Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

Veronica Grieneisen talks to GARNet!

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Published on: September 5, 2017

Veronica Grieneisen (John Innes Centre) shows much excitement for her science as we discuss a recent PNAS paper entitled ‘Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root’
http://www.pnas.org/content/early/2017/08/17/1705833114.abstract
https://www.jic.ac.uk/directory/veronica-grieneisen/

Lars Ostergaard talks to GARNet

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Published on: August 31, 2017

Lars Ostergaard has an enthusuastic discussion with GARNet about his groups recent paper published in The Plant Cell entitled: Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis’.
http://www.plantcell.org/content/early/2017/08/13/tpc.17.00389
https://www.jic.ac.uk/directory/lars-ostergaard/

Find his discussion about a previous paper here: https://www.youtube.com/watch?v=POWspYw6aXs

SEB-GARNet Meeting on PTMs

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Published on: August 29, 2017

The SEB and GARNet are organising an exciting conference entitled ‘From Proteome to Phenotype: role of post-translational modifications‘ at the University of Edinburgh in December this year.

The registration for this meeting is now open and the full programme is below.

In addition GARNet are hosting an extra workshop that is led by Dr Alex Jones (University of Warwick). This workshop is open to just 30 delegates who will be selected from interested delegates who have registered for the main meeting. There is the opportunity to apply to attend the workshop on the main registration page.

The workshop is intended to help early career researchers get started using proteomics. We will introduce sample preparation methods for common research goals such as “total” soluble protein extraction, enrichment of phosphopeptides and affinity enrichment of fusion proteins. We’ll discuss how best to approach proteomic service providers and the type of information and quality controls that can help to ensure your experiments succeed. After this introductory session we will have short talks from Hirofumi Nakagami (MPIPZ) on phosphoproteomics, Kathryn Lilley (Cambridge) on organelle proteomics and Piers Hemsley (James Hutton Institute) on SLIAC quantification and S-acylation. These talks will be interspersed with data analysis sessions and discussions regarding the troubleshooting of common errors. We will then consider how to evaluate and critically access mass spectrometric data. Our objective is to have a very open discussion throughout and delegates will be required requested to bring a laptop to work through provided examples and fully participate in discussions throughout the day.


In addition GARNet will provide up to ten £200 travel grants for early career researchers who have registered for the workshop before November 3rd.

Information about these grants can be found on the SEB website.


Arabidopsis Research Roundup: August 23rd

There is a bumper crop of papers in this weeks UK Arabidopsis Research Roundup! First up is a remarkable piece of work from George Bassel’s (University of Birmingham) lab that defines the network of cellular interactions that occur in the hypocotyl. Second and third are papers from the JIC in which Lars Ostergaard’s group uncovers the extent of the ETTIN signaling network and Caroline Dean‘s and Martin Howard’s labs provide evidence for a two step progression toward stable gene silencing following vernalisation at the FLC locus. Fourthly is a study that includes members of Alex Webb’s group (University of Cambridge) as co-authors that investigates the link between the circadian clock and night time starch metabolism. Fifth is a paper from Christine Foyer (University of Leeds) that looks at the effect of commonly used inhibitors on cellular redox state and gene expression. The next paper includes Phillip Carella (SLCU) as a co-author and looks at the role of classic flowering time genes on the phenomenon of Age-Related Resistance and finally Lee Sweetlove’s (University of Oxford) lab has published a methods paper for the analysis of photorespiration in non-photosynthetic tissues.


Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017) Topological analysis of multicellular complexity in the plant hypocotyl. Elife http:/​/​dx.​doi.​org/10.7554/eLife.26023

Open Access

George Bassel (University of Birmingham) is the corresponding author on this work that provides fantastic images of the plant hypocotyl taken as part of an analysis on the cell growth dynamics in this organ. They show that Arabidopsis epidermal atrichoblast cells demonstrate a reduced path length that coincides with preferential movement of small molecules through these cells. They analysis this process in various mutants showing which gene activities were necessary for the construction of this pattern. In addition they compared topological features in Arabidopsis, Poppy and Foxglove, showing that cell interactions and path length determinants differ between these organisms. Overall this manuscript defines the network principles that control complex organ construction as well as a function for higher order patterning.


Simonini S, Bencivenga S, Trick M, Ostergaard L (2017) Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell 10.1105/tpc.17.00389

Open Access

Last year Lars Ostergaard (JIC) discussed a paper from his lab on the GARNet YouTube channel in which they defined a new auxin-signaling paradigm that involved the non-canoical Auxin Response Factor ETTIN. This follow up to that study investigates the genetic network controlled by ETTIN activity and defines a range of developmental processes dependent on ETTIN auxin sensing. Furthermore by looking at direct ETTIN targets they suggest that this protein acts as a central node for the coordination of auxin signaling in the shoot. Finally their analysis of the effect of auxin on interactions between ETTIN and other transcription factors indicates that these are important factors in the diverse set of growth process controlled by auxin.


Yang H, Berry S, Olsson TSG, Hartley M, Howard M, Dean C (2017) Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis. Science 10.1126/science.aan1121

This is another manuscript resulting from the extremely fruitful collaboration between the labs of Caroline Dean and Martin Howard at the John Innes Centre. This paper again focuses on the FLC locus and provides evidence for a new mechanism that defines how the binding of a subset of PRC2 factors nucleates a small region (<500bp) of chromatin at the FLC TSS, causing an increase in the repressive H3K27me2 histone mark. This metastable region serves as the seed for the development of stable epigenetic marks across the length of the locus through the activity of other distinct Polycomb factors. This occurs after a cold treatment and causes the spread of H3K27me2 repression. The novelty of this work is in the distinct temporal separation of phases of silencing, which ultimately result in the repression of FLC expression after a prolonged cold treatment.


Seki M, Ohara T, Hearn TJ, Frank A, da Silva VCH, Caldana C, Webb AAR, Satake A (2017) Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism. Sci Rep. 10.1038/s41598-017-08325-y

Open Access

Research from Alex Webb’s group at the University of Cambridge features in the ARR for the second consecutive week, again on a similar topic. On this occasion they collaborate with Japanese colleagues to investigate the role of the circadian clock on determining the nighttime usage rate of starch that has accumulated during the day. They used a phase oscillator model to explain the link between the speed of the clock, starch breakdown and the maintenance of sucrose homeostasis. In addition they use Arabidopsis sugar response mutants to show that the circadian clock measures amount of cellular sucrose, which then controls the dynamics of starch breakdown.


Karpinska B, Alomrani SO, Foyer CH (2017) Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling. Philos Trans R Soc Lond B Biol Sci. 10.1098/rstb.2016.0392 Open Access

Christine Foyer (University of Leeds) is the corresponding author on this paper that looks at the effect of cellular oxidation on retrograde signaling between chloroplasts, mitochondria and the nucleus. They use a novel in vivo redox reporter to measure the effect of commonly used organelle inhibitors on cellular redox state. They discovered that these inhibitors cause a variety of effects on redox state and gene expression, which differed dependent on cell type. Researchers should be aware of these effects when they are drawing conclusions from their own experiments using these inhibitors.


Wilson DC, Kempthorne CJ, Carella P, Liscombe DK, Cameron R (2017) Age-Related Resistance in Arabidopsis thaliana Involves the MADS-domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol Plant Microbe Interact 10.1094/MPMI-07-17-0172-R

Phillip Carella is a Research Fellow at SLCU and this work from this previous lab in Canada investigates Arabidopsis Age-Related Resistance (ARR), a process that requires SA accumulation, which is then thought to act as an antimicrobial agent. The ARR response is lacking in plants containing a mutation in for the SHORT VEGETATIVE PHASE (SVP) gene. These svp plants have reduced SA, thought to be due to uncoupled overactivity of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 gene. Overall this study shows that the flowering time gene SVP plays a complementary role in the control of SA accumulation, which confers ARR to older plants.


