8 Years of OpenPlant

As the final round of OpenPlant funding comes to a close, we look back on the past eight years of work contributing to academic excellence in plant synthetic biology, open and responsible research and creating a community of like-minded scientists across Cambridge and Norwich.

In 2015, OpenPlant was established as one of six National Synthetic Biology Research Centres. A collaboration between the University of Cambridge, the John Innes Centre and the Earlham Institute, OpenPlant was founded with three aims:

1. to​ ​create​ ​a​ ​hub​ ​for​ ​interdisciplinary​ ​exchange​ ​between​ ​Cambridge​ ​and​ ​Norwich,​ ​between the​ ​fundamental​ ​and​ ​applied​ ​sciences,​ ​that​ ​will​ ​underpin​ ​advances​ ​in​ ​UK​ ​agriculture​ ​and bioproduction.

2. to​ ​establish​ ​systems​ ​for​ ​the​ ​open​ ​exchange​ ​of​ ​new​ ​plant​ ​tools​ ​and​ ​DNA​ ​components that​ ​will​ ​promote​ ​commercial​ ​innovation​ ​and​ ​international​ ​scientific​ ​exchange.

3. to​ ​explore​ ​the​ ​wider​ ​implications​ ​of​ ​the​ ​technology​ ​at​ ​local​ ​and​ ​global​ ​scales.​ ​This​ ​will bring​ ​together​ ​a​ ​wide​ ​range​ ​of​ ​engineers,​ ​scientists​ ​and​ ​policy​ ​developers​ ​to​ ​explore new​ ​technologies​ ​and​ ​possible​ ​models​ ​for​ ​sustainable​ ​agriculture,​ ​bioproduction​ ​and land​ ​use.

Over the years, these aims have been achieved in various ways, including over 230 academic publications, 90 invited lectures, 130 collaborations, 320 engagement activities and 8 spin-outs, amongst others. To round up our achievements we wanted to highlight a few of the areas in which we believe OpenPlant has excelled and added immense value, both to the academic community and beyond.

Development of New Tools and Technologies

As set out in our original aims, the development of new tools for plant synthetic biology has been a core element of OpenPlant throughout the years. This aspect has focused not just on creating new tools, but also on ensuring that our research tools can be shared and freely used by academia and industry across the world. This “two-tier” model of innovation highlights the need for a shared base of basic resources that can be used to make innovation both more efficient and more equitable. OpenPlant has been instrumental in helping to develop this shared base of tools for the plant science community. Achievements include the development of multiple plant synthetic biology toolkits, including the OpenPlant toolkit, the Cyanogate toolkit and the Chlamydomonas reinhardtii MoClo toolkit, as well as the development of more efficient transformation systems in wheat. Additionally, the establishment of a common syntax for plant DNA parts and the development of the OpenMTA, have allowed open sharing and reuse of our materials.

OpenPlant Toolkits

Wheat Transformation

Common Syntax

OpenMTA

Training and Career Development

Beyond our core research, OpenPlant has also worked hard to support our researchers with training and career development. Over the years, OpenPlant has employed 56 postdocs, students, research assistants and administrators, along with 23 group leaders. Of those, 23% have gone on to lead their own research groups, 16% have gone into industry, and 5% have gone into policy work. Workshops and initiatives to support our staff and students have included 14 technical training courses, 98 teams participating in the Biomaker Challenge, 73 teams funded by the OpenPlant Fund and two No-Code Training for Biology courses for researchers at Cambridge and Norwich.

Biomaker Challenge

OpenPlant Fund

No-Code Programming for Biology

OpenPlant Events

Influence on Policy, Practice & the Public

In line with the OpenPlant ethos of open and responsible research and innovation, we have made a concerted effort to understand and translate our research in the wider context of society, into policy, education and public engagement. Projects such as DNA Dave and Global Garden Workshops, as well as our long-standing collaborations with the Science and Art (SAW) Trust have communicated work done by OpenPlant researchers to the general public, as well as inspiring young scientists to engage with art and science practice. The SynBio4Schools initiative has also brought plant synthetic biology into schools, introducing students and teachers to cutting edge research aligned with the UK national curriculum. OpenPlant researchers have also contributed to discussions on development of appropriate regulation for new genome editing technologies, for example through workshops and seminars for DEFRA, contributions to the Food Standards Agency advisory committee, horizon scanning workshop and public dialogue. OpenPlant working groups have also addressed the use of genetic resources in the age of the Nagoya Protocol, capacity building for the bioeconomy in Africa and the development of an Open Material Transfer Agreement.

