CENTRE FOR SYNTHETIC BIOLOGY OF FINE AND SPECIALITY CHEMICALS

Lead Research Organisation: University of Manchester
Department Name: Chemistry

Abstract

The SYNBIOCHEM Centre will be a UK and European Centre of Excellence for Synthetic Biology in relation to fine and speciality chemicals and production. It will provide a national focus that spearheads UK academic and industrial research to accelerate the application of synthetic biology in fine and speciality chemicals production and the generation of new state-of-the-art tools to facilitate this translation.

Synthetic biology is an emerging science that has the capacity to transform the UK and European industrial landscape in sustainable manufacturing processes across all industrial sectors. UK industries, from large multinationals to a large number of small and medium enterprises, are internationally well positioned to benefit from the multitude of novel technologies developed in synthetic biology laboratories. To accelerate the translation of synthetic biology towards the fine and speciality chemicals market, the Centre will unite technologies, tools and ideas that emerge from academic institutions throughout the country, harvest synergies across the industrial and scientific sectors, and address the novel ethical and regulatory challenges faced by a disruptive technology at the interface of life sciences, chemistry and engineering.

The Centre will be located in the Manchester Institute of Biotechnology, a unique cross-disciplinary research centre at the University of Manchester, bringing together more than 500 researchers with expertise in molecular biology, chemistry, engineering, material and computing science, and medicine at the forefront of international developments in synthetic biology. As part of the MIB, the Centre will build on a long and distinguished track record in spin-off formation and translating innovative research to industrial application, including a substantial portfolio of partnerships, e.g., with Syngenta, GSK, BASF and Shell.

The Centre will operate an open and inclusive approach driven by the unique industrial needs of synthetic biology. This will allow it to harness the scientific expertise of the synthetic biology community at Manchester and throughout the country, by facilitating multiple research projects positioned primarily at the Technology-Readiness Levels 1 to 3, but also including industry-driven academic-led proof-of-concept and proof-of-utility projects with partners from industry and academia at the higher Technology-Readiness Levels.

The Centre will develop major programs in the ethical and regulatory aspects faced by synthetic biology. By initiating early dialogue on responsible innovation, providing expertise, guidance and training in responsible governance of synthetic biology innovation, and promoting public engagement and training for the research community, the Centre will create the conditions for accelerated exploitation of the opportunities generated by the rapid advances in synthetic biology for the benefit of the UK economy. Colleagues at the Manchester Institute of Science Ethics and Innovation will be central to this effort to mitigate technology risks (real or perceived) associated with this new industrial revolution, while the University of Manchester Business School will develop the responsible innovation and market analysis strategies required to realize emerging opportunities as science progresses. This will be supported by analysis and stimulation of collaborative developments in this multi-disciplinary/multi-sector field.

The Centre will respond continuously and flexibly to developing needs from industry partners new scientific trends across the academic landscape. Its strategic goal is to position UK industry at the forefront of the exploiting synthetic biology for chemicals and natural products biosynthesis by providing a 'one-stop access' to world class physical infrastructure/scientific knowledge that will propel fine and speciality chemicals production towards sustainable manufacturing processes.

Technical Summary

Manchester has a unique vision for fine and speciality chemicals production using synthetic biology that has been built on a long term strategy. SYNBIOCHEM is central to this strategy and will develop a series of unique and highly integrated interdisciplinary technology platforms and a truly world-leading physical infrastructure for contemporary fine and speciality chemicals production. These technology platforms will drive multiple science programs to accelerate delivery of bespoke synthetic biology solutions for chemicals synthesis by adopting modular 'plug-and-play' platform approaches and a production pipeline that embraces the 'design-build-test-deploy' life-cycle for turning knowledge assets into innovative chemicals production solutions. Dedicated technology scientists will drive these technology platforms together with expert academic leads, and the technology platforms will be managed within the governance framework of the Centre. This will ensure rapid delivery and implementation of tools/technologies across multiple programs relevant to fine and speciality chemicals production. Our vision is that SYNBIOCHEM will become the UK and European Centre of Excellence for expertise and resources for the (re-)design, engineering and analysis of biological parts, devices and systems for sustainable fine and speciality chemicals production. SYNBIOCHEM will stimulate innovation in chemicals biosynthesis and promote leading capability development that will drive new interactions with industry and other stakeholders. SYNBIOCHEM will benefit from the highly multidisciplinary environment and collaborative culture of the Manchester Institute of Biotechnology (MIB), its extensive network of industry partners and other stakeholders, MIB's track record in technology and methodology development, and its reputation for delivering competitive biotechnology-focused research to deliver a Centre of Excellence in Synthetic Biology focussed on the fine and speciality chemicals sector

Planned Impact

The SYNBIOCHEM Centre will generate societal and economic value through integration of wide-ranging and truly innovative research in synthetic biology in the fine and speciality chemicals areas. It will accelerate the translation of novel technology and science programs along the Technology-Readiness Levels towards commercialisation, and will be the national "One-Stop Access" for integration of synthetic biology approaches in fine and speciality chemicals production in terms of technology infrastructure and scientific expertise. The societal and economic value will be generated through the Centre's open collaborative culture, strong leadership and stakeholder engagement and excellence in the foundational and multidisciplinary science that is embedded in the Centre.

