A Computational Framework for Mapping Long Range Genetic Circuits

描述(由申请人提供)：本申请涉及广泛的挑战领域：(06)使能技术和具体挑战主题：06-MH-103神经科学研究的新技术。开发基于软件(例如，信息学工具、数据分析算法的实施)、基于硬件(例如，仪器或设备)或基于生物学(例如，由条件基因表达或生物活性物质驱动)的神经科学研究技术。联系人：迈克尔·F·韦尔塔博士电话：301-443-1815电子邮件：mhuert1@mail.nih.gov建立大脑网络图是现代神经生物学和医学的主要挑战之一，尤其是遗传连接图。对社会情绪系统来说，这一需求最为明显，在这个系统中，回路的失调与最具破坏性的精神疾病、抑郁症、精神分裂症和自闭症有关。这项提议寻求部署下一代神经生物学技术和新的软件工具，以从长距离轴突投影的连续切片或边缘系统的接线图中生成针对基因的三维重建，在轴突水平和灵长类大脑的大小尺度上。这个软件将填补两个显著的空白，这两个空白严重阻碍了灵长类大脑电路图的生成。由于缺乏用于对齐连续切片和处理大型数据集的现有软件，当前的电路重建方法不能处理通过多个典型的~30？m切片的轴突投影。因此，尽管已经有了优雅的新兴方法来追踪轨迹，但目前的技术只允许对小鼠海马区的单个部分的细胞进行可视化，但阻止在系统水平上为关键问题提供答案。与其他皮质或皮质下结构的长距离联系涉及情绪或认知的调节，特别是在灵长类系统所需的规模上，目前还无法可视化。此外，目前还没有在轴突投射和DTI或MRI所定义的较大区域之间进行跳跃的程序。目前的提案利用了科学计算和成像研究所(SCI)图像重建和三维可视化专家(Tasdizen，Jones)最近(Anderson，2009)开发了视网膜三维神经电路和荧光图像重建(Roysam)的计算框架、非人灵长类大脑电路和神经解剖学专家(Angelucci，Hof)、动物和人类DTI/MRI(Hsu)专家以及轴突投影多色荧光成像专家(Korenberg，Angelucci)之间独特的多维合作。这一独特的合作项目将有助于维持两名初级调查人员和三名职业生涯早期的调查人员，并将在神经生物学和计算领域创造七个新的研究工作岗位。这四个目标将：1)以轴突分辨率生成恒河猴边缘系统(下丘脑-边缘目标的子集)神经肽投影的高信噪比多色荧光图像；2)获取400多个连续切片的图像并将其存储在大小为158 TB的镶嵌2？m堆栈中；3)将发现的精氨酸加压素和Williams综合征基因产物的下丘脑投影重建为一个连续的单一数据集；以及4)自动重建到达其目标的轴突路径。其目标是创造和整合这套新颖的软件和神经生物技术，以加速哺乳动物大脑的连接。这些技术将提供必要的关键缺失框架，用于图像采集、TB数据集的操作、连续切片重建、自动和手动轨迹跟踪、灵长类动物大脑规模的基因特定接线图或连接，以及弥合轴突投影与非人类灵长类动物MRI和DTI获得的高分辨率轨迹之间的差距。这项研究对公众健康的影响：建立大脑网络图是现代神经生物学和医学的主要挑战之一，特别是遗传连接图。对控制社会行为和情绪的大脑系统来说，这一需求最为明显。在这些系统中，神经回路的失调与最具破坏性的精神疾病、抑郁症、精神分裂症和自闭症有关，这些疾病加起来影响了1300多万美国人。创建了解这些大脑系统的解决方案将广泛加速解开许多在其他神经系统疾病中受到干扰的电路的连接，包括那些与帕金森氏症、阿尔茨海默氏症和成瘾有关的疾病。总而言之，我们正在创造的工具将通过提供与潜在大脑回路的遗传联系来改变精神疾病领域。这些知识将为预防、治疗和最终治愈精神疾病的新药靶点提供洞察力。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area: (06) Enabling Technologies and specific Challenge Topic: 06-MH-103 New technologies for neuroscience research. Develop technologies for neuroscience research that are software-based, (e.g., informatics tools, implementation of data analytic algorithms), hardware-based (e.g., instrumentation or devices), or biology-based (e.g., driven by conditional gene expression or bioactive agents). Contact: Michael F. Huerta, Ph.D., 301-443-1815, mhuert1@mail.nih.gov Establishing a network diagram of the brain is one of the major challenges of modern neurobiology and medicine, particularly a diagram of genetic connectivity. Nowhere is this need more clear than for the social-emotional system, where dysregulation of circuitry has been implicated in the most devastating mental illnesses, depression, schizophrenia and autism. This proposal seeks to deploy the next generation neurobiologic technologies and novel software tools needed to generate gene-specific 3-dimensional reconstructions from serial sections of long range axon projections or wiring diagrams of the limbic system, at the axon level and on the size scale of primate brain. This software will fill two striking gaps that have seriously hindered the generation of maps of primate brain circuitry. Blocked by lack of existing software for both aligning sequential sections and for handling large datasets, current circuit reconstruction methods cannot handle axon projections that travel through more than a single, typical ~30¿m section. Therefore, although there are elegant emerging approaches to tract tracing, current technology permits only visualization of cells in a single section of a mouse hippocampus but prevents