This paper makes me very thankful for two things:
1– Bossman is extremely neurotic about controls (this apparently, is inheritable, because I am too).
2– I dont work on a mouse virus.
If the list of potential sources of contamination in the XMRV–>prostate cancer, XMRV–>CFS stories werent long enough, here is yet another source of contamination to add to the list:
In assessing the prevalence of XMRV in prostate cancer tissue samples we discovered that eluates from naïve DNA purification columns, when subjected to PCR with primers designed to detect genomic mouse DNA contamination, occasionally gave rise to amplification products. Further PCR analysis, using primers to detect XMRV, revealed sequences derived from XMRV and pMLVs from mouse and human DNA and DNA of unspecified origin. Thus, DNA purification columns can present problems when used to detect minute amounts of DNA targets by highly sensitive amplification techniques.
DNA purification columns are ubiquitous. They are little columns with a membrane in them that DNA ‘sticks’ to, so you can wash all the garbage (proteins, extra free nucleotides, enzymes, etc) off, and then when youre done washing the DNA, you add water and the column so the DNA doesnt stick to the membrane anymore, and youve got pure DNA in water. Hurray! Purifying DNA with a kit with these kinds of columns is much faster than the old-school protocols (though we often use the old protocols because they are cheaper and you can get a higher yield, but I digress). So people use these kinds of kits to purify DNA from bacterial preps, to purify DNA from agarose or acrylamide gels, to purify DNA from PCR reactions, to purify DNA from mammalian cells, to purify genomic DNA from viruses– everyone uses these kits. Particularly, everyone uses Qiagen brand kits (we often use off-brand, again because they are cheaper, but if you want to be 100% sure of a finding, you use the Qiagen).
But apparently, because moosey mice are everywhere they are contaminating everything, including the ‘DNA purification columns’ in Qiagen kits. So if you are looking for ‘mouse DNA’, or in this case, ‘the genome of a mouse retrovirus that is present in mouse DNA but youre trying to say its in human samples’, you are screwed 11 times for every 68 columns. The contaminant? Same sequence as VP62.
There is one way around this contamination– Qiagens SUPER SPECIAL columns:
It is worth noting that QIAamp Ultraclean Production (UCP) Pathogen columns which are certified to be free of contaminating microbial DNA yielded no amplification product for IAP or MLV-related sequences in 50 “mock-extracted” columns.
Those kinds of columns are usually reserved for very specific protocols (they are ~twice the price of the regular columns, which ~twice the price of off-brand), but if you do mouse research, you might just have to use these super special columns all the time.
Or, you can go back and use old-school protocols and make all your solutions in-house.
But they might be contaminated too.
Very glad I dont do mouse research.
And just to reiterate, until the dozens and dozens and dozens of contamination issues are settled with XMRV (ignoring all of the cell bio, which implies XMRV cannot productively infect human PBMC. ignoring the animal model with implies XMRV doesnt do anything. ignoring the epidemiology, or rather, the lack of epidemiology regarding XMRV ‘infections’), the contamination issue is basic, basic science that needs to be dealt with before anyone can speak a word in support ‘XMRV IZ INFECTIN DEH PEOPLES OMFG!!!!’
Again, XMRV is not infectin deh peoples.
Also, poor Carl Zimmer tried to write about the threats researchers (and journalists, and bloggers) have gotten from the nutty XMRV–>CFS proponents. Aww 🙁