An effector-detector domain in a rice immune receptor: towards structure-guided design of new disease resistance proteins.

Lead Research Organisation: University of East Anglia
Department Name: Sainsbury Laboratory

Abstract

Every growing season, significant losses are realised to many of the world's most important crop harvests because of diseases caused by pathogenic micro-organisms, such as fungi, oomycetes and bacteria. This is against the backdrop of increasing demand for food, which continues to rise as the world's population grows and there are changes in diets. Many scientific resources, from traditional plant breeding to chemical control (e.g. fungicides/pesticides), are available to help limit the impact of pathogens on crop yield. However, many of these approaches may have only short-term effects or are environmentally unsustainable. New ways to control plant diseases are required. One way to develop novel control strategies is by understanding the intricate mechanisms of how pathogens cause disease or evade detection by the plant immune system. By understanding these processes we can develop ways to engineer plants to help them fight infection.

One mechanism used by plants to fight infection is to detect pathogen agents that are attempting alter plant cells for the benefit of the pathogen. These agents, known as "effectors", give away the presence of the pathogen and plants have evolved to sense these. This triggers a response by the plant that helps stop the infection spreading. The plant sensors can work by directly contacting the effectors, like a handshake, but the important details of how this actually occurs are not known. The plant has to be very precise about knowing if a pathogen molecule is present, and all it may have to go on is the shape of the "hand" (imagine trying to identify one person in a room of 10,000 only by the shape of their hand). The plant cell will induce death of the cell if it senses the effectors, so it has to get it right.

We have been studying the interactions of a set of pathogen effectors from a microorganism (fungus) that produces a devastating disease of rice, a major food crop that many people rely on for calories. We have been able to define the nature of the "handshake" between one of these effectors and a plant sensing protein. This is just a snapshot of the interaction, and we need to understand its implications using biochemistry and biological studies in plants. To do this we will use a number of experimental approaches. Firstly, we will define how strong the handshake is between the pathogen effector and plant sensor. Secondly, we will make small changes to the shape of the molecules and see how this affects the strength of the handshake. We will then investigate some small changes that have happened in these pathogen and plant molecules during evolution in nature, using the picture of the handshake we have determined to help us. We also wish to understand why the pathogen is producing the molecules it does, and we will ask questions about what these molecules are doing. Finally, after we understand the interactions formed by the various handshakes in this system, we will engineer a plant sensor protein that can recognise more than one pathogen molecule - which could give the plant a better chance of fighting off infection. We will also see if we can get this to work in a plant other than rice, to see if our new knowledge can help other crops recognise their pathogens.

Technical Summary

The aims of this proposal are to define the molecular mechanisms underlying recognition of a rice blast effector protein family (AVR-Pik) by an unconventional domain incorporated into rice resistance proteins (Pik-HMAs) during evolution. Arms-race co-evolution, developed through direct protein-protein interaction, has resulted in an allelic series of AVR-Pik effectors and Pik resistance proteins that show deferential recognition patterns. This affects the capability of rice cultivars to respond to infection. Understanding the structural basis of recognition between these effectors and plant resistance proteins presents opportunities to engineer novel disease resistance specificities in rice, and perhaps other plant species.

To deliver on our objectives, we propose a novel multi-disciplinary approach combining biochemistry, structural biology and plant biology, with the latter directly in the host pathosystem. Building on our preliminary data, which includes the first example of a structure of a plant pathogen effector bound to a plant intracellular immune receptor, we will interrogate the interactions between AVR-Pik effectors and Pik resistance protein domains in vitro and in planta. This will include both mutational analysis based on our structural work and also natural variants of AVR-Pik and Pik-HMA domains. Further, we have identified proteins called s-HMAs as putative susceptibility factors targeted by AVR-Pik effectors. Fascinatingly, these s-HMAs are sequence (and presumably structurally)-related to the resistance protein HMA domains. We will also characterise the interaction and activity of AVR-Pik effectors with these s-HMAs. Finally, we will use structure-guided mutagenesis to engineer Pik resistance proteins with novel, extended recognition specificities (to include as-yet unrecognised AVR-Pik alleles) and also transfer HMA-mediated recognition to NLRs of other plants.

Planned Impact

Who will benefit from this research and how will they benefit?

This project will contribute knowledge and resources of relevance to the Food Security Strategic Priority area of the BBSRC.

Academics: Details of academic beneficiaries (including details of staff training) are given in the appropriate section.

The Ag-biotech and Agrichemical industries: Despite the importance of understanding the molecular mechanisms underlying plant innate immunity and how pathogens manipulate this to cause disease, little research is conducted by industry in this area. Current disease management strategies for fungi from industry mainly focus on the use of chemical interventions (fungicides). Into the future this will be unsustainable, especially as some chemicals are due to be banned. Novel genetic strategies are required to deliver plant disease resistance in important food crops. Therefore, industry will benefit from this research through an increased knowledge of disease processes that may present new opportunities for disease management. Industry could also benefit from technological developments, such as the application of structural biology and biophysical approaches to understanding plant diseases, running alongside in planta work.

Farmers: Although a challenging aim and a long-term goal, the research in this project (alongside other studies) has the potential to impact disease management strategies in the field. This may benefit commercial farmers by, for example, limiting the need for repeated spraying of fungicides on crops. It may also benefit subsistence farming, where growers do not have access to means of chemical disease control.

Policy Makers: Government Departments and senior academics will benefit from new perspectives on opportunities for management of important crop diseases of relevance to Food Security.

The general public: Diseases such as potato and tomato late-blight are well-known to the UK public, but perhaps other important diseases that affect global food security are not so well known. As part of our research we will aim to better present such diseases through public engagement with the research. The general public will largely benefit through knowledge exchange (local interest groups, home-growers), but there is also potential for benefit of new resources.

