Emily Kolenbrander Ho

Thrilled to share our work using live imaging to understand how Epiblast (future embryo proper) and Primitive Endoderm (future extraembryonic tissues) cell fates segregate in the preimplantation mouse embryo. Gargantuan effort led by amazing @rpkimyip.bsky.social, David Denberg and Denis Faerberg!

Thank you!!

pYtags - our in vivo biosensors for receptor tyrosine kinases - in all their beauty on the cover of Cell Reports! Read more here: www.cell.com/cell-reports...

Thanks to the reviewers for their thoughtful feedback, @cp-cellreports.bsky.social for a great publishing experience, and @toettch.bsky.social and all our coauthors for making this such a fun project.

The power of pYtags is that they can readily be applied to any RTK of interest (and not just in Drosophila). I’d love to connect if you are interested in making a pYtag for your favorite RTK!

We built pYtags to detect RTK activity in Drosophila embryos and used them to learn about how developmental patterns form bsky.app/profile/emko...

Excited to share that our work building in vivo biosensors for receptor tyrosine kinases (pYtags!) is now out www.cell.com/cell-reports...

So cool! Congrats Susanna!!

Excited to share the bulk of my postdocotoral work from the @ditalialab.bsky.social on how cells interpret dynamic morphogen signaling during development! Many thanks to our collaborators & coauthors @shelbyflies.bsky.social, Massimo Vergassola, Jacqueline Janssen, and Anna Chao.

Website and registration will open soon for the West Coast SDB meeting, Aug 14–17 at Cal-Poly SLO! Abstract deadline for talks is July 7. Final deadline for abstracts (posters) and registration is July 31. We will have prizes for best undergrad, grad, and post doc presentations! #wcsdb2025 1/4

I'd like to share a little bit of happy lab news in these chaotic times: a new preprint, driven by the brilliant Qinhao Cao!
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?

An optogenetic toolkit for robust activation of FGF, BMP, and Nodal signaling in zebrafish Cell signaling regulates a wide range of biological processes including development, homeostasis, and disease. Accessible technologies to precisely manipulate signaling have important applications in ...

Happy to share a new preprint from my lab! We characterize the on/off kinetics, light dosage-dependence, and more for a suite of optogenetic signaling activators in zebrafish embryos 💡 www.biorxiv.org/content/10.1...

A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field The level of cellular organization bridging the mesoscale and whole-cell scale is coming into focus as a new frontier in cell biology. Great progress has been made in unraveling the complex physical a...

New(ish) preprint! 📰What whole-cell patterns emerge from the arrangement, morphologies, and interactions of organelles in the 3D space of the cell? What would we see if we could gather ALL the whole-cell reconstruction data that's out there in one place? www.biorxiv.org/content/10.1...
🧵 1/11

Large-scale control over collective cell migration using light-activated epidermal growth factor receptors Programmable control over tissue movement is a fundamental challenge for tissue engineering and wound healing. Suh, Thornton, et al. discovered that a light-controlled EGF receptor controls long-range...

I'm so happy to report that our preprint on light-induced collective cell migration has now been published in Cell Systems! This project was a lot of fun and will be the basis for a lot of our ongoing & future work.

Epithelial polarization by the planar cell polarity complex is exclusively non–cell autonomous For cells to polarize collectively along a tissue plane, asymmetrically localized planar cell polarity (PCP) complexes must form intercellular contacts between neighboring cells. Yet, it is unknown wh...

How many cells do you need to establish PCP? The magic number is 3! Beautiful work by Lena Basta in Danelle Devenport's lab. Happy to have contributed. www.science.org/doi/10.1126/...

Developmental systems have regions that deform actively or passively from their active neighbors. We use a ring of tissue as a model to investigate this boundary-driven morphogenesis in its biological context, learning something about gastrulation and possibly blastopore geometries in the process!

A duo of preprints on the dynamics of the first cell fate decision in mouse by Madeleine Chalifoux (first grad student in the lab!) and Maria Avdeeva (Flatiron).

We use quantitative live imaging of key cell fate determinants to follow the segregation of inner cell mass and trophectoderm lineages.

The Society for Developmental Biology has released a statement on the Unprecedented Disruptions to Biomedical Research in the United States.

Thanks Ellen!

Thanks Tim!!

Possibly! If the phosphorylated substrate was membrane localized and could be tagged with the ITAM. Jak/Stat receptors would be a good example

I’ll be starting my undergrad-powered lab this summer at Claremont McKenna College and I’m super excited to continuing exploring new signaling biology with pYtags. If you are interested in tagging your favorite RTK (in flies or in other model systems), please reach out!

Huge thanks to: @toettch.bsky.social for being an awesome advisor. Payam for developing pYtags and starting this project with me. @rpkimyip.bsky.social and @eposfai.bsky.social for amazing egg chamber imaging. Alison and Stas for gorgeous trachea imaging. And Harrison who can segment anything!

Our data is consistent with a new conceptual model for terminal patterning where a local domain of Torso activity, tuned by negative feedback, produces a long-range gradient of ERK. Check out the paper to learn more!

Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo Highlighted Article: Optogenetic dissection of the incoherent feedforward loop regulating brachyenteron in the Drosophila embryo reveals that temporal dynamics and spatial diffusion contribute to stri...

Second, Torso activity was much more restricted to the poles than the broad gradient of ERK activity, consistent with a model where the ERK gradient forms via diffusion. We previously showed the same thing with an optogenetic stimulus.

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

First, Torso activity decreased over developmental time while ERK activity was sustained at a high level. This led us to the discovery of negative feedback from the ERK pathway regulating Torso’s phosphorylation state.

We then asked what we could learn about Torso by comparing Torso activity with downstream ERK activity. Two things surprised us, highlighting that we can’t always accurately infer receptor activity from downstream signaling.

And pYtags didn’t just work for Torso! We also made pYtags for EGFR and FGFR/Btl, and those worked just as well. The pYtag strategy is so powerful because it is generalizable to any RTK of interest.

We were particularly interested in Torso, the RTK controlling terminal ERK signaling at the poles of the fly embryo. I tagged Torso with the pYtag and saw gorgeous signal at the poles just where we expected it! pYtags work in embryos!

pYtags use an exceptionally specific and orthogonal pTyr / SH2 binding pair (ITAM + ZtSH2) to recruit a fluorescently tagged protein to phosphorylated RTKs.