A population-based temporal logic gate for timing and recording chemical events: Difference between revisions
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| authors = Victoria Hsiao, Yutaka Hori, Paul W.K. Rothemund, Richard M. Murray | | authors = Victoria Hsiao, Yutaka Hori, Paul W.K. Rothemund, Richard M. Murray | ||
| title = A population-based temporal logic gate for timing and recording chemical events | | title = A population-based temporal logic gate for timing and recording chemical events | ||
| source = Molecular Systems Biology (Accepted, In press | | source = Molecular Systems Biology (Accepted, In press) | ||
| year = 2016 | | year = 2016 | ||
| type = Molecular Systems Biology article | | type = Molecular Systems Biology article | ||
| funding = ICB | | funding = ICB | ||
| url = | | url = TBD | ||
| abstract = | | abstract = | ||
Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single-cell responses that translated into analog population responses. Furthermore, when single-cell genetic states were aggregated into population-level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub-populations could be used to deduce order, timing, and duration of transient chemical events. | Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single-cell responses that translated into analog population responses. Furthermore, when single-cell genetic states were aggregated into population-level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub-populations could be used to deduce order, timing, and duration of transient chemical events. | ||
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'''Preprints''' | |||
BioRxiv DOI: [http://biorxiv.org/content/early/2015/10/27/029967| 10.1101/029967] | |||
Posted: 27 Oct 2015 | |||
Revision as of 23:23, 17 May 2016
Victoria Hsiao, Yutaka Hori, Paul W.K. Rothemund, Richard M. Murray
Molecular Systems Biology (Accepted, In press)
Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single-cell responses that translated into analog population responses. Furthermore, when single-cell genetic states were aggregated into population-level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub-populations could be used to deduce order, timing, and duration of transient chemical events.
Preprints
BioRxiv DOI: 10.1101/029967
Posted: 27 Oct 2015
