SynthSys-Mammalian: Edinburgh Mammalian Synthetic Biology Research Centre
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Biological Sciences
Abstract
The vision for Edinburgh's Centre for Mammalian Synthetic Biology (SynthSys-Mammalian) is to pioneer the development of the underpinning tools and technologies needed to implement engineering principles and realise the full potential of synthetic biology in mammalian systems. We have an ambitious plan to build in-house expertise in cell engineering tool generation, whole-cell modelling, computer-assisted design and construction of DNA and high-throughput phenotyping to enable synthetic biology in mammalian systems for multiple applications. In this way we will not only advance basic understanding of mammalian biology but also generate tools and technologies for near-term commercial exploitation in areas such as the pharmaceutical and drug testing industries, biosensing cell lines sensing disease biomarkers for diagnositics, novel therapeutics, production of protein based drugs e.g. antibodies and also programming stem cell development and differentiation for regenerative medicine applications. In parallel we will develop and implement new understanding of the social and economic impact of this far-reaching technology to ensure its benefits to society.
Technical Summary
Synthetic biology (SB) is defined in the UK Synthetic Biology Roadmap1 as 'the design and engineering of biologically based parts, novel devices and systems as well as the re-design of existing natural biological systems.' SB is both a platform technology and a translational technology (providing the link between a wide range of underpinning disciplines - ranging from biochemistry to systems biology - and practical applications in a wide range of different market sectors). We aim to pioneer the development of the underpinning tools and technologies needed to implement engineering principles and realise the full potential of synthetic biology in mammalian systems. We will 1. Establish a robust pipeline for the production and screening of synthetic transcription factors (sTFs) and synthetic chromatin editors (sCEs) based on the DNA binding domains of TAL effectors (TALEs) and the CRISPR/Cas system fused to transcriptional activators, repressors or chromatin modifiers e.g. histone deacetylases. 2. Create an in silico tool for designing small-molecule control of engineered protein and demonstrate the utility of this tool by producing novel drug-controlled proteins. 3. Assemble synthetic chromosomes and chromosomal safe harbors for introduction of synthetic genetic circuits. 4. Reduce contextual effects by building predictive models through characterizing circuit-chassis interactions at the single-cell level. 5.Engineer memory and computation synthetic genetic circuits in mammalian cells to a) deliver mechanistic information on the cell state, and responses to perturbations, e.g. drug treatments and count cell divisions. Underpinning this will be the development of standards for mammalian synthetic biology in collaboration with our partners NPL and take the concept of RRI in new directions to include: the politics of standardisation; the use of strategic mapping methodologies; and new approaches to engagement informed by speculative design.
Planned Impact
The SBRC focuses on building mammalian engineering capacity to benefit the life sciences, biotechnology and biomedicine.
Our deliverables for engaging with stakeholders are:
1) Through community building we will increase membership of the SBRC and double our total collaborative research income by Year 5. We will reach out locally by continuing Open Centre Meetings (fortnightly), organise monthly PI lunches preceded by a PI seminar, record seminars and both live webcast and disseminate online, hold an annual Away Day, publish a monthly newsletter, and further explore novel ways of engagement.
2) To be an internationally recognised brand with a reputation as a centre of excellence in synthetic bioengineering of mammalian systems. To do so, we will strengthen links to local networks for national phenotyping and regenerative medicine, champion the iGEM competition, continue to be active participants in three RCUK networks, link with other SBRCs and DNA Synthesis Centres, build additional international links (particularly in China, Korea, and Hong Kong), and work to host the meeting for the international synthetic yeast genome project and SynBioBeta.
3) By Year 5, we will have created an innovation environment for synthetic biology that balances the objectives and concerns of public, industry, policy, and academic communities. We will set up a Stakeholder Forum with members from industry, policy makers, regulators, and investors; maintain high visibility at Science Festivals; deepen our involvement in art-in-science events; host a writer in residence to help communicate our research; continue to make best use of the University's Press Gangs and Officers; maintain a dynamic suite of websites, have a Twitter account, and all researchers will create and promote "Research in a Nutshell" BioPodcasts; arrange 6-monthly, off-site, SynthSys Cafes to foster engagement and build dialogue; raise the profile of our activity across government through invitations to MSPs, Chief Scientists and NGOs; and maintain and grow international influence through our membership of government leadership committees. We will create a community of activity around the SBRC with at least two industrial SBRC members participating in training activities and in reciprocal secondment of staff.
A further key impact will be to generate highly skilled, responsible, and enthusiastic scientists and engineers that will move into research, management, or operational roles in private and public sectors, building the UK's capacity in synthetic biology.
We anticipate the generation of considerable intellectual property (IP) of commercial value. We will draw on Edinburgh Research and Innovation Business Development Executive, our International Advisory Board, our industrial partners, and the strength of our broader industrial network to expedite the translation of IP. We are a key partner of the Synthetic Biology Innovation Commercial and Industrial Translation Engine (SynbiCITE) and are heavily involved in both the Scottish Industrial Biotechnology Innovation Centre and the CENSIS Innovation Centre in Sensor and Imaging Systems. We will target new market sectors by developing marketing materials tailored to specific industries, holding an annual Industry Information Day to consolidate and broaden our links, and by developing an industry-engagement plan to meet industry through site visits, missions overseas and industry partnering events. By year 5, we plan three innovations in early stages of product development and to be in advanced discussion with 3-4 industry partners around R&D collaborations.
Finally, in addition to academic impacts through refereed journals and presentations at international conferences, SBRC outputs will be published in industry and policy journals, talks at national and international festivals, in media presentations, and through a portfolio of policy briefing notes that are widely distributed.
Our deliverables for engaging with stakeholders are:
1) Through community building we will increase membership of the SBRC and double our total collaborative research income by Year 5. We will reach out locally by continuing Open Centre Meetings (fortnightly), organise monthly PI lunches preceded by a PI seminar, record seminars and both live webcast and disseminate online, hold an annual Away Day, publish a monthly newsletter, and further explore novel ways of engagement.
2) To be an internationally recognised brand with a reputation as a centre of excellence in synthetic bioengineering of mammalian systems. To do so, we will strengthen links to local networks for national phenotyping and regenerative medicine, champion the iGEM competition, continue to be active participants in three RCUK networks, link with other SBRCs and DNA Synthesis Centres, build additional international links (particularly in China, Korea, and Hong Kong), and work to host the meeting for the international synthetic yeast genome project and SynBioBeta.
3) By Year 5, we will have created an innovation environment for synthetic biology that balances the objectives and concerns of public, industry, policy, and academic communities. We will set up a Stakeholder Forum with members from industry, policy makers, regulators, and investors; maintain high visibility at Science Festivals; deepen our involvement in art-in-science events; host a writer in residence to help communicate our research; continue to make best use of the University's Press Gangs and Officers; maintain a dynamic suite of websites, have a Twitter account, and all researchers will create and promote "Research in a Nutshell" BioPodcasts; arrange 6-monthly, off-site, SynthSys Cafes to foster engagement and build dialogue; raise the profile of our activity across government through invitations to MSPs, Chief Scientists and NGOs; and maintain and grow international influence through our membership of government leadership committees. We will create a community of activity around the SBRC with at least two industrial SBRC members participating in training activities and in reciprocal secondment of staff.
A further key impact will be to generate highly skilled, responsible, and enthusiastic scientists and engineers that will move into research, management, or operational roles in private and public sectors, building the UK's capacity in synthetic biology.
We anticipate the generation of considerable intellectual property (IP) of commercial value. We will draw on Edinburgh Research and Innovation Business Development Executive, our International Advisory Board, our industrial partners, and the strength of our broader industrial network to expedite the translation of IP. We are a key partner of the Synthetic Biology Innovation Commercial and Industrial Translation Engine (SynbiCITE) and are heavily involved in both the Scottish Industrial Biotechnology Innovation Centre and the CENSIS Innovation Centre in Sensor and Imaging Systems. We will target new market sectors by developing marketing materials tailored to specific industries, holding an annual Industry Information Day to consolidate and broaden our links, and by developing an industry-engagement plan to meet industry through site visits, missions overseas and industry partnering events. By year 5, we plan three innovations in early stages of product development and to be in advanced discussion with 3-4 industry partners around R&D collaborations.
Finally, in addition to academic impacts through refereed journals and presentations at international conferences, SBRC outputs will be published in industry and policy journals, talks at national and international festivals, in media presentations, and through a portfolio of policy briefing notes that are widely distributed.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Medical Research Council (Co-funder)
- Engineering and Physical Sciences Research Council (Co-funder)
- The Research Council of Norway (Collaboration)
- Macquarie University (Collaboration)
- Integrated DNA Technologies (Collaboration)
- Utrecht University (Collaboration)
- Oregon Health and Science University (Collaboration)
- International Gene Synthesis Consortium (Collaboration)
- Twist Bioscience (Collaboration)
- John Innes Centre (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- Cellinta (Collaboration)
- University of Manchester (Collaboration)
- Royal Netherlands Academy of Arts and Sciences (Collaboration)
- Hebrew University of Jerusalem (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- OGI Bio Ltd (Collaboration)
- Johnson & Johnson (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Kazusa DNA Research Institute (Collaboration)
- Leonardo (United Kingdom) (Project Partner)
- Charles River Laboratories (United Kingdom) (Project Partner)
- Autodesk (United States) (Project Partner)
- Defence Science and Technology Laboratory (Project Partner)
- National Physical Laboratory (Project Partner)
- Thermo Fisher Scientific (United Kingdom) (Project Partner)
- Roslin Cells (United Kingdom) (Project Partner)
Publications
Baaske J
(2018)
Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells.
in Scientific reports
Balmer A
(2016)
Five rules of thumb for post-ELSI interdisciplinary collaborations
in Journal of Responsible Innovation
Balmer, A
(2015)
Taking Roles in Interdisciplinary Collaborations: Reflections on working in Post-ELSI Spaces in the UK Synthetic Biology Community
in Science and Technology Studies
Banda G
(2019)
Understanding the emergence and evolution of new business models in the UK regenerative medicine sector
in Technology Analysis & Strategic Management
Banda G
(2018)
Evolution of Business Models in Regenerative Medicine: Effects of a Disruptive Innovation on the Innovation Ecosystem.
in Clinical therapeutics
Banda G
(2019)
Regenerative medicine as a disruptive technology: implications for manufacturing & clinical adoption
in Cell and Gene Therapy Insights
Bates M
(2017)
Genetic Constructor: An Online DNA Design Platform.
in ACS synthetic biology
Bhaskar H
(2023)
Live-cell super-resolution imaging of actin using LifeAct -14 with a PAINT -based approach
in Protein Science
Blake SM
(2016)
Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation.
in eLife
Boeke JD
(2016)
GENOME ENGINEERING. The Genome Project-Write.
in Science (New York, N.Y.)
