Developing News

Posted by the Node, on 13 September 2021

Welcome to our light-hearted look at the goings-on in the world of developmental biology in the last two weeks (or so).

Call to action

NIH funding for maintaining the model organism databases (MODs) that we know and love is under threat.

Make sure your opinion is heard: https://www.surveymonkey.com/r/5NGLNNJ

For more background: https://www.ascb.org/wp-content/uploads/2021/03/MOD-letter_for_NIH_0325213.pdf

Talking points on Twitter

Is it time to consign tSNE and UMAP plots to history?

Preprint from Lior Pachter with over 1600 tweets

Picasso embedding of the ex-utero mouse embryo E8.5 data fit to a world map boundary from Chari, et al.

You can find comments for and against on this tweetorial from Lior

And a tweetorial in reply from Tim Sainburg that got a lot of love

Which model is the best for studying human development?

A Perspective article in Nature about the Human Developmental Cell Atlas

Some responses from the #devbio community (note this article created a twitter storm, especially the size of the circles in Fig1c. We have picked out a few twitter threads)

1/2 Good project, in principle but reducing cells to bags of #genes, embryos to #UMAPs & confusing chicken & human development https://t.co/Sp6JAJDcz1 doesn't bode well for quality; @humancellatlas needs #BringBiologyBack into the project #NotInTheGenes #LookAtTheCells #CellsRUs
— A. Martinez Arias (@AMartinezArias) September 10, 2021

In 1995 three geneticists won the Nobel prize in Medicine for their earlier studies in 70s and 80s. They had discovered the fundamental genetics regulating embryo development and led the way to the cellular biology of embryonic development. 1/4 pic.twitter.com/ZNBContGg6
— Giorgio Gilestro (@giorgiogilestro) September 10, 2021

The incredulous responses last week to chick embryos developing similarly to human at early stages explains A LOT. The reality is that all research models have benefits and drawbacks. There isn’t a “best one,” and if we don’t open our minds we miss out on cool discoveries. https://t.co/KsW9SA9TR5
— 𝘿𝙧. 𝘾𝙧𝙮𝙨𝙩𝙖𝙡 𝙍𝙤𝙜𝙚𝙧𝙨 ≽(◕ ᴗ ◕)≼ 🐥🐸 (@RogersLabUCD) September 12, 2021

While I do understand all the upset about the recent @Nature paper on the comparison of model oganisms, (see Figure 1c here : https://t.co/GI6WxmEe6i) I am not sure I would be upset for the same reason.
Obviously fly is not the best system to reproduce human development, BUT…
— Levayerlab (@LevayerR) September 12, 2021

Honestly, I think we should be discussing why the frog is facing left pic.twitter.com/TA6MZ5hFfV
— Dr. Joseph Bruckner (@jjbruckner) September 12, 2021

Advice for new graduate students

There are many wonderful twitter threads offering advice to new graduate students, and indeed much of the advice is relevant to the wider community. Here are a couple of our favourites:

With the new academic year starting, and many people beginning fresh as graduate students, post-docs, or junior faculty, I have been thinking a lot about the core philosophies that govern my own perspectives on science. So I thought I would share.
Welcome to The Tao of Cheese
— Iain Cheeseman (@iaincheeseman) August 31, 2021

Starting a PhD program? Congratulations!! I have some advice if you'd like it!
— Sarah McMenamin, she/her (@skmcmena) August 24, 2021

#DevBio in preLights

Light-sheet illumination of the organoid family tree with LSTree

Three-axis classification of mouse lung mesenchymal cells reveals two populations of myofibroblasts

Epithelial-mesenchymal plasticity determines estrogen receptor positive (ER+) breast cancer dormancy and reacquisition of an epithelial state drives awakening

Extracellular mechanical forces drive endocardial cell volume decrease during cardiac valve morphogenesis

Thanks to the #DevBio community for making this such an interesting couple of weeks, especially on twitter. If you have some news that you think we should share with the developmental biology community on our blog, please get in touch at thenode@biologists.com. If you are interested in getting involved with writing preLights you can find out more here.

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Most-read posts in March

Can the post-doc shortage get even worse? by J Guillermo Sanchez
Lab meeting with the Mohlin lab
SciArt profile: Brent Foster
Lab meeting with the Soiza-Reilly lab
Exploring multi-hub conferences: interview with Sally Lowell by Teodora Andreea Rinciog
An afternoon in the museum with an exploded skull and a 3.5m python skeleton by Joyce Yu

Do you have any news to share?

Our ‘Developing news’ posts celebrate the various achievements of the people in the developmental and stem cell biology community. Let us know if you would like to share some news.

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