OpenPlant researchers advance a translational synthetic biology platform for rapid access to new drug-like molecules

Researchers in Prof Anne Osbourn's lab at the John Innes Centre, including Prof Osbourn and OpenPlant PDRA Dr Michael Stephenson, have published a new paper detailing their advances in rapidly creating and purifying gram-scale quantities of natural products that were previously not possible to synthesise. This has the potential to reinvigorate drug discovery pipelines by opening up whole regions of chemical diversity for testing and production of potentially medicinally important molecules.

Reed, J., Stephenson, M.J., Miettinen, K., Brouwer, B., Leveau, A., Brett, P., Goss, R.J., Goossens, A., O’Connell, M.A. and Osbourn, A., 2017. A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules. Metabolic Engineering. DOI: 10.1016/j.ymben.2017.06.012

Fig 2 from paper: Generation of gram quantities of triterpene using vacuum infiltration a, Vacuum infiltration of N. benthamiana plants. Plants are retained by a bespoke holder, inverted into a bath containing 10 L of A. tumefaciens suspension, and a vacuum applied. Upon release of the vacuum the infiltration process is complete. b, GFP expression in leaves from a vacuum-infiltrated plant 5 days after infiltration (leaves arranged from top left to bottom right in descending order of their height on the plant). The youngest leaves (top left) were formed post-infiltration. c, β-Amyrin purified from vacuum-infiltrated plants following transient expression.

Abstract

Plants are an excellent source of drug leads. However availability is limited by access to source species, low abundance and recalcitrance to chemical synthesis. Although plant genomics is yielding a wealth of genes for natural product biosynthesis, the translation of this genetic information into small molecules for evaluation as drug leads represents a major bottleneck. For example, the yeast platform for artemisinic acid production is estimated to have taken >150 person years to develop. Here we demonstrate the power of plant transient transfection technology for rapid, scalable biosynthesis and isolation of triterpenes, one of the largest and most structurally diverse families of plant natural products. Using pathway engineering and improved agro-infiltration methodology we are able to generate gram-scale quantities of purified triterpene in just a few weeks. In contrast to heterologous expression in microbes, this system does not depend on re-engineering of the host. We next exploit agro-infection for quick and easy combinatorial biosynthesis without the need for generation of multi-gene constructs, so affording an easy entrée to suites of molecules, some new-to-nature, that are recalcitrant to chemical synthesis. We use this platform to purify a suite of bespoke triterpene analogs and demonstrate differences in anti-proliferative and anti-inflammatory activity in bioassays, providing proof of concept of this system for accessing and evaluating medicinally important bioactives. Together with new genome mining algorithms for plant pathway discovery and advances in plant synthetic biology, this advance provides new routes to synthesize and access previously inaccessible natural products and analogs and has the potential to reinvigorate drug discovery pipelines.

Twenty-nine Biomaker Challenge projects funded plus extra deadline for proposals - 21 July 2017

Twenty-nine Biomaker Challenge projects were funded by the SRI, OpenPlant and CamBridgSens covering a huge range of biology and engineering tasks from cell-free synthetic biology to clinical devices to lab automation solutions. Due to late interest, we have added a later deadline of 21 July.

Starting in this summer for the first time, the Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. From colorimeters to microfluidics and beyond, we were looking for frugal, open source and DIY approaches to biological experiments and we found them! The proposals contained a rich set of interdisciplinary project ideas from across the University of Cambridge and Norwich Research Park, with many external collaborators from local industry, the Royal College of Art and further afield.

 The 29 awardees have now been announced (see full list below) and will shortly be documented on GitHub and the Biomaker.org website, where some proposals are already online.

Biomaker Challenge Coordinator Kyata Chihbalabala has recently joined the SRI for ten weeks to manage the programme and arrange training and meetups. The Biomaker Toolkits are now being distributed so watch this space for events coming soon!

Apply by 21 July for Biomaker Challenge Round Two!

Due to a rush of late interest, we have decided to open another round. You still have an opportunity to apply for a Biomaker Toolkit (worth £250) and £750 additional support for your biological instrumentation project.

