Towards 3D in silico modeling of the sea urchin embryonic development

Cell division geometries as central organizers of early embryo development

Early cellular patterning is a critical step of embryonic development that determines the proper progression of morphogenesis in all metazoans. It relies on a series of rapid reductive divisions occurring simultaneously with the specification of the fate of different subsets of cells. Multiple species developmental strategies emerged in the form of a unique cleavage pattern with stereotyped division geometries. Cleavage geometries have long been associated to the emergence of canonical developmental features such as cell cycle asynchrony, zygotic genome activation and fate specification. Yet, the direct causal role of division positioning on blastomere cell behavior remain partially understood. Oriented and/or asymmetric divisions define blastomere cell sizes, contacts and positions, with potential immediate impact on cellular decisions, lineage specification and morphogenesis. Division positions also instruct daughter cells polarity, mechanics and geometries, thereby influencing subsequent division events, in an emergent interplay that may pattern early embryos independently of firm deterministic genetic programs. We here review the recent literature which helped to delineate mechanisms and functions of division positioning in early embryos.

3D+time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage

The Mediterranean sea urchin, Paracentrotus lividus, has been a powerful model to study embryonic development since the late 1800s. As a model, it has the advantage of having external fertilization, it can easily be manipulated experimentally, and it has semi-transparent embryonic stages, which makes it ideal for live imaging. Embryogenesis is a highly dynamic process with intrinsic variability. The reconstruction of cell dynamics and an assessment of such variability from in vivo observations has proven to be a challenge. Here, we provide an innovative methodology for manipulation and immobilization of embryos and their long-term 3D+time imaging. We then describe the twinning procedure that allows us to assess the variability and robustness of developmental processes. We demonstrate the reconstruction of cell lineages based on automated image processing and cell tracking using the BioEmergences workflow as well as the use of interactive visualization tools (Mov-IT software) for lineage validation, correction and analysis.

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis

With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

Development by three-dimensional approaches and four-dimensional imaging: to the knowledge frontier and beyond

Many advances have been taken on elucidating embryonic development and tissue homeostasis and repair by the use of experimental strategies that preserve the three-dimensional (3D) organization and allow quantitative analysis of images over time (four-dimensional). Ranging from the understanding about the relationship between blastomeres and the events that take place during gastrulation by the use of time-lapse imaging through 3D cultures that mimic organogenesis, the advances in this area are of critical value. The studies on embryonic development without disrupting the original architecture and the development of 3D organoid cultures pave a new avenue for unprecedented experimental advances that will positively impact the emergence of new treatments applying regenerative principles for both tissue repair and organ transplant.

Quantitative and in toto imaging in ascidians: working toward an image-centric systems biology of chordate morphogenesis

Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that they can be imaged in toto with fine subcellular detail using conventional microscopes and objectives. Unlike other model organisms with particularly small embryos, ascidians have a chordate embryonic body plan that includes a notochord, hollow dorsal neural tube, heart primordium and numerous other anatomical details conserved with the vertebrates. Here we compare the size and anatomy of ascidian embryos with those of more traditional model organisms, and relate these features to the capabilities of both conventional and exotic imaging methods. We review the emergence of Ciona and related ascidian species as model organisms for a new era of image-based developmental systems biology. We conclude by discussing some important challenges in ascidian imaging and image analysis that remain to be solved.