Arabidopsis Research Roundup: June 9th

This edition of the Arabidopsis Research Roundup pleasingly includes four Open Access articles. Firstly Jose Gutierrez-Marcos leads an investigation into stress-induced memory, secondly Richard Morris is the corresponding author on a study that has developed a new model that explains waves of calcium signalling that response to environmental stresses. Thirdly is a UK-US collaboration that defines the factors that control carotenoid accumulation in seeds. Finally Chris Hawes leads a study that characterises the novel localisation of a subset of auxin biosynthetic enzymes.

Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J (2016) Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity Elife http://dx.doi.org/10.7554/eLife.13546 Open AccessStress_Model

Jose Gutierrez-Marcos is the corresponding author on this pan-European study that adds to our increasing knowledge about the role of generational memory in the response to stress. Distinct regions of the Arabidopsis genome are susceptible to fluctuations in the level of DNA methylation in response to hyperosmotic stress, a condition that persists into a following generation. This effect is transmitted through the female lineage and the authors investigate this effect in more detail by focussing on a single epigenetically targeted locus. By designing experiments that ran over a series of generations they show that a plants ‘short term memory’ is reliant on the DNA methylation machinery and is able to transmit a distinct developmental response to immediate offspring.

Evans MJ, Choi WG, Gilroy S, Morris RJ (2016) A ROS-assisted Calcium Wave Dependent on AtRBOHD and TPC1 Propagates the Systemic Response to Salt Stress in Arabidopsis Roots. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00215 Open Access

Richard Morris (JIC) leads this US-UK collaboration that investigates the downstream mechanisms that occur after the waves of ROS and Ca2+ signalling that respond to environmental stresses. The authors show that the current model for propagation of this wave, which relies upon a diffusive wave Ca2+ signalling, is unable to explain the speed of transmission of the wave. The authors develop a new model that adds a ROS-signalling component to explain the velocity of the Ca2+ wave and experimentally verify that their model could represent the in vivo situation. In addition they show that the effectiveness of this ROS-release signalling module is dependent on the activity of the vacuolar ion channel TPC1 and the NADPH Oxidase AtRBOHD.
CaWavePic
Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D (2016) ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00604 Open Access

The lead author of this US-led study is Sabrina Gonzalez-Jorge who is currently a post-doc in GARNet committee member Ian Henderson’s lab in Cambridge. This study elucidates nine loci that are involved in carotenoid homeostasis in Arabidopsis seeds and shows that plants lacking the ZEAXANTHIN EPOXIDASE (ZEP) protein have a six-fold reduction in total seed carotenoids. Natural variation within the ZEP gene is able to account for the fine-tuning of seed carotenoid content and acts upstream of two previously characterised CAROTENOID CLEAVAGE DIOXYGENASE enzymes. Importantly, and somewhat surprisingly, four of the nine Arabidopsis loci are thought to have conserved function in determining the composition of carotenoids in maize kernels. This demonstrates that studying this phenomonen in Arabidopsis is highly relevant for study of the same process in economically important crops.

Kriechbaumer V, Botchway SW, Hawes C (2016) Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway J Exp Bot.

http://dx.doi.org/10.1093/jxb/erw195 Open Access

Chris Hawes (Oxford Brookes) leads this study that localised a subset of enzymes involved in auxin biosynthesis to the endoplasmic reticulum. In addition certain of these enzymes appear to physically interact. This localisation is confirmed by showing ER microsomal fractions are able to undertake auxin biosynthesis. The auxin signalling pathway is complex and well characterised yet this finding adds another layer of regulation that might influence the dynamics of auxin activity.

Arabidopsis Research Report: May 26th

This weeks Arabidopsis Research Roundup includes six studies across a range of discplines. Firstly Alison Smith provides an excellent audio description of an investigation into the dynamics of night-time starch degradation.

Secondly three UK institutions (Durham, Exeter and Oxford Brookes) participate in a study of VAP27 membrane network proteins. Next a broad collaboration from CPIB in Nottingham then introduce a multi-scale model that helps describe Arabidopsis root development.

We also include two studies that involve collaborations with Korean researchers: Gary Loake is a contributor on a study that introduces plant RALF genes whilst Ian Henderson’s research group participates in a study into the function of the SWR1 complex in miRNA gene expression. Finally we highlight a new Plant Cell teaching tool put together by UK academics from Hull and Bristol.

