[Closes 30 May 2018] Co-ordinator for Synthetic Biology Centre

We're looking to hire a Cambridge-based coordinator for the OpenPlant SynBio Research Centre and the Cambridge SynBio Strategic Research Initiative. Application deadline is 30 May 2018.

Full details of the post can be found at http://www.jobs.cam.ac.uk/job/17351/

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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.

Fixed-term: The funds for this post are available until 30 September 2019 in the first instance.

Cell-free protein synthesis - try it with your favourite protein!

Quentin Dudley, a postdoc at the Earlham Institute, did a PhD in the Jewett lab (Northwestern University, Illinois) focused on the use of cell-free systems for the reconstitution of metabolic pathways and bioproduction of monoterpenes. Now he is using an OpenPlant Fund Award to establish cell-free platforms for protein synthesis in Norwich. Read more about this work below, and on www.biomaker.org

As part of this project he is recruiting participants for a workshop on cell-free protein synthesis to be held in mid-June in Norwich. It is an opportunity to try to express your favourite protein using a low-cost, high-throughput platform. Download the poster for details and contact quentin.dudley@earlham.ac.uk for details and questions.

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Cell-free protein synthesis

Cell-free protein synthesis (CFPS) uses crude lysates of E. coli, wheat germ, and other organisms to recapitulate transcription and translation in a test tube (Carlson et al., 2012). This enables protein production at higher throughput, shorter timescales, and simpler troubleshooting compared to expression in cells. While CFPS has several pros/cons, it is particularly powerful when testing many different protein variants/mutations with an output assay that works directly in the crude cell-free reaction.

While CFPS is getting easier to implement, buying commercial kits can get expensive and troubleshooting the first time can be challenging. In response, I’m leading a project sponsored by the OpenPlant fund to establish an in-house E. coli CFPS system (~£1 / rxn) at Norwich/Cambridge and want to compare it to a commercial wheat germ kit (£12 / rxn) for expressing proteins. We are testing a range of different proteins from various plants. If you have an interesting protein you’d like to try expressing in a cell-free system, please contact quentin.dudley@earlham.ac.uk for details!)

I’ve previously worked with CFPS as a graduate student with Michael Jewett at Northwestern University. The Jewett lab is working to develop new CFPS platforms using yeast (S. cerevisiae), chloroplasts, and CHO cells. They also are improving existing E. coli-based systems to synthesize “tricky” proteins that require complex folding environments (membrane proteins, antibodies) or contain nonstandard amino acids. During my time in the lab, I used CFPS to manufacture enzyme homologs which could then be combined to prototype metabolic pathways, for example biosynthesis of monoterpenoids.

It is a very exciting time for cell-free systems. Protein yields have increased to 2 mg/mL and a commercial company (Sutro Biopharma) has reported reaction volumes at 100 L (Zawada et al., 2011). Additionally, cell-free reactions can be freeze-dried on paper and retain full activity; several groups are using this feature to develop on-demand pharmaceuticals or simple, color-changing diagnostics for diseases such as Zika virus (Pardee et al., 2016). As this cell-free technology matures, its flexibility and programmability make it an attractive opportunity for Biomaker projects and future applications will be limited only by the creativity of researchers and developers.

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REFERENCES

Carlson, E. D., Gan, R., Hodgman, C. E., & Jewett, M. C. (2012). Cell-free protein synthesis: applications come of age. Biotechnology Advances, 30(5), 1185-1194.

Zawada, J. F., Yin, G., Steiner, A. R., Yang, J., Naresh, A., Roy, S. M., ... & Murray, C. J. (2011). Microscale to manufacturing scale‐up of cell‐free cytokine production—a new approach for shortening protein production development timelines. Biotechnology and Bioengineering, 108(7), 1570-1578.

Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., ... & Collins, J.J. (2016). Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell, 165(5), 1255-1266.

[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

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)

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.

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

[Closing March 6 - April 10] Several lectureship opportunities at Edinburgh University

Lecturer or Senior Lecturer in Synthetic Biology (vacancy ref: 042732)

We seek an excellent scientist and inspiring teacher who uses synthetic biology methods in research programmes such as genome engineering, biotechnology, metabolic engineering, genetic circuit design and engineering (both in vivo and cell free), bio-sensing, multi-cellularity and tissue engineering, regenerative medicine, novel vaccine development or addresses key questions in molecular or cell biology. The Edinburgh Genome Foundry’s facilities for automated DNA assembly can support large-scale synthetic biology and synthetic genomics research and we would be particularly enthusiastic about research programmes that took advantage of these capabilities.

Closing date – March 22nd

Contact – Prof Susan Rosser (Susan.Rosser@ed.ac.uk)

Lecturer in Biological Mass Spectrometry (vacancy ref: 042692)

We seek an excellent scientist and inspiring teacher who applies mass spectrometry (MS) in innovative ways to tackle major challenges in biology. We are looking for researcher who is addressing key questions in areas such as cell biology, structural biology, immunology, microbiology, biotechnology or systems biology, by exploiting the unique sensitivity, accuracy and resolving power of modern and emerging MS techniques.

Closing date – April 5th 2018

Contact – Prof Paul Barlow (Paul.Barlow@ed.ac.uk)

Lecturer in Computational Biology (vacancy ref: 042673)

We seek an excellent scientist and inspiring teacher who uses and develops computational and modelling techniques to address key questions in biology. We welcome applications from researchers in all areas of computational biology, and we are particularly looking for those working in the following fields: metabolism, such as the application of flux balance analysis and the analysis and interpretation of data from metabolomics and fluxomics experiments; multi-scale modelling of biological systems, including formal modelling techniques and stochastic modelling; and data science approaches to biological research, including the analysis of data from next generation sequencing.

Closing Date - 13th March 2018

Contact – Prof Peter Swain or Prof Guido Sanguinetti (Peter.swain@ed.ac.uk or gsanguin@inf.ed.ac.uk)

Lecturer in Stem cell Biology (vacancy ref 042667)

We seek an excellent scientist and inspiring teacher who addresses key questions in stem cell biology or developmental biology that are directly relevant to stem cell or regenerative biology. We particularly encourage applications from candidates who employ single cell or synthetic approaches

Closing Date – April 10th

Contact – Prof Donal O’Carroll Donal.ocarroll@ed.ac.uk

Lecturer in Molecular Crop Science (vacancy ref: 042668)

We seek a creative scientist and inspiring teacher who applies molecular approaches to address important fundamental and translational questions in plant biology that are relevant to crop improvement and food security.

Closing Date – March 15th

Contact – Prof Andrew Hudson (Andrew.hudson@ed.ac.uk)

Lectureship in Biochemistry (vacancy ref 042671)

This four-year lectureship position offers an outstanding opportunity to develop an independent teaching and research programme. We seek an excellent scientist and inspiring teacher to join a group of successful scientists with teaching and research interests across RNA and cell biology, synthetic biology, systems biology, biochemistry and biotechnology. At Edinburgh we emphasise cross-disciplinary thinking in a collaborative and well-supported environment. You will benefit from this to build your own portfolio of research and scholarship. You will make an important contribution to the development and delivery of high-quality and inspirational undergraduate and postgraduate teaching, including the opportunity to develop eLearning and on-line education initiatives. You will have a PhD in a relevant area of biology or chemistry and a published record of research, along with a successful track record of developing innovative and engaging teaching.

Closing Date – March 6

Contact – Prof Paul Barlow (paul.barlow@ed.ac.uk)

For all roles, please apply online at vacancies.ed.ac.uk

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