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
- Johannes Kepler
“It is a damn poor mind indeed which can't think of at least two ways to spell any word.”
-Andrew Jackson
I know you are but what am I
November 22, 2025 at 3:38 PM
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
-Andrew Jackson
November 21, 2025 at 2:41 PM
“It is a damn poor mind that can think of only one way to spell a word”
-Andrew Jackson
-Andrew Jackson
Awe shucks
November 21, 2025 at 3:41 AM
Awe shucks
I almost forgot
November 20, 2025 at 10:13 PM
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!
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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!
November 20, 2025 at 10:12 PM
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
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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.
November 20, 2025 at 10:12 PM
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).
November 20, 2025 at 10:12 PM
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?
November 20, 2025 at 10:12 PM
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?
There are no “O” amino acids you ding dongs
September 3, 2025 at 12:21 PM
There are no “O” amino acids you ding dongs
Alternatively if you have a red sharpie hmu
July 6, 2025 at 7:07 PM
Alternatively if you have a red sharpie hmu