You L, Yin J
Department of Chemical Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691, USA.
Pac Symp Biocomput. 2001:532-43. doi: 10.1142/9789814447362_0051.
To explore how the genome of an organism defines its growth, we have developed a computer simulation for the intracellular growth of phage T7 on its E. coli host. Our simulation, which incorporates 30 years of genetic, biochemical, physiological, and biophysical data, is used here to study how the intracellular resources of the host, determined by the specific growth rate of the host, contribute toward phage development. It is also used to probe how changes in the linear organization of genetic elements on the T7 genome can affect T7 development. Further, we show how time-series trajectories of T7 mRNA and protein levels generated by the simulation may be used as raw data to test data-mining strategies, specifically, to identify partners in protein-protein interactions. Finally, we suggest how generalization of this work can lead to a knowledge-driven simulation for the growth of any virus.
为了探究生物体的基因组如何决定其生长，我们开发了一种计算机模拟程序，用于模拟噬菌体T7在其大肠杆菌宿主内的生长情况。我们的模拟程序整合了30年来的遗传学、生物化学、生理学和生物物理学数据，在此用于研究由宿主的特定生长速率所决定的宿主细胞内资源如何促进噬菌体的发育。它还用于探究T7基因组上遗传元件线性排列的变化如何影响T7的发育。此外，我们展示了由模拟程序生成的T7 mRNA和蛋白质水平的时间序列轨迹如何可以用作原始数据来测试数据挖掘策略，具体而言，用于识别蛋白质-蛋白质相互作用中的伙伴。最后，我们提出这项工作的推广如何能够促成针对任何病毒生长的知识驱动型模拟。
