Biomaker Challenge - building collaborations through low-cost instrumentation

Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. The programme aims to facilitate exchange between the biological and physical sciences, engineering, and humanities for the development of open source biological instrumentation using commodity electronics and DIY approaches.

The inaugural 2017 cohort comprises 130 participants working in 41 teams on biological and biomedical devices, instruments, and sensors.  Participating teams received a Biomaker Toolkit and a discretionary budget for additional sensors, components, consumables, and mechanical fabrication worth up to £1000.

Teams of all sizes were considered for the grant and range from an individual to twelve people. Interdisciplinarity within participating teams is prioritised and although most participants are students or staff at the University of Cambridge, John Innes Centre or the Earlham Institute, external team members are welcome and included designers from the Royal College of Art, computer scientists from ARM, local artists, makers, and entrepreneurs.

During the challenge, we offer assistance and support providing components and access to prototyping facilities in Cambridge such as Cambridge Makespace and the Media Studio on the Cambridge Biomedical Campus. We also run periodic technical workshops and meetups to encourage teams to interact and help share skills and ideas. Participating teams will document a full set of assembly/fabrication instructions, images, and a list of components used, which are made publicly accessible via GitHub. This will enable others to replicate and build on their work for their own research questions. The challenge culminates on 21 October 2017 in a public exhibit, the Biomaker Fayre, where participants will demonstrate their creations and prizes will be awarded for especially creative and enabling projects.

The Challenge will repeat in 2018 and we look forward to seeing the projects develop with a new cohort of participants to further increase access to low-cost, open access biological tools and technologies.

Example Projects

Real-Time monitoring of cell proliferation

An absorbance sensor that can be used inside a cell culture incubator for real-time monitoring of culture medium pH and cell density. The system is able to automatically transmit this data to an email server for remote monitoring of cultured cells.

Microfluidic Turntable for molecular diagnostic testing

An Arduino controlled turntable with a stroboscope for disk visualisation on screen and optical detection for absorbance and fluorescence measurements. The disc, fabricated using a laser cutter and paper plotter, is rotated by an Arduino controlled motor. Fluid actuation is also controlled by Arduino, changing the rotation direction and revolutions per second to achieve pumping, mixing and separation.

A programmable staging mount, and an imaging platform for a microfluidics based conditioned learning hub for motile bacterial cells.

By developing a maze traversal challenge, different scenarios for chemotactic bacterial colonies to employ their decision-making machinery and navigate through the maze will be assessed. This may lead to an understanding of cognition, memory and learning in bacterial colonies.

John Innes Centre researchers develop plant-made synthetic polio vaccine

Researchers at the John Innes Centre, including OpenPlant PI Prof George Lomonossoff, and collaborators, have published research to produce a new polio vaccine in plants, using the HyperTrans transient expression system. The work, funded by the World Health Organisation, was published in Nature Communications. It is hoped that this new polio vaccine will be a move towards global eradication of the disease. The publication was covered by JIC News and the BBC.

Marsian, J., Fox, H., Bahar, M.W., Kotecha, A., Fry, E.E., Stuart, D.I., Macadam, A.J., Rowlands, D.J., & Lomonossoff, G.P. (2017) Plant-made polio type 3 stabilized VLPs—a candidate synthetic polio vaccine. Nature Communications 8, Article number: 245.

Abstract

Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.

BoomTown Fair, August 2017

Blog post written by Emma McKechnie-Welsch, and reproduced with permission from The SAW Trust. Original blog post can be found here: http://sawtrust.org/news/boomtown-festival-august-2017

Science tent at Kidztown

BoomTown Fair is an annual music and arts festival held in Winchester. It attracts up to 60,000 people a year. The festival hosts a wide range of performances across its many stages, providing visually impressive themed areas on-site.

This is also the case with Kidztown, the diverse and interactive family area. OpenPlant and the SAW Trust were key contributors to the Kidztown science tent. Children here were introduced to different natural plant-based products in a fun and engaging way. This included a carefully devised potion-making, craft and spell-writing stand.

The stand, titled "Marvellous Medicines," revolved around our periodic table of natural products. The children were tasked with making a magical potion, picking just one component from each block of the periodic table for their ingredients. The blue block contributed a plant material that would provide the colour pigmentation for the potion, including the magical element of colour change in different pH solutions. The red block contained plants with appealing scents, extracted as essential oils, to give the potion a delightful smell. Finally, the yellow block contained citrus fruit. The citric acid in this can be used to observe the colour change.

