Guest Post: If you can protoplast, you can encapsulate

The following is a guest post from the SynBio Fund project ‘Development of a microfluidic device for high-throughput analysis of genetic circuits in plant protoplasts’ from by Steven Burgess, Ivan Reyna-Llorens, Christian R. Boehm, Sara Abalde-Cela and Paul Bennett. A continuation project, entitled ‘Establishing 3D Printed Microfluidics for Molecular Biology Workflows’, was funded through the OpenPlant Fund in 2016 and recently a second OpenPlant Fund grant was awarded for the project ‘Plant-ProChip 2.0: High throughput transformation of plant protoplast’.

You can read the original post on their project blog here >>

We started this project with the aim of testing whether it is possible to use microfluidics to analyse plant protoplasts, and I think we now have the answer. After numerous rounds of testing we have improved our working method and are now able to routinely isolate and encapsulate protoplasts. This has been done for two model plant species including A. thaliana, and everyone’s favorite Bryophyte –Marchantia polymorphia, the workhorse of the OpenPlant Project for plant synthetic biology (Figure 1).

Figure 1: Encapsulation of protoplasts from model plant species

So the take home message from this project is – if you can protoplast you can encapsulate! But the story does not end here. To be of real use, this process needs to be coupled to transformation of protoplasts. As a result, we teamed up with Oleg Raitskinfrom Nicola Patron’s group at the Earlham Institute. Oleg has been optimizing protoplast isolation and transformation using Nicotiana benthamiana and had a couple of tips for improving isolation, including the use of a cork borer instead of scalpel blade for cutting up tissues to minimize mechanical damage, cutting tissue when submerged in the enzyme mix and using a high ratio of DNA to protoplasts during PEG transformation.

This was a fruitful collaboration, Oleg managed to transform protoplasts with a nuclear targeted Venus reporter and these were encapsulated by Ziyi in the Chemistry department (Figure 2).

Figure 2: Encapsulation of N. benthamiana protoplats expressing a nuclear targeted Venus reporter

So putting all this work together, we have in hand a simple, but very powerful system that opens up a whole range of possibilities for rapid phenotyping in plants (Figure 3).

Figure 3: Schematic of microfluidic analysis of plant protoplasts and some of the potential applications.

One of the stipulations of the project was to pursue science in an open manner, so we have been putting up information on the website protocols.io. I highly recommend checking out the site if you haven’t done so already, it has a great set up for disseminating protocols. Further we believe microfluidics is a great technique, so would encourage others to have a go as well!

Looking to the future there are still a few things we would like to work on, The project was briefly presented at Cambridge’s Cafe Synthetique meet-up and we had some great feedback, such as trying Calcium alginate encapsulation as a means of improving protoplast viability. Sorting of protoplasts is the next major goal, and requires redesign of a new chip, and finally improving the efficiency of protoplast transformation by developing an on-chip procedure would be a big advantage. This round of our project has come to an end, but stay tuned for future developments.

Finally I want to finish this piece with a big thanks to Cambridge Synthetic Biology SRI for funding the work, it has been a great experience, and to encourage anyone who is interested in protoplasts or microfluidics to get in contact, we are always happy to chat!

OpenCon 2016 Cambridge

November 24th, 2016, 09:30-17:00

Betty and Gordon Moore Library Wilberforce Road Cambridge CB3 oWD

OpenCon 2016 is the student and early career academic professional conference on Open Access, Open Education, and Open Data being held in Washington, DC.

The OpenCon 2016 Cambridge satellite event will bring together students, early career academic professionals and open advocates from around Cambridge (although anyone from the surrounding areas are welcome to join us!)

This year’s theme is Building Impact Through Openness.

Our goal is to support and build the open community in Cambridge. We want to empower attendees to make a difference in their respective fields through open research, data, education and access.

This year’s committee have brought together a sensational program of world leading speakers but there is also time scheduled for focus group discussion around actions that we can take to make a change in the world.

Furthermore there’s ample time set aside in the day to ensure all the attendees will be able to share their ongoing activities (in the “silent” unconference) and hopefully build new collaborations for the future.

You can follow the main OpenCon event in held in Washington DC #OpenCon, and you can join the discussion around the Cambridge satellite event at #OpenConCam2016.

We look forward to seeing you there! Please reach out if you have any questions.

For more information and booking, click here.

The event is organised by Kirstie Whitaker, on behalf of the OpenCon Cambridge organising committee

More information about this event…

Nuffield Council on Bioethics publishes Genome editing: an ethical review

The Nuffield Council on Bioethics has today published the first findings of its programme of work looking at the recent and potential impact of recent advances in genome editing such as the CRISPR-Cas9 system across many areas of biological research.

The Council found evidence that, given its technical advantages and rates of uptake, genome editing is already having an almost unprecedented impact in research. The Council considered factors such as the extent to which the ethical questions raised by applications of the technology are novel, the likelihood of imminent advances in these areas and the possible effects of these advances in fields such as health care, food production, industry and public health.

Genome editing techniques are an essential tool for synthetic biology and while centred around more standard forms of single gene editing, the report acknowledges the field (sections 7.3-7.6) and the use of gene editing in food crops (5.1-5.17)

Synthetic Biology

"Synthetic biologists are self-consciously elaborating a novel field. They see the field as transforming biology as a practical discipline, not only in relation to the adoption of technical innovations, but also epistemically and institutionally (breaking down disciplinary barriers and reimagining biology as an engineering discipline), and socially and politically (e.g. the desire to build a community and to inculcate certain norms, including those of open source publication and responsible innovation practices). While, undoubtedly, genome editing has given a fillip to synthetic biology it does not, however, seem to have the same rhetorical significance here as in other areas of biology. This might be partly attributable to the fact that the natural reservoir of metaphor for synthetic biology is technical (engineering, construction) rather than textual (editing).

