Physical Biology of Developing Systems

How do RNA molecules shape genome regulation in the nervous system? (AKAY_U26CASE) | Doctoral Training Partnership This PhD project will investigate how RNA modifications influence the activity of topoisomerase I (TOP1), a crucial enzyme that regulates DNA supercoiling during replication and transcription. Using C...

New BBSRC funded PhD opportunity in my group with Inspiralis Ltd and @conradn.bsky.social. If you are interested in RNA - protein interactions and RNA modifications check the details below for how to apply. @nrpdtp.bsky.social @biouea.bsky.social @earlhaminst.bsky.social tinyurl.com/bdzvn4dr

It was one-of-a-kind moment to meet Sir John Gurdon at @socdevbio.bsky.social meeting in 2019. Such a humble, down-to-earth personality who was deeply content with life! An exemplary scientist that one could find at the benchside playground regardless of age or career stage! May he rest in peace...

Thanks Joaquin!

An accessible microfluidic perfusion platform for time-restricted control of zebrafish embryonic patterning Pattern formation in development relies on spatially localized and timely action of cell signalling networks1,2. Understanding the dynamic nature of developmental networks requires live imaging techni...

5/5 All the 3-D printing files, and Arduino program are made available as supplementary files. Read for details: www.biorxiv.org/content/10.1...

4/5 We can further observe ERK signal dynamics with live translocation reporter (yellow), which shuttles into the nuclei (cyan) from cytoplasm at the moment MEK inhibitory drug is being perfused into the imaging chamber (~24min).

3/5 And as we perfuse 💉drugs 💊 and rinse them out in a pulsated fashion we can reconstitute somites in segmentation clock mutants (as I had done by hand in my postdoc @nature.com www.nature.com/articles/s41... ) now in a fully automated fashion, notice 5 boundaries forming at the end of movie 🐟:

2/5🐟 embryos can stably be imaged on stage in sub-cellular resolution:

1/5 Lab's first manuscript 🎉 is out @biorxivpreprint.bsky.social today! Beautifully, it is performed by a senior undergraduate thesis student, Mohammed! We developed a 3-D printed #zebrafish embryo imaging chamber 🔬and connected it to syringe pumps to be able to perfuse drugs in a timely fashion. 🧪

🚀 Our new paper is out @natmethods.nature.com!

Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.

🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/

I am excited to announce that I will be moving to IMB Mainz next year! The Winter call for the IPP PhD program is now open; if you are interested in maternal #mRNA regulation and #translation in early vertebrate development, please apply! Deadline: 16 October.

More info: www.imb.de/students-pos...

🚨 The International Developmental Mechanics Zoom Seminar Series is back on Sept 25!
🎤 We have an exciting line-up of speakers this fall. See the image below for details
🌐 Website: sites.google.com/view/devmech...
📝 Interested in presenting? Sign up here: tinyurl.com/2munv5bv

Image of Toronto

JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.

www.nature.com/naturecareer...

Please repost!

Figure 1 - Live imaging of endogenously tagged YAP-miRFP670, mScarlet-I-SOX2 and CDX2-eGFP during the first fate decision in preimplantation embryos. (A) A developmental timeline of trophectoderm (TE) and inner cell mass (ICM) specification. The first cell differentiation event, between the TE (green) and ICM (purple), initiates at the 16-cell stage, establishing distinct inner, ICM, and outer, TE, cell populations in the 32-cell stage embryo. Embryos in this study are imaged until the 32-cell stage. Days post-fertilization are denoted by embryonic day. (B) Sox2 and Cdx2 expression is regulated by YAP. In ICM cells, YAP is phosphorylated and retained in the cytoplasm, facilitating Sox2 expression. In TE cells, YAP is predominantly localized to the nucleus where it activates expression of Cdx2. (C) Time-lapse images of a representative embryo expressing YAP-miRFP670, mScarlet-I-SOX2 and H2B-miRFP670 from the 8-cell through the late 32-cell stage. A z-stack was acquired every 15 min for YAP and H2B channels, and every 30 min for the SOX2 channel. Maximum intensity projections (MIPs) are shown. Unit of time is hours. Scale bar: 10 µm. (D) Time-lapse images of a representative embryo expressing YAP-miRFP670, CDX2-eGFP and H2B-miRFP670 from the 8-cell stage through the late 32-cell stage. Scale bar: 10 µm.

