Daniel Gibbs talks to GARNet

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Published on: January 9, 2019

Daniel Gibbs discusses a recent paper published in Nature Communications entitled ‘Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2

Grants to support Conference Travel to China and Oxford.

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Published on: January 7, 2019

As the festive period passes, thoughts turn to warmer times and summer conference plans. GARNet are delighted to provide and administer grants to support attendance at two major upcoming conferences.

Royal Microscopy Society Botanical Microscopy 2019. Oxford Brookes University, April 14th-18th 2019.

Scientific Organising Committee: Chris Hawes, Beatrice Satiat-Jeunemaitre, Verena Kriechbaumer, Katja Graumann, Louise Hughes, Imogen Sparkes.

GARNet are supporting the New Technologies session of this meeting that will include invited speaker Dr Sarah Robinson as well as a tribute to Professor Ian Moore.

GARNet will also supply 10x £150 travel grants to support ECRs travel to this meeting. More details about these awards can be found here in the ‘Delegate Information’ tab:

https://www.rms.org.uk/discover-engage/event-calendar/botanical-microscopy-2019.html


International Conference on Arabidopsis Research (ICAR2019): Wuhan, China, June 16th-21st 2019.

ICAR is the largest annual conference that focuses on discovery-led research. GARNet are administering four £500 travel grants available for UK-based PhD students to attend this meeting. Please contact the GARNet coordinator Geraint Parry to obtain an application form for these awards. The early registration date for this meeting means the deadline for these travel awards is January 28th.

Any other questions about these awards then please contact Geraint Parry.

Malcolm Bennett talks to GARNet

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Published on: December 28, 2018

Malcolm Bennett discussed a recent publication in Science entitled ‘Root branching toward water involves posttranslational modification of transcription factor ARF7‘.

GARNet Research Roundup: December 21st 2018

This bumper Festive Edition of the GARNet Research Roundup begins with two papers that have Beatriz Orosa-Puente as lead author following her work on SUMOylation with Ari Sadanandom at Durham. These papers looks at the role of SUMOylation in either auxin-mediated hydropatterning or in the defence response. Malcolm Bennett at Nottingham is a co-author on both papers and provided an audio description of the auxin-focused paper on the GARNet YouTube channel.

The next three papers are from the University of Edinburgh, the first that defines the role of HECT ubiquitin ligases in the defence response, the second that conducts a proteomic analysis of the GIGANTEA-interactome and the third that introduces a set of new tools for inducible gene expression in Arabidopsis roots.

The sixth and seventh papers feature authors from the John Innes Centre. Martin Howard and Caroline Dean are corresponding authors on a multi-scale analysis of the factors that control FLC expression whilst Myriam Charpentier’s lab has contributed to an investigation about LINC complexes in Medicago.

David Salt and Levi Yant from Nottingham lead the next paper that provides an analysis of the genetic determinants of adaptation to different salt conditions.

The final three papers are from Cambridge. Firstly Ian Henderson is the corresponding author on work that looks at crossover rates in specific disease resistance loci. Second is work from the Paszkowski lab at SLCU that introduces a new method for the analysis of active retrotransposons in crop plants whilst finally James Locke, also at SLCU, uses the method of distributed delays to simplify the complexity of biological network models.


Orosa-Puente B, Leftley N, von Wangenheim D, Banda J, Srivastava AK, Hill K, Truskina J, Bhosale R, Morris E, Srivastava M, Kümpers B, Goh T, Fukaki H, Vermeer J, Vernoux T, Dinneny JR, French AP, Bishopp A, Sadanandom A , Bennett MJ (2018) Roots branch towarss water by post-translational modification of the transcription factor ARF7 Science DOI: 10.1126/science.aau3956

