Evolution

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

The close association between plants and other organisms drives the evolution of antagonistic traits in host-parasite interactions and of mutually beneficial traits in symbioses. Research at all levels of biological organisation of these interactions is increasing our knowledge of evolutionary processes in plants and associated organisms and thus our ability to manipulate them to benefit stable food production. JIC, TSL and TGAC have made major contributions to progress in this area in the Biotic Interactions ISP. We have used high-throughput technologies to accelerate discoveries about the diversity of genes involved in recognition and adaptation and the structure and evolution of genomes of plants, pests and microbes. We have been at the forefront of research that has produced detailed knowledge about the structural basis of recognition, which increasingly provides a strong foundation for understanding the molecular evolution of specific plant biotic interactions. Our work on dissection of signalling pathways is leading to opportunities to understand the evolutionary relationship of different processes involved in plant-microbe interactions. We have led developments in pathogen genomics and transcriptomics, which have revolutionised our capacity to research large populations of plant pathogens and are giving us unprecedented power to understand the evolutionary forces that shape them. Our theoretical research allows us to increasingly understand which ecological processes maintain balanced polymorphism in coevolving hosts and parasites on the one hand or, as is often the case in agriculture, fuel co-evolutionary arms races.

These breakthroughs provide the foundation for the next phase of advances in understanding the co-evolution of plants and associated organisms. We will focus on key topics in research on biological molecules, organisms, populations and communities - our combined expertise will make novel contributions to science and high strategic impact to agriculture in the UK, developing countries and elsewhere. We will exploit scientific and technical advances, particularly in high-throughput technologies, to understand the evolution of effectors that interact with host plants and to identify the processes that shape the evolution and coevolution of molecules at the interface of interactions between plants and other organisms. At the organism level, we will dissect signalling and defence pathways involved in parasitic and symbiotic interactions with the aim of understanding the evolutionary implications of the complex processes involved in plants’ interactions with the environment. We will research the evolutionary forces that shape parasite and plant populations, focussing on the adaptation of populations of important fungal pathogens to methods of crop management including resistant varieties and fungicides, and on the adaptation of plant defence mechanisms to environmental conditions related to global climate change. Our programme of work in this theme will take an innovative direction by building on previous advances in our research to understand the evolutionary dynamics of communities of organisms associated with plants, including soil microflora and multiple pests and parasites, and the interaction of these communities with plant genetic variations.

Publications

10 25 50

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Bialas A (2018) Lessons in Effector and NLR Biology of Plant-Microbe Systems. in Molecular plant-microbe interactions : MPMI

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Bueno-Sancho V (2017) Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance. in Methods in molecular biology (Clifton, N.J.)

 
Description Objective 4.1: Mechanisms of coevolution of molecules involved in plant-parasite recognition

Classification of a new phytoplasmas subgroup 16SrII-W associated with Crotalaria witches' broom diseases in Oman based on multigene sequence analysis: Crotalaria aegyptiaca, a low shrub is commonly observed in the sandy soils of wadis desert and is found throughout all regions in Oman. A survey for phytoplasma diseases was conducted. During a survey in a wild area in the northern regions of Oman in 2015, typical symptoms of phytoplasma infection were observed on C. aegyptiaca plants. The infected plants showed an excessive proliferation of their shoots and small leaves. The presence of phytoplasma in the phloem tissue of symptomatic C. aegyptiaca leaf samples was confirmed by using Transmission Electron Microscopy (TEM). In addition the extracted DNA from symptomatic C. aegyptiaca leaf samples and Orosius sp. leafhoppers were tested by PCR using phytoplasma specific primers for the 16S rDNA, secA, tuf and imp, and SAP11 genes. The PCR amplifications from all samples yielded the expected products, but not from asymptomatic plant samples. Sequence similarity and phylogenetic tree analyses of four genes (16S rDNA, secA, tuf and imp) showed that Crotalaria witches' broom phytoplasmas from Oman is placed with the clade of Peanut WB (16SrII) close to Fava bean phyllody (16SrII-C), Cotton phyllody and phytoplasmas (16SrII-F), and Candidatus Phytoplasma aurantifolia' (16SrII-B). However, the Crotalaria's phytoplasma was in a separate sub-clade from all the other phytoplasmas belonging to Peanut WB group. The combination of specific primers for the SAP11 gene of 16SrII-A, -B, and -D subgroup pytoplasmas were tested against Crotalaria witches' broom phytoplasmas and no PCR product was amplified, which suggests that the SAP11 of Crotalaria phytoplasma is different from the SAP11 of the other phytoplasmas. We propose to assign the Crotalaria witches' broom from Oman in a new lineage 16SrII-W subgroup depending on the sequences analysis of 16S rRNA, secA, imp, tuf, and SAP11 genes. To our knowledge, this is the first report of phytoplasmas of the 16SrII group infecting C. aegyptiaca worldwide.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

Chemosensory proteins in the CSP4 clade evolved as plant immunity suppressors before two suborders of plant-feeding hemipteran insects diverged: Chemosensory proteins (CSPs) are small globular proteins with hydrophobic binding pockets that have a role in detection of chemicals, regulation of development and growth and host seeking behaviour and feeding of arthropods. Here, we show that a CSP has evolved to modulate plant immune responses. Firstly, we found that the green peach aphid Myzus persicae CSP Mp10, which is delivered into the cytoplasm of plant cells, suppresses the reactive oxygen species (ROS) bursts to both aphid and bacterial elicitors in Arabidopsis thaliana and Nicotiana benthamiana. In contrast, other CSPs, including MpOS-D1, do not have this ROS suppression activity. Aphid RNA interference studies demonstrated that Mp10 modulates the first layer of the plant defence response, specifically the BAK1 pathway. Alignment of CSPs from multiple aphid species showed that Mp10 homologues uniquely have tyrosine (Y40) and tryptophan (W120) flanking the central binding region. Exchange of aromatic residues between Mp10 and MpOS-D1 showed a gain of ROS activity of MpOS-D1 and loss of this activity of Mp10. We identified Mp10 homologs in diverse plant-sucking insect species, including aphids, whiteflies, psyllids and leafhoppers, but not in other insect species, including blood-feeding hemipteran insects. Moreover, the positions of Y and W residues are conserved among these Mp10 homologs, which we found also suppress plant ROS. Together, these data and phylogenetic analyses provides evidence that an ancestral Mp10-like sequence acquired plant ROS suppression activity via gain-of-function mutations before the divergence of plant-sucking insect species over 250 million years ago.

Objective 4.2: Evolution of pathways controlling biotic interactions in plants

The role of reactive oxygen in the development of Ramularia leaf spot disease in barley seedlings: Ramularia collo-cygni is an ascomycete fungus that colonizes barley primarily as a benign endophyte, although this interaction can become pathogenic, causing the disease Ramularia leaf spot (RLS). Factors, particularly reactive oxygen species, that resulted in the transition of the fungus from endophyte to necrotrophic parasite and the development of disease symptoms were investigated. Disease development in artificially inoculated seedlings of barley varieties varying in partial resistance to RLS was related to exposure to abiotic stress prior to inoculation. Histochemical and molecular analysis determined the effect of R. collo-cygni colonization on accumulation of reactive oxygen species and antioxidant gene expression. Development of RLS on barley lines defective in antioxidant enzymes and with altered redox status or non-functional chloroplasts was compared with the accumulation of fungal biomass to determine how these factors affect disease symptom expression. Exposure to abiotic stress increased symptom development in all susceptible and most partially resistant barley varieties, in association with greater hydrogen peroxide (H2O2) levels in leaves. Decreased activity of the antioxidant enzymes superoxide dismutase and catalase in transgenic and mutant plants had no effect on the disease transition, whereas manipulation of H2O2 levels during asymptomatic growth of the fungus increased disease symptoms in most susceptible varieties but not in partially resistant plants. Barley mutants that undergo rapid loss of green leaf area when infected by R. collo-cygni or albino mutants with non-functional chloroplasts showed reduced development of RLS symptoms. These results imply that in seedlings the pathogenic transition of the normally endophytic fungus R. collo-cygni does not result from senescence as such, but rather is promoted by factors that result in changes to host reactive oxygen species. Barley varieties vary in the extent to which these factors promote RLS disease.

Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors: Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds' largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided identification of effectors including xylanase and inhibitor I9 domain containing proteins able to induce cell death in-planta. The inhibitor I9 domain was more abundant in the secretomes of a wide range of necrotising fungi relative to biotrophs. These findings provide novel targets for further dissection of the virulence mechanisms and potential avenues to control this under-characterised but important pathogen.

