Recognition

Lead Research Organisation: John Innes Centre
Department Name: UNLISTED

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Plants’ perception of molecular signatures from beneficial or pathogenic microbes and pests is critical for the establishment of symbioses or initiation of immunity. Typically, these molecular signatures are sensed by receptors at either the cell surface (PRRs) or inside cells (NLRs). Diverse microbial or pest-derived molecules can be recognised, including complex oligosaccharides, nucleotides, peptides, and proteins. Some recognition events involve direct interactions between microbial or pest molecules and plant receptors. However, indirect interactions also occur and receptors can detect changes in host molecular complexes, or the activity of a microbial molecule on host factors.

To discover components involved in perception, we will investigate the genetic and molecular basis of recognition. In addition, we will use synthetic biology approaches to develop new capabilities in nature’s toolkit. Screening diverse germplasm, or preparing diverse receptor libraries, coupled with gene editing technologies (e.g. CRISPR) to introduce and test candidate genes in target plants, is critical for identifying or expanding plant recognition repertoires both at the cell surface and inside cells. The expansion in the number of genes encoding potential cell surface PRRs in plant genomes suggests we currently underestimate the full complement of recognition specificities in the plant kingdom. Discovery and functional characterisation of these specificities will further our understanding of how plants and microbes communicate with each other at the cell surface. Natural variation in wild populations, and in close and distant crop relatives, provides a rich diversity of sources for developing as-yet unexploited resistance for crops. Although the molecular mechanisms of non-host resistance, a form of asymptomatic immunity often deployed in crop breeding, are still poorly understood, both PRR and NLR receptors are likely to contribute. An emerging but critical question is to understand how levels and localisation of PRR and NLR receptors are controlled, and how they are organised in complexes competent for the perception of microbial- or pest-derived signals.

Planned Impact

unavailable
 
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 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
 
Title You Can Call Me Al 
Description A plant pathology song [With apologies to Paul Simon] A spore lands on a leaf It wonders where it landed now Why am I not a generalist The rest of my life is so hard I need pathogenicity I want a shot at infection Don't want to end up avirulent In an avirulence graveyard HR HR Cell death in the epidermis Far away from the mesophyll ROS burst ROS burst Get these receptors away from me You know I don't find this host amusing anymore If you're a Brassicaceae I can be your parasite My name is Albugo But buddy when you call me You can call me Al A spore lands on a leaf It landed on a friendly host now Got a short little burst of infection And wo my hyphae are so long Here's my spore and haustoria What if I mutate here Who'll be my new host Now that my old-host is Gone Gone I spread back down the valley With some roly-poly shaped spores All along along There were cabbages and mustards There were shifts and jumps If you're a Brassicaceae I can be your parasite My name is Albugo But buddy when you call me You can call me Al If you're a Brassicaceae I can be your parasite My name is Albugo But buddy when you call me You can call me Al 
Type Of Art Performance (Music, Dance, Drama, etc) 
Year Produced 2020 
Impact Included to teaching and outreach material by several colleagues throughout the world 
URL https://kamounlab.tumblr.com/post/632416370219499520/you-can-call-me-al-with-apologies-to-paul
 
Description Obj 1.1: We previously identified three genes that confer non-host resistance to wheat yellow rust. We previously fine-mapped Rps7 and found it was in coupling with the barley powdery mildew resistance locus, Mla. Candidate genes for the other two loci are currently being resolved with additional fine-mapping.

Obj 1.1: We identified the causal gene (an NLR) for Rps6 using map-based cloning and transformation. Transformation of Rps6 in wheat failed to confer resistance to wheat stripe rust. Natively, Rps6 is expressed at very high levels in barley. Our current hypothesis is that the Mla6 promoter, which is functional in barley, provides too little expression in wheat. Work is underway to identify high expression promoters for wheat complementation.

Obj 1.1: Map-based cloning of Rps8, a wheat stripe rust resistance gene in barley, narrowed the physical interval to a 1 Mb region. Two candidate genes were identified based on association analysis and expression polymorphisms between resistant and susceptible haplotypes. A forward genetic screen is currently underway to identify loss-of-function mutations in genes required for Rps8-mediated resistance using an establish mutagenized population in the reference barley accession Morex.

Obj 1.1: We have made excellent progress with the identification of small aphid peptides that elicit Arabidopsis thaliana defence responses in a BAK1-dependent manner. Aphid cysteine protease activity is involved in generating the aphid peptide elicitors. A prioritized list of about 30 aphid peptides are considered candidate elicitors and are being synthesized to be tested for plant defense response activation. This is a collaboration with Jan Sklenar of TSL and PhD student James Canham conducted the majority of the work. We established a collaboration with Renier van der Hoorn's group at University of Oxford to further explore how the aphid elicitor is released.

Obj 1.1: We have contributed to the identification of several novel elicitors and PRRs, as well as receptor kinases contributing to the function of plant PRRs. We optimized an immuno pull-down method, and further expanded aphid sequence databases for mass spec analyses.

Obj 1.1: We identified suppressors of plant immunity from oomycete and nematode pathogens that interfere with R-gene mediated resistance and thus alter classical gene-for-gene recognitions; we made progress in understanding the mechanisms by which these effectors suppress specific immunity.

Obj 1.1: We have generated transgenic lines of barley that contain candidate genes for Rps6, a major locus that contributes to immunity in barley to wheat stripe rust. Patent is being pursued by the 2Blades Foundation. Obj 1.1: We demonstrated that the movement of the nucleus is required for Rhizobial infection in M. truncatula.

Obj 1.1: We have reported the isolation of Rpi-amr3 (Witek et al 2016). We have since completed the isolation and definition of an allelic series of Rpi-amr1e. These alleles show only ~90% identity to each other. We also recently identified the recognized effectors for these two Rpi- genes. Mapping and further characterization of Rpi-amr4 and Rpi-amr10 are in progress. Obj 1.1: We have defined multiple Arabidopsis genes that confer resistance to Brassica juncea-infecting Albugo strains (Cevik et al 2019).

Obj 1.1: We are currently developing appropriate promoter/terminator systems for expression in wheat, as existing native promoters and terminators were found to be inadequate.

Obj 1.1: We made good progress in understanding how oomycete and nematode pathogen effectors suppress the activities of plant immune receptor network and R-gene mediated resistance.

Obj 1.1: We have further optimized purification protocols to identify aphid peptide elicitors that induce plant defence responses. We found that peptide elicitors are released by aphid-derived cysteine proteases. We have made progress with the functional characterization of aphid cysteine proteases, and found that these proteins have unusual characteristics, possibly requiring dimerization to bring together unusual residues to form active sites. Optimization of the elicitor identification is a collaboration with TSL and characterization of aphid cysteine proteases a collaboration with Renier van der Hoorn's group at Oxford University. Obj 1.1: We have published a newly discovered and very effective potato late blight resistance gene Rpi-amr1 (Witek et al 2021).

Obj 1.1: We demonstrated that plant pathogens have evolved to counteract central nodes of an NLR immune receptor network through different mechanisms. We reported the first example of a pathogen effector protein that directly binds an NLR protein to inhibit its activity.

Obj 1.1: We have screened ~50 pathovars of the bacterial pathogen Pseudomonas syringae for virulence in Marchantia polymorpha liverworts (a non-flowering, non-vascular land plant) and have identified both resistant and susceptible outcomes for future study.

Obj 1.1: We found that stable transformation of the barley powdery mildew resistance genes Mla1, Mla6, and Mla8 (driven by the Mla6 promoter) is sufficient to confer mildew resistance in single copy. In contrast, both Mla3 and Mla7 only conferred resistance to barley powdery mildew in transformed lines with multiple copies. This observation reflects the natural system, where Mla3 and Mla7 exist in multiple copies, whereas Mla1, Mla6, and Mla8 are single copy.

Obj. 1.1: To engineer a functional R gene cassette, we require the use of a single promoter to drive the expression of genes in the construct (recapitulating the expression of multicopy NLR encoding genes at their native level). To achieve this goal, we identified two genes (HORVU2Hr1G051740 and HORVU7Hr1G021510) that are expressed at similar native levels to the NLR Mla3. Using these promoters, we have generated stable transgenic lines expressing Mla3 and Mla7.

Obj. 1.1: We have provided evidence that bacterial effector proteins and lipopeptide toxins underpin virulence of Pseudomonas syringae in diverse land plants including liverworts, ferns, and angiosperms. We have purified the toxin syringomycin E for future experiments with plants.

Obj. 1.1: We have established that a single NLR is necessary and sufficient for Rps6-mediated resistance in barley to wheat stripe rust. Transformation in wheat of Rps6 has shown that it is functional and work is underway to identify suitable promoters for R gene stack development.


Obj. 1.1: We have demonstrated that a plant pathogen effector protein directly binds and inhibits the oligomerisation of an NLR protein into a resistosome.

Obj. 1.1: We continued to characterize the attributes of an aphid peptide elicitor that induces plant defence responses, including Ca2+ bursts and assessed the impact of plant receptors on the induction of Ca2+ bursts upon thrips feeding.

Obj. 1.1: We characterized plant receptors involved in recognition of aphid feeding damage and elicitors.

Obj. 1.1: We made progress with identification of a damage associated molecular pattern (DAMP) elicited during aphid feeding and identified downstream induced defence responses that suppress aphid colonization. Manuscript to be submitted soon.

Obj. 1.1: The Pisum diversity panel (224 lines) was screened with two Downy Mildew races. Both the datasets showed high correlation and about 17% of the lines showed complete resistance in both screens.

Obj. 1.1: NLRs were captured from the Pisum panel using the RenSeq approach. Both the phenotype and RenSeq data was analysed using association genetics (AgRenSeq) and a locus was identified on chromosome 5 (LGIII) which was associated with resistance in the two screens. A further locus on chromosome 2 (LGI) was identified. The genetic markers for the two loci are under development.

Obj.1.1: We showed that the model liverwort (non-flowering bryophyte) Marchantia polymorpha undergoes a conserved CC-mediated response that is similar to angiosperms like Nicotiana benthamiana.

Obj. 1.1: We showed that a cyst nematode virulence effector binds and inhibits oligomerization of a helper NLR protein by physically preventing intramolecular rearrangements required for activation.

Obj. 1.1: We have investigated the host specificity determinant Pwl2 from the rice blast fungus and shown that a CRISPR Cas9 gene edited mutant of the fungus, lacking all three copies of Pwl2 is able to cause disease in Eragrostis curvula (weeping lovegrass) validating its role as a host range determinant. We have used a diverse collection of Eragrostis cultivars to identify those that remain resistant to M. oryzae, thereby defining additional resistance specificities.

Obj. 1.1: We characterized the attributes of aphid peptide elicitors that induce plant defence responses, including Ca2+ bursts, and identified pattern recognition receptors (PRRs) involved in the response.