| Title | Crossing Kingdoms online exhibition |
| Description | The collaborative project 'Crossing Kingdoms', which involves Jane Calvert, Robert Smith, Elise Cachat and Susan Rosser from the UK Centre for Mammalian Synthetic Biology and the biological artists Ionat Zurr, Oron Catts and Tarsh Bates from the University of Western Australia, is part of an online exhibition called 'Arts Work in the Age of Biotechnology', hosted by the University of Pittsburgh, USA. |
| Type Of Art | Artistic/Creative Exhibition |
| Year Produced | 2021 |
| Impact | N/A |
| URL | https://www.artsworkintheageofbiotechnology.org/crossing-kingdoms/ |
| Description | The UK Centre for Mammalian Synthetic Biology (the 'CMSB'), hosted by the University of Edinburgh, has had a very productive year in working towards its goals for research, training, public engagement and translation. We have made excellent progress in Work Package 1 (Tools and Platform Technologies) with noteworthy success in generating libraries of synthetic transcription factors, which we are now deploying in later work packages. We are particularly excited about early evidence that cocktails of synthetic transcription factors can control stem cell differentiation as we had anticipated. These will enable us to accelerate Work Packages 3, 5 and 6 (Biotech and Medical Applications). The construction of novel genetic circuits in cells allows us to fine tune cell behaviour, of particular interest to biologics manufacturers keen to boost yield. Small molecule control of genetic circuits offers another level of sophistication for cell and tissue engineering, through drug controlled cell patterning. Progress in our research has been evidenced by an increase in publications: Currently 126. We welcomed our second cohort of six PhD students this year. The last of the covid delayed PhD cohort are writing up their thesis having benefited from bespoke training in presentation skills, team work, using social media, and working with industry. Our first Modern Apprentice completed his apprenticeship and we promoted him to Lab Technician in the Genome Foundry. Centre staff engaged actively with industry over the duration of award hosting ~90 company visits and having discussions with many more at events and conferences. This has led to numerous commercial collaborations of all sizes - from PhD sponsorship, to fee-for-service work, to exciting R&D projects. We have secured relationships with: Twist BioScience, AstraZeneca, GSK, UCB Pharma, Ingenza, Horizon Discovery, Sphere Fluidics, Agilent, FujiFilm Diosynth Biotechnology (FDBK), Synpromics (now AskBio), Thermo Scientific, Unilever, Sartorius and Berkeley Lights. We. We are exploring additional opportunities to leverage Government funding for working with industry and are exploring how to protect and exploit intellectual property arising from Work Package 1. We received an Innovate UK award for ~£1M in a joint project with Horizon Discovery and Sphere Fluidics to develop a new benchtop microfluidics system for genome and epigenome engineering. Early adopters of mammalian engineered biology are companies working in biomanufacturing. This led to a strategic partnership with FDBK to create a 'Centre of Excellence in Bioprocessing 2.0 (CEB2.0)' in partnership with the Universities of Manchester and York. FDBK committed £2m towards initial pump priming of projects and this has led to securing an EPSRC Prosperity Partnership (~£7m) to explore engineering CHO to meet the needs of modern biologics manufacturing. We continue to support a variety of outreach activities including a second SAW Trust training day (reaching over 200 school pupils across Edinburgh), the Edinburgh Science Festival and University 'Doors Open' events. We have developed strategic working relationships with Science Teachers across Scotland, developing a classroom activity aimed at Scottish Higher Biology students: in this way, we can 'train the trainers' and reach more pupils. We hired an artist-in-residence to help us devise a longer-term strategy for engagement, which will encourage more sustainable engagement with the public engagement agenda. Policy and strategy development for synthetic biology are also core to our activities: The Centre's management team are active participants in Scotland's Synthetic Biology Special Interest Group, the Industrial Biotechnology Leadership Group; the Scottish Scientific Advisory Council (SSAC), the Royal Society of Biology's Genome Editing Advisory Group; the Synthetic Biology Leadership Council. The Centre's management team and staff continue to work hard to raise the profile of our work both in the UK and internationally. We established many international links and secured informal agreements in Singapore (National University of Singapore), South Korea (Intelligent Synthetic Biology Centre), China (Tianjin, BGI). Our staff have active collaborations with Harvard University, MIT and Kyoto Uni. Staff are supporting Africa's first synthetic biology centre in Uganda. We attended research and industry conferences over the years including the Mammalian Synthetic Biology workshop (Boston and Chicago), Synthetic Biology: Engineering, Evolution & Design (SEED, Boston), SB7.0 (Singapore), IBioIC Annual Conference (Glasgow), SynBioBeta (London and San Francisco). We welcomed visitors from China, Japan, North and East Africa, and representatives from the US Office for Naval Research. We are hosting the international Mammalian Synthetic Biology Workshop in July 2022, the first time it has been held outside the US. The data manager position that was initially funded by UK CMSB and its extension funding has grown into the Bio_RDM team (Biological Research Data Management) supervised by CMSB co-I Professor Andrew Millar, as noted in previous reports. Bio_RDM supports bioscience research groups in the School of Biological Sciences and some biomedical researchers in the College of Medicine and Veterinary Medicine at the University of Edinburgh, with training, expert advice on data management including FAIR and Open practices, data management plans, a specialist data curation service, and capabilities for the management and development of data storage systems (example in Zielinski et al., Synthetic Biology 2022). Discussion of a partnership to take over this provision is ongoing between the School and the University Information Services group: if successful, this will be a long-term, strategic contribution from CMSB to the University's research environment. The team received follow-on funding to deliver 'FAIR in practice' courses to researchers as part of the UKRI-MRC Ed-DaSH award (2021-2023; PI Alison Meynert, MVM; total award £300k), and from Scottish Government (2021-2022; PI Nick Gilbert, MVM; total award £350k), to curate data and protocols from the national programme monitoring Covid-19 in wastewater (see resources linked from https://github.com/BioRDM/COVID-Wastewater-Scotland). [[internal note - Andrew Millar is not a co-I but a researcher on these two awards, so the links are not easy to track on PURE or ResearchFish]]. |
| Exploitation Route | Our first patent - of a rapid and cheap method for the production of synthetic transcription factors, the so-called STAR method - is filed and currently under licensing negotiations. One commercial collaboration (with IDT) for a multiplexing technology is under discussion. We have 2 further patents in the process of being filed one on geneomic hotspots for gene integration into CHO genomes and a secodn on a novel RNA Polymerase. To date we have had conversations with over 40 companies of which several have developed into potential projects. Of those, we have commercial collaborations in place with Sphere Fluidics and Horizon Discovery (Pollard), UCB (Rosser), Unilever (Rosser), Fujifilm (Rosser), Twist Bioscience (Cai/EGF). One are of interest is the application of the synthetic biology tools for bioproduction (e.g. biologics in CHO cells). We have secured a strategic relationship with Fujifilm as a partner in a new Centre for Bioprocessing 2.0 on the strength of their interest our research in mammalian synbio resulting in an EPSRC funded prosperity partnership. The Director has acted as an expert consultant producing reports for investment companies interested in investing in synthetic biology companies. As well as proactively engaging with industry, we also work towards helping scope policy around how to further develop the economic potential of synthetic biology. Prof Joyce Tait is a member of a number of influential UK committees, including the Prime Minister's Council for Science and Technology and the Synthetic Biology Leadership Council (SBLC) and the centre director is a member of the SBLC science and technology sub group and we have contributed extensively to the UK synthetic biology roadmaps. On a more local level have worked closely with the Scottish Synthetic Biology Special Interest Group, to develop a framework for boosting synthetic biology business in Scotland. |
| Sectors | Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | http://www.synbio.ed.ac.uk |
| Description | Research This Centre funding enabled us to us to employ 48 researchers and has made our centre one of the largest communities of mammalian synthetic biology research globally. To date, Centre staff published a total of 126 papers, articles, policy documents, features and books/chapters, with many more in preparation. Our research has been published in high impact journals including Nature Biotechnology, Nature Cell Biology Nucleic Acids Research, Nature Communications, European Journal of Neuroscience, ACS Synthetic Biology, and PNAS reflecting the pioneering nature of our research. This activity is also reflected in our ability to win new research funding: Centre PIs and staff have participated in leveraging ~£59M in new funding of which ~£27M was with industry/investors enabling the progression and development of many staff on to new projects in the mammalian engineering biology area and recruitment of new expertise. Industry, Innovation and Enterprise We filed 3 patents and founded three start-up companies: OGI Bio Ltd (making bioreactors affordable for biotechnology), Cellinta (gene therapy for glioblastoma) and Concinnity Genetics (RNA devices for control of gene therapy). One other start-up company - Aptalink (novel RNA production and therapeutics) - is in development. Our new spin outs alongside local companies (e.g. AskBio, TC Biopharma and Roslin Cells) together with the recent arrival of the Cell and Gene Therapy Catapult (CGTC) and on-going expansion of regenerative medicine and repair (a strategic priority across the University), provides a vibrant and exciting local commercial ecosystem that will underpin future mammalian engineering biology. Our gene therapy patent has been licensed and the technology is going into phas1 clinical trials in late 2023. Centre staff engaged actively with industry over the duration of award hosting ~100 company visits and having discussions with many more at events and conferences. This has led to numerous commercial collaborations of all sizes - from PhD sponsorship, to fee-for-service work, to large exciting R&D projects. We have secured relationships with: Fujifilm Diosynth Biotechnologies UK, AskBio, Ingenza, UCB, GSK, Sartorius, DGS Antibodies, Eyam Therapeutics, Aspen Neuroscience, Foresee Pharmaceuticals, Sphere Fluidics, Twist, Thermo Scientific and Berkeley Lights. Early adopters of mammalian engineered biology are companies working in biomanufacturing. This led to a strategic partnership with FDBK to create a 'Centre of Excellence in Bioprocessing 2.0 (CEB2.0)' in partnership with the Universities of Manchester and York. FDBK committed £2m towards initial pump priming of projects and this has led to securing an EPSRC Prosperity Partnership (~£8.7m) to explore engineering CHO to meet the needs of modern biologics manufacturing. Specialist Research Support Our Edinburgh Genome Foundry is the world's largest automated genome assembly platform and has capacity for very high throughput DNA assembly (~2,000 constructs/week) and the capability to perform high throughput transformation, selection and screening of engineered cells. The EGF's recent acquisition a £2M Berkeley Lights Beacon System for high throughput cell phenotyping and selection of individual cells funded by the BBSRC gives it unique extremely powerful engineering biology capabilities. In addition to the EGF continues to pioneer the development of high quality, open-source software for computer-aided design and manufacturing to support operators in daily operations and eventually fully automate our synthetic biology workflows. The EGF has published 62 software projects on Github with increasing visibility and recognition internationally (more than 1500 stars). The EGF's DNA Chisel, a DNA sequence optimizer software, is used by the Benchling bioinformatics platform, which has tens of thousands of users. The EGF is actively participating in the Global BioFoundry Alliance (GBA) with a particular focus on Software Group projects. The creation of a biological data management team (so-called Bio_RDM) has transformed our ways of working and provides a long lasting legacy for the future of biological research at Edinburgh. Bio_RDM was one of the examples of UK-wide best practice that underpinned the UKRI-BBSRC's Review of Data-Intensive Bioscience. The Bio_RDM team has leveraged more than double its original Centre funding, from the Wellcome Trust, UKRI-MRC and Scottish Government. Internationalisation We established many international collaborations with >30 institutions globally and secured informal agreements in Singapore (National University of Singapore), South Korea (Intelligent Synthetic Biology Centre), China (Tianjin, BGI). Our staff have active collaborations with collaborators in Europe such as the €5M (£4.21M) international collaboration being funded by an EU IMI call (CyGenTiG) designing novel culture hardware (Davies Co-I) and with colleagues in the US and Japan £860K SBE-UKRI 'Future Organisms: Synthetic Genomics and Responsible Research and Innovation in the UK, the USA and Japan' (Calvert PI). In addition, staff are supporting Africa's first synthetic biology centre in Uganda. Training the Next Generation Over the Centre's duration, we have employed 48 people (24 postdocs, 20 technical, 4 administrative/management) and trained 11 PhD students (with an additional 26 PhD students accessing Centre training programmes). Most of our fixed-term contract staff have moved on into new posts in academia or industry or continue to be supported through new grant and/or University-supported roles. We provide over 20 days of bespoke training to support personal and professional development of our early career researchers. Policy Staff have had a significant input into policy throughout the duration of the Centre. Of particular note is Joyce Tait's work with the British Standards Institution (BSI), investigating how the governance of innovative technologies, particularly in the life sciences, could be made more proportionate and adaptive to the needs of 21st century technologies. The report, Proportionate and Adaptive governance of Innovative Technologies (PAGIT), was influential in Joyce Tait's appointment to the Prime Minister's Council for Science and Technology (CST), leading to the White Paper Regulation for the Fourth Industrial Revolution and subsequently to her membership of the Regulatory Horizons Council (RHC). The BSI Responsible Innovation Guide (PAS 440) was downloaded more than 1,000 times, a record across all standards ever produced by BSI. Community Engagement We have >3,300 followers on Twitter now (from 300 at the start) and send our monthly newsletter to ~140 people. Over the 7 years of our award we have hosted 2 formal launch events, 12 major external conferences or workshops (e.g. SynBioBeta Activate events, Sc2.0, SBUK, ONR - Future Trends in SynBio), >100 'Open Centre Meetings' and hosted 149 external speakers. Our management staff alone have attended over 70 events to disseminate information about our Centre. Our public engagement activities have reached ~3,000 people (school children, carers, young adults) through various events across Edinburgh and The Lothians. We have contributed to: 'Biopolis: Tales of Urban Biology' - short stories written by professional writers in partnership with some of our scientists; a compilation of short stories ('Tales for a New Age') written by our researchers; a series of podcasts on our research; and established an Edinburgh branch of Café Synthetique. |