Periodic table of plants

Making the Potions

Once the children had selected their ingredients, they ground up the blue item (either red cabbage, berries, turmeric or selected flowers) using a pestle and mortar. They then practised using pipettes, adding 75 percent ethanol to extract the pigment. This was transferred to their potion flask. They next added the essential oil corresponding to their red item and 1 millilitre of bicarbonate of soda solution to observe the first colour change. Last of all, 35 millilitres of citric acid solution was added to create the final colour of their potion. It was explained that citric acid was the compound in citrus fruit that made it taste so sharp.

Whilst a slight fizz was observed upon adding the citric acid, due to it reacting with the bicarbonate of soda, only a very small amount of the bicarb was present. The final step involved adding a green slime of more bicarb mixed with washing up liquid, which caused the potions to fizz over and release the essential oil smell. If the kids wanted an extra colourful potion they also added food colouring gel.

Magical ingredients

Colourful results

Making potions

Marvellous Medicine's Art and Writing

Artist Molly Barrett helped the children create their own artistic potion bottle, cutting out bottle shapes from cardboard and sticking dried plant products to them. Our writer Ali Pritchard asked the children to think about what they wanted their potion to do, and they wrote a spell to cast over their potion for it to work. This was written on acetate and stuck to their art creation. 

Marvellous Medicines team members

Throughout, the children learned about a plant’s ability to make different compounds that define their features such as colour, scent and taste. They extracted the colour pigment themselves and used other natural extracts to complete their potions, observing how we can use things that plants make for our own products. The older children also learned about pH and colour indicators, a classic chemistry practical they will no doubt carry out in secondary school. A further use for plants was discovered in the art stand: the plant materials could be used as 3D elements to decorate the potion bottles.

The finished potions

The children let their creativity run wild by imagining what their natural product potion could achieve. Whilst compounds produced by plants may not be able to turn glitter into gold or the sea into Ribena, hopefully the children took away the idea that many of the compounds produced within plants can be used in ways they previously hadn't thought about. Not least, the children had lots of fun exploring ideas around magical plant extracts and many of the children returned to the stand later on.

Marvellous Medicines couldn’t have been a success without the hard-working team, who over three days helped the children through all the tasks. A big thank you goes to the team and to BoomTown for having us!

The Marvellous Medicines Team

UK SynBio Start-Up Survey published showing thriving East of England ecosystem

SynbiCITE have published the first survey of the UK synthetic biology start-up ecosystem, highlighting the changing sources of innovation and entrepreneurship at work in the sector from a macro-level perspective.

The report covers activity between 2000 and 2016 in research and development, technology transfer, industrial sectors, financing and investors. Its key finding were:

• The UK produced more than 146 synthetic biology start-ups between 2000 and 2016.
• More than half (54%) of new start-ups are tech transfer start- ups,
• Synthetic biology start-up activity is concentrated in the South-East, East of England and London (67%). With Oxford, Cambridge and London Universities producing a cluster of activity nucleating in and around London. 
• Synthetic biology start-up companies have raised over £620m of public (£56m) and private (£564m) investment in the UK since 2010. 

Dr. Stephen Chambers, CEO of SynbiCITE, commented that “Confirming the arrival of a new innovation ecosystem demands evidence: proof that variables ranging from investment, pipeline infrastructure, to talent and education are established and stable. We believe the industry has reached a critical mass of companies, showing a healthy churn of attrition and creation. Roughly 76% of all the start-ups founded in the survey period are still active and with the continuation of an effective national strategy in the future, this ecosystem will undoubtedly thrive, creating jobs and wealth while sustaining the UK’s leading role in the field.”

East of England emerged as the region with the highest number of synthetic biology start-ups after London, with spin-offs concentrated around the OpenPlant partner locations of Cambridge and Norwich. 

Read More >>

Download Report [PDF, 4MB]

Plant Science SAW projects at Tunstead primary School

Guest blog from Emma McKechnie-Welsch, a PhD student from the John Innes Centre who spent three months doing an internship in Science Engagement with OpenPlant and the SAW Trust.

Plant Science SAW projects at Tunstead primary School

Arabidopsis apical meristem. Image by Emma McKechnie-Welsch

My name is Emma and I am a PhD student working in the Cell and Developmental Biology department at the John Innes Centre. My research looks at genes functioning to facilitate controlled plant growth and development from the shoot apical meristem in Professor Robert Sablowski’s research group. My PhD funding from the BBSRC includes a three month work placement and I was keen to gain experience in science communication and outreach so arranged a joint placement with OpenPlant and the SAW trust.

On my placement I had the opportunity to design two SAW projects to discuss science relevant to my research with primary school children at Tunstead primary school. For the year 1/2 class I worked with writer Julia Webb and artist Lara Nicole and the aim was to get children thinking about the functions of different parts of a plant. For the year 5/6 class I was worked with writer Mike O’Driscoll and artist Chris Hann with a day themed around plant evolution.

