Pacific Expedition Breaksthrough Real-Time DNA
SDSU Postdoctoral Researcher Andreas Haas at Vostock island on Hanse Explorer. Photo Rob Edwards |
DNA
Sequence until now used to be considered tools strictly for clean land closed
laboratories. Studies costly, time consuming and available to few. A recent
expedition in the Pacific Ocean has had a breakthrough in next generation DNA
sequencing by successfully obtaining sequences in mid open waters aboard a
small ship. There may come a time when DNA sequencing of marine life forms will
be instant, affordable and in hands of everyone but until then this new study proves
to be a pathway into Live-Real-DNA sequencing. The value? Priceless for mapping
of species, classification of life forms, diverse industries, ecology,
conservation and medicine among other sectors.
Science
Daily reported on August 19th on the work “Sequencing at sea:
Performing real-time DNA sequencing in the middle of Pacific Ocean”.
Scientists
overcame equipment failure, space constraints and shark-infested waters to do
real-time DNA sequencing in a remote field location. Despite the setbacks, the
researchers successfully collected samples, sequenced DNA and developed new
research questions on the fly.
The
research expedition included San Diego State University computer scientist
Robert Edwards, biologist Forest Rohwer, postdoctoral scholar Andreas Haas and
graduate student Yan Wei Lim. They were
accompanied by several other researchers from the San Diego region and around
the world.
Single
handed they accomplished a breakthrough revealing the Live-Real Time DNA
Sequence is possible. In all it took the team just three weeks of their
five-island expedition. The conclusions and findings of their expedition were
published in the Journal PeerJ.
"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 of San Diego University told media referring to the general
doubts which the project set out to prove mistaken.
The
crew devised a protocol for how to run a DNA sequencer on a ship -headed first
to Tahiti with a sequencer provided by San Diego-based biotech company Life
Technologies and met with the vessel Explorer to set final course for the Line
Islands.
“Genomics
and metagenomics have revolutionized our understanding of marine microbial ecology
and the importance of microbes in global geochemical cycles. However, the
process of DNA sequencing has always been an abstract extension of the research
expedition, completed once the samples were returned to the laboratory,” the
paper published by PeerJ stated.
The
expedition to the Southern Line Islands was the “first effort to bringing next
generation sequencing to some of the most remote locations on the planet“. Following their ambitious goal the team
successfully sequenced twenty six marine microbial genomes, and two marine
microbial metagenomes using a Ion Torrent PGM platform on a Merchant Yacht
Hanse Explorer.
“Onboard
sequence assembly, annotation, and analysis enabled us to investigate the role
of the microbes in the coral reef ecology of these islands and atolls,” the
team states.
Sequencing
in the field allows for numerous advantages. The group highlights the
“elimination of the delay between sampling and sequencing. “By overcoming the
hurdles associated with sequencing on a boat in the middle of the Pacific Ocean
we proved the flexibility of the sequencing, annotation, and analysis
pipelines,” the paper concludes.
In
an Interview conducted by PeerJ Edwards revealed details of the expedition
which could change DNA Sequence for science. “This has massive implications for
ecology, but also for conservation, bioprospecting, and a whole suite of other
sequence based technologies.” Edwards assured.
“Most
people thought we were completely crazy when we said that we would do this. The
protocols for next generation sequencing are designed to be used in clean
laboratories, and the data requires high performance computing. Seawater tends
not to prolong the life of electronic components, and so everything was really
stacked against us. The computational aspects were much more challenging than
the biology. That it worked was the biggest surprise – not only to us, but also
to the naysayers who said it was impossible!,” the co-author of the paper told
PeerJ.
The
work of the group proves to have a huge impact on the world’s society “We’re
also pushing the boundaries of what is technically feasible and at the same
time learning new things about ecology and evolution, areas that we have
studied for hundreds of years,” Edwards concluded.