Ben Adler

#Phages can evade #bacterial #immunity by disrupting #antiviral signals like cA3, triggering the 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

most modern human projects do not have simple bottlenecks. simple bottlenecks are simple to solve, so our systems knock those out and scale up until they face complex, multi-dimensional or self-contradictory bottlenecks (e.g. speed vs safety).

Some good new to share: my lab was recently awarded an NIH R35/MIRA award to continue our work on conjugative plasmids and plasmid-dependent phages! 🥳 🫶NIH🫶 www.wadsworth.org/news/nih-gra...

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

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...

A major pillar of the system is paying its skilled employees below-market “subsistence stipends” and sharing their work for free. private industry knows it’s the biggest beneficiary. It doesn’t want the music to stop

YprA-family helicases provide the missing link between diverse prokaryotic immune systems: Cell Host & Microbe https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(26)00208-8

i've built laboratories. i've built deep learning models. i've been evangelizing Big Data in Bio my whole career. give me money and i'll do it a lot more

NIAID (@niaidnews.bsky.social) has awarded $6M to launch a coordinated US phage therapy research network — 3 new centers! Excited our Stanford Center for Phage Pharmaceuticals (@stanfordmedicine.bsky.social) is one, & to work w/ @gladstoneinst.bsky.social & @pghphageprogram.bsky.social! 🧵 1/

Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

Ancient wars between microbes gave us key immune defenses | @science.org | AAAS www.science.org/content/arti... #microsky #virosky #immunosky

Chemical inactivation of a bacterial immune system de-domesticates a temperate phage and promotes its spread bioRxiv from Joseph Gerdt at Indiana University with @annadragos.bsky.social www.biorxiv.org/content/10.6... #PhageSky

🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...

The paper on my Ph.D. work is fully online! We used a ribozyme that barcodes 16S rRNA to track the transduction range of phage P1 in a synthetic community and real wastewater communities, while diving deeper into the unique range conferred by P1s two tail fibers. www.nature.com/articles/s41...

Let's get ready to tumble!

asymmetry of information permeates academic science. i'm talking: conferences campus visits grant review peer review the right people can put themselves 6 months ahead of the public record.

Saying it because @kenjmloi.bsky.social didn't: This is really close to a RNA system that targets protein sequences because of wobble bases in codons. Truly amazing discovery!!

The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...

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.

Excited to share our new findings in @science.org on how the DRT3 bacterial defense system uses a reverse transcriptase that builds DNA repeats without a nucleic acid template. Microbes never cease to amaze! www.science.org/doi/10.1126/...

Excited to share the last installation of my PhD work. Worked with an all-star team on this one who really made this all come together beautifully. @ranidreamer.bsky.social @amardeeep.bsky.social @benadler.bsky.social and many others. www.cell.com/cell-reports...

10 years ago @vivekmutalik.bsky.social introduced me to the wild world of phages. Today, @lucasmoriniere.bsky.social presents a truly foundational scale bridging genomes, viruses, editing and function. Truly an amazing scale and vision for the future! Congrats to phage foundry 🌶️🌶️🌶️

📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Come join us at AITHYRA! I highly encourage anyone excited about the interplay between AI and life sciences to apply. It's been an amazing place to start a lab. Feel free to reach out to me if you have any questions about our institute

New preprint: Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector. Great work led by Sabine Grüschow www.biorxiv.org/content/10.6...

After >10 years of our lab studying bacterial cGAS-like enzymes, @hobbslabutah.bsky.social finally reconstitutes viral sensing in vitro and discovers how these ancient receptors sense phage protease enzymes to detect virion assembly and activate antiviral immunity www.biorxiv.org/content/10.6...

Really phenomenal work from the Gerdt lab at Indiana University... I hope this becomes a major boon for phage therapy: "Chemical inhibition of a bacterial immune system" www.cell.com/cell-host-mi...

Life science research is plagued with repetitive rote work. This system is designed to support, organize and execute tasks across the research stack. procurement, inventory management, equipment telemetry, safety, and regulatory can be managed with and by the system.

I’ve jumped completely off the deep end and I’m building a stateful agentic environment for computational and experimental life science research. Inspired by some of the systems I’ve seen here, but different. It’s goal oriented and research focused

NLR-like immunity in bacteria A new study from the Alex Gao lab. The scope of this work is incredible!!! www.biorxiv.org/content/10.6...

All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

On this episode of the "What's in the vault?!?!" saga...

Protein domains have no single definition, so why stick to one segmentation? 🧩 Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing. You control the granularity. 👇 🔗 doi.org/10.1093/bioi...

🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8

We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing. www.biorxiv.org/content/10.1...

📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...

I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes: www.biorxiv.org/content/10.1...

I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.

Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there... www.biorxiv.org/content/10.1...

Amazing piece of work from @rtoshiro.bsky.social & Kim Seed at UC Berkeley. 🙌 Played a tiny role in this work. Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses www.biorxiv.org/content/10.1...