Arabidopsis Research Roundup: July 3rd.

The Arabidopsis Research Roundup returns this week with selection of publications from institutions across the UK. Firstly George Bassel (Birmingham) leads a study that investigates the integration of inductive signals in the embryonic root. Secondly a group from the Oxford Brookes plant science group look into the literal linkages between the golgi apparatus and ER. Thirdly John Christie (Glasgow) and co-workers define a new variant of the phototropin receptor. Next Caroline Dean and Martin Howard (John Innes Centre) collaborate on work that defines the relationship between FLC, COOLAIR and cell size. The fifth paper is led by members of SLCU and investigates the regulatory influence of the Evening Complex of the circadian clock. The penultimate paper features work from Alison Smith’s group at the JIC that looks at dynamics of starch accumulation and degradation. Lastly is research from NIAB that defines the pathogeniticity of novel UK isolates of the fungal pathogen Verticillium longisporum.

Topham AT, Taylor RE, Yan D, Nambara E, Johnston IG, Bassel GW (2017) Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds. PNAS


Open Access

George Bassel (University of Birmingham) leads this study that identifies a decision making centre in the embryonic root that is defined by the intimate interaction between the hormones abscisic acid (ABA) and gibberellin (GA). The activity of this ‘decision centre’ is linked to both hormone transport and changes in temperature, the overall output of which is the decision to promotes seed germination or to delay until more favourable environmental conditions.

George discusses this paper on the GARNet YouTube channel.

Osterrieder A, Sparkes IA, Botchway SW, Ward A, Ketelaar T, de Ruijter N, Hawes C (2017) Stacks off tracks: a role for the golgin AtCASP in plant endoplasmic reticulum-Golgi apparatus tethering. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx167

Open Access

Anne Osterrieder and Chris Hawes (Oxford Brookes University) continue their work that looks at  the cellular dynamics of the golgi apparatus with this study that identifies the AtCASP protein as a important component that tethers the golgi to the ER. They use live-cell imaging to visualise golgi formation in cells that have different levels of AtCASP, allowing the authors to confirm that ER-golgi tethering is disrupted without the activity of this protein.

Petersen J, Inoue SI, Kelly SM, Sullivan S, Kinoshita T, Christie JM (2017) Functional Characterization of a Constitutively Active Kinase Variant of Arabidopsis Phototropin 1

J Biol Chem. http:/​/​dx.​doi.​org/10.1074/jbc.M117.799643

Open Access

John Christie (University of Glasgow) collaborates with Japanese colleagues to identify a novel variant of the phototropin receptor. Study of this variant allows a greater understanding regarding the mode of action of this protein under different light conditions, as controlled by phosphorylation.

Ietswaart R, Rosa S, Wu Z, Dean C, Howard M (2017) Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation. Cell Syst. http:/​/​dx.​doi.​org/10.1016/j.cels.2017.05.010

Open Access

Martin Howard and Caroline Dean (John Innes Centre) again collaborate on research that analyses the mode of regulation of FLC. They dissect RNA dynamics of FLC expression by single molecule in situ RNA fluorescence, showing that this is dependent on the presence of the antisense COOLAIR regulatory DNA. In the absence of COOLAIR they show FLC expression has a linear relationship with cell size but in the presence of the antisense transcript, FLC expression decreases with cell size. Overall they demonstrate FLC expression is tightly dependent on the presence of the antisense COOLAIR transcript.

Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V,, Cortijo S, Lai X,, Stöckle D, Zubieta C, Jaeger KE, Wigge PA (2017) The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat Plants.


Free to view with this URL.

Phil Wigge and Katja Jaeger (SLCU) lead this study that investigates how the evening complex of the circadian clock coordinates the expression of numerous important growth regulators. This genome wide regulation is determined by temperature and concides with the binding of phytochrome B, which provides a cellularly mechanism of this level of environmental control.

Fernandez O, Ishihara H, George GM, Mengin V, Flis A, Sumner D, Arrivault S, Feil R, Lunn JE, Zeeman SC, Smith AM, Stitt M (2017) Foliar starch turnover occurs in long days and in falling light at the end of the day. Plant Physiol. http:/​/​dx.​doi.​org/10.1104/pp.17.00601

Open Access

On this paper Alison Smith (John Innes Centre) is a co-corresponding author together with Mark Stitt from the Max Planck Institute for Molecular Plant Physiology in Potsdam. They continue their work to investigate the dynamics of starch metabolism in Arabidopsis leaves. Broadly they show the rate of starch accumulation corresponds to the photosynthetic rate whilst degradation is linked to correct functioning of the circadian clock. They investigate this process in more detail by determining how the rate of starch degradation alters dependent on the time after dawn.

