Molecular mechanisms of virulence and avirulence in the Avr3a family of Phytophthora.

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

Abstract

The oomycetes are fungus-like eukaryotic microorganisms. Several species of the oomycetes are devastating pathogens that are of great importance to world agriculture and food security. In essence, this means that they destroy crops that are critical sources of food. The word 'Phytophthora', which is a genus with the oomycete lineage means 'plant destroyer'. Phytophthora species include the organism responsible for the Irish potato famine, Phytophthora infestans, which causes a disease commonly know as 'potato blight' or 'late blight' (it also causes tomato blight), as well as pepper blight (Phytophthora capsici) and soybean root rot (Phytophthora sojae). Recently, Phytophthora ramorum has gained considerable press in the UK as it is threatening iconic trees, such as oak. Phytophthora infestans remains the best-known and, arguably, the most important oomycete pathogen. It continues to cost modern agriculture billions of pounds annually and also impacts subsistence farming in developing countries. With potato now ranked the third most important crop in the world, P. infestans is an important biotic threat to global food security. Damage caused by other Phytophthora species is also severe, on a global scale. Our long-term objective is to understand how oomycetes, particularly Phytophthora, successfully infect plants and dissect the plant processes that are affected by these pathogens. It is now well established that, like other pathogens, Phytophthora species secrete a number of proteins, termed 'effectors', that modulate the immune response of plants and enable host colonization. Deciphering the biochemical activities of effectors is critical to understanding mechanisms of pathogenesis. Among these proteins, RxLR-type effectors, named after an amino acid sequence present in the protein, are targeted to the inside of plant cells. In this proposal, we focus on a particular group of RxLR effectors that is found in the Phytophthora species mentioned above. These are all members of the Avr3a family, as they share amino acid sequence homology to the Phytophthora infestans effector Avr3a. Building on preliminary data we have already obtained, we aim to define what conserved and divergent functions these proteins have in suppressing the plant immune system. Through host factors, members of this protein family can also initiate a programmed cell-death response in plants designed to limit pathogen growth. We also aim to understand some details of how early steps in this response occur, specifically how these effectors are detected by host cell factors. This study will help to establish functional connections between pathogen proteins and plant processes. Detailed knowledge of how the Avr3a family is able to manipulate certain aspects of plant immunity and be recognized by others will improve our understanding of the infection process and enable novel strategies for engineering resistance to Phytophthora pathogens.

Technical Summary

This research proposal aims to characterize the conserved and divergent virulence activities of the Avr3a family of Phytophthora RxLR-type effectors. It will also provide insights into the molecular recognition of RxLR effectors by resistance (R)-proteins. These studies will show how Phytophthora spp. attempt to manipulate host cell processes and how the plant responds to these challenges, with the potential to deliver novel approaches to control important plant diseases. Building on our preliminary data we will use in planta expression assays to provide a comprehensive analysis of Avr3a family members' activities in interfering with pathogen-triggered-immunity (PTI) signaling pathways elicited by known PAMPs of diverse origin. We will link these activities with host protein interactions using standard biochemical approaches. We will then use structure-based mutagenesis of sites on the protein surface, predicted to encode function (based on our crystal structure of Avr3a11 from P. capsici), to dissect the functions of the Avr3a family and map them to structure. We will also build on our preliminary data to define the molecular determinants that allow recognition of different Avr3a family members by a library of variant R3a resistance proteins. Firstly, using agrobacterium-mediated co-expression in N. benthamiana we will establish which residues in variant R3a's are responsible for expanding recognition to include P. capsici Avr3a11. Secondly, we will use structure-based mutants of P. capsici Avr3a11 to define the residues in the effector that are important for R3a interaction. We will then screen the variant R3a library to discover new resistances against other Avr3a family members. Finally, we will generate transgenic N. benthamiana expressing variant R3a proteins and test whether they confer resistance to pathogens from which the cognate effector is derived.

