Pharmacopsychiatry 2010; 43: S2-S8
DOI: 10.1055/s-0030-1249666
Original Paper

© Georg Thieme Verlag KG Stuttgart · New York

Perspectives of a Systems Biology of the Synapse: How to Transform an Indefinite Data Space into a Model?

H.W. Mewes1 , 2 , B. Wachinger2 , V. Stümpflen2
  • 1Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Germany
  • 2Institute of Bioinformatics and Systems Biology (IBIS), Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
Further Information

Publication History

Publication Date:
17 May 2010 (online)

Abstract

Understanding the synapse and its role in the development of psychiatric disorders is not only a demanding but a highly relevant challenge for neuroscience. With the advancement of modern high-throughput technologies, the amount of data collected becomes incomprehensible and the volume of information intractable for the individual scientist. Why Systems Biology opens alternatives to organize information and to deduce knowledge that can be scrutinized by rationally designed experiments? We discuss some of the fundamental ideas why Systems Biology is indeed an alternative to reductionism and show an example how semantics may help to exploit the rich source of the scientific literature to generate qualitative models of functional modules.

References

  • 1 Abramov E, Dolev I, Fogel H. et al . Amyloid-beta as a positive endogenous regulator of release probability at hippocampal synapses.  Nat Neurosci. 2009;  12 1567-1576
  • 2 Barnickel T, Weston J, Collobert R. et al . Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts.  PLoS ONE. 2009;  4 e6393
  • 3 Bennett MR, Hacker PMS. Reductionism.. Philosophical Foundations of Neuroscience. Blackwell Publishing Ltd; 2003: 355-377
  • 4 Bush V. As we may think.  The Atlantic,. 1945; 
  • 5 Bertoldi M, Cellini B, D’Aguanno S. et al . Lysine 238 is an essential residue for alpha, beta-elimination catalyzed by Treponema denticola cystalysin.  J Biol Chem. 2003;  278 37336-37343
  • 6 Boogerd FC, Bruggeman FJ, Hofmeyr J-HS. et al .Introduction.. Systems Biology: Philosophical Foundations. Elsevier; 2007: 3-19
  • 7 Boutet E, Lieberherr D, Tognolli M. et al . UniProtKB/Swiss-Prot.  Methods Mol Biol. 2007;  406 89-112
  • 8 Fernandez-Busnadiego R, Zuber B, Maurer UE. et al . Quantitative analysis of the native presynaptic cytomatrix by cryoelectron tomography.  J Cell Biol. 2010;  188 145-156
  • 9 Gladwell M. Enron, Intelligenc, and the Perils of Too Much Information. What the Dog Saw.. Little, Brown and Company; 2002: 151-176
  • 10 Glessner JT, Hakonarson H. Common variants in polygenic schizophrenia.  Genome Biol. 2009;  10 236
  • 11 Gotow T, Miyaguchi K, Hashimoto PH. Cytoplasmic architecture of the axon terminal: filamentous strands specifically associated with synaptic vesicles.  Neuroscience. 1991;  40 587-598
  • 12 Haken H. Synergetics, Introduction and Advanced Topics.. Springer; 2004
  • 13 Jensen LJ, Kuhn M, Stark M. et al . STRING 8 – a global view on proteins and their functional interactions in 630 organisms.  Nucleic Acids Res. 2009;  37 D412-D416
  • 14 Keller EF. Disappearance of function from “self-organizing systems”. In: Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV, (eds) Systems Biology Philosophical Foundations. Elsevier; 2007
  • 15 Kitano H. Biological robustness.  Nat Rev Genet. 2004;  5 826-837
  • 16 Kohl P, Noble D. Systems biology and the virtual physiological human.  Mol Syst Biol. 2009;  5 292
  • 17 Lazebnik Y. Can a biologist fix a radio? – Or, what I learned while studying apoptosis.  Cancer Cell. 2002;  2 179-182
  • 18 Mattick JS. RNA regulation: a new genetics?.  Nat Rev Genet. 2004;  5 316-323
  • 19 Noble D. Claude Bernard, the first systems biologist, and the future of physiology.  Exp Physiol. 2008;  93 16-26
  • 20 Noble D. Genes and causation.  Philos Transact A Math Phys Eng Sci. 2008;  366 3001-3015
  • 21 Noble D. Prologue: mind over molecule: activating biological demons.  Ann N Y Acad Sci. 2008;  1123 xi-xix
  • 22 Stuempflen V, Barnickel T, Nenova K. Large Scale Knowledge Representation of Distributed Biomedical Information. Scaling Topic Maps: Third International Conference on Topic Map Research and Applications, TMRA 2007.. Springer; 2008: 116-127
  • 23 Westerhoff HV, Kell DB. The methodology of systems biology.. Systems Biology: Philosophical Foundations. Elsevier; 2007: 23-70
  • 24 Wolkenhauer O, Mesarovic M. Feedback dynamics and cell function: Why systems biology is called Systems Biology.  Mol Biosyst. 2005;  1 14-16

Correspondence

Prof. Dr. H. W. Mewes

Chair of Genome Oriented Bioinformatics

Life Science Centre

Weihenstephan

Technische Universität

München

Maximus-von-Imhof-Forum 3

85354 Freising-Weihenstephan

Germany

Phone: +49/089/3187 3580

Fax: +49/089/3187 3585

Email: w.mewes@helmholtz-muenchen.de

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