Improving zinc accumulation in cereal endosperm using HvMTP1, a transition metal transporter: Zinc (Zn) is essential for all life forms, including humans. It is estimated that around two billion people are deficient in their Zn intake. Human dietary Zn intake relies heavily on plants, which in many developing countries consists mainly of cereals. The inner part of cereal grain, the endosperm, is the part that is eaten after milling but contains only a quarter of the total grain Zn. Here, we present results demonstrating that endosperm Zn content can be enhanced through expression of a transporter responsible for vacuolar Zn accumulation in cereals. The barley (Hordeum vulgare) vacuolar Zn transporter HvMTP1 was expressed under the control of the endosperm-specific D-hordein promoter. Transformed plants exhibited no significant change in growth but had higher total grain Zn concentration, as measured by ICP-OES, compared to parental controls. Compared with Zn, transformants had smaller increases in concentrations of Cu and Mn but not Fe. Staining grain cross sections with the Zn-specific stain DTZ revealed a significant enhancement of Zn accumulation in the endosperm of two of three transformed lines, a result confirmed by ICP-OES in the endosperm of dissected grain. Synchrotron X-ray fluorescence analysis of longitudinal grain sections demonstrated a redistribution of grain Zn from aleurone to endosperm. We argue that this proof-of-principle study provides the basis of a strategy for biofortification of cereal endosperm with Zn.

Objective 4.3 Evolutionary processes in populations of plants and their parasites

Population structure of the ash dieback pathogen, , in relation to its mode of arrival in the UK: The ash dieback fungus, Hymenoscyphus fraxineus, a destructive, alien pathogen of common ash (Fraxinus excelsior), has spread across Europe over the past 25years and was first observed in the UK in 2012. To investigate the relationship of the pathogen's population structure to its mode of arrival, isolates were obtained from locations in England and Wales, either where established natural populations of ash had been infected by wind-dispersed ascospores or where the fungus had been introduced on imported planting stock. Population structure was determined by tests for vegetative compatibility (VC), mating type and single-nucleotide polymorphisms (SNPs). VC heterogeneity was high at all locations, with 96% of isolate pairings being incompatible. Frequencies of the MAT1-1-1 and MAT1-2-1 idiomorphs were approximately equal, consistent with H.fraxineus being an obligate outbreeder. Most SNP variation occurred within study location and there was little genetic differentiation between the two types of location in the UK, or between pathogen populations in the UK and continental Europe. There was modest differentiation between UK subpopulations, consistent with genetic variation between source populations in continental Europe. However, there was no evidence of strong founder effects, indicating that numerous individuals of H.fraxineus initiated infection at each location, regardless of the route of pathogen transmission. The ssRNA virus HfMV1 was present at moderate to high frequencies in all UK subpopulations. The results imply that management of an introduced plant pathogen requires action against its spread at the continental level involving coordinated efforts by European countries.

Potential for re-emergence of wheat stem rust in the United Kingdom: Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.

Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity: Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new races that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previous races, leading to wide-scale epidemics. Here, we used field-based genotyping to generate high-resolution data on P. striiformisgenetics and carried out global population analysis. We also undertook comparative analysis of the 2014 and 2013 UK populations and assessed the temporal dynamics and host specificity of distinct pathogen genotypes. Our analysis revealed that P. striiformis lineages recently detected in Europe are extremely diverse and in fact similar to globally dispersed populations. In addition, we identified a considerable shift in the UK P. striiformis population structure including the first identification of one infamous race known as Kranich. Next, by establishing the genotype of both the pathogen and host within a single infected field sample, we uncovered evidence for varietal specificity for genetic groups of P. striiformis. Finally, we found potential seasonal specificity for certain genotypes of the pathogen with several lineages identified only in samples collected in late spring and into the summer, whereas one lineage was identified throughout the wheat growing season. Our discovery of which wheat varieties are susceptible to which specific P. striiformis isolates, and when those isolates are prevalent throughout the year, represents a powerful tool for disease management.

Objective 4.4: Evolutionary implications of the community ecology of organisms associated with plants

Temporal and spatial field evaluations highlight the importance of the presymptomatic phase in supporting strong partial resistance in Triticum aestivum against Zymoseptoria tritici: Zymoseptoria tritici, the causal agent of septoria tritici blotch (STB), remains a significant threat to European wheat production with the continuous emergence of fungicide resistance in Z. triticistrains eroding the economic sustainability of wheat production systems. The life cycle of Z. triticiis characterized by a presymptomatic phase (latent period, LP) after which the pathogen switches to an aggressive necrotrophic stage, when lesions bearing pycnidia quickly manifest on the leaf. As minimal knowledge of the possible role of the LP in supporting STB resistance/susceptibility exists, the goal of this study was to investigate the spatial and temporal association between the LP and disease progression across three locations (Ireland - Waterford, Carlow; UK - Norwich) that represent commercially high, medium and low STB pressure environments. Completed over two seasons (2013-2015) with commercially grown cultivars, the potential of the LP in stalling STB epidemics was significant as identified with cv. Stigg, whose high level of partial resistance was characterized by a lengthened LP (c. 36 days) under the high disease pressure environment of Waterford. However, once the LP concluded it was followed by a rate of disease progression in cv. Stigg that was comparable to that observed in the more susceptible commercial varieties. Complementary analysis, via logistic modelling of intensive disease assessments made at Carlow and Waterford in 2015, further highlighted the value of a lengthened LP in supporting strong partial resistance against STB disease of wheat.
Exploitation Route The research is relevant to: control of insect pests and fungal pathogens by agrochemicals, plant breeding for durable broad-spectrum resistance to multiple diseases, biofortication of crops and their impact on associated microorganisms, prevention and control of invasive and re-emerging diseases, and breeding for disease resistance combined with yield and quality in arable crops.
Sectors Agriculture, Food and Drink,Environment

URL http://www.jic.ac.uk/research/plant-health/our-science/objectives/#theme-4
 
Description Research on pathology and ecological of the ash dieback fungus is being used to develop proposals for recovery of ash as a keystone species in the UK landscape. Research on wheat stem rust has been used to increase aware of the threats from accidental imports of alien diseases, and is being used to develop plans for re-establishment of barberry as a shrub in non-arable regions of England. Research on Ramularia leaf spot of barley and Septoria tritici blotch of wheat has been used to improve methods of selecting for resistance to these diseases in combination with high yield and commercially acceptable grain quality.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Environment,Leisure Activities, including Sports, Recreation and Tourism,Transport
Impact Types Societal,Economic,Policy & public services

 
Description Advice to House of Lords on plant biosecurity, especially trees: discussion with policy advisor to HoL Energy & Environment Select Committee regarding future biosecurity for UK woodlands and farming
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description Ramularia ratings on Spring Barley Recommended List
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Meeting with AHDB, SRUC and others. Prof James Brown provided advice on ensuring that the Ramularia ratings used in the AHDB Spring Barley Recommended List reflect varieties' resistance. This involves selection of field trials which have produced appropriate datasets, requirements for training field trial officers, and improved data analysis to increase the reliability of Ramularia ratings.
 
Description Relative risk in selection of recommended cereal varieties
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Meeting with AHDB and BIOSS about "relative risk" of cereal varieties. The aim of the relative risk rating is to identify crop varieties which require low chemical inputs in relation to their economic value. Prof James Brown showed that the present system for assessing relative risk of varieties on the Wheat Recommended List does not have the desired effect and simply provides information about a limited range of field traits. He demonstrated an alternative method of assessing relative risk which encapsulates the full range of traits relevant to reducing chemical inputs. This method will enable farmers to choose wheat varieties which optimise the balance between maximising yield and minimising variable costs and chemical inputs. He has agreed to extend his analysis to the Winter and Spring Barley Recommended Lists.
 
Description BBSRC-IPA grant
Amount £1,316,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description CGIAR Inspire challenge
Amount $100,000 (USD)
Organisation CGIAR 
Sector Charity/Non Profit
Country Global
Start 10/2017 
End 09/2018
 
Description ERC Advanced Investigator
Amount € 2,500,000 (EUR)
Funding ID BLASTOFF 743165 
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 09/2017 
End 08/2022
 
Description Future Leader Fellowship awarded to Thomas Mathers
Amount £317,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 04/2021
 
Description Horizon 2020
Amount € 4,999,999 (EUR)
Funding ID 773311-2 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2018 
End 04/2022
 
Description Horizon 2020
Amount £4,999,999 (GBP)
Funding ID 773311 - RUSTWATCH 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2018 
End 05/2022
 
Description The Royal Society International Exchanges Cost Share 2017 Japan (JSPS) award for overseas travel between collaborators in the UK and Japan
Amount £50,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 03/2020
 
Description The Royal Society Kohn Fellowship awarded to Adi Kliot
Amount £65,000 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 10/2016 
End 10/2018
 
Description Zespri PhD Studentship
Amount $157,934 (NZD)
Organisation Zespri Group Limited 
Start 07/2018 
End 06/2021
 
Title Golden-Gate compatible Magnaporthe oryzae transformation vectors 
Description Golden-Gate compatible vectors for Magnaporthe oryzae transformation. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact 1/ Pennington, H.G., Youles, M., and Kamoun, S. 2017. Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors. Figshare. 2/ Pennington, H.G., Youles, M., and Kamoun, S. 2017. Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors. Figshare. Plasmids are available via AddGene. 
URL https://www.addgene.org/Sophien_Kamoun/
 
Title The RenSeq method 
Description Sequence capture of R genes (RenSeq) is being broadly applied across multiple plant species to expand knowledge of plant immune repertoires 
Type Of Material Technology assay or reagent 
Year Produced 2013 
Provided To Others? Yes  
Impact Many genes that confer stem rust resistance in wheat have been cloned using this method 
 