Engaging Society

SynBio 4 Schools

Regulation of Genetic Technologies

Working Group Reports

Further Funding and Spin-outs

As a testament to the success of OpenPlant in academic excellence and collaboration building, OpenPlant research has attracted over £35.5 million in follow-on funding. This additional funding will allow the important work done by OpenPlant to continue, and has included funding for continuing collaborations between Cambridge and Norwich, including the Engineering Biology Transition Award granted to OpenPlant PIs Anne Osbourn, Nicola Patron, Jenny Molloy and Jim Haseloff. Moreover, OpenPlant is proud to have supported the establishment and growth of eight spin outs including Beneficial Bio, Colorifix, Persephone Bio, Leaf Expression Systems, Iceni Diagnostics, The Smarter Food Company, Tropic Biosciences and HotHouse BioEngineering.

Engineering Biology Transition Award

Sustainable Bioeconomy

OpenPlant Publications

OpenPlant Reports

Finally to say, the work of OpenPlant could not have been achieved without the commitment and dedication of our staff and students, and we would like to say thank you to everyone who has worked with, and engaged with, OpenPlant over the last eight years. OpenPlant has provided a core hub​ ​for​ ​interdisciplinary​ ​exchange​ ​between​ ​Cambridge​ ​and​ ​Norwich and we hope that collaborations between the OpenPlant partners continue to thrive and drive forward cutting edge and responsible research in future.

Publication: Discovery of putative Golgi S-Adenosyl methionine transporters reveals the importance of plant cell wall polysaccharide methylation

OpenPlant PI Professor Paul Dupree recently published work in collaboration with colleagues from the University of Cambridge, The Andrés Bello National University, University of Warwick and Massachusetts Institute of Technology describing the identification of putative transporters that import SAM into the Golgi lumen in plants, providing new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

Henry Temple, Pyae Phyo, Weibing Yang, Jan J. Lyczakowski, Alberto Echevarría-Poza, Igor Yakunin, Juan Pablo Parra-Rojas, Oliver M. Terrett, Susana Saez-Aguayo, Ray Dupree, Ariel Orellana, Mei Hong, Paul Dupree

https://www.biorxiv.org/content/10.1101/2021.07.06.451061v1

Abstract

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, to date, no Golgi SAM transporter has been identified in plants. In this work, we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knock-out of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesised polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, the NMR revealed the existence of pectin ‘egg-box’ structures in intact cell walls, and showed that their formation is enhanced by reduced methyl-esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters that import SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

Vacancy: Postdoctoral Research Associate

Postdoctoral Research Associate, Developing Forecasts of Environmental Risk to Carbon Stocks in Nature-based Systems, Forest Ecology Group (Coomes Lab), Cambridge Centre for Carbon Credits (4C), University of Cambridge, Cambridge UK.

The Position

You will help to develop a standardised approach to forecast the expected permanence in carbon stocks of nature-based projects, as influenced by human activities, climate change, and other disturbance events. You will stochastically extend an existing deterministic difference-in-difference analysis so that it can be used to estimate the expected permanence of nature-based carbon stores and credits derived from them.

The modelling will involve combining a variety of different risks, from climate change to the socio-economic drivers of deforestation, and how these are modified through project interventions. Your work will necessitate foundational work on risk-modelling and its application to our automated system for generating and valuing carbon credits.

Salary: £33,309 - £40,927

Application deadline: 5 April 2022

More information on this position can be found here.

Vacancy: Postdoctoral Research Associate

Assessor of Carbon Sequestration by Nature-based Climate Solutions, Forest Ecology Group (Coomes Lab), Cambridge Centre for Carbon Credits (4C), University of Cambridge, Cambridge UK.

The Position

The successful candidate will join the Cambridge Centre for Carbon Credits (4C) which aims to verify the claims and consequences of carbon credit generating activities, to ensure these have the most beneficial impact as we transition to a net-zero future.

You will assess and track changes in carbon stocks working with other research groups and private sector partners. You will bring together appropriate, trusted primary observations from ground-based surveys with remote sensing datasets to measure and track carbon stocks through time. The contexts would include key ecosystems, such as forests and peatlands. The data products should scale to the global level and will be used as an input to our automated system for generating carbon credits.

Salary: £33,309 - £ 40,927

Application deadline: 5 April 2022

More information on this position can be found here.

Churchill Fellowship

The Churchill Trust is proud to announce that a new Churchill Fellowship will be offered from 2022 to honour the memory and legacy of the late Saskia Beer, made possible through the generous sponsorship of Colin and Maggie Beer.