| First Year Of Impact | 2022 |
| Sector | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural,Economic,Policy & public services |
| Description | Contribution to the Parliamentary Office for Science and Technology POST-Note on Environmental Principles |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| Description | Development of Agenda for Responsible Research & Innovation in ERA CoBioTech (Smith and Calvert) |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | The development of an Agenda for Responsible Research & Innovation (RRI) involved holding sessions with an international consortium of 25 different research funders across Europe (members of the European Research Area Co-fund on Biotechnologies) to advise them on integrating RRI into their funding programmes. |
| Description | European Seminar Series for Biotechnology & Society |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Robert Smith co-convened the European Seminar Series for Biotechnology & Society with the ERA-NET CoFund on Biotechnology from Sept-Nov 2020. Over 60 people from across the world attended the online seminars that ran from September - November 2020. |
| URL | https://international.fnr.de/eu-activities/european-projects/european-biotechnology-and-society-onli... |
| Description | Member and Chair of Governance Subgroup, Synthetic Biology Leadership Council, UK Government Department for Business, Energy, Innovation and Skills (BEIS) |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | UK synbio activities in the last decade were summarised in a report published by the The Synthetic Biology Leadership Council (SBLC) in 2019 and include: - over £300m of public funding has been invested into synthetic biology research and capability in the UK. - six Synthetic Biology Research Centres (SBRCs) and five DNA synthesis facilities have been established. - centres for doctoral training and a dedicated Innovation and Knowledge Centre (IKC) ensure the education and maintenance of a skilled synbio research base. - the UK has a strategic plan for synthetic biology to translate synbio opportunities into commercial outcomes. - over 150 start-up and spin out synbio companies have been founded. - a synbio community and network through KTN's Synbio SIG have been established. The SBLC's report also highlights Joyce Tait's work on Proportionate and Adaptive Governance of Innovative Technologies (PAGIT). This has contributed significantly to the UK Government's programme on Reforming the Governance of Technological Innovation, which will support a smarter approach to regulating the products of gene editing and synthetic biology. |
| URL | https://admin.ktn-uk.co.uk/app/uploads/2019/07/Synthetic-Biology-UK-A-decade-of-Rapid-Progress.pdf |
| Description | Member of Genome Project Write Ethics, Society and Policy Advisory Panel (Robert Smith) |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Member, Life Sciences Scotland Triple A (Animal Health, Aquaculture and Agribusiness) Subgroup, Life Sciences Scotland |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The Triple-A sub-sector (Animal Bioscience, Agritech and Aquaculture) is a key player in the delivery of the Life Sciences strategy in Scotland, which aims to reach a £8 billion turnover target for the life sciences sector by 2025. By bringing private sector partners together with key academic, research and enterprise bodies, the Triple-A sub-sector is contributing to create jobs and wealth for Scotland, and benefit the global community. |
| URL | https://www.scotsman.com/news/environment/how-triple-life-sciences-sub-sector-maturing-it-pushes-gro... |
| Description | Member, Prime Minister's Council for Science and Technology |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | As a member of the UK's Council for Science and Technology, Innogen Institute co-director Joyce Tait contributed to a letter to the Prime Minister on how to make the UK regulatory landscape more favourable to innovation: https://www.gov.uk/government/publications/reforming-the-governance-of-technological-innovation and to the subsequent development of the White Paper on Regulation for the Fourth Industrial Revolution published in June 2019. This white paper sets out the UK's plan to maintain a stable, proportionate regulatory approach in a period of rapid technological change that supports and stimulates new products, services and business models, with greater space for experimentation. |
| URL | https://www.gov.uk/government/publications/regulation-for-the-fourth-industrial-revolution/regulatio... |
| Description | Member, UKRI/BBSRC Transforming Food Production Advisory Group |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| URL | https://www.ukri.org/innovation/industrial-strategy-challenge-fund/transforming-food-production/ |
| Description | Oral evidence on behalf of the Royal Society of Edinburgh to House of Lords Science and Technology Committee Inquiry on Life Sciences and Industrial Strategy |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | A novel automated, aerated and affordable bioreactor technology |
| Amount | £12,253 (GBP) |
| Funding ID | BB/T003979/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 09/2019 |
| Description | BBSRC IAA |
| Amount | £19,520 (GBP) |
| Funding ID | BBSRC IAA PIII-038 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 01/2020 |
| Description | Bacterial Flagellar motor as a fast synthetic biosensor |
| Amount | $390,616 (USD) |
| Organisation | ONRG Office of Naval Research Global |
| Sector | Public |
| Country | United States |
| Start | 03/2018 |
| End | 03/2021 |
| Description | Developing an assay to measure neuron-to-neuron spread of alpha-synuclein on a microfluidcs platform |
| Amount | £164,603 (GBP) |
| Funding ID | BIOSCIE2009 |
| Organisation | UCB Pharma |
| Sector | Private |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2020 |
| Description | Development of a Publicly Available Standard (PAS) for Responsible Innovation |
| Amount | £21,000 (GBP) |
| Organisation | British Standards Institute (BSI Group) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 04/2020 |
| Description | EPSRC IAA |
| Amount | £55,360 (GBP) |
| Funding ID | EPSRC IAA PIII065 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2019 |
| End | 12/2020 |
| Description | ESRC Impact Acceleration Grant: Building Capacity for Responsible Innovation in International Biotechnology Policy Organisations |
| Amount | £18,012 (GBP) |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 08/2020 |
| Description | ESRC-AHRC UK-Japan SSH Connections grants |
| Amount | £32,449 (GBP) |
| Funding ID | ES/S013601/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 06/2020 |
| Description | Early Detection Committee - CRUK-OHSU Project Award |
| Amount | £250,000 (GBP) |
| Funding ID | C65925/A26986 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 12/2021 |
| Description | Extending the analytical capability of affordable Microbioreactors |
| Amount | £14,900 (GBP) |
| Funding ID | FF-2020-12 |
| Organisation | IBioIC |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 03/2021 |
| Description | FET |
| Amount | € 5,000,000 (EUR) |
| Funding ID | CyGenTiG |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 10/2018 |
| End | 09/2023 |
| Description | Flexible Talent and Mobility Account |
| Amount | £280,000 (GBP) |
| Funding ID | BB/S508007/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2018 |
| End | 03/2021 |
| Description | IBioIC BBSRC CASE scholarship |
| Amount | £136,450 (GBP) |
| Organisation | IBioIC |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2020 |
| End | 09/2024 |
| Description | Industrial Biotechnology Catalyst - Translation |
| Amount | £3,200,000 (GBP) |
| Funding ID | BB/M018229/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2015 |
| End | 06/2020 |
| Description | Innovate UK Open Competition |
| Amount | £999,381 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 06/2020 |
| Description | Keck Futures Initiatives |
| Amount | $100,000 (USD) |
| Organisation | W M Keck Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 06/2015 |
| End | 06/2017 |
| Description | MRC Edinburgh Cellular Genomics Consortium (eCGC) pump-priming award |
| Amount | £15,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2019 |
| Description | Molecular control of DNA replication timing in mammalian cells |
| Amount | € 2,000,000 (EUR) |
| Funding ID | ERC Grant number: 726130 |
| Organisation | European Research Council (ERC) |
| Sector | Public |
| Country | Belgium |
| Start | 10/2017 |
| End | 09/2022 |
| Description | Non-invasive monitoring of human pluripotent stem cell differentiation into midbrain dopaminergic neural cells |
| Amount | £633,615 (GBP) |
| Funding ID | MR/V00560X/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2023 |
| Description | Non-invasive monitoring of human pluripotent stem cell differentiation into midbrain dopaminergic neural cells |
| Amount | £779,597 (GBP) |
| Funding ID | MR/V00560X/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2020 |
| End | 09/2023 |
| Description | Open and healthy research cultures: bringing insights into policy and practice |
| Amount | £95,306 (GBP) |
| Funding ID | ES/W00688X/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2022 |
| Description | Optimisation of CHO for Biotherapeutic Manufacture |
| Amount | £3,608,961 (GBP) |
| Funding ID | EP/V038095/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2026 |
| Description | RAEng Chair in Emerging Technologies |
| Amount | £1,300,000 (GBP) |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2028 |
| Description | Royal Society of Edinburgh Enterprise Fellowship Cohort 17 |
| Amount | £59,232 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 03/2021 |
| Description | SBE-UKRI: Future Organisms: Synthetic Genomics and Responsible Research and Innovation in the UK, the USA and Japan |
| Amount | £512,571 (GBP) |
| Funding ID | ES/V002600/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2021 |
| End | 06/2024 |
| Description | SynCrop: Synthetic circuits for robust orthogonal production |
| Amount | £3,300,000 (GBP) |
| Funding ID | 764591 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 08/2018 |
| End | 08/2022 |
| Description | UCB studentship: A combined omics and synthetic biology approach to enhanced CHO cell engineering' |
| Amount | £2,334 (GBP) |
| Organisation | UCB Pharma |
| Sector | Private |
| Country | United Kingdom |
| Start | 10/2018 |
| End | 09/2021 |
| Description | University of Edinburgh ROSSER UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts |
| Amount | £100,000 (GBP) |
| Funding ID | BB/R506606/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 03/2019 |
| Description | University of Western Australia Research Collaboration Award |
| Amount | £13,640 (GBP) |
| Organisation | University of Western Australia |
| Sector | Academic/University |
| Country | Australia |
| Start | 01/2018 |
| End | 12/2018 |
| Description | iCURE follow on fund application (OGI Follow on fund application) |
| Amount | £249,763 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2020 |
| End | 09/2021 |
| Description | iCURe cohort C |
| Amount | £35,496 (GBP) |
| Funding ID | I-C-08 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 10/2019 |
| Title | A degron controlled synthetic transcription factors have been developed |
| Description | The nuclease-deactivated variant of CRISPR-Cas9 proteins (dCas9) fused to heterologous transactivation domains can act as a potent guide RNA sequence-directed inducer or repressor of gene expression in mammalian cells. In such a system the long-term presence of a stable dCas9 effector can be a draw-back precluding the ability to switch rapidly between repressed and activated target gene expression states, imposing a static environment on the synthetic regulatory circuits in the cell. To address this issue we have generated a toolkit of conditionally degradable or stabilisable orthologous dCas9 or Cpf1 effector proteins, thus opening options for multidimensional control of functional activities through combinations of orthogonal, drug-tunable artificial transcription factors. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | None yet it has only recently been developed and published. |
| URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662744/ |
| Title | A prototype microbiorector device |
| Description | We developed an affordable prototype microbioreactor that can automate day-to-day bacterial growth and can be widely applicable. The prototype that can operate in the batch culture and turbidostat mode, is based on significantly adapting existing microbioreactor technology, making it more user-friendly and engineering it to an off-the-shelf level, while keeping the costs down. In comparisons to current bioreactors on the market, it is an order of magnitude cheaper and we envision it can replace manual flask-based culture growth. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | We are currently in the process of spinning out a company that will place the prototype based minimal viable product on the market. |
| Title | Alpha-synuclein knock-out human embryonic stem cells |
| Description | We used CRISPR/Cas9 to knock-out the Parkinson's-related gene, alpha-synuclein (aSyn), in RC17 human embryonic stem cells. We generated a number of cell lines that are aSyn-null and confirmed thet are protein-null by western blotting. We have published the lines in the following paper: Chen Y, Dolt KS, Kriek M, Baker T, Downey P, Drummond NJ, Canham MA, Natalwala A, Rosser S, Kunath T. Engineering synucleinopathy-resistant human dopaminergic neurons by CRISPR-mediated deletion of the SNCA gene. Eur J Neurosci. 2019 Feb;49(4):510-524. doi: 10.1111/ejn.14286. |
| Type Of Material | Cell line |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | These lines have so far been shared with Dr David Beckham at UC Denver under MTA for a collarative project, and Dr Malin Parmar at Lund University. |
| URL | https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14286 |
| Title | Cell lines - human neural stem cells and glioma stem cells |
| Description | Patient-derived primary cell lines from glioma tumour specimens. Also, human foetal neural stem cell lines. Plus engineered derivatives of these. |
| Type Of Material | Cell line |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | These cell lines provide state of the art models to explore neural stem cell biology, neural development, gliomagenesis and can be directly used in drug discovery efforts. |
| Title | Drug control of CRISPR |
| Description | A modification of CRISPR effectors so that they do nothing until an activating drug (tamoxifen or RU486, depending on which construct is used) is applied to cells. At that point CRISPR is activated strongly. This is both a reaerach took and has potnetial in biosafety (emergency inactivation on transgenes). |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | None yet (too recent) |
| Title | Glycosylase base editors enable C-to-A and C-to-G base changes |
