Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies
Lead Research Organisation:
Newcastle University
Department Name: Sch of Computing
Abstract
Synthetic biology involves the design and development of novel, useful biological systems, or the redesign of those systems that exist already. This approach promises to be of major value to society. Potential applications include the production of high-value materials, such as fine chemicals and pharmaceuticals, bio-remediation, sustainable energy, medical diagnostics, and agriculture.
In Synthetic Biology novel biological genetic circuits are developed using engineering principles in order to add the new properties to a given organism - called a host or chassis. The type of chassis used will vary according to the application and the circuit. For example, for food and agriculture it is highly desirable to use organisms that have been shown to be safe for human consumption. However, currently, most circuits are designed for, and tested in, a single organism such as the commonly used bacterium Escherichia coli. Moving these circuits to another organism requires the circuit to be re-engineered and retested in the new organism, a process which is very time consuming and costly. This process of 'refactoring' slows down research and costs industry a huge amount of time, effort and money.
A major problem is that the connections between the designed genetic circuit and the chassis organism are specific to a given species of chassis. So the genetic circuit ends up being redesigned to meet the new connections required for a different species. In our project we will standardise the connection between a given genetic circuit and the chassis organism. We will develop a set of academically and industrially useful organisms where the plug-in points for the genetic circuit will be the same for each of our organisms, allowing the genetic circuit to be moved from one organism to another with changes. We refer to this standardised plug-in system as a 'bio-adaptor'.
This programme grant will initiate a new field in Synthetic Biology, called 'Portabolomics'. This is a highly novel approach that has not been achieved by any other groups to-date. The key to the success of the project is to understand the networks of molecular processes that occur in a cell, since it is these networks that will need to be modified to make the bio-adaptor. We will apply a range of the state-of-the-art computing approaches to this task including many techniques from Computing Science, including network analysis, formal methods and data mining, for which our group has a wide range of world-leading expertise.
The results of the Portabolomics project will not only be a new system of major value to UK synthetic biology research and industry, but will enhance the field of computing science as new computational techniques will need to be developed to achieve our goals.
In Synthetic Biology novel biological genetic circuits are developed using engineering principles in order to add the new properties to a given organism - called a host or chassis. The type of chassis used will vary according to the application and the circuit. For example, for food and agriculture it is highly desirable to use organisms that have been shown to be safe for human consumption. However, currently, most circuits are designed for, and tested in, a single organism such as the commonly used bacterium Escherichia coli. Moving these circuits to another organism requires the circuit to be re-engineered and retested in the new organism, a process which is very time consuming and costly. This process of 'refactoring' slows down research and costs industry a huge amount of time, effort and money.
A major problem is that the connections between the designed genetic circuit and the chassis organism are specific to a given species of chassis. So the genetic circuit ends up being redesigned to meet the new connections required for a different species. In our project we will standardise the connection between a given genetic circuit and the chassis organism. We will develop a set of academically and industrially useful organisms where the plug-in points for the genetic circuit will be the same for each of our organisms, allowing the genetic circuit to be moved from one organism to another with changes. We refer to this standardised plug-in system as a 'bio-adaptor'.
This programme grant will initiate a new field in Synthetic Biology, called 'Portabolomics'. This is a highly novel approach that has not been achieved by any other groups to-date. The key to the success of the project is to understand the networks of molecular processes that occur in a cell, since it is these networks that will need to be modified to make the bio-adaptor. We will apply a range of the state-of-the-art computing approaches to this task including many techniques from Computing Science, including network analysis, formal methods and data mining, for which our group has a wide range of world-leading expertise.
The results of the Portabolomics project will not only be a new system of major value to UK synthetic biology research and industry, but will enhance the field of computing science as new computational techniques will need to be developed to achieve our goals.