Title Field pathogenomics web interface 
Description We have formulated a web interface to host all the data that is generated under our "field pathogenomics" pathogen surveillance project in a format that is accessible to a wide audience. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The web interface is still under development but we are already getting positive responses from our industrial collaborators about the ability to use this to disseminate the data generated within our IPA. 
URL https://wheatis.tgac.ac.uk/yellowrust-map/
 
Title JENNIFER collection of ash 
Description With East Malling Research, JIC established the JENNIFER collection of ash genotypes as a national resource for research in the UK. JENNIFER = John Innes / East Malling National Nursery for Integrated Fraxinus excelsior Research 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Field trial of the JENNIFER collection planted at a site near Acle, Norfolk 
 
Description Aphid 
Organisation International Centre of Insect Physiology and Ecology (ICIPE)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We sequenced and assembled the genome of the banana aphid, which is a big pest on banana in Kenya.
Collaborator Contribution The ICIPE partners provided banana aphid samples for sequencing.
Impact Genome sequences of banana aphid and other aphid species will be compared. There is an agreement of how to write this up for a publication.
Start Year 2017
 
Description Collaboration on dispersal of wheat rust pathogens 
Organisation Aarhus University
Department Department of Agroecology
PI Contribution Writing a workpackage for an EU Horizon 2020 research programme, RustWatch
Collaborator Contribution Contributing to the workpackage
Impact The RustWatch application will be funded, subject to final contract negotiations
Start Year 2017
 
Description Collaboration on dispersal of wheat rust pathogens 
Organisation University of Peshawar
PI Contribution Writing a workpackage for an EU Horizon 2020 research programme, RustWatch
Collaborator Contribution Contributing to the workpackage
Impact The RustWatch application will be funded, subject to final contract negotiations
Start Year 2017
 
Description Collaboration on emerald ash borer 
Organisation East Malling Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Identification of suitable Fraxinus excelsior accessions from the JENNIFER collection for emerald ash borer trials. Data analysis. Leading the publication.
Collaborator Contribution RBG Kew: Formation of collaboration and planning experiments. EMR: Provision of plant material for EAB experiments. OSU: Conduct of experiments and data analysis.
Impact Data on response of UK Fraxinus excelsior to emerald ash borer in controlled trials.
Start Year 2016
 
Description Collaboration on emerald ash borer 
Organisation Ohio State University
Country United States 
Sector Academic/University 
PI Contribution Identification of suitable Fraxinus excelsior accessions from the JENNIFER collection for emerald ash borer trials. Data analysis. Leading the publication.
Collaborator Contribution RBG Kew: Formation of collaboration and planning experiments. EMR: Provision of plant material for EAB experiments. OSU: Conduct of experiments and data analysis.
Impact Data on response of UK Fraxinus excelsior to emerald ash borer in controlled trials.
Start Year 2016
 
Description Collaboration on emerald ash borer 
Organisation Royal Botanic Gardens, Kew
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Identification of suitable Fraxinus excelsior accessions from the JENNIFER collection for emerald ash borer trials. Data analysis. Leading the publication.
Collaborator Contribution RBG Kew: Formation of collaboration and planning experiments. EMR: Provision of plant material for EAB experiments. OSU: Conduct of experiments and data analysis.
Impact Data on response of UK Fraxinus excelsior to emerald ash borer in controlled trials.
Start Year 2016
 
Description Collaboration with Jack Vossen 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Exchange of materials/expertise
Collaborator Contribution Exchange of materials/expertise
Impact Wu, C.-H., Abd-El-Haliem, A., Bozkurt, T.O., Belhaj, K., Terauchi, R., Vossen, J.H., and Kamoun, S. 2017. NLR network mediates immunity to diverse plant pathogens. Proceedings of the National Academy of Sciences USA, 114:8113-8118.
Start Year 2013
 
Description Collaboration with NIAB on adaptation of Septoria tritici to wheat varieties 
Organisation National Institute of Agronomy and Botany (NIAB)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Tests of virulence of Septoria isolates on a differential set of wheat varieties.
Collaborator Contribution Leading project. Testing virulence of Septoria on modern wheat varieties. Knowledge exchange.
Impact Disciplines: Plant pathology. Plant breeding.
Start Year 2016
 
Description Collaboration with Prof. Ryohei Terauchi 
Organisation University of Kyoto
Country Japan 
Sector Academic/University 
PI Contribution Exchange of materials/expertise. Exchange of visits.
Collaborator Contribution Exchange of materials/expertise. Exchange of visits.
Impact Kobayashi, M., Hiraka, Y., Abe, A., Yaegashi, H., Natsume, S., Kikuchi, H., Takagi, H., Saitoh, H., Win, J., Kamoun, S., and Terauchi, R. 2017. Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. BMC Genomics, 18:897. Bialas, A., Zess, E.K., De la Concepcion, J.C., Franceschetti, M., Pennington, H.G., Yoshida, K., Upson, J.L., Chanclud, E., Wu, C.-H., Langner, T., Maqbool, A., Varden, F.A., Derevnina, L., Belhaj, K., Fujisaki, K., Saitoh, H., Terauchi, R., Banfield, M.J., and Kamoun, S. 2017. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., Yoshida, K., Uemura, A., Oikawa, K., Abe, A., Urasaki, N., Matsumura, H., Babil, P., Yamanaka, S., Matsumoto, R., Muranaka, S., Girma, G., Lopez-Montes, A., Gedil, M., Bhattacharjee, R., Abberton, M., Kumar, P.L., Rabbi, I., Tsujimura, M., Terachi, T., Haerty, W., Corpas, M., Kamoun, S., Kahl, G., Takagi, H., Asiedu, R., and Terauchi, R. 2017. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology, 15:86. Wu, C.-H., Abd-El-Haliem, A., Bozkurt, T.O., Belhaj, K., Terauchi, R., Vossen, J.H., and Kamoun, S. 2017. NLR network mediates immunity to diverse plant pathogens. Proceedings of the National Academy of Sciences USA, 114:8113-8118. Yoshida, K., Saunders, D.G., Mitsuoka, C., Natsume, S., Kosugi, S., Saitoh, H., Inoue, Y., Chuma, I., Tosa, Y., Cano, L.M., Kamoun, S., and Terauchi, R. 2016. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics, 18:370.
 
Description Collaboration with USDA/NCSU on fungicide resistance in cereal mildew. 
Organisation U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
Sector Public 
PI Contribution Wheat mildew isolates, methods for testing fungicide resistance, data analysis, molecular genetics.
Collaborator Contribution Wheat mildew isolates, methods for testing fungicide resistance, data analysis, molecular genetics.
Impact Disciplines: Plant pathology, crop protection, molecular genetics, statistics.
Start Year 2015
 
Description Collaboration with Vivianne Vleeshouwers 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Exchange of materials/expertise
Collaborator Contribution Exchange of materials/expertise
Impact Domazakis, E., Wouters, D., Visser, R., Kamoun, S., Joosten, M.H., and Vleeshouwers, V.G.A.A. 2018. The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans. Molecular Plant-Microbe Interactions Derevnina, L., Dagdas, Y.F., De la Concepcion, J.C., Bialas, A., Kellner, R., Petre, B., Domazakis, E., Du, J., Wu, C.-H., Lin, X., Aguilera-Galvez, C., Cruz-Mireles, N., Vleeshouwers, V.G.A.A. and Kamoun, S. 2016. Nine things to know about elicitins. New Phytologist, 212:888-895. Giannakopoulou, A., Bialas, A., Kamoun, S., and Vleeshouwers, V.G.A.A. 2016. Plant immunity switched from bacteria to virus. Nature Biotechnology, 34:391-392. Du, J., Verzaux, E., Chaparro-Garcia, A., Bijsterbosch, G., Keizer, L.C.P., Zhou, J., Liebrand, T.W.H., Xie, C., Govers, F., Robatzek, S., van der Vossen, E.A.G., Jacobsen, E., Visser, R.G.F., Kamoun, S., and Vleeshouwers, V.G.A.A. 2015. Elicitin recognition confers enhanced resistance to Phytophthora infestans in potato. Nature Plants, 1:15034.
 
