#NewResearch Structure of a functional archaellum in bacteria of the Chloroflexota phylum #MicroSky @archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social ‬ @mariejoest.bsky.social @sgribaldo.bsky.social www.nature.com/articles/s41...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Please re-post: Interested in chromatin and its evolution? Good news! There's still time to join us in beautiful Catalonia (9-12 Dec) to discuss eukaryotic, bacterial, archaeal, and viral chromatin and how it all hangs together meetings.embo.org/event/24-evo... Abstract deadline: 30 September

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

Please re-post: If you know (or are!) somebody who might fancy doing a PhD (Oct 2026 start) in my group @oxfordbiochemistry.bsky.social, working on chromatin evolution in prokaryotes (or other things we're interested in), please have a look at www.bioch.ox.ac.uk/supervisors-...

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬? In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments! 👇 Check out all the details in Paula’s thread! Hint: 🐇 (most of the time)

I was #TWiMAdjacent about the much missed Elio Schaechter. I tried to discuss an article later, but I was stressed for time. The first part about Elio is so worth your time, as is the paper I discussed, about how archaea make enzymes that break down the bacterial cell wall! asm.org/podcasts/twi...

Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...

I cannot fully put into words what publishing this Review has meant to me, so I leave you with how we closed the paper. "The humble bacterium is still a relevant tool for the study of the underlying mechanisms that are conserved throughout life." 🧪🧫🧬📚 doi.org/10.1093/gene...

When we started sampling soil to isolate Bacilli and other bacterial species within @cemist.bsky.social, I did not expect that so many direct and indirect publications and numerous chapters in 6 PhD theses in my group will originate from those efforts 🧵 [1/n]

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

📣 ABSTRACT DEADLINE EXTENDED UNTIL 18TH AUGUST! Register here: register.oxfordabstracts.com/event/75604?... Abstract submission: app.oxfordabstracts.com/stages/79029...

Archaea-on-bacteria action! @romainstrock.bsky.social @tobiaswarnecke.bsky.social &co show that many #archaea encode #peptidoglycan hydrolases, which specifically target #bacterial cell walls, experimentally confirming the killing capacity of 2 of these enzymes @plosbiology.org 🧪 plos.io/4lrJBBa

This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to @ahocher.bsky.social‬, @valeriesoo.bsky.social‬, Pauline Misson, @tobiaswarnecke.bsky.social‬ and MRC LMS Proteomics. A thread 🔽 journals.plos.org/plosbiology/...

@romainstrock.bsky.social work is out! Why should you care? Because it helps shift our view of archaea — from rare extremophiles to not-so-passive bystanders. Some archaea can also fend off bacteria. Glad to be part of this cool project from @tobiaswarnecke.bsky.social. Opens lots of Questions.

Very happy to see this work published + getting the recognition it deserves! Archaea are very cool + understudied organisms and we are only scratching the surface! Since the preprint last year, we (@romainstrock.bsky.social) have included more evidence of bacteria getting killed by archaeal arsenal.

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it? Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

Very happy to announce our new paper on the evolution of metabolism is out now! royalsocietypublishing.org/doi/10.1098/... With @tweethinking.bsky.social @sabifo4.bsky.social @ssolo.bsky.social Davide Pisani, Tim Lenton and @phil-donoghue.bsky.social (1/2)

Really exciting and important tree microbiome paper published in @nature.com ‘A diverse and distinct microbiome inside living trees’ 👏 www.nature.com/articles/s41...

Archaea never stop to surprise us! 🌞 @bejalab.bsky.social @galitzlil.bsky.social discovered that marine archaea use carotenoid "antennas" to capture blue light, transferring the energy to their rhodopsin pumps. A huge leap in microbial photobiology! www.nature.com/articles/s41...

Photo of the Day: Just Following Orders. An 89 year old woman is arrested in London for opposing the genocide in Gaza & supporting Palestine Action. According to the UK Government, this is the face of terrorism in 2025. Credit to the photographer, Chris Ratcliffe, for AFP.

What’s your favorite food fact that is true but sounds totally made up? I’ll start: about half of the mushrooms produced across the United States of America each year (more than 300 million pounds of mushrooms in recent years) are produced in *one county* in Pennsylvania.

Crab-like creatures are famed for having evolved five times in evolutionary history. But anteaters have evolved at least 12 times--in half the evolutionary span. Cool story by @jakebuehler.bsky.social for @science.org

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

For the first time since she was freed from an immigration prison, Rümeysa Öztürk speaks. And she does so by ... writing: "Writing is the heart of freedom of expression. Unbelievably, this single opinion piece, published in our student newspaper, would lead to my arrest and detention."

🚨 New preprint alert! We report what might be the first mechanistic link between gut Archaea and human disease. Methanobrevibacter smithii is enriched in CRC patients—and boosts growth of cancer-associated bacteria like F. nucleatum. www.biorxiv.org/content/10.1... @archaeasky @microbiomesky

MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures pubmed.ncbi.nlm.nih.gov/40615379/ #cryoem

from www.instagram.com/yeweijun98 Slime molds eat the microbes on decaying plants but not the microbes on decaying animals. Badhamia (Physarum) polycephala is an unusually adventurous eater who also enjoys mushrooms, oats, and probably a number of other things! I wonder what's up with the peanut

Very happy to finally have this out! Thank you to my awesome PhD supervisors and all the co-authors!!

It’s a bacterium-eats-bacterium world… www.science.org/doi/10.1126/...

An amoeba with teeth. When building its shell, Netzelia corona selects sharp grains of quartz and positions them around its aperture with the tips pointing inward. I took a few closeups, yesterday. #ProtistsonSky #amoebae #peatlands #MEvoSky

🔥 New and HOT in Chemical Science! “Enhancing binding affinity predictions through efficient sampling with a re-engineered BAR method: a test on GPCR targets” by Sangbae Lee and Art Cho et al. from Korea University, inCerebro, and Atomatrix Read it: pubs.rsc.org/doi/D5S...

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Archaea xkcd.com/3095/

BindEnergyCraft claims to improve BindCraft performance using an energy-based objective. "Code will be released soon."

Excellent piece by @julieparsonnet.bsky.social on infectious diseases as root causes of a number of chronic human diseases; pausing research on bacterial and viral infections will limit efforts to cure neurodegeneration, autoimmune, metabolic disease as well as cancer substack.com/inbox/post/1...

One of my favorite history of science books: "Brave Genius" It's about Jacques Monod, discoverer of the lac operon, who risked everything to fight fascism/Nazis as a part of the French Resistance, along with his buddy Albert Camus. Be like Jacques. www.penguinrandomhouse.com/books/213596...

#Bacteria use weapons to outcompete rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social! www.biorxiv.org/content/10.1... #Chromatin #Asgard #Archaea #cryoEM

Molecular design of a therapeutic LSD analogue with reduced hallucinogenic potential | PNAS #lsd #psychedelics #jrt #rdd #drugdesign

🐈 Why are some cats orange? A tiny change in cat DNA switches off signals that usually make dark fur, turning it orange instead. This also explains why tortoiseshell cats have patchy colours. 🔗 www.cell.com/current-biol... #SciComm 🧪 #Cats

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬 www.biorxiv.org/content/10.1...

A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others peppr.vant.ai