Orosa B, Yates G, Verma V, Srivastava AK, Srivastava M, Campanaro A, De Vega D, Fernandes A, Zhang C, Lee J, Bennett MJ, Sadanandom A (2018) SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity. Nat Commun. doi: 10.1038/s41467-018-07696-8 Open Access

http://science.sciencemag.org/content/362/6421/1407

Beatriz Orosa-Puente is the lead author on two publications that have arisen from a collaboration between the labs of Ari Sadanandom at Durham and Malcolm Bennett at Nottingham. In the first paper Beatriz is co-first author with Nicola Leftley and Daniel von Wangenheim in research that links the auxin response, SUMOylation and the search for water. They reveal a novel mechanism for controlling the auxin response in which SUMOylation regulates the interaction between the ARF7 and IAA3 proteins. In turn this controls asymmetric expression of genes downstream of ARF7 and determines how different parts of the root response to the presence or absence of water.

The second paper continues with the Sadanandom lab’s focus on SUMOylation, in this case during control of the defence response. They show that SUMO is conjugated to the FLAGELLIN-SENSITIVE 2 (FLS2) receptor that senses bacterial flagellin. This releases downstream cytoplasmic effectors and enhances the immune response. The authors show that there is additional complexity to this system by also showing that flagellin induces degradation of the deSUMOylating enzyme Desi3a, thus allowing the plant to make a stronger immune response.


Furniss JJ, Grey H, Wang Z, Nomoto M, Jackson L, Tada Y, Spoel SH (2018) Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity. PLoS Pathog. doi: 10.1371/journal.ppat.1007447 Open Access

James Furniss is the lead author on this paper from the lab of current GARNet Chairman Steven Spoel at the University of Edinburgh. They show that a family of HECT domain-containing ubiquitin protein ligases (UPLs) are involved in defence responses mediated by the hormone salicylic acid (SA). Upl3 mutants show reprogramming of the entire SA transcriptional response and they are unable to establish immunity against a hemi-biotrophic pathogen, demonstrating their key role in this important process.


https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.13311

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, LeBihan T, Halliday KJ, Imaizumi T, Millar AJ (2018) Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis. FEBS Lett. doi: 10.1002/1873-3468.13311 Open Access

This paper is a collaboration between researchers in Edinburgh and Seattle for which Johanna Krahmer is lead author. They used a proteomic approach to identify proteins that interacted with a tagged-version of the key circadian regulator GIGANTEA. They successfully identified the novel transcription factor CYCLING DOF FACTOR (CDF)6. CDF6 was confirmed as interacting with GI and playing a role in the control of flowering. The time series of proteomic data produced in this study is available for use by any other interested researcher.

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD006859


Machin FQ, Beckers M, Tian X, Fairnie A, Cheng T, Scheible WR, Doerner P (2018) Inducible reporter/driver lines for the Arabidopsis root with intrinsic reporting of activity state. Plant Journal. doi: 10.1111/tpj.14192

Frank Qasim Machin is the lead author on this Technical Advance from Peter Doerner’s lab at the University of Edinburgh. They have developed a Gateway-based system for tightly controlled inducible expression across all the major cell types of the Arabidopsis roots. They have fully characterised reference driver lines that can be adapted for specific experimental requirements and hope that this contributes towards enhancing reproducibility of qualitative and quantitative analyses.


https://www.sciencedirect.com/science/article/pii/S2405471218304368?via%3Dihub

Antoniou-Kourounioti RL, Hepworth J, Heckmann A, Duncan S, Qüesta J, Rosa S, Säll T, Holm S, Dean C, Howard M (2018) Temperature Sensing Is Distributed throughout the Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization. Cell Syst. doi: 10.1016/j.cels.2018.10.011 Open Access

This work results from the successful collaboration between Caroline Dean and Martin Howard at the John Innes Centre and includes Rea Antoniou-Kourounioti and Jo Hepworth as co-first authors. They attempt to understand how the upregulation of VERNALIZATION INSENSITIVE3 (VIN3) and silencing of FLOWERING LOCUS C (FLC) is controlled during fluctuating temperatures over month-long time scales. They develop a mathematical model that integrates information from hour, day and month-long datasets to show that temperature is sensed across the entire regulatory network and not focussed on specific nodes. This allows a final effect to only be realised once all parts of the network have been appropriately changed. This model with matches new field data and therefore represents a predictive tool for the effects of climate change on plant growth.