Synthetic biology does, however, offer an insight into possible ways of approaching genome editing as an innovation within research and industry that is essentially different to the translational approaches of biomedicine or, again, public health innovations. Owing, in part, to the different cultures that are integral to synthetic biology (e.g. that of computer science) and in part to lessons about innovation learned from the observation of other fields (e.g. nanotechnology), it has been common for synthetic biologists to adopt responsible innovation practices from the outset. These tend to see ethical reflection and social engagement as longitudinally integral to their practice (‘ethical by design’), as both guiding and governing research, rather than as challenges or decisions to be addressed at particular stages."

Plants

"Genome editing is currently used in research into plant breeding. Possible commercial uses include improvements in yield and pest resistance, increased drought tolerance, and increased nutritional benefit.

The impact of genome editing techniques is perhaps less revolutionary in plants than in humans, given the already long history of breeding strategies that have changed the genetic characteristics of virtually all crops – including selective breeding and first generation ‘genetically modified’ plants (mainly involving the insertion of genes that do not naturally occur in those plants).

However, genome editing could significantly speed up the progress of breeding programmes. It is thought that genome editing could reduce the time needed to generate the desired genetic characteristics in a plant population from 7-25 years to as few as 2-3 years since its target specificity effectively bypasses the need to go through a number of plant generations to achieve a particular genetic combination.

Depending on the regulatory and economic conditions, it could open up the field to smaller companies and, potentially, drive the development of characteristics other than the main commercially important traits like herbicide resistance."

Read the full report >>

Synthetic Biology at Cambridge Science Festival gets a special mention at Cambridge BID Awards 2016

The Plant and Life Sciences Marquee was a roaring success at Cambridge Science Festival, scooping a prize at the Cambridge BID awards Awards 2016. OpenPlant's synthetic biology stand was highly rated by the public mystery shoppers and got a special mention in their final report!

OpenPlant offered a glimpse into synthetic biology at the Cambridge Science Festival and also showcased open technologies for science by demonstrated open source hardware developed with support from the OpenPlant Fund and SynBio Fund.

Making some weird and wonderful biological circuits

A disassembled phone explained the idea that by knowing how each of the individual simple components work (a dialling pad to input your desired number, a vibrating receiver coil to change the electrical signal into a sound wave) you can build more elaborate systems and by applying this idea to biology the public made weird and wonderful new lifeforms like a cat whose nose turns purple when a disease is nearby or a sprouts that taste of strawberries when it snows.

Cambridge Science Festival conducted some ‘Mystery Shopping’ as part of its evaluation strategy in 2016 and our home, The Plant and Life Sciences Marquee, was one of several weekend, hands-on spaces that were visited by evaluators. Our stand and team scored exceptionally highly with a 94.3% public approval rating!

The marquee was honoured at the 2016 CambridgeBID (Business Improvement District) Awards and Elisabeth Burmeister of the Sainsbury Laboratory collected the award on behalf of all the volunteers and sponsors who made the event a success.

Congratulations to all of the OpenPlant and SynBio SRI student and Faculty members involved!

University of Cambridge Department of Plant Sciences welcomes independent Fellows

The Department of Plant Sciences hosts significant synthetic biology research including OpenPlant and the SynBio SRI. It is currently welcoming independent research fellows who wish to apply to join the Department.

We welcome approaches to host candidates who are applying for independent Fellowships, such as Royal Society University Research Fellowships, BBSRC Sir David Phillips, NERC or EU Marie Curie awards. The Department has an excellent tradition for supporting Research Fellows in terms of providing financial support for laboratories and equipment, and PhD studentship opportunities, as well as promoting career development and collaborative expertise.

Potential candidates should contact the Head of Department, Professor Alison Smith (hod@plantsci.cam.ac.uk) or Department Administrator, Catherine Butler (cek31@cam.ac.uk) initially, after which they should approach Group Leaders from the Department (http://www.plantsci.cam.ac.uk/research) who are most closely allied to their area of research interest. Applications will be co-ordinated by the Department Resources Committee. Contact should be made at least 6 months before any deadline for submission. We welcome applications from individuals who wish to be considered for part-time or other flexible working arrangements.

The Department of Plant Sciences sits within the School of Biological Sciences, with undergraduate teaching integrated through the Natural Sciences Tripos (NST). Postgraduate recruitment and training is offered either directly or indirectly via BBSRC or NERC Doctoral Training Programmes (http://www.plantsci.cam.ac.uk/grads/). The Department maintains teaching and research specialisms across a wide range of plant science disciplines (from molecular and developmental biology, through cell-signalling, biochemistry and physiology to epidemiology, ecology and ecosystem modelling) with 18 academic staff leading active research groups, 4 independent research fellows (funded by the Royal Society, EC and NERC), 4 senior research associates, 55 post-doctoral researchers and 42 support staff. Research grant income in 2014/15 was £6M, with the Department currently administering a total of 68 grants with a combined value of £26.5M from a variety of sources, including research councils, Royal Society, charities, EU, industry and government agencies.