Education: Through engagement with schools, the education sector has the potential to benefit from the research through knowledge exchange. Especially relevant is the long-term potential of the research to contribute to food security, global sustainability (limiting potentially damaging chemical inputs into the environment) and to enthusing the next generation of scientists.

Staff training: This project will employ a PDRA and a PGRA. As part of the research they will receive specific training in diverse experimental techniques that could benefit a future career in research. They will also receive training in generic 'transferable' skills such as writing, oral presentation and outreach to the public and schools. These latter skills would be beneficial in any employment sector.

Publications

10 25 50
 
Title A biologist's poem 
Description This 'real and singular thing'. A piece of code in its own genome. A copy from the past, multipliable, repeatable, yet mutable. You couldn't help feeling that you had stolen this sequence from its owner. You had transferred a piece of life into the human consciousness. with apologies to Wim Wenders /w @SaskiaHogenhout 
Type Of Art Creative Writing 
Year Produced 2018 
Impact Positive feedback on social media 
URL http://kamounlab.tumblr.com/post/170774045435/a-biologists-poem
 
Title I Will Survive (biotroph remix) 
Description A plant pathology inspired song. I Will Survive (biotroph remix) [with apologies to Gloria Gaynor] Oh, no, not I I will survive Oh, as long as I know how to infect you I'll stay alive I've got all my life to live I've got all my spores to give And I'll survive I will survive, hey, hey 
Type Of Art Creative Writing 
Year Produced 2018 
Impact >15K impressions on social media and ~250 engagements 
URL https://twitter.com/KamounLab/status/1098214166723215361
 
Title Video animation: Plants have an immune system and it's complicated 
Description Just like humans, plants have an immune system that they use to fend off pathogens and pests. Research involving plant immunity was guided by Harold Flor's influential "gene-for-gene" model but this model is now supplanted by a more complex view of pant immunity. Disease resistance genes appear to work together in intricate networks that enable plants to detect and resist parasites more effectively. An in-depth understanding of the immune system can help us breed disease resistant crops. 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact ~10K views on YouTube 511 engagements and >20K impressions on Twitter 
URL https://youtu.be/mlp2mQTEVtQ
 
Description Pathogen effectors that bind host targets. Engineered and mutated immune receptors with improved activities.
Exploitation Route Advance basic understanding of plant immunity.
Fundamental understanding of immune receptors function.
Assist in plant breeding and biotechnology.
Sectors Agriculture, Food and Drink,Environment,Other

URL https://www.ncbi.nlm.nih.gov/pubmed/?term=kamoun+AND+banfield
 
Description The team contributed to the response to the wheat blast outbreak in Bangladesh. Since February 2016, a new fungal disease was spotted in wheat fields across Bangladesh and neighboring India. We are applying cutting-edge pathogenomics and genome editing technologies to address the problem.
Sector Agriculture, Food and Drink,Education,Environment,Other
Impact Types Societal,Policy & public services

 
Description Advisory Committee Chair, International Congress of Plant Pathology (ICPP18) in Boston, MA
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact ICPP 2018 adopted the theme "Plant Health is Earth's Wealth" for ISPP 2013-2018 recognising that plant pathogens don't just threaten food security and well-being. They also affect, forest and fibre systems, natural ecosystems, biodiversity and environmental harmony, and impede trade and market access. And, phytopathology research has also been a central focus for discovery and development in biotechnology and plant-microbial molecular biology. For our profession - people are the pivotal element, and while in the coming years, the ISPP will maintain a focus on plant disease impacts on food security, it should and will also foster attention to all facets of our profession through our Congresses, subject matter committees and our website, newsletter and Journal. In this light, the ISPP taskforce on global food security which has more than achieved it objectives will now become a Commission working in the same way as other ISPP Subject Matter Committees. https://www.isppweb.org/newsletters/pdf/48_8.pdf One of the major outcomes was the proposal for a code of ethics for plant health emergencies: * to foster ethical conduct * to support communication and collaboration * to ensure that decisions are based on the best available evidence See https://www.isppweb.org/newsletters/pdf/48_12.pdf
URL https://www.isppweb.org/newsletters/pdf/48_8.pdf
 
Description CABANA External Advisory Committee
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact What is CABANA? CABANA is a capacity strengthening project for bioinformatics in Latin America. It aims to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme focusing on three challenge areas - communicable disease, sustainable food production and protection of biodiversity. CABANA is orchestrated by an international consortium of ten organisations - nine in Latin America and one in the UK. CABANA is funded by the Global Challenges Research Fund (GCRF) - part of the UK Aid Budget - from October 2017 to December 2021.
URL http://www.cabana.online
 
Description Comment on Court of Justice of the European Union (CJEU) ruling-Organisms obtained by mutagenesis are GMOs and are, in principle, subject to the obligations laid down by the GMO Directive
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Impact This ruling ignores advances in plant bioediting that make this technology more precise than so-called "conventional mutagenesis". Bioediting can be also be used to recapitulate natural variations into cultivated varieties of crops. This ruling closes the door to many beneficial genetic modifications such as breeding of disease resistant plants that require much less pesticide input. A sad day for European plant science. Disseminated via Science Media centre and social media.
URL http://kamounlab.tumblr.com/post/176262512395/comment-on-court-of-justice-of-the-european-union
 
Description Global preparedness for emerging diseases
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact To build resilience against unintentional spread of crop disease threats, we present the argument for a global surveillance system (GSS) for de-risk global food supplies and increase resilience to crop diseases. The model for the GSS draws on lessons learned from established national and regional plant protection organizations and on measures implemented in more developed countries. The GSS would extend these agricultural biosecurity measures into LDCs, enhancing overall global food protection. The conference on "Building resilience against crop diseases: A global surveillance system" is supported by the Rockefeller Foundation and will be held Feb. 12-16, 2018, at The Bellagio Center in Lake Como, Italy. Simone Staiger, Head of Knowledge Management and Learning at CIAT, is facilitating the meeting.
URL http://kamounlab.dreamhosters.com/storify/RFBellagio_storify.html
 
