OpenPlant Coverage

New publications from the Baulcombe lab

OpenPlant PI David Baulcombe and colleagues recently published two papers: (1) on the miRNA-Argonaute machinery in the unicellular green alga Chlamydomonas reinhardtii, and (2) on the application of miRNAs for regulation of synthetic gene systems in this organism:

Chung  et al . (2019): “Figure 1: Structural features of  Chlamydomonas  Argonautes.”

Chung et al. (2019): “Figure 1: Structural features of Chlamydomonas Argonautes.”

Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression

Betty Y.-W. Chung, Adrian Valli, Michael J. Deery, Francisco J. Navarro, Katherine Brown, Silvia Hnatova, Julie Howard, Attila Molnar & David C. Baulcombe

Sci Rep. 2019; 9: 11091. doi: 10.1038/s41598-019-47415-x


The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identifed as the predominant miRNA with efects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.

Navarro and Baulcombe (2019): “Figure 1: Construction of a synthetic circuit to measure miRNA-dependent gene repression.”

Navarro and Baulcombe (2019): “Figure 1: Construction of a synthetic circuit to measure miRNA-dependent gene repression.”

miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii

Francisco J. Navarro and David C. Baulcombe

ACS Synth Biol. 2019 February 15; 8(2): 358–370. doi:10.1021/acssynbio.8b00393.


microRNAs (miRNAs), small RNA molecules of 20–24 nts, have many features that make them useful tools for gene expression regulation — small size, flexible design, target predictability and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3’UTRs, miRNA decoys and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

OpenPlant PI Julian Hibberd and colleagues published their work on the transcription factor binding repertoire associated with C3 and C4 photosynthesis:

Burgess et al. (2019): “Fig 6: Hyper-conserved cis-elements in grasses recruited into C4 photosynthesis.”

Burgess et al. (2019): “Fig 6: Hyper-conserved cis-elements in grasses recruited into C4 photosynthesis.”

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

Steven J Burgess, Ivan Reyna-Llorens, Sean Ross Stevenson, Pallavi Singh, Katja Jaeger, and Julian M Hibberd

Plant Cell. 2019. pii: tpc.00078.2019. doi: 10.1105/tpc.19.00078.


The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3 Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.

Hive BioLab, the first community/DIYBio lab in Ghana, launches @hivebiolab


Hive BioLab is the first community/DIYBio lab in Ghana dedicated to the rapid prototyping of ideas in biology, research, enterprising bio-startups by helping and providing resources to students and graduates to translate science to businesses.

HiveBioLab is now active on twitter: @hivebiolab

A Biomaker team has made it to the final of the BBSRC Innovator of the Year 2019 Awards


A Biomaker team with participants from Quadram Institute Bioscience (QIB), the Earlham Institute (EI), the John Innes Centre (JIC) and the University of Oxford, has developed a small scale speed breeding cabinet, which has qualified them for the final of the BBSRC Innovator of the Year 2019 Awards. Read more about this story here:

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Osbourn Science 2019.large.jpg

OpenPlant scientists Hans-Wilhelm Nützmann and Anne Osbourn demonstrate that model plant Arabidopsis thaliana produces a range of specialized triterpenes that direct the assembly and maintenance of a specific microbial community within and around its roots. Their work, which was part of a collaborative effort, was recently published in Science:

Ancheng C. Huang, Ting Jiang, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai, Anne Osbourn

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Science (2019) Vol. 364, Issue 6440, eaau6389
DOI: 10.1126/science.aau6389


Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community.

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

Tuncel et al fig 3.png

OpenPlant scientists Aytug Tuncel, Nicola Patron and Alison Smith demonstrate that Cas9-mediated mutagenesis of starch-branching enzymes has the potential to generate new, potentially valuable starch properties.

