The Centrifuge Queen

So, I’ve spent another week in Natural History Museum but this time instead of chatting with dung Beatles I’ve turned to playing with DNA :)  The conclusion from all of the week work is: YES, I WANT TO BE A SCIENTIST! I mean, I even find pipetting an exciting job!

Well, it’s not only pipetting that I’ve been doing, in fact, I’ve done some pretty good lab-work, it went something like this:

The research is on Brosimum alicastrum (Maya Nut) with an aim to understand the geographical patterns of the populations of this species in the Central and South America; this is an important step in order to help to make the reforestation of this species more sustainable.  During my week I was responsible for extracting DNA from the leaf samples of this tree that were collected in Panama. In addition to getting the DNA sequence that later will be used for phylogenetic tree building, we also investigated whether drying samples in a microwave (they are usually dried using silica granules that suck out the water from the sample (these are the same granules that are found in a small bag with a notice ‘not edible’ when buying shoes) has any effect on the quality of DNA. Often in a fieldtrip silica is not so readily available and microwave can usually be found in any hotel, moreover, microwaved samples look much better than the silica dried ones. All in all, if microwaved samples provide the same quality DNA that would make the life of researchers much easier!

 

The process of DNA extraction starts with grinding the samples into powder, mixing them with a special buffer, centrifuging them, adding chloroform and centrifuging again. These steps are not precise; the protocol also involves lots of storing in specific temperatures, collecting suspensions, adding RNAse to get rid of any RNA molecules, etc. After all of this you end up with a clear solution to which you add another million of buffers, make another million of centrifuge turns and then hope that you have some DNA trapped in a tiny filter in the eppendorf tube :). As my supervisor nicely put it “by the end of the day you will be the centrifuge queen”, I would also add that by the end of the day you will not feel your thumb or have a blister on it due to the million times you have to open and close the eppendorf tubes! (I wouldn’t be surprised if in the families that have long-run science history they tend to have thumbs with a very tough skin on them). To check if you actually have DNA you then run many electrophoreses- I was lucky!!!

 

If you are lucky then you can do PCR, which is a very sensitive process and any contamination will make all of your efforts go to trash… The DNA we got from extraction was any DNA that can be found in a cell but then when we did the PCR we added specific forward and reverse primers for a small region on the chloroplast genome, so after the sequencing all the information you get is about this short stretch of chDNA.

Something that was an entirely new thing for me was the analysis of DNA sequences. What you get from sequencing lab is just lots of letters and curves but then you need to edit them and match forward and reverse sequences. It’s a bit of subjective process, which is why I will be a bit more critical about the sequence data in papers, but it’s, I think, another example of puzzle collecting in science, which makes it quite a fun process!

And that’s it! Or at least what I’ve managed to do during the week. The sequence data will be later used to construct phylogenetic trees.

All in all, it has been an amazing week! Interesting work, more knowledge and intelligent people – what more can you wish! I’ve basically got a private tutoring session for lab practice, nice isn’t it?  Oh, and they have a common room on the roof of nhm- I mean, come on, can it get any better?!

 

2 thoughts on “The Centrifuge Queen

  1. nice…nice bands in PCR. sequencing however did not show gud peaks.
    and analysis by Mega gr88 going!!!
    keep it up!!!
    :)

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