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.

Organisations

Publications

10 25 50

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Adachi H (2019) A resistosome-activated 'death switch'. in Nature plants

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Andolfo G (2019) Alien Domains Shaped the Modular Structure of Plant NLR Proteins. in Genome biology and evolution

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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.)

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Carvajal-Yepes M (2019) A global surveillance system for crop diseases. in Science (New York, N.Y.)

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Chaudhari Y (2019) The ORFeome: A Functional Genomics Community Resource. in Molecular plant-microbe interactions : MPMI

 
Title A biologist's poem 
Description This 'real and singular thing'. A piece of code in its own genome. A copy from the past, multipliable, repeatable, yet mutable. You couldn't help feeling that you had stolen this sequence from its owner. You had transferred a piece of life into the human consciousness. with apologies to Wim Wenders /w @SaskiaHogenhout 
Type Of Art Creative Writing 
Year Produced 2018 
Impact Positive feedback on social media 
URL http://kamounlab.tumblr.com/post/170774045435/a-biologists-poem
 
Title I Will Survive (biotroph remix) 
Description A plant pathology inspired song. I Will Survive (biotroph remix) [with apologies to Gloria Gaynor] Oh, no, not I I will survive Oh, as long as I know how to infect you I'll stay alive I've got all my life to live I've got all my spores to give And I'll survive I will survive, hey, hey 
Type Of Art Creative Writing 
Year Produced 2018 
Impact >15K impressions on social media and ~250 engagements 
URL https://twitter.com/KamounLab/status/1098214166723215361
 
Title MARPLE diagnostics hub development in Ethiopia 
Description We interviewed a number of researchers from each of the five MARPLE diagnostics hubs being established in Ethiopia 
Type Of Art Film/Video/Animation 
Year Produced 2019 
Impact The video has been extremely useful for promoting the project and thereby assisiting in exploring opportunities for follow-on funding. 
 
Title Mobile And Real-time PLant disEase (MARPLE) diagnostics: Impact interviews 
Description We interviewed a number of researchers in Ethiopia to capture the impact of our methodology development. 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact The video has been extremely useful for promoting the methodology and thereby in achieving follow-on funding. 
 
Title Mobile And Real-time PLant disEase (MARPLE) diagnostics: pipeline artwork 
Description We developed a graphic to illustrate our new methodology and make it easier for partners to follow. 
Type Of Art Image 
Year Produced 2018 
Impact This artwork has been utilised to convey the steps of the pipeline with partners and demonstrate its simplicity. 
URL https://acaciaafrica.org/marple-diagnostics/
 
Title Video animation: Plants have an immune system and it's complicated 
Description Just like humans, plants have an immune system that they use to fend off pathogens and pests. Research involving plant immunity was guided by Harold Flor's influential "gene-for-gene" model but this model is now supplanted by a more complex view of pant immunity. Disease resistance genes appear to work together in intricate networks that enable plants to detect and resist parasites more effectively. An in-depth understanding of the immune system can help us breed disease resistant crops. 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact ~10K views on YouTube 511 engagements and >20K impressions on Twitter 
URL https://youtu.be/mlp2mQTEVtQ
 
Description Objective 4.1: Mechanisms of coevolution of molecules involved in plant-parasite recognition

NLR network mediates immunity to diverse plant pathogens (PNAS, 2017)
Plant and animal nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins often function in pairs to mediate innate immunity to pathogens. However, the degree to which NLR proteins form signaling networks beyond genetically linked pairs is poorly understood. In this study, we discovered that a large NLR immune signaling network with a complex genetic architecture confers immunity to oomycetes, bacteria, viruses, nematodes, and insects. The network emerged over 100 Mya from a linked NLR pair that diversified into up to one-half of the NLRs of asterid plants. We propose that this NLR network increases robustness of immune signaling to counteract rapidly evolving plant pathogens.

Classification of a new phytoplasma subgroup 16SrII-W associated with Crotalaria witches' broom diseases in Oman based on multigene sequence analysis (BMC Microbiology, 2017)
Crotalaria aegyptiaca, a low shrub, is found throughout all regions in Oman. During a survey in 2015, typical symptoms of phytoplasma infection were observed on C. aegyptiaca plants. The presence of phytoplasma in the phloem tissue of symptomatic C. aegyptiaca leaf samples was confirmed by Transmission Electron Microscopy and the presence of phytoplasma DNA from symptomatic leaves and Orosius sp. leafhoppers was confirmed. Phylogenetic analysis placed Crotalaria witches' broom phytoplasmas within the clade of Peanut WB (16SrII) but in a separate sub-clade from all the other phytoplasmas belonging to Peanut WB group. Further data suggested that the SAP11 of Crotalaria phytoplasma is different from the SAP11 of other phytoplasmas. We proposed to assign the Crotalaria witches' broom from Oman in a new lineage 16SrII-W subgroup.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species (Genome Biology 2017)
The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. The majority of insect herbivores colonise a small number of closely related host species but remarkably, the green peach aphid, Myzus persicae, a highly destructive pest of many important crops, colonises plant species across 40 families. 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. Genetically identical individuals were able to colonise distantly related hosts through differential regulation of genes belonging to aphid-expanded gene families, including multigene clusters. RNAi-mediated knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. The generalist aphid pest M. persicae is thus able to colonise diverse host plant species in the absence of genetic specialisation, by rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

Comparative analysis of targeted long read sequencing approaches for characterization of a plant's immune receptor repertoire (BMC Genomics, 2017)
The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Wild relatives of crops are a key source of new genetic resistance to pathogens. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. We demonstrated how MinION sequence data can be used for RenSeq and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline.

Resistance gene cloning from a wild crop relative by sequence capture and association genetics (Nature Biotechnology, 2018)
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.

Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize (PLoS Pathogens, 2019)
We published a manuscript showing that phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. We showed that a SAP11 homolog of Maize Bushy Stunt Phytoplasma (MBSP), which has a range primarily restricted to maize, destabilizes specifically TB1/CYC TCP transcription factors, affecting axillary branching and leaf development. In maize, it also affects male and female inflorescence development. SAP11 from Aster Yellows phytoplasma Witches' Broom (AY-WB) promotes fecundity of the leafhopper vector on Arabidopsis and modulates the expression of leaf defence response genes that are induced by this leafhopper. These data provide evidence that class II TCPs have overlapping but also distinct roles in regulating development and defence in a dicot and a monocot plant species that is likely to shape SAP11 effector evolution depending on the phytoplasma host range.

We have identified a number of potential Puccinia striiformis f. sp. tritici (Pst) susceptibility factors in wheat using an unconventional field-based approach. Pst-infected field samples were collected, RNA-seq analysis undertaken using our "field pathogenomics" approach, and gene expression profiles compared between wheat varieties with differing levels of susceptibility to Pst infection. This has started to uncover new insight into how Pst manipulates its host during the infection process. For instance, one gene we thoroughly characterised encodes a branched-chain amino acid aminotransferase (TaBCAT1). TaBCAT1 tetraploid double TILLING mutant lines were created that showed a significant increase in resistance to Pst infection and infection by the closely related wheat stem rust pathogen (Puccinia graminis f. sp. tritici). Further functional characterisation suggests that TaBCAT1 regulates amino acid homeostasis in the cell and by doing so, coordinates the activation of salicylic acid-mediated defence responses in wheat. This analysis is currently being submitted for publication and discussions have been initiated with multiple breeding companies due to its role as a potential susceptibility factor that could be manipulated to provide durable resistance to Pst.
Prof Sophien Kamoun has articulated a model that describes how NLRs evolve from multifunctional singletons into functionally specialized pairs and networks.
Prof Sophien Kamoun has shown how mini-chromosomes independently emerge from structural rearrangements of core-chromosomes and might contribute to adaptive evolution of the blast fungus.

Prof Jonathan Jones has cloned recognized effectors from Phytophthora for amr1 and amr3.

Role of Effector-Sensitivity Gene Interactions and Durability of Quantitative Resistance to Septoria Nodorum Blotch in Eastern U.S. Wheat (Frontiers in Plant Science, 2020)
We have reviewed the evidence on breeding for resistance of wheat to Septoria nodorum blotch (Parastagonospora nodorum) in the USA and Europe. We conclude that wheat cultivars have durable quantitative SNB resistance, largely controlled by undefined polygenes, and that interactions between major Snn resistance genes and pathogen necrotrophic effectors are of limited importance in breeding for resistance to this disease.

Durability of Quantitative Resistance in Crops: Greater Than We Know? (Annual Review of Phytopathology, 2019)
Quantitative resistance (QR) to crop diseases has usually been much more durable than major-gene, effector-triggered resistance. It has been observed that the effectiveness of some QR has eroded as pathogens adapt to it, especially when deployment is extensive and epidemics occur regularly, but it generally declines more slowly than effector-triggered resistance. Changes in aggressiveness and specificity of diverse pathogens on cultivars with QR have been recorded, along with experimental data on fitness costs of pathogen adaptation to QR, but there is little information about molecular mechanisms of adaptation. Some QR has correlated or antagonistic effects on multiple diseases. Longitudinal data on cultivars' disease ratings in trials over several years can be used to assess the significance of QR for durable resistance in crops. We argued that published data likely underreport the durability of QR, owing to publication bias.


Objective 4.2: Evolution of pathways controlling biotic interactions in plants

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (BMC Evolutionary Biology, 2018)
Disease outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops but the underlying mechanisms of genome evolution and phenotypic plasticity remain poorly understood. Recurrent outbreaks of late blight of potato and tomato, caused by the oomycete Phytophthora infestans, have been primarily caused by the successive rise and migration of pandemic asexual lineages. We showed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

The role of reactive oxygen in the development of Ramularia leaf spot disease in barley seedlings (Annals of Botany, 2018)
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). 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. Exposure to abiotic stress increased symptom development in barley varieties, in association with greater hydrogen peroxide levels. Decreased activity of antioxidant enzymes in transgenic and mutant plants had no effect on the disease transition, whereas manipulation of peroxide levels during asymptomatic growth of the fungus increased disease symptoms in most susceptible varieties. Barley 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 is promoted by factors that result in changes to host reactive oxygen species.

Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors (Scientific Reports, 2017) Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds' largest food crops including wheat, rice, maize and soybean. To date, little has been known about the pathogenicity mechanisms employed by R. solani. 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 able to induce cell death in-planta. These findings provide potential avenues to control this under-characterised but important pathogen.

Speed breeding is a powerful tool to accelerate crop research and breeding (Nature Plants, 2018)
Speed breeding in growth chambers and glasshouses for crop breeding and model plant research (Nature Protocols 2018)
We contributed to the developed of a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes of crop plants, including cereals, legumes, crucifers and chenopods. We demonstrated that speed breeding in fully enclosed, controlled-environment growth chambers could accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allowed rapid generation cycling with the potential for adaptation to larger-scale crop improvement programs. Integration of speed breeding with other modern crop breeding technologies offers exciting opportunities for accelerating research on disease resistance and other traits in a wide range of species, accelerating the rate of crop improvement. The second paper cited above provides detailed protocols for speed breeding.

Objective 4.3 Evolutionary processes in populations of plants and their parasites

The ash dieback invasion of Europe was founded by two genetically divergent individuals (Nature Ecology & Evolution 2018)
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. We contributed to the assembly and annotation of a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan revealed a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. The European population was founded by two divergent haploid individuals, divergence between which represents ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

Population structure of the ash dieback pathogen, in relation to its mode of arrival in the UK (Plant Pathology 2018)
To investigate the relationship of the Hymenoscyphus fraxineus population structure to its mode of arrival in the UK, isolates were obtained from locations 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 and frequencies of mating type idiomorphs were 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 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 results imply that management of an introduced plant pathogen requires action against its spread at the continental level involving coordinated efforts by European countries.

Pathogenomic analysis of wheat yellow rust lineages detects seasonal variation and host specificity (Genome Biology & Evolution, 2017)
Recent disease outbreaks caused by emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. 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. We used field-based genotyping to reveal that P. striiformis lineages recently detected in Europe are extremely diverse and in fact similar to globally dispersed populations and to identify a considerable shift in the UK P. striiformis population structure. Furthermore, we uncovered evidence for varietal specificity for genetic groups of P. striiformis and for seasonal specificity of certain genotypes of the pathogen.

Potential for re-emergence of wheat stem rust in the United Kingdom (Communications Biology, 2019)
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. We investigated if 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 reported 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 suggested increasingly conducive conditions for infection. We documented 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, may severely harm wheat and barley production.

Shifting the limits in wheat research and breeding using a fully annotated reference genome (Science, 2018)
We contributed to the fully annotated and ordered genome sequence of wheat, including regulatory sequences and genome-diversity information. This is a breakthrough advance in the capacity to investigate wheat, the most important crop in the UK and one of the leading crops world-wide. The value of the annotated assembly for molecular breeding and research was exemplified by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage. The reference genome sequence will enable easy access to sequence information to precisely define the necessary changes in the genomes for breeding programs.

We are continuing to integrate our MARPLE (Mobile And Real-time PLant disEase) diagnostics platform for near real-time, strain level diagnostics of Pst within the wheat rust early warning system in Ethiopia. Our partnership (JIC, CIMMYT and EIAR) and integration of this system with disease forecasting programmes has positioned Ethiopia as a world leader in pathogen diagnostics and forecasting. Our work that led to the creation of MARPLE diagnostics was recognised by receipt of the Innovator of the Year award for international impact from BBSRC in 2019. This award and support of the CGIAR Inspire challenge and the Delivering Genetic Gain in Wheat project is now facilitating the development of five MARPLE hubs at strategic locations across the major wheat growing regions in Ethiopia. Building on initial trials of the methodology in 2018, we carried out a more detailed workshop in-country in 2019 and visited all five MARPLE hubs. We now have a two-month training program planned for 2020 to support the adoption of the methodology, with assistance from four BBSRC-funded PhD students as part of their professional training. Furthermore, we are supporting the integration of MARPLE diagnostics into the UK Cereal Pathogen Virulence Survey (UKCPVS) and adoption more widely of the methodology by surveillance labs across Europe.