Aytug Tuncel, Kendall R. Corbin, Jennifer Ahn‐Jarvis , Suzanne Harris, Erica Hawkins, Mark A. Smedley, Wendy Harwood, Frederick J. Warren, Nicola J. Patron, Alison M. Smith

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

Plant Biotechnology Journal


We investigated whether Cas9‐mediated mutagenesis of starch‐branching enzymes (SBEs) in tetraploid potatoes could generate tuber starches with a range of distinct properties. Constructs containing the Cas9 gene and sgRNAs targeting SBE1, SBE2 or both genes were introduced by Agrobacterium‐mediated transformation or by PEG‐mediated delivery into protoplasts. Outcomes included lines with mutations in all or only some of the homoeoalleles of SBE genes, and lines in which homoeoalleles carried several different mutations. DNA delivery into protoplasts resulted in mutants with no detectable Cas9 gene, suggesting the absence of foreign DNA. Selected mutants with starch granule abnormalities had reductions in tuber SBE1 and/or SBE2 protein that were broadly in line with expectations from genotype analysis. Strong reduction of both SBE isoforms created an extreme starch phenotype, as reported previously for low‐SBE potato tubers. HPLC‐SEC and 1H NMR revealed a decrease in short amylopectin chains, an increase in long chains and a large reduction in branching frequency relative to wild‐type starch. Mutants with strong reductions of SBE2 protein alone had near‐normal amylopectin chain length distributions and only small reductions in branching frequency. However, starch granule initiation was enormously increased: cells contained many granules of < 4 μm and granules with multiple hila. Thus large reductions in both SBEs reduce amylopectin branching during granule growth, whereas reduction of SBE2 alone primarily affects numbers of starch granule initiations. Our results demonstrate that Cas9‐mediated mutagenesis of SBE genes has the potential to generate new, potentially valuable starch properties without integration of foreign DNA into the genome.

The protosteryl and dammarenyl cation dichotomy in polycyclic triterpene biosynthesis revisited: has this ‘rule’ finally been broken?

Stephenson Osbourn Fig 5.gif

OpenPlant postdoc Michael Stephenson, and group leaders Rob Field and Anne Osbourn at the John Innes Centre in Norwich, reveal novel insights into triterpene biogenesis in their recent paper.

Stephenson MJ,  Field RA,  and  Osbourn A (2019) The protosteryl and dammarenyl cation dichotomy in polycyclic triterpene biosynthesis revisited: has this ‘rule’ finally been broken? Natural Product Reports, DOI: 10.1039/c8np00096d


The triterpene alcohols represent an important and diverse class of natural products. This diversity is believed to originate from the differential enzymatically controlled cyclisation of 2,3-oxidosqualene. It is now a well-established presumption that all naturally occurring tetra- and penta-cyclic triterpene alcohols can be rationalised by the resolution of one of two intermediary tetracyclic cations, termed the protosteryl and dammarenyl cations. Here, a discussion of typical key triterpene structures and their proposed derivation from either of these progenitors is followed by comparison with a recently reported novel pentacyclic triterpene orysatinol which appears to correspond to an unprecedented divergence from this dichotomous protosteryl/dammarenyl view of triterpene biogenesis. Not only does this discovery widen the potential scope of triterpene scaffolds that could exist in nature, it could call into question the reliability of stereochemical assignments of some existing triterpene structures that are supported by only limited spectroscopic evidence. The discovery of orysatinol provides direct experimental evidence to support considering more flexibility in the stereochemical interpretation of the biogenic isoprene rule.

Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis

Temple Dupree Fig 1_cropped.jpg

OpenPlant postdoc Henry Temple, in Prof Paul Dupree’s lab at the University of Cambridge, has published his discovery of a novel role for members of the DUF579 protein family in plant cell wall modification.

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez‐Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct,


All members of the DUF579 family characterized so far have been described to affect the integrity of the hemicellulosic cell wall component xylan: GXMs are glucuronoxylan methyltransferases catalyzing 4‐O–methylation of glucuronic acid on xylan; IRX15 and IRX15L, although their enzymatic activity is unknown, are required for xylan biosynthesis and/or xylan deposition. Here we show that the DUF579 family members, AGM1 and AGM2, are required for 4‐O–methylation of glucuronic acid of a different plant cell wall component, the highly glycosylated arabinogalactan proteins (AGPs).

miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii

OpenPlant postdoc Francisco Navarro, in Prof David Baulcombe’s lab at the University of Cambridge, has published his work on regulation of synthetic gene circuits by miRNA in Chalmydomonas reinhardtii, in ACS Synthetic Biology. This work describes a new mechanism for regulation that can be used in in new synthetic biology applications in this green algae chassis.

