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).

Publications

10 25 50
 
Title Nicotiana, biofoundry. 
Description An artistic interpretation inspired by plant systems for bioproduction of natural products developed with artist and designer, Karen Ingram. 
Type Of Art Artwork 
Year Produced 2018 
Impact Published as part of 'Convergent Visions' Faesthetic #15 produced in partnership with SXSW for the SXSW Art Program 2018. Presented at SXSW Interactive 2018. 
URL http://think.faesthetic.com/archives/9687
 
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. We have also established a number of additional automated assays including growth assays for microbes.
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. The Earlham DNA Foundry is now providing access to automated workflows as a service. New workflows are bing developed in collaboration with other reserachers that will be offered as services in the future. In addition, early career reserachers have been trained in the use of automated laboratory platforms at the Foundry.
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.earlham.ac.uk/earlham-dna-foundry
 
Description Engagement with All-Party Parliamentary Group on Agriculture and Food for Development: Implications of the 2018 European Court of Justice ruling on genome editing
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Engagement with the Parliamentary Scientific Committee: implications of the 2018 European Court of Justice ruling on Genome Editing
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Expert member of the plant synthetic biology working group for the European Food Standards Agency (EFSA)
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
 
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 Science and Technology Committee, House of Commons - implications to the UK of the 2018 Euporean Court of Justice ruling on Genome Editing
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
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 17ALERT Mid-range equipment initiative - 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 ERA CoBioTech
Amount € 1,643,000 (EUR)
Funding ID BB/021554/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description IPA Industrial Partnering Award - An improved bioproduction system for proteins and small molecules
Amount £420,676 (GBP)
Funding ID BB/P010490/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2020
 
Description OpenPlant - Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 09/2018 
End 07/2019
 
Title Automated preparation of crystallization screening solutions. 
Description The workflow allows the automated generation of 96 different crystallization solutions, and their aliquots in 96 deep well blocks to a total of 480 samples. The workflow is available to the research community as service. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact The workflow is available to the research community reducing cost in consumables. This method will allow us to develop automated approaches to more complex crystallization solutions, minimizing human errors and cost. 
 
Title High-throughput fermentation screening for yeast with real-time monitoring of biomass, pH and dissolved oxygen 
Description The BioLector is a microfermentator able to mimic small bioreactor conditions allowing simultaneously high-throughput fermentation procedures and live monitoring of parameter such as OD, temperature, pH and fluorescence emission. Using this system, we were able to monitor five yeast strains biomass production, pH values and dissolved oxygen in real time throughout the culture duration. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact This method has been develop to increase the service porfolio of the EI DNA Foundry and phenotipically characterise yeast with industrial interest and compare strains for their ability to heterologously express a set of high-value proteins or metabolites. Provided as service at the DNA Foundry Facility 
 
Description CyanoSource : An automated mutant library and synthetic biology resource facility for the model cyanobacterium Synechocystis sp. PCC 6803 
Organisation University of East Anglia
Department School of Biological Sciences UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution Quotation for Grant application to develop CyanoSource, the first mutant library and plasmid resource facility for the model cyanobacterium Synechocystis sp. PCC 6803.
Collaborator Contribution Grant application
Impact Development of new DNA assembly workflow from PCR amplicons at the EI DNA Foundry.
Start Year 2018
 
Description CyanoSource : An automated mutant library and synthetic biology resource facility for the model cyanobacterium Synechocystis sp. PCC 6803 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Quotation for Grant application to develop CyanoSource, the first mutant library and plasmid resource facility for the model cyanobacterium Synechocystis sp. PCC 6803.
Collaborator Contribution Grant application
Impact Development of new DNA assembly workflow from PCR amplicons at the EI DNA Foundry.
Start Year 2018
 
Description Engineering plant responses to environmental nitrogen 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution Contributed epxertise in genome engineering in plants. Contributed to two joint grant proposals.
Collaborator Contribution Contributed expertise on epigenetics and plant nitrogen reponse networks. Contributed to two joint grant proposals.
Impact Two collaborative grant proposals submitted: NSF-BIO, USDA-NIFA and BBSRC joint activity - Early Concept Grants for Exploratory Research (EAGER) - Breakthrough Technologies to Advance Crop Breeding. BBSRC-NSF Lead Agency Opportunity - Synthetic approaches to address fundamental biological questions.
Start Year 2018
 
