Levayer Lab

Not sure how the community will be consulted, but if so this will be really critical and time to be vocal...delegating our peer judgement (admittedly imperfect) to LLM feels like removing the cornerstone of how science works. If this is the way it goes, I'd rather become a teacher or bake bread🤷‍♂️

European Research Council (ERC)@erc.europa.eu

As the discussion turns to potential actions, research communities must be consulted and engaged. As a first step, we will explore a joint community survey.

science.orgU.K. funder uses ‘AI triage’ to reject grant proposals—leaving researchers dismayedThe AI-based assessment, which wasn’t explicitly described in the funding call, has raised privacy and fairness concerns

Here it is...by delegating decision to non transparent AI models we generate an incentive for grant applicants to use AI writing to tweak system and the vicious/absurd feedback loop is set (which all started by an overload of grant application driven by AI writing). www.science.org/content/arti...

@marionbaraban.bsky.social

To be honnest, I would almost find it more acceptable to have a real random decision process as it was partially implemented in the SNF. At least, the "random" triage does not generate wrong incentive impacting the way you write a grant proposal and does not trigger such loop...

Levayer Lab reposted

John Stott

@jpsastro.bsky.social

Had a UKRI funded grant proposal rejected at the "AI triage stage". "This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review." 🧪 #academicsky

Levayer Lab reposted

Marion Baraban

A funded postdoctoral position is available at the IBPS, Sorbonne University/CNRS/INSERM in Paris, to investigate the formation of the olfactory organ in zebrafish. We are looking for an postdoctoral researcher with expertise in transcriptomics and bioinformatics, (scRNAseq analysis).

Only one week left to apply ! Check below for more details but the course will be great. Please spread the word 🙏

Levayer Lab@levayerr.bsky.social

📢master or PhD student interested in cell biology ? There are spots left for the Molecular Biology of the Cell course @pasteur.fr. Check the amazing list of lecturers + 1 week practical pocking choano cytokeleton with @thibautbrunet.bsky.social team. Registration 👇 www.pasteur.fr/fr/nous-conn...

Not every cell react the same way to caspase activation. In our recent study (led by @tomcumming.bsky.social and initiated by @avillars.bsky.social ), we tried to better understand what explains this difference and outlined a role of past caspase exposure 👇 www.nature.com/articles/s41...

This work was a pretty long process initiated at the end of @avillars.bsky.social PhD and taken over by @tomcumming.bsky.social with the essential contribution of Andela Davidovic. It is a small step, but it helps to get closer to a "predictive" understanding of cell death in vivo.

A big thanks for the essential support provided by @erc.europa.eu, la ligue contre le caner and @pasteur.fr !

You may wonder how this "memory" is molecularly encoded ? Well...we do as well and despite trying many candidates (that you will find in the big supp fig. Supp 5 and 6) we could not find anything obvious.

Most likely this could be based on partial cleavage of numerous substrates affecting the susceptibility to extrusion and where timescale is defined by protein turnover (but this still remains to be proven).

Can we now use it to "bias" apoptosis ? We performed a very mild activation of optocaspase in clones and let them develop. Cells in the clones were 3x more likely to die compared to neighbouring cells, suggesting that this previous priming sensitise them to "later" developmental caspase activation.

Overall, this revealed complex business taking place downstream of terminal caspase activation. There is a lot of heterogeneity between cells that encompass temporal information and relative information between neighbours.

Can we now also better predict the physiological death ? We previously found a negative feedback where the first extruding cell blocks apoptosis in the direct neighbours through ERK activation. This implies that cell death decision is not fully autonomous and is about who is the "fastest" to die.

So can we predict who among neighbours will be the first ? Using time serie forest (machine learning adapted to use temporal features) we could predict in close to 80% of the case who will the first using relative present and past caspase activity among neighbours

Can we go back to the previous experiment and explain the heterogeneity we observed ? Actually the domain of high sensitivity revealed by the global pulse of caspase are mostly explained by the history of cells. Doing the same expt. after "erasing" past caspase removed most of the spatial bias.

This also explains a good deal of cell to cell heterogeneity. Accordingly, the cells that are more likely to die upon a pulse of optogenetic caspases are the one that were already exposed in the past.

So what explains then this heterogeneity ? We looked systematically at geometrical/signaling/spatial features that may correlate with the caspase activity at which cells engage in apoptosis. The correlation matrix you see below outlines a clear neg. correlation with past caspase activation.

In other words, cells already exposed to caspase in the last 3-5 hours die at lower caspase activity. We used again the optogenetic caspase to validate this prediction using pulses of activation separated in time comparing contralateral regions exposed 1 or 2 times and confirming the "priming"

We checked this in the Drosophila pupal notum segmenting ~20,000 cells and checking systematically at which caspase activity cells engage in cell extrusion and cell death. Using the "derivative" of the GC3Ai caspase sensor was quite predictive but revealed a large heterogeneity of thresholds

Not only we found cell to cell differences, but also global spatial pattern of caspase sensitivity. Using an optogenetic caspase that we previously developed (optoDronc) and doing mild global activation revealed zones much more sensitive to caspases.

irbbarcelona.orgIRB Barcelona International PhD Fellowships - Extraordinary call 2026The following will be offered in this call:Up to 8 FPI positions associated with the “Proyectos de Generación de Conocimiento 2025” Call (funded by the Agencia Estatal de Investigación AEI- MICINN).Ch...

