OpenPlant ERASynBio Summer School in New Phytologist

New Phytologist have published a report on the OpenPlant ERASynBio Summer School in plant synthetic biology authored by Nicola Patron, Colette Matthewman and collaborators at BBSRC.

European science policy is reflecting the increasing importance of synthetic biology as a tool to drive cutting-edge scientific developments. Significant strategic investment has been made, coordinated by the European Research Area Network for synthetic biology (ERASynBio), to ensure European synthetic biology research is coherent and world-leading. Strategies to achieve this include providing high-quality training for the next generation of synthetic biologists, and fostering international collaborations across a range of disciplines (ERASynBio, 2014). To realize these aims, ERASynBio has funded annual summer schools to bring together early career researchers from across ERASynBio partner countries for world-class synthetic biology training and networking. The second of these summer schools, which ran on 14–20 September 2014 at the John Innes Centre, Norwich, UK, was designed to provide the participants with ‘An introduction to synthetic biology in plant systems’ in conjunction with OpenPlant, a collaborative plant-focussed Synthetic Biology Research Centre linking the University of Cambridge, John Innes Centre and The Sainsbury Laboratory.

‘… an invaluable and enjoyable opportunity for early career researchers to learn from and engage with world-leading experts in plant synthetic biology.’

Read more via New Phytologist Carmichael, R. E., Boyce, A., Matthewman, C., & Patron, N. J. (2015). An introduction to synthetic biology in plant systems. New Phytologist, 208(1), 20-22. DOI: 10.1111/nph.13433

Plant Methods Thematic Series on Gene Editing

The sponsor of the upcoming CRISPR workshop, Plant Methods, is inviting submissions to its new thematic series on Plant Genome Editing.

The series is being launched in conjunction with the GARNet-OpenPlant CRISPR-Cas Workshop to be held at the JIC Norwich on 7-8 September 2015.

The exciting field of genome editing is advancing rapidly and precise genome editing techniques have already become an important tool for both fundamental research and plant biotechnology.

The thematic series, which will include invited reviews by Holger Puchta (Karlsruher Institut für Technologie), Sandeep Kumar (Dow AgroSciences) and Carolyn Lawrence-Dill (Iowa State University), will cover all aspects of genome editing technologies as applied to plant research (both for crop plants and model organisms). GARNet will also collaborate with Nicola Patron to produce a commentary article from the CRISPR workshop.

Potential topics include, but are not limited to:

• Alternative methods for targeted genome editing (including CRISPR-Cas and zinc finger nickases)

• New technologies for synthetic biology

• Computational tools for genome editing

Manuscripts in the categories of Review, Methodology, Research Article, Software or Databases will be considered.

Find out more via GARNet

Algae Biotech Experience at Cambridge

On the 25^th of July, fifteen 6^th form students selected from sevens schools across East Anglia were invited to spend the day at University of Cambridge to learn about algae research and biotechnology. The event was hosted by PhD students Anthony Riseley, Dept of Biochemistry and Johan Ulrich Kudahl, Dept of Plant Sciences and with support from the Biochemical Society, Dept. of Biochemistry and the Marie Curie training network, Photo.Comm.

The Algae Biotech Experience (ABE) was an event which aimed to:

1. Engage the students into the importance and relevance of microbiology in the 21^st century;
2. Challenge the students to conducting real scientific experiments and molecular techniques such as PCR and phycobilisome extractions and;
3. Help the students to discover the importance of algae science in our daily life and its relevance to helping solve problems such as the energy crisis and food security.

The day included wet lab practicals (PCR, phycobilisome extractions), computational projects (bioinformatics/protein structure visualisation), a lecture from a Cambridge scientist, a lab tour and microscopy of various algae species.

OpenPlant at the UK Synthetic Biology 2015 Conference

Three OpenPlant group leaders spoke at the recent UK Synthetic Biology Conference: Nicola Patron (The Sainsbury Laboratory) Development and Application of Standards for Plant Synthetic Biology

Anne Osbourn (John Innes Centre) Making new molecules

Alison Smith (University of Cambridge) Using synthetic biology approaches to allow predictable metabolic engineering in algae

The full conference schedule can be found here and there are plans for a 2016 conference in Edinburgh with more involvement from PhD students and postdocs. You can see some highlights from #SBUK2015 below!