Description Collaboration with partners in Ireland on Septoria of wheat 
Organisation Teagasc
PI Contribution Supervision of M.Sc. student. Planning experiments. Field trials in England. Interpretation of data in relation to literature on Septoria. Input to writing paper.
Collaborator Contribution Teagasc: Led the research. Did the majority of field trials (in Ireland) and the data analysis. Led writing of paper.
Impact Paper in Plant Pathology. Successful M.Sc. thesis. Advice to Department of Agriculture, Food and Marine (Ireland) on disease control in crops.
Start Year 2014
 
Description Collaboration with partners in Ireland on Septoria of wheat 
Organisation University College Dublin
Department School of Biology and Environmental Science
Country Ireland 
Sector Academic/University 
PI Contribution Supervision of M.Sc. student. Planning experiments. Field trials in England. Interpretation of data in relation to literature on Septoria. Input to writing paper.
Collaborator Contribution Teagasc: Led the research. Did the majority of field trials (in Ireland) and the data analysis. Led writing of paper.
Impact Paper in Plant Pathology. Successful M.Sc. thesis. Advice to Department of Agriculture, Food and Marine (Ireland) on disease control in crops.
Start Year 2014
 
Description Establishment of JENNIFER population of ash genotypes 
Organisation East Malling Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Production of replicated clones of 328 Fraxinus accessions in the JENNIFER collection, for future research on ash including ash dieback, resistance to herbivores and phenological traits.
Collaborator Contribution East Malling: Cloning the Fraxinus accessions by grafting. Norfolk CC and Forest Research: Provision of trial sites with deer fence for ash dieback trials.
Impact Planted field trial near Acle, Norfolk, January 2018.
Start Year 2015
 
Description Establishment of JENNIFER population of ash genotypes 
Organisation Forest Research
Country United Kingdom 
Sector Public 
PI Contribution Production of replicated clones of 328 Fraxinus accessions in the JENNIFER collection, for future research on ash including ash dieback, resistance to herbivores and phenological traits.
Collaborator Contribution East Malling: Cloning the Fraxinus accessions by grafting. Norfolk CC and Forest Research: Provision of trial sites with deer fence for ash dieback trials.
Impact Planted field trial near Acle, Norfolk, January 2018.
Start Year 2015
 
Description Establishment of JENNIFER population of ash genotypes 
Organisation Norfolk County Council
Country United Kingdom 
Sector Public 
PI Contribution Production of replicated clones of 328 Fraxinus accessions in the JENNIFER collection, for future research on ash including ash dieback, resistance to herbivores and phenological traits.
Collaborator Contribution East Malling: Cloning the Fraxinus accessions by grafting. Norfolk CC and Forest Research: Provision of trial sites with deer fence for ash dieback trials.
Impact Planted field trial near Acle, Norfolk, January 2018.
Start Year 2015
 
Description Formal research collaboration with Abdullah Al-Sadi, Sultan Qaboos University, Muscat, Oman. 
Organisation Sultan Qaboos University
Department Department of Crop Sciences
Country Oman 
Sector Academic/University 
PI Contribution Provided intellectual input into investigating an important pathogen of lime trees in Oman, and hosted Ali Al-Subhi, PhD student at Sultan Qaboos University, to conduct molecular research on the pathogen for 6 months in 2015/2016 and 3 months in 2017.
Collaborator Contribution Provided funding for research conducted by the visiting PhD student and hosted me to visit phytoplasma-infected lime orchards and vegetable farms in Oman.
Impact Co-authored scientific publications, including Al-Subhi et al., 2017. BMC Microbiol. 17: 221.
Start Year 2014
 
Description Formal research collaboration with Chih-Horng Kuo, Academia Sinica, Taipei, Taiwan 
Organisation Academia Sinica
Department Institute of Plant and Microbial Biology
Country Taiwan, Province of China 
Sector Academic/University 
PI Contribution I provided intellectual input into the development of the research question, approaches and methodology. My team provided knowledge about the biology of the organisms, collected biological material, extracted DNA and generated raw reads of genome sequence data.
Collaborator Contribution The partner assembled the genome reads into contigs and annotated the genomes.
Impact Several co-authored publications, for example: Orlovskis et al., 2017. Ann Bot. 119: 869-884.
Start Year 2014
 
Description Formal research collaboration with Cock van Oosterhout, University of East Anglia, Norwich, UK 
Organisation University of East Anglia
Department School of Environmental Sciences UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution Our time provides knowledge, resources and materials for the insect-plant interaction research system.
Collaborator Contribution The Van Oosterhout team provides knowledge on evolutionary biology and population genetics.
Impact We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We are co-authors on Mathers et al., 2017. Genome Biology, and a paper that is being submitted this month. We assisted postdoctoral researcher Thomas Mathers with the writing of a Future leader fellowship application, which was succesful (starts Apr 2018).
Start Year 2013
 
Description Formal research collaboration with David Swarbreck, Earlham Institute, Norwich, UK 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Our time provides knowledge, resources and materials for the insect-plant interaction research system.
Collaborator Contribution The Swarbreck team provides knowledge on bioinformatics and genomics, including genome and transcriptome assembly pipelines and genome annotations.
Impact We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We are co-authors on Mathers et al., 2017. Genome Biology, and a paper that is being submitted this month. We assisted postdoctoral researcher Thomas Mathers with the writing of a Future leader fellowship application, which was succesful (starts Apr 2018).
Start Year 2010
 
Description Formal research collaboration with Henryk Pospieszny, Institute of Plant Protection, Poznan, Poland 
Organisation Institute of Plant Protection, National Research Institute
Country Poland 
Sector Public 
PI Contribution My lab hosted Agnieszka Zwolinska, a PhD student at the Institute of Plant Protection, Oct 2016 - Mar 2017. Agnieszka conducted work on the HFSP collaborative project.
Collaborator Contribution The team in Poznan collects plant and insect samples in northern and southern regions of Poland for the HFSP project; the samples are assayed for the presence of phytoplasma strains and effector genes.
Impact We wrote a HFSP project proposal together that was funded. We hold regular Skype meetings (in average, once in the 6 weeks) to discuss progress and results.
Start Year 2014
 
Description Formal research collaboration with Joao Spotti-Lopes, University of Sao Paolo - College of Agriculture (ESALQ) 
Organisation University of Sao Paulo
Department College of Agriculture
Country Brazil 
Sector Academic/University 
PI Contribution Provided intellectual input into development of a collaborative research proposal, expertise in specific research methodologies and trained staff in molecular biology methods. Members of the partner team visited my team to gain experience with molecular biology techniques and discuss project progress. These included: - Visit of JSL to Hogenhout lab, 11-18 Sep. 2013. - Visit of JSL to Hogenhout lab, 20-24 Oct. 2014. - Visit of postdoctoral researcher Maria Cristina Canale from JSL lab, March - Dec, 2014.
Collaborator Contribution Provided intellectual input into development of a collaborative research proposal, expertise in specific research methodologies and trained and hosted staff for conducting field-based experiments. Members of my team visited the partner lab for field trips and collection of MBSP isolates and leafhoppers from infected maize fields. These included: - Field trip and processing of samples in Brazil of a PhD student in my team, 18 May - 8 June, 2013. - Visit of Hogenhout to partner lab, 28-31 Oct, 2013. - Field trip and processing of samples in Brazil, 6-21 June, 2014. - Visit and processing of samples in Brazil, 19-23 Oct, 2015.
Impact We published several papers together, e.g. Orlovskis et al., 2017. Ann. Bot. 119: 869-884, and are working on a few other manuscripts.
Start Year 2013
 
Description Formal research collaboration with Lan-Qin Xia and Ju-Lian Chen, CAAS, Beijing, China 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution My group provides aphid genomics information to the project.
Collaborator Contribution CAAS contributed aphid samples and transgenic wheat to achieve plant-mediated RNAi of aphids to the project
Impact We sequenced the genomes of many wheat-colonizing aphid species. The genomes have been assembled. Annotation pipeline for the genomes is under construction.
Start Year 2016
 
Description Formal research collaboration with Martina Seruga-Music, University of Zagreb, Croatia 
Organisation University of Zagreb
Department Department of Molecular Biology
Country Croatia 
Sector Academic/University 
PI Contribution Provided expertise on genome-wide analyses and identification and functional characterization of effectors of phytoplasmas. Hosted members of the Croatia team several times and helped the team to obtain a research grant in Croatia.
Collaborator Contribution The Croatia team provided useful sequence information to my team and contributed to the writing of publications.
Impact Exchanged useful data and co-published scientific publications. Another publication is in preparation and will be submitted in March 2018.
Start Year 2010
 
Description Formal research collaboration with Oxitec 
Organisation Oxitec Ltd
Country United Kingdom 
Sector Private 
PI Contribution My group provides knowledge, data and resources on whiteflies and other hemipteran insects.
Collaborator Contribution Oxitec provides information on insect transformation technologies and design of transformation plasmids.
Impact Obtained a iCASE PhD student fellowship. Hired PhD student Rebecca Corkill. Rebecca is making good progress with the project.
Start Year 2015
 
Description Formal research collaboration with Richard Immink, Wageningen University and Research Centre, The Netherlands 
Organisation University of Wageningen
Department Department of Plant Sciences
Country New Zealand 
Sector Academic/University 
PI Contribution We provided knowledge on phytoplasma virulence proteins that interfere with plant development and involved the Wageningen team into a interdisciplinary project proposal that received funding from HFSP.
Collaborator Contribution The Wageningen team provided expertise on plant transcription factors targeted by phytoplasma effectors and helped us with interpretation of the plant developmental phenotypes. They are co-investigators on our HFSP grant.
Impact We received funding for a HFSP research project. We co-published a paper: MacLean et al., 2014. PLoS Biol. 12(4):e1001835. We co-supervise postdoctoral researchers. We hold regular Skype meetings (in average once per 6 months) for the past 3 years.
Start Year 2014
 
