A team of researchers at the San Diego State University have successfully carried out real-time DNA sequencing at sea. The team included biologist Forest Rohwer, computer scientist Rob Edwards, PhD scholar Andreas Haas and graduate student Yan Wei Lim. Findings of the study appeared in the journal PeerJ. It’s the first time that DNA sequencing has been done out in the field in real-time. The five-island expedition over a three-week period took place last year.
Life Technologies provided scientists the DNA sequencing equipment
Biologists at the San Diego State University have traveled to the Line Islands several times over the last decade. They would collect and analyze the coral habitat to understand the kind of organism that live there, and how they compete for resources. But it was always cumbersome. They had to wait until they got back to the laboratory to take a look at their data.
So, Edwards came up with an ambitious plan to somehow bring the expensive piece of the DNA sequencing equipment to the sea. Many people initially doubted his plan. They were hesitant to take a $500,000 equipment into the middle of the Pacific without any assurance that it’s going to be coming back, Edwards said in a news release.
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Then Edwards and his colleagues devised a protocol for how to run a DNA sequencer on a ship. Finally, San Diego-based biotechnology company Life Technologies provided them a sequencer. That was not the end to their problems. Hurdles were manifold when they reached the Line Islands. Touch screen of the DNA sequencing machine broke during the transit. Edwards had to hack into the sequencer’s software to make it run with his laptop.
Challenges to real-time DNA sequencing at sea
Accommodating all the various pieces of equipment was another challenge. The sequencer was set up in the laundry room. It was the lowest point in the vessel, so it would sway the least as the ship rocked. They set up the DNA isolation station in the cabin. The dining room hosted the PCR machine. Doctoral student Lim was given the responsibility of calibrating the sequencer. DNA sequencing usually takes just 15 minutes. But it took about five hours because of the boat’s sway.
And then there were sharks. Every time scientists dove into the reef to collect samples, they could count 20-30 sharks nearby. Despite all the hurdles, researchers collected samples, sequenced their DNA and developed new hypotheses. In total, they sequenced 26 bacterial genomes.