Noise-aided computation within a synthetic gene network through morphable and robust logic gates.

@article{Dari2011NoiseaidedCW,
  title={Noise-aided computation within a synthetic gene network through morphable and robust logic gates.},
  author={Anna Dari and Behnam Kia and Xiao Wang and Adi R. Bulsara and William L. Ditto},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  year={2011},
  volume={83 4 Pt 1},
  pages={
          041909
        }
}
  • A. DariBehnam Kia W. Ditto
  • Published 11 April 2011
  • Engineering
  • Physical review. E, Statistical, nonlinear, and soft matter physics
An important goal for synthetic biology is to build robust and tunable genetic regulatory networks that are capable of performing assigned operations, usually in the presence of noise. In this work, a synthetic gene network derived from the bacteriophage λ underpins a reconfigurable logic gate wherein we exploit noise and nonlinearity through the application of the logical stochastic resonance paradigm. This biological logic gate can emulate or "morph" the AND and OR operations through varying… 

Creating morphable logic gates using logical stochastic resonance in an engineered gene network

The idea of Logical Stochastic Resonance is adapted and applied to an autoregulatory gene network in the bacteriophage λ. This biological logic gate can emulate or morph the AND and OR gates, through

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The intriguing results of this study show that it is possible to build a biological logic block that can emulate or switch from the AND to the OR gate functionalities through externally tuning the system parameters, and are underpinned by the presence of an optimal amount of random fluctuations.

Reprogrammable biological logic gate that exploits noise

The possibility to exploit noise when it cannot be eliminated is demonstrated and the LSR paradigm is adapted to a single-gene network derived from the bacteriophage λ and from the yeast S. cerevisiae, demonstrating that in both cases there is an optimal amount of noise.

Plasticity of the truth table of low-leakage genetic logic gates

This article shows that the function of a common class of synthetic genetic AND and NAND gates is not completely dictated by the circuit connectivity, even if promoter leakage is very small, and all these functionalities are compatible with the physiological range of parameter values.

Engineering of regulated stochastic cell fate determination

This work uses synthetic biology approaches to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors.

Information-based measures for logical stochastic resonance in a synthetic gene network under Lévy flight superdiffusion.

The synchronization degree of the mutual information for the accomplished logical stochastic resonance of two repressive proteins of the synthetic gene network is analyzed by synchronization variances, which shows that those mutual information changes almost synchronously.

Control of logic gates by dichotomous noise in energetic and entropic systems.

  • M. DasD. Ray
  • Physics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2013
It is shown how the input-output correspondence can be controlled by an external exponentially correlated dichotomous noise optimizing the logical response which exhibits a maximum at an intermediate value of correlation time.

References

SHOWING 1-10 OF 95 REFERENCES

Designer gene networks: Towards fundamental cellular control.

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for

Noise-based switches and amplifiers for gene expression.

A model describing the regulation of gene expression and the effects of noise are developed and it is suggested that an external noise source could be used as a switch and/or amplifier for gene expression.

Intrinsic noise in gene regulatory networks

An analytic model is used to investigate the emergent noise properties of genetic systems and finds for a single gene that noise is essentially determined at the translational level, and that the mean and variance of protein concentration can be independently controlled.

A molecular noise generator

Two designs of a molecular noise generator that allow for the flexible modulation of the noise profile of a target gene are presented, demonstrating how it could be used to ascertain the robust or fragile properties of a genetic circuit.

Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.

The construction of synthetic transcriptional cascades comprising one, two, and three repression stages are reported, which enable us to analyze sensitivity and noise propagation as a function of network complexity.

Tuning and controlling gene expression noise in synthetic gene networks

This work introduces TATA box mutations into promoters driving TetR expression and shows that these mutations can be used to effectively tune the noise of a target gene while decoupling it from the mean, with negligible effects on the dynamic range and basal expression.

DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS

This work presents an approach that couples libraries of diversified components with in silico modeling to guide predictable gene network construction without the need for post hoc tweaking, and produces a synthetic gene network acting as a predictable timer, modifiable by component choice.

Engineering stability in gene networks by autoregulation

Simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli are designed and constructed and the gain of stability produced by negative feedback is shown.

Engineered gene circuits

Synthetic gene networks will lead to new logical forms of cellular control, which could have important applications in functional genomics, nanotechnology, and gene and cell therapy.

A synthetic oscillatory network of transcriptional regulators

This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.
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