I had a lot of fun working on this collaboration and revisiting the scRNAseq data. Although I work on zebrafish now, I still haven't forgotten my spiralian roots. Thanks @chemamd.bsky.social @baxevanislab.bsky.social and Elaine Seaver for the opportunity.
Logo for the Undiagnosed Diseases Network (UDN). It shows a the letter UDN is different colors that overlap to form the analogous colors.
Today is #RareDiseaseDay & we are celebrating by highlighting the invaluable work of the Undiagnosed Diseases Network (UDN)! Formed in 2020, it aims to solve the most challenging medical mysteries using advanced technologies. In this thread, we will highlight their use of the #zebrafish model. 1/5 🧪
Happy International Day of Women & Girls in Science! Today & everyday I am grateful for the opportunity to work alongside & learn from this talented group of women scientists. Funded by grants from the NIH, this team is working to understand how the gut microbiome affects our digestive health.
Switching fields or wanting to become an expert in #zebrafish research?
The @mblscience.bsky.social 2026 Zebrafish Development & Genetics course offers a fantastic opportunity to learn from leaders in the field!
Application deadline: March 2
Please spread the word!
www.mbl.edu/education/ad...
A very well deserved award for a wonderful scientist and mentor. My time in Jeff’s lab has undoubtedly been one of the most enjoyable and enlightening periods in my scientific career.
Happy New Year! NEW LAB PREPRINT testing how best4+ intestinal epithelial cells develop! best4+ cells are conserved across vertebrates and altered in IBD & colorectal cancer. But they were first molecularly IDed in 2019. We barely know anything about them yet! What do they do?? HOW DO THEY GET MADE?
Understanding best4+ cell development will shed light on whether changes in best4+ cells during disease are a result of intestinal dysfunction or contribute to disease progression, as well as how best4+ cells might be therapeutically manipulated.
Given their broad conservation, they are likely to have an essential role that has been selected for across evolution, though their functions remain to be determined. Here, we identify key elements of its gene regulatory network that are likely conserved across vertebrates.
We found that best4+ cells don't absorb nutrients, are not essential to regulate gut pH following acidic challenge, but exhibit heterogeneity in intracellular pH across different regions of the gut.
Since best4+ cells have only been recently molecularly described, their function remain a mystery. We used our meis1b mutants and generated novel ablation models to test some previously proposed best4+ cell functions.
pbx3a is not required for best4+ cell specification but instead shapes spatially defined gene expression patterns within best4+ cells, acting anteriorly to activate anterior markers and repress several putatively posterior markers.
Similarly, from our previous work, and conservation of meis1b and pbx3a as candidate TFs, we created whole gene deletion mutants and performed scRNAseq to understand what roles these factors play in best4+ cell development.
We found that meis1b is essential for best4+ cell identity.
Based on our previous work, as well as conservation of notch2 as a cell-type specific best4+ cell marker across evolution, we tested if Notch signaling is required for specifying best4+ cells. We found Notch signaling oppositely affected best4+ cell and enterochromaffin cell fates.
There remains a debate whether best4+ cells have an absorptive or secretory origin. We had previously predicted from our Daniocell paper that best4+ cells originate from secretory progenitors in the intestine. In this study, we lineage traced secretory progenitors to test our previous predictions.
We perform the first in vivo live imaging of these cells and identify a diversity of cell morphologies with dynamic projections.
We perform the first electron microscopy of these projections and identify associated vesicles, suggesting a role in cellular communication.
We compare best4+ cells across animals to establish their conserved expression program.
But how to explain that best4+ cells absent in mice? We identified which intestinal cell types in mice express the conserved best4+ cell-specific program using previously published scRNAseq data
Closing out 2025 with our new preprint where
@jeffreyafarrell.bsky.social and I explore development and function of zebrafish intestinal best4+ cells – molecularly described in 2019, conserved in evolution, absent in 🐭, and altered in inflammatory bowel disease.
www.biorxiv.org/content/10.6...
Check out our recent preprint, "Live longitudinal imaging of meningeal cerebrovascular injury and its sequelae in adult zebrafish."
lnkd.in/gN7z6th4
Yaaay! Great to have you back!
If you’re interested in joining our new lab at @uarizona.bsky.social as a #labmanager, please send a CV and brief cover letter to surabhinav@arizona.edu. Experience with zebrafish husbandry is a must, and experience in molecular biology or microscopy is a plus. You get to set the rules!
#zebrafish
I am delighted to announce that I will be starting as an Assistant Professor at the University of Arizona in Spring 2026. Our lab will study intestinal best4+ cells in zebrafish. We are seeking a lab manager with previous zebrafish experience – come build with us.
surlab-gastro.my.canva.site
Ok, friends! If you’re a Daniocell user, it’s now available again outside of the NIH. Very sorry for any inconvenience this posed for any of you and thanks for your patience. We’re taking additional steps to hopefully prevent similar outages in the future. Happy surfing 🎣
Transitions in development – an interview with Jeffrey Farrell
@jeffreyafarrell.bsky.social talks about becoming a group leader, his insights on advocacy for developmental biology and his belief in unifying single-cell biology with classical approaches.
journals.biologists.com/dev/article/...
I’m doing fine, hope to catch up with you next week at IZFC
Big congratulations Kristen!!! This is such wonderful news.
For more customized analysis using our zebrafish timecourse dataset available in Daniocell, check out this amazing resource DaniocellDesktop. Extremely happy to see this brainchild of @jeffreyafarrell.bsky.social out in the wild.
Spiralia enthusiasts!! 🐚🐙🐌💛
Our amazing speaker for the Spiralia Satellite symposia at the #PASEDB2025
Néva Meyer, Associate Professor, Clark University
Organizers: Christina Zakas and @albertinlab.bsky.social
#evodevo #pasedb #spiralia
Jeff Farrell about to start his seminar
5 people at dinner
It was so awesome to have @jeffreyafarrell.bsky.social here to give a departmental seminar today!!
Timeline of important technological developments in zebrafish research.
With a published genome & advancements in gene editing, the field of #zebrafish genetics has exploded in recent decades. We take a look back at major achievements in this infographic. For more, read this book chapter by @varshneylab.social et al (2015)($) doi.org/10.1016/bs.a... #ZebrafishFunFacts 🧪
Organ regeneration in the zebrafish. Summary of some of the organs and tissues used for regeneration studies in zebrafish. Preferred injury models are annotated for each organ. Image and text credit to Marques et al. (2019) https://doi.org/10.1242/dev.167692
Masters of regeneration? #Zebrafish are capable of regenerating their fins, spinal cord, pancreas, skin, retina, heart, liver, brain, tendons, hair cells, & kidney. For more info on this amazing species, read this primer on regeneration: journals.biologists.com/dev/article/... #ZebrafishFunFacts 🧪
