Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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BrAPI-an application programming interface for plant breeding applications
Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar E. ; Birkett, Clay ; Calaminos, Viana C. ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D. ; Finkers, Richard ; Yanxin Gao, Star ; Ghaffar, Mehmood ; Glaser, Philip ; Guignon, Valentin ; Hok, Puthick ; Kilian, Andrzej ; König, Patrick ; Lagare, Jack Elendil B. ; Lange, Matthias ; Laporte, Marie Angélique ; Larmande, Pierre ; LeBauer, David S. ; Lyon, David A. ; Marshall, David S. ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas A. ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramírez-González, Ricardo H. ; Rathore, Abhishek ; Raquel, Angel Manica ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul D. ; Simon, Reinhard ; Verouden, Maikel - \ 2019
Bioinformatics 35 (2019)20. - ISSN 1367-4803 - p. 4147 - 4155.

MOTIVATION: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. AVAILABILITY AND IMPLEMENTATION: More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at The BrAPI specification and the developer tools are provided as free and open source.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Blin, Kai ; Shaw, Simon ; Steinke, Katharina ; Villebro, Rasmus ; Ziemert, Nadine ; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann - \ 2019
Nucleic acids research 47 (2019)W1. - ISSN 0305-1048 - p. W81 - W87.

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' ( has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.

Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield
Woodcock, B.A. ; Garratt, M.P.D. ; Powney, G.D. ; Shaw, R.F. ; Osborne, J.L. ; Soroka, J. ; Lindström, S.A.M. ; Stanley, D. ; Ouvrard, P. ; Edwards, M.E. ; Jauker, F. ; McCracken, M.E. ; Zou, Y. ; Potts, S.G. ; Rundlöf, M. ; Noriega, J.A. ; Greenop, A. ; Smith, H.G. ; Bommarco, R. ; Werf, W. van der; Stout, J.C. ; Steffan-Dewenter, I. ; Morandin, L. ; Bullock, J.M. ; Pywell, R.F. - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723

How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture.

Differences in the gene transcription state of Botrytis cinerea between necrotic and symptomless infections of lettuce and Arabidopsis thaliana
Emmanuel, C.J. ; Kan, J.A.L. van; Shaw, M.W. - \ 2018
Plant Pathology 67 (2018)9. - ISSN 0032-0862 - p. 1865 - 1873.
Lactuca sativa - Botrydial - Endophyte - Latent - Systemic - Transcription

Botrytis cinerea can establish long-lived, symptomless, systemic infections in plant species. It is unclear how the fungus colonizes plant tissues without causing tissue damage and necrosis. Three hypotheses are: (i) the fungus state is similar in the two forms of infection, but the plant defences are more effective, leading to multiple small quiescent centres; (ii) excreted molecules that would trigger plant defences are suppressed; (iii) signal exchanges occur avoiding both extensive host cell death and complete spatial restriction of the pathogen. These hypotheses were tested by comparing transcript levels of a set of B. cinerea genes between symptomless and necrotizing infections. Four genes were analysed that participate in signalling pathways required for virulence, as well as five genes that directly participate in causing host cell death or degrading plant cell wall polysaccharides. In lettuce, necrotic infections on detached leaves (12-48 h after inoculation) had similar gene expression patterns to necrotic infections on leaves 44 days after inoculation of the seedlings. Symptomless infections on leaves that expanded after inoculation of young seedlings had similar fungal gene expression patterns at 14, 24 and 34 days after inoculation, which clearly differed from those in necrotizing infections. In Arabidopsis thaliana, there were differences in gene expression patterns between droplet inoculations on leaves, resulting in necrotic lesions, and symptomless infections in stems and leaves. The fungal gene expression patterns differed in detail between lettuce and A. thaliana. The observations suggest that the physiological state of B. cinerea during symptomless infection is distinct from necrotizing infections. Plant Pathology