Planned Impact
Synthetic Biology promises to substantially contribute to the UK economy and society. The Chancellor of the Exchequer G. Osborne estimated that the "global synthetic biology market is predicted to grow to £11 billion by 2016". The potential benefits of this rapidly growing field are detailed in a number of key documents including the UK Synthetic Biology Roadmap and the Royal Society Engineering report.
The Portabolomics project, once in place, will try to ensure the widest possible economic and societal impact from the research and resources it will generate. Since we are generating a new field for the synthetic biology community, a large amount of impact will fall into the domain of academic beneficiaries and is discussed above.
However, the key outputs emerging from the project will impact on industry directly. The new Portabolomics enabled chassis, our Portabolomics design specifications and standards, and our software systems will have the most immediate impact on industry. The translation of these outputs will be carried out initially with our industrial partners but will be widened through interactions with other organisations such as SynCiTE and CPI (see pathways to impact section). The biological outputs of the project will be of direct value to these partners as described in the main document (see Strand 2 of Pathways to Impact).
The novel computational approaches to the analysis of complex systems we develop will result in novel approaches for the computational design of synthetic biological systems that will be of clear commercial value in related fields such as neuroscience. Furthermore, this project will develop a wide range of novel research outputs in the fields of computing science. These outputs will be generically applicable, not only in the computing industry but in any other fields requiring advanced data mining strategies for Big Data and network approaches, such as distributed computing and network technology.
More widely, the work of this project in closing key gaps in our knowledge of bacterial processes at the molecular level will impact directly on the process of Synthetic Biology. In turn, this impact on how Synthetic Biology is done will open up new avenues for product development and the application of Synthetic Biology in a wide range of industrial domains. Moreover, the outputs of the project will enhance the capacity of Synthetic Biology to meet the next generation of challenges in a much wider range of fields such as those outlined in the UK Synthetic Biology roadmap.
The project will also have a strong impact on the general public. Our proposed SynBioSmith Sandbox (see Pathways to Impact, strand 5) will allow the general public to carry out synthetic biology experiments without needing to be present in a laboratory. This system will provide enthusiasts such as the DIY Bio movement with an enhanced understanding of the methodology behind synthetic biology and provide access to equipment in a safe and controlled environment. Our vision is to allow the general public to carry out Synthetic Biology over the Internet in a controlled and well-regulated manner making simple Synthetic Biology accessible to everyone. Further impact on the general public will be mediated by the Responsible Innovation section of our project (see strand 1 of the Pathways to Impact), and will allow social scientists will be able to reach out to a broad range of stake holders (scientists, industrialist, NGO, Government and the public).
The Portabolomics project, once in place, will try to ensure the widest possible economic and societal impact from the research and resources it will generate. Since we are generating a new field for the synthetic biology community, a large amount of impact will fall into the domain of academic beneficiaries and is discussed above.
However, the key outputs emerging from the project will impact on industry directly. The new Portabolomics enabled chassis, our Portabolomics design specifications and standards, and our software systems will have the most immediate impact on industry. The translation of these outputs will be carried out initially with our industrial partners but will be widened through interactions with other organisations such as SynCiTE and CPI (see pathways to impact section). The biological outputs of the project will be of direct value to these partners as described in the main document (see Strand 2 of Pathways to Impact).
The novel computational approaches to the analysis of complex systems we develop will result in novel approaches for the computational design of synthetic biological systems that will be of clear commercial value in related fields such as neuroscience. Furthermore, this project will develop a wide range of novel research outputs in the fields of computing science. These outputs will be generically applicable, not only in the computing industry but in any other fields requiring advanced data mining strategies for Big Data and network approaches, such as distributed computing and network technology.
More widely, the work of this project in closing key gaps in our knowledge of bacterial processes at the molecular level will impact directly on the process of Synthetic Biology. In turn, this impact on how Synthetic Biology is done will open up new avenues for product development and the application of Synthetic Biology in a wide range of industrial domains. Moreover, the outputs of the project will enhance the capacity of Synthetic Biology to meet the next generation of challenges in a much wider range of fields such as those outlined in the UK Synthetic Biology roadmap.
