Oxford Nanopore Technologies mini… user meeting | By Jenneke Wit

My first response when arriving at the meeting was that I took a wrong turn. The venue was very flashy, polished and professional. So much so, I felt like I ended up at an Apple launch event! But my nametag was there, and listening more closely it transpired I ended up in Little Britain. Not surprising, given Oxford Nanopore Technology (ONT) hails from overseas.

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MinION versus Nokia 5110 – an approximation

ONT, the company organising this meeting, is probably best known for their hand-held sequencer, the MinION. This fancy machine, about the size my first mobile, a – yellow – Nokia 5110, can be used in the lab as well as the field to generate long reads, thousands to over a hundred thousand bases in length. A great feat, but also something that still requires a lot of tweaking and troublesooting, which is why this community meeting was so beneficial for both ONT and its users.

When the talks started it quickly became clear there was more to the meeting than an amazing venue. Talks were of a wide diversity and good quality. We were introduced to technological improvements, including an even smaller sequencer (SmidgION), new reagent kits and molecular protocols as well as a wide range of topics where ONT sequencing played an important role. Diagnosing malaria in India, looking for complex genomic rearrangements in Caenorhabditis elegans and sequencing the human genome were but a few of the exciting topics.

Over the two-day meeting, I got most out of the breakout sessions where there was ample opportunity for discussion following a set of flash talks. These were talks of the people that were getting their hands dirty. Be that in the wet lab, in the field, or behind their computers.

Arwyn Edwards, from Aberystwyth University, gave the talk that stood out most to me. He started out introducing us to cryoconite, a dust partially made up of microbes. When this dust builds up on glaciers, its dark appearance accelerates melting. For studying which microbes are present, he uses the MinION. I have a warm, well-equipped lab at my disposal, but was intrigued by what must be the most high-tech lab-in-a-bag ever. Everything from sampling, DNA-extraction, sequencing and analysis fits in this army-style rucksack and allows Arwyn and his team to study the microbe composition on site (dubbed extreme metagenomics). Evidenced by twitter, I was not the only one enthralled by this travelling lab!

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Lab-in-a-Rucksack, ready for the “MetaGenomadic” life – by Arwyn Edwards

Having done a lot of optimizing myself, it was interesting to listen to the approaches others took to tackle the same issues, and, often, come to the same conclusions. This was valid for both the molecular work as well as the concerns we were having about the computational analysis. Especially with regards “what is good data?” when sequencing longer fragments. Consensus is: with long read technologies coverage gives way to longer reads when assembling new genomes. Aiming for fewer but longer reads rather than more “short” (few kb) reads is the way forward.

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Souvenir: Personalized sleeves!

Finally, a blog on this conference wouldn’t be complete without a mention of the amazing care they took of our nutritional needs. From breakfast to dinner, everything was equally tasty and well prepared. For vegetarians and meat lovers alike, there was plenty for everyone. The eye for detail was amazing, and provided an excellent souvenir for avid tea-drinker James.

I look forward to further collaborations with those I connected with at the meeting, and would like to thank HPI and the Faculty of Veterinary Medicine at the University of Calgary for supporting my attendance.

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In a model world

My trip across the pond could not have started better. The conference on Evolutionary Biology of Caenorhabditis and other Nematodes I was about to attend coincided with the first games of the FIFA World Cup and I was lucky enough to have a stopover in Amsterdam the day of the first Dutch game. So after I made my way to my cousin’s who was hosting me for the night, a little nap and a visit to the beach, we prepared the house for guests and sat down for a game that would, fingers crossed, end in a win of 1-2 (1-2 as it was officially a home game for Spain). Even the optimist did not dare to go out on a limb and predict a higher score in favour of the Netherlands. How different did that pan out! All dressed in our obligatory orange, equipped with orange snacks in an orange-decorated garden, the mood was dampened after the first goal… Spain. Inside, where the kids were watching, it went quiet. Still, didn’t Brazil come back from 0-1 to beat Croatia by 3-1 just yesterday? ‘It’s still possible…’, we said to each other without much conviction. How different was the mood some 45 minutes later, when the scoreboard did not indicate the highly dreaded defeat, but a not-in-my-wildest-dreams-had-I-imagined-this 1-5 victory for The Netherlands!! Every goal was accompanied by a sprint through the park by the kids and a relieved laughter that became more hysterical as the goals kept coming. What a night!

The next morning it was back to business as I made my way to Hinxton. A pretty painless affair except for the cab driver telling me off for trying to get into the drivers seat 😉 The grounds at the Sanger Institute were stunning, and I was upgraded from a shared to a single room. So far, so good. During the conference got I to spend time with people I had been in touch with previously and with whom I will collaborate in the future. I also got to catch up with fellow HPI’er Andrew Rezansoff, who was brushing up on his English in this picturesque environment for a month and did some science in the process. On top of that I met a lot of new people, a number of whom I’ve been in touch with since, and a further few I now follow on Twitter. 

Pretty eyes © SciencePhotoLibrary

Working at the faculty of Veterinary Medicine at the University of Calgary, it’s been a steep learning curve the past months when attending talks on a wide variety of veterinary related subjects. Having worked on experimental evolution of ageing in fruit flies during my PhD before changing to studying drug resistance at a genomic level in Haemonchus contortus, the talks on fellow model organism Caenorhabditis where a bit like coming home. Listening to the Keynote Lecture by Patrick Phillips I got reminded of what it was like planning the ‘perfect’ experiment, controlling the environment to the finest details and having plenty of resources to turn to when things went awry. But while I was dreaming away at the thought of working with Drosophila, Phillips made it clear there is some rivalry going on. But while it might be a benefit that C. elegans can be frozen and serve as a fossil record

on which the same experiments can be repeated time and time again, you can’t deny that Drosophila have the prettiest eyes! When I was informed Wormbase had at some point even manufactured fly swatters to extinguish the competition, my initial joy at being with likeminded scientists turned into horror. What a cruel group of people I found myself surrounded by!

 

As talks continued however, I came to appreciate the beauty of working with worms. Not just the dead kind like myself, but also those with which you can undertake experimental evolution setups and create recombinant inbred lines which I was familiar with from the fly world. Plant parasitism, mating systems, genomics, speciation and diversifications where some of the topics covered, and I enjoyed learning more about the worm world immensely.

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James Wasmuth (@jdwasmuth) highlighting the importance of collaborations, as well as a major partner in crime.

Turned out worm people are not as harsh as their anti-fly-behaviour had me believe. The atmosphere during the conference was one of friendship, joy and collaboration. Several of the younger PIs are the progeny of some of the slightly older PIs. Maybe these bonds formed previously contributed to the no-nonsense, productive vibe that hovered over the grounds from June 14-17. And because talks, posters, dinner and sleeping quarters where all located on site, networking never stopped. I thoroughly enjoyed getting to know so many people and learn about their work and interests while sharing good food and drinks. I look forward to next time!

 

PS: I was relieved to find that no matter how hard I tried, the Wormbase-fly swatter appears to be a thing of the past. The only mention of it I could find online where one on a recap of the C. elegans Worm Comedy Show from 2011, and one comment on twitter. Happy collaboration and thanks for HPI for making this trip possible!

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