Bacterial Edge Detector

One of Ginkgo’s favorite biological engineers – Jeff Tabor, has just published his latest engineered biological system, a bacterial edge detector, in Cell Magazine.

edge-detector1

The edge detector is a great example of combining different biological parts (light sensors, cell-to-cell signaling molecules, reporters, and logic gates) to make a complicated engineered biological system.  In the final system, the engineered E.coli are spread in a lawn on a petri dish and light is shown on the dish in a particular shape.  The bacteria at the edge of the shape detect that they are at the interface between light and dark (this is the really amazing bit that requires communication between neighboring cells and some genetically-encoded logic) and express a reporter protein creating an outline of the shape.

This project was actually begun by Jeff and the UT Austin iGEM team in the 1st iGEM competition in 2004.  During the 4 months of the competition they didn’t manage to get the edge detector working, but they did build the first bacterial photography system (“Coliroid“) which was later published in Nature.

Hopefully Jefff’s success with the edge detector will be an inspiration for this year’s iGEM teams to go after ambitious projects!

Design Your BioBrick Systems On-the-Go

Just a quick post to let you know that Cesar from Drew’s lab has released the first version of his BioBrick Studio app for the iPhone on the iTunes Store. It lets you do some basic browsing of BioBrick parts from the Registry of Standard Biological Parts.

It’s pretty cool that Cesar is experimenting with design environments for biological systems on different platforms. Next time you’re in the lab and can’t remember which part to pull out of the freezer, grab your iPhone and use BioBrick Studio to double check. 😉

Changes coming to the Registry of Standard Biological Parts

If you haven’t visited the Registry of Standard Biological Parts lately, you should stop by and take a look. We’ve been helping out in the re-design and re-organization of the parts collection available there. Randy and Meagan are constantly looking to improve the Registry so that it is more useful to iGEM teams and academic labs. After a fair bit of consideration, this year we’ve deliberately tried to make the Registry easier to browse for newcomers. The basic idea was to try to make the Registry look more like a catalog. Thus, if you visit the Registry catalog of parts, you can browse parts and devices by type, by assembly standard, by function, by contributor, or by chassis.

For each group of parts, we’ve added text and pictures to better explain why and how you’d want to use those parts in larger systems. For example, there have long been a number of plasmid backbones available from the Registry. Depending on whether you want to assemble parts together, operate a multi-component synthetic system, express a protein or measure the behavior of a part, you might choose to use a different plasmid backbone. By visiting the plasmid backbones page, you can find all of these backbones organized and linked from one place.

The Registry is always a work in progress, so stay tuned for even more changes coming soon. And of course, we’d welcome your feedback. So take a look and let us know what you think!

Introducing the BioBrick Assembly Kit …

It’s a big day here at Ginkgo.  We’re announcing our first product in partnership with New England Biolabs — a BioBrick™ Assembly Kit designed to make part assembly a snap.

For those of you who aren’t already familiar with BioBrick parts, they are essentially just DNA fragments that encode basic biological functions like promoters, terminators, coding sequences, ribosome binding sites and more.  What makes these genetic fragments special is that they all adhere to the first BioBrick assembly standard–a cloning standard designed to make assembly of multi-part systems much simpler and faster.  It’s simpler because you use the exact same process to assemble any two BioBrick parts.  No more searching for unique restriction sites that happen to be located in a convenient place.  No more looking up whether those two restriction enzymes will work in the same buffer conditions.  It’s faster because instead of assembling your system one part at a time, BioBrick assembly lets you assemble your system hierarchically … in log(N) steps instead of N steps.  And as an added bonus, the Registry of Standard Biological Parts maintains a collection of over 3000 BioBrick parts that academic labs and iGEM teams can use and reuse to build systems.

The BioBrick standard isn’t new.  Ginkgo founder and MIT Senior Research Scientist Tom Knight invented the standard back in 2003 to make synthetic biology easier.  Since then, the standard has been adopted by researchers around the world.  Even undergraduates with little prior lab experience use it when they participate in the annual iGEM competition.

Over the past 6 years we’ve learned a lot about how to (and how not to) assemble BioBrick parts.  Now, we’ve tried to put all that experience in one place with the BioBrick Assembly Kit and manual.  It’s specially designed for those folks who might be new to synthetic biology and BioBrick part assembly.  We’re especially excited to be releasing this product in partnership with NEB – a company with deep roots in the recombinant DNA technology that paved the way for synthetic biology. Please search for the BioBrick offerings on NEB’s website and give them a try.  We’re always looking to make biological engineering even easier, so please let us know how it works for you.

BioBrick™ is a trademark of The BioBricks Foundation.

P.S. A special shout-out goes to Mac Cowell and Lauren McCarthy from DIYbio.org for help with the graphics and photos for the BioBrick Assembly Manual.

Happy [Belated] Birthday RFC 1!

Randy Rettberg pointed out an op-ed piece in yesterday’s NY Times on How the Internet Got Its Rules.  The piece talks about how the RFC process was critical to paving the way for the Internet.  RFC is an acronymn for “Request for Comments”.  Basically an RFC is memo that documents an idea or way of doing something.  By writing an RFC, you are deliberately trying to solicit feedback and get others to discuss and improve upon your work.

