Synthetic biology in the UK - An outline of plans and progress

Engineering biology and automation-Replicability as a design principle

Applications in engineering biology increasingly share the need to run operations on very large numbers of biological samples. This is a direct consequence of the application of good engineering practices, the limited predictive power of current computational models and the desire to investigate very large design spaces in order to solve the hard, important problems the discipline promises to solve. Automation has been proposed as a key component for running large numbers of operations on biological samples. This is because it is strongly associated with higher throughput, and with higher replicability (thanks to the reduction of human input). The authors focus on replicability and make the point that, far from being an additional burden for automation efforts, replicability should be considered central to the design of the automated pipelines processing biological samples at scale-as trialled in biofoundries. There cannot be successful automation without effective error control. Design principles for an IT infrastructure that supports replicability are presented. Finally, the authors conclude with some perspectives regarding the evolution of automation in engineering biology. In particular, they speculate that the integration of hardware and software will show rapid progress, and offer users a degree of control and abstraction of the robotic infrastructure on a level significantly greater than experienced today.

Navigating the Frontier of Synthetic Biology: An AI-Driven Analytics Platform for Exploring Research Trends and Relationships

The field of synthetic biology has experienced rapid growth in recent years, leading to an overwhelming amount of literature that can make it difficult to comprehend the scope and trends of the discipline. In this study, we employ topic modeling to comprehensively map research topics within synthetic biology, revealing subtopics and their relationships, as well as trends over time. We utilize metadata to identify the most significant journals and countries in the field and discuss potential policy impact on the research output. In addition, we investigate co-authorship networks to analyze collaborations among authors, institutions, and countries. We believe that our findings could serve as a valuable resource for gaining a deeper understanding of synthetic biology and provide a foundation for analyzing other disciplines.

Public biofoundries as innovation intermediaries: the integration of translation, sustainability, and responsibility

The emergence and evolution of engineering biology, and its potential to address multiple global challenges is associated with the rise of biofoundries. These innovation intermediaries are facilities that employ advanced automation and computational analytics to accelerate engineering biology applications. Yet, for biofoundries to fully achieve their promise of generating applications that address grand societal challenges, they need to meet three key challenges: translation of research technology and its commercialization, attention to sustainability, and responsible innovation. Using web content analysis and interviews, this paper explores the functions and capabilities undertaken by existing public biofoundries, the extent to which they address these three challenges, and opportunities and models for enhancement. We also probe the roles undertaken by three other contrasting types of innovation intermediaries to identify practices and opportunities for integration and partnering with public biofoundries. We find that public biofoundries exhibit relatively strong capabilities for research translation, whereas efforts toward sustainability and responsibility are generally less prominent. For biofoundry enhancement, we propose an organisational model based on external partnering where public biofoundries are positioned as intermediaries within regional innovation systems. The framework put forward is reproducible and could be used in other contexts for assessing innovation intermediary organisational functions and capabilities toward meeting societal challenges.

Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis

The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of Saccharomyces cerevisiae that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.

Engineering the expression of plant secondary metabolites-genistein and scutellarin through an efficient transient production platform in Nicotiana benthamiana L

Plant natural products (PNPs) are active substances indispensable to human health with a wide range of medical and commercial applications. However, excessive population growth, overexploitation of natural resources, and expensive total chemical synthesis have led to recurrent supply shortages. Despite the fact that the microbial production platform solved these challenges, the platform still has drawbacks such as environmental pollution, high costs, and non-green production. In this study, an efficient platform for the production of PNPs based on the transient expression system of Nicotiana benthamiana L. combined with synthetic biology strategies was developed. Subsequently, the feasibility of the platform was verified by a simple "test unit." This platform was used to synthesize two high-value PNPs: genistein (5.51 nmol g^-1 FW) and scutellarin (11.35 nmol g^-1 FW). Importantly, this is the first report on the synthesis of scutellarin in heterologous plants. The platform presented here will possibly be adopted for the heterologous production of genistein and scutellarin in tobacco plants as a novel and sustainable production strategy.

Synthetic biology in Europe: current community landscape and future perspectives

Synthetic biology has captivated scientists' imagination. It promises answers to some of the grand challenges society is facing: worsening climate crisis, insufficient food supplies for ever growing populations, and many persisting infectious and genetic diseases. While many challenges remain unaddressed, after almost two decades since its inception a number of products created by engineered biology are starting to reach the public. European scientists and entrepreneurs have been participating in delivering on the promises of synthetic biology. Associations like the European Synthetic Biology Society (EUSynBioS) play a key role in disseminating advances in the field, connecting like-minded people and promoting scientific development. In this perspective article, we review the current landscape of the synthetic biology community in Europe, discussing the state of related academic research and industry. We also discuss how EUSynBioS has helped to build bridges between professionals across the continent.

