OpenPlant Blog — OpenPlant

Collaboration including OpenPlant researchers discovers that C4 photosynthesis has co-opted an ancient C3 regulatory code

Collaboration including OpenPlant researchers discovers that C4 photosynthesis has co-opted an ancient C3 regulatory code

Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state.

Borba AR, Serra TS, Górska A, Gouveia P, Cordeiro AM, Reyna-Llorens I, Kneřová J, Barros PM, Abreu IA, Oliveira MM, Hibberd JM, Saibo NJM.

Molecular Biology and Evolution, Volume 35, Issue 7, July 2018, Pages 1690–1705.

https://doi.org/10.1093/molbev/msy060

[Close 22 Apr 2018] Two Sr / Research Assocaite positions in Protein Design

Two positions are available in the laboratory of Professor Dek Woolfson, University of Bristol

For more information on the Woolfson group see: http://www.chm.bris.ac.uk/org/woolfson/index.html

For informal enquiries please contact: d.n.woolfson@bristol.ac.uk

Senior Research Associate / Research Associate in Protein Design for Biotechnology

http://www.jobs.ac.uk/job/BIT158/senior-research-associate-research-associate-in-protein-design-for-biotechnology/

A position for a postdoctoral research associate is available to work on a protein design in biotechnology project in the laboratory of Professor Dek Woolfson.  The group is internationally leading in the development of protein design for applications in chemical and synthetic biology.  The successful applicants will join a vibrant research team that combines bioinformatics and computational design, peptide and protein chemistry, biophysics and structural biology, and cell biology.  Expertise in peptide chemistry and biophysical methods would be a distinct advantage for this particular post, and applicants from these areas are particularly encouraged to apply.  However, we are keen to receive applications from ambitious and energetic individuals across the chemical and biochemical sciences or bioengineering with an interest in advancing protein design and its applications generally.

This post in protein design for biotechnology is for one year, and it is funded by a European Research Council Proof-of-Concept grant.  The project will explore the use of a-helical barrels recently discovered and developed in the Woolfson lab (Thomson et al. (2014) Science 346:485-488) in the area of biosensing. Researchers with a background in peptide chemistry, surface chemistry and/or fluorescence spectroscopy/microscopy are strongly encouraged to apply.  An active interest in driving the translation of this basic research into biotechnology applications of societal benefit would be an advantage.

Senior Research Associate / Research Associate in Protein Design

http://www.jobs.ac.uk/job/BIP002/senior-research-associate-research-associate-in-protein-design

A position for a postdoctoral research associate is available to work on protein design in the laboratory of Professor Dek Woolfson.  The group is internationally leading in the development of protein design for applications in chemical and synthetic biology.  The successful applicant will join a vibrant research team that combines bioinformatics and computational design, peptide and protein chemistry, biophysics and structural biology, and cell biology.  Expertise in computational biochemistry and/or structural biology would be a distinct advantage for this post, and applicants from these areas are particularly encouraged to apply.  However, we are keen to receive applications from ambitious and energetic individuals across the chemical and biochemical sciences or bioengineering with an interest in advancing protein design and its applications generally.

The post is available for an initial two-year period and is extendable to a further two years upon a successful start to the project.  This is funded by a grant from the Biotechnology and Biological Research Council of the UK.  The post-holder would be joined in year 2 by an expert in machine learning and virtual reality (VR) working in the laboratory of Dr David Glowacki (Chemistry, Bristol).  Together, these two post-doctoral research associates will develop VR methods to aid and advance the computational design of completely new proteins building on research programmes across the two labs (Thomson et al. (2014) Science 346:485-488; Wood et al. (2017) Bioinformatics 33:3043-3050; https://arxiv.org/pdf/1801.02884.pdf).  There will also be considerable opportunity to work with the international experimental and computational protein design and engineering communities.

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

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

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
 
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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

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.


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

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.

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)

Opportunity to join an exciting new start-up to develop insect tracking and quantification device via IoT

An exciting opportunity is available to work with a young up-and-coming start-up company.  As part of their research development, they are interested in creating an IoT demo device for insect tracking and quantification and could use some engineering help.

They are looking to make a device that can:

  1. Use vision tech to classify broad categories of insects
  2. Combine cloud-based hyper-localized data (weather conditions, time, etc.) with pollinator data. 
  3. Develop an IoT edge device
  4. Design a chemical release mechanism controlled electronically

The position is temporary to begin with, with a view to develop a permanent position in the future if the fit is right. The position would be based in London, but the company are open to applicants who aren't based in London, but are happy to travel on occasion.