We have undertaken the first survey of common barberry for rust infection across the UK and identified many sites where barberry infected by stem rust can be found adjacent to cereal crops. Stem and yellow rust pathogens require two hosts to complete their life cycles, undertaking asexual reproduction on cereals and sexual reproduction on Berberis (including Mahonia), where recombination can lead to emergence of novel genotypes. Eradication of common barberry (B. vulgaris) in the UK drove stem rust to almost complete extinction. However, over the past decade, barberry planting has reinitiated and is advancing in many major wheat growing regions. Part of this is due to active re-planting to enhance habitat for the endangered Barberry Carpet moth (Pareulype berberata), whose current only known food source is B. vulgaris. We have also initiated an iCASE studentship (start date Oct-19) to evaluate alternate food sources, with the aim of maintaining habitat and thereby biodiversity without posing any increased risk to cereal production, if wheat stem rust does re-emerge in the UK. Furthermore, integrating biological data and mathematical modelling we have started to develop a risk model to help guide future re-planting efforts and identify potential high-risk hedgerows that may need monitoring in future.

We have developed a rapid, high-throughput and cost-effective method for environmental DNA sample preparation and analysis. We have used this to conduct a major metagenomic analysis of microbiota associated with Arabidopsis and other plants growing in harsh soil conditions.

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

A versatile method for assessing pathogenicity of Hymenoscyphus fraxineus to ash foliage (Forest Pathology, 2018)
We developed a method for inoculating rachises of Fraxinus excelsior (European or common ash) with Hymenoscyphus fraxineus, which is faster than previous methods and allows associated foliar symptoms to be assessed on replicate leaves. A fivepoint disease progress scale of symptom development was developed. The method revealed variation in aggressiveness of H. fraxinus isolates and may be suitable for assessing the resistance of F. excelsior and other Fraxinus species to dieback. The in vitro growth rate of H. fraxineus isolates was highly correlated with disease progress. This method underpins current research on trade-offs between responses of ash to Chalara ash dieback and to invertebrate herbivores.

Temporal and spatial field evaluations highlight the importance of the presymptomatic phase in supporting strong partial resistance in Triticum aestivum against Zymoseptoria tritici (Plant Pathology, 2018)
Zymoseptoria tritici, the causal agent of septoria tritici blotch (STB), is a significant threat to European wheat production. The life cycle of Z. triticiis characterized by a presymptomatic phase (latent period, LP) after which the pathogen switches to an aggressive necrotrophic stage. We investigated the spatial and temporal association between the LP and disease progression across three locations with a range STB disease pressures. It was shown that the length of the LP contributed significant to high partial resistance to STB, but once the LP had, subsequent disease progress was as rapid as in more susceptible varieties. The implication is that selection for longer LP will promote strong partial resistance of wheat to STB.

We published a manuscript: Mathers et al., 2019. Sex-specific changes in the aphid DNA methylation landscape'. Mol. Ecol. 28: 4228-4241.

We sequenced the 2.6 Gb genome of Xylella fastidiosa insect vector Philaenus spumarius (Dataset published in 10.5281/zenodo.3368384), also known as the meadow spittle bug, which is a common insect species in the UK. We generated whole genome sequence data of 116 P. spumarius individuals collected in different habitats and on diverse plant species across the UK and are aligning these sequences to the genome sequence for population structure analyses.

We launched SapfeedersHub (http://sapfeedershub.jic.ac.uk/index.html) that has the objective to provide the wider community with full datasets of genome assemblies and associated annotations of aphids, spittlebugs and other sap-feeding hemipteran insect species.

As part of a collaboration with the Molecules from Nature ISP, Prof Sophien Kamoun has mapped and characterised the Pseudomonas metagenomic adaptations that occur in response to irrigation in potato field soil.

Prof Jonathan Jones has used Super Follow-on Funding to deploy Rpi gene stacks in potato.

Resistance of European ash (Fraxinus excelsior) saplings to larval feeding by the emerald ash borer (Agrilus planipennis) (Plant People Plant, 2019)
European ash is a significant tree commercially, ecologically, and culturally. It is currently threatened by two invasive species, the fungus that causes ash dieback and the emerald ash borer (EAB) beetle. We showed that saplings of European ash are much less susceptible to EAB than black ash, which has suffered severe damage in North America, but have similar resistance to Manchurian ash, which coexists with EAB in East Asia. Selecting ash with stronger resistance to dieback is unlikely to decrease its resistance to EAB. As we do not know what the combined effect of ash dieback and EAB will be on European ash, biosecurity measures are needed to exclude EAB from Western Europe.
Exploitation Route The research covers a very wide range of academic and non-academic applications. We have done internationally leading research in a wide range of subjects, which raises key questions and offers new opportunities across a wide range of topics relevant to pathogen evolution and host-parasite coevolution, for example in the evolution of plant recognition systems and long-range dispersal of pathogens. Other research advances knowledge of important diseases such as ash dieback, rusts of wheat and Ramularia leaf spot of barley, and thus suggests opportunities for control.

Regarding non-academic applications, our research is relevant to management of insect pests and fungal pathogens. Results of our research are applicable to improved control by agrochemicals, plant breeding for durable broad-spectrum resistance to multiple pests and diseases, prevention and control of invasive and re-emerging diseases, and breeding for disease resistance combined with yield and quality in arable crops.

The methods we have developed for gene discovery by high-throughput sequencing and genomics can be applied very widely to many traits in many species, not just plants. We have applied them more extensively to discovery of NLR pathogen recognition genes in cereals but this is a powerful technology with many applications. The wheat genome sequence, to which we contributed expertise on identifying pathogen recognition genes and other genes involved in plant defence, is another major advance which promises to accelerate greatly research and breeding for this very important crop species.

Research on evolution of pests and pathogens is important in plant disease control, e.g. by breeding, agrochemicals and interception at ports, because the effectiveness of these measures relies on them being targetted to the correct species. For example, the technology we have developed for field pathogenomics of cereal rusts supports pathology research to build up a wider, more detailed picture of pathogen population dynamics.

In research on microbial communities, QTLs and other loci in barley and wheat that control beneficial microbial colonisation will feed into sustainable cereal breeding efforts. In addition, we have identified biocontrol strains and antimicrobial natural products with activity against PsaV and other pathogenic bacteria.

Our research on European ash indicates that populations of ash which are resistant to dieback may also be able to resist attack by another alien species, the emerald ash borer beetle. Our work implies that rigorous biosecurity measures are required to exclude EAB from the UK in order to give the native ash population time to recover from the ash dieback epidemic. If this happens, we expect that a healthy ash population may be re-established in the UK in a few hundred years' time.

Our research on methods of breeding for disease resistance indicates that non-race-specific, "background" resistance, which does not involve effector recognition and is largely controlled by dispersed polygenes, is likely to be durable. Breeding strategies based on selection of this type of resistance are likely to provide resistance which is sufficiently effective and sufficiently durable to protect arable crops against a wide range of pests and diseases.
Sectors Agriculture, Food and Drink,Energy,Environment,Leisure Activities, including Sports, Recreation and Tourism,Transport

URL http://www.jic.ac.uk/research/plant-health/our-science/objectives/#theme-4
 
Description The research in the Evolution theme largely concerns pests and diseases of practical importance and thus has had and will have numerous impacts. Research on pathology and ecology of ash dieback is feeding into proposals for recovery of ash as a keystone species in the UK landscape. JIC researchers have played a prominent part in developing DEFRA's strategy for management of ash in the UK's natural environment and commercial forestry and in working with industry and third-sector organisations to promote recovery of ash from ash dieback and protection from emerald ash borer. 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. Prof James Brown and Prof Paul Nicholson have advised AHDB and the plant breeding industry on methods of scoring and rating varieties for resistance to Ramularia, Septoria, rust and Fusarium, for the benefit of the UK farming industry generally. JIC researchers have developed a system called MARPLE for rust diagnostics and are working on capacity building for rust research with colleagues in Ethiopia. Our partnership with CIMMYT and EIAR has achieved significant impact, that includes: (i) Secondment of an EIAR scientist to JIC for in-depth training in MARPLE diagnostics, providing extensive skills and knowledge in this area that is currently being transferred to researchers in-country. (ii) Wider training of EIAR scientists by JIC in September 2018 at EIAR Holeta offered knowledge and capacity building in mobile sequencing capability. CIMMYT and EIAR now have a nanopore sequencer and the capability to utilise it in-country. Further, structured, in-country, training events are planned for 2019. (iii) EIAR Holeta is now a model "hub" that will be replicated in 2019 in three further locations in Ethiopia (led by EIAR scientists) to provide rapid diagnostic capacity throughout the main wheat growing regions and permit sentinel monitoring of yellow rust races on an annual basis. Through this project, Ethiopia has now become the lead nation in Africa with a robust, rapid monitoring system for important transboundary diseases. Having accurate and rapid yellow rust diagnostics will benefit not only 5 million wheat-dependent farming families in country, but also wheat farmers in the entire region. Deployment of the first MARPLE diagnostics hub by JIC scientists occurred in September 2018. Development of MARPLE has continued in 2019, building capacity across three locations: (i) In Ethiopia, our partnership with CIMMYT and EIAR has achieved significant impact, that over the past year includes detailed training of EIAR scientists during a three-day workshop led by JIC in November 2019 at the EIAR Holeta hub. In preparation for rolling out the methodology to four additional hubs (led by EIAR scientisits), MARPLE kits are now in-country and a two-month training schedule has been arranged for July-August 2020. This will provide rapid diagnostic capacity throughout the main wheat growing regions and permit sentinel monitoring of yellow rust races on an annual basis. Through this project, Ethiopia has now become the lead nation in Africa with a robust, rapid monitoring system for important transboundary diseases. Having accurate and rapid yellow rust diagnostics will benefit not only 5 million wheat-dependent farming families in country, but also wheat farmers in the entire region. (ii) To promote uptake of the methodology across disease surveillance labs in Europe we provided a four-day training course in MARPLE diagnostics through the RustWatch program (https://agro.au.dk/forskning/projekter/rustwatch/) in November 2019. (iii) To ensure the UK specifically benefits from the development of this methodology we are also working closely with the UK Cereal Pathogen Virulence Survey (UKCPVS) to support its integration and thereby equip the UK with the latest genomic-based pathogen surveillance tools. Prof Jonathan Jones welcomed the Prime Minister's statement in July 2019 that the UK's bioscience sector should be "liberated" from anti-genetic modification rules and that UK scientist should develop blight resistant crops "that will feed the world". Prof Jones was later interviewed about this on BBC Radio 4's Today programme. The Rpi-vnt1 gene is now being deployed commercially in the US, and the Rpi-amr3 gene will be. Our collaboration with Folium Science has been successful, and has led to the creation of highly effective Guided Biotic treatments for two major plant pathogens (P. syringae and X. campestris). These treatments are now in the development stage. We have begun work on designing Guided Biotics against major global plant pathogens as part of the next stage of the company's agritech strategy. Folium currently employ two PDRAs in Dr Jake Malone's lab supported by the InnovateUK funding. The company is currently seeking co-development partners to expand the agritech branch of the business. Prof Saskia Hogenhout has had significant engagement with industrial partners, Syngenta and SESVanderHave, in her research on phytoplasma diseases and their aphid vectors. This has led to regular exchange of knowledge and methods, and submission of two patent applications. It has also led to an iCASE studentship proposal in collaboration with Syngenta and the Liverpool School of Tropical Medicine. The student will start his iCASE studentship in Oct 2020. Prof Hogenhout has had regular engagement with policymakers, government staff and the general public as part of her leadership role in the BRIGIT consortium, which researches Surveillance and response capacity for Xylella fastidiosa. She has provided information to policymakers, government staff and the general public about the biology of the plant pathogen Xylella fastidiosa and its insect vectors. She has held discussions with policymakers and government staff about mitigation procedures if this pathogen were to be introduced into the UK. She has launched a BRIGIT website with links to video, databases and information resources about Xylella and its insect vectors. Prof Sophien Kamoun has developed new tools and resources for the research community. He has made use of his extensive collaborative networks to widely disseminate new tools and resources. He has reported novel protocols and methods through online platforms (protocols.io) and distributed biomaterial through Addgene. He hosted the First Seminar Series at which students and postdocs give their first invited seminar. To date, six Early Career Scientists from UK, Netherlands, Austria, Japan and China, have participated in this series. He has established fully-funded collaborations with two agribusiness companies that raised a total amount of >£1.5M. Prof James Brown is now in his fourth three-term term (2019-2021) as the plant pathology specialist on AHDB's Wheat Crop Committee, which draws up the annual Recommended List of wheat varieties. This has given him the opportunity to encourage the plant breeding industry to continue improving the level of disease and pest resistance, especially durable resistance, in new wheat varieties which also have market-leading yield, quality and agronomic properties. He has also worked closely with AHDB to develop their new Adaptive Agronomic Merit Tool for variety selection. His approach to developing durable resistance is informed and motivated by his academic research on this subject (e.g. Cowger & Brown 2019, Ann Rev Phytopath) and vice-versa.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Energy,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 Advisory Committee Chair, International Congress of Plant Pathology (ICPP18) in Boston, MA
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact ICPP 2018 adopted the theme "Plant Health is Earth's Wealth" for ISPP 2013-2018 recognising that plant pathogens don't just threaten food security and well-being. They also affect, forest and fibre systems, natural ecosystems, biodiversity and environmental harmony, and impede trade and market access. And, phytopathology research has also been a central focus for discovery and development in biotechnology and plant-microbial molecular biology. For our profession - people are the pivotal element, and while in the coming years, the ISPP will maintain a focus on plant disease impacts on food security, it should and will also foster attention to all facets of our profession through our Congresses, subject matter committees and our website, newsletter and Journal. In this light, the ISPP taskforce on global food security which has more than achieved it objectives will now become a Commission working in the same way as other ISPP Subject Matter Committees. https://www.isppweb.org/newsletters/pdf/48_8.pdf One of the major outcomes was the proposal for a code of ethics for plant health emergencies: * to foster ethical conduct * to support communication and collaboration * to ensure that decisions are based on the best available evidence See https://www.isppweb.org/newsletters/pdf/48_12.pdf
URL https://www.isppweb.org/newsletters/pdf/48_8.pdf
 
Description Barberry Highways Project
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Providing further information regarding the role of barberry in potentially escalating cereal rust diversity has guided plans for future barberry re-planting efforts that now take into account proximity to cereal fields.
 
