Bio-QuBIC: Designer Gene Networks for Biocomputing Applications

eia - 0130331 - james.j。题目：生物计算应用的设计基因网络许多基本的细胞过程是由基因网络控制的，基因网络利用蛋白质- dna相互作用来调节功能。与蛋白质- dna相互作用相关的反馈回路的生物化学导致非线性效应，非线性分析工具变得非常宝贵。该项目涉及使用非线性动力学和分子生物学的技术来模拟、设计和构建生物计算应用的合成基因网络。在这里，生物计算被定义为细胞根据外部刺激做出决定的能力，在这种情况下，合成基因网络可以被视为活细胞的“控制器”。在这个项目中，一个快速切换的基因开关正在细菌细胞中建模和构建。基因开关是生物计算记忆存储的基本单元，可以在瞬态化学或热刺激下在两种稳定的表达状态之间翻转。此外，作为该项目的一部分，基于更复杂的逻辑门（即AND和OR门）的合成基因网络正在细菌细胞中设计、建模和构建。这些电路可以作为多个瞬态信号的传感器，并形成需要“if/then”结构的一般控制方案的基础。合成基因网络代表了迈向逻辑细胞控制的第一步，从而可以在DNA水平上操纵或监测生物过程。最终，编码成DNA的合成基因电路可能会被“下载”到细胞中，从而创造出一个“湿的”纳米机器人。这些细胞机器人可用于多种功能，包括体内生物传感、自主合成复杂生物材料、执行程序性细胞死亡，以及通过将生化事件转导到电子设备和从电子设备转导到微电子电路的接口。

EIA-0130331James.J. CollinsBoston UniversityTitle: Designer Gene Networks for Biocomputing ApplicationsMany fundamental cellular processes are governed by genetic networks which employ protein-DNA interactions in regulating function. The biochemistry of the feedback loops associated with protein-DNA interactions leads to nonlinear effects, and the tools of nonlinear analysis become invaluable. This project involves the use of techniques from nonlinear dynamics and molecular biology to model, design and construct synthetic gene networks for biocomputing applications. Here biocomputing is defined as representing the ability of cells to make decisions based on external stimuli, and in this context, synthetic gene networks can be viewed as "controllers" for living cells. In this project, a rapidly switching genetic toggle switch is being modeled and constructed in bacterial cells. The genetic toggle switch, which is a fundamental unit of biocomputing memory storage, can be flipped between two stable expression states using transient chemical or thermal stimuli. In addition, as part of this project, synthetic gene networks based on more complicated logic gates (i.e., AND and OR gates) are being designed, modeled and constructed in bacterial cells. These circuits can function as sensors of multiple transient signals, and form the basis for general control schemes requiring an "if/then" structure.Synthetic gene networks represent a first step towards logical cellular control, whereby biological processes can be manipulated or monitored at the DNA level. Ultimately, synthetic gene circuits encoded into DNA, might be "downloaded" into cells creating, in effect, a "wet" nano-robot. These cellular robots could be utilized for a variety of functions, including in vivo biosensing, autonomously synthesizing complex biomaterials, executing programmed cell death, and interfacing with microelectronic circuits by transducing biochemical events to and from the electronics.