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A network for Synthetic Biology Investigations
This network aims to enable efficient and consistent recording and sharing information about synthetic biology investigations. Standard such as the proposed SBI are essential to synthetic biology: safeguarding the inheritance of data and knowledge for future, and maximising its usefulness in present. The network will encourage the interaction across researchers from diverse disciplines, such as systems and synthetic biology, ontology engineering, computer science, biology, chemistry and medicine, and collaboration between academic researchers and business. It will also provide publicly accessible research annotated with SBI for use by a broader research community and industry.
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A network in plant cell wall improvement and utilisation
Plant cell walls show a large variation in different cell types, different stages of development and between different species. This variation has been exploited for many industrial applications that include fibre crops such as cotton, flax, hemp or wood, where the cell wall composition and architecture determine the physical and mechanical properties that determine their industrial uses. Similarly, certain cell walls accumulate large amounts of extractable polymers of industrial importance e.g. galactomannans, pectins gum arabic. In some cases, such as guar seed or gum arabic, there is increasing demand with a limited supply. In other cases the presence of the cell wall polymers, such as lignin, limits the utility of the cell wall and represents a barrier to better exploitation of the biomass for applications such as biofuel production. The overall aims of the network will be to develop systems biology approaches to investigating plant cell wall synthesis and structure, and synthetic biology approaches to improve these attributes in plants and their exploitation for industrial applications. The network would aim to: (1) link together people with the appropriate skills in chemistry, biochemistry, genetics and bioprocessing; (2) ensure that network members have access to the appropriate tools for their research; (3) identify the major research challenges limiting the use of plant cell wall biomass by end-users involved in IBBE and (4) begin to develop ambitious projects and tools that would address these.
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A Network of Integrating Technologies: From Plants to Products
The challenge of developing areas of science and technology with the ultimate aim of deployment is to ensure technological compatibility and this can only be facilitated by parallel development and integration. The opportunity is to integrate feedstock development (including genomics/ Phenomics) with extraction, conversion and valorisation that include biological, chemical, engineering approaches and physicochemical technologies at scale. Beyond this there is scope to integrate with producers, the associated supply chains and most importantly with consumers. By doing this we could develop multiple deployment opportunities to drive research into the commercial space and ultimately to mitigate climate change whilst supporting economic development within the UK and Europe.
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A Network on Plant Science Products (PSP)
By 2050 we will need to feed twice as many people with fewer resources of land and water, and meet the additional requirements for nutrition and health. The looming challenges of food security, adequate nutrition and sustainable agriculture define huge and compelling market opportunities. UK plant science researchers must be proactive to position UK companies to play leading roles in opening and capturing these markets. Relying on conventional academic processes for knowledge and technology transfer will neither capture the full benefit of these markets nor deliver the required increases in productivity. The challenge is to innovate by applying academic expertise in a measured and strategic manner across the whole supply chain in partnership with industry. Plant Sciences Products will provide the solution and heralds a new era of collaboration both within academia and between academia and industry. It is an innovative mechanism to connect the public investment in R&D with the UK companies at the forefront of economic growth and social responsibility. The strategic objectives of PSP are: • To form a unique academic team with a focussed vision offering clear benefits to industry, with strategic clustering of academic expertise into focused interdisciplinary teams (focus groups) to inform and respond to industry needs. • To optimize links between plant process research and industrial biotechnology in order to deliver step-change advances in industrial biotechnology. • To deliver near-term impact/economic benefit within a longer-term plan to identify and deliver significant and fundamental step-change innovation. • To integrate R&D and innovation with skills development to establish an effective cycle of research and innovation that delivers long-term and sustainable economic and social benefits to the UK. Your input and views are requested on the following: Ideas for focus groups please suggest interesting topics (such as Decreasing acrylamide production in foods; Plant Fuels, Stress detection kits; New enzymes from plants) and let us know if you would like to lead a focus group? Expressions of interest for in the "Inaugural PSP meeting", to be held in Leeds in April to bring industry and researchers together, to formalise the first forum groups; What do you think?
