GARNet2018: A Plant Science Showcase

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Published on: November 20, 2018

GARNet2018: A Plant Science Showcase

University of York: September 18th-19th

Meeting Website: https://garnet2018.weebly.com/

The biannual GARNet meeting was hosted by GARNet committee member Andrea Harper in the Ron Cooke Hub at the University of York. The aim of this two-day meeting was to showcase current technology and expertise both in UK and international plant science. To that end the GARNet Advisory Committee developed a program that included a mix of early career researchers and more established faculty. In order to support ECRs the meeting included fifteen two-minute flash talks that allowed delegates to introduce their posters before the official poster session. Added to the 10 speakers selected from submitted abstracts, the meeting gave opportunities for 25 registered delegates to present their work in a short talk.

The meeting was split into five sessions and was introduced by the GARNet chairman Jim Murray who highlighted GARNet achievements over the past four years and our plans for the future[1]. The first session was entitled ‘Large Scale Biology’ and was highlighted by Cristiane Calixto from the James Hutton Institute who provided an exciting, enthusiastic talk about their development of a new annotation for the Arabidopsis genome that provides additional support for alternatively spliced variants. In particular they are interested in plant responses to cold temperature as highlighted in a recent publication in The Plant Cell[2].

Cristiane confirmed that all of the data they have produced is freely available to the community which dovetailed nicely with the next presentation provided by Professor Andrew Millar who gave an introduction to the principles and benefits of open data in a talk entitled ‘Being more Open by Being more Productive’. Professor Millar’s talk is available online at the GARNet YouTube page[3]. In addition to this formal talk Andrew also hosted a lunchtime discussion session in which attendees gave their personal and institutional experiences of using and providing open data.


Tom Bennett presenting his thought-provoking work

Lucia Strader from Washington University in St Louis provided the opening talk in the second session that was entitled ‘Innovations in Hormone Signaling’ where she gave an overview of her group’s discoveries of novel aspects of the auxin response. Tom Bennett (University of Leeds) also gave a thought-provoking talk about the ways in which plants decide the number of flowers and branches that it ultimately forms.
Branching was the theme of the keynote talk that was provided by Ottoline Leyser who, as a previous GARNet PI and academic at the University of York , returned ‘home’ to give an overview of her group’s work on the hormone signals that control the growth of lateral buds.

The highlight of Session III: Interacting with the environment was a talk by Richard Buggs from Kew Science and QMUL that updated his current work that aims to tackle the progression of Ash Dieback. He started his talk with an amended quote from Tolstoy’s Anna Karenina that promoted the importance of model organisms and in particular Arabidopsis:

‘….in getting to know thoroughly one’s plant species, one gets to know all plant better than if one knew thousands of them….’.

Richard’s talk was really enthusiastic and highlighted why he has been such an excellent advocate for ash dieback research in the UK and beyond.


The incredible tools for wheat research presented by Cristobal Uauy

Contrary to some thoughts, GARNet activities support more than just research in Arabidopsis and Session IV: Out of Arabidopsis highlighted the great UK research occurring in Wheat and Brassica. Cristobal Uauy (John Innes Centre) and colleagues in the global wheat community have produced a remarkable set of genomic, mutant and phenotyping resources. These new tools are now establishing wheat as a viable model to conduct both mutant studies and the type of cell and molecular biology analysis previously only possible in more accessible genetic models[4]. Also working at the John Innes Centre, Rachel Wells is the project coordinator of the BBSRC-sponsored BRAVO project that aims to improve reliability, yield and quality in Brassica oilseed crops and includes a broad consortium of UK researchers[5].

George Bassel (University of Birmingham) chaired the final session that was broadly titled ‘Novel methods in Cell Biology and Imaging’ and also presented an exciting talk on his work that aims to quantify the factors that control interactions between cells and allow them to arrange into organs. The final plenary was provided by Minako Ueda who travelled from Nagoya for the meeting. Minako excitedly presented her outstanding live images of the events that occur during zygote formation and early embryogenesis. It was a fitting end to a meeting that was characterised throughout by excellent science.