Obj. 1.1: We improved methods for monitoring Ca2+ bursts in plants upon aphid and thrips feeding using the GFP-based GCaMP intensiometric reporter. We used the improved methods to screen a range of Arabidopsis thaliana mechano-, damage and PAMP receptor mutants for localized wound and touch perception. We compared the plant perceptions of localized wound and touch to those of aphid and thrips feeding. We found that a specific plant receptor is involved in the perception of localised wounding, touching and aphid and thrips feeding and downstream pH changes and defence gene induction.

Obj: 1.1: Alongside research carried out within the Pulse Crop Genetic Improvement Network (PCGIN), we have phenotyped a pea diversity panel with two races of downy mildew pathogen, Peronospora viciae f. sp. pisi. The panel was sequenced for immune receptor genes for which AgRenSeq pipeline was set-up to identify associate genetic loci. Using this, we have discovered two resistant loci for pea downy mildew pathogen. Long-read Nanopore assembly of a resistant pea line is being used to generate gene-level resolution in these regions.

Obj 1.1: We have discovered two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. The work has been published in Nature Plants (Arora et al 2023).

Obj. 1.1: We have developed efficient protocols to screen diversity panels with root rot pathogens (e.g., Fusarium sp. and Aphanomyces). This method will be used to screen a pea diversity panel to discover new resistances to these diseases.

Obj. 1.1: we found that upon direct recognition of Phytophthora infestans AVRamr1 or AVRamr3, sensor NLRs Rpi-amr1 and Rpi-amr3 activate helper NLR NRC2 to form an oligomer that does not contain molecules of the sensor NLR.

Obj. 1.2: We have unveiled mechanisms that control the assembly of PRR complexes or the abundance of key downstream signalling components (e.g. BIK1).

Obj 1.2: We made progress with the identification of plant pattern recognition receptors (PRR) of aphid peptide elicitor(s). So far ±6000 M2 generation seedlings of a EMS mutagenized reporter line were screened and 50 showed altered responses to aphid elicitor peptides. The F1 of these 50 plants will be retested and taken forward for identification of mutant loci using the MutMap approach.

Obj 1.2: We have provided new insights into how the Arabidopsis NLR pair RRS1/RPS4 recognises the effector PopP2 (paper in press in Cell Host & Microbes) Obj 1.2: We determined the crystal structure of the complex between the bacterial effector protein AvrRps4 and the integrated WRKY domain of the RRS1 NLR immune receptor, and are using these as a template to design mutations and test function.

Obj 1.2: We have isolated an allelic series of a new resistance gene (Rpi-amr1e) against potato late blight from the potato relative, Solanum americanum, and in 2017 undertook field trials of transgenic lines carrying this gene. A paper reporting RPi-amr1e is being prepared.

Obj 1.2: We unravelled the molecular mechanistic basis of how the allelic rice Pik-1/Pik-2 NLR pair recognises polymorphic pathogen proteins (effectors) from the rice blast pathogen.

Obj 1.2: We have found that the rice NLR pair Pik-1/Pik-2 form homo- and hetero-interactions in both the presence and absence of pathogen effector proteins. We also showed that these NLRs require full-length proteins and wild-type sequences at established motifs for immune signalling. We are investigating how these interactions change on effector perception to initiate signalling.

Obj 1.2: We discovered that a "mis-matched" effector from the rice blast pathogen (AVR-Pia) can be recognised by the NLR pair Pikp-1/Pikp-2. By defining the structure and affinity of this interaction we have informed the engineering of bespoke NLR receptor recognition specificities. Obj. 1.2: We characterized the mechanistic basis of auto-activity (potentially "sensitized" activity) in mis-matched pairings of rice NLR Pik alleles. This new knowledge has highlighted the importance of pairing specific NLR alleles for engineering new resistance capabilities in plants.

Obj 1.2: We have confirmed that Mla8 confers resistance to wheat yellow rust using complementation in barley. A paper detailing this result is under review.

Obj. 1.2: We discovered a requirement for multiple copies of Mla7 to confer race-specific resistance to barley powdery mildew and resistance to wheat stripe rust. Natively, Mla7 exists in a tandem array with multiple copies. Appropriate promoters that will drive expression at an equal level with a single copy T-DNA are currently being transformed into barley.

Obj. 1.2: We identified an N-terminal motif in NLR immune receptors (MADA motif) that is functionally conserved across distantly related plant species.

Obj. 1.2: We have investigated how the mechanisms of effector-triggered immunity act by promoting pathogen-triggered immunity pathways.

Obj. 1.2: We designed a series of mutants in the bacterial effector protein AvrRps4, based on the structure of this effector in complex with the integrated WRKY domain of the RRS1 NLR immune receptor. These mutants were designed to test the hypothesis that in vitro binding would correlate with in planta responses, and to validate the structure. We showed that mutants which prevent protein binding in vitro (measured by ITC) show a lack of recognition in plants, both in Nicotiana species on co-expression of effectors and NLRs, and in the host plant Arabidopsis during bacterial infection.

Obj 1.2: We revealed how the rice NLR allele Pikh encodes extended recognition specificity towards divergent AVR-Pik effectors via a single amino acid change from the allele Pikp. Further, by comparing Pikh with the Pikm allele, we showed how different NLR receptors have converged on a similar mechanism to deliver extended effector recognition.

Obj 1.2: We engineered the rice NLR Pik chassis to deliver a novel recognition event in response to the Magnaporthe oryzae effector protein PWL2. We achieved this by swapping the native Pik-HMA domain for the putative host target protein OsHIPP43.

Obj. 1.2: We found that aphid elicitors induce MAP kinase cascades and defense gene expression in a BAK1 and SOBIR1-dependent manner. Inhibition of Ca2+ release induced by the aphid elicitors eliminates this plant defence signalling. We are conducting additional work to examine the role of Ca2+ signalling in aphid-plant interactions.

Obj. 1.2: We reported on the role of phosphorylation in regulating the activity of the Arabidopsis RRS1/RPS4 paired immune receptor.

Obj. 1.2: We have cloned and tested candidate NLR receptors from Marchantia for immunity phenotypes. Initial data supports a conserved role of a CC-type NLRs in immune activation despite >450 million years of divergence from angiosperm crops.

Obj. 1.2: We have identified that the Pwl2 host range determinant for infection of Eragrostis curvula, acts as a virulence effector in rice for suppression of pattern-triggered immunity.


Obj. 1.2: We have demonstrated that the N-terminal coiled-coil (CC), RPW8, and TIR domains of diverse NLR immune receptors are functionally conserved across the green lineage (from algae to angiopserms). We further tested a subset of CC/R domains specific to non-flowering plants and discovered a conserved MAEPL motif at the N-terminus of the domain that is functionally interchangeable with the angiosperm MADA motif. This motif is critical for immune receptor domain activity when expressed in angiosperms or the liverwort Marchantia polymorpha, demonstrating deep functional conservation of NLR receptor domains.

Obj. 1.2: We revealed how intracellular receptors act to potentiate and restore the immunity activated by cell surface receptors.

Obj. 1.2: We reconstructed the evolutionary history of the Pik-1 immune receptor and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA integrated domain. We demonstrated that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes.

Obj. 1.2: Extending our study of the bacterial effector protein AvrRps4 and its interaction with the integrated WRKY domain of the RRS1 NLR immune receptor, we performed growth assays with bacteria expressing wild-type and mutant effector to support previous host immune responses. We also experimentally demonstrated a putative virulence-associated activity for AvrRps4 in preventing WRKY transcription factor binding to W-box DNA. Our AvrRps4/RRS1WRKY study has now been published.

Obj. 1.2: We engineered the rice NLR Pik chassis to contain the HMA domain of the rice NLR RGA5 and performed a mutagenesis study to regain binding and response to the cognate effector AVR-Pik. This study directly informs our work to engineer plant immune receptors for diverse recognition activities.

Obj. 1.2: Based on structural data, we have correlated binding of the rice blast effector protein AVR-Pii to the host rice exocyst complex component Exo70 with the resistance response mediated by Pii in rice.

Obj. 1.2: We have determined the crystal structure of two novel effectors from the wheat blast pathogen that are recognised by a rice intracellular NLR immune receptor and established an assay to study how protein interactions underpin immune responses. This will be used for further studies towards developing new immune receptor engineering towards this family of effectors.

Obj: 1.2: We have investigated protein:protein interactions underpinning a novel pair of putative sensor/helper immune receptors in wheat that recognise two effectors from the blast pathogen. Developing this immunity-related assay enables further study to understand mechanisms.

Obj: 1.2: We demonstrated that the N-terminal domains of plant NLR immune receptors (CC and TIR) are conserved across all major plant lineages. We further showed that non-flowering plant CC domains encode the N-terminal MAEPL motif that is functionally analogous to the angiosperm MADA.

Obj. 1.2: We proposed an activation-and-release model for paired NLR activation. This points to a distinct activation model compared with mammalian paired NLRs.

Obj. 1.2: We determined that the helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4.

Obj. 1.2: We have shown that the Magnaporthe oryzae effector Pwl2 interacts with a small heavy metal-associated protein from barley and this interaction is required for suppression of PTI responses, such as the generation of reactive oxygen species. This complements work in the Moscou and Banfield laboratories, which have investigated the role of Pwl2 in triggering Mla3-dependent resistance in barley, and its structural mechanism, respectively.

Obj. 1.2: We made progress with identification of a damage associated molecular pattern (DAMP) elicited during aphid feeding and identified downstream induced defence responses that suppress aphid colonization. A manuscript describing these results is under revision for resubmission.

Obj. 1.2: We found the helper NLR NRG1 oligomerises upon effector recognition, and that this also requires surface receptor mediated immunity

Obj. 1.3: We have demonstrated that the PRR EFR can be used to engineer anti-bacterial disease resistance in potato and Medicago. In addition, we showed that EFR expression in Medicago, while conferring resistance to a bacterial pathogen, does not impede on Rhizobium symbiosis.

Obj. 1.3: Based on in vitro and protein structural studies we have successfully engineered expanded recognition profiles of the Pikp NLR pair of rice to include previously unrecognised effectors. This was achieved via two approaches (single amino acid mutations and whole domain engineering). We are awaiting the results of transgenic rice, transformed with our engineered receptors, to see if these deliver improved disease resistance profiles.

Obj 1.3: We have discovered that an NLR at the Mla locus exists as a trans-species polymorphism that has been maintained for 24 million years. The polymorphism includes the presence or absence of an integrated Exo70F1 gene, which is involved in exocytosis and is a known target of pathogen effectors. A paper has been placed on the preprint server bioRxiv and is currently under review.

Obj 1.3: We identified novel HMA-targeting effectors from rice and wheat blast fungus, and initiated experiments to engineer NLR immune receptors to recognize and respond to these effectors

Obj 1.3: We have generated transgenic lines of wheat that contain candidate genes for Rps6, a major locus that contributes to immunity in barley to wheat stripe rust. A manuscript is currently in preparation.

