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 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

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

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

 Editing videos that explain how the focus stacking system works

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

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 ( 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:

[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 (


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 (


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 ( or


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


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 (


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 (


For all roles, please apply online at

Eleven projects pitch for funding from the OpenPlant Fund

 Aleksandr Gavrin pitching his proposal.

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 and documentation of OpenPlant Fund projects can be found at

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

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

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

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

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

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.

Screen Shot 2018-02-19 at 11.14.07.png

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

[Closes 22 Mar 2018] Vacancy for Lecturer or Senior Lecturer in Synthetic Biology at University of Edinburgh

Vacancy: Lecturer or Senior Lecturer in Synthetic Biology

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.

You will have the ability, enthusiasm and breadth of vision required to be a future leader in this rapidly moving field. You will pursue an independent research programme, working collaboratively and leading a team. You must have an established track record of relevant publications and the potential to win future investment in research, and will be expected to engage with both commercial and public research users and funders. You will be enthusiastic about teaching and student-centred learning for both undergraduate and postgraduate students.

The University of Edinburgh is a vibrant, research-driven community offering opportunities to work with internationally leading academics whose visions are shaping tomorrow’s world. The School of Biological Sciences is one of the UK’s largest and most highly rated life sciences departments, providing an innovative environment for research and teaching with a strong emphasis on interdisciplinary research. SynthSys, the Centre for Synthetic and Systems Biology, is one of the largest groupings of systems and synthetic biologists in the UK with expertise ranging from microbes to mammalian cells working on applications in biotechnology and medicine as well as contributing to foundational and fundamental research. SynthSys is highly multidisciplinary with members from the schools of engineering, informatics, chemistry, physics, social sciences, medicine as well as biological sciences. You will join a team of group leaders working at the interface between molecular cell biology and quantitative science, with strong links in biotechnology.

Informal enquiries: Prof Susan Rosser

This posts are full time and open ended.

Salary: UE08 £39,992 - £47,722 per annum / UE09: £50,618 - £56,950 per annum

Closing Date: Thursday 22nd March 2018 at 5pm (GMT)

To apply: search for #042732

Postdoc representatives sought for University of Cambridge Open Research Working Group


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

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

Remit of the Working Group

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

Level of Commitment

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

Contact if you are interested in this opportunity.

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


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

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

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

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

Apply now >>

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

[Closes 16 April] Accepting applications for the 2018 Cold Spring Harbor Laboratory Summer Course in Synthetic Biology


We are now accepting applications for the 2018 Cold Spring Harbor Laboratory Summer Course in Synthetic Biology. We encourage you, your colleagues, and/or your trainees to apply if…

  • You are a scientist whose training is well underway (senior graduate student to junior faculty and beyond).
  • You are interested in steering your research in a new direction, towards synthetic biology.
  • You are interested in a multi-disciplinary approach to biology and bioengineering. We encourage students of all backgrounds, whether the very biological or very theoretical, to apply!
  • You work in the field of synthetic biology and are interested in new techniques.

Since the course began in 2013, industry professionals, graduate students, postdocs, science educators, and junior faculty have completed our immersive two-week laboratory class. The Course will focus on how the complexity of biological systems, combined with traditional engineering approaches, results in the emergence of new design principles for synthetic biology. Students will work in teams to learn the practical and theoretical underpinnings of cutting edge research in the area of Synthetic Biology. In addition, students will gain a broad overview of current applications of synthetic biology by interacting with a panel of internationally-recognized speakers from academia and industry during seminars, lab work, social activities.

Scholarships: Several stipend awards are available for applicants who are accepted into the course. Please read details about the available stipend awards at:

In order to be considered for an award, you must specifically reference which one you are eligible for in the Stipend Request section of your application.

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


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

Registration for Crossing Kingdoms is now open.


Abstract submission

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

List of confirmed speakers:


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

Download the conference poster for your noticeboard


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

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

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

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

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

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

 For more information and to apply >>

[Closes 20 Feb 2018] Synthetic Biology Postdoc at Earlham Institute

OpenPlant PI Dr Nicola Patron is looking for a Postdoctoral Research Scientist to work on a European Research Area (ERA) CoBioTech collaborative project based in the Patron Lab at the Earlham Institute. The project will use will use synthetic biology, comparative transcriptomics, metabolic engineering and genome editing/engineering techniques to develop plants and fungi as low-cost, sustainable production platforms for biosynthesis of insect pheromones..

Apply now >>
Closing date 20th February 2018


[Closes 14 March 2018] NSF-USDA-BBSRC Joint Funding Opportunity to Develop Breakthrough Ideas and Enabling Technologies to Advance Crop Breeding and Functional Genomics

The National Science Foundation (NSF) Biological Sciences Directorate (BIO), the U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) and the UK's Biotechnology and Biological Sciences Research Council (BBSRC) have established a joint funding opportunity to support the development of breakthrough technologies that will enable significant advances in crop breeding. This opportunity aims to make high impact changes in the ability to translate basic knowledge of plant genomics to practical outcomes in crops of economic importance to the participating countries.

