Thursday, August 14, 2014

Virtual Barcodes

This weeks literature screen revealed a very interesting proof-of-principle study published by some colleagues from Brandeis University in Waltham, USA. They thought of utilizing a PCR method that was developed about ten years ago.

Linear-After-The-Exponential-PCR (LATE-PCR) is an asymmetric PCR method in which one DNA strand in a double-stranded DNA template is preferentially amplified. It is used in sequencing and hybridization probing where amplification of only one of the two strands is required. The colleagues used LATE-PCR to amplify a portion of the CO1 gene for each of five commercially available, beneficial species of soil nematodes. A set of ten low temperature Lights-On/Lights-Off consensus probes were included in the reaction mixture and were used at end-point to coat the accumulated single-stranded amplicon by dropping the temperature. Because each of the probes is mis-match tolerant, the temperature at which it hybridizes to its complementary region within the target is sequence dependent. As anticipated, each species had its own unique fluorescent signature in either three different colors, or a single color depending on which fluorophores were used to label the Lights-On probes. Each fluorescent signature was then mathematically converted to a species-specific Virtual Barcode.

This is yet another pretty cool non-sequencing method (like High Resolution Melting) which could be used in cases where rapid, low cost species identification is needed. What makes such non-sequencing methods so attractive are not only the highly reduced costs but also the flexibility of the system. One needs much less equipment and all of a sudden it becomes possible to work remotely (in the field, point-of-sale, border control etc.). 

It is great to see all these applications seeing the light of the day even more so when they hold the promise to bring us closer to the dream of every DNA Barcode aficionado - the handheld DNA Barcode gadget. Granted, this idea has a lot of potential for a variety of applications but I think at some point the authors start to overstate. 

One reason for development of this new method lies in the fact that the current approach to barcoding the tens of millions of eukaryotes on earth is slow, labor intensive and expensive. 

I am afraid that building the DNA Barcode library for all species will always be slow, labor intensive and expensive because collecting, obtaining and preparing specimens won't change much no matter what molecular high-tech we throw at the problem. If the only issue is the rate at which we can assemble DNA sequences, filter out duplicates and store everything in our databases, the job could be done by metabarcoding of entire ecosystems. But what would be the knowledge gained by such approaches? No sequence could be tied to a specimen (voucher) and all the information that comes with knowing the actual source of DNA. It is a feasible way to explore the diversity of all those unculturable micro-organisms but for most eukaryotes we should do more.

Don't get me wrong, I do like the approach using LATE-PCR but I am a bit puzzled by some of the motivation expressed in the paper. Should we consider iBOL's progress as slow? I really hope that there will be a day in the coming year were we lean back for a moment realizing that 500,000 species have indeed been assigned a DNA Barcode in just a little over a decade. A decade of which at least the first third was wasted in a battle against egos instead of engaging in proper scientific reasoning. The more all the 'barcoders' can be proud of what they accomplished in short time and against all odds. I will. Even more so because most of these DNA Barcodes won't be just naked sequences. They come with lots of valuable information attached to them.

Of course we all wish we could be faster in what we are doing. Reality is that we are still outpaced by extinction and hampered by human ignorance but I don't think limits to technology are holding us back any longer. The bottleneck is what some call the front-end of the barcoding enterprise. It is about collecting all the specimens, finding them, surveying the planet in a systematic way to ensure we didn't miss entire groups of organisms. Here is where we could save time by thinking more strategically. This is not another on of those calls for 'more collecting' or 'more money'. No doubt, more money would help, especially given that the current investments are rather modest but it is more about getting creative, making the most of the opportunities we have. Yes, we do need more collecting but perhaps we better look at new ways to accomplish that. I am talking about 'citizen scientists' and in my head this encompasses everyone from the hobby naturalist to the one who's livelihood depends on biodiversity. Not only would that increase the collecting workforce but perhaps more importantly the life that surrounds us becomes more meaningful to everyone directly involved. 

I'd like to ensure the authors of the paper (in case they ever read this post) that I didn't mean to downgrade their accomplishment by going off on a tangent. I do share they hopes that the new Virtual Barcode along with its nucleotide sequence can be added to an ever expanding Barcode of Life library of information - perhaps alongside with HMR melting curves and all future derivatives.

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