GARNet Research Roundup: July 16th

This week’s GARNet research roundup begins with a set of papers looking at aspects of the plant defence response with a focus on the cell wall. Firstly work from Mike Deeks’ lab in Exeter assesses the role of FORMIN4 during pre-invasion cell wall apposition. Secondly Sara Pose and Paul Knox (Leeds) are involved with a study looking at how altered cell wall lignin composition alters the defense response. Finally Joe McKenna and Cyril Zipfel are co-authors on a Norwegian-led study that looks at the influence of plant cell wall integrity maintenance in immune signalling.

Relatedly is a study from the Devoto lab at RHUL looks at the role of the defence hormone methyl jasmonate in Arabidopsis cell culture.

Next are two papers that research different aspects of the plant ER. Verena Kriechbaumer (Oxford Brookes) looks at plant ER-localised Lunapark proteins whilst a study from the University of Warwick provides a preliminary structural analysis of the RTNLB13 reticulon protein.

The seventh and eight papers are involved with the plant response to different growth conditions. Research from University of Nottingham looks at the response of the cortical cell layer of the root meristem to low phosphate conditions whilst work from University of Southampton investigates the relationship between nitrate and copper signaling.

The next paper is from Emily Flashman’s lab at the University of Oxford and looks at the role of plant cysteine oxidases as oxygen sensors whilst the tenth paper features John Doonan (Aberystwyth University) as a co-author and investigates how a histone acetyltransferase affects trichome development.

Finally is a paper from Pierre Baudal and Kirsten Bomblies (John Innes Centre) that uses Arabidopsis arenosa as a model to investigate the emergence of novel flowering time alleles in populations that have colonised along railway corridors.

Sassmann S, Rodrigues C, Milne SW, Nenninger A, Allwood E, Littlejohn GR, Talbot NJ, Soeller C, Davies B, Hussey PJ, Deeks MJ (2018) An Immune-Responsive Cytoskeletal-Plasma Membrane Feedback Loop in Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.014

Open Access

Stefan Sassmann is the lead author of this paper from Mike Deeks’s lab in Exeter. They investigate the role of the membrane-integrated FORMIN4 protein in the process of cell wall apposition, which occurs as part of the plant immune response and is dependent on actin dynamics. FORMIN4 is stably localised apart from the active traffic of the endomembrane system and removing its function compromises the defense response, presumably by altering actin distribution at sites of cell wall apposition. This work demonstrates that FORMIN4 acts as a key component of the pre-invasion defense response.

Gallego-Giraldo L, Posé S, Pattathil S, Peralta AG, Hahn MG, Ayre BG, Sunuwar J, Hernandez J, Patel M, Shah J, Rao X, Knox JP, Dixon RA (2018) Elicitors and defense gene induction in plants with altered lignin compositions. New Phytol. doi: 10.1111/nph.15258

Open Access

Sara Pose and Paul Knox (University of Leeds) are co-authors on this US-led study that investigates how lignin composition can influence the defence response. Plants with the same lignin content but changed lignin compositions show altered expression in genes involved with different arms of the defense response. This indicates that cell wall lignin composition plays a significant role in the plants ability to response to different sources of pathogen attack.

Engelsdorf T, Gigli-Bisceglia N, Veerabagu M, McKenna JF, Vaahtera L, Augstein F, Van der Does D, Zipfel C, Hamann T (2018) The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana. Sci Signal. doi: 10.1126/scisignal.aao3070

Joe McKenna (Imperial College, now Oxford Brookes University) and Cyril Zipfel (The Sainsbury Laboratory, Norwich) are co-authors on this Norwegian-led study that looks at the plant cell wall integrity maintenance mechanism and how it responses to the challenges of growth, development and environmental stresses. They identified a set of receptor-like kinases that are key for the responses elicted by cell wall damage (CWD). Conversely they showed that the components of the pattern-triggered immunity (PTI) signaling pathway repress responses to CWD. This study provides insights into how cell wall responses interact with downstream gene expression changes following pathogen challenge.

