High-frequency, precise modification of the tomato genome (open access)

Čermák, T., Baltes, N. J., Čegan, R., Zhang, Y., & Voytas, D. F. (2015). High-frequency, precise modification of the tomato genome. Genome biology, 16(1), 1-15. doi:10.​1186/​s13059-015-0796-9 The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequence-specific nucleases, which stimulate homologous recombination at predefined genomic sites by creating targeted DNA double-strand breaks, there are only a handful of studies that report precise editing of endogenous genes in crop plants. More efficient methods are needed to modify plant genomes through homologous recombination, ideally without randomly integrating foreign DNA.

Plant synthetic promoters and transcription factors

Liu, W., & Stewart, C. N. (2016). Plant synthetic promoters and transcription factors. Current opinion in biotechnology, 37, 36-44. doi:10.1016/j.copbio.2015.10.001 Synthetic promoters and transcription factors (TFs) have become incredibly powerful and efficient components for precise regulation of targeted plant transgene expression. Synthetic promoters can be rationally designed and constructed using specific type, copy number and spacing of motifs placed upstream of synthetic or native core promoters. Similarly, synthetic TFs can be constructed using a variety of DNA binding domains (DBDs) and effector domains. Synthetic promoters and TFs can provide tremendous advantages over their natural counterparts with regards to transgene expression strength and specificity. They will probably be needed for coordinated transgene expression for metabolic engineering and synthetic circuit applications in plants for bioenergy and advanced crop engineering. In this article we review the recent advances in synthetic promoters and TFs in plants and speculate on their future.

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

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 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

Job: Lectureship in Synthetic Biology

The Centre for Bacterial Cell Biology and Interdisciplinary Computing and Complex BioSystems (ICOS) research group are recruiting a tenured track Lectureship/Senior Lectureship (Assistant or Associate Professor in the American system) in

Synthetic Biology/Nanotechnology. Early applications are encouraged.

For informal enquires please contact the CSBB director, Professor Natalio Krasnogor.

Read more details about and how to apply for this exciting post.

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

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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.

IBioIC Exemplar Programme (closes 31 August 2015)

See IBioIC website for further information and to apply The Industrial Biotechnology Innovation Centre (IBioIC) is currently inviting applications for its fourth project competition from Micro Companies, for industry-led collaborative research projects using innovative applications in biotechnology. We request applications from projects with a total value of up to £250,000 that demonstrate a defined market need and commercial opportunity.

IBioIC aims to promote collaboration between universities and industry, to drive innovation, find commercial opportunities for new technology and ideas. The IBioIC Exemplar Programme aims to support projects that meet these criteria and that bring biotechnology closer to industrialisation.

The Exemplar Programme is available to all companies from large to micro businesses with a sliding scale of IBioIC funding. IBioIC also offer personal one-to-one project consultations to all members to assist in the development of projects.

Translational Plant Sciences Funding Seminar (30 July 2015)

See CambPlants Hub eventbrite for more info Are you an academic thinking of: - translation of basic plant science into crop science research? - integrating the latest bioscience and modelling techniques into practice? - creating collaborative work opportunities with industry? Or are you a Business interested in finding solutions from academic resources? Would you like to find out more about what funding schemes are available to support you in this?

CambPlants Hub invites you to a TRANSLATIONAL PLANT SCIENCES FUNDING SEMINAR, where you will have the opportunity to learn about the latest translational funding schemes in this area and network with academics, industry and research council representatives. Seminar Programme: 9:30 - Registration and Tea/coffee 9:55 - Welcome and Introduction 10:00 - BBSRC Translation Funding Schemes 10:20 - NERC Translation Funding Schemes 10:40 - Tea/coffee break 11:10 - Innovate UK and KTN opportunities 11:30 - H2020 Funding Schemes 12:00 - Elevator pitches from industry 12:30 - Lunch From 13:00 - Bookable 1:1 sessions with speakers from funding research councils.

Please contact ml745@cam.ac.uk to book your 1:1 session with a funder OR if you are interested in giving an elevator pitch. Do you have questions about this seminar? Contact Mariana Fazenda: ml745@cam.ac.uk.

