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DOI: 10.1055/s-0032-1304653
Mesoscopic Models of Neurotransmission as Intermediates between Disease Simulators and Tools for Discovering Design Principles
Publikationsverlauf
Publikationsdatum:
07. Mai 2012 (online)
Abstract
Two grand challenges have been declared as premier goals of computational systems biology. The first is the discovery of network motifs and design principles that help us understand and rationalize why biological systems are organized in the manner we encounter them rather than in a different fashion. The second goal is the development of computational models supporting the investigation of complex systems, in particular, as simulation platforms in personalized medicine and predictive health. Interestingly, most published systems models in biology contain between a handful and a few dozen variables. They are usually too complicated for systemic analyses of organizing principles, but they are at the same time too coarse to allow reliable simulations of diseases. While it may thus appear that the modeling efforts of the past have missed the declared targets of systems biology, we argue in this article that midsized mesoscopic models are excellent starting points for pursuing both goals in computational systems biology.
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References
- 1 Lotka A. Elements of Physical Biology. Williams and Wilkins; Baltimore: 1924. (reprinted as ‘Elements of Mathematical Biology’. Dover, New York, 1956)
- 2 von Bertalanffy L. Der Organismus als physikalisches System betrachtet. Die Naturwissenschaften 1940; 33: 521-531
- 3 Mesarović MD. Systems theory and biology – view of a theoretician. In: Systems theory and biology. Mesaroviâc MD. Editor Springer; Berlin, New York: 1968. 59-87
- 4 Savageau MA. Biochemical systems analysis: a study of function and design in molecular biology. Reading, Mass.: Addison-Wesley Pub. Co. Advanced Book Program; 1976. xvii, 379
- 5 Tomita M, Hashimoto K, Takahashi K et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 1999; 15: 72-84
- 6 Hood L. Systems biology: integrating technology, biology, and computation. Mech Ageing Dev 2003; 124: 9-16
- 7 Kitano H. ed. Foundations of Systems Biology. MIT Press; Cambridge, MA: 2001
- 8 Kitano H. Systems biology: a brief overview. Science 2002; 295 (5560) 1662-1664
- 9 Kitano H. Computer systems biology. Nature 2002; 420: 206-210
- 10 Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science 1999; 283: 381-387
- 11 Hayer A, Bhalla US. Molecular switches at the synapse emerge from receptor and kinase traffic. PLoS Comput Biol 2005; 1: 137-154
- 12 Savageau MA. The challenge of reconstruction. The New Biologist 1991; 3: 101-102
- 13 Alon U. Simplicity in biology. Nature 2007; 446: 497
- 14 Alon U. An introduction to systems biology: design principles of biological circuits. In: Mathematical & Computational Biology. Boca Raton, FL: Chapman & Hall/CRC; 2006
- 15 Alves R, Sorribas A. Special issue on biological design principles. Math Biosci 2011; 231: 1-2
- 16 Hlavacek WS, Savageau MA. Completely uncoupled and perfectly coupled gene expression in repressible systems. J Mol Biol 1997; 266: 538-558
- 17 Savageau MA. A theory of alternative designs for biochemical control systems. Biomed Biochim Acta 1985; 44: 875-880
- 18 Schwacke JH, Voit EO. Improved methods for the mathematically controlled comparison of biochemical systems. Theor Biol Med Model 2004; 1: 1
- 19 Savageau MA. Demand theory of gene regulation. I. Quantitative development of the theory. Genetics 1998; 149: 1665-1676
- 20 Savageau MA. Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics 1998; 149: 1677-1691
- 21 Voit EO. Design principles and operating principles: the yin and yang of optimal functioning. Math Biosci 2003; 182: 81-92
- 22 Alvarez-Vasquez F, Sims KJ, Voit EO et al. Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shift. Theor Biol Med Model 2007; 4: 42
- 23 Lee Y, Chen P-W, Voit EO. Analysis of operating principles with S-system models. Math Biosc 2011; 231: 49-60
- 24 Ma’ayan A, Cecchi GA, Wagner J et al. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proc Natl Acad Sci USA 2008; 105: 19235-19249
- 25 Vodovotz Y, Constantine G, Rubin J et al. Mechanistic simulations of inflammation: Current state and future prospects. Math Biosc 2009; 217: 1-10
- 26 Curto R, Voit EO, Cascante M. Analysis of abnormalities in purine metabolism leading to gout and to neurological dysfunctions in man. Biochem J 1998; 329 (Pt 3) 477-487
- 27 Bhalla US, Iyengar R. Robustness of the bistable behavior of a biological signaling feedback loop. Chaos 2001; 11: 221-226
