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Physical Biology of Developing Systems

@pbodslab.bsky.social
195 followers 180 following 54 posts

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.

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Physical Biology of Developing Systems @pbodslab.bsky.social · 06/10/2026
An interdisciplinary #embryology book is out as #OER: @ecampusontario.bsky.social ecampusontario.pressbooks.pub/principlesof... A teamwork turned raw lecture recordings into a colloquial writeup. Please pass any feedback & critiques! @isdb.bsky.social @swedbo.bsky.social @socdevbio.bsky.social 🧪🔬
ecampusontario.pressbooks.pub
Principles of Development - An inquisitive journey into embryology -
This textbook covers key concepts of embryology and principles of development in an understandable but detailed enough pace for advanced undergraduate students. Intended audience is advanced (3rd/4th ...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 23/09/2026
Quite likely that the whole purple are individual nuclei with nucleoli false colored, much of red interconnecting cell and nuclear membranes are AI hallucinating structures from speckled raw data, and blue are some vesicles or lysosomes.
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Physical Biology of Developing Systems @pbodslab.bsky.social · 04/09/2026
Lovely work! Congratulations 🎊
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Reyes-Lamothe lab @reyes-lab.bsky.social · 02/09/2026
We’re hiring! The Biology department at McGill is hiring a tenure-track professor in Quantitative Cell Biology. We’re looking for an outstanding researcher and educator to join our community. Deadline: October 9 Info & application: mcgill.wd3.myworkdayjobs.com/McGill_Caree... Please share!
mcgill.wd3.myworkdayjobs.com
Assistant Professor in Quantitative Cell Biology - Department of Biology
Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at ...
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Kristina Stapornwongkul @kstapornwongkul.bsky.social · 06/08/2026
First published teamwork of the lab 🎉! We wrote a review about emerging concepts of how metabolism promotes, regulates and changes during gastrulation. We hope it will be useful for anyone interested in the emerging field of developmental metabolism. www.sciencedirect.com/science/arti...
sciencedirect.com
A metabolic view of gastrulation: Coordinating signalling, epigenetics and morphogenesis
Gastrulation is the morphogenetic process by which the single-layered pluripotent epiblast is reorganised into the three germ layers and the basic bod…
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callista yee @csybio.bsky.social · 06/08/2026
hiiii everyone! my department @zoology.ubc.ca is hiring an assistant professor in cell and developmental biology! deadline is october 1! academicjobsonline.org/ajo/jobs/32408 // please share!!!!!
academicjobsonline.org
University of British Columbia, Department of Zoology
Job #AJO32408, Assistant Professor in Cell and Developmental Biology, Department of Zoology, University of British Columbia, Vancouver, British Columbia, CA
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Physical Biology of Developing Systems @pbodslab.bsky.social · 28/07/2026
Single author work by Dr. Wieschaus with lovely microscopy 🧪🤩! from the discussion:Although powerful, the logic behind [mutant] approach is always indirect, given that the phenotype one sees is produced by the genes that remain, not the gene that was removed. journals.biologists.com/dev/article/...
journals.biologists.com
Maternal patterning in early Drosophila embryos: how much information can single maternal gradients supply?
Highlighted Article: Comparison of the patterning capacity of Drosophila embryos that have only one of the three maternal gradients known to control anterior posterior patterning.
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Mike Piacentino @mikepiacentino.bsky.social · 21/07/2026
Come join us! 🔬🐣 The Piacentino Lab at Johns Hopkins @hopkinsmedicine.bsky.social is recruiting a postdoc to study membrane lipids, cell migration, and invasion in neural crest and embryonic models! @socdevbio.bsky.social @ascbiology.bsky.social #devbiol #cellbio #lipids
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Esteban Hoijman @estebanhoijman.bsky.social · 03/07/2026
Join us on a journey into the dynamics of cells during embryo development. We are offering a fully funded PhD position to investigate cell behavior using cutting-edge quantitative live imaging at the interface of Development, Immunity, and Tissue Biology. embryobioimaging.com
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Physical Biology of Developing Systems @pbodslab.bsky.social · 20/06/2026
Most distant #organizer transplants arrived: #cells from ctenophore convince a cnidarian to make a second embryo axis! Organizers (possibly) are pushed back to eumetazoan ancestor... 🧪 www.nature.com/articles/s41...
nature.com
A blastoporal organizer in a ctenophore - Nature
Experiments using the comb jelly Mnemiopsis leidyi and the sea anemone Nematostella vectensis reveal that the emergence of a core signalling pathway may have been a key innovation enabling the transit...
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Pablo J. Sáez @pjsaez.bsky.social · 04/06/2026
1 week to start🔥 New @focalplane.bsky.social webinar series focused on #CellMigration, register & join us▶️, it will be fun! pls spread the word, in the next one, ECRs could apply to show their work ;) ▶️ to register: focalplane.biologists.com/2026/05/29/n... @dgz.bsky.social @the-node.bsky.social
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Mélanie Laurin @melanielaurin.bsky.social · 22/05/2026
SAVE THE DATE for the 13th Canadian Developmental Biology Conference — March 7–10, 2027 — bringing together researchers, trainees, and innovators in developmental biology from across Canada and beyond.
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Physical Biology of Developing Systems @pbodslab.bsky.social · 10/05/2026
Really beautiful work Ali, lots of inspiring findings! Here we had thought (for amphioxus) even a tailbud gradient may be dispensible for sequential segmentation: febs.onlinelibrary.wiley.com/doi/10.1111/... Do you think eels carry a posterior gradient despite their horseshoe shaped signal center?
share.google
FEBS Press
Sequential segmentation is widespread among organisms from plants to basal chordates and humans. Three prerequisites can be proposed for sequentially segmenting species: first, presence of a cell sig....
