陳昱嘉 Yu-Chia Chen

👇👇👇 New preprint dropped! Where we dive deep into the factors that restrict pluripotent stem cells to make the RIGHT cell types in the RIGHT place in planarians. Many surprises in this very exciting story. @kuangtse.bsky.social

Still vividly remember the 🤯 moment seeing the planarian regenerate growing (sometimes) paired, supernumerary pharynges during my rotation with @carrieadler.bsky.social.

Thank you Carrie for letting me have fun with this cool project and thanks Kuang-Tse for putting together this lovely story!! 🙏

New preprint alert! 🚨 Check out this awesome highlight thread by @kuangtse.bsky.social -- How does a pluripotent stem cell differentiate into the correct cell type at the right location? 🧐

Line of zebrabow embryos that have different colors based on the cell lineage. They are sorted by color to form a rainbow.

Full spectrum of ‘zebrabow’ embryos. Credit to @jhenninger.bsky.social. #ZebrafishZunday 🧪

It’s time for another #FluorescenceFriday! 👩‍🎨🎨🔬🫀multi-color labeled zebrafish heart with mosaic expression of diverse myl7:color plasmids 🏳️‍🌈🌈

A modular platform for bioluminescent RNA tracking - Nature Communications Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...

Nice paper from Jenn Prescher and colleagues on tags for bioluminescence imaging of RNAs. www.nature.com/articles/s41...

Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia https://www.biorxiv.org/content/10.1101/2024.12.01.626237v1 The acoel worm Hofstenia miamia (H. miamia) has recently emerged as a model organism for studying wh

Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia https://www.biorxiv.org/content/10.1101/2024.12.01.626237v1

Thrilled to present our latest BioRXiv on brain/body interactions during defensive freezing behaviour! (www.biorxiv.org/content/10.1...). You might think that a frozen animal has, well, frozen muscle activity, right? Wrong! Underneath the still surface of a fly, something in the legs is beating… 🧵

Welcome to the #devbiolwriteclub Bluesky Boot Camp! I’ll be posting here regularly with thoughts and exercises to help scientists become better writers. Let’s start by managing expectations: I will NOT help you write better. I WILL help you become a better writer. 🧵 1/10

Slingjaw wrasse ink print with damselfishes

Slingjaw wrasse print with jaws extended

During thanksgiving, I sometimes wish that I was a slingjaw wrasse. They can extend their jaws 1/3 of their entire body length. Perfect for getting seconds without standing up. We printed one today from a specimen we collected in Okinawa

I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases Embryogenesis is commonly viewed through a tree model of cell differentiation, which does not adequately represent the spatiotemporal modulation of cell multipotency underlying morphogenesis. Here we ...

(1) How can we build complex structures from a limited set of progenitors and cell types? In our new preprint, we describe patterns of cell fate decisions during early development and (in some cases) identify molecular correlates of different behaviors.

www.biorxiv.org/content/10.1...

(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why

#NewPI achievement unlocked: the first
#obrownlab publication is officially accepted (🍾) about #zebrafish #glia (green) and the vasculature (magenta). Thanks to our reviewers and congrats to all of the lab members! What a great 1st paper experience. Happy #fluorescencefriday ya'll!

Another go-to graph for "AHA!" moments: phylogenetic trees. This @embl.org hosted interactive tree viz tool is intuitive and so so so customizable.

I heard that today is #Caturday 🐱

"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...

In this review @gracebower.bsky.social & I discuss recent evidence showing that, unlike canonical enhancers, long-range enhancers located hundreds of kb from their targets rely on additional mechanisms to ensure robust gene activation during mammal development. www.sciencedirect.com/science/arti...

Calcein staining showing the skeleton on the aboral side of a juvenile sea star (Patiria miniata)
Everything looks better with a rainbow LUT 🌈😊
#microscopy #echinoderms #fluorescence

"A picture contains 1,000 projects."

Acrobeles roundworm head, photo by Kaiden Power @wormkaiden.bsky.social

How many open questions about ECM patterning can you find in these pictures?

7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies

Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing

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Cell state transitions are decoupled from cell division during early embryo development - Nature Cell Biology Kukreja et al. show that blocking cell division in zebrafish does not affect differentiation of major cell types during gastrulation and segmentation, but it does decelerate differentiation of particu...

Cell division is NOT a must for differentiation during early zebrafish embryogenesis.
www.nature.com/articles/s41...

For not quite #FluorescenceFriday, here are pluteus larvae of sea urchin under polarized light 👾🚀

#FluorescentFriday
#Zebrafish

Visualization of neutrophil migration kinetics after tailfin wound at a whole animal scale.

We need more research done at a whole-animal scale... so much we don't ask because we're just looking at the small local wound under the 🔬

Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas Despite the functional importance of the vertebral skeleton, little is known about how individual vertebrae elongate or achieve disproportionate lengths as in the giraffe neck. Rodent tails are an abu...

Excited to share work that @ceriweber.bsky.social started and drove in my lab. Tails!! We know a lot about limb bone growth, but vertebrae have completely different embryonic and evolutionary origins. What controls growth and proportion in the vertebral skeleton?

www.biorxiv.org/content/10.1...

Baby flounder have an eye on each side, BUT as the flounder grows the eye 'wanders'. First creeping up slowly, then cresting the skull as a living eyeball hat. From there it tumbles to the other side, reshaping bone & muscle, & the fish goes flat
📸Jonathan Jarrell www.facebook.com/groups/26060...

Single-molecule states link transcription factor binding to gene expression - Nature A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...

Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...

Thrilled to share: out in @natureportfolio.bsky.social (!) just in time for Thanksgiving, the dinosaurian history of how your turkey does the twist. Fibular reduction enabled mid-drumstick mobility, unlocking extreme knee long-axis rotation in theropods 🍗🦖🧵 www.nature.com/articles/s41586-024-08251-w

The case against simplistic genetic explanations of evolution Summary: Extreme traits in animals, from the origin of limbs to the loss of tails, capture public attention. This Review argues that scientists should not seek simple explanations for how they evolved...

Please read and share this ⬇️

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