Bömer M, O’Brien JA, Pérez-Salamó I, Krasauskas J, Finch P, Briones A, Daudi A, Souda P, Tsui TL, Whitelegge JP, Paul Bolwell G, Devoto A (2018) COI1-dependent jasmonate signalling affects growth, metabolite production and cell wall protein composition in Arabidopsis. Ann Bot. doi: 10.1093/aob/mcy109

Open Access

Moritz Bömer works with Alessandra Devoto at Royal Holloway University of London and leads this research that looks at the effect of MeJA treatment on growth and gene expression in Arabidopsis cell culture. They demonstrate that both MeJA treatment or COI1 overexpression causes changes in the abundance of proteins involved in cell wall loosening as well as altered levels of primary metabolites alanine, serine and succinic acid. This work demonstrates a close link between hormone signaling, the defence response and the metabolic profile of Arabidopsis cells.

Dr Devoto and her academic colleagues at RHUL are profiled in the latest GARNish newsletter available for download from the GARNet website.

Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C (2018) Arabidopsis Lunapark proteins are involved in ER cisternae formation. New Phytol. doi: 10.1111/nph.15228

Open Access

Verena Kriechbaumer from Oxford Brookes University leads this research that investigates the in planta function of novel ER network-shaping proteins called Lunaparks (LNP). They show that these proteins localise to the entire ER network in Arabidopsis. They use confocal microscopy to show that altering the level of LNP gene expression changes ER morphology, possibly by regulating the formation of ER cisternae.

Chow M, Sklepari M, Frigerio L, Dixon AM (2018) Bacterial expression, purification and biophysical characterization of the smallest plant reticulon isoform, RTNLB13 Protein Expr Purif. doi: 10.1016/j.pep.2018.06.015

Open Access

Michael Chow worked with Lorenzo Frigerio and Ann Dixon at the University of Warwick to provide a preliminary structure and topology analysis of the plant RTNLB13 reticulon protein. This ER-associated integral membrane protein was expressed in bacteria and then a variety of analysis techniques were used to suggest that RTNLB13 has a high level of self-association and protein-membrane interactions.

Janes G, von Wangenheim D, Cowling S, Kerr I, Band L, French AP, Bishopp A (2018) Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions Front Plant Sci. doi: 10.3389/fpls.2018.00735

Open Access

George Janes works with Anthony Bishopp at the University of Nottingham and leads this study that looks at root meristem development under low phosphate conditions. They show that in phosphate-limiting conditions the cortex layer of the root meristem contains almost double the number of cells, which results in a greater number of root hair-forming epidermal cells. As this change can occur within 24hrs the rapidity of the response represents a significant adaptation to a changing root environment.

Hippler FWR, Mattos-Jr D, Boaretto RM, Williams LE (2018) Copper excess reduces nitrate uptake by Arabidopsis roots with specific effects on gene expression J Plant Physiol. doi: 10.1016/j.jplph.2018.06.005

Open Access

Franz Hippler (University of Southampton) leads this UK-Brazil collaboration showing that growth of Arabidopsis plants in excess copper conditions causes a downregulation in nitrate uptake. This is due to both direct and indirect changes on the gene expression of nitrate transporters as well as a reduction in transcript level of the plasma membrane proton pump, AHA2. This effect was altered when copper levels were reduced demonstrating that copper toxicity acts at the level of nitrate transport and homeostasis.

White MD, Kamps JJAG, East S, Taylor Kearney LJ, Flashman E (2018) The Plant Cysteine Oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors J Biol Chem.

doi: 10.1074/jbc.RA118.003496

Open Access

Mark White is the lead author on this work from the lab of Emily Flashman at the University of Oxford in which they look at the role of plant cysteine oxidases (PCOs) as oxygen sensors. They assessed the kinetics of each of AtPCO1 to AtPCO5 proteins and show that the most catalytically competent isoform is AtPCO4, in terms of both responding to O2, and oxidizing hypoxic responsive proteins. This work validates an O2-sensing role for the PCOs and provides evidence for functional differences between members of this enzyme family.

