Practical Synthetic Biology: Plants, Agriculture and the Environment
Lead Research Organisation:
UNIVERSITY OF CAMBRIDGE
Department Name: Plant Sciences
Abstract
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Technical Summary
Recent technical advances in biology have given rise to a different class of cellfree and transient expression systems that are both cheap to deploy and have huge potential benefit for the provision of a wide variety of diagnostics, sensors, vaccines and research materials. We propose to bring together key UK and African scientists and application specialists to explore the development and deployment of these new systems, which (i) avoid the complications, delays and regulatory uncertainty associated with uncontained of GMOs, while (ii) providing high level, low cost training opportunities and capacity building.
Planned Impact
unavailable
Organisations
Publications
Guzman-Chavez F
(2022)
Constructing Cell-Free Expression Systems for Low-Cost Access.
in ACS synthetic biology
| Description | The grant funded a symposium and knowledge sharing workshop to come up with recommendations for GCRF funding in the area of synthetic biology. Key findings include: 1) The UK and Africa share a common goal with the need to develop improved synthetic biology training in schools, universities, community labs and industry. International efforts to develop open standards and protocols for DNA parts and tools will provide a major impetus for technology transfer to Africa and synthetic biology can provide better solutions for: (i) rapid-response production of vaccines and biologics, (ii) point-of-use diagnostics and field biosensors, (iii) agricultural crop improvement using non-transgenic (genome editing) tools, and (iv) harnessing local biodiversity to build a sustainable bioeconomy. In each of these applications, the development of practical solutions and social impact requires: (i) shared curricula for training and biotechnology education in resource-poor communities and institutes; (ii) building local expertise through exchange and shared knowledge. 2) Cell-free synthetic biology offers an excellent platform for basic and applied research in the African context: These new technologies are relatively low-cost, but their adoption in Africa is limited by deficits in technical training, poor access to new research materials, inadequate laboratory facilities, and lack of strategic partnerships with other African and international research institutions. Since hte workshop, this has led to major research collaborations and a £1.5m EPSRC GCRF grant on low-cost viral diagnostics. 3) We developed recommendations that capacity-building based on open technologies and exchange should be a major component of any funding initiative. This was justified in the workshop report and drew on the increasing availability of legal tools and business models to accompany use of foundational open technologies e.g. the Open Material Transfer Agreement (http://openmta.org). 4) Our priority areas for call topics relating to capacity development include: (i) Teaching and training resources to support fast and frugal innovation in bioengineering in low-resource environments; (ii) Adoption of cell-free expression systems for rapid prototyping; (iii) Transient plant-based expression for production of vaccines and bioeconomy-related biologicals; (iv) Responsible harnessing of plant and microbial biodiversity in synthetic biology; (v) Low-cost and instrument-free diagnostics. |
| Exploitation Route | We anticipate that these finding will inform future research calls from the UK Research Councils and other agencies and that was the intended audience. Our workshop and report led to Cambridge hosting a visit by the Director of Biotechnology at the South African Department of Science and Technology, who was involved in discussions around the ways the South African government could support the recommendations. It has also fed into a report to the UN Global Environment Facility which is under preparation. We continue to distribute the report at meetings such as the OpenPlant Forum and highlight to a range of actors from academia, civil society and industry the opportunities presented in areas such as agriculture, biomanufacturing and diagnostic development. |
| Sectors | Agriculture Food and Drink Education Environment Government Democracy and Justice Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| URL | https://www.openplant.org/global-challenges/ |
