Electrical and Computer Engineering Department, Concordia University, 1455 Blvd. De Maisonneuve Ouest, Montreal, H3G 1M8, Quebec, Canada.
Département de génie logiciel et des technologies de l'information, École de Technologie Supérieure, 1100 Notre-Dame St W, Montreal, H3C 1K3, Quebec, Canada.
Biosystems. 2024 Dec;246:105281. doi: 10.1016/j.biosystems.2024.105281. Epub 2024 Aug 2.
Building on and extending existing definitions of robustness and evolvability, we propose and utilize new formal definitions, with matching measures, of robustness and evolvability of systems with genotypes and corresponding phenotypes. We explain and show how these measures are more general and more representative of the concepts they stand for, than the commonly used/referenced measures originally proposed by Wagner. Further, a versatile digital modeling approach (BNK) is proposed that is inspired by NK systems. However, unlike NK systems, BNK incorporates a genotype and a phenotype, in addition to fitness. We develop and apply an Evolutionary Algorithm to a BNK-modeled system to find different types of perfect oscillators. We then map the resulting oscillating systems to possible genetic circuit realizations. Continuing with the synthetic biology theme, we also investigate the effect of noise in DNA synthesis on the predicted functionality of a DNA-based biosensor (i.e., its robustness), and we carry out a theoretical assessment of the evolvability of different types of ribozymes, undergoing directed evolution.
在现有稳健性和可进化性定义的基础上，我们提出并利用新的形式定义，以及与之匹配的度量方法，用于具有基因型和相应表型的系统的稳健性和可进化性。我们解释并展示了这些度量方法比 Wagner 最初提出的常用/参考度量方法更通用，更能代表它们所代表的概念。此外，还提出了一种受 NK 系统启发的通用数字建模方法（BNK）。然而，与 NK 系统不同的是，BNK 除了适应度之外，还包含基因型和表型。我们开发并应用了一种进化算法到 BNK 模型系统中，以找到不同类型的完美振荡器。然后，我们将产生的振荡系统映射到可能的遗传电路实现。继续合成生物学的主题，我们还研究了 DNA 合成中的噪声对基于 DNA 的生物传感器（即其稳健性）预测功能的影响，并对经历定向进化的不同类型核酶的可进化性进行了理论评估。