Description Formal research collaboration with Russel Groves, University of Wisconsin, Madison, USA 
Organisation University of Wisconsin-Madison
Department Department of Entomology
Country United States 
Sector Academic/University 
PI Contribution We involved the University of Wisconsin team into a HFSP research proposal that got funded.
Collaborator Contribution The University of Wisconsin team collects phytoplasma-infected plant and leafhopper samples from all over the USA for the HFSP-funded project.
Impact We received funding for collaborative HFSP project. We hold regular progress meeting (in average once/6 weeks). We co-supervise postdoctoral researchers and PhD students. We are writing up a manuscript.
Start Year 2014
 
Description Formal research collaboration with Syngenta 
Organisation Syngenta International AG
Department Syngenta Ltd (Bracknell)
Country United Kingdom 
Sector Private 
PI Contribution Provide information about aphid biology and genomics, and mechanisms involved in aphid adjustment to diverse plant species and pesticides.
Collaborator Contribution Contributed 10% cash towards two BBSRC-IPA projects (2014-2017; 2017-2020) and advised on how to conduct pesticide applications. Provided aphid clones for sequencing and analyses.
Impact Made progress with understanding processes involved in aphid adjustments to plants and pesticides. This collaboration resulted in a publication: Mathers, Chen et al., 2017. Genome Biol. 18: 27. As well, the collaboration was renewed with follow-up funding, that is a BBSRC-IPA grant commencing April 2018. Held regular meetings to discuss progress, including visits of my group to Syngenta and collagues of Syngenta to JIC, and Skype and phone conference meetings.
Start Year 2014
 
Description Formal research collaboration with Tracey Chapman, University of East Anglia, Norwich, UK 
Organisation University of East Anglia
Department School of Biological Sciences UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution I am secondary supervisor on a Oxitec co-funded iCASE PhD studentship of Tracey.
Collaborator Contribution Tracey is secondary supervisor on a Oxitec co-funded iCASE PhD studentship of my group.
Impact We exchange knowledge about insect pests. We will start holding monthly journal club meetings starting Apr 2018. DIscussions to apply for research funding together are ongoing. We discuss research on the identification of sex-determination genes accross hemipteran insect species.
Start Year 2015
 
Description JENNIFER collaboration with Warwick and E.Malling 
Organisation East Malling Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Led collaboration to develop research proposal on the influence of secondary metabolites in European ash (Fraxinus excelsior) on possible trade-offs between resistances to ash dieback and to herbivores.
Collaborator Contribution Contributed to research proposal on the influence of secondary metabolites in European ash (Fraxinus excelsior) on possible trade-offs between resistances to ash dieback and to herbivores.
Impact Response-mode grant proposal submitted to BBSRC. Multi-disciplinary: pathology, entomology, genetics, population genetics, ecology, forestry, analytical chemistry, plant molecular biology.
Start Year 2017
 
Description JENNIFER collaboration with Warwick and E.Malling 
Organisation University of Warwick
Country United Kingdom 
Sector Academic/University 
PI Contribution Led collaboration to develop research proposal on the influence of secondary metabolites in European ash (Fraxinus excelsior) on possible trade-offs between resistances to ash dieback and to herbivores.
Collaborator Contribution Contributed to research proposal on the influence of secondary metabolites in European ash (Fraxinus excelsior) on possible trade-offs between resistances to ash dieback and to herbivores.
Impact Response-mode grant proposal submitted to BBSRC. Multi-disciplinary: pathology, entomology, genetics, population genetics, ecology, forestry, analytical chemistry, plant molecular biology.
Start Year 2017
 
Description JIC/FR collaboration on Chalara ash dieback 
Organisation Forest Research
Country United Kingdom 
Sector Public 
PI Contribution Research on pathology, molecular markers, population genetics and natural selection in Chalara ash dieback.
Collaborator Contribution Research on pathology, population genetics and forest management in relation to Chalara ash dieback.
Impact Papers in peer-reviewed journals: published and in press. Advice to Forestry Commission and DEFRA. Public awareness activities. Advice to forestry industry. Disciplines: plant pathology (particularly forest pathology), population genetics, forestry.
Start Year 2014
 
Description Partnership award with Matthew Baylis, University of Liverpool, UK. 
Organisation University of Liverpool
Department School of Veterinary Science Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Provide information on vector-borne diseases of plants.
Collaborator Contribution Provide information of vector-borne diseases of humans and animals.
Impact We won a US Partnering Award: Vector-borne diseases in the UK & US: common threats and shared solutions" [Matthew Baylis, PI (PI, University of Liverpool), Saskia Hogenhout (co-PI, JIC) and Simon Carpenter (co-PI, The Pirbright Institute)] BBSRC £50k, and co-organized visits of US colleagues to the UK (Dec 2016) and UK group members to the University of California, Davis (Oct 2017). We applied for a GCRF VBD network grant (£4M) together; the pre-proposal for this was selected for submission of a full proposal, and we were invited for an interview with BBSRC based on our full proposal submission. The proposal was ranked 5th out 12 proposals, and only the top 3 were funded. Finally, we are co-organizing Vector-Borne Diseases in the UK meeting, 3-4 Dec 2018 that will be hosted at the JIC.
Start Year 2016
 
Description Population genomics of the take-all/wheat/Pseudomonas biosphere 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution My team works closely with Dr Tim Mauchline and Prof Kim Hammond Kosack at RR to examine the population structure of Pseudomonas fluorescens isolates in wheat fields that have been infected with the pathogenic fungal disease take-all. We hope to understand the microbiological underpinnings of the phenomenon of take-all suppressive soils.
Collaborator Contribution Prof Hammond-Kosack provides access to her ongoing wheat field trial sites. Dr Mauchline isolates Pseudomonas and other soil microbial samples and does much of the phylogenetic analysis and plant-microbe assays associated with the study.
Impact To date, we have published two research papers (TH Mauchline, et al. Environmental microbiology 17 (11), 4764-4778, and DD Nguyen, et al. Nature Microbiology 2 (1), 16197) and a review (see URL above) based on this collaboration. A PhD student is now working on downstream elements of this project, and we have applied for follow-on research funding.
Start Year 2013
 
Description "Building resilience against crop diseases: a global surveillance system (GSS)" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Rockefeller funded workshop to discuss the development of a global pathogen surveillance system
Year(s) Of Engagement Activity 2018
 
Description A biologist's poem 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A poem to inspire about biology
Year(s) Of Engagement Activity 2017
URL http://kamounlab.tumblr.com/post/170774045435/a-biologists-poem
 
Description A view from the lab - blog interview 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview for a science blog - A View From The Lab.
Year(s) Of Engagement Activity 2018
 
Description AHDB Wheat Recommended List 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Prof James Brown is the pathology specialist on AHDB Wheat Crop Committee, which draws up the Recommended List. Impact: attention to broad-spectrum, durable resistance in recommended wheat varieties. The Wheat Recommended List reaches tens of thousands of farmers in the UK and Ireland and has a major impact throughout north-west Europe. It is a crucial document for the plant breeding industry. Typically the regular meetings are a Planning Meeting in May each year, a Candidate Selection meeting in September and a Recommendation meeting in November, together with other ad hoc meetings and activities.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
 
Description AHDB press release: Wheat stem rust outbreaks in Europe fuel industry collaboration 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact AHDB press release
Year(s) Of Engagement Activity 2018
 
Description Advisor, Nornex 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof James Brown was one of the two advisors to the Nornex project on ash dieback, contributing knowledge about population genetics and plant breeding.
Year(s) Of Engagement Activity 2013,2014,2015,2016
 
Description Blog entry about research project (Wheat Side Story) 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Blog post on research project
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/articles/wheat-side-story
 
Description Booklet on 'Identification and field scoring guide for ramularia leaf spot' published by AHDB 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Contributed to booklet on 'Identification and field scoring guide for ramularia leaf spot' by Neil Havis (SRUC) and James Brown (JIC), published in January 2018 by AHDB Cereals & Oilseeds, Information Sheet 60.
Year(s) Of Engagement Activity 2018
URL https://cereals.ahdb.org.uk/media/1340591/is60a-ramularia-guide-january-2018-v2.pdf
 
Description Breeders Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact The John Innes Centre holds an annual Breeders' Day that provides an opportunity to hear first-hand from our scientists about our science and how it impacts crop breeding and farming.
Year(s) Of Engagement Activity 2016
 
Description Cereal Rust Foundation 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof James Brown is chairman of the Cereal Rust Foundation, which organises the International Cereal Rust and Powdery Mildew Conferences, held every 3-4 years.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013
 
Description Conflict of interests: How do plants sense and integrate environmental signals. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited speaker at: Thermomorphogenesis 2016, (25 - 27 August 2016), Halle, Germany.
Year(s) Of Engagement Activity 2016
 
Description Conflict of interests: How do plants sense and integrate environmental signals? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited talk at BOKU, University of Natural Resources and Life Sciences, Vienna, Austria
April 2016
Year(s) Of Engagement Activity 2016
 
Description CropLife FoodHeroes Series: What inspires plant scientists and why is their job so important? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Why did you want to be a plant scientist?

