A Morphology and Gene Expression Atlas for Drosophila Embryogenesis

描述（由申请人提供）：动物包括复杂的、动态的、三维的细胞阵列，这些细胞在组织学类型、形状、大小、位置和其他特征方面彼此不同。这些差异以及由此产生的更高级的组织/形态结构，它们反过来产生，最终来自胚胎发生过程中发展的复杂的基因表达模式。深入了解这些复杂的，在形态和基因表达的定量变化将需要一个详细的，精确的描述形态和表达动力学在细胞分辨率。我们建议创建一个定量的，细胞分辨率的基因表达和形态学的胚胎发育的模型动物之一：果蝇。这一目标将扩展我们以前的工作，已经建立了一套活的和固定的胚胎成像和图像分析方法，提供了第一个定量描述的基因表达和形态在细胞分辨率的一个完整的早期阶段果蝇胚胎，并揭示了以前未知的功能，该系统的生物学。然而，在这些初步研究中分析的早期胚盘胚胎具有相对简单的结构，其由围绕蛋黄的约6000个细胞的单层组成。在胚盘阶段之后--在10小时的过程中--三个有丝分裂周期，大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幼虫器官的形成。为了准确地捕捉这种复杂性的巨大增加，我们建议对我们的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给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，这是可能的图像在整个果蝇胚胎发育的所有细胞，并建议一种方法来创建一个形态框架上的基因表达定量。在过去的二十年里，细胞分辨率图谱的可用性对线虫的分析是一个布恩。我们提出的更复杂的，定量的，果蝇胚胎发生的计算模型将不可避免地至少作为重要的资源，苍蝇社区，并将开辟基于数据的方式，组织形成和相关的基因调控网络的计算建模。 公共卫生相关性：我们的项目，以创建一个定量的，细胞分辨率的基因表达和胚胎发生的形态图将产生工具，这将显着推进基础生物学研究。将动物胚胎转换成其身体平面，细胞位置，细胞命运和组织位置的计算图谱，沿着基因表达的细胞分辨率图，将提供一个便携式解剖和表达图谱，可以由任何研究人员解剖和观察。这个电子胚胎图谱不仅是一个非常宝贵的教育工具，而且将允许3D解剖学的细胞分辨率解剖分析，将揭示调控途径，允许新型的计算系统生物学，它将整合解剖学与分子发育遗传学。

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.