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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    Cadena de valor en la red de tomate de árbol (Solanum betaceum) en Ecuador
    Moreno-Miranda, Carlos ; Molina, José Isaac ; Ortiz, Jacqueline ; Peñafiel, Carla ; Moreno, Raúl - \ 2020
    Agronomia mesoamericana 31 (2020)1. - ISSN 1021-7444 - p. 13 - 29.
    Coordination - Horticulture - Market - Strategy - Unit of production

    Introduction. The fruit and vegetable sector in Ecuador has shown promising performance in domestic and international markets. Likewise, this sector has faced problems of a social, economic and productive nature in its structure and articulations, which until now require intervention. Objective. The objective of this study was to analyze in a descriptive way the structure of the tree tomato agro-food network. Materials and methods. This study was carried out in the provinces of Cotopaxi, Tungurahua, and Chimborazo, Ecuador, during the period between the second quarter of 2016 and the end of 2017. The study applied a systemic methodology aimed at the identification and characterization of stages, agents and activities (primary and support), and the analysis of network governance mechanisms. Results. The present study showed the main social and productive characteristics, horizontal and vertical sizing; and the proposal of strategies focused on improving their productive performance. Conclusions. The inclusion of women, the sense of associativity of processors and distributors, and the training of producers in topics related to post-harvest, and good agricultural practices, would significantly improve the economic performance of the network, and also encourage greater participation of the agents involved. The network requires increasing the area allocated to tree tomato cultivation, and the application of greenhouse production systems that increase yields.

    Local supply of lignocellulosic biomass to paper industry in Gelderland : Development of circular and value-added chains
    Vural Gursel, Iris ; Groenestijn, Johan van; Elbersen, Wolter ; Schelhaas, Mart-Jan ; Nabuurs, Gert-Jan ; Kranendonk, Remco ; Jong, Anjo de; Leeuwen, Myrna van; Smits, Marie-Jose - \ 2020
    Wageningen : Wageningen Food & Biobased Research (Wageningen Food & Biobased Research report 2046) - ISBN 9789463954105 - 38
    Changes in food access by mestizo communities associated with deforestation and agrobiodiversity loss in Ucayali, Peruvian Amazon
    Blundo-Canto, Genowefa ; Cruz-Garcia, Gisella S. ; Talsma, Elise F. ; Francesconi, Wendy ; Labarta, Ricardo ; Sanchez-Choy, Jose ; Perez-Marulanda, Lisset ; Paz-Garcia, Paula ; Quintero, Marcela - \ 2020
    Food Security (2020). - ISSN 1876-4517
    Agrobiodiversity - Ecosystem services - Food security - Household dietary diversity score - Land use change

    Few longitudinal studies link agricultural biodiversity, land use and food access in rural landscapes. In this paper, we test the hypothesis that, in a context of economic change, cash crop expansion is associated with deforestation, reduced agrobiodiversity and changes in food access. For this purpose, we analysed data collected from the same 53 upland and floodplain mestizo households in Ucayali, Peru, in 2000 and 2015. We found an emerging transition towards less diversified food access coupled with loss of forest cover and reduced agricultural biodiversity. In 2015, diets appeared to rely on fewer food groups, fewer food items, and on products increasingly purchased in the market compared to 2000. Wild fruits and plants were mentioned, but rarely consumed. Agricultural production systems became more specialised with a shift towards commercial crops. Peak deforestation years in the 15-year period appeared linked with incentives for agricultural expansion. Our results suggest an overall trend from diversified productive and “extractive” systems and more diverse food access, towards specialized productive systems, with less diverse food access and stronger market orientation (both in production and consumption). The assumption in the food and agricultural sciences that increased income and market-orientation is linked to improved food security, is challenged by our integrated analyses of food access, agrobiodiversity, land use and forest cover. Our results highlight the importance of longitudinal, multidimensional, systemic analyses, with major implications for land use, food and health policies. The potential risks of parallel homogenisation of diets and agricultural production systems require interdisciplinary research and policies that promote integrated landscape approaches for sustainable and inclusive food systems.

