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Fellow microbial immunity, mobile elements, and plasmid enthusiasts: the paper of our wonderful @BruriaSamuel on anti-defense genes in plasmids is now published in @Nature!!!
Check out her thread below for highlights of our new results.
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Check out her thread below for highlights of our new results.
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Meet The Shielded Plasmid🛡️🧬
Our new @Nature paper reveals how plasmids outsmart bacterial defenses during conjugation.
It's all about being in the right place at the right time! The positioning of anti-defense genes boosts transfer efficiency🧵(1/7) nature.com/articles/s4158…
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Burstein lab retweeted
🧵New paper out in @Msystems! We mapped the pan-genome #T6SS effector arsenal of #Pantoea agglomerans. The surprise: its weapons live in dynamic genomic armories that mix antibacterial attack with anti-phage defense. 1/n doi.org/10.1128/msyste…
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Burstein lab retweeted
Genome language models learn from DNA shaped by billions of years of evolution, but steering them can be challenging. Designing phages with Evo 2 previously meant fine-tuning on thousands of genomes, but ICL succeeds with just four examples across tasks.
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Burstein lab retweeted
Out now in Molecular Cell! Retrons protect bacteria from phage infection, and this one has one of the craziest mechanisms we’ve ever seen. (1/8) cell.com/molecular-cell…
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Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!!
biorxiv.org/content/10.648…
biorxiv.org/content/10.648…
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Burstein lab retweeted
For all phage defence pholks - registration for the Symposium on the Immune Systems of Bacteria 2027 is now open! 20-22nd July, 2027, Churchill College, Cambridge, UK. See you there! sisb2027.info
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Check out recent work:
Artificial genetic augmentation of T6SS activity affects effector repertoire and host toxicity | Microbiology Spectrum journals.asm.org/doi/10.1128/sp…
In collaboration with @GerlicL
Artificial genetic augmentation of T6SS activity affects effector repertoire and host toxicity | Microbiology Spectrum journals.asm.org/doi/10.1128/sp…
In collaboration with @GerlicL
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Burstein lab retweeted
1/5 Telomerase has long been linked to chromosome maintenance in eukaryotes. Now, we show that telomerase-like activity is also present in bacteria, shedding new light on its ancient origins.
Excited to share that our work on DRT10 is now out in @Nature!
nature.com/articles/s4158…
Excited to share that our work on DRT10 is now out in @Nature!
nature.com/articles/s4158…
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The most important briefings of the day.
Karl Deisseroth, professor of bioengineering and of psychiatry and behavioral sciences, shares the news of his Nobel Prize with his kids.
Karl Deisseroth, professor of bioengineering and of psychiatry and behavioral sciences, shares the news of his Nobel Prize with his kids.
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So many bacterial genomes are being edited… Could we spot them in the wild even without obvious markers??? Worry not! Our @EdanGabay has you covered. In our new preprint, she pinpoints such genes disrupting the natural genomic "grammar": biorxiv.org/content/10.648… 1/4
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No unified large dataset of engineered bacterial genomes. So we built scalable simulations of random and potentially harmful gene insertions. We trained a classifier on those, along with natural sequences and natural occurrences of the inserted genes as hard negatives. 3/4
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After fine-tuning on potentially malicious insertions, the model reached 0.95 AUROC and 0.95 AUPRC. This indicates that such edits do leave detectable genomic-context signatures, without relying on marker genes or predefined databases. Congrats @EdanGabay!!! 👏👏👏 4/4
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Burstein lab retweeted
Genomes are full of dark matter of unknown functions.
We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.
We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.
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Burstein lab retweeted
Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.
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ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use.
We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
github.com/PacesaLab/Bind…
We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
github.com/PacesaLab/Bind…
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VIPR is now out in @ScienceMagazine!
What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins.
So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins.
So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR.
We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets.
Thread + link below.
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Burstein lab retweeted
Chromatin structure controls defense island expression!
Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and beats anti-defense proteins but raises toxicity. Lab strains still hide novel immunity modules!
biorxiv.org/content/10.648…
Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and beats anti-defense proteins but raises toxicity. Lab strains still hide novel immunity modules!
biorxiv.org/content/10.648…
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Also a highly experimental port of these models into WebGPU, allowing direct prediction on your 💻: localfold.org
WARNING: will drain battery🪫, overheat 🔥💻 & eat your data plan 📱
Started by Martin Steinegger as AF2 port to WebGPU martin-steinegger.github.io/alphafold2-web…
(3/3)
WARNING: will drain battery🪫, overheat 🔥💻 & eat your data plan 📱
Started by Martin Steinegger as AF2 port to WebGPU martin-steinegger.github.io/alphafold2-web…
(3/3)
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Burstein lab retweeted
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim, Martin Steinegger, Milot Mirdita
🐍 pip install colabfold[alphafold]
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🐍 pip install colabfold[alphafold]
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Burstein lab retweeted
Published now in @Nature - "Long-read sequencing reveals pre-meiotic gene conversion in sperm".
We show an unexpected source of new genetic variation in human sperm, occuring earlier in development than previously thought. Check it out here: nature.com/articles/s4158…
Thread: 1/
We show an unexpected source of new genetic variation in human sperm, occuring earlier in development than previously thought. Check it out here: nature.com/articles/s4158…
Thread: 1/
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