Stockbridge Technology Centre

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Published on: March 22, 2017

Following the conclusion of the CyVerseUK workshop at the University of York I was delighted to take a brief visit to StockBridge Technology Centre (STC) to have a look at their facilities.

STC are involved in a range of research projects that involve different aspects of plant growth across many conditions and species. As well as initiating independent research projects they are equally at home working with a broad cross section of collaborators and as such sit in an excellent position to make linkages between interest groups who can be challenging to bring together.

STC has received significant public interest for the work they do, with a number of high profile appearances in the mainstream media, most recently in early March on BBC Countryfile (see from 24minutes onward). At their site in the Vale of York they have a large number of highly adaptable greenhouses that sit in alongside 70 hectares appropriate for field trials. In addition they are involved with more technology-facing projects such as the LED4Crops that is run by Dr Phillip Davis at STC.
This project is highly relevant at a time when there are concerns about UK food security and our reliance of imported produce. Use of LED technology is proving extremely useful in improving our understanding of the light regimes that are required in order to both maximise biomass production and improve different traits. This is particularly relevant as there is a growing need to work on a constant 12-month rotation.

Researchers at the LED4Crops facility work with both ornamental and food crops and they are hoping to soon gain funding to greatly expand their operation. If the potential of Stacked Urban Farming is to be realised then the type of research undertaken at STC will be critical for understanding the light conditions needed to maximise production in those sunlight-less environments.

For academic researchers STC sits at an advantageous position of being able to bridge the gap between basic research, industry and farmers and are therefore happy to interact with any potential partners. Although researchers at STC are unable to indepedently apply for RCUK funding they are partners on many grants and work on plenty of EU-funded projects.

Please take a look at the STC website and I’m sure they’d be delighted to host anyone who is interested in visiting their facilities.

Phill Davis will be writing a longer piece for the next issue on the GARNish newsletter so please look out for that!

Arabidopsis Research Roundup: March 17th

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Published on: March 17, 2017

This weeks UK Arabidopsis Research Roundup includes three papers featuring researchers from the University of Nottingham as well as manuscripts from Leeds, Lancaster, QMUL and The Sainsburys Lab in Norwich

Firstly Stefan Kepinski (Leeds) leads a study that investigates how Gravitropic Set Point Angle (GSA) is controlled in response to different growth factors. Secondly are two Methods papers featuring researchers from CPIB in Nottingham, the first of which is in collaboration with Lancaster University and introduces the Microphentron, which is an automated phenotyping platform that can be used for chemical biology screens. The second paper describes a non-destructive method for imaging floral tissues using CT scanning.

Ranjan Swarup is also a member of CPIB and in the next paper he has collaborated with French colleagues to investigate the role of SHR on root development in rice.

The fourth paper includes Cyril Zipfel as a co-author and investigates the role of damage-associated molecular patterns (DAMPs) in the response to pathogen attack whereas this weeks final paper is from the lab of Alexander Ruban (QMUL) and discovers the phenotypic consequences of persistent damage to PSII by photoinhibition.


Suruchi Roychoudhry, Martin Kieffer, Marta Del Bianco, Che-Yang Liao, Dolf Weijers Stefan Kepinski (2017) The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean Scientific Reports http://dx.doi.org/10.1038/srep42664

Open Access

Stefan Kepinski (University of Leeds) leads this study that involves a collaboration with Dolf Weijers from Wageningen University. They investigate the role of both auxin and environmental factors in determining gravitropic set point angle (GSA), which is a measure of the growth of lateral organs away from primary shoots and roots. They show that nitrogen and phosphorous deficiency causes opposing effects on lateral root GSA, each of which are auxin-dependent. This contrasts with previous findings from work using bean adventitious roots. They find that these differences are maintained when Arabidopsis and bean roots are treated with different auxin concentrations. Latterly they also look at the effect of different light conditions on shoot GSA and put these findings into the context of potentially altering crop growth.

Stefan takes some time to discuss this paper for the GARNet YouTube Channel.