Feike D, Seung D, Graf A, Bischof S, Ellick T, Coiro M, Soyk S, Eicke S, Mettler-Altmann T, Lu KJ, Trick M, Zeeman SC, Smith AM (2016) The starch granule-associated protein EARLY STARVATION1 (ESV1) is required for the control of starch degradation in Arabidopsis thaliana leaves Plant Cell

http://dx.doi.org/10.1105/tpc.16.00011 Open Access

This UK and Swiss study is led by Alison Smith from the John Innes Centre and investigates starch degradation that occurs during nighttime. They developed a novel screen to identify an uncharacterized mutant called early starvation 1 (esv1) that more rapidly degraded starch so that it is exhausted earlier in the night. They found that ESV1 and the related LESV1 proteins associated with starch granules within the chloroplast stroma. The authors propose that these proteins influence the organisation of the starch granule matrix, facilitating access for starch-degrading enzymes. In addition they also show that this function appears to be conserved throughout all starch-synthesizing organisms.

Professor Smith provides an audio description of this paper:

Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ (2016) Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. New Phytol. 210(4):1311-1326 http://dx.doi.org/10.1111/nph.13857

This cell biology-focused study is a collaboration between the Universities of Exeter, Durham and Oxford Brookes and investigates vesicle-associated membrane protein-associated proteins (VAPs), which form part of the network that links the plasma membrane and ER. The Arabidopsis genome contains 10 VAP homologues (VAP27-1 to -10) split into 3 clades. Members of clades I and II localise to both ER as well as to ER/PM contact sites (EPCSs) whilst clade II members are only found at the PM, all discovered through transient expression experiments in tobacco. Interestingly the localisation to the EPCSs is associated with the cytoskeleton but does not require the presence of that underlying structure. These proteins are expressed in most cell types and when their levels are altered, plants show pleiotropic phenotypes. Overall this study shows that VAP27 proteins are required for ER-cytoskeleton interactions that are critical for normal plant development.

Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J (2016) A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol. S0022-5193(16)30070-4 http://dx.doi.org/10.1016/j.jtbi.2016.04.036

From http://dx.doi.org/10.1016/j.jtbi.2016.04.036

This investigation was performed at CPIB in Nottingham in collaboration with the Virtual Plant Project in Montpellier and is led by John King. The authors have developed a multi-scale computational model that allows the study of signalling networks that occurs during Arabidopsis root growth. This model was experimentally tested to investigate how it is affected by hormonal changes during root growth. The model was able to identify two novel mutants that significantly alter root length through perturbations in meristem size. In general this study demonstrates the value of multi-scale modeling as part of the process of evaluating the function of the components that define the formation of the root meristem.

Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW (2016) Comprehensive analysis of plant rapid alkalization factor (RALF) genes Plant Physiol Biochem. 106:82-90

http://dx.doi.org/10.1016/j.plaphy.2016.03.037

This Korean-led study includes a contribution from Gary Loake from the University of Edinburgh and is the first comprehensive investigation of Rapid alkalization factor (RALF) proteins across plant species. These RALF proteins are thought to be important signalling molecules in plant defense and development. This study provides information on gene structure, subcellular locations, conserved motifs, protein structure, protein-ligand interactions and promoter analysis across Arabidopsis, rice, maize and soybean. The RALF genes are phylogenetically divided into 7 clades and their mRNA upregulation following nitrosative and oxidative stresses suggests that they are function in responding to changes in cellular redox status. Overall this manuscript provides a valuable resource to prime future research into the role of RALF genes.

Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I (2016) Regulation of microRNA-mediated developmental changes by the SWR1 chromatin remodeling complex in Arabidopsis thaliana. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00332

GARNet committee member Ian Henderson (Cambridge) is a contributor on this study that is led by researchers in Seoul, South Korea. In the last ARR, Vinod Kumar described work that looked into the role of the SWR1 chromatin-remodeling complex and this study provides an insight into the role of this same SWR1 complex on microRNA (miRNA)-mediated transcriptional control. In SWR1 complex mutants (arp6, sef, and pie1), deep sequencing revealed that many miRNA types and their target mRNAs are misregulated. This further establishes the role of the SWR1 complex in the control of nucleosome occupancy, likely by mediating the exchange of H2A isoforms, for a range of genes involved in the fine-tuning of numerous developmental processes.

Hubbard, K, Dodd, A. (2016). Rhythms of Life: The Plant Circadian Clock. Teaching Tools in Plant Biology: Lecture Notes. http://dx.doi.org/10.1105/tpc.116.tt0416

Katherine Hubbard and Anthony Dodd have produced a teaching resource focused on the Circadian Clock as part of the increasingly comprehensive Plant Cell Teaching Tools. Most academics are looking to save time and this resource will allow them to do this and provides excellent coverage of the topic.