Fernie AR, Bauwe H, Sweetlove LJ (2017) Investigating the Role of the Photorespiratory Pathway in Non-photosynthetic Tissues. Methods Mol Biol 10.1007/978-1-4939-7225-8_15

Lee Sweetlove (University of Oxford) describes a protocol for evaluating the role of the photorespiration on the control of growth in non-photosynthetic tissues. This can be scaled for use in both Arabidopsis and in larger plants.

Steven Spoel talks to GARNet

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Published on: August 10, 2017

Steven Spoel (University of Edinburgh and current GARNet chairman) talks to GARNet about a recent paper in PNAS entitled ‘Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes‘. Read more about Steven’s lab here.

Meeting Report: ICAR2017 in St Louis.

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Published on: August 4, 2017

Thanks to Janina Tamborski from The Sainsbury Lab in Norwich for providing this excellent meeting report!


The most exciting (and to some the scariest) part of a large scientific conference such as the International Conference on Arabidopsis Research (ICAR) is finding the right opportunity to talk to leading scientists. Sometimes it is all about thinking on your feet, as was the case for me when my colleague knocked my drink out of my hand, resulting in a soda fountain that splashed all bystanders. Luckily one of them was Wolfgang Busch, who I had been meaning to talk to after his exciting seminar but previously lacked an opportunity to approach. After I apologised, we had a very productive discussion, proving that you can make lemonade when life gives you lemons (or a lemonade fountain).

The 28th ICAR 2017 was held at the Hyatt and Donald Danforth Plant Science Center in St. Louis. With four keynote speakers, nine plenary, nine concurrent and two poster sessions, as well as six community organised workshops, it brought together many of the best scientists in Arabidopsis research. In addition to the five-day scientific program, there were also two career workshops for early career scientists that featured panellists from both academia and industry. The mixers afterwards offered career ideas and the opportunity to further expand ones’ professional network.

Image from @huotbethany

The four keynote speakers represented the wide range of topics pursued in Arabidopsis research: Sabeeha Merchant talked about a day in the life of Chlamydomonas, Mary Lou Guerinot about ionomics and gene discovery, Keiko Torii shared her latest breakthroughs in synthetic biology and Sheng Yang He wanted to achieve understanding of the disease-climate-microbiome triangle. Keiko Torii (Washington University) amazed the audience with her interdisciplinary approaches that arose from her close collaboration with researchers at the Institute of Transformative Bio-Molecules at Nagoya University. By engineering the auxin receptor TIR1 and creating a synthetic auxin ligand, she was able to show that the acid growth response is mediated by the TIR1 pathway. This is a prime example of how synthetic biology approaches can help us find answers to questions that have proven poorly tractable in genetics. Together with her screen of chemicals that influence stomatal patterning, her research promises to yield exciting results for us to watch out for in the future.


Of particular interest to me were the great talks on how Arabidopsis interacts with and manipulates its environment. Paul Schulze-Lefert’s (MPI Cologne) work focussed on the microbiome of Arabidopsis and in particular on the endophyte C. tofildiae and its ability to promote growth and reproductive success of Arabidopsis under phosphate-limiting conditions. A successful interaction requires the host to have a functioning phosphate starvation response system and the ability to suppress its innate immunity. Cara Haney (The University of British Columbia) identified 93 genes and 63 operons in P. fluorescens that are required for survival on Col-0. She furthermore compared bacterial strains that trigger Induced Systemic Resistance (ISR) or Induced Systemic Susceptibility (ISS) that are 98% identical in their 16S RNA. Her lab identified a gene cluster that differs in ISS strains and she proposed that the production of spermidine through polyamine synthases is responsible for ISS.

