Rizzi Barbara, Peyrieras Nadine
CNRS-MDAM, UPR 3294 and BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France ; Institut des Systèmes Complexes, 57-59 rue Lhomond, Paris, France.
J Chem Biol. 2013 Sep 13;7(1):17-28. doi: 10.1007/s12154-013-0101-x.
Embryogenesis is a dynamic process with an intrinsic variability whose understanding requires the integration of molecular, genetic, and cellular dynamics. Biological circuits function over time at the level of single cells and require a precise analysis of the topology, temporality, and probability of events. Integrative developmental biology is currently looking for the appropriate strategies to capture the intrinsic properties of biological systems. The "-omic" approaches require disruption of the function of the biological circuit; they provide static information, with low temporal resolution and usually with population averaging that masks fast or variable features at the cellular scale and in a single individual. This data should be correlated with cell behavior as cells are the integrators of biological activity. Cellular dynamics are captured by the in vivo microscopy observation of live organisms. This can be used to reconstruct the 3D + time cell lineage tree to serve as the basis for modeling the organism's multiscale dynamics. We discuss here the progress that has been made in this direction, starting with the reconstruction over time of three-dimensional digital embryos from in toto time-lapse imaging. Digital specimens provide the means for a quantitative description of the development of model organisms that can be stored, shared, and compared. They open the way to in silico experimentation and to a more theoretical approach to biological processes. We show, with some unpublished results, how the proposed methodology can be applied to sea urchin species that have been model organisms in the field of classical embryology and modern developmental biology for over a century.
胚胎发生是一个具有内在变异性的动态过程，对其理解需要整合分子、遗传和细胞动力学。生物回路在单细胞水平上随时间发挥作用，需要对事件的拓扑结构、时间性和概率进行精确分析。整合发育生物学目前正在寻找合适的策略来捕捉生物系统的内在特性。“-组学”方法需要破坏生物回路的功能；它们提供的是静态信息，时间分辨率低，通常是群体平均数据，掩盖了细胞尺度和单个个体中的快速或可变特征。这些数据应与细胞行为相关联，因为细胞是生物活性的整合者。细胞动力学可通过对活生物体的体内显微镜观察来捕捉。这可用于重建三维+时间的细胞谱系树，作为模拟生物体多尺度动力学的基础。我们在此讨论在这个方向上取得的进展，从通过全时程延时成像随时间重建三维数字胚胎开始。数字标本为定量描述模式生物的发育提供了手段，这些标本可以存储、共享和比较。它们为计算机模拟实验以及对生物过程采用更具理论性的方法开辟了道路。我们展示了一些未发表的结果，说明所提出的方法如何应用于海胆物种，在过去一个多世纪里，海胆一直是经典胚胎学和现代发育生物学领域的模式生物。