Description CABANA External Advisory Committee
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact What is CABANA? CABANA is a capacity strengthening project for bioinformatics in Latin America. It aims to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme focusing on three challenge areas - communicable disease, sustainable food production and protection of biodiversity. CABANA is orchestrated by an international consortium of ten organisations - nine in Latin America and one in the UK. CABANA is funded by the Global Challenges Research Fund (GCRF) - part of the UK Aid Budget - from October 2017 to December 2021.
URL http://www.cabana.online
 
Description Comment on Court of Justice of the European Union (CJEU) ruling-Organisms obtained by mutagenesis are GMOs and are, in principle, subject to the obligations laid down by the GMO Directive
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Impact This ruling ignores advances in plant bioediting that make this technology more precise than so-called "conventional mutagenesis". Bioediting can be also be used to recapitulate natural variations into cultivated varieties of crops. This ruling closes the door to many beneficial genetic modifications such as breeding of disease resistant plants that require much less pesticide input. A sad day for European plant science. Disseminated via Science Media centre and social media.
URL http://kamounlab.tumblr.com/post/176262512395/comment-on-court-of-justice-of-the-european-union
 
Description Global preparedness for emerging diseases
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact To build resilience against unintentional spread of crop disease threats, we present the argument for a global surveillance system (GSS) for de-risk global food supplies and increase resilience to crop diseases. The model for the GSS draws on lessons learned from established national and regional plant protection organizations and on measures implemented in more developed countries. The GSS would extend these agricultural biosecurity measures into LDCs, enhancing overall global food protection. The conference on "Building resilience against crop diseases: A global surveillance system" is supported by the Rockefeller Foundation and will be held Feb. 12-16, 2018, at The Bellagio Center in Lake Como, Italy. Simone Staiger, Head of Knowledge Management and Learning at CIAT, is facilitating the meeting.
URL http://kamounlab.dreamhosters.com/storify/RFBellagio_storify.html
 
Description Gregor Mendel Institute of Molecular Plant Biology Science Advisory Board
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact The GMI is part of the Vienna BioCenter (VBC), one of the leading international biomedical research centers worldwide that has established itself as the premier location for life sciences in Central Europe.
URL https://www.oeaw.ac.at/gmi/
 
Description Inst. Plant and Microbial Biology (IPMB), Academia Sinica, Taiwan, Science Advisory Board.
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact Academia Sinica is Taiwan's premier government-supported academic research institution, with 31 institutes and centers representing a wide range of disciplines in the sciences and humanities. It is located in the Nankang district, on the outskirts of metropolitan Taipei. One of the Life Sciences Institutes, The Institute of Plant and Microbial Biology (IPMB) has 26 fellows (professor equivalents) whose research follows one of two central themes: the mechanisms of plant functioning or plant-microbial interactions. Some 300 support staff consisting of specialists, postdoctoral fellows, graduate students, Research Assistant and administrative personnel work under the research fellows. IPMB has modern infrastructure and equipment. An active education program is also set up, with Ph.D. students from the Taiwan International Graduate Program, Academia Sinica, or from their adjunct programs with National Taiwan University and National Central University. IPMB research fellows have previously made landmark discoveries in such areas as rice breeding and genomics, regeneration via tissue culture, virus satellite RNA, microbial circadian rhythm, etc. For a long time goal, we aim to improve the quality and quantity of research performance and achieve visibility in international scientific community. Over the past decade, IPMB has undergone a major reorganization and rejuvenation, and has added a number of outstanding junior fellows.
 
Description Journals 2.0: a roadmap to reinvent scientific publishing
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Promoted preprints and open science and a different, more sustainable, form of scientific publishing therefore accelerating the dissemination of science and reducing the exorbitant costs of scientific publishing. This vision describes a radically different publishing model that would reinvent the concept of a scientific journal into a live and open forum of scientific debate and analysis. This model centers on a full integration of the preprint ecosystem into the journal interface. The journal would only accept submission of articles that have been posted as preprints. All evaluations and commissioned reviews of submitted articles would be published as soon as received on the journal website and linked to the preprint version. Editors would operate as always sifting through submitted papers and seeking external reviewers when necessary. But they will also consider author-led and community crowdsourced reviews, which would be appended to the preprint. As the reviews accumulate and revisions are submitted, the journal editors would initiate a consultation process, and when satisfied with a given version promote it to a formal article. The editor's role becomes more akin to moderator than gatekeeper. The process doesn't have to be static. As the community further comments on the article and follow-up studies are published, editors may decide to commission synthetic review or commentary articles to address emerging issues. I would also envision that the paper is linked to related articles in a "knowledge network" database, and that article tags are revised to reflect new knowledge, e.g. "independently validated". The journal would therefore become less of a static repository of scientific articles, and more of a moderated forum of scientific discussion.
URL https://zenodo.org/record/1466784#.XH2SPi2cawQ
 
Description Point of view: wither pre-publication peer review to reinvent scientific publishing
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Promoted open science and preprints among the research community therefore resulting in more rapid dissemination of scientific findings.
URL http://kamounlab.tumblr.com/post/178573217080/point-of-view-wither-pre-publication-peer-review
 
Description Project Leader of BRIGIT, a UK-wide consortium to mitigate the risks of Xylella fastidiosa outbreaks in the UK
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
Impact The BRIGIT consortium includes people from various layers of government, charities, research institutes and industry. The writing of the BRIGIT proposal and activities within BRIGIT so far increased the knowledge of the consortium members about the Xylella pathosystem and how Xylella fastidiosa may spread in the UK and harm the environment. This is likely to influence future regulations to maximize protection of the UK environment.
URL https://www.jic.ac.uk/brigit/
 
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 UKCPVS steering committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
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 France
Start 10/2017 
End 09/2018
 
Description CGIAR: - CGIAR Inspire challenge scale up
Amount $250,000 (USD)
Organisation CGIAR 
Sector Charity/Non Profit
Country France
Start 01/2019 
End 12/2020
 
Description Cash contribution to IPA grant
Amount £95,000 (GBP)
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 10/2014 
End 09/2016
 
Description Cash contribution to IPA grant
Amount £131,700 (GBP)
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 04/2018 
End 03/2021
 
Description Developing new tools for interrogating cereal invaders
Amount £3,500 (GBP)
Organisation Royal Society of Biology (RSB) 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2018 
End 09/2018
 
Description ERC Advanced Investigator
Amount € 2,500,000 (EUR)
Funding ID BLASTOFF 743165 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
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 Genotype-based monitoring for fungicide resistance management
Amount £11,213 (GBP)
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 02/2020 
End 05/2020
 
Description Gordon and Betty Moore Foundation
Amount $2,000,000 (USD)
Organisation Gordon and Betty Moore Foundation 
Sector Charity/Non Profit
Country United States
Start 03/2015 
End 06/2019
 
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 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 In kind contribution to LINK grant
Amount £414,657 (GBP)
Organisation Sesvanderhave 
Sector Private
Country Belgium
Start 04/2016 
End 09/2019
 
Description Investigation of conserved infection pathways in Puccinia species to identify novel targets for pathogen control
Amount £300,951 (GBP)
Funding ID BB/S011005/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2022
 
Description JIC-CAAS collaboration funds
Amount £100,000 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 04/2017 
End 12/2018
 
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 Charity/Non Profit
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 Charity/Non Profit
Country United Kingdom
Start 10/2016 
End 10/2018
 
Description The role of the sexual cycle in escalating wheat rust diversity in the UK
Amount £593,834 (GBP)
Funding ID BB/S003975/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 09/2021
 
Description Using a multi-disciplinary approach to tackle a formidable foe - wheat stem rust
Amount £3,500 (GBP)
Organisation Royal Society of Biology (RSB) 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2019 
End 09/2019
 
Description Zespri PhD Studentship
Amount $157,934 (NZD)
Organisation Zespri Group Limited 
Sector Private
Country New Zealand
Start 07/2018 
End 06/2021
 
Title A clone resource of Magnaporthe oryzae effectors that share sequence and structural similarities across host-specific lineages 
Description We describe a clone resource of 195 effectors of the blast fungus Magnaporthe oryzae. These clones are freely available as Golden Gate compatible entry plasmids. Our aim is to provide the community with an open source effector clone library to be used in a variety of functional studies. Plant pathogens secrete effectors that play central roles in subjugating plants for colonization. Effectors typically have signal peptides, and occasionally carry conserved folds and motifs (Lo Presti et al.,2015; Franceschettiet al., 2017). Magnaporthe oryzae(Syn. Pyricularia oryzae) is an important plant pathogenthat is able to infect around 50 species of both wild and cultivated grasses including important cereals of the Poaceae family. M. oryzaeis mostly known to cause rice blast but can also cause disease on other crops such as barley, wheat, foxtail millet, and finger millet. The global population of Magnaporthe is composed of genetically differentiated lineages which, in some cases, still exhibit a measurable degree of gene flow (Gladieux et al.,2018). Fungal isolates from each of those lineages show a preference for a specific host and also encode distinct repertoires of effector genes (Yoshida et al.,2016). The first genomic sequence of Magnaporthe oryzaewas released in 2005 for the lab strain 70-15 and allowed to predict a large set of secreted proteins such as enzymes involved in secondary metabolism and virulence-associated factors including putative effectors (Dean et al.,2005). Recently an increasing number of genome sequences of isolates from different lineages have become available, allowing the research community to perform comparative genomic studies (Chiapello et al.,2015; Yoshida et al.,2016). Many of the validated effectors of M. oryzae are known as the MAX (MagnaportheAVRs and ToxB like) effectors. These effectors, while showing little primary sequence similarity, share a conserved structural fold composed of 6 ß-sheets alternating in an anti-parallel manner (de Guillenet al., 2015). The MAX family has been largely expanded in Magnaportheas those effectors account for 5-10% of the effector repertoire and for 50% of the already cloned effectors of Magnaporthe(de Guillenet al., 2015). Indeed, the identification of structural motifs enables more sensitive predictions of effectors from pathogen genomes compared to sequence similarity searches (Franceschettiet al., 2017). The aim of this project was to computationally identify a set of M. oryzaeeffectors from the main host-specific lineages and develop an open access clone resource for functional analyses. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? Yes  
Impact Distributed >100 samples to several laboratories via addgene. 
URL http://doi.org/10.5281/zenodo.3268775
 
Title Coomassie Brilliant Blue (CBB) staining for Rubisco is an appropriate loading control for western blots from plant material 
Description Background - Having an adequate loading control for a western blot is essential for the interpretation of the results. There are two common loading control methods for western blots of proteins from plant material: (i) using specific antibodies to detect for a reference protein, such as actin, tubulin, or GAPDH (Li et al. 2011); and (ii) treating the membrane with Ponceau or Coomassie stains to assay the levels of a constitutively expressed protein, such as Rubisco (Zhang et al. 2017; Lim et al. 2018; Zhuo et al. 2014). Comparative studies in the mammalian biology field have determined that these loading control methods-antibody detection versus staining-are roughly equivalent in their linearity (Romero-Calvo et al. 2010; Wilender and Ekblad, 2011), and thus serve as comparable quality controls. In the plant biology field, it is sometimes debated as to whether staining for Rubisco is an appropriate loading control, due to the high abundance of this protein in the cell. Results - We undertook an experiment to determine whether the range of detection of staining for Rubisco is similar to that of antibody-based detection of a reference protein. We loaded total protein extract from Nicotiana benthamiana leaves transiently expressing GFP into a gel at a range of effective sample volumes, and the resulting western blot was treated with anti-GFP antibodies as well as stained with Coomassie Brilliant Blue (CBB) (Fig. 1a). Quantification of the GFP bands in the western blot and the Rubisco bands in the CBB stained membrane indicated that these detection methods have similar linear correlations between the loading volumes of total protein extract and the detectable band intensities (Fig. 1b). In addition, quantification of a random protein of lower abundance in the CBB stained membrane also showed similar linearity (Fig. 1b). Conclusions - These results indicate that CBB staining for Rubisco can be an appropriate loading control for western blots from plant material. This representative experiment is consistent with results from other western blot experiments that we routinely perform in our laboratory. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact Feedback from social media indicates it is useful to many others. 
URL https://zenodo.org/record/2557821#.XH2gji2cbYI
 
Title Developed a collection strategy for Xylella insect vector population structure analyses in the UK 
Description Developed strategy and coordinated sampling insect vector populations at at least four different habitats at 5 locations in the UK at four time points. 
Type Of Material Improvements to research infrastructure 
Year Produced 2019 
Provided To Others? No  
Impact Assessment of population structure of Xylella fastidiosa insect vectors in the UK. The data can be used to model Xylella fastidiosa spread in the UK if the pathogen is introduced. 
 
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 Isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing 
Description A method for isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact Fungal genomes are highly dynamic and often contain supernumerary mini-chromosomes. However, our knowledge about the role of mini-chromosomes in dynamic genome rearrangements and evolution is scarce. Mini-chromosomes are usually smaller then core-chromosomes and are variable in size and numbers between individuals of a species. Mini-chromosome occurence in fungi is well documented since decades, but many genomic projects have neglected them, mainly because it was technically challenging to identify them in whole genome assemblies. Here we present a protocol for isolation of mini-chromosomes for enrichment sequencing. This allows identification of mini-chromosomes in whole genome assemblies and thus comparative genomics analyses of core- and mini-chromosomes. 
URL https://www.protocols.io/view/isolation-of-supernumerary-mini-chromosomes-from-f-9t7h6rn
 
Title Mobile And Real-time Plant disEase (MARPLE) diagnostics 
Description Capitalising on advances in sequencing technology we developed MARPLE (Mobile And Real-time PLant disEase) diagnostics, the first operational system in the world using nanopore sequence technology for rapid diagnostics and surveillance of complex fungal pathogens in situ. Our partnership (JIC, CIMMYT and EIAR) and integration of the system with disease forecasting programmes has positioned Ethiopia as a world leader in pathogen diagnostics and forecasting. Generating results within 48 hours of field sampling, this new strategy is a revolution in plant disease diagnostics and will have far-reaching implications for how plant health threats are identified and tracked into the future. 
Type Of Material Biological samples 
Year Produced 2018 
Provided To Others? Yes  
Impact This new methodology opens up new opportunities for rapid diagnostic capacity for wheat yellow rust throughout the main wheat growing regions and permit sentinel monitoring of yellow rust races on an annual basis. Through this project, Ethiopia has now become the lead nation in Africa with a robust, rapid monitoring system for important transboundary diseases. 
URL https://acaciaafrica.org/marple-diagnostics/
 
Title Nanopore sequencing of genomic DNA from Magnaporthe oryzae isolates from different hosts 
Description We report long-range sequencing of eight isolates of Magnaporthe oryzae(Syn. Pyricularia oryzae) from wheat, rice, foxtail millet and goosegrass using nanopore MinION. Our aim is to obtain chromosome-level genome assemblies that are freely available for public access to be scrutinized for genome rearrangements and structural variation. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact New collaborations. Others used the open data for their own research. Data shared openly prior to publication in formal journals. 
URL https://zenodo.org/record/2564950#.XH2f5y2cbYI
 
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. In updated methodology, we combined RenSeq with PacBio sequencing to achieve even better definition of angiosperm immune receptor repertoires 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact Many genes that confer stem rust resistance in wheat have been cloned using this method. There was also a recent submission to Bioarxiv detailing the pan NLRome of Arabidopsis thalian- the corresponding paper has now been submitted to Cell - see https://www.biorxiv.org/content/10.1101/537001v1 
 
Title DIVAS collection of ash seed 
Description Collection of seed from 20 female ash trees in Norfolk with few symptoms of ash dieback. November 2018. DIVAS = Diversity in Ash. Trees are named after female singers. A portion of seed has been deposited at RBG Kew's long-term storage facility at Wakehurst Place and the remainder has been kept at JIC. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Germination of seed for planting at a site in Norfolk. 
 