The approximately 80 delegates who attended the meeting included a majority of people from Northern universities; Leeds, York and Edinburgh. Very few delegates travelled from major plant science centres in the south of the UK. It is unclear whether the schedule was not of interest or whether researchers didn’t want to venture too far north! However this geographic distribution of delegates does highlight the importance of GARNet arranging events all around the UK.

Following the meeting we circulated a survey to delegates. Although only 19 delegates asked the questions it showed the majority very much enjoyed the meeting. However some aspects of the meeting weren’t perfect especially with the scheduling and arrangement of the second poster session. As ever we will learn from these less-than-optimal aspects of the meeting!

Thanks to SEB, British Society of Plant Pathology, the High Value Compounds from Plants Network and all our other sponsors for their support[6].


[1] https://www.youtube.com/watch?v=s44swqdW4sM

[2] http://www.plantcell.org/content/30/7/1424

[3] https://www.youtube.com/watch?v=gbuiXBH00Lw&t=150s

[4] http://www.wheat-training.com/

[5] https://www.jic.ac.uk/bravo/

[6] https://garnet2018.weebly.com/sponsors.html

GARNet Research Roundup: November 1st 2018

This week’s GARNet research roundup again features papers on a variety of topics. First is work from the University of Leeds that investigates the physical properties of callose:cellulose hydrogels and the implication for cell wall formation. Second is work from the University of York that assesses the role of the HSP90.2 protein in control of the circadian clock. The third paper features GARNet committee member Sarah McKim and looks at the genetic control of petal number whilst the next paper from the Universities of Warwick and Glasgow includes a proteomic analysis of different types of secretory vesicles.

The next two papers look at different aspects of hormone signaling. Firstly Alistair Hetherington from the University of Bristol is a co-author on a study that looks at the role of the BIG protein whilst Simon Turner’s lab in Manchester investigates the role of ABA in xylem fibre formation.

The penultimate paper includes Lindsey Turnbull from the University of Oxford and looks at the stability of epialleles across 5 generations of selection. Finally is a paper that includes researchers from TSL in Norwich who have contributed to a phosphoproteomic screen to identify phosphorylated amino acids that influence the defence response.


Abou-Saleh R, Hernandez-Gomez M, Amsbury S, Paniagua C, Bourdon M, Miyashima S, Helariutta Y, Fuller M, Budtova T, Connell SD, Ries ME, Benitez-Alfonso Y (2018) Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures. Nature Communications DOI: 10.1038/s41467-018-06820-y

https://www.nature.com/articles/s41467-018-06820-y

Open Access
Radwa Abou-Saleh is lead author on this work from Yoselin Benitez-Alfonso’s lab at the University of Leeds. (1,3)-β-glucans such as callose play an important role in plant development yet their physical properties are largely unknown. This study analyses a set of callose:cellulose hydrogel mixtures as a proxy for different cell wall conditions. They show that callose:cellulose hydrogels are more elastic than those composed of only cellulose, providing evidence that the interactions between cellulose and callose are important for the structural features of cell walls.


Davis AM, Ronald J, Ma Z, Wilkinson AJ, Philippou K, Shindo T, Queitsch C, Davis SJ (2018) HSP90 Contributes To Entrainment of the Arabidopsis Circadian Clock via the Morning Loop. Genetics. doi: 10.1534/genetics.118.301586

http://www.genetics.org/content/early/2018/10/18/genetics.118.301586.long

Open Access
Amanda Davies is the first author on this study from Seth Davies’ lab at the University of York in which they assess the role of the molecular chaperone HSP90.2 on function of the circadian clock. The show hsp90.2-3 mutant plants have a lengthened circadian period with a specific defect in the morning. This data allows the authors to better understand the pathway through which HSP90.2 functions to entrain the circadian clock.