The project will also have a strong impact on the general public. Our proposed SynBioSmith Sandbox (see Pathways to Impact, strand 5) will allow the general public to carry out synthetic biology experiments without needing to be present in a laboratory. This system will provide enthusiasts such as the DIY Bio movement with an enhanced understanding of the methodology behind synthetic biology and provide access to equipment in a safe and controlled environment. Our vision is to allow the general public to carry out Synthetic Biology over the Internet in a controlled and well-regulated manner making simple Synthetic Biology accessible to everyone. Further impact on the general public will be mediated by the Responsible Innovation section of our project (see strand 1 of the Pathways to Impact), and will allow social scientists will be able to reach out to a broad range of stake holders (scientists, industrialist, NGO, Government and the public).
Organisations
- Newcastle University (Lead Research Organisation)
- Sixfold Bioscience (Collaboration)
- Centre for Process Innovation (CPI) (Collaboration)
- NCIMB (Collaboration)
- Ingenza Ltd (Collaboration)
- LabGenius (Collaboration)
- Ingenza (United Kingdom) (Project Partner)
- Microsoft Research (United Kingdom) (Project Partner)
- University of Liverpool (Project Partner)
- Earlham Institute (Project Partner)
- Prozomix (United Kingdom) (Project Partner)
- BioProNet (Project Partner)
- Kajeka Ltd (Project Partner)
- Croda (United Kingdom) (Project Partner)
- LabGenius (United Kingdom) (Project Partner)
- European Organization for Nuclear Research (Project Partner)
- TerraVerdae BioWorks (United Kingdom) (Project Partner)
- Centre for Process Innovation (Project Partner)
- SilicoLife (Portugal) (Project Partner)
- University of Edinburgh (Project Partner)
Publications
Jiang S
(2022)
OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production.
in ACS synthetic biology
Jiang S
(2020)
NIHBA: a network interdiction approach for metabolic engineering design.
in Bioinformatics (Oxford, England)
Huo S
(2022)
Time-limited self-sustaining rhythms and state transitions in brain networks
in Physical Review Research
Huang Y
(2023)
A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis.
in Synthetic and systems biotechnology
Huang Y
(2021)
Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis.
in Sensors (Basel, Switzerland)
Hordijk W
(2018)
Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World.
in Life (Basel, Switzerland)
Hayward CJ
(2023)
Nonoptimal component placement of the human connectome supports variable brain dynamics.
in Network neuroscience (Cambridge, Mass.)
Hallinan J
(2019)
Future-proofing synthetic biology: educating the next generation
in Engineering Biology
Guyet A
(2023)
Insights into the Roles of Lipoteichoic Acids and MprF in Bacillus subtilis.