Obj 1.3: We have generated transgenic lines of wheat that contain Mla8 (=Rps7), a major locus that contributes to immunity in barley to wheat stripe rust. Work is underway to confirm expression of the transgene. We are currently developing promoter/terminator systems to drive high expression in wheat.

Obj 1.3: We characterized a suite of effectors from rice and wheat blast fungus that target HMA proteins and initiated experiments to engineer NLR immune receptors to recognize and respond to these effectors.

Obj 1.3: We determined that widely conserved attenuation of plant MAMP-Induced calcium influx by bacteria depends on multiple virulence factors, and may involve desensitization of host pattern recognition receptors (in collaboration with Cyril Zipfel and Ralph Panstruga)

Obj. 1.3: We developed constructs of the rice NLR Pik, engineered to contain an integrated domain based on OsHIPP43, for transformation of barley, rice and wheat to test for novel disease resistance against fungal pathogens in these cereal crops.

Obj. 1.3: We have developed transgenic Maris Piper potato lines that show complete resistance to late blight

Obj. 1.3: We described RefPlantNLR, a comprehensive reference dataset of experimentally validated plant NLR immune receptors. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset.

Obj. 1.3: Using fine-mapping and mutagenesis, we have discovered that Rps8, a resistance gene in barley to wheat stripe rust, is conferred by two genes, a transmembrane receptor-like kinase and Exo70. Transformation is currently underway to confirm the requirement of both genes for resistance.

Obj. 1.3: We identified a plant that could be a new potato variety, PiperPlus 1.0, that shows complete resistance to potato late blight, and improved tuber quality

Obj. 1.3: Using transformation, we have shown that Rps8-mediated resistance requires an LRR-receptor kinase and Exo70FX12. Exo70FX12 belongs to the grass-specific Exo70FX family and is the first to be associated with a function in plants.

Obj. 1.3: We transformed barley and rice with engineered constructs of the rice NLR containing the OsHIPP43 domain. These plants are currently growing in the T1 generation and will be tested in disease resistance assays.

Obj. 1.3: We have generated transgenic rice with engineered immune receptors that show an expanded recognition profile for effectors of the rice blast pathogen (AVR-Pik) that are not currently recognised in nature. This acts as a proof-of-principle for targeted engineering of immune receptors for expanded activities.

Obj. 1.3: We developed a novel strategy for resurrecting disease resistance in crop genomes by mutating NLR proteins to evade immune suppression, thereby restoring the activity of multiple disease resistance genes.

Obj. 1.3: We invented Pikobodies, a technology that endows plants with a pseudo-adaptive immune system and enables designing made-to-order plant disease resistance genes.

Obj: 1.3: We have developed KASP-based markers for the loci discovered for novel pea downy mildew resistance. These markers are being used to transfer this into other cultivars (Cameor and Prophet) by making crosses.

Obj. 1.3: We cloned new Resistance genes from Solanum americanum against both P. infestans and also P. capsica.
Exploitation Route It is still too early to say, as while the grant has now finishing it is continued with new Institute Strategic funding. We will be reporting separately to BBSRC on the outcomes of the Recognition grant as part of the direct Plant Health ISP reporting.
Sectors Agriculture

Food and Drink

Construction

Education

Environment
 
Description Narrative Impact: We (Zipfel) have started, in 2017, a multi-year partnership with the Two Blades Foundation and Monsanto to identify PRRs that can be deployed in corn to engineer resistance to fungal pathogens. We (Hogenhout) have a LINK-award and iCASE studentship with SESVanderHave, a Industrial Partnership Award with Syngenta and an iCASE studentship with Oxitec. We (Hogenhout) have an iCASE studentship starting in Oct 2020. This is a new collaboration with Syngenta and the Liverpool School of Tropical Medicine. Knowledge generated in these projects have contributed to the development of products and technologies and for assessing future directions in these companies. Some of our findings are being used for patent applications. I (Hogenhout) am the leader of BRIGIT, a consortium project co-ordinated by the John Innes Centre, that brings together ten leading UK research organisations, in a £4.85m programme aiming to improve methods of diagnosis and detection of the insect-transmitted plant parasite Xylella fastidiosa, to identify factors that could lead to its spread, and to prepare to minimise the risk of the pathogen to the UK. The project includes communication of information to diverse stakeholders, such as airport and harbour inspectors and nursery owners, and regular engagement with policymakers, government staff and the general public. We have launched a BRIGIT website with links to video, databases and information resources about Xylella fastidiosa and its insect vectors. Results from investigating the evolution of the Mla locus (Moscou Lab) have been essential and led directly to an industrial partnership. 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. We (Jones) have had our research on the plant NLR Rpi-vnt1 deployed commercially in the US, and a second NLR, Rpi-amr3, is also in progress. We (Kamoun) used open science platforms and crowdsourced community responses to address the appearance in Bangladesh of a destructive new fungal disease wheat blast. We helped recruit a team of multidisciplinary experts to apply cutting-edge genomics methods to identify the precise source of the outbreak and help to guide disease management responses. This work continues with the near-complete genome sequences of four Bangladeshi isolates from 2016 and 2017, which provide a high-resolution genome map to precisely define genetic changes in the Bangladeshi clonal lineage and monitor population changes. We (Kamoun) has established fully-funded collaborations with two agribusiness companies that raised a total amount of >£1.5M. We (TSL) have hosted a Seminar Series targeted at students and postdocs designed to give them an opportunity to present their first invited seminar. To date, six Early Career Scientists from UK, Netherlands, Austria, Japan and China, participated in this series. We continue to make use of our extensive collaborative networks to widely disseminate new tools and resources. We have reported novel protocols and methods through online platforms (protocols.io) and distribute biomaterials through Addgene. We have published an issue of the JIC Advances magazine focussed on Plant Health as part of the UN International Year of Plant Health (2020). We have planned activities to celebrate the UN International Year of Plant Health throughout the year, engaging with policy makers, funders, the general public, etc. (however, these events were seriously impacted by the Covid-19 pandemic). We are running a 366 tweet-a-day from the Plant Health twitter account (@PlantHealth3) to raise the profile of Plant Health (although this was impacted by the Covid-19 pandemic). We participated in a BBSRC discussion on strategies for developing Plant Health research in the UK (Dec 2020). We have developed transgenic potato lines carrying stacks of Rpi (resistance to P. infestans)- genes that confer complete late blight resistance against all known races of the pathogen, attracting considerable public interest. Our (Moscou) work on cloning the disease resistance genes Rps6 and Rps7 (=Mla) has identified a rapid strategy to identify functional resistance genes in angiosperms. This directly led to a funded collaboration with a non-profit company (2Blades Foundation) and industry (Kaneka Corporation) developing a trait discovery pipeline. Kamoun is a Director and scientific advisor to the start-up company Resurrect Bio https://resurrect.bio (since 2022). Kamoun obtained three fully funded industrial collaborations on NLR biology with Rijks-Zwaan, BASF and Limagrain (since 2019). We (Banfield) developed a new system for Golden Gate-based cloning of genes for protein expression in E. coli and submitted this to Addgene for further distribution. Talbot has carried out further plant health clinics and training in Kenya and Tanzania and disseminated worksheets and mobile phone apps through KALRO for blast disease diagnosis, control and pathogen surveillance. The Sainsbury Laboratory has showcased their plant health and disease research at the Royal Norfolk Show, engaging with policymakers, industry, and farmers about specific projects, such as late blight resistant GM potatoes. In 2022 TSL had a stand in the Discovery Zone which focused on educating school children. Visitors gain insight into the importance of research and genetic technologies in addressing global issues, while scientists benefit from valuable science communication experience and new perspectives from interactions with the public. Conversations on GM for disease-resistant plants were enlightening for both scientists and participants.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Education
Impact Types Societal

Economic

Policy & public services
 
Description Interview for JIC Advances magazine as part of Plant Health issue
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
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 Defining and deploying Rpi gene diversity in S. americanum to control late blight in potato
Amount £777,912 (GBP)
Funding ID BB/P021646/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2021
 
Description Dissecting Multiple Pathogen Resistance in Barley
Amount £20,000 (GBP)
Organisation Perry Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2017 
End 08/2019
 
Description ERC Advanced Investigator
Amount € 2,500,000 (EUR)
Funding ID BLASTOFF 743165 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 08/2017 
End 08/2022
 
Description Engineering CC-HMA-NLR immune receptors for disease resistance in crops (ERiC)
Amount £452,798 (GBP)
Funding ID BB/W00108X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 12/2025
 
Description Engineering cereal immunity using structure-guided design of effector/host interactions
Amount £583,766 (GBP)
Funding ID BB/V015508/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 12/2024
 
Description Engineering cereal immunity using structure-guided design of effector/host interactions.
Amount £757,706 (GBP)
Funding ID BB/V015508/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 08/2025
 
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 NLR-SEEK: Building a trait discovery platform in wheat
Amount £187,514 (GBP)
Organisation 2Blades Foundation 
Sector Charity/Non Profit
Country United States
Start 02/2018 
End 01/2021
 
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 iCASE PhD studentship
Amount £12,400 (GBP)
Organisation Oxitec Ltd 
Sector Private
Country United Kingdom
Start 09/2015 
End 09/2019
 
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 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 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 Protein-protein interaction assays 
Description Protein-protein interaction assays to identify effector-host protein interactions 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Petre, B., Win, J., Menke, F.L.H., and Kamoun, S. 2017. Protein-protein interaction assays with effector-GFP fusions in Nicotiana benthamiana. In "Wheat Rust Diseases: Methods and Protocols", S. Periyannan, ed. Methods in Molecular Biology, 1659:85-98. 
 
