BioBricks and synthetic biology

2009-09-25

in Geek stuff, Law, Science, The environment

Frog with leaves in Mud Lake

The basic impulse behind synthetic biology is one that human beings have been acting on for thousands of years: the desire to make living things serve our needs and desires better. We’ve domesticated animals, seriously altering their genomes and behaviours in the process, and turned wild crops into agricultural staples. Now, people aspire to use living things for all kinds of purposes: from synthesizing drugs and fuels to performing computations.

One of the most important developments of the Industrial Revolution was standardized parts. Originally used in firearms, having devices comprised of interchangeable components made maintenance and repair far simpler. Instead of having to make a custom widget designed to fit a particular machine, any standard widget of the right sort would do. To some extent, BioBricks are trying to do the same thing for engineered biological systems. Each consists of a DNA sequence held in a circular plasmid, with standard headers and footers. They include sites for enzymes, which allow the bricks to be chained together. Individual BioBrick ‘parts’ contain information such as how to code a particular protein. They are assembled into ‘devices’ that perform basic functions, and ‘systems’ that accomplish higher level tasks. MIT maintains a ‘catalog of parts and devices.’ There is even an iPhone application that allows the “review, annotatation, design, and implemention of standard biological parts.” An assembly kit adequate for 50 reactions can be purchased online for US$235.

One application of synthetic biology has been to make Amorphadiene, a chemical precursor to the ant-malarial drug artemisinin (mentioned here before). Producing the drug from the shrub in which it was discovered is expensive and tricky. As a result, annual demand far exceeds available supply. Producing it in engineered organisms could therefore make treatment more widely available. Amyris Biotechnologies, working with a grant from the Bill and Melinda Gates Foundation, has produced the drug using such an organism, and is hoping to have it on the market by 2012. The company’s founder hopes to eventually be able to synthesize any molecule found in a plant inside an easy-to-grow microbe.

Another mooted application would be engineering photosynthetic algae to produce and release oils, which could be collected and used as fuels. Such a process could be far more efficient than one based on growing conventional algae and then processing them for whatever quantity of oils they contain naturally.

Of course, synthetic biology does raise safety and ethical considerations. While I don’t think tinkering with genetic material is fundamentally morally different from cross-breeding plants or animals, there may be more danger of unanticipated consequences. Weighing the reality of that risk against the promise of what engineered organisms could do isn’t a straightforward task, especially in situations where the groups bearing the risk and receiving the benefits are not one and the same. Regulating the industry, and establishing legal precedents on things like liability, will be an important part of future policy- and law-making.

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. September 25, 2009 at 2:34 pm

Biohacking
Hacking goes squishy

Sep 3rd 2009
From The Economist print edition
Biotechnology: The falling cost of equipment capable of manipulating DNA is opening up a new field of “biohacking” to enthusiasts

“The template for biohacking’s future may be the International Genetically Engineered Machine (iGem) competition, held annually at the Massachusetts Institute of Technology. This challenges undergraduates to spend a summer building an organism from a “kit” provided by a gene bank called the Registry of Standard Biological Parts. Their work is possible because the kit is made up of standardised chunks of DNA called BioBricks.

As Jason Kelly, the co-founder of a gene-synthesis firm called Ginkgo BioWorks, observes, there is no equivalent of an electrical engineer’s diagram to help unravel what is going on in a cell. As he puts it, “what the professionals can do in terms of engineering an organism is really rudimentary. It’s really a tinkering art more than a predictable engineering system.” BioBricks are, nevertheless, an attempt to provide the equivalent of electronic components with known properties to the field—and using them is part of Ginkgo’s business plan. Information on BioBricks is kept public, helping the students understand which work together best.

What the students actually create, however, is left to their imaginations. And the results are often unexpected. A team from National Yang-Ming University in Taiwan conceived a bacterium that can do the work of a failed kidney; another, from Imperial College, London, worked on a “biofabricator” capable of building other biological materials.”