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 
 
Title Nextstrain for wheat yellow rust 
Description The wheat yellow rust fungus (Puccinia striiformis f.sp. tritici) is the first plant pathogen to be added to an online open source platform, Nextstrain.org. The interactive data visualization tool displays genome data by reconstructing a "phylogeny" that illustrates the differences in the genetic makeup of bacterial, viral and fungal strains. This assists researchers investigating how new pathogen strains emerge and spread. Our recent addition of the yellow rust pathogen grants researchers worldwide access to genetic data to study the disease. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact The addition of Pst to the Nextstrain interface provides researchers the ability to easily study the diversity of strains on a global scale. 
URL https://nextstrain.org/community/saunderslab/PST
 
Description Aphid 
Organisation International Centre of Insect Physiology and Ecology (ICIPE)
Country Kenya 
Sector Academic/University 
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 breeding for durable disease resistance 
Organisation North Carolina State University
Department Department of Plant Pathology
Country United States 
Sector Academic/University 
PI Contribution Statistical analysis of durability of disease resistance Contributing to a review of durable resistance
Collaborator Contribution Coordinating a review of durable resistance
Impact Review in Annual Review of Plant Pathology about durability of disease resistance Paper in Frontiers in Plant Science about durable resistance of wheat to Stagonospora nodorum blotch
Start Year 2017
 
Description Collaboration on breeding for durable disease resistance 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution Statistical analysis of durability of disease resistance Contributing to a review of durable resistance
Collaborator Contribution Coordinating a review of durable resistance
Impact Review in Annual Review of Plant Pathology about durability of disease resistance Paper in Frontiers in Plant Science about durable resistance of wheat to Stagonospora nodorum blotch
Start Year 2017
 
Description Collaboration on dispersal of wheat rust pathogens 
Organisation Aarhus University
Department Department of Agroecology
Country Denmark 
Sector Academic/University 
PI Contribution Writing a workpackage for an EU Horizon 2020 research programme, RustWatch. JIC is working on the implications of globalisation or transport and plant breeding for control of rust diseases of cereals in Europe.
Collaborator Contribution Contributing to the workpackage. AUP is working with JIC on investigating the impact of globalisation on spread of rust diseases of wheat. AU and LPPRC will work with JIC and AUP on applications of the research to proposing improved methods of rust control.
Impact The RustWatch application has been funded from June 2018 for four years. JIC's work will start in Year 2 of the project.
Start Year 2017
 
Description Collaboration on dispersal of wheat rust pathogens 
Organisation University of Agriculture
Country Pakistan 
Sector Academic/University 
PI Contribution Writing a workpackage for an EU Horizon 2020 research programme, RustWatch. JIC is working on the implications of globalisation or transport and plant breeding for control of rust diseases of cereals in Europe.
Collaborator Contribution Contributing to the workpackage. AUP is working with JIC on investigating the impact of globalisation on spread of rust diseases of wheat. AU and LPPRC will work with JIC and AUP on applications of the research to proposing improved methods of rust control.
Impact The RustWatch application has been funded from June 2018 for four years. JIC's work will start in Year 2 of the project.
Start Year 2017
 
Description Collaboration on emerald ash borer 
Organisation East Malling Research
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 A paper has been published 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 A paper has been published 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 A paper has been published on response of UK Fraxinus excelsior to emerald ash borer in controlled trials.
Start Year 2016
 
Description Collaboration on fungicide resistance in cereal powdery mildew 
Organisation North Carolina State University
Department Department of Plant Pathology
Country United States 
Sector Academic/University 
PI Contribution Experiments on fungicide resistance in wheat powdery mildew
Collaborator Contribution Experiments on fungicide resistance in wheat powdery mildew
Impact Papers in preparation
Start Year 2015
 
Description Collaboration on fungicide resistance in cereal powdery mildew 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution Experiments on fungicide resistance in wheat powdery mildew
Collaborator Contribution Experiments on fungicide resistance in wheat powdery mildew
Impact Papers in preparation
Start Year 2015
 
Description Collaboration with Cornell University on molecular evolution of fungicide resistance 
Organisation Cornell University
Country United States 
Sector Academic/University 
PI Contribution Hypothesis about molecular evolution of resistance to a fungicide used to control powdery mildew
Collaborator Contribution Test of a hypothesis about molecular evolution of resistance to a fungicide used to control powdery mildew, by sequencing a candidate resistance gene in isolates in Cornell's collection
Impact Work is in progress as of March 2019. Interdisciplinary collaboration: molecular genetics, molecular evolution, plant pathology.
Start Year 2018
 
Description Collaboration with Earlham Institute on genotypic variation in circadian rhythms 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Statistical analysis of circadian rhythms in plant genotypes.
Collaborator Contribution Experiments on circadian rhythms in plant genotypes.
Impact Draft paper.
Start Year 2018
 
Description Collaboration with East Malling Research 
Organisation East Malling Research
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We are sequencing and annotating the genome of the woolly apple aphid, a serious pest of apple trees
Collaborator Contribution The collaborator provided frozen aphids for genome and RNA sequencing
Impact We will obtain the complete genomes and transcriptomes of the woolly apple aphid, which is in a distinct clade in the aphid phylogenetic tree and useful for comparative genome analyses among aphids.
Start Year 2018
 
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 Academic/University 
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 John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Exchange of materials/expertise. Exchange of visits. The collaboration includes Mark Banfield, John Innes Centre.
Collaborator Contribution Exchange of materials/expertise. Exchange of visits.
Impact Multi-disciplinary collaboration: genetics, plant pathology, plant biology, biochemistry, biophysics, genomics, bioinformatics. Royal Society International Exchanges. 2018. "Retooling rice immunity for resistance against rice blast disease". £12,000 Varden, F.A., Saitoh, H., Yoshino, K., Franceschetti, M., Kamoun, S., Terauchi, R., and Banfield, M.J. 2019. Cross-reactivity of a rice NLR immune receptor to distinct effectors from the blast pathogen leads to partial disease resistance. bioRxiv, doi:https://doi.org/10.1101/530675. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. De la Concepcion, J.C., Franceschetti, M., Maqbool, A., Saitoh, H., Terauchi, R., Kamoun, S., and Banfield, M.J. 2018. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. Nature Plants, 4:576-585. 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. 2018. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions, 31:34-45. Fujisaki, K., Abe, Y., Kanzaki, E., Ito, K., Utsushi, H., Saitoh, H., Bialas, A., Banfield, M., Kamoun, S., and Terauchi, R. 2017. An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity. bioRxiv, doi:https://doi.org/10.1101/239400. 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 Prof. Ryohei Terauchi 
Organisation University of Kyoto
Country Japan 
Sector Academic/University 
PI Contribution Exchange of materials/expertise. Exchange of visits. The collaboration includes Mark Banfield, John Innes Centre.
Collaborator Contribution Exchange of materials/expertise. Exchange of visits.
Impact Multi-disciplinary collaboration: genetics, plant pathology, plant biology, biochemistry, biophysics, genomics, bioinformatics. Royal Society International Exchanges. 2018. "Retooling rice immunity for resistance against rice blast disease". £12,000 Varden, F.A., Saitoh, H., Yoshino, K., Franceschetti, M., Kamoun, S., Terauchi, R., and Banfield, M.J. 2019. Cross-reactivity of a rice NLR immune receptor to distinct effectors from the blast pathogen leads to partial disease resistance. bioRxiv, doi:https://doi.org/10.1101/530675. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. De la Concepcion, J.C., Franceschetti, M., Maqbool, A., Saitoh, H., Terauchi, R., Kamoun, S., and Banfield, M.J. 2018. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. Nature Plants, 4:576-585. 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. 2018. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions, 31:34-45. Fujisaki, K., Abe, Y., Kanzaki, E., Ito, K., Utsushi, H., Saitoh, H., Bialas, A., Banfield, M., Kamoun, S., and Terauchi, R. 2017. An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity. bioRxiv, doi:https://doi.org/10.1101/239400. 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 Prof. Tofazzal Islam 
Organisation Bangabandhu Sheikh Mujibur Rahman Agricultural University
Country Bangladesh 
Sector Academic/University 
PI Contribution Exchange of materials/expertise.
Collaborator Contribution Exchange of materials/expertise. Professor Islam's group is working on genomic and postgenomic analyses of wheat blast fungus, which recently emerged as a devastating pathogen of wheat in Bangladesh. He is leading a dream project titled "Mining biogold from Bangladesh"where they identified more than 600 plant probiotics potential for using as biofertilizer and biopesticides. Another important focus of Prof. Islam's group is to analyze the genomes of a number of plant probiotic bacteria potential for biocontrol of major phytopathogens and biofertilization of rice and wheat. In collaboration with Prof. Sophien Kamoun, Prof. Islam is dedicated to the promotion of open science and open data sharing (e.g., open wheat blast www.wheatblast.net) which they think very critical for rapidly addressing the emerging plant diseases.
Impact #OpenWheatBlast http://openwheatblast.net https://twitter.com/search?q=%23OpenWheatBlast&src=typd Win, J., Chanclud, E., Reyes-Avila, C.S., Langner, T., Islam, T., and Kamoun, S. 2019. Nanopore sequencing of genomic DNA from Magnaporthe oryzae isolates from different hosts. Zenodo, http://doi.org/10.5281/zenodo.2564950. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. Gupta, D.R., Reyes Avila, C., Win, J., Soanes, D.M., Ryder, L.S., Croll, D., Bhattacharjee, P., Hossain, S., Mahmud, N.U., Mehebub, S., Surovy, M.Z., Rahman, M., Talbot, N.J., Kamoun, S., and Islam, T. 2018. Cautionary notes on use of the MoT3 diagnostic assay for Magnaporthe oryzae Wheat and rice blast isolates. Phytopathology, in press. Islam, T., Croll, D., Gladieux, P., Soanes, D., Persoons, A., Bhattacharjee, P., Hossain, S., Gupta, D., Rahman, Md.M., Mahboob, M.G., Cook, N., Salam, M., Surovy, M.Z., Bueno Sancho, V., Maciel, J.N., Nani, A., Castroagudin, V., de Assis Reges, J.T., Ceresini, P., Ravel, S., Kellner, R., Fournier, E., Tharreau, D., Lebrun, M.-H., McDonald, B., Stitt, T., Swan, D., Talbot, N., Saunders, D., Win, J., and Kamoun, S. 2016. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biology, 14:84.
Start Year 2016
 
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 University of Lisbon, Portugal 
Organisation University of Lisbon
Country Portugal 
Sector Academic/University 
PI Contribution I involved colleagues at University of Lisbon in the BRIGIT project and the sequencing of genomes and transcriptomes of insect vectors of Xylella fastidiosa. I invited colleague to give lecture and exchange knowledge with BRIGIT consortium members at consortium meeting in Edinburgh, July 2019, and at the BRIGIT satellite meeting before the IS-MPMI in Glasgow, July 2019. We co-authored on a publication.
Collaborator Contribution Partners collected insects in Portugal and send these to us for sequencing. Partners engaged with BRIGIT consortium members.
Impact Generated new knowledge on population structures of X. fastidiosa insect vectors. Co-published the genome sequence of the spittle bug Philaenus spumarius as a dataset in Zenodo (DOI:10.5281/zenodo.3368385) and agreed to sequence more European Philaenus species that are potential vectors of Xylella.
Start Year 2018
 
Description Collaboration with University of Stellenbosch 
Organisation University of Stellenbosch
Country South Africa 
Sector Academic/University 
PI Contribution We will sequence and annotate the genome of one clone of Diuraphis noxia, a serious pest of wheat in South Africa and many other countries worldwide
Collaborator Contribution Contributed frozen materials for D. noxio aphids
Impact We generated a genome assembly of D. noxia.
Start Year 2016
 
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 Pais, M., Yoshida, K., Giannakopoulou, A., Pel, M.A., Cano, L.M., Oliva, R.F., Witek, K., Lindqvist-Kreuze, H., Vleeshouwers, V.G.A.A., and Kamoun, S. 2017. Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen. BMC Evolutionary Biology, 5:93. 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, 31:795-802. 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
Country Ireland 
Sector Public 
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 Collaboration with plant breeding company on an iCASE studentship 
Organisation Sesvanderhave
Country Belgium 
Sector Private 
PI Contribution PhD student in the laboratory is generating aphid genome sequence data and population structure analyses. Student is enrolled in supervisory system at JIC and engages with experienced researchers in the lab and at JIC.
Collaborator Contribution Provides staff and resources for conducting the study and involved student in research project at the company for 3 months.
Impact PhD student made excellent progress with his research and generated data useful for the host lab at JIC and the industrial partner.
Start Year 2016
 
Description Deep learning for discriminating crop diseases and breeding resistant varieties 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Research on deep learning for discriminating and quantifying different plant diseases.
Collaborator Contribution Access to field trial sites. Knowledge of current varieties. Knowledge of plant diseases in field situations. Costs of hosting iCASE student.
Impact Ongoing project.
Start Year 2018
 
Description Deep learning for discriminating crop diseases and breeding resistant varieties 
Organisation Limagrain
Country France 
Sector Private 
PI Contribution Research on deep learning for discriminating and quantifying different plant diseases.
Collaborator Contribution Access to field trial sites. Knowledge of current varieties. Knowledge of plant diseases in field situations. Costs of hosting iCASE student.
Impact Ongoing project.
Start Year 2018
 
Description Deep learning for discriminating crop diseases and breeding resistant varieties 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution Research on deep learning for discriminating and quantifying different plant diseases.
Collaborator Contribution Access to field trial sites. Knowledge of current varieties. Knowledge of plant diseases in field situations. Costs of hosting iCASE student.
Impact Ongoing project.
Start Year 2018
 
