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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    How the COVID-19 pandemic highlights the necessity of animal research
    Genzel, Lisa ; Adan, Roger ; Berns, Anton ; Beucken, Jeroen van den; Blokland, Arjan ; Boddeke, Erik H.W.G.M. ; Bogers, Willy M. ; Bontrop, Ronald ; Bulthuis, R. ; Bousema, Teun ; Clevers, Hans ; Coenen, Tineke C.J.J. ; Dam, Anne Marie van; Deen, Peter M.T. ; Dijk, K.W. van; Eggen, Bart J.L. ; Elgersma, Ype ; Erdogan, Izel ; Englitz, Bernard ; Fentener van Vlissingen, J.M. ; Fleur, Susanne la; Fouchier, Ron ; Fitzsimons, Carlos P. ; Frieling, Wilbert ; Haagmans, Bart ; Heesters, Balthasar A. ; Henckens, Marloes ; Herfst, Sander ; Hol, Elly ; Hove, Daniel van den; Jonge, Marien I. de; Jonkers, Jos ; Joosten, Leo A.B. ; Kalsbeek, Andries ; Kamermans, Maarten ; Kampinga, Harm H. ; Kas, Martien J. ; Keijer, J. ; Kersten, Sander ; Kiliaan, Amanda J. ; Kooij, Taco W.A. ; Kooijman, Sander ; Koopman, Werner J.H. ; Korosi, Aniko ; Krugers, Harm J. ; Kuiken, Thijs ; Kushner, Steven A. ; Langermans, Jan A.M. ; Lesscher, Heidi ; Lucassen, Paul J. ; Lutgens, Esther ; Netea, Mihai G. ; Noldus, Lucas P.J.J. ; Meer, Jos W.M. van der; Meye, Frank J. ; Mul, Joram D. ; Oers, Kees van; Olivier, Jocelien D.A. ; Pasterkamp, R.J. ; Philippens, Ingrid H.C.H.M. ; Prickaerts, Jos ; Pullox, Bart J.A. ; Rensen, Patrick C.N. ; Rheenen, Jacco van; Rij, Ronald P. van; Ritsma, Laila ; Rockx, Barry H.G. ; Roozendaal, Benno ; Schothorst, Evert M. van; Stittelaar, K. ; Stockhofe, Norbert ; Swaab, Dick F. ; Swart, Rik L. de; Vanderschuren, Louk J.M.J. ; Vries, Taco de; Vrij, Femke de; Wezel, Richard van; Wierenga, Corette J. ; Wiesmann, Maximilian ; Willuhn, Ingo ; Zeeuw, Chris I. de; Homberg, Judith R. - \ 2020
    Current Biology 30 (2020)18. - ISSN 0960-9822 - p. R1014 - R1018.
    Recently, a petition was offered to the European Commission calling for an immediate ban on animal testing. Although a Europe-wide moratorium on the use of animals in science is not yet possible, there has been a push by the non-scientific community and politicians for a rapid transition to animal-free innovations. Although there are benefits for both animal welfare and researchers, advances on alternative methods have not progressed enough to be able to replace animal research in the foreseeable future. This trend has led first and foremost to a substantial increase in the administrative burden and hurdles required to make timely advances in research and treatments for human and animal diseases. The current COVID-19 pandemic clearly highlights how much we actually rely on animal research. COVID-19 affects several organs and systems, and the various animal-free alternatives currently available do not come close to this complexity. In this Essay, we therefore argue that the use of animals is essential for the advancement of human and veterinary health. In this Essay, Genzel et al. make the case for animal research in light of the COVID-19 pandemic.
    Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera
    Song, Hojun ; Béthoux, Olivier ; Shin, Seunggwan ; Donath, Alexander ; Letsch, Harald ; Liu, Shanlin ; McKenna, Duane D. ; Meng, Guanliang ; Misof, Bernhard ; Podsiadlowski, Lars ; Zhou, Xin ; Wipfler, Benjamin ; Simon, Sabrina - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.

