Zenlabpasteur.bsky.social

This is a phenomenal story going from a classic genetic mystery to a sophisticated molecular mechansims, and another example of what Barbara McClintock predicted: transposons re-shape the genome in relevant ways

Intriguing set of observations on how ‘dual-aggregate gastruloids’ lead to the emergence of foregut-pharyngeal mesoderm co-development and patterning www.biorxiv.org/content/10.6... #gastruloids #MustRead

The final version of the paper presenting our tool EpiCure is now online: journals.biologists.com/dev/article/... !! Thanks again to all collaborators in this project

The last version of our EpiCure tool is now out in @dev-journal.bsky.social, a user friendly Napari plugin for epithelial segmentation curation. A bit thanks to @gaellel.bsky.social for carrying all along this joint department effort (check the details below). Feel free to use it and expand it !

Happy to share our last work on mitotic bookmarking where we describe a new role for extensively studied TFs. Heroic effort by first author Inma over many years. genesdev.cshlp.org/content/earl...

Two-year post-doctoral position available in zebrafish developmental neurobiology in the Bally-Cuif and Arimondo labs at Institut Pasteur, Paris, France

In zebrafish, neural stem cells keep producing neurons throughout life. Pasteur scientists reveal how Notch3 signaling coordinates neighboring stem cells to maintain this balance, insights relevant to brain tumours. www.pasteur.fr/en/research-... @natcomms.nature.com #Neuroscience #StemCells

Huge congrats @gaellel.bsky.social !!!! We are soooo proud of you !!!

#TalentsCNRS 🏅 Le CNRS décerne ses médailles de cristal et cristal collectif 2026, récompensant des femmes et des hommes ayant contribué à l’avancée des savoirs et à l’excellence de la recherche française. Félicitations 👏 👉 www.cnrs.fr/fr/actualite... 👉 www.cnrs.fr/fr/actualite...

After a quite long process, we are happy to share the last version of our article describing unexpected results regarding the coupling between local cell death and proliferation (heroic revision effort from @ralitzastaneva.bsky.social ) urldefense.com/v3/__https:/...

The importance of history, clarity on what we generate in a dish compared to the ground truth. The resourceful David Turner @gastruloids.bsky.social, initiated students on reproducible gastruloid generation and A-P extension. And now, into the 2nd week...

Happy to share the heroic effort of @gaellel.bsky.social to reduce our segmentation pain through EpiCure (Epithelial Curation), a napari plugin easing the curation of epithelial segmentation developed with several groups of @devstempasteur.bsky.social. www.biorxiv.org/content/10.6... See more 👇

Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

Bravo Liza, Brendan and colleagues for the elegant work on multiple live imaging strategies to untangle mechanisms of muscular dystrophy! www.nature.com/articles/s41...

🎖️Toutes nos félicitations à Sylvie Rétaux, cheffe de l'équipe DECA à NeuroPSI, qui a été nommée au grade de Chevalier de la Légion d’Honneur !

The call for abstracts is open to participate in the Ascona conference on "Neurogenesis from development to adulthood in health and disease" !

📣 Register to the 13th Advances in Stem Cell Biology Course #ASCBcourse at the @pasteur.fr @pasteuredu.bsky.social. Hands-on training in different models, embryonic stem cells, iPS cells and much more on #StemCells, #organoids. 🕘June22-July03, 2026 👉 shorturl.at/PyUHi

Great science & fruiful discussions last Friday the 14th Nov. around "the physics of Stem cells" , the 2025 Stem Cell Initiative & QBio joint symposium. An honour to have Meryem Baghdadi & David Brückner as keynote speakers, who gave inspiring talks. 🙏🙏 to all our speakers & poster presenters.

⌛1 month left to apply – 2025 PPU call for candidates We invite you to discover 4 Develpmental & Stem Cell Biology projects and 3 Immunology projects👇 🕰️Application deadline: October 20, 2025 📍Program starts: October 2026 Discover all the projects (50+) & apply: www.pasteur.fr/en/education...

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊 Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

Pathway to Independence – an interview with Joaquín Navajas Acedo. In this interview, @mads100tist.bsky.social talks about about his research vision, zebrafish and the importance of community: journals.biologists.com/dev/article/...

New preprint out! Novel transgenic lines directly read out Notch3 signaling in situ, and reveal how adult neural stem cells coordinate quiescence and stemness by integrating spatiotemporal information from Delta and Jagged ligands. Read more: doi.org/10.1101/2025...