Arabidopsis Research Roundup: May 13th

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Published on: May 13, 2016

This weeks Arabidopsis Research Roundup includes two peer-reviewed papers and the release of a preprint. Vinod Kumar from the JIC provides an audio description of a study that investigates the role of the SWR1 complex in the defence response. Secondly Jessica Metcalf from Oxford is a contributor on a study that looks at population responses of Arabidopsis to simulated climate change. Finally John Brown (University of Dundee and the James Hutton Institute) is the corresponding authors on a preprint that introduces a new Arabidopsis transcriptome annotation.

Berriri S, Gangappa SN, Kumar SV (2016) SWR1 chromatin-remodelling complex subunits and H2A.Z have non-overlapping functions in immunity and gene regulation in Arabidopsis Molecular Plant http://dx.doi.org/10.1016/j.molp.2016.04.003 Open Access

Vinod Kumar (John Innes Centre) is the corresponding author on this study that investigates the incorporation of the histone variant H2A.Z into Arabidopsis nucleosomes. This histone variant is important in the control of differential gene expression although its role in plant immunity is not well understood. H2A.Z is integrated into nucleosome by the SWR1 chromatin remodelling complex that contains a number of subunits namely PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX 6 (SWC6). Interestingly each subunit plays discrete roles in different pathogen response processes including basal resistance, enhanced resistance, effector-triggered immunity or in altered JA/ET-mediated immunity. Genome wide expression analysis reveals a role for PIE1 in the crosstalk between signalling processes and overall that SWR1c components might have distinct non-overlapping roles during gene regulation and expression.

Dr Kumar kindly provides a brief audio description of this paper:

 

Fournier-Level A, Perry EO, Wang JA, Braun PT, Migneault A, Cooper MD, Metcalf CJ, Schmitt J (2016) Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana PNAS http://dx.doi.org/10.1073/pnas.1517456113 PNASpic

Mathematician Jessica Metcalf (Oxford) is an author on this US-led study that uses Arabidopsis to investigate the effect of climate change on evolution of fitness. Over four seasons plants were grown under four climatic conditions (present day, overall increased temp, winter-warming and poleward-migration temp) and 12 traits were measured as a proxy for fitness evolution. The data was used to simulate evolutionary trajectories over a 50-100 year period. The authors found that each climatic condition resulted in different outcomes where populations with fewer founding genotypes or less initial diversity adapted less well to altered conditions. This suggests that successful adaptation to climate change is linked to the diversity within a given population prior to the change occurring.

Zhang R, Calixto C, Marquez Y, Venhuizen P, Tzioutziou N, Guo W, Spensley M, Frey N, Hirt H, James A, Nimmo H, Barta A, Kalyna M, Brown J (2016) AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data. Preprint BioRxiv http://dx.doi.org/10.1101/051938 Open Access

This preprint includes researchers from the Universities of Dundee (John Brown), Glasgow (Hugh Nimmo) and Vienna and the James Hutton Institute and introduces AtRTD2, a new transcriptome for Arabidopsis and AtRTD2-QUASI for expression analysis and quantification of alternatively spliced isoforms in RNA-seq data.

Arabidopsis Research Roundup: May 5th

There are a bumper crop of papers in this edition of the Arabidopsis Research Roundup. First from the University of Manchester is a paper that identifies a protein involved in plant programmed cell death. Secondly are two papers from the University of Bristol that highlight the role of viruses in the reflectivity of plant leaves and an assessment of the growth parameters of Arabidopsis on different soil-types. Thirdly are three papers from University of Edinburgh that either use CRISPR-Cas technology to develop virus-research plants, investigate the relationship between photoperiod and metabolism or present a method for assessment of protein S-nitrosylation. Fourthly is a paper that includes a contribution from the University of Leeds that investigates the evolutionary and functional relationship of the WOX gene family. Finally is a study that highlights the role of the AUGMIN complex during microtubule activity that includes a contribution from the University of Leicester.

In addition, although not involving Arabidopsis, we should mention an exciting study from Gerben van Ooijen (Edinburgh) that has discovered a conserved circadian mechanism based on magnesium rhythms that is linked to energy expenditure.

