Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa
Abstract

Stochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators ofNeurosporacrassa. The genetic algorithms were at least an order of magnitude faster than ensemble methods using parallel tempering and appeared to provide a globally optimum solution from a random start in the initial guess of model parameters (i.e., rate constants and initial counts of molecules in a cell). The resulting goodness of fit$${x}^{2}$$${x}^{2}$was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting$${x}^{2}$$${x}^{2}$per data point was only$${\chi }^{2}/n$$${\chi }^{2}/n$= 2,708.05/953 = 2.84. The fitted model ensemble was robust to variation in proxies for “cell size”. The fitted neutral models without cellular communication between single cells isolated by microfluidics provided evidence for onlyoneStochastic Resonance at one common level of stochastic intracellular noise across days from 6 to 36 h of light/dark (L/D) or in a D/D experiment. When the light-driven phase synchronization was strong as measured by the Kuramoto (K), there was degradation in the single cell oscillations away from the stochastic resonance. The rate constants for the stochastic clock network are consistent with those determined on a macroscopic scale of 107cells.

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Award ID(s):
Publication Date:
NSF-PAR ID:
10192589
Journal Name:
Scientific Reports
Volume:
10
Issue:
1
ISSN:
2045-2322
Publisher:
Nature Publishing Group
National Science Foundation
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