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Natural Computing
Erschienen in: Natural Computing 3/2014

01.09.2014

Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks

verfasst von: Sebastiano de Franciscis, Giulio Caravagna, Alberto d’Onofrio

Erschienen in: Natural Computing | Ausgabe 3/2014

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Abstract

In the first part of this invited paper we review the role of both extrinsic and intrinsic stochasticity in shaping the dynamics of biomolecular networks. In particular, we stress the use of bounded stochastic processes as a model of extrinsic random perturbations. In the second part, we propose three examples of molecular circuits under the influence of external fluctuations modeled by means of bounded noises. The first two examples involve the linear decay of a protein with, respectively, large or low number of molecules, so to stress different modeling approaches. The third example concerns the spatio-temporal dynamics of proteins determining the chemotaxis-driven polarization of a cell. In these examples one can observe phenomena that are dependent on the specific class of employed bounded noise.
Vorheriger Artikel An investigation into irreducible autocatalytic sets and power law distributed catalysis
Nächster Artikel A local landscape mapping method for protein structure prediction in the HP model

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Literatur
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2009) Molecular biology of the cell, 5th ed. Garland, New York
Alon U (2006) An introduction to systems biology: design principles of biological circuits. Chapman & Hall/CRC Mathematical & Computational Biology, Boca Raton, FL
Angeli D, Ferrell JE Jr, Sontag ED (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. PNAS 101(7):1822–1827CrossRef
Arnold L (1989) Random dynamical systems. Springer, Berlin
Becskei A, Serrano L (2000) Engineering stability in gene networks by autoregulation. Nature 405:590–593CrossRef
Becskei A, Kaufmann BB, van Oudenaarden AE (2000) Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 37:937–944CrossRef
Bobryk RV, Chrzeszczyk A (2005) Transitions induced by bounded noise. Phys A 358(2–4):263CrossRef
Cai CQ, Lin YK (1996) Generation of non-gaussian stationary stochastic processes. Phys Rev E 54:299CrossRef
Cai L, Friedman N, Xie XS (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440:358–362CrossRef
Caravagna G, Mauri G, d’Onofrio A (2013) The interplay of intrinsic and extrinsic bounded noises in biomolecular networks. PLoS One 8:e51174CrossRef
Caravagna G, Mauri G, d’Onofrio A (2013) Bounded extrinsic noises affecting biochemical networks with low molecule numbers. Chapter in d’Onofrio A (ed) Bounded noises in physics, biology and engineering, Birkauser, Verlag. ISBN 978-1-4614-7348-8
Caravagna G, Mauri G, d’Onofrio A (2013) NoisySIM: exact simulation of stochastic chemically reacting systems with extrinsic noises. In proceedings of the Symposium on theory of modeling and simulation vol 12, pp 1–6. Society for Computer Simulation International, San Diego, CA
Chang HH, Oh PY, Ingber DE, Huang S (2006) Stochastic approaches for systems biology. BMC Cell Biol 7:11–23CrossRef
Cinquin O, Demongeot J (2005) High-dimensional switches and the modelling of cellular differentiation. J Theor Biol 233:391–411CrossRef
deFranciscis S, d’Onofrio A (2012) Spatiotemporal bounded noises and transitions induced by them in solutions of the real Ginzburg–Landau model. Phys Rev E 86:021118CrossRef
deFranciscis S, d’Onofrio A (2013) Cellular polarization: interaction between extrinsic bounded noises and the wave-pinning mechanism. Phys Rev E 88:032709CrossRef
deFranciscis S, d’Onofrio A (2013) Spatio-temporal Sine–Wiener bounded noise and its effect on Ginzburg–Landau model. Nonlinear Dyn 74:607CrossRefMathSciNet
Detwiler PB, Ramanathan S, Sengupta A, Shraiman BI (2000) Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. Biophys J 79:2801–2817CrossRef
Dimentberg M (1988) Statistical dynamics of nonlinear and time-varying systems. Research Studies Press, BaldockMATH
