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Acta Biotheoretica

, Volume 50, Issue 4, pp 357–373 | Cite as

Hyperstructures, Genome Analysis and I-Cells

  • Patrick Amar
  • Pascal Ballet
  • Georgia Barlovatz-Meimon
  • Arndt Benecke
  • Gilles Bernot
  • Yves Bouligand
  • Paul Bourguine
  • Franck Delaplace
  • Jean-Marc Delosme
  • Maurice Demarty
  • Itzhak Fishov
  • Jean Fourmentin-Guilbert
  • Joe Fralick
  • Jean-Louis Giavitto
  • Bernard Gleyse
  • Christophe Godin
  • Roberto Incitti
  • François Képès
  • Catherine Lange
  • Lois Le Sceller
  • Corinne Loutellier
  • Olivier Michel
  • Franck Molina
  • Chantal Monnier
  • René Natowicz
  • Vic Norris
  • Nicole Orange
  • Helene Pollard
  • Derek Raine
  • Camille Ripoll
  • Josette Rouviere-Yaniv
  • Milton SaierJr.
  • Paul Soler
  • Pierre Tambourin
  • Michel Thellier
  • Philippe Tracqui
  • Dave Ussery
  • Jean-Claude Vincent
  • Jean-Pierre Vannier
  • Philippa Wiggins
  • Abdallah Zemirline
Article

Abstract

New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology.

Keywords

Cell Division Sequence Data Experimental Technique Genome Analysis Cellular Automaton 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Patrick Amar
    • 1
    • 2
  • Pascal Ballet
    • 3
  • Georgia Barlovatz-Meimon
    • 4
  • Arndt Benecke
    • 5
  • Gilles Bernot
    • 1
  • Yves Bouligand
    • 6
  • Paul Bourguine
    • 7
  • Franck Delaplace
    • 1
  • Jean-Marc Delosme
    • 1
  • Maurice Demarty
    • 8
  • Itzhak Fishov
    • 9
  • Jean Fourmentin-Guilbert
    • 10
  • Joe Fralick
    • 11
  • Jean-Louis Giavitto
    • 1
  • Bernard Gleyse
    • 12
  • Christophe Godin
    • 13
  • Roberto Incitti
    • 1
  • François Képès
    • 14
  • Catherine Lange
    • 15
  • Lois Le Sceller
    • 8
  • Corinne Loutellier
    • 15
  • Olivier Michel
    • 1
  • Franck Molina
    • 16
  • Chantal Monnier
    • 8
  • René Natowicz
    • 17
  • Vic Norris
    • 8
  • Nicole Orange
    • 18
  • Helene Pollard
    • 19
  • Derek Raine
    • 20
  • Camille Ripoll
    • 8
  • Josette Rouviere-Yaniv
    • 21
  • Milton SaierJr.
    • 22
  • Paul Soler
    • 19
  • Pierre Tambourin
    • 19
  • Michel Thellier
    • 8
  • Philippe Tracqui
    • 23
  • Dave Ussery
    • 24
  • Jean-Claude Vincent
    • 25
  • Jean-Pierre Vannier
    • 26
  • Philippa Wiggins
    • 27
  • Abdallah Zemirline
    • 3
  1. 1.Laboratoire de Méthodes Informatiques, CNRS UMR 8042Université d'EvryEvry cedexFrance
  2. 2.Laboratoire de Recherche en InformatiqueUniversité Paris-SudOrsayFrance
  3. 3.Laboratoire des Interfaces Machines IntelligentesUniversité de Bretagne OccidentaleBrestFrance
  4. 4.INSERM U492, Faculté de MédecineCreteilFrance
  5. 5.Institut des Hautes Etudes ScientifiquesBures-Sur-YvetteFrance and INSERM U417, Paris, France
  6. 6.Histophysique (EPHE) and Faculté de PharmacieAngersFrance
  7. 7.CREAEcole PolytechniqueParisFrance
  8. 8.Laboratoire des Processus Intégratifs Cellulaires, UPRESA CNRS 6037, Faculté des Sciences et TechniquesUniversité de RouenMont-Saint-AignanFrance
  9. 9.Department of Life Sciences, Ben-GurionUniversity of the NegevBe'er ShevaIsrael
  10. 10.Fondation Scientifique Fourmentin-GuilbertNoisy-Le-GrandFrance
  11. 11.Health Science CenterTexas Tech UniversityLubbockUSA
  12. 12.Laboratoire de Mathématiques de l'INSA de RouenMont-Saint-AignanFrance
  13. 13.CIRADLaboratoire de modélisation des plantesMontpellierFrance
  14. 14.ATelier de Genomique Cognitive, Département de MathématiquesUniversité d'ÉvryEvryFrance
  15. 15.Spectrométrie de Masse Bio-organique, UFR des sciencesUniversité de RouenMont-Saint-AignanFrance
  16. 16.Faculté de PharmacieIBPh - CNRS UMR 5094MontpellierFrance
  17. 17.ESIEE, Laboratoire d'InformatiqueCité DescartesNoisy le Grand cedexFrance
  18. 18.Laboratoire de Microbiologie du FroidUniversité de RouenEvreuxFrance
  19. 19.Genopole ResearchEvryFrance
  20. 20.Dept. of Physics and AstronomyUniversity of LeicesterLeicester0UK
  21. 21.Institut de Biologie Physico-ChimiqueCNRS UPR 9073ParisFrance
  22. 22.Department of BiologyUniversity of California at San DiegoLa JollaUSA
  23. 23.Laboratoire des Techniques Imagerie Modélisation CognitionCNRS UMR 5525, Faculté de MédecineLa TroncheFrance
  24. 24.Center for Biological Sequence Analysis, Dept. of BiotechnologyThe Technical University of DenmarkKgs, LyngbyDenmark
  25. 25.Polymères, biopolymères et membranes, UMR 6522 CNRSUniversité de RouenFrance
  26. 26.Hématologie-Oncologie Pédiatrique, Faculté de MédecineCHU de RouenRouenFrance
  27. 27.Genesis Research and Development Corporation Limited, ParnellAucklandNew Zealand

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