. September 25, 2009 at 2:41 pm

The Need for Heretics

Commencement Address, given at the University of Michigan, December 18, 2005

Freeman Dyson, Institute for Advanced Study, Princeton, New Jersey

“Every orchid or rose or lizard or snake is the work of a dedicated and skilled breeder. There are thousands of people, amateurs and professionals, who devote their lives to this business. Now imagine what will happen when the tools of genetic engineering become accessible to these people. There will be do-it-yourself kits for gardeners who will use genetic engineering to breed new varieties of roses and orchids. Also kits for lovers of pigeons and parrots and lizards and snakes, to breed new varieties of pets. Breeders of dogs and cats will have their kits too.

Genetic engineering, once it gets into the hands of housewives and children, will give us an explosion of diversity of new living creatures, rather than the monoculture crops that the big corporations prefer. Designing genomes will be a personal thing, a new art-form as creative as painting or sculpture. Few of the new creations will be masterpieces, but all will bring joy to their creators and variety to our fauna and flora. “

. September 25, 2009 at 3:05 pm

“In 2006, a team of Endy’s undergraduate students used BioBrick parts to genetically reprogram E. coli (which normally smells awful) to smell like wintergreen while it grows and like bananas when it is finished growing. They named their project Eau d’E Coli. By 2008, with more than a thousand students from twenty-one countries participating, the winning team—a group from Slovenia—used biological parts that it had designed to create a vaccine for the stomach bug Helicobacter pylori, which causes ulcers. There are no such working vaccines for humans. So far, the team has tested its creation on mice, with promising results.”

. September 29, 2009 at 12:08 pm

“The problem with this desire is that nature has no interest at all in the long-term benefit of humankind. Nature has no interest in anything. And even if it did, mankind has been overriding nature routinely for millennia. That’s what agriculture is all about. A natural Britain would be a woodland that could feed only a few–when not covered by the glaciers of a natural ice age. Selective breeding–a subject royalty understands in its bones–removed nature from the farmyard long before the first endonucleases started to cut up the first artificial strands of DNA.

. October 6, 2009 at 10:01 am

Startup Offers Pre-Built Biological Parts

“A new startup called Ginkgo BioWorks hopes to make synthetic-biology simpler than ever by assembling biological parts, such as strings of specific genes, for industry and academic scientists. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.) Company cofounder Tom Knight, also a research scientist at MIT, says: ‘I’m interested in transitioning biology from being sort of a craft, where every time you do something it’s done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'”

. November 4, 2009 at 11:52 am

Toyota Create New Plant Species to Offset Prius Factory CO2

Toyota have moved into the horticultural industry, creating two new species of flowers specifically developed for the grounds of the Prius plant in Toyota City, Japan.

The flowers are designed to take heat out of the atmosphere and absorb nitrogen oxides. The leaves of the flowers will also create water vapor, reduce the temperature of the factory’s surroundings, lowering the amount of energy needed to cool it.

. November 23, 2009 at 9:49 am

Glowing bacteria that finds landmines

Edinburgh University engineers have a plan to use genetically engineered bacteria that glow in the presence of explosives to detect landmines. The project is student-led, overseen by Alistair Elfick.

The bugs can be mixed into a colourless solution, which forms green patches when sprayed onto ground where mines are buried.

Edinburgh University said the microbes could be dropped by air onto danger areas.

Within a few hours, they would indicate where the explosives can be found.

The scientists produced the bacteria using a new technique called BioBricking, which manipulates packages of DNA.

. December 8, 2009 at 1:12 pm

Synthetic biology
Your plastic pal

Nov 26th 2009
From The Economist print edition
A genetically engineered bacterium makes a greener plastic

ONE of the most promising alternatives to plastics made from oil is polylactic acid (PLA). It is biodegradable, safe enough to be used as food packaging, can be processed like existing thermoplastics into coloured or transparent material and can be manufactured from renewable resources such as maize and sugarcane. Although PLA has been around for decades, it is only in recent years that advances in production techniques, particularly by Cargill, a big American agricultural group, have made it feasible to produce the material commercially. Now a group of researchers led by Lee Sang-yup of the Korea Advanced Institute of Science and Technology say they have come up with an even better way to make PLA, using the emerging science of synthetic biology.

