The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten ye...

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Autores principales:	Giulio Caravagna, Giancarlo Mauri, Alberto d'Onofrio
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/00c8a6438ee041d19cd51f436113a14a
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spelling	oai:doaj.org-article:00c8a6438ee041d19cd51f436113a14a2021-11-18T07:56:38ZThe interplay of intrinsic and extrinsic bounded noises in biomolecular networks.1932-620310.1371/journal.pone.0051174https://doaj.org/article/00c8a6438ee041d19cd51f436113a14a2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23437034/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.Giulio CaravagnaGiancarlo MauriAlberto d'OnofrioPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e51174 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Giulio Caravagna Giancarlo Mauri Alberto d'Onofrio The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
description	After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.
format	article
author	Giulio Caravagna Giancarlo Mauri Alberto d'Onofrio
author_facet	Giulio Caravagna Giancarlo Mauri Alberto d'Onofrio
author_sort	Giulio Caravagna
title	The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
title_short	The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
title_full	The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
title_fullStr	The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
title_full_unstemmed	The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
title_sort	interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/00c8a6438ee041d19cd51f436113a14a
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The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

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