Niko Geldner (University of Lausanne) showed advances in understanding transport in the root and how the mutually exclusive localisation of lignin and suberin creates an active zone of uptake. Research from his group demonstrated that patchy transporter expression in roots correlates with the position of passage cells, forming a funnel-like pattern of cells to enable nutrient uptake in mature roots. Ute Kraemer (Ruhr University Bochum) unveiled how Arabidopsis thalianas’ relative A. halleri, who can thrive on metalliferous soils, prevents cadmium accumulation and poisoning of the seeds. This cadmium tolerance is associated with a sequence polymorphism in HMA2 that leads to an early stop codon and renders the protein non-functional. Gregory Vert uncovered how the metal transporter IRT1 controls its own stability through recruitment of CIPK23 after excess metal conditions. CIPK23 consequently phosphorylates the E3 ligase IDF1 that mediates IRT1s K63 ubiquitination and leads to its endocytosis and degradation in the vacuole.


I particularly enjoyed the session “Novel Approaches”, which showcased exciting tools from hormone biosensors (Alexander Jones, SLCU) to two-photon excitation microscopy (Minako Ueda, Nagoya University) and genome editing techniques (Dan Voytas, Minnesota Center of Genome Engineering). As a cell biologist, I could not help but be amazed by the images shown by Minako Ueda that showed cytoskeleton dynamics in the zygote in astonishing detail thanks to the high resolution achieved through two-photon excitation imaging.

Image from @huotbethany

The meeting was rounded off by the last keynote speaker Sheng Yang He (Michigan State University) who managed to convey complex immune resistance and susceptibility concepts in an accessible manner. He discussed his recent publication that showed that bacterial effectors promote pathogenicity by transforming the air-filled apoplast into an aqueous environment for bacteria to flourish. His elegant approach to engineer the common host target COI1 to break the evolutionary dilemma of salicylic acid signalling was a case-study in the success of rational design in synthetic biology.


The 29th ICAR2018 will be held from the 25-29 June in Turku, Finland. I am excited to see how Arabidopsis continues to evolve. I hope to see the changes made at ICAR2017 continue, including the shift in hormone research from auxin-dominated to a focus on other hormones, in particular the brassinosteroids. Synthetic biology approaches were emerging in all disciplines and ranged from novel biosensors to receptor engineering. For the first time there was also an exciting session on translational biology that I would like to see again next year. I cannot wait to see what the conference in Turku next year has to offer.

SEB Plant Symposium on New Breeding Technologies

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Published on: July 30, 2017

Thanks to Iulia German from the University of York and the Warwick Integrative Synthetic Biology Centre for providing this outstanding review of the SEB plant section symposium.


At the beginning of July, Gothenburg was host to a fascinating discussion on New Breeding Technologies (NBTs), attended by scientists from 17 countries. This covered the applications of the technologies themselves, their legal status in the EU, and the rest of Europe, and the US, and Australia and New Zealand, the importance of getting the general public involved early in discussions about NBTs, and whether CRISPR-modified cabbage really does taste better than cabbage modified only through conventional breeding.

Image from Molecular Plant Pathology October 2016 issue. Pyott et al. engineered Turnip Mosaic Virus-resistant Arabidopsis and created letters in trays by infecting wildtype and CRISPR-Cas9-engineered mutants with the virus.

This Society for Experimental Biology plant section symposium was very timely given the increasing trendiness of CRISPR-Cas9 for editing plant genomes, the legal limbo of the technology in EU courts, and the lack of public awareness of CRISPR and what it can do.

From the Web of Science. While not as extreme as the overall trend, there is still a growth in published papers using CRISPR-Cas9.

While the efficiency of CRISPR-Cas9 in plants seems to be limited in comparison to animal cells, this appears to come with the unexpected benefit of fewer off-target effects. In fact the frequency of off-target mutations is even lower than that observed during chemical/physical mutagenesis. This does make for a hard time screening thousands of plants but that is worth it for people like Mariette Andersson, who is looking to bring a new variety of potato to market years faster than would be possible using conventional technologies, and Jean-Denis Faure who is generating Camelina sativa lines with different amounts of oleic acid content by targeting different combinations of FAD2 alleles in its hexaploid genome. Not to mention that it’s possible to screen for plants that have desired mutation but are CRISPR-cas9 transgene free (like in Attila Molnar’s work to create potyvirus-resistant Arabidopsis).

