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27/12/2014

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An engineer's view of applications

Richard Kitney anticipates a new industrial revolution

Synthetic biology aims to design and engineer biologically-based parts, devices and systems that do not exist in the natural world – as well as redesigning existing, natural biological systems.

Drugs and detectors

One current example is the creation of a new type of synthetic drug for malaria based on Artemisinin, a compound used for over 1000 years by Chinese herbalists to treat malaria. In 1972, a Chinese scientist called Tu Youyou discovered Artemisinin in the leaves of the annual wormwood plant. Jay Keasling and colleagues at UC Berkeley took this as a starting point for developing a synthetic version of the drug.

Another example is an advanced biosensor for the detection of urinary tract infection, a problem which affects thousands of people in hospital in the UK.1 Yet another is a detector for arsenic in drinking water - a major problem in Bangladesh.2  Finally, synthetic biology techniques have been applied to the development of advanced biofuels.

Engineers design synthetic biology products using strategies including bottom up; chassis; and parts, devices and systems.

Bottom up

Some biological organisms have been reconstructed by studying their DNA sequence in small sections.  These sections are then reproduced and stuck together to produce the overall organism.  It is now possible to reproduce the genome of a simple biological organism in this way. 

A good example of this approach is the work of Craig Venter and colleagues. In a paper in Science last year, they described how they had made a bacterium. They sequenced its genome and divided it into chunks, each of which contained about one twenty-fourth of the genome. They then reconstructed each chunk from the sequence data stored on a computer. Bit by bit, they assembled the chunks into the genome until it was completely reconstructed. They then re-sequenced it to show that there were no errors.

Chassis

The urinary tract infection detector can be thought of in more generic terms, as a three-stage biological device in a chassis. 

The first stage is a detector which, in the case of urinary tract infection, detects a small molecule called AHL which is associated with the infection.  The second stage is a signal booster which amplifies the detected signal.  This is then passed to the third stage which is an indicator (in this case, a green light which shines when AHL is present).  Each stage is a section of modified DNA. The combined sections of DNA are then placed in a natural chassis, for example E.Coli.  The E.Coli responds to DNA, which can be thought of as an instruction set, and produces the biologically-based sensor device.

Parts, devices and systems

Systems can be built from standard devices which, in turn, can be built from standard parts. Biological devices (and ultimately systems) can be constructed from a range of standard biological parts called BioParts.

Fully-understood standard BioParts are created and stored in a registry. Devices are designed combining a series of BioParts, rather like assembling something from Lego.  The design for a new device is usually sent, in the form of a software file, to a biological construction company such as GeneArt. The company returns the whole device in the form of DNA, which is then inserted into an appropriate chassis in order to construct the device.

Synthetic biology has strong parallels with the development of synthetic chemistry in the 19th century, which resulted in many of the great industries of the 20th century. Many observers believe that this new field will lead to new and important industries – and may ultimately spawn a new industrial revolution.

1 This work has been done by Freemont and Kitney at Imperial College.

2 This work has been done by Elfick and French at Edinburgh University.

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Richard Kitney
Richard Kitney is professor of BioMedical Systems Engineering at Imperial College London
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