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...
This application closes on Sept 15! If you're interested in a computational postdoc position in my lab, please apply here! Lots of fun science :)
Jason Nomburg@jnoms.bsky.social · 2mo agoI am hiring a computational postdoctoral fellow or bioinformatics scientist! Please apply here if interested, or share with anyone who may be. This position will be following up on our work studying the virus-host conflict. Reposts appreciated! aithyra.onlyfy.jobs/en/job/v2gwu...
A fast method for building phylogenetic trees with millions of sequences and then a model that leverages the tree structure to predict viral protein evolution! @seyonec.bsky.social @claudiadriscoll.bsky.social @garykbrixi.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
We find that nuclear Pol II drops several-fold in abundance with age. This is a somatic phenomenon–the germline seems to maintain Pol II just fine. Somatic declines in Pol II begin at the start of adulthood, a time when individuals still look young and vigorous. 11/22
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
I didn’t think I’d ever see a solar eclipse with 100% totality, but that was absolutely unreal
The July issue is live nature.com/nbt/volumes/... On the cover, @ycongzhang.bsky.social @efranzosa.bsky.social @hutlab.bsky.social introduce FUGAsseM, a method that uses microbial community data to infer the functions of previously uncharacterized gene products go.nature.com/435C4lp rdcu.be/ftNUV
AI model using AlphaFold3-predicted contact probabilities maps and reduces genome editor off-targets, enabling highly precise DNA base editing with improved specificity. #NBThighlight www.nature.com/articles/s41...
Precise DNA base editing using AlphaFold3-based contact modelling - Nature
ContactSeek is an AlphaFold3-driven model that can improve the precision of genome-editing tools.
nature.com
New preprint on bioRxiv! 🧬 “Structural mechanism of the type IX Retron-Kva2 anti-phage defense system” Led by the Nishimasu lab (Univ. Tokyo) — happy to have been part of the team! 🔗 doi.org/10.64898/202...
Structural mechanism of the type IX Retron-Kva2 anti-phage defense system
Retrons are prokaryotic genetic elements that protect bacterial cells from invading phages. The type IX retron comprises a non-coding RNA, a reverse transcriptase (RT), and dual effectors: a putative ...
doi.org
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...
Our new preprint is out! Using AI-guided design (RFdiffusion + ProteinMPNN), we engineered a plant immune receptor to recognise non-cognate pathogen effectors. Huge thanks to our amazing co-authors for making this possible! doi.org/10.64898/202...
Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.
The rapid evolution of plant pathogens poses a persistent threat to global agricultural sustainability, often outpacing the discovery and deployment of natural disease resistance genes. While bioengin...
doi.org
Thrilled to share! We present the structure of a prototypical P2 OLD and reveal that its tRNAse activity is triggered by ssDNA hairpins in phage origins or unresolved termini in RecBCD-deficient cells. Great team effort with Wang, Bikard & Nudler labs. www.biorxiv.org/content/10.6...
OLD sentinel: an abortive tRNase surveys phage replication and DNA defects in RecBCD-compromised cells
OLD, an abortive immunity protein from prophage P2, consists of an ABC ATPase sensor and a TO-PRIM nuclease effector - a core architecture shared by a large protein family, including components of ant...
biorxiv.org
The protein design team at Deepmind is hiring! We are looking for someone to run design campaigns and contribute to model improvement. Should have expertise in design applications and using wetlab data feedback to improve methods. Please RT! DM with Qs. www.google.com/about/career...
Research Scientist, Protein Design, DeepMind
As an organization, Google maintains a portfolio of research projects driven by fundamental research, new product innovation, product contribution and infrastructure goals, while providing individuals...
google.com
Happy to share a preview of recent work from E. Koonin & colleagues, revealing the widespread presence of reparative helicases as central components of prokaryotic immune systems. Written by our talented PhD student Oksana. www.cell.com/cell-host-mi...
A repair helicase unravels the tangled web of bacterial immunity
DNA repair proteins are repeatedly repurposed for antiviral immunity. In this issue of Cell Host & Microbe, Bell et al. utilized phylogenetic reconstruction of the evolutionary routes of the YprA repa...
cell.com
📄 *Magnesium as a conformational gatekeeper of KRAS: Structural dynamics and therapeutic implications* (Fig. 6b) Read the full study in Protein Science: onlinelibrary.wiley.com/doi/10.1002/...
Magnesium as a conformational gatekeeper of KRAS: Structural dynamics and therapeutic implications
Magnesium serves as an essential cofactor for small GTPases, yet its structural role in regulating KRAS conformational dynamics and nucleotide exchange remains poorly understood. Here, we combine hyd....
onlinelibrary.wiley.com
The 2027 Cambridge Diary Calendar. It’s calendar time again when you have the opportunity to help decide which images make up the Cambridge Diary 2027 Calendar. This year we will be building the calendar live online at cambridgebooks.co.uk.
Three weeks ago, we welcomed the local scientific community to join us at our headquarters in Kenmore Square for the inaugural lecture in the AI Proteins Seminar Series. Our speaker Neil King from @uwproteindesign.bsky.social delivered a superb seminar. Check it out 👇 youtu.be/OPRMfRnlx1k
Neil King: ML-based design of nanoparticle vaccines (AI Proteins Seminar Series)
YouTube video by AI Proteins
youtu.be
Imagine programming protein, DNA, and RNA systems like you would write computer code, or even by natural language prompting of an AI agent. @brianhie.bsky.social and team just made this a reality with Proto: a high-level programming language for generative biology.
Efficient generation of epitope-targeted antibodies with Germinal - @brianhie.bsky.social @synbiogaolab.bsky.social @stanford.edu @arcinstitute.org www.nature.com/articles/s41...
Efficient generation of epitope-targeted antibodies with Germinal - Nature Biotechnology
Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.
nature.com
We regret that our event on Extreme Heat: Improving governance and strengthening action around the world has been cancelled due to the red extreme heat warning issued by the UK Met Office. Our apologies to everyone who was planning to attend the event.
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...
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...
nature.com
Norway is banning generative AI for schoolchildren under 13 starting in September.
Norway says math, reading, and writing come first as it introduces AI restrictions for under-13s
Norway is taking steps to limit how generative AI can be used in schools from the start of the next school year.
techradar.com
Excited to share the latest version of FlashPPI published with @pnas.org ! And stay tuned for updates soon…👀
Tatta Bio@tattabio.bsky.social · 3mo agoOur FlashPPI paper is out in @pnas.org! FlashPPI is a model for proteome-wide protein-protein interaction prediction. 🔹4x better predictive performance & 2,400x faster than existing sequence-based methods 🔹20,000x faster than leading structure-based approaches. www.pnas.org/doi/10.1073/...
New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)
The CRISPR-Cas system in E. coli K-12 is considered inactive. We questioned whether mobile elements encode anti-CRISPRs against this system and found a highly abundant AcrIE9-AcrIE10 tandem and a novel AcrIE13 — an HTH protein more similar to Aca than known Acrs. www.pnas.org/doi/10.1073/...
A census of anti-CRISPR proteins reveals AcrIE9 and AcrIE13 as inhibitors of the Escherichia coli K12 type IE CRISPR-Cas system | PNAS
CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins....
pnas.org
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com 🌐 https://search.foldseek.com/folddisco
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
nature.com
Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco