PuntSeq; a toolbox and workflow to facilitate realtime monitoring of algal, bacterial and viral diversity in aquatic field work situations.

The PuntSeq team were awarded an OpenPlant Fund grant to develop a toolbox and workflow to facilitate realtime monitoring of algal, bacterial and viral diversity in aquatic field work situations. We caught up with them to find out how the project is progressing.

Full details of the project can be found on the biomaker.org website.

PuntSeq will be talking about their project at the Cambridge Pint of Science Festival. Get your tickets now to hear more about this project: https://pintofscience.co.uk/event/the-technology-behind-mainstream-headlines

Please give us a brief overview of your project (200 words max)

Water sampling from the River Cam

Year by year, Cambridge rowers, swimmers and punters obtain serious infections associated with pathogens obtained from the Cam river’s water. While an information and research framework that targets the involved microbial culprits is still lacking, our project PuntSeq is a citizen science effort that will provide an in-depth resolution of the Cam river pathogen landscape - with minimum expense!

Led by a small group of graduate students at different Life Science Departments of the University of Cambridge, we have designed a workflow for the hand-sized Oxford Nanopore MinIONTM DNA sequencing device. We are adapting software for processing large volumes of biological data from different spots of the Cam, and try to match our bacterial findings with physical measurements of the same water samples. A do-it-yourself Arduino station that combines signals from pH, temperature, turbidity and other sensors will ultimately help us understand how certain pathogens prefer to reside within particular environmental locations of the Cam.

We regularly communicate our efforts and findings through Twitter (@puntseq) and presentations at scientific conferences. Moreover, a video featuring our research ideas is also currently being produced in collaboration with Wolfson College, Cambridge.

What inspired the project?

Sampling from aboard a punt on the River Cam

Over the past years, we learned about sections of the river where people appear to often catch infections, by regularly talking to rowers and swimmers in frequent contact with the Cam. Despite the general knowledge of these unsafe areas of our river, the actual cause of the infection (i.e. the bacterial strain) remains unclear in many cases.

Up to now, taking a snapshot of the bacterial population living in a water body has required a laboratory with expensive equipment. Compared to previous sequencing machines, the Oxford Nanopore MinION dramatically reduces running expenses and is also very small, which makes it an ideal instrument for fieldwork applications. For us, this offers the opportunity to explore a new technology as well as to work interdisciplinarily by diving into a whole set of different fields from electrical engineering (Arduino measuring tool), to environmental research and the vision of personalised, data-driven health care.

How did the team meet?

Most of our members have known each other through their PhDs and previous degrees at Cambridge University. Many of us have worked together in other research projects and we share a passion for genomics research and citizen science. With an interdisciplinary combination of expertise in conservation biology, bioinformatics, engineering and physics, in situ sequencing of the Cam appeared as a really cool project for all of us to join in!

How has this project developed links between Cambridge and Norwich?

Our PuntSeq team started a collaboration with Prof. Rob Field’s laboratory at the John Innes Centre (JIC), Norwich. Amongst other environmental phenomenon, the Field lab studies algal blooms of the haptophyte Prymnesium parvum that has been associated with mass die-offs of fish in the Norfolk Broads. While the lab succeeded in associating the toxic algal blooms with infection of P. parvum by the DNA-virus PpDNAV (Wagstaff et al., 2017, Viruses), a quick monitoring system has been lacking.

Here, PuntSeq’s aim of establishing a fast metagenomics surveillance of water sources fit in perfectly. Two of our team members attended the Norfolk Broads stakeholder meeting of 2018, where we learned more about the algal blooms, exchanged our experience with DNA extraction methodology, and presented our own project of assessing the microbial community of the Cam. At this meeting, we started a collaboration with members of Rob Field’s lab to test if our approach was applicable to monitor the presence of P. parvum and PpDNAV in water in a cheap and fast manner. We hence combined our knowledge in DNA sequencing using the MinION technology, in subsequent data analysis and in engineering of environmental measurement tools to perform a metagenomics analysis on a sample of Norfolk’s Hickling Broad. As a preliminary result, we were able to draw a map of the bacterial and fungal community of the Broad, and we found a species of the toxic algae and also evidence of the virus.

The PuntSeq team joined a Norfolk Broads Stakeholder meeting, held at the John Innes Centre, Norwich

What has been your favourite aspect of the project so far?

Through our public outreach on Twitter and by regularly featuring our project at different events, we were able to discuss PuntSeq with peers and leaders in the field, for example to Prof. Nick Loman whose lab has been using the MinION to track the 2015 Ebola outbreak. We received very positive feedback and useful advice from members of the Field lab at the JIC and colleagues at the University of East Anglia (Dr Ben Wagstaff (JIC), Dr Jennifer Pratscher (UEA), Mr Elliot Brooks UEA) as well as from Alina Ham from Oxford Nanopore Technologies, which have already resulted in improvements to our DNA extraction and sequencing workflow.

Apart from this very well-received general interest in our project, we really enjoyed seeing that our first proper MinION run with the sample from the Norfolk Broads worked out - and that the results nicely confirmed our approach.

What is the biggest challenge the team have faced?

We have found it extremely challenging to extract high concentrations of DNA from river surface water, and it took us several iterations to significantly improve our low-cost protocol. Starting a MinION sequencing experiment without a laptop that fulfills the high RAM and storage requirements is very challenging and may lead to significant data loss: fortunately, Ms Lara Urban and Mr Jack Monahan from EBI have joined us and could both help with their high-performance institute machines. Since we had to do two overnight MinION runs and Lara couldn't fully dispense her computer for a full working day, the laptop-connected sequencing instrument needed to travel from our lab to her home - via Taxi! Last, waiting for >2 consecutive days of non-rain during a British spring, to only sample the Cam surface water under baseflow condition, hasn't necessarily led to a significant speed-up of our project...

PuntSeq MinION1

Is there something that came out of the project that you never expected at the beginning?

A working DNA extraction protocol, a working MinION and a working Arduino platform!

How has the OpenPlant Fund enabled the development of the project?

Through the generous funding of the OpenPlant grant, we have been able to purchase the MinION starter kit for $1000, different water DNA extraction kits, basic lab equipment and our set of Arduino sensors and wires. Moreover, Dr Colette Matthewman and Dr Jenny Molloy from OpenPlant have kindly brought us in touch with algal expert Dr. Ben Wagstaff, helping us to establish an ideal Cambridge-Norwich collaboration which will help us immensely in expanding the applicability of our approach to algal contamination of freshwater waterways. The Fund's excellent outreach network has helped us in amplifying results and messages of our project through social media channels, mainly via twitter, in addition to their kind provision of facilities for a MinION metagenome sequencing workshop that we will hold in Cambridge very soon.

How do you feel the project is progressing?

Since our PuntSeq project received its first financial funding around half a year ago, it has progressed very quickly. In these few months, our team has been able to learn about all steps that are necessary to perform metagenomics surveillance analyses, from environmental measurements over DNA extraction and MinION sequencing to bioinformatic post-processing of the data. Hereby, it is great to see how much we have learned from each other, but also entirely from scratch by reading subject literature, talking to experts and simply by trial and error. We are now at a stage where we have optimised all individual protocols to perform a major water sampling and sequencing effort at various locations of our river Cam. We expect to be able to provide a profound overview of the microbial community of the Cam by the end of Spring.

Overall, our outreach activities have been very successful although we did not present much data yet. Both scientific and non-scientific communities have shown strong interest in our project, we received a lot of positive feedback, won multiple best-poster-prizes at conferences and motivated many people to follow our progresses via Twitter (@puntseq). We are confident that this already large interest will further increase with our first results about the river Cam being released, and we are currently strengthening our public engagement efforts, e.g. by taking part in events like “A Pint of Science”, by producing a professional movie clip and conducting an online-survey on infection rates through direct contact with the Cam.

What are the future opportunities to take this project forward?

We founded PuntSeq to inform the general public about the merits of DNA sequencing, especially about the direct impact it might have on peoples' health. In future, we would ideally like to sample from multiple rivers of the greater Cambridgeshire area and beyond, producing a map of microbial communities along the length of respective waterway trajectories. We hope to share our findings with relevant environmental authorities in Cambridge and East Anglia, and to influence environmental conservation through genomics. Our team is also further streamlining the process from extraction of the aquatic DNA to sequencing with the MinION and automatic identification of potential pathogens in the field, so that non-specialists can perform these experiments and gain a deep insight into the beautiful science of microbiology.

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PuntSeq team members are: Mr Maximilian Stammnitz (Department of Veterinary Medicine, University of Cambridge); Ms Meltem Gürel (Cancer Research UK Cambridge Institute); Dr Philipp Braeuninger-Weimer (Centre of Advanced Photonics and Electronics, University of Cambridge); Mr Daniel Elías Martin-Herranz (European Bioinformatics Institute); Mr Daniel Kunz (Wellcome Trust Sanger Institute); Mr Christian Schwall (Sainsbury Laboratory, University of Cambridge); Ms Lara Urban (European Bioinformatics Institute); Mr Jack Monahan (European Bioinformatics Institute); Ms Surangi Perera (Department of Physiology, Development and Neuroscience, University of Cambridge); Ms Eirini Vamva (Department of Medicine, University of Cambridge); Ms Astrid Wendler (Department of Clinical Neuroscience, University of Cambridge).

Full details of the project are at biomaker.org website. Follow the team on twitter @PuntSeq

Plant powered camera trap - are you able to take on the challenge?

With the help of funding from the OpenPlant Fund, University of Cambridge researcher Dr Paolo Bombelli together with Ms Rachael Kemp and Mr Alasdair Davies of the Zoological Society of London have launched a competition to design and manufacture a prototype of a plant powered camera trap. Deadline for proposals is 30th April 2018.

An artistic representation of a plant-microbial fuel cell

Camera trapping has been transformed by technology to become a major tool for conservationists, playing a crucial role in helping to better understand the effects of threats such as climate change and habitat loss, and supply data that can be used to inform policy and practice.

However, the current popular power sources such as battery packs and solar panels, are proving inadequate in more remote areas or in less than optimum conditions, for example in tropical forest canopies.

To overcome these challenges and further develop this area of conservation technology, this interdisciplinary team are running The Plant-Powered Camera Trap Challenge, looking to power camera traps and environmental sensors, using plant-microbial fuel cells.

Are you an architect, engineer, designer or a scientist? Are you able to design and manufacture a prototype open source plant-BES (bio electrochemical system) to power a camera trap to be used in tropical rainforests? All prototypes should be able to deliver 5v and produce 5000mC of charge per day. Submit your concepts by April 30th to receive an award of £10,000 from the Arribada Initiative and OpenPlant to build and deploy your device in the field.

If you think you can take on the challenge click here to register and find out more.

OpenPlant Fund supports project to deliver report on genetic resources in the age of the Nagoya Protocol

Dr Deborah Scott and Dr Dominic Berry of the Engineering Life project (The University of Edinburgh) have published a report "Genetic resources in the age of the Nagoya Protocol and gene/genome synthesis", based on the results of an interdisciplinary workshop held in Cambridge and involving several OpenPlant colleagues and part-funded throught the OpenPlant Fund. The workshop was dedicated to exploring emerging questions and discussions around the practice of synthesising DNA in the context of global biological diversity use and regulation, in relation to the Nagoya Protocol.

