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Aude Bernheim

@audeber.bsky.social
3.4K followers 442 following 216 posts

PI at Institut Pasteur Evolution, immunity, genomics, microbiolgy. Into immunity in bacteria and its conservation in eukaryotes. Advocate for more inclusive sciences mdmlab.fr

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Reposted by Aude Bernheim
Carl Zimmer @carlzimmer.com · 27/09/2026
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
nyti.ms
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
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Aude Bernheim @audeber.bsky.social · 24/09/2026
Really great work !
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Reposted by Aude Bernheim
Christophe Zimmer @chzimmer.bsky.social · 10/09/2026
Can you tell how an antibiotic kills bacteria just by watching them under a regular microscope — without any dyes ? Yes, it turns out, at least if you are a deep neural net.
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Aude Bernheim @audeber.bsky.social · 23/09/2026
Some really cool microbiology!!! Congrats everyone 👏
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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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Jorge Moura de Sousa @jmouradesousa.bsky.social · 20/09/2026
Happy to see our work on the evolution of antiviral repertoires in P4-like satellites and their P2-like helper phages (check out the 🧵 👇) out in @narjournal.bsky.social 🔗 doi.org/10.1093/nar/... #phagesky #MicroSky #evosky
doi.org
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id
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Tatta Bio @tattabio.bsky.social · 18/09/2026
We're excited to share our new preprint! In collaboration with the @keaslinglab.bsky.social at UC Berkeley, we made gLM2 generative and used it to redesign a chimeric Type I polyketide synthase in the context of the full biosynthetic assembly line. 🧵 Preprint: www.biorxiv.org/content/10.6...
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Malcolm White @mfwhite2.bsky.social · 16/09/2026
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
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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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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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Tara Bartolec @tarabartolec.bsky.social · 20/08/2026
So happy to share that this work is finally out, now in @nature.com! Lots of new goodies since preprint so plz check it out (old thread below). Giant thank you to everybody involved + all @savitski-lab.bsky.social and @typaslab.bsky.social lab members 🙏🙏🙏 @embl.org nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Ben Morehouse @benmorehouse.bsky.social · 12/08/2026
Today we are excited to introduce you to PanDA 🐼🐼🐼, a newly uncovered antiphage system!! Attendees at @SISB2026 would have heard a little about this from graduate student Ali Nabhani back in May, but we are now out here in preprint form and delighted to share more of the details. (Thread below)
biorxiv.org
Minimal diadenylate cyclases have been co-opted to detect phage immune evasion
Many bacterial immune defenses transmit recognition of phage infection via the generation of diverse cyclic nucleotide second messengers. Phage have evolved to subvert this kind of immunity by sequest...
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Ady Ragucci @aragucci.bsky.social · 12/08/2026
Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial diadenylate cyclase domains synthesize diverse nucleotide signals in anti-phage defense
Bacterial diadenylate cyclase (DAC) enzymes synthesize the nucleotide signal 3′3′ cyclic di-AMP (3′3′-c-di-AMP) to control osmoregulation, cell-wall homeostasis, and DNA-damage responses. Here we disc...
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Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
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Landon Getz @landongetz.bsky.social · 06/08/2026
DNA glycosylases are repair enzymes, essential to all cellular life. They find chemically damaged bases and remove them so DNA can be repaired. Today in Nature Microbiology, we show bacteria have repeatedly repurposed them into antiviral immune systems 🧵 www.nature.com/articles/s41...
nature.com
Antiviral defence is a conserved function of diverse bacterial DNA glycosylases - Nature Microbiology
DNA glycosylases, typically used for DNA repair, can also protect bacteria against phages that would otherwise evade host immunity by incorporating modified bases into their genomes.
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Aude Bernheim @audeber.bsky.social · 29/07/2026
Awesome work! A must-read. What a wonderful tree. Congrats @algao.bsky.social and all the co-authors.
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Spyros Lytras @spyroslytras.bsky.social · 23/07/2026
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
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Aude Bernheim @audeber.bsky.social · 22/07/2026
Fantastic work from a brand new lab :)! Amazing to see the same folds being used by pathogens across the tree life! Congrats Jason and all authors.
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
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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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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 21/07/2026
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
nature.com
Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology
All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026
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/10.6...
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Osterman Ilya @ostermanilya.bsky.social · 09/07/2026
Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️
science.org
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 17/07/2026
Gabija restricts phage circularization & DNA replication Gabija prevents phage genome circularization & replication w/out impacting bacterial host. Exposed DNA ends & phage end-binding proteins license DNA targeting while RecBCD protects host from Gabija www.cell.com/cell-host-mi...
cell.com
Gabija restricts phage circularization and DNA replication
Gabija acts early during phage infection, preventing phage genome circularization and replication. Phage DNA end-binding proteins prevent RecBCD loading onto linear DNA, and the absence of RecBCD lice...
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Nogales Lab @nogaleslab.bsky.social · 20/07/2026
