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Hugo Vaysset

@hugovaysset.bsky.social
115 followers 125 following 0 posts

Postdoc researcher in bioinformatics/comparative genomics @sternberglab.bsky.social, Columbia University, NYC.

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Reposted by Hugo Vaysset
Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
www.biorxiv.org/content/10.6... New preprint from my lab revealing molecular conflicts between host replication and antiviral defense. RecBCD prevents this conflict by clearing immunogenic DNA ends produced during normal replication termination. #MicroSky #PhageSky
biorxiv.org
RecBCD Prevents Bacterial Autoimmunity by Clearing Self-DNA Ends Produced During Replication Termination
Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to ...
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Eirik Lågeide @eiriklag.bsky.social · 01/10/2026
Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵
biorxiv.org
NO VEIN is an ancestral immunity protein involved in plant-virus interaction
The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent...
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Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇
nature.com
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David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Kranzusch Lab @kranzuschlab.bsky.social · 17/09/2026
New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac...
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PLOS Biology @plosbiology.org · 18/09/2026
#Phages can evade #bacterial #immunity by disrupting #antiviral signals like cA3, triggering Panoptes defense systems. @mfwhite2.bsky.social &co show that Type II Panoptes detects cA3 loss and activates a CARF-TM effector to disrupt membranes & stop infection @plosbiology.org 🧪 buff.ly/1ixwg9v
Left: Organisation and mechanism of the Panoptes System. In type I Panoptes systems, mCpol is constitutively active, generating signalling molecules that inactivate the cognate effector, 2TMβ. When an infecting phage expresses a sponge protein, the cyclic oligonucleotide pool is depleted. The Panoptes effector oligomerises, leading to membrane disruption and growth arrest or cell death. Right: CARF-TM model structure and cA3 binding. Alphafold3 model of CARF-TM in complex with cA3, including POPG molecules to simulate the membrane bilayer. The position mutated to generate the truncated CARF protein is shown by black arrows.
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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Lucie Etienne @lucievirevolte.bsky.social · 31/08/2026
Insights into longevity & virus-driven adaptation from Myotis bat genomes International & fantastic collab. with @psudmant.bsky.social @denard.bsky.social Labs ! Major credit to the 2 leading scientists: Juan Vazquez & @lauterbur.bsky.social now with their own labs! You 2 rock! (1/n)
nature.com
Insights into longevity and virus-driven adaptation from Myotis bat genomes - Nature
Comparative and functional analyses of Myotis bats uncover unique patterns of adaptation in virus-interacting proteins and longevity-associated pathways, linking two hallmarks of bat biology.
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
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The EMBO Journal @embojournal.org · 10/06/2026
CapK is a bacterial DNA damage-activated kinase that phosphorylates transcriptional repressor CapS to control adjacently-encoded anti-phage immune pathway genes in response to a universal stress signal, DNA damage @kevincorbett.bsky.social and colleagues link.springer.com/article/10.1...
link.springer.com
A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression - The EMBO Journal
Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune ...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 search.foldseek.com/folddisco
nature.com
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
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Romi Hadary @romihadary.bsky.social · 03/06/2026
Excited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽. Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social ! www.nature.com/articles/s41...
nature.com
Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology
A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.
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Osterman Ilya @ostermanilya.bsky.social · 28/05/2026
🚨After 4 fantastic years in the Sorek lab @soreklab.bsky.social, I’ll be starting my own group at EMBL @embl.org bl.org Hamburg. www.embl.org/groups/oster... Metabolism-driven immunity: phages, metabolites, and discovery of new enzymes, molecules, and pathways 🦠🧬
embl.org
Osterman Group – Metabolism-driven immunity
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Tominaga K. (tomiken) @pacyc184.bsky.social · 28/05/2026
Temperate phages enhance bacterial host fitness via RNA-guided flagellar remodelling | Nature Microbiology www.nature.com/articles/s41564-026-…
nature.com
Temperate phages enhance bacterial host fitness via RNA-guided flagellar remodelling - Nature Microbiology
The prophage of a clinical Enterobacter isolate uses an RNA-guided transcription factor to alter flagellar composition, leading to enhanced bacterial motility and improved gut colonization in a mouse model.
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Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
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Sternberg Lab @sternberglab.bsky.social · 12/05/2026
1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202...
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
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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Nature Microbiology @natmicrobiol.nature.com · 27/04/2026
Out Now! Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity #MicroSky
go.nature.com
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity
Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02312-8A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.
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Bohdana Hurieva🇺🇦 @bhurieva.bsky.social · 23/04/2026
🎉Excited to share our new preprint! TIR domains from diverse animals, including human TLR4, are catalytically active and produce cyclic ADP-ribose (cADPR). This enzymatic activity is widespread in animals and conserved across the tree of life. www.biorxiv.org/content/10.6...
biorxiv.org
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Quanta Magazine @quantamagazine.org · 15/04/2026
Over two billion years, a fierce battle has raged between bacteria and the viruses that infect them. The resulting evolution has shaped the way our bodies fight disease today. @vcallier.bsky.social reports: www.quantamagazine.org/the-ancient-...
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Colin Carlson @colincarlson.bsky.social · 09/04/2026
New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...
Wildlife trade drives animal-to-human pathogen transmission over 40 years
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Nature @nature.com · 02/04/2026
Bacteria have been fighting off viruses using a huge arsenal of molecular weaponry that scientists did not know about — until now. Researchers have identified proteins that could lead to virus-fighting drugs and technologies. go.nature.com/4dqQnXI
go.nature.com
‘Treasure trove’ of antiviral proteins could inspire powerful molecular tools
Two research teams mined genomic data from bacteria to create databases containing thousands of antiviral defence proteins that could inspire powerful biotechnologies.
