Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

There
are two basic forms of animal development: mosaic (as found in roundworms and
sea squirts) and regulative (as found in amphibians and mammals). How might one
distinguish between each type of development? Using a four-dimensional spatial
representation (<i>x,y,z,t</i>), major
features of the developmental process are revealed. To establish the role of
mosaic mechanisms, we can map the cell division process to a computational
representation of <i>C. elegans</i>
embryogenesis using a directed, acyclic graph (DAG) and a differentiation code.
Mosaic development is identifiable by observing spatial localization of
progenitor and descendent cells. This three-dimensional compartmentalization
should be consistent with nesting in the cell lineage tree. Regulative
development should demonstrate spatial “smearing”, or deviations from the
compartmentalization of the mosaic process. In a complementary manner, complex
network statistics should confirm this by providing an approximation of embryo
geometry. Characterizing the spatial organization and geometry of embryos in
this way allows for heuristic indicators of developmental patterns both within
and between organisms.<br>All raw data used in this study are available at Github. <br>Lineage Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Lineage Tree DB, Differentiation Tree<br>Raw Data: https://github.com/balicea/DevoWorm/tree/master/Differentiation Tree Dataset. <br>All processed data (used in the analyses) are available from the Open Science Framework: https://osf.io/q9jvb/

动物发育存在两种基本模式：镶嵌型发育（见于线虫与被囊动物）与调节型发育（见于两栖类与哺乳类）。该如何区分这两类发育模式？借助四维空间表征（*x,y,z,t*），可揭示发育过程的核心特征。为明确镶嵌型发育机制的作用，我们可将细胞分裂过程映射至秀丽隐杆线虫（*C. elegans*）胚胎发生的计算表征模型，采用有向无环图（DAG）与分化编码进行构建。镶嵌型发育可通过观察祖细胞及其子代细胞的空间定位加以识别，这种三维区室化特征应与细胞谱系树中的嵌套结构相一致。调节型发育则会表现出空间“弥散”现象，或偏离镶嵌型发育的区室化模式。作为补充，复杂网络统计量可通过近似胚胎几何形态来验证这一差异。通过这种方式表征胚胎的空间组织与几何形态，可为物种内外的发育模式提供启发式识别指标。<br>本研究使用的所有原始数据均可在GitHub获取。<br>谱系树原始数据：https://github.com/balicea/DevoWorm/tree/master/Lineage Tree DB<br>分化树原始数据集：https://github.com/balicea/DevoWorm/tree/master/Differentiation Tree Dataset<br>所有用于分析的处理后数据均可通过开放科学框架（Open Science Framework）获取：https://osf.io/q9jvb/