Planned Impact

Plant diseases represent a significant threat to human welfare resulting in economic hardship, malnutrition, famine, and environmental degradation. Oomycetes are the most devastating pathogens of dicot plants, causing vast economic losses on important crop species and environmental damage in natural ecosystems. With the oomycetes, species are the most significant pathogens of plants. P. infestans is considered one of the most important biotic threats to global food security and annual losses in potato production caused by late blight are conservatively estimated at $6.7 billion. Management of Phytophthora spp. in the field is difficult and requires repeated applications of chemicals, some of which might be banned in the near future due to concerns over environmental damage. The breeding of resistant cultivars has seen limited success, but these resistances are often quickly overcome. Despite this, breeding resistant crops, through breeding programs or GM approaches, remains a critical approach for combating disease. The advantages conferred by engineered R-proteins with extended recognition specificities is one example of an exciting new approach that may deliver more durable resistances. Non-academic groups who would benefit from the research proposed, and be potential users of its outputs include: plant biotechnology companies; the agricultural community, including farmers (both in the UK and worldwide); policy makers; the general public (local interest groups, home gardeners, schools etc.). The PIs will take the lead on managing the impact plan. Both the PIs have excellent track records in communicating the outcomes of their research to a broad audience. Primarily this is through publication in academic journals, but also increasingly in open-source forums. We are also invited speak about our research at national/international meetings. The PIs have prior experience at writing scientific and general articles, as well as developing websites. The project offers unique training opportunities in multiple disciplines. An individual training plan will be implemented for the RAs and they will attend regular group meetings in the PI's laboratories to present their data and interact formally with colleagues. They will have weekly one-on-one meetings with their respective PI to discuss progress and direction. In addition, monthly project meetings involving the PIs, RAs and other relevant scientists will be conducted. The PDRA will also participate in relevant seminar series and present a seminar to the whole Department once a year. The RAs will also be able to interact with outstanding collaborators and meet the frequent national/international visitors to the site. The PIs regard these activities as an important part of mentorship and professional development. TSL and JIC have a Technology Transfer policy based on maintaining close links with those who are able to make use of discoveries for the benefit of society. Discoveries at TSL/JIC are monitored to establish whether they present opportunities to obtain Intellectual Property Protection (IPP). This is typically through patenting. Where impact activities include technology transfer or outreach/press releases the relevant offices at TSL/JIC will be involved. Throughout his career Kamoun has received funding from the plant biotechnology sector. We also engage with non-expert non-academic groups. For instance, Banfield is involved with initiatives to enthuse school children about science including the SAW (Science, Art and Writing) and TSN (Teacher-Scientist Network) initiatives. The JIC and TSL also engage with the local community thorough the 'Friends of the John Innes Centre' and events such as the 'Discovery Day'; Kamoun recently delivered a talk to > 200 members of the general public at a Food Security event at JIC. TSL/JIC has a dedicated communications office for release of information to the general public through websites and the media.
 
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
 
Description 1. Better underdstanding of how the pathogen virulence effector AVR3a functions.
2. Better knowledge of the immune resistance proteins R3a and I2.
3. Exploitation of this knowledge to help develop resistant plants to Phytophthora and Fusarium.
Exploitation Route Towards synthetic resistance genes.

Plants and pathogens are engaged in a co-evolutionary arms race, in which plants deploy various defense mechanisms and pathogens develop ways to modulate host processes and immunity. An important component of the plant defense machinery involves intracellular immunoreceptors of the nucleotide-binding leucine-rich repeat-containing protein family (NB-LRR). NB-LRRs typically recognize pathogen effector proteins with avirulent activities, and activate a response known as NB-LRR-triggered immunity (NTI). R3a and I2 are orthologous NB-LRRs from potato and tomato that recognize effectors of the late blight oomycete pathogen Phytophthora infestans and the wilt causing ascomycete Fusarium oxysporum f. sp. lycopersici (FOL) respectively. However, particular races of these pathogens have evolved stealthy effectors that evade recognition by R3a and I2. Our goal is to create synthetic NB-LRR mutants with expanded pathogen recognition specificities to develop broad-spectrum solutions to important plant pathogens. In a previous study we identified 8 single-residue mutations in the R3a protein that conferred expanded response to Phytophthora sp. effectors. We investigated whether these mutations alter the response profile of I2, and recovered I2 mutants with expanded spectrum of effector response from diverse pathogens. We are currently evaluating whether this expanded response correlates with a broader resistance spectrum using both transient and stable transgenic systems. These results could lead to new insights into the molecular interactions underlying pathogen perception by plants, building up our knowledge on basic and applied plant pathology.
Sectors Agriculture, Food and Drink

URL http://kamounlab.dreamhosters.com/publications.htm
 
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 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 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
 