Map showing parties to the Nagoya Protocol and Biological Diversity Convention. Image by L. Tak, CC BY-SA 4.0.

Researchers in law, synthetic biology, social science and history were brought together to consider the implications of the Nagoya Protocol for Synthetic Biology and modern biotechnology. The report summarises the presentations and discussions that took place, including conversations on drivers and implications of ABS legislation, and benefit sharing and proprietary technologies.

The latter half of the report reflects on the workshop in light of the December 2016 UN Biodiversity Convention, and considers similarities and differences in the deliberations addressed at the two events.

The report ‘serves to highlight issues not yet addressed in formal negotiations and to provide additional texture to conversations already underway’.  

Click to download the full report (1.4 MB PDF, 64 pages)

Calling all biomakers; we challenge you to find technical solutions for biology

This blog post was originally posted on the John Innes Centre Blog on 21.03.2018, and has been reproduced here with permission.

We are today launching the ‘Biomaker Challenge’; a four-month programme, taking place over the summer and challenging teams of people from different disciplines to build low-cost sensors and instruments for biology.

These could be anything from colorimeters to microfluidics and beyond. We’re looking for new, frugal and open source, DIY approaches to biological experiments.

Whether you’re a biologist looking to improve how you work, or pick up some electronics knowledge; an engineer looking to apply your skills and gain experience of practical biology or you’re just curious, we want to hear from you.

Participants will receive a Biomaker Toolkit and a discretionary budget for additional sensors, components, consumables and 3D-printing to help them realise their vision, with the entire package of support worth up to £1,000.

Teams should include at least one member who is a student or member of staff at either the University of Cambridge, John Innes Centre or the Earlham Institute, but external participants are also encouraged to join teams.

The challenge is designed to foster collaboration between institutes, therefore applications from teams composed of participants from multiple places are highly encouraged and will be looked upon favourably by the assessment panel.

Applications close on 11 May 2018.

We will be holding several events in Norwich and Cambridge to provide information about the Biomaker Challenge and help people to develop ideas, discover new collaborations or get involved with projects:

• 21 March, 7pm – Biomaker Challenge Launch, St Andrews Brewhouse, Norwich
• 9 April, 2:30-4:30pm – Challenge Info and Mixer Session, Chris Lamb Training Suite, John Innes Centre, Norwich
• 9 April, 6pm - Pre-Challenge Mixer, Postdoc Centre, 16 Mill Lane, Cambridge
• 19 April, 6:30pm - Pre-Challenge Mixer, Scholars Café Bar, Union House, University of East Anglia, Norwich

At the end of the challenge, you will be encouraged and expected to exhibit your device at a Biomaker Fayre in Cambridge on 3 November 2018.

Last year 40 interdisciplinary teams showcased their prototypes and prizes were awarded for the best technology, best biology and maker spirit.

One group develop a cell-free biological sensor to detect arsenic in water, another created a low-cost, pressurised liquid chromatography system for protein purification, and a third developed a new, cost-effective way to take a series of macro images and stacking them in order to create one larger, in-focus, image. There are tools available that already do this, but they are very expensive so this project looked at how it could be done cheaper. Encouragingly, the group have since gone on to secure additional funding to take their project further.

We aim for all biomaker projects to be publicly documented with full technical instructions and equipment specifications on Hackster.io. This provides anyone around the world with the ability to replicate or adapt what our groups have done, boosting the reach and impact their ideas can have.

Norwich biomakers

There is a Norwich hub for biomaker activities; the Norwich Biomakers meetup group, which brings together a variety of people interested in biology, design, technology, engineering, electronics, software, art and more, to learn from each other about the latest technologies and science advances.

Established in September 2017, the group organises monthly themed events and gives access to a network of nearly 140 biomakers with a broad range of expertise.

Whether biology provides the question, the solution or the inspiration, as an interdisciplinary group we can explore together to generate and share new ideas and skills, find solutions, form collaborations and most importantly, have fun.

Despite only being established for 6 months, we have already seen 3 new collaborations established between researchers on the Norwich Research Park and external people with, for example, electronics expertise, on bioelectricity projects.

We’ve also enjoyed a series of talks at these events from prestigious speakers from the University of East Anglia, as well as from the John Innes Centre and have at least 2 events, each month planned between now and July.

We are always open to new members, check out our online group to find out more and register.

The Biomaker Challenge is administered by the BBSRC/EPSRC-funded OpenPlant Synthetic Biology Research Centre and the Cambridge University Synthetic Biology Strategic Research Initiative.

Norwich Biomakers is supported by OpenPlant SBRC and Innovation New Anglia through the European Regional Development Fund.

Synthetic Biology and the Senses at Cambridge Science Festival, March 2018.

The morning shift: Some of the Cambridge Science Festival 2018 team ready for doors open.

For the third year in a row, OpenPlant teamed up with the SAW Trust and Cambridge Synthetic Biology SRI to deliver a variety of activities on our interactive stand at the Cambridge Science Festival.

While braving the icy ‘pest from the west’ we explored some of the natural products made by plants with those who dared to venture out in the chilly weather. In keeping with this year’s festival theme ‘making sense of our world’, our ‘Synbio and the senses’ stand enabled participants to extract their own plant pigment, learn how plants make proteins and meet the one and only DNA Dave!

Extracting anthocyanin from red cabbage at the Cambridge Science Festival

The main activity of the stall involved visitors extracting the anthocyanin pigments from red cabbage, getting hands on with a natural pigment and investigating its sensitivity to pH levels. Children and adults alike, seemed to have great fun pipetting out their cabbage juice, acid (lemon juice) and alkaline (bicarbonate of soda solution) onto discs of filter paper to create their own artworks.

Visitors were excited to take home a worksheet explaining the science behind the pigments, and giving instructions for doing their own extractions and experiments at home. You can find the worksheet here.