In synthetic biology, we’re trying to adopt a similar model.  The BioBricks Foundation (BBF) has launched an RFC process for synthetic biology.  There are a lot of great ideas floating around–from new protocols for assembling DNA to graphical depictions for BioBrick parts.  By writing down those thoughts and letting people comment and discuss them, hopefully the best and most useful ideas will float to the top over time.  BBF RFCs offer a faster way of getting new ideas and protocols out into circulation.  Every BBF RFC gets a number and a DOI courtesy of MIT DSpace so that the RFC is referenceable in peer-reviewed publications.

In the NY Times piece, Stephen Crocker writes, “We always tried to design each new protocol to be both useful in its own right and a building block available to others. We did not think of protocols as finished products, and we deliberately exposed the internal architecture to make it easy for others to gain a foothold.”

We need to be thinking the same way in synthetic biology.  How do we take the initial steps needed so that others can follow and build upon our work?  How do we design our parts and devices to maximize their reuse by others?

[Disclaimer: I’ve been helping out with the set up of the BBF RFC process and was one of the authors of BBF RFC 0 .]

Etech 2009: It’s like Spore, only real!

Whew! March has been a whirlwind month as evidenced by the lack of activity on the Ginkgo blog.  Barry and I had a great time at Etech.  I even got to make my own wearable electronics t-shirt in a tutorial with Leah Buechley!

Barry and I were blown away by the turn out at our Real Hackers Program DNA session.  At the session, we did ran a demo of the eTransformation Kit in which people get to program bacteria to turn red, glow in the dark or smell like banana’s — essentially the biological equivalent of installing a piece of software on a computer.  We think kits like this are a great way to educate people about biological engineering.  It also sparks important conversations about how to encourage best practices among novice and professional biological engineers alike.

For people who couldn’t make it, you can download the handout (pdf warning!) or check out Fumi Yumazaki’s Flickr photostream.  For the Japanese readers out there, Fumi also wrote up her experience at the session.

The eTransformation Kit was a group effort by Kalvin Kao, Mac Cowell, Jason Bobe, Jason Kelly, Barry Canton and myself.  Thanks to all!

And the award for “best engineer” goes to…

On Oscar weekend, this story seemed appropriate. Ginkgo founder Tom Knight is nominated as one of the top 25 most influential engineers working today by Engineering and Technology Magazine, the trade publication of the Institute of Engineering and Technology. The list includes other engineering luminaries such as Vint Cerf, James Dyson, Julia King, and Ray Ozzie. We’ll be keeping an eye on how the voting turns out…

Booting up standards in synthetic biology

Just a quick note to say that Alla Katsnelson of The Scientist has a couple of articles on recent efforts to develop technical standards in synthetic biology. The first describes the iGEM competition and its success as serving as a both a recruiting tool and testbed for engineering multi-component biological systems. It also describes some of the BioBricks Foundation’s recent work to start up an RFC process in synthetic biology. The second goes into more detail re different standardization efforts that are happening in the community. Both articles feature comments and work by Ginkgo engineers.

DIY bioengineering – recap of the recent MIT Soapbox session on DIYbio

My good friend Natalie Kuldell and I had the pleasure of participating at a recent Soapbox session hosted by the MIT Museum on DIY biology.  (Though frankly, I prefer the term DIY bioengineering, because I think hobbyists are going to be a lot more excited by what they can build than by what they can study in the natural world.)  

Probably the best part of the evening was when the audience got to answer two questions.

  1. If you could build anything out of biology, what would you build and why?
  2. What would you ask your neighbors if they were building this organism in the house next door to you?

In response to the first, some wanted to engineer bugs that would clean the bathroom for you.  Others wanted to make organisms that could consume nuclear waste.  Still others wanted to make organisms that could diagnose what was wrong with their dogs.  In response to the second, I think one audience member put it most succinctly when they asked, “Is it safe?”.

I think the DIY bioengineering community has a lot that they could contribute to synthetic biology and the world in general.  But the safety risks and public perception issues can’t be ignored.  Personally, I’d love to see the community coalesce around a DIYbioengineering model organism.  For example, some of the recent suggestions on the DIYbio.org email list have been

  1. Acinetobacter – a naturally competent BL1 organism
  2. Moss – again it’s readily transformable and it’s moss!  How cool is that!?!
  3. Halobacterium – this organism is native to the Great Salt Lake and only grows in media with high salt concentration.  This feature has the double bonus of both making media contamination by other organisms unlikely and ensuring that Halobacterium is less likely to grow elsewhere.

DIY bioengineers have different constraints than conventional molecular biologists.  By choosing a new model organism more suitable for their work, DIY bioengineers can both to break new ground in science and engineering and develop the foundational tools needed for DIY bioengineering to really take off.

New events and new faces

We are looking forward to an exciting and busy year for Ginkgo and we wish you the same. The Ginkgo team is speaking at a number of events in the coming months – keep an eye on our news page for more details.

images.jpegWe are also delighted to announce the first annual recipient of the Ginkgo BioWorks undergraduate fellowship, Matt Gethers (MIT, ’09). Matt, a Biological Engineering major and accomplished fencer, will be interning with us for the next few months as we develop some new DNA assembly technologies. Matt is the recipient of numerous other less prestigious awards, including a 2009 Rhodes Scholarship. Great to have you around Matt!