Description Gregor Mendel Institute of Molecular Plant Biology Science Advisory Board
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact The GMI is part of the Vienna BioCenter (VBC), one of the leading international biomedical research centers worldwide that has established itself as the premier location for life sciences in Central Europe.
URL https://www.oeaw.ac.at/gmi/
 
Description Inst. Plant and Microbial Biology (IPMB), Academia Sinica, Taiwan, Science Advisory Board.
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact Academia Sinica is Taiwan's premier government-supported academic research institution, with 31 institutes and centers representing a wide range of disciplines in the sciences and humanities. It is located in the Nankang district, on the outskirts of metropolitan Taipei. One of the Life Sciences Institutes, The Institute of Plant and Microbial Biology (IPMB) has 26 fellows (professor equivalents) whose research follows one of two central themes: the mechanisms of plant functioning or plant-microbial interactions. Some 300 support staff consisting of specialists, postdoctoral fellows, graduate students, Research Assistant and administrative personnel work under the research fellows. IPMB has modern infrastructure and equipment. An active education program is also set up, with Ph.D. students from the Taiwan International Graduate Program, Academia Sinica, or from their adjunct programs with National Taiwan University and National Central University. IPMB research fellows have previously made landmark discoveries in such areas as rice breeding and genomics, regeneration via tissue culture, virus satellite RNA, microbial circadian rhythm, etc. For a long time goal, we aim to improve the quality and quantity of research performance and achieve visibility in international scientific community. Over the past decade, IPMB has undergone a major reorganization and rejuvenation, and has added a number of outstanding junior fellows.
 
Description Journals 2.0: a roadmap to reinvent scientific publishing
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Promoted preprints and open science and a different, more sustainable, form of scientific publishing therefore accelerating the dissemination of science and reducing the exorbitant costs of scientific publishing. This vision describes a radically different publishing model that would reinvent the concept of a scientific journal into a live and open forum of scientific debate and analysis. This model centers on a full integration of the preprint ecosystem into the journal interface. The journal would only accept submission of articles that have been posted as preprints. All evaluations and commissioned reviews of submitted articles would be published as soon as received on the journal website and linked to the preprint version. Editors would operate as always sifting through submitted papers and seeking external reviewers when necessary. But they will also consider author-led and community crowdsourced reviews, which would be appended to the preprint. As the reviews accumulate and revisions are submitted, the journal editors would initiate a consultation process, and when satisfied with a given version promote it to a formal article. The editor's role becomes more akin to moderator than gatekeeper. The process doesn't have to be static. As the community further comments on the article and follow-up studies are published, editors may decide to commission synthetic review or commentary articles to address emerging issues. I would also envision that the paper is linked to related articles in a "knowledge network" database, and that article tags are revised to reflect new knowledge, e.g. "independently validated". The journal would therefore become less of a static repository of scientific articles, and more of a moderated forum of scientific discussion.
URL https://zenodo.org/record/1466784#.XH2SPi2cawQ
 
Description Point of view: wither pre-publication peer review to reinvent scientific publishing
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Promoted open science and preprints among the research community therefore resulting in more rapid dissemination of scientific findings.
URL http://kamounlab.tumblr.com/post/178573217080/point-of-view-wither-pre-publication-peer-review
 
Description ERC Advanced Investigator
Amount € 2,500,000 (EUR)
Funding ID BLASTOFF 743165 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 09/2017 
End 08/2022
 
Description 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 05/2017 
End 04/2019
 
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
 
Title A clone resource of Magnaporthe oryzae effectors that share sequence and structural similarities across host-specific lineages 
Description We describe a clone resource of 195 effectors of the blast fungus Magnaporthe oryzae. These clones are freely available as Golden Gate compatible entry plasmids. Our aim is to provide the community with an open source effector clone library to be used in a variety of functional studies. Plant pathogens secrete effectors that play central roles in subjugating plants for colonization. Effectors typically have signal peptides, and occasionally carry conserved folds and motifs (Lo Presti et al.,2015; Franceschettiet al., 2017). Magnaporthe oryzae(Syn. Pyricularia oryzae) is an important plant pathogenthat is able to infect around 50 species of both wild and cultivated grasses including important cereals of the Poaceae family. M. oryzaeis mostly known to cause rice blast but can also cause disease on other crops such as barley, wheat, foxtail millet, and finger millet. The global population of Magnaporthe is composed of genetically differentiated lineages which, in some cases, still exhibit a measurable degree of gene flow (Gladieux et al.,2018). Fungal isolates from each of those lineages show a preference for a specific host and also encode distinct repertoires of effector genes (Yoshida et al.,2016). The first genomic sequence of Magnaporthe oryzaewas released in 2005 for the lab strain 70-15 and allowed to predict a large set of secreted proteins such as enzymes involved in secondary metabolism and virulence-associated factors including putative effectors (Dean et al.,2005). Recently an increasing number of genome sequences of isolates from different lineages have become available, allowing the research community to perform comparative genomic studies (Chiapello et al.,2015; Yoshida et al.,2016). Many of the validated effectors of M. oryzae are known as the MAX (MagnaportheAVRs and ToxB like) effectors. These effectors, while showing little primary sequence similarity, share a conserved structural fold composed of 6 ß-sheets alternating in an anti-parallel manner (de Guillenet al., 2015). The MAX family has been largely expanded in Magnaportheas those effectors account for 5-10% of the effector repertoire and for 50% of the already cloned effectors of Magnaporthe(de Guillenet al., 2015). Indeed, the identification of structural motifs enables more sensitive predictions of effectors from pathogen genomes compared to sequence similarity searches (Franceschettiet al., 2017). The aim of this project was to computationally identify a set of M. oryzaeeffectors from the main host-specific lineages and develop an open access clone resource for functional analyses. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? Yes  
Impact Distributed >100 samples to several laboratories via addgene. 
URL http://doi.org/10.5281/zenodo.3268775
 
