The search for rotifers continues

“Thank you”, I whispered in a soft voice while driving by the rayon and plating factories surrounding Lake Orta. “Thank you for giving me a PhD”.

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Brachionus calyciflorus

The wastewater of those factories polluted the lake with copper and ammonium sulphate from approaching the mid-nineteen hundreds until the end of the last century. This history of pollution makes Lake Orta an interesting ecosystem to study, and sets the perfect stage for my PhD: the life-history responses of the rotifer Brachionus calyciflorus to past environmental changes (i.e. industrial pollution) and the underlying eco-evolutionary processes.

To study this, I (try to) resurrect rotifers from up to 80 year old lake sediments that contain their resting eggs, and compare the performance of these rotifers under different experimental treatments. As I have had some difficulties getting resting eggs from the post-pollution conditions, I decided to go to Lake Orta to get the most recent Brachionus calyciflorus: the ones that are currently swimming around.

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Sampling Lake Orta with a plankton net.

Together with Diego Fontaneto of the ‘Istituto per lo Studio degli Ecosistemi’, I drove around the lake, and found five spots to easily enter the lake to collect zooplankton with a plankton net. This net made of fine nylon mesh is pulled through the water horizontally and the animals are captured in a vial at the bottom of the net.

A quick look together with Diego revealed that we captured tons of animals, but probably no Brachionus. A more thorough look together with our summer research assistant Conor Waldock confirmed this suspicion, but we have still some bottles of water to go through, so we keep on hoping. And otherwise, our hope lies in the sediment samples of Lake Orta that I also brought back from the trip.

The reason why we didn’t find any Brachionus in our water samples? Probably because the water was still too cold due to the relatively bad summer, and there have been no big algae blooms yet of which Brachionus could profit. I guess this means I have to go back next month to again sample Italian ice cream… Ehm, Lake Orta I mean.

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Diego Fontaneto (left) and Conor Waldock looking at the harvest of the sampling day: water and mud.

Thinking hard and digging deep is facilitated by isolation

‘Think hard and dig deep, without being canalized by the ideas of others published in literature. Not very often do you get a chance like this offered to you. Take the challenge.’ And all the students participating in the Guarda Evolutionary Biology course took the dare set by Dieter Ebert, Sebastian Bonhoeffer, David Queller, and Joan Strassmann.

DSC04117In the idyllic Swiss village of Guarda, twenty-eight MSc/PhD-students interested in evolutionary biology were selected for a week of isolation, and given time to devote themselves to writing a grant proposal on any question they thought was worthwhile pursuing. The only requirements were that you had to collaborate in a group of 4-5 students, and choose a topic that was not related to your field of research at all. Oh, and you were not allowed to look for information in books or on the Internet: it was only tolerated to use the creativity of your own mind, the mind of your fellow students, and of the faculty members.

In just 15 working hours, the first draft of the grant proposal (including idea, hypotheses, and well-thought out experiment) had to be handed in. The faculty members granted every group 20 minutes to undergo their severe but justified feedback on the proposal. Six working hours after this feedback, the revised version had to be handed in, which got another feedback round. Five hours after this round, the final version and a presentation had to be ready. On top of that, there was an armchair lecture by one of the faculty members every evening, and you were (happily) obliged to offer all of them a hand cooked dinner during one of the days in the week.

DSC04061This has been one of the most inspiring courses I ever took that has brought me back to basic scientific thinking: What is an interesting and important question in (evolutionary) biology? How would you solve that question? Is your hypothetical experiment really answering that question? Does working within a group of complete strangers full of enthusiasm facilitates the brainstorming, discussing and writing-up process, or do you might have to learn a lot in how to successfully listen, be open-minded, and collaborate?

After this highly motivating and encouraging course (e.g. why not embrace serendipity in your scientific work?), we got home extremely exhausted, to find out that the project we proposed was at the moment being presented at the big Evolution meeting in North Carolina: how mutualistic interactions could alter the dynamics of natural selection.  I think that’s what you call Zeitgeist.

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Photo by Joan Strassmann

Attendance ‘Bayesian population analyis using WinBUGS’-course

‘Don’t feign to be stupid.’ This well-chosen phrase of Marc Kéry introduced some of our group members to the world of Bayesian Statistics (where the use of your previous knowledge on the parameter you’re interested in, the prior distribution, plays a role). Together with Michael Schaub, Marc taught the inspiring course entitled ‘Bayesian population analysis using WinBUGS’ based on the book of the same name.