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Physical Biology of Developing Systems @pbodslab.bsky.social · 10/04/2026
Congrats, Can and to the whole team! 🎉 Pretty cool science, evo-devo'ed from preprint to its final version a lot.
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MwahahahahahadScientist @mads100tist.bsky.social · 16/03/2026
It's out! Happy to present ITEC, a semi supervised algorithm with an extremely low error rate that can track cells in files of any size (think Terabytes!). We used it in many organisms, including zebrafish, to study how organs form and linked it to gene expression www.biorxiv.org/content/10.6... +🧪
biorxiv.org
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Kristina Stapornwongkul @kstapornwongkul.bsky.social · 17/02/2026
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!🙏
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Dmitry Kretov @dmitry-kretov.bsky.social · 06/02/2026
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...
cell.com
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 18/01/2026
#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:
Postdoctoral or Ph.D. project position ad at the physical biology of developing systems lab in McMaster University, ON, Canada.
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Physical Biology of Developing Systems @pbodslab.bsky.social · 15/01/2026
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... 🤩
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Physical Biology of Developing Systems @pbodslab.bsky.social · 05/01/2026
Pretty cool! Nobody repeated this experiment later on? Waddington had a similar one with chick and rabbit embryos in 1940s I guess.
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Naomi Moris @nmoris.bsky.social · 16/12/2025
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...
nature.com
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.
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Physical Biology of Developing Systems @pbodslab.bsky.social · 29/11/2025
#FluorescenceFriday bleed-through from yesterday #zebrafish 🐟🔬:
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Marine Biological Laboratory @mblscience.bsky.social · 28/10/2025
We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887
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Physical Biology of Developing Systems @pbodslab.bsky.social · 24/10/2025
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. 🧪
Rainbow with repeating colours over highway
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Physical Biology of Developing Systems @pbodslab.bsky.social · 20/10/2025
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
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Alper Akay @alperakay.bsky.social · 12/10/2025
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
biodtp.norwichresearchpark.ac.uk
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 09/10/2025
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
Thanks Joaquin!
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
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...
biorxiv.org
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
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).
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
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 🐟:
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
2/5🐟 embryos can stably be imaged on stage in sub-cellular resolution:
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Physical Biology of Developing Systems @pbodslab.bsky.social · 02/10/2025
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. 🧪
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John Ngo @johntngo.bsky.social · 22/09/2025
🚀 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/
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Laura Lorenzo Orts @lorenzoorts.bsky.social · 15/09/2025
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...
imb.de
Laura Lorenzo Orts
IMB Mainz
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Priti Agarwal @pritiagarwal.bsky.social · 16/09/2025
🚨 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
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Daniel Durocher @durocher1.bsky.social · 28/08/2025
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!
Image of Toronto
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Development @dev-journal.bsky.social · 10/09/2025
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/...
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.
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Misha Ahrens @mishaahrens.bsky.social · 08/09/2025
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...
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epithelial mechanics fan club @epimechfc.bsky.social · 31/08/2025
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!
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Physical Biology of Developing Systems @pbodslab.bsky.social · 21/07/2025
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..
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Physical Biology of Developing Systems @pbodslab.bsky.social · 19/07/2025
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 19/07/2025
I was seeing those in clouds frequently when doing drug induced somite experiments 🙃
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Esther Verheyen 🇨🇦 @estherverheyen.bsky.social · 17/07/2025
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.
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Physical Biology of Developing Systems @pbodslab.bsky.social · 11/07/2025
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. 🩵
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James Briscoe @jamesbriscoe.bsky.social · 09/07/2025
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...
stemcellpodcast.com
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...
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Physical Biology of Developing Systems @pbodslab.bsky.social · 09/07/2025
To see supplementary figure S39 which I have no idea how ended up there go to page 109!
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Orit Peleg @oritpeleg.bsky.social · 03/07/2025
📣 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👇
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Nimesh Chahare @onenimesa.bsky.social · 03/07/2025
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
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Vicki Metzis @vmetzis.bsky.social · 27/06/2025
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
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