| Description | 1) Policy impact: Our workshop and report led to Cambridge hosting a visit by the Director of Biotechnology at the South African Department of Science and Technology, who was involved in discussions around the ways the South African government could support the recommendations. It has also fed into a report to the UN Global Environment Facility which is under preparation. We continue to distribute the report at meetings such as the OpenPlant Forum and highlight to a range of actors from academia, civil society and industry the opportunities presented in areas such as agriculture, biomanufacturing and diagnostic development. The report was distributed to the World Economic Forum Global Future Council on Synthetic Biology by council member and co-author Dr Jenny Molloy. It informed an upcoming WEF report on changing geographies of innovation in synthetic biology which will in turn inform a planned global meeting for synthetic biology strategy during 2022 which will focus on equitable participation of actors and governments from the global South. The downstream impact of use of our findings is unclear at present but it has played a role in shaping relevant conversations at an international level. 2) Education and capacity building: the findings led to the organisation of a workshop to develop an open curriculum for cell-free synthetic biology which took place in Cambridge in July 2017 with southern African representation. We were then awarded a £1.5m EPSRC GCRF grant for low-cost viral diagnostics which included a major educational and capacity building component focused on early career researchers. We ran a successful workshop in South Africa in 2019 but follow up was disrupted by the COVID pandemic. Instead, effort has shifted to building out open educational resources for engineering biosensors for human, animal and environmental health initially with partners in South Africa and now expanded to include Kenya, Ghana, Cameroon, Chile and Ethiopia supported by a BBSRC GCRF STARS award. This 20 module course builds on many of the principles distilled during the Practical Synthetic Biology grant activities around adapting practical teaching for low-resource settings and as such will offer a unique resource for education on synthetic biology in a global context. We expect the resources to be published by the end of 2022 and to reach several hundred students by the end of 2023. |
| Sector | Education,Government, Democracy and Justice |
| Impact Types | Societal Policy & public services |
| Description | Diagnostics, prosthetics and orthotics to tackle health challenges in developing countries |
| Amount | £1,500,000 (GBP) |
| Funding ID | EP/R014000/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2018 |
| End | 02/2021 |
| Description | EPSRC GCRF Diagnostics, Prosthetics and Orthotics |
| Amount | £1,541,002 (GBP) |
| Funding ID | EP/R014000/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2018 |
| End | 02/2021 |
| Description | GCRF Pump-priming Fund |
| Amount | £80,000 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 12/2018 |
| End | 07/2019 |
| Description | Phytoelectronic soil sensing |
| Amount | £818,226 (GBP) |
| Funding ID | NE/T012293/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 11/2024 |
| Description | Shuttleworth Fellowship |
| Amount | $261,000 (USD) |
| Organisation | Shuttleworth Foundation |
| Sector | Charity/Non Profit |
| Country | South Africa |
| Start | 03/2018 |
| End | 03/2019 |
| Description | Synthetic Biology Strategic Research Initiative 2016-2019 |
| Amount | £165,000 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 09/2019 |
| Description | University of Cambridge SRI/SRN Small Grants |
| Amount | £5,000 (GBP) |
| Organisation | University of Cambridge |
| Department | Isaac Newton Trust |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 10/2018 |
| Title | Improved culture systems for the model plant system, Marchantia polymorpha |
| Description | Part of a set of new techniques and materials described in "Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha" by Susanna Sauret-Güeto, Eftychios Frangedakis, Linda Silvestri, Marius Rebmann, Marta Tomaselli, Kasey Markel, Mihails Delmans, Anthony West, Nicola J. Patron, Jim Haseloff. Preprint distributed on BioRxiv, and acceprted for publication at ACS Synthetic Biology. The manuscript describes new techniques and materials useful for low-cost growth of Marchantia plants thoughout the plant's life cycle under sterile conditions. The new approach allows the simple isolation of sterile spores for further transformation work, and a way of producing relatively large amounts of sterile material for bioproducion in the system. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | The technique is becoming widely adopted by other laboratories in the field. |
| URL | https://doi.org/10.1101/2020.02.29.971002 |
| Title | Improved vector system for bioengineering in plants |
| Description | Part of a set of new techniques and materials described in "Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha" by Susanna Sauret-Güeto, Eftychios Frangedakis, Linda Silvestri, Marius Rebmann, Marta Tomaselli, Kasey Markel, Mihails Delmans, Anthony West, Nicola J. Patron, Jim Haseloff. Preprint distributed on BioRxiv, and acceprted for publication at ACS Synthetic Biology. The manuscript describes a new set of plant transformation vectors and DNA partsthat are easier to manipulate, and useful for transformation of nuclear or plastid genomes. |
| Type Of Material | Biological samples |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Wide international distribution of a free vector and DNA parts kit via the OpenMTA, and deposit with Addgene. |
