Construction of a biological tissue model based on a single-cell model: A computer simulation of metabolic heterogeneity in the liver lobule

Hiroshi Ohno, Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita

Research output: Contribution to journalArticlepeer-review

35 Citations (Scopus)


An enormous body of information has been obtained by molecular and cellular biology in the last half century, However, even these powerful approaches are not adequate when it comes to higher-level biological structures, such as tissues, organs, and individual organisms, because of the complexities involved. Thus, accumulation of data at the higher levels supports and broadens the context for that obtained on the molecular and cellular levels. Under such auspices, an attempt to clucidate mesoscopic and macroscopic subjects based on plentiful nanoscopic and microscopic data is ot great potential value. On the other hand, fully realistic simulation is impracticable because of the extensive cost entailed and enormous amount of data required. Abstraction and modeling that balance the dual requirements of prediction accuracy and manageable calculation cost are of great importance for systems biology. We have constructed an ammonia metabolism model of the hepatic lobule, a histological component of the liver, based on a single-hepatocyte model that consists of the biochemical kinetics of enzymes and transporters. To bring the calculation cost within reason, the porto-central axis, which is an elemental structure of the lobule, is defined as the systems biological unit of the liver, and is accordingly modeled. A model including both histological structure and position-specific gene expression of major enzymes largely represents the physiological dynamics of the hepatic lobule in nature. In addition, heterogeneous gene expression is suggested to have evolved to optimize the energy efficiency of ammonia detoxificattion at the macroscopic level, implying that approaches like this may elucidate how properties at the molecular and cellular levels, such as regulated gene expression, modify higher-level phenomena of multicellular tissue, organs, and organisms.

Original languageEnglish
Pages (from-to)3-28
Number of pages26
JournalArtificial Life
Issue number1
Publication statusPublished - 2008


  • Ammonia metabolism
  • Biological simulation
  • Hepatic lobule
  • Zonal metabolic heterogeneity

ASJC Scopus subject areas

  • Computer Science (miscellaneous)
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Agricultural and Biological Sciences (miscellaneous)


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