Recording neural activities onto DNA

将神经活动记录到 DNA 上

• 批准号: 8547995
• 负责人: Edward S. Boyden
• 金额: $ 191.77万
• 依托单位: REHABILITATION INSTITUTE OF CHICAGO D/B/A SHIRLEY RYAN ABILITYLAB
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-26 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8547995
• 关键词: Achievement; Affect; Amplifiers; Area; Attention; Autistic Disorder; Back; Behavioral; Biological; Brain; Brain Diseases; Calcium; Cells; Clinical; Complement; Conscious; DNA; DNA Sequence; DNA-Directed DNA Polymerase; Data; Data Set; Development; Devices; Disease; Disease model; Dreams; Electrodes; Engineering; Epilepsy; Fostering; Funding; Generations; Goals; Healed; Health; Image; Individual; Ions; Joints; Lasers; Laws; Lead; Learning; Manuscripts; Methods; Mission; Molecular; Monitor; Mus; Neurobiology; Neurons; Neurosciences; Noise; Output; Perception; Polymerase; Property; Protein Engineering; Proteins; Public Health; Publications; Reading; Replication Error; Research; Signal Transduction; Talents; Techniques; Technology; Time; Transfection; Viral; Work; Writing; base; design; directed evolution; genome sequencing; healing; high risk; improved; in vivo; innovation; insight; instrumentation; molecular scale; nanoscale; nervous system disorder; neural patterning; novel strategies; public health relevance; relating to nervous system; research study; statistics; tool

DESCRIPTION (provided by applicant): Progress in neural recording is critical to understanding the brain and developing treatments for brain disorders. Current neural recordings can, at best, capture a few hundred interacting neurons. The number of recorded neurons is relatively small because current neural recording devices, such as electrodes, amplifiers, lasers, and cameras, are macroscopic. The objective of our research is to create neural recorders at the molecular scale, by writing neural activities onto DNA, like a molecular ticker tape. The device will consist of an engineered DNAP polymerase that can be cheaply synthesized and easily delivered to neurons, where it will write the temporal dynamics of activity of each neuron onto local DNA molecules, which can later be analyzed via increasingly cheap genome sequencing technologies. The long term goal of our research is to enable a paradigm shift, making recording instrumentation-free, easy to use, and scalable to arbitrary numbers of neurons. We will obtain the nanoscale recording device using three pipelines: (1) Polymerase design pipeline. We will search through different DNA polymerases to find a polymerase that makes many replication mistakes when ion concentrations increase, and thus when neurons are active. We will use directed protein engineering to add ion-sensitive domains. Lastly we will use high throughput protein directed evolution, to produce a polymerase with desirable properties. (2) Template design pipeline. We will design and deliver an engineered DNA template to the cell to be copied. We will utilize transfection, which is feasible but might not be convenient in some neuroscientific experiments, moving later towards viral template delivery methods, which may be simpler. (3) Statistics pipeline. The resulting DNA sequences need to be converted back into signals of neurobiological meaning. Such conversion needs to be precise, robust to various problems such as biological polymerase noise, and error-correcting. The approach is innovative, because it reinvents the concept of recording using molecular engineering to produce a device that is orders of magnitude smaller and arguably more versatile than comparable devices. The proposed research is significant, because it allows a whole range of new electrophysiological experiments. The approach will complement other emerging approaches that promise to lead to large dataset based neuroscience, e.g. connectomics. The resulting technique will be easyto- use and inexpensive, yet will promise to allow recording simultaneously from potentially arbitrary numbers of neurons, with temporal precision comparable to existing state-of-the-art calcium imaging. It promises massively increased amounts of neural data and entirely new approaches to asking deep questions about the way the brain works and how to cure disease of the brain.

描述（由申请人提供）：神经记录方面的进展对于了解大脑和开发脑部疾病的治疗方法至关重要。目前的神经记录最多只能捕获数百个相互作用的神经元。由于目前的神经记录设备，如电极、放大器、激光器、相机等都是宏观的，因此记录的神经元数量相对较少。我们研究的目标是通过将神经活动写入 DNA 来创建分子尺度的神经记录器，就像分子自动收报机磁带一样。该设备将由一种工程化的 DNAP 聚合酶组成，可以廉价合成并轻松递送到神经元，它将每个神经元活动的时间动态写入本地 DNA 分子，随后可以通过越来越便宜的基因组测序技术进行分析。我们研究的长期目标是实现范式转变，使记录无需仪器、易于使用，并且可扩展到任意数量的神经元。我们将使用三个管道获得纳米级记录装置：（1）聚合酶设计管道。我们将搜索不同的 DNA 聚合酶，以找到一种聚合酶，当离子浓度增加时，即当神经元活跃时，它会产生许多复制错误。我们将使用定向蛋白质工程来添加离子敏感结构域。最后，我们将使用高通量蛋白质定向进化来生产具有所需特性的聚合酶。 (2) 模板设计流程。我们将设计一个工程 DNA 模板并将其传送到要复制的细胞中。我们将利用转染，这是可行的，但在一些神经科学实验中可能不方便，稍后转向病毒模板传递方法，这可能更简单。 (3)统计管道。由此产生的 DNA 序列需要转换回具有神经生物学意义的信号。这种转换需要精确、稳健，能够解决生物聚合酶噪声和纠错等各种问题。这种方法是创新的，因为它重新发明了使用分子工程记录的概念，生产出比同类设备小几个数量级且可以说更通用的设备。拟议的研究意义重大，因为它允许进行一系列新的电生理学实验。该方法将补充其他新兴方法，这些方法有望带来基于大数据集的神经科学，例如神经科学。连接组学。由此产生的技术将易于使用且价格低廉，但有望允许同时记录可能任意数量的神经元，其时间精度可与现有最先进的钙成像相媲美。它承诺大量增加神经数据和全新的方法来提出有关大脑工作方式和如何治愈大脑疾病的深刻问题。