| URL | https://doi.org/10.1101/2020.02.29.971002 |
| Title | Loop Assembly |
| Description | High efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | International distribution of the vector DNAs both directly from teh lab, and through Addgene. |
| Title | Marchantia toolbox |
| Description | Publcation of a collection of 33 open source protocols for culture, handling and genetic manipulation of Marchantia polymorpha, a new model system being developed and improved as part of the OpenPlant initiative. (https://www.protocols.io/workspaces/openplant-project) |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | There are currently around 50 researchers who have subscribed to the protocol-sharing group, and many more informal participants. We are seeing increased numbers of requests for reagents and advice, and interest in Marchantia as a simple model plant system increases. |
| URL | https://www.protocols.io/workspaces/openplant-project |
| Title | Modular DNA tools for reprogramming Marchantia nuclear and chloroplast gene expression |
| Description | Deposited over 120 plasmid vectors at Addgene for distribution, under the OpenMTA, where possible. |
| Type Of Material | Biological samples |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Has facilitated use of Marchantia polymorpha as a new, simple plant model system, cemented the use of standard techniques for gene assembly in this system, and exchange of DNA parts and collaboration. |
| URL | https://www.addgene.org/Jim_Haseloff/ |
| Title | OpenMTA |
| Description | Introduction of a new MTA, the Open Material Transfer Agreement (OpenMTA), that relaxes restrictions on the redistribution and commercial use of biomaterials while maintaining aspects of standard MTAs that support widespread adoption (for example, incorporation into semiautomated administration systems). In developing the OpenMTA, our motivation was to realize a simple, standardized legal tool for sharing biological materials as broadly as possible without undue restrictions, while respecting the rights of creators and promoting safe practices and responsible research. Importantly, we wanted the tool to work within the practical realities of technology transfer and to be sufficiently flexible to accommodate the needs of many groups globally (for example, providing support for international transfers and compatibility with public and philanthropic funding policies). |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | We are seeing increasing adoption of this OpenMTA for public distribution of materials, now adopted by twenty academic reseach institutions, and a similar number of companies. Being adopted by Addgene as a major international partner. |
| URL | https://www.openplant.org/openmta/ |
| Description | Bahir Dar Biomaker Workshop |
| 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 | Biomaker Africa workshops were set up to get non-programmers up and running within a day or two. This is due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.biomaker.org/visiting-workshops |
| Description | Biomaker Challenge |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | The Biomaker Challenge calls on interdisciplinary teams to (i) build low-cost sensors and instruments for biology or (ii) develop some biological resource or outreach project. Over a number of years, the initiative has funded over 175 projects and involved hundreds of participants from a wide range of backgrounds. It has proved a great opportunity to learn new skills, collaborate with an interdisciplinary community and, in a short amount of time, develop tools and resources that are useful for real-world applications. Tools and resources developed during the Biomaker Challenge are openly documented and made freely available. |
| Year(s) Of Engagement Activity | 2017,2018,2019,2020 |
| URL | https://www.biomaker.org/projectindex |
| Description | CDT-Sumitomo online workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | UK-Japan online workshop to discuss advanced research topics and possible translation to applications |
| Year(s) Of Engagement Activity | 2021 |
| Description | Cambridge SynBio Forums |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | The SynBio Forums are sponsored by the University of Cambridge Synthetic Biology Interdisciplinary Research Centre, and feature prominent international speakers and excellent networking opportunities - they provide excellent opportunities to learn more about cutting edge synthetic biology. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019,2020 |
| URL | https://www.synbio.cam.ac.uk/events/forum |
| Description | Cell-free Synthetic Biology workshops |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Recent technical advances in the preparation of microbial cell-free extracts have given rise to a new class of highly efficient systems for gene expression that are cheap to deploy and have huge potential benefit for the provision of a wide variety of diagnostics, sensors, vaccines and research materials. Cell-free synthetic biology is thus a topic of growing interest to many groups in Cambridge and the Synthetic Biology IRC is pleased to share its programme of activities to promote and support interdisciplinary work in this space. |