Newman-Griffis AH, Del Cerro P, Charpentier M, Meier I (2018) Medicago LINC complexes function in nuclear morphology, nuclear movement, and root nodule symbiosis Plant Physiol. http://www.plantphysiol.org/content/early/2018/12/10/pp.18.01111 Open Access
Pablo del Cerro and Myriam Charpentier at the John Innes Centre are co-authors on this paper from Iris Meier’s lab at The Ohio State University. They identify and characterise the Linker of Nucleoskeleton and Cytoskeleton (LINC) family of nucleus-membrane-associated proteins. They show that, as in Arabidopsis, these proteins are required for nucleus movement in the root tip cells of Medicago truncatula and that they are an important contributor to nodulation. Both Iris and Myriam are members of the INDEPTH consortium that includes researchers who study this broad area of plant cell biology.


https://www.pnas.org/content/early/2018/12/11/1816964115.long

Busoms S, Paajanen P, Marburger S, Bray S, Huang XY, Poschenrieder C, Yant L, Salt DE (2018) Fluctuating selection on migrant adaptive sodium transporter alleles in  coastal Arabidopsis thaliana. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1816964115 Open Access

This UK-Sino-Spanish collaboration is led by David Salt and Levi Yant at the University of Nottingham. Silvia Busoms is the first author on the study that investigates the genetics of adaptive salt tolerance in a cohort of 77 individuals grown across a salinity gradient in a coastal region of Catalonia. By integrating their data with the 1135 genomes project they are able to trace the ancestry of these populations and define that growth in high salt conditions is associated with increased expression of the high-affinity K+ transporter (HKT1;1). This demonstrates that this gene plays a key role in the adaptation to salt stress.


Serra H, Choi K, Zhao X, Blackwell AR, Kim J, Henderson IR. Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes (2018) PLoS Genet. doi: 10.1371/journal.pgen.1007843 Open Access

This UK-Korean collaboration is led by the Heidi Serra and Ian Henderson at the University of Cambridge. They mapped the meiotic crossover hotspots that are located within the RAC1 and RPP13 disease resistance genes in Arabidopsis. They assessed these locations in plants with altered recombination rates and surprisingly showed that these effects have little impact at the RAC1 loci. Therefore they show that chromosome location and local chromatin environment are important for regulation of crossover activity. Overall they demonstrate that interhomolog divergence is important in shaping recombination within plant disease resistance genes and crossover hotspots.


Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, Paszkowski J (2018) Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nat Plants. doi: 10.1038/s41477-018-0320-9

Open Access with link: rdcu.be/bdLjy

For the second edition in succession, the GARNet research roundup features work from Jerzy Paszkowski’s lab at SLCU. In this case Jungnam Cho is lead author on work that has developed a new technique called ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for analysis of transposon-rich genomes from crop plants. Through characterisation of extrachromosomal linear DNA (eclDNA), ALE-seq allows the identification of active transposons. The authors use this technique in both rice and tomato and successfully identify a set of developmentally regulated transposable elements. This paper includes details of a bioinformatic pipeline that is adapted for ALE-seq data analyses, the scripts for which are available on GitHub.


Tokuda IT, Akman OE, Locke JCW. Reducing the Complexity of Mathematical Models for the Plant Circadian Clock by Distributed Delays (2018) J Theor Biol. doi: 10.1016/j.jtbi.2018.12.014

This UK-Japanese study includes James Locke at SLCU as corresponding author. They address the challenge of integrating an increasing number of parameters into large biological network models. Their system of study is the Arabidopsis circadian clock and they use the method of distributed delays to simplify the complexity of existing models. They demonstrate this effect by updating a model that explains the regulation of the PRR9 and PRR7 genes by LHY. They use recent experimental data and revise the previous model to show that it is more accurately reproduces the LHY-induction experiments of core clock genes. As stated they show that overall use of distributed delays facilitates the optimisation and reformulation of genetic network models.

