I much prefer the sharpest of criticism of a single intelligent man to the thoughtless approval of the masses - Johannes Kepler
Joined April 2014
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Antibiotics and phage go brr
🚨 New preprint! 🚨
We're excited to share our latest work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project to work on with @implosian, @baym, @TheShreyasPai, @KeplerMears, & @fernpizza
biorxiv.org/content/10.64898… 1/
Look out science twitter, @baym is starting his rotation in the lab and is already breaking things!
Arya (my best friend) does not have social media, he asked me to tweet this for him. But if you want to chat about science (or offer him a job) you can contact him at arya.casa/contact. He’ll (probably) be defending soon!
Manuscript Code: github.com/baymlab/deletion-…
Prefix-Suffix Approach: github.com/aryakaul/prefixsu…
Many thanks to co-authors @fernpizza, @KarelBrinda & @baym + GenScale/Baym lab! Funded by NIH, Packard, Pew, Sloan & @ChateaubriandUS
Some ~caveats~
🔹 We haven't proven any deletion was beneficial
🔹 No functional deletion-born fusion yet - selection analyses show mainly diversifying selection
🔹 Our method misses fusions with terminal mutations (requires exact 54bp matches)
The "deletional bias" in bacterial genomes has long been framed as destructive - the pruning away of genetic material.
Our findings suggest it might also be creative: deletions don't just remove genes, they can also build new ones!
You can try the prefix-suffix approach yourself! Find the Snakemake pipeline here github.com/aryakaul/prefixsu…
The prefix-suffix approach isn't just for fusions. We also found:
🔹 Internal deletions
🔹 Repeat prophage insertions
🔹 Variable gene cargo in mobile elements
It's a general tool for surveying structural variation at scale!
But here's the CATCH: detection depends on sampling depth.
When we queried well-sampled protein families we found significantly more fusions than from uniformly sampled families.
We're only seeing the tip of the iceberg. As databases grow, we expect to find more.