I became a scientist because I grew up being extremely curious about the natural world. I wanted to know how living organisms function. How they became the way they are. Plant pathology came later after realized that I may as well study a field of biology that is important to the human condition. This inspires me to narrow the gap between fundamental and applied research. My aim is to perform cutting-edge research and significantly advance knowledge on economically important plant pathogen systems. In contrast, much research focuses on model systems and is therefore further steps away from practical applications.

Can you explain what your job involves?

As an academic scientist, I am in the business of knowledge. My job is to generate new knowledge to advance science, and to influence others to pursue new directions, generate more knowledge and apply it to address practical problems. My job is also to communicate scientific knowledge and discoveries to my peers and to a broader audience, including the general public.

What are the plant diseases that you are working on?

I work primarily on blight and blast diseases. Throughout my career, I have worked primarily on the Irish potato famine pathogen Phytophthora infestans. More recently, I was inspired by the sense of urgency brought upon by the February 2016 Bangladeshi wheat blast epidemic to expand my research to blast fungi. I aim to apply the concepts and ideas I developed throughout my career to a problem with an immediate impact on global food security.

Can you describe how damaging these diseases can be for farmers?

Plant diseases are a major constraint for achieving food security. Losses caused by fungal plant pathogens alone account for enough to feed several billion people. Magnaporthe oryzae, the causal agent of blast disease of cereals, is among the most destructive plant pathogens, causing losses in rice production that, if mitigated, could feed up to 740 million people. This pathogen has emerged since the 1980s as an important pathogen of wheat seriously limiting the potential for wheat production in South America. In 2016, wheat blast was detected for the first time in Asia with reports of a severe epidemic in Bangladesh. The outbreak is particularly worrisome because wheat blast has already spread further to India, and is threatening major wheat producing areas in neighboring South Asian countries. Global trade and a warming climate are contributing to the spread and establishment of blast diseases as a global problem for cereal production and a present and clear danger to food security.

Why is your profession important in the challenge to feed the world?

Plant pathology delivers science-driven solutions to plant diseases. In particular, genetic solutions through disease resistant crop varieties can be sustainable and environmentally friendly.

What inspires you about your job?

Knowledge and people. The thrill of learning something new every day is addictive. Sharing the experience with others -be they students, colleagues, stakeholders or members of the public - is priceless.
Year(s) Of Engagement Activity 2017
URL https://croplife.org/industry-profile/sophien-kamoun/
 
Description CropTec 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact CropTec is the leading off-season event for the arable farming industry in the UK. Prof James Brown gave talks on both days about current advances in breeding for disease resistance, combined with yield and quality in barley and wheat.
Year(s) Of Engagement Activity 2017
 
Description European Research Council@10: the impact on science and scientists 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Scientists at the John Innes Centre and The Sainsbury Laboratory reflect on the success of the ERC over the last ten years and the impact that ERC grants have had on their science and their careers. Category: Science & Technology
Year(s) Of Engagement Activity 2017
URL https://youtu.be/qEgjYaMG0tQ
 
Description Exeter Uni: Forgotten crop pathogen may be about to return 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Exeter Uni press release
Year(s) Of Engagement Activity 2018
 
Description Farming Today 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Farming Today interview
Year(s) Of Engagement Activity 2018
 
Description Farming Today interview about breeding for Septoria resistance in wheat 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Farming Today interview about breeding for Septoria resistance in wheat.
Year(s) Of Engagement Activity 2017
 
Description GARNet Youtube Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact GARNet youtube interview about two articles published in Current Biology and Cell reports
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=L_--vJal50A
 
Description Horizon The EU Research and Innovation Magazine: AGRICULTURE--Can CRISPR feed the world? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact As the world's population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

By 2040, there will be 9 billion people in the world. 'That's like adding another China onto today's global population,' said Professor Sophien Kamoun of the Sainsbury Laboratory in Norwich, UK.

Prof. Kamoun is one of a growing number of food scientists trying to figure out how to feed the world. As an expert in plant pathogens such as Phytophthora infestans - the fungus-like microbe responsible for potato blight - he wants to make crops more resistant to disease.

Potato blight sparked the Irish famine in the 19th century, causing a million people to starve to death and another million migrants to flee. European farmers now keep the fungus in check by using pesticides. However, in regions without access to chemical sprays, it continues to wipe out enough potatoes to feed hundreds of millions of people every year.

'Potato blight is still a problem,' said Prof. Kamoun. 'In Europe, we use 12 chemical sprays per season to manage the pathogen that causes blight, but other parts of the world cannot afford this.'

Plants try to fight off the pathogens that cause disease but these are continuously changing to evade detection by the plant's immune system.
Year(s) Of Engagement Activity 2017
URL https://horizon-magazine.eu/article/can-crispr-feed-world_en.html
 
Description Horizon The EU Research and Innovation Magazine: Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact We asked a selection of European scientists which scientific breakthroughs they'd like to see in 2018.

Gene-editing to improve crop immunity

For Professor Sophien Kamoun at Sainsbury Laboratory in the UK, a breakthrough would be to adapt plant immune systems to defend them against a wider range of diseases. 'One approach would be to design improved immune receptors that can then be edited into crop genomes. This approach requires a better biochemical and biophysical understanding of how plant receptors detect pathogens and activate immunity. It also necessitates a better knowledge of pathogen diversity and (their ability to evolve). Ultimately, we require a framework to rapidly generate new disease resistance traits and introduce them into crop genomes. Only then we can keep up with rapidly evolving pathogens.'

Read also: Can CRISPR feed the world? https://horizon-magazine.eu/article/can-crispr-feed-world_en.html
Year(s) Of Engagement Activity 2018
URL https://horizon-magazine.eu/article/expect-exoplanet-atmospheres-organs-new-functions-and-fewer-traf...
 
Description IS-MPMI Interactions: Fat Cats Can Jump Over The Wall: Plant Biotic Interactions Workshop in Hohhot, Inner Mongolia, China 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact On a cloudy Norwich day in 2011, post-docs Sebastian Schornack, Sylvain Raffaele, and Tolga Bozkurt were having a typical British lunch of fish and chips with mushy peas with their supervisor Sophien Kamoun. Somehow, the discussion turned to the importance of sustained productivity. Kamoun, in his usual hyperbolic style, pointed out that now that each one of them had just published notable papers (Schornack et al., 2010; Raffaele et al., 2010; Bozkurt et al., 2011), they should beware of not behaving like "lazy fat cats" and think hard about their next papers. Not everyone left the lunch in the happiest mood. One day later, after discussion with another post-doc, Mireille van Damme, Schornack and colleagues decided to found the Lazy Fat Cat Club (#LFCats). Schornack drafted a chart and was appointed as Chairman Féi mao (fat cat in Mandarin). The #LFCats ethos is that productive research requires a significant amount of communication and knowledge exchange, and informally discussing research is a perfect way of solving roadblocks and laying paths for the future. Casual meetings took place on a regular basis at The Sainsbury Laboratory, mainly on afternoon coffee breaks. The club continued to loosely grow and several other researchers joined the #LFCats. As the members moved on to start their own labs, the #LFCats "brand" helped nurture a lasting bond. Suomeng Dong, now a professor in the Department of Plant Pathology at Nanjing Agricultural University, coined the Chinese proverb "Fat cats cannot jump over the wall" to challenge the #LFCats to work collaboratively to solve problems and "jump over the wall."

It should be noted that the #LFCats are neither lazy (well, maybe a bit sometimes) nor overweight (no comments...). Instead the club's name relates to the initial discussion and stands for the importance of moving out your comfort zone and looking forward to the next goal in science or in life. It also grew to reflect the importance of informal interactions as a means to enhance efficiency and creativity. To promote such interactions, Schornack organized the first #LFCats research meeting at the Sainsbury Laboratory Cambridge University in 2013. Dong (Nanjing Agricultural University, China) and Ruofang Zhang (Inner Mongolia University, China) led a second meeting in August 2017 in Hohhot, Inner Mongolia. The local host, Zhang, is the director of the Potato Research Center at Inner Mongolian University and the Plant Protection section in the Chinese Modern Agricultural Industry Technology System. Indeed, the autonomous region of Inner Mongolia is the largest potato production area in China and has contributed to making this country the leading potato producer in the world.

In this report, we summarize the key findings presented at the workshop.
Year(s) Of Engagement Activity 2017
URL https://www.ismpmi.org/members/Interactions/Lists/Posts/Post.aspx?ID=165
 
Description IS-MPMI Interactions: InterViews: Sophien Kamoun by Jixiang Kong 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This InterView with Sophien Kamoun, John Innes Centre, was performed by one of the 2016 IS-MPMI student travel awardees, Jixiang Kong, Gregor Mendel Institute.

JIXIANG KONG: What led you to study biology? More specifically plant-pathogen interactions.

SOPHIEN KAMOUN: I grew up with a passion for nature. As a teenager I collected insects and became fascinated by their incredible diversity. Later I took this "hobby" more seriously and I specialized in studying tiger beetles. I even published a few papers on this topic.

