PCR Results!

Thanks to all of the Maker Faire attendees who participated in the genotyping experiment. Here are the first few results. Each of the lanes (vertical columns) on the above gels represents one person's DNA. We have emailed the people with their lane numbers so they know which DNA is theirs. If there are two bands in the lane, the person has both the tasting (t) and nontasting (T) allele, and since the tasting is dominant they CAN taste the bitter substance. If they have the bigger band (the one on top) only, they have two non-tasting alleles (they are homozygous) and are non-tasters. None of these samples had only the lower (smaller) band, so NONE of these specific participants was homozygous for the tasting allele. We'll be processing the rest of the samples soon!

DIYbio NYC/BioBus Collaboration Wins MAKE Magazine Editors' Choice Award at Maker Faire

Whew! We are all just recovering from the Maker Faire weekend. It was a pretty intense two days of public interaction. But we won the Editors' Choice award- pretty good for our first Maker Faire outing.

We joined forces with Ben Dubin-Thaler and the BioBus, a mobile science classroom housed in a carbon-neutral vegetable oil-burning renovated 1970s San Francisco Transit bus. Yes, the outside of the bus has a kind of retro-70s vibe to it. But inside is where the magic really happened.


The BioBus folks provided some ultracool microscopy and we provided some DIY genotyping. Folks could come in, look at their own cheek cells magnified 400x on a phase-contrast microscope connected to a digital display screen, and then extract their DNA for PCR and restriction enzyme analysis of the TASR38 gene which determines the ability to taste a bitter compound called PTC. Tasting is dominant and non-tasting is recessive, so it was not only a lesson in personal genomics but also Medelian inheiritance. The space is compact, and the bus was stuffed with people checking us out all weekend long.

Ben explaining subcellular structure.



Our setup. We had a PCR machine, microfuge, heat block, and gel electrophoresis equipment (on a side bench). The hardest part was keeping the hordes of wee ones from grabbing the pipetmen and tubes off the table if we didn't pay attention.



We genotyped more than forty individuals during the course of the weekend. We took their email addresses and the gel photos with the test results will be posted for them to see later this week (we didn't have the time to do the electrophoresis step on the bus- we were constantly doing the DNA extraction with new volunteers).

Sung explaining Mendelian inheiritance to a father and son who genotyped themselves.



Sung with Nurit's DNA



Outside the bus, we had a great attraction for kids of all ages- extracting DNA from strawberries. It's colorful and messy, so we were mobbed from the opening moments of the Faire until closing down on Sunday. We had to run out to neighborhood bodegas multiple times to resupply ourselves with strawberries and rubbing alcohol. We even went through an entire carton of salt and a bottle of meat tenderizer.

Dan entertains the crowd:



James Jorasch from ScienceHouse tries his hand at strawberry DNA extraction.



The Faire itself was fantastic (although we could've done without the deafening roar that periodically emanated from the Jet Ponies- we were WAY too close to that attraction for comfort). We'll post more pictures of the Faire later, after we catch our collective breath!

PCR machine testing at NYC Resistor

Ah, PCR! The workhorse of biotechnology. We had a PCR machine donated to us that we hadn't test-driven, so we decided it was time. It turns on and lights up. But does it go through the cycles correctly? Russ put it through its paces with a short (300 bp) piece of DNA, and it appeared to work. We'll run it on a gel tomorrow and post the results... And, it worked beoootifully! So now that we know the machine works we can go ahead and do more involved experiments.

Oracle of Biological Engineering to speak at NYCR

Robert Carlson bridges both the NYC Resistor and DIYBio worlds – he’s an electrical engineer who turns E. coli into circuits! He famously discovered the Carlson curves, the biotech equivalent of Moore’s Law. They show that biotech is advancing at a pace consistent with digital tech.

Come join us at the NEW NYC Resistor space for an afternoon talk by Rob and discussion afterwards.

DATE: Saturday, March 13
TIME: 2:00pm – 4:00pm
LOCATION: NYCR

Here’s a video of Robert from the Economist that appeared on the DIYBio blog recently: http://diybio.org/2010/01/01/rob-carlson-discusses-diybio-and-open-source-biology-on-the-economist. And an excerpt from his Wired article where he wrote about the emergence of DIYBiology in 2005:

The era of garage biology is upon us. Want to participate? Take a moment to buy yourself a molecular biology lab on eBay. A mere $1,000 will get you a set of precision pipettors for handling liquids and an electrophoresis rig for analyzing DNA. Side trips to sites like BestUse and LabX (two of my favorites) may be required to round out your purchases with graduated cylinders or a PCR thermocycler for amplifying DNA. If you can’t afford a particular gizmo, just wait six months – the supply of used laboratory gear only gets better with time. Links to sought-after reagents and protocols can be found at DNAHack. And, of course, Google is no end of help.

