Probing delays and memory in gene activation using a gene oscilloscope

使用基因示波器探测基因激活的延迟和记忆

• 批准号: 1033316
• 负责人: Narendra Maheshri
• 金额: $ 32万
• 依托单位: Massachusetts Institute of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1033316&HistoricalAwards=false
• 关键词: Probing; delays; memory; gene; activation

This NSF award by the Biotechnology, Biochemical and Biomass Engineering program supports the development and application of a novel tool, the 'gene oscilloscope', to measure the kinetics of gene activation at the single cell level. The 'gene oscilloscope' consists of a yeast strain containing observable, dynamically controllable input transcription factor and a fluorescent reporter as the observable output. Input/output behavior is extracted from movies of single cells grown in microfluidic devices. It can be used to examine the dynamics of simple components in a gene regulatory network. The intellectual merit of this work is to quantify delays and memory in the activation of a promoter using simple lumped kinetic models that connect model parameters to promoter architecture. This work will yield mechanistic insights by comparing how different features of promoters and activators affect kinetics. In addition, it will inform and update large scale in silico modeling efforts of gene networks aimed at understanding how changes in network components lead to qualitatively different dynamics, aberrant function, and disease states. Broader impacts: Apart from basic insights into transcriptional dynamics, this work should further the concept of a gene oscilloscope and potentially enable synthetic biologists and metabolic engineers to characterize the dynamical properties of transcriptional device 'parts'. Apart from traditional research opportunities this project has and will provide both graduates and undergraduates in the PI's lab, the gene oscilloscope serves as a foundation for a set of research projects within the undergraduate Chemical-Biological Engineering laboratory. The goal is to expose the next generation of bioprocess engineers and biologists to the importance of single cell analysis in biotechnology, which traditionally has treated cultures as monolithic.

生物技术、生物化学和生物质工程项目的NSF奖项支持开发和应用一种新的工具，即“基因显微镜”，以测量单细胞水平上的基因激活动力学。“基因示波器”由酵母菌株组成，该酵母菌株含有可观察的、动态可控的输入转录因子和作为可观察输出的荧光报告基因。输入/输出行为是从微流体装置中生长的单细胞的电影中提取的。它可以用来检查基因调控网络中简单组件的动态。这项工作的智力价值是量化延迟和记忆的启动子激活使用简单的集总动力学模型，连接模型参数启动子架构。这项工作将通过比较启动子和激活子的不同特征如何影响动力学来产生机理上的见解。此外，它还将为基因网络的大规模计算机模拟工作提供信息和更新，旨在了解网络组件的变化如何导致定性不同的动力学，异常功能和疾病状态。 更广泛的影响：除了对转录动力学的基本认识，这项工作应该进一步的概念，基因示波器和潜在的合成生物学家和代谢工程师表征的动态特性的转录设备的“零件”。除了传统的研究机会，该项目已经并将在PI的实验室提供研究生和本科生，基因示波器作为一套研究项目的基础在本科化学生物工程实验室。目标是让下一代生物工艺工程师和生物学家了解生物技术中单细胞分析的重要性，传统上将培养物视为整体。