At the moment PLA is usually made in two stages. First, a source of starch or sugar, which could be an agricultural by-product, is fermented to produce lactic acid—the same substance made by the body during exercise, only in this case it comes from the bacteria exercising themselves in the fermentation process. In the second stage, lactic-acid molecules are linked into long chains, or polymers, in chemical-reaction vessels, to produce PLA. What Dr Lee and his colleagues have succeeded in doing, as they report in Biotechnology and Bioengineering, is to produce PLA directly, in a one-stage process, in bacteria. No chemical “post processing” is required.

. February 12, 2010 at 4:45 pm

Do-It-Yourself Genetic Engineering

IT ALL STARTED with a brawny, tattooed building contractor with a passion for exotic animals. He was taking biology classes at City College of San Francisco, a two-year community college, and when students started meeting informally early last year to think up a project for a coming science competition, he told them that he thought it would be cool if they re-engineered cells from electric eels into a source of alternative energy. Eventually the students scaled down that idea into something more feasible, though you would be forgiven if it still sounded like science fiction to you: they would build an electrical battery powered by bacteria. This also entailed building the bacteria itself — redesigning a living organism, using the tools of a radical new realm of genetic engineering called synthetic biology.

A City College team worked on the project all summer. Then in October, five students flew to Cambridge, Mass., to present it at M.I.T. and compete against more than 1,000 other students from 100 schools, including many top-flight institutions like Stanford and Harvard. City College offers courses in everything from linear algebra to an introduction to chairside assisting (for aspiring dental hygienists), all for an affordable $26 a credit. Its students were extreme but unrelenting underdogs in the annual weekend-long synthetic-biology showdown. The competition is called iGEM: International Genetically Engineered Machine Competition.

The team’s faculty adviser, Dirk VandePol, went to City College as a teenager. He is 41, with glasses, hair that flops over his forehead and, frequently, the body language of a man who knows he has left something important somewhere but can’t remember where or what. While the advisers to some iGEM teams rank among synthetic biology’s leading researchers, VandePol doesn’t even teach genetic engineering. He teaches introductory human biology — “the skeletal system and stuff,” he explained — and signed on to the team for the same reason that his students did: the promise of this burgeoning field thrills him, and he wanted a chance to be a part of it. “Synthetic biology is the coolest thing in the universe,” VandePol told me, with complete earnestness, when I visited the team last summer.

. September 13, 2014 at 4:55 pm

SYNTHETIC biology—the technique of moving genes from creature to creature not one at a time, but by the handful—promises much but has yet to deliver. Someone who believes it can, though, is Christina Smolke of Stanford University. And, as she and her colleagues write in Nature Chemical Biology, they think they now know one way that it might.

To do so, her team added three crucial poppy genes to some yeast cells. When provided with the appropriate chemical precursor, the modified yeast cranked out morphine and another opiate, codeine. And when one of the poppy genes was itself replaced by two genes from Pseudomonas putida, a soil bacterium, the yeast made oxycodone and hydrocodone too. Though this prototype yeast was not particularly efficient, some further tweaking converted it into a veritable drug factory—capable of cooking up 131mg of opioids (the equivalent of about 26 medical doses of diamorphine) per litre of culture over a four-day manufacturing cycle.

If Dr Smolke succeeds, and the technology is commercialised, opiates will join an antimalarial drug called artemisinin as non-protein medicines that can be made by biotechnology. Natural artemisinin is extracted from a species of wormwood that grows in China. The synthetic sort is made by Sanofi, to a recipe devised by Jay Keasling, a researcher at the University of California, Berkeley, and developed by Amyris, a firm he helped to found.

http://www.economist.com/news/science-and-technology/21614093-narcotic-drugs-could-soon-be-manufactured-yeast-new-opium-pipe

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