| Description | Current base editors (BEs) catalyze only base transitions (C to T and A to G) and cannot produce base transversions. Here we present BEs that cause C-to-A transversions in Escherichia coli and C-to-G transversions in mammalian cells. These glycosylase base editors (GBEs) consist of a Cas9 nickase, a cytidine deaminase and a uracil-DNA glycosylase (Ung). Ung excises the U base created by the deaminase, forming an apurinic/apyrimidinic (AP) site that initiates the DNA repair process. In E. coli, we used activation-induced cytidine deaminase (AID) to construct AID-nCas9-Ung and found that it converts C to A with an average editing specificity of 93.8% ± 4.8% and editing efficiency of 87.2% ± 6.9%. For use in mammalian cells, we replaced AID with rat APOBEC1 (APOBEC-nCas9-Ung). We tested APOBEC-nCas9-Ung at 30 endogenous sites, and we observed C-to-G conversions with a high editing specificity at the sixth position of the protospacer between 29.7% and 92.2% and an editing efficiency between 5.3% and 53.0%. APOBEC-nCas9-Ung supplements the current adenine and cytidine BEs (ABE and CBE, respectively) and could be used to target G/C disease-causing mutations. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Still too early |
| URL | https://www.nature.com/articles/s41587-020-0592-2 |
| Title | Helicase-AID: A novel molecular device for base editing at random genomic loci |
| Description | CRISPR-enabled deaminase base editing has become a powerful tool for precisely editing nucleotides on the chromosome. In this study DNA helicases, such as Escherichia coli DnaB, were fused to activation-induced cytidine deaminase (AID) to form enzyme complexes which randomly introduces edited bases throughout the chromosome. DnaB-AID was found to increase 2.5 × 103 fold relative to the mutagenesis frequency of wildtype. 97.9% of these edits were observed on the leading strand during DNA replication suggesting deamination to be highly coordinated with DNA replication. Using DnaB-AID, a 371.4% increase in ß-carotene production was obtained following four rounds of editing. In Saccharomyces cerevisiae Helicase-AID was constructed by fusing AID to one of the subunits of eukaryotic helicase Mcm2-7 complex, MCM5. Using MCM5-AID, the average editing efficiency of five strains was 2.1 ± 0.4 × 103 fold higher than the native genomic mutation rate. MCM5-AID was able to improve ß-carotene production of S. cerevisiae 4742crt by 75.4% following eight rounds of editing. The S. cerevisiae MCM5-AID technique is the first biological tool for generating and accumulating single base mutations in eukaryotic chromosomes. Since the helicase complex is highly conservative in all eukaryotes, Helicase-AID could be adapted for various applications and research in all eukaryotic cells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | still very early post publication |
| URL | https://www.sciencedirect.com/science/article/abs/pii/S1096717621001294?via%3Dihub |
| Title | Human Artificial Chromosome |
| Description | Human artificial chromosome isolated from synthetic DNA construct introduced into human HT1080 cell line. Similar HACs have recently been used in screening for inhibitors of human telomere maintenance (10.1158/0008-5472.CAN-18-0894) |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | none yet |
| Title | Mouse NS cell glioma models |
| Description | We have exploited CRISPR/Cas genome editing and created a wealth of derivative NS cell lines that will serve as important and useful models of the human disease. These include a set of glioma cell lines that are now being validated. |
| Type Of Material | Cell line |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | These cell lines are being used by CRUK Career Development Award holder Dr Dirk Sieger to explore glioma and microglia interactions using the zebrafish as a model system. |
| Title | Multiplexed activation in mammalian cells using a split-intein CRISPR/Cas12a based synthetic transcription factor |
| Description | The adoption of CRISPR systems for the generation of synthetic transcription factors has greatly simplified the process for upregulating endogenous gene expression, with a plethora of applications in cell biology, bioproduction and cell reprogramming. The recently discovered CRISPR/Cas12a (Cas12a) systems offer extended potential, as Cas12a is capable of processing its own crRNA array, to provide multiple individual crRNAs for subsequent targeting from a single transcript. Here we show the application of dFnCas12a-VPR in mammalian cells, with the Francisella novicida Cas12a (FnCas12a) possessing a shorter PAM sequence than Acidaminococcus sp. (As) or Lachnospiraceae bacterium (Lb) variants, enabling denser targeting of genomic loci, while performing just as well or even better than the other variants. We observe that synergistic activation and multiplexing can be achieved using crRNA arrays but also show that crRNAs expressed towards the 5' of 6-crRNA arrays show evidence of enhanced activity. This not only represents a more flexible tool for transcriptional modulation but further expands our understanding of the design capabilities and limitations when considering longer crRNA arrays for multiplexed targeting. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | It has only just been published |
| URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8754635/ |
| Title | Optogenetic control of cell death |
| Description | Cells can be saved from drug-inducible cell death by an optogenetic construct |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | It has been one of the foundations of a 5 million Euro collaborative project (CyGenTiG), in which light will be used to control morphogenesis. |
| Title | Plasmids for production of TAL effectors |
| Description | Library of plasmid parts for creation of synthetic transcription factors based on TAL effector architectures. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Publication of method was carried out. Various laboratories are accessing the plasmids. |
| URL | https://www.addgene.org/kits/pollard-star-tale-assembly/ |
| Title | non-invasive tool to control subnuclear localisation of specific loci |
| Description | By taking advantage of Cas9/CRISPR technology, we have designed a method to control sub-nuclear localisation of any genomic locus without altering its genetic or epigenetic composition. |
| Type Of Material | Biological samples |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | This method will allow to manipulate nuclear architecture without affecting primary DNA sequence. This is a fundamental tool to understand the role of nuclear architecture during gene expression control. |
| Title | two-step locus-specific targeting of big cargos |
| Description | Locus-specific insertion of big DNA cargos in the mammalian genome, without using selection markers, as never been achieved. Absence of an expressed drug-resistance or fluorescent marker is very important when the locus is heterochromatic and silent. Expression of the selection in this cases is either unsuccessful or induces changes of the chromatin state of the locus. We have devised a two step system to achieve successful targeting of these type of loci. |
| Type Of Material | Biological samples |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Our method allows controlling subnuclear localisaiton or protein tethering of heterochromatin loci without perturbing their epigenetic makeup. |
| Title | synPHARM |
| Description | SynPharm is a database of ligand-responsive protein sequences, derived from interactions from the Guide to PHARMACOLOGY and using data from the Protein Data Bank. The sequences here are obtained by identifying the protein chain that interacts with a ligand for a given Guide to PHARMACOLOGY interaction, determining the binding residues, and producing a continuous 'bind sequence' that can be used to confer drugability to another protein. Each bind sequence also contains metrics such as atomic contact ratio and proportional length, and visualisations such as the residue distance matrix, to allow you to better judge whether a sequence is likely to be able to fold independently. The rationale for such a project was to enable the development of orthogonal molecular switches - switches which only respond to an exogenous molecular trigger, which itself will not interfere with endogenous receptors. |
| Type Of Material | Data analysis technique |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Text written March 2017: We have used the tool to generate druggable versions of Cas9 and cpf1 for inducible gene editing (paper in preparation). The database was put on full public release so recently that we are not yet aware of external impacts, but we have just added a Google Analytics counter to track external use. |
| URL | http://synpharm.guidetopharmacology.org/ |
| Description | Collaboration in the design and use of human artificial chromosomes |
| Organisation | National Institutes of Health (NIH) |
| Department | National Cancer Institute (NCI) |
| Country | United States |
| Sector | Public |
| PI Contribution | We have isolated plasmids that have been used to create new two-domain human artificial chromosomes. |
| Collaborator Contribution | They constructed one of the plasmids used in this construction. They also provided facilities where Elisa Pesenti learned how to analyse these plasmids. Lastly, they performed Southern Blot Analysis of several of the human Artificial Chromosomes that we isolated. |
| Impact | There have been many outputs from this collaboration. The two relevant to the present grant are shown in my research portfolio. |
| Description | Collaboration with Cellinta |
| Organisation | Cellinta |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Spin out from lab of Prof Steve Pollard |
| Collaborator Contribution | Ongoing collaboration in the area of cancer gene therapy |
| Impact | NA |
| Start Year | 2020 |
| Description | Collaboration with Dr Elise Cachat |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Elise Cachat was the post-doc on this grant, but partly on the strength of what she achieved she now has an independent position and we now collaborate as equals. |
| Collaborator Contribution | Experimental design and computer modelling. |
| Impact | Publication: Cachat E, Liu W, Davies JA (2017) Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards synthetic tissue development. Eng Biol 1: doi: 10.1049/enb.2017.0013 |
| Start Year | 2016 |
| Description | Collaboration with OGI Bio Ltd |
| Organisation | OGI BIO LTD |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | In this collaboration, we will develop a bioreactor with in situ imaging capability. By doing so we will access information on microbial cell shape, which is currently inaccessible with high throughput. The collaboration is through an IBioIC and BBSRC CASE studentship. |
| Collaborator Contribution | The company will offer 6-month placement during which the student will have the opportunity to participate and learn about commercialization efforts of the technology we will develop as part of the studentship. |
| Impact | An IBioIC BBSRC CASE scholarship was secured commencing in 2020. |
| Start Year | 2020 |
| Description | Collaborative Partner on Australian Research Council Centre of Excellence in Synthetic Biology |
| Organisation | Macquarie University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Named Collaborative Partner on Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, $35,000,000 AUD (£18,500,000 GBP), January 2020 - December 2026. |
| Collaborator Contribution | Invited visits to the ARC Centre for Synthetic Biology |
| Impact | The collaboration only started in January 2020 so no outcomes have resulted yet. The collaboration is multi-disciplinary, involving biologists, engineers, computer scientists, lawyers and social scientists. |
| Start Year | 2020 |
| Description | Foundry becomes the first academic member of the International Gene Synthesis Consortium (IGSC) |
| Organisation | International Gene Synthesis Consortium |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The University of Edinburgh's Genome Foundry has become the first academic member of the International Gene Synthesis Consortium (IGSC), an association of the world's leading gene synthesis companies working to safeguard the rapidly-emerging field of gene synthesis. The IGSC was founded in 2009 by the world's leading gene synthesis companies to advance biosecurity across the industry. In April 2015, the IGSC became a California not-for-profit 501(c)(3) corporation under charter and by laws developed to facilitate broader membership and community participation. The IGSC's goals are (a) to educate gene synthesis companies and the public regarding sequence and customer screening of synthetic gene orders; (b) to identify and prevent the unauthorized synthesis and sale of inappropriate sequences; and (c) to coordinate development of ongoing best practices. For more information about membership or the IGSC screening process, please visit www.genesynthesisconsortium.org. |
| Collaborator Contribution | The IGSC was founded in 2009 by the world's leading gene synthesis companies to advance biosecurity across the industry. In April 2015, the IGSC became a California not-for-profit 501(c)(3) corporation under charter and by laws developed to facilitate broader membership and community participation. The IGSC's goals are (a) to educate gene synthesis companies and the public regarding sequence and customer screening of synthetic gene orders; (b) to identify and prevent the unauthorized synthesis and sale of inappropriate sequences; and (c) to coordinate development of on going best practices. For more information about membership or the IGSC screening process, please visit www.genesynthesisconsortium.org. |
| Impact | This collaboration requires that all parties adhere to the gene screening guidelines to ensure biosecurity. |
| Start Year | 2016 |
| Description | Integrated DNA Technologies |
| Organisation | Integrated DNA Technologies |
| Country | United States |
| Sector | Private |
| PI Contribution | We worked with IDT to test via early access their reagents for CRISPR genome editing to knock-in epitope tags. |
| Collaborator Contribution | The partners provided £10K worth of reagents for testing. These were synthetic RNAs and long DNA oligonucleotide repair templates. |
| Impact | We have created a large panel of mouse and human engineered neural and glioma stem cell lines with knockin reporters. These are used as research tools. |
| Start Year | 2017 |
| Description | Isolation and analysis of human artificial chromosomes |
| Organisation | Kazusa DNA Research Institute |
| Country | Japan |
| Sector | Private |
| PI Contribution | Dr. Pesenti visited the Kazusa DNA Institute, and while there constructed a large hybrid plasmid for use in isolation of two-domain human artificial chromosomes. She also transfected this into cells and placed those cultures under selection. Later on when we were sent cell lines bearing HACs, she want on and obtained clones, each bearing a single HAC. |
| Collaborator Contribution | They provided two 60 kb plasmids and taught Dr. Pesenti how to ligate them. After she did the ligation and transfected the plasmids into cells, they grew the cells under selection and later sent her a selection of cell lines which their preliminary analysis showed to have acquired artificial chromosomes or insertions into chromosome arms. |
| Impact | There have been many outputs from this collaboration. The two relevant to the present grant are shown in my research portfolio. |
| Description | Janssen Pharmaceuticals |
| Organisation | Johnson & Johnson |
| Department | Janssen Pharmaceuticals |
| Country | United States |
| Sector | Private |