After high school in Tunisia, I went to Paris with the firm intention of studying biology and becoming an entomologist. However, I was disappointed by how badly taught zoology was-too much emphasis on taxonomy and little mechanistic thinking. Instead, I became drawn to the more rigorous methods and approaches of molecular biology, and I ended up majoring in genetics. I reconciled this major with my natural history interests by taking multiple modules in evolution and reading a lot on the subject.

Plant pathology came later when I moved from Paris to the University of California-Davis for my Ph.D. The fellowship I received stipulated that I should study plant biology. It wasn't by choice but rather by accident. But I quickly became engrossed in molecular plant pathology and I really liked that this science involves interactions between multiple organisms. However, for many years I missed a direct connection between the lab work and the field.

JK: If you would not have chosen the topic of plant-pathogen interactions, what would you choose?

SK: Definitely, entomology. I'm still fascinated by insects, especially beetles. I feel we know so little about their biology, especially from a mechanistic angle. They are so diverse and yet most insect research focuses on a few species, such as Drosophila. There are so many fascinating questions, for example, about the evolution of insect behavior and the underlying genes. Also, insects can be important crop pests and disease vectors. This is a very fertile area of research that I highly recommend to early career scientists.

JK: How do you envision large-scale "omics" approaches in studying plant immunity?

SK: Omics are just another tool. They're powerful tools but they're still methods we use to answer questions. I advise everyone to frame their research based on questions and then look for the best methods to answer these questions.

This said, genomics has transformed biology in a fundamental way. It's a new way of doing business. We now have catalogs of plant and pathogen genes, so the challenge is to link genes to function rather than discovering the genes per se. Another key aspect is that genomics is a great equalizer. Model systems are less important than in earlier days. One can make a lot of progress with a genome and a few functional assays. For example, consider the progress made in discovering effectors in obligate parasites. This would have been almost unthinkable in the pre-genomics age. This is why I wish to see more early career scientists explore the diversity of pathogen systems rather than working on established model systems.

JK: Social media is changing the way of communication rapidly. However, the scientific communication on social media is just emerging. How do you see the direction of social media in the future regarding the impact on science? Will social media replace or minimize some conventional communication such as conferences?

SK: Communication is an essential function of being a scientist. We're not only in the business of producing new knowledge but it's also our obligation to communicate knowledge to our peers and the public. These days social media became a major medium for communication in science. It's an efficient way to filter through the incessant flow of information, stay up to date, and broadly broadcast new knowledge. It also enables us to expand our network way beyond traditional colleagues. I interact on Twitter with teachers, farmers, journalists, etc. I also use it, of course, to communicate with colleagues and share information and insights. I also find Twitter immensely entertaining. Scientists have a lot of humor.

I don't think social media will replace the need for direct contact and interaction between peers. I think we still would want to break off our daily routine and meet in person with colleagues. However, I wish we could start rethinking the format of scientific conferences. Both the fairly detailed oral presentations and poster sessions could be improved if they were combined with some sort of Internet interaction. Twitter is already transforming how scientists interact at conferences but we could do better.

JK: What advice would you provide to young researchers who are in their early scientific career?

SK: Don't follow the herd. Take chances. Look beyond the current trends both in terms of experimental systems and questions, and ask provocative questions.
Year(s) Of Engagement Activity 2017
URL https://www.ismpmi.org/members/Interactions/Lists/Posts/Post.aspx?ID=152
 
Description Invited Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk at VIB Ghent, Belgium. Talking about the research findings of the project.
Year(s) Of Engagement Activity 2016
 
Description Invited talk at University of Potsdam: Perception and integration of environmental signals in plants. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited Talk at Institute for Biochemistry and Biology, University of Potsdam, Germany.
Year(s) Of Engagement Activity 2016
 
Description JIC 50 years Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Participant at JIC 50 years Open Day
Year(s) Of Engagement Activity 2017
 
Description JIC Industry showcase event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact JIC Industry showcase event
Year(s) Of Engagement Activity 2018
 
Description JIC press release: First report in decades of a forgotten crop pathogen 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact JIC press release
Year(s) Of Engagement Activity 2018
 
Description JIC50 Molecular Microbiology presentation 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Contributed to the design and running of the molecular microbiology department stall at the JIC 50 year open day.
Year(s) Of Engagement Activity 2017
 
Description Meeting with Natural England, about ash dieback 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Prof James Brown updated science advisor to Natural England on current situation of ash dieback, prospects for recovery and future threats to woodland
Year(s) Of Engagement Activity 2017
 
Description NIAB NEWS: New study on wheat stem rust calls for close monitoring 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact NIAB news article
Year(s) Of Engagement Activity 2018
URL http://www.niab.com/news_and_events/article/429
 
Description New Phytologist workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact New Phytologist/DFG SPP1819-funded workshop "Molecular mechanisms underlying the rapid evolution of plant-microbe interactions"
Year(s) Of Engagement Activity 2018
 
Description Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Lecture to the public as part of Norwich Science festival, explaining the science and relevance of plant-microbial interactions in the soil. Positive audience feedback including two people who expressed interest in the JIC as a potential future workplace.
Year(s) Of Engagement Activity 2017
 
Description Outreach at BIO school - Bringing scientists to you event at Marshland High School (Peterborough) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Outreach at BIO school - Bringing scientists to you event at Marshland High School (Peterborough)
Year(s) Of Engagement Activity 2017
 
Description Outreach at BIO school - Sports Days for Boys 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Outreach at BIO school - Sports Days for Boys 2017
Year(s) Of Engagement Activity 2017
 
Description Pathogenomics workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Trainer on Pathogenomics workshop organised by The Sainsbury Laboratory
Year(s) Of Engagement Activity 2017
 
Description Perception and integration of environmental signals in plants 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited talk at: Arabidopsis 2016: Emerging Challenges in Plant Biology, Mohali, India
March 2016
Year(s) Of Engagement Activity 2016
 
Description Presentation on fungicide resistance in cereal powdery mildew 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Talk to UK Cereal Pathogen Virulence Survey stakeholders meeting, March 2018. Talk written by Corinne Arnold (Ph.D. student) but given by her supervisor, James Brown, as she was working with her collaborator in the USA at the time.
Year(s) Of Engagement Activity 2018
 
Description Presentation to visiting agricultural students from Hogeschool, Ghent 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Presentation to a visiting group of agricultural students from Homeschool in Ghent.
Year(s) Of Engagement Activity 2017
 
Description Press release - John Innes Centre scientists solve 60 year old Septoria mystery 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Press release. Articles published in local newspapers and farming press. Led to interview on Farming Today on Radio 4.
Year(s) Of Engagement Activity 2017
 
Description Putting it together: How do plants sense and integrate seasonal signals? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk at: Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France. This has led to the establishment of a collaboration involving scientists from France and Spain.
Year(s) Of Engagement Activity 2017
 
Description RustFight (Denmark) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof James Brown was one of two members of the advisory panel for the RustFight project coordinated by Aarhus University in Denmark, contributing knowledge of genetics and plant breeding.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
 
Description SlideShare: Pathogenomics of emerging plant pathogens: too little, too late 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Slides: Pathogenomics of emerging plant pathogens: too little, too late. Presented at the conference "Building resilience against crop diseases: A global surveillance system", February 14, 2018, Rockefeller Foundation Bellagio Center in Lake Como, Italy.
Year(s) Of Engagement Activity 2018
URL https://www.slideshare.net/SophienKamoun/pathogenomics-of-emerging-plant-pathogens-too-little-too-la...
 
Description South African Agritech 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Visit by six wheat scientists from South Africa and an FCO representative to JIC. The party learnt about current JIC activities relating to yield, crop physiology, bioinformatics, plant pathology and plant breeding technology.
Year(s) Of Engagement Activity 2018
 
Description Stranger in a strange land: the experiences of immigrant researchers 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Published in Genome Biology: Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

International collaborations are key to advancing scientific research globally and often require mobility on the part of researchers. Migration of scientists enables the spread of ideas and skills around the world, giving researchers the opportunity to follow the best resources. Of course, migration adds a new set of challenges to the already monumental task of starting and running a lab. Genome Biology spoke to Sophien Kamoun, Rosa Lozano-Durán, and Luay Nakhleh about their personal experiences.

What influenced your choice to move to your current country?

SK: There is this old German expression "wo die Musik spielt"-you go where it's happening, where the "music is played". I think that sums it up. When I was a student in the 1980s, almost everyone wanted to do a Ph.D. in the USA. I felt that to have the best training and to be among the best, I had no choice but to study in the USA. I think that was a pretty correct assessment of the state of affairs in the 1980s. Indeed, I had a fantastic experience at the University of California, Davis. Also, at that time, Europe wasn't really open to non-Western scientists, and international mobility wasn't recognized like it is today [1]. Later, I moved to the Netherlands and then back to the USA before landing in my current position at The Sainsbury Laboratory (TSL) in Norwich, UK. I moved to Norwich exactly 10 years ago, primarily because of the reputation of the laboratory as a center of excellence for plant pathology research and the generous support provided by David Sainsbury through the Gatsby Foundation. I have had a phenomenal time at TSL these past 10 years, where I have had the opportunity to work with outstanding scientists from perhaps about 30-40 countries. An interesting point is that when TSL was founded in 1988, all the group leaders were British [2], but currently our principal investigators are from all over the world [3]. I think TSL truly reflects the emergence of the #ScienceisGlobal movement on social media [4], which is so evident in the UK and other corners of Europe.

