DIYbio NYC

PCR Results!

2010-10-20T18:48:00.001-07:00

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

2010-09-27T12:40:00.000-07:00

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

2010-06-16T17:40:00.000-07:00

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

2010-03-03T19:18:00.000-08:00

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

2010-01-20T18:42:00.000-08:00

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

2010-01-01T08:08:00.000-08:00

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

2009-12-02T22:32:00.000-08:00

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

2009-12-02T22:27:00.000-08:00

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

2009-12-02T21:22:00.000-08:00

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

2009-12-02T20:28:00.000-08:00

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!

2009-09-21T08:04:00.000-07:00

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.

DIYbioNYC hosts hands-on DNA extractions at ConfluxCity 2009

2009-08-27T13:10:00.000-07:00

Explore the blueprints that underlie life in NYC’s urban public spaces. Join DIYBio at the greenmarket in Tompkins Square Park to extract DNA from locally grown produce!

DIYbioNYC will be presenting this playful DNA Extraction party as part of ConfluxCity, an event to be held throughout New York on Sunday September 20th, the final day of the annual Conflux festival.

When: Sunday, September 20th from 1:00-3:00pm

Where: Tompkins Square Park (E. 7th Street & Ave A)

From our flyer:

"Imagine exploring New York from the inside out. Most of daily interactions with the city take place in the psychological space that starts from the self and extends into the human-scale world. But there’s an invisible puppet master behind life in New York—one that creates the whole but remains out of sight, too small to see, locked behind our clothes, our skins, even the membranes of our cells. Imagine putting on special set of glasses that enlarged the tiny and shucked away the quotidian. Imagine going to a Tompkins Square Greenmarket, but instead of seeing people doing their daily fruit and vegetable shopping, you saw a schematic for the fruit, the plant that grew them, the lineage of plants before it, even the pathogens it fought along the way. You’d be seeing the world through DNA.After buying some produce at the market, visit our outdoor lab at the SW edge of the park. With some common household objects, and a little guidance from our citizen scientists, you’ll extract the DNA from your produce, and see your food, your life, your daily routines from the inside out."

From the Conflux website:

"Conflux is the annual New York festival for contemporary psychogeography, the investigation of everyday urban life through emerging artistic, technological and social practice. At Conflux, visual and sound artists, writers, urban adventurers and the public gather for four days to explore their urban environment."

"People from a wide variety of backgrounds and cultures come together at the festival to re-imagine the city as a playground, a space for positive change and an opportunity for civic engagement. The Village Voice describes Conflux as a 'network of maverick artists and unorthodox urban investigators… making fresh, if underground, contributions to pedestrian life in New York City, and upping the ante on today’s fight for the soul of high-density metropolises.'
From architects to skateboarders, Conflux participants have an enthusiasm for the city that’s contagious. Over the course of the long weekend the sidewalks are literally transformed into a mobile laboratory for creative action. With tools ranging from traditional paper maps to high-tech mobile devices, artists present walking tours, public installations and interactive performance, as well as bike and subway expeditions, workshops, a lecture series, a film program and live music performances at night."

This promises to be great fun. Hope to see you all there!

Sorry it's taken so long...

2009-05-14T12:44:00.000-07:00

..but only one person (Nurit) managed to capture video of the completion of the lab experiment where we transfected E. coli with a plasmid containing the GFP gene. And I had to get it from her in order to make the Part 2 video. So here it is, finally:

For the next lab-type meeting we decided to use another Carolina kit to purify the green fluorescent protein from the transformed E. coli and visulize it with black light and via electrophoresis. So we are slowly building our repertoire of standard molecular techniques...

Anyone who has an interest in this sort of stuff is welcome to stop by our meetings and get all nerdy with us. And Dan always seems to have none but the best brands of beer on hand.

Creating Glowing Green Bacteria for Earth Week

2009-04-24T08:21:00.000-07:00

The day before Earth Day, we gathered at Dan's apartment in lovely Park Slope to do our first biotechnology experiment. We used a kit developed for high school students. It had a detailed manual with safety instructions. Basically, E. coli K12 is so safe that you could drink it with no ill effects (although it would taste horrible). We decided to wear gloves anyway, although they were not necessary. The kit is for use in a classroom, with no lab coats, gloves, or eye protection needed. No hazardous chemicals are used, and the E. coli bacteria is easily killed in 10% bleach. So we filled a bucket with it and dumped all our used disposables into it as we worked. We covered the table with plastic, as well as the floor near the workspace. That way we could wipe any spills up, and wipe it down afterwards with the 10% bleach.

