You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org

www.science.org/doi/10.1126/...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

Phage DisCo! Our targeted phage discovery method in press today: journals.asm.org/doi/10.1128/...

Perfectly timed with our four summer undergrad's first successful phage hunt... disco lights in the lab to mark the occasion 🕺

My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

Thanks Kep same to you🫡

(7/7) We’d love to hear your thoughts, and if you are at the RNA conference in San Diego this week, I am presenting this work at P2-353 in the second poster session!

(6/7) We highlight a few stories: evidence for retroposition into phage-specific loci, unique CapR domains not reported in group II intron-encoded homing endonucleases, and the presence of a group II intron in an annotated Inovirus, the first group II intron noted in a single stranded DNA organism.

(5/7) We use three lines of evidence along with Infernal hits. (1) The presence of full-length intronless homologs of genes the group II’s are inserted in. (2) Identification of pseudoknotted tertiary base-pairing not modeled by Infernal. (3) Similarity of intron-encoded ORFs to known group II ORFs.

(4/7) Recent accelerations in Infernal, a profile SCFG-based search and alignment tool from our lab, allow us to find these large RNAs across large genomic and metagenomic datasets.

(3/7) We wondered if they haven’t been widely identified in phage because they are challenging to find — they have low primary sequence similarity. Luckily, their splicing mechanism dictates strong conservation in parts of their secondary structure.

(2/7) Group II introns are self-splicing RNAs and the speculative ancestor of our own nuclear spliceosomal introns. They are widely known in bacterial, archaeal, and eukaryotic orgenallar genomes, but considered absent in phage.

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!

www.biorxiv.org/content/10.1...

Final grad paper is officially out! Grateful for the incredible team and all the support along the way!
www.nature.com/articles/s41...

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
🧵🧪

Congratulations!!

Llamas, dolphins and measles? Oh my!

So thankful this story is finally breaking containment from my time in the Manguso Lab at the Broad. Using pieces from viruses and llamas we engineered selective cell specific viral like particles with reduced immunogenicity for in vivo gene delivery

rnahub.og
A webserver to generate RNA alignments with secondary structure assessment

www.biorxiv.org/content/10.1...

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics!
(1/n) www.biorxiv.org/content/earl...