Title Coomassie Brilliant Blue (CBB) staining for Rubisco is an appropriate loading control for western blots from plant material 
Description Background - Having an adequate loading control for a western blot is essential for the interpretation of the results. There are two common loading control methods for western blots of proteins from plant material: (i) using specific antibodies to detect for a reference protein, such as actin, tubulin, or GAPDH (Li et al. 2011); and (ii) treating the membrane with Ponceau or Coomassie stains to assay the levels of a constitutively expressed protein, such as Rubisco (Zhang et al. 2017; Lim et al. 2018; Zhuo et al. 2014). Comparative studies in the mammalian biology field have determined that these loading control methods-antibody detection versus staining-are roughly equivalent in their linearity (Romero-Calvo et al. 2010; Wilender and Ekblad, 2011), and thus serve as comparable quality controls. In the plant biology field, it is sometimes debated as to whether staining for Rubisco is an appropriate loading control, due to the high abundance of this protein in the cell. Results - We undertook an experiment to determine whether the range of detection of staining for Rubisco is similar to that of antibody-based detection of a reference protein. We loaded total protein extract from Nicotiana benthamiana leaves transiently expressing GFP into a gel at a range of effective sample volumes, and the resulting western blot was treated with anti-GFP antibodies as well as stained with Coomassie Brilliant Blue (CBB) (Fig. 1a). Quantification of the GFP bands in the western blot and the Rubisco bands in the CBB stained membrane indicated that these detection methods have similar linear correlations between the loading volumes of total protein extract and the detectable band intensities (Fig. 1b). In addition, quantification of a random protein of lower abundance in the CBB stained membrane also showed similar linearity (Fig. 1b). Conclusions - These results indicate that CBB staining for Rubisco can be an appropriate loading control for western blots from plant material. This representative experiment is consistent with results from other western blot experiments that we routinely perform in our laboratory. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact Feedback from social media indicates it is useful to many others. 
URL https://zenodo.org/record/2557821#.XH2gji2cbYI
 
Title Golden-Gate compatible Magnaporthe oryzae transformation vectors 
Description Golden-Gate compatible vectors for Magnaporthe oryzae transformation. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact 1/ Pennington, H.G., Youles, M., and Kamoun, S. 2017. Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors. Figshare. 2/ Pennington, H.G., Youles, M., and Kamoun, S. 2017. Golden-Gate compatible Magnaporthe oryzae protoplast transformation vectors. Figshare. Plasmids are available via AddGene. 
URL https://www.addgene.org/Sophien_Kamoun/
 
Title Isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing 
Description A method for isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact Fungal genomes are highly dynamic and often contain supernumerary mini-chromosomes. However, our knowledge about the role of mini-chromosomes in dynamic genome rearrangements and evolution is scarce. Mini-chromosomes are usually smaller then core-chromosomes and are variable in size and numbers between individuals of a species. Mini-chromosome occurence in fungi is well documented since decades, but many genomic projects have neglected them, mainly because it was technically challenging to identify them in whole genome assemblies. Here we present a protocol for isolation of mini-chromosomes for enrichment sequencing. This allows identification of mini-chromosomes in whole genome assemblies and thus comparative genomics analyses of core- and mini-chromosomes. 
URL https://www.protocols.io/view/isolation-of-supernumerary-mini-chromosomes-from-f-9t7h6rn
 
Title Nanopore sequencing of genomic DNA from Magnaporthe oryzae isolates from different hosts 
Description We report long-range sequencing of eight isolates of Magnaporthe oryzae(Syn. Pyricularia oryzae) from wheat, rice, foxtail millet and goosegrass using nanopore MinION. Our aim is to obtain chromosome-level genome assemblies that are freely available for public access to be scrutinized for genome rearrangements and structural variation. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact New collaborations. Others used the open data for their own research. Data shared openly prior to publication in formal journals. 
URL https://zenodo.org/record/2564950#.XH2f5y2cbYI
 
Title Protein-protein interaction assays 
Description Protein-protein interaction assays to identify effector-host protein interactions 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Petre, B., Win, J., Menke, F.L.H., and Kamoun, S. 2017. Protein-protein interaction assays with effector-GFP fusions in Nicotiana benthamiana. In "Wheat Rust Diseases: Methods and Protocols", S. Periyannan, ed. Methods in Molecular Biology, 1659:85-98. 
 