Description Establishment of JENNIFER population of ash genotypes 
Organisation East Malling Research
Country United Kingdom 
Sector Charity/Non Profit 
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 collaboration with Fera, UK 
Organisation Fera Science Limited
Country United Kingdom 
Sector Public 
PI Contribution I involved colleauges at Fera in the BRIGIT project
Collaborator Contribution FERA colleagues lead Work Package 2 (WP2) of the BRIGIT project. The main goal of WP2 is to optimize and improve technologies for diagnostics of Xylella fastidiosa in diverse plant species, including trees. Another FERA colleague is involved in WP3 of the BRIGIT project. The main goal of WP3 is to better understand the migration patterns of X. fastidiosa insect vectors in the UK. FERA colleagues are involved in the social sciences aspect of WP4 of the BRIGIT project. The main goal of WP4 is to model the potential pathways of spread of X. fastidiosa in the UK.
Impact Protocol optimization for diagnostics of Xylella fastidiosa has started.
Start Year 2018
 
Description Formal collaboration with Forest Research, England and Scotland 
Organisation Forest Research
Country United Kingdom 
Sector Public 
PI Contribution Involved colleagues at Forest Research in the BRIGIT project
Collaborator Contribution Collaborator 1 at Forest Research leads Work Package 1 (WP1) of the BRIGIT project. The main aims of WP1 are to develop activities to involved citizen scientists and stakeholders in the BRIGIT project and develop databases with information on various aspects of Xylella fastifiosa and its insect vectors. Collaborator 2 at Forest Research is involved in WP2 of the BRIGIT project. WP2 is focused on developing diagnostics for X. fastidiosa and is lead by colleagues at Fera. Collaborator 3 at Forest Research is involved in developing the social sciences aspect of WP4 of the BRIGIT project.
Impact Planning of citizen scientist and stakeholder activities have started.
Start Year 2018
 
Description Formal collaboration with Natural Environment Research Council 
Organisation Centre for Ecology & Hydrology (CEH)
Country United Kingdom 
Sector Public 
PI Contribution Involved Natural Environment Research Council colleague in the BRIGIT project
Collaborator Contribution 1. Leads Work Package 4 of the BRIGIT project; 2. Models the potential pathways of spread of Xylella fastidiosa in the UK
Impact Started to collate data from project partners to do the modelling and interacts with scientists in Europe to help develop the model.
Start Year 2018
 
Description Formal collaboration with Science and Advice for Scottish Agriculture 
Organisation Science and Advice for Scottish Agriculture
Country United Kingdom 
Sector Public 
PI Contribution I involved colleagues at SASA in the BRIGIT project
Collaborator Contribution Colleagues at SASA are involved in Work Package (WP) 2 and 3 of the BRIGIT project. WP2 is aimed at optimizing and further developing technologies for diagnostics of Xylella fastidiosa within BRIGIT, and WP3 is aimed at better understanding the migration of X. fastidiosa insect vectors in the UK.
Impact Work on WP2 and WP3 have started
Start Year 2018
 
Description Formal collaboration with University of Salford 
Organisation University of Salford
Country United Kingdom 
Sector Academic/University 
PI Contribution Involved colleague in the BRIGIT project.
Collaborator Contribution Colleague participates in Work Package (WP4) of the BRIGIT project. WP4 is modelling the potential pathways of spread of Xylella fastidiosa in the UK.
Impact Collation of data for the modelling of WP4 has started.
Start Year 2018
 
Description Formal collaboration with University of Stirling 
Organisation University of Stirling
Country United Kingdom 
Sector Academic/University 
PI Contribution Involved colleague in the BRIGIT project.
Collaborator Contribution Colleague participates in Work Package 4 (WP4) of the BRIGIT project. The aim of WP4 is to model the potential pathways of spread of Xylella fastidiosa in the UK.
Impact Collating data for starting the modelling of WP4 of BRIGIT has started.
Start Year 2018
 
Description Formal collaboration with University of Sussex 
Organisation University of Sussex
Country United Kingdom 
Sector Academic/University 
PI Contribution I involved collaboratort in the BRIGIT project
Collaborator Contribution Collaborator contributes Entomology expertise to the BRIGIT project
Impact 1. Funding of the BRIGIT project by UKRI Strategy Priority Fund. 2. Access to UK database of amateur and professional entomologists to collect candidate insect vector species of Xylella fastidiosa.
Start Year 2018
 
Description Formal research collaboration with Academia Sinica, Taipei, Taiwan 
Organisation Academia Sinica
Department Institute of Plant and Microbial Biology
Country Taiwan, Province of China 
Sector Academic/University 
PI Contribution Development of the research question, approaches and methodology. Provided knowledge about the biology of the organisms, collected biological material, extracted DNA and generated raw reads of genome sequence data. Invited groupe leader at Academia Sinica to the BRIGIT consortium meeting of July 2019 in Edinburgh.
Collaborator Contribution Assembled the genome reads into contigs and annotated the genomes. Contributed a talk and exchanged knowlede on Xylella comparative genome analyses with WP2 members of the BRIGIT consortium at the BRIGIT consortium meeting of July 2019 in Edinburgh. Contributed a talk at the BRIGIT satellite meeting before the IS-MPMI meeting of July 2019, Glasgow.
Impact Several co-authored publications. Exchanged information on Xylella genome sequence comparisons that is useful for developing diagnostics protocols in WP2 of the BRIGIT project.
Start Year 2014
 
Description Formal research collaboration with Chinese Academy of Agricultural Sciences (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 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 Colleagues 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 Institute of Plant Protection, Poznan, Poland 
Organisation Institute of Plant Protection, National Research Institute
Country Poland 
Sector Public 
PI Contribution My lab hosted a PhD student of the Institute of Plant Protection at JIC, Oct 2016 - Mar 2017. The student 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 were 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 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 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 PhD student of Sultan Qaboos University at JIC 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.
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 Formal research collaboration with 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 Knowledge, resources and materials for the insect-plant interaction research system.
Collaborator Contribution Colleague's 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 co-authored on publications. We assisted postdoctoral researchers with the writing of a succesful Future Leader Fellowship application.
Start Year 2013
 
Description Formal research collaboration with 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 ESALQ group leader to Hogenhout lab, 11-18 Sep. 2013. - Visit of ESALQ group leader to Hogenhout lab, 20-24 Oct. 2014. - Visit of ESALQ postdoctoral researcher to Hogenhout 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. 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 Co-authored several publications.
Start Year 2013
 
Description Formal research collaboration with 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 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 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 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 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" 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 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 co-organized the Vector-Borne Diseases in the UK meetings, 3-4 Dec 2018 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 Retaining the Ashes collaboration with Warwick and E.Malling 
Organisation East Malling Research
Country United Kingdom 
Sector Charity/Non Profit 
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. As well as coordinating the project, JIC is working on plant pathology, entomology and transcriptomics.
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. EMR is working on different aspects of plant pathology, complementary to the work at JIC. Warwick is working on metabolomics, coordinated with research at JIC on transcriptomics.
Impact Response-mode grant proposal funded by BBSRC. Multi-disciplinary: pathology, entomology, genetics, population genetics, ecology, forestry, analytical chemistry, plant molecular biology.
Start Year 2017
 
Description Retaining the Ashes collaboration with Warwick and E.Malling 
Organisation Max Planck Society
Department Max Planck Institute for Chemical Ecology
Country Germany 
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. As well as coordinating the project, JIC is working on plant pathology, entomology and transcriptomics.
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. EMR is working on different aspects of plant pathology, complementary to the work at JIC. Warwick is working on metabolomics, coordinated with research at JIC on transcriptomics.
Impact Response-mode grant proposal funded by BBSRC. Multi-disciplinary: pathology, entomology, genetics, population genetics, ecology, forestry, analytical chemistry, plant molecular biology.
Start Year 2017
 
Description Retaining the Ashes 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. As well as coordinating the project, JIC is working on plant pathology, entomology and transcriptomics.
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. EMR is working on different aspects of plant pathology, complementary to the work at JIC. Warwick is working on metabolomics, coordinated with research at JIC on transcriptomics.
Impact Response-mode grant proposal funded by BBSRC. Multi-disciplinary: pathology, entomology, genetics, population genetics, ecology, forestry, analytical chemistry, plant molecular biology.
Start Year 2017
 
Title Annotation of genes encoding long non-coding RNAs in aphid genomes 
Description We developed a pipeline to annotate genes for long non-coding RNAs in aphid genomes 
Type Of Technology Software 
Year Produced 2018 
Impact We have the sequences of aphid candidate long non-coding RNAs 
 
Title Improve aphid genome assembly pipeline 
Description We optimized methods to improve aphid genome assemblies using existing software 
Type Of Technology Software 
Year Produced 2018 
Impact We obtained high quality chomosome level assemblies of aphid genomes 
 
Title Improved aphid genome annotation pipeline 
Description We work with the Earlham Institute to optimize annotation of aphid genomes 
Type Of Technology Software 
Year Produced 2019 
Impact Improved annotation of aphid genomes. 
 
Title K-PIE: using K-means algorithm for Percentage Infection symptoms Estimation 
Description The K-means algorithm is one of the most effective clustering methods that has been widely used in plant disease detection. Herein, we developed a script termed K-PIE (K-means algorithm for Percentage Infection symptoms Estimation) that utilises the k-means algorithm to analyse images of both yellow and stem rust infected wheat leaves to estimate the percentage of disease symptoms based on colour analysis. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2019 
Impact This method has been adopted for rapid quantification of disease symtoms. 
URL https://zenodo.org/record/3584148#.XmISpy2caUk
 
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 #MPMI2019Posters 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact We published the Kamoun Lab posters presented at #ICMPMI2019 Congress on Molecular Plant-Microbe Interactions, Glasgow, July 14-18, on @ZENODO_ORG.

Kudos to all authors for their amazing contributions!

Joe Win, Mauricio Contreras, Benjamin Petre, Tolga O Bozkurt, Martin H Schattat, Jan Sklenar, Sophien Kamoun. (2019). Host-interactor screens of RXLR effectors reveal plant processes manipulated by Phytophthora. Zenodo. http://doi.org/10.5281/zenodo.3351297

Mauricio Contreras, Benjami
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/186817612845/mpmi2019posters-we-published-the-kamoun-lab
 
Description #OpenWheatBlast 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Wheat blast is a fearsome fungal disease of wheat. It was first discovered in Paraná State of Brazil in 1985. It spread rapidly to other South American countries such as Bolivia, Paraguay, and Argentina, where it infects up to 3 million hectares and causes serious crop losses. Wheat blast was also detected in Kentucky, USA, in 2011. Wheat blast is caused by a fungus known as Magnaporthe oryzae (syn. Pyricularia oryzae). There is a risk that wheat blast could expand beyond South America and threaten food security in wheat growing areas in Asia and Africa.

In February 2016, wheat blast was spotted in Bangladesh- its first report in Asia. Wheat is the second major food source in Bangladesh, after rice. The blast disease has, so far, caused up to 90% yield losses in more than 15000 hectares. Scientists fear that the pathogen could spread further to other wheat growing areas in South Asia.

The Twitter hashtag #openwheatblast serves as a communication tool to provide the latest on this fearsome disease and update a broad audience of news related to the ongoing pandemic.
Year(s) Of Engagement Activity 2016,2017,2018,2019
URL https://twitter.com/search?q=kamounlab%20openwheatblast&src=typd
 
Description 2Blades: the story behind the scientist 
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 We sat down with Sophien to find out more about the story behind the scientist:

Could you explain your research in 5 words?
Never bet against the pathogen.

Okay, now in a few more words..
Plants have an immune system, and it's complicated. This drives rapid evolution of pathogens, so we aim to understand the similarities in mechanisms of virulence and adaptation between plant pathogens and the disease-resistance toolkit and regulatory networks that underlie plant immunity.

Could you explain one technique you use regularly?
CRISPR-Cas9 gene editing. We love it, it's totally transformed how we do research. The best way to explain this is that the genome is like a book, consisting of text, and with CRISPR-Cas9 we can modify just a few specific letters in the book. This is the ultimate in precision for genetic modification.

What about your field of research is most exciting to you right now?
The most exciting area to me is how we're finding evolutionary similarities between immune receptors from different plant species, in terms of how they activate immunity. These similarities are both evolutionary and functional.

What keeps you busy when you're not in the lab?
Traveling, walking, movies, food.

What would you be doing if you weren't a scientist?
I would be a scientist - there's no other option! I would be a scientist even if wasn't paid for it!

What's the most enjoyable thing about your job?
The sense of excitement when you discover something new and then sharing that experience with your colleagues.

How has the 2Blades Foundation been beneficial to your work?
2Blades has brought a high degree of professionalism and expertise to The Sainsbury Laboratory in terms of our capacity to interact with industrial partners. We didn't have this before, so it's been a highly synergistic interaction.
Year(s) Of Engagement Activity 2019
URL http://2blades.org/voices/prof-sophien-kamoun/
 
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 Adaptive Agronomic Merit Tool 
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 James Brown developed the concept for the Adaptive Agronomic Merit tool and worked with AHDB staff to refine the version of the tool which will shortly be released. This enables farmers to choose crop varieties which maximise yield potential, minimise risks of unexpected variable costs, or a balance between the two.
Year(s) Of Engagement Activity 2018,2019
 
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. James Brown has been invited to remain on the committee for a further three years from 2019 to 2021, making 12 years in total.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
URL https://cereals.ahdb.org.uk/varieties/ahdb-recommended-lists.aspx
 
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 AI in Biology 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I organised a workshop on Artificial Intelligence in Biology to discuss challenges amongst the community.
Year(s) Of Engagement Activity 2018
 
Description AI talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk on "Deep Learning for Disease Surveillance" at a workshop on AI for plant biology and agriculture, ATI, 16th December 2019
Year(s) Of Engagement Activity 2019
 
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 An Exclusive Interview with Sophien Kamoun FRS regarding Genome Editing Technology and Wheat Blast 
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 An Exclusive Interview with Sophien Kamoun FRS regarding Genome Editing Technology and Wheat Blast by Bangladesh Channel 24
Year(s) Of Engagement Activity 2019
URL https://youtu.be/yaPJF-p3zgE
 
Description BASF visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to BASF scientists involved in plant protection and biotechnology on current research on fusarium head blight and opportunities for collaboration with scientists at JIC across a broad spectrum of plant and microbial research relevant to the area of crop protection.
Year(s) Of Engagement Activity 2018
 
Description BBC Farming Today Interview 25th October 2018 
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 Interview for BBC Farming Today on the CJEU ruling on Genome Editing as a form of genetic modification, subject to the same regulation as transgenic crops, and the likely effect of this ruling on agricultural innovation in Europe. The interview covered genome editing technologies, the potential for crop improvement, the details of the ruling, the contrast with other international jurisdications, and the potential effect on agriculture in Europe.
Year(s) Of Engagement Activity 2018
 
