Yeast Phenome analysis with super-hidimensional morphological profiling

• Project/Area Number: 24370002
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Genetics/Genome dynamics
• Research Institution: The University of Tokyo
• Principal Investigator: OHYA Yoshikazu 東京大学, 新領域創成科学研究科, 教授 (20183767)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000); Fiscal Year 2014: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2013: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2012: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
• Keywords: 出芽酵母 / 表現型解析 / 画像解析 / 細胞形態 / 自然淘汰 / 遺伝子破壊株 / 液泡 / 酸性化 / バイオイメージング / システムズバイオロジー / オーミクス / オルガネラ

Outline of Final Research Achievements

The primary goal of automated morphological analysis of subcellular structures using image extraction and quantification is to ensure objectivity and reproducibility. A well-designed experiment followed by appropriate statistical analyses can provide a wealth of biologically meaningful information. With regard to budding yeast, it is essential to quantitatively study the phenotype of numerous sets of mutants to extract genetically and biologically meaningful information. In this study, we addressed some of the biological findings to which quantitative morphological analysis has contributed significantly.

Research Products

• [Journal Article] Plant-derived antifungal agent poacic acid targets β-1,3-glucan (2015)
  • 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
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Ohnuki S, Okada H, Ohya Y. (2015)
  • Author(s): Image-based prediction of drug target in yeast.
  • Journal Title: Methods Mol Biol Volume: 1263 Pages: 319-327
  • DOI: 10.1007/978-1-4939-2269-7_24
  • ISBN: 9781493922680, 9781493922697
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains (2014)
  • Author(s): Yang M, Ohnuki S, Ohya Y
  • Journal Title: BMC Genomics Volume: 15 Issue: 1 Pages: 932-932
  • DOI: 10.1186/1471-2164-15-932
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data. (2014)
  • Author(s): Okada H, Ohnuki S, Roncero C, Konopka JB, Ohya Y
  • Journal Title: Mol Biol Cell Volume: 25 Pages: 222-233
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data. (2014)
  • Author(s): Okada H, Ohnuki S, Roncero C, Konopka JB, Ohya Y.
  • Journal Title: Molecular biology of the cell Volume: 25(2) Issue: 2 Pages: 222-33
  • DOI: 10.1091/mbc.e13-07-0396
  • Peer Reviewed
• [Journal Article] Dynamic changes in brewing yeast cells in culture revealed by statistical analyses of yeast morphological data. (2013)
  • Author(s): Ohnuki S, Enomoto K, Yoshimoto H, Ohya Y.
  • Journal Title: Journal of bioscience and bioengineering Volume: 117(3) Issue: 3 Pages: 278-84
  • DOI: 10.1016/j.jbiosc.2013.08.005
  • Peer Reviewed / Open Access
• [Journal Article] Organelle acidification is important for localisation of vacuolar proteins in Saccharomyces cerevisiae. (2013)
  • Author(s): Matsumoto R
  • Journal Title: Protoplasma Volume: 250 Issue: 6 Pages: 1283-1293
  • DOI: 10.1007/s00709-013-0510-2
  • Peer Reviewed
• [Journal Article] Profilin is required for Ca^<2+> homeostasis and Ca^<2+>-modulated bud formation in yeast. (2013)
  • Author(s): Yoshida M1, Ohnuki S, Yashiroda Y, Ohya Y.
  • Journal Title: Molecular genetics and genomics Volume: 288(7-8) Issue: 7-8 Pages: 317-28
  • DOI: 10.1007/s00438-013-0752-x
  • Peer Reviewed
• [Journal Article] Vanillin Inhibits Translation and Induces Messenger Ribonucleoprotein (mRNP) Granule Formation in Saccharomyces cerevisiae: Application and Validation of High-Content, Image-Based Profiling (2013)
  • Author(s): Iwaki A, Ohnuki S, Suga Y, Izawa S and Ohya Y
  • Journal Title: PLoS ONE Volume: 8(4) Issue: 4 Pages: 61748-61748
  • DOI: 10.1371/journal.pone.0061748
  • Peer Reviewed
• [Journal Article] Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast. (2013)
  • Author(s): Yvert G, Ohnuki S, Nogami S, Imanaga Y, Fehrmann S, Schacherer J. Ohya Y.
  • Journal Title: BMC systems biology Volume: 7 Issue: 1 Pages: 54-54
