PhD project: Multi-scale computational analysis of embryonic variability in ascidians

A PhD project proposal to be carried out in Patrick Lemaire’s lab at CRBM, Montpellier, France, in tight collaboration with Grégoire Malandain, Morpheme INRIA team, Sophia-Antipolis, France. Funding is conditional upon selection by the CBS2 doctoral school‘s entrance jury.

Why study ascidians?

The embryonic development of ascidians, a group of marine invertebrates, is remarkably conserved, at the single cell level, between individuals of a given species and between species, even if they diverged up to 400 MY ago.  Ascidian genomes, however, evolve particularly rapidly. The remarkably simple and transparent ascidian embryos are thus ideal to study developmental systems drift and to identify constraints that could explain the exceptional evolutionary precision and stability of embryonic morphologies.

The proposed project

We propose a computational PhD project, which will use experimental data collected in the team or in public databases to characterise inter-individual and inter-species variability at the geometric, mechanical and transcriptional scales.

This project will involve the development of concepts and computer tools to study and measure, at each scale studied, the variability of different parameters (variability of cell lineages, cell lifetimes, orientation of cell division, pressures, surface and line tensions, gene expression, etc.). These studies will lead to a reflection on the concept of the average embryo and on its computational representation. The tools developed will open the way to the quantitative study of robustness to environmental and genetic perturbations, and to the identification of bridges between scales of analysis (search for co-varying parameters across scales).

What is available to start the project?

The project will benefit from the conceptual and methodological developments made over the last 10 years by the hosting teams and their collaborators (see references below). These breakthroughs (ASTEC, MorphoNet, Aniseed) place them in a unique position to analyse, experimentally and computationally, the variability of animal embryogenesis, whether natural or in response to environmental or experimental perturbations.

Using these advanced tools, we generated high resolution geometric and mechanical descriptions of 7 embryos of the ascidian Phallusia mammillata, over several hours of development and with a 2 minutes time resolution. You can view a short video highlighting this works.

These embryos and tools constitute a solid basis for the proposed PhD project. The embryo collection is currently expanding to include more WT Phallusia embryos as well as embryos cultured in response to environmental (temperature, salinity, pH) or genetic perturbations.

How to apply?

The ideal candidate will have successfully graduated from a Master’s programme in computer science, bioinformatics or physics recognized by France. S/He will have strong computational skills and some knowledge of developmental biology. A working knowledge of English (B2) is needed. There is no prerequisite in French.

To apply to the project, please contact P. Lemaire (patrick.lemaire[at]crbm.cnrs.fr) as soon as possible and by May 11, 2022 at the latest with a motivation letter, a CV and the names and contact details of 2 academic referees including the PhD supervisor.

References

Guignard L. *, Fiuza U.-M. *, Leggio B., Laussu J., Faure E., Michelin G., Biasuz K., Hufnagel L., Malandain G. #, Godin C. #, Lemaire P.# (2020) Contact-area dependent cell communications and the morphological invariance of ascidian embryogenesis. Science, 369 :6500 eaar5663

Dardaillon, J; Dauga, D; …; Dantec, C.#; Lemaire, P#. (2019) ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Res. 48(D1): D668-D675

Leggio, B; Laussu J; Carlier, A; Godin, C; Lemaire, P and Faure, E (2019) MorphoNet: An interactive online morphological browser to explore complex multi-scale data. Nat Commun. 10(1):2812

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