Description BBC Look East Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I was interviewed about the potential impact of Brexit on scientific research at The Sainsbury Laboratory and the Norwich Research Park. The interview covered the type of research carried out across the NRP, the degree of international collaboration, and the importance of European Commission funding to research projects.
Year(s) Of Engagement Activity 2018
 
Description BBC Radio Norfolk Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I was interviewed on the potential effects of Brexit on research at The Sainsbury Laboratory, John Innes Centre and across the Norwich Research Park. The interview covered the type of research underway across the institutes, the international nature of research at TSL and JIC and the importance of European Commission funding to research programmes in Norwich.
Year(s) Of Engagement Activity 2018
 
Description BGRI workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited speaker at conference.
Year(s) Of Engagement Activity 2018
 
Description BGRI: 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 Pathogenomics workshop outline:
Recent advances in next-generation sequencing technologies have provided new opportunities to integrate high-resolution genotype data into pathogen population studies. In this workshop, we will cover some of the bioinformatics analysis incorporated into the newly developed "Field Pathogenomics" technique. This approach utilizes next-generation sequence data to accelerate pathogen diagnostics, whilst providing detailed genotypic sub-structure of pathogen populations at an unprecedented resolution. Using next-generation sequence data generated from a selection of wheat yellow rust isolates, participants will determine how related they are to each other. To this aim, they will work stepwise through a series of exercises that will include (1) QC analysis of next-generation sequence data, (2) sequence alignments, (3) SNP calling, and (4) phylogenetic analysis. At the completion of the workshop participants will be familiar with next-generation sequence data and its potential for performing high-resolution population analyses.
Year(s) Of Engagement Activity 2018
 
Description BIAZA Field Conservation and Native Species Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation to raise awareness of the barberry carpet moth.
Year(s) Of Engagement Activity 2019
 
Description BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen 
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 In a paper recently published in BMC Evolutionary Biology, an international team of scientists describes how evasion of host immunity by a clonal variant of the potato blight pathogen Phytophthora infestans is associated with variation in gene expression without any apparent underlying genetic changes. We asked the senior authors of the study, Vivianne G.A.A. Vleeshouwers, Hannele Lindqvist-Kreuze and Sophien Kamoun, to tells us about their work.

What did you find?


Wild potato
We studied two different races of the Irish potato famine pathogen, and we discovered that the difference invirulence between these races could not be ascribed to a genetic difference but rather to a difference in the expression of the underlying virulence gene. This adds to our knowledge of how this important scourge on world agriculture evolves to evade plant immunity.

Why is this work important?

As our colleague Mark Gijzen tweeted, "is this a rare and unusual curiosity or another example of a widespread biological phenomenon?" Indeed, there are few other examples in related plant pathogens, including the soybean root rot pathogen that Mark studies. This finding has far reaching implications. It indicates that these pathogens can evolve even more rapidly than anticipated thus counteracting the efforts of plant breeders to deploy disease resistant crops.

Are potato varieties resistant to the pathogen available?

Yes, there are. But there are several examples of potato cultivars that were initially resistant to late blight when farmers started to grow them, but succumbed to the disease a few years later. The ability to switch on and off virulence genes such as we found in this research may partly explain why the pathogen is so effective at overcoming the plants defense barriers.

There are potato varieties initially resistant to Phytophthora infestans that have succumbed to late blight a few years later.
What is currently done to control the disease?

Susceptible potato cultivars must be protected by repeated applications of fungicides. If left unchecked, the disease will destroy the leaves and stems in a matter of days as in the pictured trial plot of potato varieties in the highlands of Peru.

Is chemical protection the only way to control late blight?

In nature, there are wild relatives of the cultivated potato and many of them can withstand the disease (see image of potato variety field trial). Breeders identify the genes in these plants and introduce them to cultivated potato through crosses or genetic transformation.

How did you put this project together?

We studied an Andean lineage of the Irish potato famine pathogen known as EC-1 so the project had an international flavor from day one. Ours was a wide reaching multinational collaboration bringing together scientists based in the UK, Japan, Netherlands, USA, Philippines, and Peru. It's how science often goes on these days. Experts from all over the world team up to solve problems, make new discoveries and advance our knowledge.

Anything you would have done differently?

DNA sequencing technology develops so fast that by the time the paper gets published you wish you could apply a different method. It also takes more time to analyze the data, write up the paper etc. than to generate the sequence data. This can be frustrating.

You posted the paper in bioRxiv before submission. Why?

Why not? Posting the article on bioRxiv enabled us to share our findings with our colleagues and hear about it from the community as soon as possible. The tweet by Mark Gijzen we referred to above is an example of such feedback. Posting a preprint relieves some of the delays associated with publishing. It's a liberating feeling to finish writing up a paper and immediately share it with anyone who's interested.
Year(s) Of Engagement Activity 2018
URL https://blogs.biomedcentral.com/bmcseriesblog/2018/07/09/phenotypic-plasticity-pandemic-lineage-iris...
 
Description BarbRE project launch 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Annual project event to raise awareness of the role of Berberis in the life cycle of the wheat rust pathogens.
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/event/barberry-rust-explorer-launch-evening/
 
Description BarbRE website 
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 To raise awareness of the project and as a forum to advertise our launch event we generated a project-focused website: https://barbre.co.uk
Year(s) Of Engagement Activity 2019
URL https://barbre.co.uk
 
Description Bioinformatics & Wheat Genomics workshop - South Africa 
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 To train partners in South Africa in bioinformatics skills.
Year(s) Of Engagement Activity 2019
 
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 Breeders 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 Industry/Business
Results and Impact Breeder's Day at the JIC. A CASE PhD student from my lab (Alba Pacheco-Moreno) spent the day talking with agronomists, breeders, etc. about her work examining the relationship between soil dwelling, beneficial bacteria and different barley cultivars. This work aligns closely with our research in the Evolution sub-theme of Plant Health.
Year(s) Of Engagement Activity 2018
 
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 Chair of Insectary Platform Steering Committee 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Chair of committee that ensures that the JIC Insectary/Entomology Technology Platform is well managed, proactive, effective, state of the art and resourced to meet the Institutes' science needs.
Year(s) Of Engagement Activity 2017,2018,2019
 
Description Chair of Technical Platform Oversight Committee (TPOC) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Chair the committee that ensures that all JIC Technology Platforms are collectively well managed, proactive, effective, state of the art and resourced to meet the Institutes' science needs.
Year(s) Of Engagement Activity 2017,2018,2019
 
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 Cyrielle Ndougonna: Chair, Norwich Bioscience Institutes Africa Initiative (NBIAI) 
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 Cyrielle Ndougonna has been Chair of the Norwich Bioscience Institutes Africa Initiative (NBIAI) since 2019

The NBIAI is an interdisciplinary platform where all students and staff across the NBI can connect and share their interest in research, with a focus on Africa. It contributes to strengthening the interactions between the Institutes and their African research partners by supporting joint outreach and training programmes and by facilitating the integration of African researchers visiting the NBI campus.

The NBIAI is supported by the Earlham Institute, the John Innes Centre, the Quadram Institute and the Sainsbury Laboratory.
Year(s) Of Engagement Activity 2019,2020
URL https://twitter.com/NBI_Africa
 
Description Defra Ash Research Strategy 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Workshop on Defra Ash Research Strategy to develop policy on management of Chalara ash dieback in the UK. James Brown (JIC) gave a talk on prospects for evolution of resistance of ash to dieback by natural selection, and on possible trade-offs between resistance to dieback and responses to invertebrates.
Year(s) Of Engagement Activity 2019
 
Description Dhaka Tribune: Fighting the fungi that destroy wheat 
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 Newspaper article following interview by Bangladeshi science reporter Reaz Ahmed.

The article was on the front page of the Dhaka Tribune.

Scientists in UK, Bangladesh join hands in applying genome editing to develop a novel variety capable of withstanding the fearsome fungal disease - wheat blast


An international scientific collaboration is employing genome editing techniques to develop novel blast resistant wheat to save the second most important food crop in South Asia from a future devastation.

The move comes at a time when authorities in Bangladesh and in the Indian state of West Bengal are pursuing 'wheat holiday' policy - restricting wheat cultivation for a stipulated time in targeted areas - in a desperate attempt to curb the spread of deadly wheat blast disease.

This fungal disease has long been confined largely within the wheat growing regions of South America. But in 2016, it struck wheat fields of Bangladesh, in its first outbreak in Asia, causing colossal crop damage and sending alerts in bordering regions of India.

Scientists from United Kingdom and Bangladesh, involved in the process of developing blast resistant wheat through genome editing, told Dhaka Tribune that they have already identified the wheat gene where they are going to apply 'molecular scissors' and do the editing, thereby effectively driving away the fungi responsible for the blast in wheat fields.

"Once we're done with the task in our laboratory (in UK), hopefully by the end of this year we'll be sending the edited version to Bangladesh for Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) lab to do the necessary probing prior going for field test," Prof Dr Sophien Kamoun, Group Leader, Sophien Kamoun Group at the UK's The Sainsbury Laboratory (TSL) told this correspondent on Tuesday.

Tunisian-born Dr Sophien, a British Royal Society Fellow, made the science jargons easy for a layman's understanding as he explained, "The fungi hold a key and wheat has a lock and every time fungi get favourable weather they apply the key to unlock wheat thereby feasting on the plant. What essentially we'll do is fortify the lock system failing fungi's key in opening it."

Dr Sophien, a former plant pathology professor of Ohio State University, had joined hands with his TSL colleague Prof Nicholas J Talbot and other co-scientists in discovering the genome sequence of pathogen responsible for wheat blast when it first struck in Asia invading eight major wheat growing districts in Bangladesh in 2016.
Year(s) Of Engagement Activity 2019
URL https://www.dhakatribune.com/bangladesh/agriculture/2019/03/02/fighting-the-fungi-that-destroy-wheat
 
Description Dialogue with Drayton Manor regarding barberry carpet moth programme 
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 This was a formal meeting to raise awareness regarding the role of barberry in the wheat rust lifecycle. In addition, this led to a new research program developing as an outcome of these discussions.
Year(s) Of Engagement Activity 2018
 
Description Discovery of 'death switch' mechanism in plants may yield stronger crops: Scientists 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Chinese scientists have discovered a possible "death switch" mechanism in plant's immune system that triggers infected cells to self-destruct, thus limiting the spread of the disease and keeping other parts of the plant healthy, official media here reported on Friday. Scientists said the discovery provides clues to cell death control and immunity for plants, and they hope further research can lead to a new generation of disease-resistant crops that use significantly less pesticide and are more environmentally friendly.

The research was done by scientists from Tsinghua University and the Chinese Academy of Sciences' Institute of Genetics and Development Biology.

About 20 years ago, scientists discovered that plants, like animals, have robust immune systems that can protect them from pathogens including viruses, fungi, bacteria and parasites.

Plants also have a unique "lure and catch" immune response to deal with pathogens that have breached their cellular defence, but exactly how this worked remained unknown, Zhou Jianmin, a researcher at the institute and one of the main scientists behind the study was quoted by the state-run China Daily reported.

To probe this mystery, Zhou and his team investigated a protein called AvrAC, which is produced by a bacterial pathogen that causes black rot on cabbage. The bacterium injects AvrAC into plant cells, where it acts as a "biochemical weapon" weakening the plant's immune system.

They discovered that some plants have evolved to carry a resistance protein called ZAR1 that can detect bacterial proteins like AvrAC. These plants use special proteins as "bait" and trick the bacterial protein into attacking them instead. While the bait is being attacked, ZAR1 is activated to form a multiprotein structure called resistosome, Zhou said.

The resistosome inserts itself into the cell's membrane and triggers it to destroy itself along with the invading pathogens, thus protecting other healthy cells, he said.

In addition to discovering this defence mechanism, Zhou and his associates from the Tsinghua University created structural models of the resistosome from their research. This allows other scientists to examine its composition and functions more closely.

"The 'death switch' is usually harmless to the plant because it only affects diseased cells, which are a tiny portion of the entire plant," Zhou said.

"Understanding and taking advantage of this mechanism can help us create new disease-resistant crops that rely on their own immune system to fend off pathogens and thus greatly reduce the need of pesticide, which is good for the environment," he said.

Sophien Kamoun, a plant pathologist at the Sainsbury Laboratory in the United Kingdom, said in a video interview that the recent discovery is important because it shows what resistosome looks like for the first time and it proposes a "totally new model" for plant pathology and immunity.

The discovery is a huge step toward the "dream of designing new resistant genes from scratch. And once we know how the system works, we can harness it for the benefit of agriculture," he was quoted by the Daily as saying.

Kang Zhensheng, a professor of plant pathologist at Northwest Agriculture and Forestry University in Yangling, Shaanxi province, called the discovery a "milestone" that will "lead the fields of plant pathology and immunity for the foreseeable future".

Zhou Xueping, the director of the Chinese Academy of Agricultural Sciences' Institute of Plant Protection, said Chinese agriculture constantly faces serious threats from diseases and pests, and a good solution to these problems is to boost the crops' own immunity.

"Once we have a better understanding of the procedure, we might be able to create some intricate genetic designs that allow precise deterrence against diseases and pests, while ensuring crop yield," he said adding further research may lead to a new generation of disease-resistant crops.
Year(s) Of Engagement Activity 2019
URL https://www.newsnation.in/science/news/discovery-of-death-switch-mechanism-in-plants-may-yield-stron...
 
