Real-Time Genome Sequence can be Done at Sea: Researchers
A team of researchers state that it is possible to conduct a real-time genome sequencing at sea.
The four-member team from the San Diego University has become the first research group to take out a half-a-million dollar worth of equipment - the DNA sequencer - to an investigation site in the Pacific Ocean.
Their expedition is documented in an article published in the journal PeerJ.
The three-week, five-island trip took place in 2013. The team included San Diego State University computer scientist Rob Edwards, biologist Forest Rohwer, postdoctoral scholar Andreas Haas and graduate student Yan Wei Lim.
The team sequenced 26 bacterial genomes along with two metagenomes, which assess the entire DNA present in a given region. Samples were collected from southern Line Islands' numerous coral reefs.
The researchers said that they had to face several hurdles during the ambitious project. First, scientists dread hauling expensive equipment in the middle of nowhere.
"People are a little bit hesitant to take a half-million-dollar piece of equipment into the middle of the Pacific if you're not sure it's going to be coming back," Edwards said in a news release.
San Diego-based biotech company Life Technologies provided the DNA sequencer for the research.
The team then had to plan a protocol for the study as this was the first time that anyone was trying to sequence DNA in a remote location. The laundry room of the ship MY Hanse Explorer was converted into a makeshift laboratory, while the upper aft deck became a temporary microbiology lab.
Calibrating the sequencer usually takes about 15 minutes under normal conditions. Aboard the Explorer, this simple process took as many as five hours.
Sample collection was also a major issue as the researchers had to invade shark territory to look for specimens.
The researchers have now established that they can collect and process data at the study site. Next, they plan on doing more complex research and collect more data.
"At the end of the day, we were able to come up with the data we needed," Edwards said in a news release. "But when we go back next time, we're going to be better prepared."