Burrell T, Fozard S, Holroyd GH, French AP, Pound MP, Bigley CJ, James Taylor C, Forde BG (2017) The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology. Plant Methods

http://dx.doi.org/10.1186/s13007-017-0158-6 Open Access

This methods paper is a collaboration between the Universities of Lancaster and Nottingham led by Brian Forde that describes the Microphenotron. This device has been developed to facilitate chemical biology screens on in vivo plant tissues. This allows for the automated screening of either dicot or monocot roots or aerial tissues that have been grown on media infused with whichever chemical is relevant for the intended expriments. In situ GUS screening is also possible allowing for researchers to integrate information about growth and gene expression. The use of ‘Phytostrips’ in a 96-well format allows for high-throughput screening that is aligned with AutoRoot automated image analysis software to provide a rapid and facile method for undertaking small scale phenotypic screens. The Microphenotron facility is housed at the Lancester University, who are extremely open to collaboration so please get in contact if you are interested in using the facility.


Tracy SR, Gómez JF, Sturrock CJ, Wilson ZA, Ferguson AC (2017) Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (µCT) Plant Methods. http://dx.doi.org/10.1186/s13007-017-0162-x Open Access

Alison Ferguson is the corresponding author on this methods paper that includes GARNet committee member Zoe Wilson and Saoirse Tracy from Dublin. They have developed a technique using X-ray µCT scanning to image developing flowers in Arabidopsis and barley plants, taking advantage of the excellent Hounsfield facility at the University of Nottingham. They show that the technique can be hugely beneficial for plant phenotyping by providing a non-destructive method of analyzing live floral development and how this can response to changes in the growth environment. Members of the Hounsfield facility are happy to discuss any potential collaborative work and future access to these type of facilities will hopefully be improved through the UKs involvement in the pan-european EMPHASIS project.


Henry S, Dievart A, Fanchon D, Pauluzzi G, Meynard D, Swarup R, Wu S, Lee CM, Gallagher K, Périn C (2017) SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev Biol. http://dx.doi.org/10.1016/j.ydbio.2017.03.001

Ranjan Swarup (CPIB) is a co-author on this study that includes French and US researchers. Previously they had shown that expression of rice SHORTROOT (OsSHR) genes could compliment the Arabidopsis shr mutant. In this study they show that overexpression of OsSHR and AtSHR in rice roots causes growth of wider, shorter roots that have an increased number of cortical cell layers. This demonstrates that the mechanisms that control the differentiation of cortical cell layers is conserved throughout land plants, with SHR being a key determinant in this process.


de Azevedo Souza C, Li S, Lin AZ, Boutrot F, Grossmann G, Zipfel C, Somerville S (2017) Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses. Plant Physiol. http://dx.doi.org/10.1104/pp.16.01680

Cyril Zipfel (The Sainsbury Lab) is a co-author on this study from the lab of Shauna Somerville in California that focuses on the concept of damage-associated molecular patterns (DAMPs). These can be defined as cell wall breakdown components and stimulate the same defence responses as more fully characterised pathogen- or microbe-associated molecular patterns (PAMPs). Intuitively this makes sense as during infection many pathogens will cause cell wall breakdown. The authors show that cellulose-derived oligomers trigger a signalling response similar to that caused by oligogalacturonides or chito-oligomers but that lacks an increase in ROS or in callose deposition. These results confirm that cellulose-derived signals feed into the plants mechanism for cell wall scanning and acts synergistically with other signals that result from pathogen attack.


Tian Y, Ungerer P, Zhang H, Ruban AV (2017) Direct impact of the sustained decline in the photosystem II efficiency upon plant productivity at different developmental stages. J Plant Physiol. http://dx.doi.org/110.1016/j.jplph.2016.10.017

Image from http://www.sciencedirect.com/science/article/pii/S0176161717300433

Alexander Ruban (QMUL) leads this Sino-UK collaboration that investigates how the photoinhibiton of photosystem II impacts overall plant growth. In this study they use lincomycin to block chloroplast protein synthesis, which prevents the plant from restoring PSII function after photoinhibitory damage. Treated plants accumulate less starch and showed reduced above-ground biomass. This leads to a decrease in seed yield. Perhaps unsurprisingly this research shows that restoring the full function of PSII after photoinhibition to key to maintaining normally functioning electron transport rate that leads into metabolic production and growth rate.

Arabidopsis Research Roundup: March 6th.

