了解植物生物钟的补充方法
Complementary approaches to understanding the plant circadian clock
摘要：
生物钟是一种振荡的遗传网络，帮助生物体适应24小时的昼夜循环。绿色的Tauri Ostreococcus tauri的时钟是迄今为止发现的最简单的植物时钟。作为一个实验系统，它的许多优点有利于测试计算预测。我们提出了一个模型的Ostreococcus时钟的随机过程代数生物PEPA，并利用其映射到不同的分析技术，如常微分方程，随机模拟算法和模型检查。该系统的分子数量少，测试了微分方程连续近似的极限。我们研究连续确定性和离散随机方法之间的差异。随机模拟和模型检查使我们能够制定新的假设系统的行为，如在恒定的光照条件下，在单细胞中的自我维持振荡的存在。我们研究如何在模型检查的背景下对黎明和黄昏的时间进行建模，我们使用模型检查来计算关键生化物质的概率分布如何随时间变化。这些表明表达水平的相对变化在峰值表达时最小，使得峰值时间成为最佳实验阶段标记。在这些分析的基础上，我们使用进化系统生物学的方法来研究mRNA降解速率的变化如何影响可能影响适应性的关键蛋白质的阶段。我们探讨如何强大的生物钟是对这种潜在的突变变化，其基础生物化学。我们的工作表明，多种方法可以更全面地了解时钟。
英文摘要：
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