The general public will benefit from the open dialogue established by the Centre on the opportunities and risks associated with SynBio applications, through education and outreach activities. The public will be able to contribute their views to the ongoing debate on ethical aspects and help shape pathways to responsible innovation in the field. The Centre will actively provide opportunities for dialogue, bring together expertise (both in synthetic biology science and ethics) to provide the information needed to form informed opinions, and ensure public perspectives are gathered and deliberated upon at an early stage. The insights gained will contribute to the design of effective and responsible research, innovation and governance strategies for emerging synthetic biology technologies.

UK industries across a large range of sectors (e.g., fine chemicals, energy and fuels, pharmaceuticals and therapeutics, biomedical engineering and sensing, agriculture and food) will benefit from the expertise in the Centre and the accelerated access to advances in synthetic biology research. IP generation through activities in the Centre will lead to increased UK-based patent applications, licensing opportunities and potential spin out activity. The activities of the Centre will provide UK companies with a competitive advantage on the global market, based on more efficient and sustainable use of resources and the resulting increase in economic performance. Science in the synthetic biology field is advancing rapidly, and the Centre will progress synthetic biology technology-based applications on route to market by 2020 and beyond. The accelerated transfer of responsible synthetic biology technologies to industrial applications will support cleaner production processes (e.g. green chemistry), more sustainable manufacturing and energy sources (e.g. biofuels), and contribute to the creation of jobs and wealth within the UK chemicals and natural products industries and wider economy.

The UK academic synthetic biology community will benefit from early engagement with responsible synthetic biology research and innovation considerations. Early engagement with industrial partners will enable research at the cutting edge of synthetic biology science that is relevant to market trends. The resulting increased international visibility of UK synthetic biology activities and the intersector networking opportunities will stimulate excellence in synthetic biology research throughout the UK. The multidisciplinary interaction across scientific domains (biology, chemistry, computational science, engineering and the social sciences) will further strengthen the UK research base in synthetic biology. Synthetic biology human capital development throughout the UK will benefit from the inter-institution, interdisciplinary and intersectoral capabilities of the Centre. Students (UG and PG) and academic researchers will benefit from training, mentoring and other Centre activities to advance synthetic biology research applications, industrial engagement, entrepreneurship, and deliberation of responsibility in synthetic biology research and innovation and its societal and economic implications.

Publications

10 25 50
 
Title Illustrations 
Description We hosted the author and book illustrator, Lynne Chapman in our laboratories and meetings where she created alternative perspectives of our activities in a series of sketches. 
Type Of Art Artwork 
Year Produced 2016 
Impact We have used the drawings on our website and printed materials. Displays of the artwork were featured in Manchester exhibitions open to the general public. 
 
Title Perfomance Poetry 
Description SYNBIOCHEM worked with Matt Pranesh a performance poet who presented his take on Synthetic Biology and its future impact at an ESOF spin off activity (evening performance) hosted in the John Rylands Library, Manchester. 
Type Of Art Performance (Music, Dance, Drama, etc) 
Year Produced 2016 
Impact This was an interesting interaction of scientists and a poet which resulted in a public performance highlighting SynBio. 
 
Description EU-IBISBA (ESFRI Candidature submission)
Geographic Reach Europe 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
Description External advisor for European Commission Scientific Committee on Emerging and Newly Identified Health Risks on synthetic biology
Geographic Reach Europe 
Policy Influence Type Citation in other policy documents
Impact Made huge impact on the policy for defining Synthetic Biology, identifying the risks for Synthetic Biology and future recommendations in Synthetic Biology risk assessment at a European level.
 
Description Strategic review for Industrial Challenge Fund
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description Transatlantic perspective on emerging issues in biological engineering
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a national consultation
 
Description UK Policy Jisc FAIR in Practice
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description UK SynBio Strategic plan 2016
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description BBSRC
Amount £1,170,000 (GBP)
Funding ID BB/N023536/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 08/2021
 
Description BBSRC ALERT 16
Amount £341,417 (GBP)
Funding ID BB/R000093/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 05/2018
 
Description BBSRC ALERT 16
Amount £214,394 (GBP)
Funding ID BB/R000069/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2017 
End 07/2018
 
Description BBSRC BIOCATNET award
Amount £46,647 (GBP)
Funding ID IB-SCA 001. 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Department Networks in Industrial Biotechnology and Bioenergy (NIBB)
Sector Academic/University
Country United Kingdom
Start 11/2017 
End 02/2018
 
Description BBSRC FTMA
Amount £141,550 (GBP)
Funding ID BB/R506497/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 03/2019
 
Description BBSRC International award
Amount £43,786 (GBP)
Funding ID BB/N021037/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 07/2020
 
Description BBSRC Japan Partnering award
Amount £51,000 (GBP)
Funding ID BB/N021975/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 06/2020
 