    Identification of conditionally essential genes for Streptococcus suis infection in pigs
    Arenas, Jesús ; Zomer, Aldert ; Harders-Westerveen, Jose ; Bootsma, Hester J. ; Jonge, Marien I. De; Stockhofe-Zurwieden, Norbert ; Smith, Hilde E. ; Greeff, Astrid De - \ 2020
    Virulence 11 (2020)1. - ISSN 2150-5594 - p. 446 - 464.
    infection - pathogenesis - Streptococcus suis - Tn-Seq - transposon mutagenesis - zoonotic pathogen

    Streptococcus suis is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for S. suis infection. We created Tn-Seq libraries in a virulent S. suis strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in ex vivo models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in S. suis pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs.

    The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)
    Halbritter, Aud H. ; Boeck, Hans J. De; Eycott, Amy E. ; Reinsch, Sabine ; Robinson, David A. ; Vicca, Sara ; Berauer, Bernd ; Christiansen, Casper T. ; Estiarte, Marc ; Grünzweig, José M. ; Gya, Ragnhild ; Hansen, Karin ; Jentsch, Anke ; Lee, Hanna ; Linder, Sune ; Marshall, John ; Peñuelas, Josep ; Kappel Schmidt, Inger ; Stuart-Haëntjens, Ellen ; Wilfahrt, Peter ; Vandvik, Vigdis ; Abrantes, Nelson ; Almagro, María ; Althuizen, Inge H.J. ; Barrio, Isabel C. ; Beest, Mariska Te; Beier, Claus ; Beil, Ilka ; Carter Berry, Z. ; Birkemoe, Tone ; Bjerke, Jarle W. ; Blonder, Benjamin ; Blume-Werry, Gesche ; Bohrer, Gil ; Campos, Isabel ; Cernusak, Lucas A. ; Chojnicki, Bogdan H. ; Cosby, Bernhard J. ; Dickman, Lee T. ; Djukic, Ika ; Filella, Iolanda ; Fuchslueger, Lucia ; Gargallo-Garriga, Albert ; Gillespie, Mark A.K. ; Goldsmith, Gregory R. ; Gough, Christopher ; Halliday, Fletcher W. ; Hegland, Stein Joar ; Ploeg, Martine van der; Verbruggen, Erik - \ 2020
    Methods in Ecology and Evolution 11 (2020)1. - ISSN 2041-210X - p. 22 - 37.
    best practice - coordinated experiments - data management and documentation - ecosystem - experimental macroecology - methodology - open science - vegetation

    Climate change is a world-wide threat to biodiversity and ecosystem structure, functioning and services. To understand the underlying drivers and mechanisms, and to predict the consequences for nature and people, we urgently need better understanding of the direction and magnitude of climate change impacts across the soil–plant–atmosphere continuum. An increasing number of climate change studies are creating new opportunities for meaningful and high-quality generalizations and improved process understanding. However, significant challenges exist related to data availability and/or compatibility across studies, compromising opportunities for data re-use, synthesis and upscaling. Many of these challenges relate to a lack of an established ‘best practice’ for measuring key impacts and responses. This restrains our current understanding of complex processes and mechanisms in terrestrial ecosystems related to climate change. To overcome these challenges, we collected best-practice methods emerging from major ecological research networks and experiments, as synthesized by 115 experts from across a wide range of scientific disciplines. Our handbook contains guidance on the selection of response variables for different purposes, protocols for standardized measurements of 66 such response variables and advice on data management. Specifically, we recommend a minimum subset of variables that should be collected in all climate change studies to allow data re-use and synthesis, and give guidance on additional variables critical for different types of synthesis and upscaling. The goal of this community effort is to facilitate awareness of the importance and broader application of standardized methods to promote data re-use, availability, compatibility and transparency. We envision improved research practices that will increase returns on investments in individual research projects, facilitate second-order research outputs and create opportunities for collaboration across scientific communities. Ultimately, this should significantly improve the quality and impact of the science, which is required to fulfil society's needs in a changing world.