This NSF-BIO, USDA-NIFA and BBSRC Joint Activity is soliciting Early Concept Grants for Exploratory Research (EAGER) proposals to support development of breakthrough ideas and technologies to speed the development for new crop varieties.

See more information below and at this page >>

There remain significant bottlenecks to improving crop varieties even if new traits or natural variants are identified, such as producing hybrids, understanding recombination, and epigenetic inheritance as examples. Translation of basic knowledge to practical outcomes can be accelerated by key emerging technologies that exploit genomics rapidly and effectively. This EAGER opportunity invites proposals to overcome these barriers to crop breeding in highly innovative and transformative ways. Investigators considering this opportunity should articulate how the enabling technologies would be used to improve crop breeding.

Areas of research that await breakthrough advances and are appropriate for this EAGER opportunity include, but are not limited to, the following:

  • Advancing genome editing technology to generate new phenotypes for greater genetic gain
  • Achieving reliable and high throughput production of doubled haploids from genotypes that are currently recalcitrant to chromosome doubling to accelerate the breeding process in cereals and other crops
  • Controlling and understanding meiotic recombination to tap into inaccessible genetic resources in areas of low recombination and enabling whole genome manipulation
  • Modifying epigenetic inheritance to facilitate phenotypic changes related to environmental responses
  • Understanding mechanisms of heterosis, thereby generating and exploiting hybrid vigor for crop improvement

For this EAGER opportunity, emphasis should be on developing enabling technologies that will impact crops or model crop systems. Projects that focus solely on sequencing will not be considered. Funded projects relevant to the goals of the International Wheat Yield Partnership (IWYP) will be invited to become IWYP Aligned Projects.

Proposed studies should be potentially transformative and must be considered "high-risk, high-payoff" to achieve the goal of making technological breakthroughs to promote crop breeding. Studies should be compatible with the budget (up to $300,000 for US components and up to £200,000 for UK components) and time limits (2 years) of the EAGER funding mechanism. For collaborative US/UK EAGER projects, BBSRC will fund UK researchers up to £200,000 and NSF or NIFA will fund US researchers up to $300,000 including indirect costs. US only EAGERS are limited to $300,000 total including indirect costs. Further details are provided below for budgetary limits for UK partners. EAGER proposals may originate from US-UK partnerships or from US-only applicants. EAGERs solely involving UK applicants are not permitted. For more information on EAGERs, please review NSF Proposal & Award Policies & Procedures Guide (PAPPG).

More information >>


Bio-solar panel developed by researchers at University of Cambridge and Imperial College London

A two-in-one solar bio-battery and solar panel has been created by researchers who printed living cyanobacteria and circuitry onto paper.

Cyanobacteria are photosynthetic micro-organisms that have been on Earth for billions of years. They are thought to be the primary reason why the Earth’s atmosphere is oxygen rich. Several synthetic biology groups in Cambridge are working on these useful organisams, including OpenPlant PI Prof Chris Howe and OpenPlant Fund grantee Dr Paolo Bombelli (both Department of Biochemistry).

Together with researchers from Imperial College London and Central Saint Martins, they demonstrated that cyanobacteria could be used as an ink and printed from an inkjet printer in precise patterns onto electrically conductive carbon nanotubes, which were also inkjet-printed onto the piece of paper. The team showed that the cyanobacteria survived the printing process and were able to perform photosynthesis so that small amounts of electrical energy could be harvested over a period of 100 hours.

A bio-solar panel made in this way, the approximate size of an iPad, could power a simple digital clock, and in separate experiments, a small LED light bulb.

The team suggest their breakthrough could lead to new types of electrical devices that are made from paper and printed photosynthetic bacteria. These could include disposable power supplies integrated into paper-based sensors for monitoring patients with diabetes or devices that resemble wallpaper but are in fact environmental sensors for monitoring air quality in the home.

Dr Marin Sawa, a co-author from the Department of Chemical Engineering at Imperial College London, said: “We think our technology could have a range of applications such as acting as a sensor in the environment. Imagine a paper-based, disposable environmental sensor disguised as wallpaper, which could monitor air quality in the home. When it has done its job it could be removed and left to biodegrade in the garden without any impact on the environment.” 

New type of renewable energy

The solar bio-battery pushes forward research into a new type of renewable energy technology currently being developed by scientists globally called microbial biophotoltaics (BPV). It exploits the ability of cyanobacteria and other algae that use photosynthesis to convert light energy into an electrical current using water as the source of electrons.

One of the advantages of using BPVs to harvest energy from cells like cyanobacteria is that they can produce small amounts electricity in daylight and carry on producing it even in the dark from molecules produced in the light.

Some of the current limitations that scientists have previously faced when developing BPVs are that they are expensive to make, have low power output, and a short lifespan. All these drawbacks have prevented scientists from being able to scale up the technology to an industrial level.

The team says their approach of using an off-the-shelf inkjet printer to construct BPVs demonstrates a potential method for easily scaling up the technology, which may pave the way for its wider use.

