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Susceptibility

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

Plant recognition and response processes are modulated so that plants become susceptible to colonisation. To promote colonisation, pathogens and pests produce virulence factors, called effectors, which interact with specific plant targets to re-programme plant pathways, a process referred to as effector-triggered susceptibility. Effectors include proteins, mimics of plant hormones and non-proteinaceous toxins28. Some effectors induce dramatic developmental changes in plants, such as pustules, galls and witch’s brooms that provide a local habitat for the pests or pathogens and that promote their dispersal. In other cases, particularly in beneficial symbiotic associations, signal exchange between the microbe and the plant activates developmental processes that facilitate colonisation of the host plant. With the knowledge that we have already generated on effectors, their targets and associated signalling processes, we are in a unique position to investigate the specificities of effector-target interactions and the signalling pathways activated to regulate downstream processes that eventually promote plant colonisation.

Research on effectors has not only led to a better understanding of the biology of colonisers, but has also uncovered important plant processes. For example, effectors led to the discovery of plant factors that mediate cell identity and cell division31-34, identification of plant transcription factors with dual roles in plant development and plant defence responses and the elucidation of novel components of intra- and intercellular trafficking processes. We will investigate the functions of these plant factors targeted by effectors and use this new knowledge to manipulate the balance between defence responses and yield, resistance to necrotrophic versus biotrophic pathogens, and responses to harmful versus beneficial organisms.

We have shown that a wide range of factors have major impacts on the outcome of plant-biotic interactions. For example, higher temperatures can increase susceptibility to pathogens and affect interactions with beneficial non-symbiotic diazotrophic soil bacteria. In addition, soil Pseudomonas spp. modulate plant defence responses that directly and indirectly affect plant interactions with pathogens, pests and symbionts and plant growth. However, it is not clear how signals from the environment ultimately define the outcome of plant-biotic interactions. Uncovering these mechanisms will be important for understanding how alterations in the environment, such as climate change, will impact on susceptibility to plant pathogens and pests and the ability of plants to establish interactions with symbionts.

Planned Impact

unavailable

Organisations

 
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 Cover illustration 
Description Contributed an artistic drawing to illustrate the science described in Huang et al. 2021. Cell 184(20):5201-5214. The art piece was selected for the front page of the 30 Sep 2021 issue of Cell. Image credit: Hsuan Pai (The Sainsbury Laboratory) and Weijie Huang (The John Innes Centre). 
Type Of Art Artwork 
Year Produced 2021 
Impact The art piece advertises discoveries made in plant research to the broad scientific readership of the journal Cell. The art piece is creative and has high artistic value. As such the work can be used in multiple ways, such as wall decorations or other purposes. 
URL https://www.cell.com/cell/issue?pii=S0092-8674(20)X0021-3
 
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 Work with artist Henry Driver 
Description Henry Driver worked with Catherine Jacott and Myriam Charpentier to produce artwork on mycorrhizal symbiosis for an art installation 'Regenerate' 
Type Of Art Artwork 
Year Produced 2019 
Impact Too early to measure impacts 
URL https://www.henrydriverartist.com/regenerate.html
 
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. 3.1:

Geminivirus:
We used the geminivirus C4 protein (effector) to identify that the host receptor-like kinases BAM1 and BAM2 mediate the cell-to-cell transport of small RNAs.

Liberibacter:
- We characterized the virulence activity of the effector SDE1, which is produced by the citrus Huanglongbing-associated bacterial pathogen Liberibacter asiaticus. We showed that SDE1 promotes citrus susceptibility by triggering premature senescence.
- We determined gene expression profiles in the citrus Huanglongbing-associated bacterial pathogen Liberibacter asiaticus in citrus vs insect vector. We found virulence genes and functions that are potentially associated with the interaction and colonization of the bacterium in these distinct hosts.
- We supplied vectors and expertise to the Coaker lab to enable the identification of cell-to-cell mobile effectors of Liberibacter solanacearum https://www.biorxiv.org/content/10.1101/2021.09.10.459857v1.full

Phytoplasma:
- We found that 14 effectors of the obligate bacterial pathogen Phytoplasma interact with a range of plant transcription factors that have fundamental roles in regulating plant development (Marrero et al., 2020. Biorxiv https://doi.org/10.1101/2020.02.13.946517).

Pseudomonas:
- We discovered that pathogens extensively utilize effectors proteins to manipulate NAD metabolism in order to promote disease. These results demonstrate how pathogen manipulation of small molecules is an important virulence strategy.
- We showed how mRNA translation in the soil bacterium Pseudomonas fluorescens is regulated by cGMP in order to respond globally to changes in the environment.
- We have continued our research into cyclic-di-GMP control of mRNA translation by ribosomal modification. We show that this control system (RimABK) is widespread in nature, with regulatory variations in different bacterial species. We have shown that cyclic-di-GMP controls the secretion of a subset of Type III plant effectors during plant infection, and this in turn enables the development of tissue chlorosis and necrosis in infected plant tissue. We have identified the plant effector targets, and bacterial secretory mutants that present an asymptomatic phenotype, despite infection otherwise proceeding normally.
- We have characterised a new bacterial translational regulator (RsmQ), which controls plasmid transmission, motility, and biofilm formation in rhizosphere-associated, plant growth promoting bacteria. We have completed our characterisation of the plasmid-borne translational regulator RsmQ and show that it hijacks phenotypes including chemotaxis and biofilm formation in rhizosphere-associated bacteria.
- We have characterised a second plasmid-borne colonisation regulator, SpoQ, and show that it functions as a transcriptional regulator that controls horizontal plasmid transmission, motility and biofilm formation by binding to conserved binding sites on the host chromosome.
- In collaboration with researchers at Sheffield and Manchester Universities, we have examined how microbial fitness in the rhizosphere is affected by large conjugative plasmids. We show that the genomes of bacteria in the rhizosphere accumulate compensatory mutations in a core signalling pathway in response to plasmid carriage, and this is partially ameliorated by deletion of the plasmid-borne regulatory gene rsmQ.
- We have characterised the trehalose and glycogen biosynthesis pathways in Pseudomonas spp. and show that they are important for survival on man-made surfaces (P. aeruginosa) and for efficient plant infection (P. syringae). We showed how different polysaccharide biosynthesis pathways in Pseudomonas syringae combine to enable effective surface attachment and survival during the initial stages of plant infection.
- We characterised a small regulatory protein, Rmf, that links biofilm formation to antimicrobial tolerance in Pseudomonas aeruginosa. We show that this protein is vital for biofilm formation under conditions of antimicrobial stress, and are currently examining the clinical consequences of this finding in collaboration with Mark Webber at QIB and Freya Harrison at Warwick University.

Magnaporthe oryzae:
- We determined the crystal structure of the complex between the Magnaporthe oryzae effector protein PWL2 and the rice heavy-metal domain (HMA) containing protein OsHIPP43, and studied the strength of binding between these proteins in vitro. Further, we studied the interaction of natural variants of PWL2 with OsHIPP43, and demonstrated conserved high-affinity binding.
- We showed how the expanded AVR-Pik-like (APikL) effectors in different Magnaporthe oryzae lineages interact with specific host HMA-domain containing proteins. We revealed how a single amino acid polymorphism in APikL2 expands the host target binding spectrum of this effector. This has implications for our understanding of how effectors could evolve following a pathogen host jump.
- We have identified the putative target of the Pwl2 effector protein delivered by the rice blast fungus Magnaporthe oryzae during rice infection, as a small heavy metal-associated protein-encoding gene.
- We have characterised the effector repertoire of M. oryzae and shown that structurally conserved, but sequence un-related, effectors are temporally co-regulated during plant infection. This includes the MAX and ART classes of rice blast effectors.
- We have identified the MEP family of effectors in M. oryzae and demonstrated that they are co-ordinately expressed during rice infection in temporally co-regulated groups.
- We have identified the target of the Mep3 effector in M. oryzae as a chloroplast protein involved in immunity and reactive oxygen species generation. We have shown that Mep 3 is delivered to the chloroplast during infection.
- We have demonstrated that the Mep1 effector of Magnaporthe oryzae is a septin-dependent secreted protein delivered at the base of the appressorium into newly infected rice cells.
- We determined the solution structure (by NMR) of the rice blast effector AVR-Pias, revealing a new alpha-helical "staple" fold and are in the process of defining host interactors for this effector.
- We validated the structure of the rice blast effector AVR-Pii with the host target Exo70F2/3 by mutagenesis and biochemical studies of interaction.
- In collaboration with Barbara Valent's research group (Kansas State University, USA), we have found evidence that effector uptake by rice cells during blast infection may require clathrin-mediated endocytosis (CME). Using a combination of gene silencing, live cell imaging and mutant analysis, we have shown that CME takes place at the biotrophic interfacial complex, which forms a specialised interface between host and pathogen.

Fusarium:
- We collaborated with the Takken lab (University of Amsterdam) to establish that the Fusarium effectors Six5 and Avr2 do not regulate callose deposition at plasmodesmata, despite enabling an increase in cell-to-cell trafficking. https://doi.org/10.3389/fpls.2022.910594
-

Colletotrichum higginsianum:
- We performed a screen of effectors from the fungal Arabidopsis pathogen Colletotrichum higginsianum for mobility between host cells. This revealed effectors that are hypermobile (move further than expected) and effectors that modify plasmodesmata. Hypermobile effectors target a range of defence and growth associated host processes (https://www.biorxiv.org/content/10.1101/2021.01.13.426415v1).

Oomycetes:
- The Irish potato famine pathogen, an oomycete, targets the plant autophagy machinery.
- We have defined AvrAmr1 and AvrAmr3, the recognised effectors for the late blight resistance genes Rpi-amr1 and Rpi-amr3.
- We have used biochemical and structural approaches to understand the molecular mechanistic basis of how the Phytophthora infestans effector PexRD24 (PITG_04314) interacts with the host target PP1c (protein phosphatase 1c) from potato. We showed that PexRD24 acts as a mimic of a phosphatase regulatory subunit via its C-terminal KVxF motif.
- We performed a screen of effectors from the oomycete Arabidopsis pathogen Hyaloperonospora arabidopsidis for mobility between host cells. This revealed effectors that are hypermobile (move further than expected). One hypermobile effector increases cell-to-cell connectivity and suppresses host defence. https://www.biorxiv.org/content/10.1101/2022.01.24.477405v1
- We identified new effectors from potato late blight that are recognized by Solanum americanum intracellular immune receptors.
- We showed that a single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum. Bentham et al. PLOS Pathogens 2021.
- We showed that an extracellular proteolytic cascade in tomato activates immune protease, and that this pathway is in turn inhibited by pathogen effectors.
- We have identified novel susceptibility factors that are directly hijacked by Phytophthora effectors. Mutants of a susceptibility factor led to enhanced resistance to Phytophthora in Arabidopsis. This susceptibility factor is therefore a promising target for genetic engineering in order to enhance disease resistance.

Aphids:
- In a screen with 167 bacterial, oomycete, nematode and aphid effectors, we found that none of the of the candidate aphid effectors suppressed the cell death response triggered by the NRC-dependent disease resistance proteins Prf and Rpi-blb (Derevnina et al., 2021. Biorxiv doi: https://doi.org/10.1101/2021.02.03.429184).
- We have identified a new family of aphid virulence factors/effectors that are candidate long non-coding (lnc) RNAs. The lncRNA genes differentially regulate in the first stages of M. persicae adjustment upon plant host change to 9 plant species from 5 families. Some of these aphid lncRNA transcripts translocate into plants and migrate systemically. In planta heterologous expression of one of these lncRNAs promotes aphid fecundity, whereas their knock-down via RNAi in aphids reduces aphid fecundity. The work was published in Chen et al., 2020. Proc. Natl. Acad. Sci. 117(23):12763-12771. We received funding via a BBSRC responsive mode grant (BB/V008544/1) to further the work on aphid RNA effectors.
- Plant targets of 4 aphid effectors were identified.


Obj. 3.2:

Geminivirus:
- We showed that the geminivirus C4 protein targets receptors at plasmodesmata during an infection and interferes with the movement of siRNAs, thus suppressing host defense against the virus.

Phytoplasma:
- We found that SAP05 protein effectors of the obligate parasite phytoplasma simultaneously prolong plant lifespan and induce witch's broom-like proliferations (Huang et al., 2021. Biorxiv doi: https://doi.org/10.1101/2021.02.15.430920). These effectors mediate degradation of members of two large plant zinc finger transcription factor families, GATAs and SPLs, via interaction with the 26S proteasome subunit, the ubiquitin receptor RPN10. SAP05 uniquely bridges host targets and RPN10 to form a ternary complex. Remarkably, SAP05-mediated degradation does not require substrate ubiquitination. SAP05 effectors are widespread in divergent phytoplasmas - some target GATAs and other SPLs. RPN10 homologues are conserved in plants and insects, but SAP05 does not bind insect RPN10. A two-amino-acid substitution in plant RPN10 mimics the insect ortholog and generates a functional variant resistant to the SAP05 activity. Our work shows how a single parasite effector co-opts a host susceptibility factor to degrade multiple transcription factors resulting in a plethora of developmental modulations in the plant host. We published that phytoplasma effector protein SAP05 degrades members of the large plant GATA and SPL transcription factor families in a ubiquitin-independent manner via recruiting the 26S proteasome receptor RPN10 (Huang et al. 2021. Cell 184: 5201-5214).
- We studied the effect of phytoplasma Candidatus Phytoplasma mali (P. mali) colonization on the physiology of its insect vector, the psyllid Cacopsylla melanoneura (Weil et al., 2020. Insect Biochem. Mol. Biol. 127:103474. doi: 10.1016/j.ibmb.2020.103474). We made progress with the functional characterization of three phytoplasma effector proteins that interact with proteins of insect vectors (Kliot et al., 2021. In preparation).

Pseudomonas:
- For studying Pseudomonas bacteria, we established a collaboration with Xiufang Xin (CEPAMS) to examine the role of bacterial EPS in facilitating 'water soaking' during early-stage Pto infections. Moreover, we defined the regulation of the osmo-/desiccation stress molecules trehalose and alpha-glucan during plant association.

Streptomyces:
- We have shown that root-associated Streptomyces species confer benefits on their plant hosts, including increased growth and protection against disease (Worsley et al.., 2020. Appl Env Microbiol. 86: e01053-20). We also reported that the endophytic root compartment of bread wheat plants (elite varieties Axona, Cadenza, Paragon, Soissons and Tonic) is dominated by Streptomyces bacteria suggesting it is a major niche for this genus. It appears to be a mutually beneficial symbiosis whereby the plants feed the bacteria and in return the bacteria confer growth benefits and protection against disease (Prudence et al., 2021. Submitted 09/02/2021).
- Only three out of the more than 900 known species of Streptomyces colonise the wheat root endosphere. These bacteria feed on plant metabolites in the endosphere but are outcompeted for these in the rhizosphere. Our hypothesis is the endophytes establish a symbiosis with the plant hosts and provide growth promoting benefits in return

Symbiotic bacteria/symbiosis:
- For Rhizobium, we identified two plant genes encoding vacuolar iron transporters that are important for establishing the symbiosis between the model legume Medicago and Rhizobium bacteria. One gene (VTL4) is expressed early during symbiosis and affects the infection process, whereas the other gene (VTL8) is expressed later and is critical for the bacteria to obtain nitrogen-fixing competency. We also found that the electron transport components from plant organelles can functionally replace their electron transfer counterparts in bacteria to support nitrogenase activity. This may simplify our synthetic biology approach to engineer nitrogen fixation in plants, since endogenous electron transport chains present in plant organelles can function to transfer electrons to nitrogenase.
- We identified a transporter protein required for iron transport from the host plant to symbiotic bacteria. Without a functional transporter, the partially established bacteria become iron-limited and fail to progress to the next developmental stage, in which they fix nitrogen. Walton et al 2020 Plant Physiol.