Description BBSRC Partnering award
Amount £51,000 (GBP)
Funding ID BB/N021975/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 07/2020
 
Description BBSRC responsive mode Munro
Amount £462,081 (GBP)
Funding ID BB/N006275/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 06/2019
 
Description BBSRC slola Micklefield
Amount £1,168,602 (GBP)
Funding ID BB/N23536/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2016 
End 01/2021
 
Description BBSRC-FASEP
Amount £2,082,439 (GBP)
Funding ID BB/P01738X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2017 
End 12/2021
 
Description Dstl award
Amount £99,601 (GBP)
Funding ID DSTLX1000104112 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 07/2016 
End 03/2020
 
Description Dstl award
Amount £108,000 (GBP)
Funding ID 1000101995 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 05/2016 
End 05/2017
 
Description Dstl award
Amount £83,220 (GBP)
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 04/2017 
End 01/2018
 
Description Dstl award
Amount £96,407 (GBP)
Funding ID DSTLX-100012335 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 07/2017 
End 06/2018
 
Description Dstl award
Amount £107,544 (GBP)
Funding ID 1000101995 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2017
 
Description Dstl award
Amount £99,000 (GBP)
Funding ID 10000104112 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 07/2016 
End 03/2017
 
Description Dstl award
Amount £500,000 (GBP)
Funding ID DSTLX1000101893 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 08/2016 
End 07/2019
 
Description EPSRC materials
Amount £401,000 (GBP)
Funding ID EP/N025504/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 05/2019 
End 05/2019
 
Description EU H2020
Amount £304,312 (GBP)
Funding ID MS SPIDOC 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 09/2018 
End 08/2021
 
Description EU H2020
Amount £100,399 (GBP)
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 01/2017 
End 12/2019
 
Description EU H2020 chassis
Amount £1,168,602 (GBP)
Funding ID 720793-2 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 01/2017 
End 12/2020
 
Description EU H2020 chassis
Amount £1,289,926 (GBP)
Funding ID 720793-2 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2017 
End 12/2020
 
Description EU H2020 chassis
Amount £819,061 (GBP)
Funding ID 764364 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 01/2018 
End 10/2021
 
Description EU H2020-GARRI-2015-1
Amount € 1,486,175 (EUR)
Funding ID 710500 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 06/2016 
End 11/2018
 
Description EU H2020-GARRI-2015-1
Amount £148,000 (GBP)
Funding ID 710500 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 06/2016 
End 11/2018
 
Description Future Biomanufacturing Research Hub
Amount £10,284,509 (GBP)
Funding ID EP/S01778X/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 04/2019 
End 03/2026
 
Description H2020 Infrastructure
Amount € 5,000,000 (EUR)
Funding ID H2020: IBISBA 1.0 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 09/2017 
End 08/2021
 
Description OLEAginous yeast platforms for FINE chemicals - OLEFINE
Amount £408,476 (GBP)
Funding ID ERC H2020-NMBP-BIO-2016 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2018 
End 12/2021
 
Description ONRG
Amount £13,980 (GBP)
Funding ID N62909-17-1-2052 
Organisation ONRG Office of Naval Research Global 
Sector Public
Country United States
Start 05/2017 
End 06/2017
 
Description Royal Society
Amount £229,000 (GBP)
Funding ID 1000101995 
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 12/2016 
End 12/2018
 
Description ShikiFactory
Amount £8,000,000 (GBP)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2019 
End 12/2022
 
Description The aspergillus fumigatus gene and non-coding RNA knockout library.
Amount £771,344 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2021
 
Description UCB CASE
Amount £80,000 (GBP)
Organisation UCB Pharma 
Sector Private
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description University matched funding
Amount £500,000 (GBP)
Organisation University of Manchester 
Sector Academic/University
Country United Kingdom
Start 08/2016 
End 07/2019
 
Title Automated Directed Evolution library-screening platform 
Description Our Directed Evolution (DE) library-screening platform automates cell culture (colony picking, bacterial culture and protein expression) and protein purification (His-tag purification) processes in 96-well format. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Our Directed Evolution (DE) library-screening platform is providing methods that have supported the evolution of key enzymes in the chemical synthesis of mono-terpenes. 
 
Title Automated Ligase Cycling Reaction 
Description We have created an automated optimised ligase cycling reaction assembly platform for assembling genetic pathways to allow fully automated generation of large pathway libraries. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact This method is now providing automated generation of large pathway libraries to a wide cohort of users. 
 
Title GenORator 
Description A novel methodology for creating variant libraries for directed evolution, which enables the mutation of large numbers of amino acid codons simultaneously in a controlled and precise manner. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact A patent application has been submitted to protect this methodology and its commercial use is currently being developed through proof-of-concept funding with companies. 
 