We used scientific images at the start of the day to catalyse inquisitiveness about the science we were going to explore, and provide inspiration for the poetry and art sessions.

Root cross-section of Penstemon venustus

Image credit: G. von Arx (Own work), shared via Wikimedia Commons under CC BY-SA 3.0 licence. Root cross-section (30 microns) of Penstemon venustus. Lignified tissue is stained red

Floating dandelion seeds

Image credit: PiccoloNamek, shared via Wikimedia Commons under CC BY-SA 4.0 licence, https://commons.wikimedia.org/w/index.php?curid=528340.

Bee Orchid flower

Image credit: Donald Macauley from Carshalton, Surrey, UK - Bee Orchid Uploaded by Amada44, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=24915600.

Pollen from wild mahonia flowers imaged by scanning electron microscope

Image credit: Kim Findlay, John Innes Centre. Shared via NRP image library, under CC BY 4.0 licence.

Bee covered in pollen

Image from http://www.newtonsapple.org.uk/plant-pollinators/

Petty spurge pollen grain

Image credit: Kim Findlay, John Innes Centre. Shared via NRP image library, under CC BY 4.0 licence.

Close up of Fish hook cactus spikes

Image credit: SKsiddhartthan, shared via Wikimedia Commons under CC BY-SA 4.0 licence.

Fruit capitula with hooked spines and flexible hairs to attach to animal fur

Image credit: Stefan.lefnaer, shared via Wikimedia Commons under CC BY-SA 4.0 licence, https://commons.wikimedia.org/w/index.php?curid=56785572.

 

Practical Science with Year 1/2

Build a plant game, played with year 1/2 class

To start off the lesson we played a “build a plant” game to get more familiar with the main parts of a plant, their function, and what plants use from their environment to grow. Each child also put a cut flower in coloured water to think about the use of the stem. Then the children were given a selection of fruit and vegetables and asked to decide what part of the plant each came from. They were given a flower to look more closely at the reproductive parts and think about how seeds are formed by pollination. Finally, they looked at different types of seeds in a seed kit and we discussed the different types of seed dispersal tactics plants use.

 

Practical Science with Year 5/6

The children dissected plants to look up close at the reproductive parts under the microscope.

We began by guessing the number of different plant species on earth and the children suggested why plants are useful. In groups, they were given cards representing each component of photosynthesis and had to arrange them to think about the process. We covered pollination and its importance for increasing genetic variation.

The children dissected plants to look up close at the reproductive parts under the microscope. I covered different types of seed dispersal and the importance of varying environmental conditions for evolution. Then children carried out DNA extraction from strawberries after learning a bit about what DNA was and how important it was in controlling the appearance of the plant, with a single mutation in a gene coding region potentially greatly changing this. Following on from DNA extraction there was a game to match the numbers of genes to different organisms.

 

After the morning science sessions the children had poetry and art sessions based on the content. Here are some poems and images from the Year 5/6 group (age 10/11):

 

The Year 1/2 children (age 4/5) wrote poems as if they were a seed growing up, and made flower hand puppets after designing a flower:

The children really engaged with the scientific learning aspect of the day which was great. Lots of the children thought about the questions I asked to the classes and gave insightful answers, as well as wanting to ask questions throughout the lesson/ activities. When asked about their favourite part of the day, at least half the children listed specific sections of the science morning.

The poems produced by the year 5/6 children really showcased the children’s interest in understanding genetics and how growth and development of organisms are controlled. The younger children were enthusiastic about looking at different types of seeds, bringing back different types they had found in their school grounds at break time to show me. It was great for them to think about the different stages of growth a plant goes through from seed to eventually producing a flower, including difficulties different environmental conditions could cause, while writing their poems.

The children were really excited about getting to do an afternoon of art although the activities designed weren’t quite as expected. The art didn’t centre around drawing on paper but producing 3D art pieces. The younger children gave lots of personality to their individual hand puppets and used them to help communicate their poetry whilst the older children focused on the scientific pictures provided and gave interpretations of pollen and seed dispersal, as well as the protective mechanism of the cactus.

From this experience, I could see how integration of science with writing and art can help children associate science more closely with creative thought, rather than a regimented, inflexible learning process, which makes the subject inaccessible to some children. The teachers were impressed with the pieces the children managed to produce and the level of thought about scientific processes they reached, which I think was largely down to the different approach to education SAW days take.

OpenPlant and the OpenMTA feature in 'Learning by Sharing' at SB 7.0

Prof Jim Haseloff, Dr Nicola Patron and BioBricks Foundation Legal Director Dr Linda Kahl who pioneers the OpenMTA initiative with which OpenPlant is collaborating, all presented in the 'Learning by Sharing' session at SB 7.0 in Singapore, 13-16 June 2017.

