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.


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 <a href="http://dirt.iplantcollaborative cialis site” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Digital Imaging of Root Traits’]);” target=”_blank”>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. 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. 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 . 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.

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.

Arabidopsis Research Roundup: April 1st.

This weeks Arabidopsis Research Roundup contains an eclectic mix of investigations. Firstly is a study from Peter Unwin that investigates the molecular factors that control interactions between plants and nematode parasites. Secondly is a study led by John Christie that investigates the factors that control hypocotyl curvature. Thirdly is a fascinating proof-of-concept synbio-style study from Rothamstead Research where an algal gene is transferred into Arabidopsis in the hope of developing a phytomediation-based solution to heavy metal contamination. Fourthly is a study from David Bass that catalogues protist species that feed on leaf-microorganisms whilst finally John Carr heads a study that compares RNA-dependent RNA polymerases from Arabidopsis and Potato.

Eves-van den Akker S, Lilley CJ, Yusup HB, Jones JT, Urwin PE (2016) Functional C-terminally encoded plant peptide (CEP) hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis. Mol Plant Pathol.

This study is a collaboration between researchers at the Universities of Dundee and Leeds, led by Peter Unwin. The focus of the paper is the interaction of Plant-Parasitic Nematodes (PPNs) with their plant hosts. PPNs stimulate redifferentiation of vascular tissues to form ‘feeding structures’ that benefit the parasite. This process is mediated by a diverse family of effector proteins termed C-terminally Encoded Peptide plant hormone mimics (CEPs). This study investigates the CEPs from the nematode Rotylenchulus reniformis and suggests that these peptides evolved de novo in this organism. They show that the activity of a synthetic peptide corresponding to RrCEPs causes a reduction in primary root elongation whilst upregulating a set of genes including the nitrate transporter AtNRT2.1. The authors propose that CEPs evolved in R. reniformis to allow sustained biotrophy by upregulating a specific set of feeding-responsive genes and by limiting the size of the feeding site produced. This study represents an exciting introduction to a currently under-researched area within plant-pathogen interactions.

Sullivan S, Hart JE, Rasch P, Walker CH, Christie JM (2016) Phytochrome A Mediates Blue-Light Enhancement of Second-Positive Phototropism in Arabidopsis. Front Plant Sci. 7:290 Open AccessFrontiersPHOT1

John Christie (Glasgow) is the corresponding author on this investigation into the role of the blue-light receptor phototropin 1 (phot1) during hypocotyl phototropism. Curvature of this organ is enhanced by treatment by red-light mediated by the phytochromeA receptor. However this study shows that pre-treatment with blue-light can also enhance this hypocotyl curvature although this did not occur at higher light intensities. In addition phototropic enhancement was also lacking when PHOT1 is expressed only in the hypocotyl epidermis. Therefore the study shows that the phyA impact on phot1 signaling is restricted to low light intensities and in tissues other than the epidermis.

Zhong Tang, Yanling Lv, Fei Chen, Wenwen Zhang, Barry P. Rosen, and Fang-Jie Zhao (2016) Arsenic Methylation in Arabidopsis thaliana Expressing an Algal Arsenite Methyltransferase Gene Increases Arsenic Phytotoxicity J. Agric. Food Chem. Open Access ArsM

This synthetic biology-focused study is led by Fang-Jie Zhao at Rothamstead Research. The authors take an algal gene (arsM) that allows the transformation of inorganic arsenic to a more volatile methylated version. The biological activity of this enzyme was successfully transferred to two different Arabidopsis ecotypes. However interestingly these transgenic plants became more sensitive to arsenic in growth media suggesting that the new methylated arsenic intermediate is more phytotoxic than inorganic arsenic. Therefore this study demonstrates a negative consequence of this project that attempted to engineer arsenic tolerance in plants. Once again this demonstrates that nature rarely acts predictably and any great ideas usually need to be tested in vivo.

Ploch S, Rose L, Bass D, Bonkowski M (2016) High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae J Eukaryot Microbiol.

After a fantastic opening line in the abstract, ‘The largest biological surface on earth is formed by plant leaves’, this study includes the work of David Bass from the Natural History Museum in London. They investigate the abundance of protists that associate with leaf-inhabiting microorganisms, the “phyllosphere microbiome“. Their findings demonstrate that protists should be considered an important part of the diversity of plant-interacting microbial organisms.

Hunter LJ, Brockington SF, Murphy AM, Pate AE, Gruden K, MacFarlane SA, Palukaitis P, Carr JP (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases Sci Rep. 6:23082 Open Access

John Carr (Cambridge) is the UK-lead on this collaboration with Slovenian and Korean researchers. They primarily investigate the role of the RDR1 RNA-dependent RNA polymerase (RDRs) in potato. In Arabidopsis the RDR1 gene contributes to basal viral resistance but potato plants deficient in StRDR1 do not show altered susceptibility to three different plant viruses. In addition they perform a phylogenetic analysis on the RDR genes and identify a novel RDR7 gene that is only found in Rosids (but not Arabidopsis.

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