OpenPlant Forum 2015: blog by Dr Colette Matthewman

bannerimage1-marchantia

A number of events took place in Cambridge as part of Cambridge Open Technology Week. At the heart of the activities was the OpenPlant Forum a two-day meeting bringing together experts from a range of sectors to discuss developing open technologies for plant synthetic biology.

What was remarkable about the Forum was the strikingly varied and multi-disciplinary agenda covering intellectual property, policy and regulation, responsible research and innovation and open science as well as an excellent scientific programme.

The first day of the Forum focussed on foundational technologies that facilitate exchange and freedom to operate in research environments. The second day concentrated on application of these technologies to trait engineering, and open source routes to innovation and industry.

In between talks, Dr Jenni Rant showcased outputs from Science Art Writing (SAW) Trust synthetic biology public engagement workshops, including a Marchantia themed game.

Kicking off events, Tom Knight, a computer engineer now widely considered the ‘father of synthetic biology’, talked about how synthetic biology aims to make an engineering discipline of biology. He commented that “biologists tend to like complexity, while engineers like it simple”.

Dr Nicola Patron described her recent efforts with OpenPlant and the international community, to bring together a common standard for the assembly of plant DNA parts. Many of the scientific talks described DNA parts collections for gene regulation or for producing high value chemicals in plants.

Professor Anne Osbourn highlighted the value of genetic and chemical diversity in plants, explaining for example that plant P450 enzymes can achieve things that test-tube chemistry can’t. Further examples were seen in talks by Dr Yang Zhang and Dr Stephanie Brown who are exploiting this plant natural diversity for production of heath promoting and anti-cancer compounds in tomato and yeast.

Openness was a running theme across the two days with social scientist Dr Jane Calvert emphasizing how open biology, open innovation and opening up are all critical to the future of synthetic biology. Professor Chas Bountra talked about his ground-breaking work in novel drug discovery, explaining that drug discovery is too expensive, risky and slow, and open science and pooling of resources can speed up research and share the risks. Dr Linda Kahl outlined the need for new legal tools to improve freedom to operate for researchers in both academia and industry, and her work to create an Open Material Transfer Agreement in collaboration with OpenPlant.

Next year the OpenPlant Forum comes to the Norwich Research Park, from 25 – 27 July 2016.

OpenPlant is funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC).

Source: OpenPlant Forum 2015: blog by Dr Colette Matthewman

SBOL 2.0 Specification Released

The SBOL editors are pleased to announce the official release of the next major version of the Synthetic Biology Open Language (SBOL). The SBOL 2.0 specification is available online at: http://sbolstandard.org/downloads/specification-data-model-2-0/ Major new capabilities of SBOL version 2.0 over the prior 1.x include: - Beyond DNA, designs can include RNA, proteins, and other components - Designs can associate function with structure and link to external models - Rich annotation of biological designs, for integration with non-SBOL design information

This specification is complemented by the 2.0 beta release of libSBOLj (available at: https://github.com/SynBioDex/libSBOLj/releases), a library implementing the SBOL 2.0 specification in order to allow simple integration of the new SBOL capabilities into software tools.

Thanks, -Jake Beal (SBOL Editor, on behalf of the SBOL community)

First common standard for assembly of DNA parts in plant SynBio published

Dr Nicola Patron

Supported by OpenPlant, Dr Nicola Patron of The Sainsbury Laboratory, Norwich, has led development of the first common standard for the assembly of DNA parts for plant synthetic biology.

Published today in New Phytologist as a Viewpoint article, this standard has been agreed between the inventors and developers of several Type IIS cloning technologies, the leaders of numerous plant bioengineering consortia and leaders of international plant science.

In the article, Nicola and her co-authors describe a common syntax of twelve fusion sites to enable the facile assembly of eukaryotic transcriptional units.

The manuscript received favourable support in the peer review process. One reviewer commented that “ …this is somewhat of a landmark publication that will massively influence all plant synthetic biology to come and shows the community in this field to be ahead of their colleagues in other areas.” Another remarked that “this paper will be a catalyst for further discussion around standardization not only in plants but in synthetic biology in general.”

