Code and data for "Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing bacteria"

Experimental data gathered and code used for the simulations employed in the manuscript "Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing bacteria".
In the "shift simulations" folder, you can find the simulation of a base model, which can be used to reproduce the oscillatory behavior induced by nutrient shifts. In addition, there is a code for the numerical computation of the steady-state conditions.
In the "CHI BIO DATA" folder, you can find the data gathered during the chi bio experiments.
In the "Microfluidic (30 degrees) data" folder, you can find the data gathered during the microfluidic experiments performed at 30 degrees.
For more information on the data and code, please refer to the method section of the paper.

Abstract
Current theories of bacterial growth physiology demonstrate impressive predictive power but are often phenomenological, lacking mechanistic detail. Incorporating such details would significantly enhance our ability to predict and control bacterial growth under varying environmental conditions. The "Flux Controlled Regulation" (FCR) model serves as a reference framework, linking ribosome allocation to translation efficiency through a steady-state assumption. However, it neglects ppGpp-mediated nutrient sensing and transcriptional regulation of ribosomal operons. We propose a mechanistic model that extends the FCR framework by incorporating three key components: (i) the amino acid pool, (ii) ppGpp sensing of translation elongation rate, and (iii) transcriptional regulation of protein allocation by ppGpp-sensitive promoters. Our model aligns with observed steady-state growth laws and makes testable predictions for unobserved quantities. Here, we show that during environmental changes, the incoherent feedback between sensing and regulation generates oscillatory relaxation dynamics, a behavior that we support by new and existing experimental data.

本数据集包含论文《耦合氨基酸池与核糖体池的非相干反馈可在生长细菌中引发阻尼振荡》（Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing bacteria）中所用模拟实验的采集数据与代码。
在「shift simulations」文件夹中，可获取基础模型的模拟脚本，用于复现营养物转移诱导的振荡行为；此外还包含稳态条件数值计算的代码。
在「CHI BIO DATA」文件夹中，可获取CHI BIO实验中采集的实验数据。
在「Microfluidic (30 degrees) data」文件夹中，可获取30摄氏度条件下开展的微流控实验采集的数据。
如需了解数据与代码的更多细节，请参阅论文的方法部分。

摘要
当前细菌生长生理学理论具备出色的预测能力，但大多仅为现象学描述，缺乏机制层面的细节。补充此类机制细节，将显著提升我们在多变环境条件下预测与调控细菌生长的能力。「通量调控模型（Flux Controlled Regulation，FCR）」是一个参考框架，它通过稳态假设将核糖体分配与翻译效率关联起来。但该模型忽略了ppGpp介导的营养物感知以及核糖体操纵子的转录调控过程。本研究提出了一个拓展FCR框架的机制模型，纳入三项核心组分：(i) 氨基酸池；(ii) ppGpp介导的翻译延伸速率感知；(iii) ppGpp敏感启动子介导的蛋白质分配转录调控。该模型与已观测到的稳态生长规律相符，同时可对未观测的生理量给出可验证的预测结果。本研究证实，在环境变化过程中，感知与调控之间的非相干反馈会引发振荡弛豫动力学行为，该结论得到了新采集与已有实验数据的支持。