Amplitude metrics for cellular circadian bioluminescence reporters.
Amplitude metrics for cellular circadian bioluminescence reporters.
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DOI：
10.1016/j.bpj.2014.10.026
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发表时间：
2014-12
影响因子：
3.4
通讯作者：
Peter C. St. John;Stephanie R. Taylor;John H. Abel;F. Doyle
中科院分区：
文献类型：
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作者：
Peter C. St. John;Stephanie R. Taylor;John H. Abel;F. Doyle
来自细胞报告者的生物发光节律已经成为用于量化昼夜基因表达中的振荡的最常见方法。这些实验系统可以揭示由昼夜节律干扰引起的相位和幅度变化，并且可以与数学模型结合使用，以进一步深入了解时钟幅度调节的机制基础。然而，生物发光实验跟踪的平均输出从数以千计的嘈杂，非耦合振荡器，模糊了一个给定的刺激对遗传调控网络的直接影响。在许多情况下，尚不清楚振幅的变化是由于基因表达水平的个体变化还是由于群体一致性的变化。虽然这样的系统可以使用显式随机模拟建模，这些模型是计算繁琐，并限制分析洞察振幅变化的机制。因此，我们开发的理论和计算工具，以近似的平均表达水平在大人口的非相互作用的振荡器，并进一步定义计算效率的振幅响应计算来描述相位相关的振幅变化。在单细胞水平上，一个机械的非线性常微分方程模型被用来计算每个细胞的扰动的瞬态响应，而人口水平的动态捕捉耦合到一个相位密度函数的详细模型。我们的分析表明，在单个细胞或群体水平介导的幅度变化可以区分在组织水平的生物发光数据，而不需要单细胞测量。我们证明了该方法的有效性，通过模拟实验生物发光配置文件的光敏成纤维细胞，调和两个看似矛盾的研究的结论。该建模框架允许体外生物发光实验和计算机常微分方程模型之间的直接比较，并将导致更好地定量了解影响时钟振幅的因素。
Bioluminescence rhythms from cellular reporters have become the most common method used to quantify oscillations in circadian gene expression. These experimental systems can reveal phase and amplitude change resulting from circadian disturbances, and can be used in conjunction with mathematical models to lend further insight into the mechanistic basis of clock amplitude regulation. However, bioluminescence experiments track the mean output from thousands of noisy, uncoupled oscillators, obscuring the direct effect of a given stimulus on the genetic regulatory network. In many cases, it is unclear whether changes in amplitude are due to individual changes in gene expression level or to a change in coherence of the population. Although such systems can be modeled using explicit stochastic simulations, these models are computationally cumbersome and limit analytical insight into the mechanisms of amplitude change. We therefore develop theoretical and computational tools to approximate the mean expression level in large populations of noninteracting oscillators, and further define computationally efficient amplitude response calculations to describe phase-dependent amplitude change. At the single-cell level, a mechanistic nonlinear ordinary differential equation model is used to calculate the transient response of each cell to a perturbation, whereas population-level dynamics are captured by coupling this detailed model to a phase density function. Our analysis reveals that amplitude changes mediated at either the individual-cell or the population level can be distinguished in tissue-level bioluminescence data without the need for single-cell measurements. We demonstrate the effectiveness of the method by modeling experimental bioluminescence profiles of light-sensitive fibroblasts, reconciling the conclusions of two seemingly contradictory studies. This modeling framework allows a direct comparison between in vitro bioluminescence experiments and in silico ordinary differential equation models, and will lead to a better quantitative understanding of the factors that affect clock amplitude.