  • DOI: 10.1186/1752-0509-7-54
  • Peer Reviewed
• [Journal Article] Analysis of the biological activity of a novel 24-membered macrolide JBIR-19 in Saccharomyces cerevisiae by the morphological imaging program CalMorph. (2012)
  • Author(s): Shinsuke Ohnuki, et al.
  • Journal Title: FEMS Yeast Res Volume: 12 Pages: 293-304
  • Peer Reviewed
• [Presentation] High-Resolution Phenotyping to Elucidate Essential Complex Cellular Processes (2014)
  • Author(s): Yoshikazu Ohya
  • Organizer: Yeast Phenome Meeting
  • Place of Presentation: NYU, New York, USA
  • Year and Date: 2014-09-26
  • Invited
• [Presentation] Distinct roles of cell wall biogenesis in yeast morphogenesis (2014)
  • Author(s): 2) Yoshikazu Ohya
  • Organizer: The 10th International Mycological Congress
  • Place of Presentation: Bangkok, Thai
  • Year and Date: 2014-08-04 – 2014-08-07
  • Invited
• [Presentation] The cell wall contributes to phenotypic robustness in budding yeast (2013)
  • Author(s): Yoshikazu Ohya
  • Organizer: The 2013 ASCB Annual Meeting
  • Place of Presentation: New Orleans Ernest N. Morial Convention Center (New Orleas, USA)
  • Invited
• [Presentation] 微細藻類の多機能画像解析ソフトウェア (2012)
  • Author(s): 大貫 慎輔
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場 マリンメッセ福岡
  • Year and Date: 2012-12-13
• [Presentation] 出芽酵母の細胞形態プロファイリングとダイナミクスの解析 : 画像から見えないものを見る (2012)
  • Author(s): 大矢 禎一
  • Organizer: バイオイメージ・インフォマティクスワークショップ2012
  • Place of Presentation: 理化学研究所神戸 発生・再生科学総合研究センター
  • Year and Date: 2012-11-01
  • Invited
• [Presentation] 新規生理活性物質JBIR-19は細胞形態の伸長とアクチンの脱局在を引き起こす (2012)
  • Author(s): 大貫 慎輔
  • Organizer: 酵母遺伝学フォーラム第45回研究報告会
  • Place of Presentation: 京都大学宇治キャンパス おうばくプラザ きはだホール
  • Year and Date: 2012-09-06
• [Presentation] 出芽酵母の形態形成における細胞壁の各構成成分の役割 (2012)
  • Author(s): 岡田 啓希
  • Organizer: 酵母遺伝学フォーラム第45回研究報告会
  • Place of Presentation: 京都大学宇治キャンパス おうばくプラザ きはだホール
  • Year and Date: 2012-09-04
• [Presentation] 出芽とCa2+恒常性維持の連携機搆 (2012)
  • Author(s): 吉田 光範
  • Organizer: 酵母遺伝学フォーラム第45回研究報告会
  • Place of Presentation: 京都大学宇治キャンパス おうばくプラザ きはだホール
  • Year and Date: 2012-09-04
• [Presentation] Image-based systems biology in the budding yeast Saccharomyces cerevisiae (2012)
  • Author(s): Yoshikazu Ohya
  • Organizer: ICSB The 13th International Conference on Systems Biology
  • Place of Presentation: Toronto University (Toronto, CANADA)
  • Year and Date: 2012-08-21
  • Invited
• [Presentation] Chemical-genetic approaches for the elucidation of cell wall biogenesis in Saccharomyces cerevisiae (2012)
  • Author(s): Shinsuke Ohnuki
  • Organizer: ICSB The 13th International Conference on Systems Biology
  • Place of Presentation: Toronto University (Toronto, CANADA)
  • Year and Date: 2012-08-20
• [Presentation] Profilin is required for Ca (2+) homeostasis and bud formation (2012)
  • Author(s): Mitsunori Yoshida
  • Organizer: 2012 Yeast Genetics and Molecular Biology Meeting
  • Place of Presentation: Princeton University (Princeton, USA)
  • Year and Date: 2012-08-03
• [Presentation] Multi-target drugs induce complex morphological changes in the budding yeast Saccharomyces cerevisiae. (2012)
  • Author(s): Shinsuke Ohnuki
  • Organizer: 2012 Yeast Genetics and Molecular Biology Meeting
  • Place of Presentation: Princeton University (Princeton, USA)
  • Year and Date: 2012-08-01
• [Presentation] Chemical-genetic analysis on the elucidation of cell wall biogenesis in Saccharomyces cerevisiae (2012)
  • Author(s): Yoshikazu Ohya
  • Organizer: 5th International Conference on Molecular Mecha-nisms of Fungal Cell Wall Biogenesis
  • Place of Presentation: Hotel Zora, Kravata Conference Hall (CROATIA)
  • Year and Date: 2012-06-08
  • Invited
• [Remarks] 生命応答システム分野
  • URL: http://ps.k.u-tokyo.ac.jp/
• [Remarks] 生命応答システム分野
  • URL: http://ps.k.u-tokyo.ac.jp/
• [Remarks]
  • URL: http://ps.k.u-tokyo.ac.jp/
• [Patent(Industrial Property Rights)] 細胞観察装置、細胞観察方法及びそのプログラム (2012)
  • Inventor(s): 大矢禎一他
  • Industrial Property Rights Holder: JST
  • Industrial Property Rights Type: 特許
  • Filing Date: 2012-11-28