A Morphology and Gene Expression Atlas for Drosophila Embryogenesis

描述（由申请人提供）：动物由复杂的、动态的、三维的细胞阵列组成，这些细胞在组织学类型、形状、大小、位置和其他特征上彼此不同。这些差异——以及由此产生的高级组织/形态结构——最终源于胚胎发育过程中复杂的基因表达模式。要深入了解这些复杂的形态学和基因表达的定量变化，需要在细胞分辨率下对形态学和表达动态进行详细、精确的描述。我们建议创建一个定量的，细胞分辨率的基因表达和形态的所有胚胎发育的模式动物之一：果蝇黑腹。这一目标将扩展我们之前的工作，我们已经建立了一套活的和固定的胚胎成像和图像分析方法，提供了第一个在细胞分辨率下完整的早期果蝇胚胎的基因表达和形态的定量描述，并揭示了该系统以前未知的生物学特征。然而，在这些初步研究中分析的早期囊胚胚胎具有相对简单的结构，由围绕蛋黄的约6000个细胞组成的单层组成。胚层阶段后，经过10小时的三个有丝分裂周期，大的细胞运动和复杂的分化模式导致70多种细胞类型和所有主要的幼虫器官的形成。为了准确地捕捉这种复杂性的巨大增长，我们建议对成像和图像分割策略进行重大改进，建立基于学习的分类方法来将细胞分配到特定的细胞类型和组织，并开发更复杂的可视化工具来探索数据。我们的初步数据表明，在果蝇胚胎发生过程中，对所有细胞进行成像是可能的，并提出了一种方法来创建一个形态学框架，并在此框架上量化基因表达。在过去的二十年里，定性细胞分辨率图谱的可用性对秀丽隐杆线虫的分析是一个福音。我们提出的更复杂、定量的果蝇胚胎发生计算模型将不可避免地为果蝇群落提供至少同样重要的资源，并将为组织形成和相关基因调控网络的基于数据的计算建模开辟道路。

DESCRIPTION (provided by applicant): Animals comprise complex, dynamic, three dimensional arrays of cells which differ from each other in histological type, shape, size, location, and other characteristics. These differences-and the resulting higher order tissue/morphological structures that they in turn generate-ultimately derive from intricate patterns of gene expression that develop during embryogenesis. A deep understanding of these complex, quantitative changes in morphology and gene expression will require a detailed, precise description of morphological and expression dynamics at cellular resolution. We propose to create a quantitative, cellular resolution map of gene expression and morphology for all of embryo development for one of the most studied model animals: Drosophila melanogaster. This goal will extend our previous work which has established a suite of live and fixed embryo imaging and image analysis methods that have provided the first quantitative description of gene expression and morphology at cellular resolution of an intact early stage Drosophila embryo and have revealed previously unknown features about the biology of this system. The early stage blastoderm embryos analyzed in these initial studies, however, have a relatively simple structure that is comprised of a single layer of some 6000 cells surrounding a yolk. After the blastoderm stage-over the course of ten hours-three mitotic cycles, large cell motions and complex patterns of differentiation lead to the formation of over 70 cell types and all major larval organs. To accurately capture this great increase in complexity, we propose to make major improvements in our imaging and image segmentation strategies, establish learning based classification methods to assign cells to specific cell types and tissues, and develop more sophisticated visualization tools to allow exploration of the data. Our preliminary data show that it is possible to image all cells throughout Drosophila embryogenesis and suggest a way to create a morphological framework on which to quantitate gene expression. The availability of a qualitative cellular resolution atlas has been a boon to the analysis of C elegans over the last twenty years. Our proposed more sophisticated, quantitative, computational model of Drosophila embryogenesis will inevitably be at least as significant resources to the fly community and will open the way for data based, computational modeling of tissue formation and the associated gene regulatory networks. PUBLIC HEALTH RELEVANCE: Our project to create a quantitative, cellular resolution map of gene expression and morphology of embryogenesis will produce tools which will significantly advance basic biological research. Converting an animal embryo into a computational atlas of its body plan, cell positions, cell fate and tissue locations, along with a cellular resolution map of gene expression, will provide a portable anatomical and expression atlas that can be dissected and observed by any researcher. This electronic embryonic atlas, will not only be an invaluable educational tool, but will allow cellular resolution anatomical analyses of anatomy in 3D, will shed light on the regulatory pathways, allow new types of computational systems biology and it will integrate anatomy with molecular developmental genetics.