Bonus Projects

The view of a data scientist - BONUS BIO-C3 & BONUS INSPIRE

I share here my lessons while working in BONUS BIO-C3 and INSPIRE as a "data scientist". I call myself a “marine biologist”, but my career was decided in the first day of my PhD studies, when I opened “R” instead of the lab door. I can never be thankful enough for my supervisor for showing me that door. This path of data scientist placed me on the rollercoaster of co-operations with many research groups. And on the way, I hope, I learned something of the plankton and the sea too.
20.09.2017 18:54

Successful introduction of Eurytemora to the lab

Despite of the modern project-based funding system, science also needs surprises, mistakes and adventures to progress.


With two Bonus projects INSPIRE and BIO-C3 coming close to the end, I say we succeeded to get to the unknown grounds several times, as far as I know.

One such example was definitely the Baltic Sea measozooplankton data compilation, and the vast amounts of data it brought together. Although this action was not budgeted or even listed in the proposals in the beginning, those two projects still brought together relevant people (and paid also my salary).

But I also have another example, smaller in scale, but in the best spirit. Working with the zooplankton data from Baltic Sea, I became interested in several species. One in particular – Eurytemora affinis, a small estuarine copepod. This species is remarkable for its global distribution, wide salinity and temperature tolerance, and massive production. Despite of being heavily grazed by many predators, also in Baltic Sea, it still can be found in high numbers in most of the brackish ecosystems where it lives.


From in silico to in vitro


Earlier this year we published a research paper, where we focus on this species in the Pärnu Bay. Inspired by the findings, we decided that we should also run some simple experiments on this species, and figure out, among other things, the physiological optimums of the Pärnu Bay population. 

Such experiments require this species to be grown in the lab for several generations. At least in our institute, no one had succeeded with it before. But they have succeeded in many other labs worldwide.

I decided to give it another go. First I collected all the experience from people who had tried it before in our institute. 

Then I did some literature research, of how it had been grown in other labs. I even wrote to one of these labs for advice.

I asked for help from my ex-supervisor, a phytoplankton ecologist, how to grow the food (we needed something smallish and nutritious), in addition, he also gave me some room in his lab. 

And then, with all preparations done, I joined the first monitoring cruise that went out to the Pärnu Bay, in May, to bring my first live sample of these copepods to the lab.


Doing experiments is like gardening!

For someone like me – a pure data scientist until this point – it was a pure thrill! Seeing these animals jumping around in my live sample left me breathless, and in despair, at first. I knew there must be at least two species, but I could not even tell them apart, and even less catch the ones I needed. I took several photos of animals that I accidentally caught, and sent them to one of my older colleagues, who kept telling me that “no, sorry, but that’s still not Eurytemora. Eurytemora has much slimmer body, longer legs, and a pointy head.” And then he sent me two photos, one Acartia, the other Eurytemora. Even on his photos, I could not see these pointy heads and long legs. At least in the beginning. Until I did! Only few hours later after the light had hit me, there was no way anymore, that I could mix them up. Amazing transition!

eaffinis_vs_acartia
Acartia on the left, Eurytemora on the right. Note the pointy head, long legs and slimmer body!

In the first round of my experiments, many of the animals were covered with kind of parasites – small ciliates, from the group Vorticella, that were attached to my copepods and used them as transportation. Some of them looked quite sad under their burden. This, one of my colleagues told me, was the main problem he came across when trying to grow these animals for longer time.

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Overgrowing ciliates, from the group Vorticella.

But since I developed a careful method of “washing” my animals from one generation to the next (through small filtered water droplets), I managed to get rid of this parasite by the second generation already.


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Beautiful clean female with eggs and spermatophores.


Finale

While the pilot experiment was running, I did quite some literature research, and realized that it makes not much sense to study the effects of food density and temperature on them anymore. For one, it has been done so much already, and plenty of knowledge is there. And second, this knowledge will not be transferrable to the real world communities, which experience varying temperatures and food conditions during their life.

 

Hence, for the time being, and until I get a really interesting idea and hypothesis to test, I terminated my cultures, with an important conclusion nevertheless: I can grow E. affinis in the lab without problems, I know what to feed them, how to keep them clean of parasites, and how to start and initiate the experiments.

Now I just need a good idea!

 


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