Physical Biology of Developing Systems
@pbodslab.bsky.social
We are located at @mcmasteruniversity.bsky.social McMaster University Biology/Physics departments studying early vertebrate embryo patterning with quantitative tools!
www.physicalbiology.ca
posts by M. Fethullah Simsek.
www.physicalbiology.ca
posts by M. Fethullah Simsek.
Pinned
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. 🧪
Reposted by Physical Biology of Developing Systems
We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887
October 28, 2025 at 6:43 PM
We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887
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
October 20, 2025 at 5:29 PM
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
Reposted by Physical Biology of Developing Systems
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
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...
biodtp.norwichresearchpark.ac.uk
October 12, 2025 at 7:43 PM
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...
Prof. Sir John Gurdon (1933-2025). It is with great sadness that I share the news of the death of a father of the Xenopus field, Professor Sir John Gurdon. www.xenbase.org/xenbase/doNe... #science #devbio #xenopus #frogs
October 9, 2025 at 12:41 AM
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...
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. 🧪
October 2, 2025 at 2:27 AM
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. 🧪
Reposted by Physical Biology of Developing Systems
🚀 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/
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/
September 22, 2025 at 6:27 PM
🚀 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/
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/
Reposted by Physical Biology of Developing Systems
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...
More info: www.imb.de/students-pos...
Laura Lorenzo Orts
IMB Mainz
www.imb.de
September 15, 2025 at 12:13 PM
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...
More info: www.imb.de/students-pos...
Reposted by Physical Biology of Developing Systems
🚨 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
🎤 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
September 16, 2025 at 6:08 PM
🚨 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
🎤 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
Reposted by Physical Biology of Developing Systems
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!
www.nature.com/naturecareer...
Please repost!
August 28, 2025 at 6:34 AM
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!
www.nature.com/naturecareer...
Please repost!
Reposted by Physical Biology of Developing Systems
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/...
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/...
September 10, 2025 at 3:42 PM
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/...
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/...
Reposted by Physical Biology of Developing Systems
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...
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...
September 8, 2025 at 4:25 PM
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...
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...
Reposted by Physical Biology of Developing Systems
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!
August 31, 2025 at 12:00 PM
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!
Reposted by Physical Biology of Developing Systems
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 $$ infusion, the Canadian research ecosystem is never going to survive and thrive.
July 17, 2025 at 7:44 PM
CIHR rant here: our panel funded 6 (!!) out of 42 applications. That is only 14% success rate. That is as bad as the worst of times. So much good science left unfunded, labs closing, skilled workers let go. Without a $$ infusion, the Canadian research ecosystem is never going to survive and thrive.
Reposted by Physical Biology of Developing Systems
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...
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...
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...
stemcellpodcast.com
July 9, 2025 at 8:00 AM
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...
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...
Reposted by Physical Biology of Developing Systems
📣 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👇
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👇
July 3, 2025 at 1:11 AM
📣 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👇
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👇
Reposted by Physical Biology of Developing Systems
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
Or maybe quickly deflating those inflated tissues?
New #EpithelialMechanics pre-print: doi.org/10.1101/2025...
🧵 with pressure control, multiscale buckling, controlled wrinkling
July 3, 2025 at 2:23 PM
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
Or maybe quickly deflating those inflated tissues?
New #EpithelialMechanics pre-print: doi.org/10.1101/2025...
🧵 with pressure control, multiscale buckling, controlled wrinkling
Reposted by Physical Biology of Developing Systems
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
June 27, 2025 at 3:07 PM
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
Reposted by Physical Biology of Developing Systems
🥰 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
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
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...
actu.epfl.ch
June 24, 2025 at 5:53 PM
🥰 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
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
Reposted by Physical Biology of Developing Systems
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....
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.
doi.org
June 23, 2025 at 4:43 PM
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....
Reposted by Physical Biology of Developing Systems
June 13, 2025 at 9:31 PM
Reposted by Physical Biology of Developing Systems
🔔 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
🧵⤵️
“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶
🔗 www.biorxiv.org/content/10.1...
#devbio #biophysics
🧵⤵️
June 11, 2025 at 4:47 PM
🔔 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
🧵⤵️
“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
June 4, 2025 at 1:26 AM
Link to the research: www.cell.com/developmenta... @cp-devcell.bsky.social
Reposted by Physical Biology of Developing Systems
#Science #Biologie
"Information Processing in Biological Systems"
🖥️ Les vidéos colloque organisé par le Pr @thomaslecuit.bsky.social, titulaire de chaire Dynamiques du vivant, sont disponibles.
👉 www.college-de-france.fr/fr/agenda/co...
"Information Processing in Biological Systems"
🖥️ Les vidéos colloque organisé par le Pr @thomaslecuit.bsky.social, titulaire de chaire Dynamiques du vivant, sont disponibles.
👉 www.college-de-france.fr/fr/agenda/co...
May 28, 2025 at 2:22 PM
#Science #Biologie
"Information Processing in Biological Systems"
🖥️ Les vidéos colloque organisé par le Pr @thomaslecuit.bsky.social, titulaire de chaire Dynamiques du vivant, sont disponibles.
👉 www.college-de-france.fr/fr/agenda/co...
"Information Processing in Biological Systems"
🖥️ Les vidéos colloque organisé par le Pr @thomaslecuit.bsky.social, titulaire de chaire Dynamiques du vivant, sont disponibles.
👉 www.college-de-france.fr/fr/agenda/co...
Great work by @nicoleedwds.bsky.social and colleagues!
🔎 Spotted in @cp-devcell.bsky.social!
Researchers from @cincychildrens.bsky.social, among others, used DSHB's anti-Cdh1 [5D3] mAb in a study on the mutation of orthologous genes and how it affects trachea-esophageal morphogenesis in Xenopus.
📄 tinyurl.com/4h6562ed
🧫 dshb.biology.uiowa.edu/5D3
Researchers from @cincychildrens.bsky.social, among others, used DSHB's anti-Cdh1 [5D3] mAb in a study on the mutation of orthologous genes and how it affects trachea-esophageal morphogenesis in Xenopus.
📄 tinyurl.com/4h6562ed
🧫 dshb.biology.uiowa.edu/5D3
June 3, 2025 at 12:07 AM
Great work by @nicoleedwds.bsky.social and colleagues!