A Morphology and Gene Expression Atlas for Drosophila Embryogenesis

描述(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--以及由此产生的更高层次的组织/形态结构--最终源于胚胎发育过程中复杂的基因表达模式。要深入理解这些复杂的、定量的形态和基因表达变化，需要详细、准确地描述细胞分辨率下的形态和表达动态。我们建议为研究最多的模式动物之一的黑腹果蝇创建一个定量的、细胞分辨率的基因表达和形态图谱，用于所有胚胎的发育。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，这些方法首次提供了完整早期果蝇胚胎细胞分辨率下的基因表达和形态的定量描述，并揭示了该系统生物学上以前未知的特征。然而，在这些初步研究中分析的早期胚泡胚胎的结构相对简单，只有一层约6000个细胞围绕着一个卵黄。在胚胎期之后--超过10小时的过程--三个有丝分裂周期，大的细胞运动和复杂的分化模式导致形成70多种细胞类型和所有主要的幼虫器官。为了准确捕捉这种复杂性的大幅增加，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。我们的初步数据显示，有可能对整个果蝇胚胎发育过程中的所有细胞进行成像，并提出了一种方法来创建一个量化基因表达的形态框架。在过去的二十年里，定性细胞分辨率图谱的出现对线虫的分析是一个福音。我们提出的更复杂的、定量的、计算的果蝇胚胎发生模型将不可避免地至少作为苍蝇群落的重要资源，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。 与公共卫生相关：我们的项目是创建一个量化的胚胎发生基因表达和形态的细胞分辨率图，这将产生显著促进基础生物学研究的工具。将动物胚胎转化为其身体平面、细胞位置、细胞命运和组织位置的计算图谱，以及基因表达的细胞分辨率地图，将提供一个便携式的解剖和表达图谱，任何研究人员都可以解剖和观察。这一电子胚胎图谱不仅将是一种无价的教育工具，而且将使细胞解析解剖学在3D中进行，将揭示调控途径，允许新型计算系统生物学，并将解剖学与分子发育遗传学相结合。

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.