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 🌶️🌶️🌶️
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
📣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
ofc, you need to be able easily classify your particles and afford Cryo facilities (using somewhat risky samples), but this is inspiring from a speed-running life science research point of view
I love this concept -- plasmid to Cryo structure in a day!
www.biorxiv.org/content/10.1...
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 (🧵)
Ah, this is amazing work! 🤩🤩
Big congratulations to the team!
🚨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...
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
#microsky #phagesky #phage defence
Thanks, @crypticprophage.bsky.social for pointing it out on “the other side”
www.science.org/doi/10.1126/...
A mysterious lactamase-nuclease module found in multiple defense systems finally solved ! Congrats @owentuck.bsky.social et al. !
Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.
Huge congrats to Owen, Jason, and team! Such a fun story