in mBio
| Description | In Synthetic Biology novel biological functionality is developed using sound computational and engineering principles in order to add new properties to a given organism - called a host or chassis. The type of chassis used will vary according to the application and the circuit. However, currently, most research innovations are designed for, and tested in, model organisms such as the commonly used bacteria Escherichia coli or Bacillus Subtilis. Moving these circuits to another organism requires the circuit to be re-engineered and re-tested, a process which is very time consuming and costly. This process of 're-coding' slows down research and costs industry a huge amount of time, effort and money. Our international team of world leading researchers are developing a new field in Synthetic Biology, termed 'Portabolomics'. We are taking a novel approach to standardise the connection between a given genetic circuit and the chassis organism by the development of a 'bio-adapter'. This will negate the need to re-engineer and re-test the circuit when moving it to another organism (or chassis). Portabolomics is at the crossroads of the digital and bio economies and a true breakthrough in the portability of living systems - we want synthetic biologists to be able to engineer new microbial systems in the lab and then port these directly into another species on a large scale without the risk of any unpredictable outcomes. A range of state-of-the-art computing approaches will be applied to understand the networks of molecular processes that occur in a bacterial cell. Together with our wet lab expertise in bacterial replication, transcription and translation we hope to develop a new system of major value to synthetic biology research and industry. In parallel researchers in our team will explore the ethical, legal and social issues to inform a responsible design process for current and future work. Jointly funded by the Engineering and Physical Sciences Research Council (EPSRC), Newcastle University and industry, the £7.5million project will investigate how advances in the Digital Economy and Synthetic Biology could be synergised to engineer new living systems that behave in a predictable way in order to make industrial uptake easier. |
| Exploitation Route | Too early to say (only 1st year of operation out of 5) |
| Sectors | Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://portabolomics.ico2s.org/ |
| Description | Statement of problem or technology : ------------------------------------------------------------ During the course of this research, we found out there is an acute systemic deficit in the way the R&D and commercialization of engineered microorganisms are done both in academia and industry. A major frustration we identified through customer segment research is the irreproducibility of previous results, which of course has been widely reported both in the specialised media (e.g. Nature, Science, etc) and the general public media. Irreproducibility of cell bioengineering results is due, in large part, to (a) fragmented documentation and mislabelled/missing samples (i.e. the "what is in this cell line?" question) and (b) lack of transparency and traceability of engineered cell lines (i.e. the "who, when, where and why" built this cell line question). As a result, thousands of billable hours are lost due to a lack of necessary tools to address these points and keep track jointly and persistently of cell lines and their data footprint. A similar problem confronted the IT community and it solved it with Version Control Repositories (VCR). VCRs are at the heart of the software development life-cycle of IT companies worldwide both large and small. VCRs store programmers' files with the history of changes made to these files, either by individuals or teams, automatically maintained and tracked by the system. It enables traceability, backtracking (if necessary) as well as branching new versions. Radically increases software teams' productivity and creates an ecosystem of innovation around software projects. Engineering biologists, whose work is not dissimilar to programmers (except in that they program living organisms by altering their DNA), currently utilise suboptimal solutions for tracking their genetic programmes, data and living samples, and lack an integrated version control experience for genetic engineering teams. Context ------------- We commissioned a market research report from our project collaborators the Centre for Process Innovation (CPI, biologics) about microbes & microbial products in industry. The report indicates that the total global market for both was worth $170.5 billion in 2017, and $186.3 billion in 2018 and that the 2023 market is expected to approach $302.4 billion. These figures work out to a 10.2% projected CAGR between 2018 and 2023. Most of this market consists of microbial products such as biopharmaceuticals and biofuels made using yeasts, bacteria and other microbes. CPI also identified markets for 'whole' microbes (e.g., biofertilizers, biopesticides, probiotics) that totalled more than $8.5 billion in 2017. The market for 'whole' microbes is projected to be $12.7 billion in 2023. Perhaps more tantalising, a recent report from McKinsey and Company32 estimates that 60% of the world's materials input could be manufactured using biological means with an estimated combined market value of $2T to $4T by 2030 to 2040. Approach