GARNet Research Roundup: December 7th 2018

The first four papers in this GARNet Research Roundup includes research from Norwich Research Park. Firstly members of Jonathan Jones’ lab have identified a new Avr gene from Hyaloperonospora arabidopsidis. Secondly Anne Osbourn’s lab characterises two novel arabinosyltransferases that are involved in the plant defence response. Thirdly Cathie Martin’s group is involved in a study that investigates the biosynthesis of the metabolite ubiquinone. Finally in research from NRP is from Silke Robatzek’s lab, where they use a novel quantitative imaging system to characterise stomatal mutants.

The next two papers arise from work at SLCU, firstly looking at the possible role of a novel transposon family during gene-shuffling and secondly a paper that investigates the structure of an important component of the strigolactone signaling pathway.

The seventh paper from Peter Eastmond’s lab at Rothamsted Research identifies a novel gene involved in seed oil composition. The penultimate paper is from Peter Unwin at the University of Leeds and assesses the cell wall composition of ‘giant’ root cells induced by nematode Meloidogyne spp. Finally is a methods paper that describes how microCT imaging can be used to measure different leaf parameters.


Asai S, Furzer O, Cavik V, Kim DS, Ishaque N, Goritschnig S, Staskawicz B, Shirasu K, Jones JDG (2018) A downy mildew effector evades recognition by polymorphism of expression and subcellular localization. Nature Communications doi: 10.1038/s41467-018-07469-3

https://www.nature.com/articles/s41467-018-07469-3

Open Access

Shuta Asai from Jonathan Jones’ lab at The Sainsbury Lab, Norwich is the lead-author on this study that looks at co-evolution of host and pathogen resistance genes. The relationship between Hyaloperonospora arabidopsidis (Hpa) and Arabidopsis is defined by the gene-for-gene model of host Resistance (R) genes and pathogen Avirulence (AVR) genes. In this study the authors identify the HaRxL103Emoy2 AVR gene that is recognised by the R gene RPP4 and how this resistance is broken by altered expression or cellular localization.


Louveau T, Orme A, Pfalzgraf H, Stephenson M, Melton RE, Saalbach G, Hemmings  AM, Leveau A, Rejzek M, Vickerstaff RJ, Langdon T, Field R, Osbourn AE (2018) Analysis of two new arabinosyltransferases belonging to the carbohydrate-active enzyme (CAZY) glycosyl transferase family 1 provides insights into disease resistance and sugar donor specificity. Plant Cell. doi: 10.1105/tpc.18.00641

Open Access

This research from the John Innes Centre, East Maling and Aberystwyth University is led by Thomas Louveau and Anne Osbourn and characterises two new arabinosyltransferases from oat and soybean. These enzymes are involved in the production of saponins that are involved in defence responses. These enzymes normally transfer arabinose to their substrates but through targeted mutations the authors modified one of them to instead transfer glucose. This study provides insights into the specifics of ‘sugar-donation’ and has identified potential novel targets for manipulating defence responses in two crop species.


Soubeyrand E, Johnson TS, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E,  Martin C, Wilson MA, Basset G (2018) The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. Plant Cell. 2018 Nov 14. pii: tpc.00688.2018. doi: 10.1105/tpc.18.00688

Open Access

This US-led study includes members of Cathie Martin’s lab at the John Innes Centre as co-authors in which they investigate the flavonoid-biosynthesis pathway, in particular the land-plant-specific synthesis of ubiquinone. They used Arabidopsis and tomato mutants to dissect the ubiquinone biosynthesis pathway, revealing that the B-ring of the specalised metabolite kaempferol is incorporated into the primary metabolite ubiquinone.