Ge Y, Cai YM, Bonneau L, Rotari V, Danon A, McKenzie EA, McLellan H, Mach L, Gallois P (2016) Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in Arabidopsis. Cell Death Differ. http://dx.doi.org/10.1038/cdd.2016.34 Open Access

The corresponding author of this paper is Patrick Gallois from the University of Manchester and includes contributions from Hazel McLellan in Dundee almongside Chinese and Austrian collaborators. This study investigates the role of caspase proteins on control of programmed cell death in plants. This research area has been hindered by the apparent lack of plant caspase orthologues despite pharmacological evidence that proteins with caspase activity are active in plants. The authors use a labeled caspase-3 inhibitor to identify the Arabidopsis Cathepsin B3 (AtCathB3) protein as having caspase activity, which was verified using recombinant proteins during in vitro enzyme assays. AtCathepsinB1,2,3 triple mutant plants demonstrate a reduction in PCD induced by different stresses and explains why caspase inhibitors are effective tools for studying PCD in plants. The core Cathepsin B protein is evolutionarily conserved suggesting that an ancestral pathway exists that controls PCD, the details of which require further study.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2016) The Effects of Plant Virus Infection on Polarization Reflection from Leaves. PLoS One. 11(4):e0152836 http://dx.doi.org/ 10.1371/journal.pone.0152836 Open Access

Gary Foster’s research group at the University of Bristol collaborate with others at the University of York and in Australia for this study that investigates how plant viruses may modify gene expression to benefit their own transmission. They show that Potato virus Y and Cucumber mosaic virus (CMW), which both are transmitted by aphids, significantly reduce the amount of polarised light that is reflected from abaxial leaf surfaces of tobacco plants particularly when compared to the effects caused by non-insect vectored viruses. However this effect was not shown in Arabidopsis leaves infected by a variety of differently transmitted viruses. Interestingly ECERIFERUM6 (CER6) transcripts accumulate to higher levels following infection with insect vectored viruses and as this gene is involved in cuticle wax synthesis the authors suggest that induced changes in cuticle composition might be key in understanding how viruses encourage predation by their insect vectors. Finally the authors discuss the overall adaptive significance of these results.

Drake T, Keating M, Summers R, Yochikawa A, Pitman T, Dodd AN (2016) The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media. PLoS One. 11(4):e0153625 http://dx.doi.org/ 10.1371/journal.pone.0153625 Open AccessPeatPic

GARNet committee member Anthony Dodd, also from the University of Bristol, leads this study into the growth of Arabidopsis on peat-free media, which was motivated by the unsustainable use of peat-based composts. They found that biomass accumulation and seed yield were reduced on peat-free media and that some types of this media was more suspectible to fungal contamination. Overall vegetative phenotypic parameters were similar between plants grown on peat-based or peat-free media, indicating that this type of media will be appropriate for future analysis. However the seed yield was usually reduced, indicating that experiments looking at post-phase change phenotypes might not be as comparable between plants growth on media with different amount of peat.

Pyott DE, Sheehan E, Molnar A (2016) Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants Mol Plant Pathol. http://dx.doi.org/10.1111/mpp.12417

Attila Molnar (Edinburgh) is the corresponding author on this study that uses the transformative technology CRISPR/Cas9 to engineer Arabidopsis plants that are resistant to potyvirus infection. This is achieved by targeting the genes encoding the translation initiation factor eIF(iso)4E that had been previously identified as being critical for viral establishment. Importantly they subsequently selected transgene-free plants that have no phenotypic changes when compared to wildtype growth under standard conditions. As the potyvirus Turnip Mosaic Virus is an important pathogen for vegetable crops this is potentially an extremely powerful technique for generating virus-resistance food crops.

Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M (2016) Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis Plant Cell Environ. http://dx.doi.org/10.1111/pce.12754

This German–led study aims to connect the expression of photoperiod-length responsive circadian clock-regulated genes with those involved in metabolic processes such as starch degradation and includes a contribution from Professor Andrew Miller from the Edinburgh SynthSys Centre. The authors assess global gene expression by transcript profiling at photoperiods ranging from 4-18 hours and found that changes in transcript abundance at dawn throughout these photoperiods were as large as changes seen in individual experiments when comparing dawn and dusk. These complex interactions revealed coordinated regulation of key metabolic processes and begins to demonstrate how metabolism is linked to photoperiod.

Homem RA, Le Bihan T, Yu M, Loake GJ (2016) Identification of S-Nitrosothiols by the Sequential Cysteine Blocking Technique Methods Mol Biol. 1424:163-74. http://dx.doi.org/10.1007/978-1-4939-3600-7_14

This paper from the lab of Gary Loake (Edinburgh) describes the methods they use to investigate the role of protein S-nitrosylation in the immune responses of Arabidopsis. These are based on a modification of the biotin-switch technique, which they term sequential cysteine blocking.