By establishing a standard for the wider plant community Nicola and her colleagues will facilitate the sharing of standard parts for plants between scientists. It also sets a basis for the development of software and hardware that will support accelerated design and automated assembly. Their vision is to develop an extensive catalogue of standardised, characterised DNA parts to accelerate plant bioengineering.

The establishment of a DNA assembly standard for plants is an important and timely step in plant synthetic biology.

Dr Jim Haseloff at the University of Cambridge said: “The publication of a common syntax for plant DNA parts is a landmark for the adoption of engineering principles in multicellular organisms. It is the result of wide cooperation between researchers across the plant biology field, and sets the scene for greater scientific exchange and innovation in crop improvement.”

Read the paper: ‘Standards for plant synthetic biology: a common syntax for exchange of DNA parts’

Edited from the post Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio which appeared first on The Sainsbury Laboratory.

Source: Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio

The first GM oilseed crop to produce omega-3 fish oils in the field

See more at BBSRC website

In a landmark paper published today in the journal Metabolic Engineering Communications, scientists at Rothamsted Research have announced the first year results of the field-scale trial of Camelina oilseed plants genetically engineered to make omega-3 fish oils in their seeds.

Omega-3 fish oils specifically long-chain polyunsaturated fatty acids (omega-3 LC-PUFA) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are acknowledged by the medical community to be beneficial components of the human diet. The primary dietary sources of EPA & DHA are marine fish, either wild or farmed (aquaculture). Although some types of omega-3 fats are available from other sources in the human diet (such as flax seeds), the nutritionally-beneficial omega-3 LC- PUFA EPA & DHA are only available from marine sources. Fish, like humans, accumulate the omega-3 fish oils by feeding on other organisms in the marine food chain or, in the case of farmed fish, through fishmeal and fish oil in feed.

Farmed fish is a rapidly growing sector, and today over half of the fish consumed worldwide comes from aquaculture. As the production of fish through aquaculture increases so does the need to find alternative sources of omega-3 fish oils. Rothamsted's new data – which demonstrates an important proof of concept that a crop plant can be engineered to synthesise these beneficial fatty acids in seeds – provides hope for sustainable land-based sources of omega-3 fish oils, thereby releasing pressure from the oceans.

Dr Olga Sayanova, the senior Rothamsted Researcher who developed the GM Camelina plants, commented: “We are delighted with the results of our first year field trial. Finding a land-based source of feedstocks containing omega-3 fish oils has long been an urgent priority for truly sustainable aquaculture. Our results give hope that oilseed crops grown on land can contribute to improving the sustainability of the fish farming industry and the marine environment in the future."

Rothamsted scientists, strategically funded by BBSRC, have already shown that they can successfully engineer Camelina sativa plants to produce non-native EPA and DHA, by introducing a set of seven synthetic genes based on the DNA sequences found in photosynthetic marine organisms. Although previous experiments in glasshouses had given positive indications for the performance of this trait, this trial demonstrated the stability of the trait and the ability of the GM Camelina plants to synthesise useful quantities of fish oils without any negative effects on yield. Monitoring of the plants grown in the field showed no obvious phenotypic differences in the growth, flowering or seed-set of the GM Camelina plants when compared to the non-GM control plants.

Professor Johnathan Napier, leading the GM Camelina programme at Rothamsted Research, said: “The omega-3 fish oil trait that we have developed is probably the most complex example of plant genetic engineering to be tested in the field. This is a globally-significant proof of concept and a landmark moment in the effort to develop truly sustainable sources of feed for fish farms.”

The field trial conducted at Rothamsted Research’s experimental farm continues this year. In the field this year two GM Camelina lines are sown as well as the non-GM controls. One line is the same as the one described in the current publication making EPA and DHA. The second one is a GM Camelina line that makes only EPA. Analyses and comparisons will be conducted between the two lines.

The field trial and the associated laboratory analyses are funded by the government-supported Biotechnology and Biological Sciences Research Council (BBSRC). The scientific paper published today is available in open-source format from the journal Metabolic Engineering Communications.

