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

规定有机体形式和功能的规则编码在基因组中。多年来，一个 各种方法已经被用来阐明治理的基本计划和机制 不同器官或结构的大小和形式。这些策略包括用于识别基因的遗传策略。 控制发育事件的产品，以及提供分子洞察力的生化进展 了解在发育过程中个体细胞之间的交流是如何完成的。当信息 理论和数学模型已经在整合遗传和分子方面取得了进展 开发，这些方法从根本上受到一个简单的事实的限制，即大多数测量 指导这些应用(无论是遗传的还是生化的)通常是从缺乏 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研究一个理论、定量和计算项目 斯普林港实验室(CSHL)，重点是活体细胞成像和原位测序 发育过程中的基因表达和细胞谱系分析技术。在我的博士后期间 经过培训，我开发了一种原位RNA测序技术，这种技术通常可以用来确定 基因组范围内基因表达的空间和信息异质性。作为一个独立的 研究人员I已经将这项技术应用于监测发育中组织中的基因表达。这些方法 允许同时测量上下文中数千个单个细胞中的基因表达模式 处于发育中的细胞谱系。虽然概念很简单，但这一重大进步将允许动态和暂时的 基因表达的变化直接与三维结构联系在一起，使数学 在没有先前限制的情况下对关键发展过程进行建模。 首先，我们将重点了解基因表达模式中的振荡，包括 通过细胞周期调节，调节生长因子信号传导。具体地说，我们将确定周期性模式 足以产生控制细胞大小和形状的形态发生场 发展中的结构或这些模式如何有助于这些过程的稳健性在体内。我们会 也确定了梯度相关的转录起始/延伸的分子机制 RNA原位直接测序。振荡基因表达与形态梯度相关 转录起始/延长对细胞命运承诺干细胞的影响(在组织中很重要 再生和动态平衡)，这些方法可以用来剖析多个 体内的遗传途径。总而言之，我们有概念框架、生物问题、前沿 技术和严谨的科学环境，以更好地表征驱动组织的生物力量 形态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