Find out more about how to apply >>

Acknowledgements

Judging Panel: Dr Emre Ozer (ARM Ltd), Dr Stephanie Reichel (CRUK Cambridge Institute), Dr Dan MacLean (Earlham Institute), Prof Jim Haseloff (Department of Plant Sciences, University of Cambridge), Dr Alexandre Kabla (Engineering Department, University of Cambridge), Dr Oliver Hadeler (Chemical Engineering and Biotechnology, University of Cambridge).

Sponsors: ARM Ltd, New England Biolabs

 

The Funded Projects

1. A cell-free sensor platform for the quantification of arsenic concentrations in drinking water.
2. A Device for Real-Time Monitoring of Protein Synthesis.
3. A low cost reusable microfluidic device for the detection of antibiotic resistant genes in bacteria isolated from patient samples.
4. A low cost, point-of- care device to measure blood haemoglobin levels, using calorimetry and infrared spectroscopy.
5. A low-cost colorimeter for accurate detection of colour changes in medical diagnostic tests
6. A low-cost, pressurized liquid chromatography system for protein purification
7. A microdroplet incubator to establish 3D organoids cultures from oesophageal adenocarcinoma.
8. A sensor to improve the accuracy of stereotactic brain biopsies for the diagnosis of brain tumours
9. An artificial habitat to investigate Boquila trifoliata mimicry
10. Cheap Do-It- Yourself Small Volume UV Spectrometer for Nucleic Acid and Protein Quantitation
11. Detecting alterations in ionic concentrations associated with different cellular states
12. Detecting pathogens in sewage sludge
13. Developing a self-regulating control system for intravenous drug administration -- using aminoglycosides as an example
14. Development of an anti-TFF3 functionalized surface to capture of Barrett’s oesophagus cells
15. DIY bioacoustics
16. Field portable colorimeter
17. Functional membrane-based integrated biosensing devices for detection and quantitation of specific nucleic acids and other biomolecules
18. Handheld syringe pump with heating element
19. KNOW-FLOW: A low-cost programmable blood flow system
20. Low Cost Wearable Sensors Strain Sensors for illness identification via Gait, Posture and muscle usage
21. Low-Cost Multispectral Imagery for UAV-based Vegetation Monitoring
22. Macrophotography of fern gametophytes using a DIY focus stacking system.
23. Microfluidic Turntable for molecular diagnostic testing
24. OptoFlow: Optical flow rate measurement for microfluidics
25. Puzzle-solving Bacterial Pet: Imaging Platform for Microfluidics-based Reinforced Learning with Motile Bacterial Cells
26. Remote Environment Controller for Experiments in Extreme Environments
27. Sci-Fi Cam
28. Ultrasonic Plant Height System for High- Throughput Plant Phenotyping
29. Real-Time monitoring of cell proliferation

Biomaker Challenge is sponsored by BBSRC/EPSRC through OpenPlant Synthetic Biology Research Centre (www.openplant.org) and the University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative (www.synbio.cam.ac.uk) and the Sensors Strategic Research Network (www.sensors.cam.ac.uk).

Call for abstracts for SynBio UK 2017

SynBio UK conference will showcase UK Synthetic Biology research and to create a focal point for the community, embracing its diversity and fostering its growth and engagement. Submit your abstract to the scientific programme now.

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, supportive of young talent, and driven to exceptional research with meaningful outcomes.

Synthetic Biology UK is a conference for the UK synthetic biology community and we look forward to seeing a good cohort from the Cambridge Synthetic Biology community attending!

SynBio UK 2017 is hosted by the Manchester SynBio Research Centre, SYNBIOCHEM, which specialises in synthetic biology for fine and speciality chemicals production.

Abstracts must be submitted by Monday 25 September 2017. Oral communication slots are available at this meeting. 

SPEAKERS INCLUDE

• Anil Wipat (Newcastle University, United Kingdom)
• Jason Chin (MRC Laboratory of Molecular Biology, United Kingdom)
• Jens Nielsen (Chalmers University of Technology, Sweden)
• Luke Alphey (Pirbright, United Kingdom)
• Perdita Barran (University of Manchester, United Kingdom

[Closes 14 July 2017] Postdoctoral Researcher - Single Cell Genomics

Job Vacancy: Postdoctoral Researcher to lead the development of next-gen sequencing tech to analyse single cells

The Macaulay Group at the Earlham Institute (formerly TGAC) is looking for an enthusiastic Postdoctoral Researcher to lead the development and implementation of next generation sequencing technologies to analyse single cells. This is an exciting opportunity to work on a BBSRC-funded project to explore transcriptional and epigenetic heterogeneity in individual haematopoietic stem and progenitor cells.