Synthetic Biology at Cambridge Science Festival gets a special mention at Cambridge BID Awards 2016

The Plant and Life Sciences Marquee was a roaring success at Cambridge Science Festival, scooping a prize at the Cambridge BID awards Awards 2016. OpenPlant’s synthetic biology stand was highly rated by the public mystery shoppers and got a special mention in their final report!

 OpenPlant offered a glimpse into synthetic biology at the Cambridge Science Festival and also showcased open technologies for science by demonstrated open source hardware developed with support from the OpenPlant Fund and SynBio Fund.

MAKING SOME WEIRD AND WONDERFUL BIOLOGICAL CIRCUITS

A disassembled phone explained the idea that by knowing how each of the individual simple components work (a dialling pad to input your desired number, a vibrating receiver coil to change the electrical signal into a sound wave) you can build more elaborate systems and by applying this idea to biology the public made weird and wonderful new lifeforms like a cat whose nose turns purple when a disease is nearby or a sprouts that taste of strawberries when it snows.

Cambridge Science Festival conducted some ‘Mystery Shopping’ as part of its evaluation strategy in 2016 and our home, The Plant and Life Sciences Marquee, was one of several weekend, hands-on spaces that were visited by evaluators. Our stand and team scored exceptionally highly with a 94.3% public approval rating!

The marquee was honoured at the 2016 Cambridge BID (Business Improvement District) Awards and Elisabeth Burmeister of the Sainsbury Laboratory collected the award on behalf of all the volunteers and sponsors who made the event a success.

Congratulations to all of the OpenPlant and SynBio SRI student and Faculty members involved!

SETTING UP THE 3D PRINTER AND OPEN HARDWARE STAND AT CAMBRIDGE SCIENCE FESTIVAL

Fuel Your Passion for Engineering Biology at SynBioBeta SF 2016 (Oct. 4th-6th) - Special offer on registration

SynBioBeta SF 2016 - Fuel Your Passion for Engineering Biology, Oct. 4th-6th, (San Francisco, CA) SynBioBeta SF 2016 is the prime conference for the synthetic biology industry – bringing the global community together to drive technology and business forward. This conference features a program full of talks from key thought-leaders, decision makers, and tech pioneers. Networking opportunities amongst key industry leaders provides an environment rich for expanding your company’s reach. Make critical connections ideal for business growth or launching your next product. If you are an active part of the synthetic biology industry and have a passion for making biology easier to engineer, then this is a must attend event. Highlighted topics for this year include the future of food, biosecurity, engineered cell therapies, DNA storage, public engagement, and more!

Open Plant Network Gets 20% Off Registration. Use Code OPNSAVE20Learn More & Register

The Power of Plants: OpenPlant visits Latitude Festival

A team of OpenPlant Scientists from the John Innes Centre, the University of Cambridge, and collaborators from Imperial College and University College London worked together to deliver an exciting range of activities for families visiting the Kids Area at Latitude Festival in July 2016. Latitude is a mixed arts festival that attracts over 10,000 visitors a year, who enjoy the rich mix of thought-provoking performances and interactive workshops. Our stand, entitled ‘The Power of Plants’, was an exhibit that led visitors on a journey looking at traditional uses of plants, how plant selective breeding has produced the food crops that we recognise today, tracking the evolution of our relationship with plants through science to introduce the synthetic biology approach, and some of the modern uses of plants and algae that bioengineering enables.

Activities included leaf printing to explore variation in the brassica family, a pairs game to match modern crop varieties to their ancient ancestors, pigment extraction and making bath bombs to explore traditional uses of plants and the chemicals they produce, infiltrating tobacco leaves (with water) to learn how scientists introduce new DNA into plants and to discover how vaccines can be made in plants. The second half of the display focussed on algae and visitors learnt about algae and it’s many uses (including the variety of algae-derived pigments used in food), seeing an algae printer in action (created by designer Marin Sawa), learning about bioreactors and measuring algal cell density using a mobile phone app (both bioreactor and app were developed as part of the OpenPlant Fund project: Big Algae Open Experiment), and learning about the difference between a lemon battery and electric currents produced by algae and plants. We exhibited both plants and algae that had been wired up so that the current could be measured with a volt meter.

We had a hugely positive response, both to the science exhibited and to the aesthetics of our stand which was covered in plants, algae bioreactors, science related graphics, and fronted by 5 beautiful giant willow flowers created by Mat Rant, and decorated by the OpenPlant team.

Our stand even smelt good, thanks to the 100s of lavender bath bombs that were being made. Though the smell at times became a little too much for our volunteers who had to step out of the tent for some fresh air and a coffee to counter the sleep-inducing effects of the lavender!

If you want to have a go yourself at pigment extraction and creating electricity from plants, Co-Lab and OpenPlant have teamed up to run a weekend workshop in September 2016 to bring together scientists, designers, and anyone else with an interest to develop new project ideas: http://openscienceschool.org/colabopenplant/

A Big Algae Open Experiment blog post can be found here.

Many thanks to all volunteers:
Colette Matthewman (OpenPlant, John Innes Centre, Norwich), Jenni Rant (The SAW Trust, Norwich), Alys Barr (OpenPlant, John Innes Centre, Norwich), Michael Stephenson (OpenPlant, John Innes Centre, Norwich), Dorota Jakubczyk (O’Connor Lab, John Innes Centre, Norwich), Matt Heaton (John Innes Centre, Norwich), Daisy Rant (Norwich), Paolo Bombelli (Big Algae Open Experiment, University of Cambridge), Brenda Parker (Big Algae Open Experiment, University College London), Marc Jones (Big Algae Open Experiment, John Innes Centre, Norwich), Marin Sawa (Algal printer, Imperial College London), Katrin Geisler (Smith Lab, University of Cambridge).

