Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes
www.science.org/doi/10.1126/...
Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!
Linking below previous thread on our findings
Stunning new structural analysis and mechanism for Tmn anti-phage defense by @fnobrega.bsky.social
www.biorxiv.org/content/10.6...
A tremendous story about a defense system that triggers plasmolysis! It was an incredibly exciting puzzle to crack. Huge thanks to @fnobrega.bsky.social for the opportunity to work on this!
Made a short video as a response. 3 questions remain for me.
1) What is the definition of a "DEl activity," and how is it being communicated to NIH staff so they can determine whether a grant qualifies?
(Continued below)
Nature research paper: Convergent MurJ flippase inhibition by phage lysis proteins
go.nature.com/4aAWHKb
β‘οΈ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? π€
π§΅π
MicrobeAtlas is now published in Cell. πππ¦
Explore the paper and resource to see what large-scale microbiome data reveal about global ecological patterns:
www.cell.com/cell/fulltex...
For a concrete application, see our recent work on βCommunity conservatismβ:
www.nature.com/articles/s41...
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... π§΅π
Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...
Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org !
Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these.
www.ebi.ac.uk/about/news/u...
FYI were starting weird structure/evolution/biology stuff at Glasgow University!
If you're interested let me know! Tell your friends!
CRYO www.jobs.gla.ac.uk/job/research...
BIOINFO www.jobs.gla.ac.uk/job/research...
TECHNICIAN www.jobs.gla.ac.uk/job/technici...
#science #hiring #evolution
My colleague Victor Tobiasson has just started his lab at the University of Glasgow and is recruiting postdocs! If youβre into structural biology and non-model organisms, this is a great place to be! Check out his new eukaryogenesis paper that is out today: www.nature.com/articles/s41...
Dominant contribution of Asgard archaea to eukaryogenesis www.nature.com/articles/s41...
Neisseria gonorrhoeae carries an unusually large number of restrictionβmodification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...
Congrats! It is a tremendous project! ΧΧ ΧΧΧ Χ©ΧΧ
Job AD. Research Directions:
1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao
2. Study of hypermutability and selection using population cohorts with E. Koch
3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
Protein domains have no single definition, so why stick to one segmentation? π§©
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. π
π doi.org/10.1093/bioi...
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
Happy to be part of this tremendous effort lead by @fnobrega.bsky.social to build a community-driven collection of Klebsiella strains & phages.
Keep an eye on the Felixviridae, these phages are wild and seem to swap huge genome segments with ease ππ§¬
Congratulations! Well deserved!
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
Gluing a bulky host protein onto an immune surveillance complex is a wild mechanism of viral immune evasion!
@natmicrobiol.nature.com
#phagesky #phage #microsky
www.nature.com/articles/s41...
Two days left to apply for a PhD or postdoc position in my lab!
Here is the full letter:
collections.nlm.nih.gov/catalog/nlm:...
Last year it was discovered that a single bacterial NLR-like protein can recognize multiple, structurally unrelated phage proteins (BΓ©chon et al, Kibby et al)
Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
@prczhaoyansong.bsky.socialβs deep dive into the dark matter of compost communities is now out π Genomic islands hijack jumbo phagesβwhose capsids enable transfer of large tracts of DNAβshedding new light on the scale & scope of phage-mediated gene flow π
www.pnas.org/doi/10.1073/...
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!
For more information and how to apply, see below π
Please RT!
