A Plant and Microbe DNA Foundry to support Earlham Institute’s Institute Strategic Programmes (ISPs) and the UK BioScience Community and BioEconomy

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

The Plant and Microbe DNA Foundry (NC2) will provide a national resource for the UK bioscience community to engage with the high-throughput laboratory automation facilities at Earlham Institute (EI). Focusing on nanoscale DNA construct assembly from standard parts, allied with validation by next-generation sequencing via Earlham Institute’s National Capability in Genomics and Single Cell (NC1), NC2 will provide access to DNA assembly at scale and also to toolkits and collections of standard DNA parts submitted under an Open Material Transfer Agreement (OMTA).

NC2 will complement the strengths of the Norwich Research Park, providing researchers with a platform to perform large-scale experiments. NC2 benefits from essential, local multi-disciplinary expertise. This will enable new research directions and approaches to drive innovation contributing to UK SynBio sector growth, one of the UK’s ‘Eight Great Technologies’.


This will be extended by educating researchers about biological standards and automated parallel DNA assembly through training delivered through EI’s National Capability in Advanced Training (NC4).
 
Description The Earlham DNA Foundry has established workflows for the automated, nanoscale fabrication of DNA molecules from standard DNA parts. This has been done using published molecular tools as well as tools developed in collaboration with laboratories in the OpenPLant Synthetic Biology Reserach Centre. The validation of these assemblies to single-base resolution has been achieved by coupling the fabrication workflow to Next Generation sequencing. High-throughput low-cost miniaturised Illumina® Nextera XT protocols have been implemented on the Illumina MiSeq platforms and workflows on the Galaxy platform have been put in place to enable users without scripting skills to execute data analysis. In collaboration with the Liverpool Gene Mill, an alternate validation method has been developed on the Pacific Biosciences RSII sequencing platfor. The latter is particularly useful for validating constructs with repetitive elements).
Exploitation Route in the majority of UK laboratories it is still typical for postgraduate students and postdoctoral researchers to spend anything from days to weeks at the bench making just handfuls of individual DNA constructs. The Earlham DNA Foundry has developed workflows that enable the assembly of very large constructs from standardised DNA parts at exceptionally low cost and with minimal effort that would benefit many laboratories. It is currently developing additional automated workflows that will couple these nanoscale DNA assembly and delivery techniques to the downstream growth and phenotyping of cell cultures. This will enable UK researchers in the biosciences to pursue ambitious, large-scale projects that are not possible in their own institutions.
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Invited submission to the ad hoc technical expert group (AHTEG) on digital sequence information on genetic resources of the the Convention on Biological Diversity
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
URL https://www.cbd.int/abs/dsi-gr/ahteg.shtml#submissions
 
Description Submission to the International Treaty on Plant Genetic Resources for Food and Agriculture ( ITPGRFA) on access and benefit sharing of digital sequence information
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
 
Description Bioreactor capability for the Plant and Microbe DNA Foundry
Amount £358,963 (GBP)
Funding ID BB/R000433/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2017 
End 08/2018
 
Description Software for DNA Foundries 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-development of LIMS software for DNA foundries
Collaborator Contribution Co-development of LIMS software for DNA foundries
Impact New software and publication of software
Start Year 2015
 
Description Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture 
Organisation National Institute of Biology
Country Slovenia 
Sector Charity/Non Profit 
PI Contribution Co-applicant on funding application
Collaborator Contribution Co-applicant on funding application
Impact Sucessful funding application (ERA-CoBioTech).
Start Year 2017
 
Description Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture 
Organisation Spanish National Research Council (CSIC)
Department Institute for Plant Molecular and Cellular Biology
PI Contribution Co-applicant on funding application
Collaborator Contribution Co-applicant on funding application
Impact Sucessful funding application (ERA-CoBioTech).
Start Year 2017
 
Description Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture 
Organisation Technical University of Darmstadt
Country Germany 
Sector Academic/University 
PI Contribution Co-applicant on funding application
Collaborator Contribution Co-applicant on funding application
Impact Sucessful funding application (ERA-CoBioTech).
Start Year 2017
 
Description The effect of codon usage on translation rate 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-applicant of seed-funding application
Collaborator Contribution Co-applicant of seed-funding application
Impact Sucessful application for seed-funding from the Norwich Reserach Park
Start Year 2016
 
