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!


Synthetic biology contest: Today!

I just wanted to take the time to remind everyone that the io9 synthetic biology contest will be over at midnight tonight.

That is it, folks. The deadline is only about five or so hours away. I hope those of you thinking of participating already have a good thing going. It had been two months since the contest was announced, now that I think about it. I am glad to say that my entry is ready to be submitted within few minutes as well.

Now I can only wait and see. I just hope lots of people came up with very unusual ideas. Give a breadth of fresh air to the field, so to speak.

Wordie=Not too wordy.

A little update on the state of my life first. I have been working on something that might be awesome for the io9 madscience contest. Although I am approaching the contest through a sort of team-based brainstorming and responsibility sharing method, I have become increasingly aware of my limited understanding of the molecular biology and genomics, so there are a whole lot of things I need to brush up on before the contest deadline of August 25 midnight PST. So no blog posts about nothing for a while, folks.  I would like to take advantage of this moment to urge anyone still not aware of the awesome coolness that is the io9 madscience contest on synthetic biology to get cracking for that secret mad science idea you have been hoarding to yourself, and drag all your friends and families with you into participating.

Despite the busy lifestyle I lead between the study for all the crazy exams and the field of synthetic biology, I also manage to surf the web and fish out interesting websites… Which might suggest that I am not actually busy but I assure you that I am nearly numb from all the busy-ness that is my life. Eating fast and sleeping less does wonders for time micromanagement-on-the-go. Anyway, I came across this website, wordie during one of my excursion around the Internet. It is one of the many web 2.0 based sites we see popping up all around these days, with emphasis on entering and making lists of words, while sharing those lists and favoriting other peoples lists and words… Basically a web 2.0 community website devoted to the pursuit of lexicographical side of the world. The feeling and layout of the website reminded me of the eponymous everything2 for some odd reason… And I believe that the spirit and purpose of the website is not very far from some of the more obvious characteristics of the everything2 as well. Which is a good thing.

I was rather surprised to find out that the *words* I could enter into the website database were not necessarily limited to words in dictionaries, or words in any form, actually. One of the most commented on words at the wordie website at the moment is *shaken baby syndrome* which is quite clearly something you will not find in any dictionary that came off the printing press. There are a number of words in foreign language, like Chinese (though such are few at the moment, who knows what will happen in the future?), with the function to make diverse lists and being able to favorite words I especially like being some of the more notable, and welcomed features.

What I especially love about the wordie webpage is its design. Just white background and black letters, with the fonts I find attractive for some odd reason. I think the wordie blog Errata is especially representative of the minimalist aesthetics underlying the design of the main wordie webpage. It is simple, it gets the point across, it is easy to access using variety of Internet-enabled devices, and the service as a whole seem to integrate well with other Internet/communication services, which I admit is a work-in-progress but shows great potential nonetheless. Sometimes people underestimate what can be done with simple arrangement of black things on white spaces and certain choices of fonts.

I like what I have seen so far of the wordie. I think this is a service I see myself using frequently for a long time, whether it be entering an interesting word I found, or tagging and commenting numerous words already present in the webpage. If you have a minute or two to spare, maybe you might want to give it s try as well. Who knows, maybe it will even increase your vocabulary.

Mad science contest!

Who in their right mind does not want to become a mad scientist? Underneath the prim and proper veneer of sanity and polite gestures, I know that there is a darker longing gravitating us toward the callings of mad science.

Yet the fact of life is, there are usually few opportunities, if any, to pursue and perfect the dream of mad science in this world, whether it be societal taboo or physical restraints. In the light of the scared world we live in, I am very happy to announce the contest for mad scientists, aimed primarily at the emerging field of synthetic biology.

There are two categories of the contest, and each category offers a delicious prize for the taking. The category one is the more realistic mad scientists in all of us. You are supposed to work with the real BioBrick parts and form an artificial synthetic organism/something to sate the mad genius inside you and possibly even help the world in the process. The prize for the category one winner is an all-expense paid trip to Hong Kong for the upcoming Synthetic Biology 4.0 conference and a chance to present your work before the whos who of the synthetic biology scene today.

The category two is the one for the imaginative madhouses in all of us. While scientific reasoning behind your creation must be present to certain plausible extent, the second category does not force you to figure out real PCR amplification rates or the roles of each specific BioBrick parts, something you should be proficient with should you decide to compete in the first category of the contest. Instead, category two seem to be leaning toward discovering truly imaginative applications of the tenets of synthetic biology and possible social/industrial implications of such a noble craft.

This is not a contest cooked up by bunch of enthusiastic crackpots either. Some of the judges are full-time professional devotees/founders of the very field of synthetic biology itself, like Drew Andy.

So spread the news, and get all of your families and friends involved. This is a contest for the mad scientists of the world, and we really need diverse and crazy ideas that deserve the mantle.