| PI Contribution | We have collaborated with Janssen in a drug screening project as part of the National Phenotypic Screening Centre - Phenomoics discovery initiative (PDi). We have performed a small molecule screen in search of compounds that affect glioblastoma stem cell self-renewal, making use of an engineer Sox2 knockin reporter line. |
| Collaborator Contribution | Janssen has provided libraries of their small molecules, chemiinformatics support, access to the tool compounds for validation. |
| Impact | Outputs are new hits to support future anticancer drug discovery efforts against glioblastoma. |
| Start Year | 2017 |
| Description | Membership of UK BioFoundries Alliance |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Collaborator Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Impact | Web site in development. Shared protocols. |
| Start Year | 2020 |
| Description | Membership of UK BioFoundries Alliance |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Collaborator Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Impact | Web site in development. Shared protocols. |
| Start Year | 2020 |
| Description | Membership of UK BioFoundries Alliance |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Collaborator Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Impact | Web site in development. Shared protocols. |
| Start Year | 2020 |
| Description | Membership of UK BioFoundries Alliance |
| Organisation | University of Manchester |
| Department | Manchester Institute of Biotechnology MIB |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Collaborator Contribution | The Edinburgh Genome Foundry has become a partner in the UK BioFoundries Alliance network. Role - organising meetings and developing web portal. |
| Impact | Web site in development. Shared protocols. |
| Start Year | 2020 |
| Description | Molecular Dynamic modelling of nucleosome interarctions with Transcription factors |
| Organisation | Royal Netherlands Academy of Arts and Sciences |
| Department | Hubrecht Institute |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | By generating various mutants forms of transcription factors and measuring the biochemical affinity to nucleosomes in vitro and to chromatin in cells, we have identified important regions for nucleosome binding. |
| Collaborator Contribution | Using Molecular dynamics modelling, our collaborators used our experimental data to model the three dimensional structure of transcription factors in complex with nucleosomes. |
| Impact | Organized joint meeting. manuscript under preparation. |
| Start Year | 2017 |
| Description | Ramified Rolling Circle Amplification for nucleosomal DNA synthesis |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | We have used DNA synthesized by our collaborators to reconstitute nucleosomes in vitro |
| Collaborator Contribution | To enable studies on native, genomic nucleosomes, our collaborators establshed an efficient and flexible method to produce nucleosomal DNA based on rolling circle amplification (RCA). |
| Impact | manuscript under revision |
| Start Year | 2017 |
| Description | Reprogramming pancreatic cancer (PDAC) to discover early markers |
| Organisation | Oregon Health and Science University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We aim to profile the chromatin landscape of PDAC during reprogramming to iPSCs using ATAC-seq and ChIP-seq for histone marks. Characterizing these chromatin-barriers would be particularly important as we reason it will reveal the essential epigenetic transition from the PanIN to PDAC stages. |
| Collaborator Contribution | Our collaborator will reprogram a large number of PDAC tissue from human patients to iPSC to model cancer progression in mice. |
| Impact | CRUK-OHSU project award |
| Start Year | 2019 |
| Description | Roundtable on Responsible Research and Innovation with the Research Council of Norway |
| Organisation | Research Council of Norway |
| Country | Norway |
| Sector | Public |
| PI Contribution | Robert Smith, along with Koichi Mikami, Jusaku Minari and Arisa Ema held a round table meeting with the Research Council of Norway to discuss policies for Responsible Research and Innovation. |
| Collaborator Contribution | The Research Council of Norway hosted the meeting in their offices in Oslo on 12th September 2019. |
| Impact | A future workshop is planned in June 2020 bringing together funders from Japan, the UK, Norway and the USA to discuss policies for Responsible Research and Innovation. |
| Start Year | 2019 |
| Description | Transcription factors lineage specificity during reprogramming |
| Organisation | Hebrew University of Jerusalem |
| Department | Hebrew University Hadassah Medical School |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | We are using wide variety of genomic approaches including ChIP-seq, RNA-seq, Mnase-seq and ATAC-seq combined with bioinformatics to define how various combinations of transcription factors engage the genome and establish specific cell identity during reprogramming adult cells to embryonic stem cells and trophoblast cells |
| Collaborator Contribution | Our collaborators have developed various methods of reprogramming to trophoblasts and embryonic stem cells and have carried out RNA-seq and ATAC-seq at different stages of reprogramming. |
| Impact | Manuscript under preparation. two grants submitted |
| Start Year | 2016 |
| Description | Twist bioscience |
| Organisation | Twist Bioscience |
| Country | United States |
| Sector | Private |
| PI Contribution | Testing of double stranded DNA blocks synthesised for targeting vector production. |
| Collaborator Contribution | Provision of double stranded DNA blocks synthesised for targeting vector production. |
| Impact | Production of novel engineered cell lines. |
| Start Year | 2018 |
| Title | An affordable, modular microbioreactor |
| Description | Development of the modular bioreactor capable of culturing between 5-20ml of culture with the option of turbidostat is protected by know-how. |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | 2019 |
| Licensed | No |
| Impact | Based on the know-how we spun out OGI Bio Ltd. |
| Title | CHO CELL MODIFICATION |
| Description | The present disclosure relates to the modification of Chinese hamster ovary (CHO) cells at specific genomic loci that bestows the capability of receiving and expressing exogenous nucleic acid, for an extended period, as well as to methods of modifying the genome of a (CHO) cell, such that an exogenous nucleic acid sequence can be introduced, maintained and expressed by the modified CHO cell, for an extended period. |
| IP Reference | WO2022123242 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2022 |
| Licensed | No |
| Impact | The patent is currently being evaluated for licensing by 3 companies |
| Title | TRANSGENE EXPRESSION SYSTEM |
| Description | A system to limit the expression of a vector-derived transgene within a window that alleviates the disease-causing genetic deficiency without producing overexpression toxicity is described. This provides for 'dosage-insensitivity', whereby cells or tissues receiving more vector-derived transgene are disproportionately suppressed through an in-built single gene circuit that can regulate adaptively. |
| IP Reference | WO2022003348 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2022 |
| Licensed | Yes |
| Impact | The patent has been licensed by the company Neurogene and the technology is going into phase 1 clinical trials in 2023 |
| Title | BandWitch |
| Description | BandWitch is fragment analysis framework. Given a batch of assemblies, BandWitch will suggest the best enzymatic digestion to create easily-interpretable patterns for all constructs. Then, when the constructs have been experimentally digested and migrated, BandWitch provides methods to validated the batch and generate informative reports indicating which constructs are structurally correct, and helping to troubleshoot constructs with invalid band patterns. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | BandWitch is used routinely at the Edinburgh Genome Foundry where it significantly accelerated the construct validation work-flow. One manuscript for publication in preparation. |
| URL | https://github.com/Edinburgh-Genome-Foundry/BandWitch |
| Title | BioDare2 |
| Description | BioDare2 is a free, public, online resource for the visualisation and analysis of rhythmic data, designed for biological timeseries, especially derived from gene expression reporters and other synthetic or natural biological outputs controlled by the 24-hour biological clock (circadian clock). The resource includes extensive online documentation that explains the mathematical basis of the eight analysis methods that are provided, and a dedicated YouTube channel of video tutorials. This ResearchFish upload relates to the 2020-2021 version of the resource supported by UK_CMSB, and described in a publication of 2021 (Zielinski, T., Hay, J. & Millar, A. J. doi: 10.1007/978-1-0716-1912-4_2), including: - public sharing of and access to data sets, with a simple search function - rhythm detection analysis using the eJTK method, and - associated heatmap visualisations, both of which are suitable for short timeseries of 'omic data such as transcriptomics. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | BioDare2 is used by international researchers, with approximately 200 unique users worldwide, to contribute to their ongoing research. The impacts are mostly in research publications. |
| URL | https://biodare2.ed.ac.uk/ |
| Title | Caravagene |
| Description | Simple library to plot and highlight DNA design |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This library is routinely used at the Edinburgh Genome Foundry to communicate designs to customers in the setup stage of custom assembly projects |
| URL | https://github.com/Edinburgh-Genome-Foundry/Caravagene |
| Title | Cell counter |
| Description | The software automatically counts numbers of cells in a given sequence of images. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | The software will likely be a part of a spin-out company and a device in development. We are currently looking into protecting it. |
| Title | DNA Chisel |
| Description | A flexible, extensible Python library to optimize nucleotide sequences with respect to constraints and objectives. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | Used routinely at the Foundry to help customers shape their projects (go from human-formulated specifications to an actual DNA nucleotides sequence) and save time and money by maximizing the chances of assembly success. One publication in preparation. |
| URL | https://github.com/Edinburgh-Genome-Foundry/DnaChisel |
| Title | EMMA-DB (now DAB) |
| Description | In-progress web application for Computer-Aided-Design of genetic constructs, with integrated ordering to the Edinburgh Genome Foundry. The application allows to manage genetic parts for different leading assembly standards (MoClo, EMMA, etc.), to browse the parts repository of the EGF and other users, and to design constructs from these parts, and to send the order to the EGF. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | The software will serve as a customer front-end for the foundry, allowing for the planning and manufacturing of customer orders with minimal human intervention. As of February 2018 it is released in an alpha version for tests by a restricted group of customers. It supports mostly the EMMA assembly standard, and is being extended to support other standards and reach a bigger community. The software also proposes some novel approaches to construct design and may be the subject of a publication later on in 2018. |
| URL | https://dab.genomefoundry.org/ |
| Title | Edinburgh Genome Foundry File Management System |
| Description | Server and network configuration allowing to transfer files from or to different computers of the Edinburgh Genome Foundry (and in particular robot computers) in a friendly, safe, and traceable way. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | The EGF file management system strengthens the EGF operations in several ways. (1) By allowing files to be easily moved from an operator's computer to a robot's computer, it decreases the time necessary to set up robotic operations and reduces the risk of human error by file confusion. (2) By backing up all the managed files, the file manager ensures that no information is lost. (3) By keeping a trace of files histories, the file manager enables to recover information about past robotic runs, thus ensuring good traceability and making troubleshooting of operations easier - we can know at any time what exact protocol was ran on each robot at any given date. |
| Title | Edinburgh Genome Foundry Website |
| Description | Customer front of the Edinburgh Genome Foundry, with informations on the Foundry's services, products, software efforts, team, and contact details. the website also features an interactive strain ordering application. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2016 |
| Impact | The website if one of the main elements of the Edinburgh Genome Foundry's online presence strategy, allowing the Foundry to market its activity globally. The development of the website has also established a visual identity of the Foundry. |
| Title | Fitderiv |
| Description | The software is written to provide a tool for estimating growth rates from optical density data and uses that language (although it can process any other type of data too). It has been described in more detail in the following publication Swain P S**, Stevenson K, Leary A, Montano-Gutierrez L F, Clark I B N, Vogel J and Pilizota T. Inferring time-derivatives, including cell growth rates, using Gaussian processes. Nature Communications 2016;7:13766 and made openly available at http://swainlab.bio.ed.ac.uk/software/fitderiv/ |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | The software is currently used by several research groups and expected to be adopted wider (publication date is December 2016) |
| URL | http://swainlab.bio.ed.ac.uk/software/fitderiv/ |
| Title | Genedom |
| Description | Genedom is a python library for managing the domestication of genetic parts (i.e. the modification of their sequence so as to make them compatible with a given genetic assembly standard). Genedom binds together a sequence optimizer, genetic standards informations, and a reporting routines, to automate the domestication of large batches in an easy and human-friendly way. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | Genedom can do in a minute a task which would take a human operator a full day, and avoids human mistakes which can be very costly at this step. It has been used to quickly domesticate and order hundreds of parts for Edinburgh Genome Foundry cuistomers. |
| URL | https://edinburgh-genome-foundry.github.io/genedom/ |
| Title | Golden Hinges |
| Description | A library to find collections of compatible overhangs for Type-2S restriction-based assembly. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | The early version of the library was used to help in the design of the overhangs of the EMMA standard, which is now a main product of the EGF. The library has been further used to compute overhangs for 4+ custom design projects at the Foundry. |
| URL | https://github.com/Edinburgh-Genome-Foundry/GoldenHinges |
| Title | Icebreaker |
| Description | Python library to communicate with the JBEI-ICE DNA sequence manager. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | This library is now a central piece of software in the Edinburgh Genome Foundry as it provides our internal web applications with the informations (DNA sequence and sample availability) from our sequence manager. It saves hours of work to human operators weekly by automatically processing the upload or download of hundreds of DNA parts sequences. |