Blog post written by: Colette Matthewman
Photos by: Matt Heaton and Alys Barr

OpenPlant Forum 2016: Reprogramming Agriculture with SynBio

Many early efforts of synthetic biology have focussed on the engineering of microbes, especially for the growing biotech industry. In contrast to single cell microbes, multi-cellular organisms such as plants present a higher level complexity, take longer to engineer, and the regulatory system can be a tough and time consuming to navigate - but there are huge opportunities for delivering social, environmental and economic benefits through efforts to reprogramme plants and agriculture. They come with their own distinct set of ethical, legal, social and economic questions. The above were topics central to discussions at the 2016 OpenPlant Forum. Over one hundred people from various disciplines assembled to hear about some of the recent advances in crop and feedstock engineering, discover the latest tools to support innovation in this field, and to reflect on and discuss the ethical, legal, social, and economic questions.

Events kicked off at the John Innes Conference Centre, Norwich, with a networking evening and industry showcase, including two exciting new local developments: Martin Stocks (Plant BioScience Ltd) talked about Leaf Systems®, a translational facility being built to scale up protein and chemical production in plants; and Tony West gave a preview of the new DNA Foundry at the Earlham Institute, which has since been officially launched.

The first full day of the Forum opened with a double bill of keynotes from Allan Green (CSIRO) and Jonathan Napier (Rothamsted) talking about their impressive efforts engineering oilseed crops. It continued with a case study of AB Sugar's Wissington sugarbeet processing site, providing an inspiring processing model for maximising production from a feedstock and it's byproducts. This was followed by a cross-discipline exploration of some recent advances and future opportunities for reprogramming agriculture. In the final session of the day, Spencer Adler (Bioeconomy Capital) gave an investors perspective, followed by a lively debate on the ethical, legal, social and economic considerations of developments in this area. Discussions continued into the night at the conference dinner.

Day two grounded the discussions back in the technical, with a focus on tools to support synthetic biology, especially in plants. The day started with Tom Knight opening the curtains to an exhilarating view of Ginkgo Bioworks and some of their latest developments. Moving back to plant chassis, advances establishing the liverwort Marchantia as a simple plant chassis were showcased alongside work developing tools and methods for other plant chassis. The final session of the event focussed on tools to enable innovation through sharing of knowledge, data and materials - a key focus of the OpenPlant Synthetic Biology Research Centre.

Steven Burgess and Cindy Chan have published a detailed write-up of the OpenPlant Forum on the PLOS Synbio Community blog: Seven Developments in SynBio: Science, Patents and Ethics | OpenPlant Forum 2016

Blog post written by Colette Matthewman Photos by Matt Heaton

OpenPlant Forum 2016: Reprogramming Agriculture with SynBio

Many early efforts of synthetic biology have focussed on the engineering of microbes, especially for the growing biotech industry. In contrast to single cell microbes, multi-cellular organisms such as plants present a higher level complexity, take longer to engineer, and the regulatory system can be a tough and time consuming to navigate – but there are huge opportunities for delivering social, environmental and economic benefits through efforts to reprogramme plants and agriculture. They come with their own distinct set of ethical, legal, social and economic questions. The above were topics central to discussions at the 2016 OpenPlant Forum. Over one hundred people from various disciplines assembled to hear about some of the recent advances in crop and feedstock engineering, discover the latest tools to support innovation in this field, and to reflect on and discuss the ethical, legal, social, and economic questions.

Events kicked off at the John Innes Conference Centre, Norwich, with a networking evening and industry showcase, including two exciting new local developments: Martin Stocks (Plant BioScience Ltd) talked about Leaf Systems®, a translational facility being built to scale up protein and chemical production in plants; and Tony West gave a preview of the new DNA Foundry at the Earlham Institute, which has since been officially launched.

The first full day of the Forum opened with a double bill of keynotes from Allan Green (CSIRO) and Jonathan Napier (Rothamsted) talking about their impressive efforts engineering oilseed crops. It continued with a case study of AB Sugar’s Wissington sugarbeet processing site, providing an inspiring processing model for maximising production from a feedstock and it’s byproducts. This was followed by a cross-discipline exploration of some recent advances and future opportunities for reprogramming agriculture. In the final session of the day, Spencer Adler (Bioeconomy Capital) gave an investors perspective, followed by a lively debate on the ethical, legal, social and economic considerations of developments in this area. Discussions continued into the night at the conference dinner.

Day two grounded the discussions back in the technical, with a focus on tools to support synthetic biology, especially in plants. The day started with Tom Knight opening the curtains to an exhilarating view of Ginkgo Bioworks and some of their latest developments. Moving back to plant chassis, advances establishing the liverwort Marchantia as a simple plant chassis were showcased alongside work developing tools and methods for other plant chassis. The final session of the event focussed on tools to enable innovation through sharing of knowledge, data and materials – a key focus of the OpenPlant Synthetic Biology Research Centre.

