EXTENSION OF THE CONKLIN NOMENCLATURE: HOW STEREOTYPED IS THE ASCIDIAN EMBRYO DEVELOPMENT?

The goal of this internship is to investigate the stereotypy of development in ascidian embryos, and to propose extensions of the Conklin nomenclature.

Tunicates are an appealing model for developmental biology for a number of reasons. It is the closest relative of vertebrates from a phylogenetic point of view [Delsuc, 2018]. The embryo development is highly reproducible (ie stereotyped) during the first stages of the embryogenesis in ascidians [Lemaire 2011], which is the largest group inside tunicates. This stereotypy allowed the development of nomenclatures [Kofold, 1893; Castle, 1896; Conklin, 1905] from optical microscopy observations, which provide unambiguous names for the embryo cells for the first stages of the development.

Current live microscopy techniques allow the acquisition of temporal sequences of 3D images with a spatio-temporal resolution high enough to follow embryo development at sub-cellular scale [Keller, 2013]. Among them, the light sheet microscopy [Krzic, 2012] allows to image developing embryos of ascidians from the very early stages to the gastrulation stage and beyond. On the one hand, a first study [Guignard, 2020] has already permits to extract cell characteristics and lineages for a dozen of embryos (of wild type ascidians), each acquisition being made of more than a hundred of 3D images. In addition, cells can be named in the first developmental stages, based on [Conklin, 1905]. Unpublished results demonstrate a strong reproducibility of cell naming with respect to geometrical (cell position), and topological (cell neighbourhood) considerations. This suggests that cell naming can be learnt from exemplars. On the other hand, the acquisition duration, that may go beyond the gastrulation, exceeds the capacities of the Conklin nomenclature. The difficulty arises from the fact that Conklin’s nomenclature is built upon the geodesic distance (on the embryo surface) towards the vegetal pole, which is no more applicable as soon divisions get internalized. Attempts have been done to pursue Conklin’s nomenclature, but only in specific tissues [Nicol, 1998a,b].

The goal of this internship is to investigate an automated extension of the Conklin nomenclature for the whole embryo. First, based on the existing segmented temporal series, the stereotypy of cell division will be assessed based on local neighbourhoods. Second, it will investigated whether it is possible, with respect to anterior cleavages, to name unambiguous the resulting daughter while preserving the geometric spirit of Conklin’s rules. These rules aimed at giving unambiguous names (numerical values) to the two cells resulting from a division, the smaller label being given to the cell closest to the vegetal pole. Anterior cleavages may be then transformed into a vector field, which indicates the numbering to be applied, and that can be extrapolated to name future divisions, while newly named divisions will help updating it.

Requirements:
1.	 Last year of master in computer sciences or applied mathematics
2.	Knowledge in image processing, preferably 3D
3.	Computer skills: programming (python), image processing/graphics libraries
4.	Written and spoken English

Practical information:
1.	This work takes place in a collaboration between CRBM (P. Lemaire’s team) and Morpheme, a joint research team between INRIA, CNRS and the University of Nice Côte d’Azur.
2.	This internship is located in Sophia Antipolis (French Riviera).
3.	This internship is remunerated.
4.	To candidate, please send a curriculum vitae, referees coordinates and a motivation letter to
•	Grégoire Malandain (Gregoire.Malandain@inria.fr)

Bibliography
Castle, WE (1896). The early embryology of ciona intestinalis, Flemming (L.). Bulletin of the Museum of Comparative Zoology, vol. XXVII, n. 7, pp 202-310
Conklin EG (1905). The Organization and Cell-Lineage of the Ascidian Egg. J. Acad., Nat. Sci. Phila. 13, 1.
Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP (2018). A phylogenomic framework and timescale for comparative studies of tunicates. BMC Biol. 16(1):39.
Guignard, L., Fiuza, U.-M., Leggio, B., Laussu, J., Faure, E, Michelin, G., Biasuz, K. Hufnagel, L., Malandain, G., Godin, C. and Lemaire, P. (2020). Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis. Science, 369(6500), eaar5663
Keller, PJ (2013). Imaging Morphogenesis:  Technological Advances and Biological  Insights. Science,  340(6137), 1234168+.
Kofold, CA (1893). On Some Laws of Cleavage in Limax. A Preliminary Notice. Proceedings of the American Academy of Arts and Sciences, Vol. 29,pp. 180-203
Krzic, U., Gunther, S., Saunders, T. E., Streichan, S. J. and Hufnagel, L. (2012). Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods 9, 730–733.
Lemaire, P. (2011). Evolutionary crossroads in developmental biology: the tunicates. Development 138, 2143–2152.
Nicol D, Meinertzhagen IA (1988a). Development of the central nervous system of the larva of the ascidian, Ciona intestinalis L. I. The early lineages of the neural plate. Dev Biol. 130(2):721-36.
Nicol D, Meinertzhagen IA (1988b). Development of the central nervous system of the larva of the ascidian, Ciona intestinalis L. II. Neural plate morphogenesis and cell lineages