Mycorrhizae:
- We developed the study on the MLO gene family to investigate their potential involvement in nodulation as well as mycorrhization in collaboration with Jeremy Murray at the Shanghai Institute for Plant Physiology and Ecology.
- We published an article about the wider role of the Mildew Resistance Locus O in mycorrhization, pollen reception and disease resistance


Magnaporthe oryzae:
- In collaboration with Michael Marletta's research group (UC-Berkeley, USA), we have characterised a novel polysaccharide mono-oxygenase (PMO). Unlike other AA9 PMOs, the M. oryzae PMO9A enzyme is not active on cellulose but shows activity on cereal-derived mixed (1?3, 1?4)-ß-D-glucans. This PMO is necessary for efficient tissue colonisation by the blast fungus.
- We have identified the Hox7 homoeodomain transcription factor as a directly phosphorylated target of the Pmk1 MAP kinase during rice infection. We have identified the set of genes regulated by hox7 during infection.
- We have identified the Vts1 transcription factor as a novel virulence determinant and direct phosphorylated target of the Pmk1 MAP kinases during rice blast infection by Magnaporthe oryzae.
- We have identified the Mst12 transcription factor as a directly phosphorylated target of the Pmk1 MAP kinase and shown how its activation leads to a major change in gene expression associated with appressorium development.
- We have identified a family of co-regulated transcription factors as targets of a hierarchical signalling cascade controlled by the Pmk1 MAP kinase, which are necessary for rice blast disease.
- In collaboration with Joris Sprakel (Wageningen University, we have used a molecular mechanosensory to directly visualise turgor generation in appressoria of the rice blast fungus. This has provided new insight into how the plasma membrane behaves under the enormous forces generated in the appressorium, showing spatial and temporal heterogeneity in membrane tension. We are using fabricated hydrophobic surfaces to measure the force of adhesion and protrusive force generation during plant infection.
- We have identified putative targets of the Sln1 turgor-sensing histidine kinase, that is necessary for rice blast disease and controls appressorium turgor generation.
- We have identified septin interacting proteins that are expressed at the rice-fungal interface during appressorium-mediated plant infection and associated with penetration peg emergence and cuticle penetration
- We have demonstrated that organelle trafficking during appressorium morphogenesis in Magnaporthe oryzae is regulated independently of autophagic cell death and is essential for plant infection.
- We have found evidence that the Target of Rapamycin (TOR) kinase is necessary for the control of autophagic cell death of the conidium during appressorium maturation and plant infection by M. oryzae. The homeostatic control of autophagy is essential for re-polarisation and cuticle rupture by the fungus.
- We have generated a set of transgenic rice and barley lines in which each cellular compartment and organelle is fluorescently marked. In this way, we are generating an atlas of the major cellular changes associated with biotrophic colonisation of plant tissue by the blast fungus. This has revealed how the structural integrity of the host plasma membrane is maintained during cell invasion by the fungus, but then lost during the onset of necrotrophic switch and symptom development, and how the host actin cytoskeleton undergoes significant re-orientation as a response to cell invasion.

Fusarium:
- Trichomes act as points of vulnerability allowing infection by Fusarium graminearum. We have identified a candidate gene that controls trichome development on glumes of the grass Brachypodium distachyon.
- We have demonstrated that the fungal pathogen Fusarium graminearum can produce ethylene (a plant hormone) that it may use to increase susceptibility in its plant host. We have identified two genes potentially involved in ethylene biosynthesis (a plant hormone) in the fungal pathogen Fusarium graminearum. Mutants disrupted in these genes have been produced and are being evaluated for altered ethylene production and virulence.
- We have identified a candidate gene involved in the host response to DON mycotoxin in Brachypodium distachyon.
Oomycetes:
- We showed that host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen.

Hemiparasite mistletoe:
- We showed that the hemiparasite Viscum album (mistletoe) is the first reported multicellular eukaryote that lacks respiratory complex I, an iron-rich protein complex in the mitochondria. A decreased capacity for mitochondrial ATP production is compensated by increased glycolytic carbon flux, which is likely an adaptation to its parasitic life style (Maclean et al 2018 Current Biology).

Aphids:
- We have analysed the up- and downregulation of candidate effector genes of the polyphagous green peach aphid Myzus persicae on divergent plant hosts. We found that specific gene (sub)families are differentially regulated depending on the plant host species. We studied the regulation of these genes over time upon aphid host change and found that some genes adjust their expression immediately in the first generation or later in the 3rd, 6th or 9th generation of the aphids on the new hosts.
- We found that a host-responsive effector family of the polyphagous aphid Myzus persicae encode cysteine proteases that upregulate on brassicaceous and downregulate on solanaceous plants. We have shown that the proteases belong to a single expanded clade and are present in aphid saliva, unlike other family members that are more dominantly expressed in other aphid organs, such as the gut. Research on the function of these saliva proteases in plants revealed that these proteins promote aphid colonisation on Arabidopsis thaliana and that they interact directly with key players in the TIR-NBS-LRR signalling pathway of A. thaliana, but not of Nicotiana benthamiana. Confocal microscopy experiments provided evidence of a role of the saliva proteases and their direct targets in chloroplast-nucleus communication.
- We have contributed to showing that the propeptide of M. persicae cysteine protease cathepsin B13 (CathB13) interacts with tobacco cytoplasmic kinase ENHANCED DISEASE RESISTANCE 1-like (EDR1-like) and triggers the accumulation of reactive oxygen species in tobacco phloem, thereby suppressing both phloem feeding and colonization of M. persicae (a collaboration with CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China). This research is building on our previous findings showing that CathB13 is part of a highly regulated M. persicae multigene family that are downregulated in M. persicae reared on Nicotiana benthamiana (Mathers et al., 2017. Genome Biol.18(1):27. doi: 10.1186/s13059-016-1145-3; Chen et al., 2020. Proc. Natl. Acad. Sci. 117(23):12763-12771). We made further progress with identifying targets of CathB that are predominantly expressed in aphid salivary glands.
- We found that an aphid effector that suppresses PTI in response to a variety of elicitor molecules PAMPs, including aphid-derived elicitors, interacts with conserved plant target proteins that have key roles in the trafficking and stabilization of membrane proteins. This effector belongs to a clade shared with homologues from other plant-feeding hemipterans, and orthologues of this effector from other sap-feeders share PTI-suppressive functions and interactions with plant targets.

Obj. 3.3:

- We investigated the modulation of plant immunity by seasonal signals. We found that a common signalling module act to coordinate growth and defense responses in response to light and temperature cues.
- Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. We have exploited fundamental understanding of this complex regulation in combination with synthetic biology to manipulate regulatory proteins and ammonia assimilation enzymes in different diazotrophs to enable them to excrete ammonia.
- From studying plant iron transporters required for biological nitrogen fixation (BFN), it emerges that, for engineering BFN in non-legume crop plants, we can potentially use homologous transporters in these crop species, but we would need to alter their expression pattern.
- We found evidence that Chevallier and Tipple barley cultivars recruit phenotypically distinct populations of Pseudomonas bacteria. Subsequently, we have developed methods to compare barley root colonisation by distinct P. fluorescens genotypes.
- We have shown that barley plants shape the accessory genomes of their associated bacterial populations by secreting complex mixtures of root exudates into the rhizosphere.
- We have identified the genes in Pseudomonas fluorescens that contribute to root exudate utilisation and ecological success in the barley rhizosphere.


Obj. 3.4:
Phytoplasma:
- We found that a two-amino-acid substitution in plant RPN10 mimics the insect ortholog and generates a functional variant resistant to the activity of phytoplasma SAP05 effector, which induces a plethora of developmental modulations in plant hosts (Huang et al., 2021. Biorxiv doi: https://doi.org/10.1101/2021.02.15.430920). RPN10 is highly conserved among plant species and phytoplasmas that have SAP05 homologs infect a wide range of plant species, including economically important crops. Introducing the two-amino-acid substitution in RPN10 homologs of crops may lead to increased phytoplasma resistance. A patent 'Methods for altering pathogen resistance' was filed with JIC (Luxembourg (LU) patent application no. 102305) in Dec 2020, and a PCT application (PCT/EP2021/086554) was filed in Dec 2021.

Symbiotic bacteria/symbiosis and nitrogen fixation:
- While attempting to express and target nitrogenase component proteins to yeast mitochondria, we discovered that one of the nitrogenase structural subunits (NifD) was susceptible to cleavage by the mitochondrial processing peptidase. This susceptibility was also conferred by the equivalent mitochondrial processing enzymes from rice, tobacco and Arabidopsis. Using synthetic biology, we engineered active variants of NifD that are resistant to cleavage by these processing enzymes, thus paving the way for engineering nitrogen fixation in plant mitochondria.
- We found that protein lipoylation in mitochondria requires Fe-S cluster assembly factors NFU4 and NFU5. Przybyla-Toscana et al 2022, Plant Physiol.
- As a first step towards engineering synthetic symbioses between N-fixing bacteria and cereal crops, we have manipulated soil nitrogen fixing bacteria to excrete ammonia to benefit plant growth. However, bacteria that release ammonia can themselves become N-deficient and therefore non-competitive in soils. To circumvent this issue, we have engineered regulatory circuits so that the bacteria only release ammonia in the presence of carbon sources that are likely to be present in plant root exudates.


Magnaporthe:
- We demonstrated that specific inhibitors of septin assembly during appressorium morphogenesis can act as broad spectrum fungicides in field scale tests for control of rice blast disease.
- We have generated rice lines containing Pi9, Pi2, pi21, and the QTL Pi35 by marker-assisted selection that are under the third year of field trial evaluation in Kenya, Tanzania, and Burkina Faso. Results from the first two years of trials are being evaluated and further introgression of resistance specificities to exclude the prevailing blast population in sub-Saharan Africa is being carried out in collaboration with KALRO (Kenya) and IRRI (The Philippines).
- As part of an international effort led by Sophien Kamoun, we have characterised wheat blast isolates from Zambia and these have informed a potential disease control strategy using the Rmg8 resistance gene. This complements the identification of new specificities for control of wheat blast by Paul Nicholson, Jonathan Jones and collaborators.

Oomycetes:
- We continued to study a large collection of CRISPR/Cas9 mutations in candidate blast fungus susceptibility S genes in barley and wheat.
- We characterized the secondary small interfering RNA pathway in Arabidopsis and soybean and found that they confer resistance to Phytophthora pathogens, possibly through host-induced gene silencing

Aphids:
- Investigations of the plant targets of aphid effectors were pursued in collaboration with the industrial partner SESVanderHave. Promising leads to improve sugar beet resistances to insects were identified.
- We made progress with identification of aphid effector targets in Arabidopsis species, oilseed rape, pea and wheat and the characterization of variants of these genes that do not interact with the aphid effector.

All pests:
- We showed that NLR immune receptor-nanobody fusions can confer plant disease resistance. Given that nanobodies can be raised against virtually any molecule, immune receptor-nanobody fusions have the potential to generate resistance against all major plant pathogens and pests.
- We invented Pikobodies, a technology that endows plants with a pseudo-adaptive immune system and enables designing made-to-order plant disease resistance genes.
- We defined the principles in the design of bioengineered made-to-order plant immune receptors.
Exploitation Route See Impact statement
Sectors Agriculture

Food and Drink

Communities and Social Services/Policy

Education

Environment

Government

Democracy and Justice

Manufacturing

including Industrial Biotechology

Culture

Heritage

Museums and Collections

Pharmaceuticals and Medical Biotechnology

Retail
 
Description Commercialisation, applications and patent applications: - Sophien Kamoun is a Director and scientific advisor to the start-up company Resurrect Bio https://resurrect.bio (since 2022). - By characterising important signalling & stress survival systems (e.g. trehalose/glycogen biosynthetic pathway), we may identify novel antimicrobial drug targets in pathogenic bacterial species, incl. plant and human pathogens. - The research on aphid effectors has strengthened our patent applications 'METHODS OF INCREASING BIOTIC STRESS RESISTANCE IN PLANTS' (WO2021048272) (filed with the industrial collaborator). - The work on the functional characterization of phytoplasma SAP05 effectors (see Obj. 3.2 above) contributed to three patent applications submitted by the KEC office of JIC. These are: 1. Methods of altering pathogen resistance. LU102305/ PCT/EP2021/086603. 2. Methods for targeted protein degradation. LU102306/ PCT/EP2021/086666. 3. Methods of altering plant architecture. LU102304/ PCT/EP2021/086554. In collaboration with Sophien Kamoun and Nick Talbot at TSL, we secured funding to hire an entrepreneur in residence who will help us to launch a start-up. - By characterising important signalling and pathogenicity pathways (e.g. antimicrobial susceptibility genes), we may identify novel antimicrobial/anti-infective drug targets in pathogenic bacterial species, incl. plant and human pathogens. - By understanding how plasmid regulators influence the behaviour of bacteria and the spread of genetic information between them, we can better understand important phenomena such as the spread of antimicrobial resistance in clinical settings and the formation of agriculturally beneficial microbial consortia in the soil. - Our work this year has led to the development of promising biocontrol strains for use against economically damaging plant pathogens. We have begun the initial stages of commercialisation of our approach to the discovery of biocontrol bacteria. - We have discovered a highly specific bacterial protease with potential for use in research and biotechnology. We are currently in the initial stages of IP protection of this finding. Work is underway to commercialise this avenue of research. - Sophien Kamoun is the founder of the charity organization GetGenome that empowers scientists by providing equitable access to genomics technology and genomics-related training and education (http://getgenome.net). A former PhD student of JIC is director and Appolinaire Djikeng, Nick Talbot and Saskia Hogenhout are on the board of Trustees. Collaborations with industry: - We have obtained three fully funded industrial collaborations on NLR biology with Rijks-Zwaan, BASF and Limagrain. (since 2019). - We established collaborative projects with a range of UK companies via IPA, LINK and iCASE studentships. - We established a new collaboration with G's Fresh, a major producer of fresh vegetables for supermarkets, to investigate disease resistance in lettuce and other crops. We are hoping to set up a consultancy with G's fresh in the short term, prior to establishing a longer-term collaboration. This impact also involves Jacob Malone from Plant Health and Sanu Arora. - We obtained BBSRC Follow-on-Funding to create gene edited lines for the Light Leaf Spot susceptibility factor, working in collaboration with the University of Hertfordshire and KWS. Public/Policy engagement: - We have participated in a BBSRC discussion on strategies for developing Plant Health research in the UK. - Providing leadership to and the writing of the final report for the BRIGIT project that finished in Sep 2021. The BRIGIT project was initiated to investigate the invasive plant pathogen Xylella fastidiosa, its insect vectors and plant hosts and assess how introductions of the pathogen into the UK may be mitigated. The BRIGIT project report and BRIGIT impacts were shared with policymakers at BBSRC, Defra, NERC and UKRI. Output generated by the BRIGIT project is used as an example and guideline for the other 8 project funded through the Bacterial Plant Diseases Programme funded by BBSRC, NERC, Defra and Scottish Government (https://bacterialplantdiseases.uk/). - Staff members organised a session of accessible science talks for schools in Oct 2022. In this session leading scientists from JIC and TSL presented their work in an accessible manner for support staff and pupils from 6 regional schools. Impact on sustainable development: - Our work with vegetable breeders in Nepal has been included in the portfolio of projects in the newly established Norwich Institute for Sustainable Development (NISD). Our work is featured on the new NISD website and links our work on crop science with studies in the Faculty of Development at University of East Anglia. - We have carried out further plant health clinics in Kenya and Tanzania and disseminated worksheets and mobile phone apps through KALRO for blast disease diagnosis, control and pathogen surveillance. - We have trained a new set of Plant Doctors using the CABI protocols, and these extension worked are working across Kenya and Tanzania in diagnostic work and pathogen surveillance, coordinated by KALRO and becA-ILRI in Nairobi. - This funding facilitates our research program on economically important diseases citrus Huanglongbing (aka greening disease) and Phytophthora diseases. The findings obtained from this research contribute to the overall understanding of the pathogen virulence and could be used to guide the development of disease resistance. - We have disseminated new tools and resources to the community. We have shared constructs of engineered NLRs around the world for transformation to improve disease resistance. We 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. - We have developed transgenic potato lines carrying stacks of Rpi- genes that confer complete late blight resistance against all known races of the pathogen. This has attracted considerable public interest. Next destination: - Staff members of group leaders have become independent group leaders at research institutes and obtained jobs in industry, charity organizations, government and journalism worldwide.
First Year Of Impact 2020
Sector Agriculture, Food and Drink,Communities and Social Services/Policy,Education,Environment,Pharmaceuticals and Medical Biotechnology,Retail
Impact Types Cultural

Societal

Economic

Policy & public services
 
Description AHDB
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Food safety
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Hosted colleague from industry for teaching lab technique
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Taught industrial partner specific lab technique.
 