Churchill Fellowships are an internationally recognised award, providing access to expertise from around the world. Applicants are empowered to design their own projects, enabling them to explore international best practice and innovation that can be applied in Australia. There is a high level of visibility and credibility associated with becoming a Churchill Fellow, as well as a responsibility to share the knowledge and skills gained overseas with the Australian community. No prescribed qualifications are required to apply for a Churchill Fellowship and the subject of proposed projects is limitless, provided there is evidence of a benefit to Australia.

Application deadline: 28 April 2022

More information about this fellowship can be found here.

EFSA Traineeships Call 2022

The European Food Safety Authority (EFSA), based in Parma, Italy is opening positions for trainees.

The position

Under the supervision of your traineeship adviser within the unit of assignment, you will have the opportunity to:

• Get a first-hand experience into the work of a scientific EU Agency, developing new competencies and skills in line with your personal interests and professional aspirations;

• Contribute to the overall objectives of the unit by supporting in drafting documents and reports, handling scientific and/or administrative work, and ensuring timely communication of outcomes;

• Contribute to specific projects and activities with new ideas and innovative solutions;

• Contribute to the planning and monitoring of the unit’s activities;

• Participate in several trainings which will help you grow professionally.

Application deadline: 25 April 2022

More information about the position can be found here.

Vacancy: Bioinformatician

Applications are invited for a Bioinformatician to join the Laboratory of Dr Falk Hildebrand at the Earlham Institute.

The role:

This post requires an experienced bioinformatician with an interest to study reconstructed microbial genomes in metagenomes (bacterial, archaeal, fungal). The post-holder will be involved in conceptualizing & implementing bioinformatic pipelines to analyse large time-series metagenomes (human gut, soil, …), based on data from 2nd and 3rd gen sequencing platforms, such as illumina, PacBio, ONT, Hi-C & single cell sequencing data. The analysis will be published in research papers that the candidate should be leading.

Salary range: £32,578 - £39,938

Application closing date: 14 April 2022

More information about this position can be found here.

OpenPlant and the SAW Trust launch a new synthetic biology resource for schools

Synthetic Biology is seen as an emerging and important multidisciplinary field, that is currently under-represented in the national curriculum and teaching resources. Collaborating with the Science, Art and Writing (SAW) Trust, researchers from across OpenPlant have produced SynBio 4 Schools; a free to use, comprehensive package of educational resources that focuses on teaching the principles of plant synthetic biology for GCSE and A Level students.

SynBio4 Schools

Inspiring the next generation of biological engineers.

Go to resource

The new resource was officially launched last month with the hosting of a live, online launch event. Teachers were invited to join the event and ask any question they might have on delivering the resources and were given the opportunity to hear more about the science behind the resource activities from some of the scientists who created them; Professor Julea Butt (University of East Anglia), Dr Nicola Patron (Earlham Institute), Dr Roger Castells Graells (University of California, LA) and Dr Shannon Woodhouse (John Innes Centre).  Dr Paolo Bombelli, who also created a resource recorded a step–by-step video on how to build a plant microbial fuel cell to compliment the set.

SynBio 4 Schools is comprised of a downloadable booklet, which covers an introduction to synthetic biology and its applications, step-by-step guides to 4 practical activities for schools to conduct and a supporting teacher notes booklet which highlights the relevance of each activity to the British school science curriculum.  There are also two videos; the previously mentioned ‘Build Your Own Plant Microbial Fuel Cell’ with Paolo Bombelli, and four introductory videos to each of the SynBio 4 Schools Activities.

Topics covered include; Building DNA Circuits, Generating Electricity From Plants, What Can Viruses Do For You? and Natural Product Synthesis. It is hoped that these activities will help schools engage more with synthetic biology practises, whilst inspiring the next generation of biological engineers.

All resources are available via the OpenPlant website and are free to use.

Vacancy: Postdoc Position - Plant Molecular Biology

Postdoc Postion, Elina Lab, Crop Science Centre, Cambridge

A post-doctoral position in Dr Natasha Yelina’s lab working on meiosis in model and crop plants at the Crop Science Centre, University of Cambridge.

Closing date: January 23rd.

For more information visit the University of Cambridge website.

https://www.jobs.cam.ac.uk/job/32757/

Independent Research Fellowships

The John Innes Centre are welcoming applications from who either hold, or wish to apply for Independent Research Fellowships (such as a UKRI Future Leaders Fellowship, or a Royal Society University Research Fellowship).

Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 7 February 2022.

