Mendeley Advisor and microbe incubater

It’s all go today. I’ve been made a Mendeley advisor, which means 1) I get to organise demonstrations of and and give talks about how to use Mendeley to manage reference lists and pdf libraries, and how to take advantage of its collaborative functionality, round UEA. Which is quite exciting. Haven’t told UEA yet, but I’m sure they’ll be fine with it… and 2) I get a free T-shirt and a fancy banner to put on my Mendeley profile (and other really cool stuff like insider access to what’s going on with Mendeley dev etc.

As part of my initiation I had to make up a Mendeley Haiku, which I’ve completely forgotten. It wasn’t very good, but it was my first ever haiku. I’ll try to retrieve it and add it in here.

Edit: Andrew at Mendeley kindly retrieved it:

Mendeley papers, share more information, make science more open.

Bit crap really.

Anyway, Mendeley is great – manage your references, with a pdf library, get the citation info automatically from the pdf, or from the web, so you don’t have to type anything in. Integrated with word processors and bibtex for inserting citations. Annotate pdf’s in your library. Sync with the web. Share with others. Collaborate. Promote yourself and share pdfs of your work. You should probably sign up right away. In case you missed it it’s http://mendeley.com! More on all that another time.

The other new thing is that I’ve taken my first steps into the world of incubation experiments, where you take natural water with all the microbes still active, and shut them away under particular conditions in order to quantify the capacity of the microbial community to perform a particular function (e.g. to take up carbon or produce oxygen due to phtosynthesis). In this particular case my officemate, long time collaborator and now lab partner Claire Hughes and I have taken water from UEA broad and we’re incubating it in bottles to try to quantify nitrification rates. This is only a proof of concept at the moment, but nonetheless the results should be quite interesting (if it works). We’re far from the first people to measure nitrification, but if our way works (taking advantage of our really high precision methods for measuring concentrations of nitrogen-containing chemicals), then we’ll be able to do it quickly and easily, even at sea.

Nitrification is a process by which reduced nitrogen (in the form of ammonium, NH4+, a close relative of ammonia gas) is oxidised to more oxygen-rich forms of nitrogen such as nitrite (NO2-) and nitrate (NO3-). This is important because it’s the key way to get nitrate in high concentrations back into the surface of the ocean (where it drives carbon uptake through algal photosynthesis) from the material which sinks down into the deep ocean (the midnight zone as it’s called in Octonauts!), disconnected from the active layer of the  ocean (the ‘sunlight zone’).

Our experiment focuses in on nitrification by incubating the water in the dark (to stop algae eating ammonium and nitrate and confusing our results) and by adding chemicals to some sets of bottles which will inhibit certain steps of the nitrification process. All bottles have extra ammonium added to make the signal easier to see.  If it works we should see ammonium decreasing and nitrate and/ or nitrite increasing increasing, except in the bottle where the ammonium to nitrite step has been inhibited by our addition of chemicals. If you’re interested in the details, or in following the progress of the experiment, you can do so at my open lab notebook.

Octonauts, my 2 year old son Oliver’s favourite tv program (with the possible exception of Chuggington) is ace, by the way!

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