| URL | https://edinburgh-genome-foundry.github.io/icebreaker |
| Title | Kappagate |
| Description | Experimental computational software to predict the difficulty of a DNA assembly using Golden-Gate like standards: given a set of parts to assemble, Kappagate will run a simulation to predict which proportion of the final clones will contain the right version of the DNA assembly. From this prediction, Kappagate can inform the experimentalist of how many clones they should pick |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Knowing how difficult a construct will be to assemble is important for a Foundry for deciding whether the order is worth taking in. Knowing how many colonies should be picked to obtain a valid clone is important for predicting costs (Quality Control is a significant part of the final assembly cost). |
| URL | https://github.com/Edinburgh-Genome-Foundry/kappagate |
| Title | Primavera |
| Description | Primavera is a framework for primer-based DNA assembly verification (Sanger sequencing and PCR validation). Given a batch of assemblies, Primavera can generate an optimal set of primers to verify the constructs, leveraging on already-available primers. Primavera can also be used to create easy-to-read validation reports from Sanger sequencing data. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Primavera is used at the Edinburgh Genome Foundry to automate the planning of sequencing batches for assembly verification. |
| URL | https://github.com/Edinburgh-Genome-Foundry/Primavera |
| Title | Saboteurs |
| Description | Saboteurs is a Python library (and associated web app) to detect failure-causing elements from success/failure data. In particular it can use logical and statistical methods to identify genetic parts associated with assembly failure. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Saboteurs is used systematically every time a batch of assembly has a high failure rate in the Edinburgh Genome Foundry. It has succesfully saved hours of troubleshooting by identifying parts whose samples were indeed corrupted. |
| URL | https://edinburgh-genome-foundry.github.io/saboteurs |
| Title | Screepy |
| Description | Pathogenicity screening framework implementing the protocol of the International Gene Synthesis Consortium (BLAST search against databases of blacklisted agents) |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | As a member of the International Gene Synthesis Consortium, the Edinburgh Genome Foundry screens DNA orders to ensure that they are safe. Pathogenicity screening is a non-trivial task with "grey areas" as the (non-)pathogenicity of a sequence is not always obvious. The Screepy framework produces comprehensive reports providing the Foundry operators with the relevant results to take an informed decision. |
| Title | Sequenticon |
| Description | Python library (and associated web app in CUBA) to generate human-friendly icons representing sequences in an unambigous way: if two sequences have the same icon, they are certainly the same sequence. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Sequenticons are used mostly in PDF reports to increase traceability in the foundry: if a customer suddenly changes a part's sequence without modifying its name, this can cause serious confusion. Using sequenticons makes it possible to understand at a glance whether two parts in two different reports are actually the same part or not. |
| URL | https://github.com/Edinburgh-Genome-Foundry/sequenticon |
| Title | Smart Assembly |
| Description | Collection of web applications for the internal operations of a DNA assembly Foundry. Leveraging on the computational software of the Edinburgh Genome Foundry, Smart provides user interfaces for order processing (validation of the order, cloning simulation, automatic enzyme selection, robotic files generation) and sample management (creating/moving/updating microplates in the sample manager, or batch-uploading new parts to the foundry's repository) |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | Smart Assembly is a central software tool of the Edinburgh Genome Foundry where it integrates together the computational software and databases of the Edinburgh Genome Foundry, allowing for the planning of assembly batches (from order validation to picklist generation), and high-level sample management (creating/moving/updating plates). |
| Title | SynBio2Easy |
| Description | A biologist-friendly tool for batch operations on the designs of synthetic biology constructs represented in the SBOL format, with metadata input from Excel that is suitable for libraries of designs. The linked version was released with the first paper revision. The software is documented and includes full end-to-end usage scenarios in the examples. The code is also available from the GitHub link below. The application was developed with input from the McCormick lab at the University of Edinburgh, developed for our joint work on their Cyanosource resource of genome-engineered cyanobacterial lines. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Just released in 2022. |
| Title | SynPharm software tools |
| Description | Tools for assisting the design of druggable proteins |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This is a foundation for the Synpharm database |
| Title | Topkappy |
| Description | Simple Python API for the Kappa simulation framework. Topkappy enables to represent chemical agents (e.g. DNA fragments) and interactions (e.g. ligation) in a programmatic way, making it possible to define and simulate complex problems with hundreds of agents and interactions. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Originally developped to support the development of Kappagate (framework for assembly difficulty prediction, also listed in the same Awards), Topkappy was eventually packaged as a project of its own as it can be useful to the community. |
| URL | https://github.com/Edinburgh-Genome-Foundry/topkappy |
| Title | Visual SBOL CSS |
| Description | Simple library to display genetic designs using the SBOL Visual language |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | Used routinely to display genetic constructs in the internal software applications of the Edinburgh Genome Foundry. |
| URL | https://github.com/Edinburgh-Genome-Foundry/SBOL-Visual-CSS |
| Title | Zymp |
| Description | Small Python library (and associated web app on CUBA) to design sequences with compact arrays of restriction sites. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Used originally to develop custom control sequences for manufacturing and quality control at the foundry, it has been packaged in the hope that it will be useful to the community. |
| URL | https://github.com/Edinburgh-Genome-Foundry/zymp |
| Title | blabel |
| Description | Blabel is a python library to programmaticaly generate labels (typically for printing stickers) with barcodes and other dsplays |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Blabel is used to print microplate barcodes and other custom labels at the Edinburgh Genome Foundry, with the day's date, correct genetic part names (via interfacing with our sequences manager) etc. |
| URL | https://edinburgh-genome-foundry.github.io/blabel |
| Title | python_codon_tables |
| Description | Small Python library providing codon optimization tables for virtually any species, either via built-in data tables, or by automatically downloading the table corresponding to a given TaxID from the internet (http://www.kazusa.or.jp) |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Since 2019 this library provides codon tables data to all applications of the Edinburgh Genome Foundry which perform codon optimization (DNA Chisel, Genedom, and projects using these). |
| URL | https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables |
| Company Name | CELLINTA LTD |
| Description | Cell and gene therapy for oncology. Building up our expertise in synthetic biology, stem cell biology and glioblastoma models |
| Year Established | 2019 |
| Impact | Seed funding secured of ~£5M. |
| Company Name | OGI BIO LTD |
| Description | Company is focused on innovation in microbioreactor market. Focusing 1st on affordable microbioreactors and continuing to innovate in the sector, by for example developing in situ bioreactor imaging capabilities. Company is expected to start employing people on 1st October 2020. |
| Year Established | 2020 |
| Impact | The company is currently in beta testing phase of its first product. |
| Company Name | CELLINTA LTD |
| Description | Work from Pollard lab (Mantas M and Ute K) has led to formation of a new spin out in March 2020. This will focus on cell and gene therapy in oncology. The initial seed investment has been >£5M |
| Year Established | 2019 |
| Impact | The company has only just started so too early for impacts. |
| Description | 'A Question of Taste' Workshops organized by University of Edinburgh at National Museum of Scotland, Edinburgh. |
| 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 | During the workshop, students (high school) discover and compare their version of a bitter taste receptor gene (their genotype) to their ability to taste the bitter compound (their phenotype). Naiming was demonstrating and helped they carry out the laboratory techniques of DNA extraction, PCR, restriction enzyme digestion and gel electrophoresis. She also gave a short talk during the workshop. |
| Year(s) Of Engagement Activity | 2018 |
| Description | BBC Arabic TV Visit |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Visit from Anees Al Qudaihi, from BBC Arabic World Service, who was making a future edition of a Science and Technology programme. |
| Year(s) Of Engagement Activity | 2016 |
| Description | BBC News Coverage |
| 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 | Media (as a channel to the public) |
| Results and Impact | Coronavirus in Scotland: Efforts to develop 'sophisticated' antibody test July 24th 2020 |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.bbc.co.uk/news/uk-scotland-53526410 |
| Description | Biological Art Public Lecture Summerhall |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Biological artists Oron Catts and Ionat Zurr presented their on-going work in collaboration with Centre researchers in an event chaired by Jane Calvert. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.ascus.org.uk/contextualising-biotechnological-artifacts/ |
| Description | Cafe Synthetique - Edinburgh |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | On 9th of October, researchers from Biology, Informatics and Engineering hosted Edinburgh's first Café Synthetique event. This monthly event aims to address the lack of public and informal events for those curious about Synthetic Biology. Monthly meetings are held with two short talks and then dialogue over pizza. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/edinburghs-first-cafe-synthetique |
| Description | Closing the Loop Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In little over a decade, synthetic biology has evolved from demonstrating proof-of-concept gene circuits in bacteria to developing a new class of therapeutic devices (theranostics). However, despite a thriving community, and some noteworthy successes, the task of assembling a predictable gene network from biomolecular parts remains a challenge. It can take many months of trial and error to produce a gene circuit with the desired behavior or phenotype. In engineering terms, we are still far from the efficient, rational 'Design-Build-Test' cycle deployed in industrial manufacturing contexts. To gain consensus about the challenges, and to discuss potential solutions, the UK Centre for Mammalian Synthetic Biology hosted a workshop on February 22nd and 23rd 2018 in Edinburgh. A principal aim of the workshop, besides knowledge exchange across the different communities, was to start to develop a roadmap document and a focused community to address these challenges through targeted funding applications. Over 50 people from US, UK and Europe attended the workshop and enjoyed two days of talks and lively discussion. They discussed four key areas: •How to automatically design synthetic gene circuits - Bio-design automation; •How to design the most informative experiments to characterize such circuits - Optimal Experimental Design; •How to use such experiments to obtain reliable mathematical models - Making sense of data; •What kind of technologies those experiments should be based on - Technology. Outputs of the meeting will be used to develop a community position paper. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/international-workshop-discuss-unmet-needs-%E2%80%98design-build-t... |
| Description | Crossing Kingdoms Exhibition at Edinburgh International Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The Edinburgh International Science Festival hosted an arts exhibit by biological artists Oron Catts and Ionat on 'Crossing Kingdoms', their collaborative work with the Centre from 31st March - 13th May 2018 at Summerhall, Edinburgh. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.summerhall.co.uk/visual-arts/pig-wings-crossing-kingdoms/ |
| Description | Doors Open Day 2017 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | This year, Doors Open was even bigger and better than last as we welcomed over 200 visitors to the Roger Land Building - home to the Centre - on Saturday 23rd September to find out more about the great science we do within its walls. As part of the national Door's Open weekend, Centre staff and Edinburgh undergraduate iGEM team, came along to engage the public with some of the great projects ongoing across the Centre and School of Biological Sciences. Children had an opportunity to engineer their own fuzzy felt engineered bacteria, watch how bacteria can clean up dirty water, and how robots can take the pain out of pipetting! We were particularly delighted to welcome members of the Colouring Outside the Lines group of autistic girls interested in STEM subjects. They came for a private viewing before the opening to the general public and asked some very challenging questions. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/synthetic-biology-opens-doors |
| Description | Doors Open Day 2019 |
| 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 | This year, we welcomed 250 visitors to the Roger Land Building on Saturday 28th September. There they enjoyed hands on arts and crafts activities to engineer their very own bugs with superpowers that could help to save the planet. Families enjoyed the challenge posed by Alessia Lepore of seeing what diversity of structure they could build with the same bioparts (aka Lego). We also had some large fluffy designer E. coli on display, which explained how synthetic biologists can redesign genetic networks with great accuracy. The event was widely enjoyed with a lot of in depth discussions on synthetic biology applications with visitors. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/open-doors-synthetic-biology-0 |
| Description | ESC Festival of Science event |
| 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 | As part of the ESRC Festival of Social Science, the Innogen Institute brought together social science researchers and scientists from the Roslin Institute and the Centre for Synthetic and Systems Biology (SynthSys) at the University of Edinburgh for a free public event exploring the opportunities arising from the latest genetic technologies and the regulatory issues they are facing. Over forty attendees had the chance to engage with researchers and through hands-on activities find out more about how gene editing works and decide what research projects they would invest in. The audience were highly engaged with a lot of follow up questions. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/stimulating-debate-barriers-new-technology-adoption |
