Reconstruction of transcription–translation dynamics with a model of gene networks

Ichinose, Natsuhiro; Yada, Tetsushi; Gotoh, Osamu; Aihara, Kazuyuki

doi:10.1016/j.jtbi.2008.09.006

Cited by 11 publications

(10 citation statements)

References 23 publications

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“…If there is no effective auto-regulation in the piecewise linear equations, the network is called a Glass network [13], and the analysis can be performed without recourse to the Filippov method. A recent application of Glass networks is found in [14]. Sigmoidal response functions have also been approximated by the so-called logoid functions, differentiable, piecewise linear functions rising from 0 to 1 in a finite interval around the threshold [15].…”

Section: Introductionmentioning

confidence: 99%

Dynamics of actively regulated gene networks

Ironi

Panzeri

Plahte

et al. 2011

Physica D: Nonlinear Phenomena

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Section: Introductionmentioning

confidence: 99%

Dynamics of actively regulated gene networks

Ironi

Panzeri

Plahte

et al. 2011

Physica D: Nonlinear Phenomena

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“…By using mathematical models to capture the biochemical reactions of genetic systems, the synthetic genetic circuits can be designed from the system level. For the synthetic genetic network with L genes, a nonlinear Hill differential equation is used to describe the biochemical reactions as follows: [5] …”

Section: Genetic Logic Gatesmentioning

confidence: 99%

“…Recently, several fundamental artificial genetic circuits have successfully been built to achieve the basic functions, for example, toggle switch, oscillator, pulse generator, genetic counter, logic evaluator, sensor, filter, and cell-cell communicator. Based on a bottom-up approach, more complicated bio-computing processes can be expected to perform specific functions, like very-large-scale integration (VLSI) circuits in electronic systems [4], [5], [6].…”

Section: Introductionmentioning

confidence: 99%

A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier

Chuang

Lin

2014

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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This paper presents a novel synthesizing genetic logic circuit design based on an existing synthetic genetic oscillator, which provides a function of frequency multiplier to synthesize a clock signal whose frequency is a multiple of that of the genetic oscillator. In the renowned literature, the synthetic genetic oscillator, known as a repressilator, has been successfully built in Escherichia coli to generate a periodic oscillating phenomenon through three repressive genes repress each other in a chain. On the basis of this fact, our proposed genetic frequency multiplier circuit utilizes genetic Buffers in series with a waveform-shaping circuit to reshape the genetic oscillation signal into a crisp logic clock signal. By regulating different threshold levels in the Buffer, the time length of logic high/low levels in a fundamental sinusoidal wave can be engineered to pulse-width-modulated (PWM) signals with various duty cycles. Integrating some of genetic logic XOR gates and PWM signals from the output of the Buffers, a genetic frequency multiplier circuit can be created and the clock signal with the integer-fold of frequency of the genetic oscillator is generated. The synthesized signal can be used in triggering the downstream digital genetic logic circuits. Simulation results show the applicability of the proposed idea.

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“…Like others, i.e., [12,19] and [38,39], we consider a simple functional form to model either repression or activation of gene transcription characterized by the values (m,n). Since genetic repression is more often observed in biochemical systems, the repression case (0,2) has been widely studied in the literature [40][41][42][43][44][45], while the activation case has been seldom used [9][10][11][12][13]. Although repression tends to stabilize a dynamical system, activation coupled with degradation can show oscillatory behavior or even complex oscillations.…”

Section: General Modelmentioning

confidence: 99%

Self-regulation in a minimal model of chemical self-replication

Lou

Peacock‐López

2011

J Biol Phys

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In biological systems, regulation plays an important role in keeping metabolite concentrations within physiological ranges. To study the dynamical implications of selfregulation, we consider a functional form used in genetic networks and couple it to a mechanism associated with chemical self-replication. For the two-variable minimal model, we find that activation can yield chemical toggles similar to those reported for gene repression in E. coli as well as more complex dynamics.

show abstract

Reconstruction of transcription–translation dynamics with a model of gene networks

Cited by 11 publications

References 23 publications

Dynamics of actively regulated gene networks

Dynamics of actively regulated gene networks

A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier

Self-regulation in a minimal model of chemical self-replication

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