Assessing the Greenhouse Gas Mitigation effect of removing bovine trypanosomiasis in Eastern Africa
MacLeod, Michael ; Eory, Vera ; Wint, William ; Shaw, Alexandra ; Gerber, Pierre J. ; Cecchi, Giuliano ; Mattioli, Raffaele ; Sykes, Alasdair ; Robinson, Timothy - \ 2018
Sustainability 10 (2018)5. - ISSN 2071-1050
Cattle health - Climate change - GLEAM - Livestock modelling - Sustainable intensification

Increasing the production of meat and milk within sub-Saharan Africa should provide significant food security benefits. However, greenhouse gas (GHG) emissions represent a challenge, as cattle production in the region typically has high emissions intensity (EI), i.e., high rates of GHG emissions per unit of output. The high EI is caused by the relatively low production efficiencies in the region, which are in turn partly due to endemic cattle diseases. In theory, improved disease control should increase the efficiency and decrease the emissions intensity of livestock production; however quantitative analysis of the potential GHG mitigation effects of improved disease control in Africa is lacking. This paper seeks to respond to this by using a hybrid modelling approach to quantify the production and emissions effects of removing trypanosomiasis from East African cattle production systems. The emissions are quantified for each cattle production system using an excel version of GLEAM, the Food and Agriculture Organization's Global Livestock Environmental Assessment Model. The results indicate that removing trypanosomiasis leads to a reduction in the emissions intensity per unit of protein produced of between 0% and 8%, driven mainly by the increases in milk yields and cow fertility rates. Despite the limitations, it is argued that the approach provides considerable scope for modelling the GHG impacts of disease interventions.

Reviewing research priorities in weed ecology, evolution and management: a horizon scan
Neve, P. ; Barney, J.N. ; Buckley, Y. ; Cousens, R.D. ; Graham, S. ; Jordan, N.R. ; Lawton-Rauh, A. ; Liebman, M. ; Mesgaran, M.B. ; Shaw, J. ; Storkey, J. ; Baraibar, B. ; Baucom, R.S. ; Chalak, M. ; Childs, D.Z. ; Christensen, S. ; Eizenberg, H. ; Fernández-Quintanilla, C. ; French, K. ; Harsch, M. ; Heijting, S. ; Harrison, L. ; Loddo, D. ; Macel, M. ; Maczey, N. ; Merotto, A. ; Mortensen, D. ; Necajeva, J. ; Peltzer, D.A. ; Recasens, J. ; Renton, M. ; Riemens, M. ; Sønderskov, M. ; Williams, M. ; Rew, Lisa - \ 2018
Weed Research 58 (2018)4. - ISSN 0043-1737 - p. 250 - 258.
Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre‐submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio‐economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system‐oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs.
The Sphagnome Project : enabling ecological and evolutionary insights through a genus-level sequencing project
Weston, David J. ; Turetsky, Merritt R. ; Johnson, Matthew G. ; Granath, Gustaf ; Lindo, Zoë ; Belyea, Lisa R. ; Rice, Steven K. ; Hanson, David T. ; Engelhardt, Katharina A.M. ; Schmutz, Jeremy ; Dorrepaal, Ellen ; Euskirchen, Eugénie S. ; Stenøien, Hans K. ; Szövényi, Péter ; Jackson, Michelle ; Piatkowski, Bryan T. ; Muchero, Wellington ; Norby, Richard J. ; Kostka, Joel E. ; Glass, Jennifer B. ; Rydin, Håkan ; Limpens, Juul ; Tuittila, Eeva Stiina ; Ullrich, Kristian K. ; Carrell, Alyssa ; Benscoter, Brian W. ; Chen, Jin Gui ; Oke, Tobi A. ; Nilsson, Mats B. ; Ranjan, Priya ; Jacobson, Daniel ; Lilleskov, Erik A. ; Clymo, R.S. ; Shaw, A.J. - \ 2018