Steven Burgess and Cindy Chan have published a detailed write-up of the OpenPlant Forum on the PLOS Synbio Community blog: Seven Developments in SynBio: Science, Patents and Ethics | OpenPlant Forum 2016

Cambridge-JIC iGEM Update: Using low-cost, well-documented, open-source hardware for synthetic biology

The OpenPlant-supported Cambridge-JIC iGEM Team are exploring open source synthetic biology tools for chloroplast engineering in algae. The following was authored by Cambridge JIC- iGEM team member Claire Restarick and is reposted with permission from the Cambridge Consultants blog. Since our initial blog post, we’ve spent many hours finalising designs for our genetic assemblies, which are now in the process of being synthesised. Once these are complete, we will begin the challenging task of completing four rounds of experiments before our deadline in September.

While our biologists are making significant headway in the lab, there have also been advancements on the hardware and engineering side. Our designs for low-cost, open-source lab equipment to support our Chlamydomonas transformation protocol have started to take shape – with the first stages of assembly taking place. This equipment will include a growth facility with light control, temperature regulation and imaging capabilities (linked to a dedicated Twitter account, @RPi_camigem2016), as well as a gene gun which, if successful, will transform cells by firing DNA-coated tungsten microparticles directly into them at high pressure.

The decision to make our hardware low cost and open source developed from recent trips to publicise our project at synthetic biology conferences in Paris and Norwich. At the Bio NightScience event hosted by the Centre de Recherches Interdisciplinaires (CRI) at the Cité des Sciences et de l’Industry, we presented our project to the conference and heard from many projects originating from Makespaces – collaborative community labs with little-to-no budget. We found its use of plant synthetic biology was hindered by the high cost of commercial equipment to culture and transform plant and algal cells. This inspired us to design low-cost equipment, which could make the area of plant synthetic biology more accessible to these creative workspaces, and other small research institutions.

The issue of documentation for open-source hardware for synthetic biology was raised repeatedly during the Open Plant Forum, hosted by the John Innes Centre in Norwich. A lack of clear, detailed protocols online makes it near impossible for the average novice builder to construct these devices. Having struggled ourselves to find appropriate parts and clear designs online, we have placed a focus on thoroughly documenting our designs, to make our open-source designs truly accessible for everyone.

To support both the hardware and biology aspects of the project, we have also continued our work on mathematical modelling, developing an open-source, integrated, kinetic model of Cas9-mediated gene insertion. We also held our first meeting with the director of the Cambridge-based Centre for Global Equality, to begin developing the human practices element of our project – understanding its impact and integrating this within the design and aims of the different parts.

Now past the halfway point of our project’s timeline, we feel well on track to meeting our project’s ambitious goals. Thanks to the continued support of our advisors at the Plant Sciences Department, and specialist advice from Cambridge Consultants, all aspects of our project are developing the potential to have an impact on both the scientific and non-scientific communities.

Note from Cambridge ConsultantsSynthetic biology has huge potential to solve many of today’s critical challenges in healthcare, agriculture, energy and the environment. That’s why Cambridge Consultants has decided to sponsor the Cambridge University team at iGEM 2016 – the international genetically engineered machine competition run by MIT. As part of our sponsorship, we are acting as mentors – giving the team access to more than 700 Cambridge Consultants engineers and scientists worldwide to help solve problems during this year’s project.

The iGEM team is also grateful for support from:

• OpenPlant
• University of Cambridge, School of Biological Sciences
• BBSRC, the Wellcome Trust, and the Society for Experimental Biology

Cambridge-JIC iGEM Update: Using low-cost, well-documented, open-source hardware for synthetic biology

The OpenPlant-supported Cambridge-JIC iGEM Team are exploring open source synthetic biology tools for chloroplast engineering in algae. The following was authored by Cambridge JIC- iGEM team member Claire Restarick and is reposted with permission from the Cambridge Consultants blog.

Since our initial blog post, we’ve spent many hours finalising designs for our genetic assemblies, which are now in the process of being synthesised. Once these are complete, we will begin the challenging task of completing four rounds of experiments before our deadline in September.

While our biologists are making significant headway in the lab, there have also been advancements on the hardware and engineering side. Our designs for low-cost, open-source lab equipment to support our Chlamydomonas transformation protocol have started to take shape – with the first stages of assembly taking place. This equipment will include a growth facility with light control, temperature regulation and imaging capabilities (linked to a dedicated Twitter account, @RPi_camigem2016), as well as a gene gun which, if successful, will transform cells by firing DNA-coated tungsten microparticles directly into them at high pressure.

The decision to make our hardware low cost and open source developed from recent trips to publicise our project at synthetic biology conferences in Paris and Norwich. At the Bio NightScience event hosted by the Centre de Recherches Interdisciplinaires (CRI) at the Cité des Sciences et de l’Industry, we presented our project to the conference and heard from many projects originating from Makespaces – collaborative community labs with little-to-no budget. We found its use of plant synthetic biology was hindered by the high cost of commercial equipment to culture and transform plant and algal cells. This inspired us to design low-cost equipment, which could make the area of plant synthetic biology more accessible to these creative workspaces, and other small research institutions.

The issue of documentation for open-source hardware for synthetic biology was raised repeatedly during the Open Plant Forum, hosted by the John Innes Centre in Norwich. A lack of clear, detailed protocols online makes it near impossible for the average novice builder to construct these devices. Having struggled ourselves to find appropriate parts and clear designs online, we have placed a focus on thoroughly documenting our designs, to make our open-source designs truly accessible for everyone.

To support both the hardware and biology aspects of the project, we have also continued our work on mathematical modelling, developing an open-source, integrated, kinetic model of Cas9-mediated gene insertion. We also held our first meeting with the director of the Cambridge-based Centre for Global Equality, to begin developing the human practices element of our project – understanding its impact and integrating this within the design and aims of the different parts.