Bourdais G, McLachlan DH, Rickett LM, Zhou J, Siwoszek A, Häweker H, Hartley M, Kuhn H, Morris RJ, MacLean D, Robatzek S (2018) The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure. Traffic. doi: 10.1111/tra.12625

This work from both Norwich Research Park and the University of Bristol is led by Gildas Bourdais and describes a high-throughput quantitative imaging, reverse genetic screen to characterize known stomatal mutants on the basis of their effect on the endomembrane system. This screen allowed them to precisely define the point in the signaling pathway at which each mutant was affected, providing a genetic framework for the control of stomatal closure. This image-based tool should be a valuable addition to future studies that aim to use quantitative image analysis.


https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1196/5198529

Catoni M, Jonesman T, Cerruti E, Paszkowski J (2018) Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling (2018) Nucleic Acids Res. doi: 10.1093/nar/gky1196

Open Access

This work was performed at SLCU in Jerzy Paszkowski’s lab by current University of Birmingham lecturer Marco Catoni and analyses the genomic impact of the mobilisation of Pack-TYPE transposons. They track the movement of these transposons over multiple generations, showing that they can insert into genic regions and that their subsequent incomplete excisions can cause deleterious effect on gene function. Over evolutionary time the action of this type of mobile element might therefore importantly influence gene shuffling.


Shabek N, Ticchiarelli F, Mao H, Hinds TR, Leyser O, Zheng N (2018) Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling. Nature. doi: 10.1038/s41586-018-0743-5

Nitzan Shabek is the lead author on his US-led paper that includes Fabrizio Ticchiarelli and Ottoline Leyser from SLCU as co-authors. This paper reveals the structure of the interaction between the Arabidopsis α/β hydrolase D14 and the D3 F-box protein, which is important for multiple aspects of strigolactone signaling. They show that structural plasticity of the D3 C-terminal α-helix, which can switch between two different forms, enables the interaction between D14 and the D53 repressor protein. Providing insight into these specific interactions is key to increasing understanding of how the D14-D3 complex influences strigolactone signaling.


Menard GN, Bryant FM, Kelly AA, Craddock CP, Lavagi I, Hassani-Pak K, Kurup S, Eastmond PJ (2018) Natural variation in acyl editing is a determinant of seed storage oil composition. Sci Rep. doi: 10.1038/s41598-018-35136-6

Open Access

This work is led from Rothamsted Research with Guillaume Menard as first author and uses the Arabidopsis MAGIC population to identify novel genetic loci involved in seed oil composition. They identified multiple QTLs associated with the quantity of the major very long chain fatty acid species 11-eicosenoic acid (20:1), showing that the enzyme LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 (LPCAT2), which is involved in the acyl-editing pathway, was the primary QTL. Subsequently they show LPCAT2 expression was key for varying seed 20:1 content and that natural variation in the capacity for acyl editing is an important determinant of oil content.


Bozbuga R, Lilley CJ, Knox JP, Urwin PE (2018) Host-specific signatures of the cell  wall changes induced by the plant parasitic nematode, Meloidogyne incognita (2018). Sci  Rep. doi: 10.1038/s41598-018-35529-7

https://www.nature.com/articles/s41598-018-35529-7

Open Access

Refik Bozbuga at the University of Leeds is first author on this study that investigates the cell wall composition of nutrient-supplying ‘giant cells’ that are induced in roots following infection with Meloidogyne spp nematodes. They analysed the cell walls of giant cells from three species (Arabidopsis, maize and aduki bean) as well as using a set of Arabidopsis mutants to characterise the possible cell wall components that might influence infection rates.