Colour Bio-factories - using genetic engineering to boost existing pathways within plants to produce natural pigments.

In addition to the pigment extraction, visitors could learn about how researchers in Cathie Martins’ lab at the John Innes Centre are now producing these anthocyanin pigments in plants, using genetic engineering to boost a native pathway. At present there is only one natural blue pigment that is available for food colouring, which is produced from an alga called spirulina. However this blue is not very strong or stable in colour. Therefore, most blue food colourants are chemically produced synthetic compounds. The research conducted by Dr Ingo Appelhagen  in the Martin lab is enabling the discovery of new, more stable, anthocyanins found in nature and the use of plant cell cultures  to produce these more stable forms in larger amounts so that they could be used as non-synthetic colourings. They can generate a range of colours, including bright blues.

Visitors were also able to have a go at putting together their own synthetic biology plant system with the use of an interactive jigsaw game in which they chose a plant species to work with, a site or organ of the plant where they could make something happen, and a signal that would cause it to happen. To complete the game, they could then learn how proteins are made from the instructions in DNA with the help of DNA Dave! DNA Dave is a robot whose mechanics describe the processes of “transcription” and “translation” through which DNA is copied, then read and translated into a protein. As with previous events, DNA Dave was an absolute hit with all the visitors, including his namesake – Sir David Attenborough! Participants were even given the chance to design their own protein that could be used by DNA Dave.

A young visitor to the Cambridge Science Festival designs her own protein.

DNA Dave helps to explain the production of proteins.

With visitor numbers reaching 1600 in our marquee alone, the day was a great success with lots of enthusiastic individuals - if a little nippy! A big thank you to all our volunteers from the University of Cambridge and the John Innes Centre, Norwich, who helped on the day and did a great job!

Biomakespace opens its doors to new members!

Biomakespace in Cambridge is a community based, open access biology and prototyping space, which aims to contribute to awareness, knowledge and innovation in engineering with biology.

Providing members with affordable access to a well-equipped lab space, as well as training and social events, the project aims to build a community of scientists, engineers, technologists, entrepreneurs, teachers, artists and members of the public, keen to work at the interface of biology and engineering.

A dedicated team have been refurbishing the lab space since September 2016 and it's doors are now open to new membership applications! 

Check out the membership page for more details

Read more in this Cambridge Network blog post

DIY macrophotography and embracing the challenge of video documentation

Dr Jennifer Deegan has been awarded an OpenPlant Fund grant to develop teaching materials to enable others to build duplicates of her focus stacking photography setup, and to capture images that can be used for teaching and publications in plant sciences. We caught up with her to find out what she has been up to and how her project is progressing.

Full details of her project can be found on the biomaker.org website.

Jennifer, please can you give a brief overview of your project?

Jennifer Deegan: The project follows on from my Biomaker 2017 project to build a low budget DIY Focus stacking photography system. The system takes photographs of tiny plant specimens about 2mm across, with the entire specimen in focus.

An image of a gametophyte fern, captured using the DIY Focus stacking photography system

In the past it was not possible to take photographs of such tiny specimens and have them fully in focus. This was because single images taken at high magnification had only a very shallow depth of field. With this new technique we take about 40 photographs of a tiny specimen, with the camera moving progressively towards the subject. Then all of the focused parts of the images are cut out and amalgamated together into one fully focused image.

Commercial systems are available to do this, but they are very expensive. The more affordable ones only move the camera in increments of 2 micrometres. This is not small enough for use at very high magnification. Our system is very cheap and can moved in increments down to about 1/128th of a micrometre.

The DIY Focus stacking photography system

As part of this OpenPlant project we have two goals:

• Document the construction of the focus stacking system so that others can copy it.
• Use the system to take plant photos that have never before been possible. These photos will then be made available for plant science teaching and text books.

What inspired the project?

JD: I have always been frustrated that there are no great photos of fern gametophytes anywhere. Fern gametophytes have a very interesting planar heart shaped structure that is brought about by a tightly choreographed series of cell divisions. In the literature they are usually drawn by hand, because they are too small to be photographed in full focus. During my career break to raise my son, I have been working at home as a volunteer, to try to build a system that can take good, full focus, high magnification photographs of these structures.

What has been your favourite aspect of the project so far?

JD: The judges asked me to document my system using videos rather than just in writing. This threw me for a loop initially as I have never made video and didn't have the equipment. However, I have managed to cobble a system together, and am loving my new craft. The time, nuance and attention to detail that is needed to make a short video is amazing. The photo below shows the many photo, video and sound files that I had to record and line up in order to create one short video.  I'm now the proud owner of a YouTube channel. (You can visit it, and the other documentation on GitHub and Hackster via www.chlorophyllosophy.uk)

Editing videos that explain how the focus stacking system works

What are the biggest challenges you have come across?

JD: There have been a lot of challenges, particularly with the transition from written documentation to video.

The biggest problem is that my laptop is ten years old and is a bit slow for editing video. It cannot play my videos at full speed, so I have to upload them to YouTube between editing session to see what they look like. Saving the files out for upload to YouTube takes 2.5 hours for each video, so it is a slow process.

The DSLR filming the focus stacking setup, with decoy camera body in place

One of my funniest solved problems is that my DSLR is the only camera that I have that can record video, but it also has to appear in the videos. I got around this problem by putting my 27-year-old film SLR as a body double in the videos. The photo to the right shows my DSLR filming the focus stacking setup, with decoy camera body in place. It’s great fun editing the sound of the camera shutter into the finished video.

My other challenge is making these rather technical videos engaging to watch. There is a definite risk of them coming over as a bit dry, and so I try to keep them short and make the images interesting. I think that if I can improve my editing equipment at some point, I could make my videos much more engaging.