| Year(s) Of Engagement Activity | 2017,2018,2019,2020 |
| URL | https://www.synbio.cam.ac.uk/initiatives/cell-free-synthetic-biology |
| Description | Invited presentation at CRI, Paris |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited presentation: Open Tools for Engineering Biology |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited presentation at online Hitachi-sponsored workshop in Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | UK-Japan online workshop to discuss advanced research projects and possible industrial translation. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Kumasi Biomaker Workshop |
| 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 | Cambridge Biomaker organisers headed to Ghana to run a two-day workshop at Kumasi Hive, an entrepreneurship and innovation hub and one of the implementing arms of the Biomaker initiative. Twenty participants gathered in Kumasi for an accelerated course in programming hardware for low-cost, open-source bioinstrumentation. Half of the participants had worked with the Biomaker system before, and together with the new participants, further developed their projects by learning to program a customisable touchscreen interface for their existing hardware. The fast-paced, energetic training sessions were broken up by project presentations from the teams, talks from researchers from Cambridge and the nearby Kwame Nkrumah University of Science and Technology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.biomaker.org/news/2019/8/29/biomaker-in-ghana-conversations-from-a-2-day-workshop-with-i... |
| Description | No-code programming online workshop |
| 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 | Organised and delivered an online workshop to provide training for non-programmers in the use of microcontrollers for scientific applications. Distributed standard hardware for the training sessions ahead of the workshop. Dec 8th and 9th 2021. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.biomaker.org |
| Description | No-code programming workshop, University of Veracruz, Mexico |
| 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 | Online workshop, co-sponsored with Prof. Mario Arteaga, University of Veracruz, Mexico - introducing research students to no-code programming for scientific instrumentation. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.biomaker.org |
| Description | Open Technology Week |
| 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 | Open Technology Week showcases and celebrates open source technologies in research and education developed across Cambridge and beyond. This multi-day event includes lectures, demos and workshops that explore examples of open technologies and their implications, featuring projects by Biomaker Challenge teams as well as makers in the community. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019 |
| URL | https://www.synbio.cam.ac.uk/initiatives/Open_Technology_Week/ |
| Description | OpenPlant Working Group on Open Curriculum Development for Cell-Free Synthetic Biology |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | In 2017 an OpenPlant working group was established which focuses on curriculum development and teaching resources for fast and frugal biotechnology, specifically cell-free synthetic biology. The first meeting of the working group took place on Thursday 27 July 2017, after the annual OpenPlant Forum. A range of key stakeholders and influencers were invited, including researchers at the cutting edge of cell-free technology, educationalists and outreach experts. The working group focused on the educational opportunities offered by cell-free systems and freeze-dried components to provide a platform for teaching synthetic biology at low-cost and without use of GMOs. The first meeting lay the groundwork for assembly of open and modular curriculum components that could be combined into different teaching frameworks across multiple disciplines, drawing on existing work from organisations such as BioBuilder, the National Centre for Biotechnology Education, Science and Plants in Schools and the ARM Education Programme. There was a high level of interest in continued activities and plans include: includ |
| Year(s) Of Engagement Activity | 2017 |
| Description | Pretoria Biomaker Workshop |
| 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 | Biomaker Africa workshops were set up to get non-programmers up and running within a day or two. This is due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.biomaker.org/visiting-workshops |
| Description | Xalapa Biomaker Workshop |
| 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 | This Biomaker workshop was run at the University of Veracruz, Xalapa, Mexico, and designed to get non-programmers up and running within a day or two. This was due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.biomaker.org/visiting-workshops |