David Phillips Fellowships (close 21 Oct 15)

See BBSRC for more details The Biotechnology and Biological Sciences Research Council invites applications for the David Phillips fellowships. These support researchers who are wishing to establish their first independent research group. The research may be in any area of science within the council’s remit, which includes research on plants, microbes, animals, and tools and technology underpinning biological research.

Applicants should hold a PhD but not hold, or have held, an open-ended academic position of lecturer level or equivalent. They should have at least three years of active postdoctoral research experience prior to June 2015.

Up to five fellowships are available. Each fellowship includes up to £1 million at 80 per cent full economic cost for personal salary and research support. The host institution should also make a substantial demonstration of support for the fellow, in terms of access to facilities and equipment, training and research costs.

ZuvaSyntha scientist and business development vacancies (based in BioPark Hertfordshire)

More info in the ZuvaSyntha website ZuvaSyntha is a young and exciting UK SME working in the rapidly expanding Industrial Biotechnology sector. Recently formed through the merger of BioSyntha Technology Ltd and ZuvaChem LLC, we are developing novel microbial-based routes to renewable intermediate and specialty chemicals.

ZuvaSyntha is planning to expand and seeks to appoint outstanding candidates for the following roles:

• Business Development Manager
• Senior Biochemist
• Scientist/Senior Scientist in Molecular Biology and Strain Development

Postdoc vacancies at SynthSys, Edinburgh (close mid- to late-July 2015)

More info from SynthSys website

Call for participation in Lean Launchpad for Synthetic Biology (apply ASASP)

As part of its innovation development programme, SynbiCITE, is pleased to offer all its partners the opportunity to participate in the Lean Launchpad for Synthetic Biology. You can now take part in this unique programme that has helped numerous would-be entrepreneurs translate research ideas into successful products and services. Translating research from the laboratory to the market place – takes more than just improving technology. It requires a parallel track of optimizing the other parts of the business that are essential for turning an idea into a profitable company.

The Lean LaunchPad for Synthetic Biology does this by helping teams rapidly:

· Define the utility of the idea before committing resources to develop it.

· Understand who their core and tertiary customers are, and the sales and marketing process required for initial sales and downstream commercialisation.

· Assess intellectual property and regulatory risk early in the process.

· Know what data will be required by future partnerships/collaborations/purchases before doing the science.

· Identify the financing vehicles before you need them.

The Lean Launchpad for Synthetic Biology is based on the Lean Launchpad programme, developed by Steve Blank in Silicon Valley. This program has been taught at Stanford, Berkley, Columbia and Caltech, and is being adopted by US NSF as part of its i-Corps curriculum. The programme was run earlier this year at Imperial College and was highly successful launching new companies and products, and teaching entrepreneurship.

The Lean Launchpad for Synthetic Biology is a ten-week long programme for 3-person teams interested in commercialising research. The programme starts on September 15 with a 3-day kickoff, and followed by nine weekly meetings, and a 2-day wrap up session on November 23-24. You will need to commit to 20 hours per week in addition to class time for this programme to be successful. The course content includes Customer Discovery and Development methods, the Business Model Canvas and topics specific to the commercialisation of synthetic biology. The goal of the programme, within the constraints of a classroom and a limited amount of time, is to create the entrepreneurial experience of an early stage start-up. Supporting each team will be a mentor, an entrepreneur or executive with deep business experience, to provide guidance.

The course will be led by Professor Jerry Engel, the Director of the NSF i-Corp programme and

Founding Executive Director Emeritus, Lester Center for Entrepreneurship at UC Berkley’s Haas School of Business. He also has over 20 years experience and success in high technology entrepreneurship and venture capital. The teaching faculty will include entrepreneurs and investors who have successfully translated scientific research into commercial products and services.

If you have an idea you want to exploit, identify its commercial potential, discover customers, collaborators and investors to realise your dreams this is the programme is for you.

Entrance is very limited. Applicants apply as teams, not individuals. The teams are required to tell us about themselves using the “Team Information” template. They also must submit a completed Business Model Canvas using the “Business Model Information” template based on a minimum of 5 interviews. Those who are interested fill in the “Lean LaunchPad Application” form, which is available from Jenny (jcm80@cam.ac.uk).

We strongly encourage you to apply ASAP.

If you would like more information or arrange a visit to discuss the programme please contact: stephen.chambers@synbicite.com