Title GeneGenie 
Description An optimised oligomer design tool for variant genetic library design. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact None as yet 
URL http://gene-genie.org
 
Title HTP MS quantification 
Description The Centre's Test team has contributed major innovative mass spectrometry (MS) screening protocols that provide rapid high-throughput quantification for our target compounds, complemented with new data analysis/processing tools. Together these are now providing vital analysis for wide-ranging projects. These include: HTP limonene quantification method using GC-QToF MS (<5-10 mins per sample (compared with >30 mins); HTP flavonoid and alkaloid targeted MS measurements using LC-QqQ MS in 96-well format with reduced screening times of approx. 2min per sample; New analysis software developed (iTERP, R2QqQ and MetTrap) R packages for rapid MS data analysis. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact These tools and methods are providing rapid identification and quantification of our target compounds and underpins much of the work in the Centre. We will make these available to wider audiences in the next year. 
 
Title Real-time screening of bacterial colonies 
Description To identify new biocatalytic activities is a widely adopted tool in biotechnology, but is constrained by the requirements for colorimetric or tag-based detection methods. Our unique label-free screening platform for biotransformations in live colonies using desorption electrospray ionization coupled with ion mobility mass spectrometry imaging (DiBT-IMMS). The screening method has been demonstrated for both ammonia lyases and P450 monooxygenases expressed within live bacterial colonies, and enables multiplexing of enzyme variants and substrate libraries simultaneously. Yan C, Parmeggiani F, Jones EA, Claude E, Hussain SA, Turner NJ, Flitsch SL, Barran PE. (2017). Real-time screening of biocatalysts in live bacterial colonies. J. American Chemical Soc. 139, 1408-11. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact This new label-free platform for screening bio-transformations in live colonies is likely to provide new knowledge and insights to identify biocatalytic activities. 
 
Title MIBiG 
Description Bacteria, fungi and plants produce an enormous variety of small functional molecules with manifold biological activities, e.g., as antibiotics, immunosuppressants, and signaling molecules. The biosynthesis of such molecules is encoded by compact genomic units (biosynthetic gene clusters). Over the past decades, hundreds of biosynthetic gene clusters encoding the biosynthesis of secondary metabolites have been characterized. Although dozens of biosynthetic gene clusters are published and thousands are sequenced annually (with or without their surrounding genome sequence), very little effort has been put into structuring this information. Hence, it is currently very difficult to prioritize gene clusters for experimental characterization, to identify the fundamental architectural principles of biosynthetic gene clusters, to understand which ecological parameters drive their evolution, and to obtain an informative 'parts registry' of building blocks for the synthetic biology of secondary metabolite biosynthesis. Therefore, developing a genomic standard for experimentally characterized biosynthetic gene clusters (e.g., Minimum Information about a BIosynthetic Gene cluster, MIBiG) would be of great value to the field of microbial secondary metabolism. Building on the MIxS standards for ecological and environmental contextualization, information on, e.g., enzyme function, substrate specificities, functional subclusters, regulatory and transport systems, operon structure, chemical moieties of the end compound and its intermediates, biosynthetic precursor compounds, compound bioactivity and molecular targets and compound toxicity could be added to allow cross-linking the information to biochemistry, pharmaceutical properties, genomic structure and ecology. Using the already developed computational pipeline for analysis of biosynthetic gene clusters antiSMASH (http://antismash.secondarymetabolites.org/), which has quickly become a standard in the field, information on characterized biosynthetic gene clusters will be linked to the untapped wealth of thousands of unknown gene clusters that have recently been unearthed by massive genome sequencing efforts. Taken together, this has the potential to guide the characterization of new metabolites by allowing to optimize the sampling of diversity at different levels and to identify the biochemical, genomic and ecological parameters that are key predictors of pharmaceutically relevant biological activities. Moreover, it can transform the unordered pile of literature on secondary metabolites into a structured and annotated catalogue of parts that can be used as building blocks to design new biochemical pathways with synthetic biology. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact MIBiG will the better description and contextualization of sequence data, of important sequence elements, with concrete biotechnological applications that will increase the visibility and applicability of the GSC and its mission in the fields of applied microbiology, synthetic biology, natural products chemistry and enzymology. 
URL http://gensc.org/projects/mibig/
 