to problem/technology ----------------------------------------------------- We created a cloud-based version control system for biotechnology that (a) keeps track and organizes the digital data produced during cell engineering and (b) molecularly links that data to the associated living samples. Barcoding protocols, based on standard genetic engineering methods, to molecularly link to the cloud-based version control system six species, including gram-negative and gram-positive bacteria as well as eukaryote cells, were developed. Our technology marks a significant step toward more open, reproducible, easier to trace and share, and more trustworthy engineering biology. Achievements ----------------------- Given the above-described rapid growth forecast for the global bioeconomy, and the importance that it has on the UK industrial strategy, we believe that traceability, transparency, and- ultimately-trustworthiness are required from cradle to grave for engineered cell lines and their engineering processes. Our work in this area resulted in several important papers[1,2,3] and the release of significant software[4] for the research community. The outcomes of our programme grant are helping to buttress the management of provenance, pedigree and integrity of engineered cell lines in a rapidly growing bioeconomy. Building on the technical achievements mentioned above, Portabolomic researchers also contributed to informing policy, for example: N8 Agrifood Food Systems Policy Hub: The UK is recognised as a major global hub for engineering biology, but the economic success of the field depends partly on public acceptance. N. Partridge (PhD student), in collaboration with Krasnogor, in a policy brief[5] suggested two key policy recommendations for improving transparency and traceability in genetic engineering. Barcoding System for genetic engineering of microorganisms: Our papers[1,2] have been influential in shaping recent European Food Safety Authority (EFSA) thinking[6] in terms of the adequacy of current guidelines on engineered microorganisms. The agency's scientific committee is recommending that engineered microbes be barcoded (as we introduced and facilitated by our CellRepo software) and adopted a simplified version of our definition of synthetic biology agent. Impact of the long-term funding, flexibility and critical mass afforded by this EPSRC programme grant ------------------------------------------------------------------------------------------------------------------------------------------------------------------- The work described here simply could not have happened with a (series of) short-term grant(s), thus a programme grant was essential to uncover and exploit these opportunities. To start with, this was an opportunity that was not written in the original case for support but emerged soon after the programme grant started. As it became clear that our consortium would be engineering a variety of strains by modifying both chromosomes and plasmids, we needed a tool that would allow us to track the engineering process. After much investigation, it became clear that no such (off-the-shelf) tool existed. Furthermore, it also became clear that many of the subprojects within Portabolomics were based on "legacy" strains, that is, strains that were engineered by other researchers within Newcastle or elsewhere for which no detailed whole genome sequence data existed and neither a definite guide nor documentation to previous genetic modifications. The available information was informally captured in various disconnected files and often related to incomplete supplementary materials in published papers. We took this gap in the Synthetic Biology toolkit as an opportunity and deployed a small number of funds for s senior software engineer to build a prototype of what we would need. In addition, one of the Portabolomics doctoral studentships was assigned to develop barcoding protocols to link engineered strains to their digital footprint. Once our first publication came out[1] it became clear that there was a lot of interest from multiple sectors of the community hence we deployed more resources (1 full-time senior software engineer and 1 senior biotechnology postdoc) to further expand the work in this area. Thus, the ability to react rapidly to an unforeseen opportunity and to flexibly and long-term deploy resources to pursue and mature this opportunity was instrumental to our success. Another key feature of the programme grant, critical mass, was also important: the original observation that led to this research would not have happened without a critical mass of multiple different labs working together in Portabolomics: only when it became clear that the problem was cross-cutting, it became a relevant and worth-to-be-solved problem. Secondly, because we had a critical mass of postdoctoral researchers, doctoral students and software engineering expertise, we could re-allocate tasks amongst the existing talent pool to free time for others to pursue this project. Thirdly, the programme grant brought together many research groups from across Newcastle's three faculties, this critical mass justified the university to support a very substantive investment in laboratory automation equipment that is underpinning our next steps in this journey. What's next? -------------------- With support from this EPSRC Programme grant that has now ended and an ongoing Royal Academy of