Kotak J, Saisana M, Gegas V, Pechlivani N, Kaldis A, Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT (2018) The histone acetyltransferase GCN5 and the transcriptional coactivator ADA2b affect leaf development and trichome morphogenesis in Arabidopsis. Planta. doi: 10.1007/s00425-018-2923-9 Open Access

John Doonan (Aberystwyth University) is a co-author on this manuscript led by Jenna Kotak and Amy Herd in the USA. They investigate plants that have mutations in the histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b. These genes have been previously demonstrated as being involved in endoreduplication and trichome branching. They show that these mutants have alterations in the number and patterning of trichome-branches and that ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.

Baduel P, Hunter B, Yeola S, Bomblies K. Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa (2018) PLoS Genet.

doi: 10.1371/journal.pgen.1007510 Open Access

Pierre Baduel and Kirsten Bomblies (John Innes Centre) lead this work that was conducted prior to Kirsten’s move to Norwich. In this study they follow the colonization of populations of Arabidopsis arenosa along mountain railway corridors. They demonstrate that selective pressure has occurred on novel alleles of flowering time genes and discuss the implications for ruderal communities linked to railways as allele conduits linked to local adaptations.

Monogram 2018 Report: Matthew Dale

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Published on: June 13, 2018

By Matthew Dale Rothamsted Research

The Monogram meeting is an annual conference where people from all parts of the UK cereal and grass community come together to share the latest advances discovered by academic researchers. The meeting attracts the interest of industrial scientists and plant breeders who are keen to learn about the latest exciting results that have been uncovered. As with every year the diverse program provides something of interest for everyone, having entire sessions dedicated to research themes, from genomic technological advances to grain development and crop end use. PhD students and post-docs, who did not give a presentation could present a poster during the poster sessions. This offered some amazing insights into the research which is being undertaken by young researchers in the UK.

This year the conference was held at the John Innes Centre, in Norwich Research Park. JIC is a fitting venue for this event, producing fantastic research for the plant science community, and contributing greatly to the presentations at Monogram.

The meeting started with the cereal bioinformatics session, during which we were updated on the advances to the various bioinformatic resources. This session highlighted the amazing advancements in the wheat genome annotation and gave a quick overview on the publicly available resources. The bioinformatics workshop was well structured and made the complexity of cereal genetics less daunting. The workshop discussed the advances in genome labelling and the transcriptome resources available, these are the key tools as a starting point for cereal molecular biologists and lay down the foundations for fascinating research to come. As this is a rapidly changing area, the session recognised this by featuring a number of presentations on new technologies and resources, such as KNetMiner, which will soon become available to us.

The conference flowed seamlessly thanks to the careful organisation of Scott Boden, Wendy Forsdick and Brande Wulff. Despite the formal nature of the presentations, interspersed with the science was an abundance of tea breaks and lunches, which allowed plenty of time for mingling with other people with common research interests. As is tradition, a large part of the socialising was done at the conference meal on the second night. The conference meal took place at the beautiful Assembly House in Norwich City Centre which was the perfect setting for yet more discussion over a delicious three course meal and drinks.

The conference was concluded with a more applied session focusing on technologies for crop improvement. This has been yet another successful Monogram and I am looking forward to seeing the advances of this ambitious cereal community in 2019.

One switch to control them all – unravelling seasonality in plants

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Published on: June 7, 2018

Written by Marie-Anne Robertson and Andrew J. Millar, of the School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.

Plants make drastic changes to their biology to survive the changing seasons. Yet we know little about how they do this – despite the important clues it could give us on how plants adapt to harsh environments. It is only by studying a long-known anomaly in patterns of gene expression that we discover one answer has been there all along.

Plants are masters at adapting to the changing world around them. Dramatic shifts from day to night, and from season to season, can bring harsh frosts or long droughts that stretch a plant’s survival abilities to its limits. The secret to success is not simply adapting to a change in conditions, instead plants anticipate predictable changes.

Over the last 30 years, molecular genetics has revealed the intricate working of plant’s circadian clock. This molecular circuitry acts as a 24 hour timekeeper, controlling over a third of their genome. It allows plants to make multiple adjustments from day to night, including the movement of leaves, flower opening and their use of nutrients and energy.