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Published on: March 6, 2017

This weeks Arabidopsis Research Roundup includes four papers that focus on different aspects of plant cell biology. Firstly Ian Henderson’s research group in Cambridge defines the role of a critical component that determines crossover frequency in plants and other eukaryotes. Secondly Karl Oparka (Edinburgh) leads a broad collaboration that defines the mechanism of unloading of solutes and macromolecules from the root phloem. Thirdly Keith Lindsey (Durham) has developed a model that describes how auxin patterns the Arabidopsis root. Finally Mike Blatt (Glasgow) is part of a group that uses Arabidopsis as a framework for the study of ABA-signaling during stomatal movement in ferns.


Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FC, Martienssen RA, Henderson IR (2017) Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev

http:/​/​dx.​doi.​org/10.1101/gad.295501.116

Open Access

GARNet committee member Ian Henderson (University of Cambridge) leads this work that features collaborators from the UK, US and Poland. They use an experimental technique that allows facile analysis of recombination rates alongside a study of Arabidopsis natural variation to isolate a QTL that is critical for maintaining the correct number of crossovers during meiosis. This HEI10 gene codes for an E3 ligase (the targets of which are currently unknown) whose copy number is a key component in the control of recombination rate. Hei10 mutants have less crossovers whilst plants with extra copies of HEI10 have an increased number, especially in sub-telomeric regions of the genome. HEI10 is a highly conserved protein, demonstrating its important role to ensure appropriate levels of recombination throughout the evolution of eukaryotes.

Ian kindly takes ten minutes to discuss this paper with GARNet on our YouTube Channel.


Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero-Perez S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ (2017) Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.24125

Open Access

Karl Oparka (University of Edinburgh) is the corresponding author of this study that includes researchers from the UK, US and Denmark. Movement of solutes and macromolecules through the plant phloem is key for the correct distribution of nutrients allowing for optimal growth. In this paper they discover that unloading of molecules from the phloem occurs via a set of specialized funnel plasmodesmata that link the phloem to adjacent pericycle cells. Remarkably they find that whereas solutes are constantly unloaded, larger proteins are released through these plasmodesmata in discrete pulses, which they describe as ‘batch unloading’. Overall this study provides evidence of a major role for the phloem-pericycle cells in the process of moving essential nutrients from the phloem into surrounding tissues.


Moore S, Liu J, Zhang X, Lindsey K (2017) A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep. http:/​/​dx.​doi.​org/10.1038/srep43004

Open Access

The work comes from the lab of Keith Lindsey (University of Durham) and developes a data-driven model that predicts the role of auxin patterning in the recovery of an Arabidopsis root following a perturbation of polar auxin transport. They demonstrate three main principles that define the role of auxin influx and efflux carriers in this process and also provide experimental validation for their predictions.


Cai S, Chen G, Wang Y, Huang Y, Marchant B, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis D, Soltis P, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH (2017)

Evolutionary Conservation of ABA Signaling for Stomatal Closure in Ferns Plant Physiol

http:/​/​dx.​doi.​org/10.1104/pp.16.01848

Open Access

Mike Blatt (University of Glasgow) is a co-author on this global study that looks into the evolution of ABA-signaling in the control of stomatal closure. Although this study is focused on this process in ferns they build their findings on the analysis of transcriptional networks from Arabidopsis. Ultimately they find that the evolution of ABA-controlled guard cells movements are important in the adaptation of ferns to a terrestrial environment.

EMPHASIS on Plant Phenotyping

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Published on: February 28, 2017

Some readers might have heard of the EMPHASIS project but the likelihood is that the majority have not……yet it might be extremely significant for the future of plant science across Europe…. which, yes, even in these uncertain times, should include UK researchers!

The European Strategy Forum on Research Infrastructures (ESFRI) supports high quality research infrastructures across all disciplines and includes diverse projects such as ELIXIR, A distributed infrastructure for life-science information  and SKA, the Square Kilometer Array Telescope. The process of receiving support from ESFRI starts with inclusion in their annual Roadmap document that leads onto a series of discussions that aim to set the official agenda for the program. This might then result in the establishment of an official infrastructure project a further 5 years later. Importantly this is a different type of project when compared to Horizon2020 or FPs as the funding does not come from a centralised EU pot but is rather distributed from within the individual participating countries.


Last year was an exciting time for European Plant Phenotyping as through the work of Belgian, German, French and UK researchers, the EMPHASIS project (European Infrastructure for multi-scale Plant Phenomics and Simulation for food security in a changing climate) was included in the ESFRI Roadmap in 2016. Within the UK, it was largely members of the UKPPN (UK Plant Phenotyping Network) who worked with the BBSRC to ensure that UK scientists were represented in the EMPHASIS project that was included in the ESFRI Roadmap.

