Barcode the World

I’ve always been curious about DNA barcoding. Interest in wides-scale DNA barcoding exercise had been around for a long time, in part due to potential for amateur scientists to contribute to cause of the sciences using relatively minimal and easily obtained equipments and reagents. There had been some high-profile events and articles involving DNA barcoding techniques applied to everyday life in recent memory, like the infamous ‘sushi-gate‘ incident. Yet how many people really know what is it and how many people have a clear understanding of how to do it? I certainly was clueless for a long time.

It’s a little weird now that I think about it. Despite doing tons of PCR reactions day-in and day-out at the Genspace lab for one reason or another, I never tried  to dig into what exactly DNA barcoding entails in its visceral, barcoded details. Well, recently some of our Genspace members including yours truly went out on a sort of field trip to the Harlem DNA lab (situated within a junior high school in Harlem) for a day-long DNA barcoding workshop in preparation for the upcoming NYC Urban Barcode Project.

And the process couldn’t be easier. In a nutshell it just involved amplifying specific segments of DNA from a sample organism and sending it in to Genewiz for sequencing. The specific DNA segment to be amplified differs slightly from the kind of organism (is it a fish? Plant? Or insects?) but in case of most vertebrate mammals you use a portion of its mitochondrial genome called cytochrome c oxidase subunit I (COI) as the bacoding region. Mitochondrial genome (something I’ve been working with a lot for the past few months, ironically enough) is ideal for this sort of genetic species identification since they hit the exact sweet spot between homogeneity and differentiation within similar branches of the phyla, due to their rate of mutation and how mtDNAs are only passed through the maternal line. If you’re interested in performing your own DNA barcoding experiment outside regular lab settings or any official competition you can do so with the pdf files of requisite primer sequences already online and just order it straight from places like IDT. While specific protocols for running the PCR and prepping samples differ from place to place (I’m still looking for that perfect optimized protocol) what you are doing is a basic PCR amplification of the specific part of the mitochondrial genome, so when push comes to shove I’m sure simple chelex based DNA extraction (crush and pop in the sample with chelex beads for 10 minutes at ~99 C, centrifuge at 13000rpm for about a minute and extract the supernatant) combined with primers and PCR mastermixes or GE PCR beads (which already contain pre-made taq polymerase and buffer mixtures for optimal performance) will work just as well, provided that the sample is fresh enough. I think I’m going to run some experiments with the materials we already have at the Genspace lab and post the results later on. Once we put together a library of verified barcoding primer parts we should be able to do some very interesting projects and classes with the NYC biology community at large.

During the barcoding workshop we had a chance to pick out our own samples and run through the barcoding process with the instructors. I picked regular house ants, some random plant Ellen brought from her garden, and a YFP producing zebrafish that’s been dead for some time (it’s a long story). I went through the DNA extraction, purification, and PCR process outlined briefly above, using appropriate primers (for students participating in the competition the Dolan DNA learning center & Harlem DNA lab will provide the kits for free!). Here’s a picture of the gel we ended up with, dyed with syber-green (thanks Oliver!).

Now I seem to have misplaced the list of what each lane does, but the point is, all the barcoding amplifications worked except for the transgenic zebrafish. And it’s not just me, transgenic fish samples prepared by everyone else failed as well, something I can only attribute to the condition of the sample at the time of the barcoding experiment. You see when living things die cells lose structural integrity and rupture all over the place, mixing existing DNA molecules within the cells with all kinds of junk and nucleases that will damage the sequence. Considering the fish was stinking up to the high heavens by the time we got it to the lab that certainly sounds like a very likely scenario to me.

All the other samples works beautifully, and we prepared about 10ul aliquots of each PCR product and sent it in to Genewiz to get sequenced (the same Genewiz I got my mitochondrial DNA sequence from). They’ll be getting back to use within few days with the sequence data we can feed into public databases of DNA barcodes to determine what kind of organisms they are.

People always talk about how the field of biotechnology is advancing by leaps and bounds, and how the infrastructural developments like massive DNA sequencing centers for cheap sequencing will change how most view life and themselves. For a person not previously versed in biology like myself this was a great opportunity to come face to face with capacity for people outside of traditional academia to contribute to the sciences, using largely off-the-shelf technologies and public databases. The entire process of obtaining the sample, amplifying a specific genome within the sample, and getting it sequenced probably cost me about $5 in terms of materials. Think about that. $5 dollars to gain some level of insight into a genetic makeup of an unknown organism, open to everyone. Although this is nowhere near the kind of stuff we can do with true deep sequencing the day is coming, and it will certainly make for a very interesting world.

If you’re interested in learning more about the NYC Urban Barcode Project or DNA barcoding process in general, feel free to contact me at sung at genspace dot org. Genspace is one of the sponsors of the NYC Urban Barcode Project and we are looking forward to input and participation from students and teachers around the city!

Wings of Genspace

With the Genspace business and other stuff I’m working on picking up steam, it’s getting increasingly difficult to come up with decent enough blog posts these days. I’m still not sure whether this is a good thing or not. I love being busy pursuing my dreams, but writing is about the only thing that’s keeping me sharp, so that worries me a little. Maybe I’m slowly slipping into some state of waking coma…. Either way, I’m doing some really interesting things, so I might as well have a record of some of them here.