Engineering Chair in Emerging Technologies to Krasnogor, we were able to expand on the technologies described above and we have used this to spin out a company, GitLife Biotech Ltd (www.gitlifebiotech.com), out of the university to commercialise the intellectual property. We believe that the long-term benefits and impact to the wider scientific community would be better served by having a dedicated vehicle that can further support user needs on an agile and more sustainable manner that might be difficult to scale based on research grants only. GitLife Biotech will continue to work closely with academic colleagues in Newcastle and other institutions, including international ones, to ensure that the services it provides are fit for purpose and support the UK's National Engineering Biology programme goals. References: -------------------- [1] J. Tellechea-Luzardo, et al. Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering. ACS Synthetic Biology, 9(3):536-545, 2020 [2] V. de Lorenzo, et al. For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is! New Biotechnology, 60(C):44-51, 2021. [3] J. Tellechea-Luzardo, et al., Versioning biological cells for trustworthy cell engineering. Nature Communications, 13(765):12, 2022 [4] cellrepo.ico2s.org [5] Partridge, N. Towards greater transparency: Digital opportunities to promote traceability in genetic engineering. Zenodo. https://doi.org/10.5281/zenodo.5343358, 2021. [6] EFSA Scientific Committee. Evaluation of existing guidelines for their adequacy for the microbial characterisation and environmental risk assessment of microorganisms obtained through synthetic biology. EFSA Journal, doi: 10.2903/j.efsa.2020.6263, 2020 |
| First Year Of Impact | 2023 |
| Sector | Digital/Communication/Information Technologies (including Software),Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural,Societal,Economic,Policy & public services |
| Description | Capital Award: Quantification for frontier engineering |
| Amount | £100,000 (GBP) |
| Funding ID | EP/S017968/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 03/2020 |
| Description | DESTINATION: AI-enabled RNA nanotechnology DElivery SysTem for INformATION transfer into cells. |
| Amount | € 3,700,000 (EUR) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 02/2020 |
| End | 01/2024 |
| Description | Engineering Data Structures Organoids (EnDROIDS) |
| Amount | £2,700,000 (GBP) |
| Funding ID | Chair in Emerging Technologies |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 02/2030 |
| Description | KTP project therapeutic DNA/RNA nanostructures |
| Amount | £64,000 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2020 |
| End | 01/2022 |
| Description | Multiscale characterization of complex materials using a combination of atomic force microscopy and optical coherence tomography |
| Amount | £487,050 (GBP) |
| Funding ID | EP/R025606/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 04/2020 |
| Description | New ways of transcription regulation learned from cyanobacteria |
| Amount | £300,000 (GBP) |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 10/2021 |
| Description | Non-canonical RNA capping in bacteria and human mitochondria |
| Amount | £300,000 (GBP) |
| Funding ID | RPG-2018-437 |
| Organisation | The Leverhulme Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 06/2022 |
| Title | Cloud Based Version Control System for Strain Engineering |
| Description | The number of engineered strains are set to dramatically increase in the future thanks to the explosion of powerful gene-editing tools. A convincing example of the pace of progress is the global scientific response to the current Covid-19 pandemic. In a matter of weeks following the outbreak, the virus was isolated and its genome sequenced and published. Less than a year later, vaccines were developed and rolled out. Despite this progress, there are still significant gaps in other areas of biotechnology and more specifically in how strain engineering is done and disseminated. To ameliorate that we created CellRepo. What is CellRepo? CellRepo is a species and strain database that uses cell barcodes to monitor and track engineered organisms. Reported in a new study in Nature Communications, the database keeps track and organises the digital data produced during cell engineering. It also molecularly links that data to the associated living samples via bio-orthogonal chromosomal barcodes |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | We are advising DEFRA on topics related to access and benefits sharing of digital sequence information |
| URL | http://cellrepo.ico2s.org |
| Description | Centre for Process Innovation |
| Organisation | Centre for Process Innovation (CPI) |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Ongoing collaboration |
| Collaborator Contribution | Ongoing collaboration |
| Impact | Multi-disciplinary |
| Start Year | 2016 |
| Description | Ingenza |
| Organisation | Ingenza Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Ongoing collaboration |
| Collaborator Contribution | Ongoing collaboration |
| Impact | Ongoing collaboration |
| Start Year | 2016 |
| Description | Labgenius |
| Organisation | LabGenius |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Ongoing collaboration |
| Collaborator Contribution | Ongoing collaboration |
| Impact | Ongoing collaboration |
| Start Year | 2016 |
| Description | NCIMB |