De novo synthesis of synthetic biology ecosystem in Slovakia: Challenges and opportunities

Synthetic biology is an engineering discipline that applies engineering principles to rationally design novel biological systems. It has the potential to contribute to solving major global challenges in a multitude of areas, from healthcare to sustainability. While the engineering biology landscape is robust and well-established in certain countries, the ecosystem and infrastructure for genetic engineering in other countries, including Slovakia, are underdeveloped. Consequently, such countries are missing the major economic and social benefits that the practical applications of the rational design of biological systems may provide. In this work, we briefly assess the status of the synthetic biology landscape in Slovakia in different areas, including research efforts, industrial participation, governmental policy, and the educational landscape. We describe the major challenges that the Slovak synthetic biology sector faces and propose a strategy that academics, policymakers, and industry could take to activate the proliferation of the Slovak synthetic biology ecosystem.

Exploring presentations of sustainability by US synthetic biology companies

The field of synthetic biology is increasingly being positioned as a key driver of a more sustainable, bio-based economy, and has seen rapid industry growth over the past 15 years. In this paper we undertake an exploratory investigation of the relationship between sustainability and synthetic biology, identifying and analyzing sustainability-related language on the public websites of 24, US-based synthetic biology companies. We observe that sustainability is a visible part of the self-presentation of the nascent synthetic biology industry, explicitly mentioned by 18 of the 24 companies. The dominant framing of sustainability on these company websites emphasizes environmental gains and "free-market" approaches to sustainability, with little explicit mention of social dimensions of sustainability such as access, justice or intergenerational equity. Furthermore, the model of sustainability presented focuses on incremental transition towards environmental sustainability through direct substitution of products and processes using bioengineered alternatives (n = 16 companies), with no change in societal consumption or policy frameworks required in order to see sustainability gains. One-third of the companies analyzed (n = 8) mention "nature" on their websites, variously framing it as a resource to be managed or as a source of inspiration; whether the latter signals a potentially more complex relationship with nature than advanced free-market models of sustainability remains to be seen. As the synthetic biology industry begins to grow in size and visibility, we suggest this is an opportune time for the community to engage in explicit deliberation about its approach to sustainability.

Setting Up an Automated Biomanufacturing Laboratory

Laboratory automation is a key enabling technology for genetic engineering that can lead to higher throughput, more efficient and accurate experiments, better data management and analysis, decrease in the DBT (Design, Build, and Test) cycle turnaround, increase of reproducibility, and savings in lab resources. Choosing the correct framework among so many options available in terms of software, hardware, and skills needed to operate them is crucial for the success of any automation project. This chapter explores the multiple aspects to be considered for the solid development of a biofoundry project including available software and hardware tools, resources, strategies, partnerships, and collaborations in the field needed to speed up the translation of research results to solve important society problems.

Plant Biosystems Design for a Carbon-Neutral Bioeconomy

Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO2, allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed. Concerted research efforts will be required for accelerating the development of plant cultivars, genotypes, or varieties that are cooptimized in the contexts of biomass-derived fuels and/or materials aboveground and enhanced carbon sequestration belowground. Here, we briefly discuss significant knowledge gaps in our process understanding and the potential of synthetic biology in enabling advancements along the fundamental to applied research arc. Ultimately, a convergence of perspectives from academic, industrial, government, and consumer sectors will be needed to realize the potential merits of plant biosystems design for a carbon neutral bioeconomy.

Developing synthetic biology for industrial biotechnology applications

Since the beginning of the 21st Century, synthetic biology has established itself as an effective technological approach to design and engineer biological systems. Whilst research and investment continues to develop the understanding, control and engineering infrastructural platforms necessary to tackle ever more challenging systems - and to increase the precision, robustness, speed and affordability of existing solutions - hundreds of start-up companies, predominantly in the US and UK, are already translating learnings and potential applications into commercially viable tools, services and products. Start-ups and SMEs have been the predominant channel for synthetic biology commercialisation to date, facilitating rapid response to changing societal interests and market pull arising from increasing awareness of health and global sustainability issues. Private investment in start-ups across the US and UK is increasing rapidly and now totals over $12bn. Health-related biotechnology applications have dominated the commercialisation of products to date, but significant opportunities for the production of bio-derived materials and chemicals, including consumer products, are now being developed. Synthetic biology start-ups developing tools and services account for between 10% (in the UK) and ∼25% (in the US) of private investment activity. Around 20% of synthetic biology start-ups address industrial biotechnology targets, but currently, only attract ∼11% private investment. Adopting a more networked approach - linking specialists, infrastructure and ongoing research to de-risk the economic challenges of scale-up and supported by an effective long-term funding strategy - is set to transform the impact of synthetic biology and industrial biotechnology in the bioeconomy.

Private and public values of innovation: A patent analysis of synthetic biology

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Patent documents are a signalling mechanism about innovation values.

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Extant patent valuation literature tends to overlook the public value of innovation.

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Both private and public value propositions are found in patent documents.

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Public value propositions are less frequent but more diverse.

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Analysing private and public values in patents offers innovation policy insights.