Synthace Integrates Powerful Automation Equipment with its High-Level Language for Biological Research

Read more on the SynbioBeta blog

At the O’Reilly Solid conference in San Francisco, a meeting dedicated to the new hardware movement and the Internet of Things, Synthace will be announcing today a partnership to integrate its Antha language with liquid handling equipment from Gilson and CyBio Northern Europe. Sean Ward, CTO of Synthace, will also be announcing a sign-up program for a closed-beta release of the Antha language that will become available in July. This release will include an automated DNA construct assembly protocol that will enable researchers to generate 24 constructs in under an hour using a Gilson Pipetmax®.

"We are delighted to be working with these leading equipment providers to bring the Internet of Things to academic, clinical and industrial laboratories through integration with our Antha platform. Improving reproducibility and productivity across biological R&D will be absolutely reliant on establishing this type of connectivity." Sean Ward, CTO of Synthace.

EUSynBioS: growing networks in Synthetic Biology

The European Association of Students and Postdocs in Synthetic Biology (EUSynBioS) founded and chaired by Department of Plant Sciences Graduate Student Christian R. Boehm continues to attract international attention.

Half a year after its establishment, the student-led initiative embraces a membership base of several hundred students and postdoctoral researchers based in 15 European countries, is supported by an Advisory Board composed of 20 accomplished principal investigators (including Dr Jim Haseloff and Dr Nicola Patron from Cambridge), and works closely with major partner organizations across the globe towards its overall goal: shaping and fostering a community of young researchers in synthetic biology by means of providing an integrative central resource for interaction and professional development.

Co-sponsored by the Cambridge-based OpenPlant initiative, the EUSynBioS Steering Committee recently participated in the SynBioBeta London 2015 conference, where the Association was introduced to an international high-profile audience and hosted a social event in the evening. An OpenDiscussion satellite workshop chaired by Christian on the second day was well-attended by students, principal investigators, and representatives from the UK research councils BBSRC, EPSRC, and the Dstl alike. He comments on the session: “We are hopeful that bringing students, principal investigators, and representatives from funding bodies into the same room like this will lead to new opportunities for the next generation of young researchers to be better involved in shaping the future of their discipline.” To foster collaboration and exchange among students and postdoctoral researchers in the field, Christian and colleagues are working towards an international symposium for the young synthetic biology community to be hosted in Europe in the near future.

Students and postdoctoral researchers active in synthetic biology can become Members of EUSynBioS by completing a short online form at http://www.eusynbios.org.

Global Food Security Cambridge Symposium — 9 July 2015

Bookings are now open for the one-day symposium taking place at the Sainsbury Laboratory on Wednesday 8^th July 2015, 9.30–4.30. The aim of the day is to learn about and be inspired by food security research taking place across the University, and explore ways in which collaboration across disciplines can bring greater impact. Speakers from all Schools in the University will be speaking on topics ranging from zoonoses to forests and food security, resource limitations on the Ugandan food system to food supply chain risks and sustainability.

The event is aimed principally at University of Cambridge researchers, and a Raven account is required to access booking details. Please contact the Initiative if this does not apply to you but you are still interested in attending.

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Programme draft [PDF]

Global Food Security Cambridge Symposium — Cambridge University Strategic Initiative in Global Food Security.

Registration and abstract submission open for Synthetic Biology UK 2015!

Synthetic Biology UK 2015: Think, develop, measure, make 1—3 September 2015 Charles Darwin House, London, UK More info

Synthetic Biology is a field that has rapidly expanded. It relies on multidisciplinary approaches and delivers transdisciplinary advances that have the potential to redefine our understanding of the natural world and to significantly contribute to our society and economy.

The UK is a world leader in science and engineering, and Synthetic Biology has been identified as an important area for our continued success. Key to that success is a cohesive, vibrant and multidisciplinary community, open to collaboration, open to advances and driven to exceptional research with meaningful outcomes.

That cannot be delivered by a single research centre, single funding body or hosted by a single learned society. The SynBio UK conference aims to showcase UK Synthetic Biology research and to create a focal point for the community, embracing its diversity and fostering its growth and its engagement with society.

