OpenPlant Fund project reports
This is a list of projects funded by OpenPlant in 2015. Full research reports will be added to this page soon!
- The Big Algal open Experiment
Dr Paolo Bombelli, Biochemistry, University of Cambridge. Dr Brenda Parker, Biochemical Engineering, UCL. Dr James Lawrence, Biochemical Engineering, UCL. Marc Jones, PhD student in Computational and Systems Biology, John Innes Centre
Algae are amazing: they recycle over half of the carbon dioxide we exhale, and form the basis of many food chains, yet we still understand very little about how they grow. In future, we may wish to cultivate algae for food, fuel, or to clean up waste water so we need to understand more about their biology! With this in mind, we have set up the Big Open Algae Experiment to help us enhance our knowledge by performing the biggest parallel algae experiment in history.
- Wireless, portable, low cost, open source hardware for monitoring plant electrophysiology
Pakpoom Subsoontorn has a Ph.D. in Bioengineering from Stanford university and currently works as a postdoctoral researcher at department of plant science, University of Cambridge. Sakonwan Kuhaudomlarp is pursuing a Ph.D. in Plant Sciences and Microbiology at the John Innes Centre. Kyle Lopin received a Ph.D. in Physiology and Biophysics from Case Western Reserve University. Settha Tangkawanit received the B.Eng. degree in Computer Engineering and M.Eng. degree in Electrical Engineering from Naresuan University. He currently works at the Department of Electrical and Computer Engineering, Faculty of Engineering, Naresuan University, Thailand.
Plant electrical signalling regulates a wide range of physiological functions including stress responses to drought and wounding. Existing tools for monitoring such signals often require the uses of cumbersome and expensive equipment in well-controlled laboratory. We aim to create a low-cost measurement tools that can function robustly in the field, collecting electrical activity profiles from multiple plants. We have tool prototype for measuring plant electrical signal coupled with radio modules for long-distance data collection. This prototype (estimated cost £40) can sense and transmit signals from Venus flytrap responding to tactile inputs (see this video for demonstration). The tool can distinguish the action potential from other disturbance.
- Whiskeroscope: rodent whisker inspired sensor for use in analysis of plant tissue structure
Jan Lyczakowski, PhD student working with Prof Paul Dupree in the Department of Biochemistry, University of Cambridge. Abhimanyu Singh, Information and Computer Engineer, BA, MEng, Cambridge University. Christie Nel, Computer Engineer, BEngSci, Stellenbosch University
Understanding mechanical properties of plant biomass is crucial for multiple industries, e.g. building construction and production of lignocellulosic biofuels. Current methods to analyse mechanical properties of biomass are slow and provide little accuracy. We have developed a novel sensor to evaluate stiffness of plant stems. The device is inspired by rodent whiskers and relies on two inputs, obtained using thin steel rod, to quantify stiffness. The instrument successfully discriminated between materials with unlike mechanical properties (steel and foam) and differently aged stem samples from willow. Whiskeroscope was also applied to study Arabidopsis thaliana stems with altered composition of cell walls.
- Open Pi-Image: A low cost-open source plant growth imaging and analysis platform
Professor Alex Webb, Department of Plant Sciences, Downing Street, Cambridge. Dr Dan MacLean, Head of Bioinformatics, The Sainsbury Laboratory
We have designed and constructed a near infrared image capture system based on a Raspberry Pi computer, PiNoir camera and custom 3D printed parts. This runs an extensible and modular open source software suite we developed called Open Pi Image that controls automated image capture and spawns image analysis. The Pi software can be accessed on any external system (e.g. a laptop) via a web server running on the Pi and the system can be embedded in inaccessible places. Open Pi Image is designed to incorporate new user provided scripts for analysis and can be easily extended and customised.