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 Recruitment of new head for the Entomology Facility at the institute
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a guidance/advisory committee
Impact Provided leadership to the JIC Entomology Facility steering committee upon retirement of Facility head and recruitment of a new Facility head. Developed a draft of a business plan, managed Entomology Facility staff in the transition period, developed a position description for the new Facility head, interviewed applicant and successfully recruited a new head.
 
Description Training MSc students in the "Global Plant Health" program (annually since 2022)
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact We are committed to offer training opportunities to students from developing countries, especially from Africa. Since 2022, we trained >20 students from African countries. We have a strong track record to place our trainees to a career in academia and industry. Many of the trainees are in PhD programs in UK, US and EU.
 
Description Training early career researchers in the research field of plant-microbe interaction
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description UK-Canada Agrifood workshop
Geographic Reach North America 
Policy Influence Type Contribution to a national consultation/review
Impact A research framework document for joint UK-Canada research projects was established for the Agrifood sector. This will result in joint funding opportunities and engagement with stakeholders. Additionally, a reciprocal workshop in Canada is currently being planned
 
Description Writing of the final BRIGIT report
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
Impact Output generated by the BRIGIT project is used as an example and guideline for the other 8 project funded through the Bacterial Plant Diseases Programme funded by BBSRC, NERC, Defra and Scottish Government (https://bacterialplantdiseases.uk/)
URL https://bacterialplantdiseases.uk/
 
Description All Aphid Effectors on DEK
Amount £689,277 (GBP)
Funding ID BB/V008544/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 03/2024
 
Description Assess sugarbeet resistance to aphids
Amount £9,870 (GBP)
Organisation Sesvanderhave 
Sector Private
Country Belgium
Start 02/2019 
End 02/2020
 
Description BBSRC-IPA grant
Amount £1,316,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 03/2021
 
Description CAS-JIC collaboration
Amount £120,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2017 
End 03/2020
 
Description CAS-John Innes Centre Centre for Excellence in Plant and Microbial Science Collaborative Research Projects - Fifth Tranche
Amount £226,000 (GBP)
Funding ID CPM23 
Organisation Chinese Academy of Sciences 
Sector Public
Country China
Start 09/2019 
End 03/2021
 
Description CEPAMS Collaborative Grant
Amount £95,066 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 02/2019 
End 07/2020
 
Description CEPAMS Newton Fund: Sino-UK excellence with impact on the Sustainable Development Goals
Amount £2,013,638 (GBP)
Funding ID BB/T004363/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2019 
End 03/2022
 
Description Cash contribution to IPA grant
Amount £131,700 (GBP)
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 03/2018 
End 03/2021
 
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 Future Leader Fellowship awarded to Thomas Mathers
Amount £317,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 04/2021
 
Description Innovate UK Industrial Research grant
Amount £176,438 (GBP)
Funding ID 6921 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 03/2018 
End 03/2019
 
Description Institute Innovation Funds
Amount £124,000 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 11/2018 
End 12/2020
 
Description Novel blast resistant wheat varieties for Bangladesh by genome editing
Amount £603,518 (GBP)
Funding ID BB/P023339/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 04/2019
 
Description Plasmid manipulation of bacterial gene regulatory networks
Amount £485,682 (GBP)
Funding ID BB/R018154/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2018 
End 09/2021
 
Description Productive and sustainable crop and ruminant agricultural systems
Amount £909,984 (GBP)
Funding ID 26527 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 03/2019 
End 04/2021
 
Description SEPBLAST: Determining the molecular basis of septin-dependent plant infection by the blast fungus Magnaporthe oryzae
Amount £2,154,515 (GBP)
Funding ID EP/X022439/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2027
 
Description Targeted protein degradation using SAP effectors (SAP-ERASER)
Amount € 2,500,000 (EUR)
Funding ID EP/X024415/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2022 
End 08/2027
 
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 Zespri PhD Studentship
Amount $157,934 (NZD)
Organisation Zespri Group Limited 
Sector Private
Country New Zealand
Start 06/2018 
End 06/2021
 
Title A clone resource of Magnaporthe oryzae effectors that share sequence and structural similarities across host-specific lineages 
Description We describe a clone resource of 195 effectors of the blast fungus Magnaporthe oryzae. These clones are freely available as Golden Gate compatible entry plasmids. Our aim is to provide the community with an open source effector clone library to be used in a variety of functional studies. Plant pathogens secrete effectors that play central roles in subjugating plants for colonization. Effectors typically have signal peptides, and occasionally carry conserved folds and motifs (Lo Presti et al.,2015; Franceschettiet al., 2017). Magnaporthe oryzae(Syn. Pyricularia oryzae) is an important plant pathogenthat is able to infect around 50 species of both wild and cultivated grasses including important cereals of the Poaceae family. M. oryzaeis mostly known to cause rice blast but can also cause disease on other crops such as barley, wheat, foxtail millet, and finger millet. The global population of Magnaporthe is composed of genetically differentiated lineages which, in some cases, still exhibit a measurable degree of gene flow (Gladieux et al.,2018). Fungal isolates from each of those lineages show a preference for a specific host and also encode distinct repertoires of effector genes (Yoshida et al.,2016). The first genomic sequence of Magnaporthe oryzaewas released in 2005 for the lab strain 70-15 and allowed to predict a large set of secreted proteins such as enzymes involved in secondary metabolism and virulence-associated factors including putative effectors (Dean et al.,2005). Recently an increasing number of genome sequences of isolates from different lineages have become available, allowing the research community to perform comparative genomic studies (Chiapello et al.,2015; Yoshida et al.,2016). Many of the validated effectors of M. oryzae are known as the MAX (MagnaportheAVRs and ToxB like) effectors. These effectors, while showing little primary sequence similarity, share a conserved structural fold composed of 6 ß-sheets alternating in an anti-parallel manner (de Guillenet al., 2015). The MAX family has been largely expanded in Magnaportheas those effectors account for 5-10% of the effector repertoire and for 50% of the already cloned effectors of Magnaporthe(de Guillenet al., 2015). Indeed, the identification of structural motifs enables more sensitive predictions of effectors from pathogen genomes compared to sequence similarity searches (Franceschettiet al., 2017). The aim of this project was to computationally identify a set of M. oryzaeeffectors from the main host-specific lineages and develop an open access clone resource for functional analyses. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? Yes  
Impact Distributed >100 samples to several laboratories via addgene. 
URL http://doi.org/10.5281/zenodo.3268775
 
Title Coomassie Brilliant Blue (CBB) staining for Rubisco is an appropriate loading control for western blots from plant material 
Description Background - Having an adequate loading control for a western blot is essential for the interpretation of the results. There are two common loading control methods for western blots of proteins from plant material: (i) using specific antibodies to detect for a reference protein, such as actin, tubulin, or GAPDH (Li et al. 2011); and (ii) treating the membrane with Ponceau or Coomassie stains to assay the levels of a constitutively expressed protein, such as Rubisco (Zhang et al. 2017; Lim et al. 2018; Zhuo et al. 2014). Comparative studies in the mammalian biology field have determined that these loading control methods-antibody detection versus staining-are roughly equivalent in their linearity (Romero-Calvo et al. 2010; Wilender and Ekblad, 2011), and thus serve as comparable quality controls. In the plant biology field, it is sometimes debated as to whether staining for Rubisco is an appropriate loading control, due to the high abundance of this protein in the cell. Results - We undertook an experiment to determine whether the range of detection of staining for Rubisco is similar to that of antibody-based detection of a reference protein. We loaded total protein extract from Nicotiana benthamiana leaves transiently expressing GFP into a gel at a range of effective sample volumes, and the resulting western blot was treated with anti-GFP antibodies as well as stained with Coomassie Brilliant Blue (CBB) (Fig. 1a). Quantification of the GFP bands in the western blot and the Rubisco bands in the CBB stained membrane indicated that these detection methods have similar linear correlations between the loading volumes of total protein extract and the detectable band intensities (Fig. 1b). In addition, quantification of a random protein of lower abundance in the CBB stained membrane also showed similar linearity (Fig. 1b). Conclusions - These results indicate that CBB staining for Rubisco can be an appropriate loading control for western blots from plant material. This representative experiment is consistent with results from other western blot experiments that we routinely perform in our laboratory. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact Feedback from social media indicates it is useful to many others. 
URL https://zenodo.org/record/2557821#.XH2gji2cbYI
 
Title 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 Insect cell based expression system 
Description We successfully setup insect cell (Sf9 cells)-based protein production system using the baculovirus bac-to-bac method. Different purification methods were tried out to obtain enough protein for crystallography. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact At least two labs at JIC and TSL are using the system. 
 
Title Integrated analysis of global genetic datasets 
Description Reductive analysis of individual signalling pathways is inherently limited in its ability to fully explain the implications of e.g. environmental change on the global regulatory network of microorganisms. In order to enable a deeper understanding of these complex signalling networks we have developed a bioinformatic pipeline that enables the simultaneous consideration of several regulatory layers, at the whole-cell scale. Using the Hfq transcriptional/translational regulatory network in the model bacterium Pseudomonas fluorescens as a test case, we used extensive 'omic-analyses to assess how hfq deletion affects mRNA abundance, translation and protein abundance. The subsequent, multi-level integration of these datasets enabled us to highlight discrete contributions by Hfq to gene regulation at different regulatory levels. This integrative approach to global signalling may be used to dissect individual signalling networks, or to understand how bacterial cells adapt to changes in their environments to a far greater resolution than is available using conventional molecular microbiology or individual 'omic analyses. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact This analytical approach has been published (Analyzing the Complex Regulatory Landscape of Hfq-an Integrative, Multi-Omics Approach, L Grenga, G Chandra, G Saalbach, CV Galmozzi, G Kramer, JG Malone, Frontiers in microbiology 8, 1784), and is currently being adapted to examine the RimABK pathway, which forms the main focus of this project. This follow-on work will be published in 2018. 
URL https://www.frontiersin.org/articles/10.3389/fmicb.2017.01784/full
 
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 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 Quantitative cell to cell mobility assay 
Description We generated dual expression, GoldenGate vectors for plant transformation that all for marking cells that are transformed and the production and tracking of a candidate cell-to-cell mobile fluorophore. We have also generated a suite of size standards that allow quantitative analysis of cell to cell mobility. This quantitative approach allows for the identification of hypermobility 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact This tool has been distributed to a US lab and used in a screen for Liberibacter effectors 
URL https://doi.org/10.1101/2021.01.13.426415
 
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 Additional file 1 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 1: Table S1. Summary of sequence data used for genome assembly and annotation. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Hybridisation_has_shaped_a...
 
Title Additional file 3 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 3: Table S2. RNA-seq pseudoalignment stats. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Hybridisation_has_shaped_a...
 
Title Additional file 4 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 4: Table S3. Genomes used for phylogenomic analysis. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Hybridisation_has_shaped_a...
 
Title Additional file 5 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 5: Table S4. Gene family clustering summary statistics. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Hybridisation_has_shaped_a...
 
Title Additional file 6 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 6: Table S5. HapCUT2 phasing statistics. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Hybridisation_has_shaped_a...
 
Title Additional file 7 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 7: Table S6. Sample information and mapping statistics for population genomic analysis of S. miscanthi and S. avenae. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_7_of_Hybridisation_has_shaped_a...
 
Title Additional file 8 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 8: Table S7. Per chromosome shared SNP counts among UK and Chinese GBS Sitobion samples. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Hybridisation_has_shaped_a...
 
Title Additional file 9 of Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Additional file 9: Table S8. Dsuite summary statistics for all combinations of UK and Chinese Sitobion lineages. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://springernature.figshare.com/articles/dataset/Additional_file_9_of_Hybridisation_has_shaped_a...
 
