Sequencing DNA in the Rainforest with Nanopore Technology

Sequencing DNA in the Rainforest with Nanopore Technology


The last few days We’ve been on an expedition in the rain forests of Ecuador and our goal was to take a portable lab into the field sequence the DNA of an organism and identify it to species in real time so this was part of a National Geographic grant and With a team of herpetologists here in Ecuador our goal was to use a new portable sequencer This is a device that was made by Oxford nanopore technologies. It’s this really cool portable gene sequencer We use some other equipment like the miniPCR and Overall we were able to take the bare bone elements of a laboratory and take it out into a very remote rainforest in Ecuador. And so why would we want to do this? essentially we are in a very biodiverse region of the planet and we went to a Region called Canande which is in the Choco rainforest of Ecuador and this region is highly diverse there are lots of species that are known some that are threatened some that are undescribed and So the problem is that this place is being deforested very rapidly So there’s a real time sensitivity to trying to understand the organisms that live there There is a very strong need to actually preserve this biodiversity here Actually bringing the sequencer to the field can save time. So we can instead of like going out in the field collecting the samples bringing it back to a lab having them send off to a different country for sequencing this can take weeks and months and In our case it took less than 24 hours It was a really exciting turnaround we went out with our portable lab And we found animals that night like vipers, geckos, frogs. All of these amazing diverse organisms And so we were able to take a small amount of blood extract DNA use PCR amplification for certain genes that are used in identifying species And then we sequenced it right than in there so in less than 24 hours we had received the information The DNA information that we could identify them to species accurately and A cool thing is that you can even do the bioinformatics in the field the only thing you need is a laptop So it’s very very easy very fast And you get actual sequence you can even run a phylogeny or blast it against the database to see what species it is in the rainforest and this has actually lots of Implications not just for conservation or for teaching people about the biodiversity in certain areas But also for labs in countries like Ecuador where all the sequencing technologies is not readily available so if we can do it in the field anyone can do it in the lab here, and so this technology really works well for Scientist here to apply it in the labs

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13 thoughts on “Sequencing DNA in the Rainforest with Nanopore Technology

  1. Great video! I'm excited to see how much faster and easier DNA barcoding in the field will be 10 to 20 years from now. Hopefully the Ecuadorian members of Tropical Herping will stop by Mashpi during my internship over the summer. I'd love to help them out and learn some more photography tips!

  2. why a miniPCR ? one of the purpose of nanapore (in addition with the miniaturization) is the fact that there is no need to amplify the signal right ?

  3. That's amazing. Do you have more videos illustrating the steps exactly of sample processing, data analysis?? Or if you can guide me to a good website plz. thanks

  4. What species samples did you use for collecting DNA, did you also have a mini centrifuge, what portable wet lab steps did you have to take prior to using the MiniPCR and MiniIon nanopore?

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