The changing seasons, however, require more dramatic biological shifts to guarantee survival. Yet we are still largely in the dark when it comes to understanding the underlying processes. What we know so far comes from detailed studies of the most obvious and visible changes, such as the flowering of many plants in spring. Flowering time is important for agriculture, because it controls when some crops can be harvested.

Plants have a surprisingly simple way of anticipating when spring is on the way. The genes controlling flowering are only expressed at particular points in the day. When this coincides with the right environmental trigger, such as longer daylight hours, it alters the behaviour of the proteins controlled by that gene, triggering flowering. In engineering, this process is called coincidence detection. It ensures that these plants avoid harsh winter conditions and risk their delicate flowers only in longer days.

Beyond beautiful spring blooms, plants must also make big shifts to many, less visible, parts of their biology, such as metabolism and energy use. The question is could a coincidence detector explain these other adjustments? This wasn’t obvious, because the best-known detector was specialised for flowering.

Plants produce a vast number of proteins with different roles in their biology. Studying changes in their levels should provide us with clues into the specific ways plants adapt. Scientists have known for a long time that although the level of some proteins are stable across the day, curiously the genes that dictate their production are still expressed in a rhythmic way. This was long seen as a biological anomaly but it turns out that we have missed the bigger picture by only studying daily rhythms.

In a new publication from Seaton et al (2018), looked at how levels of proteins change in response to the seasons – recreating seasonal daylight hours for the plant Arabidopsis, a commonly used model for other plant species. We studied the proteins involved in the most important aspects of plant biology, those involved in photosynthesis – the conversion of sunlight into energy – and those involved in the storage and use of that energy.

In all over a third of genes in Arabidopsis show a rhythm in their expression and around 1700 proteins changed their levels according to seasonal daylight hours. By simply adjusting our focus, what was once seen as a biological anomaly was revealed to be a master key, which promises to open the door to understanding seasonal change.

Many of the proteins we identified were involved in photosynthesis and energy use, but interestingly some were involved in the plant’s secondary metabolism. This has a wider range of functions including toxic and repellent chemicals that act as the plants defence system and could help to ward off seasonal pests.

The experiments also revealed that the timing of gene expression is key. Those genes with a daily peak of activity in the evening had most effect during long days whereas those that peak in the morning were more effective during short days. As so many plant genes have rhythmic expression, this type of coincidence detection, termed translational coincidence, affected hundreds of proteins in this study.

This simple, yet remarkably powerful, global ‘switching’ mechanism allows plants to make sweeping changes to their biology. Like high street shops stocking up for the upcoming season – whether it is swimwear or winter coats – plants must also select the right options from their extensive protein catalogue. When daily rhythms in gene expression work together with the newly discovered process of translational coincidence it provides plants with a powerful way of mixing and matching vast numbers of proteins to boost their survival.

Further analysis reveals that these findings may not be unique to plants. Analysing data from cyanobacteria and algae indicates translational coincidence could be applied to all photosynthetic organisms. This is starting to provide us with vital insights into how plants, and perhaps other photosynthetic organisms, cope with change. In the future, these fundamental discoveries may pave the way to fine tuning plants biology to make them better suited to harsh environments or even help to expand their geographical boundaries.

Take a look at a video about this work here:

Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

This article is licensed under the Creative Commons License: Attribution 4.0 International,

The study is reported in the following paper, which is free online: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism (2018) Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J. & Gruissem, W. Molecular Systems Biology. 14, 3, p. e7962. Link:

All the published data, analysis scripts and results are also freely available on the FAIRDOMHub,

The study involved researchers from the University of Edinburgh, Scotland; the Max Planck Institute in Golm, Germany and the ETH in Zurich, Switzerland.

The study was funded by the European Union FP7 project TiMet (award 245143).

Monogram 2018 Report: Patrycja Sokolowska

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Published on: June 5, 2018

By Patrycja Sokolowska, PhD student at Rothamsted Research

Monogram 2018 at John Innes Centre in Norwich was the first, and so far the only conference I have been to since I have started my PhD. Monogram has the established reputation to be the best cereal research meeting in the UK, and it gathers the most experienced wheat scientists and breeders, as well as PhD students and young postdoctoral researchers. My colleagues who went to the Monogram last year said it was great, so I was very excited to go and experience it for myself. I was not disappointed!

