Periodic perturbation of genetic oscillations

Zhdanov, Vladimir P.

doi:10.1016/j.chaos.2011.12.008

Cited by 12 publications

(11 citation statements)

References 66 publications

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“…The gene expression model was taken from Zhdanov [12], whose work describes the transcription-translation process. In simple terms, transcription is a set of steps that lead to the synthesis of RNA from genomic DNA.…”

Section: Gene Expression Modelingmentioning

confidence: 99%

On the Observability and State Estimation in a Class of Gene-Expression System

Aguilar-López¹,

Mata-Machuca²

2018

DSA

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The failure of available physical sensors for the online measurement of protein concentration in cells is a key problem to understanding the transition in bio-systems. In this paper, a new state observer has been designed to estimate three protein concentrations by using a gene-expression mathematical model. Interestingly, its only input is the concentration of one messenger RNA (mRNA). Similarly by differential-algebraic observability analysis is showed that the gene-expression model is indeed observable. The observer convergence was demonstrated by analysing the estimation error dynamics. In silico experiments confirm the satisfactory performance of this new observer.

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Section: Gene Expression Modelingmentioning

confidence: 99%

On the Observability and State Estimation in a Class of Gene-Expression System

Aguilar-López¹,

Mata-Machuca²

2018

DSA

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“…Multistability is a key concept of Systems Biology since the first pioneering investigations on the dynamics of genetic networks [1][2][3][4]. Indeed, it was quite soon understood -both experimentally and theoretically -that multiple locally stable equilibria allows for the presence of multiple functionalities, even in small groups of interplaying proteins [5][6][7][8][9][10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

2013

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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: the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, a model of enzymatic futile cycle and a genetic toggle switch. In and 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.

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“…The available studies of this category are focused on periodic perturbation of bistable and oscillatory networks (see, respectively, Refs. [27,28] and [29][30][31] and references therein). Complementing those studies, we show here the effect of periodic regulation on the mRNA-miRNA interplay.…”

Section: Motivationmentioning

confidence: 99%

Two novel aspects of the kinetics of gene expression including miRNAs

Zhdanov¹

2013

Open Physics

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Abstract:In eukaryotic cells, many genes are transcribed into non-coding RNAs. Small RNAs or, more specifically, microRNAs (miRNAs) form an abundant sub-class of such RNAs. miRNAs are transcribed as long noncoding RNA and then generated via a processing pathway down to the 20-24-nucleotide length. The key ability of miRNAs is to associate with target mRNAs and to suppress their translation and/or facilitate degradation. Using the mean-field kinetic equations and Monte Carlo simulations, we analyze two aspects of this interplay. First, we describe the situation when the formation of mRNA or miRNA is periodically modulated by a transcription factor which itself is not perturbed by these species. Depending on the ratio between the mRNA and miRNA formation rates, the corresponding induced periodic kinetics are shown to be either nearly harmonic or shaped as anti-phase pulses. The second part of the work is related to recent experimental studies indicating that differentiation of stem cells often involves changes in gene transcription into miRNAs and/or the interference between miRNAs, mRNAs and proteins. In particular, the regulatory protein obtained via mRNA translation may suppress the miRNA formation, and the latter may suppress in turn the miRNA-mRNA association and degradation. The corresponding bistable kinetics are described in detail.

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Periodic perturbation of genetic oscillations

Cited by 12 publications

References 66 publications

On the Observability and State Estimation in a Class of Gene-Expression System

On the Observability and State Estimation in a Class of Gene-Expression System

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

Two novel aspects of the kinetics of gene expression including miRNAs

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