Innovative technology platforms for integrated single cell analysis

Strategic Objects

Creation of Integrated Single Cell Analysis Fundamental Technology contribute to the elucidation of biological functions

Research Supervisor


Itaru Hamachi(Professor, Graduate School of Engineering, Kyoto University)

What’s New

2016.7.8 ” Detection of LacZ-Positive Cells in Living Tissue with Single-Cell Resolution ” by Mako Kamiya was published in Angewandte Chemie International Edition (July 8th 2016, online version). The Graduate School of Medicine, The University of Tokyo and JST issued a press release of its summary.
Click here.
2016.7.7 Motomu Endo was awarded German Innovation Award, The Gottfried Wagener Prize.
Click here.
2016.5.17-19 The 4th PRESTO Meeting was held in ANA Crown Plaza Hotel Kobe.
2016.4.20 Itaru Imayoshi, Mako Kamiya, Motomu Endo, Yasufumi Takahashi, Yusuke Miyanari were awarded The Young Scientists’ Prize/The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology.
2016.1.12 The 2nd CREST/PRESTO Meeting was held in National Museum of Emerging Science and Innovation.
2015.11.27-29 The 3rd PRESTO Meeting was held in Atami-New Fujiya Hotel.
2015.5.19-20 The 2nd PRESTO Meeting was held in Otsu Prince Hotel.
2015.1.15-16 The 1st PRESTO Meeting was held in Daiichi Hotel Ryogoku.
2015.1.15 The 1st CREST/PRESTO Meeting was held in Daiichi Hotel Ryogoku.

Outline

This Research Area will bring together individual researchers with technological challenges, thereby navigating their challenges towards the establishment of core technologies in next-generation single-cell analysis toolkits.
We would like aim to construct a platform made of fundamental analytical technologies that streamlines data-based single cell phenotyping. This platform is anticipated to realize quantitative, multiplexed analyses of a variety of biomolecules including nucleic acids, proteins, saccharides, lipids etc and the complex interactions at the intracellular and intercellular levels. Obviously, it requires diverse interdisciplinary approaches in nanotechnology, engineering, chemistry, optics, materials science, chemical biology, information science, which should be mixed with the steady progress in traditional biotechnology, on the basis of the deep understanding of real needs in life science communities. Therefore this Research Area welcomes ambitious young individuals to form a multidisciplinary virtual-network institute and nurtures them with its diversity to help them found their own unique technologies.
Open innovation is an integral part of this Research Area. Marketing might be considered even at the early phase in some cases, although too short-sighted project is not supported. Rather, all the PRESTO researchers are required to recognize that matured technologies must be accepted by intended users, and that the long-running development process must involve active, collaborative, and open efforts with both academic and industrial stakeholders at all times. Thus synergistically, this Research Area as a whole is committed to world-leading single cell analysis community with its potential to drive science and technology innovation.

Research Supervisor’s Policy on Call for Application, Selection, and Management of the Research Area

In life science, cell is regarded as a minimal functional unit and its analysis has been undoubtedly crucial. Cells are not homogeneous but rather heterogeneous when you look at the genome, proteome, and expressed glycome, lipids and other metabolites in their variety and amounts of individual cells, even though these seem morphologically identical. Single cell analysis, which is the main objective in this research project, represents quantitatively and exhaustively analyzing a wide range of molecular information carried on numerous biomolecules at the single cell level. Such challenges will give a breakthrough against the traditional analyses based on the averaged data from many (intrinsically heterogeneous) cells ensembles that inevitably veil the molecular details of each cell. Also, these technologies are anticipated to provide novel approaches to reply to many questions in fundamental life science and also to facilitate constructing new platforms for advanced biotechnology and medical applications.
Based on these backgrounds, we would like to recruit research proposals with high originality mainly focused on the following topics

A. Construction of fundamental technologies and tools to analyze and regulate biomolecules and/or molecular information with quantitative and exhaustive manner, toward understanding the phenotype, function, heterogeneity and/or character of individual cells at the single cell level.

a) For genome, epigenome and transcriptome as analytical targets

Research proposals for targeting these molecules are strictly required to demonstrate the proposed technologies can be really applied to single cell analysis.

b) For proteome, glycome, metabolome, and others as analytical targets

Research proposals for targeting these molecules are not limited to strict single cell analysis. Rather, challenging proposals are welcome which enable for high-throughput, functional analysis, precise regulation or imaging of these targets with extremely high spatial and temporal resolution in a small cell ensemble, toward single cell analysis and regulation as the final goal. Truly original and innovative ideas containing molecular tools, materials, biological strategies or unique systems would also be desired.