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 Dataset and Scripts for: RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs 
Description Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 442 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark the five most popular NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact The RefPlantNLR dataset should prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function. RefPlantNLR has already proven useful in interpreting a feature of the recently elucidated structure of the RPP1 resistosome (Ma et al., 2020). The authors used RefPlantNLR to determine that although most CC-NLRs contain a TT/SR motif in which the arginine interacts with ATP, a subset of TIR-NLRs contain a charged or polar substitution creating a TTE/Q motif interacting with ADP in the activated form (Ma et al., 2020). Interestingly a phylogenetically distinct subgroup of CC-NLRs known as the MIC1 group (Bailey et al., 2018) is an exception to this rule by having a TTE/Q motif in their ADP binding pocket and thus may also retain ADP binding when activated. This example shows how a carefully curated reference dataset like RefPlantNLR can facilitate data interpretation and hypothesis generation. 
URL http://doi.org/10.5281/zenodo.3936022
 
Title Datasets related to: The N-terminal executioner domains of NLR immune receptors are structurally and functionally conserved across major plant lineages 
Description Macroevolutionary dissection of NLR immune receptors across the plant kingdom. Extended data related to: "The N-terminal executioner domains of NLR immune receptors are functionally conserved across major plant lineages" bioRxiv 2022: https://doi.org/10.1101/2022.10.19.512840 Please see Zenodo repository (https://zenodo.org/records/8356791) for extended data on NLR identification, characterisation of N-terminal immune domains (sequence and alphafold-predicted structures), and comparative RNA-seq analysis of CC domain function in liverworts-vs-angiosperms. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact This works forms the basis for our continuing analyses of NLR immune receptor conservation and diversity across the plant kingdom. 
URL https://zenodo.org/records/8356791
 
Description Collaboration with Chatchawan Jantasuriyarat, Kasetart University, Thailand 
Organisation Kasetsart University
Country Thailand 
Sector Academic/University 
PI Contribution Shared research project, joint publications, grant applications, student exchange
Collaborator Contribution Shared research project, joint publications, grant applications, student exchange
Impact student exchange, joint publication
Start Year 2017
 
Description Collaboration with Hiromasa Saitoh, Tokyo University of Agriculture 
Organisation Tokyo University of Agriculture
Country Japan 
Sector Academic/University 
PI Contribution Joint publications, sharing research materials, intellectual contribution, grant applications
Collaborator Contribution Joint publications, sharing research materials, intellectual contribution, grant applications
Impact This is a new collaboration, developed from a previous collaboration. No direct outcomes yet.
Start Year 2017
 
Description Collaboration with Jack Vossen 
Organisation Wageningen University & Research
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 Lab of Ryohei Terauchi at IBRC in Iwate and Kyoto University, Japan 
Organisation Iwate Biotechnology Research Centre
Country Japan 
Sector Public 
PI Contribution Leading collaborative research project on Structure/function studies of rice blast disease and host resistance.
Collaborator Contribution Collaborative work on research project.
Impact Research publications and BBSRC grant funded (M02198X).
Start Year 2011
 
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. Ryohei Terauchi 
Organisation University of Kyoto
Country Japan 
Sector Academic/University 
PI Contribution Retooling rice immunity for resistance against rice blast disease The collaborator Prof. Kamoun is a world-renowned scientist in the field of plant-microbe interactions. Short visits of young Japanese scientists to Prof. Kamoun's laboratory to carry out collaborative studies will greatly enhance their career development by exposure to The Sainsbury Lab research environment and learning the cutting edge scientific researches implemented in the Kamoun Lab. Among the benefits, the visiting scientists will enhance their presentation skills by joining weekly lab meetings and journal clubs and present his/her own work. Overall, these activities will help foster the next generation scientists of Japan and enable them to build lasting connection with UK science. Development of durable blast disease resistant rice cultivars by engineering of NLRs and S-genes will greatly benefit Japanese rice production by ensuring high productivity and reducing the use of fungicide.
Collaborator Contribution Prof. Terauchi is a leading figure in rice research and has developed methods for genomics-based isolation of rice genes, e.g. MutMap. In addition, he is a leader in blast fungus having cloned and studied both rice immune receptors, such as Pik-1, and matching fungus effectors. Thus, UK team would greatly benefit from the collaboration not only from an intellectual perspective but also from the practical aspects of technology transfer, method development and exchange of biomaterial. Visits to Japan would be extremely productive as they will tap into years of expertise and knowledge about the rice blast system. Some of the proposed work, such as S-gene cloning by using rice inbred lines, would essentially be impossible in the UK as rice cannot be grown outdoors. Although the primary goal of this collaboration is on rice blast, this fungal disease has emerged as a significant problem on wheat and is a potential threat to Europe. This collaboration will help the Kamoun Lab transition to blast diseases, which has started in 2016 following the Bangladeshi wheat blast outbreak. Interactions with the Japanese collaborators would also ensure the success of the recently funded Advanced Investigator ERC award to Kamoun, which focuses on blast diseases.
Impact 33 publications per PubMed (March 2021) https://pubmed.ncbi.nlm.nih.gov/?term=kamoun%20AND%20terauchi&sort=date?=yes
 
Description Collaboration with Prof. Suomeng Dong 
Organisation Nanjing Agricultural University
Country China 
Sector Academic/University 
PI Contribution Transcriptome specialization following host-jumps in the Irish potato famine pathogen lineage The collaborator Prof. Kamoun is a world leading scientist in the field of plant-microbe interactions. Short visits of young Chinese scientists to Prof. Kamoun's group at The Sainsbury Lab to carry out collaboration will greatly enhance their career development by exposure to an outstanding research environment and cutting edge scientific research. Among the benefits, the visiting scientists will enhance their communication and presentation skills by joining weekly lab meetings and presenting their own work. Overall, these activities will help foster the next generation scientists of China and enable them to build lasting connections with UK science. More specifically, Chinese research community will access high-quality and large-scale PacBio sequencing of potato late blight genomes. The CRISPR/Cas9 tool that modified in this project will be shared with the wider Chinese Phytopathology community. Also, the open source aspects of the project would serve as an exemplar for the wider community. China is the biggest potato producer in the world yet late blight remains the number disease and problem of the Chinese potato crop. This project would ultimately provide useful information for engineering
Collaborator Contribution Nanjing Agricultural University (NAU) is the center of excellence for oomycete (Phytophthora) research in China. After joining NAU in 2014, Prof. Suomeng Dong has quickly developed into one of the most energetic new wave scientists in this field, having studied several aspects of Phytophthora gene regulation, such as discovering m6A DNA methylation and alternative splicing pathways. He received prestigious awards such as Chinese National Science Fund for Excellent Young investigator and National Thousand Youth Talents Plan. Thus, the UK team would greatly benefit from the collaboration not only from an intellectual perspective but also from the practical aspects of technology transfer, method development and exchange of biomaterial. Visits to China would be extremely productive as they will tap into years of experience with Phytophthora, notably CRISPR/Cas gene editing. The collaboration would not only benefit the Kamoun Lab but also other groups at TSL that have an interest in P. infestans, e.g. the groups of Jonathan Jones and Wenbo Ma. This project will also strengthen links between the Norwich and China, given Centre of Excellence for Plant and Microbial Science (CEPAMS)-a budding partnership between the Norwich based John Innes Centre and the Chinese Academy of Sciences (CAS).
Impact 11 joint publications per PubMed (March 2021) https://pubmed.ncbi.nlm.nih.gov/?term=kamoun+AND+dong
Start Year 2012
 
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 The Sainsbury Laboratory, Norwich 
Organisation The Sainsbury Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of aphid samples, (HPLC-purified) aphid extracts and plant pull downs to analyze by mass spectrometry. Contribution of aphid, microbial and plant sequence data to analyze the mass spectrometry data against.
Collaborator Contribution Sample analyses with mass spectrometry and help with interpretation of the mass spectrometry data output.
Impact - An improved understanding of the physical properties of aphid elicitors that induce PTI-like plant defense responses.
Start Year 2018
 
Description Collaboration with University of Kyoto 
Organisation University of Kyoto
Country Japan 
Sector Academic/University 
PI Contribution Collaborator is involved in a research project of a PhD student in the lab
Collaborator Contribution Collaborator provided transgenic plant lines for screening
Impact Progress made with research goals of PhD student project
Start Year 2018
 
Description Collaboration with Vivianne Vleeshouwers 
Organisation Wageningen University & Research
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 the Lab of Frank Takken 
Organisation University of Amsterdam
Department Swammerdam Institute for Life Sciences
Country Netherlands 
Sector Academic/University 
PI Contribution Exchange of materials/expertise
Collaborator Contribution Exchange of materials/expertise
Impact Publication in New Phytologist
Start Year 2016
 
Description Collaboration with the Lab of Paul Birch 
Organisation James Hutton Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Exchange of materials/expertise
Collaborator Contribution Exchange of materials/expertise
Impact N/A at this time
Start Year 2012
 
Description Collaborations with The Sainsbury Laboratory 
Organisation John Innes Centre
Department The Sainsbury Laboratory
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Provide knowledge on the aphid-plant interactions experimental system.
Collaborator Contribution Colleagues at The Sainsbury Laboratory have contributed knowledge and expertise to a PhD student project in my lab.
Impact The PhD student made good progress with achieving research goals of his PhD project.
Start Year 2017
 
Description ENS Lyon 
Organisation École normale supérieure de Lyon (ENS Lyon)
Country France 
Sector Academic/University 
PI Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Collaborator Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Impact no output yet
Start Year 2019
 
Description Evolutionary mechanisms that equip wild potato with disease resistance against the notorious late blight pathogen (Phytophthora infestans) 
Organisation Wageningen University & Research
Country Netherlands 
Sector Academic/University 
PI Contribution Recognising the disease To defend itself the first thing the plant has to do is detect the pathogen. "The plant has receptors for this, a kind of antennas. These bind tiny pieces of Phytophthora protein, which is the signal that something is wrong. This is when the defense responses kick in. So it is very important that the plant can actually detect the disease and has the right receptors in place to activate its defences", says Vleeshouwers. These receptors are located either inside or on the surface of the cell. Receptors inside the cell are encoded by specific R genes (R stands for resistance), and potato breeders take advantage of these. They develop resistant varieties by selecting for these R genes. However, the problem is that the pathogen manages to break through that resistance, time and again. "Much less is known about the receptors on the outside, on the cell surface, the Pattern Recognition Receptors (PRRs). These receptors drive more general immune responses," Vleeshouwers says. Plant breeders are currently focusing their attention on R genes, but there is still a gap to be filled in the fundamental understanding of PRRs before the potential applications and benefits of less specific defensive responses can be explored in breeding robust disease resistance. To this end, Wageningen University & Research is cooperating with the University of Tübingen (Germany) and The Sainsbury Laboratory in Norwich (UK) to study the evolution and diversification of PRRs in potato.
Collaborator Contribution PERU Vleeshouwers explains, "We have been studying a specific type of PRR receptor called PERU. It binds a special piece of Phytophthora protein, Pep-13, which triggers the potato plant to recognise the disease. It was generally assumed that PRR receptors hardly change over time (a well-known example is the very stable receptor that recognises bacteria flagella). But we found that PERU actually exhibits dynamic evolution, and changes much faster than the more well-known PRR receptors. This is a totally new insight." According to co-research leader Thorsten Nürnberger of the Centre for Plant Molecular Biology (ZMBP) at the University of Tübingen, the research results show that the evolution of immune receptors on the cell surface of plants is much more complex than we previously thought.
Impact Sustainable cultivation This insight into this type of receptors (with more to follow) paves the way for the sustainable potato of the future. This sustainable crop could have R genes encoding for specific receptors within the cells, plus enhanced general defensive responses using PRRs on the cell surface. "Before today, breeders focused on R genes. However, the resistance they offer is constantly being thwarted. By studying how wild potato species survive in an environment where they are constantly assailed by diseases, we can discover what mechanisms they use, and then introduce these mechanisms in our own potato varieties," Vleeshouwers concludes.
Start Year 2022
 
