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Special feature on UK synthetic biology resources: Edinburgh Genome Foundry

Posted on 12/10/2016

The second in a series of special features on the SynBio SIG

Dr Hille Tekotte describes the activities and services available for synthetic biologist through the Edinburgh Genome Foundry.

This article is the second in a series of special features on the SynBio SIG, which will highlight some of the fantastic resources that are available to the UK synthetic biology (SynBio) community.

In this edition, Dr. Hille Tekotte describes the activities and services available through the newly opened Edinburgh Genome Foundry, which is one of nine strategic investments in DNA synthesis made through the Synthetic Biology for Growth Programme.

From Dr. Hille Tekotte, Edinburgh Genome Foundry Manager:

The Edinburgh Genome Foundry (EGF) is a newly established facility for the automated design and assembly of large DNA constructs. Embedded within the University of Edinburgh’s Centre for Synthetic and Systems Biology (SynthSys), the EGF is ideally located to serve world leading synthetic biology research and support future advances in the life sciences and beyond.

The vision for the EGF was to create a fully automated platform using a combination of state-of-the-art hardware, innovative software and robotics, and it is well on the way to realising this ambition.

Automation enables the assembly of large DNA constructs using faster, cheaper, and more reliable methods. For example, in addition to an automated setup that can perform conventional liquid handling methodologies, the EGF platform features cutting-edge acoustic dispensing. This can handle extremely small volumes of liquid (nanolitres), thereby reducing the cost of expensive reagents and labware. Moreover, the use of automated, robotic systems allows constructs to be moved quickly and very reliably between different stages in the complex DNA assembly process. This will also allow the platform to be run 24/7, and reduce failure rates at the crucial quality control steps.

Building engineered cell lines and new industrial strains requires the management of complex systems and large datasets – at both the design and manufacturing stages. The EGF is establishing a fully integrated software pipeline that will support Computer Aided Design (CAD) and Manufacturing (CAM) of DNA. In July 2016, we will launch Genetic Constructor, a web-based DNA sequence design tool specialised for large assembly projects, which we are developing in partnership with Autodesk, the world leader in CAD/CAM software.

The Foundry will work on a wide range of projects. One of the first is the ongoing establishment of the Edinburgh Registry of Parts: This extensive collection of pre-made, functional DNA parts from key organisms is currently being compiled by the EGF and will support the rapid construction of many DNA designs.

To test the impact of the DNA constructs on cell function, the EGF will work with other Edinburgh specialist research facilities to develop and provide biological assays. The EGF is equipped for high-throughput micro-fermentations, in which biomass, pH, dissolved oxygen, fluorescence intensity and other features can be followed over time with varying nutrients. In addition, the University offers a comprehensive suite of genomics, metabolomics and proteomics capabilities as well as protein production expertise.

The EGF was the first academic member to join the International Gene Synthesis Consortium (IGSC), which addresses the biosafety, biosecurity and ethical issues surrounding DNA synthesis. As part of the IGSC, the EGF will systematically screen all customers and every synthetic gene sequence requested. Together with international governments, we will work to promote the many beneficial applications of gene synthesis technology while safeguarding biosecurity.

The EGF was funded through the UK Research Councils’ ‘Synthetic Biology for Growth’ programme and with additional investment from the University of Edinburgh’s School of Biological Sciences. The Foundry will also support the research activities of the BBSRC, EPSRC and MRC funded UK Centre for Mammalian Synthetic Biology.

If you are interested in finding out more about the EGF please contact Dr. Hille Tekotte, Edinburgh Genome Foundry Manager at: h.tekotte@ed.ac.uk or egf@ed.ac.uk, or see the website http://www.genomefoundry.org/.

 

If you are involved in a UK SynBio resource and would be interested in promoting your activities through the SynBio SIG, please contact synbiosig@ktn-uk.org.