Now past the halfway point of our project’s timeline, we feel well on track to meeting our project’s ambitious goals. Thanks to the continued support of our advisors at the Plant Sciences Department, and specialist advice from Cambridge Consultants, all aspects of our project are developing the potential to have an impact on both the scientific and non-scientific communities.

Note from Cambridge Consultants
Synthetic biology has huge potential to solve many of today’s critical challenges in healthcare, agriculture, energy and the environment. That’s why Cambridge Consultants has decided to sponsor the Cambridge University team at iGEM 2016 – the international genetically engineered machine competition run by MIT. As part of our sponsorship, we are acting as mentors – giving the team access to more than 700 Cambridge Consultants engineers and scientists worldwide to help solve problems during this year’s project.

The iGEM team is also grateful for support from:

• OpenPlant
• University of Cambridge, School of Biological Sciences
• BBSRC, the Wellcome Trust, and the Society for Experimental Biology

OpenPlant Forum 2015: blog by Dr Colette Matthewman

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

Using ‘chemical origami’ to generate customisable, high-value chemicals from plants

The following article was originally published on the John Innes Centre news feed: Using ‘chemical origami’ to generate customisable, high-value chemicals from plants. Anne Osbourn is Co-Director of OpenPlant and this work from her group is highly relevant to the efforts of OpenPlant to create toolkits for plant metabolic engineering, but was funded from other sources.

Following the discovery of a new and very valuable enzyme which folds linear molecules into different shapes, scientists at the John Innes Centre are building a ‘triterpene machine’ which will enable them to custom-build valuable chemical compounds called triterpenes and produce them in large, cost-effective quantities. Working with the pharmaceutical, agricultural and biotechnology industries, they hope to improve existing triterpenes to make better medicines with fewer side effects, or improve the specificity of pesticides. They also hope to make completely new, custom-designed triterpenes to any specification, which could lead to development of new anti-cancer drugs, agrochemicals, industrial chemicals or cosmetics.

In the ancient Japanese art of origami, different ways of folding a single sheet of paper can transform it into an aeroplane, a flower, or a bird. Plants perform origami too – not with paper, but with chemical compounds, taking individual precursor molecules and using enzymes to fold and modify them to create many different variations.

For several years, Professor Anne Osbourn of the John Innes Centre has been studying the ‘chemical origami’ that gives rise to a large group of plant compounds called triterpenes, many of which may have valuable uses in the pharmaceutical, agricultural and biotechnology industries.

Professor Osbourn said:

“Some triterpenes are currently used in drinks as foaming agents, but there are many more exciting possibilities – new medical therapies such as anti-cancer drugs, diabetes medicines and antidepressants, for example; anti-fungal agents in crop protection, or cosmetic ingredients. All of the triterpenes we know about are based on a suite of similar molecular ‘scaffolds’ – we want to understand how these scaffolds are made, ‘folded’ and ‘decorated’ so that we might be able to engineer completely new triterpenes to make new medicines and industrial chemicals, or to improve those we already have.”

In a new research article published this week in the scientific journal Proceedings of the National Academy of Sciences, Professor Osbourn, along with colleagues at the John Innes Centre and collaborators from the USA, describes how she discovered an important part of the triterpene origami process, almost by accident.

By analysing oat plants that had been exposed to a DNA-mutating chemical, the researchers “stumbled across” a handful of mutated versions of an enzyme called SAD1. SAD1 is a triterpene synthase enzyme responsible for a critical step in building triterpenes: in its normal form, it takes a linear precursor molecule called 2,3-oxidosqualene (OS for short), and turns it into a pentacyclic scaffold – a molecule with 5 carbon rings. This is then further modified by other enzymes to produce hundreds of different triterpene compounds.

However, one of the mutated forms, which differed from the normal form by one little change in the enzyme’s structure, produced tetracyclic scaffolds with four carbon rings instead – the scaffold for a completely different set of triterpenes. Incidentally, the same mutation in an equivalent gene from a different plant, Arabidopsis thaliana, gave the same results, suggesting that this ‘molecular switch’ from pentacyclic to tetracyclic triterpene production is conserved between different plant species.

Next, the scientists tried putting the mutant SAD1 gene into yeast, a fast-growing, single-celled organism, to see if it could be used to make large quantities of triterpenes. Here, the team discovered that the SAD1 enzyme favoured dioxidosqualene (DOS) as a substrate rather than OS.

“This was an exciting discovery,” said Professor Osbourn, “because we realised that we could not only modify the enzyme to produce different triterpene scaffolds, but we could also modify the building block to make different more highly oxygenated scaffolds.”

The PNAS article presents just one part of ongoing work by the Osbourn lab to harness the power of genes and enzymes to generate high-value chemicals from plants.

Professor Osbourn said:

“Here at the Norwich Research Park we’re building a ‘Triterpene Machine’; a toolkit of molecular parts we can put into yeast, or a recently developed rapid expression system using tobacco leaves, which we hope will allow us to custom-build valuable triterpenes and produce them in large, cost-effective quantities. Working with the pharmaceutical, agricultural and biotechnology industries, we hope we’ll be able to modify known triterpenes to improve their existing applications – to make better medicines with fewer side effects, or improve the specificity of pesticides, for example. We might even be able to make completely new, custom-designed triterpenes to any specification we want, which could provide us with new anti-cancer drugs, agrochemicals, industrial chemicals or cosmetics. The possibilities are potentially endless!”

