On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. temporal aspects of epigenetic information in bacteria

Research output: Contribution to journalReview article

Abstract

A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an "algebraic" system (emphasis on temporal aspects) and as a "geometric" system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from "algebraic" and "geometric" viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based "algebraic" and "geometric" studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.

Original languageEnglish
Pages (from-to)7169-7206
Number of pages38
JournalSensors (Switzerland)
Volume12
Issue number6
DOIs
Publication statusPublished - 2012 Jun
Externally publishedYes

Fingerprint

Epigenomics
bacteria
Assays
Bacteria
chips
Microfabrication
cells
Screening
DNA
Processing
Pharmaceutical Preparations
Microtechnology
Technology
Preclinical Drug Evaluations
Automatic Data Processing
Cell Communication
regeneration
organs
Regeneration
complement

Keywords

  • Adaptation
  • Agarose microchamber array
  • Algebraic viewpoint
  • Community effect
  • Epigenetic information
  • Escheirchia coli (E. coli)
  • Genetic information
  • Geometric viewpoint
  • Individuality
  • Inheritance
  • Microchamber array
  • Multi-electrode array (MEA)
  • On-chip cellomics
  • Optical tweezers
  • Photo-thermal etching
  • Population effect
  • Variability

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Atomic and Molecular Physics, and Optics
  • Analytical Chemistry
  • Biochemistry

Cite this

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title = "On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. temporal aspects of epigenetic information in bacteria",
abstract = "A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an {"}algebraic{"} system (emphasis on temporal aspects) and as a {"}geometric{"} system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from {"}algebraic{"} and {"}geometric{"} viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based {"}algebraic{"} and {"}geometric{"} studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.",
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T1 - On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. temporal aspects of epigenetic information in bacteria

AU - Yasuda, Kenji

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N2 - A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an "algebraic" system (emphasis on temporal aspects) and as a "geometric" system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from "algebraic" and "geometric" viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based "algebraic" and "geometric" studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.

AB - A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an "algebraic" system (emphasis on temporal aspects) and as a "geometric" system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from "algebraic" and "geometric" viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based "algebraic" and "geometric" studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.

KW - Adaptation

KW - Agarose microchamber array

KW - Algebraic viewpoint

KW - Community effect

KW - Epigenetic information

KW - Escheirchia coli (E. coli)

KW - Genetic information

KW - Geometric viewpoint

KW - Individuality

KW - Inheritance

KW - Microchamber array

KW - Multi-electrode array (MEA)

KW - On-chip cellomics

KW - Optical tweezers

KW - Photo-thermal etching

KW - Population effect

KW - Variability

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DO - 10.3390/s120607169

M3 - Review article

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