- 28 Kikuchi S, Fujimoto K, Kitagawa N et al. Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A. Neural Netw 2003; 16: 1389-1398
- 29 Marin-Sanguino A, Gupta SK, Voit EO et al. Biochemical pathway modeling tools for drug target detection in cancer and other complex diseases. Meth Enzym 2010; 487: 321-372
- 30 Voit EO, Brigham KL. The role of systems biology in predictive health and personalized medicine. The Open Path J 2008; 2: 68-70
- 31 Voit EO. A systems-theoretical framework for health and disease: inflammation and preconditioning from an abstract modeling point of view. Math Biosci 2009; 217: 11-18
- 32 E-Cell http://www.e-cell.org/ecell/ 2011
- 33 Glossary. Systems biology: a user’s guide. http://www.nature.com/focus/systemsbiologyuserguide/appendices/glossary.html 2011
- 34 Noble D. The Music of Life; Biology Beyond Genes. Oxford, U.K.: Oxford University Press; 2006
- 35 Full RJ, Koditschek DE. Templates and anchors: Neuromechanical hypotheses of legged locomotion on land. J Exp Biol 1999; 202: 3325-3332
- 36 Hayt WHJ, Kemmerly JE. Engineering Circuit Analyses. 3rd edn. New York: McGraw-Hill; 1978
- 37 Voit EO, Ferreira AEN. Buffering in models of integrated biochemical systems. J Theor Biol 1998; 191: 429-438
- 38 Clewley R. Inferring and quantifying the role of an intrinsic current in a mechanism for a half-center bursting oscillation: A dominant scale and hybrid dynamical systems analysis. J Biol Phys 2011; 37: 285-306
- 39 Clewley R. Encoding the fine-structured mechanism of action potential dynamics with qualitative motifs. J Comput Neurosci 2011; 30: 391-408
- 40 Tretter F. Mental illness, synapses and the brain – behavioral disorders by a system of molecules withinb a system of neurons?. Pharmacopsychiatry 2010; 43 (Suppl. 01) S9-S20
- 41 Qi Z, Miller GW, Voit EO. Computational systems analysis of dopamine metabolism. PLoS One 2008; 3: e2444
- 42 Qi Z, Miller GW, Voit EO. A mathematical model of presynaptic dopamine homeostasis: implications for schizophrenia. Pharmacopsychiatry 2008; 41 (Suppl. 01) S89-S98
- 43 Qi Z, Miller GW, Voit EO. Computational analysis of determinants of dopamine (DA) dysfunction in DA nerve terminals. Synapse 2009; 63: 1133-1142
- 44 Barbano PE, Spivak M, Flajolet M et al. A mathematical tool for exploring the dynamics of biological networks. Proc Natl Acad Sci USA 2007; 104: 19169-19174
- 45 Fernandez É, Schiappa R, Girault JA et al. DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2006; 2: e176
- 46 Lindskog M, Kim M, Wikstrom MA et al. Transient calcium and dopamine increase PKA activity and DARPP-32 phosphorylation. PLoS Comput Biol 2006; 2 (09) e119
- 47 Qi Z, Miller GW, Voit EO. The internal state of medium spiny neurons varies in response to different input signals. BMC Syst Biol 2010; 4: 26
- 48 Mahajan SD, Aalinkeel R, Reynolds JL et al. Therapeutic targeting of “DARPP-32”: A key signaling molecule in the dopaminergic pathway for the treatment of opiate addiction. Int Rev Neurobiol 2009; 88: 199-222
- 49 Fienberg AA, Hiroi N, Mermelstein PG et al. DARPP-32: Regulator of the efficacy of dopaminergic neurotransmission. Science 1998; 281 (5378) 838-842
- 50 Qi Z, Kikuchi S, Tretter F et al. Effects of dopamine and glutamate on synaptic plasticity: A computational modeling approach for drug abuse as comorbidity in mood disorders. Pharmacopsychiatry 2011; 44 (Suppl. 01) S62-S75
- 51 Bhalla US, Ram PT, Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 2002; 297: 1018-1023
- 52 Ishii K, Nokamura S, Morohashi M et al. Comparison of metabolite production capability indices generated by network analysis methods. Biosystems 2008; 91: 166-170
- 53 Matsubara Y, Kikuchi S, Sugimoto M et al. Algebraic method for the analysis of signaling crosstalk. Artif Life 2008; 14: 81-94
- 54 Yanashima R, Kitagawa N, Matsubara Y et al. Network features and pathway analyses in a signal transduction cascade. Front Neuroinform 2009; 3: 13
- 55 Shiraishi T, Matsuyama S, Kitano H. Large-scale analysis of network bistability for human cancers. PLoS Comput Biol 2010; 6: e1000851
- 56 Savageau MA. Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 1969; 25: 365-369
- 57 Torres NV, Voit EO. Pathway Analysis and Optimization in Metabolic Engineering. Cambridge, U.K.: Cambridge University Press; 2002
- 58 Voit EO. Computational Analysis of Biochemical Systems. A Practical Guide for Biochemists and Molecular Biologists. Cambridge, UK: Cambridge University Press; 2000. xii+530
- 59 Voit EO. ed. Canonical Nonlinear Modeling. S-System Approach to Understanding Complexity ed. Van Nostrand Reinhold; NY: 1991. xi+365