Works over the past decades outlined numerous non-apoptotic functions of caspases, and the large proportion of cells surviving to effector caspase activation during development. But what makes the difference between a surviving and dying cell ? Maybe a simple threshold ?

Levayer Lab reposted

Marco MILAN LAB

@milanlab.bsky.social

16 Sept

Milan Lab is recruiting a new PhD student. Deadline: October 30th. Please, spread the news. www.irbbarcelona.org/en/careers/y...

Levayer Lab reposted

Terence Tao

@teorth.bsky.social

11 Sept

A group of 25 Fields Medalists, including myself, have made a joint declaration on Math and AI: mathandai.org . We welcome additional signatories. See also this article in the Economist announcing the declaration: www.economist.com/science-and-...

mathandai.orgDeclaration — Math and AIRead the declaration and add your name.

Levayer Lab reposted

Prisca Liberali

@priscaliberali.bsky.social

8 Sept

What if we stop asking only how cells build tissues and ask how tissues shape cells? That’s what we’ll explore at Modelling Life from Tissues to Cells 🇨🇭 lakeconferences.org/conf/8334d9b...

lakeconferences.orgConference - Modelling Life from Tissues to Cells: Coordination and Robustness - Lake Conferences

8 Sept

Institut Curie, Paris, symposium: Where Form Takes Shape October 27-28th 2026 (after the yearly International Developmental Biology course) Registration before October 10th (for free !): docs.google.com/forms/d/e/1F... There will be short talks and posters selected from abstracts.

4 Sept

4 Sept

Deadline is approaching very fast (end of september). Don't hesitate to spread the word 🙏.

Levayer Lab reposted

Development

@dev-journal.bsky.social

4 Sept

The role of geometry in morphogenesis Read this Review from our special issue #DevSIextracellular by Ryan Harrison, Olivier Hamant and @timesaunders.bsky.social. journals.biologists.com/dev/article/...

journals.biologists.comEpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentationSummary: EpiCure is a napari plugin designed to optimise epithelia segmentation and tracking curation through automatic errors detection and ergonomic correction while being easily interoperable with ...

3 Sept

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 !

Gaëlle Letort@gaellel.bsky.social

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

Levayer Lab reposted

Thibaut Brunet

@thibautbrunet.bsky.social

2 Sept

🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️

biorxiv.orgRapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animalsAnimal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...

Levayer Lab reposted

Cells & Development

@cellsdev.bsky.social

28 Aug

A very intriguing story by Joao F. Botelho et al shows that in bird, the digit formation (their ✋) is not only governed by apoptosis but also due to changes in the rate of growth extension and cell division between the interdigital zone and the digital zone. So cool! #devbio doi.org/10.1016/j.cd...

Levayer Lab reposted

Carolina Rezaval

@crezaval.bsky.social

26 Aug

We’re recruiting postdocs to join our @wellcometrust.bsky.social , Decoding Competition in the Brain. How does the brain resolve competing needs and prioritise behaviour? 📅 New deadline: 15 September 🔗 Apply: rezavallab.org Please share!

rezavallab.orgHome Animals must make crucial behavioural choices on a minute by minute basis to survive in a changing environment. A long-standing enigma is, how are alternative options evaluated in the brain...

Carolina Rezaval@crezaval.bsky.social

We’re recruiting postdocs! Join our @wellcometrust.bsky.social funded programme 'Decoding competition in the brain'. How does the brain resolve competing needs and prioritise behaviour? 📅 Deadline: 1 September Apply: rezavallab.org Please share! www.jobs.ac.uk/job/DSM781/r...

jobs.ac.ukResearch Fellow (Postdoctoral) at University of BirminghamRecruiting now: Research Fellow (Postdoctoral) on jobs.ac.uk. Click for details and explore more academic job opportunities on the top job board

Levayer Lab reposted

Kate Cavanaugh

@katecavanaugh.bsky.social

25 Aug

🧵 What if one reason fertility declines with age isn’t just genetic-but mechanical? Thrilled to share our new paper in @NatureCellBio : Elevated contractility drives implantation failure in mouse embryos from aged females… here’s what we found 👇 www.nature.com/articles/s41... 1/11

nature.comElevated contractility drives implantation failure in mouse embryos from aged females - Nature Cell BiologyCavanaugh et al. show that embryos from aged mice have increased contractility and tissue viscosity on embryonic day 4.5, which leads to poor spreading and attachment. Similar age-associated mechanica...

Levayer Lab reposted

Delarue Research

@delarueresearch.bsky.social

25 Aug

Please save the date: The Microphysio Conference is back and will be held in Cargèse from April 25th to April 30th! With a great lineup of speakers, it’s an excellent opportunity to exchange ideas in fields related to organ-on-chip, organoids, bioprinting, mechanobiology, and much more! Stay tuned.

Levayer Lab reposted

Stefano Di Talia

@ditalialab.bsky.social

24 Aug

Happy to see Ashley's paper out @natphys.nature.com www.nature.com/articles/s41...

nature.comDecaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regenerationNature Physics - Zebrafish can regenerate amputated fins back to their original size. It is now shown that gradients in extracellular signal-regulated kinase activity act as rulers during fin bone...

Levayer Lab reposted

FlyBase

@flybase.bsky.social

20 Aug

Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...

nature.comTreat biological databases as infrastructure, not projectsLetter to the Editor

nature.comIntestinal stem cells count self-renewal divisions to switch multipotency - NatureIn Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing ...

20 Aug

So cells do count eventually (still need to check the details but the abstract sounds very appealing) www.nature.com/articles/s41...