Sunday, 27 January 2013

The Horseburger Protocol

But let's leave the pastures of the past and - revenons nous a nos moutons - get back to the day job.  I wrote earlier about my molecular biology lab section.  We're spending the next tuthree weeks using the enzymes (restriction endonucleases -REs) which cut DNA at particular sequences of bases pairs [e.g. an enzyme from our homely commensal E.coli, called EcoRI, cuts DNA at GAATTC].  We have a CSI protocol where DNA from 4 suspects and a crime scene sample is treated with a couple of REs, and the fragments run out on a gel. The pattern generated by The Perp will then be compared to that from the butler, the husband, the lover and the nephew-who-will-inherit-everything.  In circulating this proposal, the Course Director put a footnote "and maybe Bob would have some bioinformatics ideas on this".
As I've spent most of the last 25 years doing 'the storage retrieval and analysis of biological sequence data' aka bioinformatics, you'd think I'd have loads to contribute.  Well I didn't, and frankly I was a teeny bit teed off that They would expect me to do anything beyond float-not-drown in the deluge of my new responsibilities. But two days later, I was driving to work through a literal deluge and had the wireless off, so I could concentrate on the traffic, and . . . I had an idea <ching!>.
There has been a scandal recently in Ireland over the revelation that cheap frozen '100% beef' burgers have been packed out with horse-meat.  There is 'no health hazard whatsoever' in this but if the producers finagle the label, what else - that we cannot detect - might they finagle?  Then again, as the rhetoric has it: what do you expect if you spend €1.49 on a dozen burgers??
ANNyway, in my last job as a Comparative Immunologist, I spent a lorra time comparing DNA sequences from different species - a lot of them mammals.  So my <ching!> was for the students to e-go to NCBI in Bethesda MD and fetch out a pair homologous sequences: one from Equus caballus and the other from Bos taurus. They can then search the sequences of the genes for GAATTC and the other RE sites.  A random pair of homologous genes from two species of different mammalian Orders might be 15% different, so there should be differences in the restriction pattern, even if you have to try a couple of different enzymes.  Appropriate-technology-me likes this a lot because you can do the whole analysis with a highlighter.  But you can't expect students to carry out tedious repetitive tasks nowadays - we have software for doing that.  So I'm suggesting that they use Fuzznuc from the EMBOSS suite of binfo software, to do the grunt work for them. The Horseburger Protocol - sounds like a racey Robert Ludlum thriller.
Haven't a clue what gene to choose?  Here's a starter list: ANXA1, BRCA1, CFTR, DRD1, EFNA1, FZD3, GSTK1, HSPA1A, IFNG, JBS, KLHL3, LPAR2, MTNR1A, NECAB2, OPRD1, PELI3, QARS, RNASE1, SOCS3, TSHZ1, UBXN8, VCF, WAS, XDH, YEATS2, ZBP1.  Don't like any of those?  There are 20,000-26 = 19,974 others to choose from. Go to!

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