B. Construction of fundamental technologies and tools to analyze and regulate molecular communication, interactions and their networks with extremely quantitative and exhaustive manner, toward understanding the phenotype, function, and/or character of individual cells at the single cell level.

C. Research proposal based on bioinformatics for integrated analysis of a huge amount of (molecular) information accumulated by exhaustive analysis at the single cell level.

The cells that are the subject of analysis are not limited to prokaryote or eukaryote, and also the individual cell in complicated tissues, as well as isolated single cells. In the last two years, we accepted a diverse array of proposals, and this (last) year, we would like to receive more challenging and creative proposals from a wide range of fields. From the fields of life science and biotechnology, we welcome attractive proposals that go beyond individual specialties to include perspectives such as how the proposed research will relate to and interact with single-cell analysis technologies to open up new frontiers in science. We would also like to strongly encourage researchers from the areas of chemistry, devices, and chemical biology to propose attractive research projects not only relating to imaging but also delving into the analysis of single cells with a stronger awareness of biological questions. We are hoping for robust and challenging research topics, from a variety of fields, that are filled with creativity and that consider not only the short-term perspective but also consider objectives and prospects over the long span. Challenging but attractive and original ones are highly welcome from a variety of research fields that envision the future valuable goals.

This Research Area is going to organize talented active researchers who are interested in developing really novel technologies and methods for single cell analysis as a virtual network type of institute and encourage PRESTO members to establish only one technology in all over the world. Also, Open innovation is an integral part of this Research Area, although PRESTO research program basically supports the individual researcher. Further, we would like to let all of the PRESTO researchers recognize that the long-running development process must involve active, collaborative, and open-minded efforts with both academic and industrial stakeholders in all times. In particular, mutual communication, discussion and collaboration with CREST researchers in the same Research Area are strongly encouraged. Thus synergistically, this Research Area as a whole is committed to a world-leading single cell analysis community with its potential, so that we drive science and technology innovation.

Research Area Advisors

・Kazunari Akiyoshi
Professor, Kyoto University

・Hiroyuki Aburatani
Professor, The University of Tokyo

・Takehiko Itoh
Professor, Tokyo Institute of Technology

・Mitsuyoshi Ueda
Professor, Kyoto University

・Takeaki Ozawa
Professor, The University of Tokyo

・Hideki Kambara
Fellow Emeritus, Hitachi, Ltd.

・Yukiko Gotoh
Professor, The University of Tokyo

・Keiko Shimamoto
Manager and Exective Researcher,
Suntory Foundation for Life Sciences Bioorganic Research Institute

・Kouhei Tsumoto
Professor, The University of Tokyo

・Hiroyuki Noji
Professor, The University of Tokyo

・Yoshinobu Baba
Professor, Nagoya University

・Michiyuki Matsuda
Professor, Kyoto University

Year Started : 2014

Development of nanodiamond bioimaging for three-dimensional structural dynamics

Research Director:
Ryuji Igarashi(PRESTO Researcher, Japan Science and Technology Agency)

Development of deep imaging techniques for analyzing single cells in tissues

Research Director:
Keisuke Isobe(Research Scientist, Center for Advanced Photonics, RIKEN)

Single-cell manipulation of gene expression dynamics in three dimensional tissues

Research Director:
Itaru Imayoshi(PRESTO Researcher, Japan Science and Technology Agency)

Single cell analysis for circadian clock regulated cell fate decidion

Research Director:
Motomu Endo(Associate Professor, Graduate school of biostudies, Kyoto University)

Ultrafast fluorescence imaging for image-activated flow cytometry

Research Director:
Sadao Ota(PRESTO Researcher, Japan Science and Technology Agency)

Elucidating how fine-scale subnetworks that have a reciprocal connection and share common inputs process information

Research Director:
Fumitaka Osakada(Associate Professor, Graduate School of Pharmaceutical Sciences, Nagoya University)

RNA imaging in living cells by using novel artificial nucleic acid, SNA

Research Director:
Hiromu Kashida(Associate Professor, Graduate School of Engineering, Nagoya University)

Single cell analysis by using multifunctional fluorescence probes

Research Director:
Mako Kamiya(Lecturer, Graduate School of Medicine, The University of Tokyo)

Ultra-sensitive CE-MS Analytical System for Trace-level Proteomics Abstract

Research Director:
Takayuki Kawai(Special Postdoctoral Researcher, Quantitative Biology Center, RIKEN)

Development of Nano ElectroChemical Microscopy for Chemical Mapping

Research Director:
Yasufumi Takahashi(Associate Professor, College of Science and Engineering, Kanazawa University)

Creation of spatial cell dissection technology for disassembling single cells

Research Director:
Kyohei Terao(Associate Professor, Faculty of Engineering, Kagawa University)

