Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells

Abstract

SignificanceSynchrony, entrainment, and pattern formation are nonlinear modes of communication and collective behavior in living systems across scales. We aim to understand these complex processes by building them bottom-up in a minimal environment to unravel basic rules governing their behavior. However, it has so far been challenging to emulate spatially distributed coupled gene expression cellular reactions. We show a microfluidic device of a confined coupled system of DNA compartments programmed with nonlinear genetic oscillator and diffusion-based communication. This approach provides unique control of experimental parameters, which reveals a rich phenomenology of cell-free gene expression patterns in space and time.

Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

“…[1] Examples of networks giving temporal, or spatiotemporal, control over the concentrations of the molecules in the system include the generation of wave fronts, [2] pattern formation with as o-calledg o-fetch model, [3] oscillations, [4][5][6][7][8] supramolecular oscillators [9] synchronisation and pattern formation with multiple oscillators through diffusional spatiotemporal coupling, [10] adaptive response networks, [11] systemss howing homeostasis, [12] self-replicating systems that can diversify into differents pecies, [13] self-replicators that can transiently form micelles, [14,15] temporally controlled material properties [16][17][18] and transientv esicle, [19] droplet, [20] fibril and gel formation. [1] Examples of networks giving temporal, or spatiotemporal, control over the concentrations of the molecules in the system include the generation of wave fronts, [2] pattern formation with as o-calledg o-fetch model, [3] oscillations, [4][5][6][7][8] supramolecular oscillators [9] synchronisation and pattern formation with multiple oscillators through diffusional spatiotemporal coupling, [10] adaptive response networks, [11] systemss howing homeostasis, [12] self-replicating systems that can diversify into differents pecies, [13] self-replicators that can transiently form micelles, [14,15] temporally controlled material properties [16][17][18] and transi...…”

Gene Expression on DNA Biochips Patterned with Strand‐Displacement Lithography

“…[8] RNAa nd proteins can be exchanged between separate brushes and thus establish spatially distributed in vitro gene circuits. [9] Lithographic structuring of the brushes enables control over local concentrations,d irects the propagation of diffusive signals on the chip,a nd defines the timescale of signaling among spatially separated gene brushes.…”

Cell‐free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices

“…Likewise, other cell‐free genetic oscillatory gene networks are fabricated performing collective behavior resembling of live cells. Thus, design principles of DNA brushes to build programmable biochemical reactions can offer potential applications to autonomous sensing, distributed computing, and biomedical diagnostics (Tayar, Karzbrun, Noireaux, & Bar‐Ziv, 2017).…”

“…Genetic circuits Artificial cells capable of metabolism, programmable protein synthesis, and communication Karzbrun et al (2014) Genetic circuits Reconstitution of gene-expression oscillations in single cells, synchrony and pattern formation in populations with applications to autonomous sensing, distributed computing, and biomedical diagnostics Tayar et al (2017)…”