    Shared Socio-economic Pathways for European agriculture and food systems : The Eur-Agri-SSPs
    Mitter, Hermine ; Techen, Anja K. ; Sinabell, Franz ; Helming, Katharina ; Schmid, Erwin ; Bodirsky, Benjamin L. ; Holman, Ian ; Kok, Kasper ; Lehtonen, Heikki ; Leip, Adrian ; Mouël, Chantal Le; Mathijs, Erik ; Mehdi, Bano ; Mittenzwei, Klaus ; Mora, Olivier ; Øistad, Knut ; Øygarden, Lillian ; Priess, Jörg A. ; Reidsma, Pytrik ; Schaldach, Rüdiger ; Schönhart, Martin - \ 2020
    Global environmental change : human and policy dimensions 65 (2020). - ISSN 0959-3780
    Consistency - Integrated assessment - Land use - Narrative - Scenario - Storyline development

    Scenarios describe plausible and internally consistent views of the future. They can be used by scientists, policymakers and entrepreneurs to explore the challenges of global environmental change given an appropriate level of spatial and sectoral detail and systematic development. We followed a nine-step protocol to extend and enrich a set of global scenarios – the Shared Socio-economic Pathways (SSPs) – providing regional and sectoral detail for European agriculture and food systems using a one-to-one nesting participatory approach. The resulting five Eur-Agri-SSPs are titled (1) Agriculture on sustainable paths, (2) Agriculture on established paths, (3) Agriculture on separated paths, (4) Agriculture on unequal paths, and (5) Agriculture on high-tech paths. They describe alternative plausible qualitative evolutions of multiple drivers of particular importance and high uncertainty for European agriculture and food systems. The added value of the protocol-based storyline development process lies in the conceptual and methodological transparency and rigor; the stakeholder driven selection of the storyline elements; and consistency checks within and between the storylines. Compared to the global SSPs, the five Eur-Agri-SSPs provide rich thematic and regional details and are thus a solid basis for integrated assessments of agriculture and food systems and their response to future socio-economic and environmental changes.

    Impacts of climate change on energy systems in global and regional scenarios
    Yalew, Seleshi G. ; Vliet, Michelle T.H. van; Gernaat, David E.H.J. ; Ludwig, Fulco ; Miara, Ariel ; Park, Chan ; Byers, Edward ; Cian, Enrica De; Piontek, Franziska ; Iyer, Gokul ; Mouratiadou, Ioanna ; Glynn, James ; Hejazi, Mohamad ; Dessens, Olivier ; Rochedo, Pedro ; Pietzcker, Robert ; Schaeffer, Roberto ; Fujimori, Shinichiro ; Dasgupta, Shouro ; Mima, Silvana ; Santos da Silva, Silvia R. ; Chaturvedi, Vaibhav ; Vautard, Robert ; Vuuren, Detlef P. van - \ 2020
    Nature Energy (2020). - ISSN 2058-7546

    Although our knowledge of climate change impacts on energy systems has increased substantially over the past few decades, there remains a lack of comprehensive overview of impacts across spatial scales. Here, we analyse results of 220 studies projecting climate impacts on energy systems globally and at the regional scale. Globally, a potential increase in cooling demand and decrease in heating demand can be anticipated, in contrast to slight decreases in hydropower and thermal energy capacity. Impacts at the regional scale are more mixed and relatively uncertain across regions, but strongest impacts are reported for South Asia and Latin America. Our assessment shows that climate impacts on energy systems at regional and global scales are uncertain due partly to the wide range of methods and non-harmonized datasets used. For a comprehensive assessment of climate impacts on energy, we propose a consistent multi-model assessment framework to support regional-to-global-scale energy planning.