The conference venue was located in a lovely surroundings of Norwich and the conference itself was brilliantly organised. Morning and afternoon sessions were grouped into focus blocks with clear themes, and although I found all the sessions interesting, due to the nature of my research, the Cereals Bioinformatics Session and Grain Development and Crop End Use Session were most useful for me. Apart from the variety of talks from invited speakers and PhD students, we also had a poster session, during which I had a chance to present my work. The session meant to last for one afternoon, but it extended into the whole duration of the conference (!), which was great, because we could talk about our work for longer!

But Monogram is not only hard work! Our hosts in Norwich made sure that we have time to relax and have a chat with other attendees over a meal too. On the first day we enjoyed the barbeque and a drink, and the second day ended with a bit more formal dinner in the beautiful Assembly House.

Monogram meeting proved to be a great place to meet peers working in a very similar field. Usually, even though I am lucky enough to be doing my PhD in a crop sciences-based research institute, where quite a lot of people work on wheat, I do not get a chance to exchange my experiences with students, simply because the project we are working on are very different. Monogram gave me an amazing opportunity to meet PhD students who use similar laboratory techniques and work on organisms closely related to wheat. We had a chance to talk about our research and exchange valuable experiences. I hope we will keep in touch and I am looking forward to reading their first publications.

Overall, these were very intense but informative and fruitful three days. I am very happy that I could be a part of this year’s Monogram and I would recommend going to anyone working in the field of cereal research. I would like to thank GARNet for awarding me the travel grant to attend this conference, and making my expenses budget a little less tight! I am looking forward to the Monogram meeting in Nottingham next year! Who knows, maybe I will have a chance to present next year!

Me during my flash talk presentation, trying to lure people into visiting my poster

GARNet Research Roundup: June 4th

This weeks GARNet Research Roundup begins with a paper from researchers at the University of Dundee, James Hutton Institute, Durham University and the University of Glasgow that characterises a functional role for alternative splicing during the cold response. Second is a paper from Newcastle University that investigates the role of the OXI1 kinase during aphid predation. Third is a paper that includes University of Bristol co-authors that looks at strigolactone signaling in moss whilst the fourth paper from researchers at Leeds and QMUL studies the role of ascorbate during photosynthesis. The final paper from Warwick and York uses gene expression data from pathogen-infected plants to generate a model for predicting a strategy for synthetic engineering of the defence response.

Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell doi: 10.1105/tpc.18.00177.

Open Access

Cristiane Calixto and Wenbin Guo work with John Brown at University of Dundee and the James Hutton Institute and in this large-scale biology paper they characterise the role of alternative splicing (AS) during a stress response. RNAseq was performed on plants exposed to cold stress and they showed that hundreds of genes undergo AS just a few hours after temperature decrease and that this response is sensitive to small changes. The authors propose that AS is a mechanism to fine-tune changes in thermo-plasticity of gene expression and in addition they investigate the activity of the novel splicing factor U2B”-LIKE.

Christiane will discuss this research at the upcoming GARNet2018 meeting held at the University of York in September 2018.

Shoala T, Edwards MG, Knight MR, Gatehouse AMR. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae) (2018) Transgenic Res. doi: 10.1007/s11248-018-0078-x.

Open Access

This work is led by Tahsin Shoala in the lab of Angharad Gatehouse at Newcastle University and demonstrates a novel role for MAPK cascades in resistance to aphid predation. They investigate mutants in OXI1 kinase, a gene that activates MAPK signaling and demonstrate a reduction in the aphid population build-up. Furthermore they show that the effect of OXI works through a mechanism that involves callose deposition, demonstrated as oxi1 mutants lack the upregulation of a set of β-1,3-glucanase genes following predation.

Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S (2018) Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. New Phytol. doi: 10.1111/nph.15214

GARNet committee member Jill Harrison is a co-author on this paper that is led by Mauricio Lopez‐Obando working at Université Paris-Saclay. In Physcomitrella patens development they investigate the role of the moss ortholog of the Arabidopsis strigolactone signaling mutant MAX2. Previous work had shown that moss does response to SL signaing but they find that although Ppmax2 mutants showed defects in early development and photomorphogenesis they do not show changes in the SL response. Fascinatingly this indicates that the molecular components that control SL signaling have diverged in vascular plants and seemingly co-opted a role for MAX2 that was previously not required in mosses.

Plumb W, Townsend AJ, Rasool B, Alomrani S, Razak N, Karpinska B, Ruban AV, Foyer CH. Ascorbate-mediated regulation of growth, photoprotection and photoinhibition in Arabidopsis thaliana (2018) J Exp Bot. doi: 10.1093/jxb/ery170

William Plumb (Leeds) and Alexandra Townsend (QMUL) are the lead authors on this study that investigates the importance of ascorbate during photosynthesis. In this work they analysed the growth of ascorbate synthesis mutants that are smaller and have less biomass than wildtype plants. However these plants have normal levels of non-photoinhibiton, allowing the authors to conclude that ascorbate is needed for growth but not photoprotection.

Foo M, Gherman I, Zhang P, Bates DG, Denby K (2018) A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring. ACS Synth Biol. doi: 10.1021/acssynbio.8b00037
Mathias Foo and Iulia Gherman (University of Warwick) are lead authors on work that analyses gene expression data taken from Botrytis cinerea-infected Arabidopsis. They have identified a network of genes involved in the defence response. They validate their model against previously obtained time series data and then perturb the model in two differences ways, focused on the transcription factor CHE. This analysis demonstrates the potential of combining feedback control theory with synthetic engineering in order to generate plants that are resistant to biotic stress.

Monogram 2018 Report: Ben Sibbett

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Published on: May 29, 2018

Ben Sibbett University of Southampton

Attending Monogram 2018 gave me a fantastic insight into the broad range of high quality research that is being conducted in the small grains community. As a PhD student, working on a specific project, it can become easy to neglect research that is outside of your primary focus. In addition, it is easy to lose sight of how your own research fits into the bigger picture and how important it is to understand how your own research can be applied.

Related to applied research, I particularly enjoyed the talk given by the plenary speaker Professor Scott Haley. Professor Haley described how his group is using genomics and bioinformatics to improve wheat varieties for farmers. He touched upon the challenges of working with farmers that are responsible for thousands of hectares of farmland and the enjoyment he has had developing a relationship between scientists and farmers.

Another aspect of Monogram 2018 that I found interesting was the opportunity to learn about how technology and the tools now available to scientists working with crop species have developed. This includes how the latest wheat genome reference is being used to assist research.

Furthermore, learning about the progress that has been made in gene editing at NIAB in rice, wheat and barley was exciting. In addition to gene editing, it was fascinating to find out how the TILLING populations in wheat are now being used widely by researchers. I have used this technology in my own research so it was interesting to see how other groups have taken advantage of this resource.

Ben gives a Flash talk at Monogram 2018

Of real interest was the talk given by James Simmonds from the Uauy lab. He discussed how the generation of double and triple mutants were allowing their group to test hypotheses. He also briefly discussed the notion of speed breeding to reduce the time taken to generate these mutants which could be helpful for my own research.

Attending Monogram also gave me the opportunity to see how other PhD students were getting along in their own projects. With the support of GARNet, I presented a poster at Monogram 2017 in Bristol. This year enabled me to talk to students I had met in Bristol and discuss the progress that had been made in our respective work. I truly enjoyed the MonoGram 2018 meeting and I am extremely grateful for the support of GARNet that has allowed me to attend.

GARNet Research Roundup: May 17th

This weeks GARNet research roundup includes six excellent papers investigating many aspects of Arabidopsis cell biology. Firstly Eirini Kaiserli from Glasgow introduces a novel regulator of blue-light signaling. Second is a paper that analyses the circadian clock with single cell resolution and is led by James Locke (SLCU) and Anthony Hall (Earlham Institute). The next two papers investigate different aspects of hormone signaling, with Keith Lindsey’s group at Durham looking at the relationshop between the HYDRA protein and the auxin response whilst Ottoline Leysers group in Cambridge looks at the link between auxin and cytokinin during shoot growth. The fifth paper from Phillip Mullineaux (University of Essex) provides a genome-wide analysis into the role of HEAT SHOCK TRANSCRIPTION FACTORA1b protein. The final paper from the lab of Piers Hemsley (James Hutton Institute, University of Dundee) should be of interest to many plant molecular biologists as they assess the functional significance of different epitope tags.