Description RiceCRIPR" A gene editing platform for crop improvement. 
Organisation Durham University
Department Department of Biosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Quotation for Grant Application to generate a public access genetic resource for improving rice productivity.
Collaborator Contribution Grant application
Impact None yet.
Start Year 2018
 
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
 
Title Leaf LIMS 
Description Leaf LIMS is a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact ongoing 
URL https://leaflims.github.io
 
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 AgriTech East - Pheromones for Insect Pest Control 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Ineractive presentation at Agritech East event to farmers, agronomists and the general public about biomanufacturing of insect sex pheromones for pest control in agriculture. Participants were given a brief presentation on bioproduction on insect pheromones and progressed through a 'fragrant biochemical pathway'. This was followed by small group discussions on new methods for pest control and the uses of biotechnology in agriculture.
Year(s) Of Engagement Activity 2018
 
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 lectures 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 EI DNA Foundry Tour : Nanjing Agricultural University (NAU) delegation 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The developed activity was related to the presentation of the EI DNA Foundry's capabilities to a Nanjing Agricultural University (NAU) delegation. The goal of the event was to promote UK-China collaboration and the establishment of potential pioneering projects.
Year(s) Of Engagement Activity 2019
 
Description Gatsby plant science summer school: engineering plants for farming and pharming 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Presented a lecture and particilaped in a discussion session with undergraduates as part of the Gatsby Plant Science Summer School. The summer school is an opportunity for first year undergraduate students in the UK to discover the challenge and opportunities of studying plant science. 76% of students rated this particular talk as good or very good with some very positive comments such as, 'I realised how much I loved to learn about Synthetic aspect of biology after the talk by Dr Nicola Patron
Year(s) Of Engagement Activity 2018
URL http://intobiology.org.uk/dr-nicola-patron-engineering-plants-for-farming-and-pharming/
 
Description Molecular Training Workshop for African Scientists, University of Cambridge 
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 Lectures deleivered as part of a two week training evint for agricultural research scientists, academics and PhD students from across Africa. This was followed by discussion and follow-up questions by email.
Year(s) Of Engagement Activity 2018
URL http://www.jrbiotekfoundation.org/cambridge-lab-training-2018/
 
Description Newsletter article June 2018: Unleashing the Power of Automation for Plant and Microbial Science 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This short communication about the DNA foundry at the Earlham had as main goal to voice up its capabilities, and inform the plant research community how to interact with us to help with their research.
Year(s) Of Engagement Activity 2018
URL https://www.garnetcommunity.org.uk/newsletters
 
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 and software. This group meets monthly at a variety of local spaces for events including talks, training in the use of technologies and to work on projects.
Year(s) Of Engagement Activity 2017,2018,2019
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 Presentation and discussion at Norwich Science Festival 2018 (Engineering Day) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Presentation on biomanufacturing to general public including interactive activity with biochemical pathways and debate about the meaning of the word 'natural', biological vs chemical manufacturing methods and whether manufacturing can be sustainable.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/building-with-biology/
 
Description Presentation at Automation in Synthetic Biology Workshop, University of Bristol 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk to Introduce the EI DNA Foundry to the UK SynBio community and industry/business attending the workshop.
Year(s) Of Engagement Activity 2018
URL http://www.bristol.ac.uk/brissynbio/events/2018/automation-workshop.html
 
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 The Essex Synthetic Biology School (ESBS), University of Essex, UK : 
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 Presented lectures on "Engineering Plant Genomes for Farming and Pharming" and "Sharing Biology in the Information Age: Perceived Threats of Dematerialisation and Open Data". These were followed by discussions on the use of biotechnologies in agricultures and a debate on access and benefit sharing of genetic resources. Participants reported changes in their views on the common practices used to share information relating to genetic resources as well as physical resources.
Year(s) Of Engagement Activity 2018
URL https://esbs.essex.ac.uk
 
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