    Nest attentiveness drives nest predation in arctic sandpipers
    Meyer, Nicolas ; Bollache, Loïc ; Dechaume-Moncharmont, François Xavier ; Moreau, Jérôme ; Afonso, Eve ; Angerbjörn, Anders ; Bêty, Joël ; Ehrich, Dorothée ; Gilg, Vladimir ; Giroux, Marie Andrée ; Hansen, Jannik ; Lanctot, Richard B. ; Lang, Johannes ; Lecomte, Nicolas ; McKinnon, Laura ; Reneerkens, Jeroen ; Saalfeld, Sarah T. ; Sabard, Brigitte ; Schmidt, Niels M. ; Sittler, Benoît ; Smith, Paul ; Sokolov, Aleksandr ; Sokolov, Vasiliy ; Sokolova, Natalia ; Bemmelen, Rob van; Gilg, Olivier - \ 2020
    Oikos (2020). - ISSN 0030-1299
    Arctic shorebirds - breeding behaviour - incubation recesses - incubation strategy - nest survival - parental care

    Most birds incubate their eggs to allow embryo development. This behaviour limits the ability of adults to perform other activities. Hence, incubating adults trade off incubation and nest protection with foraging to meet their own needs. Parents can either cooperate to sustain this tradeoff or incubate alone. The main cause of reproductive failure at this reproductive stage is predation and adults reduce this risk by keeping the nest location secret. Arctic sandpipers are interesting biological models to investigate parental care evolution as they may use several parental care strategies. The three main incubation strategies include both parents sharing incubation duties (‘biparental’), one parent incubating alone (‘uniparental’), or a flexible strategy with both uniparental and biparental incubation within a population (‘mixed’). By monitoring the incubation behaviour in 714 nests of seven sandpiper species across 12 arctic sites, we studied the relationship between incubation strategy and nest predation. First, we described how the frequency of incubation recesses (NR), their mean duration (MDR), and the daily total duration of recesses (TDR) vary among strategies. Then, we examined how the relationship between the daily predation rate and these components of incubation behaviour varies across strategies using two complementary survival analysis. For uniparental and biparental species, the daily predation rate increased with the daily total duration of recesses and with the mean duration of recesses. In contrast, daily predation rate increased with the daily number of recesses for biparental species only. These patterns may be attributed to two independent mechanisms: cryptic incubating adults are more difficult to locate than unattended nests and adults departing the nest or feeding close to the nest can draw predators’ attention. Our results demonstrate that incubation behaviour as mediated by incubation strategy has important consequences for sandpipers’ reproductive success.

    What do models tell us about water and sediment connectivity?
    Baartman, Jantiene E.M. ; Nunes, João Pedro ; Masselink, Rens ; Darboux, Frédéric ; Bielders, Charles ; Degré, Aurore ; Cantreul, Vincent ; Cerdan, Olivier ; Grangeon, Thomas ; Fiener, Peter ; Wilken, Florian ; Schindewolf, Marcus ; Wainwright, John - \ 2020
    Geomorphology 367 (2020). - ISSN 0169-555X
    Catchment - Connectivity - Erosion models - Model comparison

    Connectivity has been embraced by the geosciences community as a useful concept to understand and describe hydrological functioning and sediment movement through catchments. Mathematical modelling has been used for decades to quantify and predict erosion and transport of sediments, e.g. in scenarios of land use change or conservation measures. Being intrigued by both models and the connectivity concept, as a group of modellers we aimed at investigating what different models could tell us about connectivity. Therefore, we evaluated the response of contrasted spatially-distributed models to landscape connectivity features and explained the differences based on different model structures. A total of 53 scenarios were built with varying field sizes and orientations, as well as the implementation of soil conservation measures. These scenarios were simulated, for two rainfall intensities, with five event- and process-based water and soil erosion models – EROSION3D, FullSWOF_2D, LandSoil, OpenLISEM and Watersed. Results showed that rainfall amount plays the most important role in determining relative export and connected area of runoff and sediment in all models, indicating that functional aspects of connectivity were more important than structural connectivity. As for the role of structural landscape elements, there was no overall agreement between models regarding the effects of field sizes, crop allocation pattern, and conservation practices; agreement was also low on the spatial patterns of connectivity. This overall disagreement between models was unexpected. The results of this exercise suggest that the correct parameterization of runoff and sediment production and of routing patterns may be an important issue. Thus, incorporating connectivity functions based on routing would help modelling forward. Our results also suggest that structural connectivity indices may not suffice to represent connectivity in this type of catchment (relatively simple and monotonous land cover), and functional connectivity indices should be applied.