Description Collaboration with Prof. Ryohei Terauchi 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Exchange of materials/expertise. Exchange of visits. The collaboration includes Mark Banfield, John Innes Centre.
Collaborator Contribution Exchange of materials/expertise. Exchange of visits.
Impact Multi-disciplinary collaboration: genetics, plant pathology, plant biology, biochemistry, biophysics, genomics, bioinformatics. Royal Society International Exchanges. 2018. "Retooling rice immunity for resistance against rice blast disease". £12,000 Varden, F.A., Saitoh, H., Yoshino, K., Franceschetti, M., Kamoun, S., Terauchi, R., and Banfield, M.J. 2019. Cross-reactivity of a rice NLR immune receptor to distinct effectors from the blast pathogen leads to partial disease resistance. bioRxiv, doi:https://doi.org/10.1101/530675. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. De la Concepcion, J.C., Franceschetti, M., Maqbool, A., Saitoh, H., Terauchi, R., Kamoun, S., and Banfield, M.J. 2018. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. Nature Plants, 4:576-585. Bialas, A., Zess, E.K., De la Concepcion, J.C., Franceschetti, M., Pennington, H.G., Yoshida, K., Upson, J.L., Chanclud, E., Wu, C.-H., Langner, T., Maqbool, A., Varden, F.A., Derevnina, L., Belhaj, K., Fujisaki, K., Saitoh, H., Terauchi, R., Banfield, M.J., and Kamoun, S. 2018. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions, 31:34-45. Fujisaki, K., Abe, Y., Kanzaki, E., Ito, K., Utsushi, H., Saitoh, H., Bialas, A., Banfield, M., Kamoun, S., and Terauchi, R. 2017. An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity. bioRxiv, doi:https://doi.org/10.1101/239400. Kobayashi, M., Hiraka, Y., Abe, A., Yaegashi, H., Natsume, S., Kikuchi, H., Takagi, H., Saitoh, H., Win, J., Kamoun, S., and Terauchi, R. 2017. Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. BMC Genomics, 18:897. Bialas, A., Zess, E.K., De la Concepcion, J.C., Franceschetti, M., Pennington, H.G., Yoshida, K., Upson, J.L., Chanclud, E., Wu, C.-H., Langner, T., Maqbool, A., Varden, F.A., Derevnina, L., Belhaj, K., Fujisaki, K., Saitoh, H., Terauchi, R., Banfield, M.J., and Kamoun, S. 2017. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., Yoshida, K., Uemura, A., Oikawa, K., Abe, A., Urasaki, N., Matsumura, H., Babil, P., Yamanaka, S., Matsumoto, R., Muranaka, S., Girma, G., Lopez-Montes, A., Gedil, M., Bhattacharjee, R., Abberton, M., Kumar, P.L., Rabbi, I., Tsujimura, M., Terachi, T., Haerty, W., Corpas, M., Kamoun, S., Kahl, G., Takagi, H., Asiedu, R., and Terauchi, R. 2017. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology, 15:86. Wu, C.-H., Abd-El-Haliem, A., Bozkurt, T.O., Belhaj, K., Terauchi, R., Vossen, J.H., and Kamoun, S. 2017. NLR network mediates immunity to diverse plant pathogens. Proceedings of the National Academy of Sciences USA, 114:8113-8118. Yoshida, K., Saunders, D.G., Mitsuoka, C., Natsume, S., Kosugi, S., Saitoh, H., Inoue, Y., Chuma, I., Tosa, Y., Cano, L.M., Kamoun, S., and Terauchi, R. 2016. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics, 18:370.
 
Description Collaboration with Prof. Ryohei Terauchi 
Organisation University of Kyoto
Country Japan 
Sector Academic/University 
PI Contribution Exchange of materials/expertise. Exchange of visits. The collaboration includes Mark Banfield, John Innes Centre.
Collaborator Contribution Exchange of materials/expertise. Exchange of visits.
Impact Multi-disciplinary collaboration: genetics, plant pathology, plant biology, biochemistry, biophysics, genomics, bioinformatics. Royal Society International Exchanges. 2018. "Retooling rice immunity for resistance against rice blast disease". £12,000 Varden, F.A., Saitoh, H., Yoshino, K., Franceschetti, M., Kamoun, S., Terauchi, R., and Banfield, M.J. 2019. Cross-reactivity of a rice NLR immune receptor to distinct effectors from the blast pathogen leads to partial disease resistance. bioRxiv, doi:https://doi.org/10.1101/530675. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. De la Concepcion, J.C., Franceschetti, M., Maqbool, A., Saitoh, H., Terauchi, R., Kamoun, S., and Banfield, M.J. 2018. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. Nature Plants, 4:576-585. Bialas, A., Zess, E.K., De la Concepcion, J.C., Franceschetti, M., Pennington, H.G., Yoshida, K., Upson, J.L., Chanclud, E., Wu, C.-H., Langner, T., Maqbool, A., Varden, F.A., Derevnina, L., Belhaj, K., Fujisaki, K., Saitoh, H., Terauchi, R., Banfield, M.J., and Kamoun, S. 2018. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions, 31:34-45. Fujisaki, K., Abe, Y., Kanzaki, E., Ito, K., Utsushi, H., Saitoh, H., Bialas, A., Banfield, M., Kamoun, S., and Terauchi, R. 2017. An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity. bioRxiv, doi:https://doi.org/10.1101/239400. Kobayashi, M., Hiraka, Y., Abe, A., Yaegashi, H., Natsume, S., Kikuchi, H., Takagi, H., Saitoh, H., Win, J., Kamoun, S., and Terauchi, R. 2017. Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. BMC Genomics, 18:897. Bialas, A., Zess, E.K., De la Concepcion, J.C., Franceschetti, M., Pennington, H.G., Yoshida, K., Upson, J.L., Chanclud, E., Wu, C.-H., Langner, T., Maqbool, A., Varden, F.A., Derevnina, L., Belhaj, K., Fujisaki, K., Saitoh, H., Terauchi, R., Banfield, M.J., and Kamoun, S. 2017. Lessons in effector and NLR biology of plant-microbe systems. Molecular Plant-Microbe Interactions Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., Yoshida, K., Uemura, A., Oikawa, K., Abe, A., Urasaki, N., Matsumura, H., Babil, P., Yamanaka, S., Matsumoto, R., Muranaka, S., Girma, G., Lopez-Montes, A., Gedil, M., Bhattacharjee, R., Abberton, M., Kumar, P.L., Rabbi, I., Tsujimura, M., Terachi, T., Haerty, W., Corpas, M., Kamoun, S., Kahl, G., Takagi, H., Asiedu, R., and Terauchi, R. 2017. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology, 15:86. Wu, C.-H., Abd-El-Haliem, A., Bozkurt, T.O., Belhaj, K., Terauchi, R., Vossen, J.H., and Kamoun, S. 2017. NLR network mediates immunity to diverse plant pathogens. Proceedings of the National Academy of Sciences USA, 114:8113-8118. Yoshida, K., Saunders, D.G., Mitsuoka, C., Natsume, S., Kosugi, S., Saitoh, H., Inoue, Y., Chuma, I., Tosa, Y., Cano, L.M., Kamoun, S., and Terauchi, R. 2016. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics, 18:370.
 