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Acetogens & other Procaryotes able to Fix Carbon for Fuel and Chemicals
Much current attention is focused on deriving fuels and chemicals from lignocellulose through fermentation. However, developing processes that efficiently convert plant material into the necessary sugar feedstocks that are economic is proving challenging. An alternative approach is to cut out the middle man (the plant), and fix carbon (in the form of CO or CO2) directly through gas Fermentation. We are interested in forming a network that exploits this route to chemical commodity production. Our current focus is the acetogen Clostridium ljungdahlii. It will grow on a spectrum of waste gases from industry (eg., steel manufacturing, oil refining, coal and natural gas) as well as ‘synthesis gas’ (CO & H2) produced from renewable and sustainable resources, such as biomass and domestic/ agricultural wastes. This enables low carbon fuels and chemicals to be produced in any industrialized geography without consumption of valuable food or land resources. There are of course many other prokaryotic species that could be exploited in a similar way, some of which can more appropriately target C02. We would like to see a network develop that focuses on exploiting this microbial route to chemical manufacture and which tackles all of the aspects that will be necessary to turn such process into profitable industrial platforms. We need to:- • broaden the net to include the most promising microbial chassis that can be exploited in this manner • better understand and then manipulate their metabolic pathways • extend product streams through synthetic biology approaches • improve the economics of SynGas generation • improve gas fermentation systems and downstream processing • develop gas fermentation plants as biorefineries
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Adding Value to the supply chain: the development of true bio-refineries.
The discussions which have been posted so far have been focused in particular niche areas such as anaerobic digestion, cell wall manipulation or the use of waste products and biomass. All of these are worthy areas but the problems in developing a new industry based on the use of biomass requires the involvement of other sectors as well. A true refinery would utilise all of the resource which is fed into the process. This rehires substantial innovation and will of course be reliant on Industrial biotechnology developments. Isolation of products is critical and requires development in both separation technologies and in the identification of high value products or processes which can add value to the process through conversion either through the use of chemistry or IB. Participation of industry is critical in order to ensure that the products developed meet their requirements. This requires a true multidisciplinary approach bringing together different disciplines and business engagement. The predicted price of wheat this year highlights the fluctuations in biomass availability that are likely to impact on a fledgling industry and therefore understanding of this and alternative feedstock and robust enzymes capable of dealing with different inputs remains critical. The purpose of the network is to bring together both industry both large and small (from farm to product manufactures) and both institutes and academics to address though exchange of knowledge some of the key challenges that remain in developing a novel industry based on biomass. Organisers Guy Barker (Warwick Life Sciences) Kerry Kirwan (WMG) Dave Pink (HarperAdams)
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Agri-Food Waste Utilisation Network
The exploitation of abundant agricultural resources and food waste through the application of scalable technologies is essential for the sustainable production of a variety of existing and novel compounds with potential commercial applications in the chemical, packaging and food industry; these include food packaging biopolymers, oleochemicals, functional carbohydrates, and phenolic acids and other secondary products. It is therefore essential that existing and new technologies are applied for the fractionation of the biomass and the utilisation of the fractions towards the production of commercially important compounds from food and agricultural wastes, including waste from forestry and sawmills, spoilt and discarded parts of fruit and vegetables, sugar beet pulp, cereal straw and spent grain from brewing, distilling and biofuel production. To this end, a multidisciplinary approach is necessary, and the proposed network will aim to bring together researchers and industrialists working in the areas of plant science, carbohydrate chemistry, polymer science, food packaging, enzymology, process engineering and environmental science. The aims of the network will be to foster the interaction between researchers, technologists and industrialists in order to realise the potential of using food and agricultural wastes to produce biomaterials, chemicals and nutraceuticals, identify suitable agri-food waste sources, novel products as well as product applications, and propose scalable technologies for their sustainable production. It is envisaged that this will lead to the development of novel platforms for the industrial exploitation of these rich natural resources.
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Algal Industrial Biotechnology and Bioenergy
A multidisciplinary network linking academics with industry to bring together and biologists, chemists and engineers to drive forward on research challenges and delivery in algal and cyanobacterial IB and bioenergy. Build and broaden algal research in the areas of 'omics, systems biology and bioinformatics. Develop metabolic engineering and metabolic flux models in target strains focussed on production of commodity chemicals. Tackle challenges associated with scale-up and DSP. Carole Llewellyn, PML
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Anaerobes, Extremophiles, etc.; Expanding Biocatalytic Diversity
Discussion on expanding the industrially-accessible biocatalytic toolkit with unique and unusual enzymes/microbes and coupling this with chemical processing where required. The focus is on meeting the challenge of an increasingly diverse product catalogue, by utilising approaches from both biology and chemistry that exploit and develop unusual or extremely robust chemistries; and by providing appropriate processing and separation technologies for dealing with them.