More details and application here

My OpenPlant Experience: Outreach, Engagement and 3D printing

Guest blog post by Roger Castells-Graells about his OpenPlant Fund project “Accessible 3D Models of Molecules”. Roger recently won a UEA Engagement Award in recognition of the work he has done both with OpenPlant and beyond.

PhD student Roger Castells-Graells in the lab

My name is Roger and I am a PhD student in Prof. George Lomonossoff’s lab at the John Innes Centre in Norwich. My research project is about the production of virus-like particles to understand viral dynamics for future applications and to generate new bionanotechnological tools. I have a passion for science communication and public engagement and I have had numerous opportunities to communicate my science in Norwich, the UK and abroad since the start of my PhD.

My OpenPlant experience started in September 2016, when I attended a great Co-Lab workshop organized by the Open Science School and funded by an OpenPlant Fund. With this opportunity I had the chance to interact with scientists from different fields and also with designers and artists. It was an enriching experience and we developed a project called VRICKS (Virus Bricks) that aimed to generate tools to explain viruses in educational ways, like for example with paper models.

Following up from this workshop, in October 2016, I organized an activity for the Norwich Science Festival, together with Jenni Rant (The SAW Trust) and Colette Matthewman (OpenPlant), where we recreated the assembly of proteins into a virus protein coat using materials like paper and plastic, which represented the subunits of the virus. The public contributed to the assembly of a virus model, they learnt about related research from the Lomonossoff lab and they took home a build-at-home model. Over one hundred people participated in the activity during the weekend, making it a roaring success.

Presenting the virus activity and engaging with people at the Norwich Science Festival

Following up with the interest to build tools to explain biological processes, such as virus assembly, I decided to apply for and OpenPlant Fund with the project “Accessible 3D Models of Molecules”. The project team is a multidisciplinary team (molecular biology, bioinformatics and engineering) of students from JIC and University of Cambridge and with this fund we are developing models of viruses and proteins using 3D printing technologies.

3D printed virus models for the OpenPlant Fund project

Recently I presented some of the virus models in a high school with students aged 12 to 16 years old. The students enjoyed being able to handle and compare representations of real virus structures and were amazed that some of these structures were only discovered this year. When the school teacher was asked about how the use of educational 3D models in the classroom could benefit the learning process he answered that first of all it creates excitement and focuses the attention of the students. It is something completely new! It contributes to the understanding of three-dimensional models and gives the students a better sense of the reality of the object. Furthermore, it allows the students to calculate scale as it is possible to touch, measure and compare different models.

I was invited to speak at the Pint of Science Festival in Norwich in May, and gave a talk entitled “20000 Leagues under the microscope: Viruses & Nanomachines”. At the event, I passed around several models of 3D printed viruses and the public loved having the opportunity to handle them. It was a great experience and we received really positive feedback. I want to thank the organizers of Pint of Science for such a great event!

As a result of all of these activities, I was recently awarded a UEA Engagement Award 2016/17 for contribution to Public & Community Engagement, which I am very proud of.

Norwich Pint of Science Festival tweets

With thanks to my supervisor Prof. George Lomonossoff, OpenPlant and all the people that have helped, encouraged me and opened up opportunities in this last year.

[Closes 30 June 2017] Apply now for the OpenPlant Fund

The OpenPlant Fund is now open to proposals for innovative, open and interdisciplinary projects relevant to plant or in vitro Synthetic Biology. Projects run for six months and can include biological research, hardware prototyping, software, outreach and policy work.

Each project will receive up to £5k, with up to £4k up front and an additional £1k for follow-on and outreach after reporting. PhD students and postdocs are particularly encouraged to apply and external collaborators are welcome. 