Description Collaboration with Prof. Tofazzal Islam 
Organisation Bangabandhu Sheikh Mujibur Rahman Agricultural University
Country Bangladesh 
Sector Academic/University 
PI Contribution Exchange of materials/expertise.
Collaborator Contribution Exchange of materials/expertise. Professor Islam's group is working on genomic and postgenomic analyses of wheat blast fungus, which recently emerged as a devastating pathogen of wheat in Bangladesh. He is leading a dream project titled "Mining biogold from Bangladesh"where they identified more than 600 plant probiotics potential for using as biofertilizer and biopesticides. Another important focus of Prof. Islam's group is to analyze the genomes of a number of plant probiotic bacteria potential for biocontrol of major phytopathogens and biofertilization of rice and wheat. In collaboration with Prof. Sophien Kamoun, Prof. Islam is dedicated to the promotion of open science and open data sharing (e.g., open wheat blast www.wheatblast.net) which they think very critical for rapidly addressing the emerging plant diseases.
Impact #OpenWheatBlast http://openwheatblast.net https://twitter.com/search?q=%23OpenWheatBlast&src=typd Win, J., Chanclud, E., Reyes-Avila, C.S., Langner, T., Islam, T., and Kamoun, S. 2019. Nanopore sequencing of genomic DNA from Magnaporthe oryzae isolates from different hosts. Zenodo, http://doi.org/10.5281/zenodo.2564950. Valent, B., Farman, M., Tosa, Y., Begerow, D., Fournier, E., Gladieux, P., Islam, M.T., Kamoun, S., Kemler, M., Kohn, L.M.8., Lebrun, M.H., Stajich, J.E., Talbot, N.J., Terauchi, R., Tharreau, D., Zhang, N. 2019. Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Molecular Plant Pathology, 20:173-179. Gupta, D.R., Reyes Avila, C., Win, J., Soanes, D.M., Ryder, L.S., Croll, D., Bhattacharjee, P., Hossain, S., Mahmud, N.U., Mehebub, S., Surovy, M.Z., Rahman, M., Talbot, N.J., Kamoun, S., and Islam, T. 2018. Cautionary notes on use of the MoT3 diagnostic assay for Magnaporthe oryzae Wheat and rice blast isolates. Phytopathology, in press. Islam, T., Croll, D., Gladieux, P., Soanes, D., Persoons, A., Bhattacharjee, P., Hossain, S., Gupta, D., Rahman, Md.M., Mahboob, M.G., Cook, N., Salam, M., Surovy, M.Z., Bueno Sancho, V., Maciel, J.N., Nani, A., Castroagudin, V., de Assis Reges, J.T., Ceresini, P., Ravel, S., Kellner, R., Fournier, E., Tharreau, D., Lebrun, M.-H., McDonald, B., Stitt, T., Swan, D., Talbot, N., Saunders, D., Win, J., and Kamoun, S. 2016. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biology, 14:84.
Start Year 2016
 
Description #MPMI2019Posters 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact We published the Kamoun Lab posters presented at #ICMPMI2019 Congress on Molecular Plant-Microbe Interactions, Glasgow, July 14-18, on @ZENODO_ORG.

Kudos to all authors for their amazing contributions!

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

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

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

The Twitter hashtag #openwheatblast serves as a communication tool to provide the latest on this fearsome disease and update a broad audience of news related to the ongoing pandemic.
Year(s) Of Engagement Activity 2016,2017,2018,2019
URL https://twitter.com/search?q=kamounlab%20openwheatblast&src=typd
 
Description 2Blades: the story behind the scientist 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact We sat down with Sophien to find out more about the story behind the scientist:

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

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

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

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

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

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

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

How has the 2Blades Foundation been beneficial to your work?
2Blades has brought a high degree of professionalism and expertise to The Sainsbury Laboratory in terms of our capacity to interact with industrial partners. We didn't have this before, so it's been a highly synergistic interaction.
Year(s) Of Engagement Activity 2019
URL http://2blades.org/voices/prof-sophien-kamoun/
 
Description A biologist's poem 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A poem to inspire about biology
Year(s) Of Engagement Activity 2017
URL http://kamounlab.tumblr.com/post/170774045435/a-biologists-poem
 
Description 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 Article based on interview with BBC World Service programme "Four Good Things That Happened in 2016" 
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 Article based on interview with BBC World Service programme "Four Good Things That Happened in 2016"
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/news/world-38330452
 
Description CropLife FoodHeroes Series: What inspires plant scientists and why is their job so important? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Why did you want to be a plant scientist?

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

Can you explain what your job involves?

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

What are the plant diseases that you are working on?

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

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

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

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

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

What inspires you about your job?

Knowledge and people. The thrill of learning something new every day is addictive. Sharing the experience with others -be they students, colleagues, stakeholders or members of the public - is priceless.
Year(s) Of Engagement Activity 2017
URL https://croplife.org/industry-profile/sophien-kamoun/
 
Description Dhaka Tribune: Fighting the fungi that destroy wheat 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newspaper article following interview by Bangladeshi science reporter Reaz Ahmed.

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

"Once we have a better understanding of the procedure, we might be able to create some intricate genetic designs that allow precise deterrence against diseases and pests, while ensuring crop yield," he said adding further research may lead to a new generation of disease-resistant crops.
Year(s) Of Engagement Activity 2019
URL https://www.newsnation.in/science/news/discovery-of-death-switch-mechanism-in-plants-may-yield-stron...
 