I’m really enjoying making educational videos and would like to keep doing this work after the end of the OpenPlant grant. I’ve been in touch with the University Public Engagement Office, who have been very helpful, and I’m hoping to learn some tips from them.

You have been awarded both a Biomaker Challenge and OpenPlant Fund grant. How have these enabled the development of the project?

JD: My work absolutely could not have been done without these grants. Most of the work has been done through collaboration, volunteer labour, and home engineering. However, the grants paid for the microscope objectives. Without these amazing lenses, I could not have done the work.

How do you feel the project is progressing?

JD: I think it's going very well. I have four good videos already online, and a lot of written documentation. I have registered a new domain (www.chlorophyllosophy.uk) as a central doorway to all of the material, and I still have lots of ideas for other videos to make.

Two out of three of my lenses have arrived and I am looking forward to taking some great photos. My Utricularia gibba (bladderwort) plants are growing well in their casserole dish. Utricularia gibba is a small, carnivorous aquatic plant that develops traps to capture its prey. They are being studied by my collaborator Christopher Whitewoods at the John Innes Centre and I have already taken my first few photos of them, as the new traps develop. The traps have a beautiful structure, and as an aquatic plant, will be a great challenge to photograph.

I hope soon also to visit the Sainsbury Laboratory in Cambridge to photograph the trichome mutant phenotypes in Arabidopsis thaliana, belonging to my collaborator Aleksandr Gavrin. I really look forward to the challenge of photographing trichomes, that will have other trichomes behind to confuse my software.

I have also just sewn a new batch of fern spores and those plants will be a real treat to photograph when the time comes.

What are the future opportunities to take this project forward?

JD: One of the biggest pitfalls for photographers is that they become so fascinated by the stream of newer and better camera equipment, that they forget to actually take any photos. I think that in the next couple of years, it's very important that I actually take the time to take some photographs. With this new technology that I have built, and with the opportunity of my volunteer labour, these will add hugely to the body of research knowledge.

Jennifer's project is also documented on Github: https://github.com/BioMakers/Gametophyte-Fern-photography-2018/blob/master/README.md

Eleven projects pitch for funding from the OpenPlant Fund

Aleksandr Gavrin pitching his proposal.

Friday 1 December 2017, Norwich, was the day of the pitches for the 5th round of OpenPlant Fund proposals – and what an exciting set of proposals they were. Eleven proposals were pitched, ranging from development of plant tools and methods, to cell-free protein production, software and hardware development, training, and development of resources for schools in Ghana.

The OpenPlant Fund is rapidly building a dynamic community of early career plant synthetic biologists. The Fund has awarded over 60 micro-grants between 2015 and 2017 to projects facilitating exchange between University of Cambridge, the John Innes Institute and Earlham Institute in Norwich and a range of external collaborators for the development of open technologies and responsible innovation in the context of synthetic biology. Through these awards, OpenPlant aims to promote plant synthetic biology as an interdisciplinary field. This latest round of “high quality, innovative and novel ideas” – as judge Richard Hammond of Cambridge Consultants put it – highlights the engagement, motivation and drive the is present within the local community. More information on the Fund can be found at www.openplant.org/fund and documentation of OpenPlant Fund projects can be found at www.biomaker.org.

Fern gametophyte photographed by Dr Jennifer Deegan using her focus stacking photography platform. More information, images and project documentation can be found through http://chlorophyllosophy.uk/

Tools for plant synthetic biology

The first talk, coming to us via skype, pitched for funding to further develop a focus stacking photography platform for teaching and publication in plant sciences. Impressive images of fern gametophytes showed the current scope of the platform developed through the Biomaker Challenge. Presenter Jennifer Deegan (University of Cambridge) made full use of skype by demonstrating the hardware setup, explaining how it would be further developed to expand its scope, and how it would be adapted to build a cheap system for schools.

Next up, Aleksandr Gavrin (Sainsbury Laboratory, University of Cambridge) presented a proposal to make stable transgenic Medicago truncatula lines in which actin is tagged with a reporter gene as a tool for legume researchers. In another legume-focused project, Abhimanyu Sarkar (John Innes Centre) proposed to establish a transformation system for the orphan crop Grass-pea. While there were some challenging legal questions surrounding the shareability of the system, the judges recognised the urgent need for new developments in transformation.

Image by Pablo Ramdohr, shared under licence CC BY 2.0

Cell-free biology

Proposing to compare cell-free and plant expression systems for protein expression, Susan Duncan (Earlham Institute) pitched a project that would analyse synthesis of proteins, focussing specifically on transcription factors. New collaborations between groups in Norwich and Cambridge will provide Susan with a variety of transcription factors to test.

In a related, but “very independent” project, Quentin Dudley (Earlham Institute) proposed to compare protein synthesis in two different cell-free systems, E.coli and wheat germ lysates. The project aims to gather data on yield vs cost of the two systems. He extended on open invitation for people to ask him “can you try my protein”. So, get in touch if you’d like your plant protein to be tested in Quentin’s cell-free systems.

The third cell-free proposal came in via skype, with Clayton Rabideau (University of Cambridge) rubbing the sleep from his eyes to pitch from the US in the early morning hours. Clayton pitched for funding to develop a hardware system called Open-Cell, using machine learning together with microfluidics-based cell-free screening assay technology for screening of enzyme activity.

Computation and training

A third theme that came out through the pitches, was the need for computation, software development and training. Chris Penfold (University of Cambridge), who had arrived straight off a plane from Venice, proposed an ambitious project to develop a suite of computational tools to simulate large gene regulatory networks in plants and mammals. These tools aim to improve rational design and predictability in synthetic biology.