Dolzblasz A, Nardmann J, Clerici E, Causier B, van der Graaff E, Chen J, Davies B, Werr W, Laux T (2016) Stem cell regulation by Arabidopsis WOX genes Mol Plant. S1674-2052(16)30029-6 http://dx.doi.org/10.1016/j.molp.2016.04.007

This German-led study includes work from the lab of Brendan Davies at the University of Leeds and investigates the role of the WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor gene family during stem cell development and maintenance. Most members of the WUS-clade can largely substitute for WUSCHEL activity in the shoot meristem, which is absolutely dependent on a conserved WUS-box motif that is critical for the interaction with TOPLESS co-repressors. In contrast to the WUS clade, the WOX13 and WOX9 clades cannot substitute for WUS activity. The indicates that WOX control of shoot and floral meristem relies on certain currently not-fully-understood attributes of the WUS-clade of proteins.

Oh SA, Jeon J, Park HJ, Grini PE, Twell D, Park SK (2016) Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Plant J. http://dx.doi.org/10.1111/tpj.13192

David Twell (Leicester) is an author on his Korean-led study that reports on the identification of the new gem3 mutant, which displays defects in gametophytic development. Mutant plants exhibits disrupted cell division during male meiosis, at pollen mitosis I and throughout female gametogenesis. Gem3 is a hypomorphic allele of the AUGMIN subunit 6 gene, which is a component of Augmin complex responsible for microtubule (MT) nucleation in acentrosomal cells. In the gem3 mutant, the authors show that MT arrays are incorrectly distributed, likely causing the gametophyte-specific phenotypes and demonstrating a broad role for the augmin complex during sexual reproduction in flowering plants

SLS ’16: An Undergraduate’s View

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Published on: April 26, 2016

Guest Post from Sam Downs, 2nd Year Undergraduate at Cambridge University.

This April, the Sainsbury Laboratory at Cambridge university (SLCU) held its first large meeting – SLS ’16 – on Induced Plant Development. The keynote speakers were Prof. Sofie Goormachtig on root strigolactone signalling to Prof. Christian Fankhauser on growth changes in response to light, with others addressing topics ranging from large scale morphological studies to cell and molecular biology.

It was a first for me too; like most undergraduates, I hadn’t yet attended an academic conference. As I imagine many find at their first conference, it was slightly intimidating to be in a room half-full of PIs – the rest being PhD students, with their own research projects underway, wasn’t much better. There was nothing for it but to get stuck in though, and talking to people about their talks and posters proved easier than I had thought. It’s a testament to the friendliness of the plant science community that everyone was willing to explain their work from the bottom up to a passing undergrad!

As an outsider to research, it was interesting to note what people felt was important to communicate in talks and posters. They seemed to be broadly results-driven or process-driven, and I found this was especially marked in the posters; many were reporting new techniques, such as growing Arabidopsis roots on microfluidics chips, or laser imaging of cell movements, whilst others (such as Dr Dana MacGregor’s prize-winning poster on seed dormancy) drew their main interest from the phenomenon they showed. This is quite different to the way that I’ve mainly engaged with science – essentially, as an interested member of the public. This year I’ve been helping to run the Cambridge student biological society, and we’ve hosted a number of talks by UK scientists. Their talks are mainly of the former kind; essentially reporting new results, suitable for a lay audience. It was thus quite new to me to hear technique-driven presentations, and exciting too – a look above the parapet of summer exam revision (driven, of course, by an entirely different sort of result!).

What struck me most of all, though, was the hearing the questions people asked at the end of each talk. Through these, I got a stronger sense of how active researchers think about science than even the talks or the posters could. As an undergraduate, I’m used to hearing researchers talk about results, and sometimes about methods too; but the biggest difference was how the audience parsed what they heard. The questions focused on the experimental process and the physiology of the whole plant (“What happens to Rorippa aquatica if it’s in warm water, [when heat and submersion have opposite effects]?” “Is the plant’s response to UV-B modulated in the diurnal cycle?”). This is a different way of thinking (perhaps regrettably) to that taken at undergraduate level; we tend to focus more on isolated details, so the bigger picture of how a result came about in the lab and in the organism can be missed. It was a reminder to me of the challenge of getting across this gap from obsession with facts to obsession with science.

Overall, I learnt a lot in the short duration of the SLS, both about what’s going on in plant development and about life in science. I would life to thank the organisers, the speakers, and especially Geraint Parry from GARNet who offered me the opportunity to attend it.

Rorippa                   Temperature mediated developmental changes in Rorippa aquatica

UK-BRC Meeting: April 13th 2016

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Published on: April 18, 2016

The annual gathering of the UK Brassica Research Community is almost unique amongst meetings in that it’s refreshingly short and almost completely focuses on the research of postdocs and PhD students. As such it was a pleasure to attend the latest event that was held on April 13th at the John Innes Centre.