Description 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 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 Growing the Future-a UK Plant Sciences Federation and a Royal Society of Biology report featuring Innovations in #PlantHealth by TSL scientists 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Growing the Future-a UK Plant Sciences Federation and a Royal Society of Biology report has featured Innovations in #PlantHealth by TSL scientists and the broader oomycete and gene editing communities.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/182471762520/growing-the-futurea-uk-plant-sciences
 
Description Hello kids, I'm a biologist! 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact My presentation to the 9-10 year old children of the British International School of Tunis. March 21, 2019.

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

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

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

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

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

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

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

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

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

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

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

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

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

Slide 14. This stunning animation of the bacterium Xanthomonas infecting tomato plants was produced by students at Halle University working with Prof. Ulla Bonas.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/183672043215/hello-kids-im-a-biologist
 
Description Horizon The EU Research and Innovation Magazine: AGRICULTURE--Can CRISPR feed the world? 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact As the world's population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

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

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

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

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

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

Gene-editing to improve crop immunity

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

Read also: Can CRISPR feed the world? https://horizon-magazine.eu/article/can-crispr-feed-world_en.html
Year(s) Of Engagement Activity 2018
URL https://horizon-magazine.eu/article/expect-exoplanet-atmospheres-organs-new-functions-and-fewer-traf...
 
Description How to select a PhD lab? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact I regularly get this question from predocs. How do I select a PhD lab? How do I decide on a good supervisor? Should I select a lab based on a project? Below is a hodgepodge of the answers I generally give.
Year(s) Of Engagement Activity 2019
URL https://zenodo.org/record/3531916#.Xl6WJS2cbDY
 
Description IS-MPMI Interactions: Fat Cats Can Jump Over The Wall: Plant Biotic Interactions Workshop in Hohhot, Inner Mongolia, China 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact On a cloudy Norwich day in 2011, post-docs Sebastian Schornack, Sylvain Raffaele, and Tolga Bozkurt were having a typical British lunch of fish and chips with mushy peas with their supervisor Sophien Kamoun. Somehow, the discussion turned to the importance of sustained productivity. Kamoun, in his usual hyperbolic style, pointed out that now that each one of them had just published notable papers (Schornack et al., 2010; Raffaele et al., 2010; Bozkurt et al., 2011), they should beware of not behaving like "lazy fat cats" and think hard about their next papers. Not everyone left the lunch in the happiest mood. One day later, after discussion with another post-doc, Mireille van Damme, Schornack and colleagues decided to found the Lazy Fat Cat Club (#LFCats). Schornack drafted a chart and was appointed as Chairman Féi mao (fat cat in Mandarin). The #LFCats ethos is that productive research requires a significant amount of communication and knowledge exchange, and informally discussing research is a perfect way of solving roadblocks and laying paths for the future. Casual meetings took place on a regular basis at The Sainsbury Laboratory, mainly on afternoon coffee breaks. The club continued to loosely grow and several other researchers joined the #LFCats. As the members moved on to start their own labs, the #LFCats "brand" helped nurture a lasting bond. Suomeng Dong, now a professor in the Department of Plant Pathology at Nanjing Agricultural University, coined the Chinese proverb "Fat cats cannot jump over the wall" to challenge the #LFCats to work collaboratively to solve problems and "jump over the wall."

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SK: Don't follow the herd. Take chances. Look beyond the current trends both in terms of experimental systems and questions, and ask provocative questions.
Year(s) Of Engagement Activity 2017
URL https://www.ismpmi.org/members/Interactions/Lists/Posts/Post.aspx?ID=152
 
Description Interview with BBC World Service programme The Inquiry: "What Went Right in 2016" 
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 Interview with BBC World Service programme The Inquiry: "What Went Right in 2016"
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/programmes/p04ks9qk
 
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 Keynote lecture at ICPP 2018: The Edge of Tomorrow - Plant Health in the 21st Century 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ICPP2018 International Congress of Plant Pathology Plenary Session - Plant Health is Earth's Wealth, Boston, USA, Monday, July 30, 2018

The talk was broadcast on a live stream and is available on YouTube https://youtu.be/MYysIKSYY_8
Year(s) Of Engagement Activity 2018
URL http://kamounlab.tumblr.com/post/176385835530/the-edge-of-tomorrow-plant-health-in-the-21st
 
Description Le Professeur tunisien Sophien Kamoun intègre la prestigieuse Royal Society de Londres 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact News article in the North African media https://www.huffpostmaghreb.com
Year(s) Of Engagement Activity 2018
URL https://www.huffpostmaghreb.com/entry/le-professeur-tunisien-sophien-kamoun-integre-la-prestigieuse-...
 
Description 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 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 Plant pathogens at science, art, writing program (SAW). 
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 Several team members spent a day at a school to tell the kids about plant pathogens.

This was part of SAW http://www.sawtrust.org

See also http://kamounlab.tumblr.com/post/120786305365/marina-ronny-ola-and-joe-at-school-today
Year(s) Of Engagement Activity 2015
URL http://kamounlab.tumblr.com/post/120786305365/marina-ronny-ola-and-joe-at-school-today
 
Description Presentation "The Two-Speed Genomes of Filamentous Plant Pathogens" at the 2015 DOE JGI Genomics of Energy & Environment Meeting. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk at the 2015 DOE JGI Genomics of Energy & Environment Meeting "The Two-Speed Genomes of Filamentous Plant Pathogens"

http://kamounlab.tumblr.com/post/115841932400/watch-sophiens-talk-at-the-2015-doe-jgi-genomics
http://youtu.be/kogoAS_9Bgk
Year(s) Of Engagement Activity 2015
URL http://kamounlab.tumblr.com/post/115841932400/watch-sophiens-talk-at-the-2015-doe-jgi-genomics
 