providing answers to the critical questions at the systems level. The long range links to other cortical or subcortical structures involved in regulation of emotion or cognition, particularly at the scale needed for primate systems cannot yet be visualized. Moreover, there are no programs for making the leap between axon projections and larger tracts defined by DTI or MRI. The current proposal takes advantage of a unique multidimensional collaboration among the Scientific Computing and Imaging Institute (SCI) experts in image reconstruction and three-dimensional visualization (Tasdizen, Jones) who have recently (Anderson, 2009) developed a computational framework for 3-dimensional neurocircuitry of the retina and in fluorescence image reconstruction (Roysam), experts in non-human primate brain circuitry and neuroanatomy (Angelucci, Hof), experts in animal and human DTI/ MRI (Hsu), and experts in multicolor fluorescence imaging of axon projections (Korenberg, Angelucci). This unique collaborative project will help to maintain two junior investigators and three early career investigators, and will create seven new research jobs in the fields of neurobiology and computation. The four aims will: 1) Generate high signal- to-noise multicolor fluorescence images of neuropeptide projections in the macaque limbic system (hypothalamus- a subset of limbic targets) at axon resolution, 2) Acquire and store images of more than 400 serial sections in mosaic 2 ¿m stacks equal to158 terabytes, 3) Reconstruct the hypothalamic- projections found with arginine-vasopressin and a Williams syndrome gene product to a subset of limbic targets from serial images into a single continuous dataset, and 4) Automatically reconstruct axon pathways to their targets. The goal is to create and integrate this novel set of software and neurobiologic technologies that will accelerate wiring the brain of mammals. These technologies will provide the critical missing framework necessary for image acquisition, manipulation of terabyte datasets, serial section reconstruction, automatic and manual tract tracing, and gene specific wiring diagrams or connectomes at the scale of primate brains and for bridging the gap between axon projections and high resolution tracts obtained by MRI and DTI of non-human primates and humans. of this research to public health: Establishing a network diagram of the brain is one of the major challenges of modern neurobiology and medicine, particularly a diagram of genetic connectivity. Nowhere is this need clearer than for the brain system controlling social behavior and emotion, where dysregulation of circuitry has been implicated in the most devastating mental illnesses, depression, schizophrenia and autism that together affect more than 13 million Americans. Creating solutions to understand these brain systems will broadly accelerate unraveling the connectivity of many circuits that are disturbed in other neurologic diseases, including those involved in Parkinson's, Alzheimer's, and addiction. In summary, the tools we are creating will transform the field of mental illness by providing genetic links to the underlying brain circuitry. This knowledge will provide insights into new drug targets to prevent, treat, and ultimately cure mental illness.