The genesis of EMPHASIS could be traced back to the FP7-funded EPPN (European Plant Phenotyping Network) which was the starting point of the overall aim to develop complimentary tools for lab, greenhouse and field phenotyping that integrates high-tech automated platforms with computer-aided measurements and data management.


EMPHASIS-PREP takes shape.

The EMPHASIS-PREP project has now been funded by Horizon2020 and over the coming years will document the strengths and weaknesses of European plant phenotyping before producing a final document that will highlight why the entire EMPHASIS project should be supported and how it might be regulated across up-to-30 participating countries. As the money for UK scientists will come directly from RCUK, it is hoped that issues surrounding Brexit will not be as significant an issue for this scheme as it might with other centrally administered EU funding. This will support a UK research infrastructure that integrates with European partners and conforms to certain EMPHASIS-defined access requirements to researchers from across the EU.

The EMPHASIS-PREP project is split into 6 work-packages and the BBSRC have taken the lead with WP5, which tackles the legal frameworks that are needed for the project to succeed with minimal interference.


The group participating in EMPHASIS-PREP is much smaller than the proposed final EMPHASIS project so those members involved at the present time (which will be expanded over the course of the discussions) have signed the ‘EMPHASIS Manifesto’ in which they agree to work for the good of the whole future consortium.

Ultimately the aim of EMPHASIS is to host all the necessary infrastructure for state-of-the-art phenotyping and can be split into five very broad topics:

> Controlled conditions: Phenotyping platforms in (semi-) controlled conditions for high resolution and high throughput phenotyping.

> Intensive field: Smart/ Intensive field experimental sites for high throughput phenotyping

> Lean field: Translational, coordinated network of field experiments with lean, efficient phenotyping close to practical breeding setups

> Modelling: Modelling platforms for testing existing or virtual combinations of alleles in a variety of climatic scenarios and management practices

> e-Infrastructure: establish interconnections between different nodes/ installations.


The final organisation of the project will take a classic European Hub-and-Node organisation. The EMPHASIS Hub will likely reside in Germany whilst each national Node will attempt to lead the organisation of the countries phenotyping infrastructure so that it is open, inclusive and conforms to the overall aims of the EMPHASIS program.

As this is a five-year process it will clearly be extremely complicated to organise and over the coming year EMPHASIS-PREP are holding regional meetings to introduce the aims of the project and to receive feedback from those participating countries. As the project planning gains pace then these meetings may become more frequent and could be organized on an individual national level.

These early EMPHASIS-PREP meetings have three main goals:

> Inform: about the EMPHASIS project

> Document: the status of plant phenotyping in each country

> Discuss: future national plans for plant phenotyping

In the early stages of EMPHASIS-PREP the UK will be represented by the University of Nottingham specifically led by Malcolm Bennett, Darren Wells and Tony Pridmore. They will work closely with the BBSRC to ensure that UK interests are represented at each meeting. The location of each meeting can be found on the EMPHASIS website.


What does it mean for me now?

At the moment not a great deal.

Please keep an eye out for developments and then contribute any thoughts and ideas that you have when the appropriate forums are opened up. GARNet has been a contributing member of the UKPPN and as we are mandated to support community infrastructures so we will endeavor to keep the UK community informed as the project rolls forward.

Hopefully in 2018 there will be a UK-based meeting in which members of our outstanding UK plant phenotyping community will be able to submit their opinions as to the direction of travel of this field (pardon the pun) of research that has enormous significance for the development of new crop varieties to mitigate the effects of climate change and ensure global food and nutritional security.

Arabidopsis Research Roundup: February 27th

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Published on: February 28, 2017

This weeks research roundup includes just three papers and includes a study from the University of Essex that looks at the growth response of Arabidopsis plants to ‘real-life’ fluctuations in light levels. Secondly is a very different type of study from the University of York that uses Arabidopsis as a model for the development of plants that are able to accumulate catalytically active and commercially viable levels of palladium. Finally is a Chinese-led study that includes Alan Marchant (University of Southampton) as a co-author and looks at the role of the ERF74-RbohD-ROS signaling module on the response to abiotics stress.