Perrella G, Davidson MLH, O’Donnell L, Nastase AM, Herzyk P, Breton G, Pruneda-Paz JL, Kay SA, Chory J, Kaiserli E (2018) ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis. Proc Natl Acad Sci U S A.. pii: 201718099. doi: 10.1073/pnas.1718099115

Open Access

Eirini Kaiserli (University of Glasgow) leads this study that identifies the ZINC-FINGER HOMEODOMAIN 10 (ZFHD10) as a novel regulator of light signaling. ZFHD10 physically interacts with TANDEM ZINC-FINGER PLUS3 (TZP) and these proteins coassociate at promotors that are blue-light regulated. These results reveal of novel mechanism of action for the key multiple signal integrator TZP in the light regulated growth of Arabidopsis hypocotyls.

Eirini discusses this paper on the GARNet YouTube channel.

Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC (2018). Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. Elife. 26;7. pii: e31700. doi: 10.7554/eLife.31700 Open Access

This paper is led by James Locke (SLCU) and Anthony Hall (Earlham) and investigates the circadian clock at single cell resolution. They use Arabidopsis plants grown in constant environmental conditions to show two desynchronised yet robust single cell oscillations that move both up and down the root. Their results indicate that the clock shows cell-to-cell coupling and they they modeled this relationship to recapitulate the observed waves of activity. Overall their results are suggestive of multiple coordination points for the Arabidopsis clock, which is different from the mammalian system of regulation.

Short E, Leighton M, Imriz G, Liu D, Cope-Selby N, Hetherington F, Smertenko A, Hussey PJ, Topping JF, Lindsey K (2018) Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism in Arabidopsis. Development . pii: dev.160572. doi: 10.1242/dev.160572 Open Access

This collaboration between the research groups of Keith Lindsey and Patrick Hussey at the University of Durham investigates the role of the HYDRA1 (HYD1) sterol Δ8-Δ7 isomerase in epidermal patterning. This tissue shows highest HYD1 expression and hyd mutants have major root patterning defects. Tissue-specific expression of HYD1 indicates that it is involved with some type of non-cell autonomous signaling. Analysis of PIN1 and PIN2 protein expression suggests that auxin might be this functional signal

Waldie T, Leyser O (2018) Cytokinin targets auxin transport to promote shoot branching. Plant Physiol. 2018 May 1. pii: pp.01691.2017. doi: 10.1104/pp.17.01691.Open Access

This study from the lab of Ottoline Leyser (SLCU) investigates the integration between the plant hormones cytokinin and auxin. They investigate the role of cytokinin in shoot branching through analysis of Arabidopsis Response Regulators (ARRs) mutants. They show arr mutant phenotypes correlate with changes in stem auxin transport mediated by the PIN3, PIN4 and PIN7 efflux carriers, the expression of each respond to cytokinin signaling. Overall this study identifies a novel alternative pathway by which cytokinin impacts bud outgrowth through alterations in auxin transport.

Albihlal WS, Irabonosi O, Blein T, Persad R, Chernukhin I, Crespi M, Bechtold U, Mullineaux PM (2018) Arabidopsis Heat Shock Transcription FactorA1b regulates multiple developmental genes under benign and stress conditions. J Exp Bot. doi: 10.1093/jxb/ery142 Open Access

Phillip Mullineaux (University of Essex) leads this collaboration with French colleagues in a study that investigates the genome-wide targets of the HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) protein. Under non-stress ad heat-stress conditions they showed that 1000s of genes are differentially expressed with a smaller proportion of genes showing different levels of direct interaction. The indirect targets of HSFA1b are regulated through a network of 27 transcription factors and they also provide evidence for the role of hundreds of natural antisense non-coding RNA in the regulation of HSFA1b targets. Overall they show that HSFA1b is a key regulator of environmental cues to regulate both developmental genes and those involved in stress tolerance.