d’Onofrio A (2013) Multifaceted aspects of the kinetics of immunoevasion from tumor dormancy. In: Enderling H, Almog N and Hlatky L (eds.) Systems biology of tumor dormancy, advances in experimental medicine and biology, vol 734, Springer, Berlin, p 111
d’Onofrio A (ed) (2013) Bounded noises in physics, biology and engineering, Birkauser, Basel-Boston. ISBN 978-1-4614-7348-8.
d’Onofrio A (2010) Bounded-noise-induced transitions in a tumor-immune system interplay. Phys Rev E 81:021923CrossRefMathSciNet
d’Onofrio A, Gandolfi A (2010) Resistance to antitumor chemotherapy due to bounded-noise-induced transitions. Phys Rev E 82:061901CrossRefMathSciNet
Eldar A, Elowitz MB (2010) Functional role for noise in genetic circuits. Nature 467:167–173CrossRef
Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 298:1183–1186CrossRef
Gamba A, de Candia A, Di Talia S, A Coniglio A, Bussolino F, Serini G (2005) Diffusion-limited phase separation in eukaryotic chemotaxis. PNAS 102(47):16927CrossRef
García-Ojalvo J, Sancho JM, Ramírez-Piscina L (1992) Generation of spatiotemporal colored noise. Phys Rev A 46:4670CrossRef
García-Ojalvo J, Sancho JM, Ramírez-Piscina L (1992) A nonequilibrium phase transition with colored noise. Phys Lett A 168(1):35–39CrossRef
Garcia-Ojalvo J, Sancho JM, Ramirez-Piscina I (1992) Generation of spatiotemporal colored noise. Phys Rev E 46:4670
Gardiner CW (1985) Handbook of stochastic methods, 2nd edn. Springer, Berlin
Gardner TR, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in escherichiacoli. Nature 403:339–342CrossRef
Ghaemmaghami S, Huh W, Bower K, Howson RW, Belle A, Dephoure N, O’Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–743CrossRef
Gierer A, Meinhardt H (1972) A theory of biological pattern formation. Kybernetik 12:30–39CrossRef
Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comp Phys 22(4):403–434CrossRefMathSciNet
Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340–2361
Gillespie DT (1980) Approximating the master equation by Fokker–Planck-type equations for single-variable chemical systems. J Phys Chem 72:5363–5371
Gillespie DT (2000) The chemical Langevin equation. J Phys Chem 113:297–306
Glass L, Kauffman SA (1968) Logical analysis of systems comprising feedback loops. J Theor Biol 39:103–129CrossRef
Griffith JS (1968) Mathematics of cellular control processes ii positive feedback to one gene. J Theor Biol 20:209–216CrossRef
Guo W, Du LC, Mei DC (2012) Transitions induced by time delays and cross-correlated Sine–Wiener noises in a tumor-immune system interplay. Phys A 391:1270–1280CrossRef
Hasty J, Pradines J, Dolnik M, Collins JJ (2000) Noise-based switches and amplifiers for gene expression. PNAS 97(5):2075–2080CrossRef
Homburg AJ, Young TR, Gharaei M (2013) Bifurcations of random differential equations with bounded noise. In d’Onofrio A (ed) Bounded noises in physics, biology and engineering, Birkauser, Verlag. ISBN 978-1-4614-7348-8
Horsthemke W, Lefever R (2006) Noise-induced transitions: theory and applications in physics, chemistry, and biology, Series in Synergetics Springer, Berlin
Iglesias PA, Devreotes PN (2008) Navigating through models of chemotaxis. Curr Opin Cell Biol 20:35–40CrossRef
Iglesias PA, Ingalls PB (2010) Control theory and systems biology. MIT Press, CambridgeMATH
Jung P, Hänggi P (1987) Dynamical systems: a unified colored-noise approximation. Phys Rev A 35:4464CrossRef
Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467CrossRefMathSciNet
Kramer BP, Fussenegger M (2005) Hysteresis in a synthetic mammalian gene network. PNAS 102:9517–9522CrossRef
Lestas I, Vinnicombe G, Paulsson J (2010) Fundamental limits on the suppression of molecular fluctuations. Nature 467:174–178CrossRef
Losick R, Desplan C (2008) Stochasticity and cell fate. Science 320:65–68CrossRef
Mandelbrot BB (1963) The variation of certain speculative prices. J Bus (Chicago) 36:394–419CrossRef
Markevich NI, Hoek JB, Kholodenko BN (2004) Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol 164:353–359CrossRef
Meinhardt H (1999) Orientation of chemotactic cells and growth cones: models and mechanisms. J Cell Sci 17:2867
Mori Y, Jilkine A, Edelstein-Keshet L (2008) Wave-pinning and cell polarity from a bistable reaction-diffusion system. Biophys J 94:3684CrossRef
Murray JD (2002) Mathematical biology. Springer, New YorkMATH