To be doubly sure, we obtained the CDC (Center for Disease Control) guidelines for a Biosafety level 1 (BL1) lab and went down the checklist, making sure we complied. Needless to say, we did not start eating the pizza until we were done.

The one time someone (who came late) tried to bring a glass of water into the room, he was yelled at by everyone.

Ellen gave a short talk on biosafety as it applied to this experiment, and a little background on E. coli and the Green Fluorescent protein (GFP) plasmid. The she and Eric, who also has plenty of lab experience, went through the procedure with everyone else watching. And taking notes. And asking questions. And shooting photos. And filming video. It was a bit nerve-wracking, but we got through it.

A little creativity was needed to fulfill the conditions of the experiment. Dan and Ellen tested how long a big glass bowl filled with 42C water would hold temperature when an ice cold object was place in it, and figured out that putting the small tubes in it for 90 seconds would not decrease the temperature by more than one degree. The ice for the chilling of the calcium chloride transformation tubes was put through a blender to chop it finely enough. Other than that, the kit was pretty complete. We probably will do this experiment again at some point with greater participation, after everyone has had a chance to do some "dry runs" with tubes and vials containing water, and plates with nothing on them, to get used to clean technique.

At the end, we had 3 plates because we ended up dividing one of the plain Luria Broth (LB)-containing plates in half. One the LB plate we put a line down the middle, and put the E. coli + plasmid on one side and the E . coli without plasmid on the other. Each of the two LB + ampicillin (the antibiotic which will kill bacteria that did not take up the plasmid) plates got either the E. coli + plasmid or the E. coli without plasmid. If we are successful, then the ampicillin plate with the E. coli + plasmid should sprout little green friends in a couple of days...

Here's video (Part 1) of the evening:

(if you can't play this, go to the YouTube version)

April 15th Meeting - Well, here we go...

2009-04-16T09:50:00.000-07:00

We've been contacted by four reporters in the last three weeks. We knew it was bound to happen sooner or later- DIYbio is a hot news topic at the moment because not much has been written yet and there's such delicious potential for sensationalism inherent in the topic (Amateur biologists wipe out Cleveland!) Too bad this came so soon after we formed the group- we were hoping that we'd be incorporated as a nonprofit and have a written set of safety policies set up before we were forced to deal with this. But if you refuse to talk to them, it looks like you are trying to hide something, which we emphatically are NOT, so we welcomed a New York Times reporter into our midst last night, amid the high-volume chatter, clinking dishes, and pirogies of Veselka Restaurant in the East Village.

Song, Daniel, Russ and Ellen were there. Three new folks showed up: Eric, who has been communicating with us on the Google site for quite awhile, and is a molecular biologist. Nurit, who does bioart and is currently working with a group at MIT. Meredith, whose background is computer science and is fascinated by the concept of biological machines. It was great to see the ideas flying as the combination of everyone's divergent skills resulted in some really cool things we are going to follow up. We'll describe some if them in more detail in later posts as soon as we flesh out the details.

Our agenda was to finalize a mission statement for the group, to address what we think the group needs to do in order to be transparent, and to address safety issues and requirements for operating a space where labwork is performed. We were somewhat thrown off schedule by the time needed to communicate to the reporter our goals and hopes for this group, but we still were able to achieve quite a bit.

A draft mission statement was passed around, and we will post it as soon as it's finalized. From what we've read, this statement can be fine-tuned if necessary after the group incorporates, so we just want to make sure we've got the right concepts in there for the initial version. This is the first step to becoming a nonprofit, a step which we feel will make it easier to achieve our goal of productive, socially meaningful scientific research. Russ volunteered to produce the first draft of our articles of incorporation. They'll be posted in the File section of the Google group site.

In terms of transparency, we agreed that it would be useful to keep more formal meeting notes in the future. For now, we are posting in this blog and also keeping track of who attended each meeting. And we'll continue to let reporters observe our meetings. We fervently hope that they don't edit out the hard work, deep thought, and effort that's gone into ensuring this group operates safely at all times.