Under the themes of Making, Measuring, Thinking and Developing, the aim of the conference is to bring together the Synthetic Biology community in all forms in the UK to capitalise on synergies, enabling the exploration of entirely new approaches to the systematic and safe engineering of biology.

Abstract deadline: 3 July 2015 Abstract Submission is now open

Earlybird registration deadline: 3 July 2015 Registration is now open.

Oral communication slots are available at this meeting. All attendees, particularly researchers in the early stages of their career, are invited to submit a poster abstract for consideration as an oral communication.

Featured image credit: DNA by MIKI Yoshihito on Flickr, licensed under CC-BY 2.0

Tim Dafforn is Appointed BIS’s Chief Scientific Adviser

Professor Tim Dafforn has been appointed as the new Chief Scientific Adviser at the UK’s Department for Business, Innovation and Skills. Professor Dafforn took up his post on June 1st, and he succeeds Professor John Perkins CBE.

Read more at the SynBioBeta blog

EUSynBioS: growing networks in Synthetic Biology

The European Association of Students and Postdocs in Synthetic Biology (EUSynBioS) founded and chaired by Department of Plant Sciences Graduate Student Christian R. Boehm continues to attract international attention.

Half a year after its establishment, the student-led initiative embraces a membership base of several hundred students and postdoctoral researchers based in 15 European countries, is supported by an Advisory Board composed of 20 accomplished principal investigators (including Dr Jim Haseloff and Dr Nicola Patron from Cambridge), and works closely with major partner organizations across the globe towards its overall goal: shaping and fostering a community of young researchers in synthetic biology by means of providing an integrative central resource for interaction and professional development.

Co-sponsored by the Cambridge-based OpenPlant initiative, the EUSynBioS Steering Committee recently participated in the SynBioBeta London 2015 conference, where the Association was introduced to an international high-profile audience and hosted a social event in the evening. An OpenDiscussion satellite workshop chaired by Christian on the second day was well-attended by students, principal investigators, and representatives from the UK research councils BBSRC, EPSRC, and the Dstl alike. He comments on the session: “We are hopeful that bringing students, principal investigators, and representatives from funding bodies into the same room like this will lead to new opportunities for the next generation of young researchers to be better involved in shaping the future of their discipline.” To foster collaboration and exchange among students and postdoctoral researchers in the field, Christian and colleagues are working towards an international symposium for the young synthetic biology community to be hosted in Europe in the near future.

Students and postdoctoral researchers active in synthetic biology can become Members of EUSynBioS by completing a short online form at http://www.eusynbios.org.

Refreshed Version of the UK Synthetic Biology Roadmap: workshop on 16 June

The Synthetic Biology SIG team and The Knowledge Transfer Network are organizing a consultation workshop in Birmingham on June 16th to refresh the UK Synthetic Biology Roadmap, which is nearly three years old. The work is being led by Lionel Clarke, Co-chair of the UK Synthetic Biology Leadership Council. The outputs of the workshop will be presented to the Department of Business, Innovation and Skills later this autumn.

Read more on the SynBioBeta blog

Jonathan Jones elected to US National Academy of Sciences

Professor Jonathan Jones, Group Leader at The Sainsbury Laboratory and OpenPlant PI, has been elected as a foreign associate to the US National Academy of Sciences in recognition of his outstanding career researching plant-pathogen interactions.

The post Jonathan Jones elected to US National Academy of Sciences appeared first on The Sainsbury Laboratory.

SynBioBeta post on OpenPlant: Open Technologies for Plant Synthetic Biology

Reposted from the SynBioBeta Blog

Plant synthetic biology has great potential to improve sustainable bioproduction of globally important products; from foodstuffs to fibres to drugs. Advantages of plants over engineered microbes include their worldwide cultivation, their harvest on a giga-tonne scale and the existing precedent for genetically modified crops in many parts of the world. In addition to these applied benefits, plants raise interesting scientific questions and technical challenges around engineering pathways and interactions in multi-cellular, differentiating and developing organisms, adding complexity to current microbial experiments.