Vialet-Chabrand SR, Matthews JS, Simkin A, Raines CA, Lawson T (2017) Importance of fluctuations in light on plant photosynthetic acclimation Plant Physiol.

http://dx.doi.org/10.1104/pp.16.01767

Open Access

Tracy Lawson and GARNet committee member Christine Raines from the University of Essex Photosynthesis Group lead this study that aims to understand how plants respond to variation in light levels that occur over an ‘average’ day. This contrasts with the conditions used in a ‘standard’ growth chamber and they show that plant growth is significantly altered when the light levels fluctuate, even though the total amount of light that the plant receives is the same. The ultimate conclusion of the study is that the growth of plants under ‘square wave growth conditions’ does not accurately reflect what might be observed in the field. This is significant given the importance of moving research from model organisms, usually grown under controlled conditions into crop species grown in the field.

Tracy Lawson kindly takes less than ten minutes to discuss the paper with GARNet on our YouTube channel.


Harumain ZA, Parker HL, Muñoz García A, Austin MJ, McElroy CR, Hunt AJ, Clark JH, Meech JA, Anderson CW, Ciacci L, Graedel TE, Bruce NC, Rylott EL (2017) Towards financially viable phytoextraction and production of plant-based palladium catalysts. Environ Sci Technol. http://dx.doi.org/ 10.1021/acs.est.6b04821

Open Access

Elizabeth Rylott and Neil Bruce at the University of York lead this study that includes collaborators from the USA, Canada, Malaysia and New Zealand. They look into the options for phytoextraction of palladium, which forms nanoparticles in Arabidopsis roots. The metal taken from these roots had normal catalytic activity and could be obtained at up to 18g/kg dried tissue weight. These experiments were moved into mustard, miscanthus and sixteen willow species and although palladium can be taken up into the plant tissues, it could not be extracted at a level that would make it commercially viable. However the authors are confident that this is am important step toward attempts to develop field-suitable plants that can reduce the environmental impacts of palladium mining.


Yao Y,, He RJ, Xie QL,, Zhao XH,, Deng XM,, He JB,, Song L, He J, Marchant A, Chen XY,, Wu AM (2016) ETHYLENE RESPONSE FACTOR 74 (ERF74) plays an essential role in controlling a respiratory burst oxidase homolog D (RbohD)-dependent mechanism in response to different stresses in Arabidopsis. New Phytol. 213(4):1667-1681. http://dx.doi.org/10.1111/nph.14278

Alan Marchant (University of Southampton) is a co-author on this Chinese-led study that focuses on the role of the ERF74 transcription factor from the ETHYLENE RESPONSE FACTOR VII (ERF-VII) family in the response to abiotic stresses. The authors test the responses of plants with changed levels of ERF74, showing that they have altered responses to a range of stresses such as drought, light, heat and aluminum. erf74 mutants lack a typical reactive oxidative stress (ROS) burst due to low expression of the RESPIRATORY BURST OXIDASE HOMOLOG D (RbohD) protein. ERF74 directly interacts with the RbohD promotor and the paper shows that the whole ERF74-RbohD-ROS signaling module is activated in order for the plant to correctly response to a range of stresses, which each require maintenance of hydrogen peroxide homeostasis.

Passing the threshold gives a Giant output!

Categories: Cambridge University
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Published on: February 23, 2017

A recent Arabidopsis Research Roundup included a paper from Adrienne Roeder’s lab in Cornell that includes James Locke and Henrik Jonsson from SLCU. The research focuses on the Arabidopsis sepal, which has been the central theme of the Roeder lab since it was set up a few years ago. On a personal level I recall seeing a talk on this topic maybe 10 years ago and it’s always struck me as a fantastically simplistic system that can be used to answer some fundamental questions about the processes that control cell patterning.

This latest paper is focused on the important question of how adjacent cells are set on different development paths, using the giant sepal cells as an excellent model system. This type of cell type specificity is thought to develop following mild stochastic fluctuations in gene expression that lead into feedback loops that accentuate these initial differences. However this has not yet been visualized in vivo until this new manuscript in Elife

The sepal is the outermost organ of the Arabidopsis flower and its correct shape relies on the formation of giant epidermal cells that can grow up to 20% of the entire organ length. These are necessary for the correct function of the organ (to facilitate flower opening) and they form in approximately equal numbers to non-giant cells. Prior to this paper the mechanism of this patterning remained opaque as giant cells can form either adjacent to or apart from each other. The ATML1 transcription factor plays an important role in general Arabidopsis epidermal patterning and has been shown to be required for the generation of giant sepal cells. Importantly the increased size of these giant cells is facilitated by rounds of endoreduplication that can result in 64C nuclei.