    H7N9 influenza split vaccine with SWE oil-in-water adjuvant greatly enhances cross-reactive humoral immunity and protection against severe pneumonia in ferrets
    Jonge, Jørgen de; Dijken, Harry van; Heij, Femke de; Spijkers, Sanne ; Mouthaan, Justin ; Jong, Rineke de; Roholl, Paul ; Adami, Eduardo Alfredo ; Akamatsu, Milena Apetito ; Ho, Paulo Lee ; Brunner, Livia ; Collin, Nicolas ; Friede, Martin ; Ferreira, José A. ; Luytjes, Willem - \ 2020
    Vaccines 5 (2020)1. - ISSN 2076-393X

    Until universal influenza vaccines become available, pandemic preparedness should include developing classical vaccines against potential pandemic influenza subtypes. We here show that addition of SWE adjuvant, a squalene-in-water emulsion, to H7N9 split influenza vaccine clearly enhanced functional antibody responses in ferrets. These were cross-reactive against H7N9 strains from different lineages and newly emerged H7N9 variants. Both vaccine formulations protected in almost all cases against severe pneumonia induced by intratracheal infection of ferrets with H7N9 influenza; however, the SWE adjuvant enhanced protection against virus replication and disease. Correlation analysis and curve fitting showed that both VN- and NI-titers were better predictors for protection than HI-titers. Moreover, we show that novel algorithms can assist in better interpretation of large data sets generated in preclinical studies. Cluster analysis showed that the adjuvanted vaccine results in robust immunity and protection, whereas the response to the non-adjuvanted vaccine is heterogeneous, such that the protection balance may be more easily tipped toward severe disease. Finally, cluster analysis indicated that the dose-sparing capacity of the adjuvant is at least a factor six, which greatly increases vaccine availability in a pandemic situation.

    More frequent droughts slow down litter decomposition across European agroecosystems and increase the importance of earthworm functional diversity
    Silva, Pedro Martins da; Nascimento, Eduardo ; Reis, Filipa ; Briones, Maria J.I. ; Brussaard, Lijbert ; Sousa, José Paulo - \ 2020
    Applied Soil Ecology 153 (2020). - ISSN 0929-1393
    Climate change - Community weighted means - Decomposition - Ecological groups - Land-use - Niche complementarity

    Effects of increasing rainfall variability and weather extremes on litter decomposition are still uncertain, especially in agroecosystems, where the functional structure of soil communities is already affected. We conducted a mesocosm experiment to evaluate the impacts of different rain regimes and land management on litter mass loss and earthworm ecological groups (epigeic, endogeic and anecic) across European agroecosystems. We also tested if the effects of different rainfall regimes (normal, drought, flooding, intermittent) on earthworm functional diversity (FD) or community-weighted mean (CWM) of earthworm ecological groups (particularly anecic species in the case of CWM), affected litter mass loss across land-use types. We found that drought was the main factor retarding litter mass loss across European agroecosystems irrespective of management type. The effects of the rain regime on litter mass loss were coupled with the pedoclimatic conditions that were different among the studied European land-use types. Across land-use types the importance of earthworm communities for litter decomposition was higher under water depletion. These results also suggest that FD, as a proxy of niche complementarity, is crucial for the stability of the decomposition process under environmental disturbances. The FD values under drought regimes strongly indicated that climatic changes may slow down litter decomposition as a result of FD alterations that could compromise the long-term maintenance of litter mass loss. This result may be especially relevant for the European soils that are already under hydric stress, such as in most Mediterranean agroecosystems.

    Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes
    Lori, Martina ; Piton, Gabin ; Symanczik, Sarah ; Legay, Nicolas ; Brussaard, Lijbert ; Jaenicke, Sebastian ; Nascimento, Eduardo ; Reis, Filipa ; Sousa, José Paulo ; Mäder, Paul ; Gattinger, Andreas ; Clément, Jean Christophe ; Foulquier, Arnaud - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322

    Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change.

    Supplementation of lamb diets with vitamin E and rosemary extracts on meat quality parameters
    Leal, Leonel N. ; Beltrán, José A. ; Marc, B. ; Bello, José M. ; Hartog, Leo A. den; Hendriks, Wouter H. ; Martín-Tereso, Javier - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)7. - ISSN 0022-5142 - p. 2922 - 2931.
    all-rac-α-tocopheryl acetate - colour - lipid oxidation - modified-atmosphere packaging - rosemary extract - vitamin E

