Deep Science Ventures programme open to PhD graduates

Interested in working in the world of biotech start-ups? A new programme called Deep Science Ventures works with PhD graduates to create high-tech startups from scratch even if you haven’t yet found the right idea or team. Deep Science Ventures is a fully funded, full time programme which works with scientists to make the transition from technical expert to founder of a high-tech start-up. They accept up to 60 PhDs, PostDocs and industry scientists onto a 6 month programme twice per year, help you to identify the match between your passions and real world opportunities and build a team of like minded people across a range of disciplines.

Applications are open now for the October cohort. Register your interest this week to joint the next round of applicants: http://deepscienceventures.com

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

[Closes 31 Aug 2016] Job opportunity for Synthetic Biology SRI Administrative Assistant

The Synthetic Biology Strategic Research Initiative (SRI) is based in the Department of Plant Sciences. We are seeking a part-time (0.5FTE) Administrative Assistant who will work closely with the SRI Co-ordinator, Dr Jenny Molloy, in the research group of Professor Jim Haseloff (SRI Chair).

The role-holder will provide administrative support to the Synthetic Biology SRI Co-ordinator, maintain a website for the initiative, assist with events, publicity organisation, committee meetings and other related administration.

The successful candidate will have an A-Level in Biology, or equivalent; knowledge of web design and implementation; the ability to use social media as a PR tool in a professional setting; events management experience. You will have excellent communication skills and a pro-active and flexible approach.

Fixed-term: The funds for this post are available for 3 years in the first instance.

To apply online for this vacancy and to view further information about the role, see the listing on jobs.ac.uk.