Synthetic biology (SynBio) is a multidisciplinary, emergent field, evolving so fast that it still lacks a consensus definition, and its outstanding success in the last years should not hide the difficulties in defining and adopting biological standards: there are both historical and technical difficulties to reach that ambitious goal.
Nevertheless, the benefits of improving standardisation of biological systems are overwhelming and, in this framework, BioRoboost aims at:
(Re)definition of biology
Elaboration of a real-time catalogue of research needs on biological standards
Developing and offering the academic and industrial SynBio community a usable, realistic and flexible toolbox of standardized biological assets
Coordination of existing material and computational resources for standardized biology, as well as future initiatives
Anticipating societal ramifications and cultural reactions to standardized biology by engaging in a continuous conversation and informed debate with cognate stakeholders
In other words, the main goal is to further develop standards in biology in a holistic, systematic way: from the biological part to the experimental procedure in a given environment
BioRoboost in a nutshell
Standards are everywhere in our modern civilization. They work because they are robust, reliable, universal and they have a predictable behavior… in engineering. What happens in biotechnology and synthetic biology?
BioRoboost was born to foster standardization in Synthetic Biology. The question is: what can be standardized in this discipline? Metrology? Genes? Circuits? Chassis? Consortia? Protocols? In this video, Dr. Manuel Porcar (PI of the BioRoboost project), talks about why standardization is important and how BioRoboost has contributed to the use of standards in Synthetic Biology.
Synthetic Biology modifies the behaviour of cells using synthetic constructs. The cell can be imagined like the chassis of a car, in which different pieces or constructs are introduced to modify the capabilities of the chassis. Ideally, the constructs should behave in the same way independently of the chassis that is used. This is known as orthogonality. But the reality is that this does not happen, as there are pieces and constructs that are not always compatible with the chassis. How can we overcome this issue?
Our planet is home to an extraordinary diversity of microorganisms that can be found almost everywhere. Natural and artificial environments can be accessed and screened to convert unexplored communities into toolboxes of novel microbial strains and biological parts.
Technical documents known as standards include characteristics, specifications, requirements, guidance that materials, products, services and processes should comply with to ensure they are fit for purpose. In an interconnected world that is in continuous change, as the one we are living in, standards provide safety and security, compatibility and rationality to the value chains. Standards are published by a network of standardisation bodies at international and national level that work in a coordinated manner.
Pseudomonas putida is a bacterium that can be modified using synthetic biology for environmental applications, for example, developing biosensor strains, bioremediation of toxic compounds, and revalorization of waste by using it as a cheap substrate to produce complex molecules with high added value. Although P. putida possesses an optimal biochemical framework to endure the harsh conditions of nature, it also encodes non-desirable genetic traits.
Meet the Plant & Environmental Biotechnology Lab from the Department of Biochemistry and Biotechnology at the University of Thessaly (Greece), focused on standardizing molecular mechanisms and integrating synthetic biology principles to enhance basic research in metabolic engineering and to produce desired compounds at a large scale. They are developing modular tools for genome modification of plants and fungi, standard biosensors to measure the concentration of specific metabolites, and many other strategies that aim to achieve a predictable microbiome manipulation of the plant biosphere.
Check out the different work packages for more information about the state-of-the-art and goals of each task, and keep in mind that these sections will be updated throughout the project to include the results obtained.
WP1 aims at the identification and definition of the gaps and weaknesses of the standardization process, with the goal of proposing remediating strategies. This task with focus on reviewing the capability in common languages and tools (e.g. SBOL) and identifying opportunities where the development of new standards, descriptors and tools will facilitate development of the modelling field applied to SynBio.
The application of SynBio to eukaryotic systems lags considerably behind that of bacterial. WP3 will follow WP1’s lead, but focusing on standardisation in eukaryotic and multi-compartmental systems. To constrain this WP, we shall focus on a fine-grain auditing of need in two specific chassis (Saccharomyces cerevisiae and CHO cells), before conducting course-grain scoping for multi-cellular systems.
WP5 builds on the conceptual work and mapping developed in WP4: it considers variability in SB’s standardization practices, to focus specifically on how standards may enable knowledge circulation and collaboration within and across synthetic biology communities and research groups. This WP will focus on shareability and reusability as key social and ethical aspects of standards and standardization. WP5 attends to the multiple communities and moral economies of synthetic biology (building on WP4), with a special focus on SBOL – the most comprehensive attempt at making synthetic biology shareable by standardizing it.
The consortium will implement target-oriented measures for dissemination and valorization of the results, aiming to: (1) facilitate the gradual adoption of potential standards by the scientific community as well as by companies; (2) tackle the formal pipeline leading to the definition, development and adoption of standards by the Standards Development Organizations; and (3) address the educational community by producing a specialized educational kit for teachers and students on standards matters.
While Escherichia coli has been the favourite workhorse for hosting synthetic constructs so far, its default genetic, metabolic and physiological casting fails to sustain the wide range of industrial and environmental applications envisioned for SynBio agents. In order to firmly stablish a small but yet relatively comprehensive set of chassis to be used in a much wider range of biotechnological applications, we will define, for the first time, a set of microbial chassis, taking profit of them being already shaped by natural selection to fit very particular environmental conditions.
WP4 is the first of two interrelated work packages that employ social scientific research to further understand the place of standards, and standardized products and practices in different social systems, including the study of gender, ownership and responsibility dynamics. WP4 research will compile a mapping of the different communities involved in the making and using of a synthetic biology standard, and how those communities interact. It will do so using ethnographic observations of participant laboratories, and interviews with key figures in those labs. This WP will also identify and bring together appropriate analytic tools from fields like Science and Technology Studies (STS), which will serve the effort to explore the varied communities working with the standards under study.
In 2015, the EC’s Scientific Committee on Emerging and Newly Identified Health Risks (SCENIHR) identified major gaps in knowledge to be considered for performing a reliable risk assessment in SynBio. The aim of this WP is to contribute to the closure of the research gap identified by SCENIHR by: (1) enhancing the interface between science, industry and risk assessment authorities; (2) fostering the incorporation of safety relevant data and information in SynBio standards; and (3) assessing biocontainment in a standardized versus a non-standardized scenario.
Technical documents known as standards include characteristics, specifications, requirements, guidance that materials, products, services and processes should comply with to ensure they are fit for purpose. In an interconnected world that is in continuous change, as the one we are living in, standards provide safety and security, compatibility and rationality to the value chains.
Standards are published by a network of standardisation bodies at international and national level that work in a coordinated manner. In this video, Elena Ordozgoiti, Business Developer Manager at UNE, talks about standards, UNE and ISO, with a special emphasis on biotechnology and synthetic biology.