Title Magnagenes Version 1.0 
Description We report the compilation of MagnaGenes , a database which summarises all the available studies reporting phenotypic data about gene function in the blast fungus Magnaporthe oryzae. MagnaGenes includes information for 1637 genes and allows them to be sorted by putative function. For example, those with a particular role, such as 'conidiation' can be defined and grouped together. Magnagenes also contains clickable hyperlinks to the associated primary literature and to gene information held in the Ensembl and Uniprot databases. Magnagenes highlights some of the strengths and weaknesses in the Magnaporthe research community's effort to understand the genetic basis of the ability of M. oryzae to cause blast disease. It can serve as a guide to the understudied aspects of the blast fungus biology. We provide Magnagenes to the community as part of the OpenRiceBlast and Open WheatBlast initiatives. We aim to release regular updates to Magnagenes and welcome additions or corrections from the blast research community to expand the database. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Magnagenes has prov en an invaluable tool in all gene functional studies and for defining differences between rice blast and wheat blast. 
URL https://zenodo.org/record/4647766#.Yi7BXhDMI6E
 
Title Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Orthogroups and species tree Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa Species tree: SpeciesTree_rooted.txt Whole genome alignment of S. avenae, S. miscanthi, M. dirhodum and A. pisum Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz Haplotype divergence analysis (whole genome sequences) VCF files of HapCUT2 phased variants for S. miscanthi Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9): Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz VCF files of HapCUT2 phased variants for S. avenae JIC1 chromosomes (Siave_v2.1 assembly scaffolds 1 to 9): JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz Haplotype resolved assemblies of S. avenae JIC1 and S. miscanthi Langfang-1 based on HapCUT2 phasing results: JIC1_H1.Hapcut2.fa JIC1_H2.Hapcut2.fa Langfang1_H1.Hapcut2.fa Langfang1_H2.Hapcut2.fa SibeliaZ whole genome alignment of S. avenae JIC1 and S. miscanthi Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf Filtered VCF files used for population genomics analysis S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf SNAPP phylogenetic analysis configuration file and trees SNAPP configuration file: snapp.xml SNAPP log file: ut.log SNAPP posterior sample of trees: ut.trees SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://zenodo.org/record/7108777
 
Title Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids 
Description Orthogroups and species tree Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa Species tree: SpeciesTree_rooted.txt Whole genome alignment of S. avenae, S. miscanthi, M. dirhodum and A. pisum Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz Haplotype divergence analysis (whole genome sequences) VCF files of HapCUT2 phased variants for S. miscanthi Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9): Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz VCF files of HapCUT2 phased variants for S. avenae JIC1 chromosomes (Siave_v2.1 assembly scaffolds 1 to 9): JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz Haplotype resolved assemblies of S. avenae JIC1 and S. miscanthi Langfang-1 based on HapCUT2 phasing results: JIC1_H1.Hapcut2.fa JIC1_H2.Hapcut2.fa Langfang1_H1.Hapcut2.fa Langfang1_H2.Hapcut2.fa SibeliaZ whole genome alignment of S. avenae JIC1 and S. miscanthi Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf Filtered VCF files used for population genomics analysis S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf SNAPP phylogenetic analysis configuration file and trees SNAPP configuration file: snapp.xml SNAPP log file: ut.log SNAPP posterior sample of trees: ut.trees SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact As per 8 Mar 2025, the dataset has 336 views and 419 downloads 
URL https://zenodo.org/record/7108778
 
Title The transcriptome responses of Fusarium head blight and Fusarium root rot in B. distachyon 
Description Fusarium graminearum causes Fusarium head blight (FHB) and Fusarium root rot (FRR) in small-grain cereals. The host response to FRR and the transcriptome responses differences of FHB and FRR are not well studied. Using the model Brachypodium distachyon (Bd), the RNA-seq transcriptome response of Bd to F. graminearum (Fg) infection of heads and roots was carried out. Additionally, the RNA-seq transcriptome response and predicted secretome within the same infected material were performed against in vitro samples of Fg. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.cz8w9gj6k
 
Description Agricluture and Forestry University collaboration in Nepal 
Organisation Agriculture and Forestry University
Country Nepal 
Sector Academic/University 
PI Contribution Collaboration initiated on Yellow rust control in wheat, cabbage stem flea beertle in Brassicas and the agricultural supply chain in Nepal
Collaborator Contribution Expertise in these subject areas as well as facilities for collaborative research at AFU
Impact Too early to say
Start Year 2020
 
Description Aphid 
Organisation International Centre of Insect Physiology and Ecology (ICIPE)
Country Kenya 
Sector Academic/University 
PI Contribution We sequenced and assembled the genome of the banana aphid, which is a big pest on banana in Kenya.
Collaborator Contribution The ICIPE partners provided banana aphid samples for sequencing.
Impact Genome sequences of banana aphid and other aphid species will be compared. There is an agreement of how to write this up for a publication.
Start Year 2017
 
Description BASF 
Organisation BASF
Country Germany 
Sector Private 
PI Contribution Knowledge on pathways involved in resistance and susceptibility to Fusarium head blight (FHB). Knowledge on the use of model plant species to study FHB
Collaborator Contribution Knowledge on fungicide testing systems and high through put phenotyping
Impact Two iCASE studentships
Start Year 2016
 
Description Capturing novel quality and soil health traits for sustainable barley production 
Organisation New Heritage Barley Limited
Country United Kingdom 
Sector Private 
PI Contribution this is a collaborative project to characterise novel traits in barley for the brewing and distilling industries. Our contribution is to provide seed and field trial facilities as well as expertise in barley growing
Collaborator Contribution They provide expertise in association genetics and mapping. They also provide facilities and expertise for metabolomics analysis. New heritage barley is a spin-out company from the John Innes Centre that is investing in this project
Impact The collaboration only started in October 2018, with a student being recruited to the project
Start Year 2018
 
Description Capturing novel quality and soil health traits for sustainable barley production 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution this is a collaborative project to characterise novel traits in barley for the brewing and distilling industries. Our contribution is to provide seed and field trial facilities as well as expertise in barley growing
Collaborator Contribution They provide expertise in association genetics and mapping. They also provide facilities and expertise for metabolomics analysis. New heritage barley is a spin-out company from the John Innes Centre that is investing in this project
Impact The collaboration only started in October 2018, with a student being recruited to the project
Start Year 2018
 
Description Cell biology of NLR immune receptors 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution To understand the sub cellular localisation of NLR immune receptors both in their resting and activated states. Ibrahim, T., Yuen, E.L.H., Wang, H.Y., King, F.J., Toghani, A., Kourelis, J., Vuolo, C., Adamkova, V., Castel, B., Jones, J.D.G., Wu, C.-H., Kamoun, S. and Bozkurt, T.O. 2024. A helper NLR targets organellar membranes to trigger immunity. bioRxiv, doi: https://doi.org/10.1101/2024.09.19.613839. Madhuprakash, J., Toghani, A., Contreras, M.P., Posbeyikian, A., Richardson, J., Kourelis, J., Bozkurt, T.O., Webster, M.W., and Kamoun, S. 2024. A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity. Science Advances, 10:eadr2594. Selvaraj, M., Toghani, A., Pai, H., Sugihara, Y., Kourelis, J., Yuen, E.L.H., Ibrahim, T., Zhao, H., Xie, R., Maqbool, A., De la Concepcion, J.C., Banfield, M.J., Derevnina, L., Petre, B., Lawson, D.M., Bozkurt, T.O., Wu, C.-H. Kamoun, S., and Contreras, M.P. 2024. Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. PLOS Biology, 22:e3002868.
Collaborator Contribution Our partner is an expert in plant cell biology (a real cell biologist) and has contributed to imaging NLR immune receptors.
Impact Punctate plasma membrane localisation of activated NLR proteins Organellar localisation of helper NLR proteins Perihaustorial localisation of helper NLR proteins
Start Year 2021
 
Description Cell-to-cell mobility of effectors of Fusarium - Takken lab 
Organisation University of Amsterdam
Country Netherlands 
Sector Academic/University 
PI Contribution We performed callose staining to assay for plasmodesmal function in effector-expressing plant lines
Collaborator Contribution They provided all expertise and resources that relate to the pathosystem
Impact No outcomes to date
Start Year 2015
 
Description Cell-to-cell mobility of effectors or Liberibacter - Coaker lab 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution We provided vectors and expertise in assaying for cell to cell mobility of effector proteins in host tisses
Collaborator Contribution They provided all expertise and resources relating to the pathosystem
Impact A pre-print manuscript is available, https://www.biorxiv.org/content/10.1101/2021.09.10.459857v1.article-info
Start Year 2019
 
Description Collaboration with Davide Roncarati (University of Bologna) 
Organisation University of Bologna
Country Italy 
Sector Academic/University 
PI Contribution We will host a third-year PhD student for 6 months in my lab. We will train and support the student to conduct structural biology and global analysis (ChIP seq) research. The final three months of the six month placement will contribute directly to the work in this ISP theme.
Collaborator Contribution The student's living expenses and half of their lab costs will be paid by the collaboration partner. They will supply biological materials, know-how and academic support throughout.
Impact None so far
Start Year 2020
 
Description Collaboration with East Malling Research 
Organisation East Malling Research
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We are sequencing and annotating the genome of the woolly apple aphid, a serious pest of apple trees
Collaborator Contribution The collaborator provided frozen aphids for genome and RNA sequencing
Impact We will obtain the complete genomes and transcriptomes of the woolly apple aphid, which is in a distinct clade in the aphid phylogenetic tree and useful for comparative genome analyses among aphids.
Start Year 2018
 
Description Collaboration with Institute for Sustainable Plant Protection, Bari, Italy 
Organisation National Research Council
Department Institute for Sustainable Plant Protection
Country Italy 
Sector Public 
PI Contribution I invited colleague at Institute for Sustainable Plant Protection to attend and contribute a talk at the BRIGIT consortium meeting of July 2019, Edinburgh. The colleague was also invited to give a talk at the BRIGIT satellite meeting before the IS-MPMI meeting, July 2019, Glasgow.
Collaborator Contribution Colleague engaged and exchanged information on Xylella outbreaks in Italy with BRIGIT consortium members, and contributed samples of (potential) insect vectors for genome sequencing to the BRIGIT project.
Impact We will generate sequence data that can be used for development of diagnostics tools of (potential) Xylella insect vectors.
Start Year 2019
 
Description Collaboration with Liverpool School of Tropical Medicine (LSTM) 
Organisation Liverpool School of Tropical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Write iCASE studentship in collaboration with colleagues at LSTM and Syngenta. The proposal made it through the DTP process of the Norwich Research Park. We identified a suitable candidate who accepted the position.
Collaborator Contribution Contributed to the writing of the iCASE studentship.
Impact An iCASE studentship that starts Oct '20
Start Year 2019
 
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 Professor Xuewei Chen and Dr Min He, Sichuan Agricultural University, Chengdu 
Organisation Sichuan Agricultural University
Country China 
Sector Academic/University 
PI Contribution A collaboration was established to study the molecular basis of septin aggregation and interaction with plasma membranes during appressorium development by the rice blast fungus Magnaporthe oryzae. We discovered a requirement for very long chain fatty acid synthesis (VLCFA) in septin aggregation and identified a compund that would inhibit this process. this was tested as a fungicide against rice blast in field trials.
Collaborator Contribution The partners carried out extensive VLCFA tests on septin aggregation and identified the fungicidal compound, which we tested rigorously in my laboratory in independent tests.
Impact A publication was generated describing this work He M, Su J, Xu Y, Chen J, Chern M, Lei M, Qi T, Wang Z, Ryder LS, Tang B, Osés-Ruiz M, Zhu K, Cao Y, Yan X, Eisermann I, Luo Y, Li W, Wang J, Yin J, Lam SM, Peng G, Sun X, Zhu X, Ma B, Wang J, Liu J, Qing H, Song L, Wang L, Hou Q, Qin P, Li Y, Fan J, Li D, Wang Y, Wang X, Jiang L, Shui G, Xia Y, Gong G, Huang F, Wang W, Wu X, Li P, Zhu L, Li S, Talbot NJ, Chen X. (2020) Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi. Nature Microbiol. 5(12):1565-1575.
Start Year 2019
 
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 Lisbon, Portugal 
Organisation University of Lisbon
Country Portugal 
Sector Academic/University 
PI Contribution I involved colleagues at University of Lisbon in the BRIGIT project and the sequencing of genomes and transcriptomes of insect vectors of Xylella fastidiosa. I invited colleague to give lecture and exchange knowledge with BRIGIT consortium members at consortium meeting in Edinburgh, July 2019, and at the BRIGIT satellite meeting before the IS-MPMI in Glasgow, July 2019. We co-authored on a publication.
Collaborator Contribution Partners collected insects in Portugal and send these to us for sequencing. Partners engaged with BRIGIT consortium members.
Impact Generated new knowledge on population structures of X. fastidiosa insect vectors. Co-published the genome sequence of the spittle bug Philaenus spumarius as a dataset in Zenodo (DOI:10.5281/zenodo.3368385) and agreed to sequence more European Philaenus species that are potential vectors of Xylella.
Start Year 2018
 
Description Collaboration with University of Oxford 
Organisation University of Oxford
Department Department of Plant Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Visited colleagues at University of Oxford to discuss specific project and experimental approaches
Collaborator Contribution Contributed knowledge and resources for new experiments
Impact Progress with achieving research goals by graduate student and postdoctoral researcher in the lab. Making plans for a collaborative research proposal.
Start Year 2019
 
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 Academic/University 
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 Colletotrichum higginsianum manipulation of starch metabolism in plant hosts 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution I identified Colletotrichum effectors that target starch granules in plant cells. I now supervise a student with David Seung to determine the role this effector has to play in infection. My primary role is provide input, training, expertise and equipment as relates to studying the pathology aspects of the project.
Collaborator Contribution David Seung provides expertise, training and skills regarding starch chemistry and metabolism.
Impact We recruited a JIC rotation student to work on the project. The collaboration is multidisciplinary: plant-microbe interactions and carbohydrate chemistry and metabolism.
Start Year 2020
 
Description Conservation agriculture collaboration 
Organisation Shimpling Park Farm
Country United Kingdom 
Sector Private 
PI Contribution We visited Shimpling Park Farms to see how conservation agriculture practises were being used to add value to farming
Collaborator Contribution Owner of Shimpling Park Farms contributed to the development of a subsequent workshop on Conservation Agriculture
Impact A workshop was held at the John Innes Centre involving farmers and researchers, including scientists from the USA
Start Year 2017
 
Description Disease control in salad and vegetable crops 
Organisation G's Fresh Limited
Country United Kingdom 
Sector Private 
PI Contribution We had initial discussions to develop a research collaboration to imporve disease control in vegetable and salad crops, which a particular concern for the comapny
Collaborator Contribution They informed us of the nature of investigtion that they were interested in
Impact We have submitted a proposal for the company to consider as a basis for establishing a collaborative reserch partnership
Start Year 2020
 
Description Engaged with colleagues at the International Centre of Insect Physiology and Ecology (ICIPE) 
Organisation International Centre of Insect Physiology and Ecology (ICIPE)
Country Kenya 
Sector Academic/University 
PI Contribution Involved colleague at ICIPE in the GCRF-funded project to study Napier grass stunt phytoplasma
Collaborator Contribution Provided plant and insect materials for sequencing
Impact Materials are being processed
Start Year 2018
 
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 - Rafael Rivilla, Marta Martin and Jacob Malone 
Organisation Autonomous University of Madrid
Country Spain 
Sector Academic/University 
PI Contribution My research group has provided technical advice and support for the biochemistry of cyclic-di-GMP signalling analysis in Pseudomonas, including protein-nucleotide binding assays, ITC, nucleotide quantificaiton by LC/MS. We have hosted two researchers for summer visits to JIC
Collaborator Contribution My research partners are conducting molecular microbiology experiments into Pseudomonas fluorescens plant colonisation, that are informed by the biochemistry from my lab.
Impact One paper has been published so far from this collaboration: Muriel C., Arrebola E., Redondo-Nieto M., Martínez-Granero F., Jalvo B., Pfeilmeier S., Blanco-Romero E., Baena I., Malone J. G., Rivilla R., Martín M. (2018) AmrZ is a major determinant of c-di-GMP levels in Pseudomonas fluorescens F113. Scientific reports 8 p1979
Start Year 2015
 
Description Formal collaboration with BecA, Nairobi, Kenya 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We provide information on phytoplasma effectors and how they interact with plant targets. This will help the identification of resistance in Napier grass and other crops susceptible to phytoplasmas.
Collaborator Contribution The BecA team provided information on Napier grass germ plasm and genomics resources that will be mined for phytoplasma effector targets and polymorphisms in these targets that lead to insusceptibility to phytoplasma effectors.
Impact Two members of the Hogenhout group (a research assistant and PhD student) have visited BecA and ICIPE for several days. They joined a symposium and presented talks about their researcj in this symposium. They exchanged knowledge and resources.
Start Year 2017
 
Description Formal collaboration with Fera, UK 
Organisation Fera Science Limited
Country United Kingdom 
Sector Public 
PI Contribution I involved colleauges at Fera in the BRIGIT project
Collaborator Contribution FERA colleagues lead Work Package 2 (WP2) of the BRIGIT project. The main goal of WP2 is to optimize and improve technologies for diagnostics of Xylella fastidiosa in diverse plant species, including trees. Another FERA colleague is involved in WP3 of the BRIGIT project. The main goal of WP3 is to better understand the migration patterns of X. fastidiosa insect vectors in the UK. FERA colleagues are involved in the social sciences aspect of WP4 of the BRIGIT project. The main goal of WP4 is to model the potential pathways of spread of X. fastidiosa in the UK.
Impact Protocol optimization for diagnostics of Xylella fastidiosa has started.
Start Year 2018
 
