Tuesday, September 25, 2012

Barcoding at Warpspeed

Imagine an interception of potentially endangered species at a border or pest detection in shipments scheduled for transboundary movement. In both cases a rapid identification of organisms is paramount in order to facilitate border control decisions. DNA Barcoding seems the best option for identification in such situations, but its utility will further increase if results are delivered in hours rather than days. 

The quest for fast procedures to obtain useful sequences for identification is already underway fro a few years. In 2009 researchers from the University of Guelph proposed simple modified protocols that would enable to shorten a process that often takes 2 days to just 2 hours. The only drawback was that they were targeting smaller fragments with a maximum length around 400 bp and they were still using the classical steps of sequencing: DNA extraction followed by PCR and Sanger-Sequencing (with cleanup prior to sequencing). The trick was to reduce the time for each step as much as possible.

Now imagine you are able to skip a step in the process such as the isolation of the DNA which is often the most time-consuming one. Direct amplification is the buzz word for this and the community of forensic scientists are leading the way here. Companies offer rapid DNA services for law enforcement and biometric applications. They utilize commercial off-the-shelf equipment and reagents that already commonly used in forensic laboratories and capitalize on advancements in both rapid thermal cycling and direct amplification. A big step forward as with the DNA isolation out of the way you not only save time but also money on instrumental investments and chemical supplies. The question is if this can be used in a normal laboratory setting. After all most researchers are not working in a well funded crime lab. 

Do you remember the DNA Barcoding story of the Mezcal Worm? Certain mezcals, usually from the state of Oaxaca, are sold con gusano (with worm), a practice that began as a marketing gimmick in the 1940s. The worm is actually the larval form of the moth Hypopta agavis that lives on the agave plant. A group of researchers were able to retrieve DNA Barcodes from the booze (not the larva) and indeed they used direct amplification as most DNA isolation methods would have failed.

And in the not so distant future?
Direct Sequencing will be the future. No DNA isolation, no PCR reaction to provide enough target sequence copies, just sequencing. Science Fiction? Not really - certainly not at a point where we can buy kits for the every day use but for my part I am watching developments closely.

h/t Mark Stoeckle

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