So happy to share this new preprint, co-led by @erinedoherty.bsky.social! We found that 2H PDEs exceptionally widespread across the virome. They are also structurally diverse, which enables them to degrade nucleotide messengers involved in diverse bacterial immune systems.

📣 New paper alert 📣 IGI's @jenniferdoudna.bsky.social, @cresslab.bsky.social & @benadler.bsky.social team up with fellow #CRISPR pioneer Rodolphe Barrangou to engineer phages to edit diverse microbe species in their native communities in a recent @pnas.org pub. Read more: ow.ly/vZNR50WMohr 🧬🦠

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨ Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...

📢 Preprint out! Together with @reneechang.bsky.social @kranzuschlab.bsky.social and the amazing @soreklab.bsky.social, we explored viral sponges to map their diversity and function. Discovered huge diversity, including sponges that inhibit Pycsar & Type IV Thoeris! www.biorxiv.org/content/10.1...

Excited to share our new preprint co-led by @jnoms.bsky.social! Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.

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.

If you are an undergraduate student in #STEM and interested in becoming an intern at @jgi.doe.gov (or elsewhere at @berkeleylab.lbl.gov) through @energygov.bsky.social's Science Undergraduate Laboratory Internship (SULI): 🔗 education.lbl.gov/internships/... 🔗 science.osti.gov/wdts/suli

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you www.jobbnorge.no/en/available...

I'm pleased to announce that I will be starting my lab as an Assistant Professor at UMass Chan Medical School in August! My group will study phages that infect corynebacteria and mycobacteria to understand bacterial cell envelope assembly and phage gene function. Website and more info to come soon!

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥 I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com @cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social www.cell.com/cell-systems... 🧵...

Structure of the virulence-associated Neisseria meningitidis filamentous bacteriophage MDAphi Out in @pnas.org Congrats @janboehning.bsky.social @abultarafder.bsky.social Miles Graham @mathieucoureuil.bsky.social @mrclmb.bsky.social @hopitalnecker.bsky.social www.pnas.org/doi/10.1073/...

Great episode and great paper (@cp-cellhostmicrobe.bsky.social)!

urldefense.com/v3/__https:/... Feeling happy ❤️😇

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/

‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.

Read my review with @soreklab.bsky.social on the nucleotide pool as a central playground in antiviral immunity across humans, bacteria and plants! 🧍‍♀️🦠🌿 & how viruses overcome these nucleotide-based immune mechanisms 🗡️ www.nature.com/articles/s41...

Untangling phage immunity systems can be really challenging but @owentuck.bsky.social and team used phylogeny and biochemistry beautifully to show how a pair of genes got repurposed as a component in multiple defence systems.

Many antiphage effectors are single proteins that are "weapons" against viral predators. If simplicity works, why use something complex? It allows for effector paradigms. @owentuck.bsky.social and Jason Hu's show how a complex effector unearths a larger nuclease-protease paradigm in immunity 👇

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

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!

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...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

Seriously cool Microbiome Engineering work! www.science.org/doi/10.1126/...

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...

Extremely excited to share I have accepted an offer to be an Assistant Professor in the MCDB department at the University of Michigan! Go Blue! The Ledvina lab will investigate the molecular interworking of the bacterial immune systems including defense against both viral and bacterial pathogens.

Excited to see this new, and extensively-rewritten, version of our preprint up now! With @paulturnerlab.bsky.social we show how bacterial population dynamics (e.g. growth curves) can be used to accurately quantify bacteriophage infectivity 🦠 🧫🔬 #microbiology #VirEvol doi.org/10.1101/2023...

#SynBYSS Thur 10 am USA CT 162nd, May 22: Dr Alessandra Ferrari at European Research Council & Dr Amelie Skopp at Tech U. Munich @erc.europa.eu 163rd, Jun 5: Prof Sanjay Vashee at JCVI & Dr Ben Adler at UCB @jcvi.org @benadler.bsky.social Zoom link for the audience: us02web.zoom.us/j/88380504839

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

I love so many things about this: - phage defense(ish)* - new MGE ecology - model systems beyond E.coli - pretty images 📸 Check it out! 👇

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

My dept in London at Imperial (Bioengineering) is recruiting a group leader at Professor level 🧑‍🎓 Please RT. It's a great place with world-class expertise in all sorts of biomedical & biological engineering topics like synthetic biology. It's also not in the USA. www.imperial.ac.uk/jobs/search-...

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

Now online at Molecular Cell! What makes SpyCas9 such an efficient editor? Read more at: www.cell.com/molecular-ce... Congrats @honglue.bsky.social, Noor Al-Sayyad, and @kevinwasko.bsky.social!

New OA Letter: "Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis" rdcu.be/eiJVL ...engineered the tobacco rattle virus to express the RNA-guided TnpB enzyme ISYmu1 and guide RNA for transgene-free germline editing.

Pathogen outbreak in these crazy times

Very happy to share our newly published work! We engineered phages for intercellular communication in multicellular consortia and integrated it with CRISPR-based gene regulation for biocomputing. Congratulations to @astrikusuma.bsky.social @dmf-unil.bsky.social @fbm-unil.bsky.social rdcu.be/ehORO

Gene editing and many other useful biotechnology tools came from studies of bacteria fighting off viral invaders, but scientists have only begun to unlock the secrets of this microbial warfare. Read the Nature feature on what breakthroughs could be next. 🧪

Coming up Tuesday at noon Pacific – @dbikard.bsky.social of @pasteur.fr will be giving a talk on the #phage-bacteria arms race! Join us at the IGI Building in Berkeley or on Zoom: innovativegenomics.org/events/semin...

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

What a fantastic meeting and community! Leaving inspired to keep investigating novel mechanisms at the phage-host interface 🦠

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

Gene editing and many other useful biotechnology tools came from studies of bacteria fighting off viral invaders. But scientists have only begun to unlock the secrets of this ancient arms race https://go.nature.com/4lD4LOa

OK. I don't need to explain the importance of 'blue-sky' research to people on here, but this story in @nature.com is so cool! The area of research that delivered CRISPR gene editing has exploded and is turning up all kinds of cool tools for molecular biology. www.nature.com/articles/d41...

New online! Genetics, ecology and evolution of phage satellites

Giving a seminar for the Genome Engineering Seminar Series at Harvard this Monday, April 7 at 1pm EST / 10am PST! 🎙️ I’ll be talking about our Cas9 work—if you’ve ever wondered what the recipe is for high-efficiency CRISPR genome editing, come hang out!🧬💥 📍 Zoom link: harvard.zoom.us/j/94394339529

Catch @honglue.bsky.social at the Harvard Genome Engineering Seminar Series this Monday, April 7 at 1pm EST / 10am PST! If you’ve ever wondered why SpyCas9 is so efficient at genome editing, don’t miss his talk—Zoom link: harvard.zoom.us/j/94394339529