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.
I was wondering about this, too. And, of course whether they used Next Gen technologies - like 454- to do the sequencing.
I was wondering that also, especially since their other evidence for mixed strains are different colony morphologies...which again could be due to gene regulation.
There are at least a couple of reported inversions (one in the pXO1 plasmid) and one of a pathogenicity island in B. anthracis. I haven't honestly read the NY Times article in toto, so I don't know which one (if even) they're talking about.
Here's a TIGR report on sequencing a couple of B. anthracis strains after the attacks, and they identified the pXO1 inversion: http://www.sciencemag.org/cgi/content/full/296/5575/2028
B. anthracis is a very monomorphic bacterium and one should expect the genome sequence from strain to strain to be nearly identical. However, as TomJoe wrote there are reports of inversions of the pathogenicity island on the virulence plasmid, pXO1. Interestingly there are also IS elements on pXO1, possibly aiding in the inversion. This inversion could occur during propagation or sporulation or it could be from mixing two strains. If the inversion occured during propogation of a single colony, you would expect this to be the only difference, given the monomorphic nature of the bacterium. If the culture were mixed from two separate sources, then additional SNPs might be found that could differentiate the strains besides the inverted piece.
By the way, do we have any IDists complaining about the assumptions behind sequencing anthrax DNA?
After all, the Designer might very well have chosen to give two different strains of anthrax the exact same DNA. Who knows, what with their whacky, whimsical, unpredictable Designer, who makes malaria for the fun of it?
Since there's absolutely nothing in principle to accept the results of sequencing within species as indicating that normal processes of heredity, mutation, and natural selection are operating, while denying the same type of processes being responsible across species, families, and phyla, they really ought to be against the "naturalistic assumptions behind anthrax sequencing.
I just thought I'd reiterate how potentially threatening ID is, even to normal discovery processes in tracking down and prosecuting biological terrorists.