| Organisation | NCIMB |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We help NCIMB in evaluating version control of microorganisms biobanking |
| Collaborator Contribution | They provided biobanking and cell identification expertise |
| Impact | On going collaboration |
| Start Year | 2017 |
| Description | Sixfold Biotech |
| Organisation | Sixfold Bioscience |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We have worked closely with our colleagues at Sixfold bioscience to extend some of the technology developed in Portabolomics with the aim of applying it to next generation drug delivery systems |
| Collaborator Contribution | Sixfold introduced us to the challenges in Nucleic Acid-based therapies and we have been able to expand our research areas towards that direction. This resulted in a new KTP and H2020 joint project with them |
| Impact | This is multidisciplinary. Hast resulted in knowledge transfer from industry to academic and vice versa. New grants. |
| Start Year | 2020 |
| Title | Infobiotics Workbench |
| Description | Infobiotics Workbench (IBW) - a computer-aided design suite for synthetic biology that assists the synthetic biologist in an informed, iterative workflow of system specification, verification, simulation and biocompilation. IBW incorporates well-established design principles that guide both experienced and non-experienced biologists in refining a putative functionality into a formally-specified document for fabricating a nucleotide sequence after undergoing verification and simulation. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | N/A at this time |
| URL | https://infobiotics.org/index.html |
| Title | Simbiotics |
| Description | Simbiotics is a 3D simulation tool offering a range of modelling features to describe bacterial populations. Bacterial cells are represented as discrete geometric entities which may have internal processes and interact with their environment. Modellers may describe specific bacterial behaviour, environmental factors and the spatial arrangement of cellular populations, this is achieved via composing library modules into a model specification. Modules describe specific features to be simulated and are parameterisable, the library is extendable to allow for novel models of relevant processes to be added to the tool. Simulations can be run on mulit-threaded and multi-CPU environments to ensure the platform can represent industrially relevant systems. Simbiotics can be initialised via common standards experimentalists use such as microscopy image data and SBML models, allowing for the rapid development of 3D population models. An optional live 3D rendering and data graphing is available, alternatively exporting data in common formats (CSV and JSON) allow for the integration of Simbiotics into existing tools such as Blender or PovRay. The tool requires minimal programming experience to use. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | N/A |
| URL | http://ico2s.org/software/simbiotics.html |
| Title | Version Control System for Strain Engineering |
| Description | As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and computing science, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agile, reproducible and transparent while, at the same time, limiting the security and safety of synthetic biology constructs. To partially address some of these problems, this paper presents an approach for physically linking engineered cells to their digital footprint - we called it digital twinning. This enables the tracking of the entire engineering history of a cell line in a specialised version control system for collaborative strain engineering via simple barcoding protocols. We implemented this as a web application. We used CellRepo to document the key milestones throughout the process of cell engineering, characterisation and barcoding described earlier. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Impact | We are exploring routes for commercialisation of an enhanced version of this software |
| URL | https://cellrepo.ico2s.org/ |
| Company Name | GITLIFE BIOTECH LTD |
| Description | The company set the global standard in the management of provenance and integrity for biological assets, enabling the potential of synthetic biology to be realised worldwide. It accomplishes this by setting the international standard for version control and biological asset integrity while enabling collaboration between governmental, commercial, academic and NGO entities. |
| Year Established | 2023 |
| Impact | The company only started trading in 2023. |
| Website | https://www.gitlifebiotech.com |
| Description | Cafe Scientifique (popular science talk to public) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Café Scientifique is a popular science talk format aimed at the general public. It is embedded within the Café Culture series at Newcastle. It provides a show-case for research and an opportunity for the general public to ask questions and debate issues. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Engagement with night-time visitors to the Great North Museum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | PEALS researcher, Ken Taylor, and his Portabolomics colleague Dr Emanuela Torelli, took part in the Great North Museum (GNM) European Researcher's Evening on September 27th. The GNM opened its doors to visitors for an evening event at which University research is presented at stands at different points among the museum collections. There are also short presentations by the researchers. The event consisted of two short presentations: 1) on DNA and RNA origami research and 2) work on responsible research and innovation. Both talks were well received, and the stand attracted attention from around a quarter of all the visitors. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Gallery exhibition of artwork linked toresearch project |