I was impressed by how they managed to cover almost the whole book within 5 days: starting with a gentle introduction to the analysis of distribution, abundance and population dynamics using a Bayesian framework, followed by an introduction to the software WinBUGS and implementation of mixed models in it, and finishing with some examples of the implementation of Integrated Population Models in WinBUGS. Lectures were alternated with useful exercises.

I think all the participants are after this course better trained in making a balanced decision whether they want to make use of the full knowledge they have, or use the veil of stupidity to make big discoveries (Schwartz, 2008).

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If everything else fails, try Triops

Sometimes Science is nothing more than checking assumptions. This holds true whether you are a theoretical biologist (e.g. checking model assumptions), experimental biologist (e.g. checking assumptions of experimental design), or just love doing statistics (as we all do). During the first weeks of my PhD, I found out that I perhaps needed to check the basic assumption my supervisor has about me: that I would be able to let eggs hatch in the lab. Until now, I have been unable to let the desired rotifer eggs hatch, but I can proudly announce that since five days we have some pets in our office: Triops! These crustaceans are considered ‘living fossils’, and just as the rotifers I’m investigating, their eggs can remain in a state of diapause for a prolonged period of time.

Assumption “I have the capacity to let resting eggs hatch under laboratory conditions”: Check!

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Triops X, one of our new office pets
Triops X, one of our new office pets

Tied to two females and more will follow… – Preparations for rotifer resurrection ecology

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My science: all about bags of mud

Today I felt like going on a first (blind) date: being nervous and excited at the same time. Or perhaps this is more what marriage feels like: eager to be tied to your partner(s) for the coming years while knowing it has a high change of being a love-hate relationship. Today, my diapausing females arrived.

They were brought to our lab by Diego Fontaneto and Stefano Gerli of the Istituto per lo Studio degli Ecosistemi. Just like a first date I didn’t know what to expect, and I couldn’t trust that the outside would be a representation of the inside (which of course is the most important part): I was given bags of mud.

The mud comes from different layers of the sediment cores obtained from Lake Orta in Italy. This mud harbours the resting eggs (diapausing females) of the rotifers I will be using to investigate the relative contribution of ecological and evolutionary processes involved in the populations’ responses to changing environments. More information on how I will use resurrection ecology to address this topic will follow hopefully relatively soon.

Resting egg of Brachionus calyciflorus
Resting egg of Brachionus calyciflorus

Diego and Stefano taught us the necessary knowledge and skills on how to extract the eggs from the sediment. As I expected to find a lot of eggs in the mud, I had already designed a small experiment to be able to put the females directly to scientific use. However, in the small sample we investigated, we could only find 2 resting eggs of the rotifer species I will be using (Brachionus calyciflorus). As this is by far not enough for a proper experiment, we decided to put the females on hold: we stored them in the fridge.

To make up for the non-exciting mud picture, hereby a picture of what everyone thinks Science is about: green bubbly liquid. This is how we culture our algae, which we use as a food source for the rotifers.

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What Science is presumed to be all about: green bubbly liquid

Meet the Rotifer Family

IMG_1387As from Thursday onwards, we are now part of the Family of Rotiferologists. This will be the most important family to deal with in my coming PhD years. Arpat, Stefan and I were welcomed by Diego Fontaneto (Uncle Rotifer) at the ‘Istituto per lo Studio degli Ecosistemi’ in Verbania (Italy). This Institute resides in a big manor house near an idyllic lake: the perfect place to retreat to when one has to write up an article as there is no distraction besides some thorough scientific discussion (which is always welcome) and the sound of calling gulls.

The scientists at this Institute have great knowledge on aquatic ecosystems and the invertebrates that are part of such an ecosystem (for example rotifers). During the two days we visited them, they have shared their knowledge on how to resurrect resting eggs from sediment cores obtained from Lake Orta (a great place to eat an ice cream). So now we are able to bring the past back to life in our lab in Zürich.

More information on the details of my PhD project and the bizarre world of rotifers will follow relatively soon. So keep an eye on this blog if you want to know why even the NASA thinks that rotifers are rather exciting animals…

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