New Phytologist 217 (2018)1. - ISSN 0028-646X - p. 16 - 25.
ecological genomics - ecosystem engineering - evolutionary genetics - genome sequencing - niche construction - peatlands - Sphagnome - Sphagnum
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
Intestinal microbiota in infants at high risk for allergy : Effects of prebiotics and role in eczema development
Wopereis, Harm ; Sim, Kathleen ; Shaw, Alexander ; Warner, John O. ; Knol, Jan ; Kroll, J.S. - \ 2018
Journal of Allergy and Clinical Immunology 141 (2018)4. - ISSN 0091-6749 - p. 1334 - 1342.e5.
Allergy - Butyrate - Eczema - Gastrointestinal - Infants - Lactate - Microbiome - Microbiota - Prebiotics - Short-chain fatty acids
Background: Development of the gut microbiota in infancy is important in maturation of the immune system. Deviations in colonization patterns have been associated with allergic manifestations such as eczema, but exact microbiome dysfunctions underlying allergies remain unclear. We studied the gut microbiota of 138 infants at increased risk of allergy, participating in a clinical trial investigating the effectiveness of a partially hydrolyzed protein formula supplemented with nondigestible oligosaccharides on the prevention of eczema. Objective: The effects of interventions and breast-feeding on fecal microbiota were investigated. Additionally, we aimed to identify microbial patterns associated with the onset of eczema. Methods: Bacterial taxonomic compositions in the first 26 weeks of life were analyzed by using 16S rRNA gene sequencing. Additionally, fecal pH and microbial metabolite levels were measured. Results: Fecal microbial composition, metabolites, and pH of infants receiving partially hydrolyzed protein formula supplemented with nondigestible oligosaccharides was closer to that of breast-fed infants than that of infants receiving standard cow's milk formula. Infants with eczema by 18 months showed temporal differences that were marked by decreased relative abundances of Parabacteroides and Enterobacteriaceae at 4 weeks and decreased relative abundances of lactate-utilizing bacteria producing butyrate at 26 weeks, namely Eubacterium and Anaerostipes species, supported by increased lactate and decreased butyrate levels. Conclusions: We showed that a partially hydrolyzed protein infant formula with specific prebiotics modulated the gut microbiota closer to that of breast-fed infants. Additionally, we identified a potential link between microbial activity and onset of eczema, which might reflect a suboptimal implementation of gut microbiota at specific developmental stages in infants at high risk for allergy.
Catchment hydrology during winter and spring and the link to soil erosion: A case study in Norway
Starkloff, Torsten ; Hessel, Rudi ; Stolte, Jannes ; Ritsema, Coen - \ 2017
Nordic Hydrology 4 (2017)1. - ISSN 0029-1277
Infiltration - Modelling - SHAW - Snow - Soil erosion - Soil freezing

