How does regeneration differ from development?

Marie Curie PhD fellowship

Deadline for applications:   31 March 2023
Expected starting date:        1 October 2023
A 3-year PhD fellowship in regenerative biology is available at the Institut de Génomique Fonctionnelle de Lyon (IGFL) in France. The fellowship is funded by the Marie Curie doctoral network REGENERATE-IT.

Thesis/research topic

The research project will focus on understanding to what extent regeneration mirrors development. Our team has recently established transgenic, live imaging, and genomics approaches to study leg regeneration in the crustacean Parhyale hawaiensis (Paris et al. 2022). Parhyale can regenerate their legs throughout their lifetime. The regenerated legs are faithful replicas of the original legs generated during development (Almazan et al. 2022), but the transcriptional and cellular dynamics associated with leg development and regeneration are significantly different (Sinigaglia et al. 2022 and unpublished). These observations suggest that identical structures could be generated by distinct mechanisms. The recruited fellow will have the opportunity to probe this question using molecular genetics, imaging and genomics resources established in our team.
Different projects can be envisaged in this context, depending on the candidate's skills and interests, including:
1) Discovering to what extent the same genetic instructions are used to generate a leg during embryonic development and regeneration, by identifying the cis-regulatory elements of key patterning genes and comparing their activity during development and regeneration in transgenic animals.
2) Reconstructing putative gene regulatory networks (GRNs) operating during leg development and regeneration based on bioinformatic analyses of single-cell RNAseq and chromatin profiling data, validating selected nodes, and comparing their roles in development and regeneration with in vivo experiments.
3) Identifying the progenitors of different cell types during regeneration, based on the reconstruction of cell trajectories using snRNseq data, the establishment of Brainbow-like labeling tools, live microscopy and cell tracking.
Our experimental model, the crustacean Parhyale
A regenerating leg, a few days after amputation
The leg regeneration blastema consists of a few hundred cells

Work environment

The recruited  fellow will join the Comparative Developmental Biology and Regeneration team of the Institut de Génomique Fonctionnelle de Lyon (IGFL), located at the campus of the École Normale Supérieure de Lyon in the south of Lyon, France. The IGFL offers a stimulating scientific environment, focusing on the interfaces of animal development, physiology and evolution. The research team is international and the working language is English. (Speaking French is not required.)
The fellow will also be part of the wider community of fellows in the REGENERATE-IT doctoral network, comprising 12 laboratories across Europe. Fellows will participate in the training activities organized by the network, including secondments, in which s/he will be hosted for research/training visits in a partner laboratory.
The fellow will be enrolled as a PhD student in the École Normale Supérieure de Lyon, and will be co-supervised by Michalis Averof and Mathilde Paris.

Training, meetings and research exchanges

The fellow will receive training in molecular and developmental genetics, microscopy and genomics by the host lab, in the context of the research project, as well as training in regenerative biology in the context of the REGENERATE-IT doctoral network. The training will be adapted to the needs of the fellow and the selected project (see above).
This fellowship will involve periods of training/research in the laboratories of other REGENERATE-IT partners and participation in yearly meetings and summer schools organized by the network, to take full advantage of the wide range of expertise available in the network. The fellow will have opportunities to develop presentation, writing and other transferable skills, and to participate in outreach activities.

Eligibility / Qualifications

Applicants should have a Masters degree in science, preferably  in the molecular biosciences (molecular, cellular and developmental biology, genetics, or genomics). Practical experience in developmental biology, genetics, microscopy, genomics or bioinformatics will be appreciated. Strongly motivated students from other disciplines (e.g. physics) are also encouraged to apply.

Applicants should be able to communicate well in English.

Candidates of all nationalities may apply, but they must not have resided or carried out their main activity (work, studies, etc.) in France for more than 12 months in the 3 years immediately prior to their appointment (short stays such as holidays are not taken into account).

Applicants should submit a motivation letter and a CV.
IGFL, the host institute, located in the south of Lyon
Lyon is a historic vibrant city of ~1 million
View from IGFL's 3rd floor, where our lab is located
Marie Curie doctoral network meeting
Join our team! (team photo from 2020)