Description Formal research collaboration with SESVanderHave 
Organisation Sesvanderhave
Country Belgium 
Sector Private 
PI Contribution My research group has provided advise on strategies to obtain aphid resistant sugar beet, exchanged knowledge on research progress in plant-insect interactions of the lab, and wrote BBRSC-LINK award to fund research.
Collaborator Contribution SESVanderHave provides access to sugar beet breeding lines, genome sequence resources for these lines and insecticide-free field sites for collection of aphid populations in UK and Europe. They also funded a postdoctoral researcher in my group for one year, contributed 50% in-kind funds for the BBSRC-LINK award and funds a iCASE studentship in my group. PhD student Roland Wouters was recruited for the iCASE project. Roland is making good progress.
Impact Generated knowledge on plant-insect interactions. Organized visits of the SESVanderHave team to JIC (two times per year) and my group at JIC to SESVanderHave headquarters in Tienen, Belgium (two times per year). Organized regular Skype calls to discuss research progress and ideas for future research.
Start Year 2013
 
Description Partnership with 2Blades Foundation 
Organisation Two Blades Foundation
Country United States 
Sector Charity/Non Profit 
PI Contribution Discovery program for plant immune receptors
Collaborator Contribution know-how, biological material and plant transformation
Impact Scientific and economic outputs, incl. patents.
Start Year 2017
 
Description Plant Response Biotech 
Organisation Plant Response Biotech S.L.
Country Spain 
Sector Private 
PI Contribution This is an iCASE studentship with Plant Response Biotech. We have generated transgenic tomato homozygous lines expressing individual Arabidopsis receptor kinases belonging to the sub-family XII of LRR-RLKs. We have generated single and multiple insertional Arabidopsis mutants for LRR-RLK sub-family XII members.
Collaborator Contribution The lines generated above will be tested at the end of year at Plant Response Biotech by the student employed in this project for disease resistance. The partner will provide lab space, consumable costs, access to growth chambers, access to relevant pathogens, and access to proprietary plant-derived and microbial elicitors.
Impact not applicable yet.
Start Year 2015
 
Description Structural studies of plant NLRs by cryo-EM 
Organisation University of Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution As part of a project to investigate the potential of using plant expression systems to produce plant intracellular immune receptors (NLRs) for structural studies, we expressed and purified the plant NLRs NRC4 and Pikp-1 from N. benthamiana. This was accomplished through epitope tagging and gel filtration. This material was then tested for suitability for structural studies by cryo-EM using the equipment and expertise at the University of Leeds
Collaborator Contribution Our partners in Leeds provided expert advice and experimental knowledge towards optimising our experiments and access to the relevant equipment.
Impact A BBSRC grant application has been submitted that, in part, built on the data acquired during this collaboration. We are awaiting a decision.
Start Year 2017
 
Description UNC 
Organisation University of North Carolina at Chapel Hill
Country United States 
Sector Academic/University 
PI Contribution exchange of published and unpublished biomaterials; sharing of unpublished data
Collaborator Contribution exchange of published and unpublished biomaterials; sharing of unpublished data
Impact no output yet
Start Year 2019
 
Description University of Geneva 
Organisation University of Geneva
Department Faculty of Sciences
Country Switzerland 
Sector Academic/University 
PI Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Collaborator Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Impact no outputs yet
Start Year 2019
 
Description University of Tuebingen 
Organisation Eberhard Karls University of Tübingen
Country Germany 
Sector Academic/University 
PI Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Collaborator Contribution exchange of published and unpublished biomaterials, sharing of unpublished data
Impact stil no outputs
Start Year 2019
 
Description Wheat Disease Early Warning Advisory System (Wheat DEWAS) 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution CIMMYT has launched the Wheat Disease Early Warning Advisory System (Wheat DEWAS), funded through a $7.3 million grant from the Bill & Melinda Gates Foundation and the United Kingdom's Foreign, Commonwealth & Development Office, to enhance crop resilience to wheat diseases. Wheat DEWAS is designed to help safeguard wheat productivity and advance sustainable agricultural practices in collaboration with international partners, including researchers at the John Innes Centre, The Sainsbury Laboratory and GetGenome.
Collaborator Contribution Led by David Hodson from CIMMYT and Maricelis Acevedo from Cornell University, this ambitious project brings together a global team of experts. Professor Sophien Kamoun is particularly delighted to expand collaboration with CIMMYT and African scientists, developing and expanding the cutting-edge platforms for genomic surveillance of wheat pathogen. Open science and international collaborations were at the core of the successful tracing and identification of wheat blast clones after the devastating wheat disease spread to two other continents. By creating the website Open Wheat Blast, the rapid sharing of data was facilitated between researchers, which proved crucial for tracking wheat blast pathogens and ensured that all contributions were appropriately credited. This resulting publication was recently highlighted as an exemplary way of working with the Global South in an article calling for more collaborative authorship practices. GetGenome, a charitable initiative that aims to provide equitable access to genomic technologies, was inspired by these principles and is designed to enable open science and data sharing with contributions properly credited from the start.
Impact The combination of rapid identification of emerging variants together with pathotyping to assess the variants' potential to impact wheat production will inform the generation of a list of Variants of Concern. This valuable data will be shared with project partners and contribute to the deployment of effective disease management strategies.
Start Year 2023
 
Title COLD SHOCK PROTEIN RECEPTORS AND METHODS OF USE 
Description Methods are provided for enhancing the resistance of plants to plant pathogens. The methods involve transforming a plant with a nucleic acid construct comprising a nucleotide sequence that encodes a cold shock protein receptor for a cold shock protein. Further provided are nucleic acid molecules, transformed plants, plant cells, and seeds and methods of using the transformed plants and seeds in agriculture. 
IP Reference WO2017062790 
Protection Patent application published
Year Protection Granted 2017
Licensed No
Impact Discussions in progress with companies, as well as massive interest from the community to implement this approach to identify additional novel immune receptors.
 
Title LATE BLIGHT RESISTANCE GENE FROM SOLANUM AMERICANUM AND METHODS OF USE 
Description Compositions and methods and for enhancing the resistance of plants to a plant disease caused by a Phytophthora species are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of a plant to a plant disease caused by a Phytophthora species comprise introducing a nucleic acid molecule encoding an R gene product into a plant cell. Additionally provided are methods for using the plants in agriculture to limit plant disease. 
IP Reference WO2016182881 
Protection Patent application published
Year Protection Granted 2016
Licensed Yes
Impact None yet, beyond licensing to Simplot We are using Rpi-amr3 in our HAPI grant
 
Title LATE BLIGHT RESISTANCE GENES AND METHODS OF USE 
Description Compositions and methods and for enhancing the resistance of plants to a plant disease caused by a Phytophthora species are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of a plant to a plant disease caused by a Phytophthora species comprise introducing a nucleic acid molecule encoding an R gene product into a plant cell. Additionally provided are methods for using the plants in agriculture to limit plant disease. 
IP Reference WO2018112356 
Protection Patent application published
Year Protection Granted 2018
Licensed Yes
Impact we have carried out field trials with Rpi-amr1e
 
Title METHODS OF ENHANCING THE RESISTANCE OF PLANTS TO BACTERIAL PATHOGENS 
Description Methods are provided for enhancing the resistance of plants to bacterial pathogens. The methods involve transforming a plant with a polynucleotide molecule comprising a plant promoter operably linked to a nucleotide sequence that encodes a plant receptor that binds specifically with bacterial elongation factor-Tu. Further provided are expression cassettes, transformed plants, seeds, and plant cells that are produced by such methods. 
IP Reference WO2010062751 
Protection Patent granted
Year Protection Granted 2010
Licensed Yes
Impact several crops expressing EFR are now being generated across the world, with some of them being son tested in field trials.
 
Title METHODS, MEANS AND COMPOSITIONS FOR ENHANCING AGROBACTERIUM-MEDIATED PLANT CELL TRANSFORMATION EFFICIENCY 
Description Higher eukaryotes sense microbes through perception of pathogen-associated molecular patterns (PAMPs). The flagellin receptor FLS2 represents so far the only known pattern recognition receptor (PRR) in Arabidopsis. Arabidopsis plants detect a variety of PAMPs including specific epitopes of the bacterial proteins flagellin and EF-Tu. Here, we show that flagellin and EF-Tu activate a common set of signalling events and defence responses, but without clear additive or synergistic effects. Treatment with either PAMP results in increased receptor sites for both PAMPs, a finding employed in a reverse-genetic approach to identify the receptor kinase EFR as the EF-Tu receptor. Transient expression of EFR in Nicotiana benthamian 
IP Reference WO2007068935 
Protection Patent application published
Year Protection Granted 2007
Licensed Yes
Impact not applicable at this stage
 
Title POTYVIRUS RESISTANCE GENES AND METHODS OF USE 
Description Compositions and methods and for enhancing the resistance of plants to plant diseases caused by potyviruses are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of a plant to plant disease caused by a potyvirus comprise introducing a nucleic acid molecule encoding an R gene product into a plant cell. Additionally provided are methods for using the plants in agriculture to limit plant disease. 
IP Reference WO2019023587 
Protection Patent application published
Year Protection Granted 2019
Licensed Commercial In Confidence
Impact we have a manuscript published in bioarxiv and under review at plant biotech journal
 
Title WHEAT STRIPE RUST RESISTANCE GENES AND METHODS OF USE 
Description Compositions and methods for enhancing the resistance of wheat and barley plants to wheat stripe rust caused by Puccinia striiformis f. sp. tritici are provided. The compositions comprise nucleic acid molecules encoding resistance (R) gene products and variants thereof and plants, seeds, and plant cells comprising such nucleic acid molecules. The methods for enhancing the resistance of wheat and barley plants to wheat stripe rust comprise introducing a nucleic acid molecule encoding an R gene product into a wheat or barley plant cell. Additionally provided are methods for using the wheat and barley plants in agriculture to limit wheat stripe rust. 
IP Reference US2018320195 
Protection Patent application published
Year Protection Granted 2018
Licensed Yes
Impact Identification of a functional resistance gene from barley against wheat stripe rust, a major pathogen of wheat. The gene is currently being tested in wheat for function, with the plan to include it in resistance gene cassettes.
 
Title QKbusco 
Description A set of scripts that merge BUSCO orthologous genes for phylogenetic analysis. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Development of the most comprehensive phylogenetic tree of the Poales. Scripts can be used by anyone seeking to develop a phylogenetic tree from diverse data sets (genome or transcriptome). 
URL https://github.com/matthewmoscou/QKbusco
 
Title QKcartographer 
Description A set of scripts for preparing data, for QTL analysis using QTL Cartographer 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact These scripts predominantly enable researchers to utilise command line-based QTL Cartographer, coupled with R, to generate ggplot2-based plots. 
 