ATML1 is expressed in all sepal cells yet only a subset of these will become giant. By using ATML1-overexpression lines together with a simple genetic analysis, the authors show that gene dosage of the ATML1 gene determines the number of giant cells that form (constitutive ATML1 expression have all giant cells). The mechanism by which this dosage results in a mixed cell fate was unclear until they found (using a line containing a fluorescent ATML1-Citrine protein) that ATML1 expression fluctuated far more in the sepal cells than did other genes expressed in the same tissue.

The authors used some fantastic live imaging to show that there are high levels of ATML1 expression in cells destined for giant fate. Although this was not an absolute relationship (as some smaller cells also showed high ATML1 expression), they mathematically demonstrate that obtaining a high threshold of ATML1 correlated about 70% of the time with uptake of giant cell fate.

Finer detail was added to this picture when it became clear that obtaining this threshold at a particular phase of the cell cycle was much more strongly correlated with giant-cell fate. If this threshold is obtained when DNA content was 4C (occurring after DNA replication in G2 phase of the cell cycle) then in 80% of the time the cell became giant. As the authors state ‘a cell is competent to respond to high levels of ATML1 mainly during G2 to induce giant cell formation’.


Finally the authors used plants with a mutation in the LGO gene (LOSS OF GIANT CELLS FROM ORGANS), which have sepals with no giant cells, to determine whether there was feedback control of ATML1 once giant cell fate had been determined. The lgo mutant is epistatic to atml1 and consistent with this observation they show that ATML1 fluctuates normally in the lgo mutant but that this signal does not lead to endoreduplication and giant cell formation. Therefore there is no feedback loop that features endoreduplication and ATML1; rather there is a linear mechanism in which ATML1 fluctuations set in motion endoreduplication, which then continues independent of those ongoing fluctuations.

 

This data was then used to develop a model that could precisely predict the location of giant cell formation based on this information about rapid yet relatively small fluctuations in ATML1 levels.
  Overall this study is an outstanding example of using technological advances in live imaging in a simple experimental system to help develop an understanding of a complex regulatory system. It remains to be seen whether this type of threshold-fluctuation model is important for patterning in other tissues. However this case is an scientific tour of force, demonstrating what is possible when technical advances are put together with careful measurements and inspired experimental planning!

Arabidopsis Research Roundup: February 20th

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Published on: February 19, 2017

This weeks Arabidopsis Research Roundup begins with two papers that look at endogenous and exogenous causes of cell proliferation. Firstly Mike Bevan (JIC) leads a team that looks into the role of controlled protein degradation in this process whilst secondly, Peter Etchells from Durham is a co-author on a study that investigates how nematode pathogens stimulate cell proliferation at the site of infection.

Thirdly is work featuring Cyril Zipfel and colleagues from TSL that looks at how autophosphorylation controls the activity of calcium dependent protein kinases. Fourthly is a broad collaboration led by Richard Mott (UCL) that uses genomic structural variation to identify novel loci. Next Simon Turner from the University of Manchester phylogenetically defines the RALK peptide lineages across plant species. Finally researchers at the University of York conduct a structural analysis of the Arabidopsis AtGSTF2 glutathione transferase.


Dong H, Dumenil J, Lu FH, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y, Bevan MW (2017) Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis.

Genes Dev. http:/​/​dx.​doi.​org/10.1101/gad.292235.116

Open Access


Mike Bevan (John Innes Centre) is the corresponding author of this study that also includes researchers from labs in Belgium, Germany and China. They investigate a fundamental determinant of organ shape, the pattern of cell proliferation that leads to final cell size. They show that two RING E3 ligases activate the DA1 peptidase that in turn affects the stabilization and activity of a range of other proteins including the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22. Overall this results in continued cell proliferation and repression of endoreduplication, which ultimately serves to regulate the timing of the transition from cell proliferation to organ differentiation.

Mike discusses the science surrounding this paper on the GARNet YouTube channel.


