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

Abstract

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.

High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years

“…Although the exact phylogeny of Tunicata remains controversial [ 15 , 55 – 57 ], most paleontological studies indicate that the diversification of Tunicata dates back to the early Cambrian (ca. 525 Mya) [ 58 ]. Thus, the precision of our cell lineage data opens an entirely new horizon for evolutionary analyses and interpretation.…”

Single-cell analysis of cell fate bifurcation in the chordateCiona

“…We compared the expression level from 64-cell through hatching larva of the TFs which were upregulated in muscle, mesenchyme and endoderm compared to their sibling cell types at their initial bifurcation. We find that these TFs generally fall into one of two categories: some are expressed for only a short time window whereas others show persistent and/or increasing expression ( Figure 5 The Ciona notochord has been intensively studied as a model for understanding tissue-specific gene expression and morphogenesis [63][64][65][66][67][68][69][70][71][72]. This is the first study to To analyze if these genes were in fact notochord specific, we extracted the average expression value of each of these genes in all of the other cell clusters at the 64-cell stage.…”

Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex

“…In toto live-imaging can visualize the movement of individual cells and their interactions with the surrounding cells within the whole developing tissue (Megason and Fraser, 2007;Veeman and Reeves, 2015;McDole et al, 2018). This would enable a direct assessment of non-cell-autonomous effects exerted by the neighboring cells on an individual cell or vice versa.…”