Jan Sklenar (The Sainsbury Laboratory, Norwich) presented a proposal to bring together proteomics experts and bioinformaticists with expertise in R software. To do this, the group propose a series of workshops for knowledge exchange and training to help both disciplines understand each other. Following these workshops, the team will work together to integrate the ‘R for Proteomics’ package, developed at the University of Cambridge, into Norwich proteomics workflows and further develop the software suite. Jan’s driving motivation for the project is to “be more efficient” and require “less manual interference” for proteomics analysis.

A final computational project was pitched by Aaron Bostrom (Earlham Institute) who talked about mutant worms and Raspberry Pi’s in a proposal to develop a training programme designed around sensing hardware for data collection and machine learning for plant synthetic biology projects.

An artistic representation of a plant-microbial fuel cell, submitted in Paolo Bombelli's proposal

International activities

Two energetic presenters pitched projects focussed on engaging directly with an international group. Paolo “the plant electrician” Bombelli (University of Cambridge) pitched for match-funding to enable him to run an international biodesign competition for the development of prototypes for a plant-microbial fuel cell to be used in remote jungle regions as an environmentally friendly power supply for a sensor and camera-trap to be used by Zoologists.

Waving his hands as he introduced himself, PhD student Hans Pfalgraz (University of East Anglia and John Innes Centre) proposed a project, working with Kumasi Hive innovation hub and the Lab_13 Ghana practical science education project, to take inspiration from previous OpenPlant projects and develop open source practical teaching activities, testing these in Ghana and then making more widely available for schools in other low-resource settings.

What the judges say

“This was a great event and I thoroughly enjoyed it. It felt like we visited all four corners of science in a couple of hours. The proposals were of a high standard and well presented with some fascinating new ideas to understand and discuss. Well done to all involved.’”

— Richard Hammond, Technology Director and Head of Synthetic Biology at Cambridge Consultants

“It was a great day, very good science, creativity and a warm welcome. Thanks for the invite!”

— Ward Hills, CEO at OpenIOLabs

“We heard a number of compelling and original ideas, the majority being led by early career researchers. It was particularly impressive to see so many new collaborations and networks being built, both between the Open Plant Research Institutes and with external partners.”

— Dr Nicola Patron, Synthetic Biology Group Leader, Earlham Institute

New report from the OpenPlant IP Working Group: Towards an Open Material Transfer Agreement

View the full report >>

The OpenPlant Intellectual Property (IP) Working Group was formed to examine IP norms and policies that impede innovation in plant synthetic biology. The result was the development of the Open Material Transfer Agreement (OpenMTA), a legal tool for sharing DNA parts and other biological materials that allows IP-free sharing of foundational tools while promoting the scaling and commercialisation of novel advanced technologies.

OpenPlant is a collaborative initiative between the University of Cambridge, the John Innes Centre and the Earlham Institute in Norwich. It is a synthetic biology research centre focused on the development of open technologies for plant synthetic biology. As part of this initiative, the OpenPlant Intellectual Property (IP) Working Group was formed to examine current IP norms and policies that impede innovation in plant synthetic biology and develop pragmatic solutions.

OpenPlant is building a collectionof promoters to drive expression of fluorescent markers in the liverwort Marchantia polymorpha which will be shared with the plant synthetic biology community. Image: Bernardo Pollak, Haseloff Lab, University of Cambridge

The Working Group met at the University of Cambridge on 30 July 2015 to solicit input on the design specifications for an open material transfer agreement (OpenMTA), a legal tool that complements the BioBrick® Public Agreement and supports the sharing of DNA components as tangible material. The second aim was to gather and prioritise actionable goals for creating and sustaining an international platform of open technologies for plant synthetic biology.

This report provides background and context for our discussions then summarises the observations of the 23 participants, who included researchers, technical experts, and legal practitioners from academic, industry, and non-profit organisations.

“We believe steps to facilitate exchange of DNA parts and tools will substantially speed the take-up of new technologies in plant synthetic biology.”

The OpenPlant IP Working Group continued discussions through monthly calls and drafted several comment pieces and conference presentations. After extensive consultation, the text of the OpenMTA Master Agreement is published, initial signatories are invited and the first transfers of materials are beginning to take place, including transfer of bacterial DNA parts from Stanford University to the J Craig Venter Institute. Work continues to address the other issues identified in this report in the context of sharing OpenPlant-derived tools and technologies.

The authors welcome feedback on this report and invite suggestions for concrete actions enabling the creation and maintenance of platforms for sharing open biotechnologies. 

For more information on the OpenMTA, see http://openmta.org

Postdoc representatives sought for University of Cambridge Open Research Working Group

The Open Research Working Group will convene in Lent Term 2018 to define and develop the University’s approach to open research, including open access to publications and open research data. The working group is seeking two postdoc representatives with some background or interest in open research, one from STEM and one from AHSS.

This opportunity may appeal to those working in the open technology area, with OpenPlant or who have received OpenPlant or SynBio Fund support and have some interest in or experience of open research.

Remit of the Working Group

The Open Research Working Group will be convened in the Lent Term 2018 to clarify the University’s needs and expectations on Open Research. The group will define and agree on the University’s stance on Open Research and help shape service, infrastructure and policy developments in response to the Open Research agenda. Broadly speaking, Open Research is taken to mean the overall drive towards sharing (data, method, outputs) of University research, and the changing research and dissemination practices intended to maximise public access to these. Open Research is inclusive of Open Access to research publications and doctoral theses and the processes and planning involved in research data management which can, where appropriate, lead to the sharing of Open Data.

Level of Commitment

The working group is a short-term commitment of 4-5 meetings between Feb and June 2018. It is an excellent opportunity to voice the perspective of postdocs in how the University addresses this important topic, as well as valuable experience for an academic careers.

Contact james.brown@admin.cam.ac.uk if you are interested in this opportunity.

