Genetically identifying nematodes with a portable lab

I’m so happy my first first-author scientific paper (which you can find here, if you’re up for the challenge) is published! Here’s a summary of what I have been doing these last four years, beautifully illustrated by my friend Rachel Glover.

The bottom line is that we combined a portable molecular biology lab, the Bento Lab, with a portable DNA sequencer, the MinION. With these two techniques combined we can now genetically identify nematodes all over the world, even in remote field sites.

Im my paper I looked at the DNA of nematodes, microscopically small worms. DNA is made up of letters, and the combinations of these letters create codons (like words) and genes (like sentences). Nematodes are common parasites of humans, great apes and other animals, they are a crucial component of soil ecosystems and are abundant in marine environments. Many researchers are interested in learning which species of nematodes are present in different environments.

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Counting steps

When I was in Namibia I was following around baboons in a desert landscape. We followed them all day, from sunrise to sunset. And even though I loved the experience, it wasn’t always easy.

It was the African winter, which meant near freezing night temperatures while you’re sleeping in your tent. Then there were the early rises, before sunset (maybe around 5AM), to make sure we’d get to the troop in time. That required a physically hard walk, which was especially daunting if the baboons were on a far away sleeping cliff. There was the carrying around five litres of water to stay properly hydrated during the long warm days. And only then there was the actual follow of the troop during the day, wherever they went.

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Recently my boyfriend and I were in Scotland, where we camped next to Loch Achray. From our tent we had a beautiful view of Ben A’an, a 454 metres (1,491 ft) high mountain. Yes, I’m aware of the fact that in the UK a mountain is officially defined as a peak of 600 metres (1,969 ft) or higher. However, given that the highest point in the Netherlands is 322 metres (1,058 ft), I personally classify Ben A’an to be a mountain.

We woke up to a clear day and the tantalising view across the lake seemed to draw us towards Ben A’an. Described by my ‘Wild’ guidebook as ‘giving perhaps the best views-to-effort ratio of any Scottish mountain’, we knew we had to make the ascent. So up we went, my boyfriend sometimes slowing me down when my enthusiasm would make me speed up to an unsustainable pace. We saw a beautiful mansion disguised as a castle, heard a stream rumble, passed a bridge and walked along a big sad stretch of cleared trees. And then the steep part came. The part about which I questionably asked: ‘Ehm, do you think it’s that peak?’. Until we caught the glimpse of a bright red jacket and realised that, indeed, the last part of the climb would be that steep.

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En passant

While I focussed on Steinbeck, the baboon I was following, something attracted my attention out of the corner of my eye. In  between the scarce bushes a steenbok walked in our direction. He look at me for a moment, after which he lost interest: the baboons didn’t seem to think I was a danger, so the otherwise so skittish steenbok seemed to draw the same conclusion. The next 15 minutes he was browsing next to us, searching for fresh green leaves in the arid desert. Only giving way to the few baboons that approached him a bit too close, he imperturbably continued his path, until he moved out of my sight.

Like Jonah on the mountain

Then the Lord God provided a leafy plant and made it grow up over Jonah to give shade for his head to ease his discomfort, and Jonah was very happy about the plant. But at dawn the next day God provided a worm, which chewed the plant so that it withered. When the sun rose, God provided a scorching east wind, and the sun blazed on Jonah’s head so that he grew faint. He wanted to die, and said, “It would be better for me to die than to live.”
Jonah 4:6-8, NIV

In Tsaobis I felt like Jonah every now and then. He sat on a hill overlooking Nineveh, I regularly sat on a hill overlooking baboons. I can relate most, however, to how he must have felt when his tree, and with that his shade, was taken from him. Continue reading

Emotional encounters

Average maximum temperature: 24,1 °C
Average minimum temperature: 7,4 °C
Sunrise: 06:34
Sunset:  17:22

Olifantsrus, Ethosa
In the dark of the night I saw him slowly moving towards me. Instead of moving around the tight bushes, he passed right through the scarce undergrowth. The branches scraped his grey skin, which made a scraping sound. He continued along the waterside seemingly unbothered, with a clear goal in mind. At five meters from the observation hide the elephant came to a stop at the waterhole, under the window where I was sitting. In the red light I saw how he used his trunk to carefully search for water. A loud slurping sound grew from below me, after which he moved his trunk to his mouth to empty it: it sounded as if someone emptied a bucket of water. Every time he repeated this ritual, I amazed myself about the peculiarity of his trunk. I was so close I could see every muscle in his trunk contract. Big wrinkles showed, especially when his trunk was at his lips. Breathless I watched the impressive show. How did I deserve this, crossed my mind while the emotions got to me, that I get to experience all of this?

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Monkey bussiness

Average maximum temperature: 30 °C
Average minimum temperature: 13 °C
Sunrise: 06:23
Sunset: 17:23

Somewhere in the Swakop River, Northwest
The shade provides some shelter from the heat, but not a lot. It’s half past one and the sun is at its highest point. I’m surrounded by the rustling and munching of the baboons, while a slight breeze occasionally blows around my head. Straight ahead of me are the hills we’ll undoubtedly climb in the remaining six hours of daylight, behind me are the hills we’ve already concurred. We’re following J-troop, who’s notoriously eager to climb. The hills might be a physical challenge, I prefer them over the woodland we’re currently in. We have to follow the baboons the whole day, and that’s a lot easier on the open rocks compared to the dense vegetation of the woodlands.

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That’s why they call it cloudforest

A weekend in El Copé sketched the beautiful nature that is captured on these images. I was surrounded by scenic beauty, in the rol of a silent witness. On an altitude of 1600 meters we were bordering north and south: de mountain range Serranía de Tabasará divides Panama in humid tropical rainforest on the Caribbean side and montane forest on the Pacific side (north respectively south). On a clear day National Park Omar Torrijos is one of the few places in Panama where you can see both the Caribbean as the Pacific coast. We were fortunate enough to feel surrounded by the cloud forest: the veil of clouds deprived us of the view of both coastlines, but placed us on an island amid a sea of mist.

Hold on to me

We sat there holding hands. Or better said, she was holding my hand with her foot. Her hands were occupied clasping my leg, by which it was pressed against her cage. Preciosa is a spider monkey, and she’s depressed. And that makes sense, if you’ve been kept in a too small cage for years, in an establishment that was open each night until 3 am. Drunk men would lure her with food, to break the bones in her stretched arms and fingers with their intoxicated power. Now she tries to grab a piece of banana with her deformed, grown together fingers.

Holding 'hands' Continue reading


Like all the other nights, this one also feels like a warm blanket around me. There has been little rain lately, so it’s not clammy. With my big backpack filled with field equipment I walk over the path, carefully holding my two speakers in my hands. The slope is steep, will I get my speakers down in one go? Carefully I balance, and then a small jump. I look back: how I’ll get them back up is a care for later.

I set up my new experiment (read here about my previous one). Speaker on one side, speaker on the other side. In this new experiment we investigate the influence of habitat on the predation preference of bats. Does vegetation affect the echolocation of bats? Aside from that, there is the suspicion that vegetation influences the amount of flies bothering the frogs. The speakers play the sound of the tùngara frogs (listen here), sometimes with vegetation on top of the speakers and other times without. With this experiment, we hope to see an interaction between vegetation and predation risk by bats or parasitic load by the bloodsucking flies. I put the cameras in their place, so they can be the silent witnesses of the visiting bats. The fly traps are ready to catch ignorant flies with their stickiness. Infrared lights, cameras, action! Continue reading