Title QKdomain 
Description A set of scripts that can be used for protein domain analysis. The majority of which are developed to process files for input/output to/from InterProScan, MEME Suite, and phylogenetic analysis. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Used in several manuscripts to analyse protein domain structure. Broadly useful to anyone seeking to study proteins with complex domain structure. 
URL https://github.com/matthewmoscou/QKdomain
 
Title QKgenome 
Description A set of scripts for converting genomes based on resequencing information. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Used in several manuscripts in preparation to analyze intraspecific variation. The scripts are being used by a number of collaborators to analyze population level data. 
URL https://github.com/matthewmoscou/QKgenome
 
Title QKphylogeny 
Description A set of scripts for phylogenetic tree assessment and editing. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Used by several groups and other software packages as dependencies for the analysis of multiple sequence alignments and phylogenetic trees. 
URL https://github.com/matthewmoscou/QKphylogeny
 
Title QKutilities 
Description Suite of scripts for manipulating sequence data, analyzing protein sequence, and parsing GFF3 files. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Scripts were used in the publication of Hiebert, Moscou et al. (2020) Nature Communcations. Open access ensure reproducibility and access to broader audiences. 
URL https://github.com/matthewmoscou/QKutilities
 
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, Benjamin Petre, Tolga Bozkurt, Joe Win, & Sophien Kamoun. (2019). Phytophthora RXLR-WY effectors cooperate to modulate host vesicle trafficking. Zenodo. http://doi.org/10.5281/zenodo.3349841

Erin Zess, Yasin Dagdas, Abbas Maqbool, Tolga O Bozkurt, Mark Banfield, & Sophien Kamoun. (2019). Effector adaptation in a host-specialized lineage of Phytophthora. Zenodo. http://doi.org/10.5281/zenodo.3349901

Chih-Hang Wu, & Sophien Kamoun. (2019). A genetically unlinked NLR network that modulates plant immunity against diverse pathogens originated from an ancestral gene cluster. Zenodo. http://doi.org/10.5281/zenodo.3350801

Hiroaki Adachi, Mauricio Contreras, Adeline Harant, Chih-hang Wu, Lida Derevnina, Toshiyuki Sakai, Sophien Kamoun. (2019). A widely conserved N-terminal motif in the coiled-coil domain of NLR immune receptors is required for activation of hypersensitive cell death. Zenodo. http://doi.org/10.5281/zenodo.3349850

Thorsten Langner, Luis B. Gomez-Luciano, Adeline Harant, Joe Win, & Sophien Kamoun. (2019). The dark matter of genomics: mini-chromosomes as drivers of host adaptation in the blast fungus. Zenodo. http://doi.org/10.5281/zenodo.3349735

Yohann Petit, Joe Win, Thorsten Langner, Adeline Harant, Ryohei Terauchi, Mark Banfield, & Sophien Kamoun. (2019). New effectors from the multihost blast fungus Magnaporthe oryzae target HMA domain containing host proteins. Zenodo. http://doi.org/10.5281/zenodo.3352212
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 brief introduction to Pioneering Women in Plant Pathology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact In this video, Sophien Kamoun briefly introduces the inspiring book "Pioneering Women in Plant Pathology".

Learn about pioneering woman plant pathologists Johanna Westerdijk, Eva Sansome, and................Rosalind Franklin.

The book was published by the American Phytopathological Society and edited by Jean Ristaino. Get your own copy at https://my.apsnet.org/ItemDetail?iProductCode=43597
Year(s) Of Engagement Activity 2020
URL https://youtu.be/Mr5XC5d_gfg
 
Description Academic presentation to Chinese Academy of Sciences (CAS), Shanghai, China (Virtual) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Academic presentation to Chinese Academy of Sciences (CAS), Shanghai, China (Virtual)
Year(s) Of Engagement Activity 2021
 
Description ActualFruitVeg: Los tomates y la diversidad 
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 News article in Spanish magazine about genome edited tomato Tomelo.

Sophien Kamoun, estudia las enfermedades de las plantas en el Laboratorio de Sainsbury en Inglaterra, y en marzo su equipo publicó un documento que describía un tomate que habían modificado. Utilizando la técnica de edición de genes Crispr / Cas9 , el grupo de Kamoun cortó un trozo de un gen llamado Locus O resistente a los hongos, o Mlo. Esa eliminación hace que el tomate sea resistente al mildiu polvoriento, un grave problema agrícola que requiere una gran cantidad de productos químicos para controlar.

El "Tomelo" de Kamoun se parece mucho a un tomate natural, un mutante con la misma resistencia. "Al menos en las plantas de tomate que tenemos, no hubo diferencia detectable entre el mutante y el tipo salvaje", dice Kamoun.

El trabajo de Kamoun está detenido. Las regulaciones europeas convierten a las plantas genéticamente modificadas en ilegales. Los investigadores como Kamoun pueden tener conocimientos y hacer ensayos científicos para modificar la genética de las plantas pero no pueden llevarlos a ensayarlos en el campo. No pueden registrar estas plantas y comercializar variedades de tomates genéticamente modificados. En EEUU hay más oportunidades en ésta actividad científica. En Europa hay un gran signo de interrogación; "estoy muy frustrado por esto, tengo que ser honesto. Científicamente, esta planta, el "Tomelo" no es diferente de cualquier mutante que obtengamos de la reproducción tradicional o la mutagénesis tradicional, explica Kamoun
Year(s) Of Engagement Activity 2018
URL https://actualfruveg.com/2018/06/09/los-tomates-y-la-diversidad/
 
Description Agence nationale de la recherche - Co-vice chair of CES20 panel 
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 ANR grant panel review, influencing the research direction of science in France.
Year(s) Of Engagement Activity 2020
URL https://anr.fr/
 
Description Agence nationale de la recherche - Co-vice chair of CES20 panel 
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 ANR grant panel review, influencing the research direction of science in France.
Year(s) Of Engagement Activity 2020
URL https://anr.fr/
 
Description Agence nationale de la recherche - Member of CES20 panel 
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 ANR grant panel meeting, decisions influence the scientific direction of France. Panel includes predominantly international scientists.
Year(s) Of Engagement Activity 2019
URL https://anr.fr/
 
Description AgriGenomics, BOKU seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk to postgraduate students and faculty at BOKU for improving plant health.
Year(s) Of Engagement Activity 2021
 
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 Appointed to Deputy Chair BBSRC Responsive mode committee B 
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 Appointed to Deputy Chair BBSRC Responsive mode committee B - committee reviews responsive mode grants for scientific projects, awarding funding for successful applications
Year(s) Of Engagement Activity 2019
 
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 BBSRC Grant Review Panel 19RM1 - Deputy Chair 
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 BBSRC Resopnsive Mode grant panel meeting
Year(s) Of Engagement Activity 2019
 
Description BBSRC Grant Review Panel 19RM2 - Deputy Chair 
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 BBSRC grant review panel
Year(s) Of Engagement Activity 2019
 
Description BBSRC Grant Review Panel 19RM3 - Deputy Chair 
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 BBSRC grant review panel
Year(s) Of Engagement Activity 2020
 
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 Biologist: "The mobilization of our country's scientists has been impressive" 
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 Professor Sophien Kamoun, group leader at the Sainsbury Laboratory, discusses how he and his colleagues have pivoted from studying plant pathogens to tracing a human pathogen at the heart of a global emergency, and how scientists unable to access wet labs can still contribute to research.

Can you describe what your role involved before the COVID-19 pandemic and how your focus has changed because of the pandemic?

I normally investigate topics related to plant pathology and plant immunity. The COVID-19 pandemic hasn't changed the focus of my research, but I was tasked within our laboratory to coordinate projects on innovations that could rapidly scale-up diagnostics.

Please tell us about any COVID-19 related projects you have been involved with and what they have achieved so far.
We used a bottom-up approach, which fits best with the ethos of The Sainsbury Laboratory. First we made an open call for ideas and volunteers in late March. I was truly impressed by the willingness of many of our scientists-from students to team leaders-to contribute their expertise and know-how.
Two teams immediately came together and sprung into action. One team has focused on implementing the Cas13a/SHERLOCK method for SARS-CoV-2 detection, while the second one is working on adapting "toehold switch" detection to this coronavirus. At the moment we are still testing these protocols with synthetic controls and haven't yet worked with clinical samples.

We're interested in how science works during a crisis, and how scientists have responded to these unprecedented circumstances. What have you done differently owing to this being an urgent, emergency situation?

First, it's important to appreciate that people respond differently to a crisis like this. My first advice to everyone in my team and my collaborators was to carefully consider their own mental state and address any anxiety they may experience. I personally find exercise, meditation music and connecting with friends and family to be very helpful in relieving stress. It's rather useless to try to get intellectual work done when you're in the wrong frame of mind. This is true at any time but it's even more relevant during this situation. So just like athletes before a sporting event, scientists need to learn to chill and relax.

The second advice is to revisit objectives and expectations. I advised my team to have a plan. What are your revised goals? How realistic are they? What would it take to achieve them?
Perhaps there is also a silver lining in this crisis. In biology, everyone has been busy producing huge amounts of data. But if the data isn't shared and published, it's generally useless. Now that we are kept away from the wet labs, perhaps there is more time to process and share unpublished datasets. If you have such data, then this is the time to curate it and share it. There are many open platforms that allow you to publish datasets and barebone mini-publications, which shouldn't take that long to produce.

The prevailing paradigm in biology is that those who produce the data are expected to publish it. But why should that always be the case? If the dataset is worth sharing, then anyone who curates it and analyses it should be in a position to publish it (with due credit to everyone involved of course). That still would be a valued and valuable contribution to add to a CV. We have identified such old unpublished datasets in my lab, and we hope that any extra time offered by this situation would allow us to share and release these data in the coming weeks.

How are you communicating information from your work so that it can be utilised around the world?

Beyond the typical channels, social media continues to serve as a key medium for communicating and disseminating information. Many scientists are on Twitter and I have been posting more frequently on Facebook to reach out to scientists in developing countries given that they tend to be more active on this platform. For instance, Facebook has proven important for sharing knowledge with communities and help groups in Tunisia, my country of origin.

It's also worth highlighting the key role that preprint servers have played in this crisis. First, preprints, such as bioRxiv and medRxiv, have accelerated the dissemination of new COVID-19 research. Second, preprints allow immediate sharing of all those papers that scientists are writing up during lockdowns. As an affiliate for bioRxiv, I get to see and approve submitted papers, and there has been up to 200 papers in the queue. I don't think the classic journal model can cope with such a surge in submissions as the system is overloaded. Just imagine how we would cope without bioRxiv at the moment! All that good science that would be held up for months and months for no one to see.