- Open Labware for plant electrophysiology
Dr. Carlos A. Lugo, postdoctoral researcher in the bioinformatics group in The Sainsbury Laboratory. Dr. Marco Aita, University of Cambridge/Wellcome Trust Senior Internship for Interdisciplinary Research Fellow. Mr Christian R. Boehm, PhD student in Plant Sciences at Haselhoff’s Lab in the university of Cambridge, Mr Guru Vighnesh Radhakrishnan, PhD Student at the John Innes Centre in Prof. Giles Oldroy’s group. Dr Marielle Vigouroux, Bioinformatics and Computational Biology, John Innes Centre
In order to investigate electrical responses to mechanical and other external stimuli, our project consisted of replicating an open source Arduino shield which receives, amplifies and transmits “ECG”s from plant tissues into a computer or other circuits. We harnessed the electrical signals to trigger responses in a) other plants, b) other circuits. The resultant board’s schematics and other experimental tools such as manipulators and signal transducers are published on a dedicated project page including files for producing boards and 3D printed parts. A number of kits are available to give away to schools and labs interested in the system.
- Developing novel selection markers for plant transformation to advance live-imaging techniques
Fernan Federici, assistant professor at Department of Molecular Genetics and Microbiology, director of the Synthetic Biology Centre at PUC University-Chile and research associate at Cambridge University. Katharina Schiessl, Post Doc working on nodule organogenesis in the Oldroyd Group at the John Innes Centre. Leonie Luginbuehl is a PhD student in the Oldroyd group at the John Innes Centre; studying the transcriptional regulation during symbiosis signalling in Medicago; experience in Golden Gate cloning, hairy root transformation, nodulation and mycorrhization assays. Guru Rhadakrishnan, PhD student working with Giles Oldroyd at the John Innes Centre on the evolution of signalling events during plant-microbe interactions; expertise in Marchantia transformation.
A total of 25 DNA parts were synthesized, including tissue specific promoters and coding sequences of fluorophores and chromophores. Level 1 and level 2 GOLDEN GATE plasmids were generated and transformed into Medicago Hairy roots. Subsequently, selection markers were tested to see if they were detectable under the stereomicroscope and images were taken using confocal microscopy. It was found that the nuclear-envelope localised fluorophore dtomato, expressed under the Lotus UBIQUITIN promoter, was detectable under the stereomicroscope and could therefore provide a novel selection marker for live imaging. Furthermore, it was found that the BEARSKIN promoter was not detectable in the lateral root cap but expressed at the base of the induced hairy root callus. No significant colour change was observed in the roots transformed with the chromoproteins.
- Responsible Innovation and Open innovation with Large BioResources: Goals, Challenges and Proposals
Dr Kathy Liddell, Herschel Smith Senior Lecturer for Intellectual Property in the Faculty of Law at the University of Cambridge. She is the Director of the recently established Centre for Law, Medicine and Life Sciences (LML) and Deputy Director for the Centre for Intellectual Property and Information Law. John Liddicoat, also from the Centre for Law, Medicine and Life Sciences. John is the recently appointed Philomathia Post Doctoral Fellow in Intellectual Property Law and Genomics, a position awarded by the School of Humanities and Social Science. Dr Rob Doubleday, Director of the Centre for Science and Policy. The Centre for Science and Policy promotes engagement between the University, policy professionals, experts in the sciences and engineering, business leaders, early career researchers and others who have an interest in the relationship between science and policy. Dr Nicola Patron is a molecular and synthetic biologist at The Sainsbury Laboratory (TSL).
On 28 January 2016, the Centre for Law, Medicine and Life Sciences together with the Centre for Science and Policy, and OpenPlant hosted a workshop on responsible and open innovation with large bio-resources. The central question the workshop tackled was: whether, and to what extent, policies of openness are appropriate for successful innovation with bio-resources in synthetic biology and genomics. Closely related to this question was: how does one implement openness effectively in bio-resources intellectual property policies? A report will shortly be circulated on this workshop, detailing the stimulating conversations that took place at this event.