Description Formal collaboration with Forest Research, England and Scotland 
Organisation Forest Research
Country United Kingdom 
Sector Public 
PI Contribution Involved colleagues at Forest Research in the BRIGIT project
Collaborator Contribution Collaborator 1 at Forest Research leads Work Package 1 (WP1) of the BRIGIT project. The main aims of WP1 are to develop activities to involved citizen scientists and stakeholders in the BRIGIT project and develop databases with information on various aspects of Xylella fastifiosa and its insect vectors. Collaborator 2 at Forest Research is involved in WP2 of the BRIGIT project. WP2 is focused on developing diagnostics for X. fastidiosa and is lead by colleagues at Fera. Collaborator 3 at Forest Research is involved in developing the social sciences aspect of WP4 of the BRIGIT project.
Impact Planning of citizen scientist and stakeholder activities have started.
Start Year 2018
 
Description Formal collaboration with Natural Environment Research Council 
Organisation UK Centre for Ecology & Hydrology
Country United Kingdom 
Sector Public 
PI Contribution Involved Natural Environment Research Council colleague in the BRIGIT project
Collaborator Contribution 1. Leads Work Package 4 of the BRIGIT project; 2. Models the potential pathways of spread of Xylella fastidiosa in the UK
Impact Started to collate data from project partners to do the modelling and interacts with scientists in Europe to help develop the model.
Start Year 2018
 
Description Formal collaboration with Royal Horticultural Society 
Organisation Royal Horticultural Society
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Involved the Royal Horticultural Society in the BRIGIT project.
Collaborator Contribution Colleagues at Royal Horticultural Society developed a database of plant species susceptible to Xylella fastidiosa.
Impact Dr. Gerard Clover has been hired as the Engagement Officer for the BRIGIT project and works 4 days per week at the JIC
Start Year 2018
 
Description Formal collaboration with Science and Advice for Scottish Agriculture 
Organisation Science and Advice for Scottish Agriculture
Country United Kingdom 
Sector Public 
PI Contribution I involved colleagues at SASA in the BRIGIT project
Collaborator Contribution Colleagues at SASA are involved in Work Package (WP) 2 and 3 of the BRIGIT project. WP2 is aimed at optimizing and further developing technologies for diagnostics of Xylella fastidiosa within BRIGIT, and WP3 is aimed at better understanding the migration of X. fastidiosa insect vectors in the UK.
Impact Work on WP2 and WP3 have started
Start Year 2018
 
Description Formal collaboration with University of East Anglia 
Organisation University of East Anglia
Department School of Economics
Country United Kingdom 
Sector Academic/University 
PI Contribution Involved the colleague in the BRIGIT project
Collaborator Contribution Colleague contributes towards accomplishing goals in WP4 of the BRIGIT project
Impact WP4 of BRIGIT is making good progress
Start Year 2019
 
Description Formal collaboration with University of Salford 
Organisation University of Salford
Country United Kingdom 
Sector Academic/University 
PI Contribution Involved colleague in the BRIGIT project.
Collaborator Contribution Colleague participates in Work Package (WP4) of the BRIGIT project. WP4 is modelling the potential pathways of spread of Xylella fastidiosa in the UK.
Impact Collation of data for the modelling of WP4 has started.
Start Year 2018
 
Description Formal collaboration with University of St Andrews 
Organisation University of St Andrews
Department Department of Geography & Sustainable Development
Country United Kingdom 
Sector Academic/University 
PI Contribution I involved colleague at University of St Andrews in the BRIGIT project
Collaborator Contribution Dr Rehema White contributes to teh goals of WP4 in the BRIGIT project.
Impact Work on WP4 has been going as planned.
Start Year 2019
 
Description Formal collaboration with University of Stirling 
Organisation University of Stirling
Country United Kingdom 
Sector Academic/University 
PI Contribution Involved colleague in the BRIGIT project.
Collaborator Contribution Colleague participates in Work Package 4 (WP4) of the BRIGIT project. The aim of WP4 is to model the potential pathways of spread of Xylella fastidiosa in the UK.
Impact Collating data for starting the modelling of WP4 of BRIGIT has started.
Start Year 2018
 
Description Formal collaboration with University of Sussex 
Organisation University of Sussex
Country United Kingdom 
Sector Academic/University 
PI Contribution I involved collaboratort in the BRIGIT project
Collaborator Contribution Collaborator contributes Entomology expertise to the BRIGIT project
Impact 1. Funding of the BRIGIT project by UKRI Strategy Priority Fund. 2. Access to UK database of amateur and professional entomologists to collect candidate insect vector species of Xylella fastidiosa.
Start Year 2018
 
Description Formal research collaboration with Academia Sinica, Taipei, Taiwan 
Organisation Academia Sinica
Department Institute of Plant and Microbial Biology
Country Taiwan, Province of China 
Sector Academic/University 
PI Contribution Development of the research question, approaches and methodology. Provided knowledge about the biology of the organisms, collected biological material, extracted DNA and generated raw reads of genome sequence data. Invited groupe leader at Academia Sinica to the BRIGIT consortium meeting of July 2019 in Edinburgh.
Collaborator Contribution Assembled the genome reads into contigs and annotated the genomes. Contributed a talk and exchanged knowlede on Xylella comparative genome analyses with WP2 members of the BRIGIT consortium at the BRIGIT consortium meeting of July 2019 in Edinburgh. Contributed a talk at the BRIGIT satellite meeting before the IS-MPMI meeting of July 2019, Glasgow.
Impact Several co-authored publications. Exchanged information on Xylella genome sequence comparisons that is useful for developing diagnostics protocols in WP2 of the BRIGIT project.
Start Year 2014
 
Description Formal research collaboration with Chinese Academy of Agricultural Sciences (CAAS), Beijing, China 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution My group provides aphid genomics information to the project.
Collaborator Contribution CAAS contributed aphid samples and transgenic wheat to achieve plant-mediated RNAi of aphids to the project
Impact We sequenced the genomes of many wheat-colonizing aphid species. The genomes have been assembled. Annotation pipeline for the genomes is under construction.
Start Year 2016
 
Description Formal research collaboration with Earlham Institute, Norwich, UK 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Our time provides knowledge, resources and materials for the insect-plant interaction research system.
Collaborator Contribution Colleagues team provides knowledge on bioinformatics and genomics, including genome and transcriptome assembly pipelines and genome annotations.
Impact We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We are co-authors on Mathers et al., 2017. Genome Biology, and a paper that is being submitted this month. We assisted postdoctoral researcher Thomas Mathers with the writing of a Future leader fellowship application, which was succesful (starts Apr 2018).
Start Year 2010
 
Description Formal research collaboration with Institute of Plant Protection, Poznan, Poland 
Organisation Institute of Plant Protection, National Research Institute
Country Poland 
Sector Public 
PI Contribution My lab hosted a PhD student of the Institute of Plant Protection at JIC, Oct 2016 - Mar 2017. The student conducted work on the HFSP collaborative project.
Collaborator Contribution The team in Poznan collects plant and insect samples in northern and southern regions of Poland for the HFSP project; the samples were assayed for the presence of phytoplasma strains and effector genes.
Impact We wrote a HFSP project proposal together that was funded. We hold regular Skype meetings (in average, once in the 6 weeks) to discuss progress and results.
Start Year 2014
 
Description Formal research collaboration with Oxitec 
Organisation Oxitec Ltd
Country United Kingdom 
Sector Private 
PI Contribution My group provides knowledge, data and resources on whiteflies and other hemipteran insects.
Collaborator Contribution Oxitec provides information on insect transformation technologies and design of transformation plasmids.
Impact Obtained a iCASE PhD student fellowship. Hired PhD student Rebecca Corkill. Rebecca is making good progress with the project.
Start Year 2015
 
Description Formal research collaboration with 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 Formal research collaboration with Syngenta 
Organisation Syngenta International AG
Department Syngenta Ltd (Bracknell)
Country United Kingdom 
Sector Private 
PI Contribution Provide information about aphid biology and genomics, and mechanisms involved in aphid adjustment to diverse plant species and pesticides.
Collaborator Contribution Contributed 10% cash towards two BBSRC-IPA projects (2014-2017; 2017-2020) and advised on how to conduct pesticide applications. Provided aphid clones for sequencing and analyses.
Impact Made progress with understanding processes involved in aphid adjustments to plants and pesticides. This collaboration resulted in a publication: Mathers, Chen et al., 2017. Genome Biol. 18: 27. As well, the collaboration was renewed with follow-up funding, that is a BBSRC-IPA grant commencing April 2018. Held regular meetings to discuss progress, including visits of my group to Syngenta and collagues of Syngenta to JIC, and Skype and phone conference meetings.
Start Year 2014
 
Description Formal research collaboration with Tracey Chapman, University of East Anglia, Norwich, UK 
Organisation University of East Anglia
Department School of Biological Sciences UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution I am secondary supervisor on a Oxitec co-funded iCASE PhD studentship of Tracey.
Collaborator Contribution Tracey is secondary supervisor on a Oxitec co-funded iCASE PhD studentship of my group.
Impact We exchange knowledge about insect pests. We will start holding monthly journal club meetings starting Apr 2018. DIscussions to apply for research funding together are ongoing. We discuss research on the identification of sex-determination genes accross hemipteran insect species.
Start Year 2015
 
Description Formal research collaboration with University of East Anglia, Norwich, UK 
Organisation University of East Anglia
Department School of Environmental Sciences UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution Knowledge, resources and materials for the insect-plant interaction research system.
Collaborator Contribution Colleague's team provides knowledge on evolutionary biology and population genetics.
Impact We obtained two BBSRC-IPA collaborative grants with Syngenta. We co-supervise postdoctoral researchers and PhD students. We co-authored on publications. We assisted postdoctoral researchers with the writing of a succesful Future Leader Fellowship application.
Start Year 2013
 
Description Formal research collaboration with University of Sao Paolo - College of Agriculture (ESALQ) 
Organisation Universidade de São Paulo
Department College of Agriculture
Country Brazil 
Sector Academic/University 
PI Contribution Provided intellectual input into development of a collaborative research proposal, expertise in specific research methodologies and trained staff in molecular biology methods. Members of the partner team visited my team to gain experience with molecular biology techniques and discuss project progress. These included: - Visit of ESALQ group leader to Hogenhout lab, 11-18 Sep. 2013. - Visit of ESALQ group leader to Hogenhout lab, 20-24 Oct. 2014. - Visit of ESALQ postdoctoral researcher to Hogenhout lab, March - Dec, 2014.
Collaborator Contribution Provided intellectual input into development of a collaborative research proposal, expertise in specific research methodologies and trained and hosted staff for conducting field-based experiments. Members of my team visited the partner lab for field trips. These included: - Field trip and processing of samples in Brazil of a PhD student in my team, 18 May - 8 June, 2013. - Visit of Hogenhout to partner lab, 28-31 Oct, 2013. - Field trip and processing of samples in Brazil, 6-21 June, 2014. - Visit and processing of samples in Brazil, 19-23 Oct, 2015.
Impact Co-authored several publications.
Start Year 2013
 
Description Formal research collaboration with University of Wisconsin, Madison, USA 
Organisation University of Wisconsin-Madison
Department Department of Entomology
Country United States 
Sector Academic/University 
PI Contribution We involved the University of Wisconsin team into a HFSP research proposal that got funded.
Collaborator Contribution The University of Wisconsin team collects phytoplasma-infected plant and leafhopper samples from all over the USA for the HFSP-funded project.
Impact We received funding for collaborative HFSP project. We hold regular progress meeting (in average once/6 weeks). We co-supervise postdoctoral researchers and PhD students. We are writing up a manuscript.
Start Year 2014
 
Description Formal research collaboration with Wageningen University and Research Centre, The Netherlands 
Organisation Wageningen University & Research
Department Department of Plant Sciences
Country New Zealand 
Sector Academic/University 
PI Contribution We provided knowledge on phytoplasma virulence proteins that interfere with plant development and involved the Wageningen team into a interdisciplinary project proposal that received funding from HFSP.
Collaborator Contribution The Wageningen team provided expertise on plant transcription factors targeted by phytoplasma effectors and helped us with interpretation of the plant developmental phenotypes. They are co-investigators on our HFSP grant.
Impact We received funding for a HFSP research project. We co-published a paper: MacLean et al., 2014. PLoS Biol. 12(4):e1001835. We co-supervise postdoctoral researchers. We hold regular Skype meetings (in average once per 6 months) for the past 3 years.
Start Year 2014
 
Description Improving Vegetable Crops in Nepal 
Organisation University of East Anglia
Department School of International Development UEA
Country United Kingdom 
Sector Academic/University 
PI Contribution Including the Nepal Project in the portfolio of projects in the new Norwich Institute for Sustainble Development
Collaborator Contribution Our partners at UEA are contributing expertise in international development and business studies to address the research topic of improving vegetabe production in Nepal
Impact Too early
Start Year 2021
 
Description Limagrain wheat blast 
Organisation Limagrain
Country France 
Sector Private 
PI Contribution knowledge on genetics of wheat blast resistance
Collaborator Contribution germplasm
Impact iCASE studentship funded
Start Year 2017
 
Description Partnership award with University of Liverpool, UK. 
Organisation University of Liverpool
Department School of Veterinary Science Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Provide information on vector-borne diseases of plants.
Collaborator Contribution Provide information of vector-borne diseases of humans and animals.
Impact We won a US Partnering Award: Vector-borne diseases in the UK & US: common threats and shared solutions" and co-organized visits of US colleagues to the UK (Dec 2016) and UK group members to the University of California, Davis (Oct 2017). We applied for a GCRF VBD network grant together; the pre-proposal for this was selected for submission of a full proposal, and we were invited for an interview with BBSRC based on our full proposal submission. The proposal was ranked 5th out 12 proposals, and only the top 3 were funded. Finally, we co-organized the Vector-Borne Diseases in the UK meetings, 3-4 Dec 2018 hosted at the JIC.
Start Year 2016
 
Description Partnership with Defra 
Organisation Department For Environment, Food And Rural Affairs (DEFRA)
Country United Kingdom 
Sector Public 
PI Contribution I engaged with Defra colleagues and upper management to develop the BRIGIT proposal. We are currently working on response policies in the event Xylella fastidiosa is detected in the UK and strategies for integration of outcomes of the BRIGIT project in these reponse policies.
Collaborator Contribution Contribution of a wide range of knowledge on policy making and (methods for) collection of data for the BRIGIT project.
Impact We have weekly meetings when Dr. Sutton-Croft is at the John Innes Centre at one day per week.
Start Year 2018
 
Description Plasmid manipulation of translational regulation in bacteria 
Organisation University of Reading
Department School of Biological Sciences Reading
Country United Kingdom 
Sector Academic/University 
PI Contribution In addition to intellectual input, my lab provides specialist resources and research skills in molecular microbiology, protein biochemistry and plant-microbe interaction to this collaboration.
Collaborator Contribution Sheffield University (Brockhurst lab) are providing skills in evolutionary microbiology, soil microbiology and mathematical/statistical modelling. Reading University (Jackson lab) are providing intellectual input and know-how relating to bacterial genetics and microbiology. Both partners are funded by a companion grant to this one.
Impact None so far
Start Year 2018
 
