March 30, 2007

Just what is a wambenger?

I've been putting off putting up an explanation of my honours project for a while because everytime I think about it, I find out something more about it's scope, techniques or just what exactly it is I'm supposed to be doing. University census date was on Tuesday. So according to stipulation of my scholarship and HECS agreement, I have gone past the point of no return.

My supervisor is keen on marsupial immunology. So it's no real surprise that I'm working with marsupials, and I'm examining genes involved in the immune system.

Genes? That makes it a molecular biology project. But I still have an immunology supervisor.

What I'm going to do is utilise some predicted cytokine gene sequences from the Opossum, Monodelphis domestica, (a highly utilised laboratory marsupial that recently had a completed genome project), and use those sequences to design degenerate primers in order to detect, amplify, clone and sequence the same genes in two Dasyurid species (carnivorous marsupials - yes, they are related to Devils); the Mulgara and Phascogale (also known as a Wambenger). Then I get lots of praise, heaps of research grant offers, gazillions of published papers, a TV show and a bit of paper with my name on it. Maybe...

...maybe not.

The trouble is that these are predicted sequences. They haven't been confirmed yet. They are the more reliable predictions, but still only predictions. Additionally marsupial immunology, especially the genetic side, has yet to reach the same level of characterisation as "normal" mammals, this makes my work a bit harder. And even harder, because the two marsupials I'm dealing with are really rare and endangered and even less characterised. Not to mention they aren't really all that close to South American Opossums phylogenically.

In the mean time I'm learning how to competently utilise all sorts of genetic alignment programs like CLUSTAL, BLAST, PRIMER3, PRETTY. I'm also trying really hard to resist the urge of gouging out my eyes after staring through 3 pages of CLUSTALW alignments, only to realise I forgot to run the mouse gene in there.

Hooray! study life! At least I have a shared office, not a cubicle farm.


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