Plant synthetic biology is a young field and requires the development of tools and techniques to deal with additional complexity, such as improved genome editing, DNA synthesis and assembly at chromosomal or genomic scales. Supply of plant DNA parts is expected to increase rapidly, which is why the sharing and characterization of these components is a priority; particularly in the liverwort Marchantia, which appears to be a promising candidate for a plant synthetic biology model organism. Tools identified as necessary to support these developments include hardware and software for automation of high-throughput assembly and characterization, plant-relevant software models, data repositories and standards to increase interoperability of the parts and their associated data.

Right: Image of Marchantia

The OpenPlant initiative is a BBSRC-EPSRC funded synthetic biology centre, based at the University of Cambridge, the John Innes Centre and The Sainsbury Laboratory in Norwich, that aims to address these foundational requirements and then apply them to engineer traits including plant metabolic pathways and natural product synthesis routes. Applications include input to major programmes addressing grand challenges for energy and food security. For example, carbohydrate engineering for improved yield of biofuels or studying Marchantia to inform a synthetic approach to nitrogen-fixing in cereals, where it could have major implications for fertilizer use. Metabolic diversity in plants supplies us with important drugs, flavorings and agrochemicals in addition to impacting plant ecology and protection, so another OpenPlant project concerns optimizing enzymes and engineering gene clusters to synthesize these compounds.

OpenPlant aims to shape working practices and norms in these early stages of plant synthetic biology, by promoting interdisciplinary exchange, the development of standards and responsible innovation. It promotes an ecosystem of open technologies giving researchers and small companies greater freedom to operate within a two-tier IP system. IP-free circulation of foundational tools and DNA parts should accelerate uptake, innovation and entrepreneurship; allowing exploration of new models for decentralized ownership, control and manufacture of synthetic plant technologies. Protecting inventions representing novel combinations and applications of these low-level components preserves investment and retains commercial prospects, while also promoting alternative business models.

Innovation in plant biotechnology, particularly in high-value areas such as crops, is increasingly constrained by intellectual property (IP) protection, sometimes restricting access to genetic tools. This can impede the ability of innovative synthetic biology programmes to succeed. Commercial entities from entrepreneurial startups to large multinationals already struggle through patent thickets when bringing products to market and both academic-industrial exchange and sharing among researchers is restricted by terms and conditions in materials transfer agreements. OpenPlant experiments with openness as a means to aid innovation, particularly as the scale of DNA systems increases and the number of parts and tools involved in creating an engineered organism grows. Openness also offers greater access to research tools for the development of synthetic plant products that have implications for global sustainability and international development, and that may rely on decentralized projects to address local needs.

These efforts are part of a broader ongoing exploration of open practices and commons-based knowledge production among many communities. Open source strategies have proved fruitful in software and computing, from multimillion dollar commercial companies such as RedHat built on the basis of openly distributed code, through to projects such as the Raspberry Pi and its associated open software interfaces, which are wildly popular among educators and makers, including scientists. CERN, a scientific organisation with a strong history of successful technology transfer, heavily promotes open source hardware projects. Their repository hosts over 100 projects, with 16 companies actively engaged in testing or producing hardware based on technologies developed at CERN.

Open research practices have been promoted at the grassroots of several academic communities and are fast becoming a focus of funding agencies hoping to leverage their potential for accelerating research and innovation and reducing inequities in access to knowledge. One project employing an approach analogous to OpenPlant is the Structural Genomics Consortium, a public-private partnership for drug discovery that restricts IP protection of any results until the later stages of clinical trials, thus moving the pre-competitive boundary later in the discovery pipeline. As per a recent evaluation report, its open access approach is considered a significant incentive for investment by commercial partners owing to better facilitation of downstream research and increased competitiveness further down the value chain. The benefits of sharing were felt by the companies involved to outweigh any risks and associated with late-stage IP protection.  Other projects such as Open Source Malaria have also described how open approaches accelerated their research, including via industrial partnerships.

In summary, OpenPlant is performing cutting edge synthetic biology research while also exploring the potential of open technologies by engaging with diverse partners, building communities and providing incentives for open projects, such as seed funding. We will document and share what we learn from our approach to promoting innovation and entrepreneurship alongside the technologies and scientific results arising from our research. We welcome feedback from the SynBioBeta community!