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🧵1/ Dive into the fascinating world of bacterial immunity with our latest forum article on immune supramolecular assemblies! w/ @SimonJacksonNZ @rafapinilla92 doi.org/10.1016/j.tim.…. 🦠🛡️ #microbiology #phage
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Oh, you've "come across" another PhD student's data? How curious. It seems to be the very same student whose data you "came across" last time.
2/2 it's too much of a coincidence, just saying.
Keep your data away from AI companies, last warning
x.com/AnthropicAI/st…
2/2 it's too much of a coincidence, just saying.
Keep your data away from AI companies, last warning
x.com/AnthropicAI/st…
We’re sharing how our biology research team worked with Claude to map the first 3D structure of a vault particle from bacterial life.
Vault particles are a longstanding mystery. They are barrel-shaped objects, among the largest protein structures found in our cells. They were first discovered by Leonard Rome and Nancy Kedersha in 1986, but their function remains unknown.
With Claude, we’ve found results that might bring us closer to solving that mystery.
Until now, vaults were only known in the cells of complex things like animals and plants. We have shown that similar proteins from bacteria (and the viruses that infect them) can also assemble into vaults. Finding the structures in these simpler forms of life may make it easier to investigate their function in our own cells.
For our life sciences team, the project was also a demonstration of the potential (and the limitations) of using AI to accelerate science.
In our full piece, we discuss how Claude was able to dramatically speed up some stages—manually determining the vault particle’s structure would have taken weeks to months of painstaking work, but here it took days. We also discuss how Claude made some simple mistakes along the way, and how we collaborated with our machine learning researchers to address them.
Read more: anthropic.com/research/inves…
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Leighton Payne retweeted
Language models can learn new tasks from just a few examples in their prompt, with no retraining. This is called in-context learning (ICL). Now genome language models can do it too.
With a handful of examples, Evo 2 ICL generates proteins, de novo antibodies, CRISPR-Cas9 loci, nd entire bacteriophages.
We can even use the synthetic sequences iteratively to construct a chain-of-thought (CoT) and achieve harder design goals.
New work with Yukun A. Hao, @BrianHie and team 🧵
With a handful of examples, Evo 2 ICL generates proteins, de novo antibodies, CRISPR-Cas9 loci, nd entire bacteriophages.
We can even use the synthetic sequences iteratively to construct a chain-of-thought (CoT) and achieve harder design goals.
New work with Yukun A. Hao, @BrianHie and team 🧵
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New preprint 🧬
We modelled defense & anti-defense gene turnover in Enterobacteriaceae genomes and found that turnover of DEFs and anti-DEFs is evolutionarily coupled across lineages
We modelled defense & anti-defense gene turnover in Enterobacteriaceae genomes and found that turnover of DEFs and anti-DEFs is evolutionarily coupled across lineages
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Leighton Payne 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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We had dismissed TERT’s puzzling placement in bacterial RT trees as an artifact…
Then a chance encounter between @pentamorfico and @SternbergLab (working on DRT10’s mechanism @stephentang23) provided some clues! 🔍🧬
Then a chance encounter between @pentamorfico and @SternbergLab (working on DRT10’s mechanism @stephentang23) provided some clues! 🔍🧬
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…
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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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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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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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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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Happy to share we’ve been awarded an ERC StG! 🥳🎉
Massive thank you to everyone who helped us get here. Five years to explore some Qs we’re very excited about!! 🧬🔬
Massive thank you to everyone who helped us get here. Five years to explore some Qs we’re very excited about!! 🧬🔬
📣 Good news! 📣
Results of the ERC 2026 Starting Grant call are out!
Funding worth a total of €705 million will go to 421 early-career researchers across Europe.
Discover who, what and where 👉 link.europa.eu/9M3MmN
#ERCStG #HorizonEurope 🇪🇺 @EUScienceInnov
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Every good defence needs a backup 🛡️⚔️
Out now in @NatureRevMicro our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 nature.com/articles/s4157…
Every good defence needs a backup 🛡️⚔️
Out now in @NatureRevMicro our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 nature.com/articles/s4157…
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🧬 Thrilled to share our latest @biorxiv_micrbio preprint! Here we find that Retron-IX build crazy supramolecular rings scaffolded by DNA molecules that sense phage infection!🤯
biorxiv.org/content/10.648…
Read more below🧵! (1/16)
biorxiv.org/content/10.648…
Read more below🧵! (1/16)
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1/10
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
🔗biorxiv.org/content/10.648…
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
🔗biorxiv.org/content/10.648…
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It annoyed us that annotation tools aren't great at saying "I just don't know". That's a real problem for metagenomes and non-model organisms, where it usually means picking some threshold and hoping for the best. We built FAMUS to try and fix this. doi.org/10.64898/2026.… 1/8
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Thrilled to share! We present the structure of a prototypical P2 OLD and reveal that its tRNAse activity is triggered by ssDNA hairpins in phage origins or unresolved termini in RecBCD-deficient cells.
Great team effort with Wang, Bikard & Nudler labs.
biorxiv.org/content/10.648…
Great team effort with Wang, Bikard & Nudler labs.
biorxiv.org/content/10.648…
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🚨Preprint! From my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use #cryoEM to study the genome ejection of the #phage T4, revealing how the tape measure protein regulates the process @NMITaylorLab
biorxiv.org/content/10.648…
biorxiv.org/content/10.648…
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Out now! In collaboration with @LeifuChangLab, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!
Links to the articles in the following tweet:
Links to the articles in the following tweet:
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In our latest work, we characterise the Tmn defence system. We reveal plasmolysis as a new way to block phage infection, dramatically reducing secondary infections.
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🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research (1/8) biorxiv.org/content/10.110…
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research (1/8) biorxiv.org/content/10.110…
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Looking for great PhD candidates! Excited to collab with Prof Mark Szczelkun at Bristol UK, studying MADS phage defence. This will be a CASE studentship including research visits to New England Biolabs HQ in MA, USA 🤓 @NEBiolabs shorturl.at/KZGup deadline 3rd Dec
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