Can you talk us through some of the challenges of working during these strange times, for example the adaptations required to keep yourself and staff safe; trying to source in-demand equipment and reagents; or the effect on non-COVID research projects/departmental business?

The Sainsbury Laboratory and other Institutes on the Norwich Research Park reacted proactively to the crisis. I think the fact that we have a lot of contact with colleagues in China made us more attuned to the scale of the problem. We implemented social distancing and reduced occupancy policies early, in the week of March 9th.

We have made our own hand-sanitiser and distributed it widely. Some of our staff arranged to collect and distribute PPE to the hospital, including masks received from collaborators in China. In addition, several members of our Laboratory have volunteered at the Norfolk and Norwich University Hospitals to help scale-up COVID-19 diagnostics.

The laboratory is currently closed except for essential maintenance work and the COVID-19 projects. Most of the other work that is currently taking place is either computational or focused on analysing and publishing previously generated data. All meetings have moved to online platforms.

How would you describe the bioscience sector's interaction with public health bodies and Government?

I think the sector has fully engaged with the crisis. The mobilization of our country's scientists has been impressive, as evidenced for example by the number of volunteers. However, like many of my colleagues, I was surprised by the government's initial response - the general impression I had is that there was a period of laisser-faire before robust measures were implemented. It seemed imprudent to me that as Lombardy went into lockdown, you couldn't take a train from Milan to Rome but you could fly from Milan to Heathrow with absolutely no checks whatsoever upon arrival.

I was also stunned by the infamous press briefing of Thursday March 12th when the mitigation strategy of herd immunity was announced. Fortunately, the scientific community reacted strongly, and I was very impressed by the broad pushback. I agree with the view that, in due time, we must investigate what happened to be better prepared for the next pandemic.
Looking forward, I hope that there will be a better appreciation of the importance of curiosity-driven fundamental research. Let's reflect on the fact that COVID-19 diagnostics are based on PCR-a method that was discovered through a scientist's creative exploration of an idea, not through top-down impact driven research.
Year(s) Of Engagement Activity 2020
URL https://thebiologist.rsb.org.uk/biologist-covid-19/189-biologist/biologist-covid-19/2327-the-mobiliz...
 
Description Can a Biologist Fix a Smartphone? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Prof. Sophien Kamoun, FRS, will explore this idea using the smartphone as a metaphor for living organisms. He will discuss how the capacity to read and edit the genetic language encoded in the genome has enabled biologists to access the codical domain of living systems in an unprecedented fashion.
Year(s) Of Engagement Activity 2020
URL https://youtu.be/IrIQt1BHWkQ
 
Description Cereals 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Talk at the Cereals 2021 event. The talk initiated discussion with farmers and industrial representatives in the audience about future of plant based proteins.
Year(s) Of Engagement Activity 2021
 
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 Conference Talk - An 'integrated' approach to improving disease resistance 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 3rd International Conference "Plant Biotic Stresses & Resistance Mechanisms", Vienna, Austria - opportunity for researchers in the field to network, collaborate and exchange ideas
Year(s) Of Engagement Activity 2018
 
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 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 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 Don't perish! A step by step guide to writing a scientific paper 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Sophien Kamoun's presentation to the Norwich research Park PhD student. A step by step guide to writing scientific papers. April 1, 2020.

See slides at https://www.slideshare.net/SophienKamoun/dont-perish-a-step-by-step-guide-to-writing-a-scientific-paper

See summary and notes at https://kamounlab.tumblr.com/post/614297962173120512/dont-perish-a-step-by-step-guide-to-writing-a

This presentation is part of a workshop about writing scientific papers. It describes a 10 step guide for writing papers.

1. Create a folder
2. Write a story line
3. Make list of Figures
4. Finalize Figures
5. Write the Results
6. Write the Intro
7. Write the Discussion
8. Assemble the Abstract
9. Write the Title
10. Post it on bioRxiv
Year(s) Of Engagement Activity 2020
URL https://youtu.be/LUmf7vEFxYI
 
Description Effectorome meeting in Montpellier, France 
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 Conference attendance
Year(s) Of Engagement Activity 2019
 
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 Industry - Visit from Corteva and Indigro 
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 Engagement with Industry - Visit from Corteva and Indigro
Year(s) Of Engagement Activity 2022
 
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 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019
 
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 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 External Assessor for academic Tenure process at University of Dundee, UK. 2018 
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 External Assessor for academic Tenure process at University of Dundee, UK. 2018 - part of panel assessing suitability of candidate to become permanent research leader at University of Dundee
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 Farmers Guardian July 22 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact message regarding blight resistant potato "Genetic innovation is a crucial driver of productivity gains in agriculture, in reducing the environmental footprint of food production and in reducing the need for additional land to be brought into cultivation for supply to match growing demand.
Year(s) Of Engagement Activity 2022
 
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 Food Thinkers Series: 'Dysfunctional regulation of GM crops; scope for improvement post-Brexit?', Presentation for Food Research Collaboration, Centre for Food Policy (CFP) City University London, February 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Food Thinkers Series: 'Dysfunctional regulation of GM crops; scope for improvement post-Brexit?', Presentation for Food Research Collaboration, Centre for Food Policy (CFP) City University London, February 2017
Year(s) Of Engagement Activity 2016
URL http://foodresearch.org.uk/food-thinkers-dysfunctional-regulation-of-gm-crops-scope-for-improvement-...
 
Description GROW Webinar: CRISPR Crops: Plant Genome Editing Made Easy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In the second GROW Webinar, Dr. Sophien Kamoun, head of the Sainsbury Laboratory, presented on CRISPR Crops: Plant Genome Editing Made Easy, with a closer look at CRISPR advances in plant science and their relevance to genebanks and conservation.
Year(s) Of Engagement Activity 2021
URL https://vimeo.com/513893418
 
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 Hosted and led discussion about GM crops after public screening of Food Evolution during Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Hosted and led discussion about GM crops after public screening of Food Evolution during Norwich Science Festival
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/food-evolution-the-movie/
 
Description Hosting of Milind Sood, BSc student, University of Oxford, UK. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Will do a research project in my lab as part of the JIC/TSL/EI International Undergraduate Summer School programme at JIC, Jun-Aug 2019.
Year(s) Of Engagement Activity 2019
 
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 IS-MPMI Scientific Conference 
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 Attendance at International Society of Molecular Plant Microbe Interactions in Glasgow, Scotland.
Year(s) Of Engagement Activity 2019
 
Description IS-MPMI conference, Glasgow, Scotland - Local organising committee 
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 Member of local organising committee for IS-MPMI conference, Glasgow, Scotland to take place in July 2019
Year(s) Of Engagement Activity 2019
URL https://www.ismpmi.org/Congress/2019/Pages/default.aspx
 
Description ISMPMI Webinar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Webinar on the molecular basis of non-host resistance presented to appoximately 300 scientists from around the world. There was a question and answer sessions after the presentation to discuss current knowledge and gaps in the field.
Year(s) Of Engagement Activity 2021
URL https://www.ismpmi.org/members/Interactions/Lists/Posts/Post.aspx?ID=379
 
Description International Rice Blast Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference attendance
Year(s) Of Engagement Activity 2019
 
Description Interview and blog with the Genetic Literacy 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 Development of a blog based on my interaction with journalists at the Genetic Literacy project. The blog is entitled 'The grass has never been greener for engineering plant immunity and resilience'.
Year(s) Of Engagement Activity 2020
 
Description Interview for BBC News on fighting wheat stem rust 
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 Gave a telephone interview on a recent article from Science, which was a perspective piece on two major studies. Provided information related to the impact of this work on epidemiology of wheat stem rust and current challenges in countering this deadly pathogen.
Year(s) Of Engagement Activity 2017
URL http://www.bbc.co.uk/news/science-environment-42446795
 
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 on Talking Biotech podcast with Paul Vincelli 
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 http://www.talkingbiotechpodcast.com/065-plant-r-genes-and-their-applications/
Year(s) Of Engagement Activity 2017
URL http://www.talkingbiotechpodcast.com/065-plant-r-genes-and-their-applications/
 
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 Invited Seminar - Dept. of Plant Sci, University of Geneva, Switzerland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presented and discussed our lab's APH research. Had 1-to-1 meetings with several group leaders and students.
Year(s) Of Engagement Activity 2022
 
Description Invited Seminar: Dept. of Biology, University of York, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Presented research to the department and had 1-to-1 meetings with several group leaders their lines of research in addition to my own.
Year(s) Of Engagement Activity 2023
 
Description Invited Seminar: Dept. of Plant and Micro. Biol., University of Zurich, Switzerland. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited departmental seminar in the Dept. of Plant and Micro. Biol., University of Zurich, Switzerland.
Year(s) Of Engagement Activity 2023
 
Description Issue of JIC Advances magazine (January) focussed on Plant Health (Intro. to UN International Year of Plant Health) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Issue of JIC Advances magazine (January) focussed on Plant Health (Intro. to UN International Year of Plant Health)
Year(s) Of Engagement Activity 2020
 
Description Keeping up with the plant killers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The United Nations has declared 2020 the International Year of Plant Health (IYPH). In this timely talk, Prof. Sophien Kamoun introduces you to the secret life of the parasites that colonise plants. Ever since Heinrich Anton de Bary called the microbe that causes the potato blight a plant killer, we have learned much about how these microbes cause disease and fight off the plant immune system. Some of these plant pathogens even turn their plant hosts into living puppets or Zombie plants. Others are threatening our crops and driving the global food crisis. Plant pathologists like Sophien Kamoun are hard at work learning more about these parasites and applying new knowledge and technologies to build disease-resistant crops.

The speaker for this talk was Professor Sophien Kamoun, Senior Scientist at The Sainsbury Laboratory and Professor of Biology at The University of East Anglia

The Linnean Society of London is the world's oldest active biological society. Founded in 1788, the Society takes its name from the Swedish naturalist Carl Linnaeus (1707-1778).

https://www.linnean.org/

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Year(s) Of Engagement Activity 2020
URL https://youtu.be/R5GJWHmq2_k
 
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 Keynote speaker at ISMPMI meeting Glasgow 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I was plenary speaker at ISMPMI meeting Glasgow 2019
Year(s) Of Engagement Activity 2019
 
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 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 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 New research to understand disease resistance in crops 
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 Other audiences
Results and Impact Press release
Year(s) Of Engagement Activity 2022
URL https://www.diamond.ac.uk/Science/Research/Highlights/2022/new-research-understand-disease-resistanc...
 