The aim of the fund is to promote the development of plant Synthetic Biology as an interdisciplinary field and to facilitate exchange between the University of Cambridge, the John Innes Centre, and the Earlham Institute for the development of open technologies and responsible innovation in the context of Synthetic Biology.

More information can be found here: https://www.openplant.org/openplant-fund/

Cell-free technology startup founded by former OpenPlant Fellow awarded funding by RebelBio.

Cell-Free Tech is a brand new start up company specialising in giving people the ability to do biological research, without the need for expensive tools and infrastructure. Based at the Microbiology Department of the University College Cork, Cell-free Tech is part of RebelBio, an accelerator programme that helps life sciences innovators, academics, biomakers and citizen scientists to change the world with biology.

Former OpenPlant Fellow Thomas Meany has helped found an exciting new startup company based on making cell-free technology more accessible. Meany founded the startup this year in collaboration with Ian McDermott (Chief Scientific Officer Cell-Free Tech), and together they have been awarded funding from the accelerator programme RebelBio and SOSV (a venture capital and investment management firm)to take cell-free technology out of the lab and into the world.

Originally a physicist by trade, Meany undertook a OpenPlant/Wellcome Trust ISSF Interdisciplinary Fellowship, co-supervised in the Haseloff and Hall groups (Department of Plant Sciences and Department of Chemical Engineering and Biotechnology respectively), where he applied his computing and engineering skills to the field of synthetic biology. It was through his involvement in the SynBio SRI activities around cell-free systems, such as our recent workshop ‘Programmable biology in the test tube’, that he realised the potential of cell free systems to provide exciting and simple tools with which to do biological research.

In vitro or cell-free synthetic biology uses cell extracts rather than whole cells, programming them with DNA to produce chemicals or encode logic circuits that respond to their environment. The technology can be used to create vital biomolecules like insulin, or to generate stunning coloured, glow in the dark proteins. Since it doesn’t involve genetic engineering or extensive resources, cell-free technology can be used without the need for expensive facilities or infrastructure. Meany became increasingly fascinated by the concept: “I just loved the idea of doing biology anywhere, being able to make and create things with biology on a tabletop is fascinating.”

It was around this time Meany collaborated with SRI Steering Committee Member Helene Steiner (Royal College of Art and Microsoft Research Cambridge) on a series of cell-free workshops for the Royal College of Art (RCA) Biodesign Challenge,  aimed at making synthetic biology tools accessible to art and design students. It was through these events it became clear there was a great deal of interest in cell-free systems among the public. However, a recurring problem was that there was little scope for people to get involved, due to the lack of availability of affordable tools. Meany realised the potential for providing cheap, effective materials and after meeting Ian McDermott, a biochemist with experience in founding a business startup, they realised they think the same way. “Biology today is like computing in the late 1980s, simply awaiting an explosion of innovation. Technologies are developing faster than ever but some key platform technologies are still missing. People need to be able to access biology at an affordable price, in their own homes or workplaces and without enormous infrastructure” - explained Meany.

After communicating their vision to Bill Liao (Founder of RebelBio and SOSV investment partner) during a RebelBio conference, it was clear that their passion for cell-free technology was shared. Meany and McDermott left their University roles and with investment from RebelBio and SOSV, the team have set about producing the first publicly available low cost bio-prototyping kit at large scale, while directly reaching consumers through active market research. The kits will include a collection of 50 tubes containing individual cell-free extract alongside a set of plasmids that can be added to the extracts to produce colours, fluorescence and odours. Meany hopes universities, students, designers and makers or hobbyists from all backgrounds will be interested. “We are building the platform technology that will allow innovators from all backgrounds to engineer the materials of the future. Our hope is that the community will build on our initial projects to create and share amazing ideas of their own. We want to see biosensors, paper diagnostics and open-source insulin produced using our kits!” - Meany.

If you would like to contact Cell-free Tech to find out more or to get involved, please get in touch. They are eager to work with members of the Cambridge synthetic biology community. For more information on Cell-Free Tech, please click here.

If you are interested in learning more about cell-free technology, the SynBio SRI is currently running a series of events in this area, such as the OpenPlant Forum, OpenPlant Fund, and training workshops. For more information about these initiatives and upcoming events, please click here.

