Physical Biology of Developing Systems

We‘re looking for a motivated Master student to join our team!

Do you want to optogenetically control metabolic activity to see how metabolism affects patterning and morphogenesis? 💡🧫🧬🔬

Then please apply!
#optogenetics #metabolism #devbio #hESCs

Please RT. Thank you!🙏

RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions Kretov et al. introduce RBPscan, an RNA-editing-based platform that measures how RNA-binding proteins engage their targets in living cells. This approach quantifies the binding strength of protein-RNA...

I am thrilled to share our paper introducing RBPscan, a novel approach to profile RNA–protein interactions in living cells. Free access link at the end ⬇️ 🧵 1/
www.cell.com/molecular-ce...

Postdoctoral or Ph.D. project position ad at the physical biology of developing systems lab in McMaster University, ON, Canada.

#Canada 🍁 has opened prestigious CIRTA fellowship for internationally based candidates in Ph.D. and postdoctoral levels. We (Physical biology of developing systems lab at McMaster University) are interested in recruiting through that stream. Please apply / spread the word for those interested:

Oh my god, @biologyopen.bsky.social put this newbie next to John Gurdon in their @biologists.bsky.social 100-year anniversary cover dedicated to reviewers! What a lovely gift and coincidence for closing the year... 🤩

Pretty cool! Nobody repeated this experiment later on? Waddington had a similar one with chick and rabbit embryos in 1940s I guess.

Modelling co-development between the somites and neural tube in human trunk-like structures - Nature Cell Biology Makwana, Tilley et al. generate human stem cell-based trunk-like structures approximating Carnegie stage 13–14 of development. They use them to model and study the development of the thoracic and lumbar trunk.

Lovely little pre-Christmas present to see this out @natcellbio.nature.com! Some 🔥 new results in here since the biorvix incl (1) a new RARE-GFP reporter ✳️🙌, (2) additional NMP quantification 🔢, (3) no neural tube patterning on RA inhibition 🙅 etc. Enjoy! 😍 www.nature.com/articles/s41...

#FluorescenceFriday bleed-through from yesterday #zebrafish 🐟🔬:

We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887

Rainbow with repeating colours over highway

A picture snapped with phone camera today: a rare 'supernumerary' #rainbow over Hamilton with repeating colour sequence due to very small droplet sizes giving rise to interference patterns of #light by its #wave nature. 🧪

Fascinating timelapses of #somite clock with cadherins from Kageyama Lab @dev-journal.bsky.social : journals.biologists.com/dev/article/...! A new player in clock and #fgf gradient cross-talk besides previously discovered Dusps linking both transcriptional and post-translationally. 🧪🔬 #devbio

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. 🩵