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Links 1 through 10 of 38 by Charlie Schick tagged syntheticbiology

"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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"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.

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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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"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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"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.

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"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."

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.

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"One of UCSF’s brightest young scientists and a key member of the Bay Area’s emerging synthetic biology community is heading east."

[via @jrkelly]

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"Here we demonstrate that novel proteins from this binary patterned library can rescue E. coli cells that lack certain natural proteins required for cell viability. ... These findings show that an organism, which would otherwise not grow, can be sustained by macromolecules devised in the laboratory."

Wow. Just, wow. I really can't express how cool this is.

Why hadn't this been done before? I know I've considered this experiment at one time, but maybe long sequences were just not possible. I don't know. Or maybe, folks thought about it but just really never did it. Heh.

And you gotta love the ability to select for very rare events in microorganisms. Note that the folks above chose a "neighborhood" of adjacent possibles, proteins more likely to fold rather than totally random sequences [And I'm seeing how this can be extended with combinatorial approaches.]. Some of the experiments I have planned for Practical Microbes indeed depend on this.

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