How an open approach to patents could help build a sustainable future

This article by Dr Frank Tietze, Lecturer in Technology and Innovation Management at the University of Cambridge was originally published at The Conversation on 15 May 2017, licensed under CC-BY-ND 4.0. See the original article here and in The Independent.

Dr Tietze is a co-convenor with the SynBio SRI and OpenPlant of an upcoming CRASSH Faculty Research Group on Open IP in emerging technologies.

Nadezda Murmakova/Shutterstock

To sustain a population of 9.7 billion people by 2050 the world is going to need innovations that make careful use of the available resources, human and environmental. Key industry sectors such as energy, water, agriculture and transport are already under pressure to move to more sustainable methods of production and consumption. However, there are barriers in the way.

One of these lies in how the world manages the creation and ownership of inventions and ideas. A protectionist approach to intellectual property is designed to protect and prolong the lifecycle of existing technologies, and allow innovators to capture the profits from their creations. In a paper published with colleagues from universities in Germany and India, we examined how this also makes it harder for new and more sustainable technologies to be developed and adopted. That explains why there are now other approaches being used to move key sectors to more sustainable systems and end this status quo.

Electric car manufacturer Tesla, has been doing just that. Tesla CEO Elon Musk “shocked” the world in 2014 when he announced that his company was joining the open source movement and giving away its patents for free.

It is important to understand the rationale here. Why would a company that had worked so hard to develop and protect its technology from its global car manufacturer competitors suddenly give its technology away for free?

Switching track

Tesla initially developed a patent portfolio to protect its technology. However, Tesla’s concern that it would be overwhelmed once established car makers ramped up their production of electric cars never came to pass.

Instead, it saw the electric car market stagnate at less than 1% of total vehicle sales. So Tesla changed its strategy from trying to prevent others from building electric cars to trying to encourage them into the market.

Part of the reasoning here is that if more electric cars are built, then more battery recharging stations will be built too. This would make electric cars become more visible, and a more conventional choice. Tesla believes that an open intellectual property strategy can strengthen rather than diminish its position by building the size of the electric car market, and as a result, build its own share of the total automotive market.

This kind of careful management of intellectual property at company level, supported by policy-level awareness, can be a powerful way to support the same kinds of transitions to more sustainable technologies in other industries too.

Power companies need to adapt. Chiu Ho-yang/Flickr, CC BY-NC-SA

Energy supply faces an array of difficulties: the depletion of natural resources; air pollution and greenhouse gas emissions; nuclear risks; and security of supply. The water supply sector is restricted by water scarcity, pollutants, extreme environmental events such as flooding and costs associated with supplying water to communities in poor countries and remote communities. The agri-food sector, meanwhile, is under pressure to sustainably produce more food and to address malnutrition in poor countries.

For these industries to navigate a path around these problems, new knowledge and the innovations that follow will be essential. And in knowledge economies, intellectual property can either be an enabler or an inhibitor.

Taking the medicine

If the ownership of intellectual property is fragmented in an industry, it can slow down technology innovation and uptake, such as in the electronics industry where multiple players own complementary patents. However, firms can instead open up their innovation processes and move away from jealously guarded, internal cultures, where intellectual property is used to protect and prolong lifecycles. This change may see knowledge sharing that leads to accelerated innovation cycles and a more rapid uptake of sustainable alternatives throughout a sector: just what Tesla was hoping for in electric vehicles.

This approach to intellectual property, so-called “open IP”, is well advanced and mature in the software industry and healthcare. It has given access to life-saving medicines to millions of people, particularly in developing countries through patent pools, such as the Medicine Patent Pool. This kind of project relies on multinational pharmaceutical companies sharing their intellectual property, but small companies can also play a strategic roles in creating these new, more sustainable systems, and it’s not all about open IP.

Plumpy'Nut is handed out in Kenya. DFID /Flickr, CC BY

As progress in technology is cumulative, there will always be phases of “closed IP” for small companies to build up their portfolio. This can also be a strategy designed to make a social impact. Take Nutriset, which manufacturers food for famine relief. It protects both its invention, Plumpy’Nut, and its entire business model by patents. Plumpy’Nut is a peanut-based paste for the treatment of severe malnutrition and can be administered at home rather than through a supervised hospital treatment. As a result it can treat more patients.

