The circulation of cerebrospinal fluid (CSF) plays pivotal roles for body axis formation and brain development. During embryogenesis, CSF is rich in particles and proteins and flows bidirectionally in the central canal. The origins of bidirectional flow and its impact on development are unknown. Experiments combined with modeling and simulations demonstrate that the bidirectionality of CSF flow is generated locally by caudally-polarized motile cilia confined to the ventral wall of the central canal. Such active bidirectional flow of the CSF accelerates the long-range transport of particles propagating rostrally and caudally. In addition, spontaneous muscle contractions increase local CSF flow and consequently enhance long-range transport of extracellular lipidic particles. Focal ablation of the channel connecting brain ventricles to the central canal reduces embryo length, indicating that long-range transport contributes to embryonic growth. Our study also demonstrates that at this early stage, motile cilia ensure the proper formation of the central canal.

Figure1_CSFFlow

Code to analyze videos of beads flowing in CSF to compute the CSf flow profile /TestFile / Dataset of all profiles extrema with code to plot them similarly to what is performed in figure 1

transparent_reporting

Transparent reporting from eLife

Figure2_Cilia

Code to analyze dynamics of motile cilia from spinning disk fluorescence imaging + dataset of analyzed cilia and test file. According to figure 2 of the article

Figures2And4_DiameterCentralCanal

This .zip contains the datapoints of central canal diameter for WT embryos and various ciliary mutants, as well as the Matlab code to generate the plots in fugres 2 and 4. It also contains the code to perform the semi-automatic measurement of the central canal diameter, and the entire dataset (Confocal 3-D imaging of a dye filling the central canal) for Foxj1a vs WT siblings measurements.

Figure5_FlowVsContraction

Datapoints of Flow increase vs contraction strength associated to last panel of figure 5

Figure7_Funnel

Datapoints of funnel diameter and length associated with the first panels of figure 7

Figure7_Growth

large field images of Wt larvae 30 hours after ablation of central canal at embryonic stage. The . zip also contains the datapoints of length and angle of all embryos, as well as the Matlab code to reproduce associated panels in figure 7

Github directory with all the codes used in the article

Figure3_VelocityProfile

In order to access and plot the data corresponding to the velocity profiles and streamlines in Figure 3. Theoretical and numerical predictions are compared to a superposition of in vivo measured velocity profiles.

Figure6_Simulations

Data and codes enabling to reproduce the panels B and C1 of the figure 6, representing numerical simulations accounting for transport of particles coupling diffusion and convection in a model central canal.

Figure6_Transport

Datapoints and theoretical curve related to Taylor-Aris diffusion and long-range transport measurements.

Figure2_Cilia

Code and test file to analyze cilia motility in the central canal of Tg:B-actin arl13-GFP 30 hpf embryos.

Figure8_Growth_Revised

large field images of Wt larvae 30 hours after ablation of central canal at embryonic stage. The . zip also contains the datapoints of length and angle of all embryos, as well as the Matlab code to reproduce associated panels in figure 7
Figure8_Growth.zip

Figure7_Canals

2Photon Imaging datasets of injected dyes and immunohistochemistry revealing the 3 canals connecting the brain ventricles to the central canal. The full dataset is shared as .sld files (can be opened with Fiji) as well as a few .tif files with regions of interest. The measurement of the length and diameter of the diencephalospinal canal can be found in this dataset as well. These observations and measurements are associated with figure 7 of the main manuscript
Empty.zip