Engineer position, 12 months starting Oct. 1st, 2025, to study the role of NOTCH3 in human iPSC-derived neurogenesis models. Solid previous expertise required in cell culture, notably iPSCs, and organoid generation. Send CV, motivation letter and reference letter(s) to laure.bally-cuif@pasteur.fr

New call for research Group Leaders at Institut Pasteur Paris !

Just published in Development (@biologists.bsky.social): doi.org/10.1242/dev....

On Mon 18/11, we held a mini symposium on the novel perspectives in human embryo research @institutpasteur. Lively discussions thanks to our prominent speakers/chair Thanks to Nicolas Rivron; Alain Chédotal; Cécile Martinat; Ken McElreavey; Bernadette De Bakker and the chair Alfonso Martinez Arias

This also draws yet another parallel between physiological regulation stem cell pools and oncogenesis, which has been referred to as a process through which cells become “asocial” and cease to coordinate with their neighbors (18/18)

Although we were not able to identify what advantage this confers for NSC homeostasis, this non-canonical maintenance of Notch effectors illustrates different scales of quiescence regulation with some cells seemingly being able to listen less to their neighbors (17/18)

In vivo experiments confirmed that expression of nr2f1b in zebrafish NSCs is associated with a weaker response to Notch inhibition and functional experiments with morpholinos or electroporations of nr2f1b confirmed its ability to decrease sensitivity to Notch inhibition. (16/18)

Interestingly NR2F1 had previously been identified as a regulator of Notch signaling in the mouse inner ear (journals.biologists.com/dev/article/...), with downregulation of Notch effectors in NR2F1 knock-out mutants (15/18)

Using a gradient boosting method derived from SCENIC applied to both control and treated cells, we identified NR2F1/Coup-TF1 in sillico as a putative regulator enabling this resistance to Notch inhibition. (14/18)

Finally, we also identified that one cluster of cells barely responded to Notch inhibition, maintained expression of Notch effectors and did not upregulate genes associated with NSC activation. (13/18)

Although there are obvious differences between parenchymal astrocytes in mouse and astrocyte-like RGs in zebrafish, this suggests that comparative studies focusing on these cells might help better understand how to promote brain regeneration. (12/18)

The reported properties of the induced activation of these cells indeed shared similarities with that of astrocyte-like NSCs in the zebrafish pallium, such as participation in regeneration or reliance on Notch signaling (11/18)

Harmonizing the different reports of cell classification led us to consider that the cells that had been described as latent NSCs under different names in different publications were in fact likely the same population of parenchymal astrocytes close to the lateral ventricles. 10/18

Using the set of genes which we previously identified as allowing for distinction between murine RGL and astrocytes, we reclassified qNSC1 cells as astrocytes, in accordance with scRNAseq and in situ data from A Cebrian-Silla and methylome data from LPM Kremer. (9/18)

We found that the distinction between qNSC1 and qNSC2 had not been made in most cases even when the cells belonging to each group were present in the dataset. (8/18)

To get a clearer picture we re-analyzed scRNA-seq datasets encompassing the SVZ, generated by the labs of F Doetsch (@doetschlab.bsky.social), A Martin Villalba, J Frisen, S Linnarsson (@slinnarsson.bsky.social), J Biernaskie, N Rajewsky, F Miller, A Alvarez Buylla and O Raineteau. (7/18)

A similar phenomenon had been described in mouse astrocytes and putative subventricular zone (SVZ) radial glia-like (RGL) (called qNSC1) which respond to injury. (6/18)

In particular we found that one group of NSCs, recently described as being very similar to mouse parenchymal astrocytes, is efficiently recruited by Notch inhibition leading to the appearance of a cell state defined by co-expression of astrocytic and activating NSCs markers. (5/18)

With scRNAseq after 24hours of Notch inhibition we found that most cells had responded, but not in the same way. (4/18)

We attempted to push NSCs out of quiescence using Notch inhibition to see if previously identified clusters reacted differently to a pro-activation stimulus. (3/18)

Drawing from previous characterization of the heterogeneity of adult Neural Stem Cells (qNSCs) in the zebrafish pallium and the prediction that some of that heterogeneity comes from differences in quiescence depth (2/18)

New pre-print from the lab out on @biorxivpreprint (www.biorxiv.org/content/10.1...). 1/18