John Cumbers recently asked the BioBricks list about how best to run a ligation reaction. Based on the literature and the experience in my lab, here is what we have found works well –

…stick with the normal NEB ligase buffer. Make sure it still has DTT and ATP (not too many freeze/thaw cycles of the BUFFER). Note that the NEB ligase is provided in vast overabundance, and that very little ligase is required. The units tell the story — read them. See this paper for optimization:

Yoshino Y, Ishida M, Horii A. A new 10-min ligation method using a modified buffer system with a very low amount of T4 DNA ligase: the “Coffee Break Ligation” technique. Biotechnol Lett. 2007 Oct;29(10):1557-60. Epub 2007 Jun 21. PMID: 1758103

Note that buffers containing PEG react poorly to heat inactivation of the ligase, inhibiting transformation efficiency.

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.

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.

We 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!

Can’t keep a ginkgo tree down, apparently.

On a completely unrelated note, if you use restriction enzymes as much as we do this recent paper in NAR we came across will be pretty useful to you – The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases (Wei et al, from NEB, freely available).

Carl Zimmer on his Discover Magazine blog predicts that Obama’s choice of Steve Chu as Energy Secretary will be a boon for synthetic biology.  We hope so!

Here’s a link to a video of Steve’s talk at the Synthetic Biology 2.0 conference at Berkeley in 2006 (RealPlayer needed, unfortunately).  You can find the videos from the other talks at SB2.0 here.

The always interesting Seed Magazine reports on the work of Mac Cowell and DIYBio to bring biology to the masses. In a long interview, Mac lays out his vision of how amateurs can contribute to biological research in a similar manner to how amateur computer scientists were, and continue to be, so influential in (silicon-based) computer programming.

As an added bonus, Seed also contains an article written by Ginkgo’s own Jason Kelly about the evolution of genetic engineering from the very first recombinant DNA experiments through to the iGEM competition today. He highlights the renewed sense of excitement and possibility about responsible and constructive engineering of biology. Much of this excitement stems from the enthusiasm, talent (and dance skills) of the iGEM teams.

Well, time for me to make an appearance on the blog.  Now that Barry has added authorship, my delinquence has become obvious.  Just wanted to flag a New York Times article about bringing back Mammoths.  One of my favorite synthetic biologists – George Church has some interesting comments in the article.  On a side note, I recommend catching one of George’s talks if you have a chance – be sure to look out for the spinning tRNA (if you don’t see it at some point in the talk, you might be watching an imposter):

The approach George recommends is starting with the genome of a close relative of the Mammoth such as the African Elephant and then making the necessary changes to convert the elephant genome to match the recently sequenced Mammoth genome.  The elephant/mammoth egg could then (possibly) be brought to term by an African Elephant.  Development is a pretty robust process, so maybe it would work.

He also describes a new technology out of his lab that might be able to automate the large number of genome changes needed to pull off such a feat.  I suspect he’s talking in part about the good work described in this patent application by one of his graduate students (and another of my favorite synthetic biologists) Harris Wang.  

George also mentions that making zoos better isn’t as high on his list as addressing major world problems like the energy crisis.  I agree with that, though I have to say that de-extincting species isn’t too far down there.

An exposé of the discrimination and prejudice rampant in tomato society.

(Photo originally uploaded by leungski)

Sorry to get this post up somewhat late, the afternoon has been somewhat hectic. Slovenia once again had an extremely strong project and in the opinion of the judges were deserving of the grand prize.

Slovenia developed some very nice vaccine technology to fight Helicobacter pylori. The first part of the project was to engineer a live Helicobacter strain that expresses an antigen to trigger both the innate and adaptive immune response. The second half of the project involved engineering a constitutively active variant of TLR (toll-like receptor) to remove the requirement for receptor agonists. The latter has the potential to be a novel general strategy for developing vaccines.

Congratulations also to Freiburg and Caltech who were first and second runner’s up respectively.

Thanks are due to the organizers and the judges for such a well-organized weekend.

(The image above shows some of the crowd during the award ceremony and Tom Richard, head judge, bathed in light).

Quick update. Last night the judges whittled down the teams to six finalists. They are all presenting once more this morning before the grand prize winner is awarded.

The finalists are – Berkeley, Caltech, Slovenia, NYMU Taipei, Freiburg, and Harvard.

Berkeley just did a great job and Caltech is up next…

Stay tuned.