    BACKGROUND: Supranutritional supplementation of lamb diets with α-tocopherol is an effective method to reduce lipid oxidation and colour deterioration in meat products. However, alternative antioxidant sources have been proposed to replace the supranutritional vitamin E applications. RESULTS: Indoor concentrate-fed Rasa Aragonesa male lambs (n = 480) were supplemented with increasing levels of all-rac-α-tocopheryl acetate (0.25, 0.5, 1.0 g kg−1 compound feed), rosemary extract (0.20, 0.40, or 0.80 g kg−1 compound feed), or rosemary extract embedded in a fat matrix (0.20, 0.40, or 0.80 g kg−1 compound feed) for 14 days before slaughter. The longissimus thoracis et lumborum muscle from three lambs per pen (18 lambs per treatment) were modified-atmosphere packaged (70% O2 + 30% CO2) and maintained under retail conditions for 14 days. Supranutritional supplementation with antioxidants had no effect (P > 0.05) on average daily weight gain, feed intake, and feed efficiency. Rosemary extract supplementation (with or without fat embedment) had no effect on lipid oxidation, myoglobin forms, or colour stability parameters, regardless of the dose. All vitamin E supplementation levels significantly affected lipid oxidation, colour stability (L*, C*, and h), myoglobin forms, and meat discoloration parameters compared with non-supplemented lambs. CONCLUSIONS: This study demonstrates that, unlike vitamin E, neither dose nor protection of the rosemary extract had an effect on lipid oxidation or meat colour stability of lambs during the 14 days of storage under retail conditions.

    Exploring potential of non-destructive and non-invasive sensors in food supply chains
    Bouzembrak, Y. ; Chauhan, A. ; Daniels, F.M.J. ; Gavai, Anand ; Gonzales Rojas, Jose ; Kamphuis, C. ; Marvin, H.J.P. ; Meesters, Lydia ; Mishra, Puneet ; Müller-Maatsch, Judith ; Ouweltjes, W. ; Paillart, M.J.M. ; Petie, R. ; Petropoulou, Anna ; Plantenga, F.D.M. ; Rijgersberg, H. ; Top, J.L. ; Tsafaras, I. ; Ummels, Meeke ; Breukelen, Anouk van; Weesepoel, Y.J.A. - \ 2020
    - 1 p.
    Exploring potential of non-destructive and non-invasive sensors in food supply chains
    Chauhan, Aneesh ; Bouzembrak, Yamine ; Daniels, Freek ; Gavai, Anand ; Gonzales Rojas, Jose ; Kamphuis, J. ; Marvin, Hans ; Meesters, Lydia ; Mishra, Puneet ; Mueller-Maatsch, J. ; Ouweltjes, J. ; Paillart, Maxence ; Petie, Ronald ; Petropoulou, Anna ; Plantenga, Faline ; Rijgersberg, Hajo ; Top, Jan ; Tsafaras, Ilias ; Ummels, Meeke ; Breukelen, Anouk van; Weesepoel, Yannick - \ 2020
    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    CGIAR modeling approaches for resource-constrained scenarios : I. Accelerating crop breeding for a changing climate
    Ramirez-Villegas, Julian ; Molero Milan, Anabel ; Alexandrov, Nickolai ; Asseng, Senthold ; Challinor, Andrew J. ; Crossa, Jose ; Eeuwijk, Fred van; Ghanem, Michel Edmond ; Grenier, Cecile ; Heinemann, Alexandre B. ; Wang, Jiankang ; Juliana, Philomin ; Kehel, Zakaria ; Kholova, Jana ; Koo, Jawoo ; Pequeno, Diego ; Quiroz, Roberto ; Rebolledo, Maria C. ; Sukumaran, Sivakumar ; Vadez, Vincent ; White, Jeffrey W. ; Reynolds, Matthew - \ 2020
    Crop Science 60 (2020)2. - ISSN 0011-183X - p. 547 - 567.

