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?