William Navarre

Powerful CRISPR system inserts whole gene into human DNA ‘Directed’ evolution in the laboratory creates an editing tool that outperforms classic CRISPR systems.

www.nature.com/articles/d41...
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'

GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra

Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs

github.com/arcInstitute...

Wow.

Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus
Finally out in PLOS Pathogens. Congrats Hannah Ochner and co-authors. @mrclmb.bsky.social

journals.plos.org/plospathogen...

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...

The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha

Beautiful!

Finally in peer-reviewed form: Mapping the ultrastructural topology of the corynebacterial cell surface. @bupbuse.bsky.social @vikramalva.bsky.social

Please also see concurrent beautiful work from @adriasogues.bsky.social and Han Remaut.

People spend a lot of time wondering why the left is worse at using independent media to control the national narrative.

A useful exercise is to ask why the left is also worse at selling snake oil and pyramid schemes, because I think the reasons are basically exactly the same.

@nytimes.com - it’s not “deportation” if you aren’t returned to your home country and you’re put in a foreign prison without a trial or any legal representation. Call it what it is and quit obfuscating.

I wouldn’t make an equivalent argument on this point. Saying “other labs are ALSO bad” has no bearing on whether the wuhan lab was/was not the source.

The money isn’t really an issue since it wasn’t pulled from grants that would have gone elsewhere. The problems are much bigger and more complex. First it will promote distrust (science playing God). It will also make people think we can ‘science’ our way out of ecological destruction.

Couldn't agree more that 'avoiding jargon when explaining a niche scientific concept to a non-expert' is not the same thing as 'dumbing it down'. If anything a reliance on jargon more often shows you don't have an innate and intuitive understanding of the topic.

Excited to share a main project from my PhD, out now in
@naturecomms.bsky.social! 📝
We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱
nature.com/articles/s41...
Take a look! Thread below... 🧵

Wow

Plasmid-driven strategies for clone success in Escherichia coli - Nature Communications Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of ...

Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️

www.nature.com/articles/s41...

Quick weekend read when you get the chance! I’m excited to announce that the preprint for a major chapter of my thesis work is out on BioRxiv! In this study, we highlight the essential role that pyrimidine metabolism plays in promoting activity of the SaeRS TCS in Staphylococcus aureus! 1/3

She's right, of course, but her tone throughout is similar to the condescending and arrogant 'deplorables' comment she made years ago. I'd think twice before forwarding this opinion piece to any Trump voter in your extended family. It won't change their minds about anything.

My lab cultivated a number of microbes from the murine gut and compared the genomes of the isolates to genomes from metagenomic assemblies. It wasn't encouraging. MAGs for some species were pretty good but most MAGs were chimeric.

If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!

#MicroSky

Amazing news! Welcome (back?) to Canada!

we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯

Sorry I thought red was Canada and blue was US. Not age.

I was looking at the suicide rates. Did I read that chart incorrectly?

Why was Canada so much worse in the 90s? Also stark that, despite more focus on mental health, the rates in both US and CAN have been going up throughout the 2000s. Ugh.

THIS IS INCREDIBLE! Cohen Children’s Medical Center has confirmed that it has successfully ELIMINATED sickle cell disease from Sebastien Beauzile, using the groundbreaking genetic treatment Lyfgenia. He has made HISTORY by becoming the FIRST in New York to be CURED of sickle cell anemia! 🧪🧵⬇️

1/ @nabroderick.bsky.social and @harmitmalik.bsky.social have posed questions asking how to US students may seek opportunities outside the US (EU and Canada). As a Department Chair in Canada in #immunosky, I offer my perspective in this "bluetorial".

What if We Can't Rely on PubMed? - Absolutely Maybe PubMed is incredibly reliable. And a lot depends on it. It’s an ecosystem built around MEDLINE, the steady feed of new publications…

Hate that it has come to this, but it's time to consider PubMed vulnerable to enshittification. My latest post @plos.org discusses the lines we need to fight to hold – and alternatives we can rely on internationally:

absolutelymaybe.plos.org/2025/02/14/w...

#medlibs

the ASF is sooooo not a complete mouse microbiota.

Pass it on.
#StandWithUkraine