    Crop improvement efforts aiming at increasing crop production (quantity, quality) and adapting to climate change have been subject of active research over the past years. But, the question remains ‘to what extent can breeding gains be achieved under a changing climate, at a pace sufficient to usefully contribute to climate adaptation, mitigation and food security?’. Here, we address this question by critically reviewing how model-based approaches can be used to assist breeding activities, with particular focus on all CGIAR (formerly the Consultative Group on International Agricultural Research but now known simply as CGIAR) breeding programs. Crop modeling can underpin breeding efforts in many different ways, including assessing genotypic adaptability and stability, characterizing and identifying target breeding environments, identifying tradeoffs among traits for such environments, and making predictions of the likely breeding value of the genotypes. Crop modeling science within the CGIAR has contributed to all of these. However, much progress remains to be done if modeling is to effectively contribute to more targeted and impactful breeding programs under changing climates. In a period in which CGIAR breeding programs are undergoing a major modernization process, crop modelers will need to be part of crop improvement teams, with a common understanding of breeding pipelines and model capabilities and limitations, and common data standards and protocols, to ensure they follow and deliver according to clearly defined breeding products. This will, in turn, enable more rapid and better-targeted crop modeling activities, thus directly contributing to accelerated and more impactful breeding efforts.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    In vitro toxicological characterisation of the antifungal compound soybean toxin (SBTX)
    Arantes, Mariana Reis ; Peijnenburg, Ad ; Hendriksen, Peter J.M. ; Stoopen, Geert ; Almeida, Thiago Silva ; Souza, Terezinha Maria ; Farias, Davi Felipe ; Carvalho, Ana Fontenele Urano ; Rocha, Talita Magalhães ; Leal, Luzia Kalyne Almeida Moreira ; Vasconcelos, Ilka Maria ; Oliveira, Jose Tadeu Abreu - \ 2020
    Toxicology in Vitro 65 (2020). - ISSN 0887-2333
    Antifungal agent - Cytotoxicity - SBTX - Toxicogenomics

    Soybean toxin (SBTX) is a protein isolated from soybean seeds and composed of two polypeptide subunits (17 and 27 kDa). SBTX has in vitro activity against phytopathogenic fungi such as Cercospora sojina, Aspergillus niger, and Penicillium herguei, and yeasts like Candida albicans, C. parapsilosis, Kluyveromyces marxiannus, and Pichia membranifaciens. The present study aimed to analyze in vitro whether SBTX causes any side effects on non-target bacterial and mammalian cells that could impede its potential use as a novel antifungal agent. SBTX at 100 μg/mL and 200 μg/mL did not hinder the growth of the bacteria Salmonella enterica (subspecies enterica serovar choleraesuis), Bacillus subtilis (subspecies spizizenii) and Staphylococcus aureus. Moreover, SBTX at concentrations up to 500 μg/mL did not significantly affect the viability of erythrocytes, neutrophils, and human intestinal Caco-2 cells. To study whether SBTX could induce relevant alterations in gene expression, in vitro DNA microarray experiments were conducted in which differentiated Caco-2 cells were exposed for 24 h to 100 μg/mL or 200 μg/mL SBTX. SBTX up-regulated genes involved in cell cycle and immune response pathways, but down-regulated genes that play a role in cholesterol biosynthesis and platelet degranulation pathways. Thus, although SBTX did not affect bacteria, nor induced cytotoxity in mammalian cells, it affected some biological pathways in the human Caco-2 cell line that warrants further investigation.

    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.
    Ovulatory response of weaned sows to an altered ratio of exogenous gonadotrophins
    Manjarín, Rodrigo ; García, Jose Carlos ; Hoving, Lia ; Soede, Nicoline M. ; Maj, Magdalena ; Tejerina, Juan Carlos Dominguez de; Kirkwood, Roy N. - \ 2020
    Animals 10 (2020)3. - ISSN 2076-2615
    Follicle - Gonadotrophins - Ovulation - Sows

    At weaning, 33 mixed parity Hypor sows received either an injection of 400 IU equine chorionic gonadotrophin and 200 IU human chorionic gonadotrophin (hCG) (PG600; n = 13), PG600 with an additional 200 IU hCG 24 h later (Gn800; n = 11), or served as non‐injected controls (n = 9). All gonadotrophin treated sows received an injection of 750 IU hCG at 80 h after weaning to induce ovulation (designated as time 0 h). At 0, 24, 36, 40, 44, 48, and 60 h, all sows were subject to transrectal ultrasonography to determine numbers and sizes of large (>6 mm) follicles and time of ovulation. The interval from injection of 750 IU hCG to ovulation was shorter in Gn800 compared to PG600 sows (p = 0.02), and more Gn800 sows had ≥9 preovulatory follicles compared to PG600 and controls (p = 0.02 and 0.003, respectively). Follicular cysts were evident in both PG600 and Gn800 sows.