Nutriset says that it uses patents to enable the development of local production plants for Plumpy’Nut and to protect those in emerging nations from being taken over by global manufacturing sites in more developed countries. The local production of Plumpy’Nut helps with creating skills and employment in the regions where Nutriset’s product is most needed.

An open approach to intellectual property has clear advantages in popularising and establishing new and widespread sustainable technologies, but there is a rationale in some cases for sticking to the more traditional approach. The trick now is to discover when and where different sectors and innovators deploy each strategy. The grand open IP gestures in the mould of Tesla can force through rapid structural advances; a small peanut paste supplier shows that patent protection can still help put the building blocks in place.

Frank Tietze, Lecturer in Technology and Innovation Management, University of Cambridge

This article was originally published on The Conversation. Read the original article.

[Closes 6 Jul 2017] DST-NRF Fellowships for UK Early Career Researchers - Synthetic Biology Opportunities in South Africa

This Newton Fund opportunity allows early career UK researchers to spend 3-6 months working with a South African research group.

The SynBio SRI has a network of researchers in South Africa with whom we can connect interested researchers and an invitation from Dr Karl Rumbold at the University of the Witwatersrand, Johannesburg for Fellows who might like to join lab and/or field-based projects including synthetic biology and biocatalysis.

Find out more about the call here >>

[Closes 21 June 2017] OpenPlant PDRA researching regulatory elements of cyanobacteria

Applications are invited for a Postdoctoral Research Associate position in Prof Christopher Howe's lab as part of the Cambridge OpenPlant Synthetic Biology Centre. OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre, the Sainsbury Laboratory and the Earlham Institute, funded by BBSRC and EPSRC.

This position is aimed at identifying regulatory elements of cyanobacterial genes enabling control of gene expression in response to environmental electrical potential. Prof Howe's group has pioneered the development of 'biophotovoltaic' systems (McCormick et al. (2015) Energy & Environmental Science 8:1092) for the generation of electrical power from photosynthetic microorganisms. This post will analyse the transcriptional responses of cyanobacteria in biophotovoltaic devices.

Experience in the molecular biology of cyanobacteria, and in recombinant DNA techniques applied to microorganisms is essential. A PhD in a relevant subject is essential. Experience of electrochemistry is desirable, but not essential.

The appointee needs to be able to take up the post by 1 Sept 2017.

Fixed-term: The funds for this post are available for 24 months in the first instance.

For more information and to apply see the jobs.cam.ac.uk listing >>

OpenPlant Scientists take part in Norwich Pint of Science Festival

In May 2017, the Pint of Science festival returned to Norwich. The festival, which is held over a few days, was a huge success, with many events being sold out days in advance. Each event offers the audience the chance to meet scientists at their local pub and discuss their latest research in an informal and welcoming atmosphere, whilst sipping on their favourite pint.

Two sell out events where those of OpenPlant Project Leader Professor George Lomonossoff and his PhD student Roger Castells-Graells, and a second event with OpenPlant’s Norwich-based Director, Professor Anne Osbourn.

George’s talk was entitled ‘Just Eat Your Greens – A New Way of Vaccinating?’ and took place at the York Tavern. It covered the use of a highly efficient transient expression system developed in his laboratory. This Hypertrans® system allows for the relatively quick and cheap production of large quantities of virus-like particles in plants, which have been proven to be effective as experimental vaccines.

Roger presented ‘20,000 Leagues Under the Microscope: Viruses & Nanomachines’ taking the audience on a journey into the nano world of viruses. During the entertaining talks, the audience took part in various activities such as making a virus molecule out of pipe cleaners and creating virus inspired sketches on beer mats.

The following evening, Anne took to the stage at the St Andrews Brewhouse to present her ‘Finding Drugs in The Garden’ talk. Anne’s inspiring talk invited people into the plant kingdom to hear about its very own chemistry toolkit. She presented her teams current work harnessing the DNA that encodes the pathways to these chemicals and using them to produce designer molecules for medicinal, agricultural and industrial applications.

For the scientists taking part in the festival, it has proven to be a great platform on which to reach the public to talk about their research and build an understanding of their work within the local city of Norwich. After such well received talks and events, we very much look forward to the return of the Pint of Science Festival in 2018.