The variety and flexibility of CRISPR gene editing is increasing, with the possibility for nicks, double-stranded breaks, Cas9-nuclease fusions, dead Cas9-repressor/activator fusions, polycistronic systems, and a myriad of promoters and terminators to choose from.


The second point of discussion, the legal debate surrounding CRISPR is nicely summarised in this SEB article. It started with a history lesson on GMO regulation in the 70s after the ability to transfer genes from any organism to any other organism sparked safety discussions and a moratorium as laid out by the 1974 Paul Berg letter. The US was then first to develop regulations against these novel organisms. As a side note, the reason “novel” organisms are regulated rather than “risky” organisms is mainly because in a legal context it was easier to define something novel than something risky – however this has encouraged the train of thought that “novel” organisms are somehow more dangerous than “natural” organisms (another thing that emerged from this NBT meeting is how much scientists hate misuse of the word “natural”). All countries seem to have some legal variation on this “novel organism” theme, with some more lenient than others – Canada for example does not regulate plants with novel traits that do not possess an environment risk.

However, this process-based regulation is very outdated and not reflective of the current situation and advances in biotechnology. It would be better to include product-based rather than process-based rules ie plants should not be regulated based solely on the methods used to produce them (process-based) but based on the risks presented by the GM plant products.

There is no strict regulation if the technique involves mutagenesis, transfer of genes from sexually compatible organisms or non-inheritable changes. As CRISPR-edited plants fall into the “mutagenesis” category, we agreed that the same regulation should apply.
The crux of the debate surrounding NBTs: are they more like conventional breeding techniques or gene modification techniques? Image from: [1]


The world (other than Sweden and Denmark, which have declared that CRISPR-edited organisms are not GM) is looking to the EU to lead the way in making regulations, but the EU has been stalling.

As to how to present CRISPR to the public, the situation boils down to: people make decisions based on their principles and beliefs when presented with very complex information, so if scientists unite behind one success story for CRISPR that will appeal to people’s imagination and values, then the battle is half won. It’s all about planting the flag early. As Craig Cormick learned from surveying Australians, the bulk of the population is neither highly opposed to or greatly in favour of new technologies (they are penguins – image below). Given convincing arguments, they are likely to move to either side. In the case of NBTs, the public are not likely to be in favour of them without being given a context: it’s the difference between asking “What do you think of CRISPR – should it be used?” and “What do you think of using CRISPR to make X product?”

Image from Craig Cormick

The public’s attitudes towards new technologies: at polar ends of the spectrum are small groups of “polar bears” which are either highly opposed to or highly in favour of the technology. Most of the population falls into a cautious group in the middle who decides based on the risks presented and the application of the technology.


One of the organisers, Swedish Stefan Jansson, has been doing a fair bit to normalise the use of NBTs in food by growing his own CRISPR-modified cabbage and cooking up a feast with it. The recipe for tagliatelle with CRISPRy fried vegetables, along with Stefan’s blog detailing how he grew the cabbage, fought moths and ate the first CRISPR meal ever with reporter Gustaf Klarin, can be found here. He’s gone on tour with his cabbage to countries like Norway in order to start a discussion and hopefully persuade the legal authorities to pass the same laws as Sweden regarding the classification of NBTs. He is also adamant about refusing to say what has been modified in the cabbage – good luck finding a targeted point mutation amongst all the other spontaneous mutations that arise in the genome! What we do know for sure is that CRISPRy cabbage tastes delicious – especially when prepared by the culinary geniuses at Sjömagasinet.

All in all, the SEB New Breeding Technologies was a fantastic meeting, with great food and company. I’m always looking forward to the GARNet plant gene editing workshop at the University of Bristol on March 26-27th 2018!

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