RL-D: Three years ago, having worked as a postdoctoral researcher for almost four years, I was eager to establish my own laboratory. I had known what I wanted to devote my research to for a long time and could not wait to get started. Unfortunately, the economic climate in Europe, where I am originally from and where I was working at the time, was not particularly propitious for science in academia, with research budgets being slashed and increasing competition-not the most favorable situation for new group leaders, I heard over and over again. My partner was also a scientist at the same career stage, and so we needed to find two positions, not just one, complicating matters even more. One day, just by chance, we came across a job advertisement for group leader positions at the Shanghai Center for Plant Stress Biology in China. We had heard about the place-a new institute with the ambition to become a powerhouse for plant sciences. I was very excited at the prospects of leading my own research group, and that excitement overrode any qualms or self-imposed geographical restrictions. I am also fortunate enough to have an incredibly supportive family and friends who unconditionally encouraged me to pursue my scientific career, even if that involved moving far away; they may not always understand the nitty-gritty details of what I do, but they know how important it is for me.
It was my first job application, and I was offered the position following an interview at the center. They were willing to support me and give me the freedom to develop my own research program-it was an unbeatable opportunity to start my independent career. And the fact that I would be living in Asia, with the immense chance to broaden my experience that entailed, added some extra appeal (despite the slight vertigo I also felt). There was not much to think about, really-it was a deal I simply could not turn down.

LN: I was born to a Christian Arab family in Israel and did my undergraduate studies at the Technion (Israel Institute of Technology). Although I was an atheist by the time I started my studies at the Technion, I still considered myself to be "culturally" Christian, in that I celebrated Christmas and New Year with my family (eating and drinking, not going to church!). However, almost every year, my exams were scheduled on December 25th and January 1st (the Fall semester in Israel starts in October and ends in February). Being unable to take exams on different dates affected my performance in my studies and my interest in pursuing graduate studies at the same institution. Also, more generally, I was the only Christian Arab student in my class, and one of a handful of Arab students; I never felt comfortable at the time. So, I decided to pursue graduate studies in computer science outside Israel. The choice to come to the USA was an easy one because the USA had (and still has, in my opinion) the best graduate programs in computer science.
Year(s) Of Engagement Activity 2017
URL https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1370-4
 
Description Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Taproot is the podcast that digs beneath the surface to understand how scientific publications in plant biology are created. In each episode, co-hosts Liz Haswell and Ivan Baxter take a paper from the literature and talk about the story behind the science with one of its authors.

This episode features Sophien Kamoun, a Senior Scientist at the Sainsbury Laboratory in Norwich, UK. He was born in Tunisia, and got his Maitrise from Pierre & Marie Curie Univ., Paris, France. He then moved to the United States where he did both a Ph.D. and postdoc at the University of California, Davis. He then went to Wageningen University in The Netherlands, where he was a Senior Research Scientist for three years. Sophien started as an Assistant Professor in the Department of Plant Pathology at Ohio State University, Wooster, where he rose through the ranks to Full Professor before moving in 2007 to the Sainsbury Lab where he has been ever since. During this time he was Head of the Laboratory for several years. He has received many awards, and is an elected member of AAAS and EMBO, and has served on many editorial boards.

In this episode, the hosts and Sophien discuss a recent collaborative paper (Islam et al., 2016, BMC Biology) that really embodies the concepts of open science. It addresses the source and characterization of a newly discovered wheat blast in Bangladesh. Wheat blast is a fungal disease that affects grasses that are a huge threat to food security. The authors report the geographical distribution of this new disease, characterize the disease symptoms of affected plants, and isolate and validate the causal fungus. Most strikingly, they performed RNA sequencing on symptomatic and asymptomatic leaves and show that RNA from these infected leaves aligns to the genome of a Brazilian wheat blast strain. They conclude that the Bangladesh isolate of wheat blast is phylogenetically related to the Brazilian wheat blast, rather than an unknown or new lineage.

Listen to this episode to hear Sophien, Ivan, and Liz discuss the science in this paper, how the project started, and how it developed into a peer-reviewed publication. Also discussed is the importance of redefining what is meant by scientific "impact", and new ways to do science in the plant pathology community and beyond
Year(s) Of Engagement Activity 2017
URL https://plantae.org/taproot-episode-1-season-1-extreme-open-science-and-the-meaning-of-scientific-im...
 
Description Thought for Food challenge 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Competition - students in the group developed a web app called "Patch It App". The entry reached the top 20 teams and was invited to Amsterdam where they delivered a presentation about the novel application for urban farmers during the pop-up pitch session on the second day.
Year(s) Of Engagement Activity 2017
URL https://www.tffchallenge.com
 
Description Three-horizons, Agritech East Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact A workshop to provide an opportunity to find out how next generation sequencing technologies and high performance computing are being applied to answer the biological challenges of our time.
Year(s) Of Engagement Activity 2016
 
Description UK Cereal Pathogen Virulence Survey 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Prof James Brown is chairman of the management committee of the UK Cereal Pathogen Virulence Survey, which monitors and reports changes in populations of biotrophic pathogens of cereal crops (rusts and powdery mildews). This is an essential activity for plant breeders to select parents of crosses and design pathology trials, and provides background information for the AHDB Recommended List committee. It has an indirect impact on tens of thousands of tillage farmers in the UK and Ireland.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013
 
Description UKCPVS Event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Participant at UKCPVS Event
Year(s) Of Engagement Activity 2017
URL http://www.niab.com/pages/id/316/UKCPVS
 
Description Visit to JIC by students from Hogeschool Gent, Belgium 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Visit to JIC by c.30 students of agriculture and horticulture from Hogeschool Gent, Belgium, who learnt about current research on plant science at JIC.
Year(s) Of Engagement Activity 2017
 
Description What's up with preprints? And why I'm bothering with them. 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact What's up with preprints? And why I'm bothering with them. A few answers to @hormiga post about why he's not bothering with preprints.
Year(s) Of Engagement Activity 2017
URL http://kamounlab.tumblr.com/post/163409024195/whats-up-with-preprints-and-why-im-bothering
 
Description Wired: Who Wants Disease-Resistant GM Tomatoes? Probably Not Europe 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact ENGINEERING A TOMATO resistant to a pernicious fungal disease doesn't seem like it'd be the easiest part of a plant pathologist's job. But compared to getting that tomato to market? It's a snap.

At least, that's how Sophien Kamoun sees it. Kamoun studies plant diseases at the Sainsbury Laboratory in England, and in March his team published a paper describing a tomato they'd tweaked. Using the gene-editing technique Crispr/Cas9, Kamoun's group snipped out a piece of a gene called Mildew Resistant Locus O, or Mlo. That deletion makes the tomato resistant to powdery mildew, a serious agricultural problem that takes a lot of chemicals to control.

Kamoun's "Tomelo" actually looks a lot like a naturally occurring tomato, a mutant with the same resistance. "At least in the tomato plants we have, there was no detectable difference between the mutant and the wild type," Kamoun says. "Obviously we'd need to do more detailed field trials, but there was certainly nothing obvious."

But for now, that's where Kamoun's work stops. European regulations make the tomato essentially illegal-he and others can do the science, but probably can't get it to field trials, and certainly can't get it to market. "There's more clarity in the US. One could probably get approval. But in Europe, it's a big question mark," he says. "I'm very frustrated by this, I have to be honest. Scientifically this plant is no different from any mutant we'd get from traditional breeding or traditional mutagenesis. I really don't understand what the problem is."
Year(s) Of Engagement Activity 2017
URL https://www.wired.com/2017/05/wants-disease-resistant-gm-tomatoes-probably-not-europe/?mbid=social_t...
 
Description Women in computing blog series at the EI website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Blog post to promote women in computing
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/articles/women-computing-pilar-corredor-moreno
 
Description YouTube: BLASTOFF - Keeping Up With A Cereal Killer 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Via UC Berkeley Events. Center for Emerging and Neglected Diseases (CEND) at UC Berkeley facilitates innovative solutions for infectious disease challenges. Berkeley, CA.
Year(s) Of Engagement Activity 2018
URL https://youtu.be/FCS5y_qX8n0
 
Description Youth STEMM awards 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact A ceremony for The Youth STEMM Award (YSA) which provides a focused and engaging framework for young people aged 13-18 to further their passion, knowledge and skills in STEMM (Science, Technology, Engineering, Maths and Medicine).
Year(s) Of Engagement Activity 2017
URL https://www.jic.ac.uk/news-and-events/news/2016/07/new-youth-stemm-award-recognises-success-end-year...
 
Description http://hpc.ilri.cgiar.org/beca/training/jic_beca_2016/index.html 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Trainer on workshop "Advancing cereals genetic research using the latest genomic and germplasm resources" BecA-ILRI Hub, Nairobi, Kenya
Year(s) Of Engagement Activity 2017
URL http://hpc.ilri.cgiar.org/beca/training/jic_beca_2016/index.html