In reading this NY Times story about the anthrax investigation, this statement about how the presence of an inversion (a region of flipped DNA) puzzled me (italics mine):
The genome of various stocks of the Ames strain of anthrax used in the attacks were almost identical in all the 5 million chemical letters of their DNA. But researchers found enough differences in the attack strain to provide a reasonable chance of identifying its source.
The chief difference was that a stretch of DNA was flipped head to tail in some bacteria in the attack strain, but not in any other samples.
Further, the attack strain contained bacteria with both the flipped and the unflipped DNA, showing that it was a mixture of two strains, which analysts later found reflected a mix of origins — 85 percent from the Dugway Proving Ground of the Army in Utah and 15 percent added at Fort Detrick, according to one person close to the investigation.
Does anyone know more about this inversion? In many bacteria, inversions are used as regulatory mechanisms–when the DNA is in one direction, nearby genes are turned on, and when in the other, they’re turned off. Like so (this is a made up example for illustrative purposes only):
(usually these regions are hundreds of bases long)
Bacteria have mechanisms that specifically do this (it’s a screwy way to regulate a gene, but that’s what many bacteria do; consider it evidence for the Theory of Fucking Stupid Design). Depending on how the bacteria were cultured, it’s possible to get strains in one orientation or the other, or…a mixture. In genomics, recent work by Julian Parkhill and his colleagues showed that these variable regions (and others, such as regions that copy themselves) can be detected during genomic sequencing, but will often considered to be errors unless you know you should be looking for these inversions and duplications.
So, does anyone know more about this B. anthracis inversion? A quick Medline search didn’t yield anything. It’s not obvious, without more information, that this is evidence of a culture formed by mixing two strains.