Apply now for eLife Innovation Sprint - bringing cutting-edge technology to open research

The eLife Innovation Sprint is a two-day challenge on 10-11 May 2018 for developers, designers, technologists and researchers to collaboratively prototype innovations that bring cutting-edge technology to open research.

The eLife Innovation Initiative have been working to improve research transparency and accessibility, and accelerate discovery in the life sciences, by developing open-source technologies in collaboration with the wider community. They have heard many excellent ideas for transforming how the latest science is shared, built upon and recognised, and  they want to create a space that would help translate these ideas into action.

By bringing ideators, creators and users together for the Innovation Sprint, they hope to provide space, time and access to diverse skill sets for the community to develop their ideas into prototypes and forge new collaborations.

eLife invite you — whether change maker or web wrangler, UX champion or data tinkerer — to apply to participate in person.

Apply now >>

Applications will close at 9am GMT on March 5 2018, and we aim to communicate the outcome of each application by March 23 2018.

[Closes 28 Feb] Early registration now open for Crossing Kingdoms: an international synthetic biology symposium

Crossing Kingdoms is an international 3 day-event bringing together scientists from the microbial, animal and plant fields to present their results and highlighting how knowledge from these different life forms provide tools for synthetic biology innovations and applications.

Registration for Crossing Kingdoms is now open.

 

Abstract submission

Submissions for oral and poster presentations  are welcome.  To submit a pdf or Word file containing your abstract please complete the electronic submission form here.

List of confirmed speakers:

• Pamela Silver, Harvard University
• Matias Zurbriggen, University of Düsseldorf
• Chang Liu, UC Irvine
• Dan Voytas, University of Minnesota
• Ben Blount, Imperial College
• Sean Cutler, UC Riverside
• Alison Smith, University of Cambridge
• Giles Oldroyd , Sainsbury Laboratory – University of Cambridge
• Anne Osbourn, John Innes Centre

Organisers:

Alain Tissier (Halle) and Philip Wigge (Cambridge).
Supported by the German Ministry of Education and Research (BMBF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC) and ERA-SynBio.

Download the conference poster for your noticeboard

[Closes 12 Mar 2018] OpenPlant and SynBio SRI seek new Coordinator - apply now!

The University of Cambridge is seeking a Co-ordinator for two Synthetic Biology research initiatives. The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI).

We are seeking a Co-ordinator for two Synthetic Biology research initiatives at the University of Cambridge. The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI). The purpose of the role is to help develop and implement a strategy that will enable both initiatives to become known leaders in the field and sustainable in the longer term.

OpenPlant (http://openplant.org) is a consortium funded by BBSRC and EPSRC comprising 20 labs spanning the University of Cambridge, John Innes Centre and the Earlham Institute (Norwich). The work of the Research Centre is intended to promote novel research on tools and applied traits for plant synthetic biology, open sharing of foundational technologies, and responsible innovation. The role-holder will work with the OpenPlant Directors and Management Group, including the OpenPlant Project Manager based in Norwich, to co-ordinate a variety of activities within the Research Centre.

The SynBio SRI (http://synbio.cam.ac.uk) aims to catalyse interdisciplinary exchange between engineering, physics, biology and social sciences to advance Synthetic Biology at the University of Cambridge. The role-holder will work with the SRI Co-Chairs and Steering Committee to develop, plan and deliver the SRI's vision and strategy. They will facilitate efforts to promote development of open technologies, build shared resources, and provide a hub for networking and discussion.

Responsibilities will also include co-ordinating seed funding competitions such as the Biomaker Challenge and OpenPlant Fund; organising formal and informal scientific meetings and forums; developing and managing relationships with stakeholders within and external to the University; seeking small and large-scale funding for future activities. The role-holder is additionally responsible for ensuring that synthetic biology activities in Cambridge are actively communicated and promoted, and is supported by the part-time SynBio SRI Events and Communication Co-ordinator.

The successful candidate will have a PhD in a relevant field and knowledge of Synthetic Biology research, policy and practice. They will have the ability to foster relationships with and between academics at all levels in an interdisciplinary context, and build partnerships with companies, funders and policy makers. A successful track record in attracting research funding would be advantageous. Excellent organisational and communications skills are essential, together with proven problem-solving skills and initiative.

 For more information and to apply >>

Call for Proposals: 5th International Synthetic & Systems Biology Summer School - SSBSS 2018

The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The 2018 Summer School will take place July 25-29, 2018 at Certosa di Pontignano in Tuscany, Italy.

The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment.

Deadlines

Application: March 31, 2018

Oral Presentation/Poster Submission: March 31, 2018

Notification of Decision for Oral/Poster Presentation: April 28, 2018

Register here >>

Keynote Speakers

* PATRICK YIZHI CAI, University of Manchester, UK

* JOHN GLASS, J. Craig Venter Institute, USA

* PHILIPP HOLLIGER, MRC Laboratory of Molecular Biology, Cambridge, UK

* JENS NIELSEN, Chalmers University of Technology, Sweden

* HARRIS WANG, Columbia University, USA

* RON WEISS, MIT, USA

* LUCA ZAMMATARO, Yale University, USA

Speakers 

* Barbara Di Camillo, University of Padova, Italy

* Simone Furini, University of Siena, Italy

* Emanuele Domenico Giordano, University of Bologna, Italy

* Rodrigo Ledesma-Amaro, Imperial College London, UK

* Velia Siciliano, Italian Institute of Technology, Italy

Links

• More information on website >>
• Email via ssbss@icas.xyz
• Facebook >>

Prof Giles Oldroyd joins Sainsbury Lab to engineer nitrogen-fixing cereals

Prof Giles Oldroyd, an OpenPlant PI who directs a Bill and Melinda Gates Foundation programme of research to engineer nitrogen-fixing cereals has recently joined the Sainsbury Lab at University Cambridge after 15 years at the John Innes Centre in Norwich.