Emerging science and technology fields are increasingly expected to provide solutions to societal grand challenges. The promise of such solutions frequently underwrites claims for the public funding of research. In parallel, universities, public research organizations and, in particular, private enterprises draw on such research to actively secure property rights over potential applications through patenting. Patents represent a claim to garner financial returns from the novel outcomes of science and technology. This is justified by the potential social value promised by patents as they encourage information sharing, further R&D investment, and the useful application of new knowledge. Indeed, the value of patents has generated longstanding academic interest in innovation studies with many scholars investigating its determinants based on econometric models. Yet, this research has largely focused on evaluating factors that influence the market value of patents and the gains from exclusivity rights granted to inventions, which reflect the private value of a patent. However, the patent system is a socially shaped enterprise where private and public concerns intersect. Despite the notion of the social utility of inventions as a patenting condition, and evidence of disconnection between societal needs and the goals of private actors, less attention has been paid to other interpretations of patent value. This paper investigates the various articulations of value delineated by patents in an emerging science and technology domain. As a pilot study, we analyse patents in synthetic biology, contributing a new analytical framework and classification of private and public values at the intersections of science, economy, and society. After considering the legal, business, social and political dimensions of patenting, we undertake a qualitative and systematic examination of patent content in synthetic biology. Our analysis probes the private and public value propositions that are framed in these patents in terms of the potential private and public benefits of research and innovation. Based on this framework, we shed light on questions of what values are being nurtured in inventions in synthetic biology and discuss how attention to public as well as private values opens up promising avenues of research in science, technology and innovation policy.

Aligning sustainability assessment with responsible research and innovation: Towards a framework for Constructive Sustainability Assessment

Emerging technologies are increasingly promoted on the promise of tackling the grand challenge of sustainability. A range of assessment and governance approaches seek to evaluate these claims, but these tend to be applied disparately and lack widespread operationalisation. They also face specific challenges, such as high levels of uncertainty, when it comes to emerging technologies. Building and reflecting on both theory and practice, this article develops a framework for Constructive Sustainability Assessment (CSA) that enables the application of sustainability assessments to emerging technologies as part of a broader deliberative approach. In order to achieve this, we discuss and critique current approaches to analytical sustainability assessment and review deliberative social science governance frameworks. We then develop the conceptual basis of CSA - blending life-cycle thinking with principles of responsible research and innovation. This results in four design principles - transdisciplinarity, opening-up, exploring uncertainty and anticipation - that can be followed when applying sustainability assessments to emerging technologies. Finally, we discuss the practical implementation of the framework through a three-step process to (a) formulate the sustainability assessment in collaboration with stakeholders, (b) evaluate potential sustainability implications using methods such as anticipatory life-cycle assessment and (c) interpret and explore the results as part of a deliberative process. Through this, CSA facilitates a much-needed transdisciplinary response to enable the governance of emerging technologies towards sustainability. The framework will be of interest to scientists, engineers, and policy-makers working with emerging technologies that have sustainability as an explicit or implicit motivator.

Anticipating governance challenges in synthetic biology: Insights from biosynthetic menthol

This paper advances an anticipatory governance framework to investigate and prepare for the potential implications of an emerging technology. Within the growing domain of synthetic biology, we draw on an end-to-end assessment of biosynthetic menthol that incorporates consideration of multiple dimensions of production and use. Based on documentary analysis, available data, and interviews, our approach unfolds in three steps. First, we map the sociotechnical transition in menthol production, comparing existing agricultural and chemical production methods with new biosynthetic processes - or what we call the biological (bio) turn. Second, we explore the rationales, promises and expectations of menthol's bio-turn and explore the drivers of transition so as to clarify which goals and values innovation is addressing. Third, we reflect on the opportunities and challenges of such a transition to put forward an agenda for responsible innovation and anticipatory governance. The bio-turn in menthol is analysed through five responsible innovation dimensions: the potential distribution of benefits and burdens; social resilience; environmental sustainability; infrastructure and business models; and public perception and public interest. We consider the implications of our analysis both for the responsible development and application of synthetic biology for menthol and for the broader assessment and sociotechnical construction of emerging technologies.

Developing a graduate training program in Synthetic Biology: SynBioCDT

This article presents the experience of a team of students and academics in developing a post-graduate training program in the new field of Synthetic Biology. Our Centre for Doctoral Training in Synthetic Biology (SynBioCDT) is an initiative funded by the United Kingdom's Research Councils of Engineering and Physical Sciences (EPSRC), and Biotechnology and Biological Sciences (BBSRC). SynBioCDT is a collaboration between the Universities of Oxford, Bristol and Warwick, and has been successfully running since 2014, training 78 students in this field. In this work, we discuss the organization of the taught, research and career development training. We also address the challenges faced when offering an interdisciplinary program. The article concludes with future directions to continue the development of the SynBioCDT.

Scaling up genetic circuit design for cellular computing: advances and prospects

Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

Tracking the emergence of synthetic biology

Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.