| Description | Edinburgh Cafe Synthetique |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | SynthSys researchers organised an Edinburgh Chapter of cafe Synthetique and have run a series of events focused around our research. This has been very well attended attracting ~190 participants |
| Year(s) Of Engagement Activity | 2019,2020 |
| URL | https://www.cafesynthetique.com/ |
| Description | Edinburgh Doors Open Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | This year, the Centre welcomed 367 visitors to the Roger Land Building on Saturday 29th September where they explored science as varied as synthetic biology through to infectious diseases. The Centre provided hands on arts and crafts activity, designed by Dr Gaynor Campbell, to explain how we can engineer in novel features to cells to make them useful tools to fight major global challenges. Kids also got involved with designing and building plasmids to encode their features of choice - from oil munching bacteria to new enamel for teeth. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/doors-open-day-attracts-more-visitors |
| Description | Edinburgh Doors Open Day 2015 |
| 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 | On September 26th, SynthSys opened the Waddington Building to the public for the first time during the Doors Open event. Over the course of the day we had 75 visitors come to explore about our multidisciplinary research that brings biology together with engineering. We had exhibits from the lab of Dr Timm Krueger who offered hands-on interactive on a novel method for sorting cells, useful potentially in medicine. The lab of Prof Chris French explained how cells can be engineered to detect arsenic in drinking water, a project that may help the 100 million people at risk in developing countries. Members from the lab of Dr Patrick Cai offered a fun demonstration of the value of high-throughput and automated technology for printing cells (see photos). Dr Louise Horsfall's lab treated guests to the wonders of fluorescent bacteria and how bugs can be designed to clean up contaminated soil. Finally, visitors could actually check for themselves how climate change impacts on plant growth by playing with parameters of a model generated in the lab of Professor Andrew Millar. Edinburgh Doors Open Day is organised by the Cockburn Association (Edinburgh's Civic Trust). Now in its 25th year, the event has become one of the capital's most popular free days out. For the day Edinburgh's most architecturally, culturally and socially significant buildings are opened to the public. Many of our visitors asked probing questions about our research and several were potential undergraduate students considering training in synthetic biology. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.synthsys.ed.ac.uk/news/opening-doors-synthsys |
| Description | Edinburgh Doors Open Day 2016 |
| 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 | Over 70 visitors enjoyed learning about synthetic biology and its many applications at the Edinburgh Doors Open event in the Roger Land Building on Saturday 24th at the King's Buildings Campus. Staff and postgraduate students from SynthSys, and this year's Edinburgh iGEM team, came along to explain more about their research and the power of synthetic biology. They were joined by staff from the Centre for Regenerative Medicine, who explained how stem cells are being used to create cells suited for therapy. Children had an opportunity to engineer their own fuzzy felt bugs, parents contemplated stem cells under a microscope and visitors were amazed at the metal munching power of microbes. Many of our visitors were quite unaware of the work we do and its potential impact for society. There were many animated conversations from both adults and children about synthetic biology. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/open-doors-synthetic-biology |
| Description | Edinburgh International Science Festival |
| 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 | The Centre took synthetic biology to the Edinburgh Science Festival from March 31st to April 4th. Part of the School of Biological Science's 'Biodiscoveries' activities, the Centre sought to explain the fundamentals of synthetic biology to the primary school age visitors and their carers and to showcase some of the exciting research projects underway in Edinburgh. Over 2,500 attended the event, with lots of questions and interactions from the young visitors. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/fuzzy-felt-festival-science |
| Description | Edinburgh Science Festival - Synthetic Biology |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Edinburgh Science Festival talk on Synthetic Biology |
| Year(s) Of Engagement Activity | 2019 |
| Description | Exhibit at a Festival |
| 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 | Centre members braved the erratic Edinburgh summer weather to build bugs with kids of all ages at the annual Meadows Festival. Over 100 children came along during the event to design and build bugs with super powers that could help to save the planet. The activity, designed by Dr Gaynor Campbell, explains very simply how we can engineer in novel properties to cells to make them useful tools in the fight to address many global challenges. Participating kids totally got with the programme and built some fantastic creations - and all in a friendly GM-free environment. It also provided an opportunity to explain the Centre's research to parents and carers. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/building-superbugs-meadows |
| Description | Exhibitor at 2016 Industrial Biotechnology Showcase |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Centre showcased its research activities and industry partnerships to over 400 delegates attending the annual conference of the Industrial Biotechnology Innovation Centre (IBioIC) in Glasgow on January 28th and 29th. We had a stand within the exhibition hall displaying pop-up banner and marketing materials. Professor Susan Rosser, Director of the Centre for Mammalian Synthetic Biology, chaired a session on the challenges and opportunities arising from synthetic biology. The meeting generated many new leads with key industry players and other potential academic collaborators. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/synthsys-exhibits-annual-industrial-biotechnology-innovation-centr... |
| Description | Exhibitor at IBioIC Annual Conference Jan 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | The Centre sponsored an exhibition stand at the third Annual Conference of the Industrial Biotech Innovation Centre (IBioIC), which attracted over 400 delegates over two days in late January. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/delivering-impact-industrial-biotech-conference-2017 |
| Description | Exhibitor at IBioIC Annual Conference Jan 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Sponsored a session on synthetic biology at the 2018 Fourth Annual Conference of the Industrial Biotechnology Innovation Centre. Prof Joyce Tait chaired the sponsored session on synthetic biology spin outs. The exhibit and sponsorship helps to raise the profile of the synthetic biology research ongoing in Edinburgh; our continued visibility is key to driving new connections and collaborations with industry. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Exhibitor at KTN Chemistry and Industrial Biotechnology (IB) Showcase in York |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | The Centre attended the KTN Chemistry and Industrial Biotechnology (IB) Showcase in York on Sept 20 and 21 representing the Synthetic Biology Research Centres and Facilities across the UK, which now amounts to ~£300 million UK Government investment. The Centre Director chaired a session on Synthetic Biology during the event. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/full-speed-ahead-uk-bioeconomy |
| Description | Exhibitor at SynBioBeta London 2016 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | The Centre had a stand at SynBioBeta in London April 2016 alongside our other sister BBSRC funded SynBio Research Centres. Several hundred delegates attended from the UK and overseas. The meeting enabled us to network with other colleagues from across the UK and beyond, network with industry executives and investors and also better understand the commercial synbio landscape. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/synbioblog-synbiobeta-london-2016 |
| Description | Exhibitor at SynbiTECH Meeting, London |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | n late June, the Centre attended the first "SynbiTECH" synthetic biology industry conference in London's QEII Conference Centre in Westminster. The conference brought together several hundred academic researchers, industrialist and investors together to share opinions, insights and expertise. Along with the other five Synthetic Biology Research Centres, the UK Mammalian Synthetic Biology Research Centre had a stand during the event, enabling it to generate several new business leads. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/2019-synbitech |
| Description | Formal Launch of the UK Centre for Mammalian Synthetic Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The Centre was officially launched on October 7th at a day-long event attended by over 100 delegates from academia, industry and government/NGOs. There was an overview of the vision of the centre and some of the key work packages. One of our Board members provided a keynote talk and discussion by industry. During the event we also hosted first SynBioBeta Activate event in Scotland with over 80 attendees. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.synthsys.ed.ac.uk/news/uk-centre-mammalian-synthetic-biology-launched |
| Description | Foundry official launch event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | To celebrate the EGF opening, the University hosted a second SynBioBeta Activate! event in Scotland in partnership with Scottish Enterprise. This event attracted nearly 200 delegates and delivered a lively afternoon of discussion and debate on the role of automation and robotics in synthetic biology. There was a lineup of distinguished international speakers with an inspiring keynote from Ye Yin, CEO of BGI who talked about their ambitious plans in synthetic biology. Delegates then enjoyed short presentations from some of the leaders in DNA design and assembly automation including Cambridge Consultants, Labcyte, Thermo Scientific, Pacific Biosciences, Autodesk, m2p Labs. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/edinburgh-map-dna-design-and-construction |
| Description | Hosted visits to the Edinburgh Genome Foundry by diverse groups. These included scientists, politicians, undegraduate and prospective students, as well as representatives of industrial companies and funding agencies. |
| 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 | Other audiences |
| Results and Impact | Visitors to the facility had a brief introduction to the aims of the work and technology involved in the Edinburgh Genome Foundry. This was typically followed by a visit to see the state-of-the-art in operation. Visitors were always stimulated to ask further questions about the operation of the facility and the wider goals of synthetic biology. 2-3 tours were conducted per week throughout the year. |
| Year(s) Of Engagement Activity | 2016,2017,2018 |
| Description | Hosting two Foundation Apprentices |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Staff from the Centre and wider School of Biological Sciences hosted two Foundation Apprentices during the summer. Foundation Apprenticeships are a relatively new scheme that provide senior school students an opportunity to carry out some workplace learning in more vocational subjects. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/building-solid-foundations-next-generation |
| Description | International Workshop - Future Trends in Synthetic Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A group of 50 leading synthetic biologists gathered at the Edinburgh Centre for Carbon Innovation in Edinburgh on May 16 and 17 to discuss 'Future Trends in Synthetic Biology.' Hosted by the UK Centre for Mammalian Synthetic Biology the purpose of the 2-day workshop was to discuss and report on current research progress in the field of synthetic biology, and discern focal points for future, related disruptive technologies and applications. The workshop was an invitation-only, closed-door event to provide an opportunity for participants to discuss their perspective without bias. During the event there was animated discussion around a range of topics, from the application of synthetic biology to accelerate the production of high value chemicals, materials and medicines, through to heated debate on issues such as proportionate governance, biosecurity and ethics. At the end, delegates discussed what measures might be needed to help move synthetic biology to the next levels. Issues such as universal standards, identify 'grand challenges' focusing the community on a shared goal, and coordinating all relevant stakeholders were discussed. A white paper discussing the discussion of the meeting and its recommendation will be shared with the community when completed. The Centre would like to thanks the US Office of Naval Research Global and the Department of Homeland Security for sponsoring this event and in particular to Dr Patrick Rose (ONR Global) for all his support with its organisation and delivery. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/centre-hosts-future-trends-workshop |
| Description | Laboratory Tours for Children with Cancer, Cancer Research UK and The Brain Tumour Charity |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Supporters |
| Results and Impact | Laboratory tour of facilities and discussion about brain cancer and progress being made. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018 |
| Description | MSP visit to Foundry |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Visit from local MSPs Ian Murray and Daniel Johnson |
| Year(s) Of Engagement Activity | 2016 |
| Description | Midlothan Science Festival - Exhibit |
| 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 | Alazne Dominguez came up with a clever, hands-on approach for building a dialogue around synthetic and systems biology. They engaged with 94 kids (aged 5 to 11) with the concepts of synthetic biology and bioinformatics through an activity titled: Decoding and Designing. Why? They wanted to show the simplicity of these apparently complicated concepts in a fun and educative way through interactive activities. We attended two events within the festival: First, the 'Science Alive Gala Day' at Lasswade High School, Bonnyrigg and then the 'Computer Festival' at IKEA, Straiton. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/decoding-and-designing-out-and-about-midlothian-science-festival |
| Description | Midlothian Science Festival 2016 |