Description Discussions with DEFRA about ash research requirements 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Discussion with DEFRA officials about the impact of current research on ash dieback, notably research at JIC, for policy on control of ash dieback and for international trade in live plants, timber and firewood. These conclusions of the discussion fed into a strategy meeting held in January 2019 and will thus feed into a strategy document being written by DEFRA.
Year(s) Of Engagement Activity 2018
 
Description Engagement with BBSRC as part of the BRIGIT project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Have weekly meetings with policy makers at BBSRC about new policies that may be developed to reduce the risk of Xylella fastidiosa outbreaks in the UK
Year(s) Of Engagement Activity 2018,2019
 
Description Engagement with Defra, Forest Research and APHA as part of the BRIGIT project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Have weekly meetings with policy makers at Defra about new policies that may be developed to reduce the risk of Xylella fastidiosa outbreaks in the UK
Year(s) Of Engagement Activity 2018,2019
 
Description Engagement with Fera as part of the BRIGIT project 
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 Have weekly meetings with Fera about status of Xylella fastidiosa diagnostics that may influence new policies for reducing risk of X. fastidiosa outbreaks in the UK
Year(s) Of Engagement Activity 2018,2019
 
Description Engagement with Oxitec 
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 Regular meetings with Neil Morrison for supervisory meetings and discussing research progress of the iCASE studentship.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
 
Description Engagement with Syngenta 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Regular meetings with colleagues at Syngenta, Jealott's Hill, UK, and Switserland and USA to discuss project proposals and research progress on aphids.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
 
Description Engagement with the Royal Horticulticultural Society as part of the BRIGIT project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Third sector organisations
Results and Impact Have weekly meetings with staff member of RHS to develop a stakeholder engagement plan for BRIGIT
Year(s) Of Engagement Activity 2018,2019
 
Description Engaging Images Public Art and Poetry Exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Image competition to inspire engagement with NRP scientists.
Year(s) Of Engagement Activity 2019
 
Description European Fusarium Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Over 200 delegates from across the globe attended the meeting. My presentation sparked many questions and further discussions on the implications of our findings for improving the resistance of wheat to FHB and reducing the risk of mycotoxins accumulating in grain and posing a threat to consumers
Year(s) Of Engagement Activity 2018
 
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 Everything you wanted to know about research integrity but never dared to ask 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Sophien Kamoun's talk to the Norwich research Park PhD student. May 7, 2019.
Year(s) Of Engagement Activity 2019
URL https://www.slideshare.net/SophienKamoun/everything-you-wanted-to-know-about-research-integrity-but-...
 
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 Exploring the science behind taste and flavour at Norwich Food and Drink Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Volunteer with British Science Association.
Year(s) Of Engagement Activity 2018
 
Description FIRST INVITED SEMINAR SERIES 
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 FIRST INVITED SEMINAR SERIES

Kiki Kots, Wageningen University, The Netherlands
"Shining a light on oomcyete biology; live cell imaging of the Phytophthora cytoskeleton"
Monday November 11, 2019

Huang Tan, Shanghai Center for Plant Stress Biology, China
"Study the role of pectin in pathogen associated molecular pattern pattern (PAMP)-triggered inhibition of growth/immunity"
Monday October 14, 2019

Chuyun Gao, Nanjing Agricultural University, China
"NLR immune receptor Rpi-vnt1 provides light-dependent resistance against Irish famine pathogen by guarding chloroplast protein GLYK"
Thursday September 17, 2019

Alexandre Leary, Imperial College London
"A plant RabGAP negatively regulates autophagy and immunity to the Irish potato famine pathogen Phytophthora infestans"
Tuesday August 7, 2018

Soichiro Asuke, Kobe University, Japan
"Elucidating the genetic mechanism of host parasitic specialization of Pyricularia oryzae to wheat"
Tuesday June 5, 2018

Michael Schon, Gregor Mendel Institute of Molecular Plant Biology, Austria
"Utilizing RNA ends for tissue-specific transcriptome assembly and degradome analysis"
Friday February 16, 2018
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/188924706750/first-invited-seminar-series-fiss
 
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 Fighting the fungi that destroy wheat 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Scientists in UK, Bangladesh join hands in applying genome editing to develop a novel variety capable of withstanding the fearsome fungal disease - wheat blast


An international scientific collaboration is employing genome editing techniques to develop novel blast resistant wheat to save the second most important food crop in South Asia from a future devastation.

The move comes at a time when authorities in Bangladesh and in the Indian state of West Bengal are pursuing 'wheat holiday' policy - restricting wheat cultivation for a stipulated time in targeted areas - in a desperate attempt to curb the spread of deadly wheat blast disease.

This fungal disease has long been confined largely within the wheat growing regions of South America. But in 2016, it struck wheat fields of Bangladesh, in its first outbreak in Asia, causing colossal crop damage and sending alerts in bordering regions of India.

Scientists from United Kingdom and Bangladesh, involved in the process of developing blast resistant wheat through genome editing, told Dhaka Tribune that they have already identified the wheat gene where they are going to apply 'molecular scissors' and do the editing, thereby effectively driving away the fungi responsible for the blast in wheat fields.

"Once we're done with the task in our laboratory (in UK), hopefully by the end of this year we'll be sending the edited version to Bangladesh for Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) lab to do the necessary probing prior going for field test," Prof Dr Sophien Kamoun, Group Leader, Sophien Kamoun Group at the UK's The Sainsbury Laboratory (TSL) told this correspondent on Tuesday.

Tunisian-born Dr Sophien, a British Royal Society Fellow, made the science jargons easy for a layman's understanding as he explained, "The fungi hold a key and wheat has a lock and every time fungi get favourable weather they apply the key to unlock wheat thereby feasting on the plant. What essentially we'll do is fortify the lock system failing fungi's key in opening it."

Dr Sophien, a former plant pathology professor of Ohio State University, had joined hands with his TSL colleague Prof Nicholas J Talbot and other co-scientists in discovering the genome sequence of pathogen responsible for wheat blast when it first struck in Asia invading eight major wheat growing districts in Bangladesh in 2016.

Prof Dr Tofazzal Islam, who teaches biotechnology at Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, joined hands with them and together they launched an open source wheat blast website, creating a forum for world's scientific fraternity to look into a disease that the International Maize and Wheat Improvement Center (CIMMYT) fearedwas a potential threat to South Asia's future food security.
Year(s) Of Engagement Activity 2019
URL https://www.dhakatribune.com/bangladesh/agriculture/2019/03/02/fighting-the-fungi-that-destroy-wheat
 
Description Forest Pathology Workshop 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Workshop on Forest Pathology, held at Bodmin and Bodelva, Cornwall and Powderham Castle, Devon.
Year(s) Of Engagement Activity 2019
 
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 Gates Grand Challenges Event 
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 Invited to take part in discussion regarding the future of pathogen surveillance methodologies.
Year(s) Of Engagement Activity 2018
 
Description Growing the Future-a UK Plant Sciences Federation and a Royal Society of Biology report 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Growing the future is a report from the UK Plant Sciences Federation (UKPSF), a special advisory committee of the Royal Society of Biology. Launched in January 2019, the report highlights to policymakers and others the excellence of plant science in the UK, and its importance to the biosciences, the economy, and society both at home and around the world. In Growing the future, the UKPSF describes the potential of plant science to improve fundamental knowledge, enable better diet quality, increase crop productivity, enhance environmental sustainability and create new products and manufacturing processes.

The report section on Plant health highlighted our research on potato late blight which dates back to the 1990s and has established the fundamental knowledge that has now enabled commercialisation of the first GMO potato plants among various applications.

The report also highlighted our work on gene editing in tomato, notably the development of the fungus resistant tomato line Tomelo, which was highlighted by a picture taken from our publication Nekrasov, V., Wang, C., Win, J., Lanz, C., Weigel, D., and Kamoun, S. 2017. Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Scientific Reports, 7:482.
Year(s) Of Engagement Activity 2018,2019
URL https://www.rsb.org.uk/policy/groups-and-committees/ukpsf/about-ukpsf/growing-the-future-report
 
Description Growing the Future-a UK Plant Sciences Federation and a Royal Society of Biology report featuring Innovations in #PlantHealth by TSL scientists 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Growing the Future-a UK Plant Sciences Federation and a Royal Society of Biology report has featured Innovations in #PlantHealth by TSL scientists and the broader oomycete and gene editing communities.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/182471762520/growing-the-futurea-uk-plant-sciences
 
Description Hello kids, I'm a biologist! 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact My presentation to the 9-10 year old children of the British International School of Tunis. March 21, 2019.

Here you can find notes, acknowledgements and links to the videos:

Slide 1. The action shot is from this interview with CropLife International. More on my background can be found on the Wikipedia English and French pages, and these interviews "Stranger in a strange land: the experiences of immigrant researchers" and ISMPMI Interactions InterViews. For popular science writing, check the PlantVillage article "https://medium.com/@plantvillage/keeping-up-with-the-plant-destroyers-9c0047899683".

Slide 3. The Australian outback ~1994 with our clunky Ford Falcon. With @SaskiaHogenhout.

Slide 4. You go there to chase insects and instead insects start chasing you #fieldworkfail #Australia

Slide 5. This Scanning Electron Microscopy shot of a tiger beetle head is courtesy of Charles R. Krause who captured it in 1982 on a Hitachi S-500 SEM.

Slide 6. Rivacindela eburneola, Cicindelidae, Coleoptera. I took this shot in 1994 at Lake Gilmore, Western Australia.

Slide 7. The fastest running insect in the world. BBC Earth.

Slide 8. Ed Yong's National geographic piece on The Predator That Becomes Blind When It Runs After Prey.

Slide 9. Cornell University Daniel Zurek and Cole Gilbert study on how tiger beetles use their antennae to sense obstacles at high speed.

Slide 10. What's in this picture? #PlantBlindness

Slide 11. The time-lapse video of potato plants infected by the Irish famine pathogen Phytophthora infestans was produced by Remco Stam.

Slide 12. I received the image of the potato farmer from Dr. Tarlochan Thind, Punjab Agricultural University. He is quoted in this story about potato late blight in India.

Slide 13. Different varieties of potato are either destroyed by the blight pathogen Phytophthora infestans or fully resistant (immune). The photo is courtesy of Vivianne Vleeshouwers at Wageningen University.

Slide 14. This stunning animation of the bacterium Xanthomonas infecting tomato plants was produced by students at Halle University working with Prof. Ulla Bonas.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/183672043215/hello-kids-im-a-biologist
 
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 How to select a PhD lab? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact I regularly get this question from predocs. How do I select a PhD lab? How do I decide on a good supervisor? Should I select a lab based on a project? Below is a hodgepodge of the answers I generally give.
Year(s) Of Engagement Activity 2019
URL https://zenodo.org/record/3531916#.Xl6WJS2cbDY
 
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 International Cereal Rusts and Powdery Mildews Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited keynote speaker.
Year(s) Of Engagement Activity 2018
URL https://www.eiseverywhere.com/ehome/268483
 
Description Interview on Radio 4 Today program re GM crop regulation post Brexit 
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 Schools
Results and Impact Interview on Today program re GM crop regulation post Brexit
Year(s) Of Engagement Activity 2019
 
Description Interview with Matthew Gudgin on BBC Radio 
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 Sophien Kamoun's interview with Matthew Gudgin on BBC Radio following election as Fellow of the Royal Society. This includes a discussion of plant blindness.
Year(s) Of Engagement Activity 2018
URL http://kamounlab.tumblr.com/post/173740235230/sophiens-interview-with-matthew-gudgin-on-bbc
 
Description Introduction to bioinformatics and wheat genomics 
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 Workshop aims:
Expertise in the field of bioinformatics has become indispensable in most genetic or genomic research and applied approaches. This need has exceeded the level and rate at which plant genomics scientists have been trained in bioinformatics in South Africa. This workshop aimed to provide much-needed hands-on training in bioinformatics, wheat genomics and sequencing technologies by leading UK experts that are highly competent researchers and experienced trainers in these fields.
Year(s) Of Engagement Activity 2019
 
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 research seminar at CAS institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a research seminar at IGDB, Beijing, China on 16 Mar 2018. Research fellow Thomas Mathers in my lab also contributed a talk.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at iDiv, Leipzig, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited by PhD students to give a research presentation at the Integrative Biodiversity Research Institute (iDiv), Halle-Jena-Leipzig, Germany, 18 Apr 2018. I was hosted by Crispus Mbaluto, PhD student at iDiv.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at the Max Planck Institute, Cologne, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a research seminar at the Max Planck Institute for Plant Breeding, Cologne, Germany. Approximately 50 people, including PhD students, attended.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at the annual Life Sciences conference, Beijing, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk in a paralell session focused on insect pests at the Life Sciences Conference, Beijing, China, 28-31 Oct '19.
Year(s) Of Engagement Activity 2018
 
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 JIC student showcase 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact To provide examples of future career opportunities.
Year(s) Of Engagement Activity 2019
 
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 Keynote lecture at ICPP 2018: The Edge of Tomorrow - Plant Health in the 21st Century 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ICPP2018 International Congress of Plant Pathology Plenary Session - Plant Health is Earth's Wealth, Boston, USA, Monday, July 30, 2018

The talk was broadcast on a live stream and is available on YouTube https://youtu.be/MYysIKSYY_8
Year(s) Of Engagement Activity 2018
URL http://kamounlab.tumblr.com/post/176385835530/the-edge-of-tomorrow-plant-health-in-the-21st
 
Description Le Professeur tunisien Sophien Kamoun intègre la prestigieuse Royal Society de Londres 
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 News article in the North African media https://www.huffpostmaghreb.com
Year(s) Of Engagement Activity 2018
URL https://www.huffpostmaghreb.com/entry/le-professeur-tunisien-sophien-kamoun-integre-la-prestigieuse-...
 
Description MARPLE website 
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 We have generated a project website to raise awareness of the project: https://acaciaafrica.org/marple-diagnostics/
Year(s) Of Engagement Activity 2016,2018
URL https://acaciaafrica.org/marple-diagnostics/
 
Description Meeting with Butterfly Conservation regarding the barberry carpet moth program 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This discussion was focused on raising awareness regarding the role of barberry in the life cycle of the wheat rust pathogens.
Year(s) Of Engagement Activity 2018
 
Description Meeting with HE Mr. Slim Khalbous Ministre de l'Enseignement Supérieur et de la Recherche Scientifique of Tunisia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact A busy week in Tunisia. A great honour to receive the Presidential Research Award from HE Mr. Slim Khalbous Ministre de l'Enseignement Supérieur et de la Recherche Scientifique. Also, present at the ceremony were Mme Samia Charfi Directrice Générale de la Recherche Scientifique et M. Abdelmajid Ben Amara Directeur Général de l'Enseignement Supérieur.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/183671401535/a-busy-week-in-tunisia-a-great-honour-to-receive
 
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 Member Scientific Resources Committee 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Member of a committee that decides on purchases of all types of scientific equipment and organization of JIC infrastructure.
Year(s) Of Engagement Activity 2017,2018,2019
 
Description Member of supervisory committee of PhD student at University of Wisconsin, Madison, USA 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Aug 2018 - current: Member of supervisory committee of PhD student Shannon Piper, University of Madison, Wisconsin, USA.
Year(s) Of Engagement Activity 2018,2019
 
Description Microbes in Norwich symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact The Microbes in Norwich symposium showcased the wide variety of microbiological research taking place on the Norwich Research Park, improving links between researchers and research bodies and driving high quality research and open communication between scientists. Contributing institutions included the University of East Anglia, the John Innes Centre, The Sainsbury Laboratory, the Quadram Institute, the Earlham Institute and the Norfolk and Norwich University Hospital. 240 participants ranging from undergraduates to project leaders took part in this one day event.