In the Nordic countries, soil erosion rates in winter and early spring can exceed those at other times of the year. In particular, snowmelt, combined with rain and soil frost, leads to severe soil erosion, even, e.g., in low risk areas in Norway. In southern Norway, previous attempts to predict soil erosion during winter and spring have not been very accurate owing to a lack of catchment-based data, resulting in a poor understanding of hydrological processes during winter. Therefore, a field study was carried out over three consecutive winters (2013, 2014 and 2015) to gather relevant data. In parallel, the development of the snow cover, soil temperature and ice content during these three winters was simulated with the Simultaneous Heat and Water (SHAW) model for two different soils (sand, clay). The field observations carried out in winter revealed high complexity and diversity in the hydrological processes occurring in the catchment. Major soil erosion was caused by a small rain event on frozen ground before snow cover was established, while snowmelt played no significant role in terms of soil erosion in the study period. Four factors that determine the extent of runoff and erosion were of particular importance: (1) soil water content at freezing; (2) whether soil is frozen or unfrozen at a particular moment; (3) the state of the snow pack; and (4) tillage practices prior to winter. SHAW performed well in this application and proved that it is a valuable tool for investigating and simulating snow cover development, soil temperature and extent of freezing in soil profiles.

Dynamics and ordering of weakly Brownian particles in directional drying
Noirjean, Cecile ; Marcellini, Moreno ; Deville, Sylvain ; Kodger, Thomas E. ; Monteux, Cécile - \ 2017
Physical Review Materials 1 (2017)6. - ISSN 2475-9953

Drying of particle suspensions is an ubiquitous phenomenon with many natural and practical applications. In particular, in unidirectional drying, the evaporation of the solvent induces flows which accumulate particles at the liquid/air interface. The progressive buildup of a dense region of particles can be used, in particular, in the processing of advanced materials and architectures while the development of heterogeneities and defects in such systems is critical to their function. A lot of attention has thus been paid to correlating the flow and particle dynamics to the ordering of particles. However, dynamic observation at the particle scale and its correlation with local particle ordering are still missing. Here we show by measuring the particle velocities with high frame rate laser scanning confocal microscopy that the ordering of weakly Brownian particles during unidirectional drying in a Hele-Shaw cell opened on one side depends on the velocity of particles that impinge at the pinned liquid/solid interface. Under the ambient and experimental conditions presented in the following, the particle velocities accumulate in two branches. A higher degree of ordering is found for the branch of faster particle velocity which we explain by an increase in the pressure drop which drags the particles into a denser packing as the flow velocity increases. This counterintuitive behavior is the opposite to what is found with Brownian particles, which can reorganize by Brownian motion into denser packing during drying, as long as the flow velocity is not too high. These results show that different kinetic conditions can be used to obtain dense, defect-free regions of particles after drying. In particular, it suggests that rapid, directional drying could be used to control the crystallinity of particle deposits.

What if the trucks stop coming? : exploring the framing of local food by cooperative food retailers in New Mexico
Constance, Cheron Z. - \ 2017
Wageningen University. Promotor(en): J.S.C. Wiskerke, co-promotor(en): L.G. Horlings; L. Shaw. - Wageningen : Wageningen University - ISBN 9789463431941 - 261
food - agricultural products - cooperatives - cooperative farm enterprises - food products - new mexico - voedsel - landbouwproducten - coöperaties - coöperatieve landbouwbedrijven - voedselproducten - new mexico

Proponents of local food cite a variety of economic and environmental advantages of short food supply chains. Consumer interest in local food has also offered a point of differentiation for many players in the food industry, including restaurants and grocery stores. Engaging with local food has significant challenges, however, and many production and distribution systems engender and support more diffuse food provisioning, not less. Though food can travel thousands of miles from its point of origin to consumption, many cooperative (co-op) grocery stores have long sold locally-produced food and have deep ties to their supplier communities. This thesis offers case studies of two co-ops in the natural and organic food sector and examines how they think about and work with local food. The theories of embeddedness (after Polanyi) and diverse economies (from Gibson-Graham) undergird the analyses of these co-ops’ involvement with local food and how the cooperative business model relates to it.

Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts
Shaw, Michael W. ; Emmanuel, Christy J. ; Emilda, Deni ; Terhem, Razak B. ; Shafia, Aminath ; Tsamaidi, Dimitra ; Emblow, Mark ; Kan, Jan A.L. Van - \ 2016
Frontiers in Plant Science 7 (2016). - ISSN 1664-462X

Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. Botrytis cinerea and Botrytis pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.
Another Continental Vulture Crisis : Africa's Vultures Collapsing toward Extinction
Ogada, Darcy ; Shaw, Phil ; Beyers, Rene L. ; Buij, Ralph ; Murn, Campbell ; Thiollay, Jean Marc ; Beale, Colin M. ; Holdo, Ricardo M. ; Pomeroy, Derek ; Baker, Neil ; Krüger, Sonja C. ; Botha, Andre ; Virani, Munir Z. ; Monadjem, Ara ; Sinclair, Anthony R.E. - \ 2016
Conservation Letters (2016). - ISSN 1755-263X - p. 89 - 97.
Asian vulture crisis - Bushmeat - Illegal wildlife trade - Poisoning - Scavenger - Traditional medicine - Vulture population decline

Vultures provide critical ecosystem services, yet populations of many species have collapsed worldwide. We present the first estimates of a 30-year Pan-African vulture decline, confirming that declines have occurred on a scale broadly comparable with those seen in Asia, where the ecological, economic, and human costs are already documented. Populations of eight species we assessed had declined by an average of 62%; seven had declined at a rate of 80% or more over three generations. Of these, at least six appear to qualify for uplisting to Critically Endangered. Africa's vultures are facing a range of specific threats, the most significant of which are poisoning and trade in traditional medicines, which together accounted for 90% of reported deaths. We recommend that national governments urgently enact and enforce legislation to strictly regulate the sale and use of pesticides and poisons, to eliminate the illegal trade in vulture body parts, as food or medicine, and to minimize mortality caused by power lines and wind turbines.

