Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa
Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa
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DOI：
10.1038/s41598-020-72213-1
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发表时间：
2020-09-16
影响因子：
4.6
通讯作者：
Arnold, J.
中科院分区：
文献类型：
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作者：
Caranica, C.;Al-Omari, A.;Arnold, J.
利用遗传算法的集合方法确定了时钟的随机网络，该方法捕获了神经孢子虫单细胞振荡器的振幅和周期变化。遗传算法比使用并行回火的集成方法至少快一个数量级，并且似乎在模型参数（即速率常数和细胞中分子的初始计数）的初始猜测中从随机开始提供全局最优解。所得的拟合优度chi(2)与使用并行回火的集成方法产生的解决方案相比大约减半，每个数据点的chi(2)仅为chi(2)/n = 2,708.05/953=2.84。拟合的模型集合对“细胞大小”代理的变化具有鲁棒性。通过微流体分离的单细胞之间没有细胞通信的拟合中性模型提供了证据，证明在6至36小时的光照/暗（L/D）或D/D实验中，在一个共同水平的随机细胞内噪声中只有一个随机共振。根据Kuramoto (K)测量，当光驱动的相位同步较强时，在远离随机共振的单细胞振荡中存在退化。随机时钟网络的速率常数与在10(7)个细胞的宏观尺度上确定的速率常数一致。
Stochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators of Neurosporacrassa. 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 chi(2) was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting chi(2) per data point was only 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 only one Stochastic 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 10(7) cells.