Quantitative analysis of the biological forces and their context in tissue patterning

生物体的形式和功能的规则被编码在基因组中。多年来，A 各种各样的方法已经被用来阐明基本的计划和管理机制 不同器官或结构的大小和形式。这些包括遗传策略，用于识别基因 控制发育事件的产品，以及提供分子见解的生物化学进展 在发育过程中个体细胞之间的交流是如何完成的。虽然信息 理论和数学建模已经在整合遗传和分子方面取得了进展， 发展，这些方法从根本上受到一个简单事实的限制， 指导这些应用（遗传学或生物化学）通常来自实验环境， 在体内发现的空间或时间的丰富性。 我的研究团队准备在Cold解决一个理论，定量和计算程序 Spring Harbor Laboratory（CSHL），重点是体内细胞成像和原位测序 基因表达和细胞谱系分析技术。在我的博士后期间， 培训，我开发了一种原位RNA测序技术，可以普遍用于确定 基因表达在全基因组范围内的空间和信息异质性。作为一个独立 研究者我已经采用了这项技术来监测发育中组织的基因表达。这些方法 能够同时测量环境中数千个单细胞中的基因表达模式， 一个发育中的细胞谱系。虽然概念简单，但这一重大进展将允许动态和时间 基因表达的变化与三维结构直接相关，使数学 在没有事先限制的情况下对关键发育过程进行建模。 首先，我们将重点了解基因表达模式的振荡，包括那些 由细胞周期介导，调节生长因子信号传导。具体来说，我们将确定周期性模式 的基因表达足以产生一个形态发生场，控制大小和形状， 开发结构或这些模式如何有助于这些过程在体内的鲁棒性。我们将 还确定了梯度相关的转录起始/延伸的分子机制， 直接RNA原位测序。振荡基因表达和形态发生梯度相关的 转录起始/延伸影响细胞命运定型干细胞的方面（在组织中重要 再生和稳态），这些方法可用于剖析多种细胞因子的作用。 体内的遗传途径。总之，我们有概念框架，生物学问题，前沿 技术和严格的科学环境，以更好地表征驱动组织的生物力 形式和功能的模式化和发展。 1

Rules specifying form and function of an organism are encoded in the genome. Over the years, a variety of approaches have been leveraged to elucidate the underlying programs and machinery that govern the size and form of different organs or structures. These include genetic strategies, employed to identify gene products that control developmental events, and biochemical advances that have provided molecular insights into how communication between individual cells during development is accomplished. While information theory and mathematical modeling have made inroads toward integrating genetic and molecular aspects of development, these approaches are fundamentally limited by the simple fact that most measurements that guide these applications (either genetic or biochemical) are often derived from experimental contexts that lack the spatial or temporal richness found in vivo.  My research team is prepared to address a theoretical, quantitative, and computational program at Cold Spring Harbor Laboratory (CSHL) with an emphasis on in vivo cellular imaging and in situ sequencing technologies for gene expression and cell lineage analysis during development. During my postdoctoral training, I developed an in situ RNA sequencing technology that can be generally employed to determine the spatial and informational heterogeneity of gene expression in a genome-wide manner. As an independent investigator I have adapted this technology to monitor gene expression in developing tissues. These methods enable the simultaneous measurement of gene expression patterns in thousands of single cells in the context of a developing cell lineage. While simple in concept, this major advance will allow dynamic and temporal changes in gene expression to be directly tied to three-dimensional architecture, enabling the mathematical modeling of key developmental processes in the absence of prior limitations. Initially, we will focus on understanding how oscillations in gene expression pattern, including those mediated by the cell cycle, modulate growth factor signaling. Specifically, we will determine if cyclical patterns of gene expression are sufficient to generate a morphogenic field that controls the size and shape of developing structures or how these patterns contribute to the robustness of these processes in vivo. We will also determine the molecular mechanisms of gradient-associated transcriptional initiation/elongation using direct RNA sequencing in situ. Both oscillatory gene expression and morphogen gradient-associated transcriptional initiation/elongation impact aspects of cell fate commitment stem cells (important in tissue regeneration and homeostasis) and these approaches can be used to dissect the contribution of multiple genetic pathways in vivo. In summary, we have the conceptual framework, biological questions, cutting-edge technologies, and rigorous scientific environment to better characterize the biological forces driving tissue patterning and development of form and function.   1