Mathers AW, Hepworth C, Baillie AL, Sloan J, Jones H, Lundgren M, Fleming AJ,  Mooney SJ, Sturrock CJ (2018) Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography. Plant Methods. doi:  10.1186/s13007-018-0367-7

Open Access
This paper from the Universities of Nottingham, Sheffield and Lancaster provides a methodology that uses a microCT image pipeline to measure leaf intercellular airspace and to provide quantitative data on descriptors of leaf cellular architecture. They measured 6 different plant species, showing that this 3D method generates an improved dataset when compared to traditional 2D methods of measurement.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-018-0367-7

30th International Conference on Arabidopsis Research

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Published on: December 5, 2018

Chinese researchers publish a lot of papers in which Arabidopsis is the primary organism of study. The 2018 MASC annual report showed that in 2017 Chinese researchers published 1318 papers, which was over double the number published by researchers in the USA.

This is the exciting backdrop for the 30th International Conference for Arabidopsis Research (ICAR) that will take place in Wuhan on June 16th-21st 2019.

The conference website went live last weekend: http://icar2019.arabidopsisresearch.org/index.html


ICAR is the largest annual conference that focuses almost exclusively on discovery-led fundamental plant research. The only time ICAR has been held in China was for ICAR2007. This remains the highest ever attended ICAR with over 1400 delegates yet took place at a time when Chinese researchers published ‘just’ 248 papers, which was a 1/3 of the number published by US researchers.

At that time China was beginning its research relationship with fundamental plant science but in 2019 it is very much the most productive nation.

There is understandable excitement for ICAR2019 as it will undoubtedly be the most highly attended ICAR and will introduce excellent Chinese research to a global conference that is conducted in English.

The organisers have kept student registration cheap at $350 for early bird registration. However be aware that on February 1st his deadline is early in the year. Abstract submission for an oral presentation is on March 1st. General registration ends on May 1st.

International attendees require a VISA to enter China so make sure you apply early to your home consulant. More information on this can be found here: http://icar2019.arabidopsisresearch.org/visa.html 

To encourage UK PhD students to attend the meeting GARNet are administering a set of 4 £500 studentships. If you are interested in these awards please contact Geraint Parry
geraint@garnetcommunity.org.uk

GARNet Research Roundup: November 22nd 2018

This GARNet Research Roundup begins with two studies from the University of Sheffield. First is research from Jurriaan Ton’s lab that looks at the interaction between CO2 concentration, the soil microbiome and plant growth. The second paper from Matt Davey and Peter Quick looks at the effect of cold acclimation on freezing tolerance in Arabidpsis lyrata.

The third study includes authors from Dundee and Durham and also looks at an impact of altered CO2 concentrations, in this case on nitrogen assimilation.

The next paper looks at the role of a GA signaling module on endosperm expansion during seed germination and includes authors from Nottingham and Birmingham.

The fifth paper includes Richard Morris at the JIC as a co-author and looks at the relationship between calcium signaling and changes in cellular pH. The penultimate study features co-authors from Warwick and Exeter in work that looks at the role of 3′-O-β-D-ribofuranosyladenosine during plant immunity. Finally is a paper that includes Steve Long from Lancaster and characterises the rubisco-chaperone BSD2.


Williams A, Pétriacq P, Beerling DJ, Cotton TEA, Ton J (2018) Impacts of Atmospheric CO(2) and Soil Nutritional Value on Plant Responses to Rhizosphere Colonization by Soil Bacteria. Front Plant Sci. doi: 10.3389/fpls.2018.01493

https://www.frontiersin.org/articles/10.3389/fpls.2018.01493/full

Open Access

Alex Williams is the lead author of this paper and works with Jurriaan Ton at the University of Sheffield. The impact of the soil rhizosphere on plant growth is emerging as an important growth determinant. In this paper the authors assess the role of altered [CO2] and soil carbon (C) and nitrogen (N) concentration in the colonisation of Arabidopsis roots by two different bacteria. Firstly they showed that altered [CO2] did not change the growth dynamics of the saprophytic bacteria Pseudomonas putida KT2440 and was independent of soil C or N. In contrast growth of the rhizobacterial strain Pseudomonas simiae WCS417 was sensitive to both changing [CO2] and soil composition. These results show the importance of the interaction between atmospheric CO2 and soil nutritional status during plant interactions with soil bacteria.