| 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 | We took our 'Master Biobuilder' to he Midlothian Science Festival over a weekend in October. This enables us to reach out to less advantaged regions around Edinburgh and share our interest in Synthetic Biology. There was good engagement as this event from visitors. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Participation in AGM at Uganda Virus Research Institute |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | On February 8-10, Prof Susan Rosser, Prof Alistair Elfick and Dr Liz Fletcher attended the AGM of the MUII-Plus DELTAS programme held in Entebbe, Uganda, at the Uganda Virus Research Institute. The MUII-Plus programme is well established and is directed largely to exploring the aetiology and pathology of infectious diseases pertinent to Sub Saharan Africa. The research initiative is funded by the Wellcome Trust, UK Aid and NEPAD and its long-term vision is to train African leaders in bioinformatics, immunity and infectious diseases, which it is doing admirably well. Over three days, the Edinburgh team got a great insight of endemic diseases such as parasitic infections (Schistosomiasis, Trypanosomiasis), tuberculosis and HIV, which continue to be the source of major sources of ill health in Uganda and Sub-Saharan Africa (SSA) more widely. An analysis of the ongoing research and areas of unmet needs will follow. On the first day of the event, the Centre team presented to >50 delegates on what synthetic biology was and the many opportunities to deploy it towards research challenges for infection and immunity. This was certainly a new area of research to most individuals in the room, many of them quite taken (if not amazed!) at the potential opportunities arising. Several discussions have arisen about applications for synthetic biology, including potential collaborative projects with UK-based researchers who had also attended the event. We later ran a workshop, facilitated by Alison Gray (Skillfluence) on 'Creative Problem Solving' bringing together 25 senior managers and researchers from the University of Makerere and local hospital for a brainstorm. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/exploring-grand-challenges-uganda |
| Description | Participation in Big Bang Science Weekend in Wigtown |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The Big Bang Weekend is an annual event that explores different aspects of science for the public. This year the topic was 'Is it alive?' which explored what we mean by life at both large and small scales. There were great presentations on robots and artificial intelligence, whether or not there is life out there in space, and a comedian's exploration of human consciousness (or lack thereof). There were a series of talks for the general public. Around 80 people attended the presentation. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/should-vegans-eat-yeast |
| Description | Participation in Royal Society of Biology careers event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshops on careers for biology graduates, held at the University of Highlands and Islands, and attended mainly by professional careers advisors, with some undergraduate attendance too. It was intended for the careers advisors. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Pint of Science 2019 event dedicated to synthetic biology on May 22. |
| 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 | The Centre supported a Pint of Science 2019 event dedicated to synthetic biology on May 22. For three evenings in May, beer met biology through some engaging presentations (in some cases performances) by some of the Centre researchers. Sophie Stone expanded the vision of the audience talking about the notions of the human and our bodies on synthetic biology. Dr Gaynor Campbell showed her skills as a budding stand-up comedian taking us on the origins of genetic manipulation through to some rather dubious DIY biohacking. Prof Lynne Regan then used us some fun facts about the role of the proteins and their biomedical importance - props from large building bricks included. During the night, the audience had the opportunity to draw their own genetically augmented product - with prizes for the most artistic and the craziest ideas. Dr Elisa Pesenti from the UK Centre for Mammalian Synthetic Biology coordinated this year's event which was a sell-out success. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/cheers-centre-supports-pint-science-2019-evening |
| Description | Presentation of the Edinburgh Genome Foundry and uses of synthetic biology at a University Open Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Edinburgh Genome Foundry (EGF) staff presented a poster and some hands on material to explain to interested members of the general public, what the work in the EGF involves, why automation of processes is especially important in the field of synthetic biology and how synthetic biology will be of great importance for the future. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Rear Admiral David Hahn, Chief of US Naval Research and Director of Innovation, Technology Requirements |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The Centre was delighted to host Rear Admiral David Hahn, Chief of US Naval Research and Director of Innovation, Technology Requirements, and his Flag Aide Lieutenant Jason Penland on May 9th. The visit provided an update on ONR funded research (Pilizota) as well as a general discussion around the opportunities for synthetic biology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/chief-us-naval-research-visits-centre |
| Description | Sci-Art Collaboration and Exhibit |
| 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 | For two weeks in January 2018, SynthSys and Science Technology and Innovation Studies (STIS) jointly hosted pioneering biological artists Ionat Zurr, Oron Catts and Tarsh Bates from SymbioticA: the Centre of Excellence in Biological Arts at the University of Western Australia. While at SynthSys, Zurr, Catts and Bates initiated a research on a project on cross-kingdom cell fusion in synthetic biology between mammalian and yeast cells, to explore how the novel entities produced by these cell fusions challenge existing scientific and cultural classification systems. When borders are crossed - be they biological, geographical or conceptual - the sense of excitement and exhilaration is blended with unease. . During their visit Zurr gave a talk at the SynthSys Open Centre, Bates gave a STIS seminar, Zurr and Catts give a public lecture at Summerhall. Their work-in-progress was then exhibited at the Edinburgh International Science Festival (31st March - 15th April 2018) and the Western Australia Art Gallery in September 2018. The SynthSys/SymbioticA collaboration will also be the topic of a panel at the Quite Frankly Conference, which will take place at the University of Western Australia in October 2018, and opportunities will be explored for further developing this collaborative work. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/crossing-kingdoms-and-disciplines-living-art-synthsys |
| Description | Sci-Screen Presentation |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | A Sci-Screen event provided a light-hearted backdrop for Centre members to engage the audience of Edinburgh Skeptics in a more serious dialogue about science, its representation and its communication. Dr Jane Calvert of SynthSys and Science, Technology and Innovation Studies, provided an introduction to media monsters and the necessity for human connectivity respectively. Synthetic Biology could be viewed as a looming technological monster - who and how do we manage this for the greater good. Over 40 people turned up for this event which provoked a lot of heated debate. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/young-frankenstein-%E2%80%93-cautionary-tale-or-valuable-lesson |
| Description | Science Art Training Workshops |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | We welcomed Jenni Rant and the SAW Training team back to Edinburgh for our second annual training event bringing their innovative approach to teaching science to children using the power of words and pictures. This year, thanks to support from Lorna Macdonald, Principal Officer Creative Learning for Schools and Lifelong at the City of Edinburgh Council, we had great participation from local primary school teachers for the entire day. We subsequently ran workshops in seven primary schools reaching over 200 children in the Edinburgh region. This activity is in demand from teachers and children and we plan to train our local PE practitioners in the University to deliver the training. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-second-year |
| Description | Science Art Workshop |
| 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 | Astrid Jaekel, a teaching Fellow and course coordinator of first year illustration at the Edinburgh College Art was keen to bring science into her classroom; the resulting - 'Long Story Short' - is based on the idea of the Illustrator becoming part of the storytelling chain. First, they absorb and process information and then they turn the resulting story into artwork that will serve as a storytelling device. As part of a 5-week long storytelling project, first year Illustration students met with three practitioners from different fields: Master storyteller David Campbell, Sculptor Duncan Robertson and Scientist Prof Bill Earnshaw. Each gave insight into their professions and the relevance of storytelling within their practice. The final task of the project took inspiration from scientific methods of research as well as collaborations between artists and scientists. In response to the events of this day, students had to create an illustrated, sequential, narrative piece containing a minimum of four panels. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/science-muse |
| Description | Science Art Writing Training for Schools 2017 |
| 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 | A group of 20 teachers, scientists, poets and artists went 'back to school' to learn the SAW Trust's innovative approach to teaching science with a view to applying this in schools. Over May/June they then developed and delivered innovative workshops for primary school children in five local schools. This was a great success and all schools felt that the activities enriched their teaching of the science subjects. Several schools are interested in participating again. The activity has also enabled further engagement with key members of local education authority and Councis looking to better work with Higher Education and around the area of creativity and multidisciplinarity. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-science-art-workshop |
| Description | Science Art Writing Training for Schools 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | A group of 32 teachers, scientists, writers and artists attended to learn more about the SAW Trust's fun and innovative approach to teaching science through pictures and words. Jenni Rant (SAW training lead and scientist) and colleagues Mike O'Driscoll (writer) and Chris Hann (poet) inspired the room with ways to explore DNA and cells using everything from pipe cleaners and paints to balloons and polystyrene balls. The 'class of 2018' excelled themselves in their creative interpretations of the cell structure. At the end of the day, the trainers selected seven teams to develop and take workshops into schools in the Edinburgh and the Lothians. We subsequently ran workshops in 5 schools across the Edinburgh region reaching 180 children. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.synthsys.ed.ac.uk/news/saw-trust-inspires-again |
| Description | Scientist Next Door |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The Scientist Next Door project aims to support families by creating a new inclusive culture and learning science together. The website www.scientist-next-door.org is a platform to provide interesting materials, experiments and to organise calls. Families can participate in video-calls around a topic of their interest with a group of scientists, and ask them questions and do experiments together, guided or demonstrated by scientists. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ed.ac.uk/biology/synthsys/news-and-events/news-2020/talk-to-your-scientist-next-door |
| Description | SynBioBeta London 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | The Centre had a joint exhibit at the London SynBioBeta conference in April 2017. This 2 day event brings together industry, investors and researchers in synthetic biology and is a flagship event for synthetic biology in the UK. Attendance > 500. Centre manager chaired a session on Synthetic Biology and Novel Materials. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.synthsys.ed.ac.uk/news/synbiobeta-london-2017 |
| Description | The Rt Hon Lord Henley, Parliamentary Under Secretary of State at the Department for Business, Energy and Industrial Strategy (BEIS) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Rt Hon Lord Henley, Parliamentary Under Secretary of State at the Department for Business, Energy and Industrial Strategy (BEIS), visited the Centre for Synthetic and Systems Biology. He was provided an overview of the University's plan to develop a biotech hub linking together the many areas of expertise in this highly multidisciplinary field. Lord Henley requested further information about the challenges and opportunities for synthetic biology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.synthsys.ed.ac.uk/news/business-minister-visits-centre-and-foundry |
| Description | Translation of covid-19 research into multiple languages |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | SynthSys students, postdocs and group leaders are among more than fifty people who have contributed their scientific and linguistic knowledge to make translations of the presentations at the Edinburgh Coronavirus workshop available in over twenty languages. Providing factual and unbiased interpretations of insights emerging from Covid-19 research is critical. The Edinburgh Infectious Diseases Community came together to make information much more accessible for people whose first language is not English. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ed.ac.uk/biology/synthsys/news-and-events/news-2020/university-project-makes-covid-19-in... |
| Description | Webinar: Colony picking in a fully automated DNA assembly workflow |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this webinar Edinburgh Genome Foundry staff members described how they integrated for the first time a particular piece of equipment (a colony picker from Molecular Devices) in the workflow of automated DNA assembly. This is valuable information for researchers or industry who want to set up a similar setup and also educational for students and other audience to understand the automated workflow of DNA assembly, a key process in the growing field of synthetic biology. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Wigtown Big Bang Weekend 2018 |
| 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 | The Big Bang Weekend is an annual event that explores different aspects of science for the public in Wigtown, Scotland's Book Town. This year the topic was 'Is it alive?' which explored what we mean by life at both large and small scales. There were great presentations on robots and artificial intelligence, whether or not there is life out there in space, and a comedian's exploration of human consciousness (or lack thereof). Centre affiliated social scientist, Dr Erika Szymanski, wowed the audience at the Big Bang Weekend in Wigtown with a sparkling presentation on yeast, its genome and how we should take better care of it. Around 80 people attended the talk and there were many questions. Erika got a lot of very positive feedback. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.bbc.co.uk/news/uk-scotland-south-scotland-42902773 |
| Description | Workshop 'What can art, STS and synthetic biology do together?' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Centre co-hosted a workshop with artists at the University of Western Australia to explore the intersections between art, synthetic biology and social science. It involved artists, designers and synthetic biologists from Australia, the UK and the USA. |
| Year(s) Of Engagement Activity | 2018 |