[23 June 2017] Apply now for Biomaker Challenge!

Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. From colorimeters to microfluidics and beyond, we’re looking for frugal, open source and DIY approaches to biological experiments.

The challenge is open to students and staff at the University of Cambridge, John Innes Centre and the Earlham Institute. Participants will receive a Biomaker Toolkit and a discretionary budget for additional sensors, components, consumables and 3D-printing worth up to £1000.

For more information, to join a mixer event and to apply by 23 June 2017, see www.synbio.cam.ac.uk/biomakerchallenge

Co-organised by: OpenPlant, Synthetic Biology SRI, CamBridgeSens.

Postdoctoral Research Fellow positions available at CSIRO

The Commonwealth Scientific and Industrial Research Organisation (CSIRO) is advertising several postdoctoral research fellow positions for recent PhD graduates, including in areas relevant to synthetic biology.

The Commonwealth Scientific and Industrial Research Organisation (CSIRO) is the federal government agency for scientific research in Australia. Its chief role is to improve the economic and social performance of industry, for the benefit of the community. CSIRO works with leading organisations around the world, and CSIRO Publishing issues journals with the latest research by leading scientists on a broad range of subjects.

The postdoctoral research fellow positions advertised are to undertake independent research under the mentoring of more senior scientists within the framework of a personal development program. Positions are available across the entire spectrum of CSIRO research activity and are aimed at recent PhD graduates with little or no postgraduate experience.

The positions listed have several deadlines. In addition, more positions are likely to be advertised on their site in future.

For more information on the positions available, please click here.

SMART-map Industrial Dialogue on Synthetic Biology

In March 2017, Dr Colette Matthewman joined participants from industry, civil society, funding bodies and academia for an Industrial Dialogue on Synthetic Biology as part of the EU-funded SMART.map project (http://projectsmartmap.eu). The workshop was held at the Manchester Institute of Biotechnology.

The SMART.map project is developing RoadMAPs to Societal Mobilisation for the Advancement of Responsible Industrial Technologies. Its goal is to define and implement concrete roadmaps for the responsible development of technologies and services in three key time-changing fields: precision medicine, 3D printing in biomedicine and synthetic biology.

The Manchester dialogue provided a framework for discussions on the challenges facing synthetic biology companies, especially in the area of responsible research and innovation (RRI) and the development of concepts for tools that could help industry to engage with and integrate RRI into their synthetic biology working practice more easily. Read more in this blog and the video below.

OpenPlant Fund contributes to publication of methods for single molecule RNA FISH in Arabidopsis root cells

Researchers from the John Innes Centre have published a method for accurate quantification and localization of mRNA in fixed plant samples by detection of individual mRNA molecules. This work was in part supported through the OpenPlant Fund.

Duncan, S., Olsson, T.S.G., Hartley, M., Dean, C., Rosa S., 2017. Single Molecule RNA FISH in Arabidopsis Root Cells. Bio-protocol 7(8): e2240.

Abstract

Methods that allow the study of gene expression regulation are continually advancing. Here, we present an in situ hybridization protocol capable of detecting individual mRNA molecules in plant root cells, thus permitting the accurate quantification and localization of mRNA within fixed samples (Duncan et al., 2016; Rosa et al., 2016). This single molecule RNA fluorescence in situ hybridization (smFISH) uses multiple single-labelled oligonucleotide probes to bind target RNAs and generate diffraction-limited signals that can be detected using a wide-field fluorescence microscope. We adapted a recent version of this method that uses 48 fluorescently labeled DNA oligonucleotides (20 mers) to hybridize to different portions of each transcript (Raj et al., 2008). This approach is simple to implement and has the advantage that it can be readily applied to any genetic background.

The cutting edge of Synthetic Botany reviewed by OpenPlant researchers

Cambridge researchers including OpenPlant Director Prof Jim Haseloff  and OpenPlant PI Dr Nicola Patron (Earlham Institute) have reviewed the state of art and future prospects for Synthetic Botany - the application of synthetic biology to engineering nuclear and chloroplast genomes in plants.

