Modular systems approach to understanding the interaction of adaptive and monostable and bistable threshold processes

IET Systems Biology

Volumn 5, Issue 2, 2011, Pages 81-94

  Seaton, D ^a   Krishnan, J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE MODULES; BIFURCATION ANALYSIS; BISTABLES; CELLULAR SIGNAL TRANSDUCTION; CELLULAR SYSTEM; MODULAR SYSTEM; MONOSTABLE; NUMERICAL SIMULATION; RELATIVE TIME; THRESHOLD PROCESS; TRANSIENT SIGNAL;

BACTERIOPHAGES; BIFURCATION (MATHEMATICS);

SIGNAL TRANSDUCTION;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; PHYSIOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 79952593286     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2009.0061     Document Type: Article

References (30)

1. Tyson, J.J., Chen, K.C., and Novak, B.: 'Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell', Curr. Opin. Cell. Biol., 2003, 15, p. 221-23110.1016/S0955-0674(03)00017-6
2. Alon, U.: 'An introduction to systems biology: design principles of biological circuits', (Chapman & Hall 2006)
3. Drengstig, T., Ueda, H.R., and Ruoff, P.: 'Predicting perfect adaptation motifs in reaction kinetic networks', J. Phys. Chem. B, 2008, 112, p. 16752-1675810.1021/jp806818c 1089-5647
4. Ma, W., Trusina, A., El-Samad, H., Lim, W.A., and Tang, C.: 'Defining network topologies that can achieve biochemical adaptation', Cell, 2009, 138, p. 760-77310.1016/j.cell.2009.06.013
5. El-Samad, H., Kurata, H., Doyle, J.C., Gross, C.A., and Khammash, M.: 'Surviving heat shock: control strategies for robustness and performance', Proc. Natl. Acad. Sci. USA, 2005, 102, p. 2736-274110.1073/pnas.0403510102 0027-8424
6. Zhang, Q., and Andersen, M.: 'Dose response relationship in anti-stress gene regulatory networks', PLoS Comput. Biol., 2007, 3, p. e2410.1371/journal.pcbi.0030024
7. Ni, E., Drenstig, T., and Ruoff, P.: 'The control of the controller: molecular mechanisms for robust perfect adaptation and temperature compensation', Biophys. J., 2009, 97, p. 1244-125310.1016/j.bpj.2009.06.030 0006-3495
8. Muzzey, D., Gomez-Uribe, C.A., Mettetal, J.T., and van Oudenaarden, A.: 'A systems-level analysis of perfect adaptation in yeast osmoregulation', Cell, 2009, 138, p. 160-17110.1016/j.cell.2009.04.047
9. Wark, B., Lundstrom, B., and Fairhall, A.: 'Sensory adaptation', Curr. Opin. Neurobiol., 2007, 17, p. 429-42310.1016/j.conb.2007.07.001
10. Friedlander, T., and Brenner, N.: 'Adaptive response by state-dependent inactivation', Proc. Natl. Acad. Sci. USA, 2009, 106, p. 22558-2256310.1073/pnas.0902146106 0027-8424
11. Yi, T.M., Huang, Y., Simon, M.I., and Doyle, J.: 'Robust perfect adaptation in bacterial chemotaxis through integral feedback control', Proc. Natl. Acad. Sci. USA, 2000, 97, p. 4649-465310.1073/pnas.97.9.4649 0027-8424
12. Levchenko, A., and Iglesias, P.: 'Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils', Biophys. J., 2002, 82, p. 50-6310.1016/S0006-3495(02)75373-3 0006-3495
13. Huang, C., and Ferrell, J.: 'Ultrasensitivity in the mitogen-activated protein kinase cascade', Proc. Natl. Acad. Sci. USA, 1996, 93, p. 10078-1008310.1073/pnas.93.19.10078 0027-8424
14. Ferrell, J.: 'Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs', Trends Biochem. Sci., 1996, 21, p. 460-46610.1016/S0968-0004(96)20026-X
15. Goldbeter, A., and Koshland, D.E.: 'An amplified sensitivity arising from covalent modification in biological systems', Proc. Natl. Acad. Sci. USA, 1981, 78, p. 6840-684410.1073/pnas.78.11.6840 0027-8424
16. Ferrell, J.E., and Xiong, W.: 'Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible', Chaos, 2001, 11, p. 227-23610.1063/1.1349894 1054-1500
17. Bagowski, C.P., and Ferrell, J.E.: 'Bistability in the JNK cascade', Curr. Biol., 2001, 11, p. 1176-118210.1016/S0960-9822(01)00330-X
18. Angeli, D., Ferrell, J.E.J., and Sontag, E.D.: 'Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems', Proc. Natl. Acad. Sci. USA, 2004, 101, p. 1822-182710.1073/pnas.0308265100 0027-8424
19. Ramakrishnan, N., and Bhalla, U.: 'Memory switches in chemical reaction space', PLoS Comput. Biol., 2008, 4, p. e100012210.1371/journal.pcbi.1000122
20. Bhalla, U., and Iyengar, R.: 'Emergent properties of networks of biological signaling pathways', Science, 1999, 283, p. 381-38710.1126/science.283.5400.381 0036-8075
21. Hayer, A., and Bhalla, U.: 'Molecular switches at the synapse emerge from receptor and kinase traffic', PLoS Comput. Biol., 2005, 1, p. e2010.1371/journal.pcbi.0010020
22. Klipp, E., Nordlander, B., Kruger, R., Gennemark, P., and Hohmann, S.: 'Integrative model of the response of yeast to osmotic shock', Nat. Biotechnol., 2005, 23, p. 975-98210.1038/nbt1114
23. Sontag, E.: 'Remarks on feedforward circuits, adaptation, and pulse memory', IET Syst. Biol., 2010, 4, p. 39-5110.1049/iet-syb.2008.0171
24. Behar, M., Hao, N., Dohlman, H.G., and Elston, T.C.: 'Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways', Biophys. J., 2007b, 93, p. 806-82110.1529/biophysj.107.107516 0006-3495
25. Koshland, D.: 'A response regulator model in a simple sensory system', Science, 1977, 196, p. 1055-106310.1126/science.870969 0036-8075
26. Krishnan, J.: 'Signal processing through a generalized module of adaptation and spatial sensing', J. Theor. Biol., 2009, 259, p. 31-4310.1016/j.jtbi.2009.02.015
27. Kholodenko, B.: 'Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades', Eur. J. Biochem., 2000, 267, p. 1583-158810.1046/j.1432-1327.2000.01197.x
28. Thomson, M., and Gunawardena, J.: 'Unlimited multistability in multisite phosphorylation systems', Nature, 2009, 460, p. 274-27710.1038/nature08102 0028-0836
29. Barkai, N., and Leibler, S.: 'Robustness in simple biochemical networks', Nature, 1997, 387, p. 913-91710.1038/43199 0028-0836
30. Behar, M., Dohlman, H.G., and Elston, T.C.: 'Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks', Proc. Natl. Acad. Sci. USA, 2007a, 104, p. 16146-1615110.1073/pnas.0703894104 0027-8424