- Development of new codon optimization tools and development of a synthetic gene expression system in the green alga Chlamydomonas reinhardtii
Francisco Navarro, Molecular Biologist with a keen interest in developing new gene expression tools in Chlamydomonas. Marielle Vigouroux, Computational biologist at the John Innes Centre
Most organisms share the same genetic code, based on three nucleotide codons that encode for one amino acid. However, synonymous codons (which specify a single amino acid) are not used at equal frequency by different species. We were interested in assessing the impact of codon usage in protein production in the green alga Chlamydomonas reinhardtii. We have performed sequence analysis, and developed a platform for measuring the production of a reporter protein, which can be used for testing gene variants. Our analysis, protocols, and materials will be useful for transgene design and expression in the alga.
- The use of synthetic biology tools to define the roles of LysM receptor-like kinases in legumes and cereals
Feng Feng received his Ph.D. in plant biology from Tsinghua University, China. Now working in Prof. Giles Oldroyd’s Laboratory at the John Innes Centre. He is part of the Bill and Melinda Gates Foundation-funded programme that has pioneered the use of synthetic biology strategies in biotechnology. Ronelle Roth, research associate in Dr Uta Paszkowski's group (Cambridge). She was awarded a Marie Curie FP7-PEOPLE-IEF Fellowship in 2014 to work on beneficial plant-fungal interactions.
We have synthesized a number of golden gate modules including gene promoters, coding sequences and terminators and got the final constructs required for this project using gold gate cloning technology. Secondly, we have already expressed these constructs in Nicotiana benthamiana to check the protein expression, now we are focusing on transforming these constructs in Medicago and rice to detect defense and symbiosis phenotype.
- Quick analytical system for plastid genome modifications
We set out to provide the synthetic biology community with a quick Pulsed-Field Gel Electrophoresis (PFGE)-based analytical system for plastid genome modifications. The project led to a number of educational resources, including protocols for the sample plugs preparation for PFGE of plastid and BAC DNA and for PFGE analysis of plastid and BAC DNA using CHEF-DRII PFGE system. All protocols will be open and publicly available. OpenPlant Fund will be also acknowledged in the manuscript containing relevant PFGE protocol, which is currently in press.
- Channeling targeted DNA double strand breaks into alternative repair pathways
Dr Ian Henderson, Dr Natasha Yelina, Patrick Diaz (Department, of Plant Sciences, University of Cambridge), Dr Sebastian Schornack (The Sainsbury Laboratory, University of Cambridge), Meiogenix (Paris)
We have expressed TAL DNA binding domains fused to the FokI nuclease under meiotic promoters (e.g. DMC1, SPO11) in Arabidopsis. The aim of this work is to target DNA double strand breaks to specific sites in the genome, in order to bias initiation of meiotic recombination. Our preliminary data show that while these nucleases are expressed in meiotic-stage floral buds they do not support wild type levels of crossover recombination when the endogenous nuclease (SPO11-1) is mutated. Additionally these transgenic lines show occurrence of developmental phenotypes, leading us to the hypothesis that the resulting DSBs enter a mutagenic pathway. To investigate this in this project we are performing whole genome DNA sequencing and mutation discovery. This has been performed using support from the OpenPlant project and bioinformatic mutation discovery is ongoing. In parallel we have crossed these nuclease lines to mutants in canonical and alternative end joining pathways to test the hypothesis that we can shunt DSBs into crossover recombination via removing competing repair pathways. These lines will be grown and DNA sequencing repeated, in addition to phenotypic analysis in the next part of this project.
- Engineering Marchantia polymorpha chloroplasts for the production of high-value specialized terpenes
Aymeric Leveau & Tessa Moses, Post Doctoral Scientiss, Department of Metabolic Biology, John Innes Centre, Christian R. Boehm, Graduate Student, Department of Plant Sciences, University of Cambridge
Originally, three independent operon-like synthetic constructs should be built to achieve de novo synthesis of mono-, sesqui- and triterpenes in M. polymorpha chloroplasts. GoldenGate modules of coding sequences to be expressed in M. polymorpha were synthesized. However, two major issues were encountered during the project, including problems with transforming M. polymorpha chloroplasts with large constructs, and an assembly defect of the 2A peptide system used for generating the clusters. To circumvent these obstacles, constructs allowing nuclear transformation of M. polymorpha and subsequent chloroplast targeting of the proteins were designed and a new 2A peptide system has been created and is currently being evaluated.