The videos of all talks are now online at the BioBricks Vimeo site.

Prof Jim Haseloff (Director, OpenPlant at University of Cambridge)

Dr Nicola Patron (Earlham Institute)

Dr Linda Kahl (BioBricks Foundation)

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

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.

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.

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

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.

Report on Synthetic biology start-ups in the UK and worldwide

On 2nd December 2016, Cambridge Consultants published a report prepared for the UK Synthetic Biology Leadership Council, on Synthetic biology start-ups in the UK and worldwide.

The report highlights that the UK has a vibrant SynBio start-up community, leading in Europe and second only to the US and that SynBio tools are the larfgest sector, including strain engineering, hardware and DNA synthesis.

The full report can be found here: https://www.cambridgeconsultants.com/sites/default/files/documents/resources/synbio_start-ups_in_the_uk_and_worldwide.pdf

[Closes 21 April 2017] OpenPlant Research Associate in Prof. Alison Smith's lab, Cambridge University

Applications are invited for a Postdoctoral Research Associate position in Prof. Alison Smith's lab as part of the Cambridge OpenPlant Synthetic Biology Centre. OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre, TSL and the Earlham Institute, funded by BBSRC and EPSRC, which promotes interdisciplinary exchange, open technologies and responsible innovation for sustainable agriculture and conservation.

This position is aimed at generating novel regulatory elements based on riboswitches for plant and algal biotechnology. Riboswitches are sequences within the mRNA that respond to metabolites or other small molecules to alter production of the encoded protein, and offer flexible and tuneable elements to control transgene expression.

You will join the multidisciplinary team in central Cambridge at the Department of Plant Sciences, where the group focuses on a range of algal molecular biology and biotechnology projects. The principal tasks will be:

i) To identify riboswitches from diverse organisms that have already been characterised and shown to regulate transgene expression in their native hosts. These RNA sensors will be used in the generation of new expression platforms that allow metabolite-inducible expression of transgenes. To meet this objective the design, construction and testing of the different elements of these expression platforms will follow synthetic biology principled approaches.

ii) To test the responsiveness of the different riboswitches for the control of transgene expression in different photosynthetic eukaryotic organisms (including microalgae and plants).

Experience in recombinant DNA techniques is essential. Knowledge of systems or synthetic biology is highly desirable, as is familiarity with microbiology, metabolic engineering, and/or metabolism. The successful candidate should have the capacity to communicate effectively, work as part of a team, and take a lead role in the design and execution of the research programme as required. In addition, the PDRA will be expected to be involved in supporting junior scientists in the laboratory. You should hold a PhD in a relevant subject.

• Salary: £29,301-£38,183
• Fixed-term: The funds for this post are available for 2 years, in the first instance.
• Closing date: 21 April 2017
• Download: Further details
• You can apply online for this vacancy. You will need to register an account (if you have not already) and log in before completing the online application form.
• Please upload your CV with publication list, and covering letter to support your application.
• Please quote reference PD11744 on your application and in any correspondence about this vacancy.

The interviews are scheduled to be held in the week beginning 8 May 2017.

Please note if you have not received any news from us 1 month after the closing date you should consider that on this occasion your application has been unsuccessful.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

New Report release Webinar from National Academies of Sciences, Engineering, and Medicine (March 9th, 2017)

Preparing for Future Products of Biotechnology, a consensus report from the National Academies of Sciences, Engineering, and Medicine, was released on Thursday, March 9, 2017.

View Release Presentation Slides Here

The report describes the new types of biotechnology products likely to emerge over the next 5-10 years and assesses whether future products could pose different types of risks relative to existing products. It also identifies the scientific capabilities, tools, and expertise needed to support the oversight of these products by the U.S. regulatory system.

The Webinar Recording Will Be Posted Soon

The report release briefing featured:

– Welcome and introductions

• Bruce B. Darling, Executive Officer, National Academies of Sciences, Engineering, and Medicine

– A presentation by the Chair of the report’s authoring committee

• Dr. Richard M. Murray, Member of the National Academy of Engineering, Thomas E. and Doris Everhart Professor of Control and Dynamical Systems and Bioengineering, California Institute of Technology

– A Q&A session with study committee members

• Dr. Richard M. Murray, Member of the National Academy of Engineering, Thomas E. and Doris Everhart Professor of Control and Dynamical Systems and Bioengineering, California Institute of Technology
• Dr. Steven P. Bradbury, Professor of Environmental Toxicology, Iowa State University
• Dr. Mary E. Maxon, Biosciences Area Principal Deputy, Lawrence Berkeley National Laboratory