“A team led by Jay Keasling, a bioengineer at the Joint BioEnergy Institute in Emeryville, California, worked to extend the strategy to make more commonly used fuels. They used Escherichia coli, a bacterium into which it’s relatively easy to insert new genes. They started by creating two strains of E. coli, inserting genes for breaking down cellulose in one and genes for breaking down hemicellulose in the other. They then split each of these two strains into three groups and to each group added genes for one of three different metabolic pathways that allow the microbes to make chemical precursors for either gasoline, diesel, or jet fuel.”
Nice step towards making this happen.
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“A tiny spare bedroom is not an ideal space for a high tech biofabrication facility. To get to the one Josh Perfetto is putting together, visitors must walk all the way to the back of his mostly unfurnished house in Saratoga, California—through the kitchen, past some empty rooms, across a den with a lone couch—then climb a poorly lit staircase and round a corner.”
A really nice article on the state of gadgets DIYbiologists are creating on their own to do their biology. Very fun.
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“The researchers tweaked the genes that allow P. aeruginosa to detect other members of its species and put this synthetic genetic code into E. coli’s genome. They also gave E. coli a gene for making a modified pyocin that is toxic to P. aeruginosa. By linking the pyocin gene to the sensing genes, the researchers ensured that when the E. coli detected P. aeruginosa in the vicinity, it would fill itself with large amounts of pyocin and become a biological time bomb.”
Really clever construction of a microbe that senses a pathogen, accumulates the toxin to kill it, and then explodes to release the toxin. A good first version and should be interesting to see how the tool develops.
Read this article…
 Here’s another speaker for my proposed panel for SXSW [http://panelpicker.sxsw.com/ideas/view/10348] on DIYbio.
James King is a speculative designer working in the field of biological science to investigate the implications of future biotechnologies. He collaborates with scientists and works between the lab and studio to design potential applications for their research. Together they imagine what might be possible if technologies developed in the lab become adopted by people in their everyday lives. This results in objects, films and images that are exhibited in order to elicit debate on the desirable and undesirable qualities of future biotechnologies.
I first met him at iGEM 09, where he was part of the Cambridge team, who developed pigmented E coli, called “E. chromi”. Together with Daisy Ginsberg, he built an amazing (multi-) award-winning fantasy about the bio-political-cultural future of coloured organisms (and coloured poop). He also speculates on the measurement of what is life (Cellularity) and explored the meaning of artificial meat.
What drives him is his curiosity “to understand what biotech will really mean in everyday life.” I asked him what he’d be doing if he weren’t a speculative designer. He said, he’d actually want to “spend half my time as an interaction designer working with less-speculative technologies for today’s tech companies. I’d be doing more of that.”
When I asked him what the panelists should tell the SXSW crowd about the future and impact DIYbio. He pointed out that, “at moment, DIYBio is about demystifying biotechnology. Lifting back the curtain and showing people that its not magic and certainly not macabre. I’m not sure what the role of the citizen-scientist is in the future and whether they’ll be able to compete with large, well-funded labs, but the DIYBio community is a melting pot of designers, hackers, PHDs, ethicists and from this, new and exciting ways of working are bound to emerge.”
I’m looking forward to adding James perspective to the panel.
“Here I’ll try to give a high-level picture of Ginkgo’s pipeline for organism engineering. If you’ve checked out our webpage, you’ll see that we have several different organism engineering projects happening at Ginkgo that span several different hosts. Our goal was to build out a pipeline that could support the engineering of all these very different organisms for very different purposes but that uses a shared pipeline. To accomplish this goal, we deliberately opted to decouple design from fabrication. Ginkgo organism engineers place requests via our CAD/CAM/LIMS software system. Those requests are then batched and run on Ginkgo’s robots.”
This is indeed exciting. These folks are among the most experienced in synthetic biology and they are finally taking their engineering skills to the next level. They are reducing organism creation to a CAD request to an automated pipeline by an organism engineer. Really cool. [See more here: http://ginkgobioworks.com/works.html]
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“European scientists have created an Escherichia coli strain with a separate genome using chlorinated DNA. The genome should be unable to transfer back into unmodified bacteria, leading to what the researchers call a ‘genetic firewall’.”
First arsenic, now chlorine. In my grad school days, we were studying DNA-protein interactions by modifying specific atoms on the DNA. With this bacteria, it would be interesting to see how the overall biochemistry and enzymatic changes. Opens up a whole new way of studying biochemistry.
And I’d really like to know how they set up their continuous culture system.
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“Approved barely a month ago, the $30 million Living Foundries program should be sending out a request for proposals in the next few weeks and making awards several months from now. With its investment, over the next 3 years DARPA will support academic and corporate researchers for developing and applying an engineering framework to biology for biomanufacturing.”
Here’s a nice summary of the DARPA announcement made at the synthbio conference a few weeks back. Good to see the government funding agencies starting to pick up interest in synthbio and the practical uses of synthbio. The next 5 years should be quite interesting for those who are already doing synth bio. Also, big investments like this will get lots of students and post-docs flocking to synthbio, with a strong impact in 5-10 years. Yup. It’s gonna be great.
Read this article…
 I’ve been thinking of what to do at SXSW Interactive next year around Biology.
Biology at SXSW? It’s not as far-fetched as you’d think. The trends I see are the new bio hackspaces popping up, all the open source feeling around sharing bio tools, and so much discussion around design in biology. While SXSW Interactive is really a digerati mecca, I think there’s space for spill over into biology.
And it’s not like SXSW hasn’t been courting the scientists. For example, in 2010, there was a panel on citizen science. Then in 2011, Craig Center spoke and there was a panel on biomimicry.
My current (very unformed) thoughts are that we could have a Designing Biology panel, covering synthbio, synthetic aesthetics, DIYbio, practical microbiology, folks biology, and food design. If we want to go further, we could organize some sort of workshop with folks from GenSpace, BioCurious, or the BioBus doing what they do well – getting folks excited about Biology (maybe even at a local Uni in case the BioBus can’t be there). We could also have a screening party of bio vids, such as the Synthbio Documentary.
Ambitious? Absolutely. But we need to shoot for something. And seems this might end up with many moving parts and need proper project management, marketing, and so forth (cross that bridge when we get there).
What do you folks think? Suggestions and comments, please!
I want to at least suggest something for the SXSW panel picker by July 15th (unless someone has already suggested something).
“Should young, bright, and idealistic biotechnology students spend their summer coming up with technologies for oil companies to exploit so that they can more cleanly and efficiently pump greenhouse gases into the atmosphere, or should they be trying to come up with new fuels, new processes, new systems, new industries that can some day actually be good? iGEM is an inspirational experience, where you can meet hundreds of amazing students doing hundreds of amazing and creative things. Let’s not stifle their creativity and potential for change by having them try to make a fundamentally flawed and dangerous system less bad.” [by @thisischristina]
Well stated. Building bugs to keep extracting oil or cleaning up something that shouldn’t be dirtied is a complication upon a complication. And having to do so to be able to learn synthbio and to get funding gets awkward. Awkward if you have ethics, that is.
Bookmarked in Delicious.
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