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 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 Vivianne Vleeshouwers 
Organisation Wageningen University & Research
Country Netherlands 
Sector Academic/University 
PI Contribution Exchange of materials/expertise
Collaborator Contribution Exchange of materials/expertise
Impact Pais, M., Yoshida, K., Giannakopoulou, A., Pel, M.A., Cano, L.M., Oliva, R.F., Witek, K., Lindqvist-Kreuze, H., Vleeshouwers, V.G.A.A., and Kamoun, S. 2017. Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen. BMC Evolutionary Biology, 5:93. Domazakis, E., Wouters, D., Visser, R., Kamoun, S., Joosten, M.H., and Vleeshouwers, V.G.A.A. 2018. The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans. Molecular Plant-Microbe Interactions, 31:795-802. Derevnina, L., Dagdas, Y.F., De la Concepcion, J.C., Bialas, A., Kellner, R., Petre, B., Domazakis, E., Du, J., Wu, C.-H., Lin, X., Aguilera-Galvez, C., Cruz-Mireles, N., Vleeshouwers, V.G.A.A. and Kamoun, S. 2016. Nine things to know about elicitins. New Phytologist, 212:888-895. Giannakopoulou, A., Bialas, A., Kamoun, S., and Vleeshouwers, V.G.A.A. 2016. Plant immunity switched from bacteria to virus. Nature Biotechnology, 34:391-392. Du, J., Verzaux, E., Chaparro-Garcia, A., Bijsterbosch, G., Keizer, L.C.P., Zhou, J., Liebrand, T.W.H., Xie, C., Govers, F., Robatzek, S., van der Vossen, E.A.G., Jacobsen, E., Visser, R.G.F., Kamoun, S., and Vleeshouwers, V.G.A.A. 2015. Elicitin recognition confers enhanced resistance to Phytophthora infestans in potato. Nature Plants, 1:15034.
 
Description #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 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 ActualFruitVeg: Los tomates y la diversidad 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact News article in Spanish magazine about genome edited tomato Tomelo.

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

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

El trabajo de Kamoun está detenido. Las regulaciones europeas convierten a las plantas genéticamente modificadas en ilegales. Los investigadores como Kamoun pueden tener conocimientos y hacer ensayos científicos para modificar la genética de las plantas pero no pueden llevarlos a ensayarlos en el campo. No pueden registrar estas plantas y comercializar variedades de tomates genéticamente modificados. En EEUU hay más oportunidades en ésta actividad científica. En Europa hay un gran signo de interrogación; "estoy muy frustrado por esto, tengo que ser honesto. Científicamente, esta planta, el "Tomelo" no es diferente de cualquier mutante que obtengamos de la reproducción tradicional o la mutagénesis tradicional, explica Kamoun
Year(s) Of Engagement Activity 2018
URL https://actualfruveg.com/2018/06/09/los-tomates-y-la-diversidad/
 
Description BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In a paper recently published in BMC Evolutionary Biology, an international team of scientists describes how evasion of host immunity by a clonal variant of the potato blight pathogen Phytophthora infestans is associated with variation in gene expression without any apparent underlying genetic changes. We asked the senior authors of the study, Vivianne G.A.A. Vleeshouwers, Hannele Lindqvist-Kreuze and Sophien Kamoun, to tells us about their work.

What did you find?


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

Why is this work important?

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

Are potato varieties resistant to the pathogen available?

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

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

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

Is chemical protection the only way to control late blight?

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

How did you put this project together?

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

Anything you would have done differently?

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

You posted the paper in bioRxiv before submission. Why?

Why not? Posting the article on bioRxiv enabled us to share our findings with our colleagues and hear about it from the community as soon as possible. The tweet by Mark Gijzen we referred to above is an example of such feedback. Posting a preprint relieves some of the delays associated with publishing. It's a liberating feeling to finish writing up a paper and immediately share it with anyone who's interested.
Year(s) Of Engagement Activity 2018
URL https://blogs.biomedcentral.com/bmcseriesblog/2018/07/09/phenotypic-plasticity-pandemic-lineage-iris...
 
Description 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 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 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 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Growing the future is a report from the UK Plant Sciences Federation (UKPSF), a special advisory committee of the Royal Society of Biology. Launched in January 2019, the report highlights to policymakers and others the excellence of plant science in the UK, and its importance to the biosciences, the economy, and society both at home and around the world. In Growing the future, the UKPSF describes the potential of plant science to improve fundamental knowledge, enable better diet quality, increase crop productivity, enhance environmental sustainability and create new products and manufacturing processes.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Slide 14. This stunning animation of the bacterium Xanthomonas infecting tomato plants was produced by students at Halle University working with Prof. Ulla Bonas.
Year(s) Of Engagement Activity 2019
URL https://kamounlab.tumblr.com/post/183672043215/hello-kids-im-a-biologist
 
Description 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 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 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 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 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