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.
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