Virus and host factors affecting the clinical outcome of Bluetongue Virus infection
Caporale, M. ; Gialleonorado, L. ; Janowicz, A. ; Wilkie, G. ; Shaw, A. ; Savini, G. ; Rijn, P.A. van; Mertens, P. ; Ventura, M. ; Palmarini, M. - \ 2014
Journal of Virology 88 (2014)18. - ISSN 0022-538X - p. 10399 - 10411.
serotype 8 - culicoides-sonorensis - northern europe - british sheep - cattle - goats - ceratopogonidae - pathogenesis - replication - population
Bluetongue is a major infectious disease of ruminants caused by bluetongue virus (BTV), an arbovirus transmitted by Culicoides. Here, we assessed virus and host factors influencing the clinical outcome of BTV infection using a single experimental framework. We investigated how mammalian host species, breed, age, BTV serotypes, and strains within a serotype affect the clinical course of bluetongue. Results obtained indicate that in small ruminants, there is a marked difference in the susceptibility to clinical disease induced by BTV at the host species level but less so at the breed level. No major differences in virulence were found between divergent serotypes (BTV-8 and BTV-2). However, we observed striking differences in virulence between closely related strains of the same serotype collected toward the beginning and the end of the European BTV-8 outbreak. As observed previously, differences in disease severity were also observed when animals were infected with either blood from a BTV-infected animal or from the same virus isolated in cell culture. Interestingly, with the exception of two silent mutations, full viral genome sequencing showed identical consensus sequences of the virus before and after cell culture isolation. However, deep sequencing analysis revealed a marked decrease in the genetic diversity of the viral population after passaging in mammalian cells. In contrast, passaging in Culicoides cells increased the overall number of low-frequency variants compared to virus never passaged in cell culture. Thus, Culicoides might be a source of new viral variants, and viral population diversity can be another factor influencing BTV virulence.
Botrytis species: relentless necrotrophic thugs or endophytes gone rogue?
Kan, J.A.L. van; Shaw, M.W. ; Grant-Downton, R.T. - \ 2014
Molecular Plant Pathology 15 (2014)9. - ISSN 1464-6722 - p. 957 - 961.
sclerotinia-sclerotiorum - disease development - oxalic-acid - gray mold - cinerea - plant - infection - flowers - diversity - fruits
Plant pathology has a long-standing tradition of classifying microbes as pathogens, endophytes or saprophytes. Lifestyles of pathogens are categorized as biotrophic, necrotrophic or hemibiotrophic. Botrytis species are considered by many to be archetypal examples of necrotrophic fungi, with B.¿cinerea being the most extensively studied species because of its broad host range and economic impact. In this review, we discuss recent work which illustrates that B.¿cinerea is capable of colonizing plants internally, presumably as an endophyte, without causing any disease or stress symptoms. The extent of the facultative endophytic behaviour of B.¿cinerea and its relevance in the ecology and disease epidemiology may be vastly underestimated. Moreover, we discuss the recent discovery of a novel Botrytis species, B.¿deweyae, which normally grows as an endophyte in ornamental daylilies (Hemerocallis), but displays facultative pathogenic behaviour, and is increasingly causing economic damage. We propose that the emergence of endophytes ‘gone rogue’ as novel diseases may be related to increased inbreeding of hybrid lines and reduced genetic diversity. These observations lead us to argue that the sometimes inflexible classification of pathogenic microbes by their lifestyles requires serious reconsideration. There is much more variety to the interactions of Botrytis with its hosts than the eye (or the plant pathologist) can see, and this may be true for other microbes interacting with plants.
Consolidating the shared area of investigation between planning theory, risk theory and ethical inquiry
Basta, C. - \ 2012