Description Presentation Plant pathology in the post-genomics era at BASF Science Symposium: sustainable food chain - from field to table, Jun 23-24, 2015, Chicago 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A presentation at the BASF Science Symposium: sustainable food chain - from field to table, Jun 23-24, 2015, Chicago.
Year(s) Of Engagement Activity 2015
URL http://kamounlab.tumblr.com/post/122151022390/plant-pathology-in-the-post-genomics-era
 
Description Presentation and debate: What are world class science outputs? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A presentation on What are world class science outputs?
NRP Doctoral Training Programme Summer Conference 2015, The Assembly House, Norwich, Thursday 18th June
Year(s) Of Engagement Activity 2015
URL http://kamounlab.tumblr.com/post/121748816600/what-are-world-class-science-outputs
 
Description Public Lecture: Keeping up with the plant destroyers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Tuesday 9 December, 6.30pm
Inaugural Lectures Autumn 2014
University of East Anglia

Keeping up with the plant destroyers
Professor Sophien Kamoun (School of Biological Sciences / The Sainsbury Laboratory)
Attendance is free and open to all. Free drinks reception after the talk.
Year(s) Of Engagement Activity 2014
URL http://kamounlab.tumblr.com/post/100740813820/tuesday-9-december-630pm-inaugural-lectures
 
Description Quote by Daily Star, a major newspaper in Bangladesh in article titled: Worry over wheat again. 
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 Tweet quoted by Daily Star, a major newspaper in Bangladesh in article titled: Worry over wheat again.

Prof Sophien Kamoun of the UK's Sainsbury Laboratory, who along with Prof Islam and other international experts launched -- wheatblast.org -- a website dedicated to the cause of fighting wheat blast, also tweeted on Thursday, "Wheat blast detected in Meherpur, Bangladesh. Let's hope it doesn't take off like last year."
Year(s) Of Engagement Activity 2017
URL http://www.thedailystar.net/frontpage/worries-over-wheat-again-1348564
 
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 SlideShare: Pathogenomics of emerging plant pathogens: too little, too late 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Slides: Pathogenomics of emerging plant pathogens: too little, too late. Presented at the conference "Building resilience against crop diseases: A global surveillance system", February 14, 2018, Rockefeller Foundation Bellagio Center in Lake Como, Italy.
Year(s) Of Engagement Activity 2018
URL https://www.slideshare.net/SophienKamoun/pathogenomics-of-emerging-plant-pathogens-too-little-too-la...
 
Description Stranger in a strange land: the experiences of immigrant researchers 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Published in Genome Biology: Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

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

What influenced your choice to move to your current country?

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

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

LN: I was born to a Christian Arab family in Israel and did my undergraduate studies at the Technion (Israel Institute of Technology). Although I was an atheist by the time I started my studies at the Technion, I still considered myself to be "culturally" Christian, in that I celebrated Christmas and New Year with my family (eating and drinking, not going to church!). However, almost every year, my exams were scheduled on December 25th and January 1st (the Fall semester in Israel starts in October and ends in February). Being unable to take exams on different dates affected my performance in my studies and my interest in pursuing graduate studies at the same institution. Also, more generally, I was the only Christian Arab student in my class, and one of a handful of Arab students; I never felt comfortable at the time. So, I decided to pursue graduate studies in computer science outside Israel. The choice to come to the USA was an easy one because the USA had (and still has, in my opinion) the best graduate programs in computer science.
Year(s) Of Engagement Activity 2017
URL https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1370-4
 
Description Talking Biotech Podcast - Plant Disease Networks 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Plant disease resistance is a complicated arms race between the plant and pathogens. Bacteria, viruses and fungi evolve in lock-step with plants, creating new ways to overcome new disease resistance strategies. Resistance to disease has a foundation in the gene-for-gene model, a model that hypothesizes that plants and pathogens have a molecular relationship with each other that mediates pathogenicity. Today's podcast features Drs. Lida Derevnina and Chih-Hang Wu, postdoctoral researchers with Sophien Kamoun (@KamounLab) at the Sainsbury Laboratory (@TheSainsburyLab) in Norwich, England. They describe the new thinking of disease resistance as a number of complex layers that integrates many gene-for-gene interactions with other mechanisms in mediating plant defense. Hosted by Paul Vincelli (@pvincell).
Year(s) Of Engagement Activity 2018
URL http://www.talkingbiotechpodcast.com/146-plant-disease-networks/
 
Description Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Taproot is the podcast that digs beneath the surface to understand how scientific publications in plant biology are created. In each episode, co-hosts Liz Haswell and Ivan Baxter take a paper from the literature and talk about the story behind the science with one of its authors.

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

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

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

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

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

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

Quel est le meilleur moyen de lutter contre les revues prédatrices ?
Par la transparence. Je suis pour un système << publish & filter >>, et non l'inverse, où le peer-review se fait sur des plateformes dédiées comme PREreview, après mise en ligne du preprint. Les maisons d'édition historiques ne sont pas forcément un gage de qualité du peer-review même si les chercheurs se cachent souvent derrière le fait qu'un article est publié dans Nature pour ne pas se poser de questions. Cela peut être très dangereux, comme nous montre le cas de l'article liant vaccination et autisme, qui a finalement été retiré mais 18 ans après sa publication.
Year(s) Of Engagement Activity 2019
URL http://sco.lt/5RgfkO
 
Description Video commentary on the structure and activation mechanism of NLR type plant immune receptor ZAR1 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Stunning news from China! Check CCTV13 news report on the resistosome featuring Jijie Chai and Jian-Min Zhouwith a brief cameo by yours truly. This program's audience share was ~2.3% or about 30 million people give or take

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

It's truly cause for celebration. At long last, a structure o
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/184056312400/stunning-news-from-china-check-cctv13-news-report
 
Description 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 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