- Documentation Tool for Open Plant Technologies
Tobias Wenzel, PhD student, Winton Scholar and NanoDTC Associate, Dept. of Physics and Dept. of Biochemistry. Johan Henriksson, Postdoctoral Researcher, European Molecular Biology Laboratory – EBI. Carlos Lugo (Carlos.Lugo@sainsbury-laboratory.ac.uk), Postdoc, Sainsbury Laboratory and John Innes Centre in Norwich. External collaborator: Luka Mustafa, Shuttleworth Foundation Fellow, IRNAS
We have successfully built an open source hardware documentation software and an online repository called DocuBricks (DocuBricks.com). We arrived at a software tool that is (according to feedback of users) easy to use and helpful in a wide range of hardware projects and saves documentations in a modular and accessible XML format. The database is citable and the first biology related documentations have been uploaded – many more are to follow from Open Plant Fund projects and the Open Science Hardware Movement. We will continue to develop DocuBricks to serve as a high quality repository for Open Science Hardware.
- Strengthening synthetic biology capacity in Kenya through bioinformatics training
Richard Smith-Unna, PhD student in Plant Sciences at Cambridge University. Vicky Schneider, leads the 361° Division and is part of the Senior Management Team at TGAC in Norwich. Jelena Aleksic, the Director of Bioinformatics at TReND in Africa, the charity organising the Kenya bioinformatics course. Richard Pilling, Director of Big Data and Analytics at Intel.
From 30th November to 5th December 2015, 37 students from nine African countries attended our course, held at ICIPE in Nairobi, Kenya. The course involved six days of theory and practical work, starting from the principles of Unix and programming, through to advanced scientific programming and visualisation. Towards the end of the week students worked on specific analysis methods in various areas of genetics and genomics, with a special focus session on synthetic biology. An ongoing student-led study group, coordinated online, will help the students keep the momentum from the course going. The course is booked to repeat next year.
- Setting up an open synthetic biology lab in Abuja, Nigeria
Richard Smith-Unna, PhD student in Plant Sciences at Cambridge University, applying bioinformatics methods to studying C4 photosynthesis. Chinyere Okoro, postdoc at the Sanger Institute working on the genomics of infectious diseases. Ibukun Akinrinade, PhD student in molecular biology in Portugal. Vicky Schneider, leads the 361° Division and is part of the Senior Management Team at TGAC in Norwich. Jelena Aleksic, Director of Bioinformatics at TReND in Africa, the charity organising the Kenya bioinformatics course.
As part of developing a synthetic biology lab in Bingham University, Abuja, We have been able to successfully collect equipment donations sufficient to set up a running molecular biology lab in Bingham University, Nigeria. These facilities were acquired from kind donations from Institutes in Switzerland and the UK. The shipment to Nigeria is underway. In addition, a laboratory space has been allocated in the University to set up the equipment. Preparations for the workshop is now in top gear as logistics are been arranged and course materials are being prepared. The anticipated date for the workshop is August, 2016.
- Facilitating synthetic biology literature mining and searching for the plant community
Robert Davey, joined TGAC in February 2010 as the lead software engineer on the MISO LIMS project, which was released as an open source framework in June 2012. He went on to become the Core Bioinformatics Project Leader, and was then appointed as Data Infrastructure and Algorithms (DIA) Group Leader in late 2012. Ksenia Krasileva, Group Leader with a joint appointment at The Genome Analysis Centre and The Sainsbury Laboratory. Ksenia joined Norwich Research park in December 2014 moving from University of California Davis where she held Fellowship from National Institute of Food and Agriculture (NIFA) to develop functional genomic tools for wheat working with Jorge Dubcovsky. Nicola Patron, molecular and synthetic biologist at The Sainsbury Laboratory (TSL), a world-leading research institute working on the science of plant-microbe interactions. Richard Smith-Unna, PhD student, Plant Sciences Cambridge. Peter Murray-Rust, a (retired but highly active) chemist in Cambridge University.