Navarro F, Baulcombe DC (2019). miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii. ACS Synthetic Biology, [Epub ahead of print]


microRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation - small size, flexible design, target predictability and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

OpenPlant Forum 2018: Engineering Plants for Bioproduction

Blog post by Dr Colette Matthewman

Over the past decade, synthetic biology has focussed much of its effort on microbial chassis as platform for bioproduction. The single cell simplicity and rapid life-cycles of these organisms, the prevalence of biological tools and the existing industry infrastructure for fermentation have made microbes a tempting playground for synthetic biologists wishing to make a range of chemicals and biomolecules, from flavours and fragrances to distributed manufacturing of highly complex metabolites for medicine, and an increasing number of companies are finding success in this arena (e.g. Ginkgo Bioworks, Amyris, Evolva, Antheia).

More recently, plants have been showing serious promise as viable production platforms for complex chemicals and biomolecules which in many cases simply can’t be made in single celled microbes. This year, the OpenPlant Forum explored some of the latest advances in plant bioproduction with inspiring talks from invited speakers and OpenPlant researchers highlighting a promising and exciting future for plant synthetic biology.

OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

The first morning of the Forum focused on tools for refactoring regulation and simple test platforms for plant synthetic biology. Prof. Ian Small (University of Western Australia) opened the meeting with a keynote on the potential for using engineered RNA bonding proteins to control organelle gene expression. OpenPlant PI, Prof. Paul Dupree described research in his on engineering of polysaccharide structures in plants. We also had the first examples of plant production platforms: Dr Ingo Appelhagen presented his recently published work on the production of colourful anthocyanin molecules in plant cell cultures, while Dr Eva Thuenemann introduced the HyperTrans system developed in the Lomonossoff lab at the John Innes Centre for the transient expression of proteins in Nicotiana benthamiana, a wild relative of tobacco. Eva is working on plant-based production of a protein that could be used in a vaccine against East Coast Fever, a devastating disease in cattle in Africa. The HyperTrans platform is used by the Lomonossoff lab and recently established company Leaf Expression Systems to produce therapeutic proteins and virus-like particles for vaccines, including recent work on a new vaccine for the eradication of Polio.

The afternoon session explored the cutting edge in production of complex plant-derived natural products in yeast, with a keynote from Prof. Christina Smolke (Stanford University), followed with an insight into the engineering of triterpene production in N. benthamiana by Dr James Reed in the Osbourn lab (John Innes Centre), recently reviewed in Plant Cell Reports. These projects rely heavily on chemical and enzymatic biodiversity in nature. Dr Sam Brockington (University of Cambridge) talked about harnessing the global network of botanic gardens for access to plant diversity for metabolic engineering and synthetic biology, introducing a global database of living plant, seed and tissue collections called “Plant Search” – a perfect sedgeway into a panel discussion on Harnessing Global Biodiversity where Sam was joined by Dr Nicola Patron (Earlham Institute), Mr David Rejeski (Environmental Law Institute), and Dr Jenni Rant (SAW Trust). The discussions ranged from public opinion on synthetic biology (explored through the Global Garden workshop) and benefit sharing and dematerialisation, through to how blockchain (like the bitcoin) is being used in environmental contexts and whether blockchain technology trends can be applied to create/assign value for biodiversity.

Prof. Ralf Reski with his moss bioreactors

Prof. Ralf Reski with his moss bioreactors

Day two of the Forum continued on a theme of “Tools for Metabolic Engineering” with Prof. Claudia Vickers (University of Queensland) opening by introducing the Future Science Platform in Synthetic Biology that she leads at CSIRO, as well as numerous tools developed in her research lab. Claudia was followed by a trio of OpenPlant postdocs describing analysis to unravel the genetics of divergent metabolic pathways in Brassicaceae (Dr Zhenhua Liu), a search for new synthetic biology tools based on diversity of natural triterpene oxidation (Dr Michael Stephenson) and tools for engineering Marchantia’s chloroplasts (Dr Eftychis Frangedakis).

Moving on from the tools, we explored further plant-based bioproduction platforms, starting with an inspirational keynote from Prof. Ralf Reski (University of Freiburg) on the moss Physcomitrella patens that Ralf’s lab has established as a production platform for biopharmaceuticals, leading to foundation of the company Greenovation, which produces moss-aGal (agalsidase) for the treatment of Fabry disease, a rare but painful and potentially deadly disease. Subsequently, we heard from Prof. Alison Smith (University of Cambrige) about “Designer algae” and work towards predictable metabolic engineering in microalgae, and from Dr Eugenio Butelli (John Innes Centre) about the Tomato as a biofactory for making health promoting flavonoids.

