Pretty sure the same pack took one of my neighbor’s pets in broad daylight last Saturday afternoon. (Westwood apartments, a few blocks away from this attack).

Looking forward to him in Slow Horses next season

By my second quarter, I ran out of money and got a job washing dishes & filling tip boxes in a plant biochem lab. Soon, I was helping with benchwork and was hooked forever.

The subject I loved and was good at in HS was geology, but my teacher said the only jobs were working for oil companies … so that was out. Reading "The Breakthrough" was my first exposure to research, so I started college as Chem Engineering/MatSci major.

The guy that shot that news footage (and later made some Oregon-related documentaries) was the guest speaker at our retreat in grad school in the late 90s. I'm pretty sure he showed us more exploding-whale footage than is available on YouTube.

Based on blast, the insertion is also found in the very popular pGWB binary vectors as well. (Between the LB and NOS promoter.)

In the case of pCB302, the insertion is inside the T-region but on the opposite side of the selectable marker from the cloning region so we never saw it until I converted it for GoldenGate. Pretty much every transgenic Arabidopsis line I made for 20 years had an extra 525-bp tpnA fragment.

Until someone can synthesize a host strain without active transposable elements, we just have to be vigilant. Insertions are rare and there aren't many places one can insert without affecting plasmid function and also evading typical insert screenings. Whole-plasmid sequencing helps.

We've found a couple transposon insertions in plasmids in recent years. One was likely a new insertion after using NEB's PCR cloning kit. NEB claimed nobody else complained, so it was likely a one-off. The other was also in the parent binary vector, pCB302, but wasn't noticed until WholePlasmidSeq.

So, is the entire paper complete bunk from using outdated methods? or can we explain the discrepancies with something not considered at the time? (These two tables are the only data in the paper.)

When it crossed my mind this week, I remembered that the genome of this moss (Funaria hygrometrica) has now been sequenced (@peterszovenyi.bsky.social lab) and the 0.7±0.02 A:G ratio should have been >1 given the genome’s %GC being <50% (at least for genes I’ve sampled). That's a huge discrepancy.

The reason this initially caught my eye was because almost every auxin-induced gene I'd looked at had long-ish G tracts in their 5′ UTRs. Nevertheless, the back-of-the-envelope calculations couldn’t make sense of this paper's values.

Combined with Table 1 that showed that bud cells have >10× more RNA than protonemal cells, that’d be a huge jump in the amount of G bases. (I like the use of "µµg" instead of pg!)

Long before single-cell transcriptomics, they were able to measure total base compositions of DNA and RNA from microdissected individual cells. They measured these values for protonemal filament cells and bud cells and noticed a huge jump in G in bud cells. (Internal control DNA was unchanged.)

It looks like 'Rethinking Fandom' was already in the LibGen database (illegally) used to train Meta's AI. (A bunch of my papers were in it.) www.theatlantic.com/technology/a...

I caught the New Albany reference