Monniaux M, Pieper B, McKim SM, Routier-Kierzkowska AL, Kierzkowski D, Smith RS, Hay A. The role of APETALA1 in petal number robustness. Elife. doi: 10.7554/eLife.39399

https://elifesciences.org/articles/39399

Open Access
GARNet committee member Sarah McKim is a co-author on this paper, that is led by Marie Monniaux, which includes research from her time at the University of Oxford. This work from the Hay lab in Cologne compares petal number in Arabidopsis thaliana, in which the number is invariant, and Cardamine hirsute, in which it varies. They show that petal number robustness can be attributed to the activity of the APETALA1 (AP1) floral regulator and that AP1 masks the activity of several genes in Arabidopsis but not in Cardamine.


Waghmare S, Lileikyte E, Karnik RA, Goodman JK, Blatt MR, Jones AME (2018) SNAREs SYNTAXIN OF PLANTS 121 (SYP121) and SYP122 mediate the secretion of distinct cargo subsets . Plant Physiol. doi: 10.1104/pp.18.00832

http://www.plantphysiol.org/content/early/2018/10/23/pp.18.00832.long

Open Access

This collaboration between the Universities of Glasgow and Warwick is led by Sakharam Waghmare, who works with Mike Blatt in Glasgow. This study uses proteomic approaches to characterise the secretory cargos within vesicles decorated with either of the SNARE proteins SYNTAXIN OF PLANTS 121 (SYP121) or SYP122. Genetic analysis suggests that SYP121 and SYP122 have redundant functions but this new research is able to identify cargo proteins that are either contained within both types of vesicle or that are specific to one or the other.


Zhang RX, Ge S, He J, Li S, Hao Y, Du H, Liu Z, Cheng R, Feng YQ, Xiong L, Li C, Hetherington AM, Liang YK (2018) BIG regulates stomatal immunity and jasmonate production in Arabidopsis. New Phytol. doi: 10.1111/nph.15568

Alistair Hetherington is a co-author on this China-based study led by Ruo‐Xi Zhang from Wuhan. This work adds to some recent interest in the BIG protein; in this study showing that it is involved in the interaction between JA and ethylene signaling during stress responses. In a complex set of interactions they show that the BIG protein differently alters opposing arms of the JA signaling pathway providing additional evidence that this protein is a key regulator of plant hormone signaling, albeit by a set of as yet unknown mechanisms.


Campbell L, Etchells JP, Cooper M, Kumar M, Turner SR. An essential role for Abscisic acid in the regulation of xylem fibre differentiation. Development. doi: 10.1242/dev.161992

This work from Simon Turner’s lab at the University of Manchester is led by Liam Campbell and identifies a novel role for ABA in the formation of xylem fibres during secondary thickening of the Arabidopsis hypocotyl. The action of ABA doesn’t alter the xylem:phloem ratio but rather the activity focuses on the formation of fibres within the already defined xylem tissue.


Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U (2018) Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-06932-5

https://www.nature.com/articles/s41467-018-06932-5

Open Access
Lindsey Turnbull (University of Oxford) is a co-author on this paper from Ueli Grossniklaus’ group in Zurich. Marc Schmid is lead author of the study that investigates the inheritance of Arabidopsis epialleles over 5 generations during conditions of simulated selection. The authors show that variations in methylation state are subject to selection and do indeed contribute to adaptive responses


Kadota Y, Liebrand TWH, Goto Y, Sklenar J, Derbyshire P, Menke FLH, Torres MA, Molina A, Zipfel C, Coaker G, Shirasu K (2018) Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector- and PAMP-triggered immunity in plants. New Phytol. doi: 10.1111/nph.15523

Members of Cyril Zipfel’s group at The Sainsbury lab in Norwich are co-authors on this paper led by Yasuhiro Kadota from the RIKEN in Yokohama. They use a phosphoproteomic screen to identify a set of newly identified phosphorylation sites on membrane-associated proteins involved in effector-triggered immunity (ETI). Some of these phosphosites overlap with those known to be important for pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), indicating a convergence of signaling control of both these pathways to certain key residues.

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