    The use and performance of survey-based pre-recruit abundance indices for possible inclusion in stock assessments of coastal-dependent species
    Pape, Olivier Le; Vermard, Youen ; Guitton, Jérome ; Brown, Elliot J. ; De Wolfshaar, Karen E. Van; Lipcius, Romuald N. ; Støttrup, Josianne G. ; Rose, Kenneth A. - \ 2020
    ICES Journal of Marine Science 77 (2020)5. - ISSN 1054-3139
    coastal nursery - forecast - juvenile habitat - recruitment - stock assessment - survey
    We reviewed the use of survey-based pre-recruit abundance indices in short-term recruitment forecasts for fish species relying on coastal habitats at the juvenile stage and that are assessed by ICES. We collated information from stock assessment reports and from a questionnaire filled out by the stock assessors. Among the 78 stocks with juvenile coastal dependence, 49 use short-term forecasts in stock assessment. Survey-based pre-recruit abundance indices were available for 35 of these stocks, but only 14 were used to forecast recruitment. The questionnaire indicated that the limited use of survey-based pre-recruit abundance indices was primarily due to sampling inefficiency, which may preclude reliable recruitment estimates. The sampling is inefficient because the juvenile coastal distribution is outside the geographical area covered by large-scale surveys or targeted coastal surveys are conducted on limited spatial and temporal scales. However, our analysis of the relationship between survey-based pre-recruit indices and assessment-generated recruitment indices revealed that survey-based pre-recruit abundance indices were sufficiently accurate to provide useful information for predicting future recruitment. We recommend expansion of the use of survey-based indices of pre-recruit abundance in stock assessment and recruitment forecasting, and consideration of how to include
    juveniles in ongoing and future surveys.
    Can we use satellite-based soil-moisture products at high resolution to investigate land-use differences and land-atmosphere interactions? A case study in the Savanna
    Román-Cascón, Carlos ; Lothon, Marie ; Lohou, Fabienne ; Ojha, Nitu ; Merlin, Olivier ; Aragonés, David ; González-Dugo, María P. ; Andreu, Ana ; Pellarin, Thierry ; Brut, Aurore ; Soriguer, Ramón C. ; Díaz-Delgado, Ricardo ; Hartogensis, Oscar ; Yagüe, Carlos - \ 2020
    Remote Sensing 12 (2020)11. - ISSN 2072-4292
    DISPATCH - Heterogeneity - Land use - Satellite data - Savanna - SMOS-BEC - Soil moisture

    The use of soil moisture (SM) measurements from satellites has grown in recent years, fostering the development of new products at high resolution. This opens the possibility of using them for certain applications that were normally carried out using in situ data. We investigated this hypothesis through two main analyses using two high-resolution satellite-based soil moisture (SBSM) products that combined microwave with thermal and optical data: (1) The Disaggregation based on Physical And Theoretical scale Change (DISPATCH) and, (2) The Soil Moisture Ocean Salinity-Barcelona Expert Center (SMOS-BEC Level 4). We used these products to analyse the SM differences among pixels with contrasting vegetation. This was done through the comparison of the SM measurements from satellites and the measurements simulated with a simple antecedent precipitation index (API) model, which did not account for the surface characteristics. Subsequently, the deviation of the SM from satellite with respect to the API model (bias) was analysed and compared for contrasting land use categories. We hypothesised that the differences in the biases of the varied categories could provide information regarding the water retention capacity associated with each type of vegetation. From the satellite measurements, we determined how the SM depended on the tree cover, i.e., the denser the tree cover, the higher the SM. However, in winter periods with light rain events, the tree canopy could dampen the moistening of the soil through interception and conducted higher SM in the open areas. This evolution of the SM differences that depended on the characteristics of each season was observed both from satellite and from in situ measurements taken beneath a tree and in grass on the savanna landscape. The agreement between both types of measurements highlighted the potential of the SBSM products to investigate the SM of each type of vegetation. We found that the results were clearer for DISPATCH, whose data was not smoothed spatially as it was in SMOS-BEC. We also tested whether the relationships between SM and evapotranspiration could be investigated using satellite data. The answer to this question was also positive but required removing the unrealistic high-frequency SM oscillations from the satellite data using a low pass filter. This improved the performance scores of the products and the agreement with the results from the in situ data. These results demonstrated the possibility of using SM data from satellites to substitute ground measurements for the study of land-atmosphere interactions, which encourages efforts to improve the quality and resolution of these measurements.

    Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs
    Yang, Bin ; Cui, Leilei ; Perez-Enciso, Miguel ; Traspov, Aleksei ; Crooijmans, Richard P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Archibald, Alan ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, Martien A.M. ; Huang, Lusheng ; Megens, Hendrik Jan - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X - 1 p.

    An amendment to this paper has been published and can be accessed via the original article.

    Plastome phylogeography in two African rain forest legume trees reveals that Dahomey Gap populations originate from the Cameroon volcanic line
    Demenou, Boris B. ; Migliore, Jérémy ; Heuertz, Myriam ; Monthe, Franck K. ; Ojeda, Dario I. ; Wieringa, Jan J. ; Dauby, Gilles ; Albreht, Laura ; Boom, Arthur ; Hardy, Olivier J. - \ 2020
    Molecular Phylogenetics and Evolution 150 (2020). - ISSN 1055-7903
    African rain forest - Cameroon volcanic line - Colonization origin - Dahomey gap - Phylogeography - Plastid genome sequencing

    Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) – a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments – was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Recent Progress and Recommendations on Celiac Disease From the Working Group on Prolamin Analysis and Toxicity
    Scherf, Katharina A. ; Catassi, Carlo ; Chirdo, Fernando ; Ciclitira, Paul J. ; Feighery, Conleth ; Gianfrani, Carmen ; Koning, Frits ; Lundin, Knut E.A. ; Schuppan, Detlef ; Smulders, Marinus J.M. ; Tranquet, Olivier ; Troncone, Riccardo ; Koehler, Peter - \ 2020
    Frontiers in Nutrition 7 (2020). - ISSN 2296-861X
    barley - celiac disease - gluten - gluten-free diet - Prolamin Working Group - rye - wheat

    Celiac disease (CD) affects a growing number of individuals worldwide. To elucidate the causes for this increase, future multidisciplinary collaboration is key to understanding the interactions between immunoreactive components in gluten-containing cereals and the human gastrointestinal tract and immune system and to devise strategies for CD prevention and treatment beyond the gluten-free diet. During the last meetings, the Working Group on Prolamin Analysis and Toxicity (Prolamin Working Group, PWG) discussed recent progress in the field together with key stakeholders from celiac disease societies, academia, industry and regulatory bodies. Based on the current state of knowledge, this perspective from the PWG members provides recommendations regarding clinical, analytical and legal aspects of CD. The selected key topics that require future multidisciplinary collaborative efforts in the clinical field are to collect robust data on the increasing prevalence of CD, to evaluate what is special about gluten-specific T cells, to study their kinetics and transcriptomics and to put some attention to the identification of the environmental agents that facilitate the breaking of tolerance to gluten. In the field of gluten analysis, the key topics are the precise assessment of gluten immunoreactive components in wheat, rye and barley to understand how these are affected by genetic and environmental factors, the comparison of different methods for compliance monitoring of gluten-free products and the development of improved reference materials for gluten analysis.

    Experimental bottom trawling finds resilience in large-bodied infauna but vulnerability for epifauna and juveniles in the Frisian Front
    Tiano, Justin C. ; Reijden, Karin J. van der; O'Flynn, Sarah ; Beauchard, Olivier ; Ree, Sietse van der; Wees, Jelmer van der; Ysebaert, Tom ; Soetaert, Karline - \ 2020
    Marine Environmental Research 159 (2020). - ISSN 0141-1136
    Beam trawling - Benthic ecology - Biodiversity - Pulse trawling - Sediment profile imagery - Side-scan sonar - Underwater video