Depotter J, Rodriguez-Moreno L, Thomma BP, Wood T (2017) The emerging British Verticillium longisporum population consists of aggressive Brassica pathogens. Phytopathology http:/​/​dx.​doi.​org/10.1094/PHYTO-05-17-0184-R

Tom Wood (NIAB) is the corresponding author of this study that characterises four new UK isolates of the fungal pathogen Verticillium longisporum. The pathogenticity of V.longisporum was tested on Arabidopsis alongside three other Brassica crops. They demonstrate that the UK isolates were unusually aggressive yet this was not consistent across all Brassica cultivars with different fungal lineages showing different effects on oil seed rape, cabbage or cauliflower.

End of an Era at GARNet

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Published on: June 30, 2017

Today is a sad one at GARNet HQ as we are losing Ruth Bastow to pastures new (a position with ELIXIR at the Earlham Institute).

Ruth has been involved with GARNet for well over a decade, first as full time coordinator and more recently as the part-time support for Charis Cook and myself.

Over those years Ruth has established GARNet as the respected voice for UK academic plant sciences. She is rightly extremely well regarded by the few who have served on the advisory board, the many who attended the (now) biennial GARNet meeting or the thousands who have used the resources on the GARNet website.

During this time Ruth’s vision has grown broader as she has played significant roles in the establishment of both the UK Plant Science Federation and the Global Plant Council. Without her vision none of these organisations would have survived so it is important that those of us still involved respect her legacy by focusing on maintaining the strength of these organisations.

One of Ruth’s finest contributions to the UK Plant Science community was in the organisation of the International Conference for Arabidopsis Research (ICAR) in Edinburgh in 2009. Hopefully the community can again bring this excellent meeting back to the UK in the coming years…

On a personal level it has been a pleasure to be Ruth’s friend and colleague since we met as starting PhD students at the University of Warwick in 1997(!).

Best of luck to Ruth in her new role. Fortunately for us and the entire global plant science community she will remain as an advisor for both GARNet, the GPC and the Multinational Arabidopsis Steering Committee (MASC).

ICAR2017 Review

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Published on: June 28, 2017

Last week the excellent International Conference on Arabidopsis Research (ICAR) took place in St Louis. This global meeting moves between North America, Europe and Asia on a rolling three year cycle. This years attendance was less than in recent years but for that reason it provided a great opportunity for attendees to get to grips with the excellent science in the presentations and the poster sessions without being overwhelmed by the amount of information.

The full abstract book can be downloaded here.

The meeting included an excellent amount of interaction on social media, which included plenty of dedicated tweeters! Bethany Huot has done a great job of putting the activity from the twitterverse into these daily Storify articles. Please take a look at them.

Day 1: So it begins

Day 2: ROAR on!

Day 3: The Weed Stampede.

Day 4: Rocking and Rolling.

Day 5: Finding our Quiescent Centre.

During the after-conference come-down and return to ‘normal’ life it can be difficult to keep track of what you heard and why it was important. Therefore we have put together a file that lists the speaker affiliation and the research that they discussed during their talks. Sorry this is limited to the talks that GARNet attended…

Down the review here (excel file): ICAR17_Review

The ICAR2018 meeting will be in Turku, Finland. See you there!


Arabidopsis Research Roundup: June 6th

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Published on: June 5, 2017

This weeks Arabidopsis Research Roundup includes three studies that are led from Norwich Research Park and another from the University of Nottingham. In the latter case Rupert Fray leads an investigation into the scarcely researched process of N6-adenosine methylation of RNA. The next two papers involve members of the Sainsbury lab in Norwich and investigate either the RPS4-RRS1 or FERONIA-LLG1 defence signaling pathways. Finally is a study that originates from the John Innes Centre links the defence response with biotic predation and calcium signaling.

Růžička K,, Zhang M, Campilho A,, Bodi Z, Kashif M, Saleh M, Eeckhout D,, El-Showk S, Li H,, Zhong S,, Jaeger G,, Mongan NP, Hejátko J, Helariutta Y,, Fray RG (2017) Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol. http:/​/​dx.​doi.​org/10.1111/nph.14586

Open Access
Rupert Fray (University of Nottingham) is the corresponding author on this global collaboration that investigates the poorly understood yet essential phenomenon of mRNA N6-adenosine methylation (m6A). They used a combination of experimental techniques to identify a range of proteins that are necessary for this process. These proteins include the E3 ubiquitin ligase HAKAI that, when its expression is reduced, causes a range of phenotypes, including aberrant root vascular formation. The targets of the HAKAI E3 ligase are still to be determined but the authors suspect that this type of interaction will have relevance across eukaryotic species.