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Aude Bernheim @audeber.bsky.social · 02/04/2026
How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
science.org
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Jens Hör @jenshoer.bsky.social · 21/03/2026
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...
biorxiv.org
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Nature @nature.com · 21/03/2026
AlphaFold database now includes 1.7 million 'homodimers' - comprising two interacting strands of the same molecule go.nature.com/4sjP69b
go.nature.com
AlphaFold hits ‘next level’: the AI tool now includes protein pairing
Nature - The database of 200 million protein-structure predictions now includes homodimers, adding new biological relevance.
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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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Edoardo Gianni @edogia.bsky.social · 13/02/2026
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n
science.org
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
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Victor Tobiasson @victortobiasson.bsky.social · 18/01/2026
Dominant contribution of Asgard archaea to eukaryogenesis. tldr; Best guess, ~ 50% of conserved eukaryotic protein families are from from Asgard archaea! #science #biology #evolution #nature #bioinformatics www.nature.com/articles/s41...
nature.com
Dominant contribution of Asgard archaea to eukaryogenesis - Nature
A survey of the reconstructed gene set of the last eukaryotic common ancestor shows a consistent link between Asgard archaea and the origin of numerous, functionally diverse eukaryotic genes, dem...
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Aaron Whiteley @aaronwhiteley.bsky.social · 18/01/2026
I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
A phage protein screen identifies triggers of the bacterial innate immune system - Nature Microbiology
A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.
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Manuel Ares-Arroyo @aresarroyom.bsky.social · 14/01/2026
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...
biorxiv.org
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Luisa De Sordi @luisadesordi.bsky.social · 05/01/2026
🚨 New paper from our lab in Cell Reports @cp-cellreports.bsky.social, led by Clara Douadi! We show that bacteriophages can cross the intestinal barrier, with increased translocation in Crohn's disease. 🔗 www.cell.com/cell-reports... Many thanks to all the authors!
cell.com
Differential translocation of bacteriophages across the intestinal barrier in health and Crohn’s disease
Intestinal barrier integrity is crucial for gut homeostasis. Douadi et al. show that bacteriophages can cross this barrier without causing damage and that translocation rates depend on the barrier sta...
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BejaLabTechnion @bejalab.bsky.social · 04/01/2026
Phage-associated Cas12p nucleases require binding to bacterial thioredoxin for activation and cleavage of target DNA www.nature.com/articles/s41...
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Nature @nature.com · 16/12/2025
All living organisms face the problem of parasites - but what happens when DNA has invaded the genome? go.nature.com/3MDiJCq
go.nature.com
SOS: RNA-processing mechanism rescues genes from invasive DNA
Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix.
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Aude Bernheim @audeber.bsky.social · 15/12/2025
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...
biorxiv.org
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
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Erez Yirmiya @erezyirmiya.bsky.social · 04/12/2025
I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...
biorxiv.org
Systematic discovery of TIR-based immune signaling systems in bacteria
Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...
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Marcin J. Suskiewicz @msuskiewicz.eurosky.social · 17/11/2025
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
rdcu.be
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
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Sternberg Lab @sternberglab.bsky.social · 14/11/2025
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge. Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
science.org
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
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Lucie Etienne @lucievirevolte.bsky.social · 12/11/2025
📖Latest from the lab: Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶‍♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n www.nature.com/articles/s41...
nature.com
Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations - Nature Ecology & Evolution
A search for analogues of the human SAMD9/9L antiviral genes identifies convergent evolution of this gene family in the bacterial and animal kingdoms, with species-specific and recent genomic signatur...
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Patrick Pausch @patrick-pausch.bsky.social · 06/11/2025
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
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Osterman Ilya @ostermanilya.bsky.social · 06/11/2025
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
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Max Renner @maxrenner.bsky.social · 03/11/2025
Our new preprint is out 🥳🥳🥳 Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence? 👇
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Landon Getz @landongetz.bsky.social · 30/10/2025
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
doi.org
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...
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Paul Rainey @paulbrainey.bsky.social · 28/10/2025
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...
pnas.org
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...
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Mohammed AlQuraishi @moalquraishi.bsky.social · 28/10/2025
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
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Svetlana Dodonova @dodonova-sveta.bsky.social · 28/10/2025
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
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Aude Bernheim @audeber.bsky.social · 17/10/2025
Many antiphage systems use NAD+, in many ways. @hugovaysset.bsky.social reviewed them all! Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity! www.cell.com/molecular-ce...
cell.com
The multifaceted roles of NAD+ in bacterial immunity
In this review, Vaysset and Bernheim examine how nicotinamide adenine dinucleotide (NAD+) is a key player in diverse and widespread bacterial antiphage defense systems and phage counterdefense. The au...
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Sternberg Lab @sternberglab.bsky.social · 26/03/2025
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
biorxiv.org
Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase
Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...
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Ben Adler @benadler.bsky.social · 01/10/2025
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...
nature.com
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
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Ben Morehouse @benmorehouse.bsky.social · 01/10/2025
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
nature.com
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
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