Jeff Dean (the Biochemist) @jeffdean@qoto.org

Merge ahead ⚠️

This #HubbleFriday image showcases the peculiar galaxy merger known as Arp-Madore 417-391.

At 671 million light-years away, this merger is the result of two galaxies that were distorted by gravity and twisted together into a ring: https://go.nasa.gov/3Vphfe5
#Hubble

Holy moly. This is gonna be a time sink of massive dimensions. Much of the Boston Public Library's vinyl collection digitized on archive.org

Lots of stuff you know and lots more you don't.

https://archive.org/details/vinyl_bostonpubliclibrary

#music #publiclibrary #vinyl #archiveorg

Some very cool science from
Scott Hensley's lab published today in Science points a way to a potential universal #flu vaccine. If this works in people, this could prime us against all known flu hemagglutinins, dramatically lowering the risks flu pandemics pose. https://www.statnews.com/2022/11/24/experimental-flu-vaccine-developed-using-mrna-seen-as-potential-game-changer/

Culminating in this beautiful figure made by https://twitter.com/Bincoral - Posidonia retained most of the ethylene pathway (can make and receive), Amphibolis can only make, Zostera can do neither!
We think that has to do with their microbiome, Amphibolis might be feeding someone with ACC!

From a cross-post convo on the other site with @cj_battey and others. How to find inversions? A short 🧵 .

The short answer is, it's hard.

Best bet is lots of crosses and genotyping to find markers in reverse order. But that's time consuming and expensive.

An increasingly good option is whole-genome assembly. Cheap long reads means we can now assembly a 2.5Gb maize genome for maybe ~$5K. Inversions are super easy to see in dotplots.

"The mere existence of such a cell should be one of the great astonishments of the earth."

"People ought to be walking around all day, all through their waking hours calling to each other in endless wonderment, talking of nothing except that cell.”

by Lewis Thomas, from "The Medusa and the Snail"

Watch a Salamander emerge From a Single Cell https://www.youtube.com/watch?v=SEejivHRIbE

#DevBio

This paper has not gotten enough attention! We are moving towards large-scale genomics. They reannotated 488 genomes in a comparatve way!
"TOGA integrates gene annotation with orthology inference at scale"

https://www.biorxiv.org/content/10.1101/2022.09.08.507143v1

We know phylogenomics can suffer from bias by annotation method: https://pubmed.ncbi.nlm.nih.gov/35588743/

I'm working on a similar solution, but only 283 genomes to start. Now I've got something to compare to. Mine will be a bit more #Rust-y, though.The possibilities are exciting.

What is the fediverse anyway? We’re continuing our series on the topic with an overview of how this new interoperable social media works. https://www.eff.org/deeplinks/2022/11/leaving-twitters-walled-garden

#Introduction: I am an Associate Professor at UNC Charlotte studying the connection between #protein folding and disease.

When proteins are made in the cell, they come out as a string of amino acids. To function in the cell, this string needs to fold into a complex 3D shape. Many of our proteins need help to fold correctly. This is where molecular #chaperones come in. These proteins work as custodians of the cell by folding proteins. We work on the Hsp70 chaperone in yeast and cancer cells.

What’s up for 2023? I’m @CSHL as Artist-in-Residence to develop a book. Working title “Secret of the Flower Codes.”

I’ll talk to scientists using #AI and #CRISPR to help plants adapt to climate change. Draw and write about #genomics #bioinformatics #SynBio #genome engineering. Fun!

The NIH Advisory Committee to the Director is starting a working group on “Re-envisioning NIH-supported Postdoctoral Training.” Slide deck here has some data and details: https://acd.od.nih.gov/documents/presentations/11032022_ACD_Working_Group_Postdoc.pdf

What would you like them to know? What would you like them to do?

🍄 "#Fungi at Home" 🍄

#SciArt by Ernst Friedrich Heyn (1841-1894) for The Natural History of Plants, Vol. 2 (1895) by Anton Kerner von Marilaun, translated from the original German by Francis Wall Oliver with the assistance of Mary Frances MacDonald and Marian Busk.

View in Biodiversity Heritage Library: https://www.biodiversitylibrary.org/page/13623976

#FungiFriday #mycology #mushrooms

Interesting article by @hildabast on the big Mastodon migration, and more specifically about academics, scholars migrating from twitter to science mastodon instances.

https://absolutelymaybe.plos.org/2022/11/13/mapping-the-mastodon-migration-is-it-a-one-way-trip-or-an-each-way-bet-for-science-twitter/

When I was seven or eight, I was given a copy of the “Ladybird Book of Butterflies & Moths”. The idea was to record seeing each one of the several dozen varieties of butterfly and moths illustrated in the book and when you had ticked off all the varieties in the book, you could send off for a badge or a certificate, or something like that.
The area where I lived was particularly blessed with species variety in the butterfly world as it encompassed chalk down land, salt marsh, ancient woodland on clay soil and a variety of other habitats. This meant that I had little difficulty finding most of the butterflies in the book, but one particular species evaded me: the European swallowtail, “Papilio machaon”. This was not surprising as it is found, to this day, in the UK only around the Norfolk Broads and even there it is rather rare.
I pestered my mother for months to take me to somewhere where we would see a swallow tail and no matter how often she explained that the only place we would be likely to see one was, back in those days, 3/4 of a day's journey on the train. I was distraught; inconsolable, even! I cried, I sobbed, I begged, but all to no avail; in the end, I just had to accept that my ladybird book of butterflies would never be complete!
I had almost completely forgotten about the ladybird book of butterflies until a few months back when a swallowedtail butterfly appeared in my garden. I have never seen one before, nor since. It took me right back to my childhood and the gamut of emotions that I endured due to that damned book of butterflies.
The only problem I have now is “what the hell did I do with that sodding book?”

#alttext
A yellow swallowtail butterfly feeding on the purple Buddleia blossom in my garden in Luxembourg. A rare species even over here!

“This article processing charge is to cover the costs of peer review, copyediting, typesetting, long-term archiving, and journal management.”

OK, it’s good that MDPI explicitly say what the #APCs are (supposedly) needed for. However:

– #peerreview is done for free, only the *management* of the peer review is done by the #publisher.
– Copyediting? What copyediting?
– Typesetting? There are LaTeX and Word templates, the #typesetting is done by the authors, for free.
– Long-term archiving is done by the national library.

So, what remains is “journal management,” i.e., counting the money.

Cool demonstration of cell-free antimicrobial peptides coupled with deep learning by Amir Pandi and Tobias Erb lab

https://www.biorxiv.org/content/10.1101/2022.11.19.517184v1

Thank you very much for the follows. I’m really loving this fab, gentle space! As a newbie I thought I would just introduce myself. I’ve always been very passionate about the natural world & became a #ForestSchool practitioner for this reason. In my spare time I am obsessed with #fungi #wildflowers & #NativeOrchids & try to recreate them in wool felt ( see pic) I love our wild flora, the bedrock upon which so much of our wildlife depends & I am proud to lead #WildFlowerHour every Sunday 8-9pm 🌿🌸