Whipping up a storm

I’ve been out of the burble-sphere for a while as it’s been a busy term and I’ve been fully occupied with other things, principally two new projects that I’m setting up in school. One, a bee keeping club, is currently in the hive building stage and there’s nothing very exciting to report yet.

But the other is proving to be one of the most fun, interesting, challenging and exciting things I’ve been involved with at school…. and yet it nearly didn’t happen!

It started at a conference I went to in Birmingham last year. One of the other speakers described this amazing project where A-level students were doing original molecular research into Multiple Sclerosis. I was stunned. And immediately wanted to set up something similar. But despite attending the IRIS symposium at the Wellcome Trust HQ in London – amazing building – and finding a small group of students desperate to carry out this kind of research – we could not locate a single research group in Oxford who were interested in this kind of collaboration.

But then, at another conference this October – a school science conference in Tonbridge – I ran into Becky Parker again and she started enthusing about their Whipworm Genome project. I wasn’t immediately sold – it wasn’t the kind of hands-on, micro-pipetting/PCR-ing/gel electrophoresing/fluorescent visualising that I knew my students craved. Sitting in front of a computer scanning a genome for possible genes? I couldn’t see the appeal…

But she took my details, put me in touch with the head honcho at the Whipworm Genome HQ, and I signed up, thinking I might get 5 or 6 of the best Year 13 students interested.

Got that wrong.

I gave an assembly outlining this horrible Neglected Tropical Disease (neglected because only poor people get it, and who cares about them?). I described the project – bioinformatics/genomics – and what it would involve.

Whipworm Genome intro

Note the last slide – a screenshot from the Apollo software involved. I told them not to panic – it was as much a mystery to me as it was to them. I told them we would figure it out together, that I fully expected them to be teaching me, just as my 11 year old son schools me on how to play Clash of Clans….

And something struck a chord. A combination, I think, of:

  • genuine, original research – when they look at a whipworm gene, they are the first person to ever examine it
  • cutting edge technology – gene curating of whole organism genomes is Where It’s At…
  • a challenging and very steep learning curve (more on this in a mo!)
  • a worthwhile project – this might actually make a difference – it’s got immediate relevance
  • it’s online software, so you can do it anywhere you have a computer and internet access
  • looks good on CV/personal statement
  • immediately relevant to A-level…

Whatever it was, I currently have 86 girls signed up. I fully expect some of these to drop out, but not many. The interest and motivation is fantastic.

And it’s been a brilliant learning experience for me. I’ve never analysed a genome before, never curated a gene, never used the Apollo software. So having to do all that, whilst simultaneously trying to figure out how to teach it to students who currently don’t know a huge amount about DNA, has been hugely satisfying.

I started them off with a crash course on DNA

DNA intro for Whipworm Project

– the key bits for this project are understanding the concept of an anti-parallel 5′-3′ double helix; knowing about base pairs; knowing about introns and exons (or CDSs); knowing about UTRs (new to me!); knowing the identify of START codons and STOP codons; understanding that DNA gives rise to RNA which is translated into protein.

That’s a lot to take in for students who don’t know much about the basics of DNA!

But even being familiar with this doesn’t make the Apollo on-line software immediately accessible. So I had to practise with lots of examples and slowly build up a sense of how to do it, what to look for, how to trim or lengthen or adjust the computer gene predictions to what actually matches the evidence.

Because this is the really interesting bit. There are sequences that a computer has identified as looking a bit like a gene. But the computers often get it wrong. The student then has to compare the computer predictions to other data (principally RNA sequence data) derived from living whipworm cells, to see if the prediction matches what’s actually going on in real life…. and then adjust the predicted gene accordingly.

It’s fascinating, compelling and extraordinary. The power of the software, the sheer quantity of data, the elegance of the program, are all strongly addictive. At the moment, we’re just trying it out, running through a section on Chromosome 1 (whipworms have 3 chromosomes) for quality control issues. But just before Xmas, we should get our very own unique section of Whipworm Genome to annotate. Can’t wait!!!

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