I Like Big Gels and I Cannot Lie…

My dissertation research looks at the importance of biodiversity of seaweeds, particularly how it affects nutrient cycling and productivity. And since biodiversity includes everything from the diversity of genes to the diversity of species, sometimes a field ecologist has to get down and dirty with the molecular branch of ecology. It’s been a bit of a rocky transition for me, with no previous molecular experience and a lot of field research happening it’s taken me awhile to work out the proper protocols.

So over the next few weeks (before the holiday break and before the grant budget expires!), I am working overtime to get through the last batch of DNA samples so that I can get information on the genetic structure of my study populations. I work a brown alga called Fucus vesiculosus, which is found on rocky shores throughout the temperate North Atlantic.   I sampled my populations such that I could get information on genetic diversity not only across latitudes but also across tide height along the shore. This way I have context for my regional and shore-level experiments and can (hopefully) make more informed predictions.

To get that amount of information a large number of individuals have to be sampled, their DNA has to be extracted, and then a good number of microsatellite loci have to be amplified for each individual. Right now (budget allowing), I am working with 475 individuals and 6 loci for a total of 2850 amplifications. Of course I don’t want to send these samples off to the sequencer blindly, so I run them out on a gel to check that the amplifications worked – thankfully the lab I am collaborating with has a rather large gel rig that can hold 123 samples at a time so I don’t have to use the standard 36 sample boxes that I would normally use.

 

Small (left) gel rigs hold about 1/3 the number of samples of a large (right) gel rig.
Small (left) gel rigs hold about 1/3 the number of samples of a large (right) gel rig.

 

If you need to find me over the next few weeks check the lab bench!

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