Description Plasmid manipulation of translational regulation in bacteria 
Organisation University of Sheffield
Country United Kingdom 
Sector Academic/University 
PI Contribution In addition to intellectual input, my lab provides specialist resources and research skills in molecular microbiology, protein biochemistry and plant-microbe interaction to this collaboration.
Collaborator Contribution Sheffield University (Brockhurst lab) are providing skills in evolutionary microbiology, soil microbiology and mathematical/statistical modelling. Reading University (Jackson lab) are providing intellectual input and know-how relating to bacterial genetics and microbiology. Both partners are funded by a companion grant to this one.
Impact None so far
Start Year 2018
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Private 
PI Contribution Knowledge of genetics of disease resistance in wheat including new sources of resistance and associated genetic markers
Collaborator Contribution germplasm, DNA marker information, breeder know-how
Impact iCASE PhD studentship and scientific publications
 
Description Secobra 
Organisation Secobra Recherche
Country France 
Sector Private 
PI Contribution information on the relationship between plant height and disease susceptibility
Collaborator Contribution Germplasm and field trial testing of populations
Impact new sources of resistance to Fusarium head blight
Start Year 2012
 
Description The role of plasmodesmata in F. graminearum infection 
Organisation Chinese Academy of Sciences
Department Shanghai Institute of Plant Physiology and Ecology
Country China 
Sector Academic/University 
PI Contribution We are screening F. graminearum effectors for subcellular localisation with a particulare focus on plasmodesmata association. We will take responsibility for characterisation of any effectors of interest.
Collaborator Contribution The Tang lab provide gene expression data and expertise relating to F. graminearum pathology and handling.
Impact CAS-JIC CEPAMS collaborative project, £226k
Start Year 2019
 
Description UCD 
Organisation University College Dublin
Country Ireland 
Sector Academic/University 
PI Contribution tools for using model plant species to investigate genetics of resistance to root diseases
Collaborator Contribution coordinating programme and liaising with the European Commission
Impact Identification of candidate genes involved in resistance to root diseases in cereals
Start Year 2014
 
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
 
Description With Najing Agricultural University on Phytophthora genome sequencing and genetic manipulation 
Organisation Nanjing Agricultural University
Country China 
Sector Academic/University 
PI Contribution This is our project. We provide research concept, goal, materials and biological questions.
Collaborator Contribution Our collaborators are expert on Phytophthora genetics. They help us generate Phytophthora mutants.
Impact Not multi-disciplinary. The outcome will be joint publications that report related research discoveries.
Start Year 2023
 
Description With Structural biologists in Chinese Academy of Sciences 
Organisation Chinese Academy of Sciences
Country China 
Sector Public 
PI Contribution This is a collaboration on our project. We provide the conceptual framework, biological questions and materials.
Collaborator Contribution The collaborators are structural biologists who solved the structure of the proteins of our interest.
Impact The collaboration is multidisciplinary. Together, we have solved the crystal structures of pathogen effectors as well as effector-host target complexes. This work has been published in 2023 (Li et al., Cell). The postdoc Hui Li in my group and a graduate student Jinlong Wang in the collaborator's group are co-first authors.
Start Year 2022
 
Description With Texas A&M University (USA) 
Organisation Texas A&M University
Country United States 
Sector Academic/University 
PI Contribution We contribute to the concept of the project.
Collaborator Contribution Our partner offers their expertise in the biochemical characterization of small RNA-associated enzymes and has been doing related experiments to strengthen this research.
Impact This collaboration is not multi-disciplinary. The outcome of this collaboration will be joint authorship in a publication, which will report discoveries made by this project.
Start Year 2023
 
Description With University of East Anglia, School of Chemistry, Pharmacy and Pharmacology 
Organisation University of East Anglia
Department School of Chemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution We collaborate with Dr. Andrew Beekman (Associate professor of Medicinal Chemistry) to design peptide and chemical inhibitors that target the Phytophthora effectors in order to inactivate their virulence functions. My group contributes to this collaboration by offering the biological and mechanistic insights into effector-host interactions. We also test the candidate inhibitors for their effect on disrupting effector-host target interactions as well as disease resistance.
Collaborator Contribution Dr. Beekman's group contributes to this collaboration by designing inhibitors based on the structure of the effector-host target interaction interface.
Impact Since this collaboration is relatively recent, it has not led to any significant outcomes yet. This collaboration is multi-disciplinary, combining molecular biology, plant pathology with protein chemistry and AI-based modeling.
Start Year 2024
 
Title METHODS FOR TARGETED PROTEIN DEGRADATION 
Description The present invention relates to a fusion protein for use in ubiquitin-independent protein degradation. The invention also relates to methods for the use of the fusion protein in targeted protein degradation, modulating physiological responses and therapy. 
IP Reference WO2022129621 
Protection Patent / Patent application
Year Protection Granted 2022
Licensed Commercial In Confidence
Impact We have received additional funding and hired staff to take the technology further.
 
Title METHODS OF ALTERING PLANT ARCHITECTURE 
Description The invention relates to a method of altering plant architecture, the method comprising expressing the phytoplasma effector, SAP05. 
IP Reference WO2022129557 
Protection Patent / Patent application
Year Protection Granted 2022
Licensed No
Impact We have received additional funding and hired staff who will explore possibilities to use patents for launching a start-up company.
 
Title MODULATING PLANT RESPONSES TO ACTIVITIES OF PATHOGEN VIRULENCE FACTORS 
Description The invention relates to methods of engineering a host to become resistant or increase the resistance of a host to a vector-borne pathogen. In one example, there is a provided a method of engineering a plant to become resistant to phytoplasma. 
IP Reference WO2022129579 
Protection Patent / Patent application
Year Protection Granted 2022
Licensed No
Impact We have received additional funding and hired staff who will explore possibilities to use patents for launching a start-up company.
 
Title POLYMORPHISM FOR PATHOGEN RESISTANCE 
Description A method to select for plant resistance towards Hemipteran insects and/or towards Hemipteran-borne pathogens, the corresponding markers, mutants, isolated protein, recombinant constructs, and plant or plant part. 
IP Reference WO2021048269 
Protection Patent application published
Year Protection Granted 2021
Licensed No
Impact A method to select for plant resistance towards hemipteran insects and/or towards Hemipteran-borne pathogens, the corresponding markers, mutants, isolated protein, recombinant constructs, and plant or plant part.
 
Company Name Pfbio 
Description Pfbio develops biological alternatives to agrochemicals for use in crop farming. 
Year Established 2022 
Impact The company is working towards its first prototype product, supported by a combination of industry-linked grants and private investment.
Website http://pfbio.co.uk
 
Company Name Resurrect Bio 
Description Resurrect Bio develops gene editing technology designed to resurrect R-genes in crops such as soy, aiming to provide a more sustainable alternative to chemical agricultural controls. 
Year Established 2021 
Impact Delivering disease resistance traits. Integrating AI into plant disease resistance breeding.
Website http://resurrect.bio
 
Description "Diverse regulatory control of nitrogen fixation in proteobacteria" International Conference on Nitrogen Fixation 2019, Wuhan, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Plenary talk at a major international meeting introducing students to the potential for deriving agronomic benefit from manipulation of associative diazotophs
Year(s) Of Engagement Activity 2019
 
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 A taste of Genetic Diversity: demonstration activity for the John Innes Centre open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A demonstration of our research was performed at an open day at the John Innes Centre, involving hands on activities and discussion on the theme of 'a taste of genetic diversity. The activities involved showing how brassicas were used in baby leaf salads, and how heritage barley varieties were used in brewing beer
Year(s) Of Engagement Activity 2017
 
Description A view from the lab - blog interview 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview for a science blog - A View From The Lab.
Year(s) Of Engagement Activity 2018
 
Description 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 AgroSight 
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 Hosted and discussed potential research project on phytoplasma pathogens of oil palms in Columbia with Mayke Santos, AgroSIght, Cambridge, UK.
Year(s) Of Engagement Activity 2017
 
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 Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology, Joinville, Santa Catarina, Brazil May 26th to 29th, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a keynote talk entitled "Strategies to utilise biological nitrogen fixation to supply nitrogen to cereal crops". This talk emphasised that allthough the practice of applying chemical fertilisers to increase crop yields has had an enormous impact on world agriculture it has resulted in severe agronomic and environmental penalties, including eutrophication of aquatic systems and atmospheric pollution. In order to circumvent this nitrogen conundrum, it has been proposed that biological nitrogen fixation (BNF) could be exploited to provide a more sustainable alternative to the use of nitrogen fertilisers in agriculture. I outlined two potential approaches to circumvent this conundrum: firstly, the engineering of diazotrophic bacteria that can excrete ammonia as a nitrogen source for plants and secondly, the direct engineering of the nitrogen-fixing enzyme, nitrogenase into cereals.
Year(s) Of Engagement Activity 2018
 
Description Attended Annual conference of the Italian Society for Crop Genetics 
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 Attended scientific conference 'Science and innovation for sustainable agriculture intensification: the contribution of plant genetics and breeding' of the Italian Society for Crop Genetics, presented invited lecture and engaged with colleagues.
Year(s) Of Engagement Activity 2019
 
Description Attended Australasian Plant Pathology Society (APPS) meeting, Melbourne, Australia 
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 Attended and presented at the annual Australasian Plant Pathology Society meeting. Met with colleagues who work on approaches to prevent Xylella from spreading in Australia and New Zealand and neighbouring countries. Established international contacts for the BRIGIT project. Exchanged knowledge about a wide range of (invasive) insect-transmitted plant pathogens that cause threats to agriculture worldwide.
Year(s) Of Engagement Activity 2019
URL https://www.apps2019.org/
 
Description Attended Gatsby Plant Science Annual Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Attended the annual meeting on behalf of Gatsby-funded graduate student
Year(s) Of Engagement Activity 2019
 
Description Attended Introductory programme for UvA professors 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Participated in an introductory programme for UvA professors. The Executive Board of the University of Amsterdam offers this programme to all newly appointed UvA professors, to facilitate them in their new role in the academic community and as UvA representatives. The programme offered insights and tools that helped strengthen personal effectiveness in daily work situations including extending network within the UvA. It also allows to gain more insight into the role and position of a UvA professor, meet colleagues and exchange experiences plus learn more about Dutch academic leadership codes. Furthermore, organizational and financial aspects of the university will be highlighted as well as current developments within the UvA and the role of academic leadership.
Year(s) Of Engagement Activity 2019
 
Description BASF visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to BASF scientists involved in plant protection and biotechnology on current research on fusarium head blight and opportunities for collaboration with scientists at JIC across a broad spectrum of plant and microbial research relevant to the area of crop protection.
Year(s) Of Engagement Activity 2018
 
Description BBC Farming Today Interview 25th October 2018 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview for BBC Farming Today on the CJEU ruling on Genome Editing as a form of genetic modification, subject to the same regulation as transgenic crops, and the likely effect of this ruling on agricultural innovation in Europe. The interview covered genome editing technologies, the potential for crop improvement, the details of the ruling, the contrast with other international jurisdications, and the potential effect on agriculture in Europe.
Year(s) Of Engagement Activity 2018
 
Description BBC Look East Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I was interviewed about the potential impact of Brexit on scientific research at The Sainsbury Laboratory and the Norwich Research Park. The interview covered the type of research carried out across the NRP, the degree of international collaboration, and the importance of European Commission funding to research projects.
Year(s) Of Engagement Activity 2018
 
Description BBC Radio Norfolk Interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I was interviewed on the potential effects of Brexit on research at The Sainsbury Laboratory, John Innes Centre and across the Norwich Research Park. The interview covered the type of research underway across the institutes, the international nature of research at TSL and JIC and the importance of European Commission funding to research programmes in Norwich.
Year(s) Of Engagement Activity 2018
 
Description BBRO 
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 Discussed opportunities for collaboration with BBRO with Mark Stevens (Centrum Building, NRP, Norwich, UK).
Year(s) Of Engagement Activity 2017
 
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 Bangladesh wheat blast 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion with primary Bangladesh wheat researcher on wheat blast resistance
Year(s) Of Engagement Activity 2018
 
Description Barley to Beer: Science into Practise 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited presentation at the Moleculr Biology of Plant Pathogens meeting, Norwich, Uk. The primary audience is PhD students
Year(s) Of Engagement Activity 2019
 
Description BecA 
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 GCRF project discussions with Sita Ghimire (BecA, Nairobi, Kenya)
Year(s) Of Engagement Activity 2017
 
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 Breeder day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentations to invited individuals from the wheat breeding and food/feed beverage supply chain
Year(s) Of Engagement Activity 2015,2016,2017
 
Description CONNECTED 
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 Attended and participated in network discussions of CONNECTED UK Launch conference, Bristol, UK (hosted by Gary Foster, Neil Boonham and Nicola Spence), 29-31 Jan '18.
Year(s) Of Engagement Activity 2018
 
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 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 Coauthor on paper on risks of mirror bacteria 
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 Coauthor on paper on risks of mirror bacteria. Some followup media engagement
Year(s) Of Engagement Activity 2024
URL https://pubmed.ncbi.nlm.nih.gov/39666824/
 
Description Conference attendance 
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 Brassica Research commuity is an informal meeting where researchers can present their latest results to academia and industry
Year(s) Of Engagement Activity 2020
 
Description Contributed an 'Accessible Science Talk' for the Research and Support Staff Voice (RSSV) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact The JIC Research and Support Staff Voice (RSSV) organised a day (9 Oct 2018) of talks as part of the JIC Annual Science Meeting, delivered by top scientists from JIC and TSL. Every talk was accessible to a wide audience including scientists, support and partnership staff and communicates the great work carried out at JIC and TSL, presented in a manner that will be understandable and interesting for all.
Year(s) Of Engagement Activity 2018
 
Description Contribution of two lectures for BIO-3C20 Molecular Plant-Microbe Interactions course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact Postdoctoral researcher Adi Kliot in my lab will contribute two lectures in the BIO-3C20 Molecular Plant-Microbe Interactions, Spring Semester, University of East Anglia, March 2019.
Year(s) Of Engagement Activity 2019
 
Description Crop Doctors - New Scientist Live 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I presented alongside Prof Mark Banfield and Dr Christine Faulkner in the New Scientist Live event representing and talking about research in the Plant Health ISP. Following presentations, I stayed online and answered many questions regarding GM technologies and plant disease.
Year(s) Of Engagement Activity 2020
 
Description Crop Doctors - New Scientist Live 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I presented alongside Prof Nick Talbot and Prof Mark Banfield in the New Scientist Live event representing and talking about research in the Plant Health ISP. Following presetations, I stayed online and answered many questions regarding GM technologies and plant disease.
Year(s) Of Engagement Activity 2020
 
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 Developing Markets for Heritage Malts 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation at the Great Lakes Hop and Barley Conference, Detroit, Michigan. The audience comprised farmers, maltsters, brewers, researchers
Year(s) Of Engagement Activity 2017
 
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 Discussion with BASF 
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 Discussion on wheat disease resistance with representative of BASF
Year(s) Of Engagement Activity 2023
 
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 Dutch students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation of work on importance of research on disease resistance
Year(s) Of Engagement Activity 2016,2017,2018
 
Description Dynamic Cell IV British Society for Cell Biology International Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Invited speaker, talk entitled: Investigating the cell biology of plant infection by the rice blast fungus Magnaporthe oryzae
Year(s) Of Engagement Activity 2021
 
Description EMBO plenary lecture "Exploiting fundamental understanding of nitrogen fixation for potential agricultural benefit" Stockholm Sweden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A major international conference related to biological nitrogen fixation and sustainable agriculture
Year(s) Of Engagement Activity 2018
 
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 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Discussions with Defra Animal and Plant Health and Welfare directorate
Year(s) Of Engagement Activity 2023
 
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 SV 
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 Three-monthly meetings with industrial collaborators
Year(s) Of Engagement Activity 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 Fusarium Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Over 200 delegates from across the globe attended the meeting. My presentation sparked many questions and further discussions on the implications of our findings for improving the resistance of wheat to FHB and reducing the risk of mycotoxins accumulating in grain and posing a threat to consumers
Year(s) Of Engagement Activity 2018
 
Description European Research Council@10: the impact on science and scientists 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Scientists at the John Innes Centre and The Sainsbury Laboratory reflect on the success of the ERC over the last ten years and the impact that ERC grants have had on their science and their careers. Category: Science & Technology
Year(s) Of Engagement Activity 2017
URL https://youtu.be/qEgjYaMG0tQ
 
Description Everything you wanted to know about research integrity but never dared to ask 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Sophien Kamoun's talk to the Norwich research Park PhD student. May 7, 2019.
Year(s) Of Engagement Activity 2019
URL https://www.slideshare.net/SophienKamoun/everything-you-wanted-to-know-about-research-integrity-but-...
 