This research was funded by the Biotechnology and Biological Sciences Research Council, the John Innes Foundation and a Norwich Research Park Studentship Award.

Photo by Frost Museum 

Using ‘chemical origami’ to generate customisable, high-value chemicals from plants

The following article was originally published on the John Innes Centre news feed: Using ‘chemical origami’ to generate customisable, high-value chemicals from plants. Anne Osbourn is Co-Director of OpenPlant and this work from her group is highly relevant to the efforts of OpenPlant to create toolkits for plant metabolic engineering, but was funded from other sources.

Following the discovery of a new and very valuable enzyme which folds linear molecules into different shapes, scientists at the John Innes Centre are building a ‘triterpene machine’ which will enable them to custom-build valuable chemical compounds called triterpenes and produce them in large, cost-effective quantities. Working with the pharmaceutical, agricultural and biotechnology industries, they hope to improve existing triterpenes to make better medicines with fewer side effects, or improve the specificity of pesticides. They also hope to make completely new, custom-designed triterpenes to any specification, which could lead to development of new anti-cancer drugs, agrochemicals, industrial chemicals or cosmetics.

In the ancient Japanese art of origami, different ways of folding a single sheet of paper can transform it into an aeroplane, a flower, or a bird. Plants perform origami too – not with paper, but with chemical compounds, taking individual precursor molecules and using enzymes to fold and modify them to create many different variations.

For several years, Professor Anne Osbourn of the John Innes Centre has been studying the ‘chemical origami’ that gives rise to a large group of plant compounds called triterpenes, many of which may have valuable uses in the pharmaceutical, agricultural and biotechnology industries.

Professor Osbourn said:

“Some triterpenes are currently used in drinks as foaming agents, but there are many more exciting possibilities – new medical therapies such as anti-cancer drugs, diabetes medicines and antidepressants, for example; anti-fungal agents in crop protection, or cosmetic ingredients. All of the triterpenes we know about are based on a suite of similar molecular ‘scaffolds’ – we want to understand how these scaffolds are made, ‘folded’ and ‘decorated’ so that we might be able to engineer completely new triterpenes to make new medicines and industrial chemicals, or to improve those we already have.”

In a new research article published this week in the scientific journal Proceedings of the National Academy of Sciences, Professor Osbourn, along with colleagues at the John Innes Centre and collaborators from the USA, describes how she discovered an important part of the triterpene origami process, almost by accident.

By analysing oat plants that had been exposed to a DNA-mutating chemical, the researchers “stumbled across” a handful of mutated versions of an enzyme called SAD1. SAD1 is a triterpene synthase enzyme responsible for a critical step in building triterpenes: in its normal form, it takes a linear precursor molecule called 2,3-oxidosqualene (OS for short), and turns it into a pentacyclic scaffold – a molecule with 5 carbon rings. This is then further modified by other enzymes to produce hundreds of different triterpene compounds.

However, one of the mutated forms, which differed from the normal form by one little change in the enzyme’s structure, produced tetracyclic scaffolds with four carbon rings instead – the scaffold for a completely different set of triterpenes. Incidentally, the same mutation in an equivalent gene from a different plant, Arabidopsis thaliana, gave the same results, suggesting that this ‘molecular switch’ from pentacyclic to tetracyclic triterpene production is conserved between different plant species.

Next, the scientists tried putting the mutant SAD1 gene into yeast, a fast-growing, single-celled organism, to see if it could be used to make large quantities of triterpenes. Here, the team discovered that the SAD1 enzyme favoured dioxidosqualene (DOS) as a substrate rather than OS.

“This was an exciting discovery,” said Professor Osbourn, “because we realised that we could not only modify the enzyme to produce different triterpene scaffolds, but we could also modify the building block to make different more highly oxygenated scaffolds.”

The PNAS article presents just one part of ongoing work by the Osbourn lab to harness the power of genes and enzymes to generate high-value chemicals from plants.

Professor Osbourn said:

“Here at the Norwich Research Park we’re building a ‘Triterpene Machine’; a toolkit of molecular parts we can put into yeast, or a recently developed rapid expression system using tobacco leaves, which we hope will allow us to custom-build valuable triterpenes and produce them in large, cost-effective quantities. Working with the pharmaceutical, agricultural and biotechnology industries, we hope we’ll be able to modify known triterpenes to improve their existing applications – to make better medicines with fewer side effects, or improve the specificity of pesticides, for example. We might even be able to make completely new, custom-designed triterpenes to any specification we want, which could provide us with new anti-cancer drugs, agrochemicals, industrial chemicals or cosmetics. The possibilities are potentially endless!”

This research was funded by the Biotechnology and Biological Sciences Research Council, the John Innes Foundation and a Norwich Research Park Studentship Award.

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Image by Ftiercel [Public domain], shared via Wikimedia Commons

Synthetic Biology UK 2016

14—16 November 2016: Dynamic Earth, Edinburgh, UK

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.

Topics covered in this meeting will be published in Biochemical Society Transactions

Abstract deadline: 12 September 2016 Abstract submission is now available

Earlybird registration deadline: 12 September 2016

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.

Student Bursaries are available for this meeting. Not a member of the Biochemical Society? Join today and save up to £100 on your registration fee.

For more information, including the full program, please see here.

SYNENERGENE Forum 24-25th June 2016 Amsterdam

Synthetic Biology – visions of the future

SYNENERGENE Forum 24-25th June 2016 Amsterdam

The SYNENERGENE Forum is a large public event which will discuss the promises and implications of synthetic biology from a societal perspective.