The Forum was wrapped up for this year with a session on Sharing and Techno-Social Platforms, with an introduction from OpenPlant’s Prof Jim Haseloff, followed by Dr Linda Kahl (BioBricks Foundation) on the latest with the Open Material Transfer Agreement (Open MTA) which has been developed in collaboration with OpenPlant to enable sharing of DNA parts (publication coming soon!). Next up, Dr Joanne Kamens from not-for-profit plasmid distribution company, Addgene, revealed the freshly launched plant resource page and spoke about the upcoming adoption of the Open MTA as an option under which plasmids can be shared. Finally, Dr Richard Sever from bioRxiv spoke about preprint opportunities for synthetic biology.

Join us in Cambridge for the OpenPlant Forum 2019 | 29 – 31 July

Save the date!

Colour bio-factories: anthocyanin production in plant cell cultures

Bioreactors with engineered tobacco (left) and wild-type grape (right) cell cultures.

Bioreactors with engineered tobacco (left) and wild-type grape (right) cell cultures.

OpenPlant Postdoc, Ingo Appelhagen, in Prof Cathie Martin's lab in the John Innes Centre has recently published an article in the journal Metabolic Engineering about his research to develop a system for production of high-levels of anthocyanins in plant cell cultures.

Anthocyanins give many fruits and flowers their red, purple or blue colouration. The martin lab are interested in the beneficial effects of anthocyanins in our diets and their use as natural colourants in the food and cosmetic industries.



Appelhagen I, Wulff-Vester AK, Wendell M, Hvoslef-Eide AK, Russell J, Oertel A, Martens S, Mock HP, Martin C, Matros A (2018). Colour bio-factories: Towards scale-up production of anthocyanins in plant cell cultures. Metabolic Engineering. Doi:


Anthocyanins are widely distributed, glycosylated, water-soluble plant pigments, which give many fruits and flowers their red, purple or blue colouration. Their beneficial effects in a dietary context have encouraged increasing use of anthocyanins as natural colourants in the food and cosmetic industries. However, the limited availability and diversity of anthocyanins commercially have initiated searches for alternative sources of these natural colourants. In plants, high-level production of secondary metabolites, such as anthocyanins, can be achieved by engineering of regulatory genes as well as genes encoding biosynthetic enzymes. We have used tobacco lines which constitutively produce high levels of cyanidin 3-O-rutinoside, delphinidin 3-O-rutinoside or a novel anthocyanin, acylated cyanidin 3-O-(coumaroyl) rutinoside to generate cell suspension cultures. The cell lines are stable in their production rates and superior to conventional plant cell cultures. Scale-up of anthocyanin production in small scale fermenters has been demonstrated. The cell cultures have also proven to be a suitable system for production of 13C-labelled anthocyanins. Our method for anthocyanin production is transferable to other plant species, such as Arabidopsis thaliana, demonstrating the potential of this approach for making a wide range of highly-decorated anthocyanins. The tobacco cell cultures represent a customisable and sustainable alternative to conventional anthocyanin production platforms and have considerable potential for use in industrial and medical applications of anthocyanins.

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:

My OpenPlant Experience: Outreach, Engagement and 3D printing

Guest blog post by Roger Castells-Graells about his OpenPlant Fund project “Accessible 3D Models of Molecules”. Roger recently won a UEA Engagement Award in recognition of the work he has done both with OpenPlant and beyond.


PhD student Roger Castells-Graells in the lab

PhD student Roger Castells-Graells in the lab

My name is Roger and I am a PhD student in Prof. George Lomonossoff’s lab at the John Innes Centre in Norwich. My research project is about the production of virus-like particles to understand viral dynamics for future applications and to generate new bionanotechnological tools. I have a passion for science communication and public engagement and I have had numerous opportunities to communicate my science in Norwich, the UK and abroad since the start of my PhD.

My OpenPlant experience started in September 2016, when I attended a great Co-Lab workshop organized by the Open Science School and funded by an OpenPlant Fund. With this opportunity I had the chance to interact with scientists from different fields and also with designers and artists. It was an enriching experience and we developed a project called VRICKS (Virus Bricks) that aimed to generate tools to explain viruses in educational ways, like for example with paper models.

Following up from this workshop, in October 2016, I organized an activity for the Norwich Science Festival, together with Jenni Rant (The SAW Trust) and Colette Matthewman (OpenPlant), where we recreated the assembly of proteins into a virus protein coat using materials like paper and plastic, which represented the subunits of the virus. The public contributed to the assembly of a virus model, they learnt about related research from the Lomonossoff lab and they took home a build-at-home model. Over one hundred people participated in the activity during the weekend, making it a roaring success.