Description University of Osaka metabolomics 
Organisation Osaka University
Country Japan 
Sector Academic/University 
PI Contribution We aim:To establish strong and successful research collaborations in the analytical area of synthetic biology for fine and speciality chemical between top research groups in the UK and Japan for added potential value to BBSRC and JST science portfolios; Share access to top quality research facilities, technical knowledge and expertise in both institutions, and benefit from the added strengths implied by the complementarity of instrumentation at each institute, helping develop imaging MS as a functional tool in synthetic biology; Provide early career scientists/postdoctoral fellows an opportunity to develop their own expertise and ideas by experiencing international groups and helping prepare their own independent grant applications; Establish joint proof-of-concept research resulting in joint grant applications and collaborative partnerships
Collaborator Contribution The Osaka team will help to establish joint proof-of-concept synthetic biology based research using novel imaging mass spectrometry platforms in tandem with established untargeted metabolomics methodologies;To establish strong and successful research collaborations in the analytical area of synthetic biology for fine and speciality chemical between top research groups in the UK and Japan for added potential value to BBSRC and JST science portfolios; Share access to top quality research facilities, technical knowledge and expertise in both institutions, and benefit from the added strengths implied by the complementarity of instrumentation at each institute, helping develop imaging MS as a functional tool in synthetic biology; Establish joint proof-of-concept research resulting in joint grant applications and collaborative partnerships
Impact The project has just started but we have already started collaborations with the University of Osaka metabolomics group by inviting them to Manchester and holding a Bacterial Metabolomics Workshop on 24th June 2016 with invited speakers: Nicola Zamboni (ETH Zurich), Eiichiro Fukusaki (Osaka University), Karsten Hiller (University of Luxemburg), Sanjay Swarup (National University of Singapore), Shuichi Shimma (Osaka University), Sastia Putri (Osaka University), Rainer Breitling (University of Manchester). In 22-27 May 2017, Katherine Hollywood (named from Manchester) visited Osaka for one week; Eriko Takano and Rainer Breitling visited University of Osaka 14th March 2017 and both gave a seminar to the MSc and PhD students; PhD student Katsuaki Nitta visited to University of Manchester, 26 June-31 July 2017 to learn Streptomyces cultivation techniques and the QExactive analysis; Eriko Takano visited Aug 2017 and had a close discussion with Sastia Putri, Prof Fukusaki and Katsuaki Nitta on the project; Dr Kamila Schmidt (1 Oct - 12 Oct 2018) and Prof Eriko Takano (1- 17 Oct 2018) visited University of Osaka, Prof Fukusaki's lab to work together with Sastia Putri and Katsuaki Nitta on Streptomyces metabolomics using wt M145 strain versus antibiotic overproducer to determine possible metabolic engineering strategies arising from the semi-targetted metabolomics analysis-- this is a multidisciplinary collaboration: synthetic biology, metabolomics, computational modelling; Takano, Breitling lab in University of Manchester had several Skype conferences with Fukusaki lab, Sastia Putri and Katsuaki Nitta on metabolic modelling of Streptomyces coelicolor -- this is a multidisciplinary collaboration: metabolomics, computational modelling; Takano has been invited to be a honorary Professor/Cross-appointment at the University of Osaka, allowing her to stay in Osaka for 4 weeks/year; A new project collaboration has started with a MSc student Marvin Nathanael Iman, who is in the Fukusaki lab.
Start Year 2016
 
Title Biosynthetic Mint: 
Description A partnership with GlaxoSmithKline resulted in a UoM patent for producing a menthol isomer. 
IP Reference US20160289702 
Protection Patent granted
Year Protection Granted 2016
Licensed Commercial In Confidence
Impact None
 
Title Compositions and methods for recombinant biosynthesis of propane 
Description New synthetic biology routes to renewable bio-propane. 
IP Reference US20170218401 
Protection Patent application published
Year Protection Granted 2017
Licensed Yes
Impact None to date
 
Title Monoterpenoid biosynthesis 
Description This follows on from the early patenting of the biosynthetic routes to menthol and the second patent protects the identity of a key evolved enzyme derived from keto steroid isomerase. 
IP Reference GB1719530.6 
Protection Patent granted
Year Protection Granted 2017
Licensed No
Impact None as yet.
 
Title Polyketides 
Description Field of the Invention The present invention relates to a method for expressing a soluble type II polyketide synthase (PKS) in an E.coli host, the method comprising introducing a nucleic acid sequence 
IP Reference 1810747.4 
Protection Patent application published
Year Protection Granted 2018
Licensed No
Impact Nothing yet
 
Title Variant Nucleotide Library 
Description The application related to the GenORator methodology for creating variant libraries for directed evolution. 
IP Reference GB1709308.9 
Protection Patent application published
Year Protection Granted 2017
Licensed No
Impact This work is being developed through further proof-of-concept funding.
 
Title Biochem4j 
Description A freely available graph database of integrated chemical, reaction, enzyme and taxonomic data, based on the neo4j database. biochem4j (71) has applications in pathway elucidation, enzyme selection and metabolic modelling, acting as a knowledge base which brings together distributed data into an integrated and queryable system. It currently contains relevant information of known relationships between reactions (36765), chemicals (19735), enzymes (245704) and organisms (8431). Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R. (2017). biochem4j: Integrated and extensible biochemical knowledge through graph databases. PloS one, 12, e0179130. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This graph database is providing the Centre with an extended knowledge base to inform our chemical pathway design. 
URL http://biochem4j.org
 
Title CodonGenie 
Description Freely available web application for designing ambiguous codons to support these protein mutagenesis applications. Given a user-defined target collection of amino acids and an intended host organism, CodonGenie will design and analyse all ambiguous codons that encode the required amino acids. The codons are ranked according to their efficiency in encoding the required amino acids while minimising the encoding of additional amino acids and stop codons. Swainston N, Currin A, Green L, Breitling R, Day PJ, Kell DB. (2017). CodonGenie: optimised ambiguous codon design tools. PeerJ Computer Science, 7, e120. DOI: 10.7717/peerj-cs.120. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Impact This in silico design tool provides optimal design of biosynthetic parts to support higher efficiency use and support for protein mutagenesis applications. 
URL http://codon.synbiochem.co.uk
 
