On the fourth floor of the newest building on the Wageningen University campus, twenty master’s students stare at a screen with bated breath. Just before that, one of them dropped a DNA sample from wolf droppings on the Veluwe in a nanopore sequencer, a device the size of a snack bar. It is busy with the DNA analysis, which can be followed live on the screen. They don’t have to wait long. In a few minutes you will see which animals the Dutch newcomer has eaten.
Just three years ago, DNA research looked very different, explains lab coordinator and molecular ecologist Reindert Nijland. The analysis was done in a special laboratory and it sometimes took up to three months to get the results. That made a practical like this, in which students get to work themselves, almost impossible. It was limited to the preliminary steps: collecting samples, isolating DNA, multiplying with PCR. After that preparation process, it was the lab’s turn.
Sequencer
With the new sequencer, no external lab is involved. The analysis is now beeped in a few minutes. It’s also cheaper, more manageable and well on the way to accuracy. Feel free to call it revolutionary, says Nijland. His fellow biologists from other universities also use this term, when asked for a response. That is promising.
The core of the device, developed by Oxford Nanopore Technologies, is a surface of half by one and a half centimeters. There are 2,048 minute holes in it (the nanopores), each 1 nanometer in diameter. Fill the space above it with the DNA sample. Some of the DNA strands reach the holes and are pulled through. The device measures the resistance between the strand and the hole, which is translated into a series of letters (example: tgcgaaaaaag† The software puts those strings of letters one after the other. The result is the DNA sequence.
For most studies, a small part of the complete DNA is enough, the analysis is then done in a few seconds. But if you want to map the entire genome – one complete set of genes – of a bread sponge from the North Sea, the analysis still takes twenty hours, student Fabian Timpen (24) has learned. In his experiment, he compares the result with the already known genome of an Icelandic congener. This will help determine how diverse the species is – the more diverse, the healthier and the better it is likely to adapt to climate change.
It is typically a study that would not have been possible without the new technique, says Nijland. ‘Twenty hours seems long, but previously it would have taken months to map an entire genome. When it comes to something well-known like cod or herring, money is sometimes made available, but a sponge? Nobody puts that much money into that.’
Wildflowers
On the other side of the room, students Agata Marchi (24) and Niek Palmen (22) are studying insects. They have collected DNA on wild flowers and the question now is: which pollinators have visited them? They soon have a bite. The flowers turn out to be a dna gold mine: several species of flies, aphids, mosquitoes, butterflies, there is an earwig on a comfrey root. ‘Really cool’, they both think. ‘You used to have to spend hours looking at flowers to measure biodiversity. This is much easier and more accurate.’
The term ‘biodiversity’ is often used. The method is therefore perfect for measuring it, says Nijland. Not only on land but also at sea, as in his own research. ‘We collect seawater and analyze which DNA can be found in it. That is much easier, cheaper and less harmful than the old method, in which we have to go out to sea several times a year with large boats to catch fish.’
Another advantage: ‘You can immediately start working with your samples in the middle of the jungle, they don’t have to go back to a lab first. Everything you need fits in a backpack.’ Accessibility also opens doors for countries where it is not possible to set up an expensive DNA lab just like that. For example, the technology in West Africa was already deployed to detect new mutations of the Ebola virus. Nijland fantasizes even further. ‘What if you could measure DNA in real time at the bottom of a buoy in the sea? Or can you keep track of what a shark eats with a DNA tracker? The separate techniques are already there, they just need to be combined.’
Meanwhile, a long string of letters appears on the screen: the DNA analysis from the wolf poop has been completed. Nijland opens the DNA database and searches for a match. When the outcome appears on the screen, there is cautious laughter. ‘100% Homo sapiens’. Did the wolf feast on a human? Nope, says Nijland, some human DNA simply got in during the preparation. Even the most revolutionary technique takes some practice.