Description New scientist live food and agriculture event The crop doctors. 
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 New scientist live food and agriculture event The crop doctors.
Year(s) Of Engagement Activity 2020
 
Description Norwich Science Festival 2017 
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 The Sainsbury Laboratory, including members of my research group, actively participated in the Norwich Science Festival, which showcases research currently going on at The Sainsbury Laboratory. Several hands on activates promote the general public engagement in science, including stamp a leaf in agar and Nicotiana infiltrations. Our booth is highly visited, with over 1,000 interactions experienced during the breadth of the Festival.
Year(s) Of Engagement Activity 2017
URL http://norwichsciencefestival.co.uk/about/norwich-science-festival-2017/
 
Description Norwich Science Festival 2018 
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 The Sainsbury Laboratory, including members of my research group, actively participated in the Norwich Science Festival, which showcases research currently going on at The Sainsbury Laboratory. Several hands on activates promote the general public engagement in science, including stamp a leaf in agar, a late blight demonstration, child-friendly microscopy, and Nicotiana infiltrations. Our booth is highly visited, with over 1,000 interactions experienced during the breadth of the Festival.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/
 
Description Norwich Science Festival 2019 
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 The Sainsbury Laboratory, including members of my research group, actively participated in the Norwich Science Festival, which showcases research currently going on at The Sainsbury Laboratory. Several hands on activates promote the general public engagement in science, including stamp a leaf in agar, a fact session on genetically modified crops, child-friendly microscopy, and Arabidopsis necklaces (by transplanting Arabidopsis into a 1.5 mL microcentrifuge tube). Our booth is highly visited, with over 1,000 interactions experienced during the breadth of the Festival.
Year(s) Of Engagement Activity 2019
URL https://norwichsciencefestival.co.uk/
 
Description Open Science in the Age of Pandemics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented at the Annual Meeting of the Southern African Society for Plant Pathology, January 20th, 2021. Hosted by FABI https://www.fabinet.up.ac.za
Year(s) Of Engagement Activity 2021
URL https://youtu.be/PGh-klsemiM
 
Description Organised session of accessible science talks for schools 
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 Leading scientists from JIC and TSL presented their work in a accessible manner for support staff and pupils from 6 regional schools.
Year(s) Of Engagement Activity 2022
 
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 PAG2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Talk at the Plant and Animal Genome Conference 2022
Year(s) Of Engagement Activity 2022
 
Description Participation in autumn workshop of The Sainsbury Laboratory 
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 Participated in the autumn workshop of The Sainsbury Laboratory. A PhD student in my group gave a talk and received substantial feedback.
Year(s) Of Engagement Activity 2019
 
Description Plantae: LOCKDOWN CONVERSATIONS How to tide over the Covid-19 pandemic? 
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 "Revisit your objectives and expectations. Have a plan"

1. This current lockdown seems to be unprecedented in recent history. How is your lab coping up?
These are challenging and uncertain times for all of us and for our friends and families. I have encouraged everyone in my lab to regularly check in and update the team on how they are doing and so on. I have also encouraged everyone to make use of the lab network as much as possible to stay connected and seek help as needed. We've also continued our lab meeting through Zoom and started a weekly journal club.
2. What pieces of suggestion would you offer early career researchers on utilizing this time?
First, it's important to appreciate that people respond differently to situations like this. My first advice would be to carefully consider your own mental state and address any anxiety you may experience. I think it's useless to try to get intellectual work done when you're in the wrong frame of mind. This is generally true and it's even more relevant during this time. So, just like an athlete before a sporting event, scientists need to learn to chill and relax.

The second point is to revisit your objectives and expectations. Have a plan.
Otherwise, it's been said elsewhere that researchers can engage in a number of activities that do not require a wet lab: writing, reading, training, computational analyses etc. In biology, everyone has been busy producing data. It's data, data, data! But if the data isn't shared and published, it's generally useless. Now, perhaps there is more time to process and share unpublished datasets. There are many open platforms that allow you to publish datasets and bare-bone mini-publications, which shouldn't take that long to produce.

If the dataset is worth sharing, then anyone who curates it and analyses it should be in a position to publish it (with due credit to everyone involved of course). That still would be a valued and valuable contribution to add to a CV. We have identified such old unpublished datasets in my lab, and we hope that the extra time offered by this situation would allow us to share and release these data in the coming weeks.
3. How is the cooperation of members in your lab and institute? How do you keep track of their work progress?
It's the same as always. We continue our weekly lab meeting and that's our primary forum through which lab members update everyone about their projects. We also have ad-hoc team meetings as needed. The only difference is that this has gone online, but Zoom is working just fine and I'm amazed at how quickly everyone has adjusted to this model.
4. Some journals have come up with guidelines to support researchers in this time of difficulty. What do you think is the role of journals at this time and what more do you think they can do?
I'm much more interested in highlighting the key role of preprint servers in this crisis. First, preprints, such as bioRxiv and medRxiv, have accelerated the dissemination of new COVID-19 research. Second, preprints allow immediate sharing of all those papers that scientists are writing up during lockdowns. I don't think the classic journal model can cope with a surge in submissions as the system is already overloaded. Many articles will get stuck in the outdated model of journal pre-publication peer review. Just imagine how we would cope without bioRxiv at the moment. All that good science would be held up for months and months for no one to see except for an editor and a few reviewers.
5. Do you think this time might serve as a cooling-off period for researchers from the usual monotony of lab work? If so, how productive do you foresee the immediate future after the restoration of normalcy?
Scientific research should never be monotonous. Who says planning, executing and interpreting experiments can be boring? As my friend and colleague Ken Shirasu likes to remind us, "Science is the ultimate entertainment for humankind." So just enjoy and cherish being a scientist whether you're in a lab or at home.
Year(s) Of Engagement Activity 2020
URL https://community.plantae.org/article/5518989600502056934/lockdown-conversations
 
Description Presentation at North Dakota State University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dissemination of research results to the faculty of Plant Pathology at North Dakota State University (NDSU), as well as post-graduate and undergraduate students at NDSU. In addition to discussing scientific outcomes, this presentation was critical for establishing and maintaining additional collaborative projects with members of the department.
Year(s) Of Engagement Activity 2020
 
Description Presentation at Technische Universität München 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presentation to university faculty and students on map-based cloning of genes involves in resistance to non-adapted pathogens including Rps6, Rps7, and Rps8.
Year(s) Of Engagement Activity 2018
 
Description Presentation at the International Conference on Plant Pathology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented work encompassing the cloning of Rps7 (Mla) and Yrr1, Yrr2, and Yrr3 in Brachypodium.
Year(s) Of Engagement Activity 2018
 
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 for research paper 
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 Press release about a research publications
Year(s) Of Engagement Activity 2018
 
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 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 Royal Norfolk Show 2022 
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 The Sainsbury Laboratory showcases their plant health and disease research at the Royal Norfolk Show, engaging with policymakers, industry, and farmers about specific projects, such as late blight resistant GM potatoes. In 2022 TSL had a stand in the Discovery Zone which focused on educating school children. Visitors gain insight into the importance of research and genetic technologies in addressing global issues, while scientists benefit from valuable science communication experience and new perspectives from interactions with the public. Conversations on GM for disease-resistant plants were enlightening for both scientists and participants.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description Royal Society Creating Connections Conference 2023 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The aim of the Genetic Technologies for Agriculture session was to bring together representatives from academia, industry and policymaking to discuss the role of genetically modified organisms in plant breeding and how GMOs should be regulated. Jonathan Jones chaired the session and discussions were captured to inform Royal Society Proposals for Outcomes-Based regulation in plants
Year(s) Of Engagement Activity 2023
URL https://royalsociety.org/science-events-and-lectures/2023/01/creating-connections-east-of-england/
 
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 2013,2014,2015,2016,2017,2018,2019
URL https://www.scoop.it/topic/mpmi
 
Description Seminar at the University of Georgia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Departmental seminar describing our recent work on 'Innovations in the plant immune system'. A total of 100 scientists and students were present.
Year(s) Of Engagement Activity 2021
 
Description Seminar given at Recent Advances in Molecular Plant Pathogen Interactions (RAMPPI), NIT Durgapur, India (Virtual) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar given at Recent Advances in Molecular Plant Pathogen Interactions (RAMPPI), NIT Durgapur, India (Virtual)
Year(s) Of Engagement Activity 2021
 
Description Seminar given in Genetics, Kasetsart University, Bangkok 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar given in Genetics, Kasetsart University, Bangkok
Year(s) Of Engagement Activity 2020
 
Description Seminar given in Plant Sciences, University of Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Seminar given in Plant Sciences, University of Cambridge
Year(s) Of Engagement Activity 2019
 
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 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 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 Television interview with BBC World News 
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 A video interview with BBC World News discussing the impact of wheat stem rust on worldwide wheat production, the impact of two recent studies on understanding the epidemiology of the pathogen, and the future outlook for crop protection.
Year(s) Of Engagement Activity 2017
 
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 The Biochemist: How to trick a plant pathogen? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Plants can get sick too. In fact, they get infected by all types of microbes and little critters. But plants have evolved an effective immune system to fight off pathogen invasion. Amazingly, nearly every single plant cell is able to protect itself and its neighbours against infections. The plant immune system gets switched on when one of its many immune receptors matches a ligand in the pathogen. As a consequence of a long evolutionary history of fighting off pathogens, immune receptors are now encoded by hundreds of genes that populate the majority of plant genomes. Understanding how the plant immune system functions and how it has evolved can give invaluable insights that would benefit modern agriculture and help breeding disease-resistant crops.
Year(s) Of Engagement Activity 2020
URL https://portlandpress.com/biochemist/article/42/4/14/226035/How-to-trick-a-plant-pathogen
 
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 Twitter campaign highlighting the UN International Year of Plant Health. 366 tweet-a-day throughout 2020. 
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 Twitter campaign highlighting the UN International Year of Plant Health. 366 tweet-a-day throughout 2020.
Year(s) Of Engagement Activity 2020
 
Description VISCEA - Plant Biotic Stresses and Resistance Mechanisms III, International organising committee 
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 VISCEA - Plant Biotic Stresses and Resistance Mechanisms III, International conference
Year(s) Of Engagement Activity 2018
 
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 of a full length NLR immune receptor and much more.

And you heard it first on Twitter.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/184056312400/stunning-news-from-china-check-cctv13-news-report
 
Description Visit from Corteva and Indigro 
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 Knowledge exchange
Year(s) Of Engagement Activity 2022
 
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 Workshop with ARIA Programme Director, Angie Burnett 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact A workshop hosted by JIC and led by ARIA programme Director Dr Angie Burnett, to discuss plans for her future funding programme on programmable plants
Year(s) Of Engagement Activity 2023
 
Description YTRB Interview Series: Sophien Kamoun...à la poursuite de l'émerveillement perpétuel 
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 Invité du jour, Pr. Sophien Kamoun, Group Leader au Sainsbury Laboratory, Norwich, UK, et expert mondialement connu des plant pathogens, entre autre...nous parle de sa philosophie de la science...
Year(s) Of Engagement Activity 2020
URL https://youtu.be/UumHQ6P7mAI
 
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