Genspace is in full swing, and Ellen’s busy running her biotech crashcourse, with other group-wide projects planned out already. Who would have thought we’d actually have a functioning biotech lab in NYC two years ago? Kudos to the people who stood by us all this time. Just having a lab is not enough though, we’ll be introducing some pretty awesome projects soon, just stay tuned!

I have so many things I want to write about now that I’m finally sitting in front of a computer and logged into my blogging account… But good things need time to mature, like hot pot. So I think I’ll just write about that one thing I’m supposed to talk about in this post 🙂

So we (me and Oliver) are planning to launch a high altitude microbial sampler into the stratosphere and do metagenomic analysis of whatever the samples we can gather from there. Right now I’m thinking of about 25~30km altitude, which should be around temperature range of -50 ~ -20 degrees C, which is really cold but not quite as cold as the furthest reaches of antarctica. Just to give you a scale of how high we’re going, latest version of Boeing 747 has top service ceiling of about 13km altitude. Our device will be flying at or above the double that altitude. Here’s an interesting picture of the Earth taken around 20 km.

Now simply launching a weather balloon into the stratosphere with some minor circuits, GPS and a digital camera would be simple. In fact, if it’s all I wanted I can just walk out there and launch my own balloon-sat right now. Yet, what’s the point in doing what everybody else is already doing, am I right? Now that we have a working biology lab we need to do something to bring my love of space together with my love of biology. Which means microbiome sequencing using samples taken from the above.

You see, there’s practically no real research data on the microbiome of the high altitudes. Considering the resilience of life (if you throw bunch of fruits out into the space from ISS, they’ll survive -kind of) and interlinked atmospheric conditions of the planet as a whole, we personally find it impossible to think that the realm of high altitude is totally devoid of life. There are papers out there tracing back to the era of the cold war suggesting that the maximum height of the planetary biosphere might in fact reach far beyond conventional height, with some evidences suggesting spore presence at mesosphere (~80km).

In order to have at least modestly reliable results from our experiment however, we need to design a device that can remain sterile to and from the stratosphere that will function despite heavy shaking, blistering cold, and falling. So far we’ve been making good headway into design and building of the device (Oliver is practically a McGuyver, with PhD in molecular biology) but it’s been a whole lot tougher than simply throwing together balloons, parachute and a camera that most of these projects tend to do. I’ve accumulated some interesting resources and research results during the course of the project, and will be uploading it to the net soon so that other people can follow in our footsteps and do their own high altitude sampling as well. Maybe it would be possible to grow this into an international program of sorts, considering the nature of the kind of organisms that might be found in the stratospheric range (if we find anything at all).

Recently we launched a simple tethered balloon sat to take pictures of Brooklyn from above. The contraption really had nothing to do with the sampler we’ll be launching, but it still gave us a good feel for what the real launch in the future might feel like.

The balloons were attached to a simple digital camera, a 1.99 semi disposable that took really horrible pictures. I’ll try to find a good one or two and post it later.

We launched the balloon on top of the Genspace building. The weather condition was really great, not too much wind at all. The sunlight was beautiful as well.

I’m one of those kids who used to stay up late at night thinking about the space, the high sky where the deep blue voids split over a thin red line of the sun rising, or setting somewhere over the distant part of the planet. Really, to this day the images still have the power to stir my heart, and make me feel like a human being. This is a meager start but who knows, maybe somebody’s already working on a synthetic biology satellite design that might one day take to the skies 😉

Genspace Grand Opening

December 10th was the big day. NYC will never be the same. Let me elaborate: after two years of blood, sweat, and labor (only a few tears), we finally announced the birth of Genspace to the world on December 10th. The preparation leading to the big day way typical of the ragtag crew of Genspace: chaotic, intense, lasting way past most people’s bedtime, but mysteriously it worked out in the end.

Everyone showed up: art students, scientists, writers, and long lost faces from two years ago. Turns out two tables filled to the brim with food, wine and beer weren’t quite enough to accommodate the bio-curious (not to confuse our counterpart in SF crowd in the city. It’s almost funny how we worried that no one would turn up.

The entire laboratory was strewn with Christmas lights. A light box illuminated an algae bioreactor in testing at the space. Screens were set up showing videos of microscopic organisms, and on our desktop in the study a live feed of the strawberry tissue  streamed from $12 USB microscope in the lab. Even our neighbor Chris pulled out all the stops, demonstrating his  ‘animal sense’ contraption for people to try out.

We still have ways to go, however. We need to reach out to the population of the city and show them that science is within reach. We need to work ever harder to break the walls surrounding learning and practice of science, and we need to create ever more ingenious, useful, and beautiful things.

The Genspace grand opening isn’t about the past two years, it’s about the future from here on out. Let’s bring back the romance between the sciences and the public.  I am proud to be a founding member of the first community biotech laboratory in NYC.

Who knows, maybe we really will end up changing the world for the better.