Title PartsGenie 
Description A new web application for the design of reusable synthetic biology parts. PartsGenie offers simultaneous codon optimisation, RBS design, CDS RBS removal, assembly compatibility and synthesis compatibility. It is designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such designs in community-developed data standards such as Synthetic Biology Open Language (SBOL), and the sharing of designs in journal-recommended data repositories (JBEI-ICE). It facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie has been used for the design of most synthetic DNA used in the SYNBIOCHEM Centre and elsewhere in the MIB and is now freely available to the wider synthetic biology community. Dobson PD, Batista-Navarro R, Ananiadou S, Mendes P, Kell DB, Swainston N. A Metabolic reaction balancing web service for computational systems biology. BMC Syst Biol. In review. Aug. 2017. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact A new design tool for the design and optimisation and dissemination of reusable synthetic biology parts in a single application. 
URL http://parts.synbiochem.co.uk
 
Title RetroPath2.0 
Description To expand access to diverse chemical targets we have continued to develop our retrosynthesis approach that explores the chemical biosynthetic space. RetroPath2.0 provides an automated open source workflow based on generalized reaction rules that performs retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its ease of use and the versatility of its applications make this tool a valuable addition to the biological engineer workbench. We demonstrated its application for the identification of alternative biosynthetic routes through enzyme promiscuity. Furthermore, we demonstrated its ability to perform inverse molecular design and search bioactive molecules over chemical space, providing an automated procedure for chemical target prioritization. Delépine B, Duigou T, Carbonell P, Faulon JL. (2017). RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45, 158-70. Koch M, Duigou T, Carbonell P, Faulon JL. (2017). Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9(1):64. Lopez O, Pastor M, Sanz F, Carbonell P. (2018). Hepatotoxicity prediction by systems biology modelling of disturbed metabolic pathways using gene expression data. Methods in Molecular Biology, volume "Computational Toxicology", In press. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This new in silico design tool explores chemical biosynthetic space to identify optimum biosynthetic routes and associated enzymes for new synthetic gene pathway design that will enable biosynthetic routes towards the synthesis of chemical compounds in microorganisms. 
URL http://www.myexperiment.org/workflows/4987.html
 
Title Selenzyme 
Description The online enzyme selection tool for metabolic pathway design, Selenzyme, is helping us to mine candidate enzyme sequences for any desired target reaction or set of reactions in a pathway. The tool combines multiple data sources and screening of target reactions not necessarily existing in databases, allowing the search for alternative routes or pathways leading to non-natural products. Selenzyme uses our biochem4j graph database as its main data source. Selenzyme also provides bespoke sequence selection for automated workflows where a resulting pathway design is submitted to the next stage of the pipeline. Carbonell P, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL. Selenzyme: Enzyme selection tool for pathway design. Bioinformatics. Accepted. Sept. 2017. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This in silico design tool is providing the Centre with alternative enzyme pathways for the production of natural and non-natural products in our biosynthetic production lines. 
URL http://selenzyme.synbiochem.co.uk
 
Title SensiPath 
Description SensiPath (http://sensipath.micalis.fr/): web server (co-developed with Micalis/INRA) to identify putative biochemical transformations of our target compounds to allow identification of easily detectable compounds for screening and identification of potential biosensors. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Open Source License? Yes  
Impact New in silico modelling tool for identification of biochemical transformations made available for wider use. 
URL http://sensipath.micalis.fr/
 
Company Name C3 Biotechnologies Ltd 
Description A licensing company for technology that enables production of bio-propane 
Year Established 2015 
Impact None yet - too early
 
Description Blog posts 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The secretive 'second world' of human synthetic biology (A. Balmer, The Guardian, 18/05/16); Synthetic Biology: Reshaping the Future (PLOS SynBio Blog 1/16) https://t.co/v91JxkPFWf.
Year(s) Of Engagement Activity 2016
URL https://www.theguardian.com/science/political-science/2016/may/18/the-secretive-second-world-of-huma...
 
Description British Science Week 
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 SYNBIOCHEM researchers and our iGEM team hosted an interactive demonstration of fragrance compounds at the UoM annual British Science Week fair (14-17/03/17) and engaged visitors (~1100 students, ages 9 - 14) with the potential of synthetic biology approaches for green and sustainable chemical manufacture. Our RRI researchers also ran a stand collecting opinions on the production of menthol using synthetic biology (Annex 7).
Year(s) Of Engagement Activity 2017
 
Description College presentation Japan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Senior Experimental Officer, Adrian Jervis employed on the SYNBIOCHEM grant delivered a talk and Q&A session to Hiroo Gakuen Junior and High School pupils, Japan.
Year(s) Of Engagement Activity 2016
 