Report of 2-day workshop (hack) held at TGAC 2016-03-10/11
The workshop centered on novel methods for discovering information about plants from the existing literature ("Content Mining"). We prepared ContentMine software specifically for the workshop on the basis that "anyone can run it and get useful results ". Everyone was asked to install the software on whatever platform they commonly used (Mac, Windows, Unix). There were few problems and most people were running within an hour. A typical example was "find all you can about diseases of oats" using EuropePubMedCentral (with over 1 million Open Access papers). This retrieves about 500 papers, which were further filtered for chemicals, diseases, species, etc. and displayed within a minute or two, significantly increasing the speed of knowledge-driven scientific discovery. We also jointly made considerable improvements to the software and have agreed to meet regularly to take this forward.
Hot Tomato: Complementation of the Capsaicin Biosynthetic Pathway to Engineer Spicy Tomatoes
Implementation of a synthetic transcriptional AND gate in the chloroplast of Chlamydomonas reinhardtii
Advancing the ability to image single RNA molecules at the cellular level
Establish a Procedure for Rapid Identification of Genetic Parts for Use in Algal Biotechnology
A synthetic biology approach to investigating arbuscular mycorrhizal symbiosis in Marchantia paleacea
Desktop plant experiment box
Environmental sensor networks based on plant electrical signalling.
Establishing 3D Printed Microfluidics for Molecular Biology Workflows
Universal precise large area colony scanning stage with measurement and selection tool integration
Development of an Open Source Autonomous Imaging Station for Distribution in High Schools, Universities, and Emerging DIY Scientific Communities.
Co-lab OpenPlant - interdisciplinary workshops of science art and design
ynthetic Biology for Schools: A multidisciplinary approach
Plant-ProChip 2.0: High throughput transformation of plant protoplast
Translating Nitrogen Use Efficiency from models to crops
The Green Mother Machine Reloaded
Development of a Low-Cost Micro-Environment Device for Root-Nutrient Interaction
DNA-mediated fusion of spheroplasts with synthetic liposomes
Ambient temperature preservation of cell-free TX-TL reagents for use in synthetic biology
Developing teaching resources for rapid, open and combinatorial genetic circuit fabrication in cell-free systems.
Accessible 3D Models of Molecules
Light sheet microscopy of cell sheet folding in Volvox
Developing Cell-Free Genetic Circuits and their Electronic Counterparts as Educational Tools for SynBio Students.
Funded SynBio SRI projects
Engineering of self cloning brewer’s yeast for novel terpene profiles in beer.
3D printed microscope
Interactive web based software for genetic circuit design
Novel bioluminescent reporters
Flexible, low cost, live cell imaging platform
Faster engineering of cyanobacteria
Finding new recombinases
The Green Mother Machine: A microfluidics device for cyanobacteria
SynBio Student Society
SynBioHub: Patent information system for synthetic biology
Synthesis of novel optimised lux reporters for eukaryotic systems
CamOptimus: Self-contained user-friendly multi-parameter optimisation platform for non-specialist experimental biologists
Reliable IP-free system for inter-chassis transfer of the high molecular weight DNA
A piezoelectric bio-platform to image and stimulate cellular interactions
Interactive web-based software tool for biological circuit design (Extension plan)
Development of a microfluidic device for high-throughput analysis of genetic circuits in plant protoplasts.
Low cost solution for high throughput bacterial electrotransformation
CELLUWIN: 3D printing for cellulose
Organotypic cultures as tools for functional screening of drugs to promote oligodendrocyte differentiation and CNS myelination.