By: Dan Mead, the 25th Anniversary Sequencing Project Coordinator
Date: 29/01/2018
[Because gathering samples is proving to be quite a major task, I'm going to split this across several posts]
First things first - find a sample
The first, and often most difficult, part of getting a sample for the 25 genomes project is finding out where from.
There are a number of reasons for this but it essentially boils down to the fact that the Sanger Institute has always focused¹ on human health and disease so we don’t have a particularly great list of contacts for this project.
¹There have been some dalliances into other areas in the past, notably; Cod, Coelocanth (it’s fish, known as a ‘living fossil’, although I prefer something that implies it’s been a long-term success like ’Pan-eon species’, a description I may have made up), Tasmanian Devil Cancer, Tomato and a butterfly
The ones that are most difficult to get are the ones that the steering group decided upon independently, this is because without a scientist/researcher/expert putting forward the species there isn’t anywhere to start from.
This is where working in science has a great advantage- collaboration. In the fields of Agricultural, Plant & Animal and Environment/Ecology sciences half of all articles were written by multiple institutions by 2009² and if the trend has continued it should be over 60% by now.
²Gazni, A., Sugimoto, C. R. and Didegah, F. (2012), Mapping world scientific collaboration: Authors, institutions, and countries. J. Am. Soc. Inf. Sci., 63: 323–335. doi: 10.1002/asi.21688
This is one reason why we need to collaborate more and will be subject of a later post.
How traditional biologists and computer biologists work together. #CartoonYourScience by @redpen/blackpen https://twitter.com/redpenblackpen
(for more like this check out the wonderful @redpenblackpen)
In practice this should mean that us scientists are a helpful bunch, and it turns out this is true. Whereas cold-calling/emailing people about the ‘accident you’ve been recently involved in’ or ‘the security breach on you Microsoft device’ are extremely annoying [pro-tip, pass the phone to your pre-school child if this happens, the results are normally quite amusing] doing the same to a scientist to offer them free sequencing of their species of interest is generally quite warmly received!
Getting a Golden Eagle('s DNA)
So lets’ have a closer look at some of the species, firstly the Golden Eagle.
I would have thought that this would be a tricky one - they’re protected by a bunch of laws/regulations which means that without special licences you can’t mess with them. In fact even the locations of the nests are a closely guarded secret as they are still being illegally killed or the eggs are taken by collectors.
Turns out that a quick google and one email can lead to a great result, although it’s tinged with a bit of sadness which I’ll get to in a bit. I initially contacted Professor Anna Meredith at Edinburgh University with a general ‘can you help me with blah, blah, blah’ as she works with a number of species we were interested in (in this case I was actually after Red Squirrels) and she forwarded this on to Dr. Rob Ogden, also at Edinburgh.
As it turns out he is already working on Golden Eagles and was planning on doing some sequencing with some collaborators in Japan (they have eagles there too). Even better he had samples already from (here’s the sad bit) chicks that had died in the nest (plus one found rather suspiciously in a long abandoned nest).
So, one sample down, 24 to go!
[By the way I’m not going to go into the logistics and ENORMOUS cost of shipping things on dry ice, just assume that things arrive magically, but I may expand on why they need shipping this way some other time.]
Something squirreled away
Anna couldn’t help out with the Red Squirrel however, so I asked the National Trust who maintain a lot of the areas where these cute little critters still live:
UK Squirrel Distribution Maps, 1945 and 2010. Image Credit: Craig Shuttleworth, RSST
A nice lady called Laura put me in touch with the Head of Conservation (David Bullock) who in turn linked me to Andrew Brockbank at Formby Point who then led me to Kat Fingland (Nottingham Trent University) and Rachel Cripps (Red Squirrel Officer). All this took about a month and a bit but I finally had the right people. Thankfully we didn’t need any extra licencing to get some samples as they were already collecting from animals that had died from natural or accidental causes.
2 down, 23 to go!
Ethical and responsible sampling
It’s worth mentioning at this point that for this project we want to limit the impact of our sampling as much as possible and therefore have had it approved by our AWERB (Animal Welfare and Ethical Review Body). What this means is that wherever possible we do not kill any animals solely for the project, although in practice this is easier said than done and it does create some difficulties.
- For some animals this is not a problem as they are large enough that we can take a small amount of blood (less than 1ml) but others are too small for this to be possible (pipistrelle bats for example weigh around 5g and have only 0.5ml blood in total). This means that we need to get hold of whole animals AND as some of our species are protected (Golden Eagle, Red Squirrel etc.) they need to have already passed away for us to be able to use them.
- Another related issue is that the protected species need special licences to take blood samples from even if they are large enough for this to be possible. Given the amount of time for the project it’s not really an option, so again we need naturally passed on animals.
- The nature of the sequencing technology we’re using means that we need to get really long bits of DNA (upwards of 150,000 base pairs - that’s the A-T/G-C parts of DNA). The problem is that when we use animals that have died of natural causes we need to find and sample them really quickly: as soon as the animal dies the DNA begins to break up through the natural decomposition process.
- The really small critters (invertebrates like the Roesel’s Cricket for example) are next to impossible to find when they’ve died, as they tend to be eaten by other things and are hard to spot unless they move. In these cases we have no choice but to take live creatures and euthanise them as humanely as possible.
- Plants and fungi are somewhere in the middle, we need quite a lot of material (DNA extraction is more difficult), but ethically it’s acceptable to take bigger samples, so in these cases we take cuttings or fruiting bodies.
So that’s it for this one, more on sample collection to come…
About the author:
Dan Mead is the 25th Anniversary Sequencing Project Coordinator, for the 25 Genomes Project for the Wellcome Sanger Institute, Cambridge.