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Anaerobic digestion and the ‘dirty’ biorefinery
We would like to form a network of people interested in developing the idea of a biorefinery for bulk chemical production that does not require aseptic conditions. Our own area of expertise in this is the manipulation of anaerobic digestion so as to allow the accumulation of acid intermediates (e.g. butyric and propionic acids) in % concentrations that can then be extracted using advanced membrane technology or pervaporation techniques. We can control these reactions to some extent by controlling the syntrophy between the acid fermenters, acetogens and methanogens by a variety of techniques, including choice of waste feedstock, manipulation and availability of trace elements and kinetic conditions in the reactors. We would like to team up with groups who have interests in further refining these products or in their subsequent conversion to value-added materials (e.g. bioplastics, liquid fuels, sterilants). Product/energy carrier routes are also possible in multiphase reactor systems and we do not discount methane as a co-product to meet energy demands, or as a substrate in further fermentation. Our major objective is to avoid the need to work with sterile culture media, allowing the use of waste feedstocks to produce intermediate value products in bulk quantities.
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Anaerobic digestion network
There is huge industrial interest in anaerobic digestion at the moment, covering a variety of different feedstocks, process technologies and configurations and prime purposes from renewable energy production to waste management. The networks promoted by industry (REA, ADBA, ADOWG) have been very successful, and everyone may benefit from coordinated input from academic research in this field. If we put forward a network in AD what would you like to see as the priimary research focus? e.g. extension to new substrates, development of new technologies, improved understanding of process fundamentals, microbial communities, integration of AD with other biomass technologies (ethanol, biodiesel etc), process modelling and integration, rapid assessment and monitoring tools etc. We need your ideas to help formulate this.
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Applications of synthetic biology in vaccine production and innovation
This network is proposed to cover a range of technologies designed to exploit new opportunities in the application of synthetic biology methods to vaccine design and manufacture. It will include (but is not necessarily confined to) the following: 1. Engineering of biosynthetic pathways for adjuvants; creation of novel, modified biomolecules which can bias the stimulation of a desired response (eg Th1/Th2 balance) 2. Development of methods for optimization of antigen presentation and delivery 3. Engineering of glycoconjugates, capsular polysaccharide and other complex oligosaccharides related to vaccine formulation 4. Novel approaches to vaccine production (eg expression of antigens in heterologous hosts) It is anticipated that the outputs of the network will have applications in: 1. Routine human and animal health vaccination programmes, through the modification of current, well established vaccines to improve coverage, efficacy and other properties 2. Development of vaccines against new diseases, or diseases which were previously problematic to address using older methods 3. Biosecurity and emergency preparedness- development of an academic and industrial network which is able to respond rapidly to public and animal health emergencies, triggered through emergence of new disease forms (eg influenza), entirely new disease threats and bioterrorism The network membership should cover: 1. Academic- fundamental bioscience disciplines including molecular biosciences, microbiology, virology and immunology; also medical and veterinary practitioners in infectious disease 2. Industrial- commercial manufacturers of vaccines and related products 3. Regulatory authorities eg MHRA, Health England Thoughts and suggestions welcome.
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Biohydrogen
Hydrogen is potentially the cleanest of all fuels. Engineers can burn it if they really want (and no polution will result) but it is also versatile (can be used in fuel cells to generate electricity). Hydrogen is also an important feedstock in industrial processes - but 99% of the H2 in use at the moment is made by the steam reformation of fossil fuels. There must be a solution to this problem that biologists, and their collaborators, can solve. Some microbes produce hydrogen naturally, but it has proven a real challenge not only to harness this but to improve and boost H2 production. Biohydrogen is often overlooked by the biofuel/bioenergy community in favor of carbon-based alternatives. Rather then drop H2 into a single huge "Biofuel" network, it may be better off as a separate network of experts.
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BioProcess Design Network
We would like to propose a new network to focus on Bioprocess Design. This merges previous proposals on Multiscale Modelling (Imperial) and Predicting Bioreactor Performance (Sheffield). Our goal is to make possible the rapid design of efficient and safe bioprocesses to allow businesses to invest with confidence in new biomanufacturing process. This will be achieved through a combination of whole process modelling and better characterisation of unit operations involving cells or biomolecules: bioreactors, separations, protein product formulation, etc. The current poor characterisation of these operations confounds our ability to predict whole process performance, which introduces an unacceptable level of commercial risk. By combining appropriate modelling and laboratory technologies we will characterise these operations to generate more realistic whole process models. The parent discussions that spawned this new proposal had considerable interest from CPI, Brunel, Sheffield and other universities, plus chemical manufacturers and suppliers. We would like to combine forces or build links to other proposals, including: - Understanding the full production cycle from biomass to target chemicals - Genotype to Metabolic Phenotype - Meeting Separation Challenges in Industrial Biotechnology - Bioprocessing Network (based upon BRIC) - Bioprocess Safety, Security and Risk Network We have a strong network assembled and are keen to attract further academic, industrial and supplier expertise in the following areas: - Chemical Engineering for Reactor Modelling - Control Engineering - Scale-down technologies - Separations - Formulation - Metabolomics - PAT technologies - Bioreactors - Microbial expression platforms - Mammalian expression platforms
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Bioprocess Safety, Security and Risk Network
From a process safety perspective, the main hazards associated with industrial-scale processes have traditionally been of a toxic or flammable nature, with much effort being put into the assessment of human health and environmental risks. Although engineered biological processes operate at ‘near’ ambient temperature and pressure, and should therefore be inherently safer from a traditional process safety perspective, other hazards come into place. These are often complex, controversial, and not necessarily the main focus of research. There is, for instance, much room for quantitative studies into the survival, evolution and persistence of GMOs in the environment, their potential for impacting human health and/or ecosystems, and the business/corporate risk ramifications from these. This information would indeed help address current public perception issues with synthetic biology and biotechnology in general, and inform risk assessment frameworks and regulations early on, so that they act as catalysts of technology rather than barriers to development. A ‘Bioprocess safety, security and risk’ network would underpin the IBBE programme by addressing safety, security and risk implications of the proposed technologies and networks. It would also cover the characterisation of potential impacts on human health and the environment, where uncertainty could act as a barrier to commercial scale implementation. Alternatively, the’ bioprocess safety, security and risk’ theme could be addressed within each of the proposed networks individually. Any thoughts?