Although it is perhaps the most prominent interdisciplinary theme to have emerged in the past decades, in the domain of planning studies the prevention of technological risks has only recently started the pathway towards a rigorous theoretical definition (Boholm and Lofsted 2004; Hayden Lesbirel and Shaw 2005; Schmidt-Thomé 2006). This article is a further contribution and tries to delimit the shared area of investigation among risk theories, planning theories and ethical inquiry. In particular it discusses the matter of accounting technological risk, and its counterpart safety, as an explicit spatial design factor; this, not only in relation to the immediate context of risk-bearing installations but rather in relation to the overall distribution of risks in society. This latter consideration relates to the inherently normative nature of the practice of risk prevention, whose moral implications cannot be limited to the site-specific context of hazards; it is in fact the overall risk distribution in society, taking place through planning instruments, that needs to be considered. This article is part of a series of writings that aim at promoting a debate on what theoretical perspectives different disciplinary domains can contribute with in order to elaborate a solid and consistent planning discourse on technological risks. As such it constitutes a contribution to the streams of research of the referenced sociology, planning, risk and ethics scholars.
Challenges to the Future - Conservation of the Antarctic
Chown, S.L. ; Lee, J.E. ; Hughes, K.A. ; Barnes, J. ; Bergstrom, D.M. ; Convey, P. ; Cowan, D.A. ; Crosbie, K. ; Dyer, G. ; Frenot, Y. ; Grant, S.M. ; Herr, D. ; Kennicutt, M.C. ; Lamers, M.A.J. ; Murray, A. ; Possingham, H.P. ; Reid, K. ; Riddle, M.J. ; Ryan, P.G. ; Sanson, L. ; Shaw, J.D. ; Sparrow, M.D. ; Summerhayes, C. ; Terauds, A. ; Wall, D.H. - \ 2012
Science 337 (2012)6091. - ISSN 0036-8075 - p. 158 - 159.
The Antarctic Treaty System, acknowledged as a successful model of cooperative regulation of one of the globe's largest commons (1), is under substantial pressure. Concerns have been raised about increased stress on Antarctic systems from global environmental change and growing interest in the region's resources (2, 3). Although policy-makers may recognize these challenges, failure to respond in a timely way can have substantial negative consequences. We provide a horizon scan, a systematic means for identifying emerging trends and assisting decision-makers in identifying policies that address future challenges (2, 3). Previous analyses of conservation threats in the Antarctic have been restricted to matters for which available evidence is compelling (4). We reconsider these concerns because they might escalate quickly, judging from recent rapid environmental change in parts of Antarctica and increasing human interest in the region (see the map). We then focus on a more distant time horizon.
Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen
Cooke, D.E.L. ; Cano, L.M. ; Raffaele, S. ; Bain, R.A. ; Cooke, L.R. ; Etherington, G.J. ; Deahl, K.L. ; Farrer, R.A. ; Gilroy, E.M. ; Goss, E.M. ; Grünwald, N.J. ; Hein, I. ; Maclean, D. ; McNicol, J.W. ; Randall, E. ; Oliva, R.F. ; Pel, M. ; Shaw, D.S. ; Squires, J.N. ; Taylor, M.C. ; Vleeshouwers, V.G.A.A. ; Birch, P.R.J. ; Lees, A.K. ; Kamoun, S. - \ 2012
PLoS Pathogens 8 (2012)10. - ISSN 1553-7366
phytophthora-infestans populations - late blight - microsatellite markers - genotypic diversity - clonal lineages - rxlr effectors - plant - resistance - expression - virulence
Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics
Variation in European harbour seal immune response genes and susceptibility to phocine distemper virus (PDV)
McCarthy, A.J. ; Shaw, M. ; Jepson, P.D. ; Brasseur, S.M.J.M. ; Reijnders, P.J.H. ; Goodman, S.J. - \ 2011
Infection, Genetics and Evolution 11 (2011)7. - ISSN 1567-1348 - p. 1616 - 1623.
subacute sclerosing-panencephalitis - measles-virus - conservation genetics - cellular receptor - whole-genome - disease - association - vitulina - polymorphisms - populations
