Michalis Averof

I like this concept of the genome as a compressed representation of an organism. Not like a ZIP file that recreates the same file in smaller form, but more like an AI model where a compact sequence (DNA) generates an organism through probabilistic interactions using molecules that it encodes itself.

Mapping of NGS reads to a reference genome
@mbsj-official.bsky.social

"This cover depicts The Bridge in the NGS Rain where people are being exposed to torrents of genomic information [...]. The man standing in the middle of the bridge is pictured deep in thought, considering how to utilize this sequence data set of the ALDH2 gene." @mbsj-official.bsky.social

Just discovered the wonderful covers of 'Genes to Cells', the journal of the Molecular Biology Society of Japan @mbsj-official.bsky.social – absolutely beautiful!

here some examples inspired by mitosis, CRISPR, the DNA helix, and plant pigments

À quoi ressemble le quotidien dans un laboratoire de recherche ?
En 2025, Arthur Monternier, étudiant en art, a passé six mois dans notre laboratoire. Il raconte son expérience dans cette bande dessinée.

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How is everyday life in a research lab?
Last year Arthur Monternier, an art student, joined our lab for 6 months. He conveys his experience in this comic strip.

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nice work! are you assuming that mayflies represent the ancestral state? why are there no changes is the long branch leading to mayflies?

Happy new year to all!

(photo by Karl Blossfeldt, Art Forms in Nature, 1928)

you can find them all here: libraryofbabel.info/About.html

I see, thank you. As a naive outsider, I'm interested in the scientific question, not much in the personal differences.

In biology we can probably live with "immensely complex", no? Would it be fair to conclude that you differ in your assessment of how likely and how complex these models could be?

how large is it?

Yes. But independently of this move, ERC is undeniably contributing to the latter.

I suspect this is EU trying to respond to the mess in USA, without really adressing the problem at home. ERC probably operating under a lot of constraints.

Assholes no, that's unfair to the ERC. But I do agree that more (smaller) grants are needed, rather than larger ones. There's a big gap to fill between national- and ERC-level grants. Independent of age.

That's what 'the napolitans' we up to when they briefly invaded our lab! Wonderful memories from December 2021 and November 2022. Congratulations!!

Our ultimate goal: exploring biology beyond well established research organisms, by building tools that will make new things visible

Ending 🧵 with a marker for visualising chanoflagellates, closest unicellular relatives of animals, by @jujumathieu.bsky.social and @thibautbrunet.bsky.social

By studying these markers in a multiple organisms, we could identify ones that label the cell membrane most clearly and consistently across species (circle sizes represent how well markers perform in each species). Gathering the info involved more than 10 research labs.
see doi.org/10.1101/2024... 🧵

Some of the markers do not label the cell surface clearly, but shuttle across different parts of the cell. You can see in this early crustacean embryo, how the fluorescence pattern changes as the cells multiply. The video was made by Manon Koenig, Irene Karapidaki and @berylbiologist.bsky.social

🧵

Our lab studies how animals regenerate their body, e.g. how crustaceans regenerate broken legs. One of our aims is to understand if regeneration re-uses the gene networks that built the legs in the first place. Arthur Monternier, an artist in our team, captured the question in this cartoon.

And this is the surface of the larvae of mediterranean stinging jellyfish. It's composed of cells measuring about a hundredth of a millimetre in size. The cells' outlines are visible thanks to fluorescent markers identified by Clara Deleau and @cnidevo.bsky.social

see doi.org/10.1101/2024...

🧵

These are embryos of a jellyfish, made up of cells that are about a fiftieth of a millimetre in size. Their outlines are visible thanks to fluorescent markers identified by Sarah Asaf and @clytia-vlfr.bsky.social

see doi.org/10.1101/2024...

🧵

What are these?

You are looking at embryos of a sea squirt. Each of the 'soap bubbles' is a living cell, about a fourtieth of a millimetre in size. The outlines of the cells are visible thanks to fluorescent markers identified by Hitoyoshi Yasuo @hitoyas.bsky.social

see doi.org/10.1101/2024... 🧵

the basis of optimism is sheer terror (Oscar Wilde); perhaps this applies here

The paper describes initial screens to identify tags that work, but yes, that's something to test once you have found them. Effect will also depend on level of expression, i.e. on the driver you use. In Platy, we noticed that high expression of some reporters can delay development (fig. S7).

Yes, we cited your paper. First results from drosophila (from @yghavi.bsky.social) suggest there are other interesting tags to consider – get in touch if you're interested.

Experiments in several other species are still ongoing, and toolkit is available to anyone willing to give it a try

Thanks to all the collaborators (too many to list here), it's been a great pleasure to do this together

4/4

We identified efficient membrane-localising tags in each of the 10 animals we tested. A few tags worked in every species!

The project was also an exciting venture into open science – sharing resources openly before publication – and collaborating with >10 labs studying different organisms.

3/4

Project started a year ago, when we gathered a set of 11 tags, made them easy to test as mRNA that can be injected in eggs, and sent to 30 labs around the world. We present the results of testing these tags in animals as diverse as sea urchin, beetle, crustacean, worm, sea anemone & jellyfish.

2/4

A toolkit for testing membrane-localising tags across species Transgenic markers and tools have revolutionised how we study cells and developing organisms. Some of the elements needed to construct those tools are universally applicable (e.g. fluorescent proteins...

How can we see the cells that make up a living organism? Membrane-localising tags can drive fluorescent proteins to the cell's outer membrane, making their outlines visible. But the tags don't work well in all organisms. How do you find one for your species of interest? 🧵

Check our latest preprint