Critical dynamics in genetic regulatory networks: examples from four kingdoms.
Critical dynamics in genetic regulatory networks: examples from four kingdoms.
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DOI：
10.1371/journal.pone.0002456
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发表时间：
2008-06-18
期刊：
影响因子：
3.7
通讯作者：
Aldana M
中科院分区：
文献类型：
--
作者：
Balleza E;Alvarez-Buylla ER;Chaos A;Kauffman S;Shmulevich I;Aldana M
在生物体中，不同基因的协调表达对于在有机体可能受到的随机外部扰动下维持功能至关重要。为了应对这种外部变异性，遗传网络的全球动态必须具备两个核心属性。(A)它必须足够强大，以保证在广泛的外部条件下的稳定性，以及(B)它必须足够灵活，以识别和整合可能有助于有机体改变和适应不同环境的特定外部信号。这种稳健性和适应性之间的妥协已经在运行在有序和混沌之间的相变边缘的动力系统中观察到。这样的系统被称为关键系统。因此，临界性是动力系统的一种精确的、可测量的、具有良好特性的特性，它使生物体的稳健性和适应性共存成为可能。在这项工作中，我们研究了已报道的酿酒酵母、大肠杆菌和枯草杆菌基因转录网络的动态特性，以及黑腹葡萄球菌的片段极性基因网络和拟南芥的花发育网络。我们使用数百个微阵列实验来推断基因之间调控相互作用的性质，并将这些数据应用到遗传网络的布尔模型中。我们的结果表明，就目前可用的实验数据而言，正在研究的五个网络确实运行在接近临界点的位置。这一结果的普遍性表明，基因水平的临界性可能构成了一种基本的进化机制，它产生了我们观察到的周围动态强大的生命形式的巨大多样性。
The coordinated expression of the different genes in an organism is essential to sustain functionality under the random external perturbations to which the organism might be subjected. To cope with such external variability, the global dynamics of the genetic network must possess two central properties. (a) It must be robust enough as to guarantee stability under a broad range of external conditions, and (b) it must be flexible enough to recognize and integrate specific external signals that may help the organism to change and adapt to different environments. This compromise between robustness and adaptability has been observed in dynamical systems operating at the brink of a phase transition between order and chaos. Such systems are termed critical. Thus, criticality, a precise, measurable, and well characterized property of dynamical systems, makes it possible for robustness and adaptability to coexist in living organisms. In this work we investigate the dynamical properties of the gene transcription networks reported for S. cerevisiae, E. coli, and B. subtilis, as well as the network of segment polarity genes of D. melanogaster, and the network of flower development of A. thaliana. We use hundreds of microarray experiments to infer the nature of the regulatory interactions among genes, and implement these data into the Boolean models of the genetic networks. Our results show that, to the best of the current experimental data available, the five networks under study indeed operate close to criticality. The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us.
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影响因子：
11.6
作者：
Espinosa-soto, C;Padilla-Longoria, P;Alvarez-Buylla, ER
通讯作者：
Alvarez-Buylla, ER
DOI：
10.1209/0295-5075/2/10/001
发表时间：
1986-11-15
期刊：
EUROPHYSICS LETTERS
影响因子：
--
作者：
DERRIDA, B;STAUFFER, D
通讯作者：
STAUFFER, D
影响因子：
64.8
作者：
Lux, T;Marchesi, M
通讯作者：
Marchesi, M
DOI：
10.1016/j.physa.2007.05.050
发表时间：
2007-10-15
影响因子：
3.3
作者：
Karlsson, Fredrik;Hoernquist, Michael
通讯作者：
Hoernquist, Michael
DOI：
10.1049/ip-syb:20050079
发表时间：
2006-07-01
期刊：
IEE PROCEEDINGS SYSTEMS BIOLOGY
影响因子：
--
作者：
Chaves, M.;Sontag, E. D.;Albert, R.
通讯作者：
Albert, R.