Synthetic biology From the beginning of this century synthetic biology has emerged as a new engineering science of life. It uses the rapidly increasing possibilities for both “reading” and “writing” DNA to design and synthesize living cells and biological systems with functions that do not exist in nature. Synthetic biology offers new options for innovation in the fields of health care and sustainable production of energy and materials, but may also more and more become a subject of public controversy about potential risks and commercial exploitation of natural resources.

Responsible research and innovation In order to deal with the governance challenges resulting from this tension, we need to establish conditions for responsible research and innovation (RRI) in the field. As a European mobilization and mutual learning action plan, involving nearly thirty parties from all over Europe, SYNENERGENE contributes to this aim. During the two-day Forum event we want to share our RRI experiences and achievements with relevant stakeholders and publics, including scientists, civil society organizations, industry and policy makers, and discuss the development of a synthetic biology agenda for the (near) future. Addressing the synthetic biology agenda implies a focus on: • Opportunities of synthetic biology relating to societal challenges • Concerns about synthetic biology relating to possible negative implications • Engagement with synthetic biology as a contribution to responsible research and innovation

Program The SYNENERGENE Forum offers a two-day program on Friday and Saturday 24-25th June in the Amsterdam Science Centre NEMO (http://www.e-nemo.nl/en/). The first day is a conference with plenary and parallel sessions focusing on core issues and activities addressed by SYNENERGENE. During the second day SYNENERGENE partners will put “synthetic biology on stage” through debates, theatrical performances and a BIO·FICTION film festival.

For full program and to register, please see here: https://www.rathenau.nl/en/agenda/synenergene-forum-2016

Exciting collaboration opportunity to test Oxford NanoPore device for soil/plant-related sequencing

Details from Simon Hazelwood-Smith at Science Practice "We are Science Practice, a design and research company focused on applying the principles of design to science. One of our interests is in ways of increasing access to scientific testing in agriculture, and we are currently developing a paper microfluidic device for testing soil nutrients like nitrates, at Imperial College London.

We also have a MinION (a pocket-sized genetic sequencing machine) from Oxford Nanopore and we would like to try using our last two MinION flow cells for agricultural testing. We are looking for a collaborator with lab access who would be interested in trying this out to see if we get any interesting results.

Currently our plan is to test nitrates in two different soil samples with our microfluidic device, and also to use MinION sequencing to identify organisms (bacteria, fungi etc.) found in these two soil samples. The aim is to see if it is possible in principle to detect a relationship between nitrate levels and nitrogen-fixing bacteria. This little project would be about two days of lab time (1 day to sequence each soil sample). However we are open to suggestions for other agriculture (e.g. plant) related sequencing projects from anyone who is interested in exploring this exciting new piece of technology with us."

If interested, please contact Jenny Molloy (jcm80@cam.ac.uk) for more information.

UK Commons Select Committee calls for 'GM and gene editing' evidence check

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The UK Commons Science and Technology Select Committee invites views on the strength of the evidence in relation to GM and gene editing.

 Please read the Government statement before submitting a comment.

• GM and Gene Editing: Government statement ( PDF 90 KB)

Comments will be pre-moderated.

Science and Technology 'evidence check' web forum homepage

The Science and Technology Committee invites views on the Government-provided evidence-check papers posted on this forum, in particular on the strength of the evidence and how well the Government's approach reflects the evidence.

• Show your workings, Institute for Government report (PDF 231.13 KB)

Taking forward the work of the Institute for Government, this exercise will help shape future Committee work, including identifying areas for scrutiny hearings or for launching inquiries. We would like submitters to address the following broad questions:

• Diagnosis: Does the Government show that it knows about the issue, its causes, effects, and scale?
• Actions/plans: Has the Government shown that any policy intervention is evidence-based, that it has assessed the strengths/weaknesses of the evidence base, and identified other policy options?
• Implementation:  Has the Government shown that the implementation method for the policy has been based on evidence on what works?
• Value for money: Are the costs and benefits understood and evidence-based?
• Testing and evaluation: Are plans for testing and evaluation adequate?

Get help to improve your research software - deadline April 29th

If you write code as part of your research, then you can get help to improve it - free of charge - through the Software Sustainability Institute's Open Call for Projects. The call closes on April 29 2016.

Apply here!

You can ask for our help to improve your research software, your development practices, or your community of users and contributors (or all three!). You may want to improve the sustainability or reproducibility of your software, and need an assessment to see what to do next. Perhaps you need guidance or development effort to help improve specific aspects or make better use of infrastructure.

We accept submissions from any discipline, in relation to research software at any level of maturity, and are particularly keen to attract applications from BBSRC and ESRC funding areas.

The Software Sustainability Institute is a national facility funded by the EPSRC. Since 2010, the Institute's Research Software Group[1] has assisted over 50 projects across all the UK Research Councils. In an ongoing survey, 93% of our previous collaborators indicated they were "very satisfied" with the results of the work. To see how we've helped others, you can check out our portfolio of past and current projects[2].

A typical Open Call project runs between one and six months, during which time we work with successful applicants to create and implement a tailored work plan. You can submit an application to the Open Call at any time, which only takes a few minutes, at http://bit.ly/ssi-open-call-projects.

We’re also interested in partnering on proposals. If you would like to know more about the Open Call, or explore options for partnership, please get in touch with us at info@software.ac.uk.