Prof. Giles Oldroyd is a leading investigator in plant-symbiotic interactions, with a particular focus on the signalling processes that allow the establishment of nitrogen-fixing and arbuscular mycorrhizal associations. His work has provided the genetic underpinnings to understand the symbiosis signalling pathway that allows rhizobial recognition in legumes and mycorrhizal associations in most plants. He explained his interests in an introductory post on the SLCU website:

"I spent 15 years working at the John Innes Centre, attempting to understand how plants perceive symbiotic microorganisms present in the rhizosphere. Having contributed to a detailed understanding of symbiosis signalling, I now want to understand how this signalling process activates the developmental changes in the root leading to the formation of a nodule and intracellular bacterial infection."

“I am very excited by the prospect that some day this research could address one of the greatest limitations to agricultural productivity”

— Prof Giles Oldroyd, SLCU

Prof Oldroyd now leads an international programme funded by the Bill and Melinda Gates Foundation and the BBSRC that is attempting to engineer cereal recognition of rhizobial bacteria as the first step towards engineering nitrogen-fixing cereals.

"There remains much to be discovered before we are likely to be able to transfer nitrogen fixation to cereals. However, I am very excited by the prospect that some day this research could address one of the greatest limitations to agricultural productivity and I am particularly motivated by the fact that the beneficiaries of my work could be some of the poorest people on the planet."

The SynBio SRI welcomes the Oldroyd Lab to Cambridge and we look forward hearing more about their work in plant synthetic biology.

Prof Giles Oldroyd's homepage at SLCU >>

Essex Synthetic Biology Summer School: 2-6 July 2018

The Essex Synthetic Biology School (ESBS) is an intensive 5-day summer course targeting students and early career scientists interested in learning cutting edge experimental and computational methods to design and build biological systems directly from world-renowned experts, working with bacterial, yeast, plant and mammalian systems, in fields such as cancer and healthcare research, as well as industrial, agricultural and environmental synthetic biology.

Synthetic biology is an emerging research and industrial field aiming at designing and engineering biological systems with specific functions. To do that, it integrates methods and technologies from biology, chemistry, engineering, computer science and mathematics to streamline the process of designing, building and testing biological systems. In the last 10 years, synthetic biology has contributed many ground breaking scientific results, including the first synthetic cell and the first synthetic chromosomes, and industrial applications, including the production of drugs and biofuels.

The School, located at the University of Essex in the U.K., comprises 20 lectures and 5 laboratory sessions, focusing on building pathways in bacteria and yeast.

Learn more and register by 1 June 2018 >>>

OpenPlant Fund supports open source multi-fluorescence imaging system published in PLOS One

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study supported by the OpenPlant Fund, Isaac Nuñez, Tamara Matute and collaborators describe a multi-fluorescence imaging system that integrates low-cost and open-source hardware, software and genetic resources.

The illumination and optics system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics and the box design and flexible focusing allows imaging in scales ranging from single colonies to entire plates. The team also developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, they screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins for 3-channel fluorescent imaging.

Open source Python code was developed to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, the team tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology.

Isaac Nuñez appreciated the opportunity to work on the project with the support of OpenPlant: “OpenPlant funds were important because we are generating a real impact in research and teaching through interdisciplinarity. This project not only introduced us to new modes of work based on good practices, documentation and open source licensing but also allowed us to learn from different fields such as open hardware, design, FOSS and advanced DNA fab methods.”

In order to highlight the benefits of employing an open framework, the team formed an industry partnership with the Open Source company Backyard Brains (TM), which has significant experience in creating and distributing open educational and research technology for neuroscience in Latin America and worldwide (backyardbrains.com, backyardbrains.cl). In collaboration, the team assessed the potential use of their imaging statuon in a high school environment.  Author Tamara Matute explained “We have been able to use these resources in workshops in high schools, community spaces and cultural centres; and implement advanced practicals to teach in vitro synbio, DNA fab and microbiology. The open source and low cost nature of the resources has allowed citizens to better understand the principles behind gene expression analysis and modelling”

Together, their results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. The paper was selected as Editor's Pick for the PLOS Open Source Toolkit Channel in December 2017.

Original Publication: Nuñez, I., Matute, T., Herrera, R., Keymer, J., Marzullo, T., Rudge, T., & Federici, F. (2017). Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLOS One, 12(11), e0187163.

Synthetic Biology and the Senses: volunteers wanted for Cambridge Science Festival

Synthetic biology can bring cutting edge biotechnology into everyday experiences through people's senses by harnessing the wonderful variety of colours, scents, tastes and textures produced in nature. We are looking for enthusiastic volunteers and interactive exhibits or colourful posters to illustrate the theme of 'Synthetic Biology and the Senses' at the Cambridge Science Festival Life Science Marquee on Sat 17 March 2018.

'Synthetic Biology and the Senses' is a joint exhibit by OpenPlant and the SynBio SRI and will run 10:00-16:00 on Sat 17 March 2018 on the Downing Site Lawn, with volunteers required before and after for set-up and packing down. 

We are looking for volunteers to help out and talk to visitors as well as proposing activies or exhibits of their own. In 2017 we featured exhibits including:

• Bioluminescent bacteria

• Fabrics dyed with synthetic ink from bacteria

• Micro-organisms expressing plant metabloic pathways to produce rose and patchouli scents

• Design-a-plant

• Dave the DNA Robot

 We require volunteers for various times of the day and would be very happy to have 4 people at the exhibit at all times. Two hour slots are available and volunteers can stay as long as they wish. Lunch and Science Festival T-Shirt provided!

Please register via this form.