Onsum MD, Rao CV (2009) Calling heads from tails: the role of mathematical modeling in understanding cell polarization. Curr Opin Cell Biol 21(1):74CrossRef
Paulsson BO (2011) Systems biology simulation of dynamic network states. Cambridge University Press, CambridgeCrossRef
Rao CV, Wolf D, Arkin AP (2002) Control, exploitation and tolerance of intracellular noise. Nature 420:231–237CrossRef
Ridolfi L, D’Odorico P, Laio F (2011) Noise-induced phenomena in the environmental sciences. Cambridge University Press, CambridgeCrossRefMATH
Rigney DR, Schieve WC (1977) Stochastic model of linear, continuous protein-synthesis in bacterial populations. J Theor Biol 69:761–766CrossRef
Samoilov M, Plyasunov S, Arkin AP (2005) Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. PNAS 102(7):2310–2315CrossRef
Sanft KR, Gillespie DT, Petzold LR (2011) Legitimacy of the stochastic michaelis-menten approximation. IET Sys Bio 5(1):58–69CrossRef
Semplice M, Veglio A, Naldi G, Serini G, Gamba A (2012) A bistable model of cell polarity. PLoS One 7:e30977CrossRef
Shahrezaei V, Ollivier JF, Swain PS (2008) Colored extrinsic fluctuations and stochastic gene expression. Mol Sys Biol 4:196
Siegal-Gaskins D, Grotewold E, Smith GD (2009) The capacity for multistability in small gene regulatory networks. BMC Sys Biol 3:96CrossRef
Simon Z (1965) Multi-steady-state model for cell differentiation. J Theor Biol 8:258–263CrossRef
Sugita M (1964) Functional analysis of chemical systems in vivo using a logical circuit equivalent ii the idea of a molecular automaton. J Theor Biol 4:437–467
Thattai M, Van Oudenaarden A (2001) Attenuation of noise in ultrasensitive signaling cascades. Biophys J 82:2943–2950CrossRef
Thattai M, Van Oudenaarden A (2001) Intrisic noise in gene regulatory networks. PNAS 98:8614–8619CrossRef
Thomas R (1978) Logical analysis of systems comprising feedback loops. J Theor Biol 73:631–656CrossRef
Tomas R, d’Ari R (1990) Biological feedbacks. Chapman & Hall/CRC Mathematical & Computational Biology, Boca Raton, FL
Turing AM (1952) The chemical basis of morphogenesis. Phil Trans R Soc Lond B 237(641):37–72CrossRef
Tze-Leung T, Mahesci N (2010) Stochasticity and cell fate. Science 327:1142–1145CrossRef
Ullah M, Wolkhenauer O (2011) Stochastic approaches for systems biology. Springer, BerlinCrossRefMATH
Walther GR, Marée AF, Edelstein-Keshet L, Grieneisen VA (2012) Deterministic versus stochastic cell polarisation through wave-pinning. Bull Math Biol 74:2570MATHMathSciNet
Wang L, Walker BL, Iannaccone S, Bhatt D, Kennedy PJ, Tse WT (2009) Bistable switches control memory and plasticity in cellular differentiation. PNAS 106(16):6638–6643CrossRef
Wilkinson DJ (2006) Stochastic modelling for systems biology. Chapman & Hall/CRC Mathematical & Computational Biology, Boca Raton, FLMATH
Wio HS, Lindenberg K (2003) Modern challenges in statistical mechanics. In proceedings of the AIP conference vol 658(1)
Wio Hs, Deza RR (2013) Noise-induced phenomena: effects of noises based on Tsallis statistics. In d’Onofrio A (ed.) Bounded noises in physics, biology and engineering, Birkauser, Verlag. ISBN 978-1-4614-7348-8
Wio H, Toral R (2004) Effect of non-Gaussian noises in a noise induced transition. Phys D 193:161CrossRefMATH
Xiong W, Ferrell JE Jr (2003) A positive-feedback-based bistable ’memory module’ that governs a cell fate decision. Nature 426:460–465CrossRef
Yamada T, Bork P (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Bio 10:791–803CrossRef
Zhdanov VP (2011) Interplay of bistable kinetics of gene expression during cellular growth. Phys A 390:57CrossRef
Zhdanov VP (2012) Periodic perturbation of genetic oscillations. Chaos, Solitons & Fractals 45:577–587CrossRef
Zhu WQ, Cai GQ (2013) On Bounded stochastic processes. In d’Onofrio A (ed) bounded noises in physics, biology and engineering, Birkauser, Verlag. ISBN 978-1-4614-7348-8
Metadaten
Titel
Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks
verfasst von
Sebastiano de Franciscis
Giulio Caravagna
Alberto d’Onofrio
Publikationsdatum
01.09.2014
Verlag
Springer Netherlands
Erschienen in
Natural Computing / Ausgabe 3/2014
Print ISSN: 1567-7818
Elektronische ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-014-9424-y

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