Organised by Dr Penny Hundleby on behalf of Lars Ostergaard, the ambitious schedule is a rapid dash through the ongoing research in the UK Brassica community. The majority of the work came either from the John Innes Centre or the University of York with a few less contributions from the University of Nottingham. Aside from that were also talks from TGAC, Aberystwyth, Warwick and ADAS.

uk-brc_header2

The prevailing trend of the meeting was a description of a range of Associative Transcriptomic studies that aim to discover SNPs associated with growth in a variety of conditions. These mostly are funded through the Renewable Industrial Products from Rapeseed (RIPR) Project, which is led by Ian Bancroft at York. The majority of these studies are in the early stages with researchers having identified loci of interest that are currently without further definition. Over the coming years it will be exciting to learn more about these loci and whether they will be subsequently targeted for new breeding techniques.

The format of the meeting was designed just to highlight the key points of each presenters research and the five minute schedule did just that. Established faculty are notorious for taking liberties with timings so it was to the credit of the younger presenters that everyone kept to the 5minute schedule, although the presence of a intimidating bell might have helped with that!

There were many great talks throughout the day but a few highlights included Dana Macgregor (JIC) discussing the influence of cold signaling on seed germination and Annemarie Eckes (TGAC) who introduced the utility of the Brassica Information Portal (BIP) that is supported through the RIPR grant.  Helen Holmes (ADAS) provided a real world study about the mechanics of lodging of Brassica and the incredible £50million losses that occur due to this type of wind damage. In addition it was refreshing to see research being effectively conducted with a plank of wood! Marie Bruser from Lars Ostergaard’s lab discussed her study of the uninspiringly named Arabidopsis cell cycle gene called ‘Dimer Protein B’ that plays a role in flower development and pod-shatter. She described her mixing of research in Brassica, back to Arabidopsis and then returning again to Brassica. Later this summer, Marie will be benefitting from a Gatsby Foundation/GARNet sponsored travel sponsorship to attend the ICAR meeting in Korea.

Toward the end of the meeting Eric Holub (Warwick) gave an update on an exciting project with Indian collaborators that aims to develop strategies to combat white blister rust infection in oilseed.

WhiteBlisterAn example of white blister rust (from MPMI doi:10.1094 /MPMI-21-6-0745)

Colin Miles from the BBSRC gave arguably the most enlightening talk and certainly the one that will generate the most future interest. He outlined the Global Challenges Research Fund (GCRF) that has been recently funded out from the UK Governments Department for International Development. The GCRF contains a remarkable £1.5billion and will need to be spent before the end of this government session in 2019-20. Dr Miles indicates that a funding call will be announced in the coming months although the precise nature of the grants is currently unknown. However what is clear is that any project must have a significant interaction with an overseas collaborator from a (currently unpublished) list of developing countries. The GCRF will likely encourage cross-disciplinary collaborations so Dr Miles encouraged meeting attendees to get their thinking caps on as there will be a significant portion of money available (equivalent to 3x the entire annual BBSRC budget).

Interesting times!

Thanks to the JIC/TGAC for hosting this meeting and check out the UK-BRC website over the coming weeks for a full list of PDFs from each talk. Next year the meeting will take place in May in Nottingham, hosted by Neil Graham and Martin Broadley.

UKPPN Root Phenotyping Workshop: April 2016

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Published on: April 15, 2016

The UK Plant Phenotyping Network is a BBSRC sponsored network that has supported meetings and workshops since 2012. A representative from GARNet sits on the UKPPN committee so it was a pleasure to attend the UKPPN Root Phenotyping Meeting that recently took place in the Department of Plant Science at the University of Nottingham.

For someone whose previous research involved growing Arabidopsis plates on agar plates or in controlled growth chambers, this workshop was a real eye-opener as it highlighted the excellent science that is largely aimed at discovering how plant roots interact with their local environment.

This work does mostly not involve Arabdopsis although many of the studies investigate aspects of root growth whose fundamentals have been discovered from lab-studies of the worlds favourite weed. The meeting was hosted by Professor Malcolm Bennett and some of his current Arabidopsis work involves the hydrotropic response which is perfectly aligned to the in-terra studies of how cereal and Brassica roots interact with the available nutrients and water. This work has been facilitated by an amalgamation of research grants that ultimately resulted in the building of the Hounsfield Facility. This purpose built facility contains a generous greenhouse, a human-sized automated robot and three different imagers for CT scanning.