Guo X,, Wang J, Gardner M, Fukuda H, Kondo Y, Etchells JP, Wang X, Mitchum MG. Identification of cyst nematode B-type CLE peptides and modulation of the vascular stem cell pathway for feeding cell formation. PLoS Pathog. http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006142

Open Access

Peter Etchells (University of Durham) is a co-author on this US-led study that looks at the effect of nematode-delivered CLE-like peptides on cell growth and how that impacts parasitism. This study has identified a new class of peptides from nematodes that are similar to the plant B-type CLE-like peptide TDIF (tracheary element differentiation inhibitory factor). They show that the nematodes alter the activity of the TDIF-TDR (TDIF receptor)-WOX4 signaling module during infection, whose endogenous function acts during procambial meristem cell proliferation. A variety of mutants involved in this process show reduced infection and leading to the hypothesis that WOX4 is a potential target for nematode CLEs. When exogenous nematode CLE peptides are added to Arabidopsis roots they cause massive cell proliferation. This demonstrates that this response is clearly important for the establishment of nematode infection, usually in cambial cell files.


Bender KW, Blackburn RK, Monaghan J, Derbyshire P, Menke FL, Zipfel C, Goshe MB, Zielinski RE, Huber SC (2017) Autophosphorylation-based calcium (Ca2+) sensitivity priming and Ca2+/Calmodulin inhibition of Arabidopsis thaliana Ca2+-dependent protein kinase 28 (CPK28) J Biol Chem.

http:/​/​dx.​doi.​org/10.1074/jbc.M116.763243

Cyril Zipfel (The Sainsbury Lab) features for a second consecutive week on the Arabidopsis research roundup, this time as a co-author in a study that investigates the role of autophosphorylation in the regulation of calcium (Ca2+) dependent protein kinases (CPKs). In addition they evaluated the role of Calmodulin (CaM) on the activity of CPKs, something that had been previously overlooked. Indeed they show that CPK28 is a CaM-binding protein and that autophosphorylation causes increased activity, especially in low Ca2+ concentrations. Therefore this research provides a mechanistic insight into how a cell might respond to low levels of Ca2+.


Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics. http:/​/​dx.​doi.​org/10.1534/genetics.116.192823

Open Access

Richard Mott (UCL) is corresponding author on this paper includes authors from throughout the UK, Europe and the US. They provide a new analysis of Arabidopsis populations that relies on the genome structural variation. They treat these structural variants as quantitative traits and subsequently map genetically in the same way as in a gene expression study. When a structural variant locus is linked to a genotype at a distant locus then it is designated as a site of transposition. Remarkably they show 25% of the structural variants can be assigned to the transposition events. This method of assessing structural variant loci is amendable to sequencing at low-coverage and this study identified loci that might be involved in germination and resistant to pathogens. Overall they find that genes within structural variants are more likely to be silenced and that this novel analysis technique is particularly useful when mapping transposition events.


Campbell L, Turner SR1(2017) A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. Front Plant Sci. http:/​/​dx.​doi.​org/10.3389/fpls.2017.00037

Open Access

This study from the lab of Simon Turner (University of Manchester) analyse Rapid Alkalinization Factor (RALFs) cysteine-rich peptides from across 51 plant species. They infer that these plant RALFs originate from four major clades in which the majority of the variation exists in the mature peptide sequence, indicative of clade-specific activities. Clade IV accounts for a third of the total peptides yet these lack a number of sequence features thought to be important for RALF function, which leads the authors to speculate that this clade should be thought of as containing RALF-related peptides instead of regular RALFs. Further experimental work is needed in order to define the true nature of the functional relationship between Clades I-III and Clade IV.


Ahmad L, Rylott EL, Bruce NC, Edwards R, Grogan G (2016) Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands. FEBS Open Bio. http:/​/​dx.​doi.​org/10.1002/2211-5463.12168

Open Access

This paper links plant science and structural biology in a study that was undertaken at the University of York. Plant Glutathione transferases (GSTs) have multiple roles including in the detoxification of xenobiotics as well as in various non-catalytic roles. In this work the structure of the Arabidopsis AtGSTF2 is revealed in tandem with a variety of non-catalytic partners including indole-3-aldehyde, camalexin, the flavonoid quercetrin and its non-rhamnosylated analogue quercetin. These are thought to bind to AtGSTF2 by hydrophobic interactions at either one or two symmetrical binding sites. The authors speculate that this non-catalytic binding might have a possible role in ligand transport.