ABOUT POM:

Insect pollinators provide a vital ecosystem service for crop pollination in wild plants, and over 75% of crops worldwide benefit from insect pollination through increased yields at harvest. The number of wild pollinators, especially bees is steadily declining. This documented decline poses a significant risk to the production of many crops and threatens food security.

POM encourages flies to be more efficient pollinators, in scenarios where bees are no longer as viable. Flies are already adept pollinators, being the main pollinators in urban environments, and in total, accounting for over 30% of all pollination.

POM provides horticultural growers with information on pollinators and environmental conditions and uses chemical volatiles to manage pollinating fly species, thereby increasing crop productivity, and ensuring sustainable food harvests for the future.

KEY RESPONSIBILITIES:

We are looking to find an experienced Engineer who is interested in working with a young and exciting start-up that has recently taken on investment to develop an insect tracking IoT device.

The individual should have experience with working on Raspberry Pi, Cloud computing and IoT data connectivity. The position will report weekly developments to the POM team in our London office, and reports to the Senior Engineer remotely throughout the week.

This position is a two month contract with the potential to continue with the company after
the achievement of key milestones. Project Salary: £2,300+ per month

Click here to download the job description.

Interested? Contact hello@flypollination.com

www.flypollination.com

[Closes 26 Apr 2018] Bioinformatician - Single Cell Analysis at Earlham Institute

The Core Bioinformatics Group at the Earlham Institute (EI, Norwich, UK) is looking for an enthusiastic and dedicated Bioinformatician to support developments in single cell genomics at the institute. Apply here: http://www.earlham.ac.uk/bioinformatician-single-cell-analysis

The role:

This is a collaborative project with the successful candidate joining the group of Dr. David Swarbreck and working closely with wet and dry lab scientists in the groups of Dr. Iain Macaulay and Dr. Wilfried Haerty. The post-holder will establish and implement pipelines and processes for the analysis of single genome, epigenome and transcriptome data from a wide variety of biological systems. Delivering single cell data analysis in conjunction with faculty groups, the genomic pipelines team and external collaborators.

[Closes 26 Apr 2018] Bioinformatician - Genomics Pipelines at Earlham Institute

This position is within the Core Bioinformatics group working in collaboration with Ksenia Krasileva (University of California, Berkeley). Apply here: http://www.earlham.ac.uk/bioinformatician-genomics-pipelines

The role:

This group member will be working with the latest wheat genomic data and building a toolbox for functional analyses. Specifically, the candidate will be involved in developing software tools to help understand how new variation in NLR immune receptors is generated, updating variant calling pipelines to examine natural and induced variation in complex wheat genomes and integrating this information to enable functional characterization of wheat genes. The candidate will work independently and with members of the Swarbreck (EI) and Krasileva (UC Berkeley) Groups to develop computational tools and pipelines to analyse large datasets and interpret them in a variety of biological contexts.

[Closes 19 Apr 2018] Genomics Pipelines Senior Research Assistant (Automation) at Earlham Institute

Applications are invited for Senior Research Assistant to join the Genomics Pipelines Group at the Earlham Institute. Apply at http://www.earlham.ac.uk/genomics-pipelines-senior-research-assistant-automation

The role:

The SRA will support the automation of high-throughput workflows for the Genomics Pipelines group and the DNA Foundry at the Earlham Institute. The SRA will play a key role in automating, troubleshooting and streamlining both current and future pipelines in a rapidly changing and technology-led environment. The SRA will also assist production teams with the preparation of next-generation sequencing libraries and the building and testing of engineered organisms as required by customers’ and collaborators’ projects.

The SRA will work closely with other laboratory staff in Genomics Pipelines and DNA Foundry to plan, execute and deliver scheduled high throughput and/or novel techniques. The SRA will transition complex, and cutting-edge laboratory processes onto EI’s installed base of liquid handling robotics platforms, as well as ensuring the smooth day-to-day running of laboratory automation, and deliver training to other RAs using automated protocols for deployment into production.

The SRA will ensure efficient, effective and safe operations of the automation they are responsible for. They will train Research Assistants on using automated protocols until they are handed over for production.

The SRA’s work will support Earlham’s strategic science programmes and the National Capability in Genomics and Single Cell Analysis, and DNA foundry.

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.

NorBCTwitter-Web.jpg

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

Norwich Biomakers logo.jpg

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.

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

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.

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.

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

DNA Dave helps to explain the production of proteins.

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!