Description EPS Big Green Gathering 
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 Big Green Gathering was hosted in North Campus by the Faculty of Engineering and Physical Sciences on 8th March 2016. The event sought to engage ~150 members of the public with sustainable research initiatives from across the faculty, through the use of infographics designed by researchers. The submission by the MIB, detailing the area of industrial biotechnology and including examples of research from the institute, won 1st prize in the popular votes across all three categories: most informative, most creative and most interesting. Researchers from the MIB visited Levenshulme High School on 15th March 2016 to take part in their annual science exhibition. Around 400 key stage 3 and 4 students were engaged with the research conducted at Manchester in the field of glycoscience through arts and crafts style building of glycans and the popular cell invaders video game.
Year(s) Of Engagement Activity 2016
 
Description ESOF 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ESOF - EuroScience Open Forum 2016 was held in Manchester. SYNBIOCHEM hosted:
Science program (joint with EU programme SYNENERGENE) - Synthetic Biology and the new bio-industrial revolution - how will we ensure Responsible Research and Innovation - attended by approx. 70 people with 4 science talks followed by round table discussions.
Science to Business program - Synthetic Biology - the pathway to commercialisation. panel discussion with industry leads (GSK, Synthace, ThermoFisher, SynBiCite, BioBricks Foundation).
Early Career Researcher event in the MIB - Perspectives on Synthetic Biology.
Year(s) Of Engagement Activity 2016
URL http://www.esof.eu/
 
Description ESOF sessions 
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 Half-day workshop "Opening doors on RRI" provided a unique discussion platform on putting RRI policies into practice and brought together experts from across the EU.
It featured debates and practical workshops.
Year(s) Of Engagement Activity 2016
URL http://manchester2016.esof.eu/en/the-programme/responsible-research-and-innovation.html
 
Description ESOF sessions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A science programme of short talks and dialogue session - "Will synthetic biology deliver the new Bio-industrial revolution - and how can we ensure Responsible Research and Innovation?". This session was a joint venture between SYNBIOCHEM and SYNENERGEN (EU FP7 RRI consortium).
Year(s) Of Engagement Activity 2016
URL http://manchester2016.esof.eu/en/the-programme/science-programme.html
 
Description ESOF sessions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A Science to Business Programme as part of the Euro Science Open Forum (Manchester 2016), "SynBio - the pathway to commercialization". This was a panel debate session with industry representatives and academic input.
Year(s) Of Engagement Activity 2016
URL http://manchester2016.esof.eu/en/the-programme/science-to-business-programme.html
 
Description MIB Open Day Stands/Tours 
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 Manchester Institute of Biotechnology Open Day provides an interactive science event open to schools and colleges across the North West. SYNBIOCHEM hosted an interactive stand and provided laboratory demonstrations that showcased the D/B/T pipeline at this years event (24/11/17) to approx. 180 A' Level students.
Year(s) Of Engagement Activity 2018
 
Description MIB Open Day Stands/Tours 
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 Manchester Institute of Biotechnology Open Day provides an interactive science event open to schools and colleges across the North West. SYNBIOCHEM hosted an interactive stand and provided laboratory demonstrations that showcased the D/B/T pipeline at this years event (23/11/18) to approx. 160 A' Level students.
Year(s) Of Engagement Activity 2018
 
Description MIB Open Day Stands/Tours 
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 Schools
Results and Impact At Institute Open Day members of research group presented exhibits on topics of enzyme catalysis, synthetic biology, light activated biology and 'proteins' in general. Also demonstrated use of laboratory equipment on lab-tours run for attending students. Event was well received by both students and their teachers and seemed to inspire interest in the subject.

No defined impacts realised to date
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
 
Description Multi-Lingual Science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact The Centre, supported by Dr Nick Weise (Lecturer, E-Learning Lead, MIB) has been involved with a number of Multilingual Manchester interactions at which our scientists delivered interactive science sessions at language schools at the weekend. A second visit to the local supplementary language Huaxia Mandarin School (19/03/17) introduced students to the chemistry of enzymes and sugars in Mandarin Chinese (Yan, Kwok, Weise and Huang, 19/03/17).
Year(s) Of Engagement Activity 2018
 
Description NSEW Science Fair 
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 Members of research group presented exhibit on topics of enzymes and proteins. Event was well received by both students and their teachers and seemed to inspire interest in the subject.
Additional stand on SynBio for flavours and fragrances hosted by the iGEM team (2016)

No defined impacts realised to date
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
 
Description New Scientist Live 
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 A stand on a stand on DNA and Synthetic Biology of Fragrances at the New Scientist Live which is an award-winning, mind-blowing festival of ideas and discoveries for everyone curious about science and why it matters. For four days in September, it transforms London, the world's most exciting capital city, into the most exciting place in the universe. More than 140 speakers and 100 exhibitors come together in one venue to create an unrivalled atmosphere and energy, packed with thought-provoking talks, ground-breaking discoveries, interactive experiences, workshops and performances.
Year(s) Of Engagement Activity 2018
URL https://live.newscientist.com/
 
