Everyone's least favorite lab mate

I know you are but what am I

“It is a damn poor mind that can think of only one way to spell a word”

-Andrew Jackson

Awe shucks

I almost forgot

Thanks to @baym.lol for giving me a home and the opportunity, @fernpizza.bsky.social who taught me the ropes of evolutionary biology, @wheezenfeld.bsky.social @theshreyaspai.bsky.social @nquinoneso.bsky.social, @celiasouque.bsky.social for the help along the way and the rest of the Baym lab crew!

This work highlights how interactions between MGEs can produce unique effects where both benefit from their nested existence. Furthermore, we have extended TnpB’s mechanism that sheds light on why TnpB is so successful.

So we did a similar experiment with conjugative plasmids and found that IS605 provides offensive and defensive benefits to conjugative plasmids, acting like a primitive anti-self defense mechanism to spread plasmids between cells.

Moreover we also noticed that IS605 tended to cluster in conserved plasmid regions of conjugative plasmids.

And specifically it is the RNA-guided nuclease activity that is responsible for this benefit - confirming our hypothesis!

Which we were able to show experimentally by competing plasmids in a displacement assay. We see plasmids that contain an IS605 have an enormous advantage over those that don’t, despite the IS itself being detrimental to plasmid replication

But in the context of plasmids this results in a newly inserted IS605 to reprogram TnpB to target, and destroy, all IS- plasmids within the cell. With no competition only IS+ plasmids will replicate, biasing their inheritance.

So what is going on? TnpB happens to be the ancestor to Cas12 and is also an RNA-guided nuclease. The @sternberglab.bsky.social lab figured out TnpB uses this activity to promote genomic retention by cutting excision scars - preventing IS loss.

But not all IS families followed this trend. The IS605 family deviates while its close cousin IS200 does not. This suggests that IS605 has a unique interaction with plasmids, with the additional gene carried by IS605, TnpB, likely being responsible.

Well they can just have more shots on goal. We found a consistent relationship between the chromosomal copy number of an IS co-occurrence on plasmids. The more you try the more you are likely to succeed (poetic I know).

Insertion Sequences (IS) are enriched in plasmids. Which is quite curious as plasmids often have multiple copies preventing efficient inheritance of IS+ plasmids. So how do ISs come to be on plasmids in the first place?

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...

There are no “O” amino acids you ding dongs

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!

“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!

Alternatively if you have a red sharpie hmu

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!

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.”

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

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!

Reposting with an eye catching figure because I forgot

And thank you to Rob and Kathleen for taking a chance on me when no one else would, and to all the people I got to work with and learn from in the lab!

All in all a super fun project where I first truly learned independence. More importantly I got to work alongside @kyrellosi.bsky.social and @petermaxallen.bsky.social and watch them go from bleary eyed fresh from undergrad to fully trained scientists in their own right <3