Mathematical modelling of the first fate decision

This Research Highlight showcases the work from Maria Avdeeva, Madeleine Chalifoux, Bradley Joyce, Stanislav Y. Shvartsman, Eszter Posfai @eposfai.bsky.social :

journals.biologists.com/dev/article/...

Preprint -
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...

Are different cell types like oil and water? Over a century ago, researchers found that dissociated sponges and embryonic tissues can self-assemble into functional structures. Join me, @benswedlund.bsky.social to explore the differential adhesion hypothesis & its applications in tissue engineering!

Really cool experiments to solve a developmental mystery! 👏🏻I see how torque arises, but where does the chirality come from? Why are they whirling counter clockwise as seen from dorsal? Sorry didn't dig the preprint yet..

If you can combine with a controlled (in space and/or time) chemokine signal, would be interesting to see how to win the tug of war with optogenetic pulses...

I was seeing those in clouds frequently when doing drug induced somite experiments 🙃

CIHR rant here: our panel funded 6 (!!) out of 42 applications. That is only 14% success rate. That is as bad as the worst of times. So much good science left unfunded, labs closing, skilled workers let go. Without a $$ infusion, the Canadian research ecosystem is never going to survive and thrive.

The day which will come for every single one of us... It is interestingly different to live expecting it to come near while enjoying the legacy of what has been gifted and what awaits around the corner. With much respect and support. 🩵

Ep. 299: "Spinal Cord Development" Featuring Dr. James Briscoe - The Stem Cell Podcast Dr. James Briscoe is a Group Leader at the Francis Crick Institute and Editor-In-Chief of Development. His lab uses an interdisciplinary approach, including mice, chicks, and other models, to study de...

I was interviewed recently by @stemcellpodcast.com

I witter on about morphogens, notochord, @dev-journal.bsky.social & how biology is becoming a data science

Thanks @stemcellpodcast.com for talking to me

stemcellpodcast.com/ep-299-spina...

To see supplementary figure S39 which I have no idea how ended up there go to page 109!

📣 We're on the lookout for a creative postdoc with strong computational skills!

Be the go-to person in the lab for building simple but powerful simulations that test wild ideas on biological rythems: from daily cycles of mussel groups at deep sea, to firefly flash synchronization!

More info below👇

Have you ever thought about inflating tissues?
Or maybe quickly deflating those inflated tissues?

New #EpithelialMechanics pre-print: doi.org/10.1101/2025...
🧵 with pressure control, multiscale buckling, controlled wrinkling

Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social

Self-supervised, label-free 3D cell imaging is here EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...

🥰 Self-supervised, label-free 3D cell imaging is here

Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).

And many thanks to my other awesome co-authors🙏

elifesciences.org/articles/99848

Dynamic BMP signaling regulates sclerotome induction and lineage diversification in zebrafish Summary: Loss- and gain-of-function manipulations reveal that dynamic regulation of BMP signaling is essential for the induction and diversification of the sclerotome lineage in zebrafish.

Excited to share our latest work led by my PhD student Linjun Xie on sclerotome development: Dynamic BMP signaling regulates sclerotome induction and lineage diversification in zebrafish, now published on @dev-journal.bsky.social! #zebrafish #devbio 1/8 doi.org/10.1242/dev....

It’s out! 🥳

www.science.org/doi/10.1126/...

🔔 Proud to share the preprint of my PhD work in the Petridou group @nicolettapetridou.bsky.social @embl.org ✨

“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶

🔗 www.biorxiv.org/content/10.1...

#devbio #biophysics

🧵⤵️

Link to the research: www.cell.com/developmenta... @cp-devcell.bsky.social