Description 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 FSOV 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discuss wheat disease resistance genetics with members of a consortium of French Breeding companies.
Year(s) Of Engagement Activity 2018
 
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 Frequent meetings 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 We meet four times with colleagues at Oxitex for the supervisory meeting of the PhD student. The student contributes a presentation with the latest progress on the project. We exchange knowledge.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
 
Description GCRF visit with Nepalese Researchers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A fact-finding mission to Nepal was undertaken with the aim of developing new collaborations for potential GCRF projects
Year(s) Of Engagement Activity 2017
 
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 Grain that gives good head 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Podcast about the heritage barley project with Dewing Grain Ltd
Year(s) Of Engagement Activity 2018
URL http://www.dewinggrain.co.uk/podcast-item/?id=37
 
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 Growing the drinks industry in Wales 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Visitors from the Food and Drink Wales Cluster visited the John Innes Centre and we discussed the value of diverse germplam collections in developing new flavourse and sensory attributes of drinks
Year(s) Of Engagement Activity 2019
 
Description Healthy Plants, Healthy People, Healthy Planet - Advances in genetics, genomics, structural and computational biology are revolutionising our understanding of plants and microbes. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I presented alongside Prof Dale Sanders on the main stage of the New Scientist Live event, talking about the major joint initiative between the Sainsbury Laboratory and the John Innes Centre called Healthy Plants, Healthy People, Healthy Planet (HP3), the main objectives of this project are; feeding the world, combating global health threats and meeting the challenge of climate change.
Year(s) Of Engagement Activity 2020
 
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 Heritage Malt webinar 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was invited to participate in a webinar arranged by Crips Malting Group on the subject of heritage malts for the brewing and discilling industries
Year(s) Of Engagement Activity 2020
URL https://crispmalt.com/news/webinar-11-crisps-heritage-malt-programme/
 
Description Horizon The EU Research and Innovation Magazine: AGRICULTURE--Can CRISPR feed the world? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact As the world's population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

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

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

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

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

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

Gene-editing to improve crop immunity

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

Read also: Can CRISPR feed the world? https://horizon-magazine.eu/article/can-crispr-feed-world_en.html
Year(s) Of Engagement Activity 2018
URL https://horizon-magazine.eu/article/expect-exoplanet-atmospheres-organs-new-functions-and-fewer-traf...
 
Description Hosted Alexandra Kolodyazhnaya, BSc student Novosibirsk State University, Russia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Student did a research project in my lab as part of the JIC/TSL/EI International Undergraduate Summer School programme at JIC.
Year(s) Of Engagement Activity 2018
 
Description Hosted Libby Hanwell, BSc student Biological Sciences, University of East Anglia, UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact Hosted the student for a research project in the summer of 2018 and her BSc research project from Oct-Dec '18
Year(s) Of Engagement Activity 2018,2019
 
Description Hosted Luke Sherwin, MSc student Molecular Medicine at the University of East Anglia, UK. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact MSc project for BIO_6019Y course. Luke wrote a 3000-word project and did a research project Mar-Sep 2018
Year(s) Of Engagement Activity 2018
 
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 organizing committee 
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 Local organizing committee for IS-MPMI 2019, Glasgow, UK.
Year(s) Of Engagement Activity 2018
 
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 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 at the Max Planck Institute for Plant Breeding Research (online) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a seminar to the scientists and postgraduate students at the MPI, Cologne.
Year(s) Of Engagement Activity 2020
 
Description Invited Talk - EMBO Workshop on Intercellular communication and plasmodesmata in development and disease 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Over 100 people attended the workshop to share progress in research and establish new collaborations
Year(s) Of Engagement Activity 2022
 
Description Invited keynote speech at the Experimental Plant Science conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I was one of the two keynote speakers in the annual Experimental Plant Science (EPS) conference. This conference is the major meeting for the plant science research community in the Netherland. I presented research findings and activities in my laboratory to an audience of ~500 attendees from major universities and AgTech companies, including undergraduate/graduate students, postdoctoral fellows, research staff, and group leaders. I also engaged in many scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
Description Invited research seminar at 'When Development meets Stress' symposium, CRAG, Barcelona, Spain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk on Phytoplasma at the 'When Development meets Stress' symposium, Center for Research in Agricultural Genomics (CRAG), Barcelona, Spain, 2-4 Sep 2018.
Year(s) Of Engagement Activity 2018
URL https://www.bdebate.org/en/forum/when-development-meets-stress-understanding-developmental-reprogram...
 
Description Invited research seminar at CAS institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a research seminar at IGDB, Beijing, China on 16 Mar 2018. Research fellow Thomas Mathers in my lab also contributed a talk.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at iDiv, Leipzig, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited by PhD students to give a research presentation at the Integrative Biodiversity Research Institute (iDiv), Halle-Jena-Leipzig, Germany, 18 Apr 2018. I was hosted by Crispus Mbaluto, PhD student at iDiv.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at the Max Planck Institute, Cologne, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a research seminar at the Max Planck Institute for Plant Breeding, Cologne, Germany. Approximately 50 people, including PhD students, attended.
Year(s) Of Engagement Activity 2018
 
Description Invited research seminar at the XI European Congress of Entomology, Naples, Italy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a research seminar on Phytoplasma in a parallel session focused on insect-transmitted plant pathogens and plant-insect interactions.
Year(s) Of Engagement Activity 2018
 
Description Invited seminar at ENS de Lyon, France 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave a seminar to the scientists and postgraduate students at the ENS de Lyon, France. I also spoke with number of researchers in 1-1 meetings to exchange information and identify potential collaborations and exchanges.
Year(s) Of Engagement Activity 2020
 
Description Invited seminar at the Institute for Mediterranean and Subtropical Horticulture (Malaga, Spain) 
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 invited to speak at the Institute for Mediterranean and Subtropical Horticulture (Consejo Superior de Investigaciones Científicas (CSIC). I presented research findings and activities in my laboratory to an audience including mainly graduate students, postdoctoral fellows, and group leaders. I also engaged in scientific discussions with individuals.
Year(s) Of Engagement Activity 2025
 
Description Invited seminar at the Michigan State University (USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I was invited to speak at the Department of Plant Pathology, Michigan State University. I presented research findings and activities in my laboratory to an audience including undergraduate/graduate students, postdoctoral fellows, and faculty members. I also engaged in scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
Description Invited seminar at the University of British Columbia (Canada) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I was invited to speak at the Michael Smith Laboratory at the University of British Columbia in Vancouver, Canada. I presented research findings and activities to an audience including undergraduate students, graduate students, postdoctoral fellows, and faculty members. I also engaged in scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
Description Invited seminar at the University of California Davis (USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I was invited to speak at the Department of Plant Sciences, University of California Davis. I presented research findings and activities in my laboratory to an audience including undergraduate/graduate students, postdoctoral fellows, and faculty members. I also engaged in scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
Description Invited seminar at the University of Michigan (Ann Arbor, USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I was invited to give a lecture at the University of Michigan (Molecular, Cellular and Developmental Biology program). I presented research findings and activities in my laboratory to an audience including undergraduate/graduate students, postdoctoral fellows, and faculty members. I also engaged in scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
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 JIC 50 Open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Open Day to celebrate 50 years of the John Innes Centre in Norwich, where we exhibited a stand to show isolation of microbes from soil and their influence on plant growth.
Year(s) Of Engagement Activity 2017
 
Description JIC50 Molecular Microbiology presentation 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Contributed to the design and running of the molecular microbiology department stall at the JIC 50 year open day.
Year(s) Of Engagement Activity 2017
 
Description 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/

Follow us on social media:
https://twitter.com/LinneanSociety
https://www.facebook.com/linneansociety/
https://www.instagram.com/linneansociety
Year(s) Of Engagement Activity 2020
URL https://youtu.be/R5GJWHmq2_k
 
Description Keynote Speaker, Agrinet, Chemical Biology Conference, Syngenta Jeallott's Hill, Bracknell (July 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Engagement with Syngenta scientists working on developing new chemical control methods for fungal pathogens. Ongoing engagement and funded research from 2005-2018.
Year(s) Of Engagement Activity 2018
 
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 lecture at XVI Symposium on Biological Nitrogen Fixation with Non-Legumes, Foz do Igaucu, Brazil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Lecture related to education of postgraduate students and Brazilian faculty related to innovations in plant growth promoting bacteria
Year(s) Of Engagement Activity 2018
 
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 Limagrain wheat disease 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Discussion led to Liamgrain supporting iCASE PhD proposal (successful)
Year(s) Of Engagement Activity 2016,2017
 
Description MBPP (Molecular Biology of Plant Pathogens conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact MBPP (Molecular Biology of Plant Pathogens) is a short, friendly meeting supported by BSPP but organized locally that provides an ideal platform for young researchers (typically PhD or post-doc) to network and gain their first experiences of giving a talk away from 'home base' in front of larger audiences.
Year(s) Of Engagement Activity 2019
 
Description Meeting with HE Mr. Slim Khalbous Ministre de l'Enseignement Supérieur et de la Recherche Scientifique of Tunisia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact A busy week in Tunisia. A great honour to receive the Presidential Research Award from HE Mr. Slim Khalbous Ministre de l'Enseignement Supérieur et de la Recherche Scientifique. Also, present at the ceremony were Mme Samia Charfi Directrice Générale de la Recherche Scientifique et M. Abdelmajid Ben Amara Directeur Général de l'Enseignement Supérieur.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/183671401535/a-busy-week-in-tunisia-a-great-honour-to-receive
 
Description Meeting with Norwich Institute for Sustainable Development 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Study participants or study members
Results and Impact We exchanged information and research interest with colleagues at the Norwich Institute for Sustainable Development, University of East Anglia, UK to assess posisbilities for future collaborations.
Year(s) Of Engagement Activity 2019
 
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 Microbes in Norwich symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact The Microbes in Norwich symposium showcased the wide variety of microbiological research taking place on the Norwich Research Park, improving links between researchers and research bodies and driving high quality research and open communication between scientists. Contributing institutions included the University of East Anglia, the John Innes Centre, The Sainsbury Laboratory, the Quadram Institute, the Earlham Institute and the Norfolk and Norwich University Hospital. 240 participants ranging from undergraduates to project leaders took part in this one day event.

Seminar speakers included Nick le Brun (UEA), Nick Talbot (TSL), Alison Mather (QIB), Laura Lehtovirta-Morley (UEA), Marcelo Batista (JIC), Fred Warren (QIB), Richard Leggett (EI), Gemma Langridge (QIB), David Lea-Smith (UEA), Naiara Beraza (QIB). The Plenary Speaker was Nicole Dubilier, Director of the Max Planck Institute for Marine Microbiology, Bremen, Germany. There was also a poster competition and extensive discussion sessions.
Year(s) Of Engagement Activity 2019
URL http://microbesinnorwich.org/
 
Description Mildew Locus O facilitates colonisation by arbuscular mycorrhizal fungi in angiosperms 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A presentation was given by Catherine Jacott on her receny publication at the Shanghai Institute of Plant Physiology and Ecology
Year(s) Of Engagement Activity 2019
 
Description Mistletoe press coverage 
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 Coordinated press releases on our research on mistletoe in the UK and Germany were picked up by many national newspapers (UK, Germany, Netherlands, Spain) and by New Scientist online, and by Science Magazine online. It also sparked a commissioned short article written together with professionals of science communication.
Year(s) Of Engagement Activity 2018
URL https://www.thesciencebreaker.org/breaks/evolution-behaviour/the-mystery-of-mistletoe-mitochondria
 
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 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Lecture to the public as part of Norwich Science festival, explaining the science and relevance of plant-microbial interactions in the soil. Positive audience feedback including two people who expressed interest in the JIC as a potential future workplace.
Year(s) Of Engagement Activity 2017
 
Description Novel Approaches to Durable Disease Resistance in Crop Improvement 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact I gave an lecture at Imperial College for the module on Symbiosis, Immunity and Breeding to undergraduate and postgraduate students
Year(s) Of Engagement Activity 2021
 
Description Novel Approaches to Durable Disease Resistance in Crop Improvement 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Plenary lecture at the Eurobiotech 2019 conference, Krakow, Poland
Year(s) Of Engagement Activity 2019
 
Description Online seminar for aBIOTECH, November 18, 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I was invited as a keynote speaker for an online symposium on plant biotechnology organized by the journal aBIOTECH. This symposium attracted a broad audience with >3,000 attendees globally. Funding from BBSRC was acknowledged.
Year(s) Of Engagement Activity 2022
 
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 Organiser - Botanical Microscopy Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I was an organiser of the Botanical Microscopy Conference, hosted in Norwich. I also gave a research talk. This event involved a tour of JIC Bioimaging for participants and facilitated international exchange of knowledge regarding scientific advances and new methods.
Year(s) Of Engagement Activity 2022
 
Description Organization of BRIGIT activities at the BSPP 'Our Plants, Our Future' meeting, Royal Society, London 
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 Frequently communicated with upper management of Defra to organize BRIGIT event at the 'Our Plants, Our Future' meeting, Royal Society, London. Invited plenary speaker from Brazil to talk about Xylella fastidiosa problem in citrus and practical solutions. Organized BRIGIT poster session presented by ± 20 BRIGIT consortium members.
Year(s) Of Engagement Activity 2019
URL https://www.bspp.org.uk/conferences/our-plants-our-future/
 
Description Organized and hosted a conference 
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 Member of organizing committee and host of Vector-Borne Disease in the UK 2018, JIC, Norwich, UK, 3-4 Dec 2018.
Year(s) Of Engagement Activity 2018,2019
 
Description Organizing the satellite meeting 'Dynamics and Mechanism of Insect-Transmitted Pathogens' at the IS-MPMI 
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 This satellite meeting will be organized on Sunday 14th July, 8.30 - 15.00, and brings together scientists with an interest in studying the diverse aspects of insect-transmitted plant pathogen interactions with their plant hosts and insect vectors. These pathogens cause the most destructive diseases of plants and are often responsible for eradication of entire crop industries in countries or regions. Current examples include Olive Quick Decline Syndrome (Xylella fastidiosa), citrus greening (Candidatus Liberibacter sp.), Lime Witch's Broom and Grapevine Flavescence doree (Candidatus Phytoplasma) and Cassava mosaic (geminivirus). The meeting will cover (1) Recognition and induction of immunity, (2) Effectors and modulation of insect/plant processes, (3) Epidemiology and insect transmission and (4) Genomics and Evolution. If you would like to attend or contribute to the meeting, please contact Saskia Hogenhout, Silke Robatzek, Sheng-Yang He and Steven Lindow by 15 April 2019 at the very latest.
Year(s) Of Engagement Activity 2018,2019
URL https://www.ismpmi.org/Congress/2019/program/Pages/Satellite-Meetings.aspx
 
