Friday 18 January 2013

Help from abroad

Every Weds at 0900hrs, I'm running molecular biology practical classes.  Last week we were doing 'agarose gel electrophoresis' of 'lambda DNA' that had been cut with three different 'restriction endonucleases'.  See: it's hard to describe science without using technical terms or drifting off into metaphor.
'lambda DNA' is the genome of lambda, a virus that infects E. coli.  It consists of 48,000 base pairs (bp - the As Ts Cs Gs that comprise the universal genetic code) of DNA.
'restriction endonucleases' are enzymes that cut DNA at specific sequences of bases - GAATTC for example.  They are produced by bacteria like E.coli to protect them against viruses like lambda.  If the E.coli genome can be arranged by natural selection to have no GAATTC sub-sequences, then an enzyme that will cut at that sequence will do (fatal?) damage to any incommming DNA that does have such a sub-sequence.
'agarose gel electrophoresis' hinges on the fact that DNA is negatively charged (it's an acid: DNA) and can be driven through a thin slab of jelly made from seaweed extract by an electric current.  The distance a DNA fragment travels is proportional to it's size - large fragments get slowed down by the agarose matrix while smaller ones zip through it.
What should happen is that the students cut the lambda DNA with a tuthree different RE enzymes, so that the 48,000bp are divided up into lengths characteristic of each enzyme.  After running these fragments on the gel, you should see a ladder of DNA bands.  Each track with a different pattern because it's been cut with a different RE.
Last time I was running agarose gels in anger (and frustration) was in 1989, in my disastrous foray into 'real science' molecular biology.  So the students were much more competent than me - they'd used the technique before Christmas.  Nevertheless we made a pretty complete bags of the experiment but I didn't have this confirmed until I got to see pictures of the experimental run the night before the next session.  (I'm co-teaching the course with two other competent molecular biologists and my Oppo who had the pictures went sick this week).
The task this Weds was to measure, in cm, the distance each band had travelled last week; plot distance travelled for the fragments generated by the known RE (X-axis cm) against the length of each fragment (Y-axis bp); then calculate the fragment lengths of the unknown REs by interpolation.  Neat.
So I went to bed uneasy about what we were going to measure the next day at 0900hrs with the wretched blobs, spatters and dark-matter that we'd generated the previous week . . . and woke up screaming at 4 AM.  I'd figured that, as this was bog-standard molbiol class material, there would be crisp, clean interpretable pictures of the same experiment on The Internet.  Which as we all know is infinite in extent.  It took about 20 minutes for Google'n'Me to track down such a picture, and I e-mailed it to myself-at-work and my colleagues, before dropping back to bed
Four hours later, I get to t'office to be told that the college network is down, so I can't retrieve my solution.  But I meet the students on time; harangue us all for making a hames of the experiment; try some Socratic with them to work out what went wrong; ask them to talk amongst themselves; hare along the corridor to my office to find the network lurching back to life; download the picture; print 18 copies; hare along the corridor and . . . science is back on track.
So I'd like to thank students Nguyen and Painter in Skip Lovelady's class in Redwood High School, Larkspur, California for being the cavalry for our problem by making available their quality material.

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