Liverpool GeneMill

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

Synthetic biology is an emerging field that has been described as the construction of artificial biological devices, pathways or networks or the re-engineering of existing ones. Key to this engineering process is the construction of parts or components, which are encoded in DNA. A limiting factor in synthetic biology is access to cheap, high-fidelity DNA constructs encoding the components. This proposal is to fund the Liverpool GeneMill, which will take in raw materials in the form of DNA blocks and long oligonucleotides (Ultramers) and together with pre-existing blocks and DNA stretches from biological material, weave these into high fidelity DNA constructs. This in turn will be used for genome-scale engineering and protein expression prototyping. This will be achieved through robotic automation of a manual pipeline.

Alongside the fabrication of constructs will sit a DNA computer-aided design tool, developed to fit with our pipeline. We will develop this in collaboration with a software development company (Genome Compiler), linking users with a components database and taking designs and converting this into manufacturing blueprints for the GeneMill. This will in turn link into a laboratory management system, allowing individual tracking, quality control of each project as it moves through the GeneMill.

Ultimately the GeneMill will provide a rapid, cost-effective and accessible fabrication facility for DNA parts. By removing the complexity of manufacture for the user, GeneMill will allow researchers to focus on the design and testing of the parts, devices, pathways and networks.

Technical Summary

This proposal seeks funding to form the Liverpool "GeneMill", a facility that will provide open access to DNA synthesis for the UK research community. GeneMill will follow the DNA fabrication model used by US institutes (CVI, DARPA and JGI) subcontracting out the production of pools of long oligos (250nuc) and double strand G-blocks (500-1kb). Focusing instead on the assembly and final QC of complete DNA parts. Synthetic DNA fragments will be combined with gene or gene-fragment generated by PCR from biological material, pre-existing "Bioparts" and vector backbones using Gibson assembly. We will develop high throughput QC techniques using either Sanger sequencing and next generation sequencing techniques, repairing errors with standard molecular biology approaches and a variant of Gibson assembly. The GeneMill will provide a user with access to informatics through a collaborative environment for design, manufacture, QC and project management.

In addition, GeneMill will implement technologies for re-engineering at the genome level, building TALONs proteins or CRISPR crRNA using our assembly pipeline. We will also provide a protein expression pipeline allowing the molecular phenotyping of synthetically designed proteins.

The objective GeneMill will be to remove the complexity of design and manufacture from the user and delivering high-fidelity DNA parts for synthetic biology community from genes to whole pathways.

Planned Impact

The are three very clear impacts of this proposal:

1. The generation of a North of England DNA synthesis capacity. Like in the academic research sector, we have already established a similar need for access to cheap, high-fidelity DNA constructs specifically in the area of industrial biotechnology. GeneMill fits perfectly with the Unilever/Liverpool vision of the Materials Innovation Factory and the Micro-Biorefinery, which aims to translate fundamental research into novel products. GeneMill would provide the fundamental bio-fabrication requirements for the factory. In addition, CGR already collaborates with industry in projects including general biomedical research and synthetic biology oriented research in biofuels, engineering of pathways for natural product breakdown and more. We would aim to use this user-base as a first market for the new DNA synthesis capabilities. Moreover, we would work with the Liverpool press office and Business Gateway to promote the GeneMill to businesses across the Life Science and broader science sector.

2. The establishment of synthetic biology expertise. Either together with the LSBI or on its own, GeneMill will act as a focal collaborative hub for industry to engage with synthetic biology approaches. One of the important objectives is the integrative design environment making the synthetic biology step of parts design and manufacture accessible.

3. The collaborative development of technologies and software
The CGR has a track record of working with companies developing technologies associated with next generation sequencing, including key companies like Roche, Illumina, Life Technologies, Agilent, IDT, NimbleGen and Pacific Bioscience. Many of these companies are likely to play an important part in the development of technologies around DNA synthesis and having a credible record of working collaboratively with them is important. One of the key impacts of this project will be the collaborative development and piloting of new technologies, providing early access of new technologies to UK researchers.

Intellectual property. It is possible that IP may arise from the methodological and analytical approaches developed during this project. We will liaise with Liverpool Business Gateway to ensure the timely protection of IP during the project. It will also be critical to work with IP experts at Liverpool Business Gateway to put in place access agreements for clones and vectors.

Outreach. Synthetic biology is a new and exciting field gaining a lot of press coverage, it is, therefore, important that the public is made aware of its real potential. It is also conceptually easy for the public to understand, as it is likened to technical Lego or electronic components. We will aim to work collaboratively with the Liverpool World Museum and popular science media to showcase this work. We will take on Nuffield sixth form students and undergraduates in synthetic biology summer projects. We would also plan to enter the iGEM competition.

Publications


10 25 50
 
Description We have developed a QC approach using the PACBio to sequence constructs call SMRT Gate
Exploitation Route We are publishing the work and providing it as a service.
Sectors Manufacturing, including Industrial Biotechology
 
Description We have established the GeneMill as a research pipeline for both Academic and industry to access synthetic Biology. The industrial impact is to provide industry to a new way of working and apply synthetic principle to generating new discovering and generating new materials. We are already working with Skelene, Croda and Unilever on funded projects.
First Year Of Impact 2015
Sector Agriculture, Food and Drink,Chemicals,Manufacturing, including Industrial Biotechology
Impact Types Economic
 
Description From Pathway Discovery to Re-engineering-US partnering award
Amount £49,500 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 06/2016 
End 06/2019
 
Description Overexpression of Hydrogel-Forming proteins in heterologous hosts
Amount £50,000 (GBP)
Organisation Unilever 
Department Unilever Research and Development
Sector Private
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2015 
End 11/2016