FullSizeRenderThis has allowed a better understanding of how roots interact with soils. However applying more scientific rigour to this process has only been made possible by the analysis software that has been developed at CIPB alongside this imaging technology. During the UKPPN meeting Stefan Mairhofer (CPIB) outlined the development of the Root Phenotyping Pipeline that has allowed researchers to make statistical sense of the CT data that they obtain from the Hounsfield facility. Later in the same session Stefan Gerth (Frauhofer Institute for Integrated Circuits) presented their own technology that they are using for root phenotyping with CT imaging. Finally Erik Esveld (Wageningen) introduces the potential for using XRT imaging to analyse plants grown on drained Rockwool.

Earlier in the day the meeting started with a session on field phenotyping that included an introduction to ‘Shovelomics’ from Tobias Wojciechowski (Julich). He described how they are developing methods for the imaging of whole root systems that have been dug up from the soil. As expected, one difficulty with this work is inconsistency and indeed Tobias showed that the variation between root samples in a plot was greater than that seen between different geographic genotypes isolated from Germany, Norway or Austria. The software that has been developed in house at Julich is able to take 40K images overnight and this data is held in the Digital Imaging of Root Traits (DIRT) platform,  now being administered through CyVerse. Perhaps there is no greater contrast than the physical digging up plants versus the in silico analysis on CyVerse but perfectly shows the interdiscplinary work occuring in this research area!IMG_9554

The field phenotyping session ended with an enjoyable trip out into the Sutton Bonnington research sites to have demonstrations of Electrical Resistance Tomography by Andrew Binley (this technique allows the measurement of soil water levels) and also Tractor-Mounted Soil Coring from Larry York (which produces soil cores to be used for later root analysis). Pleasingly, the soil water levels predicted by the EMI could be observed in the soil cores.

It might have been unusual for a conference to take people out into the field but it really highlighted the level of challenge that it will take to effectively phenotype a varied field populations of plants!

FullSizeRender_1The second day of the meeting focused on root imaging and modeling, with the audience blown away by the incredible images shown by Jonathan Lynch (Penn State University and University of Nottingham) generated using laser ablation tomography. In this technique root sections are destructively imaged and then digitally reconstituted using 3D software to give fantastic videos that investigate the length of root sections.

Professor Lynch discusses the importance of aerenchyma cells that are found in the cortex of many cereal plants. These essentially empty cells enable a lower overall metabolic cost, therefore clearly benefits the overall energy costs of the plant. Detailed phenotype analysis of aerenchyma has made possible by the RootScan software that has been developed in the PSU Roots lab and is freely available for use.

Later in the session Huw Jones from NIAB described a novel method for the estimation of root biomass. They put together two items that young researchers are told should never mix: soil and PCR. In this technique they perform qPCR on soil samples using primers that are specific for your plant of interest, which allows the approximation of the root biomass within the sample. This technique has also been used to estimate the interactions between plants and weeds across a range of soil depths and struck me as a relatively inexpensive way for this type of analysis, which can provide useful data about the composition of a soil sample.

The keynote talk of the modeling session was Johannes Postma (Julich) who provided an enthusiastic explanation of his attempts to link root phenotypes, soil content and plant biomass. One predicted finding that corresponded with real-life data was that plants with root aerenchyma showed increased biomass in soils with reduced phosphorous. It was excellent to hear this analysis as for much of the meeting the link between root phenotype and yield was not fully made. This is likely to do with the challenges of the imaging technology and the difficulties in fully correlating complex root phenotype with yield.

This meeting demonstrated that the field (pardon the pun) of root phenotyping has great strength especially within the UK, France and Germany. On day one of the meeting Gabriele Pastori (BBSRC) introduced the recently published European Strategy Forum on Research Infrastructures (ESFRI) Roadmap which has “identified the new Research Infrastructures (RI) of pan-European interest corresponding to the long term needs of the European research communities”. Through the work of the UKPPN and others, this document introduces a proposed area of interest in Plant Phenotyping, called EMPHASIS.

EMPHASISThis roadmap is used as an introduction to technologies for which the EU would be interested in developing cross-border infrastructure, by facilitating the legal and financial tools necessary for these type of linkages. At this early stage the EMPHASIS project has no funding associated with it yet the involvement of the BBSRC demonstrates that there is willingness on a national level to discuss future possibilities for funding this area of research. Ultimately any grant funding will come from research bodies within each contributing nation so over the next few years it is encumbent on the UK Plant Phenotyping community to decide how this which occur. Later in the meeting the leader of the French Plant Phenotyping Network (FPPN), Francois Tardieu describes how they have brought together 15 collaborator organisations to tackle phenotyping challenges (see image below)

FPPNThe UK would not look to replicate French or German efforts but rather focus on areas of expertise in which the UK is a world-leader and will provide greatest input toward a pan-European plant phenotyping network. A significant amount of work has already gone into the highlighting of this area for possible European involvement so watch this space to find out how the UKPPN and others can convince UK funders to support this wider initiative.