    LRRpredictor—a new LRR motif detection method for irregular motifs of plant NLR proteins using an ensemble of classifiers
    Martin, Eliza C. ; Sukarta, Octavina C.A. ; Spiridon, Laurentiu ; Grigore, Laurentiu G. ; Constantinescu, Vlad ; Tacutu, Robi ; Goverse, Aska ; Petrescu, Andrei Jose - \ 2020
    Genes 11 (2020)3. - ISSN 2073-4425
    Leucine-rich repeat prediction - LRR motif - LRR structure - NOD-like receptors - R proteins - Supervised learning

    Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein–protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.

    Maternal exposure to mixtures of dienestrol, linuron and flutamide. Part I: Feminization effects on male rat offspring
    Schreiber, Elga ; Garcia, Tània ; González, Neus ; Esplugas, Roser ; Sharma, Raju Prasad ; Torrente, Margarita ; Kumar, Vikas ; Bovee, Toine ; Katsanou, Efrosini S. ; Machera, Kyriaki ; Domingo, José Luis ; Gómez, Mercedes - \ 2020
    Food and Chemical Toxicology 139 (2020). - ISSN 0278-6915
    Dienestrol - Feminization effects - Flutamide - Linuron - Male rats - Mixtures

    Exposure to endocrine-disrupting compounds (EDCs) during pregnancy can result in negative health effects in later generations, including sex changes and feminization. The present study assessed the feminization effects on male offspring rats of three EDCs: Dienestrol (DIES), Linuron (LIN), and Flutamide (FLU). Sexually mature female rats were exposed from gestation day (GD) 6 until postnatal day (PND) 21 to: 0.37, 0.75, 1.5, 3.12 or 6.25 μg/kg/day of DIES, 1.5, 3, 6, 12.5, 25 or 50 mg/kg/day of LIN, 3.5, 6.7, 12.5, 25 or 50 mg/kg/day of FLU, and the following mixtures: FLU + DIES (mg/kg/day+μg/kg/day), 3.5 + 0.37, or 3.5 + 3, 25 + 0.37, or 25 + 3; FLU + LIN (mg/kg/day + mg/kg/day), 3.5 + 12.5, or 25 + 12.5; and DIES + LIN (μg/kg/day + mg/kg/day), 0.37 + 12.5, or 3 + 12.5. Anogenital distance (AGD), nipple retention (NR) and cryptorchidism were evaluated. FLU produced a decrease of AGD, an increase of NR, and an increase of cryptorchidism at the highest dose. None of these three endpoints were significantly affected by LIN or DIES treatments alone. Combinations of FLU + LIN and FLU + DIES increased NR, and decreased AGD, while DIES + LIN did not produce any effects in male pups. Results show that FLU is able to induce feminization in male pups, while binary combinations of LIN and DIES did not modify the effects produced by FLU.

    A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmland
    Cole, Lorna J. ; Kleijn, David ; Dicks, Lynn V. ; Stout, Jane C. ; Potts, Simon G. ; Albrecht, Matthias ; Balzan, Mario V. ; Bartomeus, Ignasi ; Bebeli, Penelope J. ; Bevk, Danilo ; Biesmeijer, Jacobus C. ; Chlebo, Róbert ; Dautartė, Anželika ; Emmanouil, Nikolaos ; Hartfield, Chris ; Holland, John M. ; Holzschuh, Andrea ; Knoben, Nieke T.J. ; Kovács-Hostyánszki, Anikó ; Mandelik, Yael ; Panou, Heleni ; Paxton, Robert J. ; Petanidou, Theodora ; Pinheiro de Carvalho, Miguel A.A. ; Rundlöf, Maj ; Sarthou, Jean Pierre ; Stavrinides, Menelaos C. ; Suso, Maria Jose ; Szentgyörgyi, Hajnalka ; Vaissière, Bernard E. ; Varnava, Androulla ; Vilà, Montserrat ; Zemeckis, Romualdas ; Scheper, Jeroen - \ 2020
    Journal of Applied Ecology 57 (2020)4. - ISSN 0021-8901 - p. 681 - 694.
    agri-environment schemes - bees - CAP Green Architecture - Common Agricultural Policy - Ecological Focus Areas - habitat complementarity - pollination services - pollinator conservation

    Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake. A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating taxa (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources. EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived. Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes. Policy Implications. To conserve pollinators and help protect pollination services, our expert elicitation highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer. To achieve this the Common Agricultural Policy post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and agri-environment and climate measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised.

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