Thrilled to share our collab led by Grace Hibshman with the Shipman lab! Type IX retron-Kva2 structure reveals phage detection via an HTH fold, not a primary sequence. We computationally designed triggers that program bacteria cell death, pointing toward designer antimicrobials.
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 20/07/2026
A family of lanthipeptides with anti-phage function Discovery of 2,000+ lanthipeptide biosynthetic gene clusters with anti-phage potential. Lanthivirins inhibit phage replication by targeting phage proteins & interfering with phage DNA replication. www.cell.com/cell-host-mi...
cell.com
A family of lanthipeptides with anti-phage function
Shomar, Guillaume, et al. report the genomics-driven discovery of a family of more than 2,000 lanthipeptide biosynthetic gene clusters with anti-phage potential. They experimentally demonstrate anti-p...
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 07/07/2026
🔬 Meet Spyros Lytras, one of our new G5 group leaders! Using AI to predict viral protein evolution, he's designing vaccines for strains that don't yet exist. No more waiting for threats to emerge—be ready ahead of time. The future of pandemic preparedness. 🧬 📖 www.pasteur.fr/en/research-...
pasteur.fr
Predicting viral evolution with AI
Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...
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Aude Bernheim @audeber.bsky.social · 07/07/2026
Fantastic study tackling a new aspect of bacterial immunity: defense against conjugation ! Added bonus: Mesopotamian deities are fascinating, a good reason to dive again into this civilisation.
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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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Aude Bernheim @audeber.bsky.social · 30/06/2026
Very honored by this. Deeply grateful to all lab members and collaborators for the joy of doing science together. I hope that joy is reflected in the science we produce.
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Sorek Lab @soreklab.bsky.social · 17/06/2026
Preprint: Plant pathogens cleave 2’cADPR to suppress TIR immune signaling Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Plant pathogens cleave 2'cADPR to suppress TIR immune signaling
Small molecules produced by TIR (Toll-interleukin-1 receptor) domains are essential for plant immune signaling. A central TIR-derived signal is 2'cADPR, a cyclic ADP-ribose (ADPR) molecule that is gen...
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Debnath Ghosal @debnathghosal.bsky.social · 12/06/2026
New paper alert!! We just discovered a new filament system that is widespread exclusively within CPR bacteria! www.biorxiv.org/content/10.6.... Short thread below. 🦠🔬🚀
biorxiv.org
A Novel Pilus System in Candidate Phyla Radiation Bacteria
The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15–50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primar...
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Kranzusch Lab @kranzuschlab.bsky.social · 12/06/2026
How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...
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Sofya Garushyants @garushyants.bsky.social · 12/06/2026
Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs www.sciencedirect.com/science/arti...
sciencedirect.com
YprA-family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…
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Ákos T Kovács @evolvedbiofilm.bsky.social · 12/06/2026
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity @natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino www.nature.com/articles/s41...
nature.com
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology
The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...
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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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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 · 30/05/2026
Our aRES story is finally out 😀 Beyond what was reported in the preprint, we found that aRES is activated by direct binding of the phage DNA polymerase. Another NAD-degrading defense system — and multiple phage strategies to overcome it. www.sciencedirect.com/science/arti...
sciencedirect.com
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking down the molecule nicotinamide (Nam) adenine dinucleotide (NAD+) into adenosine di…
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Miguel López Rivera @riveralopz.bsky.social · 29/05/2026
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
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Nonia Pariente @npariente.bsky.social · 29/05/2026
❤️this Perspective from @jennifergarrison.bsky.social strongly advocating that: 🥚 ovarian biology has systemic effects in women ❌has been neglected long enough thank you very much 👩‍🦳 ovarian aging should be at the center of female geroscience  Hear her roar indeed (Blsky profile)! plos.io/4dOqcZw 🧪
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Aude Bernheim @audeber.bsky.social · 28/05/2026
One of my favorite scientist in the field is opening his lab in Europe 🥳🇪🇺🧬. So happy about this and excited about the science that will come out of this lab!
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Aude Bernheim @audeber.bsky.social · 22/05/2026
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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Jakob T Rostøl @jakob-tr.bsky.social · 20/05/2026
Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...
nature.com
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
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Luuk Loeff @lloeff.bsky.social · 14/05/2026
Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵
biorxiv.org
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Naama Aviram @naamaaviram.bsky.social · 08/05/2026
That's a wrap on three days of incredible science at #SISB2026! Special thanks to @rockefeller.edu for hosting us on their beautiful campus, to our speakers and poster presenters, and most of all to this community that never fails to inspire. Can't wait for #SISB2027 🫶
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Aude Bernheim @audeber.bsky.social · 28/04/2026
Awesome!
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Kranzusch Lab @kranzuschlab.bsky.social · 27/04/2026
Congratulations to @aragucci.bsky.social and @sadieantine.bsky.social for their nuclease-NTPase work now online in final form at @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity - Nature Microbiology
A 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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Aude Bernheim @audeber.bsky.social · 23/04/2026
Bacterial immunity illuminating novel aspects of animal immunity !
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