Next Generation Sequencing – Life Forms of Sydney Harbor

Leonard Nimoy as Spock from Star Trek: The Original Series.

In the original Star Trek, Lieutenant Spock, upon beaming down to a new planet from the Starship Enterprise, would immediately pull out a Tricorder and begin scanning the environment for life forms. Results were instantaneous, providing a comprehensive view of the surrounding ecosystem within seconds.

Though we have yet to fully see such a novel invention on Earth, I’m overwhelmed today by how close we actually are to inventing the Tricoder in real life. I spent the day in lab at the Sydney Institute of Marine Science, extracting DNA from marine sediments and their invertebrate inhabitants. Thanks to support from the IGERT Program on Ocean Change at UW and from the Applied Marine and Estuarine Ecology Lab at UNSW, the genetic material I extracted will be sequenced and matched to a database of known organism sequences, in a process called DNA barcoding.

Eliza looking very serious in her white lab coat

Like DNA extractions of the old school variety, the endeavor required donning a white lab coat, goggles, and gloves, and making sure not to sneeze or shed excessively. Unlike genetic adventures past, the materials needed for the extractions were available in a self-contained kit shipped par avion from Texas — no gels or interpretation of specific sequences was needed, and the entire process for many 10s of samples took only a single work day (20 years ago, comparable work might have been the focus of an entire PhD).

Vials and pipetting tools for the final stage of DNA extractions

I hope results from the day’s genetic escapades will yield helpful information about both the microbial and invertebrate community on manmade and natural shorelines in urban settings, such as Sydney. And I’m thrilled to report there is a chance that by the end of my lifetime, I could be scanning Earth’s ecosystems, Tricoder in hand, with my best interpretation of a female embodiment of Lieutenant Spock.

Tricorder from Star Trek: The Next Generation.