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 Panel member of international proposal review committee 
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 Reviewed proposals submitted by European scientists and influenced funding decisions.
Year(s) Of Engagement Activity 2021
 
Description Participated in conference at Syngenta 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Attended Syngenta external collaboration event. Three postdoctoral lab members in my group presented research talks and updates with their project progress.
Year(s) Of Engagement Activity 2019
 
Description Participated in visit of Syngenta to the Norwich Research Park 
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 Discussed progress on current funded projects and possibilities of future projects with colleagues from Syngenta.
Year(s) Of Engagement Activity 2019
 
Description Participated summerschool, Pwani University, Kenya 
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 Co-organized a two-day course as part of the two-week AfriPlantSci summerschool for ±25 professionals and students from research institutes and university in Kenya and several other countries in sub-saharan Africa. Two PhD students of my team participated in the organization of the summerschool. Protocols we taught in the course were shared and are being used in current projects of the course participants.
Year(s) Of Engagement Activity 2019
 
Description Phillipines 
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 Communicated and wrote proposal for the Newton Afgham Programme with Karen Alviar, National Institute of Molecular Biology (BIOTECH), University of the Philippines, Los Banos. The objective was to investigate effector proteins of the cassava phytoplasma disease (CPD), which has caused massive outbreaks in the Philippines. Unfortunately, the application was considered to have eligibility problems for unclear reasons. An appeal letter was submitted (Jun 2017), but this did not help.
Year(s) Of Engagement Activity 2017
 
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 Plenary Lecture "Engineering Nitrogen fixation for Agricultural Benefit" at the XVII International Meeting of the Spanish Society of Nitrogen Fixation, Madrid ,Spain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was an opportunity to introduce students to the benefits of sustainable agriculture . Subsequently at the meeting I was invited to write a book chapter on this subject
Year(s) Of Engagement Activity 2019
 
Description Plenary talk at the American Society of Plant Biologists conference (USA) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I was invited to give a plenary presentation at the annual ASPB conference. This conference is the major meeting for the plant science research community globally. I presented research findings and activities in my laboratory to an audience of >1,000 attendees from universities and research institutes, including undergraduate/graduate students, postdoctoral fellows, research staff, and group leaders. I also engaged in many scientific discussions with individuals.
Year(s) Of Engagement Activity 2024
 
Description Plenary talk at the European Nitrogen Fixation Conference 2021 in the session "Applications of biological nitrogen fixation and environmental impact" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Plenary Session talk entitled "Optimising nitrogen delivery by root-associated diazotrophs"
Year(s) Of Engagement Activity 2021
URL https://events.au.dk/enfc2021/programme2021
 
Description Presentation to Novozymes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact presentation of research to three representatives from Novozymes, a speciality chemicals company based in Denmark
Year(s) Of Engagement Activity 2017
 
Description Presentation to Royal Engineers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Third sector organisations
Results and Impact Presentation on fungal diseases and toxins as risks to humans and food security
Year(s) Of Engagement Activity 2023
 
Description Presented a talk at Monogram 
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 Presented a talk at Monogram, JIC, Norwich, UK, 24-16 Apr 2018.
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 the Huang et al. 2021 Cell 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 Released a press release to announce the early release of the Huang et al. 2021. Cell paper on 17 Sep 2021. The paper got published in the 30 Sep 2021 issue of Cell. The title of the press release was: "The microbial molecule that turns plants into zombies - Zombie plants, witches' brooms and the curse that might contain a cure". The press release was picked up by many news agencies and websites, including The New York Times: https://www.nytimes.com/2021/10/01/science/zombie-plants-parasites.html;
Year(s) Of Engagement Activity 2021
URL https://www.jic.ac.uk/press-release/the-microbial-molecule-that-turns-plants-into-zombies/
 
Description Press release to announce BRIGIT project. 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Engaged with JIC Public Engagement Officer to launch press release 'UK consortium to combat serious threat to plant health' to announce the start of the BRIGIT project and the BRIGIT project website.

Coverage as a result of this press release included
Eastern Daily Press - Norwich scientists will lead £4.85m project to battle one of the world's most dangerous plant diseases, The Yorkshire Post - Scientists battle bug that could infect 500 species, Horticultural Trades Association, Hort Week Online, The Herald (Glasgow), Garden Design Journal, Seed Quest, The Garden.
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/press-release/uk-wide-consortium-to-combat-serious-threat-to-plant-health/
 
Description Press release to announce new appointment for the BRIGIT project 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Engaged with JIC Public Engagement Officer to launch press release 'New appointment for UK-wide Xylella pathogen consortium' for the BRIGIT project
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/news/new-appointment-for-uk-wide-xylella-pathogen-consortium/
 
Description Progress meeting with industrial collaborator 
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 progress meetings with colleagues SESVanderHave to discuss project made with BBSRC-LINK and iCASE projects.
Year(s) Of Engagement Activity 2019
 
Description Public Presentation, Café Scientifique, Phoenix Arts Centre, Exeter (June 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Public presentation of the biology of rice blast disease, given to general public and arts undergraduates at Cafe Scientifique event for public understanding of science.
Year(s) Of Engagement Activity 2018
 
Description Public outreach - Plants of the future (May 21, 2022) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact This was an open day at the Norwich Research Park with scientific exhibits, tours and family-friendly activities. I helped designed and participated in two activities (observing plant pathogens through microscope and DNA extraction), which attracted many visitors.
Year(s) Of Engagement Activity 2022
 
Description Putting it together: How do plants sense and integrate seasonal signals? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk at: Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France. This has led to the establishment of a collaboration involving scientists from France and Spain.
Year(s) Of Engagement Activity 2017
 
Description Re-introducing heritage barley: Science into practise 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited speaker at the RMI analytics Heirloom and Terrior Barley and Malt Symposium. The results of the projects including commercialisation of heritage malt were presented
Year(s) Of Engagement Activity 2018
 
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 SchoBozKa Annual Retreat 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The event is an annual retreat of the following labs to enable interactions between the team members and explore research avenues. This also includes a career development activity. The groups involved are Sebastian Schornack @dromius | Tolga Bozkurt @Tolga_Bzkrt | Lida Derevnina @lderevnina | Phil Carella @Phil_Carella | Jiorgos Kourelis @JiorgosKourelis
Year(s) Of Engagement Activity 2023,2024,2025
URL https://kamounlab.tumblr.com/post/776102920337915904/its-that-time-of-year-schobozka-running-strong
 
Description School teacher education 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact The activity involved a presentation and discussion with school teachers on the importance and relevance of plant disease in a historical and current context. The activity is aimed at providing teachers who are not experts in plant pathology to effectively provide all the relevant information required within the A-level curriculum to their students
Year(s) Of Engagement Activity 2018
 
Description Science Engagement at St. Michaels Junior School, Norwich (08/06/2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact During a science week at St. Michael's Junior School a team member was invited to speak to three classes about 'What is a scientist?'. The classes consisted of ~30 year 4 children (aged 8/9 years). The talk was based around images on a powerpoint but was largely unscripted so that the children felt able to ask questions and spark discussion. The children were introduced to the idea that there are different types of scientists, investigating all areas of the biology, chemistry and physics. This progressed onto the career of a scientist and how scientists share their knowledge locally and internationally which naturally led to speaking about how the UBNFC's work is beneficial to sustainable agriculture, economy and the environment. The clear outcome was that it gave the children an opportunity to think about science as an interesting subject to learn more about and that a science related career was accessible option to all.
Year(s) Of Engagement Activity 2017
URL http://ubnfc.org/?page_id=74
 
Description Science Media Training for group member (Training course organised by the BBSRC, training carried out by members of the BBC) 
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 Member attended an official BBSRC Media Training course for scientists. This one-day course gave background on how interviews are conducted on TV and Radio. Techniques for answering questions were given and excellent practical sessions were included. The course is designed to prepare scientists in the event that the research attracting media attention.
Year(s) Of Engagement Activity 2017
 
Description Science Week - Engagement at Bignold Junior School, Norwich 15/03/18 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Janine Wilkinson from our team was invited to talk to the children attending the Bignold Junior School in Norwich during their Science Week. Two classes of year 5 (9/10 years) were involved. The children were introduced to what skills make a good scientist, the many different types of scientists that there are as well as discussing the fact that scientists can work with each other not just in the same laboratory but globally (in the way that UK and Brazilian scientists work together). As well as the discussion, children also used the available light microscopes to look at plant cells. Both groups of children were highly engaged, interested and asked many questions. Feedback from the teachers was very positive and it was remarked that many of the children spoke about what type of scientist they would like to be when they are older after the workshop.
Year(s) Of Engagement Activity 2018
 
Description Science, Art and Writing workshop for West Earlham Junior School, Norwich (10/10/17) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact As part of the impact activities of the UBNFC, we liaised with the SAW initiative to provide a one-day practical workshop for year 4 children at a local school. SAW provided an artist and a writer who used their skills to highlight and enhance the scientific concepts given to the children. We began with a simple talk explaining the science concepts behind the practical activities; what bacteria are and the importance of nitrogen to living organisms. This talk also included a brief mention of the international nature of science, exemplified by our UK-Brazil virtual joint centre; with researchers working together on a single project but being physically located in different parts of the world. The children worked their way through three key practicals including making soil plates (so they could study the bacterial growth post workshop), using junior microscopes to investigate root nodules and pre-grown bacterial colonies and playing an educational game teaching them about symbiosis. The science principles learnt in the morning were then applied in the art and writing sessions in the afternoon. The workshop provided a legacy for the teachers to build on provided by information on the day and the bacterial cultures that developed on the agar plates in the following weeks.
Year(s) Of Engagement Activity 2017
URL http://ubnfc.org/?page_id=74
 
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 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 Session chair - IS-MPMI Congress 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact I organised a session at the IS-MPMI congress in Providence, RI, USA. I also delivered a research talk. The session seeded an exchange of ideas that led to the proposal for a collaborative publication that represents advances in the field.
Year(s) Of Engagement Activity 2022
 
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 Summerschool, Utrecht 
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 Postgraduate students
Results and Impact Presented a talk and engaed with students at the 9th Utrecht PhD Summerschool Environmental Signaling in Plants, Utrecht, The Netherlands, 28-30 Aug 2017
Year(s) Of Engagement Activity 2017
 
Description Supervisory committee members of PhD student at University of Wisconsin, USA. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Advised a PhD student about research progress and directions.
Year(s) Of Engagement Activity 2021
 
Description TSL Symposium - Plant resistance to pathogens in the face of climate change 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The symposium held on November 4th, 2024, in Norwich. This event marks the launch of the strategic partnership between The Sainsbury Laboratory and the Khalifa Center for Genetic Engineering and Biotechnology. Our collaboration aims to advance climate-resilient plant immunity research by uniting our expertise in plant-pathogen interactions specific to desert and dryland plants.
Year(s) Of Engagement Activity 2024
URL https://kamounlab.medium.com/opening-remarks-tsl-symposium-plant-resistance-to-pathogens-in-the-face...
 
Description Talk - International Congress of Molecular Plant Microbe Interactions - PDRA Mina Ohtsu 
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 Mina Ohtsu (Faulkner lab postdoc) presented her work on assaying for cell-to-cell mobility of Colletotrichum to the IC-MPMI audience. This sparked extensive discussion afterwards from several labs wanting to use her strategy to assay the same in their systems of interest. This lead us to develop a vector for this approach and we have distributed this to the Coaker lab UC Berkeley.
Year(s) Of Engagement Activity 2019
 
Description Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Taproot is the podcast that digs beneath the surface to understand how scientific publications in plant biology are created. In each episode, co-hosts Liz Haswell and Ivan Baxter take a paper from the literature and talk about the story behind the science with one of its authors.

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

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

Listen to this episode to hear Sophien, Ivan, and Liz discuss the science in this paper, how the project started, and how it developed into a peer-reviewed publication. Also discussed is the importance of redefining what is meant by scientific "impact", and new ways to do science in the plant pathology community and beyond
Year(s) Of Engagement Activity 2017
URL https://plantae.org/taproot-episode-1-season-1-extreme-open-science-and-the-meaning-of-scientific-im...
 
Description Ten things we learned in 2010-2019 (aside from everything else) 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact This last decade has been such an exhilarating period of exploration and discovery for me, my team and my collaborators that I just can't resist the urge to write this post. The decade took us through unexpected research paths that I would have never imagined ten years ago. As I'm drafting these words during my holidays break in Sri Lanka-in between tasting the local milk rice curries and soaking the soft Indian ocean December sunshine-I'm reflecting on the local proverb above and I'm using it as my lame excuse to offer you yet another list of decadal achievements.

Please note that this is my personal highly biased perspective on ten things we have learned in 2010-2019. This list is by no means meant to be comprehensive review of advances in our research field but rather a reflection of my own personal take on the scientific topics we investigate.
Year(s) Of Engagement Activity 2020
URL https://kamounlab.tumblr.com/post/190367273015/ten-things-we-learned-in-2010-2019-aside-from
 
Description 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 UK-US VBD network 
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 UK-US Vector-borne disease network meeting, University of California, Davis, 15-17 Oct 2017. Co-organized UK-US VBD network meeting with Matthew Baylis (University of Liverpool, UK) at the University of California, Davis, USA.
Year(s) Of Engagement Activity 2017
 
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 Webcast/interview Cornell Alliance for Science 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact I gave an interview with Alliance for Science Live about research on nitrogen fixing bacteria and the future of engineering this process to benefit agriculture.
The Alliance for Science from Cornell University, New York, aims to promote access to scientific innovation in areas of food security and sustainability. During the interview, I introduced the background on biological nitrogen fixation and why it is important. I described how overuse of synthetic fertilizer has caused unintentional impacts to the environment and is costly for farmers. I then went on to discuss various approaches that can be taken to engineer nitrogen fixation in order to solve the "nitrogen crisis" and hence increase agricultural sustainability.
Year(s) Of Engagement Activity 2021
URL https://allianceforscience.cornell.edu/alliance-for-science-live/event/engineering-biological-nitrog...
 
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 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
 
Description eyespot industry partners 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact informed wheat breeders on genetics of eyespot resistance and candidate resistance genes and potential trade-off between yield and protein content of grain
Year(s) Of Engagement Activity 2015,2016,2017
 
Description interview by BBC Norfolk Radio 
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 Media (as a channel to the public)
Results and Impact Wenbo Ma was interviewed by BBC Norfolk on her Ruth Allen Award by the American Phytopathological Society.
Year(s) Of Engagement Activity 2021
 
Description presentsation to the Flying Farmers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Flying farmers are a group of farmers interested to learn about the latest trends in research. the presentation involved talking to them about our work, and engaging in a discussion with them
Year(s) Of Engagement Activity 2017
 
Description school visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Delivery of the plant disease and host disease resistance components of the A level curriculum to A'level students. This was delivered alongside a presentation on the impact of plant disease on human civilisation throughout history and efforts to combat disease through plant breeding.
Year(s) Of Engagement Activity 2018
 
Description school visit (Wymondham) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Presentations on the history of plant disease and impact on society alongside plant disease and disease resistance information required for A level students
Year(s) Of Engagement Activity 2017,2018