As we contemplated how to create a safe environment for amateur labwork, several good ideas surfaced. Anyone wanting to do wetwork in our space will have to provide evidence of training (such as a degree in bioscience) or undergo training by members who possess these skills. Ellen agreed to draft a safety training procedure. Dan suggested we limit our initial wetwork to experiments that have already been vetted for safety, such as those from the curriculum of the Dolan DNA Learning Center at Cold Spring Harbor. The "green bacteria" transformation experiment we are going to try at our next meeting is actually one of those.

Since high school students have traditionally been part of iGEM teams, we discussed what our requirements would be for participation of someone under 18. Sponsorship by an existing adult member is a possibility, with the understanding that the adult member would commit to being present during wetwork. We also need to have some sort of liability waiver for all members, like what you sign when you join a gym or rock climbing club.

Space, and the procuration of it, was also a hot meeting topic. The bottom line is, we need to have a monetary commitment from the members in order to support the space. So far, we need a few more who can pony up at least $50 per month in order to support this goal. Shared or part-time space will soon become impractical if we start doing wetwork, so we are talking about a lease, and in an industrially-zoned building. Nurit and others will be exploring options.

As usual, we overstayed our welcome at the restaurant table- the waitstaff was changing shifts and our waiter wanted his tip- so we parted after about 2 hours of fruitful discussions. Next week we meet at Dan's for some more hands-on science. Stay tuned for the video!

March 24th Meeting - wordsmithing

2009-03-25T13:42:00.000-07:00

We held our March 24th meeting in a diner - the Cozy Corner on Broadway near NYU. Not only because the food was good but because we needed to discuss the evolution of our group without the delightful distraction of wet work. The attendees were Russ, Song, and Ellen. Several other folks had planned to attend, but couldn't make it. We hope they will come to the next meeting, especially since it will be more lab-oriented.

The main topics of discussion were 1) the mission of the group 2) looking for space and 3) what kind of project shall we start with?

It occurred to us that it would help us become more legit, and possibly lead to obtaining space, if we incorporate as a nonprofit with a clear mission statement and bylaws. So Russ is going to dig up a template for all this and pass it around. The consensus among those present at the meeting was that science education, public outreach and possibly advocacy would be part of the mission of the NYC DIYbio group. It will take awhile for us to hammer all this out, and the more people that participate in our group, the more brains to contribute to this. But at least the ball is now rolling...

Space, the final frontier. We are starting to amass some basic equipment, due to quick action on Ellen's part when she heard of a biotech that had gone out of business. We have some gel boxes, a transfer apparatus, a big power supply, a dry incubator, a microfuge, and a water bath. But we have no place to put it yet. Minimum requirement would be running water. We need to investigate any hackerspace or biotech space in the area. Song is going to do some research and ask around. It's not clear if there is specific biotech zoning in the New York City area. There is the possibility of renting space in a university lab if we can convince them that we have responsible oversight.

The most tantilizing question is what to do for a first project. Song passed around the abstracts from the Synthetic Biology meeting last year in Hong Kong to generate some ideas. We agreed to start writing them down and fleshing them out. This is an area that anyone can participate in, just by posting in the group. You don't even have to show up at the meetings!

The next meeting will probably be the second week in April, after Dan gets back from his trip. We plan to do more electrophoresis, this time with better control over the dyes and the samples.

March 9th Meeting

2009-03-12T11:58:00.000-07:00

Here's a brief summary of the goings-on Monday night in Park Slope. We extracted the DNA from strawberries. Using shot glasses, buffers, alcohol, salt, coffee filters, even a champagne glass, we dripped the DNA free from its luscious abode. Turns out DNA is not nearly as pretty as the fruit. It looks like snot. Then, thanks to Ellen, her jigsaw, and some plexiglass (she made us a homemade gel electrophoresis box), we attempted to separate and visualize the sheared DNA strands. After a little fun with agar-agar (never to be used again) and alligator clips, we watched something, maybe dye, maybe DNA, migrate along the gel. Most probably it was the dye, since to get any kind of accurate concentration with the agar-agar was a nightmare (it had lumps that would not go away, and we ended up filtering it through cheesecloth) and the resulting gel was VERY solid. Oh, and we did all this with a slice of pizza or beer in one hand. And we're going to do it again next time with some other substances, possibly our cheek cells. Also, we'll remember to do some planning beforehand (beer, pizza, strawberries, agarose, you know).

We made a short video of the evening's fun:

(if this version is hard to view, go to http://www.youtube.com/watch?v=s2HPVs25HlY&feature=channel_page )