| 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 | Hatton Gallery Exhibition: Origins & Endings - this included some original artwork by Marianne Wilde that was inspired by synthetic biology - the opening night was attended by 150 + people and provoked interest and discussion in our research. The exhibition is open until March 2020. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ncl.ac.uk/peals/events/item/hattongalleryexhibition.html |
| Description | Grace Goldsmith - "Engineering bacterial compartments for industrial applications" talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Grace Goldsmith presented a talk entitled "Engineering bacterial compartments for industrial applications" at the North East Postgraduate Conference that took place on the 13th November 2020. |
| Year(s) Of Engagement Activity | 2020 |
| Description | International Symposium: The implications and impacts of a responsibility agenda for synthetic biology, September 2018. |
| 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 | Title: 'The implications and impacts of a responsibility agenda for synthetic biology'. This international interdisciplinary symposium provided an important opportunity to explore and debate the implications of different models of (responsible innovation/ responsible research and innovation (RI/RRI) for a range of interested parties. The symposium brought together leading social and scientific researchers, regulators, policy advisors, and other stakeholders to discuss the scientific, social, ethical, legal and regulatory issues raised by the burgeoning development of synthetic biology. We were joined by colleagues from a range of disciplines (including science and technology studies, biochemistry, microbial genetics, biology, computer science, synthetic biology, history, law, ethics, philosophy, politics, sociology), from a range of jurisdictions and cultural experiences (including the Netherlands, Hungary, Italy, and the UK) and from a range of policy and practice backgrounds to assist these deliberations. The symposium ran over two days and included presentations and round-table discussion. Each session was chaired by either project participant or external guest. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Museum based public engagement |
| 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 | a series of 6 'pop-up' interventions ate the Great North Museum Newcastle. Activities aimed at parents and children visiting the museum with hands-on activities to engage families with an aspects of synthetic biology. The PDRA was assisted by three students from Newcastle University's Museum, Galleries and Heritage Masters courses, who collated basic information about the visitors and their interest in the 'pop/up'. The team interacted with 399 visitors (including 240 children), completing activities such as making a clock or an origami butterfly. Jigsaw puzzles were made for smaller children. All activities aimed to start conversations about aspects of synthetic biology; such as the possible uses of a circadian clock from cyanobacteria or the research being done on DNA and RNA origami nanostructures. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ncl.ac.uk/peals/news/item/spp.html |
| Description | Participation in creation of the art exhibition in Hancock Museum based on Portabolomics research project |
| 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 exhibition challenged the public view on synthetic biology and made people think in terms of the future role of research in sustainable economy |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster at 26th International Conference on DNA Computing and Molecular Programming. 2020. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | "REVNANO: An Algorithm to Reverse Engineer Scaffolded DNA/RNA Origami Designs from Sequence Information Only" poster presented at the 26th International Conference on DNA Computing and Molecular Programming. Poster made by Shirt-Ediss B, Elezgaray J, Connolly J, Torelli E, Krasnogor N. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Seminar for MSc Students, Newcastle University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | The one hour seminar was run by Dr. Ken Taylor for MSc students (Degree of Master of Science in Synthetic Biology - Course code: 5200F). The course lecturer, Dr Tim Rudge was also present. There were around 20 students. The outcome was that the students gained an introduction to the concept of responsible innovation and some of the socio-ethical issues that synthetic biology raises. |
| Year(s) Of Engagement Activity | 2021 |
| Description | museum exhibition and short film |
| 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 | This is a small exhibition of original work created by artist Marianne Wilde and including a short 'art' film about synthetic biology. It is place within the Great North Museum Newcastle and will be open until Summer 2020. |
| Year(s) Of Engagement Activity | 2020 |