Phocine distemper virus (PDV) has caused two mass mortalities of European harbour seals (Phoca vitulina) in recent decades. Levels of mortality varied considerably among European populations in both the 1988 and 2002 epidemics, with higher mortality in continental European populations in comparison to UK populations. High levels of genetic differentiation at neutral makers among seal populations allow for the possibility that there could be potential genetic differences at functional loci that may account for some of the variation in mortality. Recent genome sequencing of carnivore species and development of genomic tools have now made it possible to explore the possible contribution of variation in candidate genes from harbour seals in relation to the differential mortality patterns. We assessed variation in eight genes (CD46, IFNG, IL4, IL8, IL10, RARa, SLAM and TLR2) encoding key proteins involved in host cellular interactions with Morbilliviruses and the relationship of variants to disease status. This work constitutes the first genetic association study for Morbillivirus disease susceptibility in a non-model organism, and for a natural mortality event. We found no variation in harbour seals from across Europe in the protein coding domains of the viral receptors SLAM and CD46, but SNPs were present in SLAM intron 2. SNPs were also present in IL8 p2 and RARa exon 1. There was no significant association of SLAM or RARa polymorphisms with disease status implying no role of these genes in determining resistance to PDV induced mortality, that could be detected with the available samples and the small number of polymorphisms indentified. However there was significant differentiation of allele frequencies among populations. PDV and other morbilliviruses are important models for wildlife epidemiology, host switches and viral evolution. Despite a negative result in this case, full sequencing of pinniped and other 'non-model' carnivore genomes will help in refining understanding the role of host genetics in disease susceptibility for these viruses
Epidemiology and integrated control of Potato Late Blight in Europe
Cooke, R.J. ; Schepers, H.T.A.M. ; Hermansen, A. ; Bain, R. ; Bradshaw, N. ; Ritchie, F. ; Shaw, D.S. ; Evenhuis, A. ; Kessel, G.J.T. ; Wander, J.G.N. ; Andersson, B. ; Hansen, J.G. ; Hannukkala, A. ; Naerstad, R. ; Nielsen, B. - \ 2011
Potato Research 54 (2011)2. - ISSN 0014-3065 - p. 183 - 222.
phytophthora-infestans population - a2 mating-type - genotypic diversity - northern-ireland - foliar aggressiveness - metalaxyl resistance - great-britain - r-genes - netherlands - cultivars
Phytophthora infestans, the causal agent of late blight, is a major threat to potato production in northwestern Europe. Before 1980, the worldwide population of P. infestans outside Mexico appeared to be asexual and to consist of a single clonal lineage of A1 mating type characterized by a single genotype. It is widely believed that new strains migrated into Europe in 1976 and that this led to subsequent population changes including the introduction of the A2 mating type. The population characteristics of recently collected isolates in NW Europe show a diverse population including both mating types, sexual reproduction and oospores, although differences are observed between regions. Although it is difficult to find direct evidence that new strains are more aggressive, there are several indications from experiments and field epidemics that the aggressiveness of P. infestans has increased in the past 20 years. The relative importance of the different primary inoculum sources and specific measures for reducing their role, such as covering dumps with plastic and preventing seed tubers from becoming infected, is described for the different regions. In NW Europe, varieties with greater resistance tend not to be grown on a large scale. From the grower’s perspective, the savings in fungicide input that can be achieved with these varieties are not compensated by the higher (perceived) risk of blight. Fungicides play a crucial role in the integrated control of late blight. The spray strategies in NW Europe and a table of the specific attributes of the most important fungicides in Europe are presented. The development and use of decision support systems (DSSs) in NW Europe are described. In The Netherlands, it is estimated that almost 40% of potato growers use recommendations based on commercially available DSS. In the Nordic countries, a new DSS concept with a fixed 7-day spray interval and a variable dose rate is being tested. In the UK, commercially available DSSs are used for c. 8% of the area. The validity of Smith Periods for the new population of P. infestans in the UK is currently being evaluated.
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