Cryogenic fluorescence microscope designed for localization of individual proteins in a cell

Research Director:
Satoru Fujiyoshi(Assitant Professor, Department of Physics, School of Science, Tokto Institute of Technology)

Live imaging of hierarchical chromatin structures

Research Director:
Yusuke Miyanari(Associated professor, Okazaki Institute for Integrative Bioscience, National Institute for Natural Science)

DNA Barclock Technology to track cellular lineages at the single cell resolution

Research Director:
Nozomu Yachie(Associate Professor, Research Center for Advanced Science and Technology, The University of Tokyo)

Year Started : 2015

Application of fluid to analysis of developmental system

Research Director:
Hidehiko Inomata(Team Leader, Center for Developmental Biology (CDB), RIKEN)

Development of comprehensive analysis technology for intercellular phenotypic heterogeneity

Research Director:
Hiroshi Ochiai(PRESTO Researcher, Japan Science and Technology Agency)

Development of a single-cell nucleic acid analytical technique for understanding biological systems and its applications for medical sciences

Research Director:
Katsuyuki Shiroguchi(Unit Leader, Quantitative Biology Center (QBiC), RIKEN)

Comprehensive cell analysis by 3D histopathology

Research Director:
Etsuo Susaki(Assistant Professor, Graduate school of medicine, The University of Tokyo)

Single-cell energy perturbation and quantification in a living organism

Research Director:
Madoka Suzuki(Principal Investigator/Associate Professor, Comprehensive Research Organization, Waseda University)

Functional and molecular characterization of neuronal microcircuits located in deep brain structures to elucidate emotion regulation

Research Director:
Sayaka Takemoto-Kimura(Professor, Research Institute of Environmental Medicine, Nagoya University)

Linking dynamics of genome, transcriptome and proteome in single cells

Research Director:
Yuichi Taniguchi(Unit Leader, Quantitative Biology Center, RIKEN)

Deciphering the individuality of a cell by single molecule analysis of membrane molecule dynamics

Research Director:
Hiroko Bannai(PRESTO Researcher, Japan Science and Technology Agency)

Analysis of secretion from single cells by using droplet-based analytical system

Research Director:
Mao Fukuyama(Assistant Professor, Institute for the Promotion of University Strategy, Kyoto Institute of Technology)

Massively parallel single-cell genomics for elucidation of intra-tissue genetic heterogeneity

Research Director:
Masahito Hosokawa(PRESTO Researcher, Japan Science and Technology Agency)

Development of Single Cell Analytical Technology to Elucidate Biological Functions of Cancer Stem Cells

Research Director:
Michiya Matsusaki(Associate Professor, Graduate School of Engineering, Department of Applied Chemistry, Osaka University)

Simultaneous acquisition of methylome and transcriptome data from a single cell

Research Director:
Fumihito Miura(Lecturer, Graduate School of Medical Sciences, Kyushu University)

Development of ultimate spatiotemporal resolution AFM for visualizing membrane molecular dynamics in single living cell

Research Director:
Hayato Yamashita(Assistant Professor, Center for Science and Technology under Extreme Conditions, Graduate School of Engineering Science, Osaka University)

Unlocking the mysteries of cellular heterogeneity by single cell proteome profiling

Research Director:
Masaki Wakabayshi(Assistant Professor, Graduate school of pharmaceutical sciences, Kyoto University)

Area Activities

2016.5.17-19
The 4th PRESTO Meeting was held in ANA Crown Plaza Hotel Kobe.
The 4th PRESTO Meeting Group Photo
2016.1.12
The 2nd CREST/PRESTO Meeting was held in National Museum of Emerging Science and Innovation.
2015.11.27-29
The 3rd PRESTO Meeting was held in Atami-New Fujiya Hotel.
The 3rd PRESTO Meeting Group Photo
2015.5.19-20
The 2nd PRESTO Meeting was held in Otsu Prince Hotel.
The 2nd PRESTO Meeting Group Photo
2015.1.15-16
The 1st PRESTO Meeting was held in Daiichi Hotel Ryogoku.
The 1st PRESTO Meeting Group Photo
2015.1.15
The 1st CREST/PRESTO Meeting was held in Daiichi Hotel Ryogoku.

Quick Access

Quick Access

 News

arrow On-going

arrow Completed

Program

Program
  • CREST
  • PRESTO
  • ERATO
  • ACCEL
  • ACT-C
  • Promoting Globalization on Strategic Basic Research Programs
  • ALCA
  • RISTEX
  • ACT-I
  • s_innov
  • Development of Advanced Measurement and Analysis Systemsicon
Finish programs
  • Pamphlet