    In this study, we analysed the benthic effects of two in situ fisheries disturbance experiments using a combination of side-scan sonar, high definition underwater video, sediment profile imagery, and box core sampling techniques after conventional beam trawling and box core sampling after electric pulse trawling in a southern North Sea habitat. Acoustic and optical methods visualised the morphological changes induced by experimental beam trawling, showing the flattening and homogenisation of surface sediments. Video transects found a 94% decrease in epibenthos in beam trawled sediments compared to an untrawled control site and a 74% decrease in untrawled sediments of the same transect. Box core samples taken 5.5 h, 29 h and 75 h after trawling detected a downward trend in infaunal densities and species richness that continued after the initial impact with small-bodied and juvenile taxa being especially prone to depletion. Data from shallow sediment samples showed trawl resilience in large mud shrimps and evidence of their upward movement towards the sediment surface after disturbance. Both trawl gears induced significant changes to infaunal communities, with no differential effect between the two gears. Our results suggest that in the Frisian Front, trawling may favour the survival of deep burrowers while removing surficial macrofauna.

    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)3. - ISSN 1087-0156 - p. 272 - 276.
    Why are cluster farmers adopting more aquaculture technologies and practices? The role of trust and interaction within shrimp farmers' networks in the Mekong Delta, Vietnam
    Joffre, Olivier M. ; Vries, Jasper R. De; Klerkx, Laurens ; Poortvliet, Marijn - \ 2020
    Aquaculture 523 (2020). - ISSN 0044-8486
    Adoption - Farmer clusters - Group farming - Shrimp farming - Trust - Vietnam

    A common avenue to enable adoption of technologies and practices by small-scale producers is by means of farmer clusters. These are achieved by building networks and partnerships between farmers and other actors within the supply chain. This paper examines the role that farmer clusters play in the adoption of practices and technologies by shrimp farmers in Vietnam. Understanding the decisions that lead to adoption is important because these have a key impact on sustainable land use in aquaculture. We report on two complementary studies that test the role of farmer clusters in accessing different sources of knowledge and the trust associated with each of the knowledge sources. First, a survey (N = 193) tested the relationship between cluster membership and adoption, and showed that shrimp farmers who are members of farmer clusters are more likely to adopt three types of pond management practices (i.e. water quality management, feed input, and disease control practices). Furthermore, frequency of interaction with, and trust related to, key stakeholder actors could partly explain this relationship. Second, focus group discussions further zoomed into the dynamics that underlie the adoption of technologies and practices by cluster farmers and non-cluster farmers, respectively. We found that input retailers, buyers and hatcheries were only valued for their input on specific products and issues, but not trusted, as the information always needed being verified through testing by, amongst others, neighbors. Consequently, trust relations with these actors can be described as strongly calculative. Farmer clusters increase trust and tighten relationships between members. As a result, members trust each other when verifying information or sharing knowledge acquired from less trusted sources. On the basis of these results, we argue that reliance on existing farmer networks (i.e. clusters) is a viable tool to improve adoption of sustainable technologies and achieve land use planning objectives. Further implications for research and policy are discussed.

    Absolute quantitation of microbes using 16S rRNA gene metabarcoding : A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard
    Zemb, Olivier ; Achard, Caroline S. ; Hamelin, Jerome ; Almeida, Marie Léa De; Gabinaud, Béatrice ; Cauquil, Laurent ; Verschuren, Lisanne M.G. ; Godon, Jean Jacques - \ 2020
    MicrobiologyOpen 9 (2020)3. - ISSN 2045-8827
    16S rRNA gene - absolute count data - metabarcoding - microbiome - normalization - spike-in

    Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

    Characterization of goat prions demonstrates geographical variation of scrapie strains in Europe and reveals the composite nature of prion strains
    Nonno, Romolo ; Marina Moreno, Alberto ; Espinosa, J.C. ; Fast, C. ; Keulen, L.J.M. van; Spiropoulos, J. ; Lantier, Isabelle ; Andrèoletti, Olivier ; Pirisinu, L. ; Bari, M.A. Di; Aguilar-Calvo, Patricia ; Sklaviadis, Theodoros ; Papasavva-Stylianou, P. ; Acutis, Pier Luigi ; Acin, C. ; Bossers, A. ; Jacobs, Jorge G. ; Vaccari, G. ; Agostino, C. D'; Chiappini, B. ; Lantier, F. ; Groschup, Martin H. ; Agrimi, U. ; Torres, Juan Maria ; Langeveld, J.P.M. - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322
    Bovine Spongiform Encephalopathy (BSE) is the only animal prion which has been recognized as a zoonotic agent so far. The identification of BSE in two goats raised the need to reliably identify BSE in small ruminants. However, our understanding of scrapie strain diversity in small ruminants remains ill-defined, thus limiting the accuracy of BSE surveillance and spreading fear that BSE might lurk unrecognized in goats. We investigated prion strain diversity in a large panel of European goats by a novel experimental approach that, instead of assessing the neuropathological profile after serial transmissions in a single animal model, was based on the direct interaction of prion isolates with several recipient rodent models expressing small ruminants or heterologous prion proteins. The findings show that the biological properties of scrapie isolates display different patterns of geographical distribution in Europe and suggest that goat BSE could be reliably discriminated from a wide range of biologically and geographically diverse goat prion isolates. Finally, most field prion isolates showed composite strain features, with discrete strain components or sub-strains being present in different proportions in individual goats or tissues. This has important implications for understanding the nature and evolution of scrapie strains and their transmissibility to other species, including humans.
    Mapping travel time to assess accessibility in West Africa : The role of borders, checkpoints and road conditions
    Walther, Olivier J. ; Dambo, Lawali ; Koné, Moustapha ; Eupen, Michiel van - \ 2020
    Journal of Transport Geography 82 (2020). - ISSN 0966-6923
    Akkermansia muciniphila reduces Porphyromonas gingivalis-induced inflammation and periodontal bone destruction
    Huck, Olivier ; Mulhall, Hannah ; Rubin, George ; Kizelnik, Zev ; Iyer, Radha ; Perpich, John D. ; Haque, Nasreen ; Cani, Patrice D. ; Vos, Willem M. de; Amar, Salomon - \ 2020
    Journal of Clinical Periodontology 47 (2020)2. - ISSN 0303-6979 - p. 202 - 212.
    infection - inflammation - periodontitis - probiotic

    Aim: Akkermansia muciniphila is a beneficial gut commensal, whose anti-inflammatory properties have recently been demonstrated. This study aimed to evaluate the effect of A. muciniphila on Porphyromonas gingivalis elicited inflammation. Material and Methods: In lean and obese mice, A. muciniphila was administered in P. gingivalis-induced calvarial abscess and in experimental periodontitis model (EIP). Bone destruction and inflammation were evaluated by histomorphometric analysis. In vitro, A. muciniphila was co-cultured with P. gingivalis, growth and virulence factor expression was evaluated. Bone marrow macrophages (BMMϕ) and gingival epithelial cells (TIGK) were exposed to both bacterial strains, and the expression of inflammatory mediators, as well as tight junction markers, was analysed. Results: In a model of calvarial infection, A. muciniphila decreased inflammatory cell infiltration and bone destruction. In EIP, treatment with A. muciniphila resulted in a decreased alveolar bone loss. In vitro, the addition of A. muciniphila to P. gingivalis-infected BMMϕ increased anti-inflammatory IL-10 and decreased IL-12. Additionally, A. muciniphila exposure increases the expression of junctional integrity markers such as integrin-β1, E-cadherin and ZO-1 in TIGK cells. A. muciniphila co-culture with P. gingivalis reduced gingipains mRNA expression. Discussion: This study demonstrated the protective effects of A. muciniphila administration and may open consideration to its use as an adjunctive therapeutic agent to periodontal treatment.

    Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
    Koenen, Erik J.M. ; Ojeda, Dario I. ; Steeves, Royce ; Migliore, Jérémy ; Bakker, Freek T. ; Wieringa, Jan J. ; Kidner, Catherine ; Hardy, Olivier J. ; Pennington, R.T. ; Bruneau, Anne ; Hughes, Colin E. - \ 2020
    New Phytologist 225 (2020)3. - ISSN 0028-646X - p. 1355 - 1369.
    Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking.We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees.
    We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting.
    All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
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