Emergent bistability: Effects of additive and multiplicative noise

@article{Ghosh2012EmergentBE,
  title={Emergent bistability: Effects of additive and multiplicative noise},
  author={S Ghosh and S. Banerjee and I Bose},
  journal={The European Physical Journal E},
  year={2012},
  volume={35},
  pages={1-14}
}
Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been proposed which involves only positive feedback and no cooperativity in the regulation. An additional positive feedback loop is effectively generated due to the inhibition of cellular growth by the synthesized proteins. The mechanism, demonstrated for a synthetic… 
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26 Citations
Background Citations
3
Methods Citations
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26 Citations

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Citation Type

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References

SHOWING 1-10 OF 108 REFERENCES
Bistability, Probability Transition Rate and First-Passage Time in an Autoactivating Positive-Feedback Loop
TLDR
This paper investigates how the probability transition rate and first-passage time in an autoactivating positive-feedback loop with bistability are affected by the maximum transcriptional rate, the intensities of additive and multiplicative noises, and the correlation of additiveandmultiplicative noises.
Noise Can Induce Bimodality in Positive Transcriptional Feedback Loops Without Bistability
TLDR
Using a synthetic system in budding yeast, it is shown that positive feedback involving a promoter with multiple transcription factor (TF) binding sites can induce a steady-state bimodal response without cooperative binding of the TF.
Positive feedback, stochasticity and genetic competence.
TLDR
The appearance of bimodal protein distributions in B. subtilis cell population is explained in the framework of three possible scenarios: the system is monostable in a deterministic description and stochasticity in gene expression is solely responsible for the appearance of the two expression states.
Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.
TLDR
Stochastic bistability where the deterministic equations predict monostability and vice-versa is found; among them, bifurcations driven solely by changing the rate of operator fluctuations even as the underlying deterministic system remains unchanged are found.
Noise-based switches and amplifiers for gene expression.
TLDR
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.
Uncovering mechanisms of bistability in biological systems.
TLDR
Recent advances in both theoretical and experimental work investigating the mechanistic as well as biological basis for bistability will be presented, including the role of positive feedback loops, the potential function of dual phosphorylation cycles, and substrate competition as a means of generating ultrasensitivity.
Prediction and measurement of an autoregulatory genetic module
TLDR
This work demonstrates that isolated gene networks, coupled with proper quantitative descriptions, can elucidate key properties of functional genetic modules and lead to the modular dissection of naturally occurring gene regulatory networks.
Enhancement of cellular memory by reducing stochastic transitions
TLDR
The key parameters that determine the stability of cellular memory are explored by using the yeast galactose-signalling network as a model system and a model reveals that fluctuations are trapped more efficiently at higher Gal80p concentrations.
Fluctuations-induced switch in the gene transcriptional regulatory system.
  • Quan Liu, Ya Jia
  • Physics, Medicine
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2004
TLDR
It is found that, under large cross-correlation intensity, a successive switch process occurs with an increase of noise intensities, and a critical noise intensity exists at which the MFPT of the switch process is the largest.
Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability.
  • J. Ferrell
  • Biology, Medicine
    Current opinion in cell biology
  • 2002
TLDR
The basic properties of bistable circuits, the requirements for construction of a satisfactorybistable switch, and the recent progress towards constructing and analysing bistables signaling systems are reviewed.
...
1
2
3
4
5
...