CLARITY: fully-assembled biology

描述（由申请人提供）：研究具有局部精度和全局范围的完整系统是生物学中尚未实现的基本目标。例如，在对大脑的研究中，确定小块大脑连通性的努力虽然是开创性的，但受到这样一个事实的挑战：所得到的图谱几乎不可能被解释，因为所追踪的神经连接的全脑来源和目的地，以及在行为重大事件期间相应细胞的活动，都是未知的。相反，记录人口活动的分子、电生理或成像方法对于所记录细胞的全脑连接模式是不可知的，这在理解功能方面造成了巨大的空白。我们现在已经为解决这一挑战奠定了基础，通过将化学工程、计算光学和分子遗传学结合在一起，采用一种称为CLARITY的方法。我们将在脊椎动物中枢神经系统中开发这种方法，这对速度和复杂性具有挑战性，但随着我们为斑马鱼、啮齿动物和灵长类动物开发平台，CLARITY将适用于整个生物学。在目标1中，我们使用化学工程工具，将散射和不渗透的组织快速转化为完整但透明和大分子渗透（抗体兼容）的形式。在目标2中，我们开发了活动读出技术，旨在提取体积活动（即使在自由移动的哺乳动物中），然后将其与全局布线和分子表型联系起来。这种变革性的技术将允许快速提取系统信息（动力学、历史、布线和分子表型），从大型和完整的生物组织或器官中，无需拆卸，低至毫秒级和细胞分辨率。在Aim 3中，我们直接将CLARITY应用于行为小鼠和斑马鱼，快速获得与疾病相关的恐惧和奖励状态相关的每个细胞的全脑活动模式。这将是生物学上的一个里程碑式的成就，而且这些数据还将与同一大脑中这些细胞的完整分子和全局连接信息联系起来，所有这些信息都可以公开地进行挖掘/搜索。最后，在Aim 4中，我们设计并构建了斑马鱼，小鼠和灵长类动物的在线数据集，以广泛地服务于社区。计算基础设施将解决处理和公众访问收集的大量数据（所有生物学中最大的数据集之一）的问题，包括脊椎动物大脑中每个神经元的活动记录

DESCRIPTION (provided by applicant): Studying intact systems with both local precision and global scope is a fundamental unmet goal in biology. For example, in the study of the brain, efforts to determine connectivity of small patches of brain, though pioneering, are challenged by the fact that resulting maps will be nearly impossible to interpret because both the brainwide sources and destinations of traced wiring connections, as well as the activity of corresponding cells during behaviorally significant events, will remain unknown. Conversely molecular, electrophysiological, or imaging methods to record population activity are agnostic with regard to brain-wide wiring patterns of recorded cells, creating an enormous gap in understanding of function. We have now laid foundations for addressing this challenge, by integrating chemical engineering, computational optics, and molecular genetics in an approach termed CLARITY. We will develop the approach in the behaving vertebrate CNS, challenging for speed and complexity, but CLARITY will become applicable across biology as we develop platforms for zebrafish, rodents, and primates. In Aim 1, we bring chemical engineering tools to bear, rapidly transforming scattering and impermeable tissues into intact but transparent and macromolecule-permeable (antibody-compatible) form. In Aim 2, we develop activity-readout technology designed to extract volumetric activity (even in freely-moving mammals) that can then be linked to the global wiring and molecular phenotypes. This transformative technology will allow rapid extraction of systems information (dynamics, history, wiring, and molecular phenotypes) from large and intact biological tissues or organs without disassembly, down to millisecond-scale and cellular resolution. In Aim 3, we directly apply CLARITY to behaving mice and zebrafish, rapidly obtaining brain-wide activity patterns of every cell involved in disease-relevant states of fear an reward. This alone will be a milestone achievement in biology, but furthermore these data will also be linked to full molecular and global wiring information of those cells in the same brains, al publicly accessible for mining/searching. Finally in Aim 4 we design and build online datasets for zebrafish, mouse, and primate to broadly serve the community. Computational infrastructure will address handling and public access to the massive amount of data collected (among the largest datasets in all of biology), including the records of activity in every neuron in vertebrate brains during specific experiences linked to molecular and global wiring information. We are experienced with technology outreach and education, and will leverage this experience to achieve the full transformative mission of this new technology.