Journal ArticleDOI
A synthetic oscillatory network of transcriptional regulators
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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.Abstract:
Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function We 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 The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networksread more
Citations
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Journal ArticleDOI
Statistical mechanics of complex networks
TL;DR: In this paper, a simple model based on the power-law degree distribution of real networks was proposed, which was able to reproduce the power law degree distribution in real networks and to capture the evolution of networks, not just their static topology.
Journal ArticleDOI
Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
Journal ArticleDOI
The large-scale organization of metabolic networks
TL;DR: In this paper, the authors present a systematic comparative mathematical analysis of the metabolic networks of 43 organisms representing all three domains of life, and show that despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.
The large-scale organization of metabolic networks
Hawoong Jeong,B. Tombor,Réka Albert,Z. N. Oltavai,Albert-László Barabási,T. Dandekar,Stefan Schuster +6 more
TL;DR: This analysis of metabolic networks of 43 organisms representing all three domains of life shows that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.
Journal ArticleDOI
The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)
TL;DR: In this paper, the authors describe the rules of the ring, the ring population, and the need to get off the ring in order to measure the movement of a cyclic clock.
References
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Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
The green fluorescent protein
TL;DR: In just three years, the green fluorescent protein from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology.
Book
Escherichia coli and Salmonella :cellular and molecular biology
TL;DR: The Enteric Bacterial Cell and the Age of Bacteria Variations on a Theme by Escherichia is described.
Journal ArticleDOI
The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)
TL;DR: In this paper, the authors describe the rules of the ring, the ring population, and the need to get off the ring in order to measure the movement of a cyclic clock.
Book
The geometry of biological time
TL;DR: The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways is presented.