Dr Andrea Fantuzzi, a co-author of the study from Department of Life Sciences at Imperial College London, said: “Paper-based BPVs are not meant to replace conventional solar cell technology for large-scale power production, but instead, could be used to construct power supplies that are both disposable and biodegradable. Their low power output means they are more suited to devices and applications that require a small and finite amount of energy, such as environmental sensing and biosensors.”

New types of paper-based sensors

The researchers suggest BPVs could be used in new forms of sensors built entirely from paper, which would mean that they are cheaper and more cost effective to make with less impact on resources and the environment.

Another example for BPVs, suggest the team, is in the healthcare industry.

Dr Andrea Fantuzzi said: “Paper-based BPVs integrated with printed electronics and biosensor technology could usher in an age of disposable paper-based sensors that monitor health indicators such as blood glucose levels in patients with diabetes. Once a measurement is taken, the device could be easily disposed of with low environmental impact and its ease of use could facilitate its direct employment by the patients. Furthermore, this approach has the potential to be very cost-effective, which could also pave the way for its use in developing countries with limited healthcare budgets and strains on resources.”

Next steps

The current paper-based BPV unit is a palm size. The next step will see the team scale up their proof-of-concept to A4 size to determine the electrical output on a larger scale.

Professor Christopher Howe, a co-author from the Department of Biochemistry at the University of Cambridge, added: “This is an exciting proof-of-concept. The challenge now is to make panels that are more powerful, long-lasting and robust.”


Sawa, Marin, Andrea Fantuzzi, Paolo Bombelli, Christopher J. Howe, Klaus Hellgardt, and Peter J. Nixon. "Electricity generation from digitally printed cyanobacteria." Nature Communications 8, no. 1 (2017): 1327.

Press release text is from Imperial College London and is available under an Attribution-NonCommercial-ShareAlike Creative Commons license.

Image credit: From publication, licensed under CC-BY 4.0

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

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

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

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Application: March 31, 2018

Oral Presentation/Poster Submission: March 31, 2018

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

Register here >>

Keynote Speakers

* PATRICK YIZHI CAI, University of Manchester, UK

* JOHN GLASS, J. Craig Venter Institute, USA

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

* JENS NIELSEN, Chalmers University of Technology, Sweden

* HARRIS WANG, Columbia University, USA


* LUCA ZAMMATARO, Yale University, USA


* Barbara Di Camillo, University of Padova, Italy

* Simone Furini, University of Siena, Italy

* Emanuele Domenico Giordano, University of Bologna, Italy

* Rodrigo Ledesma-Amaro, Imperial College London, UK

* Velia Siciliano, Italian Institute of Technology, Italy


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

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

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

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

I am very excited by the prospect that some day this research could address one of the greatest limitations to agricultural productivity
— Prof Giles Oldroyd, SLCU

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

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

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

Prof Giles Oldroyd's homepage at SLCU >>

Essex Synthetic Biology Summer School: 2-6 July 2018

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

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

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

Learn more and register by 1 June 2018 >>>

[Closes 5 March 2018] 2018 CSIRO Synthetic Biology Future Science Fellowships

The CSIRO Synthetic Biology Future Science Platform (SynBioFSP) is pleased to announce the opening of the second round of CSIRO Synthetic Biology Future Science Fellowships. The scheme aims to attract outstanding national and international early-career post-doctoral researchers (equivalent to Australian Academic Levels A and B, or in exceptional circumstances, Level C) to expand Australian research capacity in synthetic biology. A key element of the SynBio FSP is establishment of a collaborative community of practice extending across CSIRO and Australia more broadly, and linking into international efforts in the field. Research projects must demonstrate an ability to build Australian capacity in synthetic biology.

Fellowships will be hosted at a Host Organisation (usually an Australian University, but other Australian research organisations may also be eligible) and will be a partnership between the Fellow, CSIRO, and the Host Organisation. Fellows will be employed by the Host Organisation but will maintain a strong linkage to CSIRO through a partnering CSIRO Mentor(s) and various joint activities designed to support development of a synthetic biology community of practice across Australia. Fellows will have a Visiting Scientist appointment at CSIRO and may spend a portion of time physically located within a CSIRO research group if appropriate for the Fellowship project.

The SynBio FSP is built on a philosophy of responsible development of synthetic biology technology, striving for ethical outcomes and working within the bounds of social acceptance. Project proposals in the social sciences, as well as in lab-based research, are encouraged.

How to apply?

Further information and application instructions for the Fellowships are available at:

Applications must be submitted by 5pm Australian Eastern Standard Time, Monday 5th March 2018.

Further enquiries can be directed to:  

We strongly encourage women, people of Australian Aboriginal and/or Torres Strait Islander descent, and other minority groups to apply.

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

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


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

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

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

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

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

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



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


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

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

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

  • Bioluminescent bacteria
  • Fabrics dyed with synthetic ink from bacteria
  • Micro-organisms expressing plant metabloic pathways to produce rose and patchouli scents
  • Design-a-plant
  • Dave the DNA Robot

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

Please register via this form or for more information, email