Huh SU, Cevik V, Ding P, Duxbury Z, Ma Y, Tomlinson L, Sarris PF, Jones JDG (2017) Protein-protein interactions in the RPS4/RRS1 immune receptor complex. PLoS Pathog.

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006376 Open Access

Jonathan Jones (The Sainsbury Laboratory, Norwich) leads this UK-funded study that includes collaborators from Bath and Exeter and looks into the function of the RPS4-RRS1 immune signaling complex. During the course of the paper they define the sub-cellular binding relationships between plant proteins RPS4, RRS1, EDS1 along with the pathogen effector AvrRps4. Furthermore they show that these protein interactions differently interact with PAD4 or SAG101. The authors demonstrate that this immune complex is highly dynamic during effector recognition and that altered proportions of each member disrupts the defence response.

Shen Q, Bourdais G, Pan H, Robatzek S, Tang D (2017) Arabidopsis glycosylphosphatidylinositol-anchored protein LLG1 associates with and modulates FLS2 to regulate innate immunity. PNAS http:/​/​dx.​doi.​org/10.1073/pnas.1614468114 Open Access

Silke Robatzek (The Sainsbury Laboratory, Norwich) is a co-author on this Chinese-led study that investigates the role of the FERONIA signaling complex in the response to pathogen PAMPs. They show that LORELEI-LIKE GPI-ANCHORED PROTEIN 1 (LLG1) is a FERONIA co-receptor and that plants deficient in llg1 are more susceptible to various pathogens even though these plants do not show general growth defects. Overall the authors show that as a coreceptor of FERONIA, LLG1 plays a central role in many PAMP-dependent signaling pathways and is a candidate for future research in this area.

Vincent TR, Avramova M, Canham J, Higgins P, Bilkey N, Mugford ST, Pitino M, Toyota M, Gilroy S, Miller TJ, Hogenhout S, Sanders D (2017) Interplay of Plasma Membrane and Vacuolar Ion Channels, Together with BAK1, Elicits Rapid Cytosolic Calcium Elevations in Arabidopsis during Aphid Feeding. Plant Cell. http:/​/​dx.​doi.​org/10.​1105/​tpc.​17.​00136 Open Access

Dale Sanders and GARNet committee member Saskia Hogenhout are corresponding authors on this study that includes researchers from the JIC and the University of Wisconsin. This research focused on the role of calcium as a signal during the response to biotic stress. They combined a fluorescent calcium biosensor (GCaMP3) during aphid predation experiments. They detected elevated calcium levels that coincided with aphid probing of leaf epidermal and mesophyll cell layers. They used the power of Arabidopsis genetics to determine that a number of known signaling molecules were involved in this process, allowing them to link biotic predation, the defence response and cellular calcium movement within a single signaling network.

Botany Live Wrap Up

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Published on: June 2, 2017

Fascination of Plants Day: Botany Live
In 2012 the European Plant Science Organisation (EPSO) started global ‘Fascination of Plants Day’, an event that aimed to raise the profile of plant science and plant scientists around the world. Since two initial consecutive years this has now switched to a biannual event that has been fully embraced by people who work in on all aspects of plant science. Details of this can be found at In the UK the events were coordinated by Dr Dario Breitel at the John Innes Centre and featured events at around 30 venues around the country.

One of these events was entitled ‘Botany Live’ and was led by Anne Osterrieder who is a lecturer in Biology and Science Communication at Oxford Brookes University as well as being the editor of the Annals of Botany blog ( The aim of this event was to use the accessible online streaming resource Periscope to bring plant science into peoples’ homes and workplaces. The organisers requested that people live-stream a ‘short peek’ into their lives as plant scientists.

Keith Edwards discusses Wheat Transformation

Over the weekend of FoPD (May 18th-21st) 32 events signed up to provide a Botany Live video. The majority of these were from the US and UK but also featured videos from Lebanon and Argentina! These videos are being uploaded to the Botany Live website ( so you can go back and check out the action!
Botany Live kicked off on the evening on May 17th (UK time) with Marcela Karey Tello-Ruiz who is the coordinator of the Gramene project in New York. She live- streamed a ‘Plant Superpowers’ session in which she interacted with a group of primary school students to share the joy of amazing plants!

