Sorry it's taken so long...

..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

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...

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

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

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 )