Davey MP, Palmer BG, Armitage E, Vergeer P, Kunin WE, Woodward FI, Quick WP (2018) Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea. BMC Plant Biol. doi: 10.1186/s12870-018-1513-0

Open Access

Matthew Davey, now working in Cambridge, collaborated with Peter Quick at the University of Sheffield on this research that looks at the tolerance of Arabidopsis lyrata to freezing. They showed that populations from locations with colder winter climates were better able to survive subzero temperatures, particular when they have been acclimated at near zero for longer periods. This demonstrates that the adaptation of plants to cold temperatures allows them to better survive freezing, although surprisingly this effect is lessened when this acclimation period does not occur.


Andrews M, Condron LM, Kemp PD, Topping JF, Lindsey K, Hodge S, Raven JA (2018) Effects of elevated atmospheric [CO2] on nitrogen (N) assimilation and growth of C3 vascular plants will be similar regardless of N-form assimilated. J Exp Bot. doi: 10.1093/jxb/ery371

This UK-New Zealand collaboration is led by Mitchell Andrews and looks at the effect of elevated [CO2] on the nitrogen (N) assimilation when the plant is exposed to a variety of different N-sources. They show that in C3 plants the overall N assimilated will be the same whether the plant is under ammonium (NH4+) nutrition or under nitrate (NO3-) nutrition. These results are contrary to previous results that suggest elevated [CO2] reduces plant growth under NO3- nutrition.


Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L (2018) A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2018.10.009 

https://www.sciencedirect.com/science/article/pii/S1674205218303356

Open Access

This Spanish-led project includes authors from the Universites of Nottingham and Birmingham. They look at the influence of a GA signalling module on endosperm cell separation, which is essential for Arabidopsis seed germination. They show the NAC transcription factors NAC25 and NAC1L control expression of the EXPANSION2 gene and that the GA signalling component RGL2 has a controlling influence by repressing this activity.


Behera S, Xu Z, Luoni L, Bonza C, Doccula FG, DeMichelis MI, Morris RJ, Schwarzländer M, Costa A (2018) Cellular Ca2+ signals generate defined pH signatures in plants. Plant Cell. doi: 10.1105/tpc.18.00655

Open Access

Richard Morris (John Innes Centre) is a co-author on this Italian-led study that investigates the role of Calcium ions in cell signalling. They use a set of genetically-encoded fluorescent sensors to visualise a link between Ca2+ signaling and changes in pH. If this link is maintained across all cell types it might represent an extra layer of complexity and control of cellular signal transduction.


Drenichev MS, Bennett M, Novikov RA, Mansfield J, Smirnoff N, Grant M, Mikhailov S (2018) A role for 3′-O-β-D-ribofuranosyladenosine in altering plant immunity. Phytochemistry. doi: 10.1016/j.phytochem.2018.10.016

https://www.sciencedirect.com/science/article/pii/S0031942218301997?via%3Dihub

This Russian-led study includes UK-based researchers Mark Bennett, Murray Grant, Nick Smirnoff and John Mansfield as co-authors. They show that the natural disaccharide nucleoside, 3′-O-β-D-ribofuranosyladenosine accumulated in plants infected with the bacterial pathogen P. syringae. Perhaps surprisingly the application of this nucleoside to the plant doesn’t effect bacterial multiplication, indicating that adds a significant metabolic burden to plants already battling new infections.


Conlan B, Birch R, Kelso C, Holland S, De Souza AP, Long SP, Beck JL, Whitney SM (2018) BSD2 is a Rubisco specific assembly chaperone, forms intermediary hetero-oligomeric complexes and is non-limiting to growth in tobacco. Plant Cell Environ. doi: 10.1111/pce.13473

Steve Long is a Professor at Lancaster Environment Centre and is a co-author on this Australia-led study that characterizes the role of the Rubisco chaperone BSD2 during Rubisco biogenesis. These results suggest this is the sole role of BSD2 and its activity is non-limiting to tobacco growth.

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

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