Everyone's least favorite lab mate
@kepatitis-c.bsky.social
I much prefer the sharpest of criticism of a single intelligent man to the thoughtless approval of the masses - Johannes Kepler “It is a damn poor mind indeed which can't think of at least two ways to spell any word.” -Andrew Jackson
Antibiotics and phage go brr
Amy Zamora@amycrobes.bsky.social · last mo.We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/
New rotation student doing his first Gibson!
Happy new year! The second big project of my PhD in Rachel Whitaker's lab is now up! 🎉 We look at how provirus infection affects the evolution of the bacterial chromosome with different types of viral induction – with CRISPRs or antibiotics. Take a peek 🦠 www.biorxiv.org/content/10.6...
Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that forms chronic infections in people with cystic fibrosis. Often P. aeruginosa strains are lysogens, infected with proviruses, that ...
biorxiv.org
🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 7mo agoNovel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
Happy to share that I’m opening my lab at the Weizmann Institute of Science! We’ll study systems-level regulation of bacterial defense, driven by RNA-protein interactions shaping cell fate. Now recruiting PhD students & postdocs tinyurl.com/4yfa55vd Please reach out and share!
What is the best strategy to win any contest? Eliminate your opponents of course. Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight. www.biorxiv.org/content/10.1...
The project has excellent lore. From contamination to a integrated tool to classify mobility, A-Dog (Arya to civilians) has found AMR gene have been increasing on MGEs likely due to the use of antibiotics. Some great graphs in here!
Michael Baym@baym.lol · 11mo agoWhat 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...
“I asked ChatGPT to generate” has replaced “Merriam Webster defines” as the new go to low effort introduction and PIs who start talks this way need to be made fun of
When I was told I’d have a summer undergrad I couldn’t have imagined how lucky I would be. Hue has no tolerance for the easy way out and takes on new challenges with an infectious positivity. One day (hopefully🤞) someone will be just as lucky to have her as a grad student. We will miss you!
I apparently deleted a important “TnpA” label from my poster so now my week is ruined but if you want to help search for more mistakes and you are at the Microbial Populations GRC come see me Wednesday
Last summer I was lucky to attend the Woods Hole Microbial Diversity course and the most important thing I got out of it was meeting Liana. Her genuine curiosity and meticulousness really shine in this super cool story on introns (i.e. the coolest RNAs around). Excited to see what you do next!
Liana Merk@bacteriyay.bsky.social · last yr.(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...
It is getting weirder and weirder seeing faceless accounts accuse jewish professors of antisemitism for bemoaning their loss of funding
My advisor @baym.lol pointedly speaking with WBUR. “I think that reason is a pretense. I think that this is an attack on Harvard as a symbol of academia in the United States.”
Lynn Jolicoeur@lynnjolicoeur.bsky.social · last yr."I'm still in shock. I know that there have been political issues around Harvard in recent weeks, but antibiotic resistance isn't one of them." My conversation with Harvard microbiologist @baym.lol, one of many researchers there who just lost millions in fed. grants. www.wbur.org/news/2025/05...
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
During my rotation I got to work on this project and I immediately knew Soumya and Han were destined to be the future leaders of science and I would be a fool to pass up a chance to work with them. Super thankful to have met, and continue to get to hang with, you guys!
Nature Biotechnology@natbiotech.nature.com · last yr.Evolution-guided protein design of IscB for persistent epigenome editing in vivo - @zhangf.bsky.social @broadinstitute.org @hhmi.org go.nature.com/44XVBph
Reposting with an eye catching figure because I forgot
Everyone's least favorite lab mate@kepatitis-c.bsky.social · last yr.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
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
Like we needed another reason for sex… But seriously this is a very cool result, surprisingly intuitive only after you read it. I interpret it is as sex delinking beneficial and deleterious mutations to enable greater adaptability. Shreyas worked super hard to figure this out, good work!
Shreyas Pai@theshreyaspai.bsky.social · last yr.Why is sex so common if it's so costly? Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)
My scientific career changed the day I met Fernando and my faith in science restored. In a world dominated by sequencing and LLMs, this project shows how much biology is hidden in plain sight waiting for the right person to make the connection, a must read for any scientist!
Fernando Rossine@fernpizza.bsky.social · last yr.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...
Greatful to have been given the opportunity to present my wacky little project at @crisprmeeting.bsky.social and thanks to @baym.lol and the rest of the lab for the support!
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