Presenting the virus activity and engaging with people at the Norwich Science Festival

Presenting the virus activity and engaging with people at the Norwich Science Festival

Following up with the interest to build tools to explain biological processes, such as virus assembly, I decided to apply for and OpenPlant Fund with the project “Accessible 3D Models of Molecules”. The project team is a multidisciplinary team (molecular biology, bioinformatics and engineering) of students from JIC and University of Cambridge and with this fund we are developing models of viruses and proteins using 3D printing technologies.

3D printed virus models for the OpenPlant Fund project  
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3D printed virus models for the OpenPlant Fund project

Recently I presented some of the virus models in a high school with students aged 12 to 16 years old. The students enjoyed being able to handle and compare representations of real virus structures and were amazed that some of these structures were only discovered this year. When the school teacher was asked about how the use of educational 3D models in the classroom could benefit the learning process he answered that first of all it creates excitement and focuses the attention of the students. It is something completely new! It contributes to the understanding of three-dimensional models and gives the students a better sense of the reality of the object. Furthermore, it allows the students to calculate scale as it is possible to touch, measure and compare different models.

I was invited to speak at the Pint of Science Festival in Norwich in May, and gave a talk entitled “20000 Leagues under the microscope: Viruses & Nanomachines”. At the event, I passed around several models of 3D printed viruses and the public loved having the opportunity to handle them. It was a great experience and we received really positive feedback. I want to thank the organizers of Pint of Science for such a great event!

As a result of all of these activities, I was recently awarded a UEA Engagement Award 2016/17 for contribution to Public & Community Engagement, which I am very proud of.

      Norwich Pint of Science Festival tweets



Norwich Pint of Science Festival tweets

Roger tweets2b.png

With thanks to my supervisor Prof. George Lomonossoff, OpenPlant and all the people that have helped, encouraged me and opened up opportunities in this last year.

OpenPlant Scientists take part in Norwich Pint of Science Festival

In May 2017, the Pint of Science festival returned to Norwich. The festival, which is held over a few days, was a huge success, with many events being sold out days in advance. Each event offers the audience the chance to meet scientists at their local pub and discuss their latest research in an informal and welcoming atmosphere, whilst sipping on their favourite pint.

Two sell out events where those of OpenPlant Project Leader Professor George Lomonossoff and his PhD student Roger Castells-Graells, and a second event with OpenPlant’s Norwich-based Director, Professor Anne Osbourn.

George’s talk was entitled ‘Just Eat Your Greens – A New Way of Vaccinating?’ and took place at the York Tavern. It covered the use of a highly efficient transient expression system developed in his laboratory. This Hypertrans® system allows for the relatively quick and cheap production of large quantities of virus-like particles in plants, which have been proven to be effective as experimental vaccines.

3D printed viruses.png

Roger presented ‘20,000 Leagues Under the Microscope: Viruses & Nanomachines’ taking the audience on a journey into the nano world of viruses. During the entertaining talks, the audience took part in various activities such as making a virus molecule out of pipe cleaners and creating virus inspired sketches on beer mats.


The following evening, Anne took to the stage at the St Andrews Brewhouse to present her ‘Finding Drugs in The Garden’ talk. Anne’s inspiring talk invited people into the plant kingdom to hear about its very own chemistry toolkit. She presented her teams current work harnessing the DNA that encodes the pathways to these chemicals and using them to produce designer molecules for medicinal, agricultural and industrial applications.


For the scientists taking part in the festival, it has proven to be a great platform on which to reach the public to talk about their research and build an understanding of their work within the local city of Norwich. After such well received talks and events, we very much look forward to the return of the Pint of Science Festival in 2018.

OpenPlant Fellow wins 2016 Wellcome Trust Image Award

fernan-maize Fernán Federici, OpenPlant Fellow at the University of Cambridge and Director of the Synthetic Biology Lab at Pontificia Universidad Católica in Chile has been awarded a Wellcome Trust Image Award for his micrograph of maize leaves, shot in the Department of Plant Sciences in collaboration with Professor Jim Haseloff.

Fernán has enjoyed considerable success with his artistic images of bacteria and plants using microscopy, winning Wellcome Trust awards in 2011 and 2012. His image has appeared in multiple media outlets, including Nature Newsthe BBC and The Guardian.