Hurst CH, Turnbull D, Myles SM, Leslie K, Keinath NF, Hemsley PA (2018) Variable effects of C-terminal tags on FLS2 function – not all epitope tags are created equal. Plant Physiol. doi: 10.1104/pp.17.01700 Open Access

This study from the Hemsley lab (James Hutton Institute, University of Dundee) is a cautionary tale on the use and interpretation of results obtained from experiments with commonly-used epitope tags. They assessed the activity of plants containing transgenic FLS2 proteins, which is a receptor-like kinase (RLKs) involved in the defence response. They show that various FLS2 C-terminal epitope fusions reveal highly variable and unpredictable outputs, indicating that the presence of different tags significantly alters protein function. This finding might require a reassessment of many experiments that rely on interpreting the function of epitope-tagged proteins and has significant for many if not all plant molecular biologists.

Reversing the Decline in Plant Science Applications to the BBSRC: analysis and recommendations from GARNet

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Published on: May 14, 2018

GARNet is a community-facing UK network funded by BBSRC through Responsive Mode that supports the delivery of outstanding plant science research. GARNet’s primary focus is supporting researchers who work on fundamental areas of plant science, particularly around the adoption of new technologies and new ways of working. Recently members of the plant science community have expressed concerns about a perceived lack of opportunities to obtain funding for fundamental plant science.

The primary mechanism for obtaining funding of this type comes through BBSRC Responsive Mode funding predominantly via Research Committee B: Plants, microbes, food and sustainability. As a service to the community, GARNet asked the BBSRC to analyse their data regarding the number of plant science applications, which is not in the public domain. The BBSRC found that the number of total plant science applications is declining in line with the number of funded projects. However the number of applications to study aspects of fundamental plant science is declining at a faster rate (Figure 1).

Therefore GARNet investigated the factors that might have contributed to this worrying trend and our findings allowed us to make a series of recommendations outlined below. The discussion and reasoning that led to these recommendations is included in a longer article that is available for download from the GARNet website.

A- showing number of submitted and successful grants from Responsive Mode that propose to work on any aspect of plant science (2014-2017) B- showing number of submitted and successful grants from Responsive Mode that propose to work on an aspect of fundamental plant science (2014-2017). Data provided by BBSRC.


1. GARNet and other UK plant science stakeholders to spread the message that the BBSRC is ‘open-for-business’ to fund world-class grants based on fundamental plant science, including Arabidopsis-only or other plant model-only research.

2. GARNet and other UK plant science stakeholders to encourage the academic community to review Responsive Mode grants and to apply to join Research Committees. Currently, this is a particularly important action point for fundamental plant scientists.

3. GARNet uncovered considerable confusion over what can be considered ‘Impact’ within Responsive Mode proposals. We recommend that BBSRC circulates updated information to potential applicants and Research Committee panel members to clarify what exactly can be considered as ‘Impact’. The BBSRC is providing a piece on this topic for GARNish issue 29, published in Summer 2018.

4. Plant scientists are encouraged to submit their proposal to Research Committee B, but where more appropriate for the proposed research program they are also invited to submit to any of the other Research Committees. Should BBSRC deem it necessary to transfer proposals between committees, they will provide applicants the choice to withdraw their proposal.

5. BBSRC to advise potential applicants that world-class fundamental research is appropriate to be included in relevant GCRF applications, provided that it includes a clear long-term path toward a demonstrable benefit in an ODA country.

6. Given the success of IPAs, we recommend BBSRC reassesses the criteria for evaluating these grants. BBSRC could look into the possibility of capping the number of successful LINK/IPA proposals to a reasonable proportion of funded applications within a single grant round. Grants of sufficient quality would be encouraged to reapply in subsequent funding rounds if they do not fit under the cap in any one round.

7. Plant scientists are encouraged to engage with BBSRC to suggest areas that are relevant for special grant calls. The BBSRC has some flexibility to use Newton Fund and GCRF calls to respond to novel areas of research interest if there is a demonstrable community need.

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