Weeding the Gems

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).

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!

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.

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 http://www.plantday.org/. 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 (https://aobblog.com/). 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 (https://botany.live/events/) 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! https://www.pscp.tv/w/1yoJMBLXagDxQ

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 (https://www.pscp.tv/w/1nAKEBqpYolGL).

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.

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 Arabidopsisresearch.org