Mike the Mad Biologist

Yesterday, I mentioned my doubts about there being two anthrax strains used in the 2001 attacks. Thanks to an article identified by reader TomJoe, I’m convinced that there was only one anthrax strain involved, if the only evidence for the existence of two strains is that there is a DNA inversion.

Just to remind everyone, this is what I mean by a DNA 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):

ON: ATTGAAGAACCA

OFF: ATAGAAGTACCA

(usually these regions are hundreds or thousands 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.

So here’s what’s written in that article TomJoe dug up (italics mine; citations removed for reading ease):

In addition to the SNPs and VNTRs detected in this analysis, we identified two large inversions in pXO1 of the Florida isolate in relation to the previously sequenced Sterne strain. The largest (44.8 kbp) occurs between coordinates 117,178 and 162,008 (using the Sterne strain coordinates). It is flanked by inverted copies of an IS1627 sequence and is centered on the pXO1 “pathogenicity island”, which includes the genes for the tripartite lethal factor toxin. Inversion of the pathogenicity island has been described; our sequence coverage data and polymerase chain reaction (PCR) amplification across the junctions show that the Florida isolate contains a mixture of both orientations.

To translate this into English, what they found is that DNA from a single bacterial isolate (or strain) of anthrax had both orientations of one inversion, and that this was confirmed using two different methods.

Now, I don’t know if the inversion is the only purported evidence for the use of two strains simultaneously. Confirmed SNPs (a SNP, or Single Nucleotide Polymorphism, is a single change in the smallest subunit of DNA; e.g., an “A” to a “T”) would indicate a two strain mix, but the inversion by itself is not sufficient evidence for a strain mix. As noted in the previous post, these types of inversions are not rare phenomena in bacteria (e.g., “phase inversion”). And if you look at the comments of that post, I wasn’t the only one who thought this.

This really does matter, since, as long as doubts remain, we’re going to be trapped in the land of the surreal. At the very least, we have to nail down the scientific evidence.

Cited article: Timothy D. Read, Steven L. Salzberg, Mihai Pop, Martin Shumway, Lowell Umayam, Lingxia Jiang, Erik Holtzapple, Joseph D. Busch, Kimothy L. Smith, James M. Schupp, Daniel Solomon, Paul Keim, and Claire M. Fraser. 2002. Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis. Science 296: 2028. DOI: 10.1126/science.1071837

Comments

  1. #1 TomJoe
    August 7, 2008

    I assume that by confirmed SNP you’re referring to SNPs which do not originate in paralogous sequences within bacteria. SNPs in those areas could potentially give us a “two strain mix” profile, though the 85/15 split would have been a bit odd. Of course, according to this report, B. anthracis only has two paralogous sequences within its genome, so the paralogous sequence issue isn’t really much of an issue in this case anyways.

  2. #2 TomJoe
    August 7, 2008

    Oh, and like you … I don’t think we’re dealing with multiple strains, just the one. And thanks for the h/t, much appreciated. :)

  3. #3 qetzal
    August 7, 2008

    Very interesting set of posts. Thanks to you and the TomJoe for the info!

    One minor nitpick. The inverted sequence should be written as the reverse complement, not just the reverse. Thus:

    ON: AT|TGAAGA|ACCA

    OFF: AT|TCTTCA|ACCA

  4. #4 enigma4ever
    August 7, 2008

    love your blog..can I add you to watergate summer ‘s blogroll ? I am now going to read your take on the anthrax? thanks..

  5. #5 enigma4ever
    August 7, 2008

    love your blog..can I add you to watergate summer ‘s blogroll ? I am now going to read your take on the anthrax? thanks..

  6. #6 John
    August 13, 2008

    The anthrax case stinks of traditional CIA dirty jobs. For one, the perpetrator was placed inside the investigation team to cover it up. For second, he was a rabid neocon and arab hater, easy to persuade to do a job he considered public duty and benefit from it. Thirdly, he was easy to blackmail due to having a family and children. Fourth, all the comments noting these facts are deleted from Slashdot.

    FWIW: CIA traditionally hires it’s assassins from among the FBI and coroners and arranges for them to be in the investigation teams to help cover up the cases.

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