Overall this was an excellent final meeting of the UKPPN grant and since the first UKPPN gathering the research community has clearly come a long way. It is hoped that the EMPHASIS project and other initiatives will continue to support plant phenotyping across all scales from molecular analysis through to whole field phenotyping and environmental considerations.

Storify of tweets from the meeting put together by the Susie Lydon at CPIB.

Arabidopsis Research Roundup: April 14th

This week Arabidopsis Research Roundup contains two studies that originate at the University of Birmingham. Firstly George Bassel kindly provides an audio description of a study that looks at the processes regulating seed germination. Secondly Juliet Coates leads an investigation into the function of evolutionarily conserved ARABIDILLO proteins. Elsewhere is a University of Edinburgh study into the tissue-specificity of PhyA responses and lastly an investigation of the phytotoxic effects of Cerium nanoparticles.

Nieuwland J, Stamm P, Wen B, Randall RS, Murray JA, Bassel GW (2016) Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6. Sci Rep. http://dx.doi.org/10.1038/srep23586 Open AccessRootTip

George Bassel (Birmingham), GARNet PI Jim Murray (Cardiff) and Jeroen Nieuwland (South Wales) are the leaders of this study that investigates the activation of the root meristem during germination, a process that requires de novo GA synthesis. Using hormone applications and genetic analysis the authors show that root meristem can begin elongation independent of germination, which is defined as occurring following both testa rupture and radicle protrusion. KRP6 is a cell cycle regulator and partially represses activation of the cell cycle by GA so krp6 mutants germinate more rapidly. Overall this study concludes that the cell cycle can uncouple the interactions of GA and ABA that act to conclude germination and promote root meristem elongation.

George Bassel kindly provides a short audio description of this paper.

Moody LA, Saidi Y, Gibbs DJ, Choudhary A, Holloway D, Vesty EF, Bansal KK, Bradshaw SJ, Coates JC (2016) An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid. New Phytol. http://dx.doi.org/10.1111/nph.13938 Open Access

This study comes exclusively from the University of Birmingham and is led by Juliet Coates. This group investigates the role of Armadillo-related ARABIDILLO proteins on branching processes across plant species. In the moss Physcomitrella patens these proteins are linked to the action of the hormone ABA on spore germination, which converges with a role for the proteins in Arabidopsis seed germination. Importantly both P.patens and Selaginella moellendorffii ARABIDILLO proteins are able to substitute for native proteins in Arabidopsis, demonstrating their conserved function. The authors conclude that these proteins were co-opted into the regulation of both sporophytic and gametophytic processes early in plant evolution.

Kirchenbauer D, Viczián A, Ádám É, Hegedűs Z, Klose C, Leppert M, Hiltbrunner A, Kircher S, Schäfer E, Nagy F (2016) Characterization of photomorphogenic responses and signaling cascades controlled by phytochrome-A expressed in different tissues. New Phytologist . http://dx.doi.org/10.1111/nph.13941 Open Access

Ferenc Nagy (Edinburgh) is the corresponding author of this Hungaro-German study that focuses on how phytochrome responses are mediated in a tissue-specific manner. Considering that phyA is expressed throughout plant tissues it remained a mystery as to how the PhyA responses are able to control plant development. This study used tissue-specific promotors to drive PHYA production in a variety of tissues and discovered that expression in a limited number of tissues is able to regulate flowering time and root growth. In addition they find evidence for the intercellular movement of PhyA. The authors conclude that the PhyA response is partly controlled by a mix of tissue-specific expression and the regulation of key downstream factors in a tissue-autonomous cell activity.

Yang X, Pan H, Wang P, Zhao FJ (2016) Particle-specific toxicity and bioavailability of cerium oxide (CeO2) nanoparticles to Arabidopsis thaliana J Hazard Mater. http://dx.doi.org/10.1016/j.jhazmat.2016.03.054

GraphThis Sino-UK-Australian study is led by Fang-Jie Zhao at Rothamstead Research. They investigate the uptake and phytotoxicity of commonly used (in consumer products) cerium oxide nanoparticles (CeO2-NPs) into Arabidopsis. At high concentrations the NP component, but not the Ce ions, were shown to have toxic effects on plant growth. These CeO2-NPs were taken up and translocated to the shoot where they aggregate in needle-like particles. This movement was independent of the type or concentation of Ce. The authors suggest this represents important information for the environmental considerations linked to the use and disposal of this type of NPs.

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