Seminar speakers included Nick le Brun (UEA), Nick Talbot (TSL), Alison Mather (QIB), Laura Lehtovirta-Morley (UEA), Marcelo Batista (JIC), Fred Warren (QIB), Richard Leggett (EI), Gemma Langridge (QIB), David Lea-Smith (UEA), Naiara Beraza (QIB). The Plenary Speaker was Nicole Dubilier, Director of the Max Planck Institute for Marine Microbiology, Bremen, Germany. There was also a poster competition and extensive discussion sessions.
Year(s) Of Engagement Activity 2019
URL http://microbesinnorwich.org/
 
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 Overcoming plant blindness in science, education, and society 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Plants are amazing organisms. They make up around 80% of all biomass on Earth, play important roles in almost all ecosystems, and support humans and other animals by providing shelter, oxygen, and food. Despite this, many people have a tendency to overlook plants, a phenomenon known as "plant blindness." Here, we explore the reasons behind plant blindness, discuss why some people are relatively unaffected by it, and promote education around plant science to overcome this phenomenon and raise awareness of the importance of plants in the wider community.
Year(s) Of Engagement Activity 2019
URL https://nph.onlinelibrary.wiley.com/doi/full/10.1002/ppp3.51
 
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 Pint of Science talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Talk to raise awareness of plant disease and genomics.
Year(s) Of Engagement Activity 2018
 
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 Presented talk at JIC "Science for Innovation Showcase" event 
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 Industry/Business
Results and Impact Presented a talk at the JIC "Science for Innovation Showcase" event, Norwich, UK, 7-8 Feb '18. I explored opportunities to collaborate with industry.
Year(s) Of Engagement Activity 2018
 
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 Press release to announce BRIGIT project 
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 Engaged with JIC Public Engagement Officer to launch press release 'UK consortium to combat serious threat to plant health' to announce the start of the BRIGIT project and the BRIGIT project website
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/press-release/uk-wide-consortium-to-combat-serious-threat-to-plant-health/
 
Description Press release to announce new appointment for the BRIGIT project 
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 Engaged with JIC Public Engagement Officer to launch press release 'New appointment for UK-wide Xylella pathogen consortium' for the BRIGIT project
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/news/new-appointment-for-uk-wide-xylella-pathogen-consortium/
 
Description Public involvement in collection of ash accessions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Collection of seed from 20 ash trees in Norfolk which show clear indications of having resistance to Chalara ash dieback. The collection was made with input from farmers, charitable organisations and members of the general public. A portion of the seed has been deposited at RBG Kew's Millennium Seed Bank. The remainder will be used in research on genetics of ash dieback and in restoration projects (plans are in progress).
Year(s) Of Engagement Activity 2018
 
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 Retaining the Ashes, emerald ash borer: 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 Public/other audiences
Results and Impact Prof James Brown was interviewed on BBC Radio 4's Farming Today programme about his work on emerald ash borer (Showalter et al. 2019, Plants People Planet).

This was followed up by radio programmes on BBC Radio Cornwall, BBC Radio Devon, BBC Radio Shropshire (2 programmes) and BBC Radio Norfolk; in online news by Yahoo! News UK & Ireland, PHYS.ORG, LongRoom.com, ScienceDaily, LongRoom.com, Tech A Peek and LiveNews.co.nz (New Zealand); and in printed and online newspapers: The Daily Telegraph, The Herald (Glasgow), East Anglian Daily Times, Eastern Daily Press, Barking Today, MailOnline, and Ipswich Star.

The total audience for the radio outlets was 12,085,000 and the total circulation of the printed publications was 375,914.
Year(s) Of Engagement Activity 2020
URL https://www.jic.ac.uk/advances/rising-from-the-ashes/
 
Description Retaining the Ashes: TV programme on BBC Look East 
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 Public/other audiences
Results and Impact Prof James Brown was interviewed and filmed on the BBC Look East regional news programme about his work on ash dieback and emerald ash borer (Showalter et al. 2019, Plants People Planet). Dr Emily Beardon and Miss Rachel Burns were filmed and interviewed about techniques for working with ash and ash dieback.

The average viewing figure for BBC Look East is 289,000, making it the most watched BBC programme in the East Region. The film of JIC's ash work was also used in other regional news programmes; the total viewing figures for the 18.30 BBC Regional News programme (combined audience from around the regions) is 4.89m, making it is the most watched regular programme on BBC1.
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=KpkQNxrWy6U
 
Description Rising from the Ashes: article in JIC's Advances magazine 
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 Rising from the ashes - Advances article on the JIC website - 2,746 page views, with 450 likes and 89 shares on social media. This makes it the most popular of all the Advances articles that have appeared on the JIC website since we started putting them up in Summer 2017.
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/advances/rising-from-the-ashes/
 
Description Rising from the ashes JIC website article 
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 Rising from the ashes JIC website article - 463 page views, Social Media (Twitter and Facebook 29 likes, 3 shares directly from JIC's account plus many others from personal FB and Twitter accounts).
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/press-release/rising-from-the-ashes/
 
Description Roundtable debate on Genome Editing for Crop Improvement with Rt Hon Michael Gove MP, Secretary of State for the Environment. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Took part in round table debate with the Secretary of State for the Environment to discuss the CJEU ruling on Genome Editing and how this was a potential impediment to innovation in crop improvement. The debate was co-ordinated by Tom Allen-Stevens and the NFU on 11th February 2018. The meeting solicited views from the science community, the soil association, the organic farming movement, Beyond GM, plant breeders, the AgBiotech industry, and the broader farming community.

There is likely to be a follow-up discussion and ongoing work to advise government on genome editing and its potential use in crop improvement.
Year(s) Of Engagement Activity 2019
 
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 Rustwatch workshop on field pathogenomics 
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 Workshop to train individuals in the MARPLE diagnostic pipeline as part of the RustWatch program (https://agro.au.dk/forskning/projekter/rustwatch/)
Year(s) Of Engagement Activity 2019
URL https://agro.au.dk/forskning/projekter/rustwatch/news-and-events/show/artikel/rustwatch-workshop-on-...
 
Description School teacher education 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact The activity involved a presentation and discussion with school teachers on the importance and relevance of plant disease in a historical and current context. The activity is aimed at providing teachers who are not experts in plant pathology to effectively provide all the relevant information required within the A-level curriculum to their students
Year(s) Of Engagement Activity 2018
 
Description Scoop.it page "Plants and Microbes" 
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 Everything related to the science of plant-microbe interactions. Curated by Kamoun Lab @ TSL

>450K page views.
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017
URL https://www.scoop.it/topic/mpmi
 
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 State of the worlds fungi 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited speaker.
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 Talk to flying farmers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talk to "flying farmer" group.
Year(s) Of Engagement Activity 2018
 
Description Talking Biotech Podcast - Plant Disease Networks 
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 Public/other audiences
Results and Impact Plant disease resistance is a complicated arms race between the plant and pathogens. Bacteria, viruses and fungi evolve in lock-step with plants, creating new ways to overcome new disease resistance strategies. Resistance to disease has a foundation in the gene-for-gene model, a model that hypothesizes that plants and pathogens have a molecular relationship with each other that mediates pathogenicity. Today's podcast features Drs. Lida Derevnina and Chih-Hang Wu, postdoctoral researchers with Sophien Kamoun (@KamounLab) at the Sainsbury Laboratory (@TheSainsburyLab) in Norwich, England. They describe the new thinking of disease resistance as a number of complex layers that integrates many gene-for-gene interactions with other mechanisms in mediating plant defense. Hosted by Paul Vincelli (@pvincell).
Year(s) Of Engagement Activity 2018
URL http://www.talkingbiotechpodcast.com/146-plant-disease-networks/
 
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 Ten things we learned in 2010-2019 (aside from everything else) 
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 This last decade has been such an exhilarating period of exploration and discovery for me, my team and my collaborators that I just can't resist the urge to write this post. The decade took us through unexpected research paths that I would have never imagined ten years ago. As I'm drafting these words during my holidays break in Sri Lanka-in between tasting the local milk rice curries and soaking the soft Indian ocean December sunshine-I'm reflecting on the local proverb above and I'm using it as my lame excuse to offer you yet another list of decadal achievements.

Please note that this is my personal highly biased perspective on ten things we have learned in 2010-2019. This list is by no means meant to be comprehensive review of advances in our research field but rather a reflection of my own personal take on the scientific topics we investigate.
Year(s) Of Engagement Activity 2020
URL https://kamounlab.tumblr.com/post/190367273015/ten-things-we-learned-in-2010-2019-aside-from
 
Description TheMetaNews: Interview-<
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 Professional Practitioners
Results and Impact Chercheur en pathologie des plantes au Royaume-Uni, Sophien Kamouns'est tout récemment fait pirater son identité par une revue prédatrice.

Comment vous êtes-vous rendu compte du piratage de votre identité ?
J'ai reçu un email du Research journal of plant pathology, qui a attiré mon attention car il me remerciait d'avoir "reviewé" des articles pour leur compte. Il y avait le mot de passe de "mon" profil en bas du mail, j'ai donc pu y accéder et réaliser que j'étais censé avoir rendu quatre rapports (très mauvais d'ailleurs), alors que je n'ai jamais travaillé pour cette revue.

Avez-vous contacté les éditeurs de la revue pour avoir des explications ?
J'en doutais au départ mais il s'agit de vraies personnes ! Un chercheur aux Etats-Unis, un autre en Chine, les deux assez reconnus. J'en ai parlé à l'administration de mon institut et nous avons décidé que je ne les contacterai pas personnellement, mais d'agir de manière formelle. Une lettre signée de mon institut est en cours de rédaction, à l'attention de la revue, ainsi que des deux éditeurs. C'est également mon employeur qui décidera s'il y a lieu d'engager des poursuites judiciaires.

Quel est le meilleur moyen de lutter contre les revues prédatrices ?
Par la transparence. Je suis pour un système << publish & filter >>, et non l'inverse, où le peer-review se fait sur des plateformes dédiées comme PREreview, après mise en ligne du preprint. Les maisons d'édition historiques ne sont pas forcément un gage de qualité du peer-review même si les chercheurs se cachent souvent derrière le fait qu'un article est publié dans Nature pour ne pas se poser de questions. Cela peut être très dangereux, comme nous montre le cas de l'article liant vaccination et autisme, qui a finalement été retiré mais 18 ans après sa publication.
Year(s) Of Engagement Activity 2019
URL http://sco.lt/5RgfkO
 
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 Training in pathogenomics methodology in Ethiopia 
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 Visiting Ethiopia to train individuals in advanced genomics-based disease surveillance techniques.
Year(s) Of Engagement Activity 2018
URL https://acaciaafrica.org/marple-diagnostics-a-pioneering-step-in-ethiopian-wheat-rust-management/
 
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 UK Cereal Pathogen Virulence Survey: Invited speaker 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Invited to share our latest results and methodology regarding pathogen diagnostics and surveillance.
Year(s) Of Engagement Activity 2019
 
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 UKCPVS stakeholder meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact UKCPVS stakeholder event.
Year(s) Of Engagement Activity 2019
 
Description Video commentary on the structure and activation mechanism of NLR type plant immune receptor ZAR1 
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 Stunning news from China! Check CCTV13 news report on the resistosome featuring Jijie Chai and Jian-Min Zhouwith a brief cameo by yours truly. This program's audience share was ~2.3% or about 30 million people give or take

More coverage via iPlants WeChat Group, which includes a cool animation by Jian-Min's Lab. Here is also the video interview commissioned by the authors and the commentary by Hiroaki Adachi and Abbas Maqbool.

It's truly cause for celebration. At long last, a structure o
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/184056312400/stunning-news-from-china-check-cctv13-news-report
 
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 WGIN Stakeholders' Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited speaker.
Year(s) Of Engagement Activity 2018
 
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 Why the future of gene-edited foods is in the balance 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Please use the sharing tools found via the share button at the top or side of articles. Copying articles to share with others is a breach of FT.com T&Cs and Copyright Policy. Email licensing@ft.com to buy additional rights. Subscribers may share up to 10 or 20 articles per month using the gift article service. More information can be found at https://www.ft.com/tour.
https://www.ft.com/content/12b978aa-0544-11e9-bf0f-53b8511afd73

Gene editing is the biggest technical advance in bioscience since the discovery of "recombinant DNA" technology - artificially mixing genetic material - in 1973. That launched the era of genetic engineering and led to the commercialisation of genetically modified (GM) crops in the 1990s. Now gene editing (GE) is for the first time giving researchers a fast, reliable way to make precise changes in specific genes. But its use in farming is in the balance after a European ruling last year equated it with heavily regulated GM.

Publicity around gene - or genome - editing has focused on human applications, and particularly the controversy about gene-edited babies born in China. Yet it also promises to transform agricultural production, for example genetically editing crops to make them resistant to disease or developing faster-growing varieties of livestock. The extent of that transformation will depend on variations in regulation around the world.

Proponents of gene editing hope it can avoid the criticism and regulatory scrutiny that slowed the introduction of GM, because it usually alters existing genes rather than adding foreign DNA to the plant. In the US and Canada, the initial response of authorities has been that gene-edited crops will not fall under the regulatory regime of genetically modified organisms (GMOs) but the EU is taking a different view.

Scientists have devised several gene editing tools but the most popular and versatile is Crispr ("clustered regularly interspaced short palindromic repeats", pronounced "crisper"), which entered the world's laboratories six years ago.
Year(s) Of Engagement Activity 2019
URL https://www.ft.com/content/12b978aa-0544-11e9-bf0f-53b8511afd73
 
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 Science seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Formal talk to encourage women to continue a career in science.
Year(s) Of Engagement Activity 2019
 
Description Women in Science seminar series in High Schools in Spain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact To encourage women to pursue a career in science.
Year(s) Of Engagement Activity 2019
 
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 Workshop on MARPLE diagnostics in Ethiopia 
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 A workshop to train individuals in the MARPLE diagnostics method to support adoption of this method in Ethiopia.
Year(s) Of Engagement Activity 2019
URL https://acaciaafrica.org/supercharged-marple-labs-to-be-fastest-rust-surveillance-system-in-africa/
 
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 The Youth STEMM Award is an achievement-based award for students in Years 9-13, designed to support and inspire the next generation of STEMM professionals. We provided an opportunity for participants to gain new knowledge about rust pathogens.
Year(s) Of Engagement Activity 2019
 
Description Youth STEMM Awards demonstration 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Youth STEMM Awards.
Year(s) Of Engagement Activity 2019
 
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