Sunday, July 22, 2012

SCIENCE SPECIAL...Viruses Turn Out to be New Apps of Biology


Viruses Turn Out to be New Apps of Biology

Synthetic biology uses synthesised DNA to create biological functions not found in nature

    Most of us would regard viruses as dangerous organisms. But synthetic biologist Andrew Hessel sees them as the apps of biology, providing infinite possibilities for us to create new living systems. From his point of view, viruses are chemical codes that add features to the organisms that they infect. Imagine the firefly. If one could transpose its magic code on other organisms, according to Hessel, we could have “trees that glow instead of the electric lamps that we use”. No one is trying to make such trees at the moment, but some scientists have already developed bacteria that glow.
The San Jose-based start-up Geneweave has just engineered a bacteriophage – a virus that infects bacteria – as a diagnostic tool for hospitals to screen their workers for bacterial infections. The phage makes the bacteria glow, thereby announcing their presence. “Viruses have more roles than we realise,” says Hessel, who works at the Singularity University in the Silicon Valley. “They are just software and we will see them become a big industry as diagnostic tools, as gene therapy, used to hunt down diseases where antibiotics don’t work, and so many other things.”
Synthetic biology is a rapidly expanding discipline that uses synthesised DNA, the genes of most living beings, to create biological functions not found in nature. These genes are edited using a computer and then synthesised from scratch using chemicals. Synthetic biologists dream of a day when they could design a gene using a computer and then ‘print’ it out the next day, the way we have begun to produce industrial products. It is considered to be a solution to our most pressing problems like environmental pollution and shortage of food and energy. Synthetic biologists hope to create food and fuel, and drugs and chemicals, without damaging the environment.
Although the subject is riddled with serious problems, scientists are taking the first tentative steps towards their goal. After 750 attempts, scientists at Stanford University, including prominent synthetic biologist Drew Endy, have found a way to write, erase and rewrite information into the DNA of bacteria called Escherichia Coli. This ability to program DNA could one day let us switch off cells when t h e y b e c o m e c a n c e ro u s. Researchers at University of Australia made a seamless couture dress out of red wine by using nonhazardous Acetobacter bacteria to transform the alcohol into cellulose fabric by pouring and wrapping it against a human body or a mold.
A bunch of students from Brown and Stanford universities are working with NASA scientists to design synthetic microbes that would help astronauts build a community on Mars. One of their projects uses bacteria to break down urea into chemicals that can then form crystals which bind Martian sand into a strong construction material. Others engineer photosynthetic bacteria to convert sunlight into chemical energy like sugar to help power other living things.
A big milestone for synthetic biology will be later this year when the first bona fide synthetic biology product, the anti-malarial drug Artemisin, hits the market. The result of a $42.6-million grant from the Bill and Melinda Gates Foundation, the drug was created by inserting genes from various organisms into E.coli. Artemisin is currently extracted from plants. It is the only drug that works against malaria, and there is a looming shortage because plants grow slowly and the demand is increasing rapidly.
Singularity University has just started Silicon Valley’s first synthetic biology incubator SynBio Startup Launchpad, which Hessel heads, to accelerate the many promises of the subject, like using viruses as apps. The first three companies selected by this incubator are these. Evolutionary Solutions, which is developing a genome synthesis device; Modern Meadow, which applies tissue-engineering techniques to produce high volumes of animal protein for food and textiles; SoilGene, which combines environmental genomics and bio-informatics to survey land for the agriculture and natural resources.
Amyris, the company that is developing synthetic – biologyderived Artemisin, is one of the big successes of this field. It was founded by Jay Keasling, a professor at the University of C a l i fo r n i a i n Berkeley and chief executive of the Joint BioEnergy Institute. Amyris is developing several petroleum-derived products using synthetic biology. It recently gave up biofuels as being too expensive. Says Nathan Hillson, Keasling’s colleague at the Joint BioEnergy Institute: “For bio-fuels, the market is pretty challenging because petroleum is so cheap. So, even companies like Amyris and LS9 are moving into high-value bio-based chemicals, like fragrances, instead.”
Scaling is in general a grand challenge for pretty much every synthetic biology application. One big reason is unpredictability of how the components work together, and all the pieces that go into making up a desired synthetic biological factory are still poorly understood. “The gap between low-level genetic circuitry and complex gene networks having robust, predictive and adaptive behaviour still challenges the scientific community,” says Cecilia E Van Cauwenberghe, Senior Research Analyst of Life Sciences and Biotech at Frost & Sullivan, a consultancy firm. Lack of standards -- Amyris for instance uses yeast while LS9 uses E.Coli -- also makes adoption and scaling that much harder.
Across the developed countries, synthetic biology is drawing big research funds from the government. The US Department of Defence’s R&D wing, Defense Advanced Research Projects Agency (DARPA), has just awarded seven synthetic biology research grants worth $15.5 million to six companies and institutions. DARPA wants them to bio-engineer and manufacture on-demand all kinds of bio-products for urgent military needs.
Despite the problems, scientists, entrepreneurs and aficionados remain upbeat. Rapid progress is being made in building blocks and the tools to use them. Animesh Ray, professor of Systems Biology at Keck Graduate Institute of Applied Life Sciences points to three major developments in academia: Stanford’s Endy is working with abstract cell circuit modules; UC San Diego’s Jeff Hasty’s research is about using single cell genes to communicate with other cells; and Harvard Medical School’s George Church is working on training these cells to communicate with each other. “Together, these developments will help synthetic biology reach new heights,” says Ray.

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