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Bioprocessing Network
Discussion thread on a proposed Bioprocessing Network to build on the BRIC club
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Biorefinery Technologies Network
Discussion thread on Biorefinery Technologies Network
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Closing the Circle: Key technologies in the circular bioeconomy.
Central concept: The emergent model for the future development of the manufacturing economy, and a necessary intermediate approach, is the reduction of the use of limited mineral resources through the increased re-use and re-cycling of materials before they become waste. This is referred to as the ‘circular economy’ (see http://www.ellenmacarthurfoundation.org/circular-economy ). However, this process is not fully circular, and simply delays – rather than avoids the point of material exhaustion, especially in the context of rapidly increasing per-capita demands. The renewable and sustainable use of biomaterials as raw materials, and their non-polluting return to the biosphere represents the only truly circular and permanently sustainable solution to this problem. This proposed network is not exclusively focussed upon existing research and activity. It seeks to bring together relevant work, but also to encourage new projects, interactions, and translatable technologies can be brought together to foster first reduced, and subsequently zero impact economic activity based upon biotechnology and the bioeconomy. It also seeks to provide an environment in which multi- and inter-disciplinary approaches are brought to bear to find new (and apply existing) solutions to this area, one in which real world solutions are proactively sought, and in which solutions, policy, and future developments in this area are developed and progressed. • Areas of activity might include (and other suggestions are certainly sought and invited): • Biofuel development and implementation, including distributed and ‘domestic scale production’. • Bioplastics and the use of natural-sourced renewable alternatives. • Material science, manufacturing processing, and design in the use of natural biomaterials, and the specific production of those replacement materials. • The identification of and development of all areas in which new bio-sourced products can replace non-renewables, or those with excessive polluting environmental footprints. • Methods of material biodegradation, biodisposal, and appropriate ‘end of life’ return of products to the biosphere. • Synthetic biology for the refinement or generation of new exploitable materials • The integrated use of biocrops for multiple / parallel applications (for example Hemp for cloth, biofuel, oils for food and non-food applications, biofuel, building materials) to enhance the overall economic impact and viability of bio-economic solutions. • The optimization of bioseparation methodologies to increase the diversity of products obtained from single bioresources and bioprocessing streams. • The application of biosolutions for environmental monitoring and bioremediation. • The integration of non-biological / ex-vivo processing with biological processing and synthetic biology to plug critical gaps in biological system functionality (including toxicity and yield limits of end products). • Behavioural and social sciences studies on the impact of biorenewable resources, and behavioural change needed for their adoption. And economic assesments of their inplementation. There will no doubt be a developing number of core technologies and applications, but the driving force of the proposal is real-world solutions to a pressing real-world problem. This proposal also has many overlaps with others, with which it might usefully deliberately interact, but it provides a wider and unifying context, and has a stronger emphasis on translatability / applicability / implementation.
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Crossing biological membranes
A fundamental biological process that will be crucial for optimising many IB activities is the efficient import of substrates into cells and export of target products. This will require: • the natural presence or engineering of appropriate selective transporters into the cell factory. • identification of heterologous transport systems using bioinformatic approaches • mechanisms to reliably overproduce and characterize transporters • manipulating the surface area volume ratio of cells • integrating heterologous transporter encoding genes into existing gene regulatory networks. This biology will impact on the efficiency of many IB processes.
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Discussions summary
A pictorial summary of discussion threads as of the 22nd February grouped by theme
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