Official FoPD day, May 18th, also saw the majority of Botany Live events. These were kicked off by Alison Bentley providing an introduction to the NIAB Innovation Farm facility prior to the Wheat Transformation Facility Wrap up meeting (see also page 38 in this edition of GARNish). This video also featured Keith Edwards, Ben Sibbett and Sinead Drea discussing their wheat research projects (

Touring the Hounsfield Facility
Dr M goes Wild at the University of Reading!

Our event dovetailed nicely with a video from Craig Sturrock and colleagues at the University of Nottingham, who gave a tour of the Hounsfield CT scanning facility.

Throughout the (UK) afternoon there were a number of short videos from Kew Gardens that introduced some of the interesting plants that they have on site! A real video highlight was a very well choreographed livestream organized by Dr Jonathan Mitchley (aka Dr M) from the University of Reading in which he interacted with a group of school children, who gave their ‘plant highlights’.

The livestream action then crossed the pond, featuring a Q+A from the Brilliant Botany blogger Claire, a tour of the ABRC laboratory facilities at Ohio State University, as well as the greenhouse facilities at the Boyce Thompson Institute in Cornell. Later in the day, the livestream switched to focus on Argentinian Women Plant Scientists!

On Saturday May 20th researchers from the University of Glasgow featured in a really exciting set of videos from their FoPD celebration at Glasgow Botanic Gardens.

Truly it was a mixed bag of events and was an excellent first attempt at using this type of media to promote plant science. Hopefully Botany Live will be repeated again with more people taking up the challenge of putting together an interesting video for the global community……and tackling the connectivity issues relies on WiFi or a good 3G signal!

Botany Live was kindly supported by the SEB, the Annals of Botany Company, Plantae, The Quiet Branches and Oxford Brookes University.

MASC Report 2016/2017

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Published on: June 2, 2017

The Multinational Arabidopsis Steering Committee (MASC) is responsible for supporting global Arabidopsis research. This is acheived through two mechanisms:

Firstly MASC members organise the annual International Conference on Arabidopsis Research (ICAR). This meeting often welcomes up to and over 1000 delegates to a location that switches between Asia, Europe and The Americas on a three-year cycle.

This years ICAR meeting in the St Louis, USA whilst the 2018 ICAR takes place in Turku, Finland.

Secondly MASC publishes an annual report (previous report can be found here) that includes updates from the MASC subcommittees (Bioinformatics, Epigenetics and Epigenomics, ORFeomics, Metabolomics, Natural Variation, Phenomics, Proteomics, Systems and Synthetic Biology), from Project Resources (such as Araport, TAIR, uNASC etc) and updates from the twenty-eight individual MASC country representatives.

In 2017 the GARNet coordinator took on the role of the MASC coordinator and has been responsible for collating the MASC Annual Report.

The PDF of the MASC Annual Report can be downloaded here.

We would encourage taking a look at this, not least to discover information about the remarkable set of collaborative tools that are available to the global research community.

More information about MASC can be found at

NIAB Wheat Transformation Resource and BotanyLive

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Published on: May 19, 2017

On May 18th (global Fascination of Plants Day btw) I had the pleasure of attending the wrap-up meeting for the first phase of the NIAB Community Resource for Wheat Transformation Facility (CRWT) at the NIAB Innovation farm site just outside Cambridge.

The CRWT is a BBSRC resource that has provided the opportunity for plant scientists without expertise in wheat transformation (aka most people) to apply to have their gene of interest introduced into hexaploid wheat. Over the course of the grant almost 120 applications have been made to this resource and 50 genes have been pushed through the CRWT pipeline. This generates plantlets that are then sent back to the applicants for further analysis. There will be a full report from this meeting in the upcoming GARNish newsletter but suffice to say it was exciting to learn about successful applications of this technology, in particular those that have directly led into future BBSRC grants from the labs of Julie Gray (Sheffield) and Matthew Paul (Rothamsted).

As part of the #BotanyLive celebration we also put together a short video to advertise NIAB and the CRWT resource. This features Alison Bentley (NIAB), Sinead Drea (University of Leicester), Ben Sibbett (University of Southampton) and Keith Edwards (University of Bristol). You can see the full video through the Periscope website: (will open in the Periscope URL)

Arabidopsis Research Roundup: May 17th

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Published on: May 17, 2017

This weeks Arabidopsis research roundup begins with a paper led by CPIB at the University of Nottingham that discovers a somewhat surprisingly mechanism controling Arabidopsis root hydrotropism. Next are two papers from the University of Leeds that firstly investigate how the JAGGED LATERAL ORGANS gene influences the auxin response and secondly looks at the role of redox regulation in the control of the cell cycle and seed development. Finally are two papers that look at different aspects of the plant pathogen interactions. Jonathan Jones from the John Innes Centre is a co-author on a paper that dissects the multiple gene expression networks that control plant immunity whilst Charles Melnyk at the Sainsbury lab in Cambridge is involved with work that investigates the hormonal control mechanisms that influence the invasion of parasitic plants.

Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM,, Owen MR,, Band LR,, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ,, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants


Open Access via access link:

Malcolm Bennett (University of Nottingham) leads a broad international collaboration that looks at the response of Arabidopsis roots to water. Surprisingly they show that this response occurs not in the root meristem but in the elongation zone and is controlled by a ABA signaling mechanism. They show that hydrotropism is dependent on cell elongation in the cortex but not in any other cell file. This is different to the gravitropic response and demonstrates that these tropisms are controlled by distinct tissue-specific mechanisms. To provide for information about this paper, lead author Daniela Dietrich joins Professor Bennett to discuss this paper on the GARNet YouTube channel and speculate on the function of different root cell layers in water uptake.

Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R (2017) The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx131 Open Access

This German-led study includes Stefan Kepinski (University of Leeds) as a co-author. They investigate the role of the JAGGED LATERAL ORGANS (JLO) transcription factor in the establishment of the stem cell niche in the root meristem. JLO interacts with auxin signaling pathway by influencing the degradation of the key regulator BODENLOS (BDL) via the TIR1-mediated degradation pathway. In jlo mutants BDL remains present in the meristem, which does not correctly develop. They discover a novel regulatory mechanism wherein the dosage of the TIR1 and AFB1 auxin receptors is reduced, which in turn prevents BDL degradation. This shows that the JLO transcription factor is a key upstream regulator of meristem formation by playing a significant role in the fine control of the auxin response.

De Simone A, Hubbard R, Vinegra de la Torre N, Velappan Y, Wilson M, Considine MJ, Soppe W, Foyer CH (2017) Redox changes during the cell cycle in the embryonic root meristem of Arabidopsis thaliana. Antioxid Redox Signal. http:/​/​dx.​doi.​org/10.1089/ars.2016.6959

Open Access

Christine Foyer (University of Leeds) collaborates with Australian and German researchers to unpick the role that redox regulation plays in the control of the plant cell cycle. They use an in vivo redox reporter (roGFP2) to show that a cycle of reduction and oxidation occurs throughout the cell cycle. Their experimental system is Arabidopsis seed germination and they show that vitamin c defective mutants with low redox buffering capacity have altered germination rates that coincide with a changed dry seed transcriptome. Overall this paper demonstrates that the cell cycle and embryo size are linked to redox regulation.

Hillmer RA, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jones JDG, Myers CL, Katagiri F (2017) The highly buffered Arabidopsis immune signaling network conceals the functions of its components. PLoS Genet. http:/​/​dx.​doi.​org/10.1371/journal.pgen.1006639

Open Access

Jonathan Jones (John Innes Centre) is a co-author on this Japanese-led research that studies the signaling networks invovled in plant immunity. They use a systems biology approach to dissect the network of interactions that occur within the transcriptome when plants are exposed to the immune stimulant flagellin-22. This analysis discovers that there are separated networks that represent pathways controlled by different higher-level signals, such as jasmonate or salicylic acid. This provides the entire network with a degree of buffering that allows a more effective response to pathogen attack. This type of network analysis is able to reveal facets of the defence response that would not be possible when using simple null mutant analysis so adds consideration detail to the already complicated story of plant-pathogen interactions

Spallek T, Melnyk CW, Wakatake T, Zhang J, Sakamoto Y, Kiba T, Yoshida S, Matsunaga S, Sakakibara H, Shirasu K (2017) Interspecies hormonal control of host root morphology by parasitic plants. PNAS


Charles Melnyk (Sainsbury Lab, Cambridge) is an author on this study led by Ken Shirasu at RIKEN and uses Arabidopsis to investigate the relationship between parasitic plants and their hosts, specifically at the level of interspecies transport via a structure called the haustorium. Haustoria are structures through which substances, such as RNA and proteins, reciprocally move between host and parasite. In this paper they look at the interaction between Arabidopsis roots and the hemiparasitic plant Phtheirospermum japonicum, demonstrating that movement of molecules between species occurs via haustoria once a vascular connection is made. Arabidopsis secondary root growth is induced under infection, a response that requires the effect of the hormone cytokinin. They look at the genetics of this interaction and show that cytokinin signaling genes are important in establishing root hypertrophy. Overall this study demonstrates the important of cytokinin during infection with parasitic plants and might be an important target to design strategies to combat these negative interactions in systems.

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