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DNA Barcoding and Citizen Science

by Ellen Jorgensen

Tags: Genetics, DNA, GeneWatch,

DNA barcoding art

Easy enough for kids and amateur scientists to use, you might say DNA barcoding is inherently democratic.

In 2008, I happened to see an intriguing news story about two New York City high school girls who had used a new DNA-based identification method to determine if their neighborhood sushi restaurants were selling mislabeled fish. That was my first encounter with the technique known as DNA barcoding. Since then, I have helped hundreds of amateur scientists use barcoding to question the identity of everything from 'heirloom' oranges to 'beef' meatballs to the diversity of Alaskan plants.

The idea of identifying species through a very short genetic sequence, rather like the manner in which a supermarket barcode identifies products, was first proposed in a 2003 paper by Dr. Paul Hebert, a researcher at the University of Guelph in Ontario, Canada. The beauty of barcoding is that even non-specialists can obtain barcodes from tiny amounts of tissue and conclusively identify a species. Compare this to standard taxonomic identification, which requires intact specimens (often impossible in situations where you want to know the identity of foodstuffs) and an expert able to distinguish subtle anatomical differences between closely-related species using morphological features like the shape and color of the organism's parts. As The New York Times put it in their article about the abovementioned 'SushiGate' kids:

"What may be most impressive about the experiment is the ease with which the students accomplished it. Although the testing technique is at the forefront of research, the fact that anyone can take advantage of it by sending samples off to a laboratory meant the kind of investigative tools once restricted to Ph.D.'s and crime labs can move into the hands of curious diners and amateur scientists everywhere."

Readers of GeneWatch are probably more aware than most of the astounding rate at which DNA science in general is progressing. What they may not know is that there is a growing movement to democratize the technology, to put it into the hands of the public for the greater good. Professional scientists like myself have been inspired to found open, public-serving laboratories that are accessible to anyone who wants to pursue a safe and useful project. Genspace, which I co-founded and direct, is a nonprofit community biolab located in Brooklyn, NY. We provide workspace, access to equipment, and mentorship in the biosciences. Genspace offers adult education courses, free public events such as open barcoding nights, low-cost lab space for inventors, and is a place for students to work on projects for science competitions. One of the best uses of community labs is the kind of DIY investigation that can tell you more about your environment, health, or food. Is that goat cheese made with cow's milk? Bring it in and we'll teach you to barcode it. Want to know if your soy milk is Roundup Ready? We can teach you to determine that too, it's an even simpler protocol than barcoding. We want everyone to become more literate in the biosciences in order to join the discussion about them from a position of knowledge as opposed to forming opinions based on ignorance and fear. And I strongly feel that the best way to learn is hands-on in the lab.

Barcoding is a regular activity at Genspace. It's a great way for amateurs to participate in real science. Although the DNA barcodes of most common species have been deposited into public databases, most of the millions of species on earth have not been barcoded yet. This gives the student or citizen scientist an opportunity to contribute to the growing public database of DNA barcodes. Genspace first began teaching barcoding as part of Cold Spring Harbor Laboratory's 2011-2012 Urban Barcode Project, a science competition for high school students. Genspace worked closely with their Harlem DNA Lab and acted as its satellite site in Brooklyn for teacher training and open lab hours to mentor students in barcoding, a relationship that continues today.

Our newest barcoding project focuses on the importance of identifying organisms to help monitor the biological effects of global climate change. Accelerating habitat destruction is particularly evident in the Alaskan landscape, where glaciers recede practically before our eyes and environmentalists attempt to preserve species diversity in the face of opposing economic interests. In Genspace's Alaska Barcode Project, we invite the general public to monthly open nights where we teach them to barcode plant samples collected from remote locations in interior Alaska.  The goal is twofold: to create a baseline survey of plants in particular areas such as the Skolai Valley in Wrangell-St. Elias National Park, and to add new identifying barcodes to the Barcode of Life Database to empower future amateur scientists to conduct similar surveys.

Part of the DNA sequence of the chloroplast gene rbcL has been designated as one of the two barcode regions for plants (the matK gene is the other region but is not used at Genspace). Barcoding a specimen starts with extracting its DNA. You only need a small piece, the diameter of a pencil eraser, to get plenty of DNA for barcoding. In a tiny plastic tube, the sample is mixed with a few drops of a solution that disrupts the cellular structure and then ground into a paste using a little plastic pestle. The DNA is then absorbed onto silica, which is washed with salt-containing buffers until all other cellular components are gone. The clean DNA is eluted off the silica with water and the barcoding region amplified using a procedure called polymerase chain reaction (PCR). The amplification is necessary to get enough material in the tube to send out for sequencing.

PCR is a standard lab technique that has become mostly automated. Prepackaged mixtures of enzymes and reaction components such as the PCR primers that target the barcoding region can be bought cheaply in bulk. All one has to do is add a minute quantity of your DNA to the PCR mix and stick it into a preprogrammed machine. What comes out is ready to be sent off for sequencing at a fee-for-service facility doing hundreds of sequencing reactions daily. The total cost for the whole procedure can be less than $20 per sample.

Our barcoding nights have been very popular. They educate people and make them more informed about cutting-edge science. There is also a social component to the project where participants often engage in discussions about the promise and the repercussions of the technology.

It wasn't that long ago that major scientific contributions were made by curious amateurs, and science itself was less of a profession and more of a hobby. The popularity of our barcoding nights might be predictive of the resurgence of such citizen science, where a diverse cross-section of the general population are enthusiastic participants in scientific inquiry. It's empowering to be able to use the latest breakthroughs to answer questions of importance to you. I can think of no better use of my time than to continue to facilitate this empowerment through my work at Genspace. And please do stop by and barcode something if you are in the neighborhood!

Ellen Jorgensen, PhD, is co-founder and President of Genspace, where she spearheads the Urban Barcode Project and other programs. She was an invited speaker at TEDGlobal 2012. Reprinted with permission from GeneWatch (Nov/Dec. 2013), a bimonthly publication of the Council for Responsible Genetics and America's first and only magazine dedicated to monitoring biotechnology's social, ethical, and environmental consequences.

Photo by Col Ford and Natasha de Vere, licensed under Creative Commons.