Plants represent the only available platform allowing sustainable bioproduction at the gigatonne scale. Combining modular body plans and developmental plasticity with capacity for photosynthesis and extensive secondary metabolism, plants are highly attractive targets for genetic engineering. However, efforts in this area have been complicated by slow growth rates, physiological complexity, and technical challenges in the handling and manipulation of plants. Furthermore, better experimental and theoretical frameworks are needed to dissect and understand the hierarchies of genetic and physical interactions shaping their multicellular behavior.  

Joint first-authors Christian Boehm and Bernardo Pollak and colleagues reviewed the state of the art in genetic engineering of the nuclear and chloroplast genomes in plants, and highlight new approaches to harnessing their potential as custom agronomic systems for large-scale production. In particular, they show how simple plant models like the liverwort Marchantia polymorpha - combined with standard DNA parts and advanced quantitative imaging technqiues - can bridge the complexity gap between microbes and higher plants. Synthetic genetic circuits proven in Marchantia may serve as valuable tools for addressing some of the major challenges in plant metabolic engineering such as the introduction of C4 photosynthesis in C3 crops or the refactoring of nitrogen fixation pathways.

Boehm CR, Pollak B, Purswani N, Patron N & Haseloff J. (2017) Synthetic Biology. CSH Perspect Biol a023887o

[Closes 23 Apr 2017] Research & Outreach Manager at Warwick Integrative Synthetic Biology Centre

The Warwick Integrative Synthetic Biology Centre (WISB) is looking for a Research & Outreach Manager. This post will suit a candidate with a background in research who wishes to develop a career in research programme management, learning and/or applying skills in financial oversight, grant proposal writing, research communication and outreach activities. The closing date for applications is 23rd April 2017.

Details can be found on http://www.jobs.ac.uk/job/AYP101/research-and-outreach-manager-75443-047/

[Closes 17 Apr 2017] Applications Scientist - Edinburgh Genome Foundry

[Closes 17-Apr-2017] Applications Scientist - Edinburgh Genome Foundry

We need a talented Application Scientist for the Edinburgh Genome Foundry (EGF), a facility for automated and high-throughput DNA assembly technologies based in the School of Biological Sciences, University of Edinburgh.

Are you looking for a unique role working in one of today’s most exciting and rapidly developing areas of science? Are you keen to get involved with the rise of automation in the lab? Then this is the role for you.

As Application Scientist you will be the responsible biologist for translating and delivering customer orders for large-scale DNA assembly using our robotic platform.

Candidates must have a graduate degree in biology plus substantial experience in relevant work. Knowledge of synthetic biology and experience with automated equipment is essential. This is an exciting opportunity to play a fundamental role in the success of an exciting and technologically advanced UK facility.

Please note that the deadline for applications is being extended to late April.

Search for Job reference number: 039193 at https://www.vacancies.ed.ac.uk

For further information contact Dr Hille Tekotte h.tekotte@ed.ac.uk

Cambridge Science Festival Stand 2.0 – Improved Design!

A family discover how proteins are made following instructions in the DNA, with the help of Nadia Radzman and DNA Dave the robot.

In 2016 we designed a new stand for the Cambridge Science Festival and were delighted with the excellent feedback and the award won by the plant and life sciences marquee where our stand and team scored exceptionally highly with a 94.3% public approval rating! We decided to build on the game we had developed, using cardboard boxes, which explains the process of transcription and translation into something bigger and better (and more professional!). We applied for an Outreach Grant from the Biochemical Society to enable us to work with a designer to realise our ultimate game and were delighted to be successful! In December 2016 a group of enthusiastic scientists met with designer Molly Barrett to begin work. Scientists Ioannis Tamvakis and Nadia Radzman provided excellent ideas for representing the scientific process, and coding an arduino to build in the electronic outputs we wanted and then the build began and at the beginning of March we were introduced to DNA Dave, the robot! 

We were very excited to give Dave his debut at the 2017 Cambridge Science Festival and we were not disappointed! The public were really keen to see what the robot could do and the process of transcription and translation of DNA to proteins was very well explained by operating Dave’s buttons, cogs and switches. We will be taking Dave to future events and he is also available for hire! You can follow his travels on Twitter using #DNAdave.

The team celebrate the end of an excellent day.