Alessandro De Simone

Gradients, waves and nematics: quantitative perspectives on regeneration Regeneration restores a damaged body part to its original size, shape and structure. Research over the last decades identified signaling pathways, cel…

Tristan Guyomar and I wrote a review on physical mechanisms coordinating regeneration - Featured: signalling/mechanical gradients, travelling waves and nematic fields - Dramatis personae: axolotls, hydra, planaria, spiny mice and zebrafish (ofc) with a jellyfish cameo

tinyurl.com/3upzrdbs

Ben! Thank you 😀 There is no day we are not grateful for your lines, protocols and discoveries!

Thank you, Stefano! And thank you for your continuing support :)

Thank you! I fully agree with you, this is an advantage of slow waves 😀

Thank you so much!

Special thanks to Prof. Franka Voigt for this great collaboration - without who this project would have not been possible. Btw, a collaboration born at #SY-STEM 2023 in Vienna quite serendipitously.

Congratulations to Coline, Tristan, and all people involved, on this important step!

This suggests a fascinating paradigm for the control of tissue regeneration: the more Erk waves sweep across the tissue, the more the tissue matures, potentially regulating future waves to tune overall growth.

These results reveal a self-regulating and spatially organized signaling circuit in which Erk activity waves shape their own inhibition landscape as they propagate, while simultaneously driving tissue maturation.

We continued our analysis by asking if Erk waves regulate other aspects of osteoblast regeneration. We discovered that Erk waves modulate the transcription of the bone maturation transcription factor osterix, which is activated in trailing transcriptional waves.

ReLUs are classic processing units of neural networks and allow proportional responses to strong stimuli, while buffering noise.

We found that the abundance of inhibitor transcripts depends on Erk activity through Rectified Linear Unit (ReLU) responses: transcript levels increase linearly with Erk activity once a threshold is crossed.

To understand how refractory periods arise, we analyzed transcriptional patterns. Together with the Voigt lab at UZH, we developed an smFISH technique for whole-mount scales. This revealed that Erk waves induce beautiful trailing waves of the inhibitor transcripts dusp5, spry2, and spry4.

We further noticed that, when two waves meet, they merge, which suggests that waves are followed by regions that are refractory to Erk activation. This refractory region is predicted to result from high concentrations of Erk inhibitors, induced by Erk itself.

Erk waves were proposed to result from an excitable system including interactions with Erk activators and inhibitors. Compatibly with excitable Erk waves theory, we observed that Erk waves can form striking spiral patterns in scales.

Erk inhibitors are predicted to tune wave frequency, which controls tissue growth.

The lab’s first pre-print! We investigated how growth-inducing Erk activity waves are regulated in regenerating zebrafish scales. We discovered that Erk waves are followed by waves of expression of their own inhibitors, as predicted by excitable waves theory. tinyurl.com/26r2cmpj

New work from @desimonelab.bsky.social lab 🌊🐟

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We have moved to this new location as we prepare to launch a new edition of the Practical Course on Developmental Biology, Quintya-2025. This course began more than 25 years ago, and we are excited to bring together an excellent lineup of faculty and students for this latest edition

We have moved to this new location as we prepare to launch a new edition of the Practical Course on Developmental Biology, Quintya-2025. This course began more than 25 years ago, and we are excited to bring together an excellent lineup of faculty and students for this latest edition

The claustrum is critical for maintaining working memory information Working memory (WM) enables the mammalian brain to temporarily store and manipulate information, supporting cognitive tasks and communication processes. Rather than depending on a single specialized a...

Dive into our latest findings on this powerful structure here: “The claustrum is critical for maintaining working memory” biorxiv.org/cgi/content/...