论文标题

部分可观测时空混沌系统的无模型预测

Resource competition in Three-gene-motif & Emergence of Feed-forward response: A Spatiotemporal Study

论文作者

Chakraborty, Priya, Roy, Ushasi, Ghosh, Sayantari

论文摘要

众所周知,在非线性动力学系统中具有几种重要含义,经常发生在基因表达基序中,并且在实验和数学上进行了很好的探索。但是,由于对核糖体,ATP,转录因子,tRNA等和相关效应等资源的要求,遗传回路的组成部分的依赖性至关重要,这在数学模型中通常被忽略。在资源有限的环境中,两个显然没有连接的基因可以争夺其各自表达的资源,并可能表现出间接的监管联系。因此,由于资源竞争,系统中完全产生了紧急响应。在这项工作中,我们已经展示了如何在三基因途径中考虑资源竞争,如何重新创建馈送前循环(FFL)的响应(FFL)。探索具有时间和时空稳定性分析的遗传系统,已经观察到有趣的瞬态和稳态反应。本文探讨的遗传基准显示了常规FFL结构的许多特征,例如响应延迟和脉冲产生。最有趣的是,在二维细胞排列中,还观察到了输入信号浓度梯度下的特征模式形成。这项研究指出了合成和细胞系统中更大的研究和探索领域,这些领域将揭示系统依赖性的新颖控制思想和独特的行为变化。

Feed-forward dynamics, which is well-known to have several important implications in nonlinear dynamical systems, frequently occurs in gene expression motifs, and has been well explored experimentally and mathematically. However, dependency of the components of a genetic circuit upon its host, due to the requirement for resources like ribosome, ATP, transcription factors, tRNA, etc., and related effects are of utmost importance, which is commonly ignored in mathematical models. In a resource-limited environment, two apparently unconnected genes can compete for resources for their respective expression and may exhibit indirect regulatory connection; an emergent response thus arises in the system completely because of resource competition. In this work, we have shown how the responses of the feed-forward loop (FFL), a well-studied regulatory genetic motif, can be recreated considering the resource competition in a three-gene pathway. Exploring the genetic system with temporal as well as spatiotemporal stability analysis, interesting transient and steady-state responses have been observed. The genetic motifs explored in this paper show many of the characteristic features of the conventional FFL structure, like response delay and pulse generation. Most interestingly, in a two-dimensional cellular arrangement, characteristic pattern formation under a concentration gradient of input signals have also been observed. This study pinpoints a larger area of research and exploration in synthetic and cellular systems, which will reveal novel controlling ideas and unique behavioral changes in the system for its context dependencies.

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