Description 2017 Youth STEMM Gold Awards 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Presentation on synthetic biology followed by a practical workshop on designing genetic circuits. Sudents then presented their ideas, asked technical questions and discussed the potential impacts of synthetic biology and biotechnology on society.
Year(s) Of Engagement Activity 2017
URL http://ysawards.co.uk
 
Description CPSC PhD course: SYNthetic BIOlogy, From pro- to eukaryotic SYStems (SYNBIOSYS) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Delivered lecuryres and workshops as part of the University of Copenhagen's CPSC PhD course: SYNthetic BIOlogy, From pro- to eukaryotic SYStems (SYNBIOSYS)
Year(s) Of Engagement Activity 2017
URL http://cpsc.ku.dk/calendar/2017/cpsc-phd-summer-course-2017-synbiosys/
 
Description Norwich Biomakers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Norwich Biomakers brings together an interdisciplinary network of people from across NorwichCity and the Norwich Science Park that share an interest in the cross-over of biology with design, technology, engineering, electronics, software, art etc. This group meets monthly at a variety of local spaces for events including talks, training in the use of technologies and to shape project plans.
Year(s) Of Engagement Activity 2017,2018
URL https://www.meetup.com/Norwich-Biomakers/
 
Description Plants in iGem Workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Workshop on Plants in synthetic biology held at the iGEM Giant Jamboree every year since 2014. Members of many international iGEM teams, industry and civil society representatives, as well as the iGEM executive team attend. The workshops comprise short talks followed by discussion (with audience participation) and information-sharing about plant synthetic biology tools and techniques.
these workshops, together with other activities have resulted in
- The establishment of a Plant Committee at iGEM
- The acceptance of parts in the Common Plant Syntax in the iGEM Registry
- The establishment of a Special Award for excellence in Plant Synthetic Biology in the iGEM competition (from 2016 onwards)
Year(s) Of Engagement Activity 2014,2015,2016
URL http://2016.igem.org/Resources/Plant_Synthetic_Biology
 
Description Science Café, Maddermarket Theatre, Norwich 19th April 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Norwich Science Café at the Maddermarket Theatre entitled "Building with Biology". A presentation and interactive activity for identification of aromatic plant natural products and understanding biosynthetic pathways. This was followed by an extensive discussion on the meaning of the words 'synthetic', 'synthesis' and 'natural' and the relative benefits to the environment and health of synthetic biology approaches for manufacturing. Audience members expressed interest in adult-focussed lab-based workshops and bio-make spaces.
Year(s) Of Engagement Activity 2017
URL https://twitter.com/scicafenorwich
 
Description Synthetic biology session and discussion panel at the London Festival of Genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Chaired a session on synthetic biology session and participated in a panel discussion at the London Festival of Genomics, 2017. This brought the synthetic biology to a new audience of industry, investors and the general public. There was a lengthy discussion with the general public, investors and industry representatives from diverse fields (e.g. computing and engineering) about the ethics and potential of biological engineering at the panel discussion and also following the workshop.
Year(s) Of Engagement Activity 2017
URL http://www.festivalofgenomicslondon.com/full-agenda
 
Description Web Article - Spotlight on Synthetic Biology. Yaomin Cao 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Interview with Yaomin Cai of Nicola Patron's DNA Foundry at Earlham Institute, on how he got into synthetic biology, how it can help us to tackle biological questions, and what the future has in store. -SOCIAL MEDIA- Engagement x92, Impressions x70456
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/spotlight-on-synthetic-biology
 
Description Web Article - Spotlight on biohacking 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Interview with Elliot Roth, founder of Spira and Indie-lab on biohacking and algae research. -SOCIAL MEDIA- ENgagement x88, Impressions x176657
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/spotlight-biohacking-elliot-roth-%E2%80%9Cit%E2%80%99s-algae-time%...
 
Description Web article - Spotlight on Synthetic Biology 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Article with a focus on Synthetic Biology. An interview with John Cumbers, founder of SynBioBeta. -SOCIAL MEDIA- Engagement x160, Impressions x159540
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/spotlight-synthetic-biology-john-cumbers
 
Description Web article for Public Engagement - What's in a genome? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 'Learning' Article to explain what's in agenome. -SOCIAL MEDIA- Engagement x 285, Impressions x 138027
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/whats-genome