Coming up next week: the third Dutch Structural Biology meeting! Now in Delft, on Sept 26. See program here: nvbmb.kncv.nl/biology-2025 with #teamtomo #cryoEM #nmrchat simulations and more (looks like) Organized by the #NVBMB (associated with KNCV)

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...

Excited to share my latest review, now published in the Royal Society theme issue on ‘The ecology and evolution of bacterial immune systems' (available OA): Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae royalsocietypublishing.org/doi/10.1098/...

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

Our Wadjet-II paper by @roisnehamelinf.bsky.social is out in polished form: www.cell.com/structure/fu... With a great preview by @kevincorbett.bsky.social & @amardeeep.bsky.social highlighting the potential of Wadjets: Wadjet—Keeping a watchful eye on circular DNA. www.cell.com/structure/fu...

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 🧵

📢 New preprint alert! We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses. This could transform phage therapy + genetic engineering. Here’s what we found 🧵 Preprint🔗: www.biorxiv.org/content/10.1...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Great opportunity to join the Leiden University Medical Center as a Junior Principal Investigator! Congratulations to this year's awardees (Marieke Barnhoorn, Edouard Fu, Lydiane Hirschler, @lloeff.bsky.social and Rajagopal Murugan)! Applications are possible for 2026: www.lumc.nl/en/news/2025...

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR The first viral sponges to inhibit Pycsar and type IV Thoeris Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

Extremely excited to share that I’m joining Columbia University @columbiauniversity.bsky.social as an Assistant Professor! We will explore how the mobile genome works—how transposons shape us, our DNA and how they can be harnessed to build useful technologies. #NewPI #RNAsky #TEsky thawanilab.org

Ever wondered why some bacteria have multiple CRISPR-Cas systems? Our new study led by Leah Smith shows how type I CRISPR systems can promote the acquisition and retention of new spacers into a co-occuring type III system. www.sciencedirect.com/science/arti...

Exciting times ahead! Today marks the first day of the Loeff Lab at Leiden University Medical Center in the Netherlands 🇳🇱. I’m thrilled to begin this new adventure and continue exploring microbial defense mechanisms and their applications through an integrative structural biology approach.

WORK! I currently have 5 (!) open positions for postdocs/PhD students in our CDlab for projects: - Nanopore protein sequencing - Archaeal CDV cell division - Microfluidics for synthetic cells - Nuclear Pore Complex - Origami mimics of peroxisomes Please apply! ceesdekkerlab.nl/come-join-us/ RT=👍

Check it out for yourself: 🔗 alphafold.ebi.ac.uk

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology www.nature.com/articles/s41... Was fun to write this piece with Dina Hochhauser! Here is a thread to explain the premises 1/

Excited to finally share this work! We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts. tinyurl.com/2uwwy4ty

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription. www.cell.com/cell/fulltex... Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...

First preprint from the Nemudryi Lab! 🍾 In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages. www.biorxiv.org/content/10.1...

Exciting work from the Nemudryi lab! Bacterial Schlafen proteins mediate antiviral immunity, just like their human homologs!

Submit your application with attached CV and motivation letter to [email protected] (applications elsewhere will be ignored). Apologies up front if I won’t be able to reply to everyone!

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity. www.biorxiv.org/content/10.1...

Preprint: “Structural modeling reveals viral proteins that manipulate host immune signaling” Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules Congrats Nitzan Tal! www.biorxiv.org/content/10.1...

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

Phage DNA modifications evade defense Phage DNA modification adds arabinose to cytosines via hydroxy linkage (5ara-hC) w/ potential double & triple arabinosylation. Arabinosylated phages are protected from DNA-targeting CRISPR-Cas & restriction modification www.cell.com/cell-host-mi...

This is wild! Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol) www.nature.com/articles/s41... www.nature.com/articles/s41...

New Preprint!! Alejandro González-Delgado accomplished a major feat on this one: ported retron recombineering, which we love so much in E. coli, into 14 new bacterial species via a massive collaborative effort involving 9 labs! www.biorxiv.org/content/10.1...

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs. Full story here: www.biorxiv.org/content/10.1...

Had a great day at @ebi.embl.org Grenoble for the Next-Gen in Infection Biology micro symposium! Big thanks to @kowaeva.bsky.social for the invite!

Can phage treat infection AND vaccinate? We found that phage treatment protects mice against re-infection by the same pathogen. Out today in PNAS. @tailor-labs.bsky.social www.pnas.org/doi/10.1073/...

We're thrilled to share the published version of our DRT9 story, online today @nature.com! Congratulations to all authors! www.nature.com/articles/s41...

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation. Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation. cryotud.github.io/locscale/

Exciting news!! Our latest paper is out in Nat. Microbiol. @natmicrobiol.nature.com We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3 www.nature.com/articles/s41...

Our new paper on MGEs in Vibrio cholerae is now out in Genome Biology and Evolution @genomebiolevol.bsky.social Huge congrats to former PhD student Natália Drebes Dörr @nataliadrebesdorr.bsky.social 🎉🍾🥳 for the great work & thx to Alexandre Lemopoulos for bioinformatics support shorturl.at/0LveK

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!

@science.org 🧫🧬❄️🔬 Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis | Science www.science.org/doi/10.1126/... @yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase

1/10 Today in @science.org in collaboration with the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

Genomes encode biological complexity, which is determined by combinations of DNA mutations across millions of bases In new work @arcinstitute.org, we report the discovery and engineering of the first programmable DNA recombinases capable of megabase-scale human genome rearrangement

#NatureMicroPicks Microbial integrons in focus 🦠🧬 Two studies showing microbial integrons encoding phage defense systems #MicroSky www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...

Great to see this out. A story that spanned continents, cities and budget codes… www.nature.com/articles/s41... Big thanks to all the teams involved! @clausenlab.bsky.social @e3chembio.bsky.social

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA cell.com/molecular-ce... Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

Quite a nice paper in Cell Step 1: Filament Assembly Step 2: Bacterial Disassembly Bacterial CBASS phospholipases form filaments on sensing cyclic dinucleotides—triggering cell membrane rupture to abort phage infection Mirrors eukaryotic immune strategies of cell “self-sacrifice” like pyroptosis

Our paper on how integrons are biobanks of novel minimal defense systems is now out www.science.org/doi/10.1126/... Two main conclusions on this excellent work led by @eloilittner.bsky.social @baptistedarracq.bsky.social 1/n

🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...

🚀 Join the Patinios Lab at the VU LSC - EMBL Partnership Institute for Genome Editing Technologies! We are looking for a Postdoctoral Researcher to join our growing team! 🔎

"Science is an investment. We will put forward a new 500 million package for 2025-2027 to support the best and the brightest researchers and scientists from Europe and around the world." — President @vonderleyen.ec.europa.eu at the ‘Choose Europe for Science' event at La Sorbonne 🇫🇷

Nature research paper: TIR domains produce histidine-ADPR as an immune signal in bacteria. https://go.nature.com/438mKVb