More on the image via the Wellcome Trust >>

Looking inside a cluster of leaves from a young maize (corn) plant reveals lots of details and organised structure. Each curled leaf is made up of lots of small cells (small green square and rectangle shapes), and inside each cell is a nucleus (orange circle), the part of the cell which stores genetic information. Maize is one of the most widely grown cereal crops in the world. It is used as a staple food, in livestock feed, and as a raw material – such as for processing into high-fructose corn syrup. Genetically modified maize crops are being grown to be resistant to pests and herbicides.

Although seeming boring when viewed with the naked eye, maize leaves have such a delicate and intricate structure under the microscope, captured so wonderfully by this picture. The level of detail as demonstrated by the image reminds us how complex even relatively simple organisms are when seen on this scale.

James Cutmore, Picture Editor of BBC Focus

The image has been made freely available to use under a Creative Commons CC-BY-NC-ND 4.0 license.

OpenPlant lab mentioned in 'Microalgae as a microcosm of plant biotech'

Logo-monserrat chlamydomonas photo

Source: Microalgae as a microcosm of plant biotech

Orlando de Lange has a blog post up on 'Microalgae as a microcosm of plant biotech' mentioning the work of Alison Smith's Lab at the University of Cambridge, plus several others using Chlamydomonas for classical biotechnology and synthetic biology. Worth a quick read!

And of course I won’t leave out synthetic biology. Several labs seem to be exploring the potential for synthetic biology with microalgae.Alison Smith’s lab in Cambridge has long studied mircroalgal metabolism, with an eye to biofuel production and has more recently begun churning out tools for engineering Chlamydomonas.

Plant Synthetic Biology at IHÉS

poster_cellular_molecular Institut des Hautes Études Scientifiques (IHÉS) held a meeting on Cellular and Molecular Biotechnology, including Synthetic Biology in Paris last week. OpenPlant was well represented by Professors Jim Haseloff and Anne Osbourn. You can find videos of their talks below and all recordings on the IHÉS youtube channel.



First common standard for assembly of DNA parts in plant SynBio published

Dr Nicola Patron

Dr Nicola Patron

Supported by OpenPlant, Dr Nicola Patron of The Sainsbury Laboratory, Norwich, has led development of the first common standard for the assembly of DNA parts for plant synthetic biology.

Published today in New Phytologist as a Viewpoint article, this standard has been agreed between the inventors and developers of several Type IIS cloning technologies, the leaders of numerous plant bioengineering consortia and leaders of international plant science.

In the article, Nicola and her co-authors describe a common syntax of twelve fusion sites to enable the facile assembly of eukaryotic transcriptional units.

The manuscript received favourable support in the peer review process. One reviewer commented that “ …this is somewhat of a landmark publication that will massively influence all plant synthetic biology to come and shows the community in this field to be ahead of their colleagues in other areas.” Another remarked that “this paper will be a catalyst for further discussion around standardization not only in plants but in synthetic biology in general.”

By establishing a standard for the wider plant community Nicola and her colleagues will facilitate the sharing of standard parts for plants between scientists. It also sets a basis for the development of software and hardware that will support accelerated design and automated assembly. Their vision is to develop an extensive catalogue of standardised, characterised DNA parts to accelerate plant bioengineering.

The establishment of a DNA assembly standard for plants is an important and timely step in plant synthetic biology.

Dr Jim Haseloff at the University of Cambridge said: “The publication of a common syntax for plant DNA parts is a landmark for the adoption of engineering principles in multicellular organisms. It is the result of wide cooperation between researchers across the plant biology field, and sets the scene for greater scientific exchange and innovation in crop improvement.”

Read the paper: ‘Standards for plant synthetic biology: a common syntax for exchange of DNA parts’

Edited from the post Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio which appeared first on The Sainsbury Laboratory.

Source: Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio

SynBioBeta post on OpenPlant: Open Technologies for Plant Synthetic Biology

Reposted from the SynBioBeta Blog

Plant synthetic biology has great potential to improve sustainable bioproduction of globally important products; from foodstuffs to fibres to drugs. Advantages of plants over engineered microbes include their worldwide cultivation, their harvest on a giga-tonne scale and the existing precedent for genetically modified crops in many parts of the world. In addition to these applied benefits, plants raise interesting scientific questions and technical challenges around engineering pathways and interactions in multi-cellular, differentiating and developing organisms, adding complexity to current microbial experiments.

