
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 出芽酵母の形態表現型に強い影響を与える遺伝子変異株の網羅的解析2017

    • Author(s)
      鈴木吾大、王洋、大貫慎輔、大矢禎一
    • Organizer
      酵母遺伝学フォーラム (東京、2017.9.11-13)
    • Related Report
      2017 Annual Research Report
  • [Presentation] 高次元形態表現型に基づく遺伝子機能特異的表現型自動抽出法の開発2017

    • Author(s)
      大貫慎輔、徐聴涛、大矢禎一
    • Organizer
      分子生物学会 (神戸、2017.12.6-9)
    • Related Report
      2017 Annual Research Report
  • [Presentation] High-dimensional and single cell phenotyping in Saccharomyces cerevisiae2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      HIHA symposium
    • Place of Presentation
      広島大学先端物質科学研究科(広島県・東広島)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] single cell phonemics in chemical genomics2016

    • Author(s)
      大矢禎一
    • Organizer
      バイオイメージインフォーマティクス
    • Place of Presentation
      大阪大学医学部(大阪府・吹田市)
    • Year and Date
      2016-06-23
    • Related Report
      2016 Annual Research Report
  • [Presentation] Application of single cell phonemics in chemical genomics2016

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      CIFAR meeting
    • Place of Presentation
      トロント(カナダ)
    • Year and Date
      2016-04-15
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 形態プロファイリングによる 細胞内標的予想2016

    • Author(s)
      大矢禎一
    • Organizer
      日本農薬学会
    • Place of Presentation
      松江
    • Year and Date
      2016-03-17
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 清酒酵母の単細胞フェノタイピング2016

    • Author(s)
      大矢禎一
    • Organizer
      酵母細胞研究会
    • Place of Presentation
      東京大学農学部(東京都・文京区)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] A cell cycle checkpoint to insure the integrity of the cell wall synthesis2016

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      LIISAIB
    • Place of Presentation
      コルドバ(アルゼンチン)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 清酒酵母今昔2016

    • Author(s)
      大矢禎一
    • Organizer
      日本酒史学会
    • Place of Presentation
      東京大学新領域(千葉県・柏市)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Monitoring and Phenotyping of Brewing and Sake Yeasts2015

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      4th ICBB in Singapore
    • Place of Presentation
      Singapore
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] New antifungal agents that inhibit cell wall synthesis2015

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Fungal Cell Wall 2015
    • Place of Presentation
      Paris, France
    • Year and Date
      2015-10-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] β-1,3-グルカンをターゲットにする新しい抗真菌剤2015

    • Author(s)
      大矢禎一
    • Organizer
      第67回日本細胞生物学会大会シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2015-06-29
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] High-dimensional morphological phenotyping in Saccharomyces cerevisiae2015

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Annual Meeting of Microbiology in Korea
    • Place of Presentation
      Changwon, Korea
    • Year and Date
      2015-04-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 酵母の形態情報を発酵・醸造に生かす in 「 発酵・醸造食品の最前線 (北本勝ひこ監修)」2015

    • Author(s)
      大矢禎一、渡辺大輔、 岡田啓希
    • Total Pages
      14
    • Publisher
      シーエムシー出版
    • Related Report
      2015 Annual Research Report
  • [Book] 日本の強みバイオテクノロジー in 「遺伝 : 生物の科学」69 (4); 332-3372015

    • Author(s)
      大矢禎一
    • Total Pages
      6
    • Publisher
      エヌ・ティー・エス
    • Related Report
      2015 Annual Research Report
  • [Remarks] 生命応答システム

    • URL

      http://ps.k.u-tokyo.ac.jp/top.html

    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-10-07  

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