Arabidopsis Research Roundup: Feb 9th

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Published on: February 14, 2017

This weeks Arabidopsis Roundup again includes a broad selection of research topics. Firstly researchers at SLCU are involved in work that describes Arabidopsis sepal development. Secondly Cyril Zipfel from TSL leads a study that adds a layer of complexity to our knowledge of cellular pathogen perception. Thirdly the group of Reiner van der Hoorn from Oxford introduces the use of a novel set of inhibitors that reveals differential activity of proteosomal subunits during bacterial infection. Finally Hugh Pritchard from Kew Gardens is a co-author on a lipidomic study of the seed dessication-stress response.

Meyer HM, Teles J, Formosa-Jordan P, Refahi Y, San-Bento R, Ingram G, Jönsson H, Locke JC, Roeder AH (2017) Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.19131

Open Access

James Locke and Henrik Jonsson (SLCU) are authors on this paper that is led by Adrienne Roeder at Cornell in the USA. The Roeder lab largely focused their research on development of the sepal. The SLCU researchers provided modeling support for this investigation into the critical role of the ATML1 gene in the differentiation of initially identical cells into giant or regular sized sepal cells. They show that there it is a threshold level of differential ATML1 expression that is key in determining cell fate. If this threshold is met during the G2 phase of the cell cycle the cells enter endoreduplication and become giant. If the threshold isn’t reached then the cells divide and remain at a ‘normal’ size. Ultimately they demonstrate a fluctuation-driven patterning mechanism that determines cell fate.

Stegmann M, Monaghan J, Smakowska-Luzan E, Rovenich H, Lehner A, Holton N, Belkhadir Y, Zipfel C (2017) The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling Science

http:/​/​dx.​doi.​org/10.1126/science.aal2541

Cyril Zipfel (The Sainsbury Lab, Norwich) is the lead author of this study that builds upon his labs work into mechanisms of pathogen perception by cell-surface receptor kinases. In this latest work they show that the SITE-1 PROTEASE (ST1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity, a response mediated via the receptor kinase FERONIA (FER). The FER protein is also involved in the formation of other immune complexes. The authors have discovered a mechanism by which FER reglates RALK signaling, indicating that they might have uncovered a more general mechanism for this key control point of immune signaling.

Misas-Villamil JC,, van der Burgh AM, Grosse-Holz F, Bach-Pages M, Kovács J,, Kaschani F, Schilasky S, Emon AE, Ruben M, Kaiser M, Overkleeft HS, van der Hoorn RA (2017) Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. Plant Journal

http:/​/​dx.​doi.​org/10.1111/tpj.13494

Reiner van der Hoorn (University of Oxford) lead this cross-Europe collaboration that introduces a range of inhibitors and probes that can discriminate between catalytic subunits of the proteasome. These tools were studied in both Arabidopsis and Nicotiana benthamiana and the authors used the plant-microbe interactions to further validate their specificity. They show that proteasomal subunits have separate paralogs that are differentiatially incorperated into the larger complex depending on an interaction with pathogenic bacteria. Aliquots of these probes are available on request from renier.vanderhoorn@plants.ox.ac.uk

The authors encourage their usage so as to increase the chance that they might become commercially available. More information from the Plant Chemetics lab.

Chen H, Yu X, Zhang X, Yang L, Huang X, Zhang J, Pritchard HW, Li W (2017) Phospholipase Dα1-mediated phosphatidic acid change is a key determinant of desiccation-induced viability loss in seeds. Plant Cell Environ.

http:/​/​dx.​doi.​org/10.1111/pce.12925

Hugh Pritchard (Kew Gardens) is a co-author on this Chinese-led study that investigates the role of phosphatidic acid (PA) on seed viability. Higher levels of PA correlated with lower seed viability after a desiccation stress. Using Arabidopsis seeds they showed that the enzyme phospholipase D α1 (PLD α1) localises to the plasma membrane following desiccation, where it produces PA. When PLD α1 was suppressed, seed recovery following desiccation improved. The authors used comparative lipidomics to compare PA levels in eight plant species and from their Arabidopsis work, they propose a new model for the mechanism by which seed desiccation effects germination rates.

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