To apply email a two-page summary of your research plan, a copy of your CV and arrange for three letters of recommendation to be emailed to fellows@jic.ac.uk

Closing date December 3rd 2021

For more information - https://www.jic.ac.uk/vacancies/independent-research-fellowships/

sciTAG: a label design and printing app created by scientists for scientists

Proper labelling practices in the lab is one of the first things students are taught at the practical courses. As a matter of fact, labelling is an essential part of data management for scientists while working in the laboratory. And if you ever worked in a lab, you must know how much time you usually spent to label every single tube, falcon, vial, bottle etc.

The Problem

Appropriate labelling is an essential research practice. It is fundamental to day-to-day operation and long-term sample storage in laboratories. Creating labels with handwriting is convenient, adaptable, and often the standard method scientists use. However, variabilities in label format and illegible messy handwriting can both lead to flawed and/or erroneous communication, resulting in, for example, loss of important biological samples. Moreover, writing labels by hand for large scale experiments or a high number of samples is time-consuming and creates ergonomic stress. The problem presented called for a labelling method that is automated, user-friendly, and affordable.

The Project

We proposed to develop an IOS app that allows biological and medical laboratories to operate in a consistent and efficient manner, by making label design and printing more accessible.

We envisaged an app which is user-friendly, automated, and compatible with affordable label printers. To accomplish our goal, we followed a stepwise approach composed of three parts: user interface design, technical structure of the app and testing the app.

Efficient label creation frees scientists from the laborious task of writing labels by hand. Consistently and systematically designed labels ensure samples stored for long term are readable and used accurately. The app will be free, meaning that convenient label printing will be accessible to the wider scientific community.

What Has Been Achieved So Far?

Our team of five is composed of a molecular biologist, a microbiologist, a geneticist, a bioinformatician and a software developer. We started by self-teaching ourselves how to design and develop an app since most of us never worked on app development before.

Interface design decisions were made not only to be attractive to potential users, but also to be functional and simplistic as possible. One aspect of the design is visual elements. We decided on aesthetic choices such as a colour scheme throughout the app. We considered colour blindness since 4.5% of the global population experience colour-blindness. Next, we decided on the name of the app: sciTAG. We did market research to make sure this name is not a trademark. Finally, we designed an app logo depicting a double-stranded DNA alongside the name of the app.

From left: Junyan Liu (Postdoctoral Researcher, Sanger Institute), Marta Matuszewska (PhD student, Department of Veterinary Medicine, University of Cambridge) Begum Akman (Research Associate, Department of Pharmacology, University of Cambridge), Chuqiao Gong (Software developer, EMBL-EBI), Ellis Kelly (PhD student, Department of Genetics, University of Cambridge)

Then, we identified the features that are crucial for our target audience. We divided the label design into two blocks by keeping it as simple as possible with choices included to create a good label.

From left to right: home screen, label design screen, prototype label in PDF format.

Next step was to layer the technical structure: first user input information used to create a printable object such as PDF. Second, to convert this object to a storable object within the app. Finally, the app had to be compatible with commercially available label printers.

What’s Next For The sciTAG Team?

With the help of the Biomarker Challenge funding, we sourced several label printers available in the market to test sciTAG app. Among these printers only one of them is specific for lab settings (very expensive!) and others are highly affordable printers that we sourced from different companies. We distributed these printers within the team, and we are planning to complete the sciTAG prototype, start testing and reporting our experiences.

After the successful tests from the team, we are planning to recruit five laboratories within University of Cambridge to further test and optimize the sciTAG app. Eventually we are aiming to make sciTAG freely available to the science community on the App Store. Further down the line we also would like to consider making our app available for android users.

Vacancy: Biofoundry Manager

Biofoundry Manager

Applications are invited for a Biofoundry Manager to join the Engineering Biology Programme at the Earlham Institute, based in Norwich.

Closing date: November 25th.

For more information visit the Earlham Institute website.

https://www.earlham.ac.uk/biofoundry-manager

Synthetic Biology UK 2021

Synthetic Biology UK 2021 will be hosted by Synthetic Biology Research Centre Nottingham, and will focus on a number of burgeoning new areas of activity, including the engineering of microbial communities, microbial-plant interactions and applications for the sustainable manufacture of materials, the circular economy and climate mitigation strategies.

Date: November 22nd

For more information and to register visit:

https://www.eventsforce.net/biochemsoc/frontend/reg/thome.csp?pageID=53019&eventID=108&CSPCHD=0000010000005HOPapInI12EMFR969aLR0xa4Zi1NHfz6Lg5Pw