Still, don’t expect to cure cancer right away, surprise your loved ones with a stylish new feather goatee, or crank out a devilish frankenbug. (Instant bioterrorism is likely beyond your reach, too.) The goodies you buy online require practice to use properly. The necessary skills may be acquired through trial and error, studying online curricula, or taking a lab course at a community college. Although there are cookbook recipes for procedures to purify DNA or insert it into a bacterium, bench biology is not easy; the many molecular manipulations required to play with genes demand real skills.

http://www.wired.com/wired/archive/13.05/view.html?pg=2

Synthetic Biology at Science House

ScienceHouse is a cool organization with a mission to "bring people together to promote and advance science." Small, infomal meetings are their specialty. Recently, two of our DIYbio NYC denizens spoke at a gathering focused on syntheric biology. Check it out on the ScienceHouse website at http://sciencehouse.com/inside-sciencehouse/2009/11/synthetic-biology/

Also, we'll soon post more about ScienceHouse, including a special workshop on Biosecurity arranged in conjunction with DIYbio NYC.

Watch video of Russ talking about DIYbio NYC:

http://www.sciencehouse.com/VideoDIYBio.html

Watch Sung explaining the BioBricks concept:

http://www.sciencehouse.com/VideoBiobricks.html

Fun with the webcam microscope

Well, we followed the advice of the Boston DIYbio group and took the webcam apart to reverse the lens properly. When we get together next week, we'll build a stage for it so we can control the focus. For now, by holding it steady and putting it near Brian's chin, we caught a pretty impressive view of his five o"clock shadow. Can you say "Too much information"?

We also tried parts of a flower- stamens and pistils- but could not hold it steady enough to get a similarly good picture.

Late night work at NYCR

Being ever hardworking, we are spending tonight at NYCR getting through some much needed management stuff and blogging. Who said science isn't cool?

BioArt NY - First Meeting

Dan and Nurit from our group went to check out the first meeting of BioArt NY at 11th Street Bar this Tuesday. Much fun and biology was had by all. Stay tuned for further updates as we work with the awesome bio artists in the city!

NYCR DNA extraction night

Cheers!

Thanks to the wonderful people at NYC Resistor, we are now doing our weekly meetings and workshops at their space (almost) every Wednesday. Here's a brief record of what we did for our first night at the space.

The night's event was a straight DNA extraction affair, except that we were doing it using cheek cells from our own body (our previous attempts were done using fruit). The protocol is about the same. While we didn't use household materials in extracting DNA this time (instead we used chemicals that came in fancy looking bottles) the ingredients are more or less the same.

We are using Gatorade, lysis solution (it's just a detergent ingredient-wise), and ice-cold alcohol.

First, we start with Gatorade to wash our mouths for one minute. After that, we spit the contents into plastic tubes and mix it with lysis solution, shaking it throughly. Then we pour cold alcohol into the mix, a highly complex operation that needs all the concentration and control one can muster.

Make sure to pour it down the wall of the tube, so you don't disturb the contents. If you're successful, you'll end up with...

The white stuff in the middle contains DNA from our own cheek cells! Some of us made a small necklace containing our own DNA, which is just plain cool (or crazy).

We were also joined by some wonderful people from the Sciencehouse who came to check out our operation. Hi guys!

Protein purification night at Dan's

Hi everyone.

It's been a while since we've uploaded anything to this blog owing to much changes and projects that we were (and are) working on. We'll be updating the blog shortly with news of what we've been doing all these days, but here's something to tide you guys over.

We held a protein purification workshop a while ago with some of our fellow members. The process itself was a simple exercise using GFP producing plasmid containing E.Coli cells

(prepared before the event itself, since introducing plasmids to E.Coli cells take a while and can't be done in a single night session). Afterward we tried to run the plasmids on gelboxes, one of

our own design and the other one sold commercially.

Here are some of the equipments we used.

While there were a few mistakes during the course of the lab, the purification of the protein itself went along swimmingly. We did have some real issues with running the gelbox though. The trials and tribulations of the commercial and DIY gelbox will be documented at a later date with pictures and possibly a video (when I'm not writing past midnight).

DNA: Everybody's Favorite Party Favor!

Well, yesterday DIYbio NYC took ConfluxCity by storm. Or maybe by goo.

The day started out auspiciously, with the Tompkins Square Greenmarket giving us a primo spot on Avenue A to set up our DNA Extraction Party table. We laid out all our supplies- dish detergent, plastic champagne glasses, salt, meat tenderizer, etc.- on our bright green table with a cool poster of our logo in front. The day was sunny and perfect for DNA-making.

There was an amazing amount of foot traffic in the park that day. The DNA extraction process seemed to fascinate people of all ages and cultures. Of course, there was the woman who asked if our oven mitts (in case the alcohol was too chilly to hold) were for sale. And the one who walked away in disgust when she found she couldn't drink the final product...

Whatever gave us the idea that our sign would explain what we were doing? 95% of the folks who stopped to look asked "What are you doing?" and when we replied "extracting DNA" the second question was always "Why, what can you DO with it?" The answer they seemed to like best was "test it to see if the fruit was genetically engineered". The second most popular answer was "if all the strawberries on earth were wiped out, you could recreate them with what's in your little test tube- just like Jurassic Park but without the bloodshed". Yes, we brought microfuge tubes so they could take their DNA home as a souvenir.