Description Pop-up stands on Menthol 
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 Menthol pop-up stands were presented by the SYNBIOCHEM RRI team at 1) The Body Experience (Manchester Museum, 18/03/2017( mainly attracted young families) and British Science week (13-17/03/17) to approx. 1000 school children.provided an opportunity to bring science into public spaces with diverse participants. These stalls invited passers-by to interact with the taste, smell, sight and touch of menthol products. Participants shared comments about their experiences with menthol products, offered thoughts about different ways of producing menthol, and views on menthol made through synthetic biology were captured (approximately 150 people stopped by providing approx. 270 postcard responses). Some people's reactions to synthetic biology focused on the use of E. coli and there were concerns that using bacteria could be problematic, whilst others were not personally worried about genetic engineering, but thought there were "other people" who would not like consumer products that were genetically engineered.
Year(s) Of Engagement Activity 2017
 
Description RI Talk - fuels of the future 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Manchester University Alumni Event: Hear from our panel of leading academics from the Manchester Institute of Biotechnology as they explore the challenges of developing the fuels of the future, the solutions we are delivering and why Manchester is leading the world in industrial biotechnology.

One of the main challenges our society faces is the dwindling level of oil reserves which we not only depend upon for transport fuels, but also plastics, lubricants and a wide range of petrochemicals. As the 21st century progresses, and we move towards more bio-based economies, we need solutions for the manufacture of chemicals that are smarter, more predictable and more sustainable.

From underpinning strategic research to the transfer of technology into the marketplace, The University of Manchester has a range of worldclass activities supporting the need for solutions that can play their part in meeting the global energy challenge.

Just as Manchester was at the heart of the Industrial Revolution, The University of Manchester is now leading the way, both nationally and across Europe, towards a bio-industrial revolution.

Panel: Professor Nigel Scrutton (Chair), Professor of Enzymology and Biophysical Chemistry, Professor David Leys, Professor of Structural Biology, Professor Eriko Takano, Professor of Synthetic Biology
Venue: The Royal Institution of Great Britain, London
Year(s) Of Engagement Activity 2018
 
Description ScienceX 
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 Scientists and engineers from the University of Manchester took over the various attractions in and around the Trafford Centre on 23rd and 24th April 2016 as part of their Science Extravaganza or ScienceX. With exhibits and activities in the main building, LEGOLAND, Chill Factore and the Sealife Centre an estimated 10,000 shoppers were engaged throughout the weekend as a non-traditional science outreach audience. Researchers from the MIB/SYNBIOCHEM were involved in coordination of and participation in ocean acidification demonstrations at the aquarium, chemistry of ice experiments at the artificial ski slope and various biotechnology-related exhibits in the main shopping areas. One participant even wrote on their feedback form that the part of the day they enjoyed the most was the main demonstration stand from the MIB:
Year(s) Of Engagement Activity 2016
 
Description ScienceX Trafford Shopping Centre 
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 As part of the UoM Faculty of Science and Engineering's strategy to engage non-traditional audiences researchers once again took over the Trafford shopping Centre (22-23/04/17) to talk to members of the general public about science and engineering. SYNBIOCHEM representatives hosted an interactive stand at the SEALIFE Centre that used simple experiments and leaflets to inform visitors about ocean acidification and provided the opportunity to learn about how the use of biotechnology could reduce atmospheric CO2 levels. SYNBIOCHEM Social science researchers engaged shoppers with synthetic biology research on menthol production. The opinions and queries received are being used as part of the Centre's RRI initiative to involve the public in the scientific development process.
Year(s) Of Engagement Activity 2018
 
Description ScienceX Trafford Shopping Centre 
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 Science stands at the Trafford Centre over the weekend in April 2018 used to communicate SYNBIOCHEM research and synthetic biology/Biotechnology in general.
Year(s) Of Engagement Activity 2018
 
Description Scientific and technological challenges in defining a new paradigm for sustainable biomaterials. 
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 SYNBIOCHEM worked closely with Dstl and the Office for Naval Research Global (ONRG) to deliver a workshop (MIB, 16-17/05/17) that explored the "Scientific and Technological challenges in defining a new paradigm for sustainable biomaterials". The meeting set out to discuss and identify the opportunities that SynBio can bring to the materials arena. The report helped define a roadmap for the development of infrastructure and expertise for the discovery, assembly and integration of widely diverse biomaterials and their composites, and the establishment of revolutionary new ways for biomaterials production and evaluation. This road map is being used to take this
convergence of SynBio and materials fields forward and develop funding for this area.
Year(s) Of Engagement Activity 2017
 
Description UKSynBio2017 
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 UKSynBio17 meeting held in Manchester was organised by Takano and Le Feuvre in partnership with the Biochemical Society (27-28/11/17). This event brought together the UK SynBio community (~230 attendees) with a fantastic line up of international keynote speakers from academia and industry, 19 selected short talks and 70 poster presentations.
Year(s) Of Engagement Activity 2014,2017
URL https://www.biochemistry.org/Events/tabid/379/MeetingNo/SA207/view/Conference/Default.aspx
 
Description UKSynBio2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact UKSynBio conference in Bristol. Attended by approximately 10 participants from SYNBIOCHEM
Year(s) Of Engagement Activity 2018