Barcodes Are Us
Usually I write about things where I see some unexpected parallel to healthcare, or something just amazed me, or outraged me (there are lots of things about healthcare like the latter). But sometimes I run across something that just delights me.
So when I inexplicably stumbled across DNA Barcoding Technology for High Throughput Cell-Nanoparticle Study, by Andy Tay, PhD, my first thought was, oh, nanoparticles, that’s always interesting, then it hit me: wait, DNA has barcodes?
We’re all used to barcodes. Pretty much every product in pretty much every store has a barcode. The barcode was invented in the late 1940’s, but didn’t really take off in popularity until the UPC (Universal Product Code) barcode. A Marsh’s Supermarket in Troy, Ohio, in 1974 was the first grocery item scanned (a pack of Wrigley’s Juicy Fruit Gum, if you are interested). The UPC barcode encodes the Manufacturer of the product, and the product code.
The now almost as ubiquitous QR codes are, essentially, two dimensional barcodes. Accordingly, they can store significantly more information.
But back to DNA barcodes. The main purpose is, as you might guess from the name, is to have a standardized way to uniquely identify species, based on their DNA (think of species as the “product”). The methods were first proposed in 2003, by Paul D N Herbert, et alia, and quickly gained traction.
Guo, et. alia, describes DNA barcoding as follows:
DNA barcode is one or more short gene sequences (generally 200–900 base pairs) taken from a standardized portion of the genome to aid species identification and discovery by employing sequence divergence based on nucleotide alignment (Emerson et al. 2011; Hebert et al. 2003a, 2004). Thus, the fundamental function of this genetic tool seeks to compare barcode sequences to reference databases to efficiently and effectively assign any biological sample to its species regardless of the visual classification of the sample.
There are databases of DNA barcodes for a variety of life forms, including plants, animals, and/or fungi; these include the BOLD system (Barcode of Life Data system), Unite, Diat.barcode, and iBOL (international Book of Life).
Unlike, say, UPC codes, which can be simply assigned, there’s not a universal way to decide which DNA sequences can be used to barcode an organism, and great care must be taken to extract and analyze it. To complicate things further, there are mini-barcodes and meta-barcodes. I’ll leave it as an exercise for the very interested reader to learn more about exactly how all that is done; for my purposes, it may as well just be magic.
DNA barcodes allow us to look at a relatively modest DNA sequence and determine what species it belongs to, which is a great help if one is identifying new species or trying to do an assessment of an ecosystem. For example, students from a collection of 50 schools in Australia collected some 14,000 specimens, submitted 12,500 new DNA barcodes to BOLD — 3,000 of which were entirely new. Project lead Dr Erinn Fagan-Jeffries said: “It is highly likely that all contributing schools have found species new to Western science which is really exciting.”
Lest you think that all DNA barcodes are good for are identification of species, researchers at the Garvin Institute of Medical Research barcoded cancer cells, in order to understand which ones were evading the immune system response and immunotherapies. “We showed that there are rare cancer cells capable of escaping the immune system and escaping treatment with immunotherapy,” said first author Louise Baldwin.
The researchers believe that “the mechanisms could be used as potential targets for therapies, to stop tumorous cells from adapting and spreading. Another future application could be in prognosis, where a high number of cells could indicate which patients might not respond to immunotherapy.”
Not bad for a barcode.
Back to the nanoparticles. Dr. Tay says: “Recently, DNA barcoding technologies have been applied to generate barcoded cells and nanoparticles to investigate heterogeneous cell-nanoparticle interactions to boost the translational application of nanomedicine.” The new techniques enable “millions of cells to be tracked over developmental and evolutionary time scales and to record cellular features in response to stimuli, including nanomedicine.”
Dr. Tay points to research by Boehnke, et. al. that “made use of barcoded cell lines to discover cell and nanoparticle features to boost nanomedicine delivery.” These and other new techniques made it easier and faster to understand which nanoparticle formulations are having the desired effects.
I mean, really, is anything cooler than injecting DNA barcodes into nanoparticles to help achieve clinical results? That’s some real 21st century medicine.
We are DNA creatures. All life that we know are based on DNA, and it’s not clear to me that we’d even recognize an organism based on anything else as life. Barcodes are not DNA’s only amazing trick. It is the nonpareil storage device; someday all our storage needs may be met using DNA (yes, I know, some argue to diamonds as the storage medium, but, really, DNA is way cooler). As Zhang, et. al. noted earlier this year, “DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale.”
Given all that, I’m still holding out hope that we’ll someday have a DNA EHR, with both the processing done in DNA and the data stored in DNA, and that we store all that in our own DNA. Tell me that’s not something that a visitor from the 22nd century wouldn’t appreciate.
There’s a whole body of work in information theory/mathematical logic about the shortest way to define statements, numbers, etc. DNA barcodes may do well at more simply describing species, but I don’t know that we couldn’t each have a unique DNA barcode — shorter than our entire genome — that could be used for many applications.
Our world would be much different without UPC barcodes, QR codes, and computers based on silicon chips, but that’s all so 20th century. In the 21st century, we better be getting used to more ways we can use DNA.
DNA barcodes — delightful, indeed.