Plant synthetic biology is a young field and requires the development of tools and techniques to deal with additional complexity, such as improved genome editing, DNA synthesis and assembly at chromosomal or genomic scales. Supply of plant DNA parts is expected to increase rapidly, which is why the sharing and characterization of these components is a priority; particularly in the liverwort Marchantia, which appears to be a promising candidate for a plant synthetic biology model organism. Tools identified as necessary to support these developments include hardware and software for automation of high-throughput assembly and characterization, plant-relevant software models, data repositories and standards to increase interoperability of the parts and their associated data.

open plant

Right: Image of Marchantia

The OpenPlant initiative is a BBSRC-EPSRC funded synthetic biology centre, based at the University of Cambridge, the John Innes Centre and The Sainsbury Laboratory in Norwich, that aims to address these foundational requirements and then apply them to engineer traits including plant metabolic pathways and natural product synthesis routes. Applications include input to major programmes addressing grand challenges for energy and food security. For example, carbohydrate engineering for improved yield of biofuels or studying Marchantia to inform a synthetic approach to nitrogen-fixing in cereals, where it could have major implications for fertilizer use. Metabolic diversity in plants supplies us with important drugs, flavorings and agrochemicals in addition to impacting plant ecology and protection, so another OpenPlant project concerns optimizing enzymes and engineering gene clusters to synthesize these compounds.

OpenPlant aims to shape working practices and norms in these early stages of plant synthetic biology, by promoting interdisciplinary exchange, the development of standards and responsible innovation. It promotes an ecosystem of open technologies giving researchers and small companies greater freedom to operate within a two-tier IP system. IP-free circulation of foundational tools and DNA parts should accelerate uptake, innovation and entrepreneurship; allowing exploration of new models for decentralized ownership, control and manufacture of synthetic plant technologies. Protecting inventions representing novel combinations and applications of these low-level components preserves investment and retains commercial prospects, while also promoting alternative business models.

Innovation in plant biotechnology, particularly in high-value areas such as crops, is increasingly constrained by intellectual property (IP) protection, sometimes restricting access to genetic tools. This can impede the ability of innovative synthetic biology programmes to succeed. Commercial entities from entrepreneurial startups to large multinationals already struggle through patent thickets when bringing products to market and both academic-industrial exchange and sharing among researchers is restricted by terms and conditions in materials transfer agreements. OpenPlant experiments with openness as a means to aid innovation, particularly as the scale of DNA systems increases and the number of parts and tools involved in creating an engineered organism grows. Openness also offers greater access to research tools for the development of synthetic plant products that have implications for global sustainability and international development, and that may rely on decentralized projects to address local needs.

These efforts are part of a broader ongoing exploration of open practices and commons-based knowledge production among many communities. Open source strategies have proved fruitful in software and computing, from multimillion dollar commercial companies such as RedHat built on the basis of openly distributed code, through to projects such as the Raspberry Pi and its associated open software interfaces, which are wildly popular among educators and makers, including scientists. CERN, a scientific organisation with a strong history of successful technology transfer, heavily promotes open source hardware projects. Their repository hosts over 100 projects, with 16 companies actively engaged in testing or producing hardware based on technologies developed at CERN.

Open research practices have been promoted at the grassroots of several academic communities and are fast becoming a focus of funding agencies hoping to leverage their potential for accelerating research and innovation and reducing inequities in access to knowledge. One project employing an approach analogous to OpenPlant is the Structural Genomics Consortium, a public-private partnership for drug discovery that restricts IP protection of any results until the later stages of clinical trials, thus moving the pre-competitive boundary later in the discovery pipeline. As per a recent evaluation report, its open access approach is considered a significant incentive for investment by commercial partners owing to better facilitation of downstream research and increased competitiveness further down the value chain. The benefits of sharing were felt by the companies involved to outweigh any risks and associated with late-stage IP protection.  Other projects such as Open Source Malaria have also described how open approaches accelerated their research, including via industrial partnerships.

In summary, OpenPlant is performing cutting edge synthetic biology research while also exploring the potential of open technologies by engaging with